"abstract","rna_related"
"although microrna-144-3p (mirna-144-3p) has been shown to suppress tumor proliferation and invasion, its function in intracerebral hemorrhage (ich)-induced secondary brain injury (sbi) remains unclear. thus, this study was designed to investigate the role of mirna-144-3p in ich. to accomplish this, we used adult male sprague-dawley rats to establish an in vivo ich model by injecting autologous blood, while cultured primary rat cortical neurons were exposed to oxyhemoglobin (oxyhb) to mimic ich in vitro . to examine the role of mirna-144-3p in ich-induced sbi, we used an mirna-144-3p mimic and inhibitor both in vivo and in vitro . following ich induction, we found mirna-144-3p expression to increase. additionally, we predicted the formyl peptide receptor 2 (fpr2) to be a potential mirna-144-3p target, which we validated experimentally, with fpr2 expression downregulated when mirna-144-3p was upregulated. furthermore, elevated mirna-144-3p levels aggravated brain edema and neurobehavioral disorders and induced neuronal apoptosis via the downregulation of fpr2 both in vivo and in vitro . we suspected that these beneficial effects provided by fpr2 were associated with the pi3k/akt pathway. we validated this finding by overexpressing fpr2 while inhibiting pi3k/akt in vitro and in vivo . in conclusion, mirna-144-3p aggravated ich-induced sbi by targeting and downregulating fpr2, thereby contributing to neurological dysfunction and neural apoptosis via pi3k/akt pathway activation. these findings suggest that inhibiting mirna-144-3p may offer an effective approach to attenuating brain damage incurred after ich and a potential therapy to improve ich-induced sbi.",1
"a mutation located in the 5'-untranslated region (5'-utr) of the nerve-specific connexin-32 mrna, previously found in a family with charcot-marie-tooth disease (cmtx), was analyzed for its effect on the expression of a reporter gene (luciferase) in transgenic mice and in transfected cells. whereas both mutant and wild-type genes appeared to be transcribed and spliced efficiently, no luciferase was detected from the mutant in either system, suggesting that the mutation affects translation of the mrna. when the 5'-utr of nerve-specific connexin-32 mrna was inserted between the two genes of a bicistronic vector and transfected into various cell lines, expression of the second gene was significantly increased. because the mutant did not facilitate translation of the second gene in the bicistronic mrna system, this result suggested that the cmtx mutation abolished function of an internal ribosome entry site (ires) in the 5'-utr of the wild-type connexin-32 mrna. the cmtx phenotype of the mutant 5'-utr further suggested that the wild-type ires was essential for the translation of the connexin-32 mrna in nerve cells. in addition, other sequence elements of the connexin-32 ires were characterized by mutation analysis. a mutation in either of the first two elements investigated showed loss of ires function, whereas mutation of a third element showed gain of function.",1
"background micrornas (mirnas) are short, non-coding rnas (~22 nt) that play important roles in the pathogenesis of human diseases by negatively regulating gene expression. although mir-196a has been implicated in several other cancers, its role in non-small cell lung cancer (nsclc) is unknown. the aim of the present study was to examine the expression pattern of mir-196a in nsclc and its clinical significance, as well as its biological role in tumor progression. methods expression of mir-196a was analyzed in 34 nsclc tissues and five nsclc cell lines by quantitative reverse-transcription polymerase chain reaction (qrt-pcr). the effect of dna methylation on mir-196a expression was investigated by 5-aza-2-deoxy-cytidine treatment and bisulfite sequencing. the effect of mir-196a on proliferation was evaluated by mtt and colony formation assays, and cell migration and invasion were evaluated by transwell assays. analysis of target protein expression was determined by western blotting. luciferase reporter plasmids were constructed to confirm the action of mir-196a on downstream target genes, including hoxa5. differences between the results were tested for significance using student's t-test (two-tailed). results mir-196a was highly expressed both in nsclc samples and cell lines compared with their corresponding normal counterparts, and the expression of mir-196a may be affected by dna demethylation. higher expression of mir-196a in nsclc tissues was associated with a higher clinical stage, and also correlated with nsclc lymph-node metastasis. in vitro functional assays demonstrated that modulation of mir-196a expression affected nsclc cell proliferation, migration and invasion. our analysis showed that mir-196a suppressed the expression of hoxa5 both at the mrna and protein levels, and luciferase assays confirmed that mir-196a directly bound to the 3'untranslated region of hoxa5. knockdown of hoxa5 expression in a549 cells using rnai was shown to promote nsclc cell proliferation, migration and invasion. finally, we observed an inverse correlation between hoxa5 and mir-196a expression in nsclc tissues. conclusions our findings indicate that mir-196a is significantly up-regulated in nsclc tissues, and regulates nsclc cell proliferation, migration and invasion, partially via the down-regulation of hoxa5. thus, mir-196a may represent a potential therapeutic target for nsclc intervention.",1
"here we describe a set of endogenous short interfering rnas (sirnas) in arabidopsis, some of which direct the cleavage of endogenous mrnas. these sirnas correspond to both sense and antisense strands of a noncoding rna (at2g27400) that apparently is converted to double-stranded rna and then processed in 21 nt increments. these sirnas differ from previously described regulatory small rnas in two respects. first, they require components of the cosuppression pathway (rdr6 and sgs3) and also components of the microrna (mirna) pathway (ago1, dcl1, hen1, and hyl1) but not components needed for heterochromatic sirnas (dcl3 and rdr2), another class of endogenous plant sirnas. second, these sirnas repress the expression of genes that have little overall resemblance to the genes from which they originate, a characteristic previously reported only for mirnas. the identification of this silencing pathway provides yet another dimension to posttranscriptional mrna regulation in plants.",1
"in saccharomyces cerevisiae, seven snrnas (snr3, 4, 5, 8, 9, 10 and 17) are retained in the nucleus under conditions in which nucleoplasmic rnas are lost, and may be nucleolar. all of these snrnas show properties consistent with hydrogen bonding to pre-ribosomal rnas; snr5 and 8 with 20s pre-rrna, snr3, 4, 10 and 17 with 35s pre-rrna and snr9 with 20-35s rna. strains lacking snr10 are impaired in growth and specifically defective in the processing of 35s rna. processing is slowed, leading to 35s rna accumulation and most cleavage occurs, not at the normal sites, but at sites which in wild-type strains are used for subsequent steps in rrna maturation.",1
"micrornas are short, endogenous non-coding rnas that act as post-transcriptional modulators of gene expression. important functions for micrornas have been found in the regulation of development, cellular proliferation and differentiation, while perturbed mirna expression patterns have been observed in many human cancers. here we present a method for specific inhibition of mirna function through interaction with lna-modified antisense oligonucleotides and report the specificity of this application. we show that lna-modified oligonucleotides can inhibit exogenously introduced mirnas with high specificity using a heterologous reporter assay, and furthermore demonstrate their ability to inhibit an endogenous mirna in drosophila melanogaster cells, leading to up-regulation of the cognate target protein. the method shows stoichiometric and reliable inhibition of the targeted mirna and can thus be applied to studies of mirna functions and validation of putative target genes.",1
"fsh plays an essential role in processes involved in human reproduction, including spermatogenesis and the ovarian cycle. while the transcriptional regulatory mechanisms underlying its synthesis and secretion have been extensively studied, little is known about its posttranscriptional regulation. a bioinformatics analysis from our group indicated that a microrna (mirna; mir-361-3p) could regulate fsh secretion by potentially targeting the fshb subunit. herein, we sought to confirm these findings by investigating the mir-361-3p-mediated regulation of fsh production in primary pig anterior pituitary cells. gonadotropin-releasing hormone (gnrh) treatment resulted in an increase in fshb synthesis at both the mrna, protein/hormone level, along with a significant decrease in mir-361-3p and its precursor (pre-mir-361) levels in time- and dose-dependent manner. using the dual-luciferase assay, we confirmed that mir-361-3p directly targets fshb. additionally, overexpression of mir-361-3p using mimics significantly decreased the fshb production at both the mrna and protein levels, with a reduction in both protein synthesis and secretion. conversely, both synthesis and secretion were significantly increased following mir-361-3p blockade. to confirm that mir-361-3p targets fshb, we designed fsh-targeted sirnas, and co-transfected anterior pituitary cells with both the sirna and mir-361-3p inhibitors. our results indicated that the sirna blocked the mir-361-3p inhibitor-mediated upregulation of fsh, while no significant effect on non-target expression. taken together, our results demonstrate that mir-361-3p negatively regulates fsh synthesis and secretion by targeting fshb, which provides more functional evidence that a mirna is involved in the direct regulation of fsh.",1
"progressive hearing loss is common in the human population, but little is known about the molecular basis. we report a new n-ethyl-n-nitrosurea (enu)-induced mouse mutant, diminuendo, with a single base change in the seed region of mirn96. heterozygotes show progressive loss of hearing and hair cell anomalies, whereas homozygotes have no cochlear responses. most micrornas are believed to downregulate target genes by binding to specific sites on their mrnas, so mutation of the seed should lead to target gene upregulation. microarray analysis revealed 96 transcripts with significantly altered expression in homozygotes; notably, slc26a5, ocm, gfi1, ptprq and pitpnm1 were downregulated. hypergeometric p-value analysis showed that hundreds of genes were upregulated in mutants. different genes, with target sites complementary to the mutant seed, were downregulated. this is the first microrna found associated with deafness, and diminuendo represents a model for understanding and potentially moderating progressive hair cell degeneration in hearing loss more generally.",1
"nodal is a member of the transforming growth factor-β superfamily that plays crucial roles during embryogenesis. recently, we have reported that nodal inhibits trophoblast cell proliferation, migration and invasion, but induces apoptosis in the human placenta. in this study, we examined the regulation of nodal by micrornas. in silico analysis of nodal 3'utr revealed a potential binding site for mir-378a-5p. in luciferase reporter assays, we found that mir-378a-5p suppressed the luciferase activity of a reporter plasmid containing nodal 3'utr but this suppressive effect was completely abolished when the predicted target site was mutated. western blot analysis showed that mir-378a-5p decreased whereas anti-mir-378a-5p increased nodal protein levels. these results indicate that mir-378a-5p targets nodal 3'utr to repress its expression. stable transfection of the mir-378a-5p precursor, mir-378a, into htr8/svneo cells enhanced cell survival, proliferation, migration and invasion. transient transfection of mature mir-378a-5p mimic, and to a lesser extent, sirna targeting nodal, produced similar effects. however, anti-mir-378a-5p inhibited cell migration and invasion. in addition, overexpression of nodal reversed the invasion-promoting effect of mir-378a-5p. furthermore, mir-378a-5p enhanced, whereas anti-mir-378a-5p suppressed, the outgrowth and spreading of extravillous trophoblast cells in first trimester placental explants. finally, mir-378a-5p was detected in human placenta throughout different stages of gestation and in preterm pregnancies, placental mir-378a-5p levels were lower in preeclamptic patients than in healthy controls. taken together, these findings strongly suggest that mir-378a-5p plays an important role in human placental development by regulating trophoblast cell growth, survival, migration and invasion, and that mir-378a-5p exerts these effects, at least in part, through the suppression of nodal expression.",1
"background micrornas (mirnas) are endogenous, small non-coding rnas that play important roles in multiple biological processes. mir-20b has been reported to participate in breast cancer tumorigenic progression, however, the functional roles are still unclear and under debating. the aim of this study is to explicit the molecular mechanism of mir-20b underlying breast cancer tumorigenesis. results in the present study, we showed that mir-20b was overexpressed in human breast cancer tissues and cell lines compared with paired adjacent normal tissues and normal cell lines, respectively. we identified pten, a well-known tumor suppressor, as the functional downstream target of mir-20b. luciferase assays confirmed that mir-20b could directly bind to the 3' untranslated region(utr) of pten and suppress translation. alteration of mir-20b expression changed pten protein level but not mrna expression in zr-75-30 and mcf-7 breast cancer cells, suggesting mir-20b regulates pten gene expression at the posttranscriptional level. furthermore, upregulation of mir-20b significantly promoted the proliferation, colony formation and dna synthesis of zr-75-30 and mcf-7 breast cancer cells. conversely, knockdown of mir-20b expression inhibited the growth of breast cancer cells in vitro and in vivo. conclusion dysregulation of mir-20b plays critical roles in the breast cancer tumorigenesis, at least in part via targeting the tumor suppressor pten. this microrna may serve as a potential diagnostic marker and therapeutic target for breast cancer.",1
"the mir-302-367 cluster is specifically expressed in human embryonic stem cells and has been shown to convert human somatic cells into induced pluripotent stem cells. here, we investigated the role of the mir-302-367 cluster in cervical carcinoma. the cluster was not endogenously expressed in cervical cancer cells, and its ectopic expression did not reprogram the cervical cancer cells to an embryonic stem cell-like state. however, ectopic expression of the mir-302-367 cluster in hela and siha cervical cancer cells inhibited cell proliferation and tumor formation by blocking the g1/s cell cycle transition. we identified a new cell cycle regulatory pathway in which the mir-302-367 cluster directly down-regulated both cyclin d1 and akt1 and indirectly up-regulated p27(kip1) and p21(cip1), leading to the suppression of cervical cancer cell proliferation. our findings suggest that the mir-302-367 cluster may be used as a therapeutic reagent for the treatment of cervical carcinoma.",1
"morphogenesis is crucial to initiate physiological development and tumor invasion. here we show that a microrna controls zonation morphogenesis by targeting hyaluronan receptor cd44. we have developed a novel system to study microrna functions by generating constructs expressing pre-mirnas and mature mirnas. using this system, we have demonstrated that expression of mir-328 reduced cell adhesion, aggregation, and migration, and regulated formation of capillary structure. protein analysis indicated that mir-328 repressed cd44 expression. activities of luciferase constructs harboring the target site in cd44, but not the one containing mutation, were repressed by mir-328. zonation morphogenesis appeared in cells transfected by mir-328: mir-328-transfected cells were present on the surface of zonating structures while the control cells stayed in the middle. mir-328-mediated cd44 actions was validated by anti-cd44 antibody, hyaluronidase, cd44 sirna, and cd44 expression constructs. in vivo experiments showed that cd44-silencing cells appeared as layers on the surfaces of nodules or zonating structures. immuno-histochemistry also exhibited cd44-negative cells on the surface layers of normal rat livers and the internal zones of portal veins. our results demonstrate that mir-328 targets cd44, which is essential in regulating zonation morphogenesis: silencing of cd44 expression is essential in sealing the zonation structures to facilitate their extension and to inhibit complex expansion.",1
"given that mir-124 is preferentially expressed in differentiating and mature neurons and external granule cells of cerebellum are thought to be cells-of-origins of medulloblastomas, we investigated if mir-124 played a role in the development of medulloblastomas. quantitative expression analysis of 29 medulloblastomas demonstrated significant down-regulation of mir-124 in 21 (72%) tumors by at least 2-fold, with 11 of them exhibiting greater than 10-fold reduced level compared to normal cerebella (p < .01). ectopic expression of mir-124 in medulloblastoma cell lines, ons-76 and daoy, inhibited cell proliferation. using computational and expression analyses, solute carrier family 16, member 1 (slc16a1) was identified as a candidate target of mir-124. transfection of mir-124 resulted in down-regulation of slc16a1 at both transcript and protein levels. reporter assay with 3' untranslated region of slc16a1 cloned downstream of the luciferase gene showed reduced luciferase activity in the presence of mir-124, providing strong evidence that mir-124 is a direct regulator of slc16a1. expression analysis further revealed that slc16a1 transcript was elevated in 26 (90%) of 29 tumors examined. knockdown of slc16a1 by sirna induced cell death in medulloblastoma cells. slc16a1 functions to efflux lactic acid during aerobic glycolysis. we speculated that inhibition of slc16a1 function resulted in a decrease of intracellular ph to a lethal level. in conclusion, our study demonstrates that mir-124 deregulation is common in medulloblastomas, and restoration of its function inhibits cell proliferation, suggesting that mir-124 may act as a growth suppressor. our findings also raise the possibility that the mir-124/slc16a1 pathway may represent a novel therapeutic target for treatment of malignant medulloblastomas.",1
"relatively little is known about the evolutionary histories of most classes of non-protein coding rnas. here we consider y rnas, a relatively rarely studied group of related pol-iii transcripts. a single cluster of functional genes is preserved throughout tetrapod evolution, which however exhibits clade-specific tandem duplications, gene-losses, and rearrangements.",1
"spaced synaptic depolarization induces rapid axon terminal growth and the formation of new synaptic boutons at the drosophila larval neuromuscular junction (nmj). here, we identify a novel presynaptic function for the calcium/calmodulin-dependent kinase ii (camkii) protein in the control of activity-dependent synaptic growth. consistent with this function, we find that both total and phosphorylated camkii (p-camkii) are enriched in axon terminals. interestingly, p-camkii appears to be enriched at the presynaptic axon terminal membrane. moreover, levels of total camkii protein within presynaptic boutons globally increase within one hour following stimulation. these effects correlate with the activity-dependent formation of new presynaptic boutons. the increase in presynaptic camkii levels is inhibited by treatment with cyclohexamide suggesting a protein-synthesis dependent mechanism. we have previously found that acute spaced stimulation rapidly downregulates levels of neuronal micrornas (mirnas) that are required for the control of activity-dependent axon terminal growth at this synapse. the rapid activity-dependent accumulation of camkii protein within axon terminals is inhibited by overexpression of activity-regulated mir-289 in motor neurons. experiments in vitro using a camkii translational reporter show that mir-289 can directly repress the translation of camkii via a sequence motif found within the camkii 3' untranslated region (utr). collectively, our studies support the idea that presynaptic camkii acts downstream of synaptic stimulation and the mirna pathway to control rapid activity-dependent changes in synapse structure.",1
"micrornas (mirnas) are thought to have an important role in tumor metastasis by regulating diverse cellular pathways. here, we describe the function and regulation network of mir-206 in gastric cancer (gc) metastasis. mir-206 expression was downregulated in gc cells especially in high metastatic potential cells and was also significantly decreased in metastatic lesions compared with their corresponding primary tumor samples. both gain- and loss-of-function studies confirmed that mir-206 significantly suppressed gc cell invasion and metastasis both in vitro and in vivo. mechanistically, paired box gene 3 (pax3) was identified as a functional target of mir-206 in gc cells. mir-206 inhibited gc metastasis by negatively regulating expression of pax3. in addition, pax3 expression was markedly higher in gc tissues than in adjacent non-cancerous tissues. gc patients with positive pax3 expression had shorter overall survival times. transwell assays and in vivo metastasis assays demonstrated that overexpression of pax3 significantly promoted the invasiveness and pulmonary metastasis of gc cells. on the other hand, downregulation of pax3 markedly reduced cell metastatic potential. mechanistic investigations indicated that prometastasis function of pax3 was mediated by upregulating downstream target met. moreover, we found that levels of pax3 and met were positively correlated in matched human gc specimens, and their coexpression was associated with poor prognoses. in conclusion, our results reveal that mir-206-pax3-met signaling is critical to gc metastasis. targeting the pathway described here may open new therapeutic prospects to restrict the metastatic potential of gc.",1
"micrornas (mirnas) are short noncoding rna molecules, which posttranscriptionally regulate genes expression and play crucial roles in diverse biological processes, such as development, differentiation, apoptosis and proliferation. here, we investigated the possible role of mirnas in the development of multidrug resistance (mdr) in human gastric and lung cancer cell lines. we found that mir-181b was downregulated in both multidrug-resistant human gastric cancer cell line sgc7901/vincristine (vcr) and multidrug-resistant human lung cancer cell line a549/cisplatin (cddp), and the downregulation of mir-181b in sgc7901/vcr and a549/cddp cells was concurrent with the upregulation of bcl2 protein, compared with the parental sgc7901 and a549 cell lines, respectively. in vitro drug sensitivity assay demonstrated that overexpression of mir-181b sensitized sgc7901/vcr and a549/cddp cells to anticancer drugs, respectively. the luciferase activity of a bcl2 3'-untranslated region-based reporter construct in sgc7901/vcr and a549/cddp cells suggests that a new target site in the 3'utr of bcl2 of the mature mir-181s (mir-181a, mir-181b, mir-181c and mir-181d) was found. enforced mir-181b expression reduced bcl2 protein level and sensitized sgc7901/vcr and a549/cddp cells to vcr-induced and cddp-induced apoptosis, respectively. taken together, our findings suggest that mir-181b could play a role in the development of mdr in both gastric and lung cancer cell lines, at least in part, by modulation of apoptosis via targeting bcl2.",1
"hepatic scavenger receptor class b type i (sr-bi) plays an important role in selective high-density lipoprotein cholesterol (hdl-c) uptake, which is a pivotal step of reverse cholesterol transport. in this study, the potential involvement of micrornas (mirnas) in posttranscriptional regulation of hepatic sr-bi and selective hdl-c uptake was investigated. the level of sr-bi expression was repressed by mirna 185 (mir-185), mir-96, and mir-223, while the uptake of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (dii)-hdl was decreased by 31.9% (p < 0.001), 23.9% (p < 0.05), and 15.4% (p < 0.05), respectively, in hepg2 cells. the inhibition of these mirnas by their anti-mirnas had opposite effects in these hepatic cells. the critical effect of mir-185 was further validated by the loss of regulation in constructs with mutated mir-185 target sites. in addition, these mirnas directly targeted the 3' untranslated region (utr) of sr-bi with a coordinated effect. interestingly, the decrease of mir-96 and mir-185 coincided with the increase of sr-bi in the livers of apoe ko mice on a high-fat diet. these data suggest that mir-185, mir-96, and mir-223 may repress selective hdl-c uptake through the inhibition of sr-bi in human hepatic cells, implying a novel mode of regulation of hepatic sr-bi and an important role of mirnas in modulating cholesterol metabolism.",1
"ribonuclease p (rnase p) is a ribonucleoprotein enzyme that cleaves precursor trna transcripts to give mature 5' ends. rnase p in eubacteria has a large, catalytic rna subunit and a small protein subunit that are required for precursor trna cleavage in vivo. although the eukaryotic holoenzymes have similar, large rna subunits, previous work in a number of systems has suggested that the eukaryotic enzymes require a greater protein content. we have purified the saccharomyces cerevisiae nuclear rnase p to apparent homogeneity, allowing the first comprehensive analysis of an unexpectedly complex subunit composition. peptide sequencing by ion trap mass spectrometry identifies nine proteins that copurify with the nuclear rnase p rna subunit, totaling 20-fold more protein than in the bacterial enzyme. all of these proteins are encoded by genes essential for rnase p activity and for cell viability. previous genetic studies suggested that four proteins might be subunits of both rnase p and rnase mrp, the related rrna processing enzyme. we demonstrate that all four of these proteins, pop1p, pop3p, pop4p, and rpp1p, are integral subunits of rnase p. in addition, four of the five newly identified protein subunits, pop5p, pop6p, pop7p, and pop8p, also appear to be shared between rnase p and rnase mrp. only one polypeptide, rpr2p, is unique to the rnase p holoenzyme by genetic depletion and immunoprecipitation studies. the large increase in the number of protein subunits over eubacterial rnase p is consistent with an increase in functional complexity in eukaryotes. the degree of structural similarity between nuclear rnase p and rnase mrp suggests that some aspects of their functions in pre-trna and pre-rrna processing pathways might overlap or be coordinated.",1
"animal microrna (mirna) target prediction is still a challenge, although many prediction programs have been exploited. mirnas exert their function through partially binding the messenger rnas (mrnas; likely at 3' untranslated regions ), which makes it possible to detect the mirna-mrna interactions in vitro by co-transfection of mirna and a luciferase reporter gene containing the target mrna fragment into mammalian cells under a dual-luciferase assay system. here, we constructed a human mirna expression library and used a dual-luciferase assay system to perform large-scale screens of interactions between mirnas and the 3'utrs of seven genes, which included more than 3,000 interactions with triplicate experiments for each interaction. the screening results showed that the 3'utr of one gene can be targeted by multiple mirnas. among the prediction algorithms, a bayesian phylogenetic mirna target identification algorithm and a support vector machine (svm) presented a relatively better performance (27% for eimmo and 24.7% for mirdb) against the average precision (17.3%) of the nine prediction programs used here. additionally, we noticed that a relatively high conservation level was shown at the mirna 3' end targeted regions, as well as the 5' end (seed region) binding sites.",1
"there has been a great expansion in the number of small regulatory rnas identified in bacteria. some of these small rnas repress the synthesis of potentially toxic proteins. generally the toxin proteins are hydrophobic and less than 60 amino acids in length, and the corresponding antitoxin small rna genes are antisense to the toxin genes or share long stretches of complementarity with the target mrnas. given their short length, only a limited number of these type i toxin-antitoxin loci have been identified, but it is predicted that many remain to be found. already their characterization has given insights into regulation by small rnas, has suggested functions for the small toxic proteins at the cell membrane, and has led to practical applications for some of the type i toxin-antitoxin loci.",1
"pkr, an interferon (ifn)-inducible protein kinase activated by double-stranded rna, inhibits translation by phosphorylating the initiation factor eif2alpha chain. we show that human ifn-gamma mrna uses local activation of pkr in the cell to control its own translation yield. ifn-gamma mrna activates pkr through a pseudoknot in its 5' untranslated region. mutations that impair pseudoknot stability reduce the ability to activate pkr and strongly increase the translation efficiency of ifn-gamma mrna. nonphosphorylatable mutant eif2alpha, knockout of pkr and pkr inhibitors 2-aminopurine, transdominant-negative pkr, or vaccinia e3l correspondingly enhances translation of ifn-gamma mrna. the potential to form the pseudoknot is phylogenetically conserved. we propose that the rna pseudoknot acts to adjust translation of ifn-gamma mrna to the pkr level expressed in the cell.",1
"a 190-nucleotide (nt) packaging signal (ps) located in the 3' end of open reading frame 1b in the mouse hepatitis virus, a group iia coronavirus, was previously postulated to direct genome rna packaging. based on phylogenetic data and structure probing, we have identified a 95-nt hairpin within the 190-nt ps domain which is conserved in all group iia coronaviruses but not in the severe acute respiratory syndrome coronavirus (group iib), group i coronaviruses, or group iii coronaviruses. the hairpin is composed of six copies of a repeating structural subunit that consists of 2-nt bulges and 5-bp stems. we propose that repeating aa bulges are characteristic features of group iia pss.",1
"purpose microrna-21 (mirna-21) has proto-oncogenic properties, although no mirna-21-specific targets have been found in head and neck squamous cell carcinoma (hnscc). further study of mirna-21 and its specific targets is essential to understanding hnscc biology. experimental design mirna expression profiles of 10 hnsccs and 10 normal mucosa samples were investigated using a custom mirna microarray. thirteen hnsccs and five normal mucosa primary tissue specimens underwent mrna expression microarray analysis. to identify mirna-21 downstream targets, oral keratinocyte cells were subjected to microarray analysis after mirna-21 transient transfection. mirna and mrna expression were validated by reverse transcription quantitative polymerase chain reaction (rt-qpcr) in a separate cohort of 16 hnsccs and 15 normal mucosal samples. microarray and bioinformatics analyses were integrated to identify potential gene targets. in vitro assays looked at the function and interaction of mirna-21 and its specific gene targets. results mirna-21 was upregulated in hnsccs and stimulated cell growth. integrated analyses identified clusterin (clu) as a potential mirna-21 gene target. clu was downregulated after forced expression of mirna-21 in normal and hnscc cell lines. the activity of a luciferase construct containing the 3'-untranslated region (utr) of clu was repressed by the ectopic expression of mirna-21. clu was also downregulated in primary hnsccs and correlated with mirna-21 overexpression. clu variant 1 (clu-1) was the predominant splice variant in hnsccs and showed growth suppression function that was reversed by mirna-21 overexpression. conclusions clu is a specific, functional target of oncogenic mirna-21 in hnsccs. clu-1 isoform is the predominant growth-suppressive variant targeted by mirna-21.",1
"micrornas (mirnas) are essential components of gene regulation, but identification of mirna targets remains a major challenge. most target prediction and discovery relies on perfect complementarity of the mirna seed to the 3' untranslated region (utr). however, it is unclear to what extent mirnas target sites without seed matches. here, we performed a transcriptome-wide identification of the endogenous targets of a single mirna-mir-155-in a genetically controlled manner. we found that approximately 40% of mir-155-dependent argonaute binding occurs at sites without perfect seed matches. the majority of these noncanonical sites feature extensive complementarity to the mirna seed with one mismatch. these noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. thus, noncanonical mirna binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.",1
"the quest for non-coding rnas (ncrnas) in the last few years has revealed a surprisingly large number of small rnas belonging to previously known as well as entirely novel classes. computational and experimental approaches have uncovered new ncrnas in all kingdoms of life. in this work, we used a shotgun cloning approach to construct full-length cdna libraries of small rnas from the eukaryotic model organism dictyostelium discoideum. interestingly, two entirely novel classes of rnas were identified of which one is developmentally regulated. the rnas within each class share conserved 5'- and 3'-termini that can potentially form stem structures. rnas of both classes show predominantly cytoplasmic localization. in addition, based on conserved structure and/or sequence motifs, several of the identified ncrnas could be divided into classes known from other organisms, e.g. 18 small nucleolar rna candidates (17 box c/d, of which a few are developmentally regulated, and one box h/aca). two ncrnas showed a high degree of similarity to the small nuclear u2 rna and signal recognition particle rna (srp rna), respectively. furthermore, the majority of the regions upstream of the sequences encoding the isolated rnas share conserved motifs that may constitute new promoter elements.",1
"mir-185 expression has been associated with many cancers. however, the roles of mir-185 in human breast cancer remain elusive. here, we found that mir-185 expression was decreased in human breast cancer tissues compared with healthy tissue controls. up-regulation of mir-185 inhibited breast cancer cell proliferation and invasion and vice versa. mir-185 was shown to bind to the 3′-untranslated region (utr) of vascular endothelial growth factor a (vegfa), and a significant inverse correlation was found between mir-185 and vegfa. vegfa overexpression partially restored the inhibition of cell proliferation and invasion that was induced by mir-185, and vice versa. additionally, vegfa expression was found to be high in human breast cancer tissues. thus, mir-185-mediated vegfa targeting may be involved in breast cancer formation.",1
"7sk rna is a highly abundant noncoding rna in mammalian cells whose function in transcriptional regulation has only recently been elucidated. despite its highly conserved sequence throughout vertebrates, all attempts to discover 7sk rna homologues in invertebrate species have failed so far. here we report on a combined experimental and computational survey that succeeded in discovering 7sk rnas in most of the major deuterostome clades and in two protostome phyla: mollusks and annelids. despite major efforts, no candidates were found in any of the many available ecdysozoan genomes, however. the additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3' and 5' stem-loop motifs, and provide evidence for a third, structurally well-conserved domain.",1
"micrornas (mirnas) play critical roles in retinoblastoma (rb) initiation and progression, aberrant expression of mir-145 had been frequently reported in cancer studies. however, the role and mechanism of its function in rb is still unclear. in this study, our data showed that mir-145 was downregulated in rb tissues and cell lines. overexpression of mir-145 suppressed rb cell proliferation, migration and invasion in vitro. adam19 was identified as a direct target of mir-145. silencing of adam19 significantly inhibited rb cell proliferation, migration and invasion. in addition, a reverse correlation between mir-145 and adam19 expression was noted in rb tissues. taken together, these findings suggested that mir-145 functions as a tumor suppressor in rb by directly targeting adam19. mir-145 could be an anticancer therapeutic target for rb patients.",1
"hodgkin lymphoma (hl) is derived from preapoptotic germinal center b cells, although a general loss of b cell phenotype is noted. using quantitative reverse transcription-polymerase chain reaction and mirna microarray, we determined the microrna (mirna) profile of hl and compared this with the profile of a panel of b-cell non-hodgkin lymphomas. the two methods showed a strong correlation for the detection of mirna expression levels. the hl-specific mirna included mir-17-92 cluster members, mir-16, mir-21, mir-24, and mir-155. using a large panel of cell lines, we found differential expression between hl and other b-cell lymphoma-derived cell lines for 27 mirna. a significant down-regulation in hl compared to non-hodgkin lymphoma was observed only for mir-150. next, we performed target gene validation of predicted target genes for mir-155, which is highly expressed in hl and is differentially expressed between hl and burkitt lymphoma. using luciferase reporter assays, we validated 11 predicted mir-155 target genes in three different hl cell lines. we demonstrated that agtr1, fgf7, znf537, zic3, and ikbke are true mir-155 target genes in hl.",1
"gata-4 is an important transcription factor involved in several developmental processes of the heart, such as cardiac myocyte proliferation, differentiation and survival. the precise mechanisms underlying the regulation of gata-4 remain unclear, this is especially true for the mechanisms that mediate the post-transcriptional regulation of gata-4. here, we demonstrate that mir-200b, a member of the mir-200 family, is a critical regulator of gata-4. overexpression of mir-200b leads to the downregulation of gata-4 mrna and a decrease in gata-4 protein levels. moreover, mir-200b not only inhibits cell growth and differentiation but also reverses the growth response mediated by gata-4, whereas depletion of mir-200b leads to a slight reversal of the anti-growth response achieved by knocking down endogenous gata-4. more importantly, the cell cycle-associated gene cyclin d1, which is a downstream target of gata-4, is also regulated by mir-200b. thus, mir-200b targets gata-4 to downregulate the expression of cyclin d1 and myosin heavy chain (mhc), thereby regulating cell growth and differentiation.",1
"how mirnas recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. several features, such as perfect pairing of the mirna seed, additional pairing in the 3' region of the mirna, relative position in the 3' utr, and the a/u content of the environment of the putative site, have been found to be relevant. here we have used a large number of previously published data sets to assess the power that various sequence and structure features have in distinguishing between putative sites that do and those that do not appear to be functional. we found that although different data sets give widely different answers when it comes to ranking the relative importance of these features, the sites inferred from most transcriptomics experiments, as well as from comparative genomics, appear similar at this level. this suggests that mirna target sites have been selected in evolution on their ability to trigger mrna degradation. to understand at what step in the mirna-induced response individual features play a role, we transfected human hek293 cells with mirnas and analyzed the association of argonaute/eif2c-mirna complexes with target mrnas and the degradation of these messages. we found that structural features of the target site are only important for argonaute/eif2c binding, while sequence features such as the a/u content of the 3' utr are important for mrna degradation.",1
"aberrant expression of dna polymerase beta, a key enzyme involved in base excision repair, leads to genetic instability and carcinogenesis. pol beta expression has been previously shown to be regulated at the level of transcription, but there is also evidence of post-transcriptional regulation, since rat transcripts undergo alternative polyadenylation, and the resulting 3'utr contain at least one regulatory element. data presented here indicate that rna of the short 3'utr folds to form a strong secondary structure (hairpin). its regulatory role was established utilizing a luciferase-based reporter system. further studies led to the identification of a protein factor, which binds to this element-the anti-apoptotic, cytoskeleton-related protein hax-1. the results of in vitro binding analysis indicate that the formation of the rna-protein complex is significantly impaired by disruption of the hairpin motif. we demonstrate that hax-1 binds to pol beta mrna exclusively in the form of a dimer. biochemical analysis revealed the presence of hax-1 in mitochondria, but also in the nuclear matrix, which, along with its transcript-binding properties, suggests that hax-1 plays a role in post-transcriptional regulation of expression of pol beta.",1
"the currently available yeast mitochondrial dna (mtdna) sequence is incomplete, contains many errors and is derived from several polymorphic strains. here, we report that the mtdna sequence of the strain used for nuclear genome sequencing assembles into a circular map of 85,779 bp which includes 10 kb of new sequence. we give a list of seven small hypothetical open reading frames (orfs). hot spots of point mutations are found in exons near the insertion sites of optional mobile group i intron-related sequences. our data suggest that shuffling of mobile elements plays an important role in the remodelling of the yeast mitochondrial genome.",1
"polycomb group (pcg) proteins exert essential functions in the most disparate biological processes. the contribution of pcg proteins to cell commitment and differentiation relates to their ability to repress transcription of developmental regulators in embryonic stem (es) cells and in committed cell lineages, including skeletal muscle cells (smc). pcg proteins are preferentially removed from transcribed regions, but the underlying mechanisms remain unclear. here, pcg proteins are found to occupy and repress transcription from an intronic region containing the microrna mir-214 in undifferentiated smc. differentiation coincides with pcg disengagement, recruitment of the developmental regulators myod and myogenin, and activation of mir-214 transcription. once transcribed, mir-214 negatively feeds back on pcg by targeting the ezh2 3'utr, the catalytic subunit of the prc2 complex. mir-214-mediated ezh2 protein reduction accelerates smc differentiation and promotes unscheduled transcription of developmental regulators in es cells. thus, mir-214 and ezh2 establish a regulatory loop controlling pcg-dependent gene expression during differentiation.",1
"previously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preq1). the enormous expansion of available genomic dna sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover novel classes. we conducted bioinformatics searches on microbial genomic dna data sets to discover numerous additional examples belonging to the two previously known riboswitch classes for preq1 (classes preq1-i and preq1-ii), including some structural variants that further restrict ligand specificity. additionally, we discovered a third preq1-binding riboswitch class (preq1-iii) that is structurally distinct from previously known classes. these findings demonstrate that numerous organisms monitor the concentrations of this modified nucleobase by exploiting one or more riboswitch classes for this widespread compound.",1
"5s rrna extends from the central protuberance of the large ribosomal subunit, through the a-site finger, and down to the gtpase-associated center. here, we present a structure-function analysis of seven 5s rrna alleles which are sufficient for viability in the yeast saccharomyces cerevisiae when expressed in the absence of wild-type 5s rrnas, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5s rrna. this analysis supports the hypothesis that 5s rrna serves to link together several different functional centers of the ribosome. data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5s rrna, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression.",1
"recent studies suggest that microrna (mirna) plays important roles in the control of immune response and tolerance. we previously found that the expression level of antimicrobial peptide gene drosomycin (drs) is decreased in mir-964 overexpressing flies. here, we further verified that mir-964 deficiency leads to hyper-activation of drs. in addition, we employed three widely-used bioinformatic algorithms to screen potential mir-964 targets. finally, we identified that mir-964 modulates toll signaling pathway, at least in part, by repressing the expression of drs. taken together, our study identifies mir-964 as a modulator of toll signaling and enriches the repertoire of immune-modulating mirnas in drosophila.",1
"micrornas (mirna) regulate complex patterns of gene expression, and the relevance of altered mirna expression to ovarian cancer remains to be elucidated. by comprehensively profiling expression of mirnas and mrnas in serous ovarian tumors and cell lines and normal ovarian surface epithelium, we identified hundreds of potential mirna-mrna targeting associations underlying cancer. functional overexpression of mir-31, the most underexpressed mirna in serous ovarian cancer, repressed predicted mir-31 gene targets including the cell cycle regulator e2f2. mir31 and cdkn2a, which encode p14(arf) and p16(ink4a), are located at 9p21.3, a genomic region commonly deleted in ovarian and other cancers. p14(arf) promotes p53 activity, and e2f2 overexpression in p53 wild-type cells normally leads via p14(arf) to an induction of p53-dependent apoptosis. in a number of serous cancer cell lines with a dysfunctional p53 pathway (i.e., ovcar8, ovca433, and skov3), mir-31 overexpression inhibited proliferation and induced apoptosis; however, in other lines (i.e., hey and ovsayo) with functional p53, mir-31 had no effect. additionally, the osteosarcoma cell line u2os and the prostate cancer cell line pc3 (p14(arf)-deficient and p53-deficient, respectively) were also sensitive to mir-31. furthermore, mir-31 overexpression induced a global gene expression pattern in ovcar8 associated with better prognosis in tumors from patients with advanced stage serous ovarian cancer, potentially affecting many genes underlying disease progression. our findings reveal that loss of mir-31 is associated with defects in the p53 pathway and functions in serous ovarian cancer and other cancers, suggesting that patients with cancers deficient in p53 activity might benefit from therapeutic delivery of mir-31.",1
"the regulation of function of endothelial cell-cell junctions is fundamental in sustaining vascular integrity. the polycistronic microrna (mir) complexes containing mir-23a-27a-24-2, and 23b-27b-24-1 are predicted to target the majority of major endothelial junctional proteins. we focus on mir-23a and mir-23b, and investigate the functional effects of these mirs on junctions. while mir-23a and 23b only differ by 1 nucleotide (g19) outside the seed region and thus are predicted to have the same targets, they function differently with mir-23a inhibiting permeability and mir-23b inhibiting angiogenesis. both mirs target the junctional attractive molecule (tight junction protein 2) zo-2 and the repulsive molecule junctional adhesion molecule c (jam-c), although the inhibition of jam-c by mir-23a is more profound than by mir-23b. the difference in potency is attributable to differences at g19 since a mutation of the t17, the g19 binding site of mir-23b in the 3'utr of jam-c restores identity. we also show that the pattern of expression of mir-23a and mir-23b and their targets are different. thus, the paralogues mir-23a and mir-23b can have profoundly different effects on endothelial cell function due at least partially to selective effects on target proteins and differences in expression patterns of the mirs. this work exposes a hitherto unappreciated complexity in therapeutically targeting mirs.",1
"bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. one of these motifs is found exclusively in the family streptococcaceae within the 5' untranslated regions (utrs) of genes encoding the hypothetical membrane protein classified as cog4708 or duf988. while the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine(1) (preq(1)) has been identified in the 5' utr of homologous genes in many firmicute species of bacteria outside of streptococcaceae. here we show that a representative of the cog4708 rna motif from streptococcus pneumoniae r6 also binds preq(1). furthermore, representatives of this rna have structural and molecular recognition characteristics that are distinct from those of the previously described preq(1) riboswitch class. preq(1) is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. additionally, the association of preq(1) binding rnas with most genes encoding proteins classified as cog4708 strongly suggests that these proteins function as transporters for preq(1) or another queuosine biosynthetic intermediate.",1
"many or all of the sites of pseudouridine (psi) formation in eukaryotic rrna are selected by site-specific base-pairing with members of the box h + aca class of small nucleolar rnas (snornas). database searches previously identified strong homology between the rat nucleolar protein nap57p, its yeast homolog cbf5p, and the escherichia coli psi synthase trub/p35. we therefore tested whether cbf5p is required for synthesis of psi in the yeast rrna. after genetic depletion of cbf5p, formation of psi in the pre-rrna is dramatically inhibited, resulting in accumulation of the unmodified rrna. protein a-tagged cbf5p coprecipitates all tested members of the box h + aca snornas but not box c + d snornas or other rna species. genetic depletion of cbf5p leads to depletion of all box h + aca snornas. these include snr30, which is required for pre-rrna processing. depletion of cbf5p also results in a pre-rrna processing defect similar to that seen on depletion of snr30. we conclude that cbf5p is likely to be the rrna psi synthase and is an integral component of the box h + aca class of snornps, which function to target the enzyme to its site of action.",1
"mir-7 (microrna-7) has been characterized as a tumour suppressor in several human cancers. it targets a number of proto-oncogenes that contribute to cell proliferation and survival. however, the mechanism(s) by which mir-7 suppresses tumorigenesis in tscc (tongue squamous cell carcinoma) is unknown. the present bioinformatics analysis revealed that igf1r (insulin-like growth factor 1 receptor) mrna is a potential target for mir-7. ectopic transfection of mir-7 led to a significant reduction in igf1r at both the mrna and protein levels in tscc cells. knockdown of mir-7 in tscc cells enhanced igf1r expression. direct targeting of mir-7 to three candidate binding sequences located in the 3'-untranslated region of igf1r mrna was confirmed using luciferase-reporter-gene assays. the mir-7-mediated down-regulation of igf1r expression attenuated the igf1 (insulin-like growth factor 1)-induced activation of akt (protein kinase b) in tscc cell lines, which in turn resulted in a reduction in cell proliferation and cell-cycle arrest, and an enhanced apoptotic rate. taken together, the present results demonstrated that mir-7 regulates the igf1r/akt signalling pathway by post-transcriptional regulation of igf1r. our results indicate that mir-7 plays an important role in tscc and may serve as a novel therapeutic target for tscc patients.",1
"sensorineural hearing loss (snhl) is the most common cause of hearing impairment. one of the essential steps to prevent progressive hearing loss is to protect spiral ganglion neurons (sgns) from ongoing degeneration. micrornas and tmprss3 (transmembrane protease, serine 3) have been reported to be involved in development of sgns and genesis of snhl. the aim of this study was to investigate the role of mir-204 and tmprss3 in sgns. effect of mir-204 on cell viability of sgns was first examined using mtt (3--2,5 diphenyl tetrazolium bromide) assay. expression of tmprss3 in sgns with or without addition of mir-204 was assessed by real-time pcr and western blot further. a luciferase reporter activity assay was conducted to confirm target association between mir-204 and 3'-utr of tmprss3. finally, role of tmprss3 on cell viability of sgns was evaluated by transfection of tmprss3 sirna. cell viability of sgns was suppressed by mir-204 in a concentration-dependent manner. overexpression of mir-204 reduced expression of tmprss3 in sgns at both mrna and protein levels. binding to the 3'-utr of tmprss3 by mir-204 was identified by luciferase assay. knockdown of tmprss3 by sirna significantly inhibits cell viability of sgns. mir-204 could be a potential therapeutic target in sensorineural hearing loss.",1
"streptomyces are predominantly soil-dwelling bacteria that are best known for their multicellular life cycle and their prodigious metabolic capabilities. they are also renowned for their regulatory capacity and flexibility, with each species encoding >60 sigma factors, a multitude of transcription factors, and an increasing number of small regulatory rnas. here, we describe our characterization of a conserved small rna (srna), scr4677. in the model species streptomyces coelicolor, this srna is located in the intergenic region separating sco4677 (an anti-sigma factor-encoding gene) and sco4676 (a putative regulatory protein-encoding gene), close to the sco4676 translation start site in an antisense orientation. there appears to be considerable genetic interplay between these different gene products, with wild type expression of scr4677 requiring function of the anti-sigma factor sco4677, and scr4677 in turn influencing the abundance of sco4676-associated transcripts. the scr4677-mediated effects were independent of rnase iii (a double stranded rna-specific nuclease), with rnase iii having an unexpectedly positive influence on the level of sco4676-associated transcripts. we have shown that both sco4676 and sco4677 affect the production of the blue-pigmented antibiotic actinorhodin under specific growth conditions, and that this activity appears to be independent of scr4677.",1
"mirnas can have pleiotropic effects by targeting multiple genes belonging to diverse signalling networks. alternatively, mirnas can enhance the potency of their cellular effects by targeting multiple genes within the same genetic pathway. previously, we and others have demonstrated that mir-335 is a potent suppressor of tumour cell migration, invasion and metastasis, in part by targeting several genes involved in these cellular processes, including rock1, mapk1, lrg1, sp1 and sox4. here, we demonstrate that direct targeting of multiple members of the formin family of actin nucleators contributes to the inhibitory effects of mir-335 in neuroblastoma cells. we demonstrate that mir-335 regulates the expression of at least five formin family members and validate three family members, fmnl3, fmn2 and daam2, as direct targets of mir-335. the contribution of the formin family genes to cancer progression and metastasis has recently begun to emerge and here we demonstrate for the first time the ability of fmn2 and daam2 to regulate tumour cell migration and invasion, using sirna-mediated inhibition of each of these formin genes. finally, we demonstrate that the formin genes, in particular fmnl3, are responsible for the protrusion of actin-rich filopodia structures that contribute to the enhanced migratory and invasive potential associated with reduced expression of mir-335. thus, direct targeting of the formin family contributes to the metastasis suppressing abilities of mir-335 by providing a direct regulatory link to the actin assembly machinery of the cell. we conclude that mir-335 is a master regulator of tumour cell migration and invasion by directly targeting a plethora of genes that effectively control cell migratory processes.",1
"aim microangiopathy due to endothelial dysfunction is a major contributing factor to the development of diabetes-induced cardiovascular disease (cvd). dysregulation of endothelial-specific micrornas (mirs) is correlated with impaired angiogenesis and cell survival. we investigated the profile of two angiomirs, mir-126, and mir-132, in the plasma of type 2 diabetic individuals without any known history of cvd as well as in the cardiac tissues collected from diabetics undergoing cardiac surgery. methods and results the presence of diabetes alone significantly decreased both angiomirs in the plasma and the myocardium. the down-regulation of angiomirs was also associated with reduced capillaries and arterioles and increased endothelial cell apoptosis, the hallmark of microangiopathy. importantly, a time course study in a type 2 diabetic mouse model confirmed that the down-regulation of angiomirs preceded endothelial apoptosis as well as alterations in the density of the microvasculature. finally, therapeutic overexpression of both angiomirs in diabetic aortic rings and human umbilical vein endothelial cells exposed to high glucose (hg) abrogated the deleterious effects of diabetes and hg on cell survival and proliferation and restored their angiogenic potential. conclusions these novel findings demonstrate that the down-regulation of angiomirs is a major underlying mechanism for the development of microangiopathy in diabetic hearts. therefore, therapeutic restoration of angiomirs could become a potential approach to combat the cardiovascular complications of diabetes.",1
"toll-like receptors (tlrs) are important pathogen recognition molecules and are key to epithelial immune responses to microbial infection. however, the molecular mechanisms that regulate tlr expression in epithelia are obscure. micro-rnas play important roles in a wide range of biological events through post-transcriptional suppression of target mrnas. here we report that human biliary epithelial cells (cholangiocytes) express let-7 family members, micro-rnas with complementarity to tlr4 mrna. we found that let-7 regulates tlr4 expression via post-transcriptional suppression in cultured human cholangiocytes. infection of cultured human cholangiocytes with cryptosporidium parvum, a parasite that causes intestinal and biliary disease, results in decreased expression of primary let-7i and mature let-7 in a myd88/nf-kappab-dependent manner. the decreased let-7 expression is associated with c. parvum-induced up-regulation of tlr4 in infected cells. moreover, experimentally induced suppression or forced expression of let-7i causes reciprocal alterations in c. parvum-induced tlr4 protein expression, and consequently, infection dynamics of c. parvum in vitro. these results indicate that let-7i regulates tlr4 expression in cholangiocytes and contributes to epithelial immune responses against c. parvum infection. furthermore, the data raise the possibility that micro-rna-mediated post-transcriptional pathways may be critical to host-cell regulatory responses to microbial infection in general.",1
"microrna 21 (mir-21) has been implicated in various aspects of carcinogenesis. however, its function and molecular mechanism in cervical squamous carcinoma have not been studied. using taqman quantitative real-time pcr and northern blot, we confirmed that mir-21 is significantly overexpressed in human cervical squamous cancer tissues and cell lines. remarkably, we showed that the level of mir-21 correlates with the tumor differentiation and nodal status by ish. furthermore, we demonstrated that mir-21 regulates proliferation, apoptosis, and migration of hpv16-positive cervical squamous cells. in order to identify candidate target genes for mir-21, we used gene expression profiling. by luciferase reporter assays, we confirmed that ccl20 is one of its target genes, which is related to the hpv16 e6 and e7 oncogenes. our results suggest that mir-21 may be involved in cervical squamous cell tumorigenesis.",1
"nidoviruses produce an extensive 3'-coterminal nested set of subgenomic mrnas, which are used to express their structural proteins. in addition, arterivirus and coronavirus mrnas contain a common 5' leader sequence, derived from the genomic 5' end. the joining of this leader sequence to different segments (mrna bodies) from the genomic 3'-proximal region presumably involves a unique mechanism of discontinuous minus-strand rna synthesis. key elements in this process are the so-called transcription-regulating sequences (trss), which determine a base-pairing interaction between sense and antisense viral rna that is essential for leader-to-body joining. to identify rna structures in the 5'-proximal region of the equine arteritis virus genome that may be involved in subgenomic mrna synthesis, a detailed secondary rna structure model was established using bioinformatics, phylogenetic analysis, and rna structure probing. according to this structure model, the leader trs is located in the loop of a prominent hairpin (leader trs hairpin; lth). the importance of the lth was supported by the results of a mutagenesis study using an eav molecular clone. besides evidence for a direct role of the lth in subgenomic rna synthesis, indications for a role of the lth region in genome replication and/or translation were obtained. similar lth structures could be predicted for the 5'-proximal region of all arterivirus genomes and, interestingly, also for most coronaviruses. thus, we postulate that the lth is a key structural element in the discontinuous subgenomic rna synthesis and is likely critical for leader trs function.",1
"micrornas (mirnas) are a class of 20-24 nt non-coding rnas that regulate gene expression primarily through post-transcriptional repression or mrna degradation in a sequence-specific manner. the roles of mirnas are just beginning to be understood, but the study of mirna function has been limited by poor understanding of the general principles of gene regulation by mirnas. here we used cne cells from a human nasopharyngeal carcinoma cell line as a cellular system to investigate mirna-directed regulation of vegf and other angiogenic factors under hypoxia, and to explore the principles of gene regulation by mirnas. through computational analysis, 96 mirnas were predicted as putative regulators of vegf. but when we analyzed the mirna expression profile of cne and four other vegf-expressing cell lines, we found that only some of these mirnas could be involved in vegf regulation, and that vegf may be regulated by different mirnas that were differentially chosen from 96 putative regulatory mirnas of vegf in different cells. some of these mirnas also co-regulate other angiogenic factors (differential regulation and co-regulation principle). we also found that vegf was regulated by multiple mirnas using different combinations, including both coordinate and competitive interactions. the coordinate principle states that mirnas with independent binding sites in a gene can produce coordinate action to increase the repressive effect of mirnas on this gene. by contrast, the competitive principle states when multiple mirnas compete with each other for a common binding site, or when a functional mirna competes with a false positive mirna for the same binding site, the repressive effects of mirnas may be decreased. through the competitive principle, false positive mirnas, which cannot directly repress gene expression, can sometimes play a role in mirna-mediated gene regulation. the competitive principle, differential regulation, multi-mirna binding sites, and false positive mirnas might be useful strategies in the avoidance of unwanted cross-action among genes targeted by mirnas with multiple targets.",1
"hedgehog (hh) pathway signaling is crucial for the maintenance of blood cell progenitors in the lymph gland hematopoietic organ present in drosophila third instar larvae. previous studies from our lab have likewise shown the importance of the mir-7 and bag of marbles (bam) genes in maintaining the progenitor state. thus, we sought to investigate a possible interaction between the hh pathway and mir-7/bam in the prohemocyte population within this hematopoietic tissue. gain of function mir-7 was able to rescue a blood cell progenitor depletion phenotype caused by patched (ptc) inhibition of hh pathway signaling in these cells. similarly, expression of a dominant/negative version of ptc was able to rescue the severe reduction of prohemocytes due to bam loss of function. furthermore, we demonstrated that suppressor of fused , another known inhibitor of hh signaling, likely serves as a translational repression target of the mir-7 mirna. our results suggest the mir-7/bam combination regulates the hh signaling network through repression of su(fu) to maintain hemocyte progenitors in the larval lymph gland.",1
"although there is abundant evidence that individual microrna (mirna) loci repress large cohorts of targets, large-scale knockout studies suggest that most mirnas are phenotypically dispensable. here, we identify a rare case of developmental cell specification that is highly dependent on mirna control of an individual target. we observe that binary cell fate choice in the drosophila melanogaster peripheral sensory organ lineage is controlled by the non-neuronally expressed mir-279/996 cluster, with a majority of notum sensory organs exhibiting transformation of sheath cells into ectopic neurons. the mir-279/996 defect phenocopies notch loss of function during the sheath-neuron cell fate decision, suggesting the mirnas facilitate notch signaling. consistent with this, mir-279/996 knockouts are strongly enhanced by notch heterozygosity, and activated nuclear notch is impaired in the mirna mutant. although hairless (h) is the canonical nuclear notch pathway inhibitor, and h heterozygotes exhibit bristle cell fate phenotypes reflecting gain-of-notch signaling, h/+ does not rescue mir-279/996 mutants. instead, we identify insensible (insb), another neural nuclear notch pathway inhibitor, as a critical direct mir-279/996 target. insb is posttranscriptionally restricted to neurons by these mirnas, and its heterozygosity strongly suppresses ectopic peripheral nervous system neurons in mir-279/996 mutants. thus, proper assembly of multicellular mechanosensory organs requires a double-negative circuit involving mirna-mediated suppression of a notch repressor to assign non-neuronal cell fate.",1
"notch (n) signaling is central to the self-renewal of neural stem cells (nscs) and other tissue stem cells. its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases. how n regulates stem cell behavior in health and disease is not well understood. here we show that n regulates bantam (ban) microrna to impact cell growth, a process key to nsc maintenance and particularly relied upon by tumor-forming cancer stem cells. notch signaling directly regulates ban expression at the transcriptional level, and ban in turn feedback regulates n activity through negative regulation of the notch inhibitor numb. this feedback regulatory mechanism helps maintain the robustness of n signaling activity and nsc fate. moreover, we show that a numb-myc axis mediates the effects of ban on nucleolar and cellular growth independently or downstream of n. our results highlight intricate transcriptional as well as translational control mechanisms and feedback regulation in the n signaling network, with important implications for nsc biology and cancer biology.",1
"lung cancer is the most common type of cancer-related death in developed countries. micrornas (mirnas) are small non-coding rnas, which regulates gene expression in cancer. recent studies demonstrate that the microrna-293-3p (mir-293-3p) may play as an oncogene or a tumor suppressor. however, its expression and roles in non-small cell lung cancer (nsclc) is not known. in this study, our purpose is to investigate the expression and roles of mir-296-3p in nsclc. the findings indicated that mir296-3p inhibited nsclc cell proliferation, enhance the drug resistance, and apoptosis. data of luciferase reporter assays demonstrated that the cx3cr1 gene was a direct regulator of tumorsuppressive mir296-3p. moreover, overexpressed cx3cr1 was confirmed in nsclc clinical specimens. inhibition of cx3cr1 could inhibit cancer cellular survival and increase chemotherapy sensitivity. there was a negative relationship between mir296-3p and cx3cr1 expression in nsclc tissues. our study elucidates that mir296-3p plays a suppressive role in nsclc by inhibiting cx3cr1 expression.",1
"objective abdominal aortic aneurysm (aaa) is characterized as a progressive dilation and degradation of the aortic wall, associated with activation of matrix metalloproteinases (mmps) and inflammation. emerging evidence indicates a role for micrornas (mirnas) in aaa pathogenesis, but it is unclear whether abdominal aortic endothelial mirnas play a role in the disease process. we aimed to identify mirnas in the abdominal aortic endothelium that play a critical role in aaa development. approach and results the mouse model of aaa induced by angiotensin ii infusion was used in this study. through a mirna array and validation study, we initially identified the murine-specific mir-712 and subsequently its human/murine homolog mir-205 as angiotensin ii-induced mirnas in the abdominal aortic endothelium in vivo and in vitro. mechanistically, mir-712 stimulated mmp activity in the aortic wall by directly targeting 2 mmp inhibitors: tissue inhibitor of metalloproteinase 3 (timp3) and reversion-inducing cysteine-rich protein with kazal motifs (reck). silencing of mir-712 and mir-205 by using anti-mir-712 and anti-mir-205, respectively, significantly decreased the aortic mmp activity and inflammation, preventing aaa development in angiotensin ii-infused apoe(-/-) mice. further, upregulation of 4 angiotensin ii-sensitive mirnas, mir-205, -21, -133b, and -378, identified in this murine study were confirmed in human aaa samples compared with nondiseased control. conclusions our results demonstrate that angiotensin ii-sensitive mir-712 and its human homolog mir-205 downregulate timp3 and reck, which in turn stimulate aortic mmp activity and inflammation, leading to aaa development. targeting these mirnas may be a novel therapeutic strategy to prevent aaa.",1
"cutaneous homeostasis and innate immunity is procured by a complex circuitry of intercellular cytokine signaling. micrornas are important posttranscriptional regulators of keratinocyte gene expression and assist in modulating the fine balance between cell proliferation and differentiation in skin. a characteristic microrna profile in inflammatory skin suggests putative functions of micrornas in perturbed cytokine production and signaling during chronic inflammatory skin conditions such as psoriasis. it remains unclear, however, why certain micrornas are aberrantly expressed during skin inflammation and if they serve pro- and/or anti-inflammatory functions. in this report, we focus on cytokine regulation by microrna-203 (mir-203), which is highly abundant in keratinocytes and upregulated in psoriatic lesions. by screening a panel of cytokines that are upregulated in psoriatic skin for regulation by mir-203, we identify the genes encoding the pro-inflammatory cytokines tnfα and il24 as direct targets of mir-203. studies of mir-203 overexpression, inhibition, and mutagenesis validate posttranscriptional regulation of tnfα and il24 by mir-203 in cell lines and primary keratinocytes. our findings suggest that mir-203 serves to fine-tune cytokine signaling and may dampen skin immune responses by repressing key pro-inflammatory cytokines.",1
"rna-based therapeutics are emerging as innovative options for cancer treatment, with micrornas being attractive targets for therapy development. we previously implicated microrna-642a-5p (mir-642a-5p) as a tumor suppressor in prostate cancer (pca), and here we characterize its mode of action, using 22rv1 pca cells. in an in vivo xenograft tumor model, mir-642a-5p induced a significant decrease in tumor growth, compared to negative control. using rna-sequencing, we identified gene targets of mir-642a-5p which were enriched for gene sets controlling cell cycle; downregulated genes included wilms tumor 1 gene (wt1), nuak1, rassf3 and skp2; and upregulated genes included igfbp3 and gps2. analysis of pca patient datasets showed a higher expression of wt1, nuak1, rassf3 and skp2; and a lower expression of gps2 and igfbp3 in pca tissue compared to non-malignant prostate tissue. we confirmed the prostatic oncogene wt1, as a direct target of mir-642a-5p, and treatment of 22rv1 and lncap pca cells with wt1 sirna or a small molecule inhibitor of wt1 reduced cell proliferation. taken together, these data provide insight into the molecular mechanisms by which mir-642a-5p acts as a tumor suppressor in pca, an effect partially mediated by regulating genes involved in cell cycle control; and restoration of mir-642-5p in pca could represent a novel therapeutic approach.",1
"co(2) sensation represents an interesting example of nervous system and behavioral evolutionary divergence. the underlying molecular mechanisms, however, are not understood. loss of microrna-279 in drosophila melanogaster leads to the formation of a co(2) sensory system partly similar to the one of mosquitoes. here, we show that a novel allele of the pleiotropic transcription factor prospero resembles the mir-279 phenotype. we use a combination of genetics and in vitro and in vivo analysis to demonstrate that pros participates in the regulation of mir-279 expression, and that reexpression of mir-279 rescues the pros co(2) neuron phenotype. we identify common target molecules of mir-279 and pros in bioinformatics analysis, and show that overexpression of the transcription factors nerfin-1 and escargot (esg) is sufficient to induce formation of co(2) neurons on maxillary palps. our results suggest that prospero restricts co(2) neuron formation indirectly via mir-279 and directly by repressing the shared target molecules, nerfin-1 and esg, during olfactory system development. given the important role of pros in differentiation of the nervous system, we anticipate that mir-mediated signal tuning represents a powerful method for olfactory sensory system diversification during evolution.",1
"spontaneous self-terminating atrial fibrillation (af) is one of the most common heart rhythm disorders, yet the regulatory molecular mechanisms underlying this syndrome are rather unclear. microrna (mirna) transcriptome and expression of candidate transcription factors (tfs) with potential roles in arrhythmogenesis, such as pitx2, tbx5, and myocardin (myocd), were analyzed by microarray, qrt-pcr, and western blotting in left atrial (la) samples from pigs with transitory af established by right atrial tachypacing. induced ectopic tachyarrhythmia caused rapid and substantial mirna remodeling associated with a marked downregulation of pitx2, tbx5, and myocd expression in atrial myocardium. the downregulation of pitx2, tbx5, and myocd was inversely correlated with upregulation of the corresponding targeting mirnas (mir-21, mir-10a/10b, and mir-1, resp.) in the la of paced animals. through in vitro transient transfections of hl-1 atrial myocytes, we further showed that upregulation of mir-21 did result in downregulation of pitx2 in cardiomyocyte background. the results suggest that immediate-early mirna remodeling coupled with deregulation of tf expression underlies the onset of af.",1
"background/aims the objective of this study was to investigate the potential role of il-17 in the development of nasopharyngeal carcinoma (npc) and to screen micrornas (mirnas) that potentially target il-17 in npc cells. methods blood was collected from npc patients and normal subjects, and plasma il-17 concentration was quantified by enzyme-linked immunosorbent assay. an immortalized normal human nasopharyngeal epithelial cell line, np69, was treated with or without human il-17 (15 ng/ml) for various times, and expression of il-1ß, il-6, il-12, and tnf-α mrna was assessed by real-time reverse transcription pcr. the candidate mirnas that potentially target il-17 were predicted by a bioinformatics strategy. the selected mir-135a mimic was transfected into primary npc cells, and cell proliferation was assessed by mtt assay. results the concentration of plasma il-17 was significantly higher in the npc patients (92.5 ± 7.3 pg/ml) than in the control subjects (56.8 ± 2.9 pg/ml). in response to il-17 treatment, the mrna expression of il-1ß and il-6 was significantly upregulated and reached a peak at 12 h, followed by a slight decrease at 24 h, while the mrna expression of il-12 and tnf-α was significantly upregulated at 12 h and remained high even at 48 h after exposure to il-17. moreover, mir-135a specifically targets il-17 and was dramatically downregulated in npc cells compared with np69 cells. transfection of exogenous mir-135a mimic resulted in significant suppression of il-17 secretion and subsequent inhibition of npc cell proliferation. conclusions blood il-17 was significantly higher in npc patients compared with normal subjects. expression of mir-135a in the cancer cells isolated from nasopharyngeal tumors was significantly lower than that in np69 cells, and suppression of il-17 by mir-135a mimic resulted in significant inhibition of npc cell proliferation. these findings suggested that downregulation of mir-135a may contribute to the development of npc via the mechanism of il-17 stimulation of proinflammatory cytokine expression.",1
"x inactivation is controlled by xist and its antisense gene, tsix, neither of which encodes a protein. xist is essential for x inactivation to occur in cis, and its differential expression is a key event in the initiation of x inactivation. xist and tsix are imprinted in the extraembryonic tissues of mouse embryos so that they are expressed from the paternal and maternal x, respectively, resulting in the preferential inactivation of the paternal x. targeted disruption of tsix causes ectopic expression of xist, suggesting that tsix negatively regulates xist in cis. however, the molecular mechanism of this antisense regulation remains unknown. here, we demonstrate that tsix transcriptionally silences xist in both embryonic and extraembryonic tissues of mouse embryos. moreover, we show that disruption of tsix impairs establishment of repressive epigenetic modifications and chromatin structure at the xist locus. we propose that tsix silences xist through modification of the chromatin structure.",1
"chronic infection with hepatotropic viruses is the main cause of chronic liver disease and cirrhosis worldwide. toll-like receptor 3 (tlr3) and toll-like receptor 7 (tlr7) are pathogen-recognition receptors that are expressed on innate immune cells. they recognize viral rna, which induces their activation, with a subsequent increase in type i interferon transcription. hepatitis c virus (hcv) infection inhibits the expression of tlr3 and tlr7; however, the mechanism by which this occurs is unclear. micrornas (mirnas) are small rnas that posttranscriptionally regulate gene expression. their aberrant expression is commonly correlated with disease status, as is the case with hcv infection. here, we found that mir-758 levels were increased in patients with hcv infection and were correlated with tlr3 and tlr7 expression levels in the patients with hcv infection, and bioinformatics analysis predicted that tlr3 and tlr7 are targets of mir-758. therefore, we postulate that hcv may increase the level of mir-758, which inhibits the expression of tlr3 and tlr7, resulting in a loss of antiviral effect. in order to test our hypothesis, we constructed an hcv core protein expression plasmid and used it to transfect liver cells. the results showed that hcv infection increased mir-758 levels and decreased tlr3/tlr7 expression. furthermore, using rt-pcr and luciferase reporter analysis, we found that mir-758 targets tlr3 and tlr7, with a subsequent decrease in ifnα and ifnβ production. in conclusion, our results highlight the upregulation of mir-758 expression by hcv as a novel mechanism contributing to downregulation of tlr3 and tlr7 in patients with hcv infection.",1
"akt2 is a crucial mediator in the tumorigenesis and thought to be an ideal target for the treatment of malignancies. increasing evidence has also shown that micrornas (mirnas) could regulate or be regulated by mrnas and they also might serve as therapeutic agencies or targets. mir-29s (mir-29a, mir-29b and mir-29c) had been approved that they decreased in gastric cancers (gc) by targeting ccnd2, mmp2 and p42.3. however, whether mir-29s would target akt2 have not been investigated in gc. here, we explored the relationship between mir-29s and akt2 and found that in gc cell lines (hgc-27 and mgc-803) and gc clinical samples the decreased levels of mir-29s accompanied by increased akt2 expression. introduction of mir-29s into gc cells resulted in decreased akt2 expression and decreased the ability of cancer cells invasion, so did the sirna-akt2. our studies revealed that mir-29s expression is downregulated in gc and they could repress the akt2 expression and the inactivation of akt and gsk3beta leading to inhibit the gc cells invasion. taken together, our findings suggested that akt2 may be one of the targets of mir29s in gastric cancer. by increasing the expression of mir-29s or decreasing akt2 expression may be promising in combating with gc.",1
"rationale viral myocarditis results from an adverse immune response to cardiotropic viruses, which causes irreversible myocyte destruction and heart failure in previously healthy people. the involvement of micrornas and their usefulness as therapeutic targets in this process are unknown. objective to identify micrornas involved in viral myocarditis pathogenesis and susceptibility. methods and results cardiac micrornas were profiled in both human myocarditis and in coxsackievirus b3-injected mice, comparing myocarditis-susceptible with nonsusceptible mouse strains longitudinally. microrna responses diverged depending on the susceptibility to myocarditis after viral infection in mice. microrna-155, -146b, and -21 were consistently and strongly upregulated during acute myocarditis in both humans and susceptible mice. we found that microrna-155 expression during myocarditis was localized primarily in infiltrating macrophages and t lymphocytes. inhibition of microrna-155 by a systemically delivered lna-anti-mir attenuated cardiac infiltration by monocyte-macrophages, decreased t lymphocyte activation, and reduced myocardial damage during acute myocarditis in mice. these changes were accompanied by the derepression of the direct microrna-155 target pu.1 in cardiac inflammatory cells. beyond the acute phase, microrna-155 inhibition reduced mortality and improved cardiac function during 7 weeks of follow-up. conclusions our data show that cardiac microrna dysregulation is a characteristic of both human and mouse viral myocarditis. the inflammatory microrna-155 is upregulated during acute myocarditis, contributes to the adverse inflammatory response to viral infection of the heart, and is a potential therapeutic target for viral myocarditis.",1
"background myocardial infarction leads to cardiac remodeling and development of heart failure. insufficient myocardial capillary density after myocardial infarction has been identified as a critical event in this process, although the underlying mechanisms of cardiac angiogenesis are mechanistically not well understood. methods and results here, we show that the small noncoding rna microrna-24 (mir-24) is enriched in cardiac endothelial cells and considerably upregulated after cardiac ischemia. mir-24 induces endothelial cell apoptosis, abolishes endothelial capillary network formation on matrigel, and inhibits cell sprouting from endothelial spheroids. these effects are mediated through targeting of the endothelium-enriched transcription factor gata2 and the p21-activated kinase pak4, which were identified by bioinformatic predictions and validated by luciferase gene reporter assays. respective downstream signaling cascades involving phosphorylated bad (bcl-xl/bcl-2-associated death promoter) and sirtuin1 were identified by transcriptome, protein arrays, and chromatin immunoprecipitation analyses. overexpression of mir-24 or silencing of its targets significantly impaired angiogenesis in zebrafish embryos. blocking of endothelial mir-24 limited myocardial infarct size of mice via prevention of endothelial apoptosis and enhancement of vascularity, which led to preserved cardiac function and survival. conclusions our findings indicate that mir-24 acts as a critical regulator of endothelial cell apoptosis and angiogenesis and is suitable for therapeutic intervention in the setting of ischemic heart disease.",1
"three elements are crucial for the programmed frameshifting in translation of dnax mrna: a shine-dalgarno (sd)-like sequence, a double-shift site, and a 3' structure. the conformation of the mrna containing these three elements was investigated using chemical and enzymatic probes. the probing data show that the structure is a specific stem-loop. the bottom half of the stem is more stable than the top half of the stem. the function of the stem-loop was further investigated by mutagenic analysis. reducing the stability of the bottom half of the stem strongly effects frameshifting levels, whereas similar changes in the top half are not as effective. stabilizing the top half of the stem gives increased frameshifting beyond the wt efficiency. the identity of the primary rna sequence in the stem-loop is unimportant, provided that the overall structure is maintained. the calculated stabilities of the variant stem-loop structures correlate with frameshifting efficiency. the sd-interaction and the stem-loop element act independently to increase frameshifting in dnax.",1
"msx1 is a key factor for the development of tooth and craniofacial skeleton and has been proposed to play a pivotal role in terminal cell differentiation. in this paper, we demonstrated the presence of an endogenous msx1 antisense rna (msx1-as rna) in mice, rats, and humans. in situ analysis revealed that this rna is expressed only in differentiated dental and bone cells with an inverse correlation with msx1 protein. these in vivo data and overexpression of msx1 sense and as rna in an odontoblastic cell line (mo6-g3) showed that the balance between the levels of the two msx1 rnas is related to the expression of msx1 protein. to analyze the impact of this balance in the msx-dlx homeoprotein pathway, we analyzed the effect of msx1, msx2, and dlx5 overexpression on proteins involved in skeletal differentiation. we showed that the msx1-as rna is involved in crosstalk between the msx-dlx pathways because its expression was abolished by dlx5. msx1 was shown to down-regulate a master gene of skeletal cells differentiation, cbfa1. all these data strongly suggest that the ratio between msx1 sense and antisense rnas is a very important factor in the control of skeletal terminal differentiation. finally, the initiation site for msx1-as rna transcription was located by primer extension in both mouse and human in an identical region, including a consensus tata box, suggesting an evolutionary conservation of the as rna-mediated regulation of msx1 gene expression.",1
"objective single nucleotide polymorphisms (snps) located at microrna (mirna) binding sites (mir-snps) can affect the expression of genes. this study aimed to identify the mir-snps associated with atherosclerosis and stroke. methods patients with ischemic stroke (n = 657) and stroke- and myocardial infarction-free volunteers (n = 1571) were enrolled. the carotid intima-media thickness (imt) was measured in the control participants. seventy-nine stroke susceptibility genes were initially selected and 13 genes were predicted to have mir-snps at their 3' untranslated regions (3'utr). the mirna arrays were used to further identify potential mir-snps. the mir-snp rs3735590 at the paraoxonase 1 (pon1) gene was finally selected and its associations with stroke and carotid imt were evaluated. the 3'utr reporter and snp functional assays were then performed to validate the results. results compared with cc genotype, patients with ct or tt genotype at rs3735590 had lower risk of ischemic stroke (or = 0.72, p = 0.036; or = 0.83, p = 0.077, respectively). among the healthy participants, the ct or tt genotype was associated with thinner imt in the internal carotid arteries in comparison with cc genotype (β = -0.76, p = 0.003; β = -0.022, p = 0.452, respectively). our findings suggested that the minor allele t had a protective effect on atherosclerosis. results from 3'utr reporter assays showed that pon1 is a direct target gene of mir-616. in plasmid constructs carrying the risk allele c at rs3735590, mir-616 inhibited the genetic expression of pon1. however, substitution of c by t at rs3735590 reduced the mir-616 binding affinity, leading to overexpression of the pon1 gene. conclusion our study is the first to show that the mir-snp at pon1 could affect genetic expression and is associated with an elevated risk for ischemic stroke and subclinical atherosclerosis.",1
"brca1, a breast and ovarian tumor suppressor, colocalizes with markers of the inactive x chromosome (xi) on xi in female somatic cells and associates with xist rna, as detected by chromatin immunoprecipitation. breast and ovarian carcinoma cells lacking brca1 show evidence of defects in xi chromatin structure. reconstitution of brca1-deficient cells with wt brca1 led to the appearance of focal xist rna staining without altering xist abundance. inhibiting brca1 synthesis in a suitable reporter line led to increased expression of an otherwise silenced xi-located gfp transgene. these observations suggest that loss of brca1 in female cells may lead to xi perturbation and destabilization of its silenced state.",1
"cyclin-dependent kinase inhibitor 1a (cdkn1a), also known as p21cip1/waf1, is a master downstream effector of tumor suppressors. in this study, we experimentally demonstrate through a high-throughput luciferase reporter screen that p21cip1/waf1 can be directly targeted by nearly 28 micrornas (mirnas). the results were further confirmed by a series of mutational analyses and luciferase reporter assays. these 28 mirnas can substantially inhibit p21cip1/waf1 expression, predominantly at translational level. many of these mirnas were upregulated in cancers and might serve as modulators of oncogenesis. furthermore, 8 of these 28 p21-regulating mirnas are located in the chromosome 19 mirna cluster, the largest mirna gene cluster in humans, and they can clearly promote cell proliferation and cell-cycle progression in choriocarcinoma cells. in conclusion, our screening strategy provides an alternative approach to uncovering mirna modulators of an individual mrna, and it has identified multiple mirnas that can suppress p21cip1/waf1 expression by directly targeting its 3' untranslated region.",1
"microrna-1 (mir-1) is preferentially expressed in cardiac muscles, and the expression has been demonstrated to be involved in cardiac development and cardiovascular diseases. here we report that mir-1 is closely related with ischemia/reperfusion injury in a rat model. the level of mir-1 is inversely correlated with bcl-2 protein expression in cardiomyocytes of the i/r rat model. in vitro, the level of mir-1 was dramatically increased in response to h(2)o(2). overexpression of mir-1 facilitated h(2)o(2)-induced apoptosis in cardiomyocytes. inhibition of mir-1 by antisense inhibitory oligonucleotides caused marked resistance to h(2)o(2). through bioinformatics, we identified the potential target sites for mir-1 on the 3' utr of bcl-2. mir-1 significantly reduced the expression of bcl-2 in the levels of mrna and protein. the post-transcriptional repression of bcl-2 was further confirmed by luciferase reporter experiments. these data demonstrated that mir-1 plays an important role in the regulation of cardiomyocyte apoptosis, which is involved in post-transcriptional repression of bcl-2.",1
"endothelial cell migration induced in response to vascular endothelial growth factor (vegf) is a crucial step of angiogenesis and it depends on the activation of the p38 map-kinase pathway downstream of vegfr2. in this study, we investigated the role of micrornas (mirnas) in regulating these processes. we found that the vegf-induced p38 activation and cell migration are modulated by overexpression of argonaute 2, a key protein in the functioning of mirnas. thereafter, we found that mir-20a expression is increased by vegf and that its ectopic expression inhibits vegf-induced actin remodeling and cell migration. moreover, the expression of mir-20a impairs the formation of branched capillaries in a tissue-engineered model of angiogenesis. in addition, the lentivirus-mediated expression of mir-20a precursor (pmir-20a) is associated with a decrease in the vegf-induced activation of p38. in contrast, these processes are increased by inhibiting mir-20a with a specific antagomir. interestingly, mir-20a does not modulate vegfr2 or p38 protein expression level. mir-20a does not affect either the expression of other known actors of the p38 map kinase pathway except mkk3. indeed, by using quantitative pcr and western blot analysis, we found that pmir-20a decreases the expression of mkk3 and we obtained evidence indicating that mir-20a specifically binds to the 3'utr region of mkk3 mrna. in accordance, the vegf-induced activation of p38 and cell migration are impaired when the mkk3 expression is knocked down by sirna. we conclude that mir-20a acts in a feedback loop to repress the expression of mkk3 and to negatively regulate the p38 pathway-mediated vegf-induced endothelial cell migration and angiogenesis.",1
"gammaherpesviruses, including the human pathogens epstein-barr virus (ebv) and kaposi's sarcoma-associated herpesvirus (kshv), establish lifelong latent infection in b cells and are associated with a variety of tumors. in addition to protein coding genes, these viruses encode numerous micrornas (mirnas) within their genomes. while putative host targets of ebv and kshv mirnas have been previously identified, the specific functions of these mirnas during in vivo infection are largely unknown. murine gammaherpesvirus 68 (mhv68) is a natural pathogen of rodents that is genetically related to both ebv and kshv, and thus serves as an excellent model for the study of ebv and kshv genetic elements such as mirnas in the context of infection and disease. however, the specific targets of mhv68 mirnas remain completely unknown. using a technique known as qclash (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of ago-associated, direct mirna-mrna interactions during lytic infection, latent infection and reactivation from latency. validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mrna targets of mhv68 mirnas, including arid1a, ctsl, ifitm3 and phc3. notably, of the 1,505 mhv68 mirna-host mrna targets identified in b cells, 86% were shared with either ebv or kshv, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus mirna targeting. pathway analysis of mhv68 mirna targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eif2 signaling, mtor signaling and protein ubiquitination, pathways also enriched for targets of ebv and kshv mirnas. these findings provide substantial new information about specific targets of mhv68 mirnas and shed important light on likely conserved functions of gammaherpesvirus mirnas.",1
"mirnas silence gene expression by repressing translation and/or by promoting mrna decay. in animal cells, degradation of partially complementary mirna targets occurs via deadenylation by the caf1-ccr4-not1 deadenylase complex, followed by decapping and subsequent exonucleolytic digestion. to determine how generally mirnas trigger deadenylation, we compared mrna expression profiles in d. melanogaster cells depleted of ago1, caf1, or not1. we show that approximately 60% of ago1 targets are regulated by caf1 and/or not1, indicating that deadenylation is a widespread effect of mirna regulation. however, neither a poly(a) tail nor mrna circularization are required for silencing, because mrnas whose 3' ends are generated by a self-cleaving ribozyme are also silenced in vivo. we show further that mirnas trigger mrna degradation, even when binding by 40s ribosomal subunits is inhibited in cis. these results indicate that mirnas promote mrna decay by altering mrnp composition and/or conformation, rather than by directly interfering with the binding and function of ribosomal subunits.",1
"the overexpression of the hmga1 proteins is a feature of human malignant neoplasias and has a causal role in cell transformation. the aim of our study has been to investigate the micrornas (mirnas or mirs) regulated by the hmga1 proteins in the process of cell transformation analyzing the mirna expression profile of v-ras-ki oncogene-transformed thyroid cells expressing or not hmga1 proteins. we demonstrate that, among the mirnas regulated by cell transformation, there are mir-10b, mir-21, mir-125b, mir-221 and mir-222 that are positively and mir-34a and mir-603 that are negatively regulated by hmga1 expression. then, we focused our attention on the mir-10b and mir-603 whose expression was dependent on the presence of hmga1 also in other cell systems. we found that mir-10b is able to target the pten gene, whereas mir-603 targets the ccnd1 and ccnd2 genes coding for the cyclin d1 and cyclin d2 proteins, respectively. moreover, functional studies showed that mir-10b and mir-603 regulate positively and negatively, respectively, cell proliferation and migration suggesting a role of their dysregulation in thyroid cell transformation.",1
"hypoxia-induced pulmonary hypertension (ph), which is characterized by vasoconstriction and subsequent structural remodeling of blood vessels, is an important event in chronic obstructive pulmonary disease patients and in people living at high altitudes. hypoxia-inducible factor-1α (hif-1α) and its regulator four-and-a-half lim (lin-11, isl-1 and mec-3) domain 1 (fhl-1) have important roles in hypoxia-induced ph. microrna-206 (mir-206) is critical for myogenesis and related diseases; however, the role of mir-206 in hypoxia-induced ph is unknown. mir-206 expression was evaluated in a hypoxic rat model and in cultured hypoxic pulmonary artery smooth muscle cells (pasmcs) using real-time quantitative pcr (rt-qpcr). hif-1α and fhl-1 expression were evaluated using rt-qpcr, western blotting, immunohistochemistry and immunofluorescence. the function of mir-206 was assessed by transfecting mir-206 mimics and inhibitors. dual-luciferase reporter gene assays and western blotting were performed to validate the target genes of mir-206. sirna targeted against fhl-1 was used to investigate the effect of fhl-1 on mir-206. flow cytometry was used to detect the cell cycle phase distribution in each group of pasmcs. significant downregulation of mir-206 in hypoxic lung tissue and pasmcs was identified, whereas hif-1α and fhl-1 were upregulated in these samples. the expression of mir-206 in the serum was different from that in the lung tissue. transfection of pre-mir mir-206 in hypoxic conditions led to increased expression of hif-1α and fhl-1 rather than abolishing hypoxia-induced hif-1α and fhl-1, as was expected, and promoted the entry of cells into the s phase and enhanced pasmc proliferation. fhl-1-targeted sirna in pasmc prevented cell proliferation and led to an increased proportion of cells in the g1 phase without altering mir-206 expression. bioinformatic analysis and dual-luciferase reporter gene assays revealed direct evidence for mir-206 targeting of hif-1α. in conclusion, hypoxia-induced downregulation of mir-206 promotes ph by targeting the hif-1α/fhl-1 pathway in pasmcs. mir-206 could be a triggering factor of early stage of hypoxia-induced ph.",1
"respiratory syncytial virus (rsv) causes substantial morbidity and life-threatening lower respiratory tract disease in infants, young children and the elderly. understanding the host response to rsv infection is critical for developing disease-intervention approaches. the role of micrornas (mirnas) in post-transcriptional regulation of host genes responding to rsv infection is not well understood. in this study, it was shown that rsv infection of a human alveolar epithelial cell line (a549) induced five mirnas (let-7f, mir-24, mir-337-3p, mir-26b and mir-520a-5p) and repressed two mirnas (mir-198 and mir-595), and showed that rsv g protein triggered let-7f expression. luciferase-untranslated region reporters and mirna mimics and inhibitors validated the predicted targets, which included cell-cycle genes (ccnd1, dyrk2 and elf4), a chemokine gene (ccl7) and the suppressor of cytokine signalling 3 gene (socs3). modulating let-7 family mirna levels with mirna mimics and inhibitors affected rsv replication, indicating that rsv modulates host mirna expression to affect the outcome of the antiviral host response, and this was mediated in part through rsv g protein expression.",1
"an internal ribosome entry segment (ires) has been identified in the 5' untranslated region (5' utr) of two members of the myc family of proto-oncogenes, c-myc and n-myc. hence, the synthesis of c-myc and n-myc polypeptides can involve the alternative mechanism of internal initiation. here, we show that the 5' utr of l-myc, another myc family member, also contains an ires. previous studies have shown that the translation of mrnas containing the c-myc and n-myc iress can involve both cap-dependent initiation and internal initiation. in contrast, the data presented here suggest that internal initiation can account for all of the translation initiation that occurs on an mrna with the l-myc ires in its 5' utr. like many other cellular iress, the l-myc ires appears to be modular in nature and the entire 5' utr is required for maximum ires efficiency. the ribosome entry window within the l-myc ires is located some distance upstream of the initiation codon, and thus, this ires uses a ""land and scan"" mechanism to initiate translation. finally, we have derived a secondary structural model for the ires. the model confirms that the l-myc ires is highly structured and predicts that a pseudoknot may form near the 5' end of the mrna.",1
"single micrornas are usually associated with hundreds of putative target genes that can influence multiple phenotypic traits in drosophila, ranging from development to behaviour. we investigated the function of drosophila mir-210 in circadian behaviour by misexpressing it within circadian clock cells. manipulation of mir-210 expression levels in the pdf (pigment dispersing factor) positive neurons affected the phase of locomotor activity, under both light-dark conditions and constant darkness. per cyclical expression was not affected in clock neurons, however, when mir-210 was up-regulated, a dramatic alteration in the morphology of pdf ventral lateral neuron (lnv) arborisations was observed. the effect of mir-210 in shaping neuronal projections was confirmed in vitro, using a drosophila neuronal cell line. a transcriptomic analysis revealed that mir-210 overexpression affects the expression of several genes belonging to pathways related to circadian processes, neuronal development, gtpases signal transduction and photoreception. collectively, these data reveal the role of mir-210 in modulating circadian outputs in flies and guiding/remodelling pdf positive lnv arborisations and indicate that mir-210 may have pleiotropic effects on the clock, light perception and neuronal development.",1
"background pulmonary hypertension (ph) is a proliferative disorder associated with enhanced proliferation and suppressed apoptosis of pulmonary artery smooth muscle cells (pasmcs). our lately study demonstrated that let-7g inhibited hypoxia-induced proliferation of pasmcs via repressing c-myc-bmi-1-p16 signaling pathway. however, the upstream of let-7g has not yet been fully defined. previous studies have shown that lox-1, a target of let-7g, could also regulate the expression of let-7g in human aortic endothelial cells. in this present study, we aimed to investigate whether there is a negative feedback regulation between microrna let-7g and lox-1 in hypoxia-induced proliferation of pasmcs. methods sd rats were exposed to hypoxia (10% o 2 , 3 weeks) to induce ph. he staining was used to evaluate pulmonary artery remodeling. in situ hybridization and immunohistochemistry were performed to assess the expression and distribution of let-7g and lox-1, respectively. mts, edu and flow cytometry were performed to evaluate pasmcs proliferation. quantitative real-time polymerase chain reaction (qrt-pcr) and western blotting were conducted to assess the expression of let-7g, lox-1, calpain-1,-2,-4, and oct-1. results the expression of let-7g was significantly down-regulated in pulmonary arteries of hypoxia-induced ph rats accompanied by pulmonary vascular remodeling, whereas let-7g mimic inhibited hypoxia-induced proliferation of pasmcs and up-regulation of lox-1 expression. lox-1 blocking reversed hypoxia-induced down-regulation of let-7g expression. calpains, protein kinase c and oct-1 were involved in negative feedback regulation between let-7g and lox-1. conclusion negative feedback regulation between let-7g and lox-1 mediated hypoxia-induced proliferation of in pasmcs.",1
"many molecular pathways involved in heart disease have their roots in evolutionarily ancient developmental programs that depend critically on gene dosage and timing. micrornas (mirnas) modulate gene dosage posttranscriptionally, and among these, the muscle-specific mir-1 is particularly important for developing and maintaining somatic/skeletal and cardiac muscle. to identify pathways regulated by mir-1, we performed a forward genetic screen in drosophila using wing-vein patterning as a biological assay. we identified several unexpected genes that genetically interacted with dmir-1, one of which was kayak, encodes a developmentally regulated transcription factor. additional studies directed at this genetic relationship revealed a previously unappreciated function of dmir-1 in regulating the polarity of cardiac progenitor cells. the mammalian ortholog of kayak, c-fos, was dysregulated in hearts of gain- or loss-of-function mir-1 mutant mice in a stress-dependent manner. these findings illustrate the power of drosophila-based screens to find points of intersection between mirnas and conserved pathways in mammals.",1
"aims atherosclerosis is the most common cause of cardiovascular disease, such as myocardial infarction and stroke. previous study revealed that microrna (mir)-134 promotes lipid accumulation and proinflammatory cytokine secretion through angiopoietin-like 4 (angptl4)/lipid lipoprotein (lpl) signaling in thp-1 macrophages. methods apoe ko male mice on a c57bl/6 background were fed a high-fat/high-cholesterol western diet, from 8 to 16 weeks of age. mice were divided into four groups, and received a tail vein injection of mir-134 agomir, mir-134 antagomir, or one of the corresponding controls, respectively, once every 2 weeks after starting the western diet. after 8 weeks we measured aortic atherosclerosis, lpl activity, mrna and protein levels of angptl4 and lpl, lpl/ low-density lipoprotein receptor related protein 1 complex formation, proinflammatory cytokine secretion and lipid levels. results despite this finding, the influence of mir-134 on atherosclerosis in vivo remains to be determined. using the well-characterized mouse atherosclerosis model of apolipoprotein e knockout, we found that systemic delivery of mir-134 agomir markedly enhanced the atherosclerotic lesion size, together with a significant increase in proinflammatory cytokine secretion and peritoneal macrophages lipid contents. moreover, overexpression of mir-134 decreased angptl4 expression but increased lpl expression and activity in both aortic tissues and peritoneal macrophages, which was accompanied by increased formation of lpl/low-density lipoprotein receptor-related protein 1 complexes in peritoneal macrophages. however, an opposite effect was observed in response to mir-134 antagomir. conclusions these findings suggest that mir-134 accelerates atherogenesis by promoting lipid accumulation and proinflammatory cytokine secretion via the angptl4/lpl pathway. therefore, targeting mir-134 may offer a promising strategy for the prevention and treatment of atherosclerotic cardiovascular disease.",1
"the mechanisms by which deregulated nuclear factor erythroid-2-related factor 2 (nrf2) and kelch-like ech-associated protein 1 (keap1) signaling promote cellular proliferation and tumorigenesis are poorly understood. using an integrated genomics and ¹³c-based targeted tracer fate association (ttfa) study, we found that nrf2 regulates mir-1 and mir-206 to direct carbon flux toward the pentose phosphate pathway (ppp) and the tricarboxylic acid (tca) cycle, reprogramming glucose metabolism. sustained activation of nrf2 signaling in cancer cells attenuated mir-1 and mir-206 expression, leading to enhanced expression of ppp genes. conversely, overexpression of mir-1 and mir-206 decreased the expression of metabolic genes and dramatically impaired nadph production, ribose synthesis, and in vivo tumor growth in mice. loss of nrf2 decreased the expression of the redox-sensitive histone deacetylase, hdac4, resulting in increased expression of mir-1 and mir-206, and not only inhibiting ppp expression and activity but functioning as a regulatory feedback loop that repressed hdac4 expression. in primary tumor samples, the expression of mir-1 and mir-206 was inversely correlated with ppp gene expression, and increased expression of nrf2-dependent genes was associated with poor prognosis. our results demonstrate that microrna-dependent (mirna-dependent) regulation of the ppp via nrf2 and hdac4 represents a novel link between mirna regulation, glucose metabolism, and ros homeostasis in cancer cells.",1
"mir-155 acts as an oncogenic mir in b-cell lymphoproliferative disorders, including waldenstrom macroglobulinemia (wm) and chronic lymphocytic leukemia, and is therefore a potential target for therapeutic intervention. however, efficient targeting of mirs in tumor cells in vivo remains a significant challenge for the development of mir-155-based therapeutics for the treatment of b-cell malignancies. in the present study, we show that an 8-mer locked nucleic acid anti-mir-155 oligonucleotide targeting the seed region of mir-155 inhibits wm and chronic lymphocytic leukemia cell proliferation in vitro. moreover, anti-mir-155 delivered systemically showed uptake in the bm cd19(+) cells of wm-engrafted mice, resulting in the up-regulation of several mir-155 target mrnas in these cells, and decreased tumor growth significantly in vivo. we also found mir-155 levels to be elevated in stromal cells from wm patients compared with control samples. interestingly, stromal cells from mir-155-knockout mice led to significant inhibition of wm tumor growth, indicating that mir-155 may also contribute to wm proliferation through bm microenvironmental cells. the results of the present study highlight the therapeutic potential of anti-mir-155-mediated inhibition of mir-155 in the treatment of wm.",1
"chronic lymphocytic leukemia (cll) is the most common human leukemia and is characterized by predominantly nondividing malignant b cells overexpressing the antiapoptotic b cell lymphoma 2 (bcl2) protein. mir-15a and mir-16-1 are deleted or down-regulated in the majority of clls. here, we demonstrate that mir-15a and mir-16-1 expression is inversely correlated to bcl2 expression in cll and that both micrornas negatively regulate bcl2 at a posttranscriptional level. bcl2 repression by these micrornas induces apoptopsis in a leukemic cell line model. therefore, mir-15 and mir-16 are natural antisense bcl2 interactors that could be used for therapy of bcl2-overexpressing tumors.",1
"the nonselective β-adrenergic receptor antagonist (β-blocker) carvedilol has been shown to protect against myocardial injury, but the detailed underlying mechanisms are unclear. we recently reported that carvedilol stimulates the processing of microrna (mir)-199a-3p and mir-214 in the heart via β-arrestin1-biased β1-adrenergic receptor (β1ar) cardioprotective signaling. here, we investigate whether these β-arrestin1/β1ar-responsive mirs mediate the beneficial effects of carvedilol against simulated ischemia/reperfusion (si/r). using cultured cardiomyocyte cell lines and primary cardiomyocytes, we demonstrate that carvedilol upregulates mir-199a-3p and mir-214 in both ventricular and atrial cardiomyocytes subjected to si/r. overexpression of the two mirs in cardiomyocytes mimics the effects of carvedilol to activate p-akt survival signaling and the expression of a downstream pluripotency marker sox2 in response to si/r. moreover, carvedilol-mediated p-akt activation is abolished by knockdown of either mir-199a-3p or mir-214. along with previous studies to directly link the cardioprotective actions of carvedilol to upregulation of p-akt/stem cell markers, our findings suggest that the protective roles of carvedilol during ischemic injury are in part attributed to activation of these two protective mirs. loss of function of mir-199a-3p and mir-214 also increases cardiomyocyte apoptosis after si/r. mechanistically, we demonstrate that mir-199a-3p and mir-214 repress the predictive or known apoptotic target genes ddit4 and ing4, respectively, in cardiomyocytes. these findings suggest pivotal roles for mir-199a-3p and mir-214 as regulators of cardiomyocyte survival and contributors to the functional benefits of carvedilol therapy.",1
"nuclear factor of activated t cells (nfat) proteins are ca(2+)-regulated transcription factors that control gene expression in many cell types. nfat proteins are heavily phosphorylated and reside in the cytoplasm of resting cells; when cells are stimulated by a rise in intracellular ca(2+), nfat proteins are dephosphorylated by the ca(2+)/calmodulin-dependent phosphatase calcineurin and translocate to the nucleus to activate target gene expression. here we show that phosphorylated nfat1 is present in a large cytoplasmic rna-protein scaffold complex that contains a long intergenic noncoding rna (lincrna), nron ; a scaffold protein, iq motif containing gtpase activating protein (iqgap); and three nfat kinases, casein kinase 1, glycogen synthase kinase 3, and dual specificity tyrosine phosphorylation regulated kinase. combined knockdown of nron and iqgap1 increased nfat dephosphorylation and nuclear import exclusively after stimulation, without affecting the rate of nfat rephosphorylation and nuclear export; and both nron-depleted t cells and t cells from iqgap1-deficient mice showed increased production of nfat-dependent cytokines. our results provide evidence that a complex of lincrna and protein forms a scaffold for a latent transcription factor and its regulatory kinases, and support an emerging consensus that lincrnas that bind transcriptional regulators have a similar scaffold function.",1
"micrornas (mirnas) are short noncoding rnas, which post-transcriptionally regulate gene expression. mirnas are transcribed as precursors and matured to active forms by a series of enzymes, including dicer. mirnas are important in governing cell differentiation, development, and disease. we have recently developed a feeder- and serum-free protocol for direct derivation of endothelial cells (ecs) from human embryonic stem cells (hescs) and provided evidence of increases in angiogenesis-associated mirnas (mir-126 and -210) during the process. however, the functional role of mirnas in hesc differentiation to vascular ec remains to be fully interrogated. here, we show that the reduction of mirna maturation induced by dicer knockdown suppressed hes-ec differentiation. a mirna microarray was performed to quantify hes-ec mirna profiles during defined stages of endothelial differentiation. mir-99b, -181a, and -181b were identified as increasing in a time- and differentiation-dependent manner to peak in mature hesc-ecs and adult ecs. augmentation of mir-99b, -181a, and -181b levels by lentiviral-mediated transfer potentiated the mrna and protein expression of ec-specific markers, pecam1 and ve cadherin, increased nitric oxide production, and improved hes-ec-induced therapeutic neovascularization in vivo. conversely, knockdown did not impact endothelial differentiation. our results suggest that mir-99b, -181a, and -181b comprise a component of an endothelial-mirna signature and are capable of potentiating ec differentiation from pluripotent hescs.",1
"the transcriptional repressor bcl6 is a critical regulator of t helper cell fate, and inhibits th2-type inflammation. we have found that microrna-21 (mir-21) is a novel target gene for bcl6 in treg cells. bcl6 represses and stat3 activates mir-21 transcription through a stat3 binding element in the promoter, indicating opposing regulation of mir-21 by the two transcription factors via the same dna site. ectopic expression of mir-21 promoted th2 differentiation in non-polarized t cells. the pro-th2 activity of mir-21 was associated with increased gata3 expression and decreased expression of the mir-21 target gene sprouty1. increased mir-21 promoted th2 and treg gene expression in wild-type tregs. mir-21 could thus help promote the th2 bias of bcl6-deficient conventional t cells and treg cells. mir21 expression is increased in th2-type inflammation, and our results define mir-21 as a critical target of bcl6, thus providing a new link between bcl6 and th2 inflammation. finally, our results reveal a novel t cell autonomous role for mir-21 in promoting th2 differentiation.",1
"the transcriptional networks that regulate embryonic stem (es) cell pluripotency and lineage specification are the subject of considerable attention. to date such studies have focused almost exclusively on protein-coding transcripts. however, recent transcriptome analyses show that the mammalian genome contains thousands of long noncoding rnas (ncrnas), many of which appear to be expressed in a developmentally regulated manner. the functions of these remain untested. to identify ncrnas involved in es cell biology, we used a custom-designed microarray to examine the expression profiles of mouse es cells differentiating as embryoid bodies (ebs) over a 16-d time course. we identified 945 ncrnas expressed during eb differentiation, of which 174 were differentially expressed, many correlating with pluripotency or specific differentiation events. candidate ncrnas were identified for further characterization by an integrated examination of expression profiles, genomic context, chromatin state, and promoter analysis. many ncrnas showed coordinated expression with genomically associated developmental genes, such as dlx1, dlx4, gata6, and ecsit. we examined two novel developmentally regulated ncrnas, evx1as and hoxb5/6as, which are derived from homeotic loci and share similar expression patterns and localization in mouse embryos with their associated protein-coding genes. using chromatin immunoprecipitation, we provide evidence that both ncrnas are associated with trimethylated h3k4 histones and histone methyltransferase mll1, suggesting a role in epigenetic regulation of homeotic loci during es cell differentiation. taken together, our data indicate that long ncrnas are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery.",1
"cooperation between dna, rna and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. here, we report that endoderm differentiation is regulated by the interaction between the long non-coding rna (lncrna) digit and the bromodomain and extraterminal domain protein brd3. brd3 forms phase-separated condensates of which the formation is promoted by digit, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. brd3 binds to histone h3 acetylated at lysine 18 (h3k18ac) in vitro and co-occupies the genome with h3k18ac. digit is also enriched in regions of h3k18ac, and the depletion of digit results in decreased recruitment of brd3 to these regions. our findings show that cooperation between digit and brd3 at regions of h3k18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncrna phase-separated condensates have a broader role as regulators of transcription.",1
"obesity, type 2 diabetes, and heart failure are associated with aberrant cardiac metabolism. we show that the heart regulates systemic energy homeostasis via med13, a subunit of the mediator complex, which controls transcription by thyroid hormone and other nuclear hormone receptors. med13, in turn, is negatively regulated by a heart-specific microrna, mir-208a. cardiac-specific overexpression of med13 or pharmacologic inhibition of mir-208a in mice confers resistance to high-fat diet-induced obesity and improves systemic insulin sensitivity and glucose tolerance. conversely, genetic deletion of med13 specifically in cardiomyocytes enhances obesity in response to high-fat diet and exacerbates metabolic syndrome. the metabolic actions of med13 result from increased energy expenditure and regulation of numerous genes involved in energy balance in the heart. these findings reveal a role of the heart in systemic metabolic control and point to med13 and mir-208a as potential therapeutic targets for metabolic disorders.",1
"in caenorhabditis elegans, the heterochronic pathway controls the timing of developmental events during the larval stages. a component of this pathway, the let-7 small regulatory rna, is expressed at the late stages of development and promotes the transition from larval to adult (l/a) stages. the stage-specificity of let-7 expression, which is crucial for the proper timing of the worm l/a transition, is conserved in drosophila melanogaster and other invertebrates. in drosophila, pulses of the steroid hormone 20-hydroxyecdysone (ecdysone) control the timing of the transition from larval to pupal to adult stages. to test whether let-7 expression is regulated by ecdysone in drosophila, we used northern blot analysis to examine the effect of altered ecdysone levels on let-7 expression in mutant animals, organ cultures, and s2 cultured cells. experiments were conducted to test the role of broad-complex (br-c), an essential component in the ecdysone pathway, in let-7 expression. we show that ecdysone and br-c are required for let-7 expression, indicating that the ecdysone pathway regulates the temporal expression of let-7 in drosophila. these results demonstrate an interaction between steroid hormone signaling and the heterochronic pathway in insects.",1
"both micrornas and alternative pre-mrna splicing have been implicated in the development of the nervous system (ns), but functional interactions between these two pathways are poorly understood. we demonstrate that the neuron-specific microrna mir-124 directly targets ptbp1 (ptb/hnrnp i) mrna, which encodes a global repressor of alternative pre-mrna splicing in nonneuronal cells. among the targets of ptbp1 is a critical cassette exon in the pre-mrna of ptbp2 (nptb/brptb/ptblp), an ns-enriched ptbp1 homolog. when this exon is skipped, ptbp2 mrna is subject to nonsense-mediated decay (nmd). during neuronal differentiation, mir-124 reduces ptbp1 levels, leading to the accumulation of correctly spliced ptbp2 mrna and a dramatic increase in ptbp2 protein. these events culminate in the transition from non-ns to ns-specific alternative splicing patterns. we also present evidence that mir-124 plays a key role in the differentiation of progenitor cells to mature neurons. thus, mir-124 promotes ns development, at least in part by regulating an intricate network of ns-specific alternative splicing.",1
"in prokaryotes, small noncoding rnas (snrnas) of 50-500 nt are produced that are important in bacterial virulence and response to environmental stimuli. here, we identified and characterized snrnas from the endosymbiotic bacteria, wolbachia, which are widespread in invertebrates and cause reproductive manipulations. most importantly, some strains of wolbachia inhibit replication of several vector-borne pathogens in insects. we demonstrate that two abundant snrnas, wsnrna-46 and wsnrna-49, are expressed in wolbachia from noncoding rna transcripts that contain precursors with stem-loop structures. wsnrnas were detected in aedes aegypti mosquitoes infected with the wmelpop-cla strain of wolbachia and in drosophila melanogaster and drosophila simulans infected with wmelpop and wau strains, respectively, indicating that the wsnrnas are conserved across species and strains. in addition, we show that the wsnrnas may potentially regulate host genes and wolbachia genes. our findings provide evidence for the production of functional snrnas by wolbachia that play roles in cross-kingdom communication between the endosymbiont and the host.",1
"hedgehog (hh) signaling plays many important roles in developmental processes and cancers. smoothened (smo) is an important signal transducer in the hh pathway, and its expression is tightly regulated by several different post-transcriptional mechanisms. however, whether micrornas (mirnas) are involved in smo regulation is still unclear. here, we found that mir-5 acts as a suppressor of the hh pathway by targeting smo. through in vivo sensor assay and in vitro luciferase assay, we found that mir-5 downregulates smo through directly binding to its 3'utr. moreover, our data indicated costal-2 (cos2) and fused (fu) do not play a role in the reduction of smo mediated by mir-5. furthermore, we determined that mir-5 not involved in notch or dpp signaling pathways by detecting target gene expression. together, our results indicate that mir-5 can specifically suppress hh signaling by directly targeting smo in drosophila.",1
"recently, researchers have uncovered the presence of many long noncoding rnas (lncrnas) in embryonic stem cells and believe they are important regulators of the differentiation process. however, there are only a few examples explicitly linking lncrna activity to transcriptional regulation. here, we used transcript counting and spatial localization to characterize a lncrna (dubbed linc-hoxa1) located ∼50 kb from the hoxa gene cluster in mouse embryonic stem cells. single-cell transcript counting revealed that linc-hoxa1 and hoxa1 rna are highly variable at the single-cell level and that whenever linc-hoxa1 rna abundance was high, hoxa1 mrna abundance was low and vice versa. knockdown analysis revealed that depletion of linc-hoxa1 rna at its site of transcription increased transcription of the hoxa1 gene cis to the chromosome and that exposure of cells to retinoic acid can disrupt this interaction. we further showed that linc-hoxa1 rna represses hoxa1 by recruiting the protein purb as a transcriptional cofactor. our results highlight the power of transcript visualization to characterize lncrna function and also suggest that purb can facilitate lncrna-mediated transcriptional regulation.",1
"once protein-coding, the x-inactivation center (xic) is now dominated by large noncoding rnas (ncrna). x chromosome inactivation (xci) equalizes gene expression between mammalian males and females by inactivating one x in female cells. xci requires xist, an ncrna that coats the x and recruits polycomb proteins. how xist is controlled remains unclear but likely involves negative and positive regulators. for the active x, the antisense tsix rna is an established xist repressor. for the inactive x, here, we identify xic-encoded jpx as an xist activator. jpx is developmentally regulated and accumulates during xci. deleting jpx blocks xci and is female lethal. posttranscriptional jpx knockdown recapitulates the knockout, and supplying jpx in trans rescues lethality. thus, jpx is trans-acting and functions as ncrna. furthermore, δjpx is rescued by truncating tsix, indicating an antagonistic relationship between the ncrnas. we conclude that xist is controlled by two rna-based switches: tsix for xa and jpx for xi.",1
"while recent insights indicate that the transcription factor krüppel-like factor 4 (klf4) is indispensable for vascular homeostasis, its exact role in proliferation and angiogenesis and how it functions remain unresolved. thus, the aim of the present study was to evaluate the role of klf4 in the proliferations of endothelial and vascular smooth muscle cells, as well as the angiogenesis. the overexpression of klf4 in endothelial cells significantly impaired tube formation. klf4 inhibited the formation of a vascular network in implanted matrigel plugs in nude mice. importantly, we found that klf4 significantly upregulated the mir-15a expression in endothelial cells and vascular smooth muscle cells, and conversely, klf4 depletion reduced the amount of mir-15a. furthermore, klf4 blocked cell cycle progression and decreased cyclin d1 expression in endothelial cells and vascular smooth muscle cells through the induction of mir-15a. intriguingly, the delivery of a mir-15a antagomir to nude mice resulted in marked attenuation of the anti-angiogenic effect of klf4. collectively, our present study provide the first evidence that mir-15a as a direct transcriptional target of klf4 that mediates the anti-proliferative and anti-angiogenic actions of klf4, which indicates that klf4 upregulation of mir-15a may represent a therapeutic option to suppress proliferative vascular disorders.",1
"background berberine is a natural alkaloid derived from a traditional chinese herbal medicine. it is known to modulate microrna (mirna) levels, although the mechanism for this action is unknown. here, we previously demonstrate that the expression of 87 mirnas is differentially affected by berberine in multiple myeloma cells. among 49 mirnas that are down-regulated, nine act as oncomirs, including mir-21. integrative analysis showed that 28 of the down-regulated mirnas participate in tumor protein p53 (tp53) signaling and other cancer pathways. mir-21 is involved in all these pathways, and is one of the most important oncomirs to be affected by berberine in multiple myeloma cells. results we confirmed that berberine down-regulated mirna-21 expression and significantly up-regulated the expression of programmed cell death 4 (pdcd4), a predicted mir-21 target. luciferase reporter assays confirmed that pdcd4 was directly regulated by mir-21. bioinformatic analysis revealed that the mir-21 promoter can be targeted by signal transducer and activator of transcription 3 (stat3). down-regulation of interleukin 6 (il6) by berberine might lead to inhibition of mir-21 transcription through stat3 down-regulation in multiple myeloma. furthermore, both berberine and seed-targeting anti-mir-21 oligonucleotide induced apoptosis, g2-phase cell cycle arrest and colony inhibition in multiple myeloma cell lines. depletion of pdcd4 by short interfering rna could rescue berberine-induced cytotoxicity in multiple myeloma cells. conclusions our results suggest that berberine suppresses multiple myeloma cell growth, at least in part, by down-regulating mir-21 levels possibly through il6/stat3. this led to increased pdcd4 expression, which is likely to result in suppression of the p53 signaling pathway. these findings may also provide new mechanistic insight into the anti-cancer effects of certain compounds in traditional chinese herbal medicines.",1
"mammalian micrornas (mirnas) pair to 3'utrs of mrnas to direct their posttranscriptional repression. important for target recognition are approximately 7 nt sites that match the seed region of the mirna. however, these seed matches are not always sufficient for repression, indicating that other characteristics help specify targeting. by combining computational and experimental approaches, we uncovered five general features of site context that boost site efficacy: au-rich nucleotide composition near the site, proximity to sites for coexpressed mirnas (which leads to cooperative action), proximity to residues pairing to mirna nucleotides 13-16, positioning within the 3'utr at least 15 nt from the stop codon, and positioning away from the center of long utrs. a model combining these context determinants quantitatively predicts site performance both for exogenously added mirnas and for endogenous mirna-message interactions. because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and sirna off-targets.",1
"microrna (mirna) has been proved to play a key role in lipid metabolism. in our previous study, mir-125b was validated to be differentially expressed in preadipocytes and adipocytes, which was also proved to involve in lipid metabolism. to explore the comprehensive targets of mir-125b in adipocytes, isobaric tag for relative and absolute quantitation (itraq) analysis was performed to obtain differentially expressed proteins in adipocytes comparing negative control (nc) and mir-125b mimic, combining with digital gene expression (dge) profiling of mrna incorporated into rna-induced silencing complex (risc) pulled down by biotinylated mir-125b mimic and targets prediction of mir-125b by three algorithms, acyl-coa dehydrogenase short chain (acads) and mitochondrial trans-2-enoyl-coa reductase (mecr) were screened out as mir-125b direct targets. luciferase reporter assay further validated that mir-125b mimic significantly inhibited the luciferase activity by targeting wild type (wt) 3'-utr compared with nc. qpcr analysis of acads and mecr mrna from adipose tissues of mir-125b knockout (ko) mice further confirmed the inhibition of mir-125b on acads and mecr expressions. here we report mir-125b play a vital role in maintaining homeostasis of fatty acid metabolism by targeting key enzyme acads and mecr in the process of fatty acid elongation and degradation.",1
"the gene encoding the mir-34a microrna is a transcriptional target of the p53 tumor suppressor protein and subject to epigenetic inactivation in colorectal cancer and numerous other tumor types. here, we combined pulsed silac (psilac) and microarray analyses to identify mir-34a-induced changes in protein and mrna expression. psilac allowed to quantify the de novo protein synthesis of 1206 proteins after activation of a conditional mir-34a allele in a colorectal cancer cell line. ∼19% of the detected proteins were differentially regulated, with 113 proteins being down- and 115 up-regulated. the proteins with a mir-34a seed-matching-sequence in the 3'-untranslated region (utr) of the corresponding mrna showed a clear bias toward translational repression. proteins involved in dna replication, e.g. the mcm proteins, and cell proliferation, were over-represented among indirectly down-regulated proteins lacking a mir-34a seed-match. the decrease in de novo protein synthesis of direct mir-34a targets correlated with reduced levels of the corresponding mrna in most cases, indicating an interdependence of both types of regulation. in addition, 43 mrnas encoding proteins not detected by psilac were down-regulated after mir-34a expression and contained mir-34a seed-matches. the direct regulation of selected mir-34a target-mrnas was confirmed using reporter assays. via down-regulation of the proteins encoded by these mrnas mir-34a presumably inhibits glycolysis (ldha), wnt-signaling (lef1), invasion/migration (axl) and lipid metabolism (acsl1, acsl4). furthermore, mir-34a may activate p53 by inhibiting its acetylation (mta2, hdac1) and degradation (yy1). in summary, mir-34a presumably participates in multiple tumor suppressive pathways by directly and indirectly suppressing the expression of numerous, critical proteins.",1
"the structure and dynamics of the polyadenylation inhibition element (pie) rna, free and bound to the u1a protein, have been examined using time-resolved fret and 2-aminopurine (2ap) fluorescence. this regulatory rna, located at the 3' end of the u1a pre-mrna, adopts a u-shaped structure, with binding sites for a single u1a protein at each bend (box 1 and box 2). the distance between the termini of the arms of the rna is sensitive to its three-dimensional structure. using cy3/cy5 fret efficiency to monitor binding of mg(2+), we show that the pie rna binds two mg(2+) ions, which results in a restriction of its distance distribution of conformations. local rna structure probing using 2ap fluorescence shows that the structure of box 2 changes in response to mg(2+) binding, thus tentatively locating the ion binding sites. steady-state fret data show that the distance r between the termini of the pie rna stems decreases from 66 a in the free rna, to 58 a when n-terminal rna binding domains (rbd1) of u1a are bound, and to 53 a when u1a proteins bind. however, anisotropy measurements indicate that both cy3 and cy5 stack on the ends of the rna. to examine the consequences of the restricted motion of the fluorophores, fret data are analyzed using two different models of motion and then compared to analogous data from the cy3/fluorescein fret pair. we conclude that the error introduced into distance calculations by stacking of the dyes is within the error of our measurements. distance distributions of the rna structures show that the intramolecular distance between the arms of the pie rna varies on the time scale of the fluorescence measurements; the mean distance is dependent on protein binding, but the breadth of the distributions indicates that the rna retains structural heterogeneity.",1
"we previously reported that mir-1 is among the most consistently down-regulated mirs in primary human prostate tumors. in this follow-up study, we further corroborated this finding in an independent data set and made the novel observation that mir-1 expression is further reduced in distant metastasis and is a candidate predictor of disease recurrence. moreover, we performed in vitro experiments to explore the tumor suppressor function of mir-1. cell-based assays showed that mir-1 is epigenetically silenced in human prostate cancer. overexpression of mir-1 in these cells led to growth inhibition and down-regulation of genes in pathways regulating cell cycle progression, mitosis, dna replication/repair and actin dynamics. this observation was further corroborated with protein expression analysis and 3'-utr-based reporter assays, indicating that genes in these pathways are either direct or indirect targets of mir-1. a gene set enrichment analysis revealed that the mir-1-mediated tumor suppressor effects are globally similar to those of histone deacetylase inhibitors. lastly, we obtained preliminary evidence that mir-1 alters the cellular organization of f-actin and inhibits tumor cell invasion and filipodia formation. in conclusion, our findings indicate that mir-1 acts as a tumor suppressor in prostate cancer by influencing multiple cancer-related processes and by inhibiting cell proliferation and motility.",1
"background wnt-signalling has an important role in renal cancer and it is modulated by genistein in other cancers. recently, micrornas (mirnas) have emerged as new regulators of gene expression. thus, we focused on mirnas to examine the regulatory mechanism of genistein on the wnt-signalling pathway in renal cell carcinoma (rcc). methods initially, we investigated the effect of genistein on wnt-signalling (topflash reporter assay (tcf reporter assays)) in renal cancer cells, and using microarray identified candidate mirnas whose expression was decreased by genistein. we performed functional analyses and investigated the relationship between mirna expression and renal cancer patient outcomes. we also did 3'utr luciferase assays to look at direct mirna regulation of wnt-signalling-related genes. results genistein promoted apoptosis while inhibiting rcc cell proliferation and invasion. genistein also decreased tcf reporter activity in rcc cells. we found that mir-1260b was highly expressed and significantly downregulated by genistein in rcc cells. the expression of mir-1260b was significantly higher in renal cancer tissues compared with normal, and significantly related to overall shorter survival. in addition, mir-1260b promoted renal cancer cell proliferation and invasion in rcc cells. the 3'utr luciferase activity of target genes (sfrp1, dkk2, smad4) was significantly decreased and their protein expression significantly upregulated in mir-1260b inhibitor-transfected renal cancer cells. conclusion our data suggest that genistein inhibited wnt-signalling by regulating mir-1260b expression in renal cancer cells.",1
"background microrna 21 (mir-21) has been demonstrated to be significantly elevated in many types of cancers, including the hepatocellular carcinoma (hcc). in the present study, we investigated the role of mir-21 in hcc by identifying its novel targets, as well as its underlying molecular mechanism. methods the expression of mitogen-activated protein kinase-kinase 3 (map2k3) in human hcc tumor tissues and adjacent non-tumor tissues was determined by immunohistochemistry staining (ihc) analysis. the 3'-untranslated region (3'-utr) of map2k3 combined with mir-21 was experimentally verified by a mirna luciferase reporter approach. moreover, the role of mir-21 in regulating hcc cell proliferation was analyzed by an mtt assay infected with mir-21mimics/sponge inhibitor adenoviral viral vectors. results by immunohistochemistry staining analysis, we found that mitogen-activated protein kinase-kinase 3 (map2k3) was strikingly repressed in the human hcc tumor tissues, in comparison with the adjacent non-tumor tissues in clinical settings. more importantly, the repression of map2k3 was inversely correlated with the expression of mir-21 in hcc. further study demonstrated that the map2k3 was a novel direct target of mir-21, which was experimentally validated by a mirna luciferase reporter approach. in hepg2 cells, inhibition of mir-21 expression with an adenoviral mir-21 sponge vector profoundly suppressed cell proliferation by up-regulating map2k3 expression at both mrna and protein levels. conclusions these results provide a clinical evidence that map2k3 may be a tumor repressor gene, and it is a direct target of mir-21 in hcc, indicating an underlying mechanism by which mir-21 is able to directly target map2k3 and inhibit its expression during the carcinogenesis of hcc, at both transcriptional and post-translational levels. this study also suggests that targeting mir-21-map2k3 pathway may be a promising strategy in the prevention and treatment of hcc.",1
"the aim of this study was to investigate the role of microrna-21 (mir-21) in the regulation of phosphatase and tensin homolog deleted from chromosome-10 (pten) expression and proliferation of endometrioid endometrial cancer (eec) cells. we performed a qrt-pcr assay with mir-21 and pten in 16 paired eec tumor tissues and adjacent non-tumor endometrium. to investigate the regulation of pten by mir-21, we designed gain- and loss-of-function of mir-21 experiments in the kle cell line by transfection with a synthetic mir-21 mimic and inhibitor. to validate the putative binding site of mir-21 in the 3' untranslated region (3'-utr) of pten messenger rna (mrna), a dual-luciferase reporter assay was carried out. to evaluate the potential effect of mir-21 on eec proliferation, we performed both overexpression experiments, using an mir-21 mimic, and inhibition assays, using an mir-21 inhibitor. mir-21 was overexpressed in eec and was inversely correlated with pten protein expression (p<0.001). mir-21 regulated pten protein expression and cell proliferation in the kle cell line and the direct binding of mir-21 to the pten 3'-utr was confirmed using a dual-luciferase reporter assay. the upregulation of mir-21 led to a significant decrease in the pten protein expression level (p=0.007). the downregulation of mir-21 led to a significant increase in pten protein (p=0.002). the expression of luciferase in the wt-pten-3'-utr-pgl3 group was downregulated in the presence of the mir-21 mimic (p=0.001). mir-21 was overexpressed in eec. in conclusion, we demonstrated that the expression of pten protein, but not mrna, was negatively directly regulated by mir-21 in the kle cell line. the overexpression of mir-21 modulated eec cell proliferation through the downregulation of pten.",1
"micrornas (mirnas) are short noncoding regulatory rna molecules that modulate protein expression by inhibiting mrna translation or promoting mrna degradation. however, little is understood about the roles of mirnas in alzheimer's disease. during a research for mirnas that are differentially expressed in cerebral cortex of appswe/psdeltae9 mice (a model for alzheimer's disease) and age-matched controls, one candidate mirna that is relatively highly expressed, mir-34a, was studied further because sequence analysis suggested a likely interaction with the 3'-untranslated region of bcl2 mrna. we show that the expression of mir-34a is inversely correlated with the protein level of bcl2 in appswe/psdeltae9 mice and age-matched controls, and mir-34a expression directly inhibits bcl2 translation in sh-sy5y cells. no effect on bcl2 mrna level was observed. western blot analysis of active caspase-3 showed higher levels in appswe/psdeltae9 mice and stable transfecant cell line of mir-34a than in controls. consistently, mir-34a knockdown through antisense lna oligonucleotides increased the level of bcl2 protein in sh-sy5y cells, which was accompanied by a decrease of active caspase-3. these findings suggested that bcl2 is an important functional target for mir-34a, and the abnormal expression of mir-34a may contribute to the pathogenesis of alzheimer's disease, at least in part by affecting the expression of bcl2.",1
"microrna-145 (mir-145) expression is downregulated in several human cancers, but its clinical and functional relevance to ovarian carcinoma has not yet been elucidated. this study addressed the hypothesis that mir-145 serves as a prognostic biomarker and a tumor suppressor that regulates the expression of high-mobility group a2 (hmga2) oncoprotein in ovarian cancer. here, we found that low mir-145 expression and hmga2 overexpression determined by qrt-pcr and immunohistochemistry significantly correlated with advanced stage, lymph node involvement, and distant metastasis in 74 ovarian carcinomas. low mir-145 expression significantly correlated with tumor recurrence and worse overall survival (hr=8.62, p = 0.039). transfection of pre-mir-145 resulted in reduced cell growth and migration, and increased apoptosis of ovarian cancer cells by tunel, colony forming, and cell migration assays. mir-145 was found to directly target hmga2 by luciferase assay and western blotting. our findings suggest that mir-145 functions as a tumor suppressor in ovarian cancer and directly targets hmga2 oncoprotein. low mir-145 and high hmga2 expressions are potential biomarkers of poor prognosis of ovarian carcinoma and mir-145 is the more powerful predictor of patient outcome.",1
"previously, aimp3 (aminoacyl-trnasynthetase-interacting multifunctional protein-3) was shown to be involved in the macromolecular trna synthetase complex or to act as a tumor suppressor. in this study, we report a novel role of aimp3/p18 in the cellular aging of human mesenchymal stem cells (hmscs). we found that aimp3/p18 expression significantly increased in senescent hmscs and in aged mouse bone marrow-derived mscs (mbm-mscs). aimp3/p18 overexpression is sufficient to induce the cellular senescence phenotypes with compromised clonogenicity and adipogenic differentiation potential. to identify the upstream regulators of aimp3/p18 during senescence, we screened for potential epigenetic regulators and for mirnas. we found that the levels of mir-543 and mir-590-3p significantly decreased under senescence-inducing conditions, whereas the aimp3/p18 protein levels increased. we demonstrate for the first time that mir-543 and mir-590-3p are able to decrease aimp3/p18 expression levels through direct binding to the aimp/p18 transcripts, which further compromised the induction of the senescence phenotype. taken together, our data demonstrate that aimp3/p18 regulates cellular aging in hmscs possibly through mir-543 and mir-590-3p.",1
"micrornas are important regulators of gene expression, yet the functional outputs of most microrna-target interactions remain elusive. here we introduce the drosophila melanogaster microrna sponge (mir-sp) as a powerful transgenic technology to dissect the function of every microrna with precise spatiotemporal resolution. mir-sps can be used to characterize tissue-specific microrna loss-of-function phenotypes, define the spatial regulation of their effectors and uncover interactions between micrornas and other genes. using themir-sp system, we identified an essential role of the conserved microrna mir-8, in neuromuscular junction formation. tissue-specific silencing revealed that postsynaptic activity of mir-8 is important for normal neuromuscular junction morphogenesis. given that mir-sps rely on a bipartite modular expression system, they could be used to elucidate the endogenous function of micrornas in any species in which conditional expression can be achieved.",1
"the male-specific lethal (msl) complex regulates dosage compensation of the male x chromosome in drosophila. here, we report the crystal structure of its msl1/msl2 core, where two msl2 subunits bind to a dimer formed by two molecules of msl1. analysis of structure-based mutants revealed that msl2 can only interact with the msl1 dimer, but msl1 dimerization is msl2 independent. we show that msl1 is a substrate for msl2 e3 ubiquitin ligase activity. chip experiments revealed that msl1 dimerization is essential for targeting and spreading of the msl complex on x-linked genes; however, msl1 binding to promoters of male and female cells is independent of the dimer status and other msl proteins. finally, we show that loss of msl1 dimerization leads to male-specific lethality. we propose that msl1-mediated dimerization of the entire msl complex is required for msl2 binding, x chromosome recognition, and spreading along the x chromosome.",1
"micrornas (mirnas) are small regulatory rnas that are between 21 and 25 nucleotides in length and repress gene function through interactions with target mrnas. the genomes of metazoans encode on the order of several hundred mirnas, but the processes they regulate have been defined for only two in c. elegans. we searched for new inhibitors of apoptotic cell death by testing existing collections of p element insertion lines for their ability to enhance a small-eye phenotype associated with eye-specific expression of the drosophila cell death activator reaper. here we report the identification of the drosophila mirna mir-14 as a cell death suppressor. loss of mir-14 enhances reaper-dependent cell death, whereas ectopic expression suppresses cell death induced by multiple stimuli. animals lacking mir-14 are viable. however, they are stress sensitive and have a reduced lifespan. mir-14 mutants have elevated levels of the apoptotic effector caspase drice, suggesting one potential site of action. mir-14 also regulates fat metabolism. deletion of mir-14 results in animals with increased levels of triacylglycerol and diacylglycerol, whereas increases in mir-14 copy number have the converse effect. we discuss possible relationships between these phenotypes.",1
"bacterial ribonuclease iii (rnase iii) is a highly conserved endonuclease, which plays pivotal roles in rna maturation and decay pathways by cleaving double-stranded structure of rnas. here we cloned rncs gene from the genomic dna of brucella melitensis, and analyzed the cleavage properties of rnase iii from brucella. we identified brucella-encoding small rna (srna) by high-throughput sequencing and northern blot, and found that srna of brucella and homo mirna precursor (pre-mirna) can be bound and cleaved by b.melitensis ribonuclease iii (bm-rnase iii). cleavage activity of bm-rnase iii is bivalent metal cations- and alkaline buffer-dependent. we constructed several point mutations in bm-rnase iii, whose cleavage activity indicated that the 133th glutamic acid residue was required for catalytic activity. western blot revealed that bm-rnase iii was differently expressed in brucella virulence strain 027 and vaccine strain m5-90. collectively, our data suggest that brucella rnase iii can efficiently bind and cleave stem-loop structure of small rna, and might participate in regulation of virulence in brucella.",1
"purpose the purpose of this study was to investigate the clinicopathologic significance and potential role of mir-200b and mir-200c in the development and progression of gastric cancer. experimental design we examined mir-200b and mir-200c expression in 36 paired normal and stomach tumor specimens, as well as gastric cancer cell lines, by quantitative real-time pcr. in addition, mir-200b and mir-200c were detected by ish using gastric cancer tissue microarrays, and the association between mir-200b and mir-200c levels and clinicopathologic factors and prognosis were analyzed. a luciferase assay was conducted for target evaluation. the functional effects of mir-200b and mir-200c on gastric cancer cells were validated by a cell proliferation assay and cell invasion and migration assays. results mir-200b and mir-200c were downregulated in the gastric cancer specimens and cell lines tested. mir-200b and mir-200c levels were significantly correlated with the clinical stage, t stage, lymph node metastasis, and survival of patients. ectopic expression of mir-200b and mir-200c impaired cell growth and invasion. in addition, when overexpressed, mir-200b and mir-200c commonly directly targeted dnmt3a, dnmt3b, and sp1 (a transactivator of the dnmt1 gene), which resulted in marked reduction of the expression of dna methyltransferases dnmt1, dnmt3a, and dnmt3b at the protein level. this effect, in turn, led to a decrease in global dna methylation and reexpression of p16, rass1a1, and e-cadherin via promoter dna hypomethylation. conclusion our findings suggest that mir-200b and mir-200c, as valuable markers of gastric cancer prognosis, may be a promising approach to human gastric cancer treatment.",1
"microrna (mirna)-133b has been revealed to be downregulated in head and neck/oral, bladder, human non-small cell lung, colorectal and esophageal squamous cell cancer. the present study examined the expression of mir-133b in renal cell carcinoma (rcc) cell lines and the effects of mirna-133b on rcc cell proliferation, migration and invasion. quantitative polymerase chain reaction was used to detect the expression of mir-133b in rcc cell lines. following transfection of mir-133b, the expression of mir-133b was examined and a cell viability assay, cell migration assay, cell invasion assay, western blot analysis and luciferase assay were conducted in rcc cell lines. the present study revealed that mirna‑133b was downregulated and inhibited cell proliferation, migration and invasion in 786-o and a498 cells. in addition, to the best of our knowledge, the present study provided the first evidence that mirna-133b may directly target matrix metallopeptidase 9 (mmp-9) in rcc. the present study also provided evidence that mirna-133b suppresses cell proliferation, migration and invasion by targeting mmp-9 in rcc cell lines. these results suggested that mirna-133b may be used for the development of novel molecular markers and therapeutic approaches to inhibit the metastasis of rcc.",1
"aberrant overexpression of the mir-17-92 polycistron is strongly associated with b-cell lymphomagenesis. recent studies have shown that mir-17-92 down-regulates the proapoptotic protein bim, leading to overexpression of bcl2, which likely plays a key role in lymphomagenesis. however, the fact that jeko-1 cells derived from mantle cell lymphoma exhibit both homozygous deletion of bim and overexpression of mir-17-92 suggests other targets are also involved in b-cell lymphomagenesis. to identify essential target(s) of mir-17-92 in lymphomagenesis, we first transfected mir-17-92 into 2 genetically distinct b-cell lymphoma cell lines: raji, which overexpress c-myc, and sudhl4, which overexpress bcl2. raji transfected with mir-17-19b-1 exhibited down-regulated expression of bim and a slight up-regulation in bcl2 expression. on the other hand, sudhl4 transfectants showed aggressive cell growth reflecting facilitated cell cycle progression at the g(1) to s transition and decreased expression of cdkn1a mrna and p21 protein (cdkn1a/p21) that was independent of p53 expression. conversely, transfection of antisense oligonucleotides against mir-17 and mir-20a into jeko-1 led to up-regulation of cdkn1a/p21, resulting in decreased cell growth with g(1) to s arrest. thus, cdkn1a/p21 appears to be an essential target of mir-17-92 during b-cell lymphomagenesis, which suggests the mir-17-92 polycistron has distinct targets in different b-cell lymphoma subtypes.",1
"small noncoding rna (srna) molecules are integral components of the regulatory machinery for many bacterial species and are known to posttranscriptionally regulate metabolic and stress-response pathways, quorum sensing, virulence factors, and more. the yop-ysc type iii secretion system (t3ss) is a critical virulence component for the pathogenic yersinia species, and the regulation of this system is tightly controlled at each step from transcription to translocation of effectors into host cells. the contribution of srnas to the regulation of the t3ss in yersinia has been largely unstudied, however. previously, our lab identified a role for the srna chaperone protein hfq in the regulation of components of the t3ss in the gastrointestinal pathogen yersinia pseudotuberculosis. here we present data demonstrating a similar requirement for hfq in the closely related species yersinia pestis. through deep sequencing analysis of the y. pestis srna-ome, we found 63 previously unidentified putative srnas in this species. we identified a yersinia-specific srna, ysr141, carried by the t3ss plasmid pcd1 that is required for the production of multiple t3ss proteins. in addition, we show that ysr141 targets an untranslated region upstream of yopj to posttranscriptionally activate the synthesis of the yopj protein. furthermore, ysr141 may be an unstable and/or processed srna, which could contribute to its function in the regulation of the t3ss. the discovery of an srna that influences the synthesis of the t3ss adds an additional layer of regulation to this tightly controlled virulence determinant of y. pestis.",1
"small nucleolar rnas (snornas) are an abundant group of noncoding rnas mainly involved in the post-transcriptional modifications of rrnas in eukaryotes. in this study, a large-scale genome-wide analysis of the two major families of snorna genes in the fruit fly drosophila melanogaster has been performed using experimental and computational rnomics methods. two hundred and twelve gene variants, encoding 56 box h/aca and 63 box c/d snornas, were identified, of which 57 novel snornas have been reported for the first time. these snornas were predicted to guide a total of 147 methylations and pseudouridylations on rrnas and snrnas, showing a more comprehensive pattern of rrna modification in the fruit fly. with the exception of nine, all the snornas identified to date in d. melanogaster are intron encoded. remarkably, the genomic organization of the snornas is characteristic of 8 duhg genes and 17 intronic gene clusters, demonstrating that distinct organizations dominate the expression of the two families of snornas in the fruit fly. of the 267 introns in the host genes, more than half have been identified as host introns for coding of snornas. in contrast to mammals, the variation in size of the host introns is mainly due to differences in the number of snornas they contain. these results demonstrate the extensive utilization of introns for coding of snornas in the host genes and shed light on further research of other noncoding rna genes in the large introns of the drosophila genome.",1
"menin, the product of the men1 gene, functions as a tumor suppressor and was first identified in 1997 due to its causative role in the endocrine tumor disorder multiple endocrine neoplasia, type 1 (men1). more recently, menin has been identified as a key player in pancreatic islet biology with the observation of an inverse relationship between menin levels and pancreatic islet proliferation. however, the factors regulating menin and the men1 gene in the pancreas are poorly understood. here, we describe the regulation of menin by mir-24 and demonstrate that mir-24 directly decreases menin levels and impacts downstream cell cycle inhibitors in min6 insulinoma cells and in βlox5 immortalized β-cells. this regulation of menin impacts cell viability and proliferation in βlox5 cells. furthermore, our data show a feedback regulation between mir-24 and menin that is present in the pancreas, suggesting that mir-24 regulates menin levels in the pancreatic islet.",1
"micrornas (mirnas) can influence lineage choice or affect critical developmental checkpoints during hematopoiesis. we examined the role of the p53-induced microrna mir-34a in hematopoiesis by gain-of-function analysis in murine bone marrow. constitutive expression of mir-34a led to a block in b cell development at the pro-b-cell-to-pre-b-cell transition, leading to a reduction in mature b cells. this block appeared to be mediated primarily by inhibited expression of the transcription factor foxp1. foxp1 was a direct target of mir-34a in a 3'-untranslated region (utr)-dependent fashion. knockdown of foxp1 by sirna recapitulated the b cell developmental phenotype induced by mir-34a, whereas cotransduction of foxp1 lacking its 3' utr with mir-34a rescued b cell maturation. knockdown of mir-34a resulted in increased amounts of foxp1 and mature b cells. these findings identify a role for mir-34a in connecting the p53 network with suppression of foxp1, a known b cell oncogene.",1
"some micrornas (mirnas) have been implicated in hepatocellular carcinoma (hcc) development and progression. however, the roles and mechanisms of several mirnas in hcc remain poorly understood. here, we report that mir-379-5p, which is down-regulated in hcc tissues and cell lines, is associated with advanced tnm stage and metastasis in hcc. the ectopic overexpression of mir-379-5p inhibited hcc cell migration, invasion, epithelial-to-mesenchymal transition (emt) and metastasis both in vitro and in vivo. conversely, mir-379 knockdown increased migration, invasion and emt in hcc cells. moreover, mir-379-5p exerted this function by directly targeting focal adhesion kinase (fak) 3'-utr and repressing fak expression, thus leading to suppression of akt signaling. furthermore, the tumor suppressive effects of mir-379-5p in hcc cells were reversed by activating akt signaling or restoring fak expression. in clinical samples of hcc, mir-379-5p negatively correlated with fak, which was up-regulated in hcc. taken together, our findings highlight the important role of mir-379-5p in regulating the emt and metastasis of hcc by targeting fak/akt signaling, suggesting that mir-379-5p may represent a novel potential therapeutic target and prognostic marker for hcc.",1
"adenosine to inosine (a-to-i) pre-mrna editing by the adar enzyme family has the potential to increase the variety of the proteome. this editing by adenosine deamination is essential in mammals for a functional brain. to detect novel substrates for a-to-i editing we have used an experimental method to find selectively edited sites and combined it with bioinformatic techniques that find stem-loop structures suitable for editing. we present here the first verified editing candidate detected by this screening procedure. we show that gabra-3, which codes for the alpha3 subunit of the gaba(a) receptor, is a substrate for editing by both adar1 and adar2. editing of the gabra-3 mrna recodes an isoleucine to a methionine. the extent of editing is low at birth but increases with age, reaching close to 100% in the adult brain. we therefore propose that editing of the gabra-3 mrna is important for normal brain development.",1
"in many adult stem cell lineages, the continuous production of functional differentiated cells depends on the maintenance of progenitor cells in an undifferentiated and proliferative state, as well as the subsequent commitment to proper terminal differentiation. in the drosophila male germline stem cell (gsc) lineage, a key differentiation factor, bag of marbles (bam), is required for the transition from proliferative spermatogonia to differentiating spermatocytes. we show that bam mrna, but not bam, is present in spermatocytes, suggesting that bam is regulated post-transcriptionally. consistent with this, repression of bam accumulation is achieved by micrornas via the bam 3'utr. when the bam 3'utr was substituted with the 3'utr of a constitutively expressed α-tubulin, bam became stabilized in spermatocytes. moreover, such a persistent expression of bam in spermatocytes was recapitulated by specifically mutating the putative mir-275/mir-306 recognition site at the bam 3'utr. in addition, overexpression of mir-275 or mir-306 in spermatogonial cells resulted in a delay of the proliferation-to-differentiation transition and resembled the bam loss-of-function phenotype, suggesting that these micrornas are sufficient to downregulate bam. finally, the failure of bam downregulation in spermatocytes affected spermatid terminal differentiation and resulted in increased male sterility. our results demonstrate that micrornas control the stem cell differentiation pathway through regulating bam, the downregulation of which is crucial for proper spermatid terminal differentiation.",1
"uncontrolled fibrosis in multiple organs is the main cause of death in systemic sclerosis (ssc), and transforming growth factor-β (tgf-β) activation plays a fundamental role in the process. our previous study demonstrated that mir-21 was significantly up-regulated in ssc fibroblasts. here, we found that tgf-β regulated the expression of mir-21 and fibrosis-related genes, and decreased smad7 expression. over-expression of mir-21 in fibroblasts decreased the levels of smad7, whereas knockdown of mir-21 increased its expression. further study using a reporter gene assay demonstrated smad7 was a direct target of mir-21. similar to human ssc, the expression of mir-21 increased in the bleomycin induced skin fibrosis. inhibition of fibrosis by treatment with anti-fibrosis drug bortezomib restored the levels of mir-21 and smad7. mir-21 may function in an amplifying circuit to enhance tgf-β signaling events in ssc fibrosis, and suggesting that mir-21 may act as a potential therapeutic target.",1
"background colorectal carcinoma (crc) is a major cause of cancer mortality. the aberrant expression of several micrornas is associated with crc progression; however, the molecular mechanisms underlying this phenomenon are unclear. methods mir-638 and sry-box 2 (sox2) expression levels were detected in 36 tumor samples and their adjacent, non-tumor tissues from patients with crc, as well as in 4 crc cell lines, using real-time quantitative rt-pcr (qrt-pcr). sox2 expression levels were detected in 90 tumor samples and their adjacent tissue using immunohistochemistry. luciferase reporter and western blot assays were used to validate sox2 as a target gene of mir-638. the regulation of sox2 expression by mir-638 was assessed using qrt-pcr and western blot assays, and the effects of exogenous mir-638 and sox2 on cell invasion and migration were evaluated in vitro using the hct-116 and sw1116 crc cell lines. results we found that mir-638 expression was differentially impaired in crc specimens and dependent on tumor grade. the inhibition of mir-638 by an antagomir promoted cell invasion and a mesenchymal-like transition (lamellipodium stretching increased and cell-cell contacts decreased, which was accompanied by the suppression of the epithelial cell marker zo-1/e-cadherin and the upregulation of the mesenchymal cell marker vimentin). a reporter assay revealed that mir-638 repressed the luciferase activity of a reporter gene coupled to the 3'-untranslated region of sox2. mir-638 overexpression downregulated sox2 expression, and mir-638 inhibition upregulated sox2 expression. moreover, mir-638 expression levels were correlated inversely with sox2 mrna levels in human crc tissues. the rnai-mediated knockdown of sox2 phenocopied the invasion-inhibiting effect of mir-638; furthermore, sox2 overexpression blocked the mir-638-induced crc cell transition to epithelial-like cells. conclusions these results demonstrate that the loss of mir-638 promotes invasion and a mesenchymal-like transition by directly targeting sox2 in vitro. these findings define mir-638 as a new, invasion-associated tumor suppressor of crc.",1
"background neurotrophins and their receptors are key molecules in the regulation of neuronal differentiation and survival. they mediate the survival of neurons during development and adulthood and are implicated in synaptic plasticity. the human neurotrophin-3 receptor gene ntrk3 yields two major isoforms, a full-length kinase-active form and a truncated non-catalytic form, which activates a specific pathway affecting membrane remodeling and cytoskeletal reorganization. the two variants present non-overlapping 3'utrs, indicating that they might be differentially regulated at the post-transcriptional level. here, we provide evidence that the two isoforms of ntrk3 are targeted by different sets of micrornas, small non-coding rnas that play an important regulatory role in the nervous system. results we identify one microrna (mir-151-3p) that represses the full-length isoform of ntrk3 and four micrornas (mir-128, mir-485-3p, mir-765 and mir-768-5p) that repress the truncated isoform. in particular, we show that the overexpression of mir-128 - a brain enriched mirna - causes morphological changes in sh-sy5y neuroblastoma cells similar to those observed using an sirna specifically directed against truncated ntrk3, as well as a significant increase in cell number. accordingly, transcriptome analysis of cells transfected with mir-128 revealed an alteration of the expression of genes implicated in cytoskeletal organization as well as genes involved in apoptosis, cell survival and proliferation, including the anti-apoptotic factor bcl2. conclusions our results show that the regulation of ntrk3 by micrornas is isoform-specific and suggest that neurotrophin-mediated processes are strongly linked to microrna-dependent mechanisms. in addition, these findings open new perspectives for the study of the physiological role of mir-128 and its possible involvement in cell death/survival processes.",1
"cellular senescence of normal human cells has by now far exceeded its initial role as a model system for aging research. many reports show the accumulation of senescent cells in vivo, their effect on their microenvironment and its double-edged role as tumour suppressor and promoter. importantly, removal of senescent cells delays the onset of age-associated diseases in mouse model systems. to characterize the role of mirnas in cellular senescence of endothelial cells, we performed mirna arrays from huvecs of five different donors. twelve mirnas, comprising hsa-mir-23a, hsa-mir-23b, hsa-mir-24, hsa-mir-27a, hsa-mir-29a, hsa-mir-31, hsa-mir-100, hsa-mir-193a, hsa-mir-221, hsa-mir-222 and hsa-let-7i are consistently up-regulated in replicatively senescent cells. surprisingly, also mir-21 was found up-regulated by replicative and stress-induced senescence, despite being described as oncogenic. transfection of early passage endothelial cells with mir-21 resulted in lower angiogenesis, and less cell proliferation mirrored by up-regulation of p21(cip1) and down-regulation of cdk2. these two cell-cycle regulators are indirectly regulated by mir-21 via its validated direct targets nfib (nuclear factor 1 b-type), a transcriptional inhibitor of p21(cip) (1) , and cdc25a, which regulates cdk2 activity by dephosphorylation. knock-down of either nfib or cdc25a shows a phenocopy of over-expressing mir-21 in regard to cell-cycle arrest. finally, mir-21 over-epxression reduces the replicative lifespan, while stable knock-down by sponges extends the replicative lifespan of endothelial cells. therefore, we propose that mir-21 is the first mirna that upon its knock-down extends the replicative lifespan of normal human cells.",1
"hypoxia-inducible factor 1 (hif-1) is a crucial transcription factor for the cellular adaptive response to hypoxia, which contributes to multiple events in cancer biology. micrornas (mirnas) are involved in almost all cellular activities such as differentiation, proliferation, and apoptosis. in this work, we use mirna microarrays to profile mirna expression in acute myeloid leukemia (aml) cells with inducible hif-1α expression, and identify 19 differentially expressed mirnas. our study shows that hif-1α represses the expression of mir-17 and mir-20a by downregulating c-myc expression. these two mirnas alleviate hypoxia and hif-1α-induced differentiation of aml cells. more intriguingly, mir-17 and mir-20a directly inhibit the p21 and stat3 (signal transducer and activator of transcription 3) expression, both of which can reverse mir-17/mir-20a-mediated abrogation of hif-1α-induced differentiation. moreover, we show in vivo that mir-20a contributes to hif-1α-induced differentiation of leukemic cells. taken together, our results suggest that hif-1α regulates the mirna network to interfere with aml cell differentiation, representing a novel molecular mechanism for hif-1-mediated anti-leukemic action.",1
"epstein-barr virus (ebv) is a tumorigenic human γ-herpesvirus, which produces several known structured rnas with functional importance: two are implicated in latency maintenance and tumorigenic phenotypes, eber1 and eber2; a viral small nucleolar rna (v-snorna1) that may generate a small regulatory rna; and an internal ribosomal entry site in the ebna1 mrna. a recent bioinformatics and rna-seq study of ebv identified two novel ebv non-coding (nc)rnas with evolutionary conservation in lymphocryptoviruses and likely functional importance. both rnas are transcribed from a repetitive region of the ebv genome (the w repeats) during a highly oncogenic type of viral latency. one novel ncrna can form a massive (586 nt) hairpin, while the other rna is generated from a short (81 nt) intron and is found in high abundance in ebv-infected cells.",1
"homeostasis of the intestine is maintained by dynamic regulation of a pool of intestinal stem cells. the balance between stem cell self-renewal and differentiation is regulated by the notch and insulin signaling pathways. dependence on the insulin pathway places the stem cell pool under nutritional control, allowing gut homeostasis to adapt to environmental conditions. here we present evidence that mir-305 is required for adaptive homeostasis of the gut. mir-305 regulates the notch and insulin pathways in the intestinal stem cells. notably, mir-305 expression in the stem cells is itself under nutritional control via the insulin pathway. this link places regulation of notch pathway activity under nutritional control. these findings provide a mechanism through which the insulin pathway controls the balance between stem cell self-renewal and differentiation that is required for adaptive homeostasis in the gut in response to changing environmental conditions.",1
"neural progenitors self-renew and generate neurons throughout the central nervous system. here, we uncover an unexpected regional specificity in the properties of neural progenitor cells, revealed by the function of a microrna--mir-9. mir-9 is expressed in neural progenitors, and its knockdown results in an inhibition of neurogenesis along the anterior-posterior axis. however, the underlying mechanism differs--in the hindbrain, progenitors fail to exit the cell cycle, whereas in the forebrain they undergo apoptosis, counteracting the proliferative effect. among several targets, we functionally identify hairy1 as a primary target of mir-9, regulated at the mrna level. hairy1 mediates the effects of mir-9 on proliferation, through fgf8 signaling in the forebrain and wnt signaling in the hindbrain, but affects apoptosis only in the forebrain, via the p53 pathway. our findings show a positional difference in the responsiveness of progenitors to mir-9 depletion, revealing an underlying divergence of their properties.",1
"background vascular hyperproliferative disorders are characterized by excessive smooth muscle cell (smc) proliferation leading to vessel remodeling and occlusion. in pulmonary arterial hypertension (pah), smc phenotype switching from a terminally differentiated contractile to synthetic state is gaining traction as our understanding of the disease progression improves. while maintenance of smc contractile phenotype is reportedly orchestrated by a mef2c-myocardin (myocd) interplay, little is known regarding molecular control at this nexus. moreover, the burgeoning interest in micrornas (mirs) provides the basis for exploring their modulation of mef2c-myocd signaling, and in turn, a pro-proliferative, synthetic smc phenotype. we hypothesized that suppression of smc contractile phenotype in pulmonary hypertension is mediated by mir-214 via repression of the mef2c-myocd-leiomodin1 (lmod1) signaling axis. methods and results in smcs isolated from a pah patient cohort and commercially obtained hpasmcs exposed to hypoxia, mir-214 expression was monitored by qrt-pcr. mir-214 was upregulated in pah- vs. control subject hpasmcs as well as in commercially obtained hpasmcs exposed to hypoxia. these increases in mir-214 were paralleled by mef2c, myocd and smc contractile protein downregulation. of these, lmod1 and mef2c were directly targeted by the mir. mir-214 overexpression mimicked the pah profile, downregulating mef2c and lmod1. antagomir-214 abrogated hypoxia-induced suppression of the contractile phenotype and its attendant proliferation. anti-mir-214 also restored pah-pasmcs to a contractile phenotype seen during vascular homeostasis. conclusions our findings illustrate a key role for mir-214 in modulation of mef2c-myocd-lmod1 signaling and suggest that an antagonist of mir-214 could mitigate smc phenotype changes and proliferation in vascular hyperproliferative disorders including pah.",1
"genetic and functional data indicate that variation in the expression of the neurotrophin-3 receptor gene (ntrk3) may have an impact on neuronal plasticity, suggesting a role for ntrk3 in the pathophysiology of anxiety disorders. microrna (mirna) posttranscriptional gene regulators act by base-pairing to specific sequence sites, usually at the 3'utr of the target mrna. variants at these sites might result in gene expression changes contributing to disease susceptibility. we investigated genetic variation in two different isoforms of ntrk3 as candidate susceptibility factors for anxiety by resequencing their 3'utrs in patients with panic disorder (pd), obsessive-compulsive disorder (ocd), and in controls. we have found the c allele of rs28521337, located in a functional target site for mir-485-3p in the truncated isoform of ntrk3, to be significantly associated with the hoarding phenotype of ocd. we have also identified two new rare variants in the 3'utr of ntrk3, ss102661458 and ss102661460, each present only in one chromosome of a patient with pd. the ss102661458 variant is located in a functional target site for mir-765, and the ss102661460 in functional target sites for two mirnas, mir-509 and mir-128, the latter being a brain-enriched mirna involved in neuronal differentiation and synaptic processing. interestingly, these two variants significantly alter the mirna-mediated regulation of ntrk3, resulting in recovery of gene expression. these data implicate mirnas as key posttranscriptional regulators of ntrk3 and provide a framework for allele-specific mirna regulation of ntrk3 in anxiety disorders.",1
"alzheimer's disease (ad) is the most common form of dementia worldwide, characterized by progressive memory impairment, behavioral changes, and, ultimately, loss of consciousness and death. recently, microrna (mirna) dysfunction has been associated with increased production and impaired clearance of amyloid-β (aβ) peptides, whose accumulation is one of the most well-known pathophysiological markers of this disease. in this study, we identified several mirnas capable of targeting key proteins of the amyloidogenic pathway. the expression of one of these mirnas, mir-31, previously found to be decreased in ad patients, was able to simultaneously reduce the levels of app and bace1 mrna in the hippocampus of 17-month-old ad triple-transgenic (3xtg-ad) female mice, leading to a significant improvement of memory deficits and a reduction in anxiety and cognitive inflexibility. in addition, lentiviral-mediated mir-31 expression significantly ameliorated ad neuropathology in this model, drastically reducing aβ deposition in both the hippocampus and subiculum. furthermore, the increase of mir-31 levels was enough to reduce the accumulation of glutamate vesicles in the hippocampus to levels found in non-transgenic age-matched animals. overall, our results suggest that mir-31-mediated modulation of app and bace1 can become a therapeutic option in the treatment of ad.",1
"micrornas (mirnas) are endogenous noncoding rnas, about 22 nucleotides in length, that mediate post-transcriptional gene silencing by annealing to inexactly complementary sequences in the 3'-untranslated regions of target mrnas. our current understanding of the functions of mirnas relies mainly on their tissue-specific or developmental stage-dependent expression and their evolutionary conservation, and therefore is primarily limited to their involvement in developmental regulation and oncogenesis. of more than 300 mirnas that have been identified, mir-1 and mir-133 are considered to be muscle specific. here we show that mir-1 is overexpressed in individuals with coronary artery disease, and that when overexpressed in normal or infarcted rat hearts, it exacerbates arrhythmogenesis. elimination of mir-1 by an antisense inhibitor in infarcted rat hearts relieved arrhythmogenesis. mir-1 overexpression slowed conduction and depolarized the cytoplasmic membrane by post-transcriptionally repressing kcnj2 (which encodes the k(+) channel subunit kir2.1) and gja1 (which encodes connexin 43), and this likely accounts at least in part for its arrhythmogenic potential. thus, mir-1 may have important pathophysiological functions in the heart, and is a potential antiarrhythmic target.",1
"rationale micrornas (mirnas), in particular mir-29b and mir-30c, have been implicated as important regulators of cardiac fibrosis. objective to perform a proteomics comparison of mirna effects on extracellular matrix secretion by cardiac fibroblasts. methods and results mouse cardiac fibroblasts were transfected with pre-/anti-mir of mir-29b and mir-30c, and their conditioned medium was analyzed by mass spectrometry. mir-29b targeted a cadre of proteins involved in fibrosis, including multiple collagens, matrix metalloproteinases, and leukemia inhibitory factor, insulin-like growth factor 1, and pentraxin 3, 3 predicted targets of mir-29b. mir-29b also attenuated the cardiac fibroblast response to transforming growth factor-β. in contrast, mir-30c had little effect on extracellular matrix production but opposite effects regarding leukemia inhibitory factor and insulin-like growth factor 1. both mirnas indirectly affected cardiac myocytes. on transfection with pre-mir-29b, the conditioned medium of cardiac fibroblasts lost its ability to support adhesion of rat ventricular myocytes and led to a significant reduction of cardiac myocyte proteins (α-actinin, cardiac myosin-binding protein c, and cardiac troponin i). similarly, cardiomyocytes derived from mouse embryonic stem cells atrophied under pre-mir-29 conditioned medium, whereas pre-mir-30c conditioned medium had a prohypertrophic effect. levels of mir-29a, mir-29c, and mir-30c, but not mir-29b, were significantly reduced in a mouse model of pathological but not physiological hypertrophy. treatment with antagomirs to mir-29b induced excess fibrosis after aortic constriction without overt deterioration in cardiac function. conclusions our proteomic analysis revealed novel molecular targets of mirnas that are linked to a fibrogenic cardiac phenotype. such comprehensive screening methods are essential to define the concerted actions of mirnas in cardiovascular disease.",1
"micrornas are important regulators of the pathogenesis of b-cell acute lymphoblastic leukaemia (b-all). in this study, we identified mir-3173 and its predicted target gene ptk2 were correspondingly differentially expressed in b-all patients. in b-all cell lines, cck-8 proliferation assay revealed that mir-3173 could inhibit the cell proliferation. moreover, transwell assay revealed that mir-3173 could also inhibit cell migration and invasion in b-all cell lines. luciferase assays revealed that mir-3173 directly bound to the 3'untranslated region of ptk2, and western blotting showed that mir-3173 suppressed the expression of ptk2 at the protein level. generally, this study indicates that mir-3173 negatively regulates ptk2 and inhibits proliferation and invasion of b-all cell lines. thus, mir-3173 may represent a potential therapeutic molecule for b-all intervention.",1
"myasthenia gravis (mg) is a t cell-dependent and b cell-mediated autoimmune disease of neuromuscular junctions and cytokines may play a crucial role in the pathogenesis and perpetuation of mg. micrornas (mirnas) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. dysregulation of mirnas has been described in various disease states. in this study, mirna microarrays identified let-7 family to be decreased in peripheral blood mononuclear cells (pbmcs) from mg patients compared to the healthy controls. we next demonstrated the differential expression of let-7 family in larger samples by quantitative real-time pcr. using a combination of bioinformatics and molecular approaches, we confirmed il-10 as a target for let-7c. il-10 expression also showed a negative correlation with let-7c expression in pbmcs from mg patients. further experiments revealed that induced levels of il-10 were inversely related to let-7c levels. we also showed that let-7c could regulate il-10 expression in jurkat cells. in summary, our results suggest that abnormal expression/regulation of micrornas may contribute to or be indicative of the initiation and progression of mg.",1
"micrornas (mirna) are small rna molecules of approximately 20 to 22 nucleotides that reduce expression of proteins through mrna degradation and/or translational silencing. each known mirna has a large number of predicted targets. members of the let-7/mir-98 family of mirnas are up-regulated at the end of embryonic development. let-7 is often down-regulated early during cancer development, suggesting that let-7-regulated oncofetal genes (log) may become reexpressed in cancer cells. using comparative bioinformatics, we have identified 12 conserved logs that include hmga2 and imp-1/crd-bp. imp-1 has growth-promoting activities through stabilization of c-myc mrna. we experimentally confirmed that imp-1 is a direct let-7 target that promotes cell growth and motility of tumor cells, and we confirmed by proteomics analysis that imp-1 and hmga2 are major mirna targets. our data suggest that a substantial part of the growth inhibitory activities of let-7 comes from suppressing the expression of imp-1. logs could be novel therapeutic targets and potential biomarkers for cancer treatment.",1
"mammalian genomes include many maternally and paternally imprinted genes. most of these are also expressed in the brain, and several have been implicated in regulating specific behavioral traits. here, we have used a knockout approach to study the function of peg13 , a gene that codes for a fast-evolving lncrna (long noncoding rna) and is part of a complex of imprinted genes on chromosome 15 in mice and chromosome 8 in humans. mice lacking the 3' half of the transcript look morphologically wild-type but show distinct behavioral differences. they lose interest in the opposite sex, instead displaying a preference for wild-type animals of the same sex. further, they show a higher level of anxiety, lowered activity and curiosity, and a deficiency in pup retrieval behavior. brain rna expression analysis reveals that genes involved in the serotonergic system, formation of glutamatergic synapses, olfactory processing, and estrogen signaling-as well as more than half of the other known imprinted genes-show significant expression changes in peg13 -deficient mice. intriguingly, these pathways are differentially affected in the sexes, resulting in male and female brains of peg13 -deficient mice differing more from each other than those of wild-type mice. we conclude that peg13 is part of a developmental pathway that regulates the neurobiology of social and sexual interactions.",1
"this study was designed to evaluate the effects of strontium on the expression levels of micrornas (mirnas) and to explore their effects on skeletal cell proliferation, differentiation, adhesion, and apoptosis. the targets of these mirnas were also studied. molecular cloning, cell proliferation assay, cell apoptosis assay, quantitative real-time pcr, and luciferase reporter assay were used. strontium altered the expression levels of mirnas in vitro and in vivo. mir-9-5p, mir-675-5p, and mir-138-5p impaired skeletal cell proliferation, cell differentiation and cell adhesion. mir-9-5p and mir-675-5p induced mc3t3-e1 cell apoptosis more specifically than mir-138-5p. mir-9-5p, mir-675-5p, and mir-138-5p targeted glycogen synthase kinase 3 β (gsk3β), atpase aminophospholipid transporter class i type 8a member 2 (atp8a2), and eukaryotic translation initiation factor 4e binding protein 1 (eif4ebp1), respectively. low-density lipoprotein receptor-related protein 5 (lrp5) played a positive role in skeletal development. mir-9-5p, mir-675-5p, and mir-138-5p damage strontium and lrp5-mediated skeletal cell proliferation, differentiation, and adhesion, and induce cell apoptosis by targeting gsk3β, atp8a2, and eif4ebp1, respectively.",1
"transforming growth factor-β (tgfβ) promotes glomerular hypertrophy and matrix expansion, leading to glomerulosclerosis. micrornas are well suited to promote fibrosis because they can repress gene expression, which negatively regulate the fibrotic process. recent cellular and animal studies have revealed enhanced expression of microrna, mir-21, in renal cells in response to tgfβ. specific mir-21 targets downstream of tgfβ receptor activation that control cell hypertrophy and matrix protein expression have not been studied. using 3'utr-driven luciferase reporter, we identified the tumor suppressor protein pten as a target of tgfβ-stimulated mir-21 in glomerular mesangial cells. expression of mir-21 sponge, which quenches endogenous mir-21 levels, reversed tgfβ-induced suppression of pten. additionally, mir-21 sponge inhibited tgfβ-stimulated phosphorylation of akt kinase, resulting in attenuation of phosphorylation of its substrate gsk3β. tuberin and pras40, two other akt substrates, and endogenous inhibitors of mtorc1, regulate mesangial cell hypertrophy. neutralization of endogenous mir-21 abrogated tgfβ-stimulated phosphorylation of tuberin and pras40, leading to inhibition of phosphorylation of s6 kinase, mtor and 4ebp-1. moreover, downregulation of mir-21 significantly suppressed tgfβ-induced protein synthesis and hypertrophy, which were reversed by sirna-targeted inhibition of pten expression. similarly, expression of constitutively active akt kinase reversed the mir-21 sponge-mediated inhibition of tgfβ-induced protein synthesis and hypertrophy. furthermore, expression of constitutively active mtorc1 prevented the mir-21 sponge-induced suppression of mesangial cell protein synthesis and hypertrophy by tgfβ. finally, we show that mir-21 sponge inhibited tgfβ-stimulated fibronectin and collagen expression. suppression of pten expression and expression of both constitutively active akt kinase and mtorc1 independently reversed this mir-21-mediated inhibition of tgfβ-induced fibronectin and collagen expression. our results uncover an essential role of tgfβ-induced expression of mir-21, which targets pten to initiate a non-canonical signaling circuit involving akt/mtorc1 axis for mesangial cell hypertrophy and matrix protein synthesis.",1
"genome-encoded micrornas (mirnas) provide a post-transcriptional regulatory layer that is important for pancreas development. however, how specific mirnas are intertwined into the transcriptional network, which controls endocrine differentiation, is not well understood. here, we show that microrna-7 (mir-7) is specifically expressed in endocrine precursors and in mature endocrine cells. we further demonstrate that pax6 is an important target of mir-7. mir-7 overexpression in developing pancreas explants or in transgenic mice led to pax6 downregulation and inhibition of α- and β-cell differentiation, resembling the molecular changes caused by haploinsufficient expression of pax6. accordingly, mir-7 knockdown resulted in pax6 upregulation and promoted α- and β-cell differentiation. furthermore, pax6 downregulation reversed the effect of mir-7 knockdown on insulin promoter activity. these data suggest a novel mir-7-based circuit that ensures precise control of endocrine cell differentiation.",1
"while the immunological dysfunction in combat veterans with post-traumatic stress disorder (ptsd) has been well documented, the precise mechanisms remain unclear. the current study evaluated the role of microrna (mir) in immunological dysfunction associated with ptsd. the presence of peripheral blood mononuclear cells (pbmc) and various lymphocyte subsets in blood collected from ptsd patients were analyzed. our studies demonstrated that the numbers of both pbmc and various lymphocyte subsets increased significantly in ptsd patients. when t cells were further analyzed, the percentage of th1 cells and th17 cells increased, regulatory t cells(tregs) decreased, while th2 cells remained unaltered in ptsd patients. these data correlated with increased plasma levels of ifn-γ and il-17 while il-4 showed no significant change. the increase in pbmc counts, th1 and th17 cells seen in ptsd patients correlated with the clinical scores. high-throughput analysis of pbmcs for 1163 mirs showed that the expression of a significant number of mirs was altered in ptsd patients. pathway analysis of dysregulated mirs seen in ptsd patients revealed relationship between selected mirnas and genes that showed direct/indirect role in immunological signaling pathways consistent with the immunological changes seen in these patients. of interest was the down-regulation of mir-125a in ptsd, which specifically targeted ifn-γ production. together, the current study demonstrates for the first time that ptsd was associated with significant alterations in mirnas, which may promote pro-inflammatory cytokine profile. such epigenetic events may provide useful tools to identify potential biomarkers for diagnosis, and facilitate therapy of ptsd.",1
"here, we show that mir-515-5p inhibits cancer cell migration and metastasis. rna-seq analyses of both oestrogen receptor receptor-positive and receptor-negative breast cancer cells overexpressing mir-515-5p reveal down-regulation of nras, fzd4, cdc42bpa, pik3c2b and mark4 mrnas. we demonstrate that mir-515-5p inhibits mark4 directly 3' utr interaction and that mark4 knock-down mimics the effect of mir-515-5p on breast and lung cancer cell migration. mark4 overexpression rescues the inhibitory effects of mir-515-5p, suggesting mir-515-5p mediates this process through mark4 down-regulation. furthermore, mir-515-5p expression is reduced in metastases compared to primary tumours derived from both in vivo xenografts and samples from patients with breast cancer. conversely, mir-515-5p overexpression prevents tumour cell dissemination in a mouse metastatic model. moreover, high mir-515-5p and low mark4 expression correlate with increased breast and lung cancer patients' survival, respectively. taken together, these data demonstrate the importance of mir-515-5p/mark4 regulation in cell migration and metastasis across two common cancers.",1
"thermo-chemotherapy has been proven to reduce the invasion capability of cancer cells. however, the molecular mechanism underlying this anti-invasion effect is still unclear. in this study, the role of thermo-chemotherapy in the inhibition of tumor invasion was studied. the results demonstrated that expression of mir-218 was downregulated in gastric cancer tissues, which had a positive correlation with tumor invasion and metastasis. in vitro thermo-chemotherapy increased mir-218 expression in sgc7901 cells and inhibited both proliferation and invasion of cancer cells. gli2 was identified as a downstream target of mir-218, and its expression was negatively regulated by mir-218. the thermo-chemotherapy induced mir-218 upregulation was also accompanied by increasing of e-cadherin expression. in conclusion, the present study indicates that thermo-chemotherapy can effectively decrease the invasion capability of cancer cells and increase cell-cell adhesion. mir-218 and its downstream target gli2, as well as e-cadherin, participate in the anti-invasion process.",1
"to investigate whether the effect of maternal dietary protein on offspring lipid metabolism is mediated by microrna (mirna), fourteen meishan sows were fed either low-protein (lp, half of standard protein (sp) level, n 7) or sp (n 7) diets throughout gestation and lactation periods. ppar-γ and ccaat/enhancer-binding protein-β (c/ebp-β) protein expression was evaluated. the expression of mirna predicted to directly target ppar-γ and c/ebp-β in the subcutaneous fat of offspring at weaning age was determined, and the functions of these potential mirna were verified. the results showed that piglet body weight and back fat thickness were significantly decreased in the lp group compared with the sp group (p<0·05). the protein level of ppar-γ was significantly decreased and c/ebp-β protein expression was also decreased, though not significantly (p=0·056), in the subcutaneous fat of the lp group. furthermore, mirna expression analysis showed that mir-130b, targeting the ppar-γ 3'-untranslated region (utr), and mir-374b, targeting the c/ebp-β 3'-utr, were significantly increased in the lp group compared with the sp group; other candidate regulatory mirna were expressed similarly in both groups. dual luciferase activity assay results indicated that mir-130b directly recognised and bound to the 3'-utr of ppar-γ and thereby suppressed ppar-γ gene expression. similar results were found for mir-374b and the 3'-utr of c/ebp-β. the present study showed that mir-130b and mir-374b are involved in the effect of maternal dietary protein on offspring lipid metabolism in pigs. these results shed new light on our understanding of the maternal effect on offspring lipid deposition.",1
"the discovery that micrornas (mirnas) play important roles in regulating gene expression via posttranscriptional repression has revealed a previously unsuspected mechanism controlling development and progenitor-cell function (reviewed in ); however, little is known of mirna functions in mammalian organogenesis. processing of mirnas and their assembly into the rna-induced silencing (risc) complex requires the essential multifunctional enzyme dicer . we found that dicer mrna and multiple mirnas are expressed in mouse skin, suggesting roles in skin- and hair-follicle biology. in newborn mice carrying an epidermal-specific dicer deletion, hair follicles were stunted and hypoproliferative. hair-shaft and inner-root-sheath differentiation was initiated, but the mutant hair follicles were misoriented and expression of the key signaling molecules shh and notch1 was lost by postnatal day 7. at this stage, hair-follicle dermal papillae were observed to evaginate, forming highly unusual structures within the basal epidermis. normal hair shafts were not produced in the dicer mutant, and the follicles lacked stem cell markers and degenerated. in contrast to decreased follicular proliferation, the epidermis became hyperproliferative. these results reveal critical roles for dicer in the skin and implicate mirnas in key aspects of epidermal and hair-follicle development and function.",1
"the dpp and fat-hippo signaling pathways both regulate growth in drosophila. dpp is a bmp family ligand and acts via a smad family dna-binding transcription factor, mad. fat-hippo signaling acts via a non-dna-binding transcriptional coactivator protein, yorkie. here, we show that these pathways are directly interlinked. they act synergistically to promote growth, in part via regulation of the microrna gene bantam, and their ability to promote growth is mutually dependent. yorkie and mad physically bind each other, and we identify a 410 bp minimal enhancer of bantam that responds to yorkie:mad in vivo and in cultured cells, and show that both yorkie and mad associate with this enhancer in vivo. our results indicate that in promoting the growth of drosophila tissues, fat-hippo and dpp signaling contribute distinct subunits of a shared transcriptional activation complex, yorkie:mad.",1
"to define a complete catalog of the genes that are activated during mouse sclerotome formation, we sequenced rna from embryonic mouse tissue directed to form sclerotome in culture. in addition to well-known early markers of sclerotome, such as pax1, pax9, and the bapx2/nkx3-2 homolog nkx3-1, the long-noncoding rna peat (pax1 enhancer antisense transcript) was induced in sclerotome-directed samples. strikingly, peat is located just upstream of the pax1 gene. using crispr/cas9, we generated a mouse line bearing a complete deletion of the peat-transcribed unit. rna-seq on peat mutant embryos showed that loss of peat modestly increases bone morphogenetic protein target gene expression and also elevates the expression of a large subset of ribosomal protein mrnas.",1
"a new paradigm of gene expression regulation has emerged recently with the discovery of micrornas (mirnas). most, if not all, mirnas are thought to control gene expression, mostly by base pairing with mirna-recognition elements (mres) found in their messenger rna (mrna) targets. although a large number of human mirnas have been reported, many of their mrna targets remain unknown. here we used a combined bioinformatics and experimental approach to identify important rules governing mirna-mre recognition that allow prediction of human mirna targets. we describe a computational program, ""diana-microt"", that identifies mrna targets for animal mirnas and predicts mrna targets, bearing single mres, for human and mouse mirnas.",1
"background the acvr1/alk-2 gene, encoding a bmp type i receptor, is mutated in fibrodysplasia ossificans progressiva, a severe form of heterotopic ossification. regulation of acvr1/alk-2 expression, still poorly understood, is likely to be controlled by transcriptional and post-transcriptional mechanisms. in our work, we focused on the functional role of the 3'utr region of the gene and on micrornas as possible modulators of the acvr1/alk-2 expression. results the acvr1/alk-2 3'utr region consists of a 1.1 kb sequence harboring several putative, well-conserved binding sites for mirnas in its proximal half, and au-rich elements in the distal one, as assessed by bioinformatic analysis. the functional role of this region was tested in presence of transcription inhibitors and in transfection experiments in different cell lines, with a acvr1/alk-2-3'utr reporter construct. by this transfection-based approach, we have also verified that three micrornas, among those predicted to target acvr1/alk-2 gene by in silico analysis, can bind its 3'utr sequence thereby modulating its expression. conclusion in this work we demonstrated that the acvr1/alk-2 transcript is unstable in presence of inhibitors of transcription. functional analysis of the 3'utr region by luciferase reporter assays showed that it plays an inhibitory role on acvr1/alk-2 gene expression. moreover, we found that specific mirnas are involved in modulating acvr1/alk-2 gene expression as suggested by binding sites prediction in its 3'utr sequence. in particular, we found that mir148b and mir365 were able to down-regulate acvr1/alk-2 expression, whereas mir26a showed a positive effect on its mrna. our data contribute to elucidate some of the mechanisms intervening in the modulation of acvr1/alk-2 expression. considering that no specific and effective treatment of fop is available, clarifying the basic mechanisms of the acvr1/alk-2 gene biology may provide means to develop innovative therapeutics approaches.",1
"background micrornas play important roles in various biological processes involving fairly complex mechanism. analysis of genome-wide mirna microarray demonstrate that a single mirna can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a mirna provokes detectable functional changes with such mild regulation. results to explore the internal mechanism of mirna-mediated regulation, we re-analyzed the data collected from genome-wide mirna microarray with bioinformatics assay, and found that the transfection of mir-181b and mir-34a in hela and hct-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high enrichment scores, suggesting that these mirnas may be important in cell growth and cell death. mir-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while mir-34a mediated contrary changes of gene expression. cell growth assays further confirmed this finding. in further study on mir-20b-mediated osteogenesis in hmscs, mir-20b was found to enhance osteogenesis by activating bmps/runx2 signaling pathway in several stages by co-repressing of pparγ, bambi and crim1. conclusions with its multi-target characteristics, mir-181b, mir-34a and mir-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual mirna targeting genes could have contributed to an additive effect. this might also be one of the modes of mirna-mediated gene regulation.",1
"objective it has been reported that microrna-195 (mir-195) protects against chronic brain injury induced by chronic brain hypoperfusion. however, neither the expression profile of mir-195 nor its potential role during acute ischemic stroke has been investigated. in this study, the authors' aim was to verify the mechanism of mir-195 in acute ischemic stroke. methods the plasma levels of mir-195 expression were assessed using real-time pcr in 96 patients with acute ischemic stroke, and the correlation with the national institutes of health stroke scale score was evaluated. in addition, cerebral infarct volume, neurological score, and levels of mir-195 and cx3cl1/cx3cr1 mrna and protein expression were assessed in mice subjected to middle cerebral artery occlusion (mcao) with or without intra-cerebroventricular infusion of lentiviral vector. the inflammatory cytokines tumor necrosis factor-α (tnfα), interleukin (il)-1β, and il-6 of mouse brains after mcao and bv2 cells treated with oxygen-glucose deprivation were measured using enzyme-linked immunosorbent assay, and apoptotic proteins were examined by western blotting. direct targeting of cx3cl1/cx3cr1 by mir-195 was determined by immunoblotting and dual luciferase assay. results in ischemic stroke patients, mir-195 was significantly downregulated and expression levels of mir-195 in these patients negatively correlated with the national institutes of health stroke scale score. in mice after mcao, mir-195 overexpression decreased infarct volume, alleviated neurological deficits, and most importantly, suppressed an inflammatory response. meanwhile, mir-195 suppressed the expression of the inflammatory cytokines tnfα, il-1β, and il-6 in vitro and in vivo. the authors further discovered that both cx3cl1 and cx3cr1 are direct targets of mir-195, but mir-195 exerts neuroprotective roles mainly through inhibiting cx3cr1-mediated neuroinflammation and subsequent neuronal cell apoptosis. conclusions taken together, these findings suggest that mir-195 promotes neuronal cell survival against chronic cerebral ischemic damage by inhibiting cx3cr1-mediated neuroinflammation. this indicates that mir-195 may represent a novel target that regulates neuroinflammation and brain injury, thus offering a new treatment strategy for cerebral ischemic disorders.",1
"the virulence gene icsa of shigella flexneri encodes an invasion protein crucial for host colonization by pathogenic bacteria. within the intergenic region vira-icsa, we have discovered a new gene that encodes a non-translated antisense rna (named rnag), transcribed in cis on the complementary strand of icsa. in vitro transcription assays show that rnag promotes premature termination of transcription of icsa mrna. transcriptional inhibition is also observed in vivo by monitoring the expression profile in shigella by real-time polymerase chain reaction and when rnag is provided in trans. chemical and enzymatic probing of the leader region of icsa mrna either free or bound to rnag indicate that upon hetero-duplex formation an intrinsic terminator, leading to transcription block, is generated on the nascent icsa mrna. mutations in the hairpin structure of the proposed terminator impair the rnag mediated-regulation of icsa transcription. this study represents the first evidence of transcriptional attenuation mechanism caused by a small rna in gram-negative bacteria. we also present data on the secondary structure of the antisense region of rnag. in addition, alternatively silencing icsa and rnag promoters, we find that transcription from the strong rnag promoter reduces the activity of the weak convergent icsa promoter through the transcriptional interference regulation.",1
"micrornas have been implicated in regulating diverse cellular pathways. although there is emerging evidence that some micrornas can function as oncogenes or tumour suppressors, the role of micrornas in mediating cancer metastasis remains unexplored. here we show, using a combination of mouse and human cells, that microrna-10b (mir-10b) is highly expressed in metastatic breast cancer cells and positively regulates cell migration and invasion. overexpression of mir-10b in otherwise non-metastatic breast tumours initiates robust invasion and metastasis. expression of mir-10b is induced by the transcription factor twist, which binds directly to the putative promoter of mir-10b (mirn10b). the mir-10b induced by twist proceeds to inhibit translation of the messenger rna encoding homeobox d10, resulting in increased expression of a well-characterized pro-metastatic gene, rhoc. significantly, the level of mir-10b expression in primary breast carcinomas correlates with clinical progression. these findings suggest the workings of an undescribed regulatory pathway, in which a pleiotropic transcription factor induces expression of a specific microrna, which suppresses its direct target and in turn activates another pro-metastatic gene, leading to tumour cell invasion and metastasis.",1
"reverse transcription of hepatitis b virus (hbv) pregenomic rna is essential for virus replication. in the first step of this process, hbv reverse transcriptase binds to the highly conserved encapsidation signal, epsilon (epsilon), situated near the 5' end of the pregenome. epsilon has been predicted to form a bulged stem-loop with the apical stem capped by a hexa- loop. after the initial binding to this apical stem- loop, the reverse transcriptase synthesizes a 4 nt primer using the bulge as a template. here we present mutational and structural data from nmr on the apical stem-loop of epsilon. application of new isotope-labeling techniques (13c/15n/2h-u-labeling) allowed resolution of many resonance overlaps and an extensive structural data set could be derived. the nmr data show that, instead of the predicted hexa-loop, the apical stem is capped by a stable ugu tri-loop closed by a c-g base pair, followed by a bulged out c. the apical stem contains therefore two unpaired pyrimidines (c1882 and u1889), rather than one as was predicted, spaced by 6 nt. c1882, the 3' neighbour to the g of the loop-closing c-g base pair, is completely bulged out, while u1889 is at least partially intercalated into the stem. analysis of 205 of our own hbv sequences and 1026 strains from the literature, covering all genotypes, reveals a high degree of conservation of epsilon. in particular, the residues essential for this fold are either totally conserved or show rare non-disruptive mutations. these data strongly indicate that this fold is essential for recognition by the reverse transcriptase.",1
"eukaryotic translation initiation factor 2 (eif2) is a g-protein that functions as a central switch in the initiation of protein synthesis. in its gtp-bound state it delivers the methionyl initiator trna (met-trna(i)) to the small ribosomal subunit and releases it upon gtp hydrolysis following the recognition of the initiation codon. we have developed a complete thermodynamic framework for the assembly of the saccharomyces cerevisiae eif2.gtp.met-trna(i) ternary complex and have determined the effect of the conversion of gtp to gdp on eif2's affinity for met-trna(i) in solution. in its gtp-bound state the factor forms a positive interaction with the methionine moiety on met-trna(i) that is disrupted when gtp is replaced with gdp, while contacts between the factor and the body of the trna remain intact. this positive interaction with the methionine residue on the trna may serve to ensure that only charged initiator trna enters the initiation pathway. the toggling on and off of the factor's interaction with the methionine residue is likely to play an important role in the mechanism of initiator trna release upon initiation codon recognition. in addition, we show that the conserved base-pair a1:u72, which is known to be a critical identity element distinguishing initiator from elongator methionyl trna, is required for recognition of the methionine moiety by eif2. our data suggest that a role of this base-pair is to orient the methionine moiety on the initiator trna in its recognition pocket on eif2.",1
"the selection of sites for pseudouridylation in eukaryotic cytoplasmic rrna occurs by the base pairing of the rrna with specific guide sequences within the rna components of box h/aca small nucleolar ribonucleoproteins (snornps). forty-four of the 46 pseudouridines (psis) in the cytoplasmic rrna of saccharomyces cerevisiae have been assigned to guide snornas. here, we examine the mechanism of psi formation in 5s and 5.8s rrna in which the unassigned psis occur. we show that while the formation of the psi in 5.8s rrna is associated with snornp activity, the pseudouridylation of 5s rrna is not. the position of the psi in 5.8s rrna is guided by snorna snr43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rrna; an internal stem-loop that is not part of typical yeast snornas also is conserved in snr43. the multisubstrate synthase pus7 catalyzes the formation of the psi in 5s rrna at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of pus7. the different mechanisms involved in 5s and 5.8s rrna pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and trna synthesis.",1
"pten is a tumor-suppressor gene that has been shown to be under the regulatory control of a pten pseudogene expressed noncoding rna, ptenpg1. here, we characterize a previously unidentified ptenpg1-encoded antisense rna (asrna), which regulates pten transcription and pten mrna stability. we find two ptenpg1 asrna isoforms, α and β. the α isoform functions in trans, localizes to the pten promoter and epigenetically modulates pten transcription by the recruitment of dna methyltransferase 3a and enhancer of zeste. in contrast, the β isoform interacts with ptenpg1 through an rna-rna pairing interaction, which affects pten protein output through changes of ptenpg1 stability and microrna sponge activity. disruption of this asrna-regulated network induces cell-cycle arrest and sensitizes cells to doxorubicin, which suggests a biological function for the respective ptenpg1 expressed asrnas.",1
"insect development and metamorphosis are regulated by the coordination of ecdysone and juvenile hormones. insect micrornas (mirnas) also act in insect development and metamorphosis by regulating genes in the ecdysone cascade. although hundreds of insect mirnas have been identified, the physiological functions of most remain poorly understood. here, we report that a conserved insect mirna, microrna-281 (mir-281), regulates the ecdysone receptor (ecr), in an isoform-specific manner in the silkworm bombyx mori. the b. mori ecr (bmecr) gene encodes three isoforms: bmecr-a, bmecr-b1 and bmecr-b2. the 3'utr regions of a and b genes, which contain multiple potential microrna targeting sites, are distinct. target prediction revealed that mir-281 may specifically target the 3'utr of bmecr-b. using a dual luciferase reporter assay in hek293t cells, we confirmed that mir-281 suppressed transcription of bmecr-b but not bmecr-a. the expression of mir-281 and bmecr-b are well coordinated in the malpighian tubules from the fourth larval molt to pupation. in the malpighian tubules of fifth instar larvae, bmecr-b protein expression was down-regulated after injection of a mir-281 mimic while up-regulated after injection of a mir-281 inhibitor. mir-281 expression was suppressed by 20-hydroxyecdysone treatments but not affected by juvenile hormone treatments. based on these findings, we propose that mir-281 participates in b. mori developmental regulation in the malpighian tubules through suppression of bmecr-b expression.",1
"background micrornas (mirnas) regulate a lot of physiological and pathological processes, including myocardial ischemia/reperfusion. recent studies reported that knockdown of mir-92a could attenuate ischemia/reperfusion-induced myocardial injury. in the present study, we examined the potential anti-apoptotic effects of mir-92a in a rat myocardiocyte cell line, and the possible role of smad7 in such actions. methodology and results in a preliminary bioinformatic analysis, we identified smad family member 7 (smad7) as a potential target for mir-92a. a luciferase reporter assay indeed demonstrated that mir-92a could inhibit smad7 expression. myocardial ischemia/reperfusion was simulated in rat h9c2 cells with 24-h hypoxia followed by 12-h reoxygenation. prior to hypoxia/reoxygenation, cells were transfected by mir-92a inhibitor. in some experiments, cells were co-transfected with sirna-smad7. the mir-92a inhibitor dramatically reduced the release of lactate dehydrogenase and malonaldehyde, and attenuated cardiomyocyte apoptosis. the mir-92a inhibitor increased smad7 protein level and decreased nuclear nf-κb p65 protein. effects of the mir-92a inhibitor were attenuated by co-transfection with sirna-smad7. conclusion inhibiting mir-92a can attenuate myocardiocyte apoptosis induced by hypoxia/reoxygenation by targeting smad7.",1
"angiogenesis is important in pathophysiological processes, including the pathogenesis of acute monocytic leukemia (aml). microrna‑21 (mir‑21) is overexpressed and exhibits oncogenic activity in cancer. however, the biological mechanism underlying the effect of mir‑21 in aml remains to be fully elucidated. in the present study, the expression levels of mir‑21 and vascular endothelial growth factor (vegf) were determined in 26 patients with aml and 28 healthy individuals. the secretion of vegf was also measured following the transfection of thp‑1 cells with mir‑21 mimic or inhibitor. the supernatants of the thp‑1 cells, which were transfected with mir‑21 mimic, inhibitor or small interfering rna (si)vegf, respectively, were used to incubate human umbilical vein endothelial cells (huvecs), following which tube formation of the huvecs was measured. mir‑21 targets were predicted using a biological target prediction website and confirmed using a luciferase assay. the effects of interleukin (il)‑12 were investigated by examining the tube formation of huvecs and the secretion of vegf following recombinant human (rh) il‑12 pretreatment. the results revealed that mir‑21 and vegf expression was significantly increased in the peripheral blood monocytes of the patients, compared with the healthy controls. there was negative correlation between the expression of il‑12 and mir‑21 in the serum of patients with aml. furthermore, supernatant vegf levels from the mir‑21 mimic‑transfected thp‑1 cells were increased, whereas a decreasing trend was observed in the mir‑21 inhibitor group. the angiogenic ability of the huvecs pretreated with supernatant from the thp‑1 cells transfected with mir‑21 mimic was higher, and was lower in thp‑1 cells co‑transfected with mir‑21 mimic and sivegf, compared with the mir‑21 mimic only group. a luciferase assay demonstrated that il‑12 was the direct target of mir‑21, and the level of il‑12 in the supernatant of thp‑1 cells transfected with mir‑21 mimic was increased. il‑12 pretreatment increased vegf expression and angiogenic ability in huvecs. the inactivation of mir‑21 or activation of its target gene may be a potential therapeutic strategy in human aml.",1
"mirna cluster mir-17-92 is known as oncomir-1 due to its potent oncogenic function. mir-17-92 is a polycistronic cluster that encodes 6 mirnas, and can both facilitate and inhibit cell proliferation. known targets of mirnas encoded by this cluster are largely regulators of cell cycle progression and apoptosis. here, we show that mirnas encoded by this cluster and sharing the seed sequence of mir-17 exert their influence on one of the most essential cellular processes - endocytic trafficking. by mrna expression analysis we identified that regulation of endocytic trafficking by mir-17 can potentially be achieved by targeting of a number of trafficking regulators. we have thoroughly validated tbc1d2/armus, a gap of rab7 gtpase, as a novel target of mir-17. our study reveals regulation of endocytic trafficking as a novel function of mir-17, which might act cooperatively with other functions of mir-17 and related mirnas in health and disease.",1
"objective the purpose of this study was to investigate the role of mir-130b in the development of multidrug-resistant ovarian cancer. methods the expression of mir-130b was assessed in ovarian tissues and cell lines by qrt-pcr. in vitro, mir-130b level was manipulated by transfection with mimics or inhibitors. methylation level of mir-130b was evaluated by quantitative methylation-specific pcr (qmsp). csf-1 expression in ovarian tissues and cells was determined by qrt-pcr, immunohistochemistry and elisa, respectively. csf-1 regulated by mir-130b was detected using dual luciferase reporter system. results down-regulation of mir-130b in ovarian cancer was associated with figo iii-iv clinical stages and poorer histological differentiation. mir-130b was downregulated in multidrug resistant ovarian cancer cells. restoration of mir-130b expression could sensitize these cells to anticancer drugs. mir-130b hypermethylation was found in ovarian cancer tissues as well as in drug resistant cell lines and the methylation level was negatively correlated with its expression. demethylation with 5-aza-cdr led to reactivation of mir-130b expression in drug resistant ovarian cancer cell lines concomitant with increase of sensibility to cisplatin and taxol. csf-1 expression was negatively associated with mir-130b level in ovarian tissues and cell lines. luciferase assay validated csf-1 is a direct target of mir-130b. knock-down of csf-1 sensitized ovarian cancer cells to anticancer drugs and could partially attenuate the resistance inducing effect of mir-130b inhibitors. conclusions downregulation of mir-130b promotes the development of multidrug resistant ovarian cancer partially by targeting the 3'-utr of csf-1, and the silencing of mir-130b may be mediated by dna methylation.",1
"background esophageal squamous cell carcinoma (escc) is the major histological type of esophageal cancer in developing countries. the prognosis and survival rate of escc are very poor. recently, micrornas (mirnas) have emerged as important regulators of cancer cell biological processes. to better understanding the molecular mechanisms by which they regulate the behavior of cancer cells is needed. methods the expression of mir-208 was examined in escc cell lines and tumor tissues by real-time pcr. proliferation capability of escc cells upon regulation of mir-208 expression was detected by mtt assay, colony formation assay, anchorage-independent growth ability assay and flow cytometry analysis. the target of mir-208 was determined by western blotting analysis, luciferase reporter assay and real-time pcr. results mir-208 was upregulated in escc cell lines and tissues. overexpression of mir-208 in escc cells increased cell proliferation, tumorigenicity and cell cycle progression, whereas inhibition of mir-208 reduced cells proliferation, tumorigenicity and cell cycle progression. additionally, sox6 was identified as a direct target of mir-208. ectopic expression of mir-208 led to downregulation of sox6 protein, which resulted in the downregulation of p21, upregulation of cyclin d1 and phosphorylation of rb. conclusions these results suggest that mir-208 represents a potential onco-mir and participates in escc carcinogenesis by suppressing sox6 expression.",1
"the covr/s two-component system regulates the transcription of many genes that are crucial for the virulence of streptococcus pyogenes (group a streptococcus, gas). previously, we demonstrated that one gene repressed directly by covr is rivr, which encodes a member of the rofa-like family of transcriptional regulators. in this study, we deleted rivr and its downstream gene rivx in a deltacovr background. microarray analysis revealed that the products of the rivrx locus exert positive control over the transcription of members of the mga regulon. using mutational analysis, we established that rivx encodes a small regulatory rna. we found that rivr enhances transcriptional activation by mga in vivo and in vitro. an m1 deltacovrdeltarivrx strain is attenuated for virulence in a murine model of invasive soft tissue infection and this attenuation is complemented by rivrx expressed from a plasmid, demonstrating the importance of the rivrx locus in pathogenesis. this study provides the first link between the covr and mga regulatory networks. by integrating the signals received through these two global regulators, gas is able to select from its repertoire different combinations of specific virulence factors to express in response to a broad spectrum of environmental conditions.",1
"cardiovascular disease has been the biggest killer in the united states for decades, with almost a million new cases each year. even though mammalian rodent neonatal cardiomyocytes show proliferative potential for up to 5 days, adult cardiomyocytes lose this ability. insufficient cardiomyocyte proliferation is one of the major reasons for the lack of regeneration of myocardial tissue, post injury. several studies have looked at the mechanisms responsible for the arrest in proliferation at an adult stage. following up on a recent study by eulalio et al 's study on functional screening of 875 mirnas for neonatal cardiomyocyte proliferation, we recently identified several mirnas that induce proliferation in naturally senescent adult cardiomyocytes. additional studies by mahmood et al 2013 have identified meis1 as the major regulator of cardiomyocyte cell cycle. in our present study we have identified three of the adult cardiomyocyte proliferation inducing mirnas to have binding sites on the 3'utr of meis1 gene by in-silico analysis and luciferase assay. additionally we found these mirnas; mir-548c-3p, mir-509-3p, and mir-23b-3p to induce significant proliferation in adult cardiomyocytes through translational inhibition of meis1. we found a significant increase in the number of acms with each mirna, in combination, and with sirna mediated inhibition of meis1 gene. we confirmed that these micrornas, through inhibition of meis1, affect its downstream targets and thereby regulate cell-cycle progression. further investigating of the mechanism of action of these mirnas can identify other treatment options for abnormalities associated with the lack of cardiac regeneration post myocardial injury.",1
"bombyx mori cytoplasmic polyhedrosis virus (bmcpv) is a major viral pathogen of silkworm and remains a big challenge to the sericultural industry. insulin-related peptide binding protein 2 (ibp2) gene, induced by bmcpv infection may play an important role in b. mori immune response. micrornas (mirnas) are small noncoding rnas that regulate gene expression at the post-transcriptional level and play an important role in various processes, including immunity and antiviral response. in this study, we identified ibp2 as one of the targets for mir-278-3p by using luciferase reporter assay. overexpression of mir-278-3p negatively regulates the expression of ibp2 in silkworm larvae and positively regulates the mrna transcript level of bmcpv. our results suggest that mir-278-3p may play an important role in bmcpv replication. it's the first report on bmo-mirnas in response to bmcpv infection and could provide a new clue to explore the molecular mechanism of bmcpv infection and host immunity.",1
"neuronal gene expression is tightly regulated in developing cns. here, we demonstrate the anti-neural function of phosphatase scp1 (small c-terminal domain phosphatase 1) during development. we further show that the neuron-enriched microrna mir-124 directly targets scp1-3' untranslated region (utr) to suppress scp1 expression. in developing spinal cord, expression of mir-124 and scp1 is complementary, and mir-124 antagonism phenocopies scp1 overexpression and vice versa. in p19 cells, mir-124 suppresses scp1 expression and induces neurogenesis, and scp1 counteracts this proneural activity of mir-124. our results suggest that, during cns development, timely down-regulation of scp1 is critical for inducing neurogenesis, and mir-124 contributes to this process at least in part by down-regulating scp1 expression.",1
"deregulated proliferation is a hallmark of cancer cells. here, we show that microrna-10b* is a master regulator of breast cancer cell proliferation and is downregulated in tumoural samples versus matched peritumoural counterparts. two canonical cpg islands (5 kb) upstream from the precursor sequence are hypermethylated in the analysed breast cancer tissues. ectopic delivery of synthetic microrna-10b* in breast cancer cell lines or into xenograft mouse breast tumours inhibits cell proliferation and impairs tumour growth in vivo, respectively. we identified and validated in vitro and in vivo three novel target mrnas of mir-10b* (bub1, plk1 and ccna2), which play a remarkable role in cell cycle regulation and whose high expression in breast cancer patients is associated with reduced disease-free survival, relapse-free survival and metastasis-free survival when compared to patients with low expression. this also suggests that restoration of microrna-10b* expression might have therapeutic promise.",1
"background the genus alphavirus includes several potentially lethal human viruses. additionally, species such as sindbis virus and semliki forest virus are important vectors for gene therapy, vaccination and cancer research, and important models for virion assembly and structural analyses. the genome encodes nine known proteins, including the small '6k' protein. 6k appears to be involved in envelope protein processing, membrane permeabilization, virion assembly and virus budding. in protein gels, 6k migrates as a doublet--a result that, to date, has been attributed to differing degrees of acylation. nonetheless, despite many years of research, its role is still relatively poorly understood. results we report that ribosomal -1 frameshifting, with an estimated efficiency of approximately 10-18%, occurs at a conserved uuuuuua motif within the sequence encoding 6k, resulting in the synthesis of an additional protein, termed tf (transframe protein; approximately 8 kda), in which the c-terminal amino acids are encoded by the -1 frame. the presence of tf in the semliki forest virion was confirmed by mass spectrometry. the expression patterns of tf and 6k were studied by pulse-chase labelling, immunoprecipitation and immunofluorescence, using both wild-type virus and a tf knockout mutant. we show that it is predominantly tf that is incorporated into the virion, not 6k as previously believed. investigation of the 3' stimulatory signals responsible for efficient frameshifting at the uuuuuua motif revealed a remarkable diversity of signals between different alphavirus species. conclusion our results provide a surprising new explanation for the 6k doublet, demand a fundamental reinterpretation of existing data on the alphavirus 6k protein, and open the way for future progress in the further characterization of the 6k and tf proteins. the results have implications for alphavirus biology, virion structure, viroporins, ribosomal frameshifting, and bioinformatic identification of novel frameshift-expressed genes, both in viruses and in cellular organisms.",1
"micrornas (mirnas) have been implicated in regulating various aspects of animal development, but their functions in neurogenesis are largely unknown. here we report that loss of mir-9a function in the drosophila peripheral nervous system leads to ectopic production of sensory organ precursors (sops), whereas overexpression of mir-9a results in a severe loss of sops. we further demonstrate a strong genetic interaction between mir-9a and senseless (sens) in controlling the formation of sops in the adult wing imaginal disc. moreover, mir-9a suppresses sens expression through its 3' untranslated region. mir-9a is expressed in epithelial cells, including those adjacent to sops within proneural clusters, suggesting that mir-9a normally inhibits neuronal fate in non-sop cells by down-regulating sens expression. these results indicate that mir-9a ensures the generation of the precise number of neuronal precursor cells during development.",1
"epithelial-mesenchymal interaction has critical roles for organ development including teeth, during which epithelial thickening and mesenchymal condensation are initiated by precise regulation of the signaling pathway. in teeth, neural crest-derived mesenchymal cells expressed pdgf receptors migrate and become condensed toward invaginated epithelium. to identify the molecular mechanism of this interaction, we explored the specific transcriptional start sites (tsss) of tooth organs using cap analysis of gene expression (cage). we identified a tooth specific tss detected in the chromosome 15qd1 region, which codes microrna-875 (mir875). mir875-5p is specifically expressed in dental mesenchyme during the early stage of tooth development. furthermore, prrx1/2 binds to the mir875 promoter region and enhances the expression of mir875. to assess the role of mir875-5p in dental mesenchyme, we transfected mimic mir875-5p into mouse dental pulp (mdp) cells, which showed that cell migration toward dental epithelial cells was significantly induced by mir875-5p via the pdgf signaling pathway. those results also demonstrated that mir875-5p induces cell migration by inhibiting pten and stat1, which are regulated by mir875-5p as part of post-transcriptional regulation. together, our findings indicate that tooth specific mir875-5p has important roles in cell condensation of mesenchymal cells around invaginated dental epithelium and induction of epithelial-mesenchymal interaction.",1
"background micrornas are small non-coding rnas that regulate post-transcriptional mrna expression by binding to 3' untranslated region (3'-utr) of the complementary mrna sequence resulting in translational repression and gene silencing. they act as negative regulators of gene expression and play a pivotal role in regulating apoptosis and cell proliferation. studies have shown that mirnas interact with p53 by regulating the activity and function of p53 through direct repression or its regulators. mammalian target of rapamycin (mtor) is an evolutionary conserved check point protein kinase that plays a major effect in the control of cell division via protein synthesis regulation. mtor regulates protein synthesis through phosphorylation and inactivation of 4e-bp1 and through phosphorylation and activation of s6 kinase 1 (s6k1). these two downstream effectors of mtor control cell growth and metabolism. in mammals, mtor protein kinase is the central node in the nutrient and growth factor signaling and p53 plays a critical role in sensing genotoxic stress. activation of p53 inhibits mtor activity, which in turn regulates its downstream targets providing a cross talk among both the signaling machinery. microrna-15 and 16 belong to a common precursor family and are highly conserved. deletion or downregulation of these two micrornas has been shown to accelerate cell division by modulating the expression of the genes involved in controlling cell cycle progression. these micrornas may function as tumor suppressors and act on the downstream targets of p53 signaling pathway. to have a better insight of the role of mir-15/16 in regulating the cross talk of p53 and mtor, we performed an in depth study in mda-mb-231 breast cancer cells by performing a gain-of-function analysis with lentiviral plasmids expressing microrna-15 and 16. methods the effect of individual micrornas on rps6kb1 was examined by using 3'-utr clones via luciferase based assays. the cell cycle effects were observed by flow-cytometric analysis. reverse transcription pcr was used to explore the expression of mtor and rps6kb1 in cells transfected with mir-15/16. results overexpression of mir-15/16 led to inhibition of cell proliferation causing g1 cell cycle arrest as well as caspase-3 dependent apoptosis. forced expression of mir-15/16 might lead to decrease in mrna level of rps6kb1, mtor. the effect was a complete reversal after treatment with anti-mirs against mir-15/16 proving the specificity of the expression. in addition, the dual luciferase reporter assays indicated a clear decrease in luciferase gene expression in cells transfected with lentiviral based mir-15 and 16 plasmids indicating that mir-15/16 directly targets rps6kb1 through its 3'-utr binding. further, these micrornas also inhibit epithelial to mesenchymal transition (emt) by targeting key proteins such as twist1 and ezh2 clearly demonstrating its crucial role in controlling cell proliferation. conclusion this study suggests that exogenous microrna-15/16 can target rps6kb1, control cell proliferation and cause apoptosis in caspase-dependent manner even in the absence of functional p53.",1
"unlabelled growing evidence indicates that deregulation of micrornas (mirnas) contributes to tumorigenesis. down-regulation of mir-195 has been observed in various types of cancers. however, the biological function of mir-195 is still largely unknown. in this study we aimed to elucidate the pathophysiologic role of mir-195. our results showed that mir-195 expression was significantly reduced in as high as 85.7% of hepatocellular carcinoma (hcc) tissues and in all of the five hcc cell lines examined. moreover, introduction of mir-195 dramatically suppressed the ability of hcc and colorectal carcinoma cells to form colonies in vitro and to develop tumors in nude mice. furthermore, ectopic expression of mir-195 blocked g(1)/s transition, whereas inhibition of mir-195 promoted cell cycle progression. subsequent investigation characterized multiple g(1)/s transition-related molecules, including cyclin d1, cdk6, and e2f3, as direct targets of mir-195. silencing of cyclin d1, cdk6, or e2f3 phenocopied the effect of mir-195, whereas overexpression of these proteins attenuated mir-195-induced g(1) arrest. in addition, mir-195 significantly repressed the phosphorylation of rb as well as the transactivation of downstream target genes of e2f. these results imply that mir-195 may block the g(1)/s transition by repressing rb-e2f signaling through targeting multiple molecules, including cyclin d1, cdk6, and e2f3. conclusion our data highlight an important role of mir-195 in cell cycle control and in the molecular etiology of hcc, and implicate the potential application of mir-195 in cancer therapy.",1
"the aberrant expression of micrornas is associated with development and progression of cancers. down-regulation of mir-124 has been demonstrated in the hepatocellular carcinoma (hcc), but the underlying mechanism by which mir-124 suppresses tumorigenesis in hcc remains elusive. in this study, we found that mir-124 suppresses the tumor growth of hcc through targeting the signal transducers and activators of transcription 3 (stat3). overexpression of mir-124 suppressed proliferation and induced apoptosis in hepg-2 cells. luciferase assay confirmed that mir-124 binding to the 3'-utr region of stat3 inhibited the expression of stat3 and phosphorylated stat3 proteins in hepg-2 cells. knockdown of stat3 by sirna in hepg-2 cells mimicked the effect induced by mir-124. overexpression of stat3 in mir-124-transfected hepg-2 cells effectively rescued the inhibition of cell proliferation caused by mir-124. furthermore, mir-124 suppressed xenograft tumor growth in nude mice implanted with hepg-2 cells by reducing stat3 expression. taken together, our findings show that mir-124 functions as tumor suppressor in hcc by targeting stat3, and mir-124 may therefore serve as a biomarker for diagnosis and therapeutics in hcc.",1
"micrornas (mirnas) are highly expressed in vertebrate neural tissues, but the contribution of specific mirnas to the development and function of different neuronal populations is still largely unknown. we report that mirnas are required for terminal differentiation of olfactory precursors in both mouse and zebrafish but are dispensable for proper function of mature olfactory neurons. the repertoire of mirnas expressed in olfactory tissues contains over 100 distinct mirnas. a subset, including the mir-200 family, shows high olfactory enrichment and expression patterns consistent with a role during olfactory neurogenesis. loss of function of the mir-200 family phenocopies the terminal differentiation defect observed in absence of all mirna activity in olfactory progenitors. our data support the notion that vertebrate tissue differentiation is controlled by conserved subsets of organ-specific mirnas in both mouse and zebrafish and provide insights into control mechanisms underlying olfactory differentiation in vertebrates.",1
"rna binding proteins and messenger rnas (mrnas) assemble into ribonucleoprotein granules that regulate mrna trafficking, local translation, and turnover. the dysregulation of rna-protein condensation disturbs synaptic plasticity and neuron survival and has been widely associated with human neurological disease. neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. here, we show in drosophila that a previously uncharacterized long noncoding rna, mimi , is required to scaffold large neuronal granules in the adult nervous system. neuronal elav-like proteins directly bind mimi and mediate granule assembly, while staufen maintains condensate integrity. mimi granules contain mrnas and proteins involved in synaptic processes; granule loss in mimi mutant flies impairs nervous system maturity and neuropeptide-mediated signaling and causes phenotypes of neurodegeneration. our work reports an architectural rna for a neuronal granule and provides a handle to interrogate functions of a condensate independently of those of its constituent proteins.",1
"the variable clinical course in chronic lymphocytic leukaemia (cll) largely depends on p53 functionality and b-cell receptor (bcr) signalling propensity; however, it is unclear if there is any crosstalk between these pathways. we show that dna damage response (ddr) activation leads to down-modulating the transcriptional factor foxp1, which functions as a positive bcr signalling regulator and its high levels are associated with worse cll prognosis. we identified microrna (mirna) mir-34a as the most prominently upregulated mirna during ddr in cll cells in vitro and in vivo during fcr therapy (fludarabine, cyclophosphamide, rituximab). mir-34a induced by ddr activation and p53 stabilization potently represses foxp1 expression by binding in its 3'-utr. the low foxp1 levels limit bcr signalling partially via derepressing bcr-inhibitory molecule cd22. we also show that low mir-34a levels can be used as a biomarker for worse response or shorter progression free survival in cll patients treated with fcr chemoimmunotherapy, and shorter overall survival, irrespective of tp53 status. additionally, we have developed a method for the absolute quantification of mir-34a copies and defined precise prognostic/predictive cutoffs. overall, herein, we reveal for the first time that b cells limit their bcr signalling during ddr by down-modulating foxp1 via ddr-p53/mir-34a axis.",1
"objective micrornas (mirs) regulate angiogenesis by posttranscriptional silencing of target genes. the significance of angiostatic mir-200b in switching on skin wound angiogenesis was tested. methods and results wounding caused imminent and transient downregulation of mir-200b in dermal wound-edge endothelial cells. derailing this injury response by lentiviral delivery of mir-200b in vivo impaired wound angiogenesis. computational prediction, target reporter luciferase assay, and western blot analysis provided first evidence that mir-200b targets globin transcription factor binding protein 2 (gata2) and vascular endothelial growth factor receptor 2 (vegfr2). overexpression of gata2 or vegfr2 in endothelial cells rescued the angiostatic effect of mir-200b in vitro. downregulation of mir-200b derepressed gata2 and vegfr2 expression to switch on wound angiogenesis, which was disrupted in diabetic wounds. treatment of endothelial cells with tumor necrosis factor-α, a proinflammatory cytokine abundant in diabetic wounds, induced mir-200b expression, silenced gata2 and vegfr2, and suppressed angiogenesis. these outcomes were attenuated using anti-mir-200b strategy. neutralization of tumor necrosis factor-α in the diabetic wounds improved wound angiogenesis and closure, which was accompanied by downregulation of mir-200b expression and desilencing of gata2 and vegfr2. conclusions injury-induced repression of mir-200b turned on wound angiogenesis. in mice with diabetes mellitus,excessive tumor necrosis factor-α induced mir-200b blunting proangiogenic functions of gata2 and vegfr2.",1
"the european large subunit ribosomal rna database compiles all complete or nearly complete large subunit ribosomal rna sequences available from public sequence databases. these are provided in aligned format and the secondary structure, as derived by comparative sequence analysis, is included. additional information about the sequences such as literature references and taxonomic information is also included. the database is available from our www server at",1
"the aim of the present study was to measure the expression of microrna (mir)-146a in liver tissues, peripheral blood mononuclear cells (pmbc) and serum from patients with hepatitis b and either liver fibrosis or cirrhosis, as well as to determine the regulatory mechanism of mir-146a. a total of 36 patients with hepatitis b and liver fibrosis and 25 patients with hepatitis b and liver cirrhosis admitted to linyi people's hospital (shandong, china) between june 2012 and february 2016 were included in the present study. reverse transcription-quantitative polymerase chain reaction was performed to determine the expression of mir-146a and interleukin (il)-6 mrna in the liver tissue, pbmcs and serum. western blotting was used to assess the expression of il-6 in liver tissues and pbmcs. an enzyme-linked immunosorbent assay was conducted to measure il-6 levels in serum. to identify the direct interaction between il-6 and mir-146a, a dual luciferase reporter assay was performed. il-6 mrna expression in liver tissues, pbmcs and serum from patients with liver cirrhosis was significantly higher than that from patients with liver fibrosis (p<0.05). furthermore, il-6 expression in liver tissues and pbmcs from patients with liver cirrhosis was enhanced and levels of il-6 protein in the serum of patients with liver cirrhosis were significantly elevated compared with patients with liver fibrosis (p<0.05). by contrast, levels of mir-146a in liver tissues, pbmcs and serum from patients with liver cirrhosis were significantly downregulated (p<0.05) compared with patients with liver fibrosis. mir-146a regulated the expression of il-6 by binding to its 3'-untranslated region. thus, in the transformation from liver fibrosis to cirrhosis, the upregulation of il-6 in liver tissues, pbmcs and serum may be associated with the downregulation of mir-146a. mir-146a directly targets il-6, which may regulate the occurrence and immune responses of hepatitis b.",1
"glioblastoma is the most common and lethal primary brain tumor. tumor initiation and recurrence are likely caused by a sub-population of glioblastoma stem cells, which may derive from mutated neural stem and precursor cells. since cd133 is a stem cell marker for both normal brain and glioblastoma, and to better understand glioblastoma formation and recurrence, we looked for dys-regulated micrornas in human cd133+ glioblastoma stem cells as opposed to cd133+ neural stem cells isolated from normal human brain. using facs sorting of low-passage cell samples followed by microrna microarray analysis, we found 43 micrornas that were dys-regulated in common in three separate cd133+ human glioblastomas compared to cd133+ normal neural stem cells. among these were several micrornas not previously associated with cancer. we then verified the micrornas dys-regulated in glioblastoma using quantitative real time pcr and taqman analysis of the original samples, as well as human gbm stem cell and established cell lines and many human specimens. we show that two candidate oncogenic micrornas, mir-363 and mir-582-5p, can positively influence glioblastoma survival, as shown by forced expression of the micrornas and their inhibitors followed by cell number assay, caspase 3/7 assay, annexin v apoptosis/fluorescence activated cell sorting, sirna rescue of microrna inhibitor treatment, as well as 3'utr mutagenesis to show luciferase reporter rescue of the most successful targets. mir-582-5p and mir-363 are shown to directly target caspase 3, caspase 9, and bim.",1
"in many mouse models of skin cancer, only a few tumors typically form even though many cells competent for tumorigenesis receive the same oncogenic stimuli. these observations suggest an active selection process for tumor-initiating cells. here, we use quantitative mrna- and mir-seq to determine the impact of hras(g12v) on the transcriptome of keratinocytes. we discover that microrna-203 is downregulated by hras(g12v). using a knockout mouse model, we demonstrate that loss of microrna-203 promotes selection and expansion of tumor-initiating cells. conversely, restoration of microrna-203 using an inducible model potently inhibits proliferation of these cells. we comprehensively identify microrna-203 targets required for hras-initiated tumorigenesis. these targets include critical regulators of the ras pathway and essential genes required for cell division. this study establishes a role for the loss of microrna-203 in promoting selection and expansion of hras mutated cells and identifies a mechanism through which microrna-203 antagonizes hras-mediated tumorigenesis.",1
"seven complete and two partial copies of is1221 variants from mycoplasma hyorhinis and mycoplasma hyopneumoniae characterized to date have established a consensus is1221 as a 1513 bp element with unique structural characteristics resembling the is3 family of bacterial insertion sequences. each is1221 copy contains highly conserved 28 bp imperfect terminal inverted repeats and three distinctive internal inverted repeats (lir, rir and iir). iir is located within the coding region of the element and it is proposed that it plays a critical role in the regulation of putative transposase expression. consensus is1221 and one particular copy, g1135.2, contain a single long open reading frame (orf). two potential initiation codons are present at nucleotide 46 (aug46) and nucleotide 397 (aug397) and both are preceded by strong ribosome-binding sites. both initiation codons can be used efficiently in an escherichia coli t7 expression system. the lir has a negative regulatory effect on translation initiation from aug46. a-1 translational frameshift event is shown to be involved in expression of the is1221 orf and results in the production of 20 kda and 6 kda truncated proteins from the respective upstream initiation codons of the is1221 orf. base substitution and deletion mutations in sequences resembling characterized motifs in documented examples of translational frameshifting resulted in a significant increase in the full-length products and a corresponding decrease in the truncated products from the is1221 orf. in contrast to the usual -1 frameshift regulatory event in the is3 family, which produces a transframe fusion product as the active transposase, is1221 may have evolved a high-frequency -1 frameshift mechanism that produces a truncated product from the upstream coding domain and thereby results in the regulated low-level production of the full-length presumptive transposase.",1
"the physiological role of escherichia coli spot 42 rna has remained obscure, even though the 109-nucleotide rna was discovered almost three decades ago. structural features of spot 42 rna and previous work suggested to us that the rna might be a regulator of discoordinate gene expression of the galactose operon, a control that is only understood at the phenomenological level. the effects of controlled expression of spot 42 rna or deleting the gene (spf) encoding the rna supported this hypothesis. down-regulation of galk expression, the third gene in the gal operon, was only observed in the presence of spot 42 rna and required growth conditions that caused derepression of the spf gene. subsequent biochemical studies showed that spot 42 rna specifically bound at the galk shine-dalgarno region of the galetkm mrna, thereby blocking ribosome binding. we conclude that spot 42 rna is an antisense rna that acts to differentially regulate genes that are expressed from the same transcription unit. our results reveal an interesting mechanism by which the expression of a promoter distal gene in an operon can be modulated and underline the importance of antisense control in bacterial gene regulation.",1
"background in our previous paper, we demonstrated that connexin 43 (cx43) was highly expressed in bladder cancer (bc) tissues. but the molecular mechanism about micrornas (mirnas) regulation upstream of cx43 in bc has not been well elucidated and remains to be further studied. microrna-139-5p (mir-139-5p) is a tumor suppressor in progression of multifarious cancers including bc. nevertheless, the underlying mechanisms of cx43/mir-139-5p in tumorigenesis of bc are still not well illustrated. the specific objective of our study was to inquiry the effect of cx43/mir-139-5p on bc progression and its underlying mechanism. methods the bioinformatics analysis softwares were applied to predict the mirnas in the upstream of cx43. first, the expression levels of mir-139-5p in bc tissues (tumor) and paracancer tissues (normal) were investigated using the data from the cancer genome atlas database. quantitative reverse transcription-polymerase chain reaction (qrt-pcr) was used to detect the mrna expression level of mir-139-5p in three human bc cell lines 5637, t24, ecv-304 and a human bladder epithelial immortalized cell line sv-huc-1 (normal control). then si-cx43, si-control, mir-139-5p mimic, and its negative control (nc) were transfected into bc cell line ecv-304. the relationship of mir-139-5p and cx43 was analyzed by dual-luciferase reporter assay. the qrt-pcr and western blotting were used to test the mrna and protein expression level of cx43. the proliferation of ecv-304 and t24 cells were examined by cell counting kit-8. the migration and invasion of ecv-304 cells were tested by transwell assay. to determine whether mir-139-5p would affect cell proliferation, migration and invasion by targeting cx43, we executed the rescue assay. the comparison between two groups was analyzed by student's t test, and comparisons among multiple samples were performed by one-way analysis of variance and a bonferroni post hoc test. results the expression of mir-139-5p was remarkably down-regulated in bc tissues (tumor vs. normal, 2.286 ± 0.017 vs. 3.211 ± 0.034, t = 11.540, p conclusion mir-139-5p, as a tumor-suppressor, repressed cell proliferation, invasion, and migration in bc, which might be achieved by regulating cx43.",1
"the genomic rna of human astrovirus was sequenced and found to contain 6797 nt organized into three open reading frames (1a, 1b, and 2). a potential ribosomal frameshift site identified in the overlap region of open reading frames 1a and 1b consists of a ""shifty"" heptanucleotide and an rna stem-loop structure that closely resemble those at the gag-pro junction of some retroviruses. this translation frame-shift may result in the suppression of in-frame amber termination at the end of open reading frame 1a and the synthesis of a nonstructural, fusion polyprotein that contains the putative protease and rna-dependent rna polymerase. comparative sequence analysis indicated that the protease and polymerase of astrovirus are only distantly related to the respective enzymes of other positive-strand rna viruses. the astrovirus polyprotein lacks the rna helicase domain typical of other positive-strand rna viruses of similar genome size. the genomic organization and expression strategy of astrovirus, with the protease and the polymerase brought together by predicted frameshift, most closely resembled those of plant leuteoviruses. specific features of the sequence and genomic organization support the classification of astroviruses as an additional family of positive-strand rna viruses, designated astroviridae.",1
"currently, multiple myeloma (mm) patients are broadly grouped into a non-hyperdiploid (nh-mm) group, highly enriched for igh translocations, or into a hyperdiploid (h-mm) group, which is typically characterized by trisomies of some odd-numbered chromosomes. we compared the micro rna (mirna) expression profiles of these two groups and we identified 16 mirnas that were downregulated in the h-mm group, relative to the nh-mm group. we found that target genes of the most differentially expressed mirnas are directly involved in the pathogenesis of mm; specifically, the inhibition of hsa-mir-425, hsa-mir-152 and hsa-mir-24, which are all downregulated in h-mm, leads to the overexpression of ccnd1, tacc3, mafb, fgfr3 and myc, which are the also the oncogenes upregulated by the most frequent igh chromosomal translocations occurring in nh-mm. importantly, we showed that the downregulation of these specific mirnas and the upregulation of their targets also occur simultaneously in primary cases of h-mm. these data provide further evidence on the unifying role of cyclin d pathways deregulation as the key mechanism involved in the development of both groups of mm. finally, they establish the importance of mirna deregulation in the context of mm, thereby opening up the potential for future therapeutic approaches based on this molecular mechanism.",1
"we screened for new structural non-coding rnas (ncrnas) in the genome sequence of the yeast saccharomyces cerevisiae using computational comparative analysis of genome sequences from five related species of saccharomyces. the screen identified 92 candidate ncrna genes. thirteen showed discrete transcripts when assayed by northern blot. of these, eight appear to be novel ncrnas ranging in size from 268 to 775 nt, including three new h/aca box small nucleolar rnas.",1
"objectives the present study aimed to explore the role of microribonucleic acid (mirna) let-7g in regulating endothelial functions. background derangement of mirnas is implicated in the pathogenesis of cardiovascular diseases. because the transforming growth factor (tgf)-β pathway plays a regulatory role in endothelial functions, mirnas targeted at tgf-β signal cascade might affect vascular health. methods bioinformatics software predicted that let-7g can influence the tgf-β pathway by targeting 3 genes. the let-7g's effects on multiple endothelial functions were first tested in endothelial cells (ecs) and then in apolipoprotein e knockout mice. blood samples from lacunar stroke patients were also examined to further support let-7g's effects on human subjects. results let-7g was experimentally confirmed to knock down the thbs1, tgfbr1, and smad2 genes in the tgf-β pathway. pai-i, one of the downstream effectors of the tgf-β pathway, was also down-regulated by let-7g. let-7g decreased ec inflammation and monocyte adhesion and increased angiogenesis via the tgf-β pathway. furthermore, let-7g reduced ec senescence through increasing sirt-1 protein. venous injection of let-7g inhibitor into apolipoprotein e knockout mice caused overgrowth of vascular intima-media, overexpression of pai-1, increased macrophage infiltration, and up-regulation of tgf-β downstream genes in the carotid arteries. let-7g's beneficial effects on ec were reduced, whereas the tgf-β pathway was suppressed by ribonucleic acid interference. restoration of the tgf-β pathway also attenuated the effects of let-7g overexpression. low serum levels of let-7g were associated with increased circulating pai-1 levels. conclusions decreased let-7g levels impair endothelial function and increase the risks of cardiovascular diseases through targeting tgf-β and sirt-1 signaling.",1
"microrna-122, an abundant and conserved liver-specific mirna, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the mir-122 target network remains incomplete. to this end, we performed argonaute crosslinking immunoprecipitation (argonaute -clip) sequencing in mir-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (hcc) and benign liver tissue to identify mirna target sites transcriptome-wide in two species. we observed a majority of mir-122 binding on 3' utrs and coding exons followed by extensive binding to other genic and non-genic sites. motif analysis of mir-122-dependent binding revealed a g-bulged motif in addition to canonical motifs. a large number of mir-122 targets were found to be species specific. upregulation of several common mouse and human targets, most notably bcl9, predicted survival in hcc patients. these results broadly define the molecular consequences of mir-122 downregulation in hepatocellular carcinoma.",1
"micrornas (mirnas) are non-coding rnas regulating gene expression post-transcriptionally. we have characterized the role of mirnas in regulating the human epidermal growth factor receptor 2 (her2)-pathway in breast cancer. we performed mirna gain-of-function assays by screening two her2 amplified cell lines (kpl-4 and jimt-1) with a mirna mimic library consisting of 810 human mirnas. the levels of her2, phospho-akt, phospho-erk1/2, cell proliferation (ki67) and apoptosis (cparp) were analyzed with reverse-phase protein arrays. rank product analyses identified 38 mirnas (q < 0.05) as inhibitors of her2 signaling and cell growth, the most effective being mir-491-5p, mir-634, mir-637 and mir-342-5p. we also characterized mirnas directly targeting her2 and identified seven novel mirnas (mir-552, mir-541, mir-193a-5p, mir-453, mir-134, mir-498, and mir-331-3p) as direct regulators of the her2 3'utr. we demonstrated the clinical relevance of the mirnas and identified mir-342-5p and mir-744* as significantly down-regulated in her2-positive breast tumors as compared to her2-negative tumors from two cohorts of breast cancer patients (101 and 1302 cases). mir-342-5p specifically inhibited her2-positive cell growth, as it had no effect on the growth of her2-negative control cells in vitro. furthermore, higher expression of mir-342-5p was associated with better survival in both breast cancer patient cohorts. in conclusion, we have identified mirnas which are efficient negative regulators of the her2 pathway that may play a role in vivo during breast cancer progression. these results give mechanistic insights in her2 regulation which may open potential new strategies towards prevention and therapeutic inhibition of her2-positive breast cancer.",1
"the large nucleus limited noncoding hsromega-n rna of drosophila melanogaster is known to associate with a variety of heterogeneous nuclear rna-binding proteins (hnrnps) and certain other rna-binding proteins to assemble the nucleoplasmic omega speckles. in this article, we show that rnai-mediated depletion of this noncoding rna dominantly suppresses apoptosis, in eye and other imaginal discs, triggered by induced expression of rpr, grim, or caspases (initiator as well as effector), all of which are key regulators/effectors of the canonical caspase-mediated cell death pathway. we also show, for the first time, a genetic interaction between the noncoding hsromega transcripts and the c-jun n-terminal kinase (jnk) signaling pathway since downregulation of hsromega transcripts suppressed jnk activation. in addition, hsromega-rnai also augmented the levels of drosophila inhibitor of apoptosis protein 1 (diap1) when apoptosis was activated. suppression of induced cell death following depletion of hsromega transcripts was abrogated when the diap1-rnai transgene was coexpressed. our results suggest that the hsromega transcripts regulate cellular levels of diap1 via the hnrnp hrb57a, which physically interacts with diap1, and any alteration in levels of the hsromega transcripts in eye disc cells enhances association between these two proteins. our studies thus reveal a novel regulatory role of the hsromega noncoding rna on the apoptotic cell death cascade through multiple paths. these observations add to the diversity of regulatory functions that the large noncoding rnas carry out in the cells' life.",1
"in recent years, a number of small rna molecules derived from snornas have been observed. findings concerning the functions of snorna-derived small rnas (sdrnas) in cells are limited primarily to their involvement in microrna pathways. however, similar molecules have been observed in saccharomyces cerevisiae, which is an organism lacking mirna machinery. here we examined the subcellular localization of sdrnas in yeast. our findings reveal that both sdrnas and their precursors, snornas, are present in the cytoplasm at levels dependent upon stress conditions. moreover, both sdrnas and snornas may interact with translating ribosomes in a stress-dependent manner. likely consequential to their ribosome association and protein synthesis suppression features, yeast sdrnas may exert inhibitory activity on translation. observed levels of sdrnas and snornas in the cytoplasm and their apparent presence in the ribosomal fractions suggest independent regulation of these molecules by yet unknown factors.",1
"telomerase is a specialized reverse transcriptase containing an intrinsic telomerase rna (tr) which provides the template for telomeric dna synthesis. distinct from conventional reverse transcriptases, telomerase has evolved a unique tr-binding domain (trbd) in the catalytic telomerase reverse transcriptase (tert) protein, integral for ribonucleoprotein assembly. two structural elements in the vertebrate tr, the pseudoknot and cr4/5, bind tert independently and are essential for telomerase enzymatic activity. however, the details of the tr-tert interaction have remained elusive. in this study, we employed a photoaffinity cross-linking approach to map the cr4/5-trbd rna-protein binding interface by identifying rna and protein residues in close proximity. photoreactive 5-iodouridines were incorporated into the medaka cr4/5 rna fragment and uv cross-linked to the medaka trbd protein fragment. the cross-linking rna residues were identified by alkaline partial hydrolysis and cross-linked protein residues were identified by mass spectrometry. three cr4/5 rna residues (u182, u187, and u205) were found cross-linking to trbd amino acids tyr503, phe355, and trp477, respectively. this cr4/5 binding pocket is distinct and separate from the previously proposed t pocket in the tetrahymena trbd. based on homologous structural models, our cross-linking data position the essential loop l6.1 adjacent to the tert c-terminal extension domain. we thus propose that stem-loop 6.1 facilitates proper tert folding by interacting with both trbd and c-terminal extension. revealing the telomerase cr4/5-trbd binding interface with single-residue resolution provides important insights into telomerase ribonucleoprotein architecture and the function of the essential cr4/5 domain.",1
"the identification of specific micrornas (mirnas) that target a given messenger rna (mrna) is essential for studies in gene regulation, but the available bioinformatic software programs are often unreliable. we have developed a unique experimental mirna affinity assay whereby a 3'utr rna is end-labeled with biotin, immobilized, and then used as a bait sequence for affinity pull-down of mirnas. after washes and release, cloning and sequencing identify the mirnas. binding affinity is quantitated by quantitative polymerase chain reaction (qpcr), comparing released and original input concentrations. as an initial demonstration, the tcf8/zeb1 mrna affinity pull-down yielded mir-200 family member mirs in the majority of clones, and binding affinity was approximately 100%; virtually all copies of mir-200c bound the immobilized mrna transcript. for validation in cells, mir-200c strongly inhibited expression of a tcf8 luciferase reporter, native tcf8 mrna, and protein levels, which contrasted with other recovered mirnas with lower binding affinities. for smad4 mrna, mir-150 (and others) displayed a binding affinity of 39% (or less) yet did not inhibit a smad4 reporter, native smad4 mrna, or protein levels. these results were not predicted by available software. this work demonstrates this mirna binding affinity assay to be a novel yet facile experimental means of identification of mirnas targeting a given mrna.",1
"potent therapeutic inhibition of the androgen receptor (ar) in prostate adenocarcinoma can lead to the emergence of neuroendocrine prostate cancer (nepc), a phenomenon associated with enhanced cell plasticity. here, we show that microrna-194 (mir-194) is a regulator of epithelial-neuroendocrine transdifferentiation. in clinical prostate cancer samples, mir-194 expression and activity were elevated in nepc and inversely correlated with ar signaling. mir-194 facilitated the emergence of neuroendocrine features in prostate cancer cells, a process mediated by its ability to directly target a suite of genes involved in cell plasticity. one such target was foxa1, which encodes a transcription factor with a vital role in maintaining the prostate epithelial lineage. importantly, a mir-194 inhibitor blocked epithelial-neuroendocrine transdifferentiation and inhibited the growth of cell lines and patient-derived organoids possessing neuroendocrine features. overall, our study reveals a post-transcriptional mechanism regulating the plasticity of prostate cancer cells and provides a rationale for targeting mir-194 in nepc.",1
"purpose micrornas (mirnas) have emerged as a class of gene expression regulators involved in immune regulation. in the present study, we investigated the role of mirna in two uveitis entities: behcet's disease (bd) and vogt koyanagi harada syndrome (vkh). methods the expression of five mirnas was studied in pbmcs, dcs, and cd4(+) t cells from bd patients with active and inactive uveitis, vkh patients with active uveitis, and healthy controls using real-time pcr. mir-155 mimics and inhibitor were transfected to dcs to evaluate the effect on dc maturation and cytokine production by these cells and cd4(+) t cells. luciferase reporter assays and western blotting were performed to identify the target gene of mir-155. results only mir-155 expression was significantly decreased in pbmcs and dcs from bd patients with active uveitis and no differences were observed in the mirna expression in cells from patients with vkh as compared with controls. overexpression of mir-155 in dcs was shown to inhibit the production of il-6 and il-1β, and to promote the expression of il-10 by these cells. mir-155 transfected dcs significantly inhibited intracellular il-17 expression in allogeneic cd4(+) t cells; however, it did not influence the expression of cell surface markers cd80, cd40, cd83, cd86, and hla-dr. luciferase reporter assays revealed that tab2 was a target gene of mir-155, which was confirmed by western blotting. conclusions the present results suggest that mir-155 expression is decreased in active bd but not in vkh patients. downregulated mir-155 may be involved in bd pathogenesis by targeting tab2.",1
"hepatocyte nuclear factor 4α (hnf4α) is essential for liver development and hepatocyte function. here, we show that transient inhibition of hnf4α initiates hepatocellular transformation through a microrna-inflammatory feedback loop circuit consisting of mir-124, il6r, stat3, mir-24, and mir-629. moreover, we show that, once this circuit is activated, it maintains suppression of hnf4α and sustains oncogenesis. systemic administration of mir-124, which modulates inflammatory signaling, prevents and suppresses hepatocellular carcinogenesis by inducing tumor-specific apoptosis without toxic side effects. as we also show that this hnf4α circuit is perturbed in human hepatocellular carcinomas, our data raise the possibility that manipulation of this microrna feedback-inflammatory loop has therapeutic potential for treating liver cancer.",1
"although specific micrornas (mirnas) can be upregulated in cancer, global mirna downregulation is a common trait of human malignancies. the mechanisms of this phenomenon and the advantages it affords remain poorly understood. here we identify a microrna family, mir-103/107, that attenuates mirna biosynthesis by targeting dicer, a key component of the mirna processing machinery. in human breast cancer, high levels of mir-103/107 are associated with metastasis and poor outcome. functionally, mir-103/107 confer migratory capacities in vitro and empower metastatic dissemination of otherwise nonaggressive cells in vivo. inhibition of mir-103/107 opposes migration and metastasis of malignant cells. at the cellular level, a key event fostered by mir-103/107 is induction of epithelial-to-mesenchymal transition (emt), attained by downregulating mir-200 levels. these findings suggest a new pathway by which dicer inhibition drifts epithelial cancer toward a less-differentiated, mesenchymal fate to foster metastasis.",1
"bmp2 and tgfβ1 are functional antagonists of pathological remodeling in the arteries, heart, and lung; however, the mechanisms in vsmcs, and their disturbance in pulmonary arterial hypertension (pah), are unclear. we found a pro-proliferative tgfβ1-stat3-foxo1 axis in vsmcs, and pparγ as inhibitory regulator of tgfβ1-stat3-foxo1 and tgfβ1-smad3/4, by physically interacting with stat3 and smad3. tgfβ1 induces fibrosis-related genes and mir-130a/301b, suppressing pparγ. conversely, pparγ inhibits tgfβ1-induced mitochondrial activation and vsmc proliferation, and regulates two glucose metabolism-related enzymes, platelet isoform of phosphofructokinase (pfkp, a pparγ target, via mir-331-5p) and protein phosphatase 1 regulatory subunit 3g (ppp1r3g, a smad3 target). pparγ knockdown/deletion in vsmcs activates tgfβ1 signaling. the pparγ agonist pioglitazone reverses pah and inhibits the tgfβ1-stat3-foxo1 axis in tgfβ1-overexpressing mice. we identified pparγ as a missing link between bmp2 and tgfβ1 pathways in vsmcs. pparγ activation can be beneficial in tgfβ1-associated diseases, such as pah, parenchymal lung diseases, and marfan's syndrome.",1
"microrna-455-5p (mir-455-5p) seems to have an anti-inflammatory role in the immune system since its expression is induced by il-10 cytokine. multiple sclerosis (ms) is a chronic demyelinating neurodegenerative disease of the central nervous system that is caused by an autoimmune inflammatory attack against the myelin insulation of neurons. the expression level of mir-455-5p and its role in ms pathogenesis has yet to be elucidated. we found that mir-455-5p expression was highly correlated with disease severity in ms patients. mir-455-5p expression inversely correlates with its inflammatory-predicted targets (myd88 and rel) in relapse- and remitting-phase patients. luciferase assays confirm that myd88 and rel are direct targets of mir-455-5p. this study represents the first report of the mir-455-5p acts as an anti-inflammatory role in ms, at least partially through targeting myd88 and rel. this study may provide important information for the use of mir-455-5p as a novel strategy to improve the severity of disease and control inflammation and attack in ms patients.",1
"x chromosome inactivation (xci) is an essential epigenetic process which involves several non-coding rnas (ncrnas), including xist, the master regulator of x-inactivation initiation. xist is flanked in its 5' region by a large heterochromatic hotspot, which contains several transcription units including a gene of unknown function, ftx (five prime to xist). in this article, we describe the characterization and functional analysis of murine ftx. we present evidence that ftx produces a conserved functional long ncrna, and additionally hosts micrornas (mir) in its introns. strikingly, ftx partially escapes x-inactivation and is upregulated specifically in female es cells at the onset of x-inactivation, an expression profile which closely follows that of xist. we generated ftx null es cells to address the function of this gene. in these cells, only local changes in chromatin marks are detected within the hotspot, indicating that ftx is not involved in the global maintenance of the heterochromatic structure of this region. the ftx mutation, however, results in widespread alteration of transcript levels within the x-inactivation center (xic) and particularly important decreases in xist rna levels, which were correlated with increased dna methylation at the xist cpg island. altogether our results indicate that ftx is a positive regulator of xist and lead us to propose that ftx is a novel ncrna involved in xci.",1
"background mir-21 is overexpressed in esophageal squamous cell carcinoma (escc) and is thought to be correlated with the development of the cancer. the target gene of mir-21 including fasl, timp3 and reck is revealed by researchers. mir-21 may be involved in the tumorgenesis of escc by targeting fasl, timp3 and reck. aims the purpose of this study was to explore the mechanism of mir-21 in the development of escc. methods mir-21 expression in escc and the matched non-malignant adjacent tissues (nmats) was examined by qrt-pcr. cell growth, cell apoptosis and cell invasion ability of ec9706 and ec-1 cells was examined after the cells were transfected with mir-21 inhibitor. the potential target genes of mir-21 including fasl, timp3 and reck were examined by western blot and luciferase reporter assay. results mir-21 expression was increased significantly in escc tissues compared with nmat. mir-21 down-regulation inhibits cell growth, cell invasion and induces cells to apoptosis. fasl, timp3 and reck are direct targets of mir-21. conclusions mir-21 down-regulation inhibits cell growth, invasion and induces cells to apoptosis by targeting fasl, timp3 and reck genes.",1
"mir-21 has been reported to be highly expressed in various cancers and to be inducible in a human promyelocytic cell line, hl-60, after phorbol 12-myristate 13-acetate (pma) treatment. to examine molecular mechanisms involved in mir-21 expression, we analyzed the structure of the mir-21 gene by determining its promoter and primary transcripts. we show that activation protein 1 (ap-1) activates the mir-21 transcription in conjugation with the swi/snf complex, after pma stimulation, through the conserved ap-1 and pu.1 binding sites in the promoter identified here. the previous findings of enhanced mir-21 expression in several cancers may therefore reflect the elevated ap-1 activity in these carcinomas. a single precursor rna containing mir-21 was transcribed just downstream from the tata box in this promoter, which is located in an intron of a coding gene, tmem49. more important, expression of this overlapping gene is completely pma-independent and all its transcripts are polyadenylated before reaching the mir-21 hairpin embedding region, indicating that mirnas could have their own promoter even if overlapped with other genes. by available algorithms that predict mirna target using a conservation of sequence complementary to the mirna seed sequence, we next predicted and confirmed that the nfib mrna is a target of mir-21. nfib protein usually binds the mir-21 promoter in hl-60 cells as a negative regulator and is swept off from the mir-21 promoter during pma-induced macrophage differentiation of hl-60. the translational repression of nfib mrna by mir-21 accelerates clearance of nfib in parallel with the simultaneous mir-21-independent transcriptional repression of nfib after pma stimulation. since exogenous mir-21 expression moderately induced endogenous mir-21, an evolutionarily conserved double-negative feedback regulation would be operating as a mechanism to sustain mir-21 expression.",1
"myosin is the primary regulator of muscle strength and contractility. here we show that three myosin genes, myh6, myh7, and myh7b, encode related intronic micrornas (mirnas), which, in turn, control muscle myosin content, myofiber identity, and muscle performance. within the adult heart, the myh6 gene, encoding a fast myosin, coexpresses mir-208a, which regulates the expression of two slow myosins and their intronic mirnas, myh7/mir-208b and myh7b/mir-499, respectively. mir-208b and mir-499 play redundant roles in the specification of muscle fiber identity by activating slow and repressing fast myofiber gene programs. the actions of these mirnas are mediated in part by a collection of transcriptional repressors of slow myofiber genes. these findings reveal that myosin genes not only encode the major contractile proteins of muscle, but act more broadly to influence muscle function by encoding a network of intronic mirnas that control muscle gene expression and performance.",1
"alzheimer's disease (ad) is a multifactorial, fatal neurodegenerative disorder characterized by the abnormal accumulation of aβ and tau deposits in the brain. there is no cure for ad, and failure at different clinical trials emphasizes the need for new treatments. in recent years, significant progress has been made toward the development of mirna-based therapeutics for human disorders. this study was designed to evaluate the efficiency and potential safety of mirna replacement therapy in ad, using mir-15/107 paralogues as candidate drug targets. we identified mir-16 as a potent inhibitor of amyloid precursor protein (app) and bace1 expression, aβ peptide production, and tau phosphorylation in cells. brain delivery of mir-16 mimics in mice resulted in a reduction of ad-related genes app, bace1, and tau in a region-dependent manner. we further identified nicastrin, a γ-secretase component involved in aβ generation, as a target of mir-16. proteomics analysis identified a number of additional putative mir-16 targets in vivo, including α-synuclein and transferrin receptor 1. top-ranking biological networks associated with mir-16 delivery included ad and oxidative stress. collectively, our data suggest that mir-16 is a good candidate for future drug development by targeting simultaneously endogenous regulators of ad biomarkers (i.e., aβ and tau), inflammation, and oxidative stress.",1
"the box c/d snornas function in directing 2'-o-methylation and/or as chaperones in the processing of ribosomal rna. we show here that snu13p (15.5 kd in human), a component of the u4/u6.u5 tri-snrnp, is also associated with the box c/d snornas. indeed, genetic depletion of snu13p in yeast leads to a major defect in rna metabolism. the box c/d motif can be folded into a stem-internal loop-stem structure, almost identical to the 15.5 kd binding site in the u4 snrna. consistent with this, the box c/d motif binds snu13p/ 15.5 kd in vitro. the similarities in structure and function observed between the u4 snrnp (chaperone for u6) and the box c/d snornps raises the interesting possibility that these particles may have evolved from a common ancestral rnp.",1
"angiogenesis, new vessel formation from pre-existing vessels, is a highly conserved event through vertebrates. however, the system for tuning angiogenesis by species-intrinsic factors is totally unknown. mir-1224 is a member of mammal-specific mirtrons, which were identified as non-canonical micrornas. we found that the expression of mir-1224 was upregulated in capillary-like tube-forming human umbilical vein endothelial cells on matrigel. enforced expression of mir-1224 stimulated tube formation, whereas repression of endogenous mir-1224 inhibited formation. enforced expression of mir-1224 enhanced vegf signaling and repressed notch signaling. the adaptor protein of clathrin-dependent endocytosis, epsin2, which has been shown to be a suppressor of angiogenesis, was a direct target of mir-1224. knockdown of epn2 stimulated tube formation, while overexpression of epn2 repressed mir-1224-mediated stimulation. our findings indicate that mir-1224 is a mammal specific modulator of angiogenesis.",1
"although aberrant reactivation of embryonic gene programs is intricately linked to pathological heart disease, the transcription factors driving these gene programs remain ill-defined. here we report that increased calcineurin/nfat signalling and decreased mir-25 expression integrate to re-express the basic helix-loop-helix (bhlh) transcription factor dhand (also known as hand2) in the diseased human and mouse myocardium. in line, mutant mice overexpressing hand2 in otherwise healthy heart muscle cells developed a phenotype of pathological hypertrophy. conversely, conditional gene-targeted hand2 mice demonstrated a marked resistance to pressure-overload-induced hypertrophy, fibrosis, ventricular dysfunction and induction of a fetal gene program. furthermore, in vivo inhibition of mir-25 by a specific antagomir evoked spontaneous cardiac dysfunction and sensitized the murine myocardium to heart failure in a hand2-dependent manner. our results reveal that signalling cascades integrate with micrornas to induce the expression of the bhlh transcription factor hand2 in the postnatal mammalian myocardium with impact on embryonic gene programs in heart failure.",1
"jnk signaling plays a critical role in both tumor promotion and tumor suppression. here, we identified clustered micrornas (mirnas) mir-306 and mir-79 as novel tumor-suppressor mirnas that specifically eliminate jnk-activated tumors in drosophila . while showing only a slight effect on normal tissue growth, mir-306 and mir-79 strongly suppressed growth of multiple tumor models, including malignant tumors caused by ras activation and cell polarity defects. mechanistically, these mirnas commonly target the mrna of an e3 ubiquitin ligase ring finger protein 146 (rnf146). we found that rnf146 promotes degradation of tankyrase (tnks), an adp-ribose polymerase that promotes jnk activation in a noncanonical manner. thus, downregulation of rnf146 by mir-306 and mir-79 leads to hyper-enhancement of jnk activation. our data show that, while jnk activity is essential for tumor growth, elevation of mir-306 or mir-79 overactivate jnk signaling to the lethal level via noncanonical jnk pathway and thus eliminate tumors, providing a new mirna-based strategy against cancer.",1
"microrna-34a (mir-34a) and sirtuin 1 (sirt1) have been extensively studied in tumour biology and longevity/aging, but little is known about their functional roles in smooth muscle cell (smc) differentiation from pluripotent stem cells. using well-established smc differentiation models, we have demonstrated that mir-34a has an important role in smc differentiation from murine and human embryonic stem cells. surprisingly, deacetylase sirtuin 1 (sirt1), one of the top predicted targets, was positively regulated by mir-34a during smc differentiation. mechanistically, we demonstrated that mir-34a promoted differentiating stem cells' arrest at g0/g1 phase and observed a significantly decreased incorporation of mir-34a and sirt1 rna into ago2-risc complex upon smc differentiation. importantly, we have identified sirt1 as a transcriptional activator in the regulation of smc gene programme. finally, our data showed that sirt1 modulated the enrichment of h3k9 tri-methylation around the smc gene-promoter regions. taken together, our data reveal a specific regulatory pathway that mir-34a positively regulates its target gene sirt1 in a cellular context-dependent and sequence-specific manner and suggest a functional role for this pathway in smc differentiation from stem cells in vitro and in vivo.",1
"circadian clocks control the timing of animal behavioral and physiological rhythms. fruit flies anticipate daily environmental changes and exhibit two peaks of locomotor activity around dawn and dusk. micrornas are small non-coding rnas that play important roles in post-transcriptional regulation. here we identify drosophila mir-210 as a critical regulator of circadian rhythms. under light-dark conditions, flies lacking mir-210 (mir-210ko) exhibit a dramatic 2 hrs phase advance of evening anticipatory behavior. however, circadian rhythms and molecular pacemaker function are intact in mir-210ko flies under constant darkness. furthermore, we identify that mir-210 determines the evening phase of activity through repression of the cell adhesion molecule fasciclin 2 (fas2). ablation of the mir-210 binding site within the 3' utr of fas2 (fas2δmir-210) by crispr-cas9 advances the evening phase as in mir-210ko. indeed, mir-210 genetically interacts with fas2. moreover, fas2 abundance is significantly increased in the optic lobe of mir-210ko. in addition, overexpression of fas2 in the mir-210 expressing cells recapitulates the phase advance behavior phenotype of mir-210ko. together, these results reveal a novel mechanism by which mir-210 regulates circadian locomotor behavior.",1
"micrornas are small noncoding rnas that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript. different combinations of micrornas are expressed in different cell types and may coordinately regulate cell-specific target genes. here, we present pictar, a computational method for identifying common targets of micrornas. statistical tests using genome-wide alignments of eight vertebrate genomes, pictar's ability to specifically recover published microrna targets, and experimental validation of seven predicted targets suggest that pictar has an excellent success rate in predicting targets for single micrornas and for combinations of micrornas. we find that vertebrate micrornas target, on average, roughly 200 transcripts each. furthermore, our results suggest widespread coordinate control executed by micrornas. in particular, we experimentally validate common regulation of mtpn by mir-375, mir-124 and let-7b and thus provide evidence for coordinate microrna control in mammals.",1
"purpose available tools for prostate cancer diagnosis and prognosis are suboptimal and novel biomarkers are urgently needed. here, we investigated the regulation and biomarker potential of the gabre∼mir-452∼mir-224 genomic locus. experimental design gabre/mir-452/mir-224 transcriptional expression was quantified in 80 nonmalignant and 281 prostate cancer tissue samples. gabre∼mir-452∼mir-224 promoter methylation was determined by methylation-specific qpcr (methylight) in 35 nonmalignant, 293 prostate cancer and 198 prostate cancer tissue samples (rp cohort 2). diagnostic/prognostic biomarker potential of gabre∼mir-452∼mir-224 methylation was evaluated by roc, kaplan-meier, uni- and multivariate cox regression analyses. functional roles of mir-224 and mir-452 were investigated in pc3 and du145 cells by viability, migration, and invasion assays and gene-set enrichment analysis (gsea) of posttransfection transcriptional profiling data. results gabre∼mir-452∼mir-224 was significantly downregulated in prostate cancer compared with nonmalignant prostate tissue and had highly cancer-specific aberrant promoter hypermethylation (auc = 0.98). functional studies and gsea suggested that mir-224 and mir-452 inhibit proliferation, migration, and invasion of pc3 and du145 cells by direct/indirect regulation of pathways related to the cell cycle and cellular adhesion and motility. finally, in uni- and multivariate analyses, high gabre∼mir-452∼mir-224 promoter methylation was significantly associated with biochemical recurrence in rp cohort 1, which was successfully validated in rp cohort 2. conclusion the gabre∼mir-452∼mir-224 locus is downregulated and hypermethylated in prostate cancer and is a new promising epigenetic candidate biomarker for prostate cancer diagnosis and prognosis. tumor-suppressive functions of the intronic mir-224 and mir-452 were demonstrated in two prostate cancer cell lines, suggesting that epigenetic silencing of gabre∼mir-452∼mir-224 may be selected for in prostate cancer.",1
"cardiac fibroblasts (cfs) are the most numerous cells in the heart and are recognized primarily for their ability to maintain both the structural integrity and the physiological functions of the heart. the transforming growth factor beta (tgf-β) signaling pathway is reportedly involved in the modulation of cf functions, including apoptosis. recent studies have indicated that microrna-101 (mir-101) attenuates the tgf-β signaling pathway, either by inhibiting the expression of tgfβ1 or by targeting transforming growth factor-β receptor type i (tgfβri). the present study aimed to determine whether mir-101 protects cfs from hypoxia-induced apoptosis and to investigate the mechanisms underlying its protective effects. the cck-8 test, electron microscopy and tunel assay results demonstrated that mir-101a/b significantly inhibited hypoxia-induced cf apoptosis. the results of western blotting, quantitative rt-pcr and immunofluorescence assays indicated that mir-101a dramatically inhibited the hypoxia-induced up-regulation of both tgfβri and p-smad 3 but not tgfβ1 in cfs. additionally, mir-101a significantly reversed the hypoxia-induced up-regulation of bax and caspase-3, the down-regulation of bcl-2 and the activation of caspase-3 in cfs. moreover, mir-101a markedly inhibited the intracellular ca(2+) (i) overload caused by hypoxia. taken together, our results suggest that mir-101a protects cfs against hypoxia-induced apoptosis by inhibiting the tgf-β signaling pathway, which may be a potential therapeutic target for heart injury.",1
"background microrna-200a (mir-200a) has been reported to regulate tumour progression in several tumours but little is known about its role in neuroblastoma. our aim was to investigate the potential role and mechanism of mir-200a in neuroblastomas. materials and methods expression levels of mir-200a in tissues were determined using rt-pcr. the effect of mir-200a and shap-2γ on cell viability was evaluated using mts assays, and target protein expression was determined using western blotting and rt-pcr. luciferase reporter plasmids were constructed to confirm direct targeting. results were reported as mean±s.e.m and differences were tested for significance using the 2-tailed students t-test. results we determined that mir-200a expression was significantly lower in neuroblastoma tumors than the adjacent non-cancer tissue. over-expression of mir-200 are reduced cell viability in neuroblastoma cells and inhibited tumor growth in mouse xenografts. we identified ap-2γ as a novel target for mir-200a in neuroblastoma cells. thus mir-200a targets the 3'utr of ap-2γ and inhibits its mrna and protein expression. furthermore, our result showed that shrna knockdown of ap-2γ in neuroblastoma cells results in significant inhibit of cell proliferation and tumor growth in vitro, supporting an oncogenic role of ap-2γ in neuroblastoma. conclusions our study revealed that mir-200a is a candidate tumor suppressor in neuroblastoma, through direct targeting of ap-2γ. these findings re-enforce the proposal of ap-2γ as a therapeutic target in neuroblastoma.",1
"c-met receptor tyrosine kinase has been regarded as a promising therapeutic target for hepatocellular carcinoma (hcc). recently, micrornas (mirnas) have been shown as a novel mechanism to control c-met expression in cancer. in this study, we investigate the potential contribution of mir-181a-5p dysregulation to the biology of c-met overexpression in hcc. herein, we found an inverse expression pattern between mir-181a-5p and c-met expression in normal, cirrhotic and hcc liver tissues. luciferase assay confirmed that mir-181a-5p binding to the 3'-utr of c-met downregulated the expression of c-met in hcc cells. overexpression of mir-181a-5p suppressed both hgf-independent and -dependent activation of c-met and consequently diminished branching-morphogenesis and invasion. combined treatment with mir-181a-5p and c-met inhibitor led to a further inhibition of c-met-driven cellular activities. knockdown of mir-181a-5p promoted hgf-independent/-dependent signaling of c-met and accelerated migration, invasion and branching-morphogenesis. in conclusion, our results demonstrated for the first time that c-met is a functional target gene of mir-181a-5p and the loss of mir-181a-5p expression led to the activation of c-met-mediated oncogenic signaling in hepatocarcinogenesis. these findings display a novel molecular mechanism of c-met regulation in hcc and strategies to increase mir-181a5p level might be an alternative approach for the enhancement of the inhibitory effects of c-met inhibitors.",1
"endothelial cells growing in high glucose-containing medium show reduced cell proliferation and in vitro angiogenesis. evidence suggests that the molecular pathways leading to these cellular responses are controlled by micrornas, endogenous post-transcriptional regulators of gene expression. to identify the micrornas and their targeted genes involved in the glucose responses, we performed the mirna signature of human umbelical vein endothelial cells (huvecs) exposed and unexposed to high glucose. among differentially expressed micrornas, we analysed mir-492 and showed that its overexpression was able to reduce proliferation, migration and tube formation of huvec. these effects were accompanied by the down-regulation of enos, a key regulator of the endothelial cell function. we showed that enos was indirectly down-regulated by mir-492 and we discovered that mir-492 was able to bind mrnas involved in proliferation, migration, tube formation and regulation of enos activity and expression. moreover, we found that mir-492 decreased vegf expression in huvec and impaired in vivo angiogenesis in a tumour xenograft model, suggesting a role also in modulating the secretion of pro-angiogenic factors. taken together, the data indicate that mir-492 exerts a potent anti-angiogenic activity in endothelial cells and therefore mir-492 seems a promising tool for anti-angiogenic therapy.",1
"mature bdnf and its precursor probdnf may both be secreted to exert opposite effects on synaptic plasticity in the hippocampus. however, it is unknown how probdnf and mature bdnf affect the excitability of gabaergic interneurons and thereby regulate gabaergic inhibition. we made recordings of gabaergic spontaneous ipscs (sipscs) in mouse dentate gyrus granule cells and found that chronic or acute bdnf reductions led to large increases in the sipsc frequencies, which were ttx (tetrodotoxin) sensitive and therefore action-potential driven. conversely, addition of mature bdnf, but not probdnf, within minutes led to a decrease in the sipsc frequency to 44%. direct recordings from fast-spiking gabaergic interneurons revealed that mature bdnf reduced their excitability and depressed their action potential firing, whereas probdnf had no effect. using the trkb inhibitor k-252a, or mice deficient for the common neurotrophin receptor p75(ntr), the regulation of gabaergic activity was shown specifically to be mediated by bdnf binding to the neurotrophin receptor trkb. in agreement, immunohistochemistry demonstrated that trkb, but not p75(ntr), was expressed in parvalbumin-positive interneurons. our results suggest that mature bdnf decreases the excitability of gabaergic interneurons via activation of trkb, while probdnf does not impact on gabaergic activity. thus, by affecting the firing of gabaergic interneurons, mature bdnf may play an important role in regulating network oscillations in the hippocampus.",1
"rationale since their discovery almost 20 years ago, micrornas have been shown to perform essential roles during tissue development and disease. although roles for micrornas in the myocardium during embryo development and cardiac disease have been demonstrated, very little is know about their role in the endocardium or during cardiac valve formation. objective to study the role of micrornas in cardiac valve formation. methods and results we show that zebrafish dicer mutant embryos, lacking mature mirnas, form excessive endocardial cushions. by screening mirnas expressed in the heart, we found that mir-23 is both necessary and sufficient for restricting the number of endocardial cells that differentiate into endocardial cushion cells. in addition, in mouse endothelial cells, mir-23 inhibited a transforming growth factor-β-induced endothelial-to-mesenchymal transition. by in silico screening of expression data with predicted mir-23 target sites combined with in vivo testing, we identified hyaluronic acid synthase 2 (has2), icat, and tmem2 as novel direct targets of mir-23. finally, we demonstrate that the upregulation of has2, an extracellular remodeling enzyme required for endocardial cushion and valve formation, is responsible for the excessive endocardial cushion cell differentiation in dicer mutants. conclusions mir-23 in the embryonic heart is required to restrict endocardial cushion formation by inhibiting has2 expression and extracellular hyaluronic acid production.",1
"vibrio cholerae is the bacterium that causes the diarrheal disease cholera. the bacteria experience a temperature shift as v. cholerae transition from contaminated water at lower temperatures into the 37 °c human intestine. within the intestine, v. cholerae express cholera toxin (ct) and toxin-coregulated pilus (tcp), two main virulence factors required for disease. ct and tcp expression is controlled by the transcriptional activator protein toxt. we identified an rna thermometer motif in the 5' utr of toxt, with a fouru anti-shine-dalgarno (sd) element that base pairs with the sd sequence to regulate ribosome access to the mrna. rna probing experiments demonstrated that the fouru element allowed access to the sd sequence at 37 °c but not at 20 °c. moreover, mutations within the fouru element (u5c, u7c) that strengthened base-pairing between the anti-sd and sd sequences prevented access to the sd sequence even at 37 °c. translation of toxt-flag from the native toxt utr was enhanced at 37 °c, compared with 25 °c in both escherichia coli and v. cholerae. in contrast, the u5c, u7c utr prevented translation of toxt-flag even at 37 °c. v. cholerae mutants containing the u5c, u7c utr variant were unable to colonize the infant mouse small intestine. our results reveal a previously unknown regulatory mechanism consisting of an rna thermometer that controls temperature-dependent translation of toxt, facilitating v. cholerae virulence at a relevant environmental condition found in the human intestine.",1
"a leucine, leucyl-trna synthetase-dependent pathway activates torc1 kinase and its downstream stimulation of protein synthesis, a major nitrogen consumer. we previously demonstrated, however, that control of gln3, a transcription activator of catabolic genes whose products generate the nitrogenous precursors for protein synthesis, is not subject to leucine-dependent torc1 activation. this led us to conclude that excess nitrogen-dependent down-regulation of gln3 occurs via a second mechanism that is independent of leucine-dependent torc1 activation. a major site of gln3 and gat1 (another gata-binding transcription activator) control occurs at their access to the nucleus. in excess nitrogen, gln3 and gat1 are sequestered in the cytoplasm in a ure2-dependent manner. they become nuclear and activate transcription when nitrogen becomes limiting. long-term nitrogen starvation and treatment of cells with the glutamine synthetase inhibitor methionine sulfoximine (msx) also elicit nuclear gln3 localization. the sensitivity of gln3 localization to glutamine and inhibition of glutamine synthesis prompted us to investigate the effects of a glutamine trna mutation (sup70-65) on nitrogen-responsive control of gln3 and gat1. we found that nuclear gln3 localization elicited by short- and long-term nitrogen starvation; growth in a poor, derepressive medium; msx or rapamycin treatment; or ure2δ mutation is abolished in a sup70-65 mutant. however, nuclear gat1 localization, which also exhibits a glutamine trnacug requirement for its response to short-term nitrogen starvation or growth in proline medium or a ure2δ mutation, does not require trnacug for its response to rapamycin. also, in contrast with gln3, gat1 localization does not respond to long-term nitrogen starvation. these observations demonstrate the existence of a specific nitrogen-responsive component participating in the control of gln3 and gat1 localization and their downstream production of nitrogenous precursors. this component is highly sensitive to the function of the rare glutamine trnacug, which cannot be replaced by the predominant glutamine trnacaa. our observations also demonstrate distinct mechanistic differences between the responses of gln3 and gat1 to rapamycin inhibition of torc1 and nitrogen starvation.",1
"the inflammation-associated cytokine interleukin-6 (il-6) can contribute to tumor growth and resistance to therapy by the activation of survival mechanisms. in several human cancers, il-6-activated survival signaling involves the signal transducers and activators of transcription (stat) factors or protein kinase cascades. micrornas (mirnas) are endogenous regulators of gene expression that are altered in expression in many cancers. however, the effect of inflammatory cytokines on mirna expression and the role of mirna in modulating il-6-mediated cell survival are unknown. we investigated the involvement of mirna in malignant cholangiocytes stably transfected to overexpress il-6, which enhances tumor growth in vivo by inhibition of apoptosis. we provide evidence that (i) mirna expression both in vitro and in vivo is altered by overexpression of il-6; (ii) selective mirnas including let-7a are up-regulated and contribute to the survival effects of enforced il-6 activity; and (iii) let-7a contributes to the constitutively increased phosphorylation of stat-3 by a mechanism involving the neurofibromatosis 2 (nf2) gene. these findings reveal a novel mechanism by which il-6 mediates tumor cell survival that may be therapeutically targeted and emphasize the presence of complex interrelationships between deregulated expression of mirna and transcription factors in human cancers.",1
"micrornas are negative regulators of protein coding genes. the liver-specific microrna-122 (mir-122) is frequently suppressed in primary hepatocellular carcinomas (hccs). in situ hybridization demonstrated that mir-122 is abundantly expressed in hepatocytes but barely detectable in primary human hccs. ectopic expression of mir-122 in nonexpressing hepg2, hep3b, and sk-hep-1 cells reversed their tumorigenic properties such as growth, replication potential, clonogenic survival, anchorage-independent growth, migration, invasion, and tumor formation in nude mice. further, mir-122-expressing hcc cells retained an epithelial phenotype that correlated with reduced vimentin expression. adam10 (a distintegrin and metalloprotease family 10), serum response factor (srf), and insulin-like growth factor 1 receptor (igf1r) that promote tumorigenesis were validated as targets of mir-122 and were repressed by the microrna. conversely, depletion of the endogenous mir-122 in huh-7 cells facilitated their tumorigenic properties with concomitant up-regulation of these targets. expression of srf or igf1r partially reversed tumor suppressor function of mir-122. further, mir-122 impeded angiogenic properties of endothelial cells in vitro. notably, adam10, srf, and igf1r were up-regulated in primary human hccs compared with the matching liver tissue. co-labeling studies demonstrated exclusive localization of mir-122 in the benign livers, whereas srf predominantly expressed in hcc. more importantly, growth and clonogenic survival of mir-122-expressing hcc cells were significantly reduced upon treatment with sorafenib, a multi-kinase inhibitor clinically effective against hcc. collectively, these results suggest that the loss of multifunctional mir-122 contributes to the malignant phenotype of hcc cells, and mir-122 mimetic alone or in combination with anticancer drugs can be a promising therapeutic regimen against liver cancer.",1
"background micrornas (mirnas) are non-coding rnas that alter the stability and translation efficiency of messenger rnas. ionizing radiation (ir) induces rapid and selective changes in mirna expression. depletion of the mirna processing enzymes dicer or ago2 reduces the capacity of cells to survive radiation exposure. elucidation of critical radiation-regulated mirnas and their target proteins offers a promising approach to identify new targets to increase the therapeutic effectiveness of the radiation treatment of cancer. principal findings expression of mir-525-3p is rapidly up-regulated in response to radiation. manipulation of mir-525-3p expression in irradiated cells confirmed that this mirna mediates the radiosensitivity of a variety of non-transformed (rpe, huvec) and tumor-derived cell lines (hela, u2-os, ea.hy926) cell lines. thus, anti-mir-525-3p mediated inhibition of the increase in mir-525-3p elevated radiosensitivity, while overexpression of precursor mir-525-3p conferred radioresistance. using a proteomic approach we identified 21 radiation-regulated proteins, of which 14 were found to be candidate targets for mir-525-3p-mediated repression. luciferase reporter assays confirmed that nine of these were indeed direct targets of mir-525-3p repression. individual analysis of these direct targets by rnai-mediated knockdown established that arrb1, txn1 and hspa9 are essential mir-525-3p-dependent regulators of radiation sensitivity. conclusion the transient up-regulation of mir-525-3p, and the resultant repression of its direct targets arrb1, txn1 and hspa9, is required for cell survival following irradiation. the conserved function of mir-525-3p across several cell types makes this microrna pathway a promising target for modifying the efficacy of radiotherapy.",1
"micrornas are endogenously expressed small, non-coding rnas that modulate biological processes by recognizing specific gene transcripts, leading to translational repression or degradation. previous work showed that the mir-17-92 cluster is highly expressed in human endothelial cells that participate in angiogenesis. in this study we showed that mir-19b-1, a component of this cluster, controls the intrinsic angiogenic activity of human umbilical vein endothelial cells (huvecs) in vitro. in silico and in vitro analyses have suggested that mir-19b-1 targets mrna corresponding to the pro-angiogenic protein, fgfr2, and blocks the cell cycle from the s phase to the g(2)/m phase transition by controlling the expression of cyclin d1. thus, mir-19b-1 may serve as a valuable therapeutic agent in the context of tumor angiogenesis.",1
"children with trisomy 21/down syndrome (ds) are at high risk to develop acute megakaryoblastic leukemia (ds-amkl) and the related transient leukemia (ds-tl). the factors on human chromosome 21 (hsa21) that confer this predisposing effect, especially in synergy with consistently mutated transcription factor gata1 (gata1s), remain poorly understood. here, we investigated the role of hsa21-encoded mir-125b-2, a microrna (mirna) overexpressed in ds-amkl/tl, in hematopoiesis and leukemogenesis. we identified a function of mir-125b-2 in increasing proliferation and self-renewal of human and mouse megakaryocytic progenitors (mps) and megakaryocytic/erythroid progenitors (meps). mir-125b-2 overexpression did not affect megakaryocytic and erythroid differentiation, but severely perturbed myeloid differentiation. the proproliferative effect of mir-125b-2 on meps accentuated the gata1s mutation, whereas growth of ds-amkl/tl cells was impaired upon mir-125b repression, suggesting synergism during leukemic transformation in gata1s-mutated ds-amkl/tl. integrative transcriptome analysis of hematopoietic cells upon modulation of mir-125b expression levels uncovered a set of mir-125b target genes, including dicer1 and st18 as direct targets. gene set enrichment analysis revealed that this target gene set is down-regulated in ds-amkl patients highly expressing mir-125b. thus, we propose mir-125b-2 as a positive regulator of megakaryopoiesis and an oncomir involved in the pathogenesis of trisomy 21-associated megakaryoblastic leukemia.",1
"accumulating evidence indicates that micrornas (mirnas) are aberrantly expressed in human cancer and contribute to the tumorigenesis, but their roles in pancreatic cancer are still largely unknown. in this study, our data showed that mir-130b was significantly downregulated in 52 pairs of pancreatic cancer tissues and five cell lines. furthermore, the deregulated mir-130b was correlated with worse prognosis, increased tumor size, late tnm stage, lymphatic invasion and distant metastasis. multivariate analysis showed that mir-130b expression was a significant and independent prognostic predictor for pancreatic cancer patients. functional studies indicated that the overexpression of mir-130b dramatically suppressed the proliferation of pancreatic cancer cells both in vitro and in vivo, which could be attributed to the induction of apoptosis and cell cycle arrest at s phase. meanwhile, an overexpressed mir-130b remarkably inhibited the invasive ability of pancreatic cancer cells. moreover, the dual luciferase assay revealed that stat3 was directly targeted by mir-130b, which was further confirmed by the inverse expression of mir-130b and stat3 in pancreatic cancer samples. our findings suggested that mir-130b might have a considerable potential in prognosis identification and application of therapy for pancreatic cancer.",1
"scn5a encodes the voltage-gated na+ channel nav1.5 that is responsible for depolarization of the cardiac action potential and rapid intercellular conduction. mutations disrupting the scn5a coding sequence cause inherited arrhythmias and cardiomyopathy, and single-nucleotide polymorphisms (snps) linked to scn5a splicing, localization, and function associate with heart failure-related sudden cardiac death. however, the clinical relevance of snps that modulate scn5a expression levels remains understudied. we recently generated a transcriptome-wide map of microrna (mir) binding sites in human heart, evaluated their overlap with common snps, and identified a synonymous snp (rs1805126) adjacent to a mir-24 site within the scn5a coding sequence. this snp was previously shown to reproducibly associate with cardiac electrophysiological parameters, but was not considered to be causal. here, we show that mir-24 potently suppresses scn5a expression and that rs1805126 modulates this regulation. we found that the rs1805126 minor allele associates with decreased cardiac scn5a expression and that heart failure subjects homozygous for the minor allele have decreased ejection fraction and increased mortality, but not increased ventricular tachyarrhythmias. in mice, we identified a potential basis for this in discovering that decreased scn5a expression leads to accumulation of myocardial reactive oxygen species. together, these data reiterate the importance of considering the mechanistic significance of synonymous snps as they relate to mirs and disease, and highlight a surprising link between scn5a expression and nonarrhythmic death in heart failure.",1
"it is largely recognized that micrornas (mirnas) function to silence gene expression by targeting 3'utr regions. however, mirnas have also been implicated to positively-regulate gene expression by targeting promoter elements, a phenomenon known as rna activation (rnaa). in the present study, we show that expression of mouse cyclin b1 (ccnb1) is dependent on key factors involved in mirna biogenesis and function (i.e. dicer, drosha, ago1 and ago2). in silico analysis identifies highly-complementary sites for 21 mirnas in the ccnb1 promoter. experimental validation identified three mirnas (mir-744, mir-1186 and mir-466d-3p) that induce ccnb1 expression in mouse cell lines. conversely, knockdown of endogenous mir-744 led to decreased ccnb1 levels. chromatin immunoprecipitation (chip) analysis revealed that ago1 was selectively associated with the ccnb1 promoter and mir-744 increased enrichment of rna polymerase ii (rnap ii) and trimethylation of histone 3 at lysine 4 (h3k4me3) at the ccnb1 transcription start site. functionally, short-term overexpression of mir-744 and mir-1186 resulted in enhanced cell proliferation, while prolonged expression caused chromosomal instability and in vivo tumor suppression. such phenotypes were recapitulated by overexpression of ccnb1. our findings reveal an endogenous system by which mirna functions to activate ccnb1 expression in mouse cells and manipulate in vivo tumor development/growth.",1
"the accurate control of cell proliferation and survival is critical for animal development. the hippo tumor suppressor pathway regulates both of these parameters by controlling the nuclear availability of the transcriptional coactivator yorkie (yki), which regulates downstream target genes together with scalloped (sd), a dna-binding protein. here we provide evidence that yki can also regulate target genes in conjunction with homothorax (hth) and teashirt (tsh), two dna-binding transcription factors expressed in the uncommitted progenitor cells of the drosophila eye imaginal disc. clonal analyses demonstrate that hth and tsh promote cell proliferation and protect eye progenitor cells from apoptosis. genetic epistasis experiments suggest that hth and tsh execute these functions with yki, in part by up-regulating the microrna bantam. a physical interaction between hth and yki can be detected in cell culture, and we show that hth and yki are bound to a dna sequence approximately 14 kb upstream of the bantam hairpin in eye imaginal disc cells, arguing that this regulation is direct. these data suggest that the hippo pathway uses different dna-binding transcription factors depending on the cellular context. in the eye disc, hth and tsh provide spatial information to this pathway, promoting cell proliferation and survival in the progenitor domain.",1
"micro-rnas (mirnas) are noncoding rnas that bind target mrna transcripts and modulate gene expression. in the cortical collecting duct (ccd), aldosterone stimulates the expression of genes that increase activity of the epithelial sodium channel (enac); in the early phase of aldosterone induction, one such gene is serum and glucocorticoid regulated kinase 1 (sgk1). we hypothesized that aldosterone regulates the expression of mirnas in the early phase of induction to control the expression of target genes that stimulate enac activity. we treated mpkccdc14 cells with aldosterone or vehicle for 1 h and used a mirna microarray to analyze differential mirna expression. we identified mir-466g as a mirna that decreased by 57% after 1 h of aldosterone treatment. moreover, we identified a putative mir-466g binding site in the 3'-untranslated region of sgk1. we constructed an sgk1 3'-untranslated region luciferase reporter and found that cotransfection of mir-466g suppressed luciferase activity in human embryonic kidney-293 cells in a dose-dependent manner. deletion or introduction of point mutations that disrupt the mir-466g target site attenuated mir-466g-directed suppression of luciferase activity. finally, we generated stably transduced mpkccdc14 cell lines overexpressing mir-466g. cells overexpressing mir-466g demonstrated 12.9-fold lower level of sgk1 mrna compared with control cells after 6 h of aldosterone induction; moreover, cells overexpressing mir-466g exhibited 25% decrease in amiloride-sensitive current after 6 h of aldosterone induction and complete loss of amiloride-sensitive current after 24 h of aldosterone induction. our findings implicate mir-466g as a novel early-phase aldosterone responsive mirna that regulates sgk1 and enac in ccd cells.",1
"meiotic recombination hot spot locus (mrhl) rna is a nuclear enriched long noncoding rna encoded in the mouse genome and expressed in testis, liver, spleen, and kidney. mrhl rna silencing in gc1-spg cells, derived from mouse spermatogonial cells, resulted in perturbation of expression of genes belonging to cell adhesion, cell signaling and development, and differentiation, among which many were of the wnt signaling pathway. a weighted gene coexpression network generated nine coexpression modules, which included tcf4, a key transcription factor involved in wnt signaling. activation of wnt signaling upon mrhl rna downregulation was demonstrated by beta-catenin nuclear localization, beta-catenin-tcf4 interaction, occupancy of beta-catenin at the promoters of wnt target genes, and top/fop-luciferase assay. northwestern blot and rna pulldown experiments identified ddx5/p68 as one of the interacting proteins of mrhl rna. downregulation of mrhl rna resulted in the cytoplasmic translocation of tyrosine-phosphorylated p68. concomitant downregulation of both mrhl rna and p68 prevented the nuclear translocation of beta-catenin. mrhl rna was downregulated on wnt3a treatment in gc1-spg cells. this study shows that mrhl rna plays a negative role in wnt signaling in mouse spermatogonial cells through its interaction with p68.",1
"recently, the role of mir-29b in colorectal carcinoma (crc) development appears to be controversial. until now, the expression and function of mir-29b in crc have not been clarified clearly. we showed that decreased expression of mir-29b usually occurred in crc cell lines and tissue samples. loss- and gain-of-function assays in vitro revealed suppressive effects of mir-29b on cell proliferation and migration. endogenous overexpression of mir-29b was sufficient to suppress aggressive behavioral phenotypes in mice. proteomic analysis showed that mir-29b involved in integrate several key biological processes. in addition, mir-29b mediated the inhibition of epithelial-mesenchymal transition (emt) and the inactivation of mitogen-activated protein kinase and phosphatidylinositol-4,5-bisphosphate 3-kinase/akt signal transduction pathway. further studies found that t lymphoma invasion and metastasis 1 (tiam1) was identified as a direct target of mir-29b. in contrast to the phenotypes induced by mir-29b restoration, tiam1-induced cell proliferation and migration partly rescued mir-29b-mediated biological behaviors. our results illustrated that mir-29b as a suppressor has a critical role in crc progression, which suggests its potential role in the molecular therapy of patients with advanced crc.",1
"unlabelled although the inflammation-associated cytokine interleukin-6 (il-6) has been implicated in cholangiocarcinoma growth, the relationship between il-6 and oncogenic changes is unknown. il-6 can increase expression of dna methyltransferase-1 (dnmt-1) and epigenetically regulate the expression of several genes, including micrornas (mirnas). dnmt-1 up-regulation occurs in hepatobiliary cancers and is associated with a poor prognosis. to understand the potential regulation of dnmt-1 by il-6-dependent mirnas, we examined the expression of a group of mirnas which have sequence complementarity to the 3'-untranslated region of dnmt-1, namely mir-148a, mir-152, and mir-301. the expression of these mirnas was decreased in cholangiocarcinoma cells. moreover, the expression of all three mirnas was decreased in il-6-overexpressing malignant cholangiocytes in vitro and in tumor cell xenografts. there was a concomitant decrease in expression of the methylation-sensitive tumor suppressor genes rassf1a and p16ink4a. using luciferase reporter constructs, dnmt-1 was verified as a target for mir-148a and mir-152. precursors to mir-148a and mir-152 decreased dnmt-1 protein expression, increased rassf1a and p16ink4a expression, and reduced cell proliferation. conclusion these data indicate that il-6 can regulate the activity of dnmt-1 and expression of methylation-dependent tumor suppressor genes by modulation of mir-148a and mir-152, and provide a link between this inflammation-associated cytokine and oncogenesis in cholangiocarcinoma.",1
"background enhanced sarcoplasmic reticulum ca(2+)-leak via ryanodine receptor type-2 (ryr2) contributes to the pathogenesis of atrial fibrillation (af). recent studies have shown that the level of ryr2 protein is elevated in atria of patients with paroxysmal af, suggesting that microrna-mediated post-transcriptional regulation of ryr2 might be an underlying mechanism. bioinformatic analysis suggests that mir-106b and mir-93, members of the mir-106b-25 cluster, could bind to ryr2-3'-untranslated region and suppress its translation. thus, we tested the hypothesis that loss of the mir-106b-25 cluster promotes af via enhanced ryr2-mediated sarcoplasmic reticulum ca(2+)-leak. methods and results quantitative real-time polymerase chain reaction showed that the levels of mature mir-106b, mir-93, and mir-25 were lower in atria of patients with paroxysmal af when compared with patients in sinus rhythm. in vitro assay showed that mir-93 reduced ryr2-3'-untranslated region luciferase activity. total ryr2 protein in atrial tissue of mir-106b-25(-/-) mice was increased by 42% when compared with wild-type littermates but still maintained a normal subcellular distribution. ca(2+)-spark frequency and total sarcoplasmic reticulum ca(2+)-leak were increased in atrial myocytes of mir-106b-25(-/-) mice. telemetry ecg recordings revealed that mir-106b-25(-/-) mice exhibited more frequent atrial ectopy and were also more susceptible to pacing-induced af than wild-type littermates. increased sarcoplasmic reticulum ca(2+)-release and af susceptibility in mir-106b-25(-/-) mice were abolished by the ryr2 blocker k201. conclusions these results suggest that mir-106b-25 cluster-mediated post-transcriptional regulation of ryr2 is a potential molecular mechanism involved in paroxysmal af pathogenesis. as such, the mir-106b-25 cluster could be a novel gene-therapy target in af associated with enhanced ryr2 expression.",1
"objective to explore the relationship between microrna-23a-3p expression and perihematomal edema (phe) in patients with acute intracerebral hemorrhage (ich) and its underlying mechanism. patients and methods clinical data and blood samples on the 3rd day after ich onset were collected. head ct was performed in each subject when admitted. serum expressions of micrornas were detected by quantitative real-time pcr (qrt-pcr). the relationship between hematoma volume and perihematomal edema was analyzed by correlation analysis. the direct binding of microrna-23a-3p and zonula occludens-1 (zo-1) was verified by luciferase activity assay and western blot, respectively. moreover, in vitro experiments were carried out by flow cytometry and cck-8 assay, respectively. results serum levels of microrna-23a-3p and microrna-130a in ich patients were remarkably higher than those in the control group, microrna-26a and microrna-146a, however, were significantly decreased. a positive correlation was observed between the microrna-23a-3p expression and the volume of relative perihematomal edema (rphe) on the 3rd day after ich (r2=0.3985; p=0.0002). up-regulation of microrna-23a-3p significantly decreased zo-1 expression in hcmec/d3 cells. results of luciferase activity assay further indicated that microrna-23a-3p directly targets the wild-type of zo-1. in vitro results suggested that microrna-23a-3p expression markedly affects the proliferation and apoptosis of hcmec/d3 cells. similar results were obtained after overexpression or knockdown of zo-1. conclusions up-regulated microrna-23a-3p in ich patients promotes the apoptosis of cerebral vascular endothelial cells by down-regulatingzo-1, thus participating in the perihematomal edema formation after intracerebral hematoma.",1
"the h/aca small nucleolar rnas (snornas) are involved in pseudouridylation of pre-rrnas. they usually fold into a two-domain hairpin-hinge-hairpin-tail structure, with the conserved motifs h and aca located in the hinge and tail, respectively. synthetic rna transcripts and extracts from hela cells were used to reconstitute human u17 and other h/aca ribonucleoproteins (rnps) in vitro. competition and uv cross-linking experiments showed that proteins of about 60, 29, 23, and 14 kda interact specifically with u17 rna. except for u17, rnps could be reconstituted only with full-length h/aca snornas. for u17, the 3'-terminal stem-loop followed by box aca (u17/3'st) was sufficient to form an rnp, and u17/3'st could compete other full-length h/aca snornas for assembly. the h/aca-like domain that constitutes the 3' moiety of human telomerase rna (htr), and its 3'-terminal stem-loop (htr/3'st), also could form an rnp by binding h/aca proteins. hence, the 3'-terminal stem-loops of u17 and htr have some specific features that distinguish them from other h/aca rnas. antibodies that specifically recognize the human gar1 (hgar1) protein could immunoprecipitate h/aca snornas and htr from hela cell extracts, which demonstrates that hgar1 is a component of h/aca snornps and telomerase in vivo. moreover, we show that in vitro-reconstituted rnps contain hgar1 and that binding of hgar1 does not appear to be a prerequisite for the assembly of the other h/aca proteins.",1
"the mammalian cerebral cortex plays a central role in higher cognitive functions and in the complex task of motor control. maternally expressed gene 3 (meg3) appears to play a role in cortical development and neurodegeneration, but the expression and regulation of meg3 in the cortex is not clear. in this study, we examined the expression of transcript variants of meg3 in the developing mouse cerebral cortex. by in situ hybridization, we found that a novel transcript variant of meg3 with 8 small exons was expressed in the developing cortex, whereas the long isoforms of meg3 (~11 kb) were enriched in corticospinal neurons (csns) in layer v of the cortex. no transcript variants of meg3 were found in the neural progenitors at e12.5, when the intergenic differential methylation region (ig-dmr) near meg3 was highly methylated. ig-dmr became demethylated at e15.5 and remained hypomethylated in early csns isolated from fezf2-egfp transgenic mice. the expression of meg3 transcript variant 1 was inversely correlated with the ig-dmr methylation level during development. moreover, expression of paternally expressed gene peg11 was limited to the upper layers, consistent with the idea that the maternally expressed gene may be preferentially transcribed in the lower layers of the cortex. the spatiotemporal expression pattern of meg3 suggests that it may participate in the early development of csns and contribute to cortical malfunctions related to aberrant imprinting in meg3.",1
"neuroblastoma (nb) is one of the most common forms of cancer in children, accounting for 15% of pediatric cancer deaths. the clinical course of these tumors is highly variable and is dependent on such factors as age at presentation, stage, ploidy and genomic abnormalities. hemizygous deletion of chromosome 1p occurs in approximately 30% of advanced stage tumors, is associated with a poor prognosis, and likely leads to the loss of one or more tumor suppressor genes. we show here that microrna (mirna)-34a (1p36.23) is generally expressed at lower levels in unfavorable primary nb tumors and cell lines relative to normal adrenal tissue and that reintroduction of this mirna into three different nb cell lines causes a dramatic reduction in cell proliferation through the induction of a caspase-dependent apoptotic pathway. as a potential mechanistic explanation for this observation, we demonstrate that mir-34a directly targets the messenger ribonucleic acid (mrna) encoding e2f3 and significantly reduces the levels of e2f3 protein, a potent transcriptional inducer of cell-cycle progression. furthermore, mir-34a expression increases during retinoic acid-induced differentiation of the sk-n-be cell line, whereas e2f3 protein levels decrease. thus, adding to the increasing role of mirnas in cancer, mir-34a may act as a suppressor of nb tumorgenesis.",1
"micrornas (mirnas) are critical to proliferation, differentiation, and development. here, we characterize gene expression in murine dicer-null adult mesenchymal stem cell lines, a fibroblast cell type. loss of dicer leads to derepression of let-7 targets at levels that exceed 10-fold to 100-fold with increases in transcription. direct and indirect targets of this mirna belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state. surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 (e3.5) and the induction of let-7 upon differentiation at e10.5. within this mid-gestation program, we characterize the let-7 target nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following mirna loss. in total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor-suppressive function.",1
"the orchestration of brain function requires complex gene regulatory networks that are modulated, in part, by micrornas (mirnas). these noncoding rnas associate with argonaute (ago) proteins in order to direct posttranscriptional gene suppression via base pairing with target transcripts. in order to better understand how mirnas contribute to human-specialized brain processes and neurological phenotypes, identifying their targets is of paramount importance. here, we address the latter by profiling ago2:rna interactions using hits-clip to generate a transcriptome-wide map of mirna binding sites in human brain. we uncovered ∼ 7,000 stringent ago2 binding sites that are highly enriched for conserved sequences corresponding to abundant brain mirnas. this interactome points to functional mirna:target pairs across >3,000 genes and represents a valuable resource for accelerating our understanding of mirna functions in brain. we demonstrate the utility of this map for exploring clinically relevant mirna binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics.",1
"animal micrornas (mirnas) regulate gene expression by inhibiting translation and/or by inducing degradation of target messenger rnas. it is unknown how much translational control is exerted by mirnas on a genome-wide scale. we used a new proteomic approach to measure changes in synthesis of several thousand proteins in response to mirna transfection or endogenous mirna knockdown. in parallel, we quantified mrna levels using microarrays. here we show that a single mirna can repress the production of hundreds of proteins, but that this repression is typically relatively mild. a number of known features of the mirna-binding site such as the seed sequence also govern repression of human protein synthesis, and we report additional target sequence characteristics. we demonstrate that, in addition to downregulating mrna levels, mirnas also directly repress translation of hundreds of genes. finally, our data suggest that a mirna can, by direct or indirect effects, tune protein synthesis from thousands of genes.",1
"calcineurin inhibitors induce nephrotoxicity through poorly understood mechanisms thereby limiting their use in transplantation and other diseases. here we define a microrna (mirna)-messenger rna (mrna) interaction map that facilitates exploration into the role of mirnas in cyclosporine-induced nephrotoxicity (cin) and the gene pathways they regulate. using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (par-clip), we isolated rnas associated with argonaute 2 in the rna-induced silencing complex (risc) of cyclosporine a (csa) treated and control human proximal tubule cells and identified mrnas undergoing active targeting by mirnas. csa causes specific changes in mirnas and mrnas associated with risc, thereby altering post-transcriptional regulation of gene expression. pathway enrichment analysis identified canonical pathways regulated by mirnas specifically following csa treatment. rna-seq performed on total rna indicated that only a fraction of total mirnas and mrnas are actively targeted in the risc, indicating that par-clip more accurately defines meaningful targeting interactions. our data also revealed a role for mirnas in calcineurin-independent regulation of jnk and p38 mapks caused by targeting of map3k1. together, our data provide a novel resource and unique insights into molecular pathways regulated by mirnas in cin. the gene pathways and mirnas defined may represent novel targets to reduce calcineurin induced nephrotoxicity.",1
"aims micrornas (mirnas) are small non-coding rnas that regulate gene expression at the post-transcriptional level by either degradation or translational repression of a target mrna. encoded in the genome of most eukaryotes, mirnas have been proposed to regulate specifically up to 90% of human genes through a process known as mirna-guided rna silencing. for the first time, we sought to test how myocardial ischaemia-reperfusion (ir) changes mir expression. methods and results following 2 and 7 h of ir or sham operation, myocardial tissue was collected and subjected to mirna expression profiling and quantification using a bioarray system that screens for human-, mice-, rat-, and ambi-mir. data mining and differential analyses resulted in 13 mirs that were up-regulated on day 2, 9 mirs that were up-regulated on day 7, and 6 mirs that were down-regulated on day 7 post-ir. results randomly selected from expression profiling were validated using real-time pcr. tissue elements laser-captured from the infarct site showed marked induction of mir-21. in situ hybridization studies using locked nucleic acid mir-21-specific probe identified that ir-inducible mir-21 was specifically localized in the infarct region of the ir heart. immunohistochemistry data show that cardiac fibroblasts (cfs) are the major cell type in the infarct zone. studies with isolated cfs demonstrated that phosphatase and tensin homologue (pten) is a direct target of mir-21. modulation of mir-21 regulated expression of matrix metalloprotease-2 (mmp-2) via a pten pathway. finally, we noted a marked decrease in pten expression in the infarct zone. this decrease was associated with increased mmp-2 expression in the infarct area. conclusion this work constitutes the first report describing changes in mir expression in response to ir in the mouse heart, showing that mir-21 regulates mmp-2 expression in cfs of the infarct zone via a pten pathway.",1
"objective the atp-binding cassette transporter a1 (abca1) protein maintains cellular cholesterol homeostasis in several different tissues. in the liver, abca1 is crucial for high-density lipoprotein biogenesis, and in the pancreas abca1 can regulate insulin secretion. in this study, our aim was to identify novel micrornas that regulate abca1 expression in these tissues. approach and results we combined multiple microrna prediction programs to identify 8 micrornas that potentially regulate abca1. a luciferase reporter assay demonstrated that 5 of these micrornas (mir-148, mir-27, mir-144, mir-145, and mir-33a/33b) significantly repressed abca1 3'-untranslated region activity with mir-145 resulting in one of the larger decreases. in hepatic hepg2 cells, mir-145 can regulate both abca1 protein expression levels and cholesterol efflux function. in murine islets, an increase in mir-145 expression decreased abca1 protein expression, increased total islet cholesterol levels, and decreased glucose-stimulated insulin secretion. inhibiting mir-145 produced the opposite effect of increasing abca1 protein levels and improving glucose-stimulated insulin secretion. finally, increased glucose levels in media significantly decreased mir-145 levels in cultured pancreatic beta cells. these findings suggest that mir-145 is involved in glucose homeostasis and is regulated by glucose concentration. conclusions our studies demonstrate that mir-145 regulates abca1 expression and function, and inhibiting this microrna represents a novel strategy for increasing abca1 expression, promoting high-density lipoprotein biogenesis in the liver, and improving glucose-stimulated insulin secretion in islets.",1
"mg2+ is the most abundant divalent cation in biological systems. it is required for atp-mediated enzymatic reactions and as a stabilizer of ribosomes and membranes. the enteric bacterium salmonella enterica serovar typhimurium harbors three mg2+ transporters and a regulatory system-termed phop/phoq-whose activity is regulated by the extracytoplasmic levels of mg2+. we have determined that expression of the phop-activated mg2+ transporter mgta is also controlled by its 5'-untranslated region (5'utr). the 5'utr of the mgta gene can adopt different stem-loop structures depending on the mg2+ levels, which determine whether transcription reads through into the mgta-coding region or stops within the 5'utr. this makes the mgta 5'utr the first example of a cation-responding riboswitch. the initiation of mgta transcription responds to extracytoplasmic mg2+, and its elongation into the coding region to cytoplasmic mg2+, which provides a singular example where the same ligand is sensed in different cellular compartments to regulate disparate steps in gene transcription. the phop-activated mg2+ transporter mgtb is also regulated by mg2+ in a strain lacking the mg2+ sensor phoq, suggesting the presence of additional mg2+-responding devices.",1
"micrornas (mirnas) comprise of a novel class of endogenous small noncoding rnas that frequently downregulate the expression of target genes. recent reports suggest that mirna-200b prevents epithelial-to-mesenchymal transition (emt) in cancer cells by targeting the e-box binding transcription factors zinc finger e-box-binding homeobox 1 (zeb1) and zinc finger e-box-binding homeobox 2 (zeb2). about 35% of active fibroblasts are derived from emt which is central to the development of progressive renal fibrosis. hence, this study was designed to assess the effect of mirna-200b on transforming growth factor-β (tgf-β1)-induced fibrotic responses in renal tubular cells. morphologically, human kidney-2 cells transfected with mirna-200b retained their epithelial cell characteristics when exposed to tgf-β1. mirna-200b significantly increased e-cadherin (p < 0.001) and reduced fibronectin mrna and protein expression (both p < 0.01) independent of phospho-smad2/3 and phospho-p38 and p42/44 signaling. increased e-cadherin expression was associated with decreased expression of zeb1 and zeb2 and repression of fibronectin was mediated through direct targeting of the fibronectin mrna, demonstrated using pmir luciferase reporter assay and site-directed mutagenesis. these results suggest that mirna-200b suppresses tgf-β1-induced emt via inhibition of zeb1 and zeb2 and the extracellular matrix protein fibronectin by directing targeting of its 3'utr mrna, independent of pathways directly involved in tgf-β1 signaling.",1
"background/aims over the past decade, heat shock protein 90 (hsp90) has emerged as a potential therapeutic target for cancer. however, the molecular mechanisms of down-regulation hsp90 expression in osteosarcoma are incompletely understood. to develop potential therapy targeting heat shock protein 90b1 (hsp90b1), we studied the roles of mir- 223 in the proliferation and apoptosis of human osteosarcoma. methods pcdna3.1(+)- mir-223 plasmid vectors were constructed and transfected into mg63 cells. co-transfection of mir-223 expression vector with pmir-hsp90b1 (the recombined vector of pmir-glotm luciferase vector containing hsp90b1-3'utr) led to the reduced activity of luciferase in a dual-luciferase reporter gene assay, suggesting that hsp90b1 is a target gene of mir-223. expression of hsp90b1 was detected by rt-pcr and western blotting analysis. cell proliferation was determined using the mtt assay. cell-cycle distribution and apoptosis were examined by flow cytometry. pi3k, p-akt, akt, mtor, bcl-2 and bid were also detected by western blotting analysis. after a mouse xenograft model of human mg63 tumors was constructed, tumor growth, microvessel density and proliferation in each group was determined. results the pcdna3.1(+)-mir-223 vector efficiently suppressed the expression of hsp90b1, while silencing mir-223 increased expression of hsp90b1. furthermore, overexpression of mir-223 results in significant inhibition of cell growth on culture plates. moreover, cancer cells showed significant g0/g1 arrest and increased apoptosis due to gene silencing. protein levels of pi3k, p-akt, mtor, and bcl-2 were decreased, whereas bid levels were increased. microvessel density as assessed by cd34 levels and cell growth by pcna levels decreased according to immunohistochemical analysis. conclusion hsp90b1 is a direct target of mir-223 and mir- 223 may have a tumor suppressor function in osteosarcoma through the pi3k/akt/mtor pathway and could be used in anticancer therapies in osteosarcoma.",1
"most of the mammalian genome is transcribed. this generates a vast repertoire of transcripts that includes protein-coding messenger rnas, long non-coding rnas (lncrnas) and repetitive sequences, such as sines (short interspersed nuclear elements). a large percentage of ncrnas are nuclear-enriched with unknown function. antisense lncrnas may form sense-antisense pairs by pairing with a protein-coding gene on the opposite strand to regulate epigenetic silencing, transcription and mrna stability. here we identify a nuclear-enriched lncrna antisense to mouse ubiquitin carboxy-terminal hydrolase l1 (uchl1), a gene involved in brain function and neurodegenerative diseases. antisense uchl1 increases uchl1 protein synthesis at a post-transcriptional level, hereby identifying a new functional class of lncrnas. antisense uchl1 activity depends on the presence of a 5' overlapping sequence and an embedded inverted sineb2 element. these features are shared by other natural antisense transcripts and can confer regulatory activity to an artificial antisense to green fluorescent protein. antisense uchl1 function is under the control of stress signalling pathways, as mtorc1 inhibition by rapamycin causes an increase in uchl1 protein that is associated to the shuttling of antisense uchl1 rna from the nucleus to the cytoplasm. antisense uchl1 rna is then required for the association of the overlapping sense protein-coding mrna to active polysomes for translation. these data reveal another layer of gene expression control at the post-transcriptional level.",1
"this study sought to determine the potential role of micrornas (mirnas) in the detrimental effects of cigarette smoke on angiogenesis and neovascularization. using large-scale mirna profiling and qrt-pcr analyses, we identified let-7f as a pro-angiogenic mirna which expression is significantly reduced in huvecs treated with cigarette smoke extracts (cse), and in the ischemic muscles of mice that are exposed to cigarette smoke (mes). in a mouse model of hindlimb ischaemia, intramuscular injection of let-7f mimic restored ischaemia-induced neovascularization in mes. doppler flow ratios and capillary density in ischemic muscles were significantly improved in mes treated with let-7f mimic. clinically, this was associated with reduced ambulatory impairment and hindlimb ischaemic damage. treatment with let-7f mimic could also rescue pro-angiogenic cell (pac) number and function (attachment, proliferation, migration) in mes. alk5 (tgf-βr1), an important modulator of angiogenesis, is a target of let-7f. here we show that alk5 is increased in huvecs exposed to cse and in the ischaemic muscles of mes. this is associated with a downstream activation of the anti-angiogenic factors smad2/3 and pai-1. importantly, treatment with let-7f mimic reduces the expression of alk5, smad2/3 and pai-1 both in vitro and in vivo. moreover, let-7f overexpression or alk5 inhibition can rescue angiogenesis in huvecs exposed to cse. cigarette smoke exposure is associated with reduced expression of let-7f and activation of the anti-angiogenic tgf-β/alk5 pathway. overexpression of let-7f using a mirna mimic could constitute a novel therapeutic strategy to improve ischaemia-induced neovascularization in pathological conditions.",1
"micrornas (mirnas) repress target genes by destabilizing mrnas and/or by inhibiting translation. the best known factor for target recognition is the so called seed--a short continuous region of watson-crick base pairing between nucleotides 2-7 of the mirna and complementary sequences in 3' untranslated regions of target mrnas. the mir-34 family consists of three conserved members with important tumor suppressor functions linked to the p53 pathway. the family members share the same seed, raising the question if they also have the same targets. here, we analyse the effect of mir-34a and mir-34c on protein synthesis by psilac. despite significant overlap, we observe that the impact of both family members on protein synthesis differs. the ability to identify specific targets of a family member is complicated by the occurrence of * strand mediated repression. transfection of mir-34 chimeras indicates that the 3'end of the mirna might be responsible for differential regulation in case of targets without a perfect seed site. pathway analysis of regulated proteins indicates overlapping functions related to cell cycle and the p53 pathway and preferential targeting of several anti-apoptotic proteins by mir-34a. we used luciferase assays to confirm that vcl and fkbp8, an important anti-apoptotic protein, are specifically repressed by mir-34a. in summary, we find that mir-34a and mir-34c down-regulate distinct subsets of targets which might mediate different cellular outcomes. our data provides a rich resource of mir-34 targets that might be relevant for clinical trials that want to implement the mir-34 family in cancer therapy.",1
"the therapy resistance of pancreatic cancer is associated with the loss of gap junction intercellular communication and connexin 43 expression. the broccoli isothiocyanate sulforaphane restored these features and therapy sensitivity. we investigated whether microrna signaling is involved. established cell lines and a patient tissue array (n = 96) were evaluated by mirna and gene array, bioinformatics, expression studies, in situ hybridization and immunohistochemistry. sulforaphane inhibited the expression of our top candidate mir30a-3p. upon transfection of mir30a-3p inhibitors, the gemcitabine bystander effect, cx43 expression and intercellular communication increased, whereas mir30a-3p mimics inhibited the luciferase activity of a cx43 3'-utr construct. mir30a-3p-overexpressing tumor xenografts had a decreased tumor volume and increased gemcitabine sensitivity. in patient tissues, a higher expression of mir30a-3p and a lower expression of cx43 correlated with malignancy. these findings provide new knowledge and suggest sulforaphane as cotreatment for pancreatic cancer.",1
"substantial data indicate that microrna 21 (mir-21) is significantly elevated in glioblastoma (gbm) and in many other tumors of various origins. this microrna has been implicated in various aspects of carcinogenesis, including cellular proliferation, apoptosis, and migration. we demonstrate that mir-21 regulates multiple genes associated with glioma cell apoptosis, migration, and invasiveness, including the reck and timp3 genes, which are suppressors of malignancy and inhibitors of matrix metalloproteinases (mmps). specific inhibition of mir-21 with antisense oligonucleotides leads to elevated levels of reck and timp3 and therefore reduces mmp activities in vitro and in a human model of gliomas in nude mice. moreover, downregulation of mir-21 in glioma cells leads to decreases of their migratory and invasion abilities. our data suggest that mir-21 contributes to glioma malignancy by downregulation of mmp inhibitors, which leads to activation of mmps, thus promoting invasiveness of cancer cells. our results also indicate that inhibition of a single oncomir, like mir-21, with specific antisense molecules can provide a novel therapeutic approach for ""physiological"" modulation of multiple proteins whose expression is deregulated in cancer.",1
"unlabelled micrornas (mirnas) are small, noncoding rna molecules that control expression of target genes. the abnormally expressed mirnas function as oncogenes or tumor suppressors in human cancer. to evaluate the abundant gene regulation of mir-221 in papillary thyroid carcinoma (ptc), we performed microarray analysis and developed a gaussia luciferase (gluc) reporter system regulated by mir-221. methods total rnas were isolated from pre-mir-221-treated normal human thyroid cells (ht-ori3) and anti-mir-221-treated papillary thyroid cells (npa). microarray analysis was performed with 44,000 probes. the messenger rna levels of target genes regulated by mir-221 were evaluated using reverse-transcription polymerase chain reaction. three types of cytomegalovirus (cmv)/gluc_3' untranslated region (utr) of homeobox b5 (hoxb5), which included a seed sequence of mature mir-221 in the 3' utr of hoxb5 after the gluc stop codon, were transfected into npa cells, and pre-mir-221 was cotransfected with cmv/gluc_3' utr of hoxb5. the gluc activities in cells were measured by luciferase assay. mice implanted with ptc-expressing gluc regulated by mir-221 were monitored with bioluminescence imaging for 6 d. results microarray analysis showed thousands of genes were directly and indirectly regulated by mir-221 and shifted the gene expression pattern of normal thyroid cells toward ptc. of several genes downregulated more than 2-fold by mir-221, messenger rna levels of hoxb5 were significantly downregulated by mir-221. also, in vitro or in vivo gluc activities using cmv/gluc_3' utr of hoxb5 systems were downregulated dose dependently by endogenous or exogenous mir-221. conclusion mir-221 overexpressed in ptc drives carcinoma gene expression patterns by directly and indirectly regulating numerous genes, including hoxb5. the bioluminescence imaging system using cmv/gluc_3' utr of hoxb5 is a useful tool for noninvasive in vivo long-term monitoring of functional targeting of mir-221.",1
"the parts of the rna genome of infectious bronchitis virus (ibv) required for replication and packaging of the rna were investigated using deletion mutagenesis of a defective rna (d-rna) cd-61 (6.1 kb) containing a chloramphenicol acetyltransferase reporter gene. a d-rna with the first 544, but not as few as 338, nucleotides (nt) of the 5' terminus was replicated; the 5' untranslated region (utr) comprises 528 nt. region i of the 3' utr, adjacent to the nucleocapsid protein gene, comprised 212 nt and could be removed without impairment of replication or packaging of d-rnas. a d-rna with the final 338 nt, including the 293 nt in the highly conserved region ii of the 3' utr, was replicated. thus, the 5'-terminal 544 nt and 3'-terminal 338 nt contained the necessary signals for rna replication. phylogenetic analysis of 19 strains of ibv and 3 strains of turkey coronavirus predicted a conserved stem-loop structure at the 5' end of region ii of the 3' utr. removal of the predicted stem-loop structure abolished replication of the d-rnas. d-rnas in which replicase gene 1b-derived sequences had been removed or replaced with all the downstream genes were replicated well but were rescued poorly, suggesting inefficient packaging. however, no specific part of the 1b gene was required for efficient packaging.",1
"rna silencing processes are guided by small rnas that are derived from double-stranded rna. to probe for function of rna silencing during infection of human cells by a dna virus, we recorded the small rna profile of cells infected by epstein-barr virus (ebv). we show that ebv expresses several microrna (mirna) genes. given that mirnas function in rna silencing pathways either by targeting messenger rnas for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression.",1
"beta1-adrenoreceptor (β1-ar) predominantly exists in the heart and β1-ar reduction is closely related to severity of heart failure (hf). in this study, our research focused on the mirnas that may repress β1-ar directly, and aim to find out new markers and target molecules for hf. we first did argonaute2 ago2 knock down experiments and confirmed that endogenous adrenoceptor beta 1 (adrb1) expression was suppressed by mirnas. to further identify which mirna suppress adrb1 expression directly, we constructed the adrb1 3'utr reporter plasmid and selected sixteen candidate mirnas. confirmed by dual-luciferase assay and western blot, we found that mir-19a suppressed adrb1 expression by directly targeting 3'utr. further expressions detection the levels of mir-19a, bnp and camp in 32 plasma samples of hf patients helped us to construct positive correlations between the expression levels of mir-19a and bnp or camp, hints mir-19a may be used as a biomarker in hf patients indicating cardiac function. in conclusion, this study confirmed mir-19a suppressed adrb1 expression by directly targeting 3'utr of adrb1 and found an positive correlation between plasma mir-19a and bnp or camp levels in hf patients, which may contributes to fully understand the hf pathogenesis and develops new therapy for hf.",1
"theiler's virus and mengo virus are representatives of the cardiovirus genus within the picornavirus family. their genome is an 8-kilobase long positive strand rna molecule. this rna molecule plays three roles in infected cells: it serves as a messenger rna, acts as a template for genome replication, and is encapsidated to form progeny virions. we observed that a cis-acting signal required for replication of theiler's virus was contained within a 130-nt stretch of the region encoding the capsid protein vp2. this rna sequence does not influence internal ribosome entry site-mediated translation initiation and thus likely acts directly as a signal for the replication complex. we found a similar signal in the vp2-coding sequence of mengo virus, and both signals could be functionally exchanged. within the replication element, a 9-nt sequence that is highly conserved among cardioviruses was shown to be essential for replication. this conserved sequence was contained in mostly unpaired regions of the rna secondary structure predicted for the replication elements of the various cardioviruses. interestingly, a similar replication element has been reported to occur in the distantly related human rhinovirus type 14, suggesting that such elements could be conserved throughout the picornavirus family. however, the different location of the replication elements in rhinovirus and cardioviruses, and the fact that they were not functionally exchangeable, is raising intriguing questions about the evolution of such signals in picornaviruses.",1
"background tumor suppressor microrna mir-145 is commonly down-regulated in colon carcinoma tissues, but its specific role in tumors remains unknown. methods in this study, the authors identified the friend leukemia virus integration 1 gene (fli1) as a novel target of mir-145. fli1 is involved in t(11;22)(q24:q12) reciprocal chromosomal translocation in ewing sarcoma, and its expression appears to be associated with biologically more aggressive tumors. results the authors demonstrated that mir-145 targets a putative microrna regulatory element in the 3'-untranslated region (utr) of fli1, and its abundance is reversely associated with fli1 expression in colon cancer tissues and cell lines. by using a luciferase/fli1 3'-utr reporter system, they found that mir-145 down-regulated the reporter activity, and this down-regulation was reversed by anti-mir-145. mutation of the mir-145 microrna regulatory element sequence in the fli1 3'-utr abolished the activity of mir-145. mir-145 decreased fli1 protein but not fli1 mrna, suggesting a mechanism of translational regulation. furthermore, the authors demonstrated that mir-145 inhibited cell proliferation and sensitized ls174t cells to 5-fluorouracil-induced apoptosis. conclusions taken together, these results suggest that mir-145 functions as a tumor suppressor by down-regulating oncogenic fli1 in colon cancer.",1
"accumulating evidence suggests that hypoxia-inducible factor 1α (hif-1α) regulates numerous mirnas and is crucial for cellular response to hypoxia. however, the relationship between hif-1α and mir-21 in hypoxic cardiomyocytes is little known. we found that hypoxia induced hif-1α and mir-21 expression. hif-1α knockdown increased cell apoptosis and reduced mir-21 expression. furthermore, we found that hif-1α transcriptionally enhanced mir-21 promoter activity by binding to its promoter, which required the recruitment of cbp/p300. in addition, we found that mir-21 inhibition increased cell apoptosis and reduced hif-1α expression, and modulated the pten/akt pathway. our results indicate that hif-1α-mir-21 feedback contributes to the adaptation of cardiomyocytes to hypoxia, and has potential as therapeutic target for myocardial ischemia.",1
"micrornas (mirs) play a key role in cancer etiology by coordinately repressing numerous target genes involved in cell proliferation, migration and invasion. the genomic region in chromosome 9p21 that encompasses mir-31 is frequently deleted in solid cancers including melanoma; however the expression and functional role of mir-31 has not been previously studied in melanoma. here, we queried the expression status and performed functional characterization of mir-31 in melanoma tissues and cell lines. we found that down-regulation of mir-31 was a common event in melanoma tumors and cell lines and was associated with genomic loss in a subset of samples. down-regulation of mir-31 gene expression was also a result of epigenetic silencing by dna methylation, and via ezh2-mediated histone methylation. ectopic overexpression of mir-31 in various melanoma cell lines inhibited cell migration and invasion. mir-31 targets include oncogenic kinases such as src, met, nik (map3k14) and the melanoma specific oncogene rab27a. furthermore, mir-31 overexpression resulted in down-regulation of ezh2 and a de-repression of its target gene rap1gap; increased expression of ezh2 was associated with melanoma progression and overall patient survival. taken together, our study supports a tumor suppressor role for mir-31 in melanoma and identifies novel therapeutic targets.",1
"micrornas (mirnas) are a class of recently discovered noncoding rna genes that post-transcriptionally regulate gene expression. it is becoming clear that mirnas play an important role in the regulation of gene translation during development. however, in mammals, expression data are principally based on whole tissue analysis and are still very incomplete. we isolated cd34(+)cd38(-) hematopoietic stem cells (hscs) from human umbilical cord blood, on the basis of cell-surface markers using fluorescence-activated cell sorting (facs). also, cd34(+) subpopulation was facs isolated as the control. next, using microarray containing oligonucleotides corresponding to 517 mirnas from human, mouse, and rat genomes, we obtained mirna gene expression profiles of both subpopulations. we focused on the hscs correlative mirnas with comparison to the control. the mirnas of particular interest were confirmed by real-time rt-pcr. hscs-overexpressed hsa-mir-520h and underexpressed hsa-mir-129 were selected for target prediction and analysis. the result showed that eif2c3 and camta1, genes related to mirnas processing or transcription regulation, were proved to be real targets for hsa-mir-129. and abcg2, involved in stemness maintaining, a real target for hsa-mir-520h. finally, we chose hsa-mir-520h, enriched in hscs but low in cd34(+) cells, for functional characterization, because of its possible role in differentiation of hscs by regulating abcg2. as a result, hsa-mir-520h transduction into cd34(+) cells greatly increased number of different progenitor colonies in colony-forming-cell assays, suggesting that hsa-mir-520h may promote differentiation of hscs into progenitor cells by inhibiting abcg2 expression. this study paves the way for identifying hsc-specific mirnas and their roles in hsc development.",1
"b7-h3, a surface immunomodulatory glycoprotein, inhibits natural killer cells and t cells. the monoclonal antibody (mab) 8h9 is specific for 4ig-b7-h3, the long and principal form of b7-h3. early results from radioimmunotherapy using 8h9 have shown promise in patients with metastatic solid tumors to the central nervous system. whereas b7-h3 transcript was ubiquitously expressed in a wide spectrum of human solid tumors as well as human normal tissues, b7-h3 protein was preferentially expressed only in tumor tissues. by quantitative reverse transcription-pcr, all three isoforms of microrna mir-29 (a, b, and c) were highly expressed in normal tissues. however, they were down-regulated in a broad spectrum of solid tumors, including neuroblastoma, sarcomas, brain tumors, and tumor cell lines. b7-h3 protein expression was inversely correlated with mir-29 levels in both cell lines and tumor tissues tested. using luciferase reporter assay, mir-29a was shown to directly target b7-h3 3' untranslated region, and knock-in and knockdown of mir-29a led to down-regulation and up-regulation, respectively, of b7-h3 protein expression. the ability of mir-29 to control b7-h3 protein expression has implications in immune escape by solid tumors. differential modulation of this key immunoinhibitory molecule in tumor versus normal tissues may advance both cell-mediated immunotherapy and antibody-based targeted strategies using the b7-h3-specific mab 8h9.",1
"rationale macrophage accumulation of cholesterol leads to foam cell formation which is a major pathological event of atherosclerosis. recent studies have shown that microrna (mir)-19b might play an important role in cholesterol metabolism and atherosclerotic diseases. here, we have identified mir-19b binding to the 3'utr of atp-binding cassette transporter a1 (abca1) transporters, and further determined the potential roles of this novel interaction in atherogenesis. objective to investigate the molecular mechanisms involved in a mir-19b promotion of macrophage cholesterol accumulation and the development of aortic atherosclerosis. methods and results we performed bioinformatics analysis using online websites, and found that mir-19b was highly conserved during evolution and directly bound to abca1 mrna with very low binding free energy. luciferase reporter assay confirmed that mir-19b bound to 3110-3116 sites within abca1 3'utr. mir-19b directly regulated the expression levels of endogenous abca1 in foam cells derived from human thp-1 macrophages and mouse peritoneal macrophages (mpms) as determined by qrt-pcr and western blot. cholesterol transport assays revealed that mir-19b dramatically suppressed apolipoprotein ai-mediated abca1-dependent cholesterol efflux, resulting in the increased levels of total cholesterol (tc), free cholesterol (fc) and cholesterol ester (ce) as revealed by hplc. the excretion of (3)h-cholesterol originating from cholesterol-laden mpms into feces was decreased in mice overexpressing mir-19b. finally, we evaluated the proatherosclerotic role of mir-19b in apolipoprotein e deficient (apoe(-/-)) mice. treatment with mir-19b precursor reduced plasma high-density lipoprotein (hdl) levels, but increased plasma low-density lipoprotein (ldl) levels. consistently, mir-19b precursor treatment increased aortic plaque size and lipid content, but reduced collagen content and abca1 expression. in contrast, treatment with the inhibitory mir-19b antisense oligonucleotides (aso) prevented or reversed these effects. conclusion mir-19b promotes macrophage cholesterol accumulation, foam cell formation and aortic atherosclerotic development by targeting abca1.",1
"sterol regulatory element-binding protein 2 (srebp-2) transcription factor has been identified as a key protein in cholesterol metabolism through the transactivation of the ldl receptor and cholesterol biosynthesis genes. here, we generated mice lacking microrna (mir)-33, encoded by an intron of the srebp2, and showed that mir-33 repressed the expression of atp-binding cassette transporter a1 (abca1) protein, a key regulator of hdl synthesis by mediating cholesterol efflux from cells to apolipoprotein a (apoa)-i. in fact, peritoneal macrophages derived from mir-33-deficient mice showed a marked increase in abca1 levels and higher apoa-i-dependent cholesterol efflux than those from wt mice. abca1 protein levels in liver were also higher in mir-33-deficient mice than in wt mice. moreover, mir-33-deficient mice had significantly higher serum hdl cholesterol levels than wt mice. these data establish a critical role for mir-33 in the regulation of abca1 expression and hdl biogenesis in vivo.",1
"the identities and roles of proteins associated with human telomerase remain poorly defined. to gain insight, we undertook an affinity purification of endogenously assembled human telomerase complexes. we show that specific subsets of h/aca, sm, and hnrnp proteins associate with active and inactive telomerase rnps, while two ntpase proteins associate preferentially with active enzyme. all three core h/aca-motif binding proteins are telomerase holoenzyme components essential for rnp accumulation. on the other hand, telomerase rnps lacking interaction with sm proteins or hnrnp c remain fully functional for telomere elongation. curiously, overexpression of either associated hnrnp protein (hnrnp c and hnrnp u) or either ntpase protein (nat10 and gnl3l) induced telomere shortening. our findings suggest that endogenous human telomerase complexes are more heterogeneous than those of single-celled eukaryotes, have predominantly shared rather than telomerase-specific proteins, and make numerous regulatory interactions.",1
"micrornas (mirnas) play critical roles in the growth, metastasis and therapeutic resistance of liver cancer. accumulating evidence suggests that mir‑498 is aberrantly expressed in several human malignancies. however, the role and underlying mechanism of mir‑498 in liver cancer remain unclear. in the present study, we investigated the potential roles and clinical value of mir‑498 in liver cancer. we found that the mir‑498 expression level was significantly lower in liver cancer patient tissues than that in healthy control tissues. the expression of mir‑498 was also decreased in liver cancer cell lines compared to that noted in a normal human normal liver cell line. mir‑498 overexpression markedly inhibited liver cancer cell proliferation, migration and invasion. mir‑498 overexpression induced cell cycle arrest and apoptosis while it suppressed epithelial‑mesenchymal transition (emt) in liver cancer cells. bioinformatic analysis and luciferase reporter assay further identified zinc finger e‑box binding homeobox 2 (zeb2) as a novel target of mir‑498. furthermore, zeb2 knockdown recapitulated the inhibitory effects of mir‑498 overexpression in liver cancer cells. zeb2 overexpression rescued the inhibition of liver cancer cell proliferation, migration, and invasion by mir‑498, indicating that zeb2 acts as a downstream effector of mir‑498 in liver cancer cells. thus, we demonstrated that mir‑498 suppresses the growth and metastasis of liver cancer cells, partly at least, by directly targeting zeb2, suggesting that mir‑498 may serve as a potential biomarker for the diagnosis and therapy of liver cancer.",1
"background & aims neurotensin promotes inflammation and colon cancer via the neurotensin-1 receptor (ntr1). micrornas (mir) regulate protein synthesis by degrading or preventing translation of mrnas. we analyzed expression of 365 different micrornas by human colonic epithelial cells (ncm460) after activation of ntr1. methods we performed microarray analysis of mrna expression by neurotensin-stimulated ncm460 cells that overexpressed ntr1. nuclear factor-κb (nf-κb) binding sites were identified and tumorigenesis was assessed using soft agar assays and xenograft analysis of severe combined immunodeficiency mice. targets of neurotensin-regulated micrornas were identified via bioinformatic, real-time polymerase chain reaction, and immunoblot analyses. we analyzed rna samples from human normal colon and tumor samples. results neurotensin stimulated differential expression of 38 micrornas, including mir-21 and mir-155, which have been associated with tumor growth and contain nf-κb binding sites. neurotensin expression increased colony formation by hct-116 cells. blocking mir-21 and/or mir-155 prevented colony formation (p conclusions ntr1 activation stimulates expression of mir-21 and mir-155 in colonocytes, via akt and nf-κb, to down-regulate pten and socs1 and promote growth of tumors in mice. levels of ntr1, mir-21, and mir-155 increase in human colon tumor samples and correlate with tumor stage.",1
"neuroepithelial cell proliferation must be carefully balanced with the transition to neuroblast (neural stem cell) to control neurogenesis. here, we show that loss of the drosophila microrna mir-8 (the homolog of vertebrate mir-200 family) results in both excess proliferation and ectopic neuroblast transition. unexpectedly, mir-8 is expressed in a subpopulation of optic-lobe-associated cortex glia that extend processes that ensheath the neuroepithelium, suggesting that glia cells communicate with the neuroepithelium. we provide evidence that mir-8-positive glia express spitz, a transforming growth factor α (tgf-α)-like ligand that triggers epidermal growth factor receptor (egfr) activation to promote neuroepithelial proliferation and neuroblast formation. further, our experiments suggest that mir-8 ensures both a correct glial architecture and the spatiotemporal control of spitz protein synthesis via direct binding to spitz 3' utr. together, these results establish glial-derived cues as key regulatory elements in the control of neuroepithelial cell proliferation and the neuroblast transition.",1
"understanding the molecular mechanism of cerebral hypoxic preconditioning (hpc)-induced endogenous neuroprotection may provide potential therapeutic targets for ischemic stroke. by using bioinformatics analysis, we found that mir-181b, one of 19 differentially expressed mirnas, may target aconitate hydratase (aco2), heat shock protein a5 (hspa5), and ubiquitin carboxyl-terminal hydrolase isozyme l1 (uchl1) among 26 changed protein kinase c isoform-specific interacting proteins in hpc mouse brain. in this study, the role of mir-181b in oxygen-glucose deprivation (ogd)-induced n2a cell ischemic injury in vitro and mouse middle cerebral artery occlusion (mcao)-induced cerebral ischemic injury in vivo, and its regulation of aco2, hspa5, and uchl1 were further determined. we found that mir-181b expression levels significantly decreased in mouse brain following mcao and in ogd-treated n2a cells. up- and downregulation of mir-181b by transfection of pre- or anti-mir-181b could negatively regulate hspa5 and uchl1 (but not aco2) protein levels as well as n2a cell death and programmed cell death in ogd-treated n2a cells. by using a t7 promoter-driven control dual luciferase assay, we confirmed that mir-181b could bind to the 3'-untranslated rergions of hspa5 and uchl1 mrnas and repress their translations. mir-181b antagomir reduced caspase-3 cleavage and neural cell loss in cerebral ischemic cortex and improved neurological deficit of mice after mcao. in addition, hspa5 and uchl1 short interfering rnas (sirnas) blocked anti-mir-181b-mediated neuroprotection against ogd-induced n2a cell injury in vitro. these results suggest that the downregulated mir-181b induces neuroprotection against ischemic injury through negatively regulating hspa5 and uchl1 protein levels, providing a potential therapeutic target for ischemic stroke.",1
"retinoids are promising agents for the treatment/prevention of breast carcinoma. we examined the role of micrornas in mediating the effects of all-trans-retinoic acid (atra), which suppresses the proliferation of estrogen receptor-positive (erα(+)) breast carcinoma cells, such as mcf-7, but not estrogen receptor-negative cells, such as mda-mb-231. we found that pro-oncogenic mir-21 is selectively induced by atra in erα(+) cells. induction of mir-21 counteracts the anti-proliferative action of atra but has the potentially beneficial effect of reducing cell motility. in erα(+) cells, retinoid-dependent induction of mir-21 is due to increased transcription of the mir21 gene via ligand-dependent activation of the nuclear retinoid receptor, rarα. rarα is part of the transcription complex present in the 5'-flanking region of the mir21 gene. the receptor binds to two functional retinoic acid-responsive elements mapping upstream of the transcription initiation site. silencing of mir-21 enhances atra-dependent growth inhibition and senescence while reverting suppression of cell motility afforded by the retinoid. up-regulation of mir-21 results in retinoid-dependent inhibition of the established target, maspin. knockdown and overexpression of maspin in mcf-7 cells indicates that the protein is involved in atra-induced growth inhibition and contributes to the atra-dependent anti-motility responses. integration between whole genome analysis of genes differentially regulated by atra in mcf-7 and mda-mb-231 cells, prediction of mir-21 regulated genes, and functional studies led to the identification of three novel direct mir-21 targets: the pro-inflammatory cytokine il1b, the adhesion molecule icam-1 and plat, the tissue-type plasminogen activator. evidence for icam-1 involvement in retinoid-dependent inhibition of mcf-7 cell motility is provided.",1
"through a computer search of dna databases, we have identified the homologs of the mgu6-47 snorna gene from the yeast schizosaccharomyces pombe, the fly drosophila melanogaster and human. the three box c/d-containing snorna genes showed no significant similarity in their sequences except for an 11 nt long complementarity to u6 snrna, suggesting that the mechanism of snorna guided snrna methylation is conserved from mammals to yeast. the corresponding snornas have been positively detected by reverse transcription and northern blotting. taking advantage of the fission yeast system, we have disrupted the yeast mgu6-47 gene and demonstrated that it is absolutely required for site-specific 2'-o-methylation of u6 at position a41. no growth differences between mgu6-47 gene-disrupted and wild-type cells were observed, suggesting that the mgu6-47 gene, as for most rrna methylation guides, is dispensable in yeast. nevertheless, it was revealed by temperature shift assay that abolition of a41 methylation in yeast u6 snrna might cause a small decrease in mrna splicing efficiency. the timing of s.pombe u6 pre-rna transport in the nucleus for splicing and methylation was also analyzed and is described.",1
"recent studies have reported that hyper-methylation in the promoter region of mirnas could silence the expression of tumor suppressive mirnas and might play significant roles in the process of tumor development. however, the potential mechanisms regarding how methylation of mirna cpg island could regulate cancer cell chemo-resistance have not yet been studied. using microarray and bsp (bisulfate sequencing pcr) assays, we found that compared with the parent sgc7901/vcr cells, expression of mir-129-5p was restored in sgc7901/vcr gastric cancer multi-drug resistant cell line treated by de-methylation reagent (5-aza-dc). using gain or loss of function assays, we found the over-expressed mir-129-5p reduced the chemo-resistance of sgc7901/vcr and sgc7901/adr cells, while down-regulation of mir-129-5p had an opposite effect. furthermore, three members of multi-drug resistance (mdr) related abc transporters (abcb1, abcc5 and abcg1) were found to be direct targets of mir-129-5p using bioinformatics analysis and report gene assays. the present study indicated that hyper-methylation of mir-129-5p cpg island might play important roles in the development of gastric cancer chemo-resistance by targeting mdr related abc transporters and might be used as a potential therapeutic target in preventing the chemo-resistance of gastric cancer.",1
"the present study is one of the few that includes tissue samples in the evaluation of target prediction algorithms designed to detect microrna (mirna) sequences that might interact with particular messenger rna (mrna) sequences. twelve different target prediction tools were used to find mirna sequences that might interact with ccl20 gene expression. different algorithms predicted controversial mirna sequences for ccl20 regulation due to a different weighting of parameters. hsa-mir-21 and hsa-mir-145 suggested by four or more programs were chosen for further investigation. possible real interaction of these mirna sequences with ccl20 gene expression was monitored using luciferase assays and expression analyses of tissue samples of colorectal adenocarcinoma by either qrt-pcr or elisa. folding status of seed-binding sites in complete mrna and 3'utr of ccl20 was predicted. prediction of mirna expression was attempted based on ccl20 expression data. eight of the target prediction tools forecasted a role for hsa-mir-21 and four mentioned hsa-mir-145 in ccl20 gene regulation. laboratory experimentation showed that ccl20 may serve as a target of hsa-mir-21 but not hsa-mir-145. expression of the molecules resulted in no clear assertion. folding of seed-binding sites was predicted to be relatively constant for the complete mrna and 3'utr. predicting mirna expression based on target gene expression was impossible. this might be attributable to the fact that effects of mirna activity may oscillate between gene product repression and activation. additional systematic studies are needed to address this issue.",1
"the pyrimidine nucleotide biosynthesis (pyr) operon in bacillus subtilis is regulated by transcriptional attenuation. the pyrr protein binds in a uridine nucleotide-dependent manner to three attenuation sites at the 5'-end of pyr mrna. pyrr binds an rna-binding loop, allowing a terminator hairpin to form and repressing the downstream genes. the binding of pyrr to defined rna molecules was characterized by a gel mobility shift assay. titration indicated that pyrr binds rna in an equimolar ratio. pyrr bound more tightly to the binding loops from the second (bl2 rna) and third (bl3 rna) attenuation sites than to the binding loop from the first (bl1 rna) attenuation site. pyrr bound bl2 rna 4-5-fold tighter in the presence of saturating ump or udp and 150- fold tighter with saturating utp, suggesting that utp is the more important co-regulator. the minimal rna that bound tightly to pyrr was 28 nt long. thirty-one structural variants of bl2 rna were tested for pyrr binding affinity. two highly conserved regions of the rna, the terminal loop and top of the upper stem and a purine-rich internal bulge and the base pairs below it, were crucial for tight binding. conserved elements of rna secondary structure were also required for tight binding. pyrr protected conserved areas of the binding loop in hydroxyl radical footprinting experiments. pyrr likely recognizes conserved rna sequences, but only if they are properly positioned in the correct secondary structure.",1
"the discovery of programmed -1 frameshifting at the hexanucleotide shift site cga_aag, in addition to the classical x_xxy_yyz heptanucleotide shift sequences, prompted a search for instances among eubacterial insertion sequence elements. is1222 has a cga_aag shift site. a genetic analysis revealed that frameshifting at this site is required for transposition.",1
"we previously reported that the g allele of rs3853839 at 3'untranslated region (utr) of toll-like receptor 7 (tlr7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (sle) in 9,274 eastern asians . here, we conducted trans-ancestral fine-mapping in 13,339 subjects including european americans, african americans, and amerindian/hispanics and confirmed rs3853839 as the only variant within the tlr7-tlr8 region exhibiting consistent and independent association with sle (pmeta = 7.5×10(-11), or = 1.24 ). the risk g allele was associated with significantly increased levels of tlr7 mrna and protein in peripheral blood mononuclear cells (pbmcs) and elevated luciferase activity of reporter gene in transfected cells. tlr7 3'utr sequence bearing the non-risk c allele of rs3853839 matches a predicted binding site of microrna-3148 (mir-3148), suggesting that this microrna may regulate tlr7 expression. indeed, mir-3148 levels were inversely correlated with tlr7 transcript levels in pbmcs from sle patients and controls (r(2) = 0.255, p = 0.001). overexpression of mir-3148 in hek-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by tlr7 3'utr segment bearing the c allele (p = 0.0003). compared with the g-allele construct, the c-allele construct showed greater than two-fold reduction of luciferase activity in the presence of mir-3148. reduced modulation by mir-3148 conferred slower degradation of the risk g-allele containing tlr7 transcripts, resulting in elevated levels of gene products. these data establish rs3853839 of tlr7 as a shared risk variant of sle in 22,613 subjects of asian, ea, aa, and amerindian/hispanic ancestries (pmeta = 2.0×10(-19), or = 1.25 ), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor mir-3148.",1
"background the multidrug resistance and distant metastasis of cholangiocarcinoma result in high postoperative recurrence and low long-term survival rates. it has been demonstrated that the ectopic expression of mir-200 suppresses the multidrug resistance and metastasis of cancer. however, the expression and function of mir-200 in cholangiocarcinoma has not yet been described. methods in this study, we identified dysregulated micrornas (mirnas, mir) in cholangiocarcinoma tissue by microarray analysis, and subsequent real-time pcr and northern blot analyses validated the expression of candidate mir. we performed functional analyses and investigated the relationship between mir-200b/c expression and the properties of cholangiocarcinoma cells. a dual luciferase assay was applied to examine the effect of mirnas on the 3'-utr of target genes, and we demonstrated the function of the target gene by sirna transfection identifying the downstream pathway via western blotting. results we found significantly downregulated expression of four mir-200 family members (mir-200a/b/c/429) and then confirmed that ectopic mir-200b/200c inhibits the migration and invasion of cholangiocarcinoma cells both in vitro and in vivo. we found that mir-200b/c influenced the tumourigenesis of cholangiocarcinoma cells including their tumour-initiating capacity, sphere formation, and drug resistance. we further found that mir-200b/c regulated migration and invasion capacities by directly targeting rho-kinase 2 and regulated tumorigenic properties by directly targeting suz12 (a subunit of a polycomb repressor complex). conclusion our study shows that mir-200b/c has a critical role in the regulation of the tumorigenic and metastatic capacity of cholangiocarcinoma and reveals the probable underlying mechanisms.",1
"in the intestine, dysregulation of mirna is associated with inflammation, disruption of the gastrointestinal barrier, and the onset of gastrointestinal disorders. this study identifies mirnas involved in the maintenance of intercellular junctions and barrier integrity. for the functional identification of barrier affecting mirnas, we took advantage of the barrier-enforcing effects of the probiotic bacterium escherichia coli nissle 1917 (ecn) which can be monitored by enhanced transepithelial resistance (ter). mirna-profiling of t84 monolayers prior and after co-incubation with ecn revealed for the first time differentially regulated mirnas (mir-203, mir-483-3p, mir-595) targeting tight junction (tj) proteins. using real-time pcr, western blotting and specific mirna mimics, we showed that these mirnas are involved in the regulation of barrier function by modulating the expression of regulatory and structural components of tight junctional complexes. furthermore, specific inhibitors directed at these mirna abrogated the disturbance of tight junctions induced by enteropathogenic e. coli (epec). the half-maximal inhibitory concentration (ic(50)) was determined to 340 nm by monitoring inhibitor kinetics. in summary, we conclude that specific mirnas effect regulatory as well as structural proteins of the junctional complex which in turn are involved in the barrier enhancing effect of ecn. hence, we suggest that the application of mirnas might be refined and further developed as a novel supportive strategy for the treatment of gastrointestinal disorders.",1
"metazoan replication-dependent histone mrnas are not polyadenylated and instead end in a conserved stem loop that is the cis element responsible for coordinate posttranscriptional regulation of these mrnas. using biochemical approaches, only a limited number of factors required for cleavage of histone pre-mrna have been identified. we therefore performed a genome-wide rna interference screen in drosophila cells using a gfp reporter that is expressed only when histone pre-mrna processing is disrupted. four of the 24 genes identified encode proteins also necessary for cleavage/polyadenylation, indicating mechanistic conservation in formation of different mrna 3' ends. we also unexpectedly identified the histone variants h2av and h3.3a/b. in h2av mutant cells, u7 snrnp remains active but fails to accumulate at the histone locus, suggesting there is a regulatory pathway that coordinates the production of variant and canonical histones that acts via localization of essential histone pre-mrna processing factors.",1
"dietary saturated fatty acids (sfa) in excess not only induce hepatic insulin resistance, but also result in type 2 diabetes (t2dm). although micrornas (mirnas) participate widely in the pathogenesis of a range of diseases through the suppression of target gene expression at the post-transcriptional level, the implications of sfa-induced mirnas in the dysregulation of metabolism, particularly in the development of insulin resistance, are largely unclear. sfa palmitate provoked an impairment of insulin signaling in hepg2 cells via a reduction in the expression of insr and irs-1 protein. the significant upregulation of mir-1271, which was presumed to target insr and irs-1 3'utrs, was observed in the palmitate-treated hepg2 cells. using a reporter gene assay, mir-1271 authentically targeted the 3'utrs of insr and irs-1. furthermore, the overexpression of mir-1271 caused a substantial decrease in insr and irs-1 expression, which led to an impairment in insulin signaling and glycogen metabolism. therefore, these findings suggest that the induction of mir-1271 by sfa palmitate promotes the development of insulin resistance by targeting insr and irs-1 in hepatocytes.",1
"in eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal rnas (rrnas) by small nucleolar rnas (snornas). we identified homologs of snorna genes in both branches of the archaea. eighteen small sno-like rnas (srnas) were cloned from the archaeon sulfolobus acidocaldarius by coimmunoprecipitation with archaeal fibrillarin and nop56, the homologs of eukaryotic snorna-associated proteins. we trained a probabilistic model on these srnas to search for more srnas in archaeal genomic sequences. over 200 additional srnas were identified in seven archaeal genomes representing both the crenarchaeota and the euryarchaeota. snorna-based rrna processing was therefore probably present in the last common ancestor of archaea and eukarya, predating the evolution of a morphologically distinct nucleolus.",1
"identification of primary microrna (mirna) gene targets is critical for developing mirna-based therapeutics and understanding their mechanisms of action. however, disentangling primary target derepression induced by mirna inhibition from secondary effects on the transcriptome remains a technical challenge. here, we utilized rna immunoprecipitation (rip) combined with competitive binding assays to identify novel primary targets of mir-122. these transcripts physically dissociate from ago2-mirna complexes when anti-mir is spiked into liver lysates. mrna target displacement strongly correlated with expression changes in these genes following in vivo anti-mir dosing, suggesting that derepression of these targets directly reflects changes in ago2 target occupancy. importantly, using a metric based on weighted mirna expression, we found that the most responsive mrna target candidates in both rip competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited mirnas. these data strongly suggest that mirna co-regulation modulates the transcriptomic response to anti-mir. we demonstrate the practical utility of this 'mir-target impact' model, and encourage its incorporation, together with the rip competition assay, into existing target prediction and validation pipelines.",1
"viroids are small non-coding parasitic rnas that are able to infect their host plants systemically. this circular naked rna makes use of host proteins to accomplish its proliferation. here we analyze the specific binding of the tomato protein virp1 to the terminal right domain of potato spindle tuber viroid rna (pstvd). we find that two asymmetric internal loops within the pstvd (+) rna, each composed of the sequence elements 5'-acagg and cucuucc-5', are responsible for the specific rna-protein interaction. in view of the nucleotide composition we call this structural element an 'ry motif'. the ry motif located close to the terminal right hairpin loop of the pstvd secondary structure has an approximately 5-fold stronger binding affinity than the more centrally located ry motif. simultaneous sequence alterations in both ry motifs abolished the specific binding to virp1. mutations in any of the two ry motifs resulted in non-infectious viroid rna, with the exception of one case, where reversion to sequence wild type took place. in contrast, the simultaneous exchange of two nucleotides within the terminal right hairpin loop of pstvd had only moderate influence on the binding to virp1. this variant was infectious and sequence changes were maintained in the progeny. the relevance of the phylogenetic conservation of the ry motif, and sequence elements therein, amongst various genera of the family pospiviroidae is discussed.",1
"the nf-κb/relish, as a core transcription factor of drosophila immune deficiency (imd) pathway, activates the transcriptions of antimicrobial peptides (amps) to combat gram-negative bacterial infections, but its role in regulating mirna expression during immune response has less been reported. we here describe a negative feedback loop of imd signaling mediated by relish/mir-275/dredd that controls drosophila immune homeostasis after escherichia coli (e. coli) infection. our results demonstrate that relish may directly activate the transcription of mir-275 via binding to its promoter in vitro and vivo, particularly mir-275 further inhibits the expression of dredd through binding to its 3'utr to negatively control drosophila imd immune response. remarkably, the ectopic expression of mir-275 significantly reduces drosophila lifespan. more importantly, our work uncovers a new mechanism by which relish can flexibly switch its role to maintain drosophila immune response and homeostasis during infection. collectively, our study not only reveals the functional duality of relish in regulating immune response of drosophila imd pathway, but also provides a new insight into the maintenance of animal innate immune homeostasis.",1
"the ski protein is a transcriptional coregulator over-expressed in melanoma. experimentally induced down-regulation of ski inhibits melanoma cell growth in vitro and in vivo. micrornas (mirnas) negatively modulate gene expression and have been implicated in oncogenesis. we previously showed that microrna-155 (mir-155) is down-regulated in melanoma cells as compared with normal melanocytes and that its ectopic expression impairs proliferation and induces apoptosis. here, we investigated whether mir-155 could mediate melanoma growth inhibition via ski gene silencing. luciferase reporter assays demonstrated that mir-155 interacted with ski 3'utr and impaired gene expression. transfection of melanoma cells with mir-155 reduced ski levels, while inhibition of endogenous mir-155 up-regulated ski expression. specifically designed small interfering rnas reduced ski expression and inhibited proliferation. however, melanoma cells over-expressing a 3'utr-deleted ski were still susceptible to the antiproliferative effect of mir-155. our data demonstrate for the first time that ski is a target of mir-155 in melanoma. however, impairment of ski expression is not the leading mechanism involved in the growth-suppressive effect of mir-155 found in this malignancy.",1
"silencing of ribosomal rna genes (rdna) requires binding of the chromatin remodelling complex norc to rna that is complementary to the rdna promoter. norc-associated rna (prna) folds into a conserved stem-loop structure that is required for nucleolar localization and rdna silencing. mutations that disrupt the stem-loop structure impair binding of tip5, the large subunit of norc, to prna and abolish targeting of norc to nucleoli. binding to prna results in a conformational change of tip5, as shown by enhanced sensitivity of tip5 towards trypsin digestion. our results indicate an rna-dependent mechanism that targets norc to chromatin and facilitates the interaction with co-repressors that promote heterochromatin formation and rdna silencing.",1
"the sterol regulatory element binding protein 2 (srebp-2) and the liver x receptor (lxr) control antagonistic transcriptional programs that stimulate cellular cholesterol uptake and synthesis, and cholesterol efflux, respectively. the clinical importance of srebp-2 is revealed in patients with hypercholesterolemia treated with statins, which reduce low-density lipoprotein (ldl) cholesterol levels by increasing hepatic expression of srebp-2 and its target, the ldl receptor. here we show that mir-33 is encoded within srebp-2 and that both mrnas are coexpressed. we also identify sequences in the 3' utr of abca1 and abcg1, sterol transporter genes both previously shown to be regulated by lxr, as targets for mir-33-mediated silencing. our data show that lxr-dependent cholesterol efflux to both apoai and serum is ameliorated by mir-33 overexpression and, conversely, stimulated by mir-33 silencing. finally, we show that abca1 mrna and protein and plasma hdl levels decline after hepatic overexpression of mir-33, whereas they increase after hepatic mir-33 silencing. these results suggest novel ways to manage hypercholesterolemic patients.",1
"most eukaryotic mrnas depend upon precise removal of introns by the spliceosome, a complex of rnas and proteins. splicing of pre-mrna is known to take place in dictyostelium discoideum, and we previously isolated the u2 spliceosomal rna experimentally. in this study, we identified the remaining major spliceosomal rnas in dictyostelium by a bioinformatical approach. expression was verified from 17 small nuclear rna (snrna) genes. all these genes are preceded by a putative noncoding rna gene promoter. immunoprecipitation showed that snrnas u1, u2, u4, and u5, but not u6, carry the conserved trimethylated 5' cap structure. a number of divergent u2 species are expressed in dictyostelium. these rnas carry the u2 rna hallmark sequence and structure motifs but have an additional predicted stem-loop structure at the 5' end. surprisingly, and in contrast to the other spliceosomal rnas in this study, the new u2 variants were enriched in the cytoplasm and were developmentally regulated. furthermore, all of the snrnas could also be detected as polyadenylated species, and polyadenylated u1 rna was demonstrated to be located in the cytoplasm.",1
"autophagy is an evolutionarily conserved process responsible for degradation and recycling of cytoplasmic components through the lysosomal machinery. it has been proved to play pivotal roles in cellular homeostasis, cell growth and organism development. moreover, abnormalities of autophagy have been linked to numerous human pathophysiologies. emerging evidence has linked leucine deprivation induced protein breakdown to autophagy, but the underlying mechanisms controlling autophagic activity in this process are not fully understood. here, we demonstrate that two members of the mir-17 microrna family, mir-20a and mir-106b, may participate in regulating leucine deprivation induced autophagy via suppression of ulk1 expression in c2c12 myoblasts. we showed that leucine deprivation downregulated mir-20a and mir-106b expression via suppression of their transcription factor c-myc. we discovered the essential autophagy gene ulk1 as cellular target of mir-20a and mir-106b. treatment of c2c12 cells with the mir-20a or mir-106b mimic decreased the endogenous ulk1 protein levels. dual luciferase reporter assay confirmed that the mirna binding sequences in the 3' utr of ulk1 contribute to the modulation of ulk1 expression by mir-20a and mir-106b. furthermore, inhibition of ulk1 expression by the mir-20a or mir-106b mimic blunted activation of autophagy induced by leucine deprivation, while suppression of endogenous mir-20a or mir-106b by specific antagomir in c2c12 cells showed normal autophagic activity. altogether, our data demonstrated that mir-20a and mir-106b regulated autophagy induced by leucine deprivation in c2c12 cells via targeting ulk1.",1
"binding of p53 to mir-34a promoter activates the expression of tumor-suppressive mir-34a. oncogenic human papillomavirus (hpv) infection downregulates mir-34a expression through viral e6 degradation of p53. in our report, we found that mir-34a specifically targets p18ink4c, a cdk4 and cdk6 inhibitor induced by e2f transactivation. hpv18(+) hela cells with ectopic mir-34a expression or by e6 sirna knockdown-induced expression of endogenous mir-34a exhibited a substantial reduction of p18ink4c in a dose-dependent manner, but had no effect on p16ink4a, another member of cdk4/6 inhibitor family. in contrast, de novo infection by oncogenic hpvs of human keratinocyte-derived raft tissues increased p18ink4c expression. suppression of endogenous mir-34a in cell lines with a mir-34a inhibitor also increased p18ink4c. we found that mir-34a suppresses the expression of p18ink4c by binding to a specific seed match in the 5' utr of p18ink4c. further investigation found remarkable increase of p18ink4c in cervical precancer lesions and cervical cancer. immunohistochemical staining of cervical tissue arrays showed increased expression of p18ink4c in 68% of cervical cancer, 8.3% of chronic cervical inflammation and 4.8% of normal cervix. although p18ink4c inhibits cell proliferation in general and regulates e2f1 expression in hct116 cells, it appears not to function as a tumor suppressor in cervical cancer cells lacking an intact g1 checkpoint because of viral e7 degradation of prb. in summary, our study demonstrates an intimate connection among oncogenic hpv e6, p53, mir-34a and p18ink4c and identifies p18ink4c as a possible biomarker for cervical cancer.",1
"dysregulated long noncoding rnas (lncrnas) have potential roles in various cancer types. the objective of this study was to investigate the expression and the underlying role of long intergenic nonprotein coding rna 115 (linc00115) in lung cancer. the relative expression of linc00115 and mir-607 in tumor tissues and cells was detected by real-time pcr. after overexpression or knockdown of linc00115 expression in tumor cells, the changes in the proliferation, migration, and invasion capacities were detected via counting kit-8 (cck-8) assay and transwell assays. the interplay among linc00115, mir-607, and integrin β1 (itgb1) was confirmed by bioinformatics analyses and luciferase reporter assay. in addition, tumor cells with linc00115 knockdown were injected into nude mice to investigate the effect of linc00115 on tumorigenesis in vivo. linc00115 was highly expressed in tumor tissues and cells. linc00115 promoted the malignant properties of tumor cells. investigation to its molecular mechanism revealed that linc00115 functioned as a competitive endogenous rna (cerna), regulating the expression of itgb1 by sponging mir-607 to affect tumor growth. the linc00115/mir-607/itgb1 signaling axis might be a novel therapeutic target in lung cancer.",1
"a novel 72 nt small nucleolar rna (snorna) called u87 was found in rat liver cells. this rna possesses the features of c/d box snorna family: boxes c, d', c', d, and 11 nt antisense element complementary to 28s ribosomal rna (rrna). the vast majority of c/d box snornas direct site-specific 2'-o-ribose methylation of rrnas. u87 rna is suggested to be involved in 2'-o-methylation of a g(3468) residue in 28s rrna. u87 rna was detected in different mammalian species with slight length variability. rat and mouse u87 rna gene was characterized. unlike the majority of c/d box snornas u87 rna lacks the terminal stem required for snorna processing. however, u87 gene is flanked by 7 bp inverted repeats potentially able to form a terminal stem in u87 rna precursor.",1
"mrp rna is a noncoding rna component of rnase mitochondrial rna processing (mrp), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal rna processing, mitochondrial dna replication, and cell cycle regulation. a recent study predicted a potential drosophila ortholog of mrp rna (cr33682) by computer-based genome analysis. we have confirmed the expression of this gene and characterized the phenotype associated with this locus. flies with mutations that specifically affect mrp rna show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. we present several lines of evidence demonstrating a role for drosophila mrp rna in rrna processing. the nuclear fraction of drosophila mrp rna localizes to the nucleolus. further, a mutant strain shows defects in rrna processing that include a defect in 5.8s rrna processing, typical of mrp rna mutants in other species, as well as defects in early stages of rrna processing.",1
"the biological mechanism of a recent discovered association of type 2 diabetes with the acaa-insertion/deletion polymorphism at the 3'utr of the igf2r gene has remained unclear. a very recently emerging novel polymorphic control layer by micrornas (mirnas) makes it possible to elucidate this issue. in this study, a prediction by web tools microinspector and miranda demonstrated that dna sequence polymorphism (dsps) acaa-insertion/deletion in igf2r 3'utr is located within the hsa-mir-657 and hsa-mir-453 binding sites. and luciferase reporter assay revealed that hsa-mir-657 acts directly at the 3'utr of the igf2r. furthermore, acaa-deletion exerted a further repression compared with acaa-insertion, indicating that hsa-mir-657 regulates igf2r gene expression in a polymorphic control manner. importantly, we also demonstrated that hsa-mir-657 can translationally regulate the igf2r expression levels in hep g2 cells. thus, our findings testify the possibility that the acaa-insertion/deletion polymorphism may result in the change of igf2r expression levels at least in part by hsa-mir-657-mediated regulation, contributing to the elucidation for the pathogenesis of type 2 diabetes and raise the possibility that mirnas or in combination with functional dna sequence polymorphism may be valuable in the treatment of human type 2 diabetes.",1
"micrornas can have subtle and combinatorial effects on the levels of the targets and pathways they act on. studying the consequences of a single microrna knockout often proves difficult as many such knockouts exhibit phenotypes only under stress conditions. this has often led to the hypothesis that micrornas buffer the effects of intrinsic and environmental stochasticity on gene expression. observing and understanding this buffering effect entails quantitative analysis of microrna and target expression in single cells. to this end, we have employed single-molecule fluorescence in situ hybridization, immunofluorescence, and high-resolution confocal microscopy to investigate the effects of mir-9a loss on the expression of the serine-protease rhomboid in drosophila melanogaster early embryos. our single-cell quantitative approach shows that spatially, the rhomboid mrna pattern is identical in wt and mir-9a knockout embryos. however, we find that the number of mrna molecules per cell is higher when mir-9a is absent, and the level and temporal accumulation of rhomboid protein shows a more dramatic increase in the mir-9a knockout. specifically, we see accumulation of rhomboid protein in mir-9a mutants by stage 5, much earlier than in wt. the data, therefore, show that mir-9a functions in the regulation of rhomboid mrna and protein levels. while further work is required to establish whether rhomboid is a direct target of mir-9 in drosophila, our results further establish the mir-9 family micrornas as conserved regulators of timing in neurogenic processes. this study shows the power of single-cell quantification as an experimental tool to study phenotypic consequences of microrna mis-regulation.",1
"ribosomal subunits are assembled on a precursor rrna that includes four spacers in addition to mature rrna sequences. the 5' external transcribed spacer (5' ets) is the most prominent one that recruits u3 snorna and a plethora of proteins during the early assembly of 90s small subunit preribosomes. here, we have conducted a comprehensive mutational analysis of 5' ets by monitoring the processing and assembly of a plasmid-expressed pre-18s rna. remarkably, nearly half of the 5' ets sequences, when depleted individually, are dispensable for 18s rrna processing. the dispensable elements largely bind at the surface of the 90s structure. defective assembly of 5' ets completely blocks the last stage of 90s formation yet has little effect on the early assembly of 5' and central domains of 18s rrna. our study reveals the functional regions of 5' ets and provides new insight into the assembly hierarchy of 90s preribosomes.",1
"micrornas (mirnas) are small noncoding rnas that regulate gene expression through imperfect base pairing with the 3' untranslated region (3'utr) of target mrna. we studied the regulation of alpha 1 (i) collagen (col1a1) expression by mirnas in human stellate cells, which are involved in liver fibrogenesis. among mir-29b, -143, and -218, whose expressions were altered in response to transforming growth factor-beta1 or interferon-alpha stimulation, mir-29b was the most effective suppressor of type i collagen at the mrna and protein level via its direct binding to col1a1 3'utr. mir-29b also had an effect on sp1 expression. these results suggested that mir-29b is involved in the regulation of type i collagen expression by interferon-alpha in hepatic stellate cells. it is anticipated that mir-29b will be used for the regulation of stellate cell activation and lead to antifibrotic therapy.",1
"the genetic networks controlling stem cell identity are the focus of intense interest, due to their obvious therapeutic potential as well as exceptional relevance to models of early development. genome-wide mapping of transcriptional networks in mouse embryonic stem cells (mescs) reveals that many endogenous noncoding rna molecules, including long noncoding rnas (lncrnas), may play a role in controlling the pluripotent state. we performed a genome-wide screen that combined full-length mesc transcriptome genomic mapping data with chromatin immunoprecipitation genomic location maps of the key mesc transcription factors oct4 and nanog. we henceforth identified four mesc-expressed, conserved lncrna-encoding genes residing proximally to active genomic binding sites of oct4 and nanog. accordingly, these four genes have potential roles in pluripotency. we show that two of these lncrnas, ak028326 (oct4-activated) and ak141205 (nanog-repressed), are direct targets of oct4 and nanog. most importantly, we demonstrate that these lncrnas are not merely controlled by mesc transcription factors, but that they themselves regulate developmental state: knockdown and overexpression of these transcripts lead to robust changes in oct4 and nanog mrna levels, in addition to alterations in cellular lineage-specific gene expression and in the pluripotency of mescs. we further characterize ak028326 as a co-activator of oct4 in a regulatory feedback loop. these results for the first time implicate lncrnas in the modulation of mesc pluripotency and expand the established mesc regulatory network model to include functional lncrnas directly controlled by key mesc transcription factors.",1
"context placental angiogenesis contributes to the pathogenesis of preeclampsia (pe) that affects 5-8% of all human pregnancies. microrna (mirna) are a class of noncoding 21- to 25-nucleotide rna that negatively regulate gene expression posttranscriptionly. objective the aim of this study was to test the hypothesis that mirna are differentially expressed in healthy term and pe placentas and a subclass of angiogenesis-associated mirna are increased by pe. design total mirna were extracted from villous placental tissues from healthy term and severe preeclamptic pregnancies. differential mirna expression was analyzed by microarray and real-time quantitative pcr. angiogenesis-associated mirna were analyzed by target prediction databases. in situ hybridization was used to localize mirna. target verification was performed by transfection of mirna precursors or antagomirs into endothelial and bewo cells and luciferase reporter assays. results three highly expressed mirna (mir-17, -20a, and -20b) were found significantly increased in pe compared with healthy term placentas (n = 10 per group). they target on the same group of genes important for angiogenesis. mir-20b was expressed primarily in villous syncytiotrophoblasts in term placenta. overexpression or inhibition of mir-20b differentially regulated mrna expression of those genes in endothelial vs. trophoblast cells. luciferase reporter assay showed that mir-20b targets ephb4 and ephrin-b2 that have been shown to be critical for early human placental development. placental ephrin-b2 mrna was significantly down-regulated in pe compared with normotensive pregnancies. conclusion mir-17, mir-20a, and mir-20b are differentially regulated in human placentas by pe. they regulate ephb4 and ephrin-b2 expression in trophoblast and endothelial cells via the same ""seed"" sequence, suggesting their roles in early placental development.",1
"lung cancer is the leading cause of cancer mortality in the world today. although some advances in lung cancer therapy have been made, patient survival is still poor. micrornas (mirnas) can act as oncogenes or tumor-suppressor genes in human malignancy. the mir-34 family consists of tumor-suppressive mirnas, and its reduced expression has been reported in various cancers, including non-small cell lung cancer (nsclc). in this study, we found that mir-34a and mir-34c target platelet-derived growth factor receptor alpha and beta (pdgfr-α and pdgfr-β), cell surface tyrosine kinase receptors that induce proliferation, migration and invasion in cancer. mir-34a and mir-34c were downregulated in lung tumors compared to normal tissues. moreover, we identified an inverse correlation between pdgfr-α/β and mir-34a/c expression in lung tumor samples. finally, mir-34a/c overexpression or downregulation of pdgfr-α/β by sirnas, strongly augmented the response to tnf-related apoptosis inducing ligand (trail) while reducing migratory and invasive capacity of nsclc cells.",1
"aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, dictyostelium discoideum however, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of amoebozoa are unicellular. previously, a novel type of noncoding rna, class i rnas, was identified in d. discoideum and shown to be important for normal multicellular development. here, we investigated class i rna evolution and its connection to multicellular development. we identified a large number of new class i rna genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. multiple genes were predicted in representatives of each major group of dictyostelia and expression analysis confirmed that our search approach identifies expressed class i rna genes with high accuracy and sensitivity and that the rnas are developmentally regulated. further studies showed that class i rnas are ubiquitous in dictyostelia and share highly conserved structure and sequence motifs. in addition, class i rna genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. our results show that class i rna is an ancient class of ncrnas, likely to have been present in the last common ancestor of dictyostelia dating back at least 600 million years. based on previous functional analyses and the presented evolutionary investigation, we hypothesize that class i rnas were involved in evolution of multicellularity in dictyostelia.",1
"background micrornas (mirnas) contribute to tumorigenesis by acting as either oncogenes or tumor suppressor genes. in this study, we investigated the role of mir-145 in the pathogenesis of uveal melanoma. methods expression profiles of mirnas in uveal melanoma were performed using agilent mirna array. quantitative real-time polymerase chain reaction was used to screen the expression levels of mir-145 in normal uveal tissue, uveal melanoma tissue, and uveal melanoma cell lines. lenti-virus expression system was used to construct mum-2b and ocm-1 cell lines with stable overexpression of mir-145. cell proliferation, cell cycle, and cell apoptosis of these mir-145 overexpression cell lines were examined by mtt assay and flow cytometry respectively. the target genes of mir-145 were predicted by bioinformatics and confirmed using a luciferase reporter assay. the expression of insulin-like growth factor-1 receptor (igf-1r), insulin receptor substrate-1 (irs-1) proteins was determined by western blotting analysis. irs-1 was knocked down in ocm-1 cells. tunel, brdu, and flow cytometry assay were performed in irs-1 knocked down ocm-1 cell lines to analyze its function. results forty-seven mirnas were up regulated in uveal melanoma and 61 were down regulated. mir-145 expression was significantly lower in uveal melanoma sample and the cell lines were compared with normal uveal sample. overexpression of mir-145 suppressed cell proliferation by blocking the g1 phase entering s phase in uveal melanoma cells, and promoted uveal melanoma cell apoptosis. irs-1 was identified as a potential target of mir-145 by dual luciferase reporter assay. knocking down of irs-1 had similar effect as overexpression of mir-145. conclusion mir-145 might act as a tumor suppressor in uveal melanoma, and downregulation of the target irs-1 might be a potential mechanism.",1
"the importance of dysregulation of microrna (mirna) expression in nonalcoholic steatohepatitis (nash) has been increasingly recognized; however, the association between altered expression of mirnas and pathophysiological features of nash and whether there is a connection between susceptibility to nash and altered expression of mirnas are largely unknown. in this study, male inbred c57bl/6j and dba/2j mice were fed a lipogenic methyl-deficient diet that causes liver injury similar to human nash, and the expression of mirnas and the level of proteins targeted by these mirnas in the livers were determined. administration of the methyl-deficient diet triggered nash-specific changes in the livers of c57bl/6j and dba/2j mice, with the magnitude being more severe in dba/2j mice. this was evidenced by a greater extent of expression of fibrosis-related genes in the livers of methyl-deficient dba/2j mice. the development of nash was accompanied by prominent changes in the expression of mirnas, including mir-29c, mir-34a, mir-155, and mir-200b. interestingly, changes in the expression of these mirnas and protein levels of their targets, including cebp-β, socs 1, zeb-1, and e-cadherin, in the livers of dba/2j mice fed a methyl-deficient diet were more pronounced as compared with those in c57bl/6j mice. these results show that alterations in the expression of mirnas are a prominent event during development of nash induced by methyl deficiency and strongly suggest that severity of nash and susceptibility to nash may be determined by variations in mirna expression response. more important, our data provide a mechanistic link between alterations in mirna expression and pathophysiological and pathomorphological features of nash.",1
"micrornas (mirnas) pair with target sequences in the 3' untranslated region of mrnas to posttranscriptionally repress gene expression. in this study, we report that tnf-mediated induction of endothelial adhesion molecules can be regulated by mirnas that are induced by tnf. specifically, e-selectin and icam-1 are targets of tnf-induced mirnas mir-31 and mir-17-3p, respectively. specific antagonism of these tnf-induced mirnas increased neutrophil adhesion to cultured endothelial cells. conversely, transfections with mimics of these mirnas decreased neutrophil adhesion to endothelial cells. these data suggest that mirnas provide negative feedback control of inflammation.",1
"malat1 is a long noncoding rna known to be misregulated in many human cancers. we have identified a highly conserved small rna of 61 nucleotides originating from the malat1 locus that is broadly expressed in human tissues. although the long malat1 transcript localizes to nuclear speckles, the small rna is found exclusively in the cytoplasm. rnase p cleaves the nascent malat1 transcript downstream of a genomically encoded poly(a)-rich tract to simultaneously generate the 3' end of the mature malat1 transcript and the 5' end of the small rna. enzymes involved in trna biogenesis then further process the small rna, consistent with its adoption of a trna-like structure. our findings reveal a 3' end processing mechanism by which a single gene locus can yield both a stable nuclear-retained noncoding rna with a short poly(a) tail-like moiety and a small trna-like cytoplasmic rna.",1
"micrornas (mirnas) are a class of naturally occurring small non-coding rnas that target protein-coding mrnas at the post-transcriptional level. our previous studies suggest that mir-21 functions as an oncogene and has a role in tumorigenesis, in part through regulation of the tumor suppressor gene tropomyosin 1 (tpm1). given that tpm1 has been implicated in cell migration, in this study we further investigated the role of mir-21 in cell invasion and tumor metastasis. we found that suppression of mir-21 in metastatic breast cancer mda-mb-231 cells significantly reduced invasion and lung metastasis. consistent with this, ectopic expression of tpm1 remarkably reduced cell invasion. furthermore, we identified two additional direct mir-21 targets, programmed cell death 4 (pdcd4) and maspin, both of which have been implicated in invasion and metastasis. like tpm1, pdcd4 and maspin also reduced invasiveness of mda-mb-231 cells. finally, the expression of pdcd4 and maspin inversely correlated with mir-21 expression in human breast tumor specimens, indicating the potential regulation of pdcd4 and maspin by mir-21 in these tumors. taken together, the results suggest that, as an oncogenic mirna, mir-21 has a role not only in tumor growth but also in invasion and tumor metastasis by targeting multiple tumor/metastasis suppressor genes. therefore, suppression of mir-21 may provide a novel approach for the treatment of advanced cancers.",1
"background accumulating evidence showed that micrornas are involved in development and progression of multiple tumors. recent studies have found that mir-181a were dysregulated in several types of cancers, however, the function of mir-181a in hepatocellular carcinoma (hcc) remains unclear. in this study we assessed the potential association between mir-181a, hbv and hcc. methods the expression of mir-181a in hbv-expressing cells was determined by using qrt-pcr. dual-luciferase reporter assay, qrt-pcr and western blot were performed to investigate the target genes of mir-181a. the effects of mir-181a on hcc proliferation were analyzed by mts and colony formation assay. tumor growth assay was used to analyze the effect of mir-181a on tumor formation. results hbv up-regulated mir-181a expression by enhancing its promoter activity. overexpression of mir-181a in hepatoma cells promoted cell growth in vitro and tumor formation in vivo. conversely, inhibition of mir-181a suppressed the proliferation of hbv-expressing cells. mechanism investigation revealed that mir-181a inhibited the expression of transcription factor e2f5 by specifically targeting its mrna 3'utr. moreover, e2f5 inhibition induced cell growth and rescued the suppressive effect of mir-181a inhibitor on the proliferation of smmc-7721 cells. interestingly, we also discovered that hbv could down-regulate e2f5 expression. conclusions those results strongly suggested that hbv down-regulated e2f5 expression, in part, by up-regulating the expression of mir-181a. up-regulation of mir-181a by hbv in hepatoma cells may contribute to the progression of hcc possibly by targeting e2f5, suggesting mir-181a plays important role in hcc development.",1
"in the recent decades, carotid angioplasty and stenting (cas) has been developed into a credible option for the patients with carotid stenosis. however, restenosis remains a severe and unsolved issue after cas treatment. restenosis is characterized by neointimal hyperplasia, which is partially caused by vascular smooth muscle cells (vsmc) proliferation. however, the molecular mechanism involved in the restenosis is still unclear. in this study, we demonstrated a functional crosstalk between two tgf-β superfamily signaling pathway members, smad3 and bmpr2, in vsmc proliferation. smad3 plays an important role in the tgf-β/smad3 signaling pathway, and is significantly upregulated in the carotid artery with restenosis to promote vsmc proliferation. in contrast, bmp receptor ii (bmpr2), an inhibitor of vsmc proliferation is downregulated in carotid restenosis. we further found that bmpr2 downregulation is mediated by mir-17-92 cluster, which is transcriptionally regulated by smad3. thus, smad3 upregulation and smad3/mir-17-92 cluster-dependent bmpr2 downregulation are likely to promote vsmc proliferation and restenosis. taken together, our results may provide novel clues for early diagnosis of carotid restenosis and developing new therapeutic strategy.",1
"micrornas (mirnas), which are short (22-24 base pairs), non-coding rnas, play critical roles in myogenesis. using solexa deep sequencing, we detected the expression levels of 229 and 209 mirnas in swine skeletal muscle at 90 days post-coitus (e90) and 100 days postnatal (d100), respectively. a total of 138 mirnas were up-regulated on e90, and 31 were up-regulated on d100. of these, 9 mirnas were selected for the validation of the small rna libraries by quantitative rt-pcr (rt-qpcr). we found that mirna-21 was down-regulated by 17-fold on d100 (p<0.001). bioinformatics analysis suggested that the transforming growth factor beta-induced (tgfβi) gene was a potential target of mirna-21. both dual luciferase reporter assays and western blotting demonstrated that the tgfβi gene was regulated by mirna-21. co-expression analysis revealed that the mrna expression levels of mirna-21 and tgfβi were negatively correlated (r = -0.421, p = 0.026) in skeletal muscle during the 28 developmental stages. our results revealed that more mirnas are expressed in prenatal than in postnatal skeletal muscle. the mirna-21 is a novel myogenic mirna that is involved in skeletal muscle development and regulates pi3k/akt/mtor signaling by targeting the tgfβi gene.",1
"oxidative stress, defined as an excess production of reactive oxygen species (ros), is shown to play an important role in the pathophysiology of cardiac remodeling including cell death and contractile dysfunction. therefore, the balance between ros production and removal of excess ros is essential in maintaining the redox state and homeostasis balance in the cell. the increased ros further activates nuclear factor-κb (nf-κb), a redox-sensitive transcription factor and promotes cell death. recently, micrornas (mirnas) have been identified as critical regulators of various pathophysiological processes of cardiac remodeling; however, nf-κb-mediated mirna's role in cardiomyocytes under oxidative stress remains undetermined. the mir-21 has been implicated in diverse cardiac remodeling; but, nf-κb-mediated mir-21 modulation in oxidative stress is currently unknown. neonatal cardiomyocytes were transfected with iκbα mutant, mir-21 mimetic, and inhibitors separately, and were challenged with h2o2. the target gene, programmed cell death 4 (pdcd4), ros activity, and nf-κb translocation were analyzed. our results indicated that nf-κb positively regulated mir-21 expression under oxidative stress, and pdcd4 was a direct target for mir-21. nf-κb further regulated the expression of pdcd4 in h2o2-induced oxidative stress. moreover, h2o2-induced ros activity and cardiomyocytes apoptosis were partly protected by overexpression of mir-21 and displayed an important role in ros-mediated cardiomyocytes injury. we evaluated a critical role of nf-κb-mediated mir-21 modulation in h2o2-induced oxidative stress in cardiomyocytes by targeting pdcd4. our data may provide a new insight of mir-21's role in cardiac diseases primarily mediated by ros.",1
"using highly sensitive microarray-based procedures, we identified eight micrornas (mirnas) showing robust differential expression between 31 laser-capture-microdissected nasopharyngeal carcinomas (npcs) and 10 normal healthy nasopharyngeal epithelial samples. in particular, mirna mir-29c was expressed at one-fifth the levels in tumors as in normal epithelium. in npc tumors, the lower mir-29c levels correlated with higher levels of multiple mrnas whose 3' utrs can bind mir-29c at target sequences conserved across many vertebrates. in cultured cells, introduction of mir-29c down-regulated these genes at the level of mrna and inhibited expression of luciferase encoded by vectors having the 3' utrs of these genes. moreover, for each of several genes tested, mutating the mir-29c target sites in the 3' utr abrogated mir-29c-induced inhibition of luciferase expression. most of the mir-29c-targeted genes identified encode extracellular matrix proteins, including multiple collagens and laminin gamma1, that are associated with tumor cell invasiveness and metastatic potential, prominent characteristics of npc. thus, we identify eight mirnas differentially expressed in npc and demonstrate the involvement of one in regulating genes involved in metastasis.",1
"the role of tumor-proximal factors in tumor plasticity during chemoresistance and metastasis following chemotherapy is well studied. however, the role of endothelial cell (ec) derived paracrine factors in tumor plasticity, their effect on chemotherapeutic outcome, and the mechanism by which these paracrine factors modulate the tumor microenvironment are not well understood. in this study, we report a novel mechanism by which endothelial mir-125a and let-7e-mediated regulation of interleukin-6 (il-6) signaling can manipulate vasculogenic mimicry (vm) formation of mda-mb-231 breast cancer cells. we found that endothelial il-6 levels were significantly higher in response to cisplatin treatment, whereas levels of il-6 upon cisplatin exposure remained unchanged in mda-mb-231 breast cancer cells. we additionally found an inverse correlation between il-6 and mir-125a/let-7e expression levels in cisplatin treated ecs. interestingly, il-6, il-6 receptor (il-6r), and signal transducer and activator of transcription 3 (stat3) genes in the il-6 pathway are closely regulated by mir-125a and let-7e, which directly target its 3' untranslated region. functional analyses revealed that endothelial mir-125a and let-7e inhibit il-6-induced adhesion of monocytes to ecs. furthermore, conditioned medium from cisplatin treated ecs induced a significantly higher formation of vm in mda-mb-231 breast cancer cells as compared to that from intact ecs; this effect of cisplatin treatment was abrogated by concurrent overexpression of mir-125a and let-7e. overall, this study reveals a novel ec-tumor cell crosstalk mediated by the endothelial mir-125a/let-7e-il-6 signaling axis, which might improve chemosensitivity and provide potential therapeutic targets for the treatment of cancer. .",1
"background results from dna microarray experiments have shown that the expression of mir-34s undergoes significant changes following spinal cord injury (sci). the present study was designed to detect changes in the expression of mir-34s and its target genes during the acute and sub-acute stages of sci. material and methods luxol fast blue (lfb) staining for myelin was used to observe the differences in the general morphology of the spinal cord after sci in a contusion model in rats. qpcr was carried out to determine the expression variation of mir-34s and its target genes during the acute and sub-acute stages of sci. the mimic technique was used to further confirm the regulatory effect of mir-34a on the potential target genes. results the expression level of mir-34a decreased immediately after sci and persisted for 21 days after sci. the expression level of mir-34c began decreasing at day 1 after sci and persisted until day 14. the expression level of mir-34b did not undergo significant change after sci. the results of double immunofluorescence and in-situ hybridization suggested that mir-34a was highly expressed in spinal cord neurons. based on our bioinformatics analysis, we postulated that mir-34a might participate in post-sci cell apoptosis by regulating the target gene notch1, and likely participated in the inflammatory response and glial scar formation by regulating the candidate genes csf1r and pdgfra, respectively. the expression levels of the candidate genes csf1r and pdgfra were consistent with notch1 after sci. the mimic technique further confirmed the regulatory effect of mir-34a on the aforementioned target genes. conclusions we postulate that mir-34a and mir-34c might participate in multiple aspects of cytobiological activities following sci. mir-34a in particular may participate in cell apoptosis, inflammatory response, and glial scar formation by regulating the target gene notch1 and candidate target genes csf1r and pdgfra respectively.",1
"the signaling environment, or niche, often governs the initial difference in behavior of an adult stem cell and a derivative that initiates a path towards differentiation. the transition between an instructive stem cell niche and differentiation niche must generally have single-cell resolution, suggesting that multiple mechanisms might be necessary to sharpen the transition. here, we examined the drosophila ovary and found that cap cells, which are key constituents of the germline stem cell (gsc) niche, express a conserved microrna (mir-124). surprisingly, loss of mir-124 activity in cap cells leads to a defect in differentiation of gsc derivatives. we present evidence that the direct functional target of mir-124 in cap cells is the epidermal growth factor receptor (egfr) and that failure to limit egfr expression leads to the ectopic expression of a key anti-differentiation bmp signal in neighboring somatic escort cells (ecs), which constitute a differentiation niche. we further found that notch signaling connects efgr activity in cap cells to bmp expression in ecs. we deduce that the stem cell niche communicates with the differentiation niche through a mechanism that begins with the selective expression of a specific microrna and culminates in the suppression of the major anti-differentiation signal in neighboring cells, with the functionally important overall role of sharpening the spatial distinction between self-renewal and differentiation environments.",1
"tissue growth has to be carefully controlled to generate well-functioning organs. micrornas are small non-coding rnas that modulate the activity of target genes and play a pivotal role in animal development. understanding the functions of micrornas in development requires the identification of their target genes. here, we find that mir-8 , a conserved microrna in the mir-200 family, controls tissue growth and homeostasis in the drosophila wing imaginal disc. upregulation of mir-8 causes the repression of yorkie , the effector of the hippo pathway in drosophila , and reduces tissue size. remarkably, co-expression of yorkie and mir-8 causes the formation of neoplastic tumors. we show that upregulation of mir-8 represses the growth inhibitor brinker , and depletion of brinker cooperates with yorkie in the formation of neoplastic tumors. hence, mir-8 modulates a positive growth regulator, yorkie , and a negative growth regulator, brinker deregulation of this network can result in the loss of tissue homeostasis and the formation of tumors.",1
"increasing evidence suggests that micrornas are involved in human carcinogenesis as tumor suppressors or oncogenes. a growing number of reports has shown that an interest has been sparked in aberrant microrna expression and how they can be used to treat human diseases, including cancer. however, their precise biological role remains largely unknown. in the present study, we aimed to identify micro-rna species involved in the regulation of tumor growth. by performing quantitative reverse transcription-polymerase chain reaction (rt-pcr) analysis, we demonstrated that mir-663 was downregulated in human gastric cancer cell lines unlike in normal cells. a transient introduction of mir-663 into the human gastric cancer cell lines bgc823 and snu5 induced morphology changes and suppression of proliferation of these cells. in addition, mir-663 alters the dna content and induces phenotypes of mitotic catastrophe in tumor cells. moreover, the liposome-mediated delivery of mir-663 suppressed the in vivo growth of the bgc823 and snu5 cells. western blot analyses performed after the introduction of mir-663 revealed upregulation of cyclin b following transfection with mir-663. our results provide evidence that downregulation of mir-663 in tumor cells may contribute to aberrant cell hyperplasia, leading to the development of gastric cancer. therefore, mir-663 might function as a potent suppressor of tumor growth.",1
"the genome of xanthomonas campestris pv. vesicatoria encodes a constitutively expressed small rna, which we designate ptarna1, ""plasmid transferred anti-sense rna"". it exhibits all hallmarks of a novel rna antitoxin that proliferates by frequent horizontal transfer. it shows an erratic phylogenetic distribution with occurrences on chromosomes in a few individual strains distributed across both beta- and gamma-proteobacteria. moreover, a homologous gene located on plasmid pmatvim-7 of pseudomonas aeruginosa is found. all ptarna1 homologs are located anti-sense to a putative toxin, which in turn is never encountered without the small rna. the secondary structure of ptarna1, furthermore, is very similar to that of the finp anti-sense rna found on f-like plasmids in escherichia coli.",1
"hepatic fam3a expression is repressed under obese conditions, but the underlying mechanism remains unknown. this study determined the role and mechanism of mir-423-5p in hepatic glucose and lipid metabolism by repressing fam3a expression. mir-423-5p expression was increased in the livers of obese diabetic mice and in patients with nonalcoholic fatty liver disease (nafld) with decreased fam3a expression. mir-423-5p directly targeted fam3a mrna to repress its expression and the fam3a-atp-akt pathway in cultured hepatocytes. hepatic mir-423-5p inhibition suppressed gluconeogenesis and improved insulin resistance, hyperglycemia, and fatty liver in obese diabetic mice. in contrast, hepatic mir-423-5p overexpression promoted gluconeogenesis and hyperglycemia and increased lipid deposition in normal mice. mir-423-5p inhibition activated the fam3a-atp-akt pathway and repressed gluconeogenic and lipogenic gene expression in diabetic mouse livers. the mir-423 precursor gene was further shown to be a target gene of nfe2, which induced mir-423-5p expression to repress the fam3a-atp-akt pathway in cultured hepatocytes. hepatic nfe2 overexpression upregulated mir-423-5p to repress the fam3a-atp-akt pathway, promoting gluconeogenesis and lipid deposition and causing hyperglycemia in normal mice. in conclusion, under the obese condition, activation of the hepatic nfe2/mir-423-5p axis plays important roles in the progression of type 2 diabetes and nafld by repressing the fam3a-atp-akt signaling pathway.",1
"to provide a bridge between in vivo and in vitro studies of eukaryotic translation initiation, we have developed a reconstituted translation initiation system using components from the yeast saccharomyces cerevisiae. we have purified a minimal set of initiation factors (elfs) that, together with yeast 80s ribosomes, gtp, and initiator methionyl-trna, are sufficient to assemble active initiation complexes on a minimal mrna template. the kinetics of various steps in the pathway of initiation complex assembly and the formation of the first peptide bond in vitro have been explored. the formation of active initiation complexes in this system is dependent on ribosomes, mrna, met-trnai, gtp hydrolysis, elf1, elf1a, elf2, elf5, and elf5b. our data indicate that elf1 and elf1a both facilitate the binding of the elf2 x gtp x met-trnai complex to the 40s ribosomal subunit to form the 43s complex. elf5 stimulates a step after 43s complex formation, consistent with its proposed role in activating gtp hydrolysis by elf2 upon initiation codon recognition. the presence of elf5b is required for the joining of the 40s and 60s subunits to form the 80s initiation complex. the step at which each of these factors acts in this reconstituted system is in agreement with previous data from in vivo studies and work using reconstituted mammalian systems, indicating that the system recapitulates fundamental events in translation initiation in eukaryotic cells. this system should allow us to couple powerful yeast genetic and molecular biological experiments with in vitro kinetic and biophysical experiments, yielding a better understanding of the molecular mechanics of this central, complex process.",1
"epithelial bicellular and tricellular junctions are essential for establishing and maintaining permeability barriers. tricellular junctions are formed by the convergence of three bicellular junctions at the corners of neighbouring epithelia. gliotactin, a member of the neuroligin family, is located at thedrosophilatricellular junction, and is crucial for the formation of tricellular and septate junctions, as well as permeability barrier function. gliotactin protein levels are tightly controlled by phosphorylation at tyrosine residues and endocytosis. blocking endocytosis or overexpressing gliotactin results in the spread of gliotactin from the tricellular junction, resulting in apoptosis, delamination and migration of epithelial cells. we show that gliotactin levels are also regulated at the mrna level by micro (mi)rna-mediated degradation and that mirnas are targeted to a short region in the 3'utr that includes a conserved mir-184 target site. mir-184 also targets a suite of septate junction proteins, including nrxiv, coracle and mcr. mir-184 expression is triggered when gliotactin is overexpressed, leading to activation of the bmp signalling pathway. gliotactin specifically interferes with dad, an inhibitory smad, leading to activation of the tkv type-i receptor and activation of mad to elevate the biogenesis and expression of mir-184.",1
"background micrornas (mirnas) are small, noncoding rnas that are believed to play fundamental roles in tumorigenesis and tumor development at the posttranscriptional level, as negative regulators of gene expression. this study was designed to evaluate the expression and anticancer effect of mir-519d in ovarian cancer. methods the expression levels of mir-519d in ovarian cancer cells and tissues were detected by taqman quantitative reverse transcriptase-polymerase chain reaction (taqman qrt-pcr; life technologies, carlsbad, ca, usa). the effects of mir-519d on ovarian cancer cell proliferation and cisplatin chemosensitivity were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide, flow cytometry, and western blotting assay. a luciferase reporter assay was performed to validate the mir-519d binding sites on the 3' untranslated region of x-linked inhibitor of apoptosis protein (xiap). the expression levels of xiap mrna and protein were examined by quantitative real-time polymerase chain reaction (qrt-pcr) and western blotting assay, respectively. results mir-519d was significantly downregulated in human ovarian cancer cell lines and tissues. overexpression of mir-519d in ovarian cancer cells decreased cell proliferation and sensitized ovarian cancer cells to cisplatin-induced cell death accompanied by increased activation of caspase 3 and cleavage of poly(adenosine diphosphate -ribose) polymerase 1. bioinformatics analysis indicated that xiap was a putative target of mir-519d. overexpression of mir-519d decreased xiap expression at both the protein and mrna levels. in contrast, inhibition of mir-519d increased xiap expression. luciferase reporter assay confirmed xiap as a direct target of mir-519d. xiap mrna and protein expression levels were inversely correlated with mir-519d expression in ovarian cancer cell lines and tissues. conclusion these findings indicate that mir-519d suppresses cell proliferation and sensitizes ovarian cancer cells to cisplatin-induced cell death by targeting the xiap transcript, suggesting that mir-519d plays a tumor-suppressive role in human ovarian cancer and highlighting the therapeutic potential of mir-519d in ovarian cancer treatment.",1
"micrornas (mirnas) are important regulators of biological processes, including host-virus interaction. this study investigated the involvement of drosophila melanogaster mir-8-5p in host-virus interaction. drosophila flies and cells challenged with drosophila c virus (dcv) were found to have lower mir-8-5p abundance compared to uninfected samples. lowering mir-8-5p abundance by experimental inhibition of the mirna led to an increase in viral accumulation, suggesting that the observed decrease in the mir-8-5p abundance during dcv infection enhances viral replication. mir-8-5p putative targets were identified and included djun, a transcription factor gene whose mammalian homologue cjun is induced by various viruses through kinase activation. increasing mir-8-5p abundance using mir-8-5p mimics resulted in a decrease in djun and gfp reporter levels. furthermore, when the putative target in djun was mutated, addition of mir-8-5p mimics did not result in the same antagonistic effect on djun. these results show negative regulation of djun by mir-8-5p and suggest that an mirna-mediated pathway is involved in djun regulation during viral infection. to analyse the role of djun during dcv infection, djun was knocked down in cells prior to dcv infection. knockdown of djun decreased dcv replication, providing evidence that djun up-regulation that is concomitant with mir-8-5p down-regulation during dcv infection supports viral replication. these results highlight the role of mirna in regulating the transcription factor gene djun and uncover a previously unrecognized mechanism by which djun is regulated during host-virus interaction.",1
"hundreds of micrornas (mirnas) are expressed in mammalian cells, where they aid in modulating gene expression by mediating mrna transcript cleavage and/or regulation of translation rate. functional studies to date have demonstrated that several of these mirnas are important during development. however, the role of mirnas in the regulation of stem cell growth and differentiation is not well understood. we show herein that microrna (mir)-134 levels are maximally elevated at day 4 after retinoic acid-induced differentiation or day 2 after n2b27-induced differentiation of mouse embryonic stem cells (mescs), but this change is not observed during embryoid body differentiation. the elevation of mir-134 levels alone in mescs enhances differentiation toward ectodermal lineages, an effect that is blocked by a mir-134 antagonist. the promotion of mesc differentiation by mir-134 is due, in part, to its direct translational attenuation of nanog and lrh1, both of which are known positive regulators of oct4/pou5f1 and mesc growth. together, the data demonstrate that mir-134 alone can enhance the differentiation of mescs to ectodermal lineages and establish a functional role for mir-134 in modulating mesc differentiation through its potential to target and regulate multiple mrnas.",1
"micrornas have emerged as regulators of smooth muscle cell phenotype with a role in smooth muscle-related disease. studies have shown that mir-143 and mir-145 are the most highly expressed micrornas in smooth muscle cells, controlling differentiation and function. the effect of mir-143/145 knockout has been established in the vasculature but not in smooth muscle from other organs. using knockout mice we found that maximal contraction induced by either depolarization or phosphatase inhibition was reduced in vascular and airway smooth muscle but maintained in the urinary bladder. furthermore, a reduction of media thickness and reduced expression of differentiation markers was seen in the aorta but not in the bladder. supporting the view that phenotype switching depends on a tissue-specific target of mir-143/145, we found induction of angiotensin-converting enzyme in the aorta but not in the bladder where angiotensin-converting enzyme was expressed at a low level. chronic treatment with angiotensin type-1 receptor antagonist restored contractility in mir-143/145-deficient aorta while leaving bladder contractility unaffected. this shows that tissue-specific targets are critical for the effects of mir-143/145 on smooth muscle differentiation and that angiotensin converting enzyme is one such target.",1
"specificity of interaction between a microrna (mirna) and its targets crucially depends on the seed region located in its 5'-end. it is often implicitly considered that two mirnas sharing the same biological activity should display similarity beyond the strict six nucleotide region that forms the seed, in order to form specific complexes with the same mrna targets. we have found that expression of hsa-mir-147b and hsa-mir-210, though triggered by different stimuli (i.e. lipopolysaccharides and hypoxia, respectively), induce very similar cellular effects in term of proliferation, migration and apoptosis. hsa-mir-147b only shares a ""minimal"" 6-nucleotides seed sequence with hsa-mir-210, but is identical with hsa-mir-147a over 20 nucleotides, except for one base located in the seed region. phenotypic changes induced after heterologous expression of mir-147a strikingly differ from those induced by mir-147b or mir-210. in particular, mir-147a behaves as a potent inhibitor of cell proliferation and migration. these data fit well with the gene expression profiles observed for mir-147b and mir-210, which are very similar, and the gene expression profile of mir-147a, which is distinct from the two others. bioinformatics analysis of all human mirna sequences indicates multiple cases of mirnas from distinct families exhibiting the same kind of similarity that would need to be further characterized in terms of putative functional redundancy. besides, it implies that functional impact of some mirnas can be masked by robust expression of mirnas belonging to distinct families.",1
"the placenta is thought to have a critical role in the pathogenesis of gestational diabetes mellitus (gdm), as gdm‑associated complications resolve following delivery. placenta-specific micrornas (mirnas) may contribute to the pathology of the development of gdm. the aim of the present study was to evaluate whether the placenta-specific mir-518d contributes to the development of gdm. it was revealed that mir-518d expression was higher in placentas taken from patients with gdm compared with control placentas, whereas the protein levels of the predicted mir-518d target gene, peroxisome proliferator-activated receptor-α (pparα), were lower in placentas from patients with gdm compared with those from control subjects. it was also demonstrated that pparα was a direct target of mir-518d with a specific binding site at the seed sequence, which determines target specificity. in the placentas of females with gdm increased levels of mir-518d were negatively correlated with the levels of pparα protein. as pparα dysregulation may be related to the development of gdm, it is suggested that upregulation of mir-518d may be associated with the pathogenesis of gdm via an effect on the regulation of pparα expression.",1
"the aberrant expression of micrornas (mirnas) has been found in various types of cancer. the present study found mir-20a to be significantly upregulated in prostate cancer compared with normal prostate tissues. the proliferation and colony formation assays revealed that the downregulation of mir-20a by mir-20a inhibitor suppresses the proliferation of mda-pca-2b cells in vitro and also inhibits tumor growth in vivo. furthermore, a gap junction protein, α 1 (cx43), was identified as a direct target gene of mir-20a. the upregulation of cx43 was detected in mda-pca-2b cells after treatment with mir-20a inhibitor both in vitro and in vivo. in conclusion, the findings show that mir-20a significantly contributes to the progression of prostate cancer by targeting cx43.",1
"aim: to explore the role of mirna-150-5p (mir-150-5p) in liver fibrosis. materials & methods: mirna expression profiles, ccl 4 -induced liver fibrosis progression and regression rodent models, quantitative real-time pcr, mir-150-5p mimics and inhibitors, cell proliferation and apoptosis detection, rna sequencing and bioinformatics analysis were employed. results: liver tissue mir-150-5p expression was positively associated with liver fibrosis progression and regression; however, mir-150-5p exhibited a cell-specific expression pattern, namely, it was enhanced in hepatocytes but reduced in hepatic stellate cells (hscs) during liver fibrosis; mir-150-5p overexpression promoted hsc apoptosis and sensitized hepatocyte apoptosis; mir-150-5p mimic had a larger influence on the transcriptomic stability of hscs than that of hepatocytes; mir-150-5p mediated activation of interferon signaling pathways might be responsible for hsc apoptosis. conclusion: mir-150-5p exhibited an opposite regulation and function pattern between hscs and hepatocytes during liver fibrosis.",1
"structured rna regions are important gene control elements in prokaryotes and eukaryotes. here, we show that the mrna of a cyanobacterial heat shock gene contains a built-in thermosensor critical for photosynthetic activity under stress conditions. the exceptionally short 5'-untranslated region is comprised of a single hairpin with an internal asymmetric loop. it inhibits translation of the synechocystis hsp17 transcript at normal growth conditions, permits translation initiation under stress conditions and shuts down hsp17 production in the recovery phase. point mutations that stabilized or destabilized the rna structure deregulated reporter gene expression in vivo and ribosome binding in vitro. introduction of such point mutations into the synechocystis genome produced severe phenotypic defects. reversible formation of the open and closed structure was beneficial for viability, integrity of the photosystem and oxygen evolution. continuous production of hsp17 was detrimental when the stress declined indicating that shutting-off heat shock protein production is an important, previously unrecognized function of rna thermometers. we discovered a simple biosensor that strictly adjusts the cellular level of a molecular chaperone to the physiological need.",1
"micrornas (mirnas) are small noncoding rnas involved in posttranscriptional gene regulation that have been shown to be involved in growth, development, function, and stress responses of various organs. the purpose of this study was to identify the mirna response to physical activity, which was related to functions such as nutrient metabolism, although the mirnas involved are currently unknown. c57bl/6 mice were divided into exercise and control groups. the exercise group performed running exercise, with a gradual increase of the load over 4 wk. on the other hand, to examine the effect of muscle inactivity, the unilateral hindlimbs of other mice were fixed in a cast for 5 days. microarray analysis for mirna in gastrocnemius revealed that mir-696 was markedly affected by both exercise and immobilization, showing opposite responses to these two interventions. peroxisome proliferator-activated receptor-gamma coactivator-1alpha (pgc-1alpha), which was increased by exercise and decreased by immobilization in the protein level, was predicted as a target regulated by mir-696. in cultured myocytes, intracellular mir-696 variation led to negative regulation of pgc-1alpha protein along with the expression of mrnas for downstream genes. in addition, we found decreases in the biogenesis of mitochondria and fatty acid oxidation in mir-696-overexpressing myocytes compared with normal control myocytes. these observations demonstrate that mir-696 is a physical activity-dependent mirna involved in the translational regulation of pgc-1alpha and skeletal muscle metabolism in mice.",1
"stable intronic sequence rnas (sisrnas) are by-products of splicing and regulate gene expression. how sisrnas are regulated is unclear. here we report that a double-stranded rna binding protein, disco-interacting protein 1 (dip1) regulates sisrnas in drosophila. dip1 negatively regulates the abundance of sisr-1 and ine-1 sisrnas. fine-tuning of sisr-1 by dip1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. drosophila dip1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of ine-1 transposable element sequences that are processed into sisrnas. dip1 presumably acts outside the satellite bodies to regulate sisr-1, which is not on the fourth chromosome. thus, our study identifies dip1 as a sisrna regulatory protein that controls germline stem cell self-renewal in drosophila.stable intronic sequence rnas (sisrnas) are by-products of splicing from introns with roles in embryonic development in drosophila. here, the authors show that the rna binding protein dip1 regulates sisrnas in drosophila, which is necessary for germline stem cell homeostasis.",1
"nuclei of higher organisms are well structured and have multiple, distinct nuclear compartments or nuclear bodies. paraspeckles are recently identified mammal-specific nuclear bodies ubiquitously found in most cells cultured in vitro. to investigate the physiological role of paraspeckles, we examined the in vivo expression patterns of two long noncoding rnas, neat1_1 and neat1_2, which are essential for the architectural integrity of nuclear bodies. unexpectedly, these genes were only strongly expressed in a particular subpopulation of cells in adult mouse tissues, and prominent paraspeckle formation was observed only in the cells highly expressing neat1_2. to further investigate the cellular functions of paraspeckles, we created an animal model lacking neat1 by gene targeting. these knockout mice were viable and fertile under laboratory growth conditions, showing no apparent phenotypes except for the disappearance of paraspeckles. we propose that paraspeckles are nonessential, subpopulation-specific nuclear bodies formed secondary to particular environmental triggers.",1
"micrornas (mirnas) control gene expression at the post-transcriptional level. however, the identification of mirnas regulating the fate of a specific messenger rna remains limited due to the imperfect complementarity of mirnas and targeted transcripts. here, we describe mitrap (mirna trapping by rna in vitro affinity purification), an advanced protocol of previously reported ms2-tethering approaches. mitrap allows the rapid identification of mirnas targeting an in vitro transcribed rna in cell lysates. selective co-purification of regulatory mirnas was confirmed for the myc- as well as zeb2-3'utr, two well-established mirna targets in vivo. combined with mirna-sequencing, mitrap identified in addition to mirnas reported to control myc expression, 18 novel candidates including not in silico predictable mirnas. the evaluation of 10 novel candidate mirnas confirmed 3'utr-dependent regulation of myc expression as well as putative non-canonical targeting sites for the not in silico predictable candidates. in conclusion, mitrap provides a rapid, cost-effective and easy-to-handle protocol allowing the identification of regulatory mirnas for rnas of choice in a cellular context of interest. most notably, mitrap not only identifies in silico predictable but also unpredictable mirnas regulating the expression of a specific target rna.",1
"epidermal growth factor receptors (egfr) expression is frequently amplified in human glioblastoma cells. nimotuzumab, a monoclonal antibody (mab) against egfr, has been used globally in clinics as an anti-cancer agent. it is largely unknown whether the blockade of mir-21, a microrna that is upregulated in glioma cells, could amplify the effects of nimotuzumab. herein, we have demonstrated that mir-21 directly targets von hippel-lindau (vhl) and peroxisome-proliferator-activated receptor α (pparα) and that mir-21 regulates egfr/akt signaling through vhl/β-catenin and the pparα/ap-1 axis. further, the expression of mir-21 is regulated by egfr via the activation of β-catenin and ap-1. these data indicate that a feedback loop exists between mir-21 and egfr. we also show that the combination of nimotuzumab and an inhibitor of mir-21 is superior to single-agent therapy. these results clarify a novel association between mir-21 and egfr in the regulation of cancer cell progression.",1
"we analyzed the leader region of human immunodeficiency virus type 1 (hiv-1) rna to decipher the nature of the cis-acting e/psi element required for encapsidation of viral rna into virus particles. our data indicate that, for rna encapsidation, there are at least two functional subregions in the leader region. one subregion is located at a position immediately proximal to the major splice donor, and the second is located between the splice donor and the beginning of the gag gene. this suggests that at least two discrete cis-acting elements are recognition signals for encapsidation. to determine whether specific putative rna secondary structures serve as the signal(s) for encapsidation, we constructed primary base substitution mutations that would be expected to destabilize these potential structures and second-site compensatory mutations that would restore secondary structure. analysis of these mutants allowed the identification of two discrete hairpins that facilitate rna encapsidation in vivo. thus, the hiv-1 e/psi region is a multipartite element composed of specific and functional rna secondary structures. compensation of the primary mutations by the second-site mutations could not be attained in trans. this indicates that interstrand base pairing between these two stem regions within the hairpins does not appear to be the basis for hiv-1 rna dimer formation. comparison of the hypothetical rna secondary structures from 10 replication-competent hiv-1 strains suggests that a subset of the hydrogen-bonded base pairs within the stems of the hairpins is likely to be required for function in cis.",1
"in the present study, the expression of microrna (mir)-365 and interleukin (il)-6 in peripheral blood mononuclear cells and serum from patients with sepsis following multiple trauma has been investigated. a total of 26 patients with sepsis following multiple trauma were included as the experimental group, whereas 21 contemporaneous patients without sepsis following multiple trauma were included as the negative control group. the expression of il-6 mrna and mir-365 was determined by reverse transcription-quantitative polymerase chain reaction, and western blot analysis was used to measure il-6 protein expression. elisa was performed to determine the secretion of il-6 protein. following stimulation with lipopolysaccharide (lps) for 24 h, thp-1 cells were used to examine the expression of mir-365 and the levels of il-6 protein and mrna in cells simulating sepsis. a dual luciferase reporter assay revealed that il-6 mrna was a direct target of mir-365. patients with sepsis following multiple trauma exhibited significantly higher il-6 mrna and protein levels than patients without sepsis (p<0.05). in addition, mir-365 expression in patients with sepsis following trauma was significantly lower than in patients without sepsis (p<0.05). similar effects were observed in thp-1 cells treated with lps. the present study demonstrated that increased expression of il-6 in patients with sepsis following multiple trauma is associated with decreased expression of mir-365. mir-365 may regulate the occurrence and immune response of sepsis following multiple trauma via il-6. these results may elucidate agents for clinical diagnosis and treatment of the disease.",1
"micrornas are involved in human carcinogenesis and cancer progression. our previous study has shown that loss of mir-338-3p expression is associated with clinical aggressiveness of hepatocellular carcinoma (hcc). however, the exact roles and mechanisms of mir-338-3p remain unknown in hcc. to determine whether and how mir-338-3p influences liver cancer cell invasion, we studied mir-338-3p in the liver cancer cell lines, and we found that mir-338-3p is down-regulated in treated cells. forced expression of mir-338-3p in sk-hep-1 cells suppressed cell migration and invasion, whereas inhibition of mir-338-3p in smmc-7721 cells induced cell migration and invasion. furthermore, smoothened (smo) was identified as a direct target of mir-338-3p. forced expression of mir-338-3p down-regulated smo and matrix metalloproteinase (mmp)-9 expression, but inhibition of mir-338-3p up-regulated smo and mmp9 expression. however, small interfering rna targeted smo reversed the effects induced by blockade of mir-338-3p. smo and mmp9 were overexpressed and associated with invasion and metastasis in hcc tissues. these data indicate that mir-338-3p suppresses cell invasion by targeting the smoothened gene in liver cancer in vitro and mir-338-3p might be a novel potential strategy for liver cancer treatment.",1
"purpose recent evidence has shown that altered patterns of microrna (mirna) expression correlate with various human cancers. we investigated the clinical significance of mir-10b and its involvement in chemotherapeutic resistance to 5-fluorouracil (5-fu), which is a key component of common chemotherapy regimens in colorectal cancer. methods quantitative rt-pcr was used to evaluate the clinicopathologic significance of mir-10b expression in 88 colorectal cancer cases. we also investigated the chemotherapeutic sensitivity to 5-fu in mir-10b-overexpressing colorectal cancer cells. to explore the mechanism of chemoresistance in mir-10b transfected cells, we examined whether mir-10b inhibits the pro-apoptotic bh3-only bcl-2 family member bim(bcl2l11), a key mediator of chemotherapy-induced cell death. results high level mir-10b expression was found to be significantly associated with high incidence of lymphatic invasion (p = 0.0257) and poor prognosis (p = 0.0057). multivariate analysis indicated that high mir-10b expression is an independent prognostic factor for survival. in vitro studies revealed that mir-10b directly inhibits pro-apoptotic bim, and the overexpression of mir-10b confers chemoresistance in colorectal cancer cells to 5-fu. conclusions mir-10b is a novel prognostic marker in colorectal cancer. moreover, the expression of mir-10b is a potential indicator of chemosensitivity to the common 5-fu-based chemotherapy regimen.",1
"background the pathways regulating the transition of mammalian cells from quiescence to proliferation are mediated by multiple mirnas. despite significant improvements in our understanding of mirna targeting, the majority of mirna regulatory networks are still largely unknown and require experimental validation. results here we identified mir-503, mir-103, and mir-494 as negative regulators of proliferation in primary human cells. we experimentally determined their genome wide target profiles using rna-induced silencing complex (risc) immunoprecipitations and gene expression profiling. analysis of the genome wide target profiles revealed evidence of extensive regulation of gene expression through non-canonical target pairing by mir-503. we identified the proto-oncogene ddhd2 as a target of mir-503 that requires pairing outside of the canonical 5' seed region of mir-503, representing a novel mode of mirna-target pairing. further bioinformatics analysis implicated mir-503 and ddhd2 in breast cancer tumorigenesis. conclusions our results provide an extensive genome wide set of targets for mir-503, mir-103, and mir-494, and suggest that mir-503 may act as a tumor suppressor in breast cancer by its direct non-canonical targeting of ddhd2.",1
"rationale mitochondria are semiautonomous cellular organelles with their own genome, which not only supply energy but also participate in cell death pathways. micrornas (mirnas) are usually 19 to 25 nt long, noncoding rnas, involved in posttranscriptional gene regulation by binding to the 3'-untranslated regions of target mrna, which impact on diverse cellular processes. objective to determine if nuclear mirnas translocate into the mitochondria and regulate mitochondrial function with possible pathophysiological implications in cardiac myocytes. methods and results we find that mir-181c is encoded in the nucleus, assembled in the cytoplasm, and finally translocated into the mitochondria of cardiac myocytes. immunoprecipitation of argonaute 2 from the mitochondrial fraction indicates binding of cytochrome c oxidase subunit 1 (mt-cox1) mrna from the mitochondrial genome with mir-181c. also, a luciferase reporter construct shows that mi-181c binds to the 3'utr of mt-cox1. to study whether mir-181c regulates mt-cox1, we overexpressed precursor mir-181c (or a scrambled sequence) in primary cultures of neonatal rat ventricular myocytes. overexpression of mir-181c did not change mt-cox1 mrna but significantly decreased mt-cox1 protein, suggesting that mir-181c is primarily a translational regulator of mt-cox1. in addition to altering mt-cox1, overexpression of mir-181c results in increased mt-cox2 mrna and protein content, with an increase in both mitochondrial respiration and reactive oxygen species generation in neonatal rat ventricular myocytes. thus, our data show for the first time that mir-181c can enter and target the mitochondrial genome, ultimately causing electron transport chain complex iv remodeling and mitochondrial dysfunction. conclusions nuclear mir-181c translocates into the mitochondria and regulates mitochondrial genome expression. this unique observation may open a new dimension to our understanding of mitochondrial dynamics and the role of mirna in mitochondrial dysfunction.",1
"telomeres are key structural elements for the protection and maintenance of linear chromosomes, and they function to prevent recognition of chromosomal ends as dna double-stranded breaks. loss of telomere capping function brought about by telomerase deficiency and gradual erosion of telomere ends or by experimental disruption of higher-order telomere structure culminates in the fusion of defective telomeres and/or the activation of dna damage checkpoints. previous work has implicated the nonhomologous end-joining (nhej) dna repair pathway as a critical mediator of these biological processes. here, employing the telomerase-deficient mouse model, we tested whether the nhej component dna-dependent protein kinase catalytic subunit (dna-pkcs) was required for fusion of eroded/dysfunctional telomere ends and the telomere checkpoint responses. in late-generation mterc(-/-) dna-pkcs(-/-) cells and tissues, chromosomal end-to-end fusions and anaphase bridges were readily evident. notably, nullizygosity for dna ligase4 (lig4)--an additional crucial nhej component--was also permissive for chromosome fusions in mterc(-/-) cells, indicating that, in contrast to results seen with experimental disruption of telomere structure, telomere dysfunction in the context of gradual telomere erosion can engage additional dna repair pathways. furthermore, we found that dna-pkcs deficiency does not reduce apoptosis, tissue atrophy, or p53 activation in late-generation mterc(-/-) tissues but rather moderately exacerbates germ cell apoptosis and testicular degeneration. thus, our studies indicate that the nhej components, dna-pkcs and lig4, are not required for fusion of critically shortened telomeric ends and that dna-pkcs is not required for sensing and executing the telomere checkpoint response, findings consistent with the consensus view of the limited role of dna-pkcs in dna damage signaling in general.",1
"in spite of being one of our most prominent bacterial pathogens, the presence of small regulatory rnas (srnas) has not previously been investigated in mycobacterium tuberculosis. post-transcriptional regulation of gene expression by srna molecules has been demonstrated in a wide range of pathogenic bacteria and has been shown to play a significant role in the control of virulence. by screening cdna libraries prepared from low-molecular weight rna from m. tuberculosis we have identified nine putative srna molecules, including cis-encoded antisense transcripts from within open reading frames and trans-encoded transcripts from intergenic regions. srnas displayed differential expression between exponential and stationary phase, and during a variety of stress conditions. two of the cis-encoded srnas were associated with genes encoding enzymes involved in lipid metabolism, desa1 and pks12. these srnas showed complementarity to multiple m. tuberculosis genes, suggesting the potential to act as both cis-encoded and trans-encoded srnas. overexpression of selected trans-encoded srnas had profound impact on growth of m. tuberculosis and m. smegmatis. this is the first experimental evidence of srnas in m. tuberculosis and it will be important to consider the potential influence of srna regulation when studying the transcriptome and the proteome of m. tuberculosis during infection.",1
"the ten-eleven translocation family of proteins (tet1/2/3, tets) converts 5-methylcytosine (5mc) to 5-hydroxymethylcytosine (5hmc), which can be further oxidized and repaired by thymine dna glycosylase (tdg), to influence gene transcription in embryonic and adult tissues. however the mechanisms of how tets and tdg levels are regulated are unknown. we show that mir-29 can directly regulate tet1-3 and tdg mrna levels through binding to their 3'utrs. mir-29 mimic decreases global 5hmc levels, a hallmark of tet activity. moreover, the mrna levels for tet3 and tdg are inversely correlated with the levels of mir-29 in aged mouse aorta implying that aging may affect methylation patterns via mirna. in summary, our data show that tets and tdg are direct targets of mir-29 and unravel a novel regulatory role for this mirna in epigenetic dna demethylation pathways.",1
"micrornas (mirnas) are 21-23 nucleotide rna molecules that regulate the stability or translational efficiency of target messenger rnas. mirnas have diverse functions, including the regulation of cellular differentiation, proliferation and apoptosis. although strict tissue- and developmental-stage-specific expression is critical for appropriate mirna function, mammalian transcription factors that regulate mirnas have not yet been identified. the proto-oncogene c-myc encodes a transcription factor that regulates cell proliferation, growth and apoptosis. dysregulated expression or function of c-myc is one of the most common abnormalities in human malignancy. here we show that c-myc activates expression of a cluster of six mirnas on human chromosome 13. chromatin immunoprecipation experiments show that c-myc binds directly to this locus. the transcription factor e2f1 is an additional target of c-myc that promotes cell cycle progression. we find that expression of e2f1 is negatively regulated by two mirnas in this cluster, mir-17-5p and mir-20a. these findings expand the known classes of transcripts within the c-myc target gene network, and reveal a mechanism through which c-myc simultaneously activates e2f1 transcription and limits its translation, allowing a tightly controlled proliferative signal.",1
"metastasis is a complex, multistep process involved in the progression of cancer from a localized primary tissue to distant sites, often characteristic of the more aggressive forms of this disease. despite being studied in great detail in recent years, the mechanisms that govern this process remain poorly understood. in this study, we identify a novel role for mir-139-5p in the inhibition of breast cancer progression. we highlight its clinical relevance by reviewing mir-139-5p expression across a wide variety of breast cancer subtypes using in-house generated and online data sets to show that it is most frequently lost in invasive tumors. a biotin pull-down approach was then used to identify the mrna targets of mir-139-5p in the breast cancer cell line mcf7. functional enrichment analysis of the pulled-down targets showed significant enrichment of genes in pathways previously implicated in breast cancer metastasis (p < 0.05). further bioinformatic analysis revealed a predicted disruption to the tgfβ, wnt, rho, and mapk/pi3k signaling cascades, implying a potential role for mir-139-5p in regulating the ability of cells to invade and migrate. to corroborate this finding, using the mda-mb-231 breast cancer cell line, we show that overexpression of mir-139-5p results in suppression of these cellular phenotypes. furthermore, we validate the interaction between mir-139-5p and predicted targets involved in these pathways. collectively, these results suggest a significant functional role for mir-139-5p in breast cancer cell motility and invasion and its potential to be used as a prognostic marker for the aggressive forms of breast cancer.",1
"periosteal expansion is a recognized response to androgen exposure during bone development and in profoundly hypogonadal adults. however, androgen also suppresses endocortical bone formation, indicating that its effects on bone are dichotomous and envelope-specific. in fact, enhanced androgen signaling has been shown to have dramatic detrimental effects on whole bone biomechanical properties in two different transgenic models with skeletally targeted androgen receptor (ar) overexpression. as the mechanisms underlying this response are uncharacterized, we compared patterns of gene expression in periosteum-free cortical bone samples derived from ar-overexpressing transgenic male mice and their wild-type counterparts. we then assessed direct androgen effects in both wild-type and ar-overexpressing osteoblasts in primary culture. among major signaling pathways associated with bone formation, focused quantitative rt-pcr (qpcr) array-based analysis of endocortical bone gene expression from wild-type vs. transgenic males identified the transforming growth factor-beta (tgf-beta) superfamily and bone morphogenetic protein (bmp) signaling as significantly altered by androgen in vivo. bioinformatic analyses indicated proliferation, osteoblast differentiation and mineralization as major biological processes affected. consistent with the in vivo array data and bioinformatic analyses, inhibition of differentiation observed with androgen exposure was reduced by exogenous bmp2 treatment of ar-overexpressing cultures to stimulate bmp signaling, confirming array pathway analysis. in addition, nonaromatizable dihydrotestosterone (dht) inhibited osteoblast proliferation, differentiation and several indices of mineralization, including mineral accumulation and mineralized nodule formation in primary cultures from both wild-type and ar-transgenic mice. these findings identify a molecular mechanism based on altered bmp signaling that contributes to androgen inhibition of osteoblast differentiation and mineralization. such detrimental effects of androgen on osteoblast function may underlie the generally disappointing results of androgen therapy.",1
"the c. elegans heterochronic gene pathway consists of a cascade of regulatory genes that are temporally controlled to specify the timing of developmental events. mutations in heterochronic genes cause temporal transformations in cell fates in which stage-specific events are omitted or reiterated. here we show that let-7 is a heterochronic switch gene. loss of let-7 gene activity causes reiteration of larval cell fates during the adult stage, whereas increased let-7 gene dosage causes precocious expression of adult fates during larval stages. let-7 encodes a temporally regulated 21-nucleotide rna that is complementary to elements in the 3' untranslated regions of the heterochronic genes lin-14, lin-28, lin-41, lin-42 and daf-12, indicating that expression of these genes may be directly controlled by let-7. a reporter gene bearing the lin-41 3' untranslated region is temporally regulated in a let-7-dependent manner. a second regulatory rna, lin-4, negatively regulates lin-14 and lin-28 through rna-rna interactions with their 3' untranslated regions. we propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory rnas triggers transitions in the complement of heterochronic regulatory proteins to coordinate developmental timing.",1
"micrornas are key regulators of many biological processes, including cell differentiation. here we show that during human monocyte-macrophage differentiation, expression of the micrornas mir-223, mir-15a and mir-16 decreased considerably, which led to higher expression of the serine-threonine kinase ikkalpha in macrophages. in macrophages, higher ikkalpha expression in conjunction with stabilization of the kinase nik induced larger amounts of p52. because of low expression of the transcription factor relb in untreated macrophages, high p52 expression repressed basal transcription of both canonical and noncanonical nf-kappab target genes. however, proinflammatory stimuli in macrophages resulted in greater induction of noncanonical nf-kappab target genes. thus, a decrease in certain micrornas probably prevents macrophage hyperactivation yet primes the macrophage for certain responses to proinflammatory stimuli.",1
"activation of the endothelium by pro-inflammatory stimuli plays a key role in the pathogenesis of a multitude of vascular diseases. angiogenesis is a crucial component of the vascular response associated with inflammatory signaling. the cd40/cd40 ligand dyad in endothelial cells (ec) has a central role in promoting vascular inflammatory response; however, the molecular mechanism underlying this component of inflammation and angiogenesis is not fully understood. here we report a novel microrna mediated suppression of endothelial cd40 expression. we found that cd40 is closely regulated by mir-424 and mir-503, which directly target its 3' untranslated region. pro-inflammatory stimuli led to increased endothelial cd40 expression, at least in part due to decreased mir-424 and mir-503 expression. in addition, mir-424 and mir-503 reduced lps induced ec sprouting, migration and tube formation. moreover, we found that mir-424 and mir-503 expression is directly regulated by peroxisome proliferator-activated receptor gamma (pparγ), whose endothelial expression and activity are decreased in response to inflammatory factors. finally, we demonstrate that mice with endothelial-specific deletion of mir-322 (mir-424 ortholog) and mir-503 have augmented angiogenic response to lps in a matrigel plug assay. overall, these studies identify a pparγ-dependent mir-424/503-cd40 signaling axis that is critical for regulation of inflammation mediated angiogenesis.",1
"the highly conserved internal stem-loop (isl) of u6 spliceosomal rna is unwound for u4/u6 complex formation during spliceosome assembly and reformed upon u4 release during spliceosome activation. the u6 isl is structurally similar to domain 5 of group ii self-splicing introns, and contains a dynamic bulge that coordinates a mg++ ion essential for the first catalytic step of splicing. we have analyzed the causes of growth defects resulting from mutations in the saccharomyces cerevisiae u6 isl-bulged nucleotide u80 and the adjacent c67-a79 base pair. intragenic suppressors and enhancers of the cold-sensitive a79g mutation, which replaces the c-a pair with a c-g pair, suggest that it stabilizes the isl, inhibits u4/u6 assembly, and may also disrupt spliceosome activation. the lethality of mutations c67a and c67g results from disruption of base-pairing potential between u4 and u6, as these mutations are fully suppressed by compensatory mutations in u4 rna. strikingly, suppressor analysis shows that the lethality of the u80g mutation is due not only to formation of a stable base pair with c67, as previously proposed, but also another defect. a u6-u80g strain in which mispairing with position 67 is prevented grows poorly and assembles aberrant spliceosomes that retain u1 snrnp and fail to fully unwind the u4/u6 complex at elevated temperatures. our data suggest that the u6 isl bulge is important for coupling u1 snrnp release with u4/u6 unwinding during spliceosome activation.",1
"dendritic cells (dcs) and macrophages play important roles in maintaining intestinal homeostasis. however, the molecular mechanisms that regulate the differentiation and responses of intestinal dcs and macrophages remain poorly understood. here, we have identified microrna mir-223 as a key molecule for regulating these processes. deficiency of mir-223 led to a significantly decreased number of intestinal cx3cr1(hi) macrophages at steady state. both intestinal cx3cr1(hi) macrophages and cd103(+) conventional dcs (cdcs) in mir-223-deficient mice exhibited a strong pro-inflammatory phenotype. moreover, mir-223-deficient monocytes gave rise to more monocyte-derived dcs (modcs) and produced more pro-inflammatory cytokines upon stimulation. using a mouse model of colitis, we demonstrated that the mir-223 deficiency resulted in more severe colitis. target gene analysis further identified that the effects of mir-223 on dcs and macrophages were mediated by directly targeting c/ebpβ. taken together, our study identifies a role for mir-223 as a critical regulator of intestinal homeostasis.",1
"many chemotherapy regiments are successfully used to treat breast cancer; however, often breast cancer cells develop drug resistance that usually leads to a relapse and worsening of prognosis. we have shown recently that epigenetic changes such as dna methylation and histone modifications play an important role in breast cancer cell resistance to chemotherapeutic agents. another mechanism of gene expression control is mediated via the function of small regulatory rna, particularly microrna (mirna); its role in cancer cell drug resistance still remains unexplored. in the present study, we investigated the role of mirna in the resistance of human mcf-7 breast adenocarcinoma cells to doxorubicin (dox). here, we for the first time show that dox-resistant mcf-7 cells (mcf-7/dox) exhibit a considerable dysregulation of the mirnaome profile and altered expression of mirna processing enzymes dicer and argonaute 2. the mechanistic link of mirnaome deregulation and the multidrug-resistant phenotype of mcf-7/dox cells was evidenced by a remarkable correlation between specific mirna expression and corresponding changes in protein levels of their targets, specifically those ones that have a documented role in cancer drug resistance. furthermore, we show that microrna-451 regulates the expression of multidrug resistance 1 gene. more importantly, transfection of the mcf-7/dox-resistant cells with microrna-451 resulted in the increased sensitivity of cells to dox, indicating that correction of altered expression of mirna may have significant implications for therapeutic strategies aiming to overcome cancer cell resistance.",1
"micrornas are small endogenous noncoding rnas that regulate protein expression by hybridization to imprecise complementary sequences of target mrnas. changes in abundance of muscle-specific microrna, mir-1, have been implicated in cardiac disease, including arrhythmia and heart failure. however, the specific molecular targets and cellular mechanisms involved in the action of mir-1 in the heart are only beginning to emerge. in this study we investigated the effects of increased expression of mir-1 on excitation-contraction coupling and ca(2+) cycling in rat ventricular myocytes using methods of electrophysiology, ca(2+) imaging and quantitative immunoblotting. adenoviral-mediated overexpression of mir-1 in myocytes resulted in a marked increase in the amplitude of the inward ca(2+) current, flattening of ca(2+) transients voltage dependence, and enhanced frequency of spontaneous ca(2+) sparks while reducing the sarcoplasmic reticulum ca(2+) content as compared with control. in the presence of isoproterenol, rhythmically paced, mir-1-overexpressing myocytes exhibited spontaneous arrhythmogenic oscillations of intracellular ca(2+), events that occurred rarely in control myocytes under the same conditions. the effects of mir-1 were completely reversed by the camkii inhibitor kn93. although phosphorylation of phospholamban was not altered, mir-1 overexpression increased phosphorylation of the ryanodine receptor (ryr2) at s2814 (ca(2+)/calmodulin-dependent protein kinase) but not at s2808 (protein kinase a). overexpression of mir-1 was accompanied by a selective decrease in expression of the protein phosphatase pp2a regulatory subunit b56alpha involved in pp2a targeting to specialized subcellular domains. we conclude that mir-1 enhances cardiac excitation-contraction coupling by selectively increasing phosphorylation of the l-type and ryr2 channels via disrupting localization of pp2a activity to these channels.",1
"molecular pathogenesis of high-grade serous ovarian carcinoma (hg-soc) is poorly understood. recent recognition of hg-soc precursor lesions, defined as serous tubal intraepithelial carcinoma (stic) in fimbria, provides a new venue for the study of early genetic changes in hg-soc. using microrna profiling analysis, we found that mir-182 expression was significantly higher in stic than in matched normal fallopian tube. further study revealed that mir-182 was significantly overexpressed in most hg-soc cases. to test whether mir-182 plays a major role in early tumourigenesis of hg-soc, we overexpressed mir-182 in immortalized ovarian surface, fallopian tube secretory cells and malignant ovarian cell lines, and found that mir-182 overexpression resulted in increased tumour transformation in vitro, and enhanced tumour invasiveness in vitro and metastasis in vivo. mechanistically, we demonstrated that the oncogenic properties of mir-182 in ovarian cancer were mediated in part by its impaired repair of dna double-strand breaks and negative regulation of breast cancer 1 (brca1) and metastasis suppressor 1 (mtss1) expression as well as its positive regulation of the oncogene high-mobility group at-hook 2 (hmga2). our findings suggest that mir-182 dysregulation confers powerful oncogenic potential in the tumourigenesis of hg-soc. copyright © 2012 pathological society of great britain and ireland. published by john wiley & sons, ltd.",1
"micrornas (mirnas) have been shown to be important in early development and maintenance of human embryonic stem cells (hescs). the mirna mir-302-367 is specifically expressed in hescs, and its expression decays on differentiation. we previously identified the structure of the gene coding for the human mir-302-367 cluster and characterized its promoter. the promoter activity was functionally validated in hescs, opening up new avenues to further investigate how these mirna molecules fit in the complex molecular network conferring ""stemness"" properties to hescs. the physiological roles of specific mirna-mrna interactions remain largely unknown. here, we investigated putative mir-302-367 mrna targets in hescs, potentially relevant for esc biology. we found that the nodal inhibitors lefty1 and lefty2 are post-transcriptionally targeted by mir-302s in hescs. functional analyses indicate that mir-302s negatively modulate the level of lefties, and become upstream regulators of the tgfβ/nodal pathway, functioning via smad-2/3 signaling. overexpression of the mir-302-367 cluster in hescs causes a delay in early hesc differentiation, as measured by enhanced levels of esc-specific transcription factors, coupled to a faster teratoma formation in mice transplanted with mir-302-367-expressing hescs and a concomitant impairment of germ layer specification, displaying robust decreased levels of early mesodermal, endodermal, and ectodermal specific markers. these findings suggest that lefty is negatively modulated by mir-302s in hescs, which plays an important role in maintaining the balance between pluripotency and germ layer specification.",1
"the kidney has long been invoked in the etiology of essential hypertension. this could involve alterations in expression of specific genes and micrornas (mirnas). the aim of the present study was to identify, at the transcriptome-wide level, mrnas and mirnas that were differentially expressed between kidneys of 15 untreated hypertensive and 7 normotensive white male subjects of white european ancestry. by microarray technology we found 14 genes and 11 mirnas that were differentially expressed in the medulla. we then selected and confirmed by real-time quantitative pcr expression differences for nr4a1, nr4a2, nr4a3, per1, and sik1 mrnas and for the mirnas hsa-mir-638 and hsa-let-7c. luciferase reporter gene experiments in human kidney (hek293) cells confirmed the predicted binding of hsa-let-7c to the 3' untranslated region of nr4a2 mrna. in the renal cortex we found differential expression of 46 genes and 13 mirnas. we then confirmed expression differences for aifm1, ambp, apoe, cd36, efnb1, ndufaf1, prdx5, ren, renbp, slc13a1, stx4, and tnnt2 mrnas and for mirnas hsa-mir-21, hsa-mir-126, hsa-mir-181a, hsa-mir-196a, hsa-mir-451, hsa-mir-638, and hsa-mir-663. functional experiments in hek293 cells demonstrated that hsa-mir-663 can bind to the ren and apoe 3' untranslated regions and can regulate ren and apoe mrna levels, whereas hsa-mir-181a regulated ren and aifm1 mrna. our data demonstrated for the first time that mirnas can regulate renin expression. the observed downregulation of 2 mirnas in hypertension could explain the elevation in intrarenal renin mrna. renin, cd36, and other mrnas, as well as mirnas and associated pathways identified in the present study, provide novel insights into hypertension etiology.",1
"the two-component regulatory system ciarh of streptococcus pneumoniae has been implicated in beta-lactam resistance, maintenance of cell integrity, competence and virulence, but the genes that are regulated directly by the system have not been defined. using transcriptional mapping, in vitro ciar binding, and in vivo analysis of ciar-mediated regulation, 15 promoters were identified to be directly controlled by the response regulator ciar. a direct repeat, tttaag-n5-tttaag, was found to be essential for ciar binding and regulation. it is present, either completely or with subtle changes, in all promoter regions. fourteen promoters of the regulon are activated by ciar, and one was found to be controlled negatively. the genes that are transcribed from these promoters included ciarh, loci that are predicted to be involved in the modification of teichoic acids (lic), in sugar metabolism (mal, man), stress response (htra), chromosome segregation (parb), protease maturation (ppma) and unknown functions. remarkably, the five strongest promoters of the ciar regulon drive expression of small rnas. these small rnas, designated csrnas for cia-dependent small rnas, are non-coding, between 87 and 151 nt in size, and show a high degree of similarity to each other. the analysis of deletion mutants in the csrna genes revealed that csrna4 and csrna5 affect stationary-phase autolysis. the identification of five small non-coding regulatory rnas opens new perspectives to approach the physiological role of the ciarh two-component regulatory system.",1
"a number of different micrornas (mirnas) have been implicated in various autoimmune diseases, including multiple sclerosis (ms). t helper (th)17 and regulatory t cells (tregs) have likewise been implicated as key players in ms, and a functional imbalance of these cell types is increasingly recognized as a key etiological factor in the disease. although specific panels of transcription factors and cytokines are known to regulate the th17/treg balance, the role of noncoding rnas remains poorly understood. the inflammatory cytokine, interleukin (il)6, appears to play a critical role in both the development of the th17 response and the inhibition of treg functions. in this research, an il6-associated mirna, mir26a, was identified, and its normally downregulated expression was shown to be highly correlated with disease severity in patients suffering from ms as well as in c57bl/6 mice with experimental autoimmune encephalomyelitis (eae; a well-established animal model of human ms). using the eae model system, in vivo silencing of mir26a was found to result in increased expression of th17-related cytokines and increased severity of eae, while overexpression of mir26a was found to result in reduced expression of th17-related cytokines and a milder form of eae. by contrast, treg cell-specific transcription factor, foxp3, was found to be positively correlated with mir26a expression. finally, mir26a was found to downregulate th17 and to upregulate treg cell function through its targeting of il6. taken together, our data indicate an important role for mir26a in maintaining the th17 and treg cell balance in ms that involves repression of il6 expression.",1
"rationale the sympathetic nervous system plays a fundamental role in the regulation of myocardial function. during chronic pressure overload, overactivation of the sympathetic nervous system induces the release of catecholamines, which activate β-adrenergic receptors in cardiomyocytes and lead to increased heart rate and cardiac contractility. however, chronic stimulation of β-adrenergic receptors leads to impaired cardiac function, and β-blockers are widely used as therapeutic agents for the treatment of cardiac disease. microrna-133 (mir-133) is highly expressed in the myocardium and is involved in controlling cardiac function through regulation of messenger rna translation/stability. objective to determine whether mir-133 affects β-adrenergic receptor signaling during progression to heart failure. methods and results based on bioinformatic analysis, β1-adrenergic receptor (β1ar) and other components of the β1ar signal transduction cascade, including adenylate cyclase vi and the catalytic subunit of the camp-dependent protein kinase a, were predicted as direct targets of mir-133 and subsequently validated by experimental studies. consistently, camp accumulation and activation of downstream targets were repressed by mir-133 overexpression in both neonatal and adult cardiomyocytes following selective β1ar stimulation. furthermore, gain-of-function and loss-of-function studies of mir-133 revealed its role in counteracting the deleterious apoptotic effects caused by chronic β1ar stimulation. this was confirmed in vivo using a novel cardiac-specific teton-mir-133 inducible transgenic mouse model. when subjected to transaortic constriction, teton-mir-133 inducible transgenic mice maintained cardiac performance and showed attenuated apoptosis and reduced fibrosis compared with control mice. conclusions mir-133 controls multiple components of the β1ar transduction cascade and is cardioprotective during heart failure.",1
"one of the first specialized collections of nucleic acid sequences in life sciences was the 'compilation of trna sequences and sequences of trna genes' ( here, an updated and completely restructured version of this compilation is presented ( the new database, trnadb, is hosted and maintained in cooperation between the universities of leipzig, marburg, and strasbourg. reimplemented as a relational database, trnadb will be updated periodically and is searchable in a highly flexible and user-friendly way. currently, it contains more than 12 000 trna genes, classified into families according to amino acid specificity. furthermore, the implementation of the ncbi taxonomy tree facilitates phylogeny-related queries. the database provides various services including graphical representations of trna secondary structures, a customizable output of aligned or un-aligned sequences with a variety of individual and combinable search criteria, as well as the construction of consensus sequences for any selected set of trnas.",1
"tobacco smoking is a risk factor for many diseases, and nicotine is a major component of tobacco. our previous work revealed that nicotine can induce myocardial fibrosis. this study aimed to investigate whether nicotine can induce cardiomyocyte apoptosis and to explore the mechanisms involved. cardiomyocytes were exposed to different nicotine concentrations for 48 h. mtt assay showed that the viability of cardiomyocytes was significantly inhibited by nicotine in a dose- and time-dependent manner. loss of mitochondrial membrane potential, nuclear and dna defragmentation determined by tunel and elisa assays, and morphological alterations all revealed the pro-apoptotic property of nicotine. meanwhile, mir-133, a muscle-specific microrna, was markedly downregulated by nicotine. consistently, caspase-9, a target gene for mir-133, was significantly upregulated, leading to an increase in caspase-3, in nicotine-treated cardiomyocytes compared to non-treated cells. furthermore, erk1/2 protein levels were considerably downregulated, along with reduction of serum response factor (srf), which is a downstream target protein of erk1/2 and an upstream transactivator of mir-133 as well. our findings therefore revealed that inhibition of the erk1/2-srf-mir-133 signaling pathway to increase caspases-9 and -3 is a novel mechanism for nicotine to induce cardiomyocyte apoptosis and these tobacco smokers.",1
"expression of several heat shock operons, mainly coding for small heat shock proteins, is under the control of rose (repression of heat shock gene expression) in various rhizobial species. this negatively cis-acting element confers temperature control by preventing expression at physiological temperatures. we provide evidence that rose-mediated regulation occurs at the post-transcriptional level. a detailed mutational analysis of rose(1)-hspa translationally fused to lacz revealed that its highly conserved 3'-half is required for repression at normal temperatures (30 degrees c). the mrna in this region is predicted to form an extended secondary structure that looks very similar in all 15 known rose elements. nucleotides involved in base pairing are strongly conserved, whereas nucleotides in loop regions are more divergent. base substitutions leading to derepression of the lacz fusion at 30 degrees c exclusively resided in potential stem structures. optimised base pairing by elimination of a bulged residue and by introduction of complementary nucleotides in internal loops resulted in rose elements that were tightly repressed not only at normal but also at heat shock temperatures. we propose a model in which the temperature-regulated secondary structure of rose mrna influences heat shock gene expression by controlling ribosome access to the ribosome-binding site.",1
"micrornas (mirnas) act as sequence-specific guides for argonaute (ago) proteins, which mediate posttranscriptional silencing of target messenger rnas. despite their importance in many biological processes, rules governing ago-mirna targeting are only partially understood. here we report a modified ago hits-clip strategy termed clear (covalent ligation of endogenous argonaute-bound rnas)-clip, which enriches mirnas ligated to their endogenous mrna targets. clear-clip mapped ∼130,000 endogenous mirna-target interactions in mouse brain and ∼40,000 in human hepatoma cells. motif and structural analysis define expanded pairing rules for over 200 mammalian mirnas. most interactions combine seed-based pairing with distinct, mirna-specific patterns of auxiliary pairing. at some regulatory sites, this specificity confers distinct silencing functions to mirna family members with shared seed sequences but divergent 3'-ends. this work provides a means for explicit biochemical identification of mirna sites in vivo, leading to the discovery that mirna 3'-end pairing is a general determinant of ago binding specificity.",1
"background hypoxia-induced renal tubular cell epithelial-mesenchymal transition (emt) is an important event leading to renal fibrosis. micrornas (mirnas) are small non-coding rna molecules that bind to their mrna targets, thereby leading to translational repression. the role of mirna in hypoxia-induced emt is largely unknown. methodology/principal findings mirna profiling was performed for the identification of differentially expressed mirnas in hk-2 cells under normal and low oxygen, and the results were then verified by quantitative real time rt-pcr (qrt-pcr). the function of mirnas in hypoxia-induced renal tubular cell emt was assessed by the transfection of specific mirna inhibitors and mimics. luciferase reporter gene assays and western blot analysis were performed to validate the target genes of mir-34a. sirna against jagged1 was designed to investigate the role of the mir-34a-notch pathway in hypoxia induced renal tubular cell emt. mirna-34a was identified as being downregulated in hypoxic renal tubular epithelial cells. inhibition of mir-34a expression in hk-2 cells, which highly express endogenous mir-34a, promoted a mesenchymal phenotype accompanied by reduced expression of the epithelial marker z0-1, e-cadherin and increased expression of the mesenchymal markers α-sma and vimentin. conversely, mir-34a mimics effectively prevented hypoxia-induced emt. transfection of mirna-34a in hk-2 cells under hypoxia abolished hypoxia-induced expression of notch1 and jagged1 as well as notch downstream signals, such as snail. western blot analysis and luciferase reporter gene assays showed direct evidence for mir-34a targeting notch1 and jagged1. sirnas against jagged1 or notch1 effectively prevented mir-34a inhibitor-induced tubular epithelial cell emt. conclusions/significance our study provides evidence that the hypoxia-induced decrease of mir-34a expression could promote emt in renal tubular epithelial cells by directly targeting notch1 and jagged1, and subsequently, notch downstream signaling.",1
"micrornas (mirnas) are generally thought to negatively regulate the expression of their target genes by mrna degradation or by translation repression. here we show an efficient way to identify mirna target genes by screening alterations in global mrna levels following changes in mirna levels. in this study, we used mrna microarrays to measure global mrna expression in three cell lines with increased or decreased levels of mir-16 and performed bioinformatics analysis based on multiple target prediction algorithms. for further investigation among the predicted mir-16 target genes, we selected genes that show an expression pattern opposite to that of mir-16. one of the candidate target genes that may interact with mir-16, adp-ribosylation factor-like protein 2 (arl2), was further investigated. first, arl2 was deduced to be an ideal mir-16 target by computational predictions. second, arl2 mrna and protein levels were significantly abolished by treatment with mir-16 precursors, whereas a mir-16 inhibitor increased arl2 mrna and protein levels. third, a luciferase reporter assay confirmed that mir-16 directly recognizes the 3'-untranslated region (3'-utr) of arl2. finally, we showed that mir-16 could regulate proliferation and induce a significant g0/g1 cell cycle arrest, which was due at least in part, to the down-regulation of arl2. in summary, the present study suggests that integrating global mrna profiling and bioinformatics tools may provide the basis for further investigation of the potential targets of a given mirna. these results also illustrate a novel function of mir-16 targeting arl2 in modulating proliferation and cell cycle progression.",1
"morgagni-type diaphragmatic hernias are rare. the overwhelming majority are discovered in children who usually present with pneumonia or sepsis. we report an unusual case of a 57-yr-old woman with a morgagni hernia presenting with pulmonary symptoms. complicating the clinical picture, the pneumonia delayed the definitive diagnosis until a lateral chest x-ray study revealed loops of bowel in the right lower lung fields. it is important to entertain abdominal etiologies in the differential diagnosis of a thoracic density.",1
"background atrial fibrillation (af) begets af in part due to atrial remodeling, the molecular mechanisms of which have not been completely elucidated. this study was conducted to identify microrna(s) responsible for electrical remodeling in af. methods and results the expression profiles of 1205 micrornas, in cardiomyocytes from patients with persistent af and from age-, gender-, and cardiac function-matched control patients with normal sinus rhythm, were examined by use of a microrna microarray platform. thirty-nine micrornas differentially expressed in af patients' atria were identified, including mir-30d, as a candidate responsible for ion channel remodeling by in silico analysis. mir-30d was significantly upregulated in cardiomyocytes from af patients, whereas the mrna and protein levels ofcacna1c/cav1.2 andkcnj3/kir3.1, postulated targets of mir-30d, were markedly reduced.kcnj3/kir3.1 expression was downregulated by transfection of the mir-30 precursor, concomitant with a reduction of the acetylcholine-sensitive inward-rectifier k(+)current (ik.ach).kcnj3/kir3.1 (but notcacna1c/cav1.2) expression was enhanced by the knockdown of mir-30d. the ca(2+)ionophore, a23187, induced a dose-dependent upregulation of mir-30d, followed by the suppression ofkcnj3mrna expression. blockade of protein kinase c signaling blunted the i-dependent downregulation of kir3.1 via mir-30d. conclusions the downward remodeling ofik.achis attributed, at least in part, to deranged ca(2+)handling, leading to the upregulation of mir-30d in human af, revealing a novel post-transcriptional regulation ofik.ach. (circ j 2016; 80: 1346-1355).",1
"lung cancer is one of the leading causes of cancer death worldwide. micrornas have been shown to be a novel class of regulators in lung cancer. here, we explored the role of mir-153 in the pathogenesis of lung cancer and its therapeutic potential. mir-153 was significantly decreased in lung cancer tissues than the adjacent tissues. the protein and mrna levels of protein kinase b (akt), which were shown to promote tumor growth, were both increased in lung cancer tissues than adjacent tissues. overexpression of mir-153 significantly inhibited akt protein expression, which were abrogated by co-transfection of amo-153, the specific inhibitor of mir-153. luciferase assay showed that transfection of mir-153 markedly suppressed the fluorescent intensity of chimeric vectors carrying the 3'utr of akt1, while produced no effect on the mutant construct, indicating that akt is regulated by mir-153. overexpression of mir-153 significantly inhibited the proliferation and migration, and promoted apoptosis of cultured lung cancer cells in vitro, and suppressed the growth of xenograft tumors in vivo. interestingly, lung cancer cells with lower endogenous mir-153 expression are more sensitive to ectopic overexpressed mir-153. the ic50 of mir-153 on lung cancer cells is positive correlated with the endogenous mir-153 level, while negative correlated with akt level. knockdown of akt expression suppressed lung cancer cell proliferation. in summary, mir-153 exerted anti-tumor activity in lung cancer by targeting on akt. the sensitivity of lung cancer cells to mir-153 is determined by its endogenous mir-153 level.",1
"emerging data implicate micrornas (mirnas) in the regulation of synaptic structure and function, but we know little about their role in the regulation of neurotransmission in presynaptic neurons. here, we demonstrate that the mir-310-313 cluster is required for normal synaptic transmission at the drosophila larval neuromuscular junction. loss of mir-310-313 cluster leads to a significant enhancement of neurotransmitter release, which can be rescued with temporally restricted expression of mir-310-313 in larval presynaptic neurons. kinesin family member, khc-73 is a functional target for mir-310-313 as its expression is increased in mir-310-313 mutants and reducing it restores normal synaptic function. cluster mutants show an increase in the active zone protein bruchpilot accompanied by an increase in electron dense t bars. finally, we show that repression of khc-73 by mir-310-313 cluster influences the establishment of normal synaptic homeostasis. our findings establish a role for mirnas in the regulation of neurotransmitter release.",1
"background paired box 6 (pax6), a highly conserved transcriptional factor, has been implicated in tumorigenesis. aim we aimed to explore the roles and molecular mechanisms of pax6 and microrna (mir-7) in colorectal cancer cells. methods tissue microarray immunohistochemistry and western blot were applied to examine the pax6 expression. real-time rt-pcr and western blot were performed to determine the expression of mir-7 and pax6. luciferase reporter assay was used to determine whether pax6 was a target of mir-7. effects of mir-7 and pax6 on colorectal cell proliferation, cell cycle progression, colony formation and invasion were then investigated. western blot was used to determine the activities of the erk and pi3k signal pathways, as well as the protein expression of mmp2 and mmp9. results the protein levels of pax6 were gradually increased, while the expression of mir-7 was gradually reduced with malignancy of colorectal cancer. pax6 was further identified as a target of mir-7, and its protein expression was negatively regulated by mir-7 in human colorectal cancer cells. overexpression of pax6 in caco-2 and sw480 cells enhanced cellular proliferation, cell cycle progression, colony formation, and invasion, while mir-7 upregulation repressed these biological processes. furthermore, the activities of erk and pi3k signal pathways, as well as the protein levels of mmp2 and mmp9, were upregulated in pax6-overexpressed caco-2 and sw480 cells but deregulated in mir-7-overexpressed caco-2 and sw480 cells. conclusions our study suggests that as a novel target of mir-7, pax6 may serve as a promising therapeutic target for colorectal cancer.",1
"vascular smooth muscle cell (vsmc) apoptosis plays an important role in vascular remodeling and atherosclerotic plaque instability. oxidative stress in diseased vessels promotes vsmc apoptosis in part by activating the c-jun n-terminal kinase (jnk) pathway, which has been identified as a molecular target of mir-92a in macrophages. here, we examined the expression and biological activity of mir-92a in vsmc. quiescent vsmc exhibited a low basal expression of mir-92a, which was positively regulated by serum stimulation and negatively regulated by h2o2. overexpression of mir-92a decreased h2o2-induced vsmc apoptosis as indicated by tunel assay and cleaved caspase-3 protein levels. using 3'utr-reporter assay, we found that mir-92a overexpression led to suppression of both mitogen-activated protein kinase kinase 4 (mkk4)- and jnk1-dependent luciferase activity. we also found that 10 mer seed match between mirna:mrna pair is more efficient than 8 mer seed match for us to identify authentic mirna target. protein levels of active phospho-jnk and phospho-c-jun, downstream targets of the mkk4-jnk1 pathway, were also decreased by overexpressing mir-92a in vsmc under oxidative stress. consistent with these findings, overexpression of mkk4 reversed the anti-apoptotic effects of mir-92a in oxidatively stressed vsmc. in conclusion, mir-92a overexpression inhibits h2o2-induced vsmc apoptosis by directly targeting the mkk4-jnk1 pathway.",1
"proper coordination of cholesterol biosynthesis and trafficking is essential to human health. the sterol regulatory element-binding proteins (srebps) are key transcription regulators of genes involved in cholesterol biosynthesis and uptake. we show here that micrornas (mir-33a/b) embedded within introns of the srebp genes target the adenosine triphosphate-binding cassette transporter a1 (abca1), an important regulator of high-density lipoprotein (hdl) synthesis and reverse cholesterol transport, for posttranscriptional repression. antisense inhibition of mir-33 in mouse and human cell lines causes up-regulation of abca1 expression and increased cholesterol efflux, and injection of mice on a western-type diet with locked nucleic acid-antisense oligonucleotides results in elevated plasma hdl. our findings indicate that mir-33 acts in concert with the srebp host genes to control cholesterol homeostasis and suggest that mir-33 may represent a therapeutic target for ameliorating cardiometabolic diseases.",1
"triple negative breast cancer lacking estrogen receptor (er), progesterone receptor and her2 account for account for the majority of the breast cancer deaths, due to the lack of specific gene targeted therapy. our current study aimed to investigate the role of mir-544 in triple negative breast cancer. endogenous levels of mir-544 were significantly lower in breast cancer cell lines than in human breast non-tumorigenic and mammary epithelial cell lines. we found that mir-544 directly targeted the 3'-untranslated region (utr) on both bcl6 and stat3 mrnas, and overexpression of mir-544 in triple negative breast cancer cells significantly down-regulated expressions of bcl6 and stat3, which in turn severely inhibited cancer cell proliferation, migration and invasion in vitro. employing a mouse xenograft model to examine the in vivo function of mir-544, we found that expression of mir-544 significantly repressed the growth of xenograft tumors. our current study reported mir-544 as a tumor-suppressor microrna particularly in triple negative breast cancer. our data supported the role of mir-544 as a potential biomarker in developing gene targeted therapies in the clinical treatment of triple negative breast cancer.",1
"glioblastomas (gbm), the most common and aggressive type of malignant glioma, are characterized by increased invasion into the surrounding brain tissues. despite intensive therapeutic strategies, the median survival of gbm patients has remained dismal over the last decades. in this study we examined the expression of mir-145 in glial tumors and its function in glioma cells. using tcga analysis and real-time pcr we found that the expression of mir-145/143 cluster was downregulated in astrocytic tumors compared to normal brain specimens and in glioma cells and glioma stem cells (gscs) compared to normal astrocytes and neural stem cells. moreover, the low expression of both mir-145 and mir-143 in gbm was correlated with poor patient prognosis. transfection of glioma cells with mir-145 mimic or transduction with a lentivirus vector expressing pre-mir 145 significantly decreased the migration and invasion of glioma cells. we identified connective tissue growth factor (ctgf) as a novel target of mir-145 in glioma cells; transfection of the cells with this mirna decreased the expression of ctgf as determined by western blot analysis and the expression of its 3'-utr fused to luciferase. overexpression of a ctgf plasmid lacking the 3'-utr and administration of recombinant ctgf protein abrogated the inhibitory effect of mir-145 on glioma cell migration. similarly, we found that silencing of ctgf decreased the migration of glioma cells. ctgf silencing also decreased the expression of sparc, phospho-fak and fak and overexpression of sparc abrogated the inhibitory effect of ctgf silencing on cell migration. these results demonstrate that mir-145 is downregulated in glial tumors and its low expression in gbm predicts poor patient prognosis. in addition mir-145 regulates glioma cell migration by targeting ctgf which downregulates sparc expression. therefore, mir-145 is an attractive therapeutic target for anti-invasive treatment of astrocytic tumors.",1
"there is a growing body of evidence about the presence and the activity of the mirisc in the nucleus of mammalian cells. here, we show by quantitative proteomic analysis that ago2 interacts with the nucleoplasmic protein sfpq in an rna-dependent fashion. by a combination of hits-clip and transcriptomic analyses, we demonstrate that sfpq directly controls the mirna targeting of a subset of binding sites by local binding. sfpq modulates mirna targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic commitment of sfpq-target mrnas that globally influences mirna modes of action. mechanistically, sfpq binds to a sizeable set of long 3'utrs forming aggregates to optimize mirna positioning/recruitment at selected binding sites, including let-7a binding to lin28a 3'utr. our results extend the mirna-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an sfpq-dependent strategy for controlling mirna activity takes place in cells, contributing to the complexity of mirna-dependent gene expression control.",1
"recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal rna (rrna) structure, functional centers, and their interactions with antibiotics. however, much less is known about how rrna function differs between prokaryotic and eukaryotic ribosomes. the core decoding sites are identical in yeast and human 18s rrnas, suggesting that insights obtained in studies with yeast rrna mutants can provide information about ribosome function in both species. in this study, we examined the importance of key nucleotides of the 18s rrna decoding site on ribosome function and aminoglycoside susceptibility in saccharomyces cerevisiae cells expressing homogeneous populations of mutant ribosomes. we found that residues g577, a1755, and a1756 (corresponding to escherichia coli residues g530, a1492, and a1493, respectively) are essential for cell viability. we also found that residue g1645 (a1408 in e. coli) and a1754 (g1491 in e. coli) both make significant and distinct contributions to aminoglycoside resistance. furthermore, we found that mutations at these residues do not alter the basal level of translational accuracy, but influence both paromomycin-induced misreading of sense codons and readthrough of stop codons. this study represents the most comprehensive mutational analysis of the eukaryotic decoding site to date, and suggests that many fundamental features of decoding site function are conserved between prokaryotes and eukaryotes.",1
"microrna-21 (mir-21) is an oncomir overexpressed in most human tumors in that it promotes malignant growth and progression by acting on multiple targets. here, we broaden the impact of mir-21 in cancer by showing that it regulates the formation of reactive oxygen species (ros) that promote tumorigenesis. key targets of mir-21 in mediating this function were sod3 and tnfα. we found that mir-21 inhibited the metabolism of superoxide to hydrogen peroxide, produced either by endogenous basal activities or exposure to ionizing radiation (ir), by directing attenuating sod3 or by an indirect mechanism that limited tnfa production, thereby reducing sod2 levels. importantly, both effects contributed to an elevation of ir-induced cell transformation. our findings, therefore, establish that mir-21 promotes tumorigenesis to a large extent through its regulation of cellular ros levels.",1
"mir-132 is a neuronal activity-regulated microrna that controls the morphology of dendritic spines and neuronal transmission. similar activities have recently been attributed to matrix metalloproteinase-9 (mmp-9), an extrasynaptic protease. in the present study, we provide evidence that mir-132 directly regulates mmp-9 mrna in neurons to modulate synaptic plasticity. with the use of luciferase reporter system, we show that mir-132 binds to the 3'utr of mmp-9 mrna to regulate its expression in neurons. the overexpression of mir-132 in neurons reduces the level of endogenous mmp-9 protein secretion. in synaptoneurosomes, metabotropic glutamate receptor (mglur)-induced signaling stimulates the dissociation of mir-132 from polyribosomal fractions and shifts it towards the messenger ribonucleoprotein (mrnp)-containing fraction. furthermore, we demonstrate that the overexpression of mir-132 in the cultured hippocampal neurons from fmr1 ko mice that have increased synaptic mmp-9 level provokes enlargement of the dendritic spine heads, a process previously implicated in enhanced synaptic plasticity. we propose that activity-dependent mir-132 regulates structural plasticity of dendritic spines through matrix metalloproteinase 9.",1
"skeletal muscle is an important and complex organ with a variety of functions in humans and animals. skeletal myogenesis is a multistep and complex process, and increasing evidence suggests that micrornas (mirnas) and long noncoding rnas (lncrnas) play critical roles in skeletal myogenesis. in this study the expression of mir-351-5p is dynamically regulated during skeletal myogenesis in vitro and in vivo. cell-counting kit-8, qrt-pcr, and edu immunofluorescence analysis showed that mir-351-5p overexpression promoted the proliferation and inhibited the differentiation of c2c12 myoblast, whereas inhibition of mir-351-5p had the opposite effect. in addition, mir-351-5p mediated the regulation of muscle fiber type transition in vivo. in vitro, loss of mir-351-5p in muscle tissues promoted muscle hypertrophy and increased slow-twitch fibers in the gastrocnemius muscles of mice. luciferase reporter assay and functional analyses demonstrated that lactamase β ( lactb) is a direct target of mir-351-5p involved in the regulation of skeletal myogenesis. expression levels of a myogenesis-associated lncrna ( lnc-mg) correlated negatively with mir-351-5p and positively with lactb during c2c12 myoblast proliferation and differentiation. further analyses showed that lnc-mg acted as a molecular sponge for mir-351-5p, demonstrating its involvement in the negative regulation of lactb by mir-351-5p during skeletal myogenesis. these findings indicate that mirna-351-5p functions in skeletal myogenesis by targeting lactb and is regulated by lnc-mg, supporting the role of the competing endogenous rna network in skeletal myogenesis.-du, j., zhang, p., zhao, x., he, j., xu, y., zou, q., luo, j., shen, l., gu, h., tang, q., li, m., jiang, y., tang, g., bai, l., li, x., wang, j., zhang, s., zhu, l. microrna-351-5p mediates skeletal myogenesis by directly targeting lactamase β and is regulated by lnc-mg.",1
"pancreatic ductal adenocarcinoma (pdac) is a highly lethal solid tumor due to the lack of reliable early detection markers and effective therapies. micrornas (mirnas), noncoding rnas that regulate gene expression, are involved in tumorigenesis and have a remarkable potential for the diagnosis and treatment of malignancy. in this study, we investigated aberrantly expressed mirnas involved in pdac by comparing mirna expression profiles in pdac cell lines with a normal pancreas cell line and found that mir-135a was significantly down-regulated in the pdac cell lines. the microarray results were validated by qrt-pcr in pdac tissues, paired adjacent normal pancreatic tissues, pdac cell lines, and a normal pancreas cell line. we then defined the tumor-suppressing significance and function of mir-135a by constructing a lentiviral vector to express mir-135a. the overexpression of mir-135a in pdac cells decreased cell proliferation and clonogenicity and also induced g1 arrest and apoptosis. we predicted bmi1 may be a target of mir-135a using bioinformatics tools and found that bmi1 expression was markedly up-regulated in pdac. its expression was inversely correlated with mir-135a expression in pdac. furthermore, a luciferase activity assay revealed that mir-135a could directly target the 3'-untranslated region (3'-utr) of bmi1. taken together, these results demonstrate that mir-135a targets bmi1 in pdac and functions as a tumor suppressor. mir-135a may offer a new perspective for the development of effective mirna-based therapy for pdac.",1
"objective low-density lipoprotein receptor-related protein-1 (lrp1) has been suggested to be a crucial regulator in the pathogenesis of abdominal aortic aneurysm (aaa) from previous genome association and animal studies. our prior study using human aortic samples has further revealed a significant reduction of lrp1 protein expression associated with aaa. however, the downregulation of lrp1 in the pathophysiology of aaa remained unresolved. we hypothesized that lrp1 downregulation may be mediated by microrna (mir) and that lrp1 may function as a scavenger of matrix metalloproteinase-9 (mmp-9), a well-known protease for degradation of extracellular matrix proteins at the aortic wall for aaa pathogenesis. this study investigated the cause of lrp1 downregulation and its potential effect on aaa pathogenesis. methods an observational study of lrp1 protein, lrp1 messenger rna (mrna), and its three predicted mir candidates (mir-205, mir-338-5p, and mir-545-3p) was first performed in aaa compared with nonaneurysmal tissues from humans, followed by a functional study testing the effect on lrp1 expression of mir-205 overexpression and knockdown in human vascular smooth muscle cells (vsmcs) explant cultured from human abdominal aortic tissues. lastly, another functional study was performed to test for the clearance of exogenous mmp-9 upon silencing of lrp1 in human vsmcs. results from the observational study, significantly higher mir-205 (p conclusions our study revealed the downregulation of lrp1 protein expression may be tightly regulated by mir-205 through translational inhibition in human vsmcs. also, such lrp1 down-regulation in vsmcs may hinder the removal of pericellular mmp-9, leading to excess mmp-9 remaining in the extracellular matrix. hence, the integrity of the vascular wall may be disrupted, promoting aaa formation.",1
"the hippo signaling pathway acts upon the yorkie transcriptional activator to control tissue growth in drosophila. activated yorkie drives growth by stimulating cell proliferation and inhibiting apoptosis, but how it achieves this is not understood. yorkie is known to activate cyclin e (cyce) and the apoptosis inhibitor diap1. however, overexpression of these targets is not sufficient to cause tissue overgrowth. here we show that yorkie also activates expression of the bantam microrna, a known regulator of both proliferation and apoptosis. bantam overexpression mimics yorkie activation while loss of bantam function slows the rate of cell proliferation. bantam is necessary for yorkie-induced overproliferation and bantam overexpression is sufficient to rescue survival and proliferation of yorkie mutant cells. finally, we show that bantam levels are regulated during both developmentally programmed proliferation arrest and apoptosis. in summary, the results show that the hippo pathway regulates expression of bantam to control tissue growth in drosophila.",1
"microrna-182 (mir-182) is significantly downregulated in human gastric tissue samples. overexpression of mir-182 suppresses the proliferation and colony formation of gastric cancer cells. however, new aspects of the mechanism are still emerging in gastric cancer. anubl1, also known as zfand4 (zinc finger, an1-type domain 4), its roles are scarely reported in cancer. in this study, we not only showed that anubl1 as an oncogene was upregulated and could promote proliferation of sgc-7901 cells, but also demonstrated that its over-expression led to a strong decrease of mir-182 expression and expression of anubl1 was in turn directly downregulated by mir-182, thereby establishing a negative feedback loop between mir-182 and anubl1. the elucidation of the mechanisms of mir-182 targeting anubl1 in gastric cancer helps us to further understand the mechanism of gastric cancer initiation and progression.",1
"overexpression of erbb2 or erbb3 is associated with cancer development and poor prognosis. in this study, we show that reactive oxygen species (ros) induce both erbb2 and erbb3 expression in vitro and in vivo. we also identify that mir-199a and mir-125b target erbb2 and/or erbb3 in ovarian cancer cells, and demonstrate that ros inhibit mir-199a and mir-125b expression through increasing the promoter methylation of the mir-199a and mir-125b genes by dna methyltransferase 1. these findings reveal that erbb2 and erbb3 expression is regulated by ros via mir-199a and mir-125b downregulation and dna hypermethylation.",1
"we have isolated clones which complement the temperature sensitivity and abnormal rrna processing pattern of the rrp2-2 mutant of saccharomyces cerevisiae we previously described. dna sequencing and restriction analysis demonstrated that all clones contain the nme1 gene encoding the rna of the ribonucleprotein particle rnase mrp. deletion analysis showed that the nme1 gene is responsible for the complementation of the rrp2-2 phenotype. a single base change was identified in the nme1 gene in the rrp2 mutant, confirming that the rrp2 and nme1 genes are identical. our experiments therefore indicate that rnase mrp, in addition to its previously reported role in formation of rna primers for mitochondrial dna replication , is involved in rrna processing.",1
"purpose to investigate the biological functions of mir-204 in human trabecular meshwork (htm) cells. methods changes in gene expression induced by mir-204 in htm cells were evaluated by gene array analysis using arrays and confirmed by quantitative-pcr (q-pcr). direct targeting of mir-204 to 12 potential novel targets was confirmed using a luciferase system, and five of them were verified by western blot analysis. effects of mir-204 on apoptosis, cell viability, and accumulation of carbonylated proteins were evaluated in htm cells treated with h(2)o(2). induction of endoplasmic reticulum (er) stress markers by tunicamycin was analyzed by q-pcr, and expression of il-8 and il-11 was analyzed by elisa. results mir-204 decreased the expression of multiple genes in htm cells. twelve genes (ap1s2, bcl2l2, birc2, edem1, ezr, fzd1, m6pr, rab22a, rab40b, serp1, tcf12, and tcf4) were validated as direct targets of mir-204. downregulation of expressions at protein levels of bcl2l2, birc2, ezr, m6pr, and serp1 were confirmed by western blot analysis. htm cells transfected with mir-204 showed increased levels of apoptosis, decreased viability, increased accumulation of oxidized proteins after h(2)o(2) treatment, decreased induction of er stress response markers, and reduced expression of inflammatory mediators il-8 and il-11. conclusions mir-204 potentially plays an important role in the regulation of multiple functions in htm cells including apoptosis, accumulation of damaged proteins, er stress response, and expression of inflammatory mediators.",1
"we have characterized a mutation that affects the trnaasp coded by yeast mitochondrial dna. comparison of the dna sequences of the trnaasp gene from a wild type strain and the mutant demonstrates that the mutant differs by a c to u base change in position 72 of the trna. this mutation abolishes mitochondrial protein synthesis, presumably because the trnaasp made from this gene cannot be charged with aspartic acid (faye, g., bolotin-fukuhara, m., and fukuhara, h. (1976) in the genetics and biogenesis of chloroplasts and mitochondria (bucher, c. t., neupert, w., sebalt, w., and werner, s., eds) pp. 547-555, north holland publishing co., amsterdam). it also reduces the amount of trnaasp transcripts in the mutant as compared to the wild type.",1
"innate immune response is the first line of host defense against pathogenic microorganisms, and its excessive or insufficient activation is detrimental to the organism. many individual micrornas (mirnas) have emerged as crucial post-transcriptional regulators of immune homeostasis in drosophila melanogaster . however, the synergistical regulation of mirnas located within a cluster on the imd-immune pathway remains obscured. in our study, a genetic screening with 52 transgenic uas-mirnas was performed to identify ten mirnas or mirna clusters, including the mir310~313 cluster, which may function on imd-dependent immune responses. the mirna rt-qpcr analysis showed that the expression of mir-310~313 cluster members exhibited an increase at 6-12 h post e. coli infection. furthermore, the overexpression of the mir-310~313 cluster impaired the drosophila survival. and the overexpression of mir-310/311/312 reduced dpt expression, an indication of imd pathway induced by gram-negative bacteria. conversely, the knockdown of mir-310/311/312 led to increases in dpt expression. the luciferase reporter expression assays and rt-qpcr analysis confirmed that mir-310~313 cluster members directly co-targeted and inhibited imd transcription. these findings reveal that the members of the mir-310~313 cluster synergistically inhibit imd-dependent immune responses by co-targeting the imd gene in drosophila .",1
"although both u1 and u2 snrnps have been implicated in the splicing process, their respective roles in the earliest stages of intron recognition and spliceosome assembly are uncertain. to address this issue, we developed a new strategy to prepare snrnp-depleted splicing extracts using saccharomyces cerevisiae cells conditionally expressing u1 or u2 snrnp. complementation analyses and chase experiments show that a stable complex, committed to the splicing pathway, forms in the absence of u2 snrnp. u1 snrnp and a substrate containing both a 5' splice site and a branchpoint sequence are required for optimal formation of this commitment complex. we developed new gel electrophoresis conditions to identify these committed complexes and to show that they contain u1 snrna. chase experiments demonstrated that these complexes are functional intermediates in spliceosome assembly and splicing. our results have implications for the process of splice site selection.",1
"mir-150 is a microrna (mirna) specifically expressed in mature lymphocytes, but not their progenitors. a top predicted target of mir-150 is c-myb, a transcription factor controlling multiple steps of lymphocyte development. combining loss- and gain-of-function gene targeting approaches for mir-150 with conditional and partial ablation of c-myb, we show that mir-150 indeed controls c-myb expression in vivo in a dose-dependent manner over a narrow range of mirna and c-myb concentrations and that this dramatically affects lymphocyte development and response. our results identify a key transcription factor as a critical target of a stage-specifically expressed mirna in lymphocytes and suggest that this and perhaps other mirnas have evolved to control the expression of just a few critical target proteins in particular cellular contexts.",1
"despite their different origins, drosophila glia and hemocytes are related cell populations that provide an immune function. drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system, whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. interestingly, the drosophila immune cells within (glia) and outside (hemocytes) the nervous system require the same transcription factor glial cells deficient/glial cells missing (glide/gcm) for their development. this raises the issue of how do glia specifically differentiate in the nervous system, and hemocytes in the procephalic mesoderm. the repo homeodomain transcription factor and panglial direct target of glide/gcm is known to ensure glial terminal differentiation. here we show that repo also takes center stage in the process that discriminates between glia and hemocytes. first, repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. second, repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. third, the lack of repo triggers the expression of hemocyte markers in glia. thus, a complex network of tissue-specific cues biases the potential of glide/gcm. these data allow us to revise the concept of fate determinants and help us to understand the bases of cell specification. both sexes were analyzed. significance statement distinct cell types often require the same pioneer transcription factor, raising the issue of how one factor triggers different fates. in drosophila , glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. while they both require the glial cells deficient/glial cells missing (glide/gcm) transcription factor, glia originate from the ectoderm, and hemocytes from the mesoderm. here we show that tissue-specific factors inhibit the gliogenic potential of glide/gcm in the mesoderm by repressing the expression of the homeodomain protein repo, a major glial-specific target of glide/gcm. repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. these cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification.",1
"to investigate the mechanism of spliceosome assembly in vivo, we performed chromatin immunoprecipitation (chip) analysis of u1, u2, and u5 small nuclear ribonucleoprotein particles (snrnps) to intron-containing yeast (s. cerevisiae) genes. the snrnps display patterns that indicate a cotranscriptional assembly model: u1 first, then u2, and the u4/u6*u5 tri-snrnp followed by u1 destabilization. cis-splicing mutations also support a role of u2 and/or the tri-snrnp in u1 destabilization. moreover, they indicate that splicing efficiency has a major impact on cotranscriptional snrnp recruitment and suggest that cotranscriptional recruitment of u2 or the tri-snrnp is required to commit the pre-mrna to splicing. branchpoint (bp) mutations had a major effect on the u1 pattern, whereas 5' splice site (5'ss) mutations had a stronger effect on the u2 pattern. a 5'ss-u1 snrna complementation experiment suggests that pairing between u1 and the 5'ss occurs after u1 recruitment and contributes to a specific u1:substrate conformation required for efficient u2 and tri-snrnp recruitment.",1
"the receptor for advanced-glycation end products (rage) is upregulated in various cancers and has been associated with tumor progression, but little is known about its expression and regulation by micrornas (mirnas) in esophageal squamous cell carcinoma (escc). here, we describe mir-185, which represses rage expression, and investigate the biological role of mir-185 in escc. in this study, we found that the high level of rage expression in 29 pairs of paraffin-embedded escc tissues was correlated positively with the depth of invasion by immunohistochemistry, suggesting that rage was involved in escc. we used bioinformatics searches and luciferase reporter assays to investigate the prediction that rage was regulated directly by mir-185. besides, overexpression of mir-185 in escc cells was accompanied by 27% (te-11) and 49% (eca-109) reduced rage expression. the effect was further confirmed in rage protein by immunofluorescence in both cell lines. the effects were reversed following cotransfection with mir-185 and high-level expression of the rage vector. furthermore, the biological role of mir-185 in escc cell lines was investigated using assays of cell viability, ki-67 staining, and cell migration and invasion, as well as in a xenograft model. we found that overexpression of mir-185 inhibited migration and invasion by escc cells in vitro and reduced their capacity to develop distal pulmonary metastases in vivo partly through the rage/heat shock protein 27 pathway. interestingly, in clinical specimens, the level of plasma mir-185 expression was decreased significantly (p = 0.002) in patients with escc compared with healthy controls (2.410; 95% ci 0.612-5.671). the value of the area under the receiver-operating characteristic curve was 0.73 (95% ci 0.604-0.855). in conclusion, our findings shed novel light on the role of mir-185/rage in escc metastasis, and plasma mir-185 has potential as a novel diagnostic biomarker in escc.",1
"long non-coding rnas (lncrnas) contribute to the regulation of gene expression in response to intra- or extracellular signals but the underlying molecular mechanisms remain largely unexplored. here, we identify an uncharacterized lncrna as a central player in shaping the meiotic gene expression program in fission yeast. we report that this regulatory rna, termed mamrna, scaffolds the antagonistic rna-binding proteins mmi1 and mei2 to ensure their reciprocal inhibition and fine tune meiotic mrna degradation during mitotic growth. mechanistically, mamrna allows mmi1 to target mei2 for ubiquitin-mediated downregulation, and conversely enables accumulating mei2 to impede mmi1 activity, thereby reinforcing the mitosis to meiosis switch. these regulations also occur within a unique mmi1-containing nuclear body, positioning mamrna as a spatially-confined sensor of mei2 levels. our results thus provide a mechanistic basis for the mutual control of gametogenesis effectors and further expand our vision of the regulatory potential of lncrnas.",1
"the signal transducer and activator of transcription 3 (stat3) signaling pathway was involved in regulation of endothelial cell survival/apoptosis and was regarded as a target for prevention of atherosclerosis or other cardiovascular diseases. factors, regulating stat3 expression and activity, have aroused a wide range of interest, such as mirnas or transcription factors. the aim of this study is to explore the role of mir-351, a mirna found not long before, in the regulation of stat3 expression and endothelial cell survival in the model mice with atherosclerosis (as). expression of mir-351 in the serum and cardiac arterial endothelial cells of the wt mice and as mice was detected. real-time qpcr analysis showed that mir-351 was upregulated in the serum and endothelial cells of the as mice, displaying an opposite expression pattern with stat3. to explore the role and mechanism of mir-351 in the endothelial cell survival, the mir-351 mimic was transfected in to the endothelial cells. mtt and trypan blue assays showed mir-351 attenuated the survival of endothelial cells. our results of the targetscan output and the 3'utr luciferase reporter assay indicated that stat3 was target of mir-351. additionally, mir-351 resisted the elevation of stat3 protein level and promotion of endothelial cell survival caused by sd19. finally, our in vitro angiogenesis assay revealed that mir-351 suppressed angiogenesis and resisted the promotion of angiogenesis caused by sd19. in conclusion, mir-351 was upregulated in the atherosclerotic mice. mir-351 can attenuate the survival of endothelial cells and suppress angiogenesis through targeting stat3 in vitro.",1
"the object of this study was to determine whether the inducer(s) of dna synthesis in mammalian cells accumulates gradually throughout the g1 period or becomes available suddenly at the g1-s transition. hela cells, synchronized at various points in the g1 period, were fused by using uv-inactivated sendai virus. early g1 cells were fused with mid-g1 or late g1 cells and late g1 cells were fused with mid-g1 cells. the g1 traverse of mono-, bi-, and trinucleated cells was studied. the bi- and trinucleated cells of mid-g1 and late g1 parents traversed the g1 period significantly faster than did their mononucleated counterparts. the reduction in the duration of the g1 period was proportional to the number and age of nuclei at the time of fusion. there was no significant difference between the mono- and binucleated cells of the early g1 parent in their rates of entry into s period. in light of these findings, a model is proposed in which the inducer(s) of dna synthesis accumulates gradually throughout the g1 period, reaching a critical level at the g1-s boundary when dna replication is initiated; after reaching a peak during early or mid-s period, it declines to below the critical level when dna synthesis ceases.",1
"aims growing evidences indicate that micrornas (mirnas) are involved in cardiac hypertrophy development. multiple mirnas have been identified as diagnostic and prognostic biomarkers of cardiac hypertrophy, as well as potential therapeutic tools. the present study aimed to investigate the functions and regulatory mechanisms of mir-21-3p in cardiac hypertrophy. methods and results decreased expression of mir-21-3p was observed in cardiac hypertrophy induced by transverse aortic constriction (tac) and angiotensin (ang) ii infusion in mice. to further explore the role of mir-21-3p in cardiac hypertrophy, raav-mir-21-3p was administered intravenously in mice. overexpression of mir-21-3p markedly suppressed tac-induced cardiac hypertrophy and also blocked ang ii-induced cardiac hypertrophy as determined by cardiac function measurement and biomarker detection. furthermore, western blot assays showed that histone deacetylase-8 (hdac8) was silenced by mir-21-3p, and luciferase reporter assays showed that mir-21-3p binds to the 3' utr of hdac8. moreover, re-expression of hdac8 attenuated mir-21-3p-mediated suppression of cardiac hypertrophy by enhancing phospho-akt and phospho-gsk3β expression. conclusion our data reveal a role of mir-21-3p in regulating hdac8 expression and akt/gsk3β pathway, and suggest that modulation of mir-21-3p levels may provide a therapeutic approach for cardiac hypertrophy.",1
"inflammatory responses are complex events occurring when the host immune system fights against invading pathogens, which are double-edged swords requiring appropriate control. micrornas (mirnas), emerging as a new layer of gene-regulation mechanism, have been reported to have crucial effects on inflammation. in the current study, we identified mir-34a, previously known for its potent tumor suppressive role, to be a novel inflammation regulator. we found that the expression of mir-34a was downregulated in macrophages after lipopolysaccharide (lps) stimulation. mir-34a mimics decreased, while the inhibition of mir-34a increased, the expression of inflammatory cytokines tumor necrosis factor- (tnf- ) and interleukin-6 (il-6) in lps treated raw264.7 cells. bioinformatics predictions revealed a potential binding site of mir-34a in 3' untranslated region (utr) of notch1 and it was further confirmed by luciferase assay. moreover, both the mrna and protein level of notch1 were downregulated by mir-34a in raw264.7. subsequently, knockdown of notch1 with either genetic or pharmacological inhibition exhibited similar effects as mir-34a mimics on lps-induced macrophage inflammatory response. furthermore, the nf-κb activation induced by lps was also significantly suppressed by mir-34a. these results together identify, for the first time, mir-34a as a negative regulator in lps-induced inflammation at least partially by targeting notch1. besides extending the knowledge of mir-34a from tumor suppressor to inflammation regulator, this study also provides an implication that compounds which can enhance mir-34a expression or mir-34a itself may hold a promise in anti-inflammatory drugs development.",1
"telomerase is the ribonucleoprotein complex that adds telomeric repeats to the ends of chromosomes. its protein subunit tert is highly conserved among eukaryotes, whereas the rna subunit varies greatly in size and sequence, hindering the identification of telomerase rnas in some important model organisms. here we report the identification and functional characterization of ter1, the telomerase rna component from fission yeast schizosaccharomyces pombe. deletion of ter1+ caused progressive shortening of telomeres and cellular senescence followed by chromosome circularization. interactions between est1 and trt1, the two known protein components of fission yeast telomerase, were dependent on ter1, supporting its role as a scaffold for the assembly of protein subunits. using a series of template mutations, we show that translocation or dissociation site variability and template-primer slippage account for the sequence heterogeneity of fission yeast telomeres.",1
"dosage-sensitive modifier screening is a powerful tool for linking genes to biological processes. use of chromosomal deletions permits sampling the effects of removing groups of genes related by position on the chromosome. here, we explore the use of inducible microrna transgenes as a complement to deficiency-based modifier screens. mirnas are predicted to have hundreds of targets. mirna overexpression provides an efficient means to reduces expression of large gene sets. a collection of transgenes was prepared to allow overexpression of 89 mirnas or mirna clusters. these transgenes and a set of genomic deficiencies were screened for their ability to modify the bristle phenotype of the cell-cycle regulator minus. sixteen mirnas were identified as dominant suppressors, while the deficiency screen uncovered four genomic regions that contain a dominant suppressor. comparing the genes uncovered by the deletions with predicted mirna targets uncovered a small set of candidate suppressors. two candidates were identified as suppressors of the minus phenotype, cullin-4 and cg5199/cut8. additionally, we show that cullin-4 acts through its substrate receptor cdt2 to suppress the minus phenotype. we suggest that inducible microrna transgenes are a useful complement to deficiency-based modifier screens.",1
"micrornas (mirnas) are small non-coding regulatory molecules that influence many biological functions, including apoptosis, but their role in the regulation of apoptosis in gastric tumor cells has not been intensively investigated. here, we showed that mir-100 was specifically upregulated in human epithelium-derived gastric cancer cells and that silencing mir-100 expression in human gastric epithelial cancer cells initiated a robust apoptotic response in vitro. our in vivo assays indicated that the development of gastric cancer was inhibited by the mir-100 antagonism via initiating apoptosis of tumor. the results presented that antagonism of mir-100 increased the expression level of hs3st2, the target gene of mir-100, and further resulted in the activation of the notch-apoptosis pathway in tumor cells. the data also revealed that silencing of mir-100 expression sensitized gastric cancer cells to chemotherapy. therefore our study presented a novel mir-100 mediated notch pathway in apoptosis of tumor cells.",1
"micrornas (mirnas) are a class of small, noncoding rnas that act as key regulators in various physiological and pathological processes. however, the regulatory mechanisms for mirnas in colorectal cancer remain largely unknown. here, we found that mir-103 is up-regulated in colorectal cancer and its overexpression is closely associated with tumor proliferation and migration. in addition, repressing the expression of mir-103 apparently inhibits colorectal cancer cell proliferation and migration in vitro and hct-116 xenograft tumor growth in vivo. subsequent software analysis and dual-luciferase reporter assay identified two tumor suppressor genes dicer and pten as direct targets of mir-103, and up-regulation of dicer and pten obtained similar results to that occurred in the silencing of mir-103. in addition, restoration of dicer and pten can inhibit mir-103-induced colorectal cancer cell proliferation and migration. our data collectively demonstrate that mir-103 is an oncogene mirna that promotes colorectal cancer proliferation and migration through down-regulation of the tumor suppressor genes dicer and pten. thus, mir-103 may represent a new potential diagnostic and therapeutic target for colorectal cancer treatment.",1
"aims aberrant vascular smooth muscle cell (vsmc) proliferation and migration contribute significantly to the development of vascular pathologies, such as atherosclerosis and restenosis. micrornas have recently emerged as critical modulators in cellular processes and the purpose of this study is to identify novel mirna regulators implicated in human aortic vsmc proliferation and migration. methods and results to identify mirnas that are differentially expressed in human vsmcs, we performed mirna microarray analysis in human aortic smooth muscle cells (smcs) at different time points after platelet-derived growth factor (pdgf) stimulation. here, we identified microrna-638 (mir-638) as a transcript that was one of the most significantly down-regulated in human vsmcs after pdgf stimulation. furthermore, we confirmed, by quantitative rt-pcr, that mir-638 is highly expressed in human vsmcs, and its expression is markedly down-regulated in a dose- and time-dependent manner upon pdgf treatment. consistent with a critical role in smc proliferation, we found that mir-638 expression was significantly up-regulated in human vsmcs cultured in differentiation medium, a condition that inhibits smc proliferation. furthermore, we identified the orphan nuclear receptor nor1 as a downstream target gene product of mir-638 and down-regulation of nor1 is critical for mir-638-mediated inhibitory effects on pdgf-induced cyclin d1 expression, cell proliferation, and migration in human aortic smcs. conclusion these results indicate that mir-638 is a key molecule in regulating human vsmc proliferation and migration by targeting the nor1/cyclin d pathway and suggest that specific modulation of mir-638 in human vsmcs may represent an attractive approach for the treatment of proliferative vascular diseases.",1
"microrna deregulation is a critical event in tumor initiation and progression. the down-regulation of microrna-138 has been frequently observed in various cancers, including tongue squamous cell carcinoma (tscc). our previous studies suggest that deregulation of mir-138 is associated with the enhanced proliferation and invasion in tscc cells. here, we seek to identify the targets of mir-138 in tscc, and explore their functional relevance in tumorigenesis. our genome-wide expression profiling experiments identified a panel of 194 unique transcripts that were significantly down-regulated in tscc cells transfected with mir-138. a comprehensive screening using six different sequence-based microrna target prediction algorithms revealed that 51 out of these 194 down-regulated transcripts are potential direct targets for mir-138. these targets include: chloride channel, nucleotide-sensitive, 1a (clns1a), g protein alpha inhibiting activity polypeptide 2 (gnai2), solute carrier family 20, member 1 (slc20a1), eukaryotic translation initiation factor 4e binding protein 1 (eif4ebp1), and rho-related gtp-binding protein c (rhoc). gnai2 is a known proto-oncogene that is involved in the initiation and progression of several different types of tumors. direct targeting of mir-138 to two candidate binding sequences located in the 3'-untranslated region of gnai2 mrna was confirmed using luciferase reporter gene assays. knockdown of mir-138 in tscc cells enhanced the expression of gnai2 at both mrna and protein levels. in contrast, ectopic transfection of mir-138 reduced the expression of gnai2, which, in consequence, led to reduced proliferation, cell cycle arrest and apoptosis. in summary, we identified a number of high-confident mir-138 target genes, including proto-oncogene gnai2, which may play an important role in tscc initiation and progression.",1
"micrornas have been demonstrated as key regulators of gene expression in the etiology of a range of diseases including alzheimer's disease (ad). recently, we identified mir-483-5p as the most upregulated mirna amongst a panel of mirnas in blood plasma specific to prodromal, early-stage alzheimer's disease patients. here, we investigated the functional role of mir-483-5p in ad pathology. using targetscan and mirtarbase, we identified the microtubule-associated protein mapt, often referred to as tau, and the extracellular signal-regulated kinases 1 and 2 (erk1 and erk2), known to phosphorylate tau, as predicted direct targets of mir-483-5p. employing several functional assays, we found that mir-483-5p regulates erk1 and erk2 at both mrna and protein levels, resulting in lower levels of phosphorylated forms of both kinases. moreover, mir-483-5p-mediated repression of erk1/2 resulted in reduced phosphorylation of tau protein at epitopes associated with tau neurofibrillary pathology in ad. these results indicate that upregulation of mir-483-5p can decrease phosphorylation of tau via erk pathway, representing a compensatory neuroprotective mechanism in ad pathology. this mir-483-5p/erk1/tau axis thus represents a novel target for intervention in ad.",1
"bag of marbles (bam) is a stem cell differentiation factor in the drosophila germ line. here, we demonstrate that bam has a crucial function in the lymph gland, the tissue that orchestrates the second phase of drosophila hematopoiesis. in bam mutant larvae, depletion of hematopoietic progenitors is observed, coupled with prodigious production of differentiated hemocytes. conversely, forced expression of bam in the lymph gland results in expansion of prohemocytes and substantial reduction of differentiated blood cells. these findings identify bam as a regulatory protein that promotes blood cell precursor maintenance and prevents hemocyte differentiation during larval hematopoiesis. cell-specific knockdown of bam function via rnai expression revealed that bam activity is required cell-autonomously in hematopoietic progenitors for their maintenance. microrna-7 (mir-7) mutant lymph glands present with phenotypes identical to those seen in bam-null animals and mutants double-heterozygous for bam and mir-7 reveal that the two cooperate to maintain the hematopoietic progenitor population. by contrast, analysis of yan mutant lymph glands revealed that this transcriptional regulator promotes blood cell differentiation and the loss of prohemocyte maintenance. expression of bam or mir-7 in hematopoietic progenitors leads to a reduction of yan protein. together, these results demonstrate that bam and mir-7 antagonize the differentiation-promoting function of yan to maintain the stem-like hematopoietic progenitor state during hematopoiesis.",1
"the distinct phenotypic and prognostic subclasses of human hepatocellular carcinoma (hcc) are difficult to reproduce in animal experiments. here we have used in vivo gene targeting to insert an enhancer-promoter element at an imprinted chromosome 12 locus in mice, thereby converting ∼1 in 20,000 normal hepatocytes into a focus of hcc with a single genetic modification. a 300-kb chromosomal domain containing multiple mrnas, snornas, and micrornas was activated surrounding the integration site. an identical domain was activated at the syntenic locus in a specific molecular subclass of spontaneous human hccs with a similar histological phenotype, which was associated with partial loss of dna methylation. these findings demonstrate the accuracy of in vivo gene targeting in modeling human cancer and suggest future applications in studying various tumors in diverse animal species. in addition, similar insertion events produced by randomly integrating vectors could be a concern for liver-directed human gene therapy.",1
"the male-specific lethal (msl) complex, which includes two noncoding rna on x (rox)1 and rox2 rnas, induces histone h4-lys16 acetylation for twofold hypertranscription of the male x chromosome in drosophila melanogaster. to characterize the role of rox rnas in this process, we have identified evolutionarily conserved functional domains of rox rnas in several drosophila species (eight for rox1 and nine for rox2). despite low homology between them, male-specific expression and x chromosome-specific binding are conserved. within rox rnas of all drosophila species, we found conserved primary sequences, such as guunuacg, in the 3' end of both rox1 (three repeats) and rox2 (two repeats). a predicted stem-loop structure of rox2 rna contains this sequence in the 3' stem region. six tandem repeats of this stem-loop region (72 nt) of rox2 were enough for targeting the msl complex and inducing h4-lys16 acetylation on the x chromosome without other parts of rox2 rna, suggesting that rox rnas might play important roles in regulating enzymatic activity of the msl complex.",1
"objective hippocampal demyelination, a common feature of postmortem multiple sclerosis (ms) brains, reduces neuronal gene expression and is a likely contributor to the memory impairment that is found in >40% of individuals with ms. how demyelination alters neuronal gene expression is unknown. methods to explore whether loss of hippocampal myelin alters expression of neuronal micrornas (mirnas), we compared mirna profiles from myelinated and demyelinated hippocampi from postmortem ms brains and performed validation studies. results a network-based interaction analysis depicts a correlation between increased neuronal mirnas and decreased neuronal genes identified in our previous study. the neuronal mirna mir-124 was increased in demyelinated ms hippocampi and targets mrnas encoding 26 neuronal proteins that were decreased in demyelinated hippocampus, including the ionotrophic glutamate receptors ampa2 and ampa3. hippocampal demyelination in mice also increased mir-124, reduced expression of ampa receptors, and decreased memory performance in water maze tests. remyelination of the mouse hippocampus reversed these changes. interpretation we establish here that myelin alters neuronal gene expression and function by modulating the levels of the neuronal mirna mir-124. inhibition of mir-124 in hippocampal neurons may provide a therapeutic approach to improve memory performance in ms patients.",1
"we previously demonstrated that downregulation of protein kinase ckii induces cellular senescence in human colon cancer hct116 cells. to investigate the role of micrornas (mirnas) in ckii downregulation during senescence, we employed computational algorithms. four mirnas (mir-186, mir-216b, mir-337-3p, and mir-760) were predicted to be mirnas against ckiiα mrna. mimics of all four mirnas jointly downregulated ckiiα expression in hct116 cells. reporter analysis and rt-pcr have suggested that these four mirnas may stimulate degradation of ckiiα mrna by targeting its 3' untranslated regions (utrs). the four mirna mimics increased senescent-associated β-galactosidase (sa-β-gal) staining, p53 and p21(cip1/waf1) expression, and reactive oxygen species (ros) production. in contrast, concomitant knockdown of the four mirnas by antisense inhibitors increased the ckiiα protein level and suppressed ckii inhibition-mediated senescence. finally, ckiiα overexpression antagonized senescence induced by the four mirna mimics. therefore, the present results show that mir-186, mir-216b, mir-337-3p, and mir-760 cooperatively promote cellular senescence through the p53-p21(cip1/waf1) pathway by ckii downregulation-mediated ros production in hct116 cells.",1
"background radiotherapy kills tumor-cells by inducing dna double strand breaks (dsbs). however, the efficient repair of tumors frequently prevents successful treatment. therefore, identifying new practical sensitizers is an essential step towards successful radiotherapy. in this study, we tested the new hypothesis: identifying the mirnas to target dna dsb repair genes could be a new way for sensitizing tumors to ionizing radiation. principal findings here, we chose two genes: dna-pkcs (an essential factor for non-homologous end-joining repair) and atm (an important checkpoint regulator for promoting homologous recombination repair) as the targets to search their regulating mirnas. by combining the database search and the bench work, we picked out mir-101. we identified that mir-101 could efficiently target dna-pkcs and atm via binding to the 3'- utr of dna-pkcs or atm mrna. up-regulating mir-101 efficiently reduced the protein levels of dna-pkcs and atm in these tumor cells and most importantly, sensitized the tumor cells to radiation in vitro and in vivo. conclusions these data demonstrate for the first time that mirnas could be used to target dna repair genes and thus sensitize tumors to radiation. these results provide a new way for improving tumor radiotherapy.",1
"nuclear factor 90 (nf90) is a double-stranded rna-binding protein implicated in multiple cellular functions, but with few identified rna partners. using in vivo cross-linking followed by immunoprecipitation, we discovered a family of small nf90-associated rnas (snar). these highly structured non-coding rnas of approximately 117 nucleotides are expressed in immortalized human cell lines of diverse lineages. in human tissues, they are abundant in testis, with minor distribution in brain, placenta and some other organs. two snar subsets were isolated from human 293 cells, and additional species were found by bioinformatic analysis. their genes often occur in multiple copies arranged in two inverted regions of tandem repeats on chromosome 19. snar-a is transcribed by rna polymerase iii from an intragenic promoter, turns over rapidly, and shares sequence identity with alu rna and two potential pirnas. it interacts with nf90's double-stranded rna-binding motifs. snar orthologs are present in chimpanzee but not other mammals, and include genes located in the promoter of two chorionic gonadotropin hormone genes. snars appear to have undergone accelerated evolution and differential expansion in the great apes.",1
"background/aims osteogenic differentiation of mesenchymal stem cells (mscs) plays a crucial role in bone regeneration and bone reparation. this complex process is regulated precisely and firmly by specific factors. recent studies have demonstrated that mir-125b regulates osteogenic differentiation, but little is known about the molecular mechanisms of this regulation. furthermore, how mir-125b regulates the osteogenic differentiation of mscs still needs elucidation. methods in the present study, human bone marrow-derived mesenchymal stem cells (hbmscs) were isolated and induced to osteoblasts with mir-125b inhibition or overexpression. qrt-pcr and western blot analysis were used to detect the expression of osteogenic marker genes and proteins. alkaline phosphatase (alp) and alizarin red (ars) staining were performed to evaluate the osteoblast phenotype. targetscan, pictar and miranda database were used to predict the target gene of mir-125b. dual luciferase reporter assay and rna interference were performed to verify the target gene. micro-ct imaging and histochemical staining were used to investigate the bone defect repair capacity of mir-125b in vivo. results we observed that mir-125b was expressed at a low level during the osteogenic differentiation of hbmscs. then, we found that osteogenic marker genes were negatively regulated by mir-125b during the course of osteogenic differentiation, suggesting that mir-125b down regulation plays an important role in the process of osteogenic differentiation. bioinformatics approaches using mirna target prediction algorithms indicated that the bone morphogenetic protein type ib receptor (bmpr1b) is a potential target of mir-125b. the results of the dual luciferase reporter assay indicated that mir-125b binds to the 3'-utr of the bmpr1b gene. we observed that knockdown of bmpr1b by sirna inhibited the osteogenic differentiation of hbmscs. furthermore, by co-transfecting cells with an mir-125b inhibitor and si-bmpr1b, we found that the osteogenic capacity of the cells transfected with mir-125b inhibitor was blocked upon knockdown of bmpr1b. in vivo, demineralized bone matrix (dbm) was composited with hbmscs as a scaffold to repair segmental femoral defects. by inhibiting the expression of mir-125b, hbmscs showed a better capacity to repair bone defects. conclusions taken together, our study demonstrated that mir-125b regulated the osteogenic differentiation of hbmscs by targeting bmpr1b and that inhibiting mir-125b expression could enhance the capacity of bone defect repair in vivo.",1
"the let-7 tumor suppressor micrornas are known for their regulation of oncogenes, while the rna-binding proteins lin28a/b promote malignancy by inhibiting let-7 biogenesis. we have uncovered unexpected roles for the lin28/let-7 pathway in regulating metabolism. when overexpressed in mice, both lin28a and lin28b promote an insulin-sensitized state that resists high-fat-diet induced diabetes. conversely, muscle-specific loss of lin28a or overexpression of let-7 results in insulin resistance and impaired glucose tolerance. these phenomena occur, in part, through the let-7-mediated repression of multiple components of the insulin-pi3k-mtor pathway, including igf1r, insr, and irs2. in addition, the mtor inhibitor, rapamycin, abrogates lin28a-mediated insulin sensitivity and enhanced glucose uptake. moreover, let-7 targets are enriched for genes containing snps associated with type 2 diabetes and control of fasting glucose in human genome-wide association studies. these data establish the lin28/let-7 pathway as a central regulator of mammalian glucose metabolism.",1
"micrornas (mirnas) are short, single-stranded, noncoding rnas that play important roles in the regulation of gene expression. we previously identified a characteristic mirna expression profile in psoriasis, distinct from that of healthy skin. one of the most downregulated mirnas in psoriasis skin was microrna-125b (mir-125b). in this study, we aimed to identify the potential role(s) of mir-125b in psoriasis pathogenesis. in situ hybridization results showed that the major cell type responsible for decreased mir-125b levels in psoriasis lesions was the keratinocyte. overexpression of mir-125b in primary human keratinocytes suppressed proliferation and induced the expression of several known differentiation markers. conversely, inhibition of endogenous mir-125b promoted cell proliferation and delayed differentiation. fibroblast growth factor receptor 2 (fgfr2) was identified as one of the direct targets for suppression by mir-125b by luciferase reporter assay. the expression of mir-125b and fgfr2 was inversely correlated in both transfected keratinocytes and in psoriatic skin. knocking down fgfr2 expression by sirna suppressed keratinocyte proliferation, but did not enhance differentiation. altogether, our results demonstrate a role for mir-125b in the regulation of keratinocyte proliferation and differentiation, partially through the regulation of fgfr2. loss of mir-125b in psoriasis skin may contribute to hyperproliferation and aberrant differentiation of keratinocytes.",1
"rnase mrp and rnase p ribonucleoproteins are structurally and functionally similar across a large evolutionary distance. to better characterize possible complex interrelationships between these two enzymes, we have employed the fission yeast schizosaccharomyces pombe. unlike saccharomyces cerevisiae, s. pombe is believed to harbour only one genetic locus for the rna component of rnase p and does not contain a known mitochondrially encoded rnase p rna. we have identified the single nuclear gene for the rna component of rnase mrp in s. pombe, mrp-1, by homology to vertebrate rnase mrp rnas. the mrp-1 gene encodes an rna of maximum mature length 400 nucleotides that shares a high degree of identity, in evolutionarily conserved regions, to both vertebrate rnase mrp rnas and s. pombe rnase p rna. disruption of mrp-1 in the diploid strain sp826 and sporulation of tetrads resulted in a 2 dead:2 viable segregation, consistent with the gene being essential. lethality is rescued by a plasmid-borne copy of mrp-1. partially purified ribonucleoprotein rnase mrp activity correctly and efficiently processed all previously characterized heterologous mitochondrial rna substrates. the compact mitochondrial genome of s. pombe contains sequence elements with > 50% identity to mammalian d-loop csbi and csbii elements. the identification of mrp-1 in s. pombe should facilitate not only comparisons between the related ribonucleoproteins rnase mrp and rnase p, but should also provide an opportunity for genetic elucidation of rnase mrp function in a situation reflective of the animal kingdom.",1
"rnase e is a key regulatory enzyme that controls the principal pathway for mrna degradation in escherichia coli. the cellular concentration of this endonuclease is governed by a feedback mechanism in which rnase e tightly regulates its own synthesis. autoregulation is mediated in cis by the 361-nucleotide 5' untranslated region (utr) of rne (rnase e) mrna. here we report the determination of the secondary structure of the rne 5' utr by phylogenetic comparison and chemical alkylation, together with dissection studies to identify the 5' utr element that mediates autoregulation. our findings reveal that the structure and function of the rne 5' utrs are evolutionarily well conserved despite extensive sequence divergence. within the rne 5' utrs are multiple rna secondary structure elements, two of which function in cis to mediate feedback regulation of rne gene expression. the more potent of these two elements is a stem-loop structure containing an internal loop whose sequence is the most highly conserved of any region of the rne 5' utr. our data show that this stem-loop functions as a sensor of cellular rnase e activity that directs autoregulation by modulating the degradation rate of rne mrna in response to changes in rnase e activity.",1
"phenylalanine hydroxylase deficient phenylketonuria (pku) is the paradigm for a treatable inborn error of metabolism where maintaining plasma phenylalanine (phe) in the therapeutic range relates to improved clinical outcomes. while phe is the presumed intoxicating analyte causal in neurologic damage, the mechanism(s) of phe toxicity has remained elusive. altered dna methylation is a recognized response associated with exposure to numerous small molecule toxic agents. paralleling this effect, we hypothesized that chronic phe over-exposure in the brain would lead to aberrant dna methylation with secondary influence upon gene regulation that would ultimately contribute to pku neuropathology. the pah(enu2) mouse models human pku with intrinsic hyperphenylalaninemia, abnormal response to phe challenge, and neurologic deficit. to examine this hypothesis, we assessed dna methylation patterns in brain tissues using methylated dna immunoprecipitation and paired end sequencing in adult pah(enu2) animals maintained under either continuous dietary phe restriction or chronic hyperphenylalaninemia. heterozygous pah(enu2/wt) litter mates served as controls for normal phe exposure. extensive repatterning of dna methylation was observed in brain tissue of hyperphenylalaninemic animals while phe restricted animals displayed an attenuated pattern of aberrant dna methylation. affected gene coding regions displayed aberrant hypermethylation and hypomethylation. gene body methylation of noncoding rna genes was observed and among these microrna genes were prominent. of particular note, observed only in hyperphenylalaninemic animals, was hypomethylation of mirna genes within the imprinted dlk1-dio3 locus on chromosome 12. aberrant methylation of microrna genes influenced their expression which has secondary effects upon the expression of targeted protein coding genes. differential hypermethylation of gene promoters was exclusive to hyperphenylalaninemic pah(enu2) animals. genes with synaptic involvement were targets of promoter hypermethylation that resulted in down-regulation of their expression. gene dysregulation secondary to abnormal dna methylation may be contributing to pku neuropathology. these results suggest drugs that prevent or correct aberrant dna methylation may offer a novel therapeutic option to management of neurological symptoms in pku patients.",1
"cell cycle arrest in response to dna damage is an important antitumorigenic mechanism. micrornas (mirnas) were recently shown to play key regulatory roles in cell cycle progression. for example, mir-34a is induced in response to p53 activation and mediates g(1) arrest by down-regulating multiple cell cycle-related transcripts. here we show that genotoxic stress promotes the p53-dependent up-regulation of the homologous mirnas mir-192 and mir-215. like mir-34a, activation of mir-192/215 induces cell cycle arrest, suggesting that multiple mirna families operate in the p53 network. furthermore, we define a downstream gene expression signature for mir-192/215 expression, which includes a number of transcripts that regulate g(1) and g(2) checkpoints. of these transcripts, 18 transcripts are direct targets of mir-192/215, and the observed cell cycle arrest likely results from a cooperative effect among the modulations of these genes by the mirnas. our results showing a role for mir-192/215 in cell proliferation combined with recent observations that these mirnas are underexpressed in primary cancers support the idea that mir-192 and mir-215 function as tumor suppressors.",1
"endothelial cell migration induced in response to vascular endothelial growth factor (vegf) is an essential step of angiogenesis. it depends in part on the activation of the p38/mapkap kinase-2/limk1/annexin-a1 (anxa1) signaling axis. in the present study, we obtained evidence indicating that mir-196a specifically binds to the 3'-utr region of anxa1 mrna to repress its expression. in accordance with the role of anxa1 in cell migration and angiogenesis, the ectopic expression of mir-196a is associated with decreased cell migration in wound closure assays, and the inhibitory effect of mir-196a is rescued by overexpressing anxa1. this finding highlights the fact that anxa1 is a required mediator of vegf-induced cell migration. mir-196a also reduces the formation of lamellipodia in response to vegf suggesting that anxa1 regulates cell migration by securing the formation of lamellipodia at the leading edge of the cell. additionally, in line with the fact that cell migration is an essential step of angiogenesis, the ectopic expression of mir-196a impairs the formation of capillary-like structures in a tissue-engineered model of angiogenesis. here again, the effect of mir-196a is rescued by overexpressing anxa1. moreover, the presence of mir-196a impairs the vegf-induced in vivo neo-vascularization in the matrigel plug assay. interestingly, vegf reduces the expression of mir-196a, which is associated with an increased level of anxa1. similarly, the inhibition of mir-196a with an antagomir results in an increased level of anxa1. we conclude that the vegf-induced decrease of mir-196a expression may participate to the angiogenic switch by maintaining the expression of anxa1 to levels required to enable p38-anxa1-dependent endothelial cell migration and angiogenesis in response to vegf.",1
"rationale mammalian cardiomyocytes withdraw from the cell cycle during early postnatal development, which significantly limits the capacity of the adult mammalian heart to regenerate after injury. the regulatory mechanisms that govern cardiomyocyte cell cycle withdrawal and binucleation are poorly understood. objective given the potential of micrornas (mirnas) to influence large gene networks and modify complex developmental and disease phenotypes, we searched for mirnas that were regulated during the postnatal switch to terminal differentiation. methods and results microarray analysis revealed subsets of mirnas that were upregulated or downregulated in cardiac ventricles from mice at 1 and 10 days of age (p1 and p10). interestingly, mir-195 (a member of the mir-15 family) was the most highly upregulated mirna during this period, with expression levels almost 6-fold higher in p10 ventricles relative to p1. precocious overexpression of mir-195 in the embryonic heart was associated with ventricular hypoplasia and ventricular septal defects in β-myosin heavy chain-mir-195 transgenic mice. using global gene profiling and argonaute-2 immunoprecipitation approaches, we showed that mir-195 regulates the expression of a number of cell cycle genes, including checkpoint kinase 1 (chek1), which we identified as a highly conserved direct target of mir-195. finally, we demonstrated that knockdown of the mir-15 family in neonatal mice with locked nucleic acid-modified anti-mirnas was associated with an increased number of mitotic cardiomyocytes and derepression of chek1. conclusions these findings suggest that upregulation of the mir-15 family during the neonatal period may be an important regulatory mechanism governing cardiomyocyte cell cycle withdrawal and binucleation.",1
"many plant viral rnas lack the 5'-cap structure that is required on all host mrnas for interacting with essential translation initiation factors. instead, uncapped viral rnas take over the host translation machinery by harbouring sequences that functionally replace the 5'-cap. recent reports reveal at least eight different classes of cite (cap-independent translation element) located in the 3'-utrs (untranslated regions) of various viruses. we describe how the structure and behaviour of each class of element differs from the other classes, suggesting that they recruit translation factors and, ultimately, the ribosome by diverse mechanisms. these results greatly expand our understanding of ways in which mrnas can recruit ribosomes, and they provide insight into the regulation of virus gene expression.",1
"amyloid precursor protein (app) has an important function in the generation of alzheimer's disease (ad). in our previous study, mir‑193b was found to be downregulated in the hippocampi of 9‑month‑old app/ps1 double‑transgenic mice using microrna (mir) array. in the present study, bioinformatic analyses showed that mir‑193b was a mir that was predicted to potentially target the 3'‑untranslated region (utr) of app. subsequently, the function of mir‑193b on app was studied. the levels of mir‑193b, exosomal mir‑193b, aβ, tau, p‑tau, hcy and apoe in samples from app/ps1 double‑transgenic mice, mild cognitive impairment (mci) and dementia of alzheimer‑type (dat) patients, were measured. the results indicated that overexpression of mir‑193b could repress the mrna and protein expression of app. the mir‑193b inhibitor oligonucleotide induced upregulation of app. binding sites of mir‑193b in the 3'‑utr of app were identified by luciferase assay. mci and dat patients had lower exosomal mir‑193b, but not total mir‑193b, in the blood as compared with the controls. dat patients had lower exosomal mir‑193b levels in blood as compared with the mci group. a decreased exosomal mir‑193b expression level was additionally observed in the cerebral spinal fluid (csf) of dat patients. negative correlations were found between exosomal mir‑193b and aβ42 in the csf of dat patients. in conclusion, these findings showed that mir‑193b may function in the development of ad and exosomal mir‑193b has potential as a novel, non-invasive, blood‑based biomarker of mci and dat patients.",1
"microrna regulation of transcript expression has been reported in patients with alzheimer's disease (ad). here, we investigate the role of microrna-146a (mirna-146a), a brain-enriched mirna, which is upregulated in ad patients. through analysis of predicted targets of mirna-146a, low-density lipoprotein receptor-related protein-2 (lrp2), a member of the ldlr family that is known to play a protective role in ad, was identified. overexpression of mirna-146a in sh-sy5y cells significantly decreased lrp2 expression, resulting in a reduction of akt activation and induction of proapoptotic caspase-3, thereby increasing cell apoptosis. thus, specific mirna-146a regulation may contribute to ad by downregulating the lrp2/akt pathway.",1
"micrornas are a class of small non-coding rnas and participate in the regulation of apoptotic program. although mir-21 is able to inhibit apoptosis, its expression regulation and downstream targets remain to be fully elucidated. here we report that the transcriptional factor foxo3a initiates apoptosis by transcriptionally repressing mir-21 expression. our results showed that doxorubicin could simultaneously induce the translocation of foxo3a to the cell nuclei and a reduction in mir-21 expression. knockdown of foxo3a resulted in an elevation in mir-21 levels, whereas enforced expression of foxo3a led to a decrease in mir-21 expression. in exploring the molecular mechanism by which foxo3a regulates mir-21, we observed that foxo3a bound to the promoter region of mir-21 and suppressed its promoter activity. these results indicate that foxo3a can transcriptionally repress mir-21 expression. in searching for the downstream targets of mir-21 in apoptosis, we found that mir-21 suppressed the translation of fas ligand (fasl), a pro-apoptotic factor. furthermore, foxo3a was able to up-regulate fasl expression through down-regulating mir-21. our data suggest that foxo3a negatively regulates mir-21 in initiating apoptosis.",1
"oligonucleotides derived from the spacer element of the histone rna 3' processing signal were used to characterize mouse u7 small nuclear rna (snrna), i.e., the snrna component active in 3' processing of histone pre-mrna. under rnase h conditions, such oligonucleotides inhibited the processing reaction, indicating the formation of a dna-rna hybrid with a functional ribonucleoprotein component. moreover, these oligonucleotides hybridized to a single nuclear rna species of approximately 65 nucleotides. the sequence of this rna was determined by primer extension experiments and was found to bear several structural similarities with sea urchin u7 snrna. the comparison of mouse and sea urchin u7 snrna structures yields some further insight into the mechanism of histone rna 3' processing.",1
"small nucleolar rnas (snornas) play an important role in eukaryotic rrna biogenesis. by combination of a computer search of embl database and experimental procedure, a novel snorna coding sequence (z8) was screened out and characterized from yeastsaccharomyces cerevisiue genome. z8 snorna gene codes a boxc/d antisense snorna which guides, deduced from structure analysis, the 2'-o-ribose methylation at u(2421) of 25s rrna. after disruption of z8 snorna gene, the methylation at corresponding site was abolished, but no gmwth delay was observed in various cultural temperatures. z8 dna is the first gene of a gene cluster consisting of three cognate snorna genes which are located on an intergenic region of chromosome xiii. this gene cluster is co-transcribed as a polycistronic precursor from a + 247 bp u snorna gene promoter, followed by processing to release individual snornas, representing a new expression pattern of snorna genes.",1
"current genome-wide microrna (mirna) expression signature analysis using deep sequencing technologies can drive the discovery of novel cancer pathways regulated by oncogenic and/or tumor suppressive mirnas. we determined the genome-wide mirna expression signature in bladder cancer (bc) by deep sequencing technology. a total of ten small rna libraries were sequenced (five bcs and five samples of histologically normal bladder epithelia (nbe)), and 13,190,619 to 18,559,060 clean small rna reads were obtained. a total of 933 known mirnas and 17 new mirna candidates were detected in this analysis. among the known mirnas, a total of 60 mirnas were significantly downregulated in bc compared with nbe. we also found that several mirnas, such as mir-1/133a, mir-206/133b, let-7c/mir-99a, mir-143/145 and mir-195/497, were located close together at five distinct loci and constituted clustered mirnas. among these clustered mirnas, we focused on the mir-195/497 cluster because this clustered mirna had not been analyzed in bc. transfection of mature mir-195 or mir-497 in two bc cell lines (boy and t24) significantly inhibited cancer cell proliferation, migration and invasion, suggesting that the mir-195/497 cluster functioned as tumor suppressors in bc. regarding the genes targeted by the mir-195/497 cluster, the targetscan algorithm showed that 6,730 genes were putative mir-195/497 targets, and 113 significantly enriched signaling pathways were identified in this analysis. the ""pathways in cancer"" category was the most enriched, involving 104 candidate target genes. gene expression data revealed that 27 of 104 candidate target genes were actually upregulated in bc clinical specimens. luciferase reporter assays and western blotting demonstrated that birc5 and wnt7a were directly targeted by mir-195/497. in conclusion, aberrant expression of clustered mirnas was identified by deep sequencing, and downregulation of mir-195/497 contributed to bc progression and metastasis. tumor suppressive mirna-mediated cancer pathways provide new insights into the potential mechanisms of bc oncogenesis.",1
"background endothelial cells (ecs) form blood vessels through angiogenesis that is regulated by coordination of vascular endothelial growth factor (vegf), notch, transforming growth factor β, and other signals, but the detailed molecular mechanisms remain unclear. methods and results small rna sequencing initially identified mir-342-5p as a novel downstream molecule of notch signaling in ecs. reporter assay, quantitative reverse transcription polymerase chain reaction and western blot analysis indicated that mir-342-5p targeted endoglin and modulated transforming growth factor β signaling by repressing smad1/5 phosphorylation in ecs. transfection of mir-342-5p inhibited ec proliferation and lumen formation and reduced angiogenesis in vitro and in vivo, as assayed by using a fibrin beads-based sprouting assay, mouse aortic ring culture, and intravitreal injection of mir-342-5p agomir in p3 pups. moreover, mir-342-5p promoted the migration of ecs, accompanied by reduced endothelial markers and increased mesenchymal markers, indicative of increased endothelial-mesenchymal transition. transfection of endoglin at least partially reversed endothelial-mesenchymal transition induced by mir-342-5p. the expression of mir-342-5p was upregulated by transforming growth factor β, and inhibition of mir-342-5p attenuated the inhibitory effects of transforming growth factor β on lumen formation and sprouting by ecs. in addition, vegf repressed mir-342-5p expression, and transfection of mir-342-5p repressed vegfr2 and vegfr3 expression and vegf-triggered akt phosphorylation in ecs. mir-342-5p repressed angiogenesis in a laser-induced choroidal neovascularization model in mice, highlighting its clinical potential. conclusions mir-342-5p acts as a multifunctional angiogenic repressor mediating the effects and interaction among angiogenic pathways.",1
"γ-synuclein is a member of the synucleins family of small proteins, which consists of three members:α, β- and γ-synuclein. γ-synuclein is abnormally expressed in a high percentage of advanced and metastatic tumors, but not in normal or benign tissues. furthermore, γ-synuclein expression is strongly correlated with disease progression, and can stimulate proliferation, induce invasion and metastasis of cancer cells. γ-synuclein transcription is regulated basically through the binding of ap-1 to specific sequences in intron 1. here we show that γ-synuclein expression may be also regulated by micro rnas (mirs) on post-transcriptional level. according to prediction by several methods, the 3'-untranslated region (utr) of γ-synuclein gene contains targets for mirs. insertion of γ-synuclein 3'-utr downstream of the reporter luciferase (luc) gene causes a 51% reduction of luc activity after transfection into skbr3 and y79 cells, confirming the presence of efficient targets for mirs in this fragment. expression of mir-4437 and mir-4674 for which putative targets in 3'-utr were predicted caused a 61.2% and 60.1% reduction of endogenous γ-synuclein expression confirming their role in gene expression regulation. on the other hand, in cells overexpressing γ-synuclein no significant effect of mirs on γ-synuclein expression was found suggesting that mirs exert their regulatory effect only at low or moderate, but not at high level of γ-synuclein expression. elevated level of γ-synuclein differentially changes the level of several mirs expression, upregulating the level of some mirs and downregulating the level of others. three mirs upregulated as a result of γ-synuclein overexpression, i.e., mir-885-3p, mir-138 and mir-497 have putative targets in 3'-utr of the γ-synuclein gene. some of mirs differentially regulated by γ-synuclein may modulate signaling pathways and cancer related gene expression. this study demonstrates that mirs might provide cell-specific regulation of γ-synuclein expression and set the stage to further evaluate their role in pathophysiological processes.",1
"microrna dysregulation is observed in different types of cancer. mir-21 up-regulation has been reported for the majority of cancers profiled to date; however, knowledge is limited on the mechanism of action of mir-21, including identification of functionally important targets that contribute to its proproliferative and antiapoptotic actions. in this study, we show for the first time that mir-21 targets multiple important components of the p53, transforming growth factor-beta (tgf-beta), and mitochondrial apoptosis tumor-suppressive pathways. down-regulation of mir-21 in glioblastoma cells leads to derepression of these pathways, causing repression of growth, increased apoptosis, and cell cycle arrest. these phenotypes are dependent on two of the mir-21 targets validated in this study, hnrpk and tap63. these findings establish mir-21 as an important oncogene that targets a network of p53, tgf-beta, and mitochondrial apoptosis tumor suppressor genes in glioblastoma cells.",1
"hepatic steatosis is a global epidemic that is thought to contribute to the pathogenesis of type 2 diabetes. micrornas (mirs) are regulators that can functionally integrate a range of metabolic and inflammatory pathways in liver. we aimed to investigate the functional role of mir-155 in hepatic steatosis. male c57bl/6 wild-type (wt) and mir-155(-/-) mice were fed either normal chow or high fat diet (hfd) for 6 months then lipid levels, metabolic and inflammatory parameters were assessed in livers and serum of the mice. mice lacking endogenous mir-155 that were fed hfd for 6 months developed increased hepatic steatosis compared to wt controls. this was associated with increased liver weight and serum vldl/ldl cholesterol and alanine transaminase (alt) levels, as well as increased hepatic expression of genes involved in glucose regulation (pck1, cebpa), fatty acid uptake (cd36) and lipid metabolism (fasn, fabp4, lpl, abcd2, pla2g7). using mirna target prediction algorithms and the microarray transcriptomic profile of mir-155(-/-) livers, we identified and validated that nr1h3 (lxrα) as a direct mir-155 target gene that is potentially responsible for the liver phenotype of mir-155(-/-) mice. together these data indicate that mir-155 plays a pivotal role regulating lipid metabolism in liver and that its deregulation may lead to hepatic steatosis in patients with diabetes.",1
"background adaptive neovascularization after arterial occlusion is an important compensatory mechanism in cardiovascular disease and includes both the remodeling of pre-existing vessels to collateral arteries (arteriogenesis) and angiogenic capillary growth. we now aimed to identify regulatory micrornas involved in the modulation of neovascularization after femoral artery occlusion in mice. methods and results using microrna-transcriptome analysis, we identified mir-155 as a downregulated microrna during hindlimb ischemia. correspondingly, inhibition of mir-155 in endothelial cells had a stimulatory effect on proliferation and angiogenic tube formation via derepression of its direct target gene angiotensin ii type 1 receptor. surprisingly, mir-155-deficient mice showed an unexpected phenotype in vivo, with a strong reduction of blood flow recovery after femoral artery ligation (arteriogenesis) dependent on the attenuation of leukocyte-endothelial interaction and a reduction of proarteriogenic cytokine expression. consistently, mir-155-deficient macrophages exhibit a specific alteration of the proarteriogenic cytokine expression profile, which is partly mediated by the direct mir-155 target gene socs-1. conclusions our data demonstrate that mir-155 exerts an antiangiogenic but proarteriogenic function in the regulation of neovascularization via the suppression of divergent cell-specific target genes and that its expression in both endothelial and bone marrow-derived cells is essential for arteriogenesis in response to hindlimb ischemia in mice.",1
"micrornas (mirnas) are a class of small regulatory rnas that are thought to be involved in diverse biological processes by regulating gene expression. numerous mirnas have been identified in various species, and many more mirnas remain to be detected. generally, hundreds of mrnas have been predicted to be potential targets of one mirna, so it is a great challenge to identify the genuine mirna targets. here, we generated the cell lines depleted of drosha protein and screened dozens of transcripts (including cyclin d1) regulated potentially by mirna-mediated rna silencing pathway. on the basis of mirna expressing library, we established a mirna targets reverse screening method by using luciferase reporter assay. by this method, we found that the expression of cyclin d1 (ccnd1) was regulated by mir-16 family directly, and mir-16 induced g1 arrest in a549 cells partially by ccnd1. furthermore, several other cell cycle genes were revealed to be regulated by mir-16 family, including cyclin d3 (ccnd3), cyclin e1 (ccne1) and cdk6. taken together, our data suggests that mir-16 family triggers an accumulation of cells in g0/g1 by silencing multiple cell cycle genes simultaneously, rather than the individual target.",1
"glioblastoma (gbm) proliferation is a multistep process during which the expression levels of many genes that control cell proliferation, cell death, and genetic stability are altered. micrornas (mirnas) are emerging as important modulators of cellular signaling, including cell proliferation in cancer. in this study, using next generation sequencing analysis of mirnas, we found that mir-127-3p was downregulated in gbm tissues compared with normal brain tissues; we validated this result by rt-pcr. we further showed that dna demethylation and histone deacetylase inhibition resulted in downregulation of mir-127-3p. we demonstrated that mir-127-3p overexpression inhibited gbm cell growth by inducing g1-phase arrest both in vitro and in vivo. we showed that mir-127-3p targeted ski (v-ski sarcoma viral oncogene homolog ), rgma (rgm domain family, member a), zwint (zw10 interactor, kinetochore protein), serpinb9 (serpin peptidase inhibitor, clade b , member 9), and sfrp1 (secreted frizzled-related protein 1). finally, we found that mir-127-3p suppressed gbm cell growth by inhibiting tumor-promoting ski and activating the tumor suppression effect of transforming growth factor-β (tgf-β) signaling. this study showed, for the first time, that mir-127-3p and its targeted gene ski, play important roles in gbm and may serve as potential targets for gbm therapy.",1
"the saccharomyces cerevisiae telomerase rna subunit is encoded by the tlc1 gene. a selection for viable alleles of tlc1 rna from a large library of random deletion alleles revealed that less than half (approximately 0.5 kb of the approximately 1.3-kb rna) is required for telomerase function in vivo. the main essential region (430 nucleotides), which contains the template for telomeric dna synthesis, was required for coimmunoprecipitation with est1p and est2p. furthermore, the subregion required for interaction with est1p, the telomerase recruitment subunit, differed from those required for interaction with est2p, the reverse transcriptase subunit. two regions of the rna distant from the template in the nucleotide sequence were required for est2p binding, but the template itself was not. having the rna secured to the protein away from the template is proposed to facilitate the translocation of the rna template through the active site. more generally, our results support a role for the telomerase rna serving as a scaffold for binding key protein subunits.",1
"in cancers with wild-type (wt) p53 status, the function of p53 is inhibited through direct interaction with mdm2 oncoprotein, a negative feedback loop to limit the function of p53. in response to cellular stress, p53 escapes the p53:mdm2 negative feedback to accumulate rapidly to induce cell cycle arrest and apoptosis. we demonstrate herein that an microrna mir-605 is a new component in the p53 gene network, being transcriptionally activated by p53 and post-transcriptionally repressing mdm2. activation of p53 upregulated mir-605 via interacting with the promoter region of the gene. overexpression of mir-605 directly decreased mdm2 expression at the post-transcriptional level but indirectly increased the transcriptional activity of p53 on mir-34a via downregulating mdm2; knockdown of mir-605 did the opposite. mdm2 inhibitor upregulated expression of both mir-34a and mir-605, which was mitigated by p53 inhibitor. mir-605 preferentially induced apoptosis in wt p53-expressing cells, an effect abolished by p53 inhibition. these results indicate that mir-605 acts to interrupt p53:mdm2 interaction to create a positive feedback loop aiding rapid accumulation of p53 to facilitate its function in response to stress.",1
"although microrna-1 (mir-1) is a known liver cancer suppressor, the role of mir-1 in apoptosis of hepatoma cells has remained largely unknown. our study shows that ectopic mir-1 overexpression induced apoptosis of liver hepatocellular carcinoma (hepg2) cells. apoptosis inhibitor 5 (api-5) was found to be a potential regulator of mir-1 induced apoptosis, using a bioinformatics approach. furthermore, an inverse relationship between mir-1 and api-5 expression was observed in human liver cancer tissues and adjacent normal liver tissues. negative regulation of api-5 expression by mir-1 was demonstrated to promote apoptosis of hepg2 cells. our study provides a novel regulatory mechanism of mir-1 in the apoptosis of hepatoma cells.",1
"resistance to chemotherapy is a major obstacle for the effective treatment of advanced ovarian cancer. the mechanism of chemoresistance is still poorly understood. recently, more and more evidence showed micrornas (mirnas) modulated many key molecules and pathways involved in chemotherapy. microrna-106a (mir-106a) has been implicated in many cancers, but its role in ovarian cancer and drug resistance still remains unexplored. this study was to investigate whether mir-106a mediated resistance of the ovarian cancer cell line a2780 to the chemotherapeutic agent cisplatin (ddp). the different levels of mir-106a in a2780 cells and their resistant variant a2780/ddp cells were identified by using real-time pcr. mtt assay and flow cytometry were used to analyze the effect of mir-106a on cisplatin resistance of these paired cells. real-time pcr, western blotting and luciferase reporter assay were applied to explore whether mcl-1 was a target of mir-106a. as compared to a2780 cells, the expression of mir-106a was down-regulated in the cisplatin resistant cell line a2780/ddp. moreover, knockdown of mir-106a dramatically decreased antiproliferative effects and apoptosis induced by cisplatin in a2780 cells, while overexpression of mir-106a significantly increased antiproliferative effects and apoptosis induced by cisplatin in a2780/ddp cells. furthermore, mir-106a inhibited cell survival and cisplatin resistance through downregulating the expression of mcl-1. mcl-1 was a direct target of mir-106a. these results suggest that mir-106a may provide a novel mechanism for understanding cisplatin resistance in ovarian cancer by modulating mcl-1.",1
"micrornas (mirnas) regulate gene expression by repressing target genes at the posttranscriptional level. since mirnas have unique expression profiles in different tissues, they provide pivotal regulation of many biological processes. the present study defined mirna expression during murine myogenic progenitor cell (mpc) proliferation and differentiation to identify mirnas involved in muscle regeneration. muscle-related gene expression analyses revealed that the time course and expression of myosin heavy chain (mhc) and transcription factors (myf5, myod, myogenin, and pax7) were similar during in vitro mpc proliferation/differentiation and in vivo muscle regeneration. comprehensive profiling revealed that 139 or 16 mirnas were significantly changed more than twofold [false discovery rate (fdr) 10-fold during mpc differentiation (fdr < 0.01). however, several previously unreported mirnas were differentially expressed, including mir-10b, -335-3p, and -682. interestingly, the temporal patterns of mir-1, -499, and -682 expression during in vitro mpc proliferation/differentiation were remarkably similar to those observed during in vivo muscle regeneration. moreover, in vitro inhibition of mir-682, the only mirna upregulated in proliferating compared with quiescent mpc, led to decreased mpc proliferation, further validating our in vitro assay system for the identification of mirnas involved in muscle regeneration. thus the differentially expressed mirnas identified in the present study could represent new regulatory elements in mpc proliferation and differentiation.",1
"the myc oncogene, which is commonly mutated/amplified in tumors, represents an important regulator of cell growth because of its ability to induce both proliferation and apoptosis. recent evidence links myc to altered mirna expression, thereby suggesting that myc-regulated mirnas might contribute to tumorigenesis. to further analyze the impact of myc-regulated mirnas, we investigated a murine lymphoma model harboring the myc transgene in a tet-off system to control its expression. microarray-based mirna expression profiling revealed both known and novel myc targets. among the mirnas repressed by myc, we identified the potential tumor suppressor mir-26a, which possessed the ability to attenuate proliferation in myc-dependent cells. interestingly, mir-26a was also found to be deregulated in primary human burkitt lymphoma samples, thereby probably being of clinical relevance. although today only few mirna targets have been identified in human disease, we could show that ectopic expression of mir-26a influenced cell cycle progression by targeting the bona fide oncogene ezh2, a polycomb protein and global regulator of gene expression yet unknown to be regulated by mirnas. thus, in addition to directly targeting protein-coding genes, myc modulates genes important to oncogenesis via deregulation of mirnas, thereby vitally contributing to myc-induced lymphomagenesis.",1
"background osteogenic differentiation of bone marrow mesenchymal stem cells (bmscs) is of much significance for bone formation, the imbalance of it would result in osteoporosis and other pathological bone defects. increasing evidences showed that long non-coding rnas (lncrnas) and mirnas played vital roles in the regulation of osteogenic differentiation. lncrna kcnq1ot1 was often regarded as an imprinted lncrna and was related to tumor progression, while its function in osteogenic differentiation remained unclear. method qrt-pcr was performed to detect the expression of kcnq1ot1, mir-214 and osteogenesis-related genes bmp2, runx2, opn, and ocn. western blotting was carried out to detect osteogenesis-related markers. the osteoblastic phenotype was evidenced by alkaline phosphatase (alp) activity and alizarin red s accumulation detection. bioinformatics and luciferase assays were used to predict and validate the interaction between kcnq1ot1 and mir-214 as well as bmp2 and mir-214. results kcnq1ot1 was significantly up-regulated during the process of osteogenic induction while mir-214 was contrarily down-regulated. knockdown of kcnq1ot1 inhibited osteogenic differentiation and down-regulated bmp2 and osteogenesis-related genes. it was also confirmed that kcnq1ot1 directly interacted with mir-214. meanwhile, mir-214 could bind to 3'utr of bmp2 and therefore inhibited its expression. furthermore, co-transfection of mir-214 inhibitor could rescue the down-regulation of bmp2 and osteogenesis-related genes and osteogenic differentiation suppression induced by kcnq1ot1 knockdown. moreover, mir-214 inhibitor significantly reversed the decreased protein levels of p-smad1/5/8, runx2 and osterix induced by shkcnq1ot1. conclusions kcnq1ot1 positively regulated osteogenic differentiation of bmscs by acting as a cerna to regulate bmp2 expression through sponging mir-214.",1
"tau is a highly abundant and multifunctional brain protein that accumulates in neurofibrillary tangles (nfts), most commonly in alzheimer's disease (ad) and primary age-related tauopathy. recently, micrornas (mirnas) have been linked to neurodegeneration; however, it is not clear whether mirna dysregulation contributes to tau neurotoxicity. here, we determined that the highly conserved brain mirna mir-219 is downregulated in brain tissue taken at autopsy from patients with ad and from those with severe primary age-related tauopathy. in a drosophila model that produces human tau, reduction of mir-219 exacerbated tau toxicity, while overexpression of mir-219 partially abrogated toxic effects. moreover, we observed a bidirectional modulation of tau levels in the drosophila model that was dependent on mir-219 expression or neutralization, demonstrating that mir-219 regulates tau in vivo. in mammalian cellular models, we found that mir-219 binds directly to the 3'-utr of the tau mrna and represses tau synthesis at the post-transcriptional level. together, our data indicate that silencing of tau by mir-219 is an ancient regulatory mechanism that may become perturbed during neurofibrillary degeneration and suggest that this regulatory pathway may be useful for developing therapeutics for tauopathies.",1
"tumor suppressor p53 plays a central role in tumor prevention. p53 protein levels and activity are under a tight and complex regulation in cells to maintain the proper function of p53. micrornas play a key role in the regulation of gene expression. here we report the regulation of p53 through mir-504. mir-504 acts as a negative regulator of human p53 through its direct binding to two sites in the p53 3' untranslated region. overexpression of mir-504 decreases p53 protein levels and functions in cells, including p53 transcriptional activity, p53-mediated apoptosis, and cell-cycle arrest in response to stress, and furthermore promotes tumorigenecity of cells in vivo. these results demonstrate the direct negative regulation of p53 by mir-504 as a mechanism for p53 regulation in cells, which highlights the importance of micrornas in tumorigenesis.",1
"background ischemic postconditioning (ipost) has aroused much attention since 2003 when it was firstly reported. the role of micrornas (mirnas or mirs) in ipost has rarely been reported. the present study was undertaken to investigate whether mirnas were involved in the protective effect of ipost against myocardial ischemia-reperfusion (ir) injury and the probable mechanisms involved. methods thirty sd rats weighing 250-300 g were equally randomized to three groups: control group, where the rats were treated with thoracotomy only; ir group, where the rats were treated with ischemia for 60 min and reperfusion for 180 min; and ipost group, where the rats were treated with 3 cycles of transient ir just before reperfusion. the extent of myocardial infarction, ldh and ck activities were measured immediately after treatment. myocardial apoptosis was detected by tunel assay. the myocardial tissue was collected after ir or ipost stimulation to evaluate the mirnas expression level by mirna-microarray and quantitative real-time rt-pcr. real-time pcr was conducted to identify changes in mrna expression of apoptosis-related genes such as bcl-2, bax and caspase-9 (casp9), and western blot was used to compare the protein expression level of casp9 in the three groups. the mirna mimics and anti-mirna oligonucleotides (amo) were transferred into the cultured neonatal cardiomyocytes and myocardium before they were treated with ir. the effect of mirnas on apoptosis was determined by flow cytometry and tunel assay. casp9, as one of the candidate target of mir-133a, was compared during ir after the mir-133a mimic or amo-133a was transferred into the myocardium. results ipost reduced the ir-induced infarct size of the left ventricle, and decreased ck and ldh levels. tunel assay showed that myocardial apoptosis was attenuated by ipost compared with ir. mirna-microarray and rt-pcr showed that myocardial-specific mir-1 and mir-133a were down-regulated by ir, and up-regulated by ipost compared with ir. furthermore, ipost up-regulated the mrna expression of bcl-2, down-regulated that of bax and casp9. western blot showed that ipost also down-regulated the casp9 protein expression compared with ir. the results of flow cytometry and tunel assay showed that up-regulation of mir-1 and mir-133a decreased apoptosis of cardiomyocytes. mir-133a mimic down-regulated casp9 protein expression and attenuated ir-induced apoptosis. conclusion mirnas are associated with the protective effect of ipost against myocardial ir injury. ipost can up-regulate mir-1 and mir-133a, and decrease apoptosis of cardiomyocyte. myocardial-specific mir-1 and mir-133a may play an important role in ipost protection by regulating apoptosis-related genes. mir-133a may attenuate apoptosis of myocardiocytes by targeting casp9.",1
"activation of microglia resulting in exacerbated inflammation expression plays an important role in degeneration of dopaminergic (da) neurons in the pathogenesis of parkinson's disease (pd). however, how this enhanced inflammation is induced in microglia remains largely unclear. here, in the mouse pd model induced by 1-methyl-4-phenyl-1,2,3,6-tetra hydropyridine (mptp), we found that mir-7116-5p in microglia has a crucial role in this inflammation. 1-methyl-4-phenylpyridinium (mpp + ) is uptaken by microglia through organic cation transporter 3 (oct3) to downregulate mir-7116-5p, an mirna found to target tumor necrosis factor alpha (tnf-α). production of tnf-α in microglia is specifically potentiated by mpp + via downregulation of mir-7116-5p to elicit subsequent inflammatory responses. furthermore, enhancement of mir-7116-5p expression in microglia in mice inhibits the production of tnf-α and the activation of glia, and further prevents loss of da neurons. together, our studies suggest that mpp + suppresses mir-7116-5p level in microglia and potentiates tnf-α production and inflammatory responses to contribute to da neuron damage.",1
"cardiomyocyte progenitor cells play essential roles in early heart development, which requires highly controlled cellular organization. micrornas (mirs) are involved in various cell behaviors by post-transcriptional regulation of target genes. however, the roles of mirnas in human cardiomyocyte progenitor cells (hcmpcs) remain to be elucidated. our previous study showed that mir-134 was significantly downregulated in heart tissue suffering from congenital heart disease, underlying the potential role of mir-134 in cardiogenesis. in the present work, we showed that the upregulation of mir-134 reduced the proliferation of hcmpcs, as determined by edu assay and ki-67 immunostaining, while the inhibition of mir-134 exhibited an opposite effect. both up- and downregulation of mir-134 expression altered the transcriptional level of cell-cycle genes. we identified meis2 as the target of mir-134 in the regulation of hcmpc proliferation through bioinformatic prediction, luciferase reporter assay and western blot. the over-expression of meis2 mitigated the effect of mir-134 on hcmpc proliferation. moreover, mir-134 did not change the degree of hcmpc differentiation into cardiomyocytes in our model, suggesting that mir-134 is not required in this process. these findings reveal an essential role for mir-134 in cardiomyocyte progenitor cell biology and provide new insights into the physiology and pathology of cardiogenesis.",1
"post-transcriptional regulation by micrornas (mirnas) is essential for complex molecular responses to physiological insult and disease. although many disease-associated mirnas are known, their global targets and culminating network effects on pathophysiology remain poorly understood. we applied argonaute (ago) crosslinking immunoprecipitation (clip) to systematically elucidate altered mirna-target interactions in brain following ischemia and reperfusion (i/r) injury. among 1,190 interactions identified, the most prominent was the cumulative loss of target regulation by mir-29 family members. integration of translational and time-course rna profiles revealed a dynamic mode of mir-29 target de-regulation, led by acute translational activation and a later increase in rna levels, allowing rapid proteomic changes to take effect. these functional regulatory events rely on canonical and non-canonical mir-29 binding and engage glutamate reuptake signals, such as glial glutamate transporter (glt-1), to control local glutamate levels. these results uncover a mirna target network that acts acutely to maintain brain homeostasis after ischemic stroke.",1
"in the last few years, micrornas (mirna) have started a revolution in molecular biology and emerged as key players in the carcinogenesis. they have been identified in various tumor types, showing that different sets of mirnas are usually deregulated in different cancers. to identify the mirna signature that was specific for oral squamous cell carcinoma (oscc), we first examined expression profiles of 148 mirnas in a panel of 18 oscc cell lines and the immortalized oral keratinocyte line rt7 as a control. compared with rt7, the expression of 54 mirnas (36.5%) was frequently down-regulated in oscc lines ( or=66.7% of 18 lines). among these 54 mirnas, we further analyzed four of these mirnas (i.e., mir-34b, mir-137, mir-193a, and mir-203), located around cpg islands, to identify tumor-suppressive mirnas silenced through aberrant dna methylation. the expression of those four genes was restored by treatment with 5-aza-2'-deoxycytidine in oscc cells lacking their expression. in addition, expression levels of the four mirnas were inversely correlated with their dna methylation status in the oscc lines. in primary tumors of oscc with paired normal oral mucosa, down-regulation of mirna expression through tumor-specific hypermethylation was more frequently observed for mir-137 and mir-193a than for mir-34b and mir-203. moreover, the ectopic transfection of mir-137 or mir-193a into oscc lines lacking their expressions significantly reduced cell growth, with down-regulation of the translation of cyclin-dependent kinase 6 or e2f transcription factor 6, respectively. taken together, our results clearly show that mir-137 and mir-193a are tumor suppressor mirnas epigenetically silenced during oral carcinogenesis.",1
"developmental growth is an intricate process involving the coordinated regulation of the expression of various genes, and micrornas (mirnas) play crucial roles in diverse processes throughout animal development. the ecdysone-responsive mirna, mir-252, is normally upregulated during the pupal and adult stages of drosophila development. here, we found that overexpression of mir-252 in the larval fat body decreased total tissue mass through a reduction in both cell size and cell number, causing a concomitant decrease in larval size. furthermore, mir-252 overexpression led to a delayed larval-to-pupal transition with defective anterior spiracle eversion, as well as a decrease in adult size and mass. conversely, adult flies lacking mir-252 showed an increase in mass compared with control flies. we found that mir-252 directly targeted mbt, encoding a p21-activated kinase, to repress its expression. notably, co-overexpression of mbt rescued the developmental and growth defects associated with mir-252 overexpression, indicating that mbt is a biologically relevant target of mir-252. overall, our data support a role for the ecdysone/mir-252/mbt regulatory axis in growth control during drosophila development.",1
"animal growth is controlled by a variety of external and internal factors during development. the steroid hormone ecdysone plays a critical role in insect development by regulating the expression of various genes. in this study, we found that fat body-specific expression of mir-276a, an ecdysone-responsive microrna (mirna), led to a decrease in the total mass of the larval fat body, resulting in significant growth reduction in drosophila. changes in mir-276a expression also affected the proliferation of drosophila s2 cells. furthermore, we found that the insulin-like receptor (inr) is a biologically relevant target gene regulated by mir-276a-3p. in addition, we found that mir-276a-3p is upregulated by the canonical ecdysone signalling pathway involving the ecdysone receptor and broad complex. a reduction in cell proliferation caused by ecdysone was compromised by blocking mir-276a-3p activity. thus, our results suggest that mir-276a-3p is involved in ecdysone-mediated growth reduction by controlling inr expression in the insulin signalling pathway.",1
"t cell senescence and exhaustion are major barriers to successful cancer immunotherapy. here we show that mir-155 increases cd8 + t cell antitumor function by restraining t cell senescence and functional exhaustion through epigenetic silencing of drivers of terminal differentiation. mir-155 enhances polycomb repressor complex 2 (prc2) activity indirectly by promoting the expression of the prc2-associated factor phf19 through downregulation of the akt inhibitor, ship1. phf19 orchestrates a transcriptional program extensively shared with mir-155 to restrain t cell senescence and sustain cd8 + t cell antitumor responses. these effects rely on phf19 histone-binding capacity, which is critical for the recruitment of prc2 to the target chromatin. these findings establish the mir-155-phf19-prc2 as a pivotal axis regulating cd8 + t cell differentiation, thereby paving new ways for potentiating cancer immunotherapy through epigenetic reprogramming of cd8 + t cell fate.",1
"in mammals, glucocorticoids (gcs) and their intracellular receptor, the glucocorticoid receptor (gr), represent critical checkpoints in the endocrine control of energy homeostasis. indeed, aberrant gc action is linked to severe metabolic stress conditions as seen in cushing's syndrome, gc therapy and certain components of the metabolic syndrome, including obesity and insulin resistance. here, we identify the hepatic induction of the mammalian conserved microrna (mir)-379/410 genomic cluster as a key component of gc/gr-driven metabolic dysfunction. particularly, mir-379 was up-regulated in mouse models of hyperglucocorticoidemia and obesity as well as human liver in a gc/gr-dependent manner. hepatocyte-specific silencing of mir-379 substantially reduced circulating very-low-density lipoprotein (vldl)-associated triglyceride (tg) levels in healthy mice and normalized aberrant lipid profiles in metabolically challenged animals, mediated through mir-379 effects on key receptors in hepatic tg re-uptake. as hepatic mir-379 levels were also correlated with gc and tg levels in human obese patients, the identification of a gc/gr-controlled mirna cluster not only defines a novel layer of hormone-dependent metabolic control but also paves the way to alternative mirna-based therapeutic approaches in metabolic dysfunction.",1
"progranulin deficiency is thought to cause some forms of frontotemporal dementia (ftd), a major early-onset age-dependent neurodegenerative disease. how progranulin (pgrn) expression is regulated is largely unknown. we identified an evolutionarily conserved binding site for microrna-29b (mir-29b) in the 3' untranslated region (3'utr) of the human pgrn (hpgrn) mrna. mir-29b downregulates the expression of luciferase through hpgrn or mouse pgrn (mpgrn) 3'utrs, and the regulation was abolished by mutations in the mir-29b binding site. to examine the direct effect of manipulating endogenous mir-29b on hpgrn expression, we established a stable nih3t3 cell line that expresses hpgrn under the control of the cytomegalovirus promoter. ectopic expression of mir-29b decreased hpgrn expression at the both mrna and protein levels. conversely, knockdown of endogenous mir-29b with locked nucleic acid increased the production and secretion of hpgrn in nih3t3 cells. endogenous hpgrn in hek 293 cells was also regulated by mir-29b. these findings identify mir-29b as a novel posttranscriptional regulator of pgrn expression, raising the possibility that mir-29b or other mirnas might be targeted therapeutically to increase hpgrn levels in some ftd patients.",1
"peripheral artery disease (pad) is an occlusive disease of limb arteries. critical limb ischemia (cli) is an advanced form of pad that is prognostically worse in subjects with diabetes and can result in limb loss, gangrene, and death, although the underlying signaling mechanisms that contribute to its development remain poorly understood. by comparing plasma samples from diabetic humans with pad and mouse models of pad, we identified mir-375 to be significantly downregulated in humans and mice during progression to cli. overexpression of mir-375 was pro-angiogenic in endothelial cells in vitro and induced endothelial migration, proliferation, sprouting, and vascular network formation, whereas mir-375 inhibition conferred anti-angiogenic effects. intramuscular delivery of mir-375 improved blood flow recovery to diabetic mouse hindlimbs following femoral artery ligation (fal) and improved neovessel growth and arteriogenesis in muscle tissues. using rna-sequencing and prediction algorithms, kruppel-like factor 5 (klf5) was identified as a direct target of mir-375 and sirna knockdown of klf5 phenocopied the effects of mir-375 overexpression in vitro and in vivo through regulatory changes in nf-kb signaling. together, a mir-375-klf5-nf-kb signaling axis figures prominently as a potential therapeutic pathway in the development cli in diabetes.",1
"adhesion of circulating monocytes to vascular endothelial cells (ecs) is a critical event leading to vascular inflammation and, hence, development of atherosclerosis. micrornas (mirs) are a class of endogenous, highly conserved, noncoding small rnas that play important roles in regulating gene expression and cellular function, as well as pathogenesis of atherosclerosis. here, we showed that oscillatory shear stress (oss) induces the expression of mir-21 at the transcriptional level in cultured human umbilical vein ecs via an increased binding of c-jun, which is a component of transcription factor activator protein-1 (ap-1), to the promoter region of mir-21. oss induction of mir-21 inhibited the translation, but not transcription, of peroxisome proliferators-activated receptor-α (pparα) by 3'-utr targeting. overexpression of mir-21 up-regulated ap-1 activation, which was attenuated by exogenous expression of pparα. oss and overexpression of mir-21 enhanced the expression of adhesion molecules vascular cell adhesion molecule-1 and monocyte chemotactic protein-1 and the consequential adhesion of monocytes to ecs. overexpression of pparα significantly attenuated the ap-1-mediated mir-21 expression. these results demonstrate a unique mechanism by which oss induces ap-1-dependent mir-21 expression, which directly targets pparα to inhibit its expression, thereby allowing activation of ap-1 and the promotion of monocyte adhesion. our findings suggest the presence of a positive feedback loop that enables the sustained induction of mir-21, thus contributing to the proinflammatory responses of vascular endothelium under oss.",1
"transfer of f-like plasmids is regulated by the finop system, which controls the expression of traj, a positive regulator of the transfer operon. f finp is a 79 base antisense rna, composed of two stem-loops, complementary to the 5' untranslated leader of traj mrna. binding of finp to the traj leader sequesters the traj ribosome binding site, preventing its translation and repressing plasmid transfer. the fino protein binds stem-loop ii of finp and traj mrna and promotes duplex formation in vitro. fino stabilizes finp, increasing its effective concentration in vivo. to determine how fino protects finp from decay, the degradation of finp was examined in a series of ribonuclease-deficient strains. using northern blot analysis, full-length finp was found to be stabilized sevenfold in an rnase e-deficient strain. the major site of rnase e cleavage was mapped on synthetic finp, to the single-stranded region between stem-loops i and ii. a secondary site near the 5' end ( approximately 10 bases) was also observed. a gst-fino fusion protein protected finp from rnase e cleavage at both sites in vitro. two duplexes between finp and traj mrna were detected in an rnase iii-deficient strain. the larger duplex resulted from extension of the finp transcript at its 3' end, suggesting readthrough at the terminator that corresponds to finp stem-loop ii. a point mutant of finp (finp305; c30u) that is unable to repress traj in the presence of fino was also characterized. the pattern of rnase e digestion of finp305 rna differed from finp, and gst-fino did not protect finp305 rna from cleavage in vitro. the half-life of finp305 rna decreased more than tenfold in vivo, such that the steady-state levels of finp305 rna, in the presence of fino, were insufficient to significantly reduce the level of traj mrna available for translation, allowing derepressed levels of transfer.",1
"micrornas (mirnas) control gene expression by binding to their target mrnas for degradation and/or translation repression and are implicated in many aspects of cellular physiology. our previous study shows that mir-29b acts as a biological repressor of intestinal mucosal growth, but its exact downstream targets remain largely unknown. in the present study, we found that mrnas, encoding wnt co-receptor lrp6 (low-density lipoprotein-receptor-related protein 6) and rna-binding protein (rbp) hur, are novel targets of mir-29b in intestinal epithelial cells (iecs) and that expression of lrp6 and hur is tightly regulated by mir-29b at the post-transcriptional level. mir-29b interacted with both lrp6 and hur mrnas via their 3'-utrs and inhibited lrp6 and hur expression by destabilizing lrp6 and hur mrnas and repressing their translation. studies using heterologous reporter constructs revealed a greater repressive effect of mir-29b through a single binding site in the lrp6 or hur 3'-utr, whereas deletion mutation of this site prevented mir-29b-induced repression of lrp6 and hur expression. repression of hur by mir-29b in turn also contributed to mir-29b-induced lrp6 inhibition, since ectopic overexpression of hur in cells overexpressing mir-29b restored lrp6 expression to near normal levels. taken together, our results suggest that mir-29b inhibits expression of lrp6 and hur post-transcriptionally, thus playing a role in the regulation of iec proliferation and intestinal epithelial homoeostasis.",1
"our previous studies have showed that chemokine receptor 4 (cxcr4) was over-expressed in laryngeal squamous cell carcinoma (lscc). however, the mechanism underlying aberrant cxcr4 expression remains unclear. to investigate the roles played by mirnas in cxcr4 over-expression in lscc, putative mir-139 was predicted through computational algorithms, including targetscan, pictar and mirbase, and luciferase reporter assay was explored to confirm that whether cxcr4 was directly regulated by mir-139. then, quantitative real-time pcr, immunohistochemistry and in situ hybridization methods were employed to detect the expression of mir-139 and cxcr4 in primary lscc tissues, normal adjacent mucosal tissues and metastatic lesions derived from 40 lscc patients in the second hospital, xi'an jiaotong university. finally, gain- and loss-of-function assays were adopted to explore the effects of mir-139 and cxcr4 on proliferation, invasion and metastasis of the human lscc cell line hep-2 in vitro and in vivo. our results showed that mir-139 dampened cxcr4 expression, and cxcr4 was directly targeted by mir-139. additionally, the expression of mir-139 was reduced in alignment with the progression of primary to metastatic lscc. moreover, an inverse correlation was observed between mir-139 and cxcr4 protein levels in lscc specimens. functional analyses demonstrated that ectopic expression of mir-139 inhibited cell proliferation, migration and metastasis of hep-2 cells in vitro and in vivo. similar to the observations seen in restoring mir-139 expression, dampening of cxcr4 expression inhibited cell growth, migration and invasion, whereas mir-139 over-expression reversed the pro-metastatic effect of cxcr4. taken together, we conclude that mir-139 targets cxcr4 and inhibits proliferation and metastasis of lscc.",1
"acute myeloid leukemia (aml) carrying npm1 mutations and cytoplasmic nucleophosmin (npmc+ aml) accounts for about one-third of adult aml and shows distinct features, including a unique gene expression profile. micrornas (mirnas) are small noncoding rnas of 19-25 nucleotides in length that have been linked to the development of cancer. here, we investigated the role of mirnas in the biology of npmc+ aml. the mirna expression was evaluated in 85 adult de novo aml patients characterized for subcellular localization/mutation status of npm1 and flt3 mutations using a custom microarray platform. data were analyzed by using univariate t test within brb tools. we identified a strong mirna signature that distinguishes npmc+ mutated (n = 55) from the cytoplasmic-negative (npm1 unmutated) cases (n = 30) and includes the up-regulation of mir-10a, mir-10b, several let-7 and mir-29 family members. many of the down-regulated mirnas including mir-204 and mir-128a are predicted to target several hox genes. indeed, we confirmed that mir-204 targets hoxa10 and meis1, suggesting that the hox up-regulation observed in npmc+ aml may be due in part by loss of hox regulators-mirnas. flt3-itd+ samples were characterized by up-regulation of mir-155. further experiments demonstrated that the up-regulation of mir-155 was independent from flt3 signaling. our results identify a unique mirna signature associated with npmc+ aml and provide evidence that support a role for mirnas in the regulation of hox genes in this leukemia subtype. moreover, we found that mir-155 was strongly but independently associated with flt3-itd mutations.",1
"the loss of microrna-122 (mir-122) expression correlates to many characteristic properties of hepatocellular carcinoma (hcc) cells, including clonogenic survival, anchorage-independent growth, migration, invasion, epithelial-mesenchymal transition, and tumorigenesis. however, all of these findings do not sufficiently explain the oncogenic potential of mir-122. in the current study, we used two-dimensional differential in-gel electrophoresis to measure changes in the expression of thousands of proteins in response to the inhibition of mir-122 in human hepatoma cells. several proteins that were upregulated on mir-122 inhibition were involved in the unfolded protein response (upr) pathway. the overexpression of mir-122 resulted in the repression of upr pathway activation. therefore, mir-122 may act as an inhibitor of the chaperone gene expression and negatively regulate the upr pathway in hcc. we further showed that the mir-122 inhibitor enhanced the stability of the 26s proteasome non-atpase regulatory subunit 10 (psmd10) through the up-regulation of its target gene cyclin-dependent kinase 4 (cdk4). this process may activate the upr pathway to prevent chemotherapy-mediated tumor cell apoptosis. the current study suggests that mir-122 negatively regulates the upr through the cdk4-psmd10 pathway. the down-regulation of mir-122 activated the cdk4-psmd10-upr pathway to decrease tumor cell anticancer drug-mediated apoptosis. we identified a new hcc therapeutic target and proclaimed the potential risk of the therapeutic use of mir-122 silencing.",1
"our expression signatures of human cancer including bladder cancer (bc) revealed that the expression of microrna-1 (mir-1) and microrna-133a (mir-133a) is significantly reduced in cancer cells. in the human genome, mir-1 and mir-133a are located on the same chromosomal region (mir-1-2 and mir-133a-1 on 18q11.2, and mir-1-1 and mir-133a-2 on 20q13.33) called cluster. in this study, we identified the novel molecular targets commonly regulated by mir-1 and mir-133a in bc. genome-wide molecular target search and luciferase reporter assays showed that prothymosin-α (ptma) and purine nucleoside phosphorylase (pnp) are directly regulated by mir-1 and mir-133a. silencing of these two genes significantly inhibited cell proliferation and invasion, and increased apoptosis in bc cells. immunohistochemistry showed that ptma expression levels were significantly higher in bc compared to normal bladder epitheliums. ptma and pnp were identified as new target genes regulated by the mir-1 and mir-133a cluster in bc. these genes may function as oncogenes contributing to cell proliferation and invasion in bc. tumor suppressive mir-1 and mir-133a-mediated novel molecular targets may provide new insights into the potential mechanisms of bc oncogenesis.",1
"identifying regulatory mechanisms that influence inflammation in metabolic tissues is critical for developing novel metabolic disease treatments. here, we investigated the role of microrna-146a (mir-146a) during diet-induced obesity in mice. mir-146a is reduced in obese and type 2 diabetic patients and our results reveal that mir-146a-/- mice fed a high-fat diet (hfd) have exaggerated weight gain, increased adiposity, hepatosteatosis, and dysregulated blood glucose levels compared to wild-type controls. pro-inflammatory genes and nf-κb activation increase in mir-146a-/- mice, indicating a role for this mirna in regulating inflammatory pathways. rna-sequencing of adipose tissue macrophages demonstrated a role for mir-146a in regulating both inflammation and cellular metabolism, including the mtor pathway, during obesity. further, we demonstrate that mir-146a regulates inflammation, cellular respiration and glycolysis in macrophages through a mechanism involving its direct target traf6. finally, we found that administration of rapamycin, an inhibitor of mtor, was able to rescue the obesity phenotype in mir-146a-/- mice. altogether, our study provides evidence that mir-146a represses inflammation and diet-induced obesity and regulates metabolic processes at the cellular and organismal levels, demonstrating how the combination of diet and mirna genetics influences obesity and diabetic phenotypes.",1
"decapentaplegic (dpp), the drosophila homolog of the vertebrate bone morphogenetic protein (bmp2/4), is crucial for patterning and growth in many developmental contexts. the dpp pathway is regulated at many different levels to exquisitely control its activity. we show that bantam (ban), a microrna, modulates dpp signaling activity. over expression of ban decreases phosphorylated mothers against decapentaplegic (mad) levels and negatively affects dpp pathway transcriptional target genes, while null mutant clones of ban upregulate the pathway. we provide evidence that dpp upregulates ban in the wing imaginal disc, and attenuation of dpp signaling results in a reduction of ban expression, showing that they function in a feedback loop. furthermore, we show that this feedback loop is important for maintaining anterior-posterior compartment boundary stability in the wing disc through regulation of optomotor blind (omb), a known target of the pathway. our results support a model that ban functions with dpp in a negative feedback loop.",1
"background the purpose of this study was to identify prostate cancer (pc) oncogenic micrornas (mirs) based on mir microarray and to investigate whether these oncogenic mirs may be useful as pc biomarkers. methods initially, we carried out mir microarray and real-time pcr using rwpe-1, pc-3, du-145 and lncap cells. to investigate the function of mir-183, we used a mir-183 knockdown inhibitor in cell growth and wound-healing assays. we used several algorithms and confirmed that they are directly regulated by mir-183. results we identified three potential oncogenic mirs (mir-146a, mir-183 and mir-767-5p). the expression of mir-183 in pc cells (pc-3, du-145 and lncap) was upregulated compared with rwpe-1 cells. mir-183 expression was also significantly higher in pc tissues compared with that in matched normal prostate tissues. additionally, mir-183 expression was correlated with higher prostate-specific antigen, higher pt and shorter overall survival. mir-183 knockdown decreased cell growth and motility in pc cells and significantly decreased prostate tumour growth in in vivo nude mice experiments. we identified dkk-3 and smad4 as potential target genes of mir-183. conclusion our data suggest that oncogenic mir-183 may be useful as a new pc biomarker and that inhibition of mir-183 expression may be therapeutically beneficial as a pc treatment.",1
"the adverse biological responses to prostheses wear particles commonly led to the failure of total hip arthroplasty. among the released cytokines, interferon-γ (ifn-γ) has been found to be a critical functional factor during osteoclast differentiation. however, the molecular mechanism underlying the regulation of ifn-γ in wear particles-induced cells still needs to be determined. four kinds of abrasive endoprosthetic wear particle were used to treat thp-1 cells, including polymethylmethacrylate (pmma), zirconiumoxide (zro 2 ), commercially pure titanium (cpti), and titanium alloy (ti-6al-7nb), with a concentration of 0.01, 0.05, 0.1, or 0.2 mg/ml for 48 h. the expression of ifn-γ and mir-29b was detected by real-time rt-pcr or elisa. luciferase reporter assay was performed to determine the regulation of mir-29b on ifn-γ. the effect of mir-29b inhibitor on the expression of wear particle-induced ifn-γ was detected. the expression of mir-29b was examined in thp-1 cells treated with tumor necrosis factor-alpha (tnf-α). the expression of ifn-γ was downregulated and the level of mir-29b was increased in thp-1 cells pretreated with wear particles. ifn-γ was a target of mir-29b. wear particles inhibited the expression of ifn-γ through mir-29b. the expression of mir-29b was significantly reduced in thp-1 cells treated with tnf-α neutralizing antibody and particles comparing to that in the cells treated with particles alone. wear particles inhibit the ifn-γ secretion in human monocytes, which was associated with the upregulating tnf-α-induced mir-29b.",1
"objective low-density lipoprotein receptor (ldlr) mediates endocytosis of ldl particles and is important in maintaining plasma cholesterol levels, thus its expression is under extensive regulation at multiple levels, including transcriptional and posttranscriptional regulation by transcription factors (tfs) and rna-binding proteins (rbps). here, we identified microrna-185 (mir-185) as a novel direct posttranscriptional regulator of ldlr and an indirect ldlr modulator through ksrp in hepatic cells. methods and results using quantitative real-time pcr (qpcr), we detected the effect of predicted ldlr-targeting mirnas and found that overexpression of mir-185 repressed ldlr expression and ldl uptake in hepg2 cells by 62.4 ± 6.0% (p = 7.0 × 10(-5)) and 32.5 ± 6.0% (p = 7.7 × 10(-4)) respectively, through directly targeting ldlr 3'utr. unexpectedly, the antisense inhibitor of mir-185 had similar repression effect on ldlr although it reduced the association of endogenous mir-185 with ldlr mrna. further experiments revealed that kh-type splicing regulatory protein (ksrp), one of the ldlr-destabilizing rbps, is also a target of mir-185. ksrp silencing reversed the repression effects of mir-185-inhibitor on ldlr. thus mir-185 regulates ldlr expression not only through directly targeting but also by a rbp-involved indirect pathway. finally, the in vivo results showed that mir-185-inhibitor upregulated hepatic ldlr expression and correlated with a decrease in plasma cholesterol level and arterial plaque area in apoe ko mice. conclusions these findings reveal that mir-185 controls cholesterol homeostasis as a key posttranscriptional ldlr modulator in hepatic cells, providing novel insight into the regulatory mechanism for ldlr expression and the anti-atherosclerosis effect of mir-185-inhibitor.",1
"micrornas (mirnas) are abundant, approximately 21-nucleotide, noncoding regulatory rnas. each mirna may regulate hundreds of mrna targets, but the identities of these targets and the processes they regulate are poorly understood. here we have explored the use of microarray profiling and functional screening to identify targets and biological processes triggered by the transfection of human cells with mirnas. we demonstrate that a family of mirnas sharing sequence identity with mirna-16 (mir-16) negatively regulates cellular growth and cell cycle progression. mir-16-down-regulated transcripts were enriched with genes whose silencing by small interfering rnas causes an accumulation of cells in g(0)/g(1). simultaneous silencing of these genes was more effective at blocking cell cycle progression than disruption of the individual genes. thus, mir-16 coordinately regulates targets that may act in concert to control cell cycle progression.",1
"the tumour suppressor p53 is a crucial regulator of cell cycle arrest and apoptosis by acting as a transcription factor to regulate a variety of genes. at least in part, this control is exerted by p53 via regulating expression of numerous micrornas. we identified two abundantly expressed micrornas, mir-16 and mir-26a, whose expression is regulated by p53 during the checkpoint arrest induced by the genotoxic drug, doxorubicin. importantly, among the targets of these mirs are two critical checkpoint kinases, chk1 and wee1. the p53-dependent augmentation of mir-16 and mir-26a expression levels led to the cell cycle arrest of tumour cells in g1/s and increased apoptosis. strikingly, the bioinformatics analysis of survival times for patients with breast and prostate cancers has revealed that co-expression of mir-16 and mir-26a correlated with a better survival outcome. collectively, our data provide a novel mechanism whereby p53 represses chk1 and wee1 expression, at least partially, via upregulation of mir-16 and mir-26a and thus sensitizes tumour cells to genotoxic therapies.",1
"pulmonary artery endothelial dysfunction is associated with pulmonary arterial hypertension (pah). based on recent studies showing that microrna (mir)-27b is aberrantly expressed in pah, we hypothesized that mir-27b may contribute to pulmonary endothelial dysfunction and vascular remodeling in pah. the effect of mir-27b on pulmonary endothelial dysfunction and the underlying mechanism were investigated in human pulmonary artery endothelial cells (hpaecs) in vitro and in a monocrotaline (mct)-induced model of pah in vivo. mir-27b expression was upregulated in mct-induced pah and inversely correlated with the levels of peroxisome proliferator-activated receptor (ppar)-γ, and mir-27b inhibition attenuated mct-induced endothelial dysfunction and remodeling and prevented pah associated right ventricular hypertrophy and systolic pressure in rats. pparγ was confirmed as a direct target of mir-27b in hpaecs and shown to mediate the effect of mir-27b on the disruption of endothelial nitric oxide synthase (enos) coupling to hsp90 and the suppression of no production associated with the pah phenotype. we showed that mir-27b plays a role endothelial function and no release and elucidated a potential mechanism by which mir-27b regulates hsp90-enos and no signaling by modulating pparγ expression, providing potential therapeutic targets for the treatment of pah.",1
"micrornas are small noncoding rnas that control gene function posttranscriptionally through mrna degradation or translational inhibition. much has been learned about the processing and mechanism of action of micrornas, but little is known about their biological function. here, we demonstrate that injection of 2'o-methyl antisense oligoribonucleotides into early drosophila embryos leads to specific and efficient depletion of micrornas and thus permits systematic loss-of-function analysis in vivo. twenty-five of the forty-six embryonically expressed micrornas show readily discernible defects; pleiotropy is moderate and family members display similar yet distinct phenotypes. processes under microrna regulation include cellularization and patterning in the blastoderm, morphogenesis, and cell survival. the largest microrna family in drosophila (mir-2/6/11/13/308) is required for suppressing embryonic apoptosis; this is achieved by differential posttranscriptional repression of the proapoptotic factors hid, grim, reaper, and sickle. our findings demonstrate that micrornas act as specific and essential regulators in a wide range of developmental processes.",1
"metazoan genomes encode an abundant collection of mrna-like, long noncoding (lnc)rnas. although lncrnas greatly expand the transcriptional repertoire, we have a limited understanding of how these rnas contribute to developmental regulation. here, we investigate the function of the drosophila lncrna called yellow-achaete intergenic rna (yar). comparative sequence analyses show that the yar gene is conserved in drosophila species representing 40-60 million years of evolution, with one of the conserved sequence motifs encompassing the yar promoter. further, the timing of yar expression in drosophila virilis parallels that in d. melanogaster, suggesting that transcriptional regulation of yar is conserved. the function of yar was defined by generating null alleles. flies lacking yar rnas are viable and show no overt morphological defects, consistent with maintained transcriptional regulation of the adjacent yellow (y) and achaete (ac) genes. the location of yar within a neural gene cluster led to the investigation of effects of yar in behavioral assays. these studies demonstrated that loss of yar alters sleep regulation in the context of a normal circadian rhythm. nighttime sleep was reduced and fragmented, with yar mutants displaying diminished sleep rebound following sleep deprivation. importantly, these defects were rescued by a yar transgene. these data provide the first example of a lncrna gene involved in drosophila sleep regulation. we find that yar is a cytoplasmic lncrna, suggesting that yar may regulate sleep by affecting stabilization or translational regulation of mrnas. such functions of lncrnas may extend to vertebrates, as lncrnas are abundant in neural tissues.",1
"small rnas (srnas) are a growing class of non-protein-coding transcripts that participate in the regulation of virtually every aspect of bacterial physiology. heterocystous cyanobacteria are a group of photosynthetic organisms that exhibit multicellular behavior and developmental alternatives involving specific transcriptomes exclusive of a given physiological condition or even a cell type. in the context of our ongoing effort to understand developmental decisions in these organisms we have undertaken an approach to the global identification of srnas. using differential rna-seq we have previously identified transcriptional start sites for the model heterocystous cyanobacterium nostoc sp. pcc 7120. here we combine this dataset with a prediction of rho-independent transcriptional terminators and an analysis of phylogenetic conservation of potential srnas among 89 available cyanobacterial genomes. in contrast to predictive genome-wide approaches, the use of an experimental dataset comprising all active transcriptional start sites (differential rna-seq) facilitates the identification of bona fide srnas. the output of our approach is a dataset of predicted potential srnas in nostoc sp. pcc 7120, with different degrees of phylogenetic conservation across the 89 cyanobacterial genomes analyzed. previously described srnas appear among the predicted srnas, demonstrating the performance of the algorithm. in addition, new predicted srnas are now identified that can be involved in regulation of different aspects of cyanobacterial physiology, including adaptation to nitrogen stress, the condition that triggers differentiation of heterocysts (specialized nitrogen-fixing cells). transcription of several predicted srnas that appear exclusively in the genomes of heterocystous cyanobacteria is experimentally verified by northern blot. cell-specific transcription of one of these srnas, nsir8 (nitrogen stress-induced rna 8), in developing heterocysts is also demonstrated.",1
"the ca(2+) sensor s100a1 is essential for proper endothelial cell (ec) nitric oxide (no) synthase (enos) activation. s100a1 levels are greatly reduced in primary human microvascular ecs subjected to hypoxia, rendering them dysfunctional. however mechanisms that regulate s100a1 levels in ecs are unknown. here we show that ecs transfected with a s100a1-3' untranslated region (utr) luciferase reporter construct display significantly reduced gene expression when subjected to low oxygen levels or chemical hypoxia. bioinformatic analysis suggested that microrna -138 (mir-138) could target the 3'utr of s100a1. patients with critical limb ischemia (cli) or mice subjected to femoral artery resection (far) displayed increased mir-138 levels and decreased s100a1 protein expression. consistent with this finding, hypoxia greatly increased mir-138 levels in ecs, but not in skeletal muscle c2c12 myoblasts or differentiated myotubes or primary human vascular smooth muscle cells. transfection of a mir-138 mimic into ecs reduced s100a1-3 'utr reporter gene expression, while transfection of an anti mir-138 prevented the hypoxia-induced downregulation of the reporter gene. deletion of the 22 nucleotide putative mir-138 target site abolished the hypoxia-induced loss of reporter gene expression. knockdown of hif1-α mediated by sirna prevented loss of hypoxia-induced reporter gene expression. conversely, specific activation of hif1-α by a selective prolyl-hydroxylase inhibitor (iox2) reduced reporter gene expression even in the absence of hypoxia. finally, primary ecs transfected with a mir-138 mimic displayed reduced tube formation when plated onto matrigel matrix and expressed less no when stimulated with vegf. these effects were reversed by gene transfer of s100a1 using recombinant adenovirus. we conclude that hypoxia-induced mir-138 is an essential mediator of ec dysfunction via its ability to target the 3'utr of s100a1.",1
"gradients of signalling and transcription factors govern many aspects of embryogenesis, highlighting the need for spatiotemporal control of regulatory protein levels. micrornas are phylogenetically conserved small rnas that regulate the translation of target messenger rnas, providing a mechanism for protein dose regulation. here we show that microrna-1-1 (mir-1-1) and mir-1-2 are specifically expressed in cardiac and skeletal muscle precursor cells. we found that the mir-1 genes are direct transcriptional targets of muscle differentiation regulators including serum response factor, myod and mef2. correspondingly, excess mir-1 in the developing heart leads to a decreased pool of proliferating ventricular cardiomyocytes. using a new algorithm for microrna target identification that incorporates features of rna structure and target accessibility, we show that hand2, a transcription factor that promotes ventricular cardiomyocyte expansion, is a target of mir-1. this work suggests that mir-1 genes titrate the effects of critical cardiac regulatory proteins to control the balance between differentiation and proliferation during cardiogenesis.",1
"micrornas (mirnas) are small silencing rnas with regulatory roles in gene expression. mirnas interact with argonaute (ago) proteins to form effector complexes that cleave target mrnas or repress translation. rice (oryza sativa) encodes four ago1 homologs (ago1a, ago1b, ago1c, and ago1d). we used rna interference (rnai) to knock down the four ago1s. the rnai lines displayed pleiotropic developmental phenotypes and had increased accumulation of mirna targets. ago1a, ago1b, and ago1c complexes were purified and further characterized. the three ago1s all have a strong preference for binding small rnas (srnas) with 5' u and have slicer activity. we cataloged the srnas in each ago1 complex by deep sequencing and found that all three ago1s predominantly bound known mirnas. most of the mirnas were evenly distributed in the three ago1 complexes, suggesting a redundant role for the ago1s. intriguingly, a subset of mirnas were specifically incorporated into or excluded from one of the ago1s, suggesting functional specialization among the ago1s. furthermore, we identified rice mirna targets at a global level. the validated targets include transcription factors that control major stages of development and also genes involved in a variety of physiological processes, indicating a broad regulatory role for mirnas in rice.",1
"using a computer program designed to search for rna structural motifs in sequence databases, we have found a hammerhead ribozyme domain encoded in the smalpha repetitive dna of schistosoma mansoni. transcripts of these repeats are expressed as long multimeric precursor rnas that cleave in vitro and in vivo into unit-length fragments. this rna domain is able to engage in both cis and trans cleavage typical of the hammerhead ribozyme. further computer analysis of s. mansoni dna identified a potential trans cleavage site in the gene coding for a synaptobrevin-like protein, and rna transcribed from this gene was efficiently cleaved by the smalpha ribozyme in vitro. similar families of repeats containing the hammerhead domain were found in the closely related schistosoma haematobium and schistosomatium douthitti species but were not present in schistosoma japonicum or heterobilharzia americana, suggesting that the hammerhead domain was not acquired from a common schistosome ancestor.",1
"regulation of amyloid-β (aβ) precursor protein (app) expression is complex. micrornas (mirnas) are expected to participate in the molecular network that controls this process. the composition of this network is, however, still undefined. elucidating the complement of mirnas that regulate app expression should reveal novel drug targets capable of modulating aβ production in ad. here, we investigated the contribution of mir-153 to this regulatory network. a mir-153 target site within the app 3'-untranslated region (3'-utr) was predicted by several bioinformatic algorithms. we found that mir-153 significantly reduced reporter expression when co-transfected with an app 3'-utr reporter construct. mutation of the predicted mir-153 target site eliminated this reporter response. mir-153 delivery in both hela cells and primary human fetal brain cultures significantly reduced app expression. delivery of a mir-153 antisense inhibitor to human fetal brain cultures significantly elevated app expression. mir-153 delivery also reduced expression of the app paralog aplp2. high functional redundancy between app and aplp2 suggests that mir-153 may target biological pathways in which they both function. interestingly, in a subset of human ad brain specimens with moderate ad pathology, mir-153 levels were reduced. this same subset also exhibited elevated app levels relative to control specimens. therefore, endogenous mir-153 inhibits expression of app in human neurons by specifically interacting with the app 3'-utr. this regulatory interaction may have relevance to ad etiology, where low mir-153 levels may drive increased app expression in a subset of ad patients.",1
"micrornas (mirnas) usually bind to their target mrnas through imperfect base pairing in the 3'-untranslated regions (3' utrs) and regulate target gene expression via post-transcriptional suppression. in recent years, computational approaches to predict mirna targets have facilitated the identification of potential target sites. in this study, we used three programs targetscan, mirdb and miranda to predict potential mirna binding sites to the fragile x gene fmr1 and picked out 61 mirnas which were predicted by all three programs for further investigation. excitingly, 5 out of these mirnas, mir-23a, mir-32, mir-124, mir-335-5p and mir-350, were experimentally verified by luciferase reporter assays. furthermore, overexpression of mir-124 in mouse embryonic neural progenitor cells (enpc) could not only significantly reduce fmr1 level, but also increase cdk4 and cyclin d1 levels which coincidently promoted enpc proliferation. our results imply that mir-124 plays an important role in the proliferation of mouse embryonic stem cells by promoting cdk4 and cyclin d1 expression through directly inhibiting fmr1 expression.",1
"here, we report a comprehensive investigation of changes in microrna (mirna) expression profiles on human keratinocyte (hk) differentiation in vitro and in vivo. we have monitored expression patterns of 377 mirnas during calcium-induced differentiation of primary hks, and have compared these patterns with mirna expression profiles of epidermal stem cells, transient amplifying cells, and terminally differentiated hks from human skin. apart from the previously described mir-203, we found an additional nine mirnas (mir-23b, mir-95, mir-210, mir-224, mir-26a, mir-200a, mir-27b, mir-328, and mir-376a) that are associated with hk differentiation in vitro and in vivo. in situ hybridization experiments confirmed mir-23b as a marker of hk differentiation in vivo. additionally, gene ontology analysis and functional validation of predicted mirna targets using 3'-untranslated region-luciferase assays suggest that multiple mirnas that are upregulated on hk differentiation cooperate to regulate gene expression during skin development. our results thus provide the basis for further analysis of mirna functions during epidermal differentiation.",1
"secreted exosomal micrornas (mirnas) mediate interorgan/tissue communications by modulating target gene expression, thereby regulating developmental and physiological functions. however, the source, route, and function in target cells have not been formally established for specific mirnas. here, we show that glial mir-274 non-cell-autonomously modulates the growth of synaptic boutons and tracheal branches. whereas the precursor form of mir-274 is expressed in glia, the mature form of mir-274 distributes broadly, including in synaptic boutons, muscle cells, and tracheal cells. mature mir-274 is secreted from glia to the circulating hemolymph as an exosomal cargo, a process requiring escrt components in exosome biogenesis and rab11 and syx1a in exosome release. we further show that mir-274 can function in the neurons or tracheal cells to modulate the growth of synaptic boutons and tracheal branches, respectively. also, mir-274 uptake into the target cells by ap-2-dependent mechanisms modulates target cell growth. in the target cells, mir-274 down-regulates sprouty (sty) through a targeting sequence at the sty 3' untranslated region, thereby enhancing mapk signaling and promoting cell growth. mir-274 expressed in glia of an mir-274 null mutant is released as an exosomal cargo in the circulating hemolymph, and such glial-specific expression resets normal levels of sty and mapk signaling and modulates target cell growth. mir-274 mutant larvae are hypersensitive to hypoxia, which is suppressed by mir-274 expression in glia or by increasing tracheal branches. thus, glia-derived mir-274 coordinates growth of synaptic boutons and tracheal branches to modulate larval hypoxia responses.",1
"during drosophila oogenesis, the endopolyploid nuclei of germ-line nurse cells undergo a dramatic shift in morphology as oogenesis progresses; the easily-visible chromosomes are initially polytenic during the early stages of oogenesis before they transiently condense into a distinct '5-blob' configuration, with subsequent dispersal into a diffuse state. mutations in many genes, with diverse cellular functions, can affect the ability of nurse cells to fully decondense their chromatin, resulting in a '5-blob arrest' phenotype that is maintained throughout the later stages of oogenesis. however, the mechanisms and significance of nurse-cell (nc) chromatin dispersal remain poorly understood. here, we report that a screen for modifiers of the 5-blob phenotype in the germ line isolated the spliceosomal gene peanuts, the drosophila prp22. we demonstrate that reduction of spliceosomal activity through loss of peanuts promotes decondensation defects in nc nuclei during mid-oogenesis. we also show that the prp38 spliceosomal protein accumulates in the nucleoplasm of nurse cells with impaired peanuts function, suggesting that spliceosomal recycling is impaired. finally, we reveal that loss of additional spliceosomal proteins impairs the full decondensation of nc chromatin during later stages of oogenesis, suggesting that individual spliceosomal subcomplexes modulate expression of the distinct subset of genes that are required for correct morphology in endopolyploid nurse cells.",1
"we report a phenomenon wherein induction of cell death by a variety of means in wing imaginal discs of drosophila larvae resulted in the activation of an anti-apoptotic microrna, bantam. cells in the vicinity of dying cells also become harder to kill by ionizing radiation (ir)-induced apoptosis. both ban activation and increased protection from ir required receptor tyrosine kinase tie, which we identified in a genetic screen for modifiers of ban. tie mutants were hypersensitive to radiation, and radiation sensitivity of tie mutants was rescued by increased ban gene dosage. we propose that dying cells activate ban in surviving cells through tie to make the latter cells harder to kill, thereby preserving tissues and ensuring organism survival. the protective effect we report differs from classical radiation bystander effect in which neighbors of irradiated cells become more prone to death. the protective effect also differs from the previously described effect of dying cells that results in proliferation of nearby cells in drosophila larval discs. if conserved in mammals, a phenomenon in which dying cells make the rest harder to kill by ir could have implications for treatments that involve the sequential use of cytotoxic agents and radiation therapy.",1
"background both nuclear receptor subfamily 2 group f member 1 (nr2f1) and micrornas (mirnas) have been shown to play critical roles in the developing and functional inner ear. based on previous studies suggesting interplay between nr2f1 and mirnas, we investigated the coregulation between nr2f1 and mirnas to better understand the regulatory mechanisms of inner ear development and functional maturation. results using a bioinformatic approach, we identified 11 potential mirnas that might coregulate target genes with nr2f1 and analyzed their targets and potential roles in physiology and disease. we selected 6 mirnas to analyze using quantitative real-time (qrt) -pcr and found that mir-140 is significantly down-regulated by 4.5-fold (p=0.004) in the inner ear of nr2f1 knockout (nr2f1(-/-)) mice compared to wild-type littermates but is unchanged in the brain. based on this, we performed chromatin-immunoprecipitation followed by qrt-pcr and confirmed that nr2f1 directly binds and regulates both mir-140 and klf9 in vivo. furthermore, we performed luciferase reporter assay and showed that mir-140 mimic directly regulates klf9-3'utr, thereby establishing and validating an example coregulatory network involving nr2f1, mir-140, and klf9. conclusions we have described and experimentally validated a novel tissue-dependent coregulatory network for nr2f1, mir-140, and klf9 in the inner ear and we propose the existence of many such coregulatory networks important for both inner ear development and function.",1
"castration of male pigs is a common practice used to reduce boar taint in commercial pork production, but it also significantly results in fat accumulation in carcass. our previous study revealed a mirna gene, ssc-mir-7134-3p that was implicated in adipogenesis. however, the relationship between ssc-mir-7134-3p and fat deposition due to castration is unknown. in the present study, we observed that ssc-mir-7134-3p targets the coding sequence (cds) region of mark4 based on bioinformatics analysis and dual-luciferase assays. experiments using silent mutations and sub-cloning showed that ssc-mir-7134-3p binds independently to two adjacent sites in the mark4 cds. subsequently, ssc-mir-7134-3p inhibits mark4 protein expression in pig fibroblast cells, being consistent with the targeting demonstrated in vitro. we found higher mark4 protein levels in the back fat of castrated pigs than in intact pigs, providing further evidence that mark4 is involved in regulation of fat deposition. in addition, one snp (g.2581a>g) in mark4 was significantly associated with the back fat trait in chinese and european pig populations. taken together, we would conclude that ssc-mir-7134-3p targets the mark4 gene for fat accumulation in the castrated male pigs.",1
"unlabelled the question of how hiv-1 interfaces with cellular microrna (mirna) biogenesis and effector mechanisms has been highly controversial. here, we first used deep sequencing of small rnas present in two different infected cell lines (tzm-bl and c8166) and two types of primary human cells (cd4(+) peripheral blood mononuclear cells and macrophages) to unequivocally demonstrate that hiv-1 does not encode any viral mirnas. perhaps surprisingly, we also observed that infection of t cells by hiv-1 has only a modest effect on the expression of cellular mirnas at early times after infection. comprehensive analysis of mirna binding to the hiv-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (par-clip) technique revealed several binding sites for cellular mirnas, a subset of which were shown to be capable of mediating mirna-mediated repression of gene expression. however, the main finding from this analysis is that hiv-1 transcripts are largely refractory to mirna binding, most probably due to extensive viral rna secondary structure. together, these data demonstrate that hiv-1 neither encodes viral mirnas nor strongly influences cellular mirna expression, at least early after infection, and imply that hiv-1 transcripts have evolved to avoid inhibition by preexisting cellular mirnas by adopting extensive rna secondary structures that occlude most potential mirna binding sites. importance micrornas (mirnas) are a ubiquitous class of small regulatory rnas that serve as posttranscriptional regulators of gene expression. previous work has suggested that hiv-1 might subvert the function of the cellular mirna machinery by expressing viral mirnas or by dramatically altering the level of cellular mirna expression. using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. moreover, hiv-1 transcripts appear to largely avoid regulation by cellular mirnas by adopting an extensive rna secondary structure that occludes the ability of cellular mirnas to interact with viral mrnas. together, these data suggest that hiv-1, rather than seeking to control mirna function in infected cells, has instead evolved a mechanism to become largely invisible to cellular mirna effector mechanisms.",1
"cardiac myxoma (cm) is a prevalent primary cardiac tumor. mir-217 plays a vital role in tumorigenesis of various cancers, however, its role and underlying molecular mechanism in human cm remain poorly understood. here, we reported that the expression of mir-217 was downregulated in cm tissues and inversely correlated with the expression of interleukin-6 (il-6) mrna. gain-of-function analysis indicated that overexpression of mir-217 inhibited the proliferation and promoted the apoptosis of the primary cm cells. bioinformatics analysis showed that il-6 was a direct target gene of mir-217, which is confirmed by the dual luciferase assays. moreover, downregulation of il-6 by small interference rna (sirna) mimicked the tumor-suppressive effects of mir-217 in cm. furthermore, rescue experiments pointed out that restoration of il-6 expression abrogated the anti-proliferative and pro-apoptotic effect induced by mir-217 overexpression in cm cells. taken together, we validated that mir-217 could act as a tumor suppressor in cm by directly targeting 3'utr of il-6 gene, indicating that manipulation of mir-217 may be a potential therapeutic strategy for cm patients.",1
"telomerase maintains cell viability and chromosomal stability through the addition of telomere repeats to chromosome ends. the reactivation of telomerase through the upregulation of tert, the telomerase protein subunit, is an important step during cancer development, yet tert protein function and regulation remain incompletely understood. despite its close sequence similarity to human tert (htert), we find that mouse tert (mtert) does not immortalize primary human fibroblasts. here we exploit these differences in activity to understand tert protein function by creating chimeric mouse-human tert proteins. through the analysis of these chimeric tert proteins, we find that sequences in the human carboxy-terminal domain are critical for telomere maintenance in human fibroblasts. the substitution of the human carboxy-terminal sequences into the mouse tert protein is sufficient to confer immortalization and maintenance of telomere length and function. strikingly, we find that htert protein accumulates to markedly higher levels than does mtert protein and that the sequences governing this difference in protein regulation also reside in the carboxy-terminal domain. these elevated protein levels, which are characteristic of htert, are necessary but not sufficient for telomere maintenance because stabilized mtert mutants cannot immortalize human cells. thus, the tert carboxy terminus contains sequences that regulate tert protein levels and determinants that are required for productive action on telomere ends.",1
"demyelinating disorders including leukodystrophies are devastating conditions that are still in need of better understanding, and both oligodendrocyte differentiation and myelin synthesis pathways are potential avenues for developing treatment. overexpression of lamin b1 leads to leukodystrophy characterized by demyelination of the central nervous system, and microrna-23 (mir-23) was found to suppress lamin b1 and enhance oligodendrocyte differentiation in vitro. here, we demonstrated that mir-23a-overexpressing mice have increased myelin thickness, providing in vivo evidence that mir-23a enhances both oligodendrocyte differentiation and myelin synthesis. using this mouse model, we explored possible mir-23a targets and revealed that the phosphatase and tensin homologue/phosphatidylinositol trisphosphate kinase/akt/mammalian target of rapamycin pathway is modulated by mir-23a. additionally, a long noncoding rna, 2700046g09rik, was identified as a mir-23a target and modulates phosphatase and tensin homologue itself in a mir-23a-dependent manner. the data presented here imply a unique role for mir-23a in the coordination of proteins and noncoding rnas in generating and maintaining healthy myelin.",1
"chronic hypoxia triggers pulmonary vascular remodeling, which is associated with de-differentiation of pulmonary artery smooth muscle cells (pasmc). here, we show that mir-20a expression is up-regulated in response to hypoxia in both mouse and human pasmc. we also observed that mir-20a represses the protein kinase, cgmp-dependent, type i (prkg1) gene and we identified two crucial mir-20a binding sites within the coding region of prkg1. functional studies showed that mir-20a promotes the proliferation and migration of human pasmc, whereas it inhibits their differentiation. in summary, we provided a possible mechanism by which hypoxia results in decreased prkg1 expression and in the phenotypic switching of pasmc.",1
"unlabelled the molecular mechanisms that regulate hadsc differentiation toward osteogenic precursors and subsequent bone-forming osteoblasts is unknown. using osteoblast precursors obtained from subcutaneous human adipose tissue, we observed that microrna-26a modulated late osteoblasts differentiation by targeting the smad1 transcription factor. introduction elucidation of the molecular mechanisms guiding human adipose tissue-derived stem cells (hadscs) differentiation is of extreme importance for improving the treatment of bone-related diseases such as osteoporosis. the aim of this study was to identify microrna as a regulator of the osteogenic differentiation of hadscs. materials and methods osteoblast differentiation of hadscs was induced by treatment with dexamethasone, ascorbic acid, and beta-glycerol phosphate. the expression of osteoblastic phenotype was evaluated after the induction by simultaneous monitoring of alkaline phosphatase activity, the expression of genes involved in osteoblastic differentiation by real-time rt-pcr, and mineralization at the same time. microrna expression was determined by northern blot, and transfection of both antisense mir-rna and sensor plasmids was done to validate the inhibitory role of microrna during hadsc osteogenesis. western blot was used to determine the expression levels of the smad1 protein. qrt-pcr analysis was used to compare the expression patterns of osteoblastic markers in transfected cells. results and conclusions we analyzed the role of microrna 26a (mir-26a) during differentiation of hadscs. northern blot analysis of mir-26a during hadsc differentiation showed increased expression, whereas expression of the smad1 protein was complementary to that of mir-26a. because the highest expression of mir-26a and the lowest expression of smad1 protein were reached at hadsc terminal differentiation, we carried out our study during the late stages of hadsc differentiation. the inhibition of mir-26a, by 2'-o-methyl-antisense rna, increased protein levels of its predicted target, smad1 transcription factor, in treated osteoblasts, upregulating bone marker genes and thus enhancing osteoblast differentiation. our data suggest a role for mir-26a in the differentiation induced by treatment with dexamethasone, ascorbic acid, and beta-glycerol phosphate of hadscs toward the osteogenic lineage by targeting its predicted target, the smad1 protein. this study contributes to a better knowledge of molecular mechanisms governing hadsc differentiation by proposing a microrna-based control of late differentiation.",1
"the regulation of mitochondrial biogenesis is under the control of nuclear genes including the master mitochondrial transcription factor a (tfam). recent evidence suggests that the expression of tfam is regulated by micrornas (mirnas) in various cellular contexts. here, we show that hsa-mir-155-5p, a prominent mirna encoded in chromosome 21, controls the expression of tfam at the post-transcriptional level. in human fibroblasts derived from a diploid donor, downregulation of tfam by hsa-mir-155-5p decreased mitochondrial dna (mtdna) content. in contrast, downregulation of tfam by hsa-mir-155-5p did not decrease mtdna content in fibroblasts derived from a donor with down syndrome (ds, trisomy 21). in line, downregulation of mitochondrial tfam levels through hsa-mir-155-5p decreased mitochondrial mass in diploid fibroblasts but not in trisomic cells. due to the prevalence of mitochondrial dysfunction and cardiac abnormalities in subjects with ds, we examined the presence of potential associations between hsa-mir-155-5p and tfam expression in heart samples from donors with and without ds. there were significant negative associations between hsa-mir-155-5p and tfam expression in heart samples from donors with and without ds. these results suggest that regulation of tfam by hsa-mir-155-5p impacts mitochondrial biogenesis in the diploid setting but not in the ds setting.",1
"mitochondrial gene expression is largely controlled through post-transcriptional processes including mitochondrial rna (mt-rna) processing, modification, decay, and quality control. defective mitochondrial gene expression results in mitochondrial oxidative phosphorylation (oxphos) deficiency and has been implicated in human disease. to fully understand mitochondrial transcription and rna processing, we performed rna-seq analyses of mt-rnas from the fission yeast schizosaccharomyces pombe rna-seq analyses show that the abundance of mt-rnas vary greatly. analysis of data also reveals mt-rna processing sites including an unusual rna cleavage event by mitochondrial trna (mt-trna) 5'-end processing enzyme rnase p. additionally, this analysis reveals previously unknown mitochondrial transcripts including the rnpb -derived fragment, mitochondrial small rnas (mitosrnas) such as mt-trna-derived fragments (mt-trfs) and mt-trna halves, and mt-trnas marked with 3'-ccacca/ccacc in s. pombe finally, rna-seq reveals that inactivation of trz2 encoding s. pombe mitochondrial trna 3'-end processing enzyme globally impairs mt-trna 3'-end processing, inhibits mt-mrna 5'-end processing, and causes accumulation of unprocessed transcripts, demonstrating the feasibility of using rna-seq to examine the protein known or predicted to be involved in mt-rna processing in s. pombe our work uncovers the complexity of a fungal mitochondrial transcriptome and provides a framework for future studies of mitochondrial gene expression using s. pombe as a model system.",1
"hepatitis b virus (hbv) infection is a leading cause of hepatocellular carcinoma worldwide. however, the strategy of hbv to escape from the host immune system remains largely unknown. in this study, we examined extracellular vesicles (evs) secreted from human hepatocytes infected with hbv. evs includeing exosomes are nano-size vesicles with proteins, mrnas, and micrornas (mirnas), which can be transmitted to different cells. we found that 104 ev associated mirnas were increased in hepatocytes more than 2-fold by hbv infection. we then selected those that were potentially implicated in immune regulation. among them, five hbv-induced mirnas were found to potentially target multiple sequences in the 3'utr of il-21, a cytokine that induces anti-viral immunity. moreover, expression of a reporter gene with the 3' utr of human il-21 mrna was suppressed by the five mirnas individually. finally, il-21 expression in cloned human t cells was down-regulated by the five mirnas. collectively, this study identified the novel 3' utr sequences of human il-21 mrna and potential binding sites of hbv-induced ev-mirnas.",1
"in eukaryotes, the 40 s ribosomal subunit serves as the platform of initiation factor assembly, to place itself precisely on the aug start codon. structural arrangement of the 18 s rrna determines the overall shape of the 40 s subunit. here, we present genetic evaluation of yeast 18 s rrna function using 10 point mutations altering the polysome profile. all the mutants reduce the abundance of the mutant 40 s, making it limiting for translation initiation. two of the isolated mutations, g875a, altering the core of the platform domain that binds eif1 and eif2, and a1193u, changing the h31 loop located below the p-site trna(i)(met), show phenotypes indicating defective regulation of aug selection. evidence is provided that these mutations reduce the interaction with the components of the preinitiation complex, thereby inhibiting its function at different steps. these results indicate that the 18 s rrna mutations impair the integrity of scanning-competent preinitiation complex, thereby altering the 40 s subunit response to stringent aug selection. interestingly, nine of the mutations alter the body/platform domains of 18 s rrna, potentially affecting the bridges to the 60 s subunit, but they do not change the level of 18 s rrna intermediates. based on these results, we also discuss the mechanism of the selective degradation of the mutant 40 s subunits.",1
"micrornas (mirnas) as one of the major epigenetic modulators negatively regulate mrnas at post transcriptional level. it was therefore hypothesized that modulation of mirnas by hexavalent chromium , a priority environmental chemical, can affect dna damage. in a genetically tractable model, drosophila melanogaster, role of maximally up-regulated mirna, dme-mir-314-3p, on dna damage was examined by exposing the third instar larvae to 5.0-20.0 μg/ml cr(vi) for 24 and 48 h. mus309, a drosophila homologue of human bloom's syndrome and predicted as one of the potential targets of this mirna, was confirmed as its target by 5'rlm-race assay. a significant down-regulation of mus309 was observed in dme-mir-314-3p overexpression strain (myo-gal4>uas-mir-314-3p) as compared with that in parental strains (myo-gal4 and uas-mir-314-3p) and in w(1118). a significant increase in dna damage including double strand breaks generation was observed in exposed myo-gal4>uas-mir-314 and mus309 mutants as compared with that in parental strain and in unexposed control. a significant down-regulation of cell cycle regulation genes (cyca, cycb and cdc2) was observed in these exposed genotypes. collectively, the study demonstrates that dme-mir-314-3p can mediate the downregulation of repair deficient gene mus309 leading to increased dna damage and cell cycle arrest in exposed organism which may affect cr(vi) mediated carcinogenesis.",1
"the sterol regulatory element binding transcription factor 2 (srebf2) gene encodes a transcription factor that activates the expression of many genes involved in the synthesis and uptake of cholesterol, fatty acids, triglycerides, and phospholipids. through bioinformatics, we found that intron 16 of the chicken srebf2 gene might encode the chicken mir-33. using quantitative rt-pcr, we detected the expression of mir-33 in a variety of chicken tissues including skeletal muscle, adipose tissue, and liver. three hundred and seventy eight genes were predicted to be potential targets of mir-33 in chickens via mirna target prediction programs ""miranda"" and ""targetscan"". among these targets, the gene fto (fat mass and obesity associated) encodes a fe(ii)- and 2-oxoglutarate-dependent nucleic acid demethylase that regulates lipid metabolism, and the possibility that its expression is negatively regulated by mir-33 in the chicken liver was therefore further studied. co-transfection and dual-luciferase reporter assays showed that the expression of luciferase reporter gene linked to the 3'-untranslated region (3'utr) of the chicken fto mrna was down-regulated by overexpression of the chicken mir-33 in the c2c12 cells (p<0.05). furthermore, this down-regulation was completely abolished when the predicted mir-33 target site in the fto 3'utr was mutated. in contrast, the expression of fto mrna in the primary chicken hepatocytes was up-regulated after transfection with the mir-33 inhibitor lna-anti-mir-33. using quantitative rt-pcr, we also found that the expression of mir-33 was increased in the chicken liver from day 0 to day 49 of age, whereas that of the fto mrna was decreased during the same age period. these data together suggest that mir-33 might play an important role in lipid metabolism in the chicken liver by negatively regulating the expression of the fto gene.",1
"mirnas are emerging as critical regulators in carcinogenesis and tumor progression. recently, microrna-122 (mir-122) has been proved to play an important role in hepatocellular carcinoma, but its functions in the context of breast cancer (bc) remain unknown. in this study, we report that mir-122 is commonly downregulated in bc specimens and bc cell lines with important functional consequences. overexpression of mir-122 not only dramatically suppressed cell proliferation, colony formation by inducing g1-phase cell-cycle arrest in vitro, but also reduced tumorigenicity in vivo. we then screened and identified a novel mir-122 target, insulin-like growth factor 1 receptor (igf1r), and it was further confirmed by luciferase assay. overexpression of mir-122 would specifically and markedly reduce its expression. similar to the restoring mir-122 expression, igf1r downregulation suppressed cell growth and cell-cycle progression, whereas igf1r overexpression rescued the suppressive effect of mir-122. to identify the mechanisms, we investigated the akt/mtor/p70s6k pathway and found that the expression of akt, mtor and p70s6k were suppressed, whereas re-expression of igf1r which did not contain the 3'utr totally reversed the inhibition of akt/mtor/p70s6k signal pathway profile. we also identified a novel, putative mir-122 target gene, pi3cg, a member of pi3k family, which further suggests mir-122 may be a key regulator of the pi3k/akt pathway. in clinical specimens, igf1r was widely overexpressed and its mrna levels were inversely correlated with mir-122 expression. taken together, our results demonstrate that mir-122 functions as a tumor suppressor and plays an important role in inhibiting the tumorigenesis through targeting igf1r and regulating pi3k/akt/mtor/p70s6k pathway. given these, mir-122 may serve as a novel therapeutic or diagnostic/prognostic-target for treating bc.",1
"rna structures are fundamentally important for rna function. dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and rna thermometers. by parallel analysis of rna structures, we mapped the rna structurome of yersinia pseudotuberculosis at three different temperatures. this human pathogen is exquisitely responsive to host body temperature (37 °c), which induces a major metabolic transition. our analysis profiles the structure of more than 1,750 rnas at 25 °c, 37 °c, and 42 °c. average mrnas tend to be unstructured around the ribosome binding site. we searched for 5'-utrs that are folded at low temperature and identified novel thermoresponsive rna structures from diverse gene categories. the regulatory potential of 16 candidates was validated. in summary, we present a dynamic bacterial rna structurome and find that the expression of virulence-relevant functions in y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mrnas.",1
"the role of mirnas in mediating insecticide resistance remains largely unknown, even for the model species drosophila melanogaster. building on prior research, this study used microinjection of synthetic mir-310s mimics into ddt-resistant 91-r flies and observed both a significant transcriptional repression of computationally-predicted endogenous target p450 detoxification genes, cyp6g1 and cyp6g2, and also a concomitant increase in ddt susceptibility. additionally, co-transfection of d. melanogaster s2 cells with dual luciferase reporter constructs validated predictions that mir-310s bind to target binding sites in the 3' untranslated regions (3'-utr) of both cyp6g1 and cyp6g2 in vitro. findings in the current study provide empirical evidence for a link between reduced mirna expression and an insecticidal resistance phenotype through reduced targeted post-transcriptional suppression of transcripts encoding proteins involved in xenobiotic detoxification. these insights are important for understanding the breadth of adaptive molecular changes that have contributed to the evolution of ddt resistance in d. melanogaster.",1
"here we report the functional characterization of pwp2, an evolutionary conserved component of the 90 s pre-ribosome. conditional depletion of the pwp2 protein in yeast specifically impairs pre-rrna proccessing at sites a(0), a(1), and a(2), leading to a strong decrease in 18 s rrna and 40 s ribosomal subunit levels. pre-ribosomal particle sedimentation analysis indicated that these defects are caused by a block in the formation of 90 s pre-ribosomes. we demonstrate that in pwp2-depleted cells the u3 small nucleolar ribonucleoprotein is not able to interact with the 35 s pre-rrna and accumulates as a free complex. similarly, other 90 s particle components such as imp3 and imp4 do not associate with the pre-rrna precursor in the absence of pwp2. in addition, we have found that after blocking u3 ribonucleoprotein assembly, pwp2 predominantly accumulates as a complex in association with five proteins: dip2, utp6, utp13, utp18, and utp21. immunoprecipitation and gradient sedimentation analysis revealed that this pwp2 small subcomplex is capable of interacting directly with the 35 s pre-rrna 5' end. taken together, these results indicate that pwp2 forms part of a stable particle subunit independent of the u3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90 s pre-ribosome.",1
"our previous studies have showed that metastasis-associated protein 3 (mta 3) is overexpressed in non-small cell lung cancer (nsclc) tissue, and increased mta3 mrna levels is a risk factor of lymph node metastasis. using bioinformatics analyses, we found that mta3 was a potential target of mir-495. however, the pathophysiological role of mir-495 and its relevance to the growth and development of nsclc have yet to be investigated. the purpose of this study was to elucidate the molecular mechanisms by which mir-495 acts as a tumor suppressor in nsclc. qrt-pcr data showed significant downregulation of mir-495 in 56 nsclc tissue samples and 5 lung cancer cell lines, compared with their adjacent normal tissue; furthermore, western blotting analysis revealed mta3 protein was overexpressed in the tumor samples compared with the matched adjacent normal tissue. mir-495 was shown to not only inhibit the proliferation of lung cancer cells (a549 and calu-3) but also to inhibit cell migration in vitro. using western blotting and luciferase assays, mta3 was identified as a target of mir-495. these findings suggest the importance of mir-495 targeting of mta3 in the regulation of lung cancer growth and migration.",1
"ribozymes are noncoding rnas that promote chemical transformations with rate enhancements approaching those of protein enzymes. although ribozymes are likely to have been abundant during the rna world era, only ten classes are known to exist among contemporary organisms. we report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. nearly 2,700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. the twister ribozyme motif provides another example of a natural rna catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving rnas.",1
"neat1 rna, a highly abundant 4 kb ncrna, is retained in nuclei in approximately 10 to 20 large foci that we show are completely coincident with paraspeckles, nuclear domains implicated in mrna nuclear retention. depletion of neat1 rna via rnai eradicates paraspeckles, suggesting that it controls sequestration of the paraspeckle proteins psp1 and p54, factors linked to a-i editing. unlike overexpression of psp1, neat1 overexpression increases paraspeckle number, and paraspeckles emanate exclusively from the neat1 transcription site. the psp-1 rna binding domain is required for its colocalization with neat1 rna in paraspeckles, and biochemical analyses support that neat1 rna binds with paraspeckle proteins. unlike other nuclear-retained rnas, neat1 rna is not a-i edited, consistent with a structural role in paraspeckles. collectively, results demonstrate that neat1 functions as an essential structural determinant of paraspeckles, providing a precedent for a ncrna as the foundation of a nuclear domain.",1
"medulloblastoma, originating in the cerebellum, is the most common malignant brain tumor in children. medulloblastoma consists of four major groups where constitutive activation of the sonic hedgehog (shh) signaling pathway is a hallmark of one group. mouse and human shh medulloblastomas exhibit increased expression of micrornas encoded by the mir-17~92 and mir-106b~25 clusters compared with granule progenitors and postmitotic granule neurons. here, we assessed the therapeutic potential of 8-mer seed-targeting locked nucleic acid (lna)-modified anti-mir oligonucleotides, termed tiny lnas, that inhibit microrna seed families expressed by mir-17~92 and mir-106b~25 in two mouse models of shh medulloblastomas. we found that tumor cells (medulloblastoma cells) passively took up 8-mer lna-anti-mirs and specifically inhibited targeted microrna seed-sharing family members. inhibition of mir-17 and mir-19a seed families by anti-mir-17 and anti-mir-19, respectively, resulted in diminished tumor cell proliferation in vitro. treatment of mice with systemic delivery of anti-mir-17 and anti-mir-19 reduced tumor growth in flank and brain allografts in vivo and prolonged the survival of mice with intracranial transplants, suggesting that inhibition of the mir-17~92 cluster family by 8-mer lna-anti-mirs might be considered for the treatment of shh medulloblastomas.",1
"dna double strand break (dsb) is one of the major damages that cause genome instability and cellular aging. the homologous recombination (hr)-mediated repair of dsbs plays an essential role in assurance of genome stability and cell longevity. telomeres resemble dsbs and are competent for hr. here we show that in budding yeast saccharomyces cerevisiae telomere recombination elicits genome instability and accelerates cellular aging. inactivation of keops subunit cgi121 specifically inhibits telomere recombination, and significantly extends cell longevity in both telomerase-positive and pre-senescing telomerase-negative cells. deletion of cgi121 in the short-lived yku80(tel) mutant restores lifespan to cgi121δ level, supporting the function of cgi121 in telomeric single-stranded dna generation and thus in promotion of telomere recombination. strikingly, inhibition of telomere recombination is able to further slow down the aging process in long-lived fob1δ cells, in which rdna recombination is restrained. our study indicates that hr activity at telomeres interferes with telomerase to pose a negative impact on cellular longevity.",1
"cis-acting rna signals are required for replication of positive-strand viruses such as the picornaviruses. although these generally have been mapped to the 5' and/or 3' termini of the viral genome, rnas derived from human rhinovirus type 14 are unable to replicate unless they contain an internal cis-acting replication element (cre) located within the genome segment encoding the capsid proteins. here, we show that the essential cre sequence is 83-96 nt in length and located between nt 2318-2413 of the genome. using dicistronic rnas in which translation of the p1 and p2-p3 segments of the polyprotein were functionally dissociated, we further demonstrate that translation of the cre sequence is not required for rna replication. thus, although it is located within a protein-coding segment of the genome, the cre functions as an rna entity. computer folds suggested that cre sequences could form a stable structure in either positive- or minus-strand rna. however, an analysis of mutant rnas containing multiple covariant and non-covariant nucleotide substitutions within these putative structures demonstrated that only the predicted positive-strand structure is essential for efficient rna replication. the absence of detectable minus-strand synthesis from rnas that lack the cre suggests that the cre is required for initiation of minus-strand rna synthesis. since a lethal 3' noncoding region mutation could be partially rescued by a compensating mutation within the cre, the cre appears to participate in a long-range rna-rna interaction required for this process. these data provide novel insight into the mechanisms of replication of a positive-strand rna virus, as they define the involvement of an internally located rna structure in the recognition of viral rna by the viral replicase complex. since internally located rna replication signals have been shown to exist in several other positive-strand rna virus families, these observations are potentially relevant to a wide array of related viruses.",1
"cisplatin-induced and atm-phosphorylated (p)-δnp63α regulates the expression of epidermal differentiation and skin barrier regulators (aqp3, casp14, alox12b, and cldn1) in squamous cell carcinoma (scc) cells by dual transcriptional and post-transcriptional mechanisms. we found that p-δnp63α bound to target gene promoters, and regulated the activity of the tested promoters in vitro. p-δnp63α was shown to upregulate mir-185-5p and downregulate let7-5p, which subsequently modulated aqp3, casp14, alox12b and cldn1 through their respective 3'-untranslated regions. the introduction of mir-185-5p into resistant scc-11m cells, which are unable to phosphorylate δnp63α, render these cells more sensitive to cisplatin treatment. further studies of the aqp3, casp14, alox12b, and cldn1 contributions to chemoresistance may assist in developing novel microrna-based therapies for human scc.",1
"little is known about the tertiary structure of internal ribosome entry site (ires) elements. the central domain of foot-and-mouth disease (fmdv) ires, named 3 or i, contains a conserved gnra motif, essential for ires activity. we have combined functional analysis with rna probing to define its structural organization. we have found that a uncg motif does not functionally substitute the gnra motif; moreover, binding of synthetic gnra stem-loops to domain 3 was significantly reduced in rnas bearing uccg or guag substitutions. the apical region of domain 3 consists of a four-way junction where residues of the gnra tetraloop are responsible for the organization of the adjacent stem-loops, as deduced from ribonucleases and dimethyl sulfate accessibility. a single a-to-g substitution in the fourth position of this motif led to a strong rna reorganization, affecting several nucleotides away in the secondary structure of domain 3. the study of mutants bearing uncg or guag tetraloops revealed lack of protection to chemical attack in native rna at specific nucleotides relative to the parental guaa, suggesting that the gnra motif dictates the organization and stability of domain 3. this effect is likely mediated by the interaction with distant residues. therefore, the gnra motif plays a crucial role in the organization of ires structure with important consequences on activity.",1
"vault rnas (vtrnas) are small, about 100 nt long, polymerase iii transcripts contained in the vault particles of eukaryotic cells. presumably due to their enigmatic function, they have received little attention compared with most other noncoding rna (ncrna) families. their poor sequence conservation makes homology search a complex and tedious task even within vertebrates. here we report on a systematic and comprehensive analysis of this rapidly evolving class of ncrnas in deuterostomes, providing a comprehensive collection of computationally predicted vtrna genes. we find that all previously described vtrnas are located at a conserved genomic locus linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. lineage-specific expansions to small vtrna gene clusters are frequently observed in this region. a second vtrna locus is syntenically conserved across eutherian mammals. the vtrnas at the two eutherian loci exhibit substantial differences in their promoter structures, explaining their differential expression patterns in several human cancer cell lines. in teleosts, expression of several paralogous vtrna genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction.",1
"cajal (coiled) bodies are conserved subnuclear organelles that are present in the nucleoplasm of both animal and plant cells. although cajal bodies were first described nearly 100 years ago, their function has remained largely speculative. here, we describe a novel class of human small nuclear rnas that localize specifically to cajal bodies. the small cajal body-specific rnas (scarnas) are predicted or have already been demonstrated to function as guide rnas in site-specific synthesis of 2'-o-ribose-methylated nucleotides and pseudouridines in the rna polymerase ii-transcribed u1, u2, u4 and u5 spliceosomal small nuclear rnas (snrnas). our results provide strong support for the idea that the cajal body, this mysterious nuclear organelle, provides the cellular locale for post-transcriptional modification of spliceosomal snrnas.",1
"micrornas (mirnas) silence gene expression by binding 3' untranslated regions of target mrnas. recent studies suggested silencing is achieved through either recruitment of eif6, which prevents ribosome assembly, or displacement of eif4e from the mrna 5' cap structure. using drosophila melanogaster cells, we show that eif6 is not required for silencing. in contrast, silencing is abolished by mutating argonaute 1 (ago1) at two conserved phenylalanine residues predicted to mediate binding to the cap structure. notably, we found these mutations also prevented ago1 from interacting with gw182 and mirnas, indicating that the essential role of these residues is unrelated to cap binding. consistently, depleting gw182 or overexpressing its ago1 binding domain relieved silencing of all reporters tested, including those lacking a poly(a) tail. together, our findings show that mirna function is effected by ago1-gw182 complexes and the role of gw182 in silencing goes beyond promoting deadenylation.",1
"the functions of micrornas (mirnas) as either oncogenes or tumor suppressors in regulating cancer-related events have been established. we analyzed the alterations in the mirna expression profile of the glioma cell line u-251 caused by ionizing radiation (ir) by using an mirna array and identified several mirnas whose expression was significantly affected by ir. among the ir-responsive mirnas, we further examined the function of mir-193a-3p, which exhibited the most significant growth-inhibiting effect. mir-193a-3p was observed to induce apoptosis in both u-251 and hela cells. we also demonstrated that mir-193a-3p induces the accumulation of intracellular reactive oxygen species (ros) and dna damage as determined by the level of γh2ax and by performing the comet assay. the induction of both apoptosis and dna damage by mir-193a-3p was blocked by antioxidant treatment, indicating the crucial role of ros in the action of mir-193a-3p. among the putative target proteins, the expression of mcl-1, an anti-apoptotic bcl-2 family member, decreased because of mir-193a-3p transfection. a reporter assay using a luciferase construct containing the 3'-untranslated region of mcl-1 confirmed that mcl-1 is a direct target of mir-193a-3p. down-regulation of mcl-1 by sirna transfection closely mimicked the outcome of mir-193a-3p transfection showing increased ros, dna damage, cytochrome c release, and apoptosis. ectopic expression of mcl-1 suppressed the pro-apoptotic action of mir-193a-3p, suggesting that mcl-1 depletion is critical for mir-193a-3p induced apoptosis. collectively, our results suggest a novel function for mir-193a-3p and its potential application in cancer therapy.",1
"persistent hyperglycemia in diabetes causes endothelial cell dysfunction. exposure to high levels of glucose, which mimics hyperglycemia, induced expression of microrna 221 (mir-221) but reduced expression of c-kit, the receptor for stem cell factor in human umbilical vein endothelial cells (huvecs). in addition, high glucose treatment impaired endothelial cell migration. incubation with the antisense mir-221 oligonucleotide amo-221 reduced expression of mir-221 and restored c-kit protein expression in huvecs treated with high levels of glucose. furthermore, amo-221 treatment abolished the inhibitory effect of high glucose exposure on huvecs transmigration. thus, under hyperglycemic conditions, mir-221 is induced in huvecs, which consequently triggers inhibition of c-kit and impairment of huvecs migration. these findings suggest that manipulation of the mir-221-c-kit pathway may offer a novel strategy for treatment of vascular dysfunction in diabetic patients.",1
"there is evidence that specificity proteins (sp), such as sp1, sp3, and sp4, are overexpressed in tumors and contribute to the proliferative and angiogenic phenotype associated with cancer cells. sp1, sp3, and sp4 are expressed in a panel of estrogen receptor (er)-positive and er-negative breast cancer cell lines, and we hypothesized that regulation of their expression may be due to microrna-27a (mir-27a), which is also expressed in these cell lines and has been reported to regulate the zinc finger zbtb10 gene, a putative sp repressor. transfection of er-negative mda-mb-231 breast cancer cells with antisense mir-27a (as-mir-27a) resulted in increased expression of zbtb10 mrna and decreased expression of sp1, sp3, and sp4 at the mrna and protein levels and also decreased activity in cells transfected with constructs containing sp1 and sp3 promoter inserts. in addition, these responses were accompanied by decreased expression of sp-dependent survival and angiogenic genes, including survivin, vascular endothelial growth factor (vegf), and vegf receptor 1 (vegfr1). moreover, similar results were observed in mda-mb-231 cells transfected with zbtb10 expression plasmid. both as-mir-27a and zbtb10 overexpression decreased the percentage of mda-mb-231 cells in s phase of the cell cycle; however, zbtb10 increased the percentage of cells in g(0)-g(1), whereas as-mir-27a increased the percentage in g(2)-m. this latter response was associated with induction of myt-1 (another mir-27a target gene), which inhibits g(2)-m through enhanced phosphorylation and inactivation of cdc2. thus, the oncogenic activity of mir-27a in mda-mb-231 cells is due, in part, to suppression of zbtb10 and myt-1.",1
"in escherichia coli, the dsba'-phoa hybrid proteins carrying an unfoldable dsba' fragment can be targeted to the envelope, where they exert their toxicity. hybrid proteins stick to the periplasmic face of the inner membrane and paralyze the export mechanism, becoming lethal if sufficiently overproduced and if not degraded by the degp protease (a. guigueno, p. belin, and p. l. boquet, j. bacteriol. 179:3260-3269, 1997). we isolated a multicopy suppressor that restores viability to a degp strain without modifying the expression level of the toxic fusion. suppression does not involve activation of the known envelope stress-combative pathways, the cpx pathway and the sigma(e) regulon. subclone analysis of the suppressor revealed a 195-bp dna fragment that is responsible for toxicity suppression. the cloned gene, called uptr, is approximately 130 bp long (including the promoter and a transcription termination signal) and is transcribed into a small rna (92 nucleotides). using site-directed mutagenesis, we found that uptr rna does not require translation for toxicity suppression. uptr-mediated action reduces the amount of membrane-bound toxic hybrid protein. uptr rna is the first example of a small rna implicated in extracytoplasmic toxicity suppression. it appears to offer a new way of suppressing toxicity, and its possible modes of action are discussed.",1
"the let-7 family of micrornas (mirnas) plays an important role on endothelial cell function. however, there have been few studies on their role under ischemic conditions. in this study, we demonstrate that let-7i, belonging to the let-7 family, rescues human brain microvascular endothelial cells (hbmecs) in an oxygen-glucose deprivation (ogd) model. our data show that the expression of let-7 family mirnas was downregulated after ogd. overexpression of let-7i significantly alleviated cell death and improved survival of ogd-treated hbmecs. let-7i also protected permeability in an in vitro blood brain barrier (bbb) model. further, let-7i downregulated the expression of toll-like receptor 4 (tlr4), an inflammation trigger. moreover, overexpression of let-7i decreased matrix metallopeptidase 9 (mmp9) and inducible nitric oxide synthase (inos) expression under ogd. upon silencing tlr4 expression in hbmecs, the anti-inflammatory effect of let-7i was abolished. our research suggests that let-7i promotes ogd-induced inflammation via downregulating tlr4 expression.",1
"hepatocellular carcinoma (hcc) is generally a fatal disease due to a paucity of effective treatment options. the identification of oncogenic micrornas that exert pleiotropic effects in hcc cells may offer new therapeutic targets. in this study, we have identified the human microrna mir-191 as a potential target for hcc therapy. inhibition of mir-191 decreased cell proliferation and induced apoptosis in vitro and significantly reduced tumor masses in vivo in an orthotopic xenograft mouse model of hcc. additionally, mir-191 was found to be upregulated by a dioxin, a known liver carcinogen, and was found to be a regulator of a variety of cancer-related pathways. our findings offer a preclinical proof of concept for mir-191 targeting as a rational strategy to pursue for improving hcc treatment.",1
"basal autophagy is tightly regulated by transcriptional and epigenetic factors to maintain cellular homeostasis. dysregulation of cardiac autophagy is associated with heart diseases, including cardiac hypertrophy, but the mechanism governing cardiac autophagy is rarely identified. to analyze the in vivo function of mir-199a in cardiac autophagy and cardiac hypertrophy, we generated cardiac-specific mir-199a transgenic mice and showed that overexpression of mir-199a was sufficient to inhibit cardiomyocyte autophagy and induce cardiac hypertrophy in vivo. mir-199a impaired cardiomyocyte autophagy in a cell-autonomous manner by targeting glycogen synthase kinase 3β (gsk3β)/mammalian target of rapamycin (mtor) complex signaling. overexpression of autophagy related gene 5 (atg5) attenuated the hypertrophic effects of mir-199a overexpression on cardiomyocytes, and activation of autophagy using rapamycin was sufficient to restore cardiac autophagy and decrease cardiac hypertrophy in mir-199a transgenic mice. these results reveal a novel role of mir-199a as a key regulator of cardiac autophagy, suggesting that targeting mirnas controlling autophagy as a potential therapeutic strategy for cardiac disease.",1
"numerous micrornas and their target mrnas are coexpressed across diverse cell types. however, it is unknown whether they are regulated in a manner independent of or dependent on cellular context. here, we explored transcriptome-wide targeting and gene regulation by mir-155, whose activation-induced expression plays important roles in innate and adaptive immunity. through mapping of mir-155 targets through differential iclip, mrna quantification with rna-seq, and 3' untranslated region (utr)-usage analysis with poly(a)-seq in macrophages, dendritic cells, and t and b lymphocytes either sufficient or deficient in activated mir-155, we identified numerous targets differentially bound by mir-155. whereas alternative cleavage and polyadenylation (apa) contributed to differential mir-155 binding to some transcripts, in most cases, identical 3'-utr isoforms were differentially regulated across cell types, thus suggesting apa-independent and cellular-context-dependent mir-155-mediated gene regulation. our study provides comprehensive maps of mir-155 regulatory networks and offers a valuable resource for dissecting context-dependent and context-independent mirna-mediated gene regulation in key immune cell types.",1
"mir-185 is a microrna (mir) that targets bruton's tyrosine kinase in b cells, with reductions in mir-185 linked to b cell autoantibody production. in hippocampal neurons, mir-185 targets both sarcoplasmic/endoplasmic reticulum calcium atpase 2 and a novel golgi inhibitor. this mir is haploinsufficient in 90-95% of individuals with chromosome 22q11.2 deletion syndrome, patients who can present with immune, cardiac, and parathyroid problems, learning disorders, and a high incidence of schizophrenia in adults. the reduced levels of mir-185 in neurons cause presynaptic neurotransmitter release. many of the 22q11.2 deletion syndrome patients have a thymic hypoplasia, which results in a peripheral t cell lymphopenia and unusual t helper cell skewing. the molecular targets of mir-185 in thymocytes are unknown. using an mir-185 t cell transgenic approach, increasing levels of mir-185 attenuated t cell development at the t cell receptor β (tcrβ) selection checkpoint and during positive selection. this caused a peripheral t cell lymphopenia. mzb1, nfatc3, and camk4 were identified as novel mir-185 targets. elevations in mir-185 enhanced tcr-dependent intracellular calcium levels, whereas a knockdown of mir-185 diminished these calcium responses. these effects concur with reductions in mzb1, an endoplasmic reticulum calcium regulator. consistent with their haploinsufficiency of mir-185, mzb1 levels were elevated in thymocyte extracts from several 22q11.2 deletion syndrome patients. our findings indicate that mir-185 regulates t cell development through its targeting of several mrnas including mzb1.",1
"psoriasis is a chronic inflammatory skin disorder mediated by cross-talk occurring between epidermal keratinocytes, dermal vascular cells and immunocytes. literature reveals that signal transducer and activator of transcription 3 (stat3), a protein involved in transmitting extracellular signals to the nucleus, is a possible important link between keratinocytes and immunocytes and is crucial to the development of psoriasis. although photochemotherapy using uv in combination with 8 methoxypsoralen is one of the most effective therapy for moderate to severe plaque psoriasis, its mechanism of action is largely unknown. herein, we studied the change in mirna profiles of cultured human keratinocytes (hacat cells) before and after in vitro puva treatment by 8 methoxypsoralen and found significant up regulation of hsa-mir-4516. we for the first time demonstrate that ectopic expression of hsa-mir-4516 directly targets stat3 protein by binding to its 3'utr in hacat cells as confirmed by luciferase reporter assays and western blot analysis. we further show that overexpression of hsa-mir-4516 downregulates stat3, p-stat3, cdk6, and ube2n proteins that are consistently upregulated in psoriasis and induces apoptosis in hacat cells. we also observed that anti-mir-4516 treatment was able to partially inhibit puva-induced apoptosis, suggesting that mir-4516 is involved in puva-induced apoptosis. taken together, these results not only indicate the mechanistic involvement of hsa-mir-4516 in puva mediated effects by down-regulating stat3 in hacat keratinocytes, but also highlight the potential of hsa-mir-4516 in development of novel therapeutic strategies. j. cell. physiol. 229: 1630-1638, 2014. © 2014 wiley periodicals, inc.",1
"here, we found that microrna-24-1 (mir-24-1) is significantly reduced in bladder cancer (bc) tissues, suggesting that it functions as a tumour suppressor. restoration of mature mir-24-1 inhibits cancer cell proliferation and induces apoptosis. forkhead box protein m1 (foxm1) is a direct target gene of mir-24-1, as shown by genome-wide gene expression analysis and luciferase reporter assay. overexpressed foxm1 is confirmed in bc clinical specimens, and silencing of foxm1 induces apoptosis in cancer cell lines. our data demonstrate that the mir-24-1-foxm1 axis contributes to cancer cell proliferation in bc, and elucidation of downstream signalling will provide new insights into the molecular mechanisms of bc oncogenesis.",1
"background micrornas (mirnas) are a class of endogenous, small and highly conserved noncoding rnas that control gene expression either by degradation of target mrnas or by inhibition of protein translation. they play important roles in cancer progression. a single mirna can provoke a chain reaction and further affect protein interaction network (pin). therefore, we developed a novel integrative approach to identify the functional roles and the regulated pin of oncomirs. results we integrated the expression profiles of mirna and mrna with the human pin to reveal mirna-regulated pin in specific biological conditions. the potential functions of mirnas were determined by functional enrichment analysis and the activities of mirna-regulated pins were evaluated by the co-expression of protein-protein interactions (ppis). the function of a specific mirna, mir-148a, was further examined by clinical data analysis and cell-based experiments. we uncovered several mirna-regulated networks which were enriched with functions related to cancer progression. one mirna, mir-148a, was identified and its function is to decrease tumor proliferation and metastasis through its regulated pin. furthermore, we found that mir-148a could reduce the invasiveness, migratory and adhesive activities of gastric tumor cells. most importantly, elevated mir-148a level in gastric cancer tissues was strongly correlated with distant metastasis, organ and peritoneal invasion and reduced survival rate. conclusions this study provides a novel method to identify active oncomirs and their potential functions in gastric cancer progression. the present data suggest that mir-148a could be a potential prognostic biomarker of gastric cancer and function as a tumor suppressor through repressing the activity of its regulated pin.",1
"background signal-regulatory protein α (sirpα) is an essential signaling molecule that modulates leukocyte inflammatory responses. however, the regulation of selective sirpα synthesis and its dynamic changes in leukocytes under inflammatory stimulation remain incompletely understood. objective we sought to identify the micrornas (mirnas) that posttranscriptionally regulate sirpα synthesis and their roles in modulating macrophage inflammatory responses. methods sirpα was induced in sirpα-negative promyelocytic cells by retinoic acid or phorbol 12-myristate 13-acetate, and the differential expression of mirnas was assessed by means of microarray and quantitative rt-pcr assays. the roles of identified mirnas in controlling sirpα synthesis in leukocytes and leukocyte inflammatory responses were determined. results we identified sirpα as a common target gene of mir-17, mir-20a, and mir-106a. during sirpα induction, levels of these 3 mirnas were all reduced, and their downregulation by retinoic acid or phorbol 12-myristate 13-acetate occurred through suppression of the c-myc signaling pathway. all mir-17, mir-20a, and mir-106a specifically bound to the same seed sequence within the sirpα 3' untranslated region and correlated inversely with sirpα protein levels in various cells. in macrophages upregulation of mir-17, mir-20a, and mir-106a by lps served as the mechanism underlying lps-induced sirpα reduction and macrophage activation. both in vitro and in vivo assays demonstrate that mir-17, mir-20a, and mir-106a regulate macrophage infiltration, phagocytosis, and proinflammatory cytokine secretion through targeting sirpα. conclusion these findings demonstrate for the first time that mir-17, mir-20a, and mir-106a regulate sirpα synthesis and sirpα-mediated macrophage inflammatory responses in a redundant fashion, providing a novel pathway in which a panel of mirnas can modulate immune polarization through regulation of macrophage activation.",1
"micrornas (mirnas) are 21-24-nucleotide non-coding rnas found in diverse organisms. although hundreds of mirnas have been cloned or predicted, only very few mirnas have been functionally characterized. embryo implantation is a crucial step in mammalian reproduction. many genes have been shown to be significantly changed in mouse uterus during embryo implantation. however, mirna expression profiles in the mouse uterus between implantation sites and inter-implantation sites are still unknown. in this study, mirna microarray was used to examine differential expression of mirnas in the mouse uterus between implantation sites and inter-implantation sites. compared with inter-implantation sites, there were 8 up-regulated mir-nas at implantation sites, which were confirmed by both northern blot and in situ hybridization. mir-21 was highly expressed in the subluminal stromal cells at implantation sites on day 5 of pregnancy. because mir-21 was not detected in mouse uterus during pseudopregnancy and under delayed implantation, mir-21 expression at implantation sites was regulated by active blastocysts. furthermore, we showed that reck was the target gene of mir-21. our data suggest that mir-21 may play a key role during embryo implantation.",1
"gastric cancer is the second leading cause of cancer-related death worldwide. herein, we investigated the role of transcription factor yin yang 1 (yy1), a multi-functional protein, in tumorigenesis of gastric cancer cells. results showed that yy1 contributed to gastric carcinogenesis of sc-m1 cells including growth, viability, and abilities of colony formation, migration, invasion, and tumorsphere formation. levels of pluripotency genes cd44, oct4, sox-2, and nanog were also up-regulated by yy1 in sc-m1 cells. additionally, the 3'-untranslated region (3'-utr) of yy1 mrna was the target of microrna-34 (mir-34) family consisting of mir-34a, mir-34b, and mir-34c. overexpression of mir-34 family suppressed carcinogenesis through down-regulation of yy1 in nugc-3 gastric cancer cells scarcely expressing mir-34 family. alternatively, knockdown of mir-34 family promoted tumorigenesis via up-regulation of yy1 in sc-m1 and az521 gastric cancer cells with higher levels of mir-34 family. the mir-34 family also affected tumorsphere ultra-structure and inhibited the xenografted tumor growth as well as lung metastasis of sc-m1 cells through yy1. expressions of mir-34a and mir-34c in gastric cancer tissues of patients were lower than those in normal tissues. taken together, these results suggest that mir-34 family-yy1 axis plays an important role in the control of gastric carcinogenesis.",1
"our recent studies of microrna (mirna) expression signatures have indicated that the mir-143/145 cluster is significantly downregulated in several types of cancer and represents a putative tumor-suppressive mirna in human cancers. the aim of this study was to investigate the functional significance of the mir-143/145 cluster in cancer cells and to identify novel molecular targets of the mir-143/145 cluster in renal cell carcinoma (rcc). the expression levels of mir-143 and mir-145 were significantly downregulated in rcc tissues compared with adjacent non-cancerous tissues. a significant positive correlation was recognized between mir-143 and mir-145 expression. restoration of mature mir-143 or mir-145 in 786-o and a498 rcc cells revealed that both mature mirnas significantly inhibited cancer cell proliferation and invasion, suggesting that the mir-143/145 cluster functioned as a tumor suppressor in rcc. gene expression data and in silico database analysis showed that the hexokinase-2 (hk2) gene, which encodes a glycolytic enzyme crucial for the warburg effect in cancer cells, was a candidate target of the mir-143/145 cluster. luciferase reporter assays showed that both mir-143 and mir-145 directly regulated hk2. in rcc clinical specimens, the expression of hk2 was significantly higher in cancer tissues than in non-cancerous tissues. silencing hk2 suppressed rcc cell proliferation and invasion, suggesting that hk2 has oncogenic functions in rcc. thus, our data showed that loss of the tumor-suppressive mir-143/145 cluster enhanced rcc cell proliferation and invasion through targeting hk2.",1
"aberrant expression of microrna (mirna) has been reported in various cancers. to clarify the role of mirna in gastric carcinogenesis, we performed mirna microarray analysis and investigated expression changes of mirnas in a 5-aza-2'-deoxycytidine (5-aza-cdr)-treated gastric cancer cell line, kato-iii. on microarray analysis, five mirnas were found to be upregulated (>3-fold) after 5-aza-cdr treatment compared with untreated cells. among them, mir-181c and mir-432as exhibited cpg islands in their upstream sequences on computational analysis, and their upregulation was verified by reverse transcription-polymerase chain reaction analyses. in particular, mir-181c upregulation was found not only in kato-iii but also in two other gastric and one colorectal cancer cell line with 5-aza-cdr treatment. decreased expression of mir-181c was observed in 9 of 16 primary gastric carcinoma (gc) cases compared with the corresponding non-cancerous stomach tissues. hypermethylation signals in the upstream region of mir-181c were observed in some cultured and primary gc cells with negative or low mir-181c expression. transfection of the precursor mir-181c molecule induced decreased growth of two gastric cancer cell lines, kato-iii and mkn45. as for targets of mir-181c, oncogenic notch4 and kras were identified by complementary dna microarray analysis after precursor mir-181c molecule transfection, computational searches of mirna target databases and reporter assaying using the 3'-untranslated regions of the two genes. these results indicate that mir-181c may be silenced through methylation and play important roles in gastric carcinogenesis through its target genes, such as notch4 and kras.",1
"the myelin sheaths that surround the thick axons of the peripheral nervous system are produced by the highly specialized schwann cells. differentiation of schwann cells and myelination occur in discrete steps. each of these requires coordinated expression of specific proteins in a precise sequence, yet the regulatory mechanisms controlling protein expression during these events are incompletely understood. here we report that schwann cell-specific ablation of the enzyme dicer1, which is required for the production of small non-coding regulatory micrornas, fully arrests schwann cell differentiation, resulting in early postnatal lethality. dicer(-/-) schwann cells had lost their ability to myelinate, yet were still capable of sorting axons. both cell death and, paradoxically, proliferation of immature schwann cells was markedly enhanced, suggesting that their terminal differentiation is triggered by growth-arresting regulatory micrornas. using microrna microarrays, we identified 16 micrornas that are upregulated upon myelination and whose expression is controlled by dicer in schwann cells. this set of micrornas appears to drive schwann cell differentiation and myelination of peripheral nerves, thereby fulfilling a crucial function for survival of the organism.",1
"as mirnas are associated with normal cellular processes, deregulation of mirnas is thought to play a causative role in many complex diseases. nevertheless, the precise contribution of mirnas in fibrotic lung diseases, especially the idiopathic form (ipf), remains poorly understood. given the poor response rate of ipf patients to current therapy, new insights into the pathogenic mechanisms controlling lung fibroblasts activation, the key cell type driving the fibrogenic process, are essential to develop new therapeutic strategies for this devastating disease. to identify mirnas with potential roles in lung fibrogenesis, we performed a genome-wide assessment of mirna expression in lungs from two different mouse strains known for their distinct susceptibility to develop lung fibrosis after bleomycin exposure. this led to the identification of mir-199a-5p as the best mirna candidate associated with bleomycin response. importantly, mir-199a-5p pulmonary expression was also significantly increased in ipf patients (94 ipf versus 83 controls). in particular, levels of mir-199a-5p were selectively increased in myofibroblasts from injured mouse lungs and fibroblastic foci, a histologic feature associated with ipf. therefore, mir-199a-5p profibrotic effects were further investigated in cultured lung fibroblasts: mir-199a-5p expression was induced upon tgfβ exposure, and ectopic expression of mir-199a-5p was sufficient to promote the pathogenic activation of pulmonary fibroblasts including proliferation, migration, invasion, and differentiation into myofibroblasts. in addition, we demonstrated that mir-199a-5p is a key effector of tgfβ signaling in lung fibroblasts by regulating cav1, a critical mediator of pulmonary fibrosis. remarkably, aberrant expression of mir-199a-5p was also found in unilateral ureteral obstruction mouse model of kidney fibrosis, as well as in both bile duct ligation and ccl4-induced mouse models of liver fibrosis, suggesting that dysregulation of mir-199a-5p represents a general mechanism contributing to the fibrotic process. mir-199a-5p thus behaves as a major regulator of tissue fibrosis with therapeutic potency to treat fibroproliferative diseases.",1
"mir-27b is reported to participate in the proliferation and differentiation of hepatic stellate cells (hscs) and to regulate fat metabolism of rat hscs by targeting retinoid x receptor α. our previous study also indicated that the recombinant p40 protein from schistosoma japonicum (rsjp40) inhibited the activation of hscs. in this study, we observed the expression of mir-27b in rsjp40-treated lx-2 cells and explored its potential mechanisms. quantitative real-time pcr showed that rsjp40 inhibits the expression of mir-27b in lx-2 cells. further results obtained by western blot and dual-luciferase reporter assay confirmed that mir-27b regulates peroxisome proliferator-activated receptor γ (pparγ) expression in rsjp40-treated lx-2 cells by targeting the 3'-utr of pparγ. 5-aza-2'-deoxycytidine (5-aza-dc), which inhibits methylation of hscs, partially reversed rsjp40-induced down-regulation expression of mir-27b in lx-2 cells. 5-aza-dc also partially reversed rsjp40-induced up-regulation expression of pparγ in lx-2 cells. the increased expression of pparγ in rsjp40-treated lx-2 cells may be partially due to mir-27b methylation. therefore, our study provides further insight into the mechanism by which rsjp40 inhibits hsc activation and provides a basis for future study of the blocking effect of rsjp40 in liver fibrosis.-zhu, d., lyu, l., shen, p., wang, j., chen, j., sun, x., chen, l., zhang, l., zhou, q., duan, y. rsjp40 protein promotes pparγ expression in lx-2 cells through microrna-27b.",1
"background mir-155 has emerged as an ""oncomir"", which is the most significantly up-regulated mirna in breast cancer. however, the mechanisms of mir-155 functions as an oncomir are mainly unknown. in this study, the aims were to investigate the effects of mir-155 on cell proliferation, cell cycle, and cell apoptosis of eralpha (+) breast cancer cells and to verify whether tp53inp1 (tumor protein 53-induced nuclear protein 1) is a target of mir-155, and tried to explore the mechanisms of mir-155 in this process. results the expression of mir-155 is significantly higher in mcf-7 cells compared with mda-mb-231 cells. ectopic expression of tp53inp1 inhibits growth of mcf-7 cells by inducing cell apoptosis and inhibiting cell cycle progression. overexpression of mir-155 increases cell proliferation and suppress cell apoptosis, whereas abrogating expression of mir-155 suppress cell proliferation and promotes cell apoptosis of mcf-7 cells. in addition, mir-155 negatively regulates tp53inp1 mrna expression and the protein expression of tp53inp1, cleaved-caspase-3, -8, -9, and p21, and luciferase reporter reveals that tp53inp1 is targeted by mir-155. conclusions tp53inp1 is the direct target of mir-155. mir-155, which is overexpressed in mcf-7 cells, contributes to proliferation of mcf-7 cells possibly through down-regulating target tp53inp1.",1
"unlabelled nuclear factor kappa b (nf-κb) is an important factor linking inflammation and tumorigenesis. in this study we experimentally demonstrated through a high-throughput luciferase reporter screen that nf-κb signaling can be directly targeted by nearly 29 micrornas (mirnas). many of these mirnas can directly target nf-κb signaling nodes by binding to their 3' untranslated region (utr). mir-195, a member of the mir-15 family, is frequently down-regulated in gastrointestinal cancers, especially in hepatocellular carcinoma (hcc). the expression level of mir-195 is inversely correlated with hcc tumor size. we further show that mir-195 suppresses cancer cell proliferation and migration in vitro and reduces tumorigenicity and metastasis in vivo. additionally, mir-195 may exert its tumor suppressive function by decreasing the expression of multiple nf-κb downstream effectors by way of the direct targeting of ikkα and tab3. conclusion multiple mirnas are involved in the nf-κb signaling pathway and mir-195 plays important inhibitory roles in cancer progression and may be a potential therapeutic target.",1
"background & aims micrornas (mirnas) have been implicated in the development and progression of human cancers. we investigated the roles and mechanisms of mir-26a in human cholangiocarcinoma. methods we used in situ hybridization and quantitative reverse transcriptase polymerase chain reaction to measure expression of mir-26a in human cholangiocarcinoma tissues and cell lines (eg, cclp1, sg231, hucct1, tfk1). human cholangiocarcinoma cell lines were transduced with lentiviruses that expressed mir-26a1 or a scrambled sequence (control); proliferation and colony formation were analyzed. we analyzed growth of human cholangiocarcinoma cells that overexpress mir-26a or its inhibitor in severe combined immune-deficient mice. immunoblot, immunoprecipitation, dna pull-down, immunofluorescence, and luciferase reporter assays were used to measure expression and activity of glycogen synthase kinase (gsk)-3β, β-catenin, and related signaling molecules. results human cholangiocarcinoma tissues and cell lines had increased levels of mir-26a compared with the noncancerous biliary epithelial cells. overexpression of mir-26a increased proliferation of cholangiocarcinoma cells and colony formation in vitro, whereas mir-26 depletion reduced these parameters. in severe combined immune-deficient mice, overexpression of mir-26a by cholangiocarcinoma cells increased tumor growth and overexpression of the mir-26a inhibitor reduced it. gsk-3β messenger rna was identified as a direct target of mir-26a by computational analysis and experimental assays. mir-26a-mediated reduction of gsk-3β resulted in activation of β-catenin and induction of several downstream genes including c-myc, cyclind1, and peroxisome proliferator-activated receptor δ. depletion of β-catenin partially prevented mir-26a-induced tumor cell proliferation and colony formation. conclusions mir-26a promotes cholangiocarcinoma growth by inhibition of gsk-3β and subsequent activation of β-catenin. these signaling molecules might be targets for prevention or treatment of cholangiocarcinoma.",1
"overactivated hepatic gluconeogenesis contributes to the pathogenesis of metabolic disorders, including type 2 diabetes. precise control of hepatic gluconeogenesis is thus critical for maintaining whole-body metabolic homeostasis. long non-coding rnas (lncrnas) have been shown to play key roles in diseases by regulating diverse biological processes, but the function of lncrnas in maintaining normal physiology, particularly glucose homeostasis in the liver, remains largely unexplored. we identified a novel liver-enriched long non-coding rna, gm10768, and examined its expression patterns under pathophysiological conditions. we further adopted gain- and loss-of-function strategies to explore the effect of gm10768 on hepatic glucose metabolism and the possible molecular mechanism involved. our results showed that the expression of gm10768 was significantly increased in the liver of fasted mice and was induced by gluconeogenic hormonal stimuli. functionally, overexpression of gm10768 activated hepatic gluconeogenesis in a cell-autonomous manner. in contrast, depletion of gm10768 suppressed hepatic glucose production both in vitro and in vivo adenovirus-mediated hepatic knockdown of gm10768 improved glucose tolerance and hyperglycemia of diabetic db/db mice. mechanistically, gm10768 sequestrated microrna-214 (mir-214) to relieve its suppression on activating transcription factor 4 (atf4), a positive regulator of hepatic gluconeogenesis. taken together, we identified gm10768 as a new lncrna activating hepatic gluconeogenesis through antagonizing mir-214 in mice.",1
"increasing evidences have illuminated the fundamental role of inflammation in mediating all stages of atherosclerosis. mir-155, a typical multi-functional mirna, has recently emerged as a novel component of inflammatory signal transduction in the pathogenesis of atherosclerosis. however, little is known about whether endothelial highly expressed mir-155 can regulate endothelial inflammation-related transcription factors and the predicted role of mir-155 as a negative feedback regulator in endothelial inflammation involved in atherosclerosis. bioinformatics analysis showed that rela (nuclear factor-κb p65) is a potential target gene of mir-155 and this was confirmed by a luciferase reporter assay. our results show that microrna-155 mediate endothelial inflammation and decrease nfкb p65 and adhesion molecule expression in tnfα-stimulated endothelial cells. transfection with mir-155 significantly inhibited tnfα-induced monocyte adhesion to endothelium. inhibition of mir-155 enhanced p65 level and endothelial inflammatory response which was counteracted through the depletion of p65 by si-p65. on the other hand, knockdown of enos, another target of mir-155, while transfecting with mir-155 inhibitor resulted in more significant inflammatory response. mir-155 is highly expressed in tnfα treated huvecs, deprived of endogenous p65 could reverse tnfα-induced upregulation of mir-155. thus, tnfα induced mir-155 may serve as a negative feedback regulator in endothelial inflammation involved in atherosclerosis by targeting nuclear transcription factor p65. these results provide a rationale for intervention of intracellular microrna as possible anti-atherosclerotic targets.",1
"micrornas are important gene regulators that could play a profound role in tumorigenesis. our previous studies indicate that mir-145 is a tumor suppressor capable of inhibiting tumor cell growth both in vitro and in vivo. in this study, we show that mir-145 exerts its function in a cell-specific manner. although mir-145 inhibits cell growth in mcf-7 and hct-116 cells, it has no significant effect on cell growth in metastatic breast cancer cell lines. however, mir-145 significantly suppresses cell invasion in these cells; in contrast, the antisense oligo against mir-145 increases cell invasion. mir-145 is also able to suppress lung metastasis in an experimental metastasis animal model. this mir-145-mediated suppression of cell invasion is in part due to the silencing of the metastasis gene mucin 1 (muc1). using luciferase reporters carrying the 3'-untranslated region of muc1 combined with western blot and immunofluorescence staining, we identify muc1 as a direct target of mir-145. moreover, ectopic expression of muc1 enhances cell invasion, which can be blocked by mir-145. of interest, suppression of muc1 by mir-145 causes a reduction of beta-catenin as well as the oncogenic cadherin 11. finally, suppression of muc1 by rnai mimics the mir-145 action in suppression of invasion, which is associated with downregulation of beta-catenin and cadherin 11. taken together, these results suggest that as a tumor suppressor, mir-145 inhibits not only tumor growth but also cell invasion and metastasis.",1
"micrornas have been implicated in hepatocellular carcinoma (hcc) metastasis, which is predominant cause of high mortality in these patients. although an increasing body of evidence indicates that mir-149 plays an important role in the growth and metastasis of multiple types of cancers, its role in the progression of hcc remains unknown. here, we demonstrated that mir-149 was significantly down-regulated in hcc, which was correlated with distant metastasis and tnm stage with statistical significance. a survival analysis showed that decreased mir-149 expression was correlated with a poor prognosis of hcc as well. we found that over-expression of mir-149 suppressed migration and invasion of hcc cells in vitro. in addition, we identified ppm1f (protein phosphatase, mg(2+)/mn(2+)-dependent, 1f) as a direct target of mir-149 whose expression was negatively correlated with the expression of mir-149 in hcc tissues. the re-expression of ppm1f rescued the mir-149-mediated inhibition of cell migration and invasion. mir-149 regulated formation of stress fibers to inhibit migration, and re-expression of ppm1f reverted the mir-149-mediated loss of stress fibers. moreover, we demonstrated that over-expression of mir-149 reduced pmlc2, a downstream effector of ppm1f, in mhcc-97h cells. in vivo studies confirm inhibition of hcc metastasis by mir-149. taken together, our findings indicates that mir-149 is a potential prognostic biomarker of hcc and that the mir-149/ppm1f regulatory axis represents a novel therapeutic target for hcc treatment.",1
"barley yellow dwarf virus (bydv) generates three 3'-coterminal subgenomic rnas (sgrnas) in infected cells. translation of bydv genomic rna (grna) and sgrna1 is mediated by the bydv cap-independent translation element (bte) in the 3' untranslated region. sgrnas 2 and 3 are unlikely to be mrnas. we proposed that accumulation of sgrna2, which contains the bte in its 5' utr, regulates bydv replication by trans-inhibiting translation of the viral polymerase from genomic rna (grna). here, we tested this hypothesis and found that: (i) co-inoculation of the bte or sgrna2 with bydv rna inhibits bydv rna accumulation in protoplasts; (ii) brome mosaic virus (bmv), engineered to contain the bte, trans-inhibits bydv replication; and (iii) sgrna2 generated during bydv infection trans-inhibits both gfp expression from bmv rna and translation of a non-viral reporter mrna. we conclude that sgrna2, via its bte, functions as a riboregulator to inhibit translation of grna. this may make grna available as a replicase template and for encapsidation. thus, bydv sgrna2 joins a growing list of trans-acting regulatory rnas.",1
"in mammals, sex differentiation depends on gonad development, which is controlled by two groups of sex-determining genes that promote one gonadal sex and antagonize the opposite one. sox9 plays a key role during testis development in all studied vertebrates, whereas it is kept inactive in the xx gonad at the critical time of sex determination, otherwise, ovary-to-testis gonadal sex reversal occurs. however, molecular mechanisms underlying repression of sox9 at the beginning of ovarian development, as well as other important aspects of gonad organogenesis, remain largely unknown. because there is indirect evidence that micro-rnas (mirna) are necessary for testicular function, the possible involvement of mirnas in mammalian sex determination deserved further research. using microarray technology, we have identified 22 mirnas showing sex-specific expression in the developing gonads during the critical period of sex determination. bioinformatics analyses led to the identification of mir-124 as the candidate gene for ovarian development. we knocked down or overexpressed mir-124 in primary gonadal cell cultures and observed that mir-124 is sufficient to induce the repression of both sox9 translation and transcription in ovarian cells. our results provide the first evidence of the involvement of a mirna in the regulation of the gene controlling gonad development and sex determination. the mirna microarray data reported here will help promote further research in this field, to unravel the role of other mirnas in the genetic control of mammalian sex determination.",1
"increasing evidence shows that abnormal microrna (mirna) expression is involved in tumorigenesis. mir-25 was previously reported to act as tumor suppressor or oncogene in diverse cancers. however, their expression, function, and mechanism in gastric cancer (gc) are not well known. here, we show that mir-25 was overexpressed in primary tumor tissues of gc patients and was significantly correlated with a more aggressive phenotype of gc in patients. mir-25 inhibition significantly decreased the proliferation, invasion, and migration of gc cells in vitro. furthermore, mir-25 repressed f-box and wd-40 domain protein 7 (fbxw7) expression by directly binding to 3-untranslated region (utr) of fbxw7, and the inverse correlation was observed between the expressions of mir-25 and fbxw7 mrna in primary gc tissues. moreover, the restoration of fbxw7 led to suppressed proliferation, invasion, and migration of gc cells. in vivo, mir-25 promotes tumor growth of gc. taken together, mir-25 promotes gc progression by directly downregulating fbxw7 expression and may be employed as a novel prognostic marker and therapeutic target of gc.",1
"background cd151 is highly expressed in breast cancer cells and has been shown to accelerate breast cancer by enhancing cell growth and motility, but its regulation is poorly understood. to explore post-translation regulation of cd151, for example micrornas, will be of great importance to claim the mechanism. methods a luciferase reporter assay was used to determine whether cd151 was a target of mir-124. the levels of cd151 mrna were detected by real-time pcr and cd151 protein expression was measured by western blot and flow cytometry. the effects of mir-124 expression on growth, apoptosis, cell cycle and motility of breast cancer cells were determined. results we discovered that mir-124 directly targets the 3' untranslated region (3'-utr) of cd151 mrnas and suppresses its mrna expression and protein translation. both sirna of cd151 and mir-124 mimics could significantly inhibit proliferation of breast cancer cell lines via cell cycle arrest but does not induce apoptosis. meanwhile, mir-124 mimics significantly inhibited the motility of breast cancer cells. conclusion mir-124 plays a critical role in inhibiting the invasive and metastatic potential of breast cancer cells, probably by directly targeting the cd151 genes. our findings highlight an important role of mir-124 in the regulation of invasion and metastasis by breast cancer cells and suggest a potential application for mir-124 in breast cancer treatment.",1
"fission yeast mei2p is an rna-binding protein required for both premeiotic dna synthesis and meiosis i. mei2p binds to a polyadenylated rna molecule, meirna, loss of which blocks meiosis i. mei2p forms a dot in meiotic prophase nuclei. here, we show that meirna is required for the nuclear localization of mei2p and is detectable in the dot. however, mei2p carrying a nuclear localization signal can produce a nuclear dot and promote meiosis i in the absence of meirna. mei2p expressed in cultured mammalian cells stays in the cytoplasm, but it accumulates in the nucleolus if meirna is coexpressed. these results indicate that meirna contributes to the promotion of meiosis i exclusively as a cofactor that assists nuclear transport of mei2p.",1
"nuclear factor kappa b (nf-κb) signaling is frequently deregulated in a variety of cancers and is constitutively active in estrogen receptor negative (er-) breast cancer subtypes. these molecular subtypes of breast cancer are associated with poor overall survival. we focused on mechanisms of nf-κb regulation by micrornas (mirnas), which regulate eukaryotic gene expression at the post-transcriptional level. in a previous genome-wide mirna screen, we had identified mir-30c-2-3p as one of the strongest negative regulators of nf-κb signaling. here we have uncovered the underlying molecular mechanisms and its consequences in breast cancer. in vitro results show that mir-30c-2-3p directly targets both tnfrsf1a-associated via death domain (tradd), an adaptor protein of the tnfr/nf-κb signaling pathway, and the cell cycle protein cyclin e1 (ccne1). ectopic expression of mir-30c-2-3p downregulated essential cytokines il8, il6, cxcl1, and reduced cell proliferation as well as invasion in mda-mb-231 breast cancer cells. rna interference (rnai) induced silencing of tradd phenocopied the effects on invasion and cytokine expression caused by mir-30c-2-3p, while inhibition of ccne1 phenocopied the effects on cell proliferation. we further confirmed the tumor suppressive role of this mirna using a dataset of 781 breast tumors, where higher expression was associated with better survival in breast cancer patients. in summary we have elucidated the mechanism by which mir-30c-2-3p negatively regulates nf-κb signaling and cell cycle progression in breast cancer.",1
"in addition to estrogen receptor modulators, retinoic acid and other retinoids are promising agents to prevent breast cancer. retinoic acid and estrogen exert antagonistic regulations on the transcription of coding genes and we evaluated here whether these two compounds have similar effects on micrornas. using an integrative approach based on several bioinformatics resources together with experimental validations, we indeed found that retinoic acid positively regulates mir-210 and mir-23a/24-2 expressions and is counteracted by estrogen. conversely, estrogen increased mir-17/92 and mir-424/450b expressions and is inhibited by retinoic acid. in silico functional enrichment further revealed that this combination of transcriptional/post-transcriptional regulations fully impacts on the molecular effects of estrogen and retinoic acid. besides, we unveiled a novel effect of retinoic acid on aerobic glycolysis. we specifically showed that it increases extracellular lactate production, an effect counteracted by the mir-210 and the mir-23a/24-2, which simultaneously target lactate dehydrogenase a and b mrnas. together our results provide a new framework to better understand the estrogen/retinoic acid antagonism in breast cancer cells.",1
"inflammation is observed at all stages of atherosclerosis. the initial stage of atherosclerosis is characterized by recruitment of leukocytes to activated endothelial cells (ecs). micrornas (mirnas) are a class of 19-25 nucleotides, non-protein-coding rnas that repress target gene expression by translational inhibition or mrna degradation. the link between mirna and endothelial functions is largely unknown. northern blot showed that mir-155 and mir-221 were highly expressed in human umbilical vein endothelial cells (huvecs) and vascular smooth muscle cells (vsmcs). bioinformatics analysis proposed ets-1, a key endothelial transcription factor for inflammation and tube formation, as a candidate target for mir-155 and mir-221/222 cluster. the effect was demonstrated by luciferase reporter assay and western blot. by using western blot, we also confirmed that angiotensin ii type 1 receptor (at1r) is a target of mir-155 in huvecs. quantitative pcr showed that ets-1 and its downstream genes, including vcam1, mcp1 and flt1, were upregulated in angiotensin ii-stimulated huvecs, and this effect was partially reversed by overexpression of mir-155 and mir-221/222. in addition, cell adhesion assay revealed overexpression of mir-155 and mir-221/222 effectively decreased the adhesion of jurkat t cells to ang ii-stimulated huvecs. besides, by targeting at1r, mir-155 can also decrease the huvecs migration in response to ang ii. in summary, huvecs highly expressed mir-155 may co-target at1r and ets-1 while mir-221/222 targets ets-1, which indirectly regulate the expression of several inflammatory molecules of ecs, and therefore attenuate the adhesion of jurkat t cells to activated huvecs and reduce huvecs migration. these findings present possible therapeutic targets in atherosclerosis.",1
"micrornas are involved in regulating the biology of cancer cells, but their involvement in chemoresistance is not fully understood. we found that mir-663 was up-regulated in our induced multidrug-resistant mda-mb-231/adm cell line and that this up-regulation was closely related to chemosensitivity. in the present study, we aimed to clarify the role of mir-663 in regulating the chemoresistance of breast cancer. microrna microarray and quantitative rt-pcr assays were used to identify differentially expressed micrornas. cell apoptosis was evaluated by annexin v/propidium iodide staining, tunel, and reactive oxygen species generation analysis. the expression of mir-663 and hspg2 in breast cancer tissues was detected by in situ hybridization and immunohistochemistry. the potential targets of mir-663 were defined by a luciferase reporter assay. bisulfite sequencing pcr was used to analyze the methylation status. we found that mir-663 was significantly elevated in mda-mb-231/adm cells, and the down-regulation of mir-663 sensitized mda-mb-231/adm cells to both cyclophosphamide and docetaxel. the overexpression of mir-663 in breast tumor tissues was associated with chemoresistance; in mda-mb-231 cells, this chemoresistance was accompanied by the down-regulation of hspg2, which was identified as a target of mir-663. mda-mb-231/adm contained fewer methylated cpg sites than its parental cell line, and mir-663 expression in mda-mb-231 cells was reactivated by 5-aza-29-deoxycytidine treatment, indicating that dna methylation may play a functional role in the expression of mir-663. our findings suggest that the overexpression of hypomethylated mir-663 induced chemoresistance in breast cancer cells by down-regulating hspg2, thus providing a potential target for the development of an microrna-based approach for breast cancer therapy.",1
"the rna-binding protein hfq plays important roles in bacterial physiology and is required for the activity of many small regulatory rnas in prokaryotes. we have previously shown that hfq contributes to stress tolerance and virulence in the gram-positive human pathogen listeria monocytogenes. in the present study, we performed coimmunoprecipitations followed by enzymatic rna sequencing to identify hfq-binding rna molecules in l. monocytogenes. the approach resulted in the discovery of three small rnas (srnas). the srnas are conserved between listeria species, but were not identified in other bacterial species. the initial characterization revealed a number of unique features displayed by each individual srna. the first srna is encoded from within an annotated gene in the l. monocytogenes egd-e genome. analogous to most regulatory srnas in escherichia coli, the stability of this srna is highly dependent on the presence of hfq. the second srna appears to be produced by a transcription attenuation mechanism, and the third srna is present in five copies at two different locations within the l. monocytogenes egd-e genome. the cellular levels of the srnas are growth phase dependent and vary in response to growth medium. all three srnas are expressed when l. monocytogenes multiplies within mammalian cells. this study represents the first attempt to identify srnas in l. monocytogenes.",1
"shortage of oxygen is one of the prime stress conditions in tissues. in this study, we looked for micrornas expressed during hypoxia and showed that mir-210 expression was upregulated in response to hypoxia in vitro and in vivo. an active form of the hif-1alpha induced the expression of mir-210, showing the involvement of the hif-1 signaling pathway in mir-210 gene transcription. furthermore, mir-210 was shown to bind to the predicted target sites of ephrin-a3 or neuronal pentraxin 1, causing repression in luciferase reporter activity. contrary to the microrna-mediated repression hypothesis, ephrin-a3 was expressed at very high levels in post-ischemic mouse hippocampus in vivo. thus, the regulatory effects of mir-210 on its targets in vivo need to be further characterized.",1
"multidrug resistance (mdr) is usually correlated with the poor prognosis of gastric cancer. in this study, we revealed a total of 11 micrornas (mirna) that regulated mdr of gastric cancer via high-throughput functional screening, and mir-508-5p reversed mdr most efficiently among these candidate mirnas. the overexpression of mir-508-5p was sufficient to reverse cancer cell resistance to multiple chemotherapeutics in vitro and sensitize tumours to chemotherapy in vivo. further studies showed that mir-508-5p could directly target the 3'-untranslated regions of abcb1 and zinc ribbon domain-containing 1 (znrd1), and suppress their expression at the mrna and protein levels. meanwhile, the suppression of znrd1 led to a decrease in abcb1. these findings suggest that a mir-508-5p/znrd1/abcb1 regulatory loop has a critical role in mdr in gastric cancer. in addition, mir-508-5p could be used as a prognostic factor for overall survival in gastric cancer. these data reveal an important role for mir-508-5p in the regulation of mdr in gastric cancer, and suggest the potential application of mir-508-5p in drug resistance prediction and treatment.",1
"aberrant microrna expression has been implicated in the development of human cancers. here, we investigated the oncogenic significance and function of mir-23b in glioma. we identified that the expression of mir-23b was elevated in both glioma samples and glioma cells, indicated by real-time polymerase chain reaction analyses. down-regulation of mir-23b triggered growth inhibition, induced apoptosis, and suppressed invasion of glioma in vitro. luciferase assay and western blot analysis revealed that vhl is a direct target of mir-23b. restoring expression of vhl inhibited glioma proliferation and invasion. mechanistic investigation revealed that mir-23b deletion decreased hif-1α/vegf expression and suppressed β-catenin/tcf-4 transcription activity by targeting vhl. furthermore, expression of vhl was inversely correlated with mir-23b in glioma samples and was predictive of patient survival in a retrospective analysis. therefore, we demonstrated that downregulation of mir-23b suppressed tumor survival through targeting vhl, leading to the inhibition of β-catenin/tcf-4 and hif-1α/vegf signaling pathways.",1
"although naturally occurring catalytic rna molecules-ribozymes-have attracted a great deal of research interest, very few have been identified in humans. here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring ribozyme in humans. the secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes. the sequence of the ribozyme exhibits a clear evolutionary path, from its appearance between ~130 and ~65 million years ago (ma), to acquiring self-cleavage activity very recently, ~13-10 ma, in the common ancestors of humans, chimpanzees and gorillas. the ribozyme appears to be functional in vivo and is embedded within a long noncoding rna belonging to a class of very long intergenic noncoding rnas. the presence of a catalytic rna enzyme in lncrna creates the possibility that these transcripts could function by carrying catalytic rna domains.",1
"background validation of physiologic mirna targets has been met with significant challenges. we employed hits-clip to identify which mirnas participate in liver regeneration, and to identify their target mrnas. results mirna recruitment to the risc is highly dynamic, changing more than five-fold for several mirnas. mirna recruitment to the risc did not correlate with changes in overall mirna expression for these dynamically recruited mirnas, emphasizing the necessity to determine mirna recruitment to the risc in order to fully assess the impact of mirna regulation. we incorporated rna-seq quantification of total mrna to identify expression-weighted ago footprints, and developed a microrna regulatory element (mre) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. these high confidence mres were used to generate candidate 'competing endogenous rna' (cerna) networks. conclusion hits-clip analysis provide novel insights into global mirna:mrna relationships in the regenerating liver.",1
"micrornas are small endogenous rnas that play important roles in the pathogenesis of human diseases, including malignancy. microrna-1 (mir-1) is downregulated in non-small cell lung cancer (nsclc); however, the underlying mechanisms by which it suppresses tumorigenesis in nsclc are largely unknown. we investigated whether phosphoinositide-3-kinase catalytic subunit alpha (pik3ca) was a novel target of mir-1 in the nsclc cell line a549, and the mechanism of mir-1 inhibition of the tumorigenic properties of a549 cells is discussed. the influence of mir-1 on a549 cells was studied by transfection with mir-1 mimics or inhibitor. mir-1 overexpression led to downregulation of pik3ca protein, but not mrna by western blot and quantitative real-time pcr, respectively. the dual-luciferase reporter assay confirmed that mir-1 targeted pik3ca directly. pik3ca downregulation by mir-1 mimics led to a significant reduction of phosphorylated akt and survivin protein, the downstream targets of the pi3k/akt pathway. cell proliferation was studied using a cell counting kit. migration and invasion were evaluated by transwell and matrigel assays, respectively. cell cycle and apoptosis were detected by flow cytometry. the results were that mir-1 upregulation inhibited a549 cell proliferation, migration, and invasion. these findings indicate that mir-1 may play an important role in the pathogenesis of nsclc by regulating pik3ca through the pi3k/akt pathway. increasing mir-1 expression may provide a novel approach for nsclc treatment.",1
"human nuclear uracil-dna glycosylase ung2 is essential for post-replicative repair of uracil in dna, and ung2 protein and mrna levels rapidly decline in g2/m phase. previous work has demonstrated regulation of ung2 at the transcriptional level, as well as by protein phosphorylation and ubiquitylation. ung2 mrna, encoded by the ung gene, contains a long 3'untranslated region (3'utr) of previously unknown function. here, we demonstrate that several conserved regions in the 3'utr are potential seed sites for micrornas (mirnas), such as mir-16, mir-34c, and mir-199a. our results show that these mirnas down-regulate ung activity, ung mrna, and ung protein levels. down-regulation was dependent on the 3'utr, indicating that the mirnas directly target the conserved seed sites in the 3'utr. these results add mirnas as a new modality to ung's increasing list of complex regulatory mechanisms.",1
"mir-124 is conserved in sequence and neuronal expression across the animal kingdom and is predicted to have hundreds of mrna targets. diverse defects in neural development and function were reported from mir-124 antisense studies in vertebrates, but a nematode knockout of mir-124 surprisingly lacked detectable phenotypes. to provide genetic insight from drosophila, we deleted its single mir-124 locus and found that it is dispensable for gross aspects of neural specification and differentiation. on the other hand, we detected a variety of mutant phenotypes that were rescuable by a mir-124 genomic transgene, including short lifespan, increased dendrite variation, impaired larval locomotion, and aberrant synaptic release at the nmj. these phenotypes reflect extensive requirements of mir-124 even under optimal culture conditions. comparison of the transcriptomes of cells from wild-type and mir-124 mutant animals, purified on the basis of mir-124 promoter activity, revealed broad upregulation of direct mir-124 targets. however, in contrast to the proposed mutual exclusion model for mir-124 function, its functional targets were relatively highly expressed in mir-124-expressing cells and were not enriched in genes annotated with epidermal expression. a notable aspect of the direct mir-124 network was coordinate targeting of five positive components in the retrograde bmp signaling pathway, whose activation in neurons increases synaptic release at the nmj, similar to mir-124 mutants. derepression of the direct mir-124 target network also had many secondary effects, including over-activity of other post-transcriptional repressors and a net incomplete transition from a neuroblast to a neuronal gene expression signature. altogether, these studies demonstrate complex consequences of mir-124 loss on neural gene expression and neurophysiology.",1
"micrornas (mirnas) are short rnas that direct messenger rna degradation or disrupt mrna translation in a sequence-dependent manner. for more than a decade, attempts to study the interaction of mirnas with their targets were confined to the 3' untranslated regions of mrnas, fuelling an underlying assumption that these regions are the principal recipients of mirna activity. here we focus on the mouse nanog, oct4 (also known as pou5f1) and sox2 genes and demonstrate the existence of many naturally occurring mirna targets in their amino acid coding sequence (cds). some of the mouse targets analysed do not contain the mirna seed, whereas others span exon-exon junctions or are not conserved in the human and rhesus genomes. mir-134, mir-296 and mir-470, upregulated on retinoic-acid-induced differentiation of mouse embryonic stem cells, target the cds of each transcription factor in various combinations, leading to transcriptional and morphological changes characteristic of differentiating mouse embryonic stem cells, and resulting in a new phenotype. silent mutations at the predicted targets abolish mirna activity, prevent the downregulation of the corresponding genes and delay the induced phenotype. our findings demonstrate the abundance of cds-located mirna targets, some of which can be species-specific, and support an augmented model whereby animal mirnas exercise their control on mrnas through targets that can reside beyond the 3' untranslated region.",1
"antiviral immunity in insects is mediated by the rna interference (rnai) pathway. viruses evade antiviral rnai by expressing virulence factors known as viral suppressors of rnai (vsr). here, we report the identification of vinr, a drosophila vsr-interacting long non-coding (lnc) rna that activates non-canonical innate immune signaling upon detection of the dsrna-binding vsr of drosophila c virus (dcv). vinr is required for the induction of antimicrobial peptide (amp) genes but dispensable for antiviral rnai. vinr functions by preventing the ubiquitin proteasome-dependent degradation of cactin, a coiled-coil and arginine-serine-rich domain-containing protein that regulates a non-cannonical antimicrobial pathway for amp induction. crispr-cas9 knockout of vinr in drosophila cells enhances dcv replication independently of antiviral rnai, and vinr-knockout adult flies exhibit enhanced disease susceptibility to dcv and bacteria. our findings reveal a counter counter-defense strategy activated by a lncrna in response to the viral suppression of the primary antiviral rnai immunity.",1
"high plasma cholesterol levels are a major risk factor for atherosclerosis. plasma cholesterol can be reduced by inhibiting lipoprotein production; however, this is associated with steatosis. previously we showed that lentivirally mediated hepatic expression of microrna-30c (mir-30c) reduced hyperlipidemia and atherosclerosis in mice without causing hepatosteatosis. because viral therapy would be formidable, we examined whether a mir-30c mimic can be used to mitigate hyperlipidemia and atherosclerosis without inducing steatosis. delivery of a mir-30c mimic to the liver diminished diet-induced hypercholesterolemia in c57bl/6j mice. reductions in plasma cholesterol levels were significantly correlated with increases in hepatic mir-30c levels. long term dose escalation studies showed that mir-30c mimic caused sustained reductions in plasma cholesterol with no obvious side effects. furthermore, mir-30c mimic significantly reduced hypercholesterolemia and atherosclerosis in apoe(-/-) mice. mechanistic studies showed that mir-30c mimic had no effect on ldl clearance but reduced lipoprotein production by down-regulating microsomal triglyceride transfer protein expression. mir-30c had no effect on fatty acid oxidation but reduced lipid synthesis. additionally, whole transcriptome analysis revealed that mir-30c mimic significantly down-regulated hepatic lipid synthesis pathways. therefore, mir-30c lowers plasma cholesterol and mitigates atherosclerosis by reducing microsomal triglyceride transfer protein expression and lipoprotein production and avoids steatosis by diminishing lipid syntheses. it mitigates atherosclerosis most likely by reducing lipoprotein production and plasma cholesterol. these findings establish that increasing hepatic mir-30c levels is a viable treatment option for reducing hypercholesterolemia and atherosclerosis.",1
"the untranslated leader of the human immunodeficiency virus type 1 (hiv-1) rna genome encodes essential sequence and structural motifs that control various replication steps. the 5' splice site or splice donor (sd) is embedded in a semistable hairpin, but the function of this structure is unknown. we stabilized this sd hairpin by creating an additional base pair and demonstrated a severe hiv-1 replication defect. a splicing defect was apparent in rna analyses of virus-infected cells and cells transfected with appropriate reporter constructs. we selected multiple virus revertants in search for interesting second-site escape pathways. most revertants acquired an additional mutation that modulated the stability of the mutant sd hairpin. one revertant acquired a single nucleotide change in the upstream dis hairpin. we demonstrate that a novel sd site is created by this upstream mutation, which obviously reduces the number of leader nucleotides that are included in spliced hiv-1 transcripts. these results suggest a novel role of rna structure in the regulation of hiv-1 splicing.",1
"posttranscriptional regulation plays a crucial role in germline and early embryonic development, but the underlying mechanisms are only partially understood. here we report the genetic and molecular analysis of the maternally and zygotically expressed microrna mir-184 in drosophila. loss of mir-184 leads to multiple severe defects during oogenesis and early embryogenesis, culminating in the complete loss of egg production. using both in vitro and in vivo assays, we characterize the relevant mir-184 targets and target sites for three of the observed phenotypes. mir-184 controls germline stem cell differentiation by tuning the dpp receptor saxophone, dorsoventral patterning of the egg shell by regulating the gurken transport factor k10, and anteroposterior patterning of the blastoderm by tuning the transcriptional repressor tramtrack69. our study highlights the importance of microrna-mediated regulation in the major developmental transitions of the female germline, and provides insights into several aspects of microrna function.",1
"the 7sk small nuclear ribonucleoprotein (snrnp) plays a central role in rna polymerase ii elongation control by regulating the availability of active p-tefb. we optimized conditions for analyzing 7sk rna by shape and demonstrated a hysteretic effect of magnesium on 7sk folding dynamics including a 7sk gauc motif switch. we also found evidence that the 5΄ end pairs alternatively with two different regions of 7sk giving rise to open and closed forms that dictate the state of the 7sk motif. we then used recombinant p-tefb, hexim1, larp7 and mepce to reconstruct a functional 7sk snrnp in vitro. stably associated p-tefb was highly inhibited, but could still be released and activated by hiv-1 tat. notably, p-tefb association with both in vitro-reconstituted and cellular snrnps led to similar changes in shape reactivities, confirming that 7sk undergoes a p-tefb-dependent structural change. we determined that the xrrm of larp7 binds to the 3΄ stem loop of 7sk and inhibits the methyltransferase activity of mepce through a c-terminal mepce interaction domain (mid). inhibition of mepce is dependent on the structure of the 3΄ stem loop and the closed form of 7sk rna. this study provides important insights into intramolecular interactions within the 7sk snrnp.",1
"the vascular response to pro-atherosclerotic factors is a multifactorial process involving endothelial cells (ecs), macrophages (macs), and smooth muscle cells (smcs), although the mechanism by which these cell types communicate with each other in response to environmental cues is yet to be understood. here, we show that mir-155, which is significantly expressed and secreted in krüppel-like factor 5 (klf5)-overexpressing vascular smooth muscle cells (vsmcs), is a potent regulator of endothelium barrier function through regulating endothelial targeting tight junction protein expression. vsmcs-derived exosomes mediate the transfer of klf5-induced mir-155 from smcs to ecs, which, in turn, destroys tight junctions and the integrity of endothelial barriers, leading to an increased endothelial permeability and enhanced atherosclerotic progression. moreover, overexpression of mir-155 in ecs inhibits endothelial cell proliferation/migration and re-endothelialization in vitro and in vivo and thus increases vascular endothelial permeability. blockage of the exosome-mediated transfer of mir-155 between these two cells may serve as a therapeutic target for atherosclerosis.",1
"bone marrow mesenchymal stem cells (bmscs) exhibit an age-dependent reduction in osteogenesis that is accompanied by an increased propensity toward adipocyte differentiation. this switch increases adipocyte numbers and decreases the number of osteoblasts, contributing to age-related bone loss. here, we found that the level of microrna-188 (mir-188) is markedly higher in bmscs from aged compared with young mice and humans. compared with control mice, animals lacking mir-188 showed a substantial reduction of age-associated bone loss and fat accumulation in bone marrow. conversely, mice with transgenic overexpression of mir-188 in osterix+ osteoprogenitors had greater age-associated bone loss and fat accumulation in bone marrow relative to wt mice. moreover, using an aptamer delivery system, we found that bmsc-specific overexpression of mir-188 in mice reduced bone formation and increased bone marrow fat accumulation. we identified histone deacetylase 9 (hdac9) and rptor-independent companion of mtor complex 2 (rictor) as the direct targets of mir-188. notably, bmsc-specific inhibition of mir-188 by intra-bone marrow injection of aptamer-antagomir-188 increased bone formation and decreased bone marrow fat accumulation in aged mice. together, our results indicate that mir-188 is a key regulator of the age-related switch between osteogenesis and adipogenesis of bmscs and may represent a potential therapeutic target for age-related bone loss.",1
"cancer pathogenesis is restricted by stresses that compromise cell division and survival. in this study, we identify mir-708, a little studied member of a set of micrornas that have been implicated in stress control, as an important tumor suppressor in renal cell carcinoma (rcc). mir-708 expression was attenuated widely in human rcc specimens. restoration of mir-708 expression in rcc cell lines decreased cell growth, clonability, invasion, and migration and elicited a dramatic increase in apoptosis. moreover, intratumoral delivery of mir-708 was sufficient to trigger in vivo regression of established tumors in murine xenograft models of human rcc. investigation of the targets of mir-708 identified the inhibitor of apoptosis protein survivin as important. sirna-mediated knockdown of survivin partially phenocopied mir-708 overexpression suggesting that the proapoptotic role of mir-708 may be mediated primarily through survivin regulation. additionally, we identified the e-cadherin regulators zeb2 and bmi1 as likely mir-708 targets. taken together, our findings define a major tumor suppressive role for mir-708, which may offer an attractive new target for prognostic and therapeutic intervention in rcc.",1
"background mirnas and other small noncoding rnas (sncrnas) are key players in post-transcriptional gene regulation. hiv-1 derived small noncoding rnas (sncrnas) have been described in hiv-1 infected cells, but their biological functions still remain to be elucidated. here, we approached the question whether viral sncrnas may play a role in the rna interference (rnai) pathway or whether viral mrnas are targeted by cellular mirnas in human monocyte derived macrophages (mdm). methods the incorporation of viral sncrnas and/or their target rnas into rna-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (par-clip) as well as high-throughput sequencing of rna isolated by cross-linking immunoprecipitation (hits-clip), which capture argonaute2-bound mirnas and their target rnas. hiv-1 infected monocyte-derived macrophages (mdm) were chosen as target cells, as they have previously been shown to express hiv-1 sncrnas. in addition, we applied small rna deep sequencing to study differential cellular mirna expression in hiv-1 infected versus non-infected mdms. results and conclusion par-clip and hits-clip data demonstrated the absence of hiv-1 rnas in ago2-risc, although the presence of a multitude of hiv-1 sncrnas in hiv-1 infected mdms was confirmed by small rna sequencing. small rna sequencing revealed that 1.4% of all sncrnas were of hiv-1 origin. however, neither hiv-1 derived sncrnas nor putative hiv-1 target sequences incorporated into ago2-risc were identified suggesting that hiv-1 sncrnas are not involved in the canonical rnai pathway nor is hiv-1 targeted by this pathway in hiv-1 infected macrophages.",1
"transposition of insertion sequence is10 is regulated by an anti-sense rna which inhibits transposase expression when is10 is present in multiple copies per cell. the anti-sense rna (rna-out) consists of a stem domain topped by a flexibly paired loop; the 5' end of the target molecule, rna-in, is complementary to the top of the loop, and complementarity extends for 35 base-pairs down one side of rna-out. we present here genetic evidence that anti-sense pairing, both in vitro and in vivo, initiates by interaction of the 5' end of rna-in and the loop domain of rna-out; other features of the reaction are discussed. in the context of this model, we discuss features of this anti-sense system which are important for its biological effectiveness, and suggest that is10 provides a convenient model for design of efficient artificial anti-sense rna molecules.",1
"the mir-221/222 cluster is significantly upregulated in malignant glioma cells and regulates the expression of multiple genes associated with glioma cell proliferation, invasion and apoptosis, which was shown in our previous studies. cx43 has been identified as a tumor suppressor and major component for the establishment of gap junction intercellular communication (gjic) in glial cells, which is frequently reduced or deleted in high-grade gliomas. according to bioinformatic analysis, connexin 43 (cx43) may be one of the target genes of mir-221/222. the aim of the present study was to validate cx43 as a target gene of mir-221/222 and to determine whether overexpression of mir-221/222 is one of the molecular mechanisms for the reduced expression of cx43 in malignant gliomas. we transfected mir-221/222 antisense oligonucleotides (as-mir-221/222) into u251 human glioblastoma cells using a lipofectamine method. northern blot analysis was conducted to detect the expression of the mir-221/222 cluster. luciferase reporter assays were exploited to confirm cx43 as a target gene of mir-221/222. cx43 expression was assessed by western blotting and immunofluorescence staining. scrape loading and dye transfer (sldt) assays were used for examination of gjic. proliferation and invasion of u251 cells were evaluated by mtt and transwell assays, respectively. cell cycle kinetics and apoptosis were determined with flow cytometry. we found that expression of the mir-221/222 cluster was significantly reduced while cx43 expression was upregulated in u251 cells transfected with as-mir-221/222, and the gjic deficiency in parental u251 cells was re-established. moreover, the luciferase activity determined by the luciferase reporter assay was enhanced in as-mir-221/222-treated cells, and cell proliferation and invasion were suppressed while apoptosis was induced. we conclude that mir-221/222 function as oncogenic micrornas in human gliomas, at least in part, by targeting cx43.",1
"the muc1 oncoprotein is overexpressed in most human breast cancers by mechanisms that are incompletely understood. the microrna, mir-125b, is downregulated in breast cancer cells. the present studies demonstrate that the muc1 3'utr contains a site for binding of the mir-125b seed region. the results show that the muc1 3'utr suppresses luciferase expression and that this effect is abrogated by mutation or deletion of the mir-125b binding site. expression of an anti-sense mir-125b in bt-549 breast cancer cells was associated with induction of muc1 protein, but not muc1 mrna, levels. the anti-sense mir-125b also increased bt-549 cell growth by a muc1-dependent mechanism. in addition, overexpression of exogenous mir-125b downregulated muc1 protein, and not muc1 transcripts, in zr-75-1 breast cancer cells. silencing of muc1 in zr-75-1 cells with a sirna has been shown to promote dna damage-induced apoptosis. in concert with these observations, mir-125b-induced decreases in muc1 levels increased the apoptotic response of zr-75-1 cells to cisplatin treatment. these findings indicate that mir-125b suppresses translation of the muc1 oncoprotein and that mir-125b thereby functions as a tumor suppressor in breast cancer cells.",1
"unlabelled deregulated cell proliferation and apoptosis play a major role in hepatocellular carcinoma (hcc). micrornas participate in the modulation of key molecules linked to hepatocarcinogenesis. purpose this study aims to investigate the role of mir-221 in the modulation of bmf, a proapoptotic bh3-only protein, and to characterize mir-221 contribution to hepatocarcinogenesis through modulation of apoptosis. experimental design transfection of mir-221 and anti-mir-221 in hcc-derived cell lines and luciferase reporter assay were used to assess bmf as a target of mir-221. modulation of mir-221 and bmf expression contributed to characterize their role in anoikis. primary hcc tissues were analyzed to assess the clinical relevance of in vitro findings. results enforced mir-221 expression caused bmf down-regulation, whereas anti-mir-221 induced its up-regulation. a luciferase reporter assay confirmed bmf as a target of mir-221. following matrix detachment, mir-221 silencing led to increased apoptotic cell death. the analysis of hcc tissues revealed an inverse correlation between mir-221 and bmf expression and a direct correlation between bmf and activated caspase-3, as a marker of apoptosis. high mir-221 levels were associated with tumor multifocality and reduced time to recurrence after surgery. conclusions our results indicate that mir-221, by targeting bmf, inhibits apoptosis. moreover, in hcc, mir-221 overexpression is associated with a more aggressive phenotype. these findings, together with the previously reported modulation of cdkn1b/p27 and cdkn1c/p57, show that mir-221 simultaneously affects multiple pro-oncogenic pathways and suggest mir-221 as a potential target for nonconventional treatment against hcc.",1
"background japanese encephalitis virus (jev) is a mosquito-borne flavivirus that causes acute viral encephalitis in humans. pigs are important amplifier hosts of jev. emerging evidence indicates that host micrornas (mirnas) play key roles in modulating viral infection and pathogenesis. however, mechanistic studies delineating the roles of mirnas in regulating host-jev interactions remain scarce. results in this study, we demonstrated that mir-124 inhibited jev replication in porcine kidney epithelial pk15 cells. furthermore, using bioinformatics tools, we identified dynamin2 (dnm2), a gtpase responsible for vesicle scission, as a target of mir-124. small interfering rna (sirna) depletion studies inicated that dynamin2 was required for efficient jev replication. we also demonstrated that upregulation of mir-124 expression corresponded to decreased expression of its target, dnm2, in the jev-infected pk15 cells. conclusions overall, these results suggest the importance of mir-124 in modulating jev replication and provide a scientific basis for using cellular mirnas in anti-jev therapies.",1
"micrornas (mirnas) have been hypothesized to function as oncogenes or tumor suppressors by targeting specific cancer-related genes. previous studies have reported that mir-223 may serve as a tumor suppressor in a number of cancer types, however, knowledge of its targets in non-small cell lung cancer (nsclc) remains limited. in the current study, mir-223 was found to inhibit cell proliferation in vitro by cck-8 assay, growth curves and an anchorage-independent growth assay in a lewis lung carcinoma (llc) cell line. mir-223 transfection in the llc cells was observed to significantly inhibit migration and invasion, induce g 2 /m arrest and decrease the expression levels of sca-1, a marker of murine stem cells. in addition, mir-223 transfection markedly suppressed akt and erk signaling, as well as insulin-like growth factor-1 receptor (igf-1r)-mediated downstream signaling, pathways that are crucial for cell proliferation and invasion in nsclc cells. analyses in c57bl/6 mice demonstrated that mir-223 suppresses tumorigenicity in vivo . using a luciferase activity assay and western blot analysis, igf-1r and cyclin-dependent kinase 2 (cdk2) were identified as direct targets of mir-223. in the present study, novel cancer-related targets of mir-223 were identified and verified in a llc cell line, indicating that mir-223 functions as a tumor suppressor, which may fine-tune the activity of the igf-1r pathway in lung cancer. therefore, increasing mir-223 expression may provide a novel approach for the treatment of nsclc.",1
"telomere maintenance by telomerase is impaired in the stem cell disease dyskeratosis congenita and during human aging. telomerase depends upon a complex pathway for enzyme assembly, localization in cajal bodies, and association with telomeres. here, we identify the chaperonin cct/tric as a critical regulator of telomerase trafficking using a high-content genome-wide sirna screen in human cells for factors required for cajal body localization. we find that tric is required for folding the telomerase cofactor tcab1, which controls trafficking of telomerase and small cajal body rnas (scarnas). depletion of tric causes loss of tcab1 protein, mislocalization of telomerase and scarnas to nucleoli, and failure of telomere elongation. dc patient-derived mutations in tcab1 impair folding by tric, disrupting telomerase function and leading to severe disease. our findings establish a critical role for tric-mediated protein folding in the telomerase pathway and link proteostasis, telomere maintenance, and human disease.",1
"muscle stem cells undergo a dramatic metabolic switch to oxidative phosphorylation during differentiation, which is achieved by massively increased mitochondrial activity. since expression of the muscle-specific mir-1/133a gene cluster correlates with increased mitochondrial activity during muscle stem cell (musc) differentiation, we examined the potential role of mir-1/133a in metabolic maturation of skeletal muscles in mice. we found that mir-1/133a downregulate mef2a in differentiated myocytes, thereby suppressing the dlk1-dio3 gene cluster, which encodes multiple micrornas inhibiting expression of mitochondrial genes. loss of mir-1/133a in skeletal muscles or increased mef2a expression causes continuous high-level expression of the dlk1-dio3 gene cluster, compromising mitochondrial function. failure to terminate the stem cell-like metabolic program characterized by high-level dlk1-dio3 gene cluster expression initiates profound changes in muscle physiology, essentially abrogating endurance running. our results suggest a major role of mir-1/133a in metabolic maturation of skeletal muscles but exclude major functions in muscle development and musc maintenance.",1
"microrna-181a binds to the 3' untranslated region of messenger rna (mrna) for renin, a rate-limiting enzyme of the renin-angiotensin system. our objective was to determine whether this molecular interaction translates into a clinically meaningful effect on blood pressure and whether circulating mir-181a is a measurable proxy of blood pressure. in 200 human kidneys from the transcriptome of renal human tissue (translate) study, renal mir-181a was the sole negative predictor of renin mrna and a strong correlate of circulating mir-181a. elevated mir-181a levels correlated positively with systolic and diastolic blood pressure in translate, and this association was independent of circulating renin. the association between serum mir-181a and systolic blood pressure was replicated in 199 subjects from the genetic regulation of arterial pressure of humans in the community (graphic) study. renal immunohistochemistry and in situ hybridization showed that colocalization of mir-181a and renin was most prominent in collecting ducts where renin is not released into the systemic circulation. analysis of 69 human kidneys characterized by rna sequencing revealed that mir-181a was associated with downregulation of four mitochondrial pathways and upregulation of 41 signaling cascades of adaptive immunity and inflammation. we conclude that renal mir-181a has pleiotropic effects on pathways relevant to blood pressure regulation and that circulating levels of mir-181a are both a measurable proxy of renal mir-181a expression and a novel biochemical correlate of blood pressure.",1
"carcinoembryonic antigen-related cell adhesion molecule 6 (ceacam6) is an important regulator of cell adhesion, invasion, and metastasis. the aim of this study was to evaluate the functional roles of ceacam6 in lung adenocarcinoma and to identify mirnas that inhibit the growth, migration, and invasion of lung adenocarcinoma cells by targeting ceacam6. ceacam6 expression is associated with poor prognosis of patients with lung adenocarcinoma, and ceacam6 has important functional roles in controlling the growth, migration, and invasion of lung adenocarcinoma cells in vitro and in vivo. furthermore, mir-29a can suppress the growth, migration, and invasion of lung adenocarcinoma cells by targeting ceacam6. therefore, mir-29a/ceacam6 axis represents a potential therapeutic target for treatment of lung adenocarcinoma.",1
"the protein fino represses f-plasmid conjugative transfer by facilitating interactions between the mrna of the major f-plasmid transcriptional activator, traj, and an antisense rna, finp. fino is known to bind stem-loop structures in both finp and traj rnas; however, the mechanism by which fino facilitates sense-antisense pairing is poorly understood. here we show that fino acts as an rna chaperone to promote strand exchange and duplexing between minimal rna targets derived from finp. this strongly suggests that fino may function to destabilize internal secondary structures within finp and traj rnas that would otherwise act as a kinetic trap to sense-antisense pairing. the energy for fino-catalyzed base-pair destabilization does not arise from atp hydrolysis but appears to be supplied directly from fino rna binding free energy. an analysis of the activities of mutants that are specifically deficient in strand exchange but not rna-binding activity demonstrates that strand exchange is essential to the ability of fino to mediate sense-antisense rna recognition, and that this function also plays a role in repression of conjugation in vivo.",1
"micro rnas (mirnas) play an important role during renal development and show a tissue-specific enrichment in the kidney. nephroblastomas, embryonal renal neoplasms of childhood, are considered to develop from nephrogenic rests (nrs) and resemble morphologically and genetically developing kidney. we therefore investigated the role of kidney-enriched mirnas in the pathogenesis of nephroblastomas. mir-192, mir-215 and mir-194 had a significantly lower expression in nephroblastomas regardless of the subtype compared with mature kidney measured by quantitative real-time-pcr. mir-141 and mir-200c showed a significantly lower expression in blastema-type and mixed-type tumors. in comparison with nrs, a significantly lower expression of mir-192, mir-194 and mir-215 was identified in blastema-type, mixed-type and stroma-type nephroblastomas and of mir-141 and mir-200c in blastema-type tumors. kidney parenchyma had a significantly higher expression of mir-192, mir-194, mir-215 and mir-200c compared with nrs. in this study, the activin receptor type 2b (acvr2b), a member of the transforming growth factor (tgf)-β pathway, was identified as single common target gene for mir-192, mir-215, mir-194, mir-141 and mir-200c in silico for the first time. the interaction between all five mirnas and acvr2b was also verified by an in vitro assay. additionally, a distinct protein expression of acvr2b was detected in 53 of 55 nephroblastomas paralleled by an upregulation of acvr2b messenger rna demonstrated in 25 nephroblastomas of all subtypes. a differential regulation of acvr2b by mirnas in nrs and nephroblastomas appears to be an important step in the pathogenesis of nephroblastomas implicating for the first time the tgf-β pathway in this process.",1
"micrornas (mirnas) are an emerging class of non-coding endogenous rnas involved in multiple cellular processes, including cell differentiation. treatment with retinoic acid (ra) results in neural differentiation of neuroblastoma cells. we wanted to elucidate whether mirnas contribute to the gene expression changes induced by ra in neuroblastoma cells and whether mirna regulation is involved in the transduction of the ra signal. we show here that ra treatment of sh-sy5y neuroblastoma cells results in profound changes in the expression pattern of mirnas. up to 42 different mirna species significantly changed their expression (26 up-regulated and 16 down-regulated). among them, the closely related mir-10a and -10b showed the most prominent expression changes. induction of mir-10a and -10b by ra also could be detected in la-n-1 neuroblastoma cells. loss of function experiments demonstrated that mir-10a and -10b are essential mediators of ra-induced neuroblastoma differentiation and of the associated changes in migration, invasion, and in vivo metastasis. in addition, we found that the sr-family splicing factor sfrs1 (sf2/asf) is a target for mir-10a -and -10b in hela and sh-sy5y neuroblastoma cells. we show here that changes in mir-10a and -10b expression levels may regulate sfrs1-dependent alternative splicing and translational functions. taken together, our results give support to the idea that mirna regulation plays a key role in ra-induced neuroblastoma cell differentiation. the discovery of sfrs1 as direct target of mir-10a and -10b supports the emerging functional interaction between two post-transcriptional mechanisms, micrornas and splicing, in the neuronal differentiation context.",1
"regulated expression of the h19 long noncoding rna gene has been well characterized as a paradigm for genomic imprinting, but the h19 rna's biological function remains largely unclear. h19 is abundantly expressed maternally in embryonic tissues but is strongly repressed after birth, and significant transcription persists only in skeletal muscle. thus, we examined the role of the h19 rna in skeletal muscle differentiation and regeneration. knockdown of h19 rna in myoblast cells and h19 knockout mouse satellite cells decreases differentiation. h19 exon1 encodes two conserved micrornas, mir-675-3p and mir-675-5p, both of which are induced during skeletal muscle differentiation. the inhibition of myogenesis by h19 depletion during myoblast differentiation is rescued by exogenous expression of mir-675-3p and mir-675-5p. h19-deficient mice display abnormal skeletal muscle regeneration after injury, which is rectified by reintroduction of mir-675-3p and mir-675-5p. mir-675-3p and mir-675-5p function by directly targeting and down-regulating the anti-differentiation smad transcription factors critical for the bone morphogenetic protein (bmp) pathway and the dna replication initiation factor cdc6. therefore, the h19 long noncoding rna has a critical trans-regulatory function in skeletal muscle differentiation and regeneration that is mediated by the micrornas encoded within h19.",1
"colorectal cancer represents one of the most challenging diseases. increasing evidence indicates that aberrant expression of micrornas (mirnas) is related to pathogenesis of colorectal cancer. cancer cells reprogram metabolic pathways to sustain higher proliferation rates. whether mechanisms underlying the role of mirna in colorectal cancer are involved in metabolic reprogramming and the mechanisms through which mirnas alter cancer metabolism are as yet unknown. herein, we show that mir-124, mir-137 and mir-340 are associated with poor prognosis of colorectal cancer. expression of these mirnas inhibits the growth of colorectal cancer cells. pkm (pyruvate kinase isozyme) alternative splicing proteins (ptb1/hnrnapa1/hnrnapa2), which control the inclusion of exon 9 (pkm1) or exon 10 (pkm2), are targeted by mir-124, mir-137 and mir-340. consequently, mir-124, mir-137 and mir-340 switch pkm gene expression from pkm2 to pkm1. high ratios of pkm1/pkm2 inhibit the glycolysis rate, but elevate the glucose flux into oxidative phosphorylation. these results demonstrate that mirnas (mir-124, mir-137 and mir-340) impair colorectal cancer growth by counteracting the warburg effect due to regulating alternative splicing of the pkm gene.",1
"unlabelled bile acid synthesis not only produces physiological detergents required for intestinal nutrient absorption, but also plays a critical role in regulating hepatic and whole-body metabolic homeostasis. we recently reported that overexpression of cholesterol 7α-hydroxylase (cyp7a1) in the liver resulted in improved metabolic homeostasis in cyp7a1 transgenic (cyp7a1-tg) mice. this study further investigated the molecular links between bile acid metabolism and lipid homeostasis. microarray gene profiling revealed that cyp7a1 overexpression led to marked activation of the steroid response element-binding protein 2 (srebp2)-regulated cholesterol metabolic network and absence of bile acid repression of lipogenic gene expression in livers of cyp7a1-tg mice. interestingly, cyp7a1-tg mice showed significantly elevated hepatic cholesterol synthesis rates, but reduced hepatic fatty acid synthesis rates, which was accompanied by increased (14) c-glucose-derived acetyl-coenzyme a incorporation into sterols for fecal excretion. induction of srebp2 also coinduces intronic microrna-33a (mir-33a) in the srebp2 gene in cyp7a1-tg mice. overexpression of mir-33a in the liver resulted in decreased bile acid pool, increased hepatic cholesterol content, and lowered serum cholesterol in mice. conclusion this study suggests that a cyp7a1/srebp2/mir-33a axis plays a critical role in regulation of hepatic cholesterol, bile acid, and fatty acid synthesis. antagonism of mir-33a may be a potential strategy to increase bile acid synthesis to maintain lipid homeostasis and prevent nonalcoholic fatty liver disease, diabetes, and obesity.",1
"since the discovery of micrornas (mirnas) only two decades ago, they have emerged as an essential component of the gene regulatory machinery. mirnas have seemingly paradoxical features: a single mirna is able to simultaneously target hundreds of genes, while its presence is mostly dispensable for animal viability under normal conditions. it is known that mirnas act as stress response factors; however, it remains challenging to determine their relevant targets and the conditions under which they function. to address this challenge, we propose a new workflow for mirna function analysis, by which we found that the evolutionarily young mirna family, the mir-310s (mir-310/mir-311/mir-312/mir-313), are important regulators of drosophila metabolic status. mir-310s-deficient animals have an abnormal diet-dependent expression profile for numerous diet-sensitive components, accumulate fats, and show various physiological defects. we found that the mir-310s simultaneously repress the production of several regulatory factors (rab23, dhr96, and ttk) of the evolutionarily conserved hedgehog (hh) pathway to sharpen dietary response. as the mir-310s expression is highly dynamic and nutrition sensitive, this signal relay model helps to explain the molecular mechanism governing quick and robust hh signaling responses to nutritional changes. additionally, we discovered a new component of the hh signaling pathway in drosophila, rab23, which cell autonomously regulates hh ligand trafficking in the germline stem cell niche. how organisms adjust to dietary fluctuations to sustain healthy homeostasis is an intriguing research topic. these data are the first to report that mirnas can act as executives that transduce nutritional signals to an essential signaling pathway. this suggests mirnas as plausible therapeutic agents that can be used in combination with low calorie and cholesterol diets to manage quick and precise tissue-specific responses to nutritional changes.",1
"objective distant metastasis is the major cause of cancer-related death in patients with colorectal cancer (crc). although the microrna-200 (mir-200) family is a crucial inhibitor of epithelial-to-mesenchymal transition (emt) in human cancer, the role of mir-200 members in the pathogenesis of metastatic crc has not been investigated. design fifty-four pairs of primary crc and corresponding matched liver metastasis tissue specimens were analysed for expression and methylation status of the mir-200 family members. functional analysis of mir-200c overexpression was investigated in crc cell lines, and cells were analysed for proliferation, invasion and migration. expression of several mir-200c target genes (zeb1, ets1 and flt1) and emt markers (e-cadherin and vimentin) in crc cell lines and tissue specimens was validated. results liver metastasis tissues showed higher expression of mir-200c (primary crc = 1.31 vs. liver metastasis = 1.59; p = 0.0014) and mir-141 (primary crc = 0.14 vs. liver metastasis = 0.17; p = 0.0234) than did primary crcs, which was significantly associated with hypomethylation of the promoter region of these mirnas (primary crc = 61.2% vs. liver metastasis = 46.7%; p conclusions mir-200c plays an important role in mediating emt and metastatic behaviour in the colon. its expression is epigenetically regulated, and mir-200c may serve as a potential diagnostic marker and therapeutic target for patients with crc.",1
"microrna (mirna) play essential roles in biological processes ranging from cellular proliferation to apoptosis. recently, mirna have also been implicated in a number of diseases including cancers. however, the targets of most mirna remain unknown. the majority of reports describing identification of mirna targets are based on computational approaches or detection of altered mrna levels despite the fact that most mirna are thought to regulate their targets primarily at the level of translational inhibition in animals. mir-21 is a mirna with oncogenic activity that is involved in various cancer-related processes such as invasion and migration. given the importance of mir-21 in tumorigenesis, we employed a quantitative proteomic strategy to systematically identify potential targets of mir-21. by knocking down the expression of endogenous mir-21 in mcf-7 breast cancer cells, we observed an increase in the abundance of 58 proteins, implying that they could be potential targets of mir-21. validation of 12 of these candidate targets in luciferase assays showed that 6 of them were likely direct targets of mir-21. importantly, the mrna of the majority of the candidate targets tested did not show a concomitant increase in abundance. overall, our results demonstrate that mir-21 affects the expression of many of its targets through translational inhibition and highlights the utility of proteomic approaches for identifying mirna targets.",1
"the bone morphogenetic protein 4 (bmp4) signaling pathway plays a critical role in the promotion and maintenance of the contractile phenotype in vascular smooth muscle cell (vsmc). misexpression or inactivating mutations of the bmp receptor gene can lead to dedifferentiation of vsmc characterized by increased migration and proliferation that is linked to vascular proliferative disorders. previously we demonstrated that vsmcs increase microrna-21 (mir-21) biogenesis upon bmp4 treatment, which induces contractile gene expression by targeting programmed cell death 4 (pdcd4). to identify novel targets of mir-21 that are critical for induction of the contractile phenotype by bmp4, biotinylated mir-21 was expressed in vsmcs followed by an affinity purification of mrnas associated with mir-21. nearly all members of the dedicator of cytokinesis (dock) 180-related protein superfamily were identified as targets of mir-21. down-regulation of dock4, -5, and -7 by mir-21 inhibited cell migration and promoted cytoskeletal organization by modulating an activity of small gtpase. thus, this study uncovers a regulatory mechanism of the vsmc phenotype by the bmp4-mir-21 axis through dock family proteins.",1
"atrial fibrillation (af) is a growing public health burden, and its treatment remains a challenge. af leads to electrical remodeling of the atria, which in turn promotes af maintenance and resistance to treatment. although remodeling has long been a therapeutic target in af, its causes remain poorly understood. we show that atrial-specific up-regulation of microrna-31 (mir-31) in goat and human af depletes neuronal nitric oxide synthase (nnos) by accelerating mrna decay and alters nnos subcellular localization by repressing dystrophin translation. by shortening action potential duration and abolishing rate-dependent adaptation of the action potential duration, mir-31 overexpression and/or disruption of nnos signaling recapitulates features of af-induced remodeling and significantly increases af inducibility in mice in vivo. by contrast, silencing mir-31 in atrial myocytes from patients with af restores dystrophin and nnos and normalizes action potential duration and its rate dependency. these findings identify atrial-specific up-regulation of mir-31 in human af as a key mechanism causing atrial dystrophin and nnos depletion, which in turn contributes to the atrial phenotype begetting this arrhythmia. mir-31 may therefore represent a potential therapeutic target in af.",1
"endothelin-1 (et-1) is a small 21-amino acid peptide that is known to exert diverse biological effects on a wide variety of tissues and cell types through its own receptors. the et-1-etra axis is frequently dysfunctional in numerous types of carcinomas, and contributes to the promotion of cell growth and migration. micrornas (mirnas) are small non-coding rnas that play a critical role in carcinogenesis through mrna degradation or the translational inhibition of cancer-associated protein-coding genes. however, the role of et-1 and the relationship between et-1 and mirnas in gastric cancer remain unknown. results of the analysis of the database of the cancer genome atlas (tcga) revealed that et-1 is significantly overexpressed in gastric cancer cells when compared with its expression in adjacent normal cells. exogenous et-1 significantly enhanced gastric cancer cell proliferation, implying that et-1 plays an oncogenic role in gastric cancer carcinogenesis. using a luciferase reporter assay we showed that 18 mirna candidates had a significant silencing effect on et-1 expression by up to 20% in hek293t cells. among them, 5 mirnas (mir-1, mir-101, mir-125a, mir-144 and let-7c) were shown to be involved in et-1 silencing through post-transcriptional modulation in gastric cancer. our data also revealed that dna hypermethylation contributes to the silenced mir-1 expression in gastric cancer cells. the ectopic expression of mir-1 significantly inhibited ags cell proliferation by suppressing et-1 expression. overall, our study revealed that et-1 overexpression may be due to dna hypermethylation resulting in the silencing of mir-1 expression in gastric cancer cells. in addition, we identified several mirnas as potential modulators for et-1 in gastric cancer, which may be used as targets for gastric cancer therapy.",1
"unlabelled micrornas (mirnas), which are inhibitors of gene expression, participate in diverse biological functions and in carcinogenesis. in this study, we show that liver-specific microrna-122 (mir-122) is significantly down-regulated in liver cancers with intrahepatic metastasis and negatively regulates tumorigenesis. restoration of mir-122 in metastatic mahlavu and sk-hep-1 cells significantly reduced in vitro migration, invasion, and anchorage-independent growth as well as in vivo tumorigenesis, angiogenesis, and intrahepatic metastasis in an orthotopic liver cancer model. because an inverse expression pattern is often present between an mirna and its target genes, we used a computational approach and identified multiple mir-122 candidate target genes from two independent expression microarray datasets. thirty-two target genes were empirically verified, and this group of genes was enriched with genes regulating cell movement, cell morphology, cell-cell signaling, and transcription. we further showed that one of the mir-122 targets, adam17 (a disintegrin and metalloprotease 17) is involved in metastasis. silencing of adam17 resulted in a dramatic reduction of in vitro migration, invasion, in vivo tumorigenesis, angiogenesis, and local invasion in the livers of nude mice, which is similar to that which occurs with the restoration of mir-122. conclusion our study suggests that mir-122, a tumor suppressor microrna affecting hepatocellular carcinoma intrahepatic metastasis by angiogenesis suppression, exerts some of its action via regulation of adam17. restoration of mir-122 has a far-reaching effect on the cell. using the concomitant down-regulation of its targets, including adam17, a rational therapeutic strategy based on mir-122 may prove to be beneficial for patients with hepatocellular carcinoma.",1
"small non-coding regulatory rnas (srnas) post-transcriptionally affect multiple phenotypes in prokaryotes and eukaryotes, yet most of the underlying regulatory mechanisms and the nature of the target mrnas remain unclear. here we report the identification and functional analysis of the novel cis-encoded srna h2cr, from the human opportunistic pathogen burkholderia cenocepacia j2315. the srna was found to negatively regulate the hfq2 mrna, through binding to part of the 5'-utr region of the hfq2 mrna, resulting in accelerated hfq2 mrna decay and reduced protein levels in exponentially growing cells. both the h2cr transcript and the hfq2 mrna are stabilized by the other b. cenocepacia rna chaperone, hfq. infection experiments using the nematode caenorhabditis elegans revealed that down-regulation of hfq2 by h2cr decreases the b. cenocepacia ability to colonize and persist within the nematode, suggesting a role for h2cr on bacterial persistence in the host.",1
"accumulating evidence indicates that some mirnas could form feedback loops with their targets to fine-tune tissue homeostasis, while disruption of these loops constitutes an essential step towards human tumorigenesis. in this study, we report the identification of a novel negative feedback loop formed between mir-139 and its oncogenic target jun. in this loop, mir-139 could inhibit jun expression by targeting a conserved site on its 3'-utr, whereas jun could induce mir-139 expression in a dose dependent manner through a distant upstream regulatory element. interestingly, aberration in this loop was found in human gastric cancer, where mir-139 was down-regulated and inversely correlated with jun expression. further functional analysis showed that restored expression of mir-139 in gastric cancer cells significantly induces apoptosis, and inhibits cell migration and proliferation as well as tumour growth through targeting jun. thus, our data strongly suggests a role of aberrant mir-139/jun negative feedback loop in the development of human gastric cancer and mir-139 as a potential therapeutic target for gastric cancer. given that mir-139 and jun are deregulated in many cancers, our findings here might have broader implication in other types of human cancers.",1
"metastasis is the major cause of poor prognosis in colorectal cancer (crc), and increasing evidence supports the contribution of mirnas to cancer progression. here, we found that high expression of mir-103 and mir-107 (mir-103/107) was associated with metastasis potential of crc cell lines and poor prognosis in patients with crc. we showed that mir-103/107 targeted the known metastasis suppressors death-associated protein kinase (dapk) and krüppel-like factor 4 (klf4) in crc cells, resulting in increased cell motility and cell-matrix adhesion and decreased cell-cell adhesion and epithelial marker expression. mir-103/107 expression was increased in the presence of hypoxia, thereby potentiating dapk and klf4 downregulation and hypoxia-induced motility and invasiveness. in mouse models of crc, mir-103/107 overexpression potentiated local invasion and liver metastasis effects, which were suppressed by reexpression of dapk or klf4. mir-103/107-mediated downregulation of dapk and klf4 also enabled the colonization of crc cells at a metastatic site. clinically, the signature of a mir-103/107 high, dapk low, and klf4 low expression profile correlated with the extent of lymph node and distant metastasis in patients with crc and served as a prognostic marker for metastasis recurrence and poor survival. our findings therefore indicate that mir-103/107-mediated repression of dapk and klf4 promotes metastasis in crc, and this regulatory circuit may contribute in part to hypoxia-stimulated tumor metastasis. strategies that disrupt this regulation might be developed to block crc metastasis.",1
"micrornas (mirnas) are small non-coding rnas that regulate gene expression by destabilizing target transcripts and/or inhibiting their translation. mirnas are thought to have roles in buffering gene expression to confer robustness. mirnas have been shown to play important roles during tissue development to control cell proliferation, differentiation and morphogenesis. many mirnas are expressed in the germ line of drosophila, and functions have been reported for a few mirnas in maintenance of stem cell proliferation during oogenesis. here, we analyse the function of drosophila mir-989 in oogenesis. mir-989 is abundant in ovaries. mutants lacking mir-989 did not display gross abnormalities affecting egg chamber formation or maturation. however, the migration of the border cell cluster was severely delayed in mir-989 mutant egg chambers. we demonstrate that mir-989 function is required in the somatic cells in the egg chamber, not in germ line cells for border cell migration. loss of mir-989 from a fraction of the border cell cluster was sufficient to impair cluster migration as a whole, suggesting a role in border cells. gene ontology analysis reveals that many predicted mir-989 target mrnas are implicated in regulating cell migration, cell projection morphogenesis, cell adhesion as well as receptor tyrosine kinase and ecdysone signalling, consistent with an important regulatory role for mir-989 in border cell migration.",1
"micrornas, a class of small and non-encoding rnas that transcriptionally or post-transcriptionally modulate the expression of their target genes, has been implicated as critical regulatory molecules in many cardiovascular diseases, including ischemia/reperfusion induced cardiac injury. here, we report microrna-145, a tumor suppressor mirna, can protect cardiomyocytes from hydrogen peroxide h₂o₂-induced apoptosis through targeting the mitochondrial pathway. quantitative real-time pcr (qpcr) demonstrated that the expression of mir-145 in either ischemia/reperfused mice myocardial tissues or h₂o₂-treated neonatal rat ventricle myocytes (nrvms) was markedly down-regulated. over-expression of mir-145 significantly inhibited the h₂o₂-induced cellular apoptosis, ros production, mitochondrial structure disruption as well as the activation of key signaling proteins in mitochondrial apoptotic pathway. these protective effects of mir-145 were abrogated by over-expression of bnip3, an initiation factor of the mitochondrial apoptotic pathway in cardiomyocytes. finally, we utilized both luciferase reporter assay and western blot analysis to identify bnip3 as a direct target of mir-145. our results suggest mir-145 plays an important role in regulating mitochondrial apoptotic pathway in heart challenged with oxidative stress. mir-145 may represent a potential therapeutic target for treatment of oxidative stress-associated cardiovascular diseases, such as myocardial ischemia/reperfusion injury.",1
"background the mechanism for inactivation of positive regulatory domain containing i (prdm1), a newly identified tumour suppressor gene in extranodal nk/t-cell lymphoma, nasal type (en-nk/t-nt) has not been well defined. the aim of the present study was to investigate the expression of prdm1 in en-nk/t-nt and analyse its downregulation by mirnas. methods prdm1 and mirna expression were evaluated in en-nk/t-nt samples by immunohistochemical analysis, qrt-pcr, and in situ hybridisation. luciferase assays were performed to verify the direct binding of mir-223 to the 3'-untranslated region of prdm1 mrna. in addition, the effect of mir-223 on prdm1 expression was assessed in nk/t lymphoma cell lines by transfecting a mir-223 mimic or inhibitor to increase or decrease the effective expression of mir-223. overall survival and failure-free survival in en-nk/t-nt patients were analysed using kaplan-meier single-factor analysis and the log-rank test. results investigation of the downregulation of prdm1 in en-nk/t-nt cases revealed that prdm1-positive staining might be a favourable predictor of overall survival and failure-free survival in en-nk/t-nt patients. however, the negative staining of prdm1 usually presented transcripts, suggesting a possible post-transcriptional regulation. mir-223 and its putative target gene, prdm1, exhibited opposite patterns of expression in en-nk/t-nt tissues and cell lines. moreover, prdm1 was identified as a direct target gene of mir-223 by luciferase assays. the ectopic expression of mir-223 led to the downregulation of the prdm1 protein in the nk/t-cell lymphoma cell line, whereas a decrease in mir-223 restored the level of prdm1 protein. conclusions our findings reveal that the downregulation of the tumour suppressor prdm1 in en-nk/t-nt samples is mediated by mir-223 and that prdm1-positive staining might have prognostic value for evaluating the clinical outcome of en-nk/t-nt patients.",1
"it is important to understand the regulation of stem cell division because defects in this process can cause altered tissue homeostasis or cancer. the cyclin-dependent kinase inhibitor dacapo (dap), a p21/p27 homolog, acts downstream of the microrna (mirna) pathway to regulate the cell cycle in drosophila melanogaster germline stem cells (gscs). tissue-extrinsic signals, including insulin, also regulate cell division of gscs. we report that intrinsic and extrinsic regulators intersect in gsc division control; the insulin receptor (inr) pathway regulates dap levels through mirnas, thereby controlling gsc division. using gfp-dap 3'utr sensors in vivo, we show that in gscs the dap 3'utr is responsive to dicer-1, an rna endonuclease iii required for mirna processing. furthermore, the dap 3'utr can be directly targeted by mir-7, mir-278 and mir-309 in luciferase assays. consistent with this, mir-278 and mir-7 mutant gscs are partially defective in gsc division and show abnormal cell cycle marker expression, respectively. these data suggest that the gsc cell cycle is regulated via the dap 3'utr by multiple mirnas. furthermore, the gfp-dap 3'utr sensors respond to inr but not to tgf-beta signaling, suggesting that inr signaling utilizes dap for gsc cell cycle regulation. we further demonstrate that the mirna-based dap regulation may act downstream of inr signaling; dcr-1 and dap are required for nutrition-dependent cell cycle regulation in gscs and reduction of dap partially rescues the cell cycle defect of inr-deficient gscs. these data suggest that mirna- and dap-based cell cycle regulation in gscs can be controlled by inr signaling.",1
"mammalian biological processes such as inflammation, involve regulation of hundreds of genes controlling onset and termination. micrornas (mirnas) can translationally repress target mrnas and regulate innate immune responses. our model system comprised primary human keratinocytes, which exhibited robust differences in inflammatory cytokine production (interleukin-6 and tumor necrosis factor-alpha) following specific toll-like receptor 2 and 4 (tlr-2/tlr-4) agonist challenge. we challenged these primary cells with porphyromonas gingivalis (a gram-negative bacterium that triggers tlr-2 and tlr-4) and performed mirna expression profiling. we identified mirna (mir)-105 as a modulator of tlr-2 protein translation in human gingival keratinocytes. there was a strong inverse correlation between cells that had high cytokine responses following tlr-2 agonist challenge and mir-105 levels. knock-in and knock-down of mir-105 confirmed this inverse relationship. in silico analysis predicted that mir-105 had complementarity for tlr-2 mrna, and the luciferase reporter assay verified this. further understanding of the role of mirna in host responses may elucidate disease susceptibility and suggest new anti-inflammatory therapeutics.",1
"hepatic nuclear factor 4α (hnf4a) is a nuclear transcription factor that regulates the expression of many genes involved in drug disposition. to identify additional molecular mechanisms that regulate hnf4a, we identified micrornas (mirnas) that target hnf4a expression. in silico analyses suggested that hnf4a is targeted by many mirnas. we conducted in vitro studies to validate several of these predictions. with use of an hnf4a 3'-untranslated region (utr) luciferase reporter assay, five of six mirnas tested significantly down-regulated (∼20-40%) the luciferase activity. in hepg2 cells, mir-34a and mir-449a also down-regulated the expression of both the hnf4a protein and an hnf4a target gene, pxr (∼30-40%). this regulation appeared without reduction in hnf4a mrna expression, suggesting that they must be blocking hnf4a translation. using additional bioinformatic algorithms, we identified polymorphisms that are predicted to alter the mirna targeting of hnf4a. luciferase assays indicated that mir-34a and mir-449a were less effective in regulating a variant (rs11574744) than the wild-type hnf4a 3'-utr. in vivo, subjects with the variant hnf4a had lower cyp2d6 enzyme activity, although this result was not statistically significant (p = 0.16). in conclusion, our findings demonstrate strong evidence for a role of mirnas in the regulation of hnf4a.",1
"the tumor microenvironment (tme) has an impact on breast cancer progression by creating a pro-inflammatory milieu within the tumor. however, little is known about the roles of mirnas in cells of the tme during this process. we identified six putative oncomirs in a breast cancer dataset, all strongly correlating with poor overall patient survival. out of the six candidates, mir-1246 was upregulated in aggressive breast cancer subtypes and expressed at highest levels in mesenchymal stem/stroma cells (mscs). functionally, mir-1246 led to a p65-dependent increase in transcription and release of pro-inflammatory mediators il-6, ccl2 and ccl5 in mscs, and increased nf-κb activity. the pro-inflammatory phenotype of mir-1246 in mscs was independent of tnfα stimulations and mediated by direct targeting of the tumor-suppressors prkar1a and ppp2cb. in vitro recapitulation of the tme revealed increased stat3 phosphorylation in breast epithelial (mcf10a) and cancer cells (sk-br-3, mcf7, t47d) upon incubation with conditioned medium (cm) of mscs overexpressing mir-1246. additionally, this stimulation enhanced proliferation of mcf10a cells, increased migration of mda-mb-231 cells and induced attraction of thp-1 monocytic cells. our data shows that mir-1246 acts as both key-enhancer of pro-inflammatory responses in mscs and putative oncomir in breast cancer, suggesting its influence on cancer-related inflammation and breast cancer progression.",1
"background dysregulation of micrornas (mirnas) in arterial dysfunction and hypertension has not been extensively investigated yet. this project determined the effects of two anti-hypertensive β1 adrenergic selective blockers on mirna expression in the dahl salt sensitive (dss) hypertensive rat model. methods and results microarray analysis showed that a set of mirnas is differently expressed in the aorta of high salt (hs) treated rats with mir-320 increased and mir-26b and -21 decreased. all of these changes were reverted to normal by nebivolol (neb, a β1 selective-blocker and β3 activator). the selective β3-adrenoceptor antagonist s-(-)-cyanopindolol (syc) counteracted the effect of neb on these mirnas. atenolol (atn, a pure β1-blocker) combined with specific β3 agonist brl37344 restored the expression of all three mirnas, similar to neb, while atn alone had only a partial effect on mir-320 expression. computational analysis found insulin growth factor-1 receptor (igf1r) as a putative target of mir-320, and phosphatase and tensin homolog on chromosome ten (pten) as a putative target of mir-26b and -21. the targets were verified by luciferase reporter assays. inhibition of mir-320 by an antisense inhibitor or neb increased igf1r expression, while mir-320 overexpression reversed the effect of neb. overexpression of mir-26b or -21 or neb decreased pten levels, while inhibition of mir-26b or -21 attenuated the effect of neb. hs diet induced downregulation of igf1r and upregulation of pten in the aorta. neb normalized the aberrant expression of igf1r and pten and also improved the impairment of vascular akt/enos signaling. moreover, both neb and atn showed to have protective effects on salt-induced hypertension, oxidative stress, and vascular remodeling. neb had a greater effect than atn. conclusions our data supports a differential mirna expression profile in salt-induced hypertension. manipulation of dysregulated mirnas by β-blockers may substantially induce alterations of gene expression and prevent arterial dysfunction and remodeling.",1
"during keratinocyte differentiation and stratification, cells undergo extensive remodeling of their actin cytoskeleton, which is important to control cell mobility and to coordinate and stabilize adhesive structures necessary for functional epithelia. limited knowledge exists on how the actin cytoskeleton is remodeled in epithelial stratification and whether cell shape is a key determinant to trigger terminal differentiation. in this paper, using human keratinocytes and mouse epidermis as models, we implicate mir-24 in actin adhesion dynamics and demonstrate that mir-24 directly controls actin cable formation and cell mobility. mir-24 overexpression in proliferating cells was sufficient to trigger keratinocyte differentiation both in vitro and in vivo and directly repressed cytoskeletal modulators (pak4, tks5, and arhgap19). silencing of these targets recapitulated the effects of mir-24 overexpression. our results uncover a new regulatory pathway involving a differentiation-promoting microribonucleic acid that regulates actin adhesion dynamics in human and mouse epidermis.",1
"liposarcoma can be an aggressive, debilitating, and fatal malignancy. in this study, we identifed mirnas associated with the differentiation status of liposarcoma to gain insight into the basis for its progression. mirna expression profiles determined in human tumors and normal fat specimens identified a dedifferentiated tumor expression signature consisting of 35 mirnas. deregulated mirna expression was confirmed in a second independent sample cohort. the mir-155 was the most overexpressed mirna and functional investigations assigned an important role in the growth of dedifferentiated liposarcoma cell lines. transient or stable knockdown of mir-155 retarded tumor cell growth, decreased colony formation, and induced g(1)-s cell-cycle arrest in vitro and blocked tumor growth in murine xenografts in vivo. we identified casein kinase 1α (ck1α) as a direct target of mir-155 control which enhanced β-catenin signaling and cyclin d1 expression, promoting tumor cell growth. in summary, our results point to important functions for mir-155 and β-catenin signaling in progression of liposarcoma, revealing mechanistic vulnerabilities that might be exploited for both prognostic and therapeutic purposes.",1
"rationale foam cell formation because of excessive accumulation of cholesterol by macrophages is a pathological hallmark of atherosclerosis, the major cause of morbidity and mortality in western societies. liver x nuclear receptors (lxrs) regulate the expression of the adenosine triphosphate-binding cassette (abc) transporters, including adenosine triphosphate-binding cassette transporter a1 (abca1) and adenosine triphosphate-binding cassette transporter g1 (abcg1). abca1 and abcg1 facilitate the efflux of cholesterol from macrophages and regulate high-density lipoprotein (hdl) biogenesis. increasing evidence supports the role of microrna (mirnas) in regulating cholesterol metabolism through abc transporters. objective we aimed to identify novel mirnas that regulate cholesterol metabolism in macrophages stimulated with lxr agonists. methods and results to map the mirna expression signature of macrophages stimulated with lxr agonists, we performed an mirna profiling microarray analysis in primary mouse peritoneal macrophages stimulated with lxr ligands. we report that lxr ligands increase mir-144 expression in macrophages and mouse livers. overexpression of mir-144 reduces abca1 expression and attenuates cholesterol efflux to apolipoproteina1 in macrophages. delivery of mir-144 oligonucleotides to mice attenuates abca1 expression in the liver, reducing hdl levels. conversely, silencing of mir-144 in mice increases the expression of abca1 and plasma hdl levels. thus, mir-144 seems to regulate both macrophage cholesterol efflux and hdl biogenesis in the liver. conclusions mir-144 regulates cholesterol metabolism via suppressing abca1 expression and modulation of mirnas may represent a potential therapeutical intervention for treating dyslipidemia and atherosclerotic vascular disease.",1
"we aimed to evaluate the expression of microrna-182 (mir-182) in triple-negative breast cancer (tnbc) tissues and the tnbc cell line mda-mb-231 and to investigate the effects of mirr-182 on the cellular behavior of mda-mb-231 and the expression of the target gene profilin 1 (pfn1), thus providing new methods and new strategies for the treatment of tnbc. quantitative real-time pcr (qrt-pcr) was utilized to evaluate the expression of mir-182 in tnbc tissues, relatively normal tissues adjacent to tnbc and the tnbc cell line mda-mb-231. forty-eight hours after the mda-mb-231 cells were transfected with the mir-182 inhibitor, qrt-pcr was utilized to detect the changes in mir-182 expression levels, and an mtt (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was utilized to determine the effects of mir-182 on cell viability. flow cytometry was adopted to determine whether mir-182 affects the proliferation rates and apoptosis levels of the mda-mb-231 cells. the transwell migration assay method was used to investigate the effects of mir-182 on the migration of the mda-mb-231 cells. a luciferase reporter gene system was applied to validate that pfn1 was the target gene of mir-182. western blot was used to measure the effects of mir-182 on the pfn1 protein expression levels in the cells. qrt-pcr results showed that compared with the relatively normal tissues adjacent to tnbc, mir-182 expression was significantly increased in the tnbc tissues and the mda-mb-231 cells (p<0.01). compared with the control group, mda-mb-231 cells transfected with the mir-182 inhibitor and incubated for 48 h showed significantly decreased mir-182 expression (p<0.01). the results of an mtt assay showed that inhibition of mir-182 in mda-mb-231 cells led to significantly reduced cell viability (p<0.05). flow cytometry analysis indicated that inhibition of mir-182 expression resulted in significantly decreased cell proliferation (p<0.05) and significantly increased levels of apoptosis (p<0.05). the results of a transwell migration assay showed that after inhibited of mir-182 expression, the number of cells passing through the transwell membranes was significantly decreased (p<0.05). the results from a luciferase reporter gene system showed that compared with the control group, the relative luciferase activity of the group transfected with the mir-182 inhibitor was significantly increased (p<0.05). western blot analysis showed that compared with the control group, pfn1 protein expression levels were significantly increased in the mda-mb-231 cells transfected with the mir-182 inhibitor and incubated for 48 h (p<0.05). in conclusion, mir-182 is upregulated in tnbc tissues and cells. it promotes the proliferation and invasion of mda-mb-231 cells and could negatively regulate pfn1 protein expression. treatment strategies utilizing inhibition of mir-182 expression or overexpression of the pfn1 gene might benefit patients with tnbc.",1
"microrna (mirna)-guided target rna expression is vital for a wide variety of biological processes in eukaryotes. currently, mirbase (version 13) lists 142 and 353 mirnas from arabidopsis and rice (oryza sativa), respectively. the integration of mirnas in diverse biological networks relies upon the confirmation of their rna targets. in contrast with the well-characterized mirna targets that are cleaved in arabidopsis, only a few such targets have been confirmed in rice. to identify small rna targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small rna-directed target cleavage by sequencing the 5' ends of uncapped rnas. one hundred and sixty targets of 53 mirna families (24 conserved and 29 rice-specific) and five targets of tas3-small interfering rnas (sirnas) were identified. surprisingly, an additional conserved target for mir398, which has not been reported so far, has been validated. besides conserved homologous transcripts, 23 non-conserved genes for nine conserved mirnas and 56 genes for 29 rice-specific mirnas were also identified as targets. besides mirna targets, the rice degradome contained fragments derived from mirna precursors. a closer inspection of these fragments revealed a unique pattern distinct from sirna-producing loci. this attribute can serve as one of the ancillary criteria for separating mirnas from sirnas in plants.",1
"the molecular controls over meiosis are poorly understood compared with those over mitosis. here, we show that s. pombe mei2, which is essential for the initiation of premeiotic dna synthesis, encodes an rna-binding protein. a temperature-sensitive mei2 mutant performs premeiotic dna synthesis but does not undergo meiotic divisions, suggesting that mei2 is required also for meiosis i. a novel, polyadenylated rna species (meirna), which suppresses this temperature-sensitive defect if overexpressed, specifically binds to mei2 both in vivo and in vitro. cells without meirna perform premeiotic dna synthesis but cannot undergo meiosis i. mutations that apparently block the rna binding ability of mei2 inhibit premeiotic dna synthesis. mei2 is thus likely to couple with another rna species to promote premeiotic dna synthesis.",1
"tgfβr1 plays an important role in tgf-β signaling transduction and serves as a tumor suppressor. our previous studies show that reduced expression of tgfβr1 is common in non-small cell lung cancer (nsclc) and tgfβr1 variants confer risk of nsclc. however, the epigenetic mechanisms underlying the role of tgfβr1 in nsclc carcinogenesis are still elusive. we investigated the function and regulation of tgf-β signaling-based mirnas in nsclc. computational algorithms predicted that the 3'-untranslated region (3'-utr) of tgfβr1 is a target of mir-142-3p. here a luciferase reporter assay confirmed that mir-142-3p can directly bind to 3'-utr of tgfβr1. overexpression of mir-142-3p in nsclc a549 cells suppressed expression of tgfβr1 mrna and protein, while knockdown of endogenous mir-142-3p led to increased expression of tgfβr1. on tgf-β1 stimulation, stable overexpression of mir-142-3p attenuated phosphorylation of smad3, an indispensable downstream effector in canonical tgf-β/smad signaling, via repression of tgfβr1 in a549 cells. furthermore, mir-142-3p-mediated down-regulation of tgfβr1 weakened tgf-β-induced growth inhibition effect, and this effect was reversed by stable knockdown of endogenous mir-142-3p in a549 cells. in nsclc tissues, mir-142-3p expression was increased and inversely correlated with tgfβr1 expression. these data demonstrate that mir-142-3p influences the proliferation of nsclc cells through repression of tgfβr1.",1
"translational regulation of the dendritically localized mrna encoding for the neurotrophin receptor trkb has important ramifications for synaptic function. we examined whether the trkb mrna is translated through an internal initiation entry site (ires). the human trkb 5' leaders are derived from the use of alternative promoters and alternative splicing, but all 5' leaders share a common exon. insertion of a full-length 5' leader, as well as the common exon into the intercistronic region of a dicistronic luciferase construct, yielded luciferase activity generated from the second cistron that was either equivalent or higher than that observed from the encephalomyocarditis virus ires. moreover, inhibiting cap-dependent translation ex vivo and in in vitro lysates had only a minimal effect on the translation of mrna containing the trkb 5' leader. dissecting the 5' leader showed that the ires is located in the exon common to all trkb 5' leaders. moreover, six regions ranging from 2 to 25 nt were identified that either promoted or inhibited ires activity. taken together, these results suggest that the 5' leader of the human trkb mrna contains multiple cis-elements that regulate internal initiation of translation and that this mechanism may contribute significantly to the translation of the trkb mrna in neuronal dendrites.",1
"background neuroblastoma remains a major cause of cancer-linked mortality in children. mir-204 has been used in microrna expression signatures predictive of neuroblastoma patient survival. the aim of this study was to explore the independent association of mir-204 with survival in a neuroblastoma cohort, and to investigate the phenotypic effects mediated by mir-204 expression in neuroblastoma. methods neuroblastoma cell lines were transiently transfected with mir-204 mimics and assessed for cell viability using mts assays. apoptosis levels in cell lines were evaluated by facs analysis of annexin v-/propidium iodide-stained cells transfected with mir-204 mimics and treated with chemotherapy drug or vehicle control. potential targets of mir-204 were validated using luciferase reporter assays. results mir-204 expression in primary neuroblastoma tumours was predictive of patient event-free and overall survival, independent of established known risk factors. ectopic mir-204 expression significantly increased sensitivity to cisplatin and etoposide in vitro. mir-204 direct targeting of the 3' utr of bcl2 and ntrk2 (trkb) was confirmed. conclusion mir-204 is a novel predictor of outcome in neuroblastoma, functioning, at least in part, through increasing sensitivity to cisplatin by direct targeting and downregulation of anti-apoptotic bcl2. mir-204 also targets full-length ntrk2, a potent oncogene involved with chemotherapy drug resistance in neuroblastoma.",1
"micrornas (mirna) represent a novel class of genes that function as negative regulators of gene expression. recently, mirnas have been implicated in several cancers. however, aberrant mirna expression and its clinicopathologic significance in human ovarian cancer have not been well documented. here, we show that several mirnas are altered in human ovarian cancer, with the most significantly deregulated mirnas being mir-214, mir-199a*, mir-200a, mir-100, mir-125b, and let-7 cluster. further, we show the frequent deregulation of mir-214, mir-199a*, mir-200a, and mir-100 in ovarian cancers. significantly, mir-214 induces cell survival and cisplatin resistance through targeting the 3'-untranslated region (utr) of the pten, which leads to down-regulation of pten protein and activation of akt pathway. inhibition of akt using akt inhibitor, api-2/triciribine, or introduction of pten cdna lacking 3'-utr largely abrogates mir-214-induced cell survival. these findings indicate that deregulation of mirnas is a recurrent event in human ovarian cancer and that mir-214 induces cell survival and cisplatin resistance primarily through targeting the pten/akt pathway.",1
"background microrna-19a (mir-19a), an oncogenic microrna, has been recently reported to target cd22 in b cell lymphoma cell lines, but its role in inflammatory response is unclear. cd22 is a negative regulator for bcr signaling, and we hypothesize that mir-19a regulates b cell response by targeting cd22 in sepsis. material and methods in order to determine whether mir-19a-cd22 pathway was involved in sepsis, and what role it played in the regulatory mechanisms, we detected the levels of mir-19a in b cells obtained from patients with sepsis, and measured the levels of mir-19a and cd22 expression in b cells activated by lps in vitro. additionally, we investigated the correlation between mir-19a and cd22, as well as the influence of this pathway on bcr signaling, in transfected b cells. results we found that septic patients displayed up-regulated mir-19a in b cells. in vitro, mir-19a was increased in activated b cells, with cd22 expression initially enhanced but subsequently decreased. moreover, overexpression of mir-19a resulted in an amplified bcr signaling, while overexpression of cd22 attenuated the effect of mir-19a and increased its expression. conclusions our study demonstrated that mir-19a and cd22 comprised a feedback loop for b cell response in sepsis, providing a potential therapeutic target to recover the immune homeostasis.",1
"background micrornas alter multiple cell processes and thus influence tumour carcinogenesis and progression. mir-100 and mir-99a have been reported to be aberrantly expressed in acute leukaemia. in this study, we focused on their functions in acute lymphoblastic leukaemia (all) and the molecular networks in which they are involved. methods mir-100 and mir-99a expression levels were measured in acute leukaemia patients by qrt-pcr. kaplan-meier analysis and log-rank tests were used to calculate the survival rate. three human all cell lines were studied. apoptosis and proliferation were analysed using sirna transfection, western blot and flow cytometry. results in vivo, mir-100 and mir-99a were down-regulated in 111 all patients, especially in high-risk groups; their expression levels were correlated with the patient's 5-year survival. in vitro, the restoration of mir-100 and mir-99a in all cells suppressed cell proliferation and increased dexamethasone-induced cell apoptosis. ectopic expression of mir-100 and mir-99a targeted fk506-binding protein 51 (fkbp51) and, in turn, influenced glucocorticoid receptor (gr) activity. meanwhile, mir-100 and mir-99a overexpression inhibited the expression of igf1r and mtor and their downstream oncogene mcl1. conclusion mir-100 and mir-99a have critical roles in altering cellular processes by targeting both the fkbp51 and igf1r/mtor signalling pathways in vitro and might represent a potential novel strategy for all treatment.",1
"background in severe obesity, as well as in normal development, the growth of adipose tissue is the result of an increase in adipocyte size and numbers, which is underlain by the stimulation of adipogenic differentiation of precursor cells. a better knowledge of the pathways that regulate adipogenesis is therefore essential for an improved understanding of adipose tissue expansion. as micrornas (mirnas) have a critical role in many differentiation processes, our study aimed to identify the role of mirna-mediated gene silencing in the regulation of adipogenic differentiation. results we used deep sequencing to identify small rnas that are differentially expressed during adipogenesis of adipose tissue-derived stem cells. this approach revealed the un-annotated mir-642a-3p as a highly adipocyte-specific mirna. we then focused our study on the mir-30 family, which was also up-regulated during adipogenic differentiation and for which the role in adipogenesis had not yet been elucidated. inhibition of the mir-30 family blocked adipogenesis, whilst over-expression of mir-30a and mir-30d stimulated this process. we additionally showed that both mir-30a and mir-30d target the transcription factor runx2, and stimulate adipogenesis via the modulation of this major regulator of osteogenesis. conclusions overall, our data suggest that the mir-30 family plays a central role in adipocyte development. moreover, as adipose tissue-derived stem cells can differentiate into either adipocytes or osteoblasts, the down-regulation of the osteogenesis regulator runx2 represents a plausible mechanism by which mir-30 mirnas may contribute to adipogenic differentiation of adipose tissue-derived stem cells.",1
"micrornas (mirnas) negatively and post-transcriptionally regulate expression of multiple target genes to support anabolic pathways for bone formation. here, we show that mir-218 is induced during osteoblast differentiation and has potent osteogenic properties. mir-218 promotes commitment and differentiation of bone marrow stromal cells by activating a positive wnt signaling loop. in a feed forward mechanism, mir-218 stimulates the wnt pathway by down-regulating three wnt signaling inhibitors during the process of osteogenesis: sclerostin (sost), dickkopf2 (dkk2), and secreted frizzled-related protein2 (sfrp2). in turn, mir-218 expression is up-regulated in response to stimulated wnt signaling and functionally drives wnt-related transcription and osteoblast differentiation, thereby creating a positive feedback loop. furthermore, in metastatic breast cancer cells but not in normal mammary epithelial cells, mir-218 enhances wnt activity and abnormal expression of osteoblastic genes (osteomimicry) that contribute to homing and growth of cells metastatic to bone. thus, mir-218/wnt signaling circuit amplifies both the osteoblast phenotype and osteomimicry-related tumor activity.",1
"unlabelled the microrna mir-150, a critical regulator of hematopoiesis, is downregulated in mixed-lineage leukemia (mll). in this study, mir-150 acts as a potent leukemic tumor suppressor by blocking the oncogenic properties of leukemic cells. by using mll-af9-transformed cells, we demonstrate that ectopic expression of mir-150 inhibits blast colony formation, cell growth, and increases apoptosis in vitro. more importantly, ectopic expression of mir-150 in mll-af9-transformed cells completely blocked the development of myeloid leukemia in transplanted mice. furthermore, gene expression profiling revealed that mir-150 altered the expression levels of more than 30 ""stem cell signature"" genes and many others that are involved in critical cancer pathways. in addition to the known mir-150 target myb, we also identified cbl and egr2 as bona fide targets and shrna-mediated suppression of these genes recapitulated the pro-apoptotic effects observed in leukemic cells with mir-150 ectopic expression. in conclusion, we demonstrate that mir-150 is a potent leukemic tumor suppressor that regulates multiple oncogenes. implications these data establish new, key players for the development of therapeutic strategies to treat mll-af9-related leukemia.",1
"one of the largest families of small rnas in eukaryotes is the h/aca small nucleolar rnas (snornas), most of which guide rna pseudouridine formation. so far, an effective computational method specifically for identifying h/aca snorna gene sequences has not been established. we have developed snogps, a program for computationally screening genomic sequences for h/aca guide snornas. the program implements a deterministic screening algorithm combined with a probabilistic model to score gene candidates. we report here the results of testing snogps on the budding yeast saccharomyces cerevisiae. six candidate snornas were verified as novel rna transcripts, and five of these were verified as guides for pseudouridine formation at specific sites in ribosomal rna. we also predicted 14 new base-pairings between snornas and known pseudouridine sites in s.cerevisiae rrna, 12 of which were verified by gene disruption and loss of the cognate pseudouridine site. our findings include the first prediction and verification of snornas that guide pseudouridine modification at more than two sites. with this work, 41 of the 44 known pseudouridine modifications in s.cerevisiae rrna have been linked with a verified snorna, providing the most complete accounting of the h/aca snornas that guide pseudouridylation in any species.",1
"genome-wide association studies (gwas) have identified hundreds of genetic variants that are associated with lipid phenotypes. however, data supporting a functional role for these variants in the context of lipid metabolism are scarce. we investigated the association of the lipoprotein lipase (lpl) variant rs13702 with plasma lipids and explored its potential for functionality. the rs13702 minor allele had been predicted to disrupt a microrna (mir) recognition element (mre) seed site (mress) for the human microrna-410 (mir-410). furthermore, rs13702 is in linkage disequilibrium (ld) with several snps identified by gwas. we performed a meta-analysis across ten cohorts of participants that showed a statistically significant association of rs13702 with triacylglycerols (tag) (p = 3.18 × 10(-42)) and high-density lipoprotein cholesterol (hdl-c) (p = 1.35 × 10(-32)) with each copy of the minor allele associated with 0.060 mmol/l lower tag and 0.041 mmol/l higher hdl-c. our data showed that an lpl 3' utr luciferase reporter carrying the rs13702 major t allele was reduced by 40% in response to a mir-410 mimic. we also evaluated the interaction between intake of dietary fatty acids and rs13702. meta-analysis demonstrated a significant interaction between rs13702 and dietary polyunsaturated fatty acid (pufa) with respect to tag concentrations (p = 0.00153), with the magnitude of the inverse association between dietary pufa intake and tag concentration showing -0.007 mmol/l greater reduction. our results suggest that rs13702 induces the allele-specific regulation of lpl by mir-410 in humans. this work provides biological and potential clinical relevance for previously reported gwas variants associated with plasma lipid phenotypes.",1
"genomic recoding by a-->i rna editing plays an important role in diversifying the proteins involved in electrical excitability. here, we describe editing of an intronless potassium channel gene. a small region of human k(v)1.1 mrna sequence directs efficient modification of one adenosine by human adenosine deaminase acting on rna 2 (hadar2). mutational analysis shows that this region adopts a hairpin structure. electrophysiological characterization reveals that the editing event (i/v) profoundly affects channel inactivation conferred by accessory beta subunits. drosophila melanogaster shaker channels, mimicking this editing event through mutation, exhibit a similar effect. in addition, we demonstrate that mrnas for the paralogous d. melanogaster shab potassium channel are edited at the same position by fly adar-a clear example of convergent evolution driven by adenosine deamination. these results suggest an ancient and key regulatory role for this residue in k(v) channels.",1
"although extensive investigation has been made on mir-29a in relation to malignancies, only a little information has been provided about the angiogenic property of this mirna so far. herein, we sought to investigate the role of mir-29a in regulating cell cycle and angiogenic phenotype of endothelial cells. the results showed that mir-29a is highly expressed and upregulated by hypoxia-mimicking reagents in human umbilical vein endothelial cells (huvec). consistent with this preliminary finding, introduction of exogenous agomir-29a, or antagomir-29a altered cell cycle progression and promoted, or repressed the proliferation and tube formation of huvec, respectively. furthermore, by using luciferase reporter assay, the expression of hbp1, a suppressor transcription factor was directly regulated by mir-29a through 3'-utr. increased or decreased hbp1 protein level was associated with the inhibition or overexpression of mir-29a, respectively. we conclude that mir-29a has a significant role in regulating cell cycle, proliferation and angiogenic properties of huvec, and this function is likely mediated through hbp1 protein at the post-transcriptional level. as a novel molecular target, mir-29a may have a potential value for the treatment of angiogenesis-associated diseases such as cardiovascular diseases and cancers.",1
"micrornas act as negative regulators of gene expression, and the altered expression of micrornas by epigenetic mechanisms is strongly implicated in carcinogenesis. here we report that the microrna-10b gene (mir-10b) was silenced in gastric cancer cells by promoter methylation. in this study, using a methylation array and bisulfate pyrosequencing analysis, we found that mir-10b promoter cpgs were heavily methylated in gastric cancers. clinicopathologic data showed that mir-10b methylation increased with patient age and occurred significantly more frequently in intestinal-type (28/44, 64%) than in diffuse-type (22/56, 39%) gastric cancers (p = 0.016). in addition, mir-10b methylation was also associated with an increase in expression of the oncogene that encodes microtubule-associated protein, rp/eb family, member 1 (mapre1; p = 0.004), which was identified as a potential mir-10b target. after 5-aza-2'-deoxycytidine treatment of gastric cancer cells, mir-10b methylation was significantly decreased, and expression of mir-10b and hoxd4, which is 1 kb downstream of mir-10b, was greatly restored. moreover, decreased mapre1 expression coincided with increased mir-10b expression, suggesting that mir-10b targets mapre1 transcription. we also found that transfection with precursor mir-10b into gastric cancer cells dramatically decreased mapre1 mrna and protein, resulting in a significant decrease in colony formation and cell growth rates. thus, we show a tumor-suppressive role for mir-10b in gastric carcinogenesis. mir-10b methylation may be a useful molecular biomarker for assessing the risk of gastric cancer development, and modulation of mir-10b may represent a therapeutic approach for treating gastric cancer.",1
"the urnadb offers aligned, annotated and phylogenetically ordered sequences of several u rnas. new to this release are rnas from u7 (14 sequences), u8 (two sequences), u11 (three sequences), u12 (two sequences), u14 (11 sequences), u18, u48 and u49. a total of 34 new sequences were aligned with the previously compiled snrnas u1, u2, u3, u4, u5 and u6.",1
"micrornas play important roles in tumor metastasis. recently, we reported that the level of mir-520b is inversely related to the metastatic potential of breast cancer cells. in this study, we investigated the role of mir-520b in breast cancer cell migration. we found that mir-520b suppressed the migration of breast cancer cells with high metastatic potential, including mda-mb-231 and lm-mcf-7 cells, although the inhibition of mir-520b enhanced the migration of low metastatic potential mcf-7 cells. we further discovered that mir-520b directly targets the 3'-untranslated region (3'utr) of either hepatitis b x-interacting protein (hbxip) or interleukin-8 (il-8), which has been reported to contribute to cell migration. surprisingly, tissue array assays showed that 75% (38:49) and 94% (36:38) of breast cancer tissues and metastatic lymph tissues, respectively, were positive for hbxip expression. moreover, overexpression of hbxip was able to promote the migration of mcf-7 cells. interestingly, hbxip was able to regulate il-8 transcription by nf-κb, suggesting that the two target genes of mir-520b are functionally connected. in addition, we found that mir-520b could indirectly regulate il-8 transcription by targeting hbxip. thus, we conclude that mir-520b is involved in regulating breast cancer cell migration by targeting hbxip and il-8 via a network in which hbxip promotes migration by stimulating nf-κb-mediated il-8 expression. these studies point to hbxip as a potential therapeutic target for breast cancer.",1
"microtubule-associated protein tau (mapt) is a gene responsible for encoding tau protein, which is tightly implicated in keeping the function of microtubules and axonal transport. hyperphosphorylated tau protein participates in the formation of neurofibrillary tangles (nfts), which characterize many neurodegenerative disorders termed tauopathies. genome-wide association studies (gwas) have demonstrated numerous single nucleotide polymorphisms (snps) located in mapt associated with various neurodegenerative diseases. thus, it has been presumed that mapt plays a crucial role in pathogenesis of neurodegeneration via affecting the structure and function of tau. here, we review the advanced studies to summarize the biochemical properties of mapt and its encoded protein, as well as the genetics and epigenetics of mapt in neurodegeneration. finally, given the potential mechanisms of mapt to neurodegeneration pathogenesis, targeting mapt and tau might present significant treatments of mapt mutation-related neurodegeneration. affirmatively, the identification of mapt is extremely beneficial for improving our understanding of the pathogenesis of various neurodegenerative diseases and developing the mechanism-based therapies.",1
"aim to investigate the mechanism by which mir-204-3p inhibits the growth of hepatocellular carcinoma (hcc) tumor endothelial cells (tecs). methods flow cytometry was used to identify hcctecs and analyze their purity. differentially expressed mirnas in hcc tecs as compared to normal hepatic sinusoidal endothelial cells (hsecs) were examined using the hmioa v4 human mirna onearray microarray. mir-204-3p showed the most significant decrease in expression and was further studied. over-expression of mir-204-3p was achieved using lentiviral transduction into tecs of hcc. the biological changes in hcc tecs before and after transduction were detected using mtt and apoptosis assays. the association between mir-204-3p and fibronectin 1 (fn1) was determined using the dual luciferase activity assay. changes in fn1 protein expression before and after transduction were detected using western blot analysis. results microarray results showed that compared to normal hsecs, 15 mirnas were differentially expressed in hcc tecs, including 6 mirnas with increased expression and 9 mirnas with decreased expression. among them, mir-204-3p showed the most significant decrease in expression (log2 = -1.233477, p = 0.000307). over-expression of mir-204-3p in hcc tecs via lentiviral transduction significantly inhibited the proliferation of hcc tecs and promoted apoptosis. results from the dual luciferase activity experiment showed that the luciferase intensity in the wild type fn1 group was significantly inhibited (p conclusion mir-204-3p acts on its potential target gene, fn1, and inhibits its expression, thus blocking the adhesion function of fn1 in promoting the growth of tecs.",1
"background micrornas (mirnas) are small non-coding rnas that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. characterisation of mirnas in adult mammalian brains by deep sequencing has been reported previously. however, to date, no small rna profiling of the developing brain has been undertaken using this method. we have performed deep sequencing and small rna analysis of a developing (e15.5) mouse brain. results we identified the expression of 294 known mirnas in the e15.5 developing mouse brain, which were mostly represented by let-7 family and other brain-specific mirnas such as mir-9 and mir-124. we also discovered 4 putative 22-23 nt mirnas: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76 nt predicted pre-mirna. we validated the 4 putative mirnas and further characterised one of them, mm_br_e15_1181, throughout embryogenesis. mm_br_e15_1181 biogenesis was dicer1-dependent and was expressed in e3.5 blastocysts and e7 whole embryos. embryo-wide expression patterns were observed at e9.5 and e11.5 followed by a near complete loss of expression by e13.5, with expression restricted to a specialised layer of cells within the developing and early postnatal brain. mm_br_e15_1181 was upregulated during neurodifferentiation of p19 teratocarcinoma cells. this novel mirna has been identified as mir-3099. conclusions we have generated and analysed the first deep sequencing dataset of small rna sequences of the developing mouse brain. the analysis revealed a novel mirna, mir-3099, with potential regulatory effects on early embryogenesis, and involvement in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development.",1
"background micrornas are noncoding regulatory rnas strongly implicated in carcinogenesis, cell survival, and chemosensitivity. here, micrornas associated with chemoresistance in ovarian carcinoma, the most lethal of gynaecological malignancies, were identified and their functional effects in chemoresistant ovarian cancer cells were assessed. methods microrna expression in paclitaxel (ptx)-resistant skpac sublines was compared with that of the ptx-sensitive, parental skov3 ovarian cancer cell line using microarray and qrt-pcr. the function of differentially expressed micrornas in chemoresistant ovarian cancer was further evaluated by apoptosis, cell proliferation, and migration assays. results upregulation of mir-106a and downregulation of mir-591 were associated with ptx resistance in ovarian cancer cells and human tumour samples. transfection with anti-mir-106a or pre-mir-591 resensitized ptx-resistant skpac cells to ptx by enhancing apoptosis (23 and 42% increase), and inhibited their cell migration (43 and 56% decrease) and proliferation (64 and 65% decrease). furthermore, zeb1 was identified as a novel target gene of mir-591, and bcl10 and caspase-7 were target genes of mir-106a, as identified by immunoblotting and luciferase assay. conclusion mir-106a and mir-591 have important roles in conferring ptx resistance to ovarian cancer cells. modulation of these micrornas resensitizes ptx-resistant cancer cells by targeting bcl10, caspase-7, and zeb1.",1
"small nucleolar rnas (snornas) are non-coding rnas that form ribonucleoproteins to guide covalent modifications of ribosomal and small nuclear rnas in the nucleus. recent studies have also uncovered additional non-canonical roles for snornas. however, the physiological contributions of these small rnas are largely unknown. here, we selectively deleted four snornas encoded within the introns of the ribosomal protein l13a (rpl13a) locus in a mouse model. loss of rpl13a snornas altered mitochondrial metabolism and lowered reactive oxygen species tone, leading to increased glucose-stimulated insulin secretion from pancreatic islets and enhanced systemic glucose tolerance. islets from mice lacking rpl13a snornas demonstrated blunted oxidative stress responses. furthermore, these mice were protected against diabetogenic stimuli that cause oxidative stress damage to islets. our study illuminates a previously unrecognized role for snornas in metabolic regulation.",1
"alzheimer's disease (ad) is the most common age-related form of dementia, associated with deposition of intracellular neuronal tangles consisting primarily of hyperphosphorylated microtubule-associated protein tau (p-tau) and extracellular plaques primarily comprising amyloid- β (aβ) peptide. the p-tau tangle unit is a posttranslational modification of normal tau protein. aβ is a neurotoxic peptide excised from the amyloid-β precursor protein (app) by β-site app-cleaving enzyme 1 (bace1) and the γ-secretase complex. micrornas (mirnas) are short, single-stranded rnas that modulate protein expression as part of the rna-induced silencing complex (risc). we identified mir-298 as a repressor of app, bace1, and the two primary forms of aβ (aβ40 and aβ42) in a primary human cell culture model. further, we discovered a novel effect of mir-298 on posttranslational levels of two specific tau moieties. notably, mir-298 significantly reduced levels of ~55 and 50 kda forms of the tau protein without significant alterations of total tau or other forms. in vivo overexpression of human mir-298 resulted in nonsignificant reduction of app, bace1, and tau in mice. moreover, we identified two mir-298 snps associated with higher cerebrospinal fluid (csf) p-tau and lower csf aβ42 levels in a cohort of human ad patients. finally, levels of mir-298 varied in postmortem human temporal lobe between ad patients and age-matched non-ad controls. our results suggest that mir-298 may be a suitable target for ad therapy.",1
"micrornas (mirnas) regulate myriad biological processes; however, their role in cell fate choice is relatively unexplored. pluripotent nt2/d1 embryonal carcinoma cells differentiate into an epithelial/smooth muscle phenotype when treated with bone morphogenetic protein-2 (bmp-2). to identify mirnas involved in epithelial cell development, we performed mirna profiling of nt2/d1 cells treated with bmp-2 at 6, 12, and 24 h, and on days 6 and 10. integration of the mirna profiling data with previously obtained gene expression profiling (gep) data of nt2/d1 cells treated with bmp-2 at the same time points identified mir-18b and mir-518b as the top two mirnas with the highest number of up-regulated predicted targets with known functions in epithelial lineage development. silencing of mir-18b and mir-518b in nt2/d1 cells revealed several up-regulated tfs with functions in epithelial lineage development; among these, target prediction programs identified foxn1 as the only direct target of both mirnas. foxn1 has previously been shown to play an important role in keratinocyte differentiation and epithelial cell proliferation. nt2/d1 and h9 human embryonic stem cells with silenced mir-18b and mir-518b showed up-regulation of foxn1 and the epithelial markers cdh1, epcam, krt19, and krt7. a 3'utr luciferase assay confirmed foxn1 to be a target of the two mirnas, and up-regulation of foxn1 in nt2/d1 cells led to the expression of epithelial markers. overexpression of the two mirnas in bmp-2-treated nt2/d1 cells led to down-regulation of foxn1 and epithelial lineage markers. these results show that mir-18b and mir-518b are upstream controllers of foxn1-directed epithelial lineage development.",1
"background recent work has identified that many long mrna-like noncoding rnas (lncrnas) are expressed in the developing nervous system. despite their abundance, the function of these ncrnas has remained largely unexplored. we have investigated the highly abundant lncrna rncr2 in regulation of mouse retinal cell differentiation. results we find that the rncr2 is selectively expressed in a subset of both mitotic progenitors and postmitotic retinal precursor cells. shrna-mediated knockdown of rncr2 results in an increase of both amacrine cells and müller glia, indicating a role for this lncrna in regulating retinal cell fate specification. we further report that rncr2 rna, which is normally nuclear-retained, can be exported from the nucleus when fused to an ires-gfp sequence. overexpression of rncr2-ires-gfp phenocopies the effects of shrna-mediated knockdown of rncr2, implying that forced mislocalization of rncr2 induces a dominant-negative phenotype. finally, we use the ires-gfp fusion approach to identify specific domains of rncr2 that are required for repressing both amacrine and müller glial differentiation. conclusion these data demonstrate that the lncrna rncr2 plays a critical role in regulating mammalian retinal cell fate specification. furthermore, we present a novel approach for generating dominant-negative constructs of lncrnas, which may be generally useful in the functional analysis of this class of molecules.",1
"micrornas (mirnas) are short non-coding rnas that regulate gene expression in plants and animals. although their biological importance has become clear, how they recognize and regulate target genes remains less well understood. here, we systematically evaluate the minimal requirements for functional mirna-target duplexes in vivo and distinguish classes of target sites with different functional properties. target sites can be grouped into two broad categories. 5' dominant sites have sufficient complementarity to the mirna 5' end to function with little or no support from pairing to the mirna 3' end. indeed, sites with 3' pairing below the random noise level are functional given a strong 5' end. in contrast, 3' compensatory sites have insufficient 5' pairing and require strong 3' pairing for function. we present examples and genome-wide statistical support to show that both classes of sites are used in biologically relevant genes. we provide evidence that an average mirna has approximately 100 target sites, indicating that mirnas regulate a large fraction of protein-coding genes and that mirna 3' ends are key determinants of target specificity within mirna families.",1
"microrna-200c (mir-200c) through repression of specific target genes has been associated with cellular transition, tumorigenesis, and tissue fibrosis. we explored the expression and functional aspects of mir-200c in genesis of leiomyomas (lyo), benign uterine tumors with fibrotic characteristic. using lyo and matched myometrium (myo; n=76) from untreated and from patients exposed to hormonal therapies (gnrh agonist (gnrha), depo-provera, and oral contraceptives), we found that mir-200c was expressed at significantly lower levels (p<0.05) in lyo as compared with myo. these levels were lower in lyo from african americans as compared with caucasians, patients experiencing abnormal uterine bleeding and those exposed to gnrha therapy. gain-of-function of mir-200c in isolated leiomyoma smooth muscle cells (lsmcs), myometrial smooth muscle cells (msmcs), and leiomyosarcoma cell line (sklm-s1) repressed zeb1/zeb2 mrnas and proteins, with concurrent increase in e-cadherin (cdh1) and reduction in vimentin expression, phenotypic alteration, and inhibition of msmc and lsmc proliferations. we further validated timp2, fbln5, and vegfa as direct targets of mir-200c through interaction with their respective 3' utrs, and other genes as determined by microarray analysis. at tissue levels, lyo expressed lower levels of timp2 and fbln5 mrnas but increased protein expressions, which to some extent altered due to hormonal exposure. given the regulatory functions of zebs, vegfa, fbln5, and timp2 on cellular activities that promote cellular transition, angiogenesis, and matrix remodeling, we concluded that altered expression of mir-200c may have a significant impact on the outcome of lyo growth, maintenance of their mesenchymal and fibrotic characteristics, and possibly their associated symptoms.",1
"mir-200b is a tumor suppressor in multiple tumors including gastric cancer, breast cancer, ovarian cancer and glioma. in this study, we detected the expression of mir-200b and analyzed its correlation with clinicopathological parameters in glioma tissues. mir-200b was downregulated in glioma tissues. and its downexpression was correlated with poor prognosis in gliomas. members of rab family, rab21, rab23, rab18 and rab3b were predicted to be novel targets of mir-200b. the direct suppression of rab21, rab23, rab18 and rab3b expressions by mir-200b was revealed by luciferase reporter assay, quantitative rt-pcr analysis and western blot. furthermore, the overall survival of patients with different expression of rabs was analyzed. the expression of rab21, rab23, rab18 and rab3b was related to the prognosis and histopathology of glioma. the patients who had the upregulation of all the four rabs had the worst outcome; those who had the downregulation of all rabs had the best outcome (p<0.001). mir-200b was a potential biomarker for glioma prognosis.",1
"the lncrna tumor suppressor candidate 8 (tusc8) plays a critical role in the development of several cancers. however, the biological functions and underlying molecular mechanisms of tusc8 with respect to breast cancer remain largely unclear. here, we found that tusc8 was significantly down-regulated in breast cancer tissues and its high expression predicted better prognosis of breast cancer patients. functionally, knock-down of tusc8 drastically promoted the proliferation, migration and invasion of breast cancer cells in vitro and facilitated tumorigenicity and metastasis in vivo . mechanistically, the results of luciferase reporter, rip and rna pull-down assays proved that tusc8 functioned as molecular sponge for mir-190b-5p. furthermore, we showed that tusc8 served as a competing endogenous rna (cerna) of myosin regulatory light chain interacting protein (mylip) through competitively binding with mir-190b-5p and suppressed breast cancer metastasis through regulating the expression of epithelial-mesenchymal transition (emt) related markers. clinically, the receiver operating characteristic curve (roc) analyses revealed that the combination usage of tusc8 and mylip might become novel promising diagnostic biomarkers for breast cancer. taken together, these results suggested that tusc8 inhibited breast cancer growth and metastasis via mir-190b-5p/mylip axis, providing us new insights into developing potential therapeutic targets for breast cancer patients.",1
"unlabelled hepatitis c virus (hcv)-mediated liver diseases are one of the major health issues in the united states and worldwide. hcv infection has been reported to modulate micrornas (mirnas) that control various cell surface receptors and gene-regulatory complexes involved in hepatic inflammation and liver diseases. we report here that specific downregulation of mirna-107 and mirna-449a following hcv infection in patients with hcv-mediated liver diseases modulates expression of ccl2, an inflammatory chemokine upregulated in patients with chronic liver diseases, by targeting components of the interleukin-6 receptor (il-6r) complex. computational analysis for dna-bound transcription factors in the ccl2 promoter identified adjacent binding sites for ccaat/cebpα, spleen focus-forming virus, proviral integration oncogene (spi1/pu.1), and stat3. we demonstrate that cebpα, pu.1, and stat3 interacted with each other physically to cooperatively bind to the promoter and activate ccl2 expression. analysis of il-6r and jak1 expression in hcv patients by quantitative pcr showed significant upregulation when there was impaired mirna-107 and mirna-449a expression, along with upregulation of pu.1 and stat3, but not cebpα. mirna-449a and mirna-107 target expression of il-6r and jak1, respectively, in vitro and also inhibit il-6 signaling and impair stat3 activation in human hepatocytes. taken together, our results demonstrate a novel gene-regulatory mechanism in which hcv-induced changes in mirnas (mirna-449a and mirna-107) regulate ccl2 expression by activation of the il-6-mediated signaling cascade, which we propose will result in hcv-mediated induction of inflammatory responses and fibrosis. importance hepatitis c virus (hcv)-induced hepatitis is a major health concern worldwide. hcv infection results in modulation of noncoding micrornas affecting major cellular pathways, including inflammatory responses. in this study, we have identified a microrna-regulated pathway for the chemokine ccl2 in hcv-induced hepatitis. understanding microrna-mediated transcriptional-regulatory pathways will result in development of noninvasive biomarkers for better disease prediction and development of effective therapeutics.",1
"the identification of ultraconserved noncoding sequences in vertebrates has been associated with developmental regulators and dna-binding proteins. one of the first of these was identified in the intergenic region between the dlx-5 and dlx-6 genes, members of the dlx/dll homeodomain-containing protein family. in previous experiments, we showed that sonic hedgehog treatment of forebrain neural explants results in the activation of dlx-2 and the novel noncoding rna (ncrna), evf-1. in this report, we show that the dlx-5/6 ultraconserved region is transcribed to generate an alternatively spliced form of evf-1, the ncrna evf-2. evf-2 specifically cooperates with dlx-2 to increase the transcriptional activity of the dlx-5/6 enhancer in a target and homeodomain-specific manner. a stable complex containing the evf-2 ncrna and the dlx-2 protein forms in vivo, suggesting that the evf-2 ncrna activates transcriptional activity by directly influencing dlx-2 activity. these experiments identify a novel mechanism whereby transcription is controlled by the cooperative actions of an ncrna and a homeodomain protein. the possibility that a subset of vertebrate ultraconserved regions may function at both the dna and rna level to control key developmental regulators may explain why ultraconserved sequences exhibit 90% or more conservation even after 450 million years of vertebrate evolution.",1
"background therapeutic plasma exchange (pe) or plasmapheresis is an extracorporeal procedure employed to treat immunological disorders. exosomes, nanosized vesicles of endosomal origin, mediate intercellular communication by transferring cargo proteins and nucleic acids and regulate many pathophysiological processes. exosomal mirnas are potential biomarkers due to their stability and dysregulation in diseases including complex regional pain syndrome (crps), a chronic pain disorder with persistent inflammation. a previous study showed that a subset of crps patients responded to pe. methods as a proof-of-concept, we investigated the pe-induced exosomal mirna changes in six crps patients. plasma cytokine levels were measured by hplc and correlated with mirna expression. luciferase assay following co-transfection of hek293 cells with target 3'utr constructs and mirna mimics was used to evaluate mirna mediated gene regulation of target mrna. transient transfection of thp-1 cells with mirna mimics followed by estimation of target gene and protein expression was used to validate the findings. results comparison of mirnas in exosomes from the serum of three responders and three poor-responders showed that 17 mirnas differed significantly before and after therapy. of these, poor responders had lower exosomal hsa-mir-338-5p. we show that mir-338-5p can bind to the interleukin 6 (il-6) 3' untranslated region and can regulate il-6 mrna and protein levels in vitro. pe resulted in a significant reduction of il-6 in crps patients. conclusions we propose that lower pretreatment levels of mir-338-5p in poor responders are linked to il-6 levels and inflammation in crps. our data suggests the feasibility of exploring exosomal mirnas as a strategy in patient stratification for maximizing therapeutic outcome of pe.",1
"micrornas (mirnas) guide posttranscriptional repression of mrnas. hundreds of mirnas have been identified but the target identification of mammalian mrnas is still a difficult task due to a poor understanding of the interaction between mirnas and the mirna recognizing element (mre). in recent research, the importance of the 5' end of the mirna:mre duplex has been emphasized and the effect of the tail region addressed, but the role of the central loop has largely remained unexplored. here we examined the effect of the loop region in mirna:mre duplexes and found that the location of the central loop is one of the important factors affecting the efficiency of gene regulation mediated by mirnas. it was further determined that the addition of a loop score combining both location and size as a new criterion for predicting mres and their cognate mirnas significantly decreased the false positive rates and increased the specificity of mre prediction.",1
"ribosomal protein s4 represses synthesis of the four ribosomal proteins (including itself) in the escherichia coli alpha operon by binding to a nested pseudoknot structure that spans the ribosome binding site. a model for the repression mechanism previously proposed two unusual features: (i) the mrna switches between conformations that are ""active"" or ""inactive"" in translation, with s4 as an allosteric effector of the inactive form, and (ii) s4 holds the 30 s subunit in an unproductive complex on the mrna (""entrapment""), in contrast to direct competition between repressor and ribosome binding (""displacement""). these two key points have been experimentally tested. first, it is found that the mrna pseudoknot exists in an equilibrium between two conformers with different electrophoretic mobilities. s4 selectively binds to one form of the rna, as predicted for an allosteric effector; binding of ribosomal 30 s subunits is nearly equal in the two forms. second, we have used s4 labeled at a unique cysteine with either of two fluorophores to characterize its interactions with mrna and 30 s subunits. equilibrium experiments detect the formation of a specific ternary complex of s4, mrna pseudoknot, and 30 s subunits. the existence of this ternary complex is unambiguous evidence for translational repression of the alpha operon by an entrapment mechanism.",1
"recent microrna expression profiling studies have documented an up-regulation of mir-146a in several angiogenesis models. however, the underlying molecular mechanism of mir-146a in the angiogenic activity of endothelial cells has not been clearly elucidated. the present study was aimed to evaluate whether mir-146a promotes angiogenesis in huvecs by increasing fgfbp1 expression via directly targeting creb3l1. mir-146a was over expressed in huvecs via lentiviral-mir-146a. expression profiling analysis found mir-146a over expression resulted in up-regulation of angiogenesis and cytokine activity associated genes including fgf2. further a combination of bioinformatics and experimental analyses demonstrated the creb3l1 as a bona fide functional target of mir-146a during angiogenesis. moreover, creb3l1 inhibited luciferase expression from fgfbp1 promoter containing only cre elements. furthermore, creb3l1 inhibited fgfbp1 expression by binding to two cre-like sites located at approximately -1780-1777 and -868-865 bp relative to the fgfbp1 transcription start site. additionally, ectopic expression of creb3l1 decreased mir-146a-induced fgf2 secretion. these findings indicate that the mir-146a-creb3l1-fgfbp1 signaling axis plays an important role in the regulation of angiogenesis in huvecs and provides a potential therapeutic target for anti-angiogenic therapeutics.",1
"micrornas (mirnas) have emerged as post-transcriptional regulators that are critically involved in the pathogenesis of a number of human cancers. recently, cyclin-dependent kinase 6 (cdk6) is found to be up-regulated in several types of human tumors and has been implicated in cancer initiation and progression. we have identified mir-107 as a potential regulator of cdk6 expression. a bioinformatics search revealed a putative target site for mir-107 within the cdk6 3' untranslated region. expression of mir-107 in gastric cancer cell lines was found inversely correlated with cdk6 expression. mir-107 could significantly suppress cdk6 3' utr luciferase reporter activity, and this effect was not detectable when the putative 3' utr target site was mutated. consistent with the results of the reporter assay, ectopic expression of mir-107 reduced both mrna and protein expression levels of cdk6, inhibited proliferation, induced g1 cell cycle arrest, and blocked invasion of the gastric cancer cells. our results suggest that mir-107 may have a tumor suppressor function by directly targeting cdk6 to inhibit the proliferation and invasion activities of gastric cancer cells.",1
"microrna-124a (mir-124a) is the most abundant microrna expressed in the vertebrate cns. despite past investigations into the role of mir-124a, inconsistent results have left the in vivo function of mir-124a unclear. we examined the in vivo function of mir-124a by targeted disruption of rncr3 (retinal non-coding rna 3), the dominant source of mir-124a. rncr3(-/-) mice exhibited abnormalities in the cns, including small brain size, axonal mis-sprouting of dentate gyrus granule cells and retinal cone cell death. we found that lhx2 is an in vivo target mrna of mir-124a. we also observed that lhx2 downregulation by mir-124a is required for the prevention of apoptosis in the developing retina and proper axonal development of hippocampal neurons. these results suggest that mir-124a is essential for the maturation and survival of dentate gyrus neurons and retinal cones, as it represses lhx2 translation.",1
"to study the effects of microrna-98 (mir-98) on human bone mesenchymal stromal cells (hbmscs). the patients undergoing hip arthroplasty were selected by inclusion/exclusion criteria for this study. the extracted hbmscs were detected of osteogenic differentiation by alizarin red s staining, and of cell phenotype by flow cytometry. bioinformatics, dual luciferase report, western blotting, rt-pcr and immunoblotting were used in our study. the hbmscs were divided into mir-98 mimics, mir-98 negative control (nc), mir-98 inhibitors, mock and mir-98 inhibitors + sibmp2 groups. human bone mesenchymal stromal cells were extracted and purified in vitro and had specific cytological morphology, surface markers and abilities of self-renewal and differentiation. compared with the nc group and mock group, the mir-98 mimics group showed increased mir-98 level while the mir-98 inhibitors group decreased mir-98 level (both p < 0.01). dual luciferase reporter showed bmp2 was the target gene of mir-98. the levels of mrna and protein expression of bmp2, protein expression of runx2, alkaline phosphatase activity and osteocalcin content significantly decreased in the mir-98 mimics group while increased in the mir-98 inhibitors group and showed no changes in the nc group and mock group (all p < 0.05). the mir-98 mimics group showed obviously declined stained red particles and the mir-98 inhibitors group showed opposite result. after lowering the expression of mir-98, osteogenic differentiation ability of hbmscs rose, which was weakened by the transfection with sibmp2. mir-98 may regulate osteogenic differentiation of hbmscs by targeting bmp2.",1
"background mir-145 is down-regulated in various human cancers. we previously demonstrated that some actin-binding proteins were targeted by several micrornas (mirnas), including mir-145, in bladder and prostate cancer (cap). the aim of this study is to determine a novel oncogenic gene targeted by mir-145 by focusing on actin-binding proteins in cap. methods we focused on the swap switching b-cell complex 70 kda subunit (swap70), which is an f-actin binding protein involved in activating b-cell transformation. a luciferase reporter assay was used to identify the actual binding sites between mir-145 and swap70 mrna. cell viability was evaluated by cell proliferation, wound healing, and matrigel invasion assays in si-swap70 transfectants. a total of 75 clinical prostate specimens were subjected to immunohistochemistry of swap70. results molecular target searches of this mirna and the luciferase reporter assay showed that swap70 was directly regulated by mir-145. silencing of swap70 studies demonstrated significant inhibitions of cell migration and invasion in cap cell lines. the swap70 positive-staining was significantly higher in percentage in the cap than in benign prostate hyperplasia tissue. conclusions down-regulation of mir-145 was a frequent event in cap, and it may have a tumor suppressive function. swap70 may be a target of mir-145, and it might have a potential oncogenic function. the novel molecular networks though which mir-145 acts, may provide new insights into the underlying molecular mechanisms of cap.",1
"propofol (2,6-diisopropylphenol) is one of the most commonly used intravenous anesthetics. anesthetics can regulate the inflammatory process; however, the mechanism remains to be fully elucidated. the present study aimed to investigate whether and how propofol affects the inflammatory reaction in human umbilical vein endothelial cells (huvecs). the expression levels of toll‑like receptor 4 (tlr4) and cluster of differentiation 14 (cd14) were determined in huvecs treated with propofol and lipopolysaccharide (lps) using western blot and reverse transcription‑quantitative polymerase chain reaction analyses. in addition, whether propofol regulated the expression of tlr4 though microrna (mir)‑21 was examined. the results showed that lps promoted the expression levels of tlr4, cd14 and tumor necrosis factor α (tnfα), and suppressed the expression of mir‑21 in huvecs. propofol suppressed the expression levels of tlr4, cd14 and tnfα, and upregulated the expression of mir‑21 in a concentration‑dependent manner. mir‑21 downregulated the expression of tlr4 at the mrna and protein levels, whereas the mir‑21 mimic reversed the effect of lps on the expression of tlr4. in addition, the mir‑21 inhibitor inhibited the downregulatory effect of propofol on the expression of tlr4. targetscan analysis showed that tlr4 was included in the list of targets of mir‑21. fluorescent reporter assays showed that the mir‑21 mimic and propofol treatment reduced the fluorescence intensity in cells transfected with a reporter vector containing the wild‑type tlr4 3'‑untranslated region. taken together, the results of the present study demonstrated that propofol regulated the expression of tlr4 in huvecs through mir‑21.",1
"microrna-mediated gene regulation is important in many physiological processes. here we explore the roles of a microrna, mir-941, in human evolution. we find that mir-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of africa. emergence of mir-941 was accompanied by accelerated loss of mir-941-binding sites, presumably to escape regulation. we further show that mir-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. human-specific effects of mir-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. taken together, these results implicate mir-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage.",1
"microrna 183 (mir-183) has been reported to inhibit tumor invasiveness and is believed to be involved in the development and function of ciliated neurosensory organs. we have recently found that expression of mir-183 increased after the induction of cellular senescence by exposure to h(2)o(2). to gain insight into the biological roles of mir-183 we investigated two potential novel targets: integrin beta1 (itgb1) and kinesin 2alpha (kif2a). mir-183 significantly decreased the expression of itgb1 and kif2a measured by western blot. targeting of the 3'-untranslated region (3'-utr) of itgb1 and kif2a by mir-183 was confirmed by luciferase assay. transfection with mir-183 led to a significant decrease in cell invasion and migration capacities of hela cells that could be rescued by expression of itgb1 lacking the 3'-utr. although mir-183 had no effects on cell adhesion in hela cells, it significantly decreased adhesion to laminin, gelatin, and collagen type i in normal human diploid fibroblasts and human trabecular meshwork cells. these effects were also rescued by expression of itgb1 lacking the 3'-utr. targeting of kif2a by mir-183 resulted in some increase in the formation of cells with monopolar spindles in hela cells but not in human diploid fibroblast or human trabecular meshwork cells. the regulation of itgb1 expression by mir-183 provides a new mechanism for the anti-metastatic role of mir-183 and suggests that this mirna could influence the development and function in neurosensory organs, and contribute to functional alterations associated with cellular senescence in human diploid fibroblasts and human trabecular meshwork cells.",1
"the hammerhead ribozyme is a small catalytic rna motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. the x-ray crystallographic structure of a hammerhead rna-dna ribozyme-inhibitor complex at 2.6 a resolution reveals that the base-paired stems are a-form helices and that the core has two structural domains. the first domain is formed by the sequence 5'-cuga following stem i and is a sharp turn identical to the uridine turn of transfer rna, whereas the second is a non-watson-crick three-base-pair duplex with a divalent-ion binding site. the phosphodiester backbone of the dna inhibitor strand is splayed out at the phosphate 5' to the cleavage site. the structure indicates that the ribozyme may destabilize a substrate strand in order to facilitate twisting of the substrate to allow cleavage of the scissile bond.",1
"glioblastoma multiforme (gbm) is the most malignant and frequent brain tumor, with an aggressive growth pattern and poor prognosis despite best treatment modalities. although chemotherapy with temozolomide (tmz) may restrain tumor growth for some months, tmz resistance is also common and accounts for many treatment failures. research into microrna's role in gbm has shown that micrornas play a key regulatory role in the gbm, making it a potential therapeutic target. in this study, we demonstrated that the lower expression of mir-181a/b/c/d subunits contributes to astrocytoma tumorigenesis, and their overexpression could inhibit the invasive proliferation of glioblastoma cells by targeting rap1b-mediated cytoskeleton remodeling and related molecular (cdc42, rhoa and n-cadherin) changes, suggesting that mir-181 was a critical regulator and might be an important target for glioblastoma treatment. tmz as a standard chemotherapeutic agent for gbm inhibited the rap1b expression and actin cytoskeleton remodeling to exert its cell killing by upregulating mir-181a/b/c/d subunits; conversely, each mir-181a/b/c/d subunit enhanced the chemosensitivity of tmz in glioblastoma cells.",1
"although the role of app and psen genes in genetic alzheimer's disease (ad) cases is well established, fairly little is known about the molecular mechanisms affecting abeta generation in sporadic ad. deficiency in abeta clearance is certainly a possibility, but increased expression of proteins like app or bace1/beta-secretase may also be associated with the disease. we therefore investigated changes in microrna (mirna) expression profiles of sporadic ad patients and found that several mirnas potentially involved in the regulation of app and bace1 expression appeared to be decreased in diseased brain. we show here that mir-29a, -29b-1, and -9 can regulate bace1 expression in vitro. the mir-29a/b-1 cluster was significantly (and ad-dementia-specific) decreased in ad patients displaying abnormally high bace1 protein. similar correlations between expression of this cluster and bace1 were found during brain development and in primary neuronal cultures. finally, we provide evidence for a potential causal relationship between mir-29a/b-1 expression and abeta generation in a cell culture model. we propose that loss of specific mirnas can contribute to increased bace1 and abeta levels in sporadic ad.",1
"purpose this study aims to profile the expressions of 156 micrornas (mirna) in hepatocellular carcinoma (hcc) and to characterize the functions of mir-222, the most significantly upregulated candidate identified. experimental design mirna expression profile in hcc tumors, matching adjacent cirrhotic livers, and cell lines was conducted using quantitative pcr. common mir-222 upregulations were further validated in a larger cohort of tumors. the functional effects of mir-222 inhibition on hcc cell lines were examined. the downstream modulated pathways and target of mir-222 were investigated by coupling gene expression profiling and pathway analysis, and by in silico prediction, respectively. luciferase reporter assay was done to confirm target interaction. results we identified a 40-mirna signature that could discriminate tumors from adjacent cirrhotic liver tissue, and further corroborated common mir-222 overexpression in tumors relative to its premalignant counterpart (55.3%; p conclusions our study showed that mir-222 overexpression is common in hcc and could confer metastatic potentials in hcc cells, possibly through activating akt signaling.",1
"rationale diosgenin (dgn), a structural analogue of cholesterol, has been reported to have the hypolipidemic and antiatherogenic properties, but the underlying mechanisms are not fully understood. given the key roles of macrophages in cholesterol metabolism and atherogenesis, it is critical to investigate macrophage cholesterol efflux and development of atherosclerotic lesion after dgn treatment. objective this study was designed to evaluate the potential effects of dgn on macrophage cholesterol metabolism and the development of aortic atherosclerosis, and to explore its underlying mechanisms. methods and results dgn significantly up-regulated the expression of atp-binding cassette transporter a1 (abca1) protein, but didn't affect liver x receptor α levels in foam cells derived from human thp-1 macrophages and mouse peritoneal macrophages (mpms) as determined by western blotting. the mir-19b levels were markedly down-regulated in dgn-treated thp-1 macrophages/mpm-derived foam cells. cholesterol transport assays revealed that treatment with dgn alone or together with mir-19b inhibitor notably enhanced abca1-dependent cholesterol efflux, resulting in the reduced levels of total cholesterol, free cholesterol and cholesterol ester as determined by high-performance liquid chromatography. the fecal 3h-sterol originating from cholesterol-laden mpms was increased in apolipoprotein e knockout mice treated with dgn or both dgn and antagomir-19b. treatment with dgn alone or together with antagomir-19b elevated plasma high-density lipoprotein levels, but reduced plasma low-density lipoprotein levels. accordingly, aortic lipid deposition and plaque area were reduced, and collagen content and abca1 expression were increased in mice treated with dgn alone or together with antagomir-19b. however, mir-19b overexpression abrogated the lipid-lowering and atheroprotective effects induced by dgn. conclusion the present study demonstrates that dgn enhances abca1-dependent cholesterol efflux and inhibits aortic atherosclerosis progression by suppressing macrophage mir-19b expression.",1
"persistent colonization of the gastric mucosa by helicobacter pylori (hp) elicits chronic inflammation and aberrant epithelial cell proliferation, which increases the risk of gastric cancer. here we examine the ability of micrornas to modulate gastric cell proliferation in response to persistent hp infection and find that epigenetic silencing of mir-210 plays a key role in gastric disease progression. importantly, dna methylation of the mir-210 gene is increased in hp-positive human gastric biopsies as compared with hp-negative controls. moreover, silencing of mir-210 in gastric epithelial cells promotes proliferation. we identify stmn1 and dimt1 as mir-210 target genes and demonstrate that inhibition of mir-210 expression augments cell proliferation by activating stmn1 and dimt1. together, our results highlight inflammation-induced epigenetic silencing of mir-210 as a mechanism of induction of chronic gastric diseases, including cancer, during hp infection.",1
"micrornas (mirnas) play an important role in proper function and differentiation of mouse embryonic stem cells (escs). we performed a systematic comparison of mirna expression in undifferentiated vs. differentiating escs. we report that 138 mirnas are increased on the induction of differentiation. we compared the entire list of candidate mrna targets of up-regulated mirnas with that of mrna down-regulated in escs on induction of differentiation. among the candidate targets emerging from this analysis, we found three genes, smarca5, jarid1b, and sirt1, previously demonstrated to be involved in sustaining the undifferentiated phenotype in escs. on this basis, we first demonstrated that smarca5 is a direct target of mir-100, jarid1b of mir-137, and we also confirmed previously published data demonstrating that sirt1 is a direct target of mir-34a in a different context. the suppression of these three mirnas by anti-mirs caused the block of esc differentiation induced by lif withdrawal. on the other hand, the overexpression of the three mirnas resulted in an altered expression of differentiation markers. these results demonstrate that mir-34a, mir-100, and mir-137 are required for proper differentiation of mouse escs, and that they function in part by targeting sirt1, smarca5, and jarid1b mrnas.",1
"riboswitches are metabolite binding domains within certain messenger rnas that serve as precision sensors for their corresponding targets. allosteric rearrangement of mrna structure is mediated by ligand binding, and this results in modulation of gene expression. we have identified a class of riboswitches that selectively recognizes guanine and becomes saturated at concentrations as low as 5 nm. in bacillus subtilis, this mrna motif is located on at least five separate transcriptional units that together encode 17 genes that are mostly involved in purine transport and purine nucleotide biosynthesis. our findings provide further examples of mrnas that sense metabolites and that control gene expression without the need for protein factors. furthermore, it is now apparent that riboswitches contribute to the regulation of numerous fundamental metabolic pathways in certain bacteria.",1
"aims hypoxia induces expression of various genes and micrornas (mirs) that regulate angiogenesis and vascular function. in this study, we investigated a new functional role of new hypoxia-responsive mir-101 in angiogenesis and its underlying mechanism for regulating heme oxygenase-1 (ho-1) and vascular endothelial growth factor (vegf) expression. results we found that hypoxia induced mir-101, which binds to the 3'untranslated region of cullin 3 (cul3) and stabilizes nuclear factor erythroid-derived 2-related factor 2 (nrf2) via inhibition of the proteasomal degradation pathway. mir-101 overexpression promoted nrf2 nuclear accumulation, which was accompanied with increases in ho-1 induction, vegf expression, and endothelial nitric oxide synthase (enos)-derived nitric oxide (no) production. the elevated no-induced s-nitrosylation of kelch-like ech-associated protein 1 and subsequent induction of nrf2-dependent ho-1 lead to further elevation of vegf production via a positive feedback loop between the nrf2/ho-1 and vegf/enos axes. moreover, mir-101 promoted angiogenic signals and angiogenesis both in vitro and in vivo, and these events were attenuated by inhibiting the biological activity of ho-1, vegf, or enos. moreover, these effects were also observed in aortic rings from ho-1(+/-) and enos(-/-) mice. local overexpression of mir-101 improved therapeutic angiogenesis and perfusion recovery in the ischemic mouse hindlimb, whereas antagomir-101 diminished regional blood flow. innovation hypoxia-responsive mir-101 stimulates angiogenesis by activating the ho-1/vegf/enos axis via cul3 targeting. thus, mir-101 is a novel angiomir. conclusion our results provide new mechanistic insights into a functional role of mir-101 as a potential therapeutic target in angiogenesis and vascular remodeling.",1
"the p63 protein plays a key role in regulating human keratinocyte proliferation and differentiation. although some p63-regulating micrornas (mirnas) have been identified in the control of epidermal homeostasis, little is known about mirnas acting downstream of p63. in this paper, we characterized multiple p63-regulated mirnas (mir-17, mir-20b, mir-30a, mir-106a, mir-143 and mir-455-3p) and elucidated their roles in the onset of keratinocyte differentiation. we identified rb, p21 and multiple mapks as targets of these p63-controlled mirnas. upon inhibition of most of these mirnas, we observed defects in commitment to differentiation that could be reversed by sirna-mediated silencing of their targets. furthermore, knockdown of mapk8 and mapk9 efficiently restored expression of the early differentiation markers keratin 1 and keratin 10 in p63-silenced primary human keratinocytes. these results highlight new mechanistic roles of multiple mirnas, particularly the mir-17 family (mir-17, mir-20b and mir-106a), as regulatory intermediates for coordinating p63 with mapk signaling in the commitment of human mature keratinocytes to early differentiation.",1
"micrornas are endogenously expressed small noncoding rnas that regulate gene expression on the posttranscriptional level. the mir-17-92 cluster (encoding mir-17, -18a, -19a/b, -20a, and mir-92a) is highly expressed in tumor cells and is up-regulated by ischemia. whereas mir-92a was recently identified as negative regulator of angiogenesis, the specific functions of the other members of the cluster are less clear. here we demonstrate that overexpression of mir-17, -18a, -19a, and -20a significantly inhibited 3-dimensional spheroid sprouting in vitro, whereas inhibition of mir-17, -18a, and -20a augmented endothelial cell sprout formation. inhibition of mir-17 and mir-20a in vivo using antagomirs significantly increased the number of perfused vessels in matrigel plugs, whereas antagomirs that specifically target mir-18a and mir-19a were less effective. however, systemic inhibition of mir-17/20 did not affect tumor angiogenesis. further mechanistic studies showed that mir-17/20 targets several proangiogenic genes. specifically, janus kinase 1 was shown to be a direct target of mir-17. in summary, we show that mir-17/20 exhibit a cell-intrinsic antiangiogenic activity in endothelial cells. inhibition of mir-17/20 specifically augmented neovascularization of matrigel plugs but did not affect tumor angiogenesis indicating a context-dependent regulation of angiogenesis by mir-17/20 in vivo.",1
"liver x receptors (lxrα and lxrβ) are key transcription factors in cholesterol metabolism that regulate cholesterol biosynthesis/efflux and bile acid metabolism/excretion in the liver and numerous organs. in macrophages, lxr signaling modulates cholesterol handling and the inflammatory response, pathways involved in atherosclerosis. since regulatory pathways of lxr transcription control are well understood, in the present study we aimed at identifying post-transcriptional regulators of lxr activity. micrornas (mirs) are such post-transcriptional regulators of genes that in the canonical pathway mediate mrna inactivation. in silico analysis identified mir-206 as a putative regulator of lxrα but not lxrβ. indeed, as recently shown, we found that mir-206 represses lxrα activity and expression of lxrα and its target genes in hepatic cells. interestingly, mir-206 regulates lxrα differently in macrophages. stably overexpressing mir-206 in thp-1 human macrophages revealed an up-regulation and mir-206 knockdown led to a down-regulation of lxrα and its target genes. in support of these results, bone marrow-derived macrophages (bmdms) from mir-206 ko mice also exhibited lower expression of lxrα target genes. the physiological relevance of these findings was proven by gain- and loss-of-function of mir-206; overexpression of mir-206 enhanced cholesterol efflux in human macrophages and knocking out mir-206 decreased cholesterol efflux from mpms. moreover, we show that mir-206 expression in macrophages is repressed by lxrα activation, while oxidized ldl and inflammatory stimuli profoundly induced mir-206 expression. we therefore propose a feed-back loop between mir-206 and lxrα that might be part of an lxr auto-regulatory mechanism to fine tune lxr activity.",1
"the importance of microrna (mirna) to vascular biology is becoming increasingly evident; however, the function of a significant number of mirna remains to be determined. in particular, the effect of growth factor regulation of mirnas on endothelial cell morphogenesis is incomplete. thus, we aimed to identify mirnas regulated by pro-angiogenic vascular endothelial growth factor (vegf) and determine the effects of vegf-regulated mirnas and their targets on processes important for angiogenesis. human umbilical vein endothelial cells (huvecs) were thus stimulated with vegf and mirna levels assessed using microarrays. we found that vegf altered expression of many mirna, and for this study focused on one of the most significantly down-regulated mirna in huvecs following vegf treatment, mir-30b. using specific mirna mimics, we found that overexpression of mir-30b inhibited capillary morphogenesis in vitro, while depletion of endogenous mir-30b resulted in increased capillary morphogenesis indicating the potential significance of down-regulation of mir-30b as a pro-angiogenic response to vegf stimulation. mir-30b overexpression in huvec regulated transforming growth factor beta 2 (tgfβ2) production, which led to increased phosphorylation of smad2, indicating activation of an autocrine tgfβ signaling pathway. up-regulation of tgfβ2 by mir-30b overexpression was found to be dependent on atf2 activation, a transcription factor known to regulate tgfβ2 expression, as mir-30b overexpressing cells exhibited increased levels of phosphorylated atf2 and depletion of atf2 inhibited mir-30b-induced tgfβ2 expression. however, mir-30b effects on atf2 were indirect and found to be via targeting of the known atf2 repressor protein jdp2 whose mrna levels were indirectly correlated with mir-30b levels. increased secretion of tgfβ2 from huvec was shown to mediate the inhibitory effects of mir-30b on capillary morphogenesis as treatment with a neutralizing antibody to tgfβ2 restored capillary morphogenesis to normal levels in mir-30b overexpressing cells. these results support that the regulation of mir-30b by vegf in huvec is important for capillary morphogenesis, as increased mir-30b expression inhibits capillary morphogenesis through enhanced expression of tgfβ2.",1
"the discovery of structured non-coding rnas (ncrnas) in bacteria can reveal new facets of biology and biochemistry. comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncrna classes in recent years. however, this general search strategy favors the discovery of more common ncrna classes, whereas progressively rarer classes are correspondingly more difficult to identify. in the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare rna classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. by implementing these methods, we discovered 224 novel ncrna classes, which include rool rna, an rna class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncrna classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory rna classes involved in a variety of biological processes. we expect that further research on these newly found rna classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncrnas.",1
"enzymes made of rna catalyze reactions that are essential for protein synthesis and rna processing. however, such natural ribozymes are exceedingly rare, as evidenced by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. indeed, only 11 distinct ribozyme classes have been experimentally validated to date. recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. herein we exploited this association to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding rna motifs that are self-cleaving rna candidates. we identified three new self-cleaving classes, which we named twister sister, pistol and hatchet, from this collection, suggesting that even more ribozymes remain hidden in modern cells.",1
"cerebellar degeneration is a devastating manifestation of cerebellar-type multiple-system atrophy (msa), a rapidly progressive neurodegenerative disease, and the exact pathogenesis is unknown. here, we examined the expression of micro-rnas (mirnas), which are short noncoding rnas, in the cerebellum of msa and the key target genes. mirna microarray found 11 mirnas with significantly different expression in msa cerebellum compared to cerebellum from age-, sex-, and postmortem interval-matched controls. mir-202 was the most upregulated in the msa samples. in silico analysis, followed by target gene luciferase assay, in vitro transfection, and western blotting in human samples showed that mir-202 downregulates oct1 (pou2f1), a transcription factor expressed in cerebellar purkinje cells. transfection of neuro-2a cells with mir-202 enhanced oxidative stress-induced cell death, and an antagomir to mir-202 inhibited this effect of mir-202. this study provides novel insight into the role of mirna in cerebellar degeneration and suggests that mir-202 is a key mirna mediating the pathogenesis of msa.",1
"loss-of-function mutations in progranulin (grn) cause ubiquitin- and tar dna-binding protein 43 (tdp-43)-positive frontotemporal dementia (ftld-u), a progressive neurodegenerative disease affecting approximately 10% of early-onset dementia patients. here we expand the role of grn in ftld-u and demonstrate that a common genetic variant (rs5848), located in the 3'-untranslated region (utr) of grn in a binding-site for mir-659, is a major susceptibility factor for ftld-u. in a series of pathologically confirmed ftld-u patients without grn mutations, we show that carriers homozygous for the t-allele of rs5848 have a 3.2-fold increased risk to develop ftld-u compared with homozygous c-allele carriers (95% ci: 1.50-6.73). we further demonstrate that mir-659 can regulate grn expression in vitro, with mir-659 binding more efficiently to the high risk t-allele of rs5848 resulting in augmented translational inhibition of grn. a significant reduction in grn protein was observed in homozygous t-allele carriers in vivo, through biochemical and immunohistochemical methods, mimicking the effect of heterozygous loss-of-function grn mutations. in support of these findings, the neuropathology of homozygous rs5848 t-allele carriers frequently resembled the pathological ftld-u subtype of grn mutation carriers. we suggest that the expression of grn is regulated by mirnas and that common genetic variability in a mirna binding-site can significantly increase the risk for ftld-u. translational regulation by mirnas may represent a common mechanism underlying complex neurodegenerative disorders.",1
"a number of studies have shown that increased app levels, resulting from either a genomic locus duplication or alteration in app regulatory sequences, can lead to development of early-onset dementias, including alzheimer's disease (ad). therefore, understanding how app levels are regulated could provide valuable insight into the genetic basis of ad and illuminate novel therapeutic avenues for ad. here we test the hypothesis that app protein levels can be regulated by mirnas, evolutionarily conserved small noncoding rna molecules that play an important role in regulating gene expression. utilizing human cell lines, we demonstrate that mirnas hsa-mir-106a and hsa-mir-520c bind to their predicted target sequences in the app 3'utr and negatively regulate reporter gene expression. over-expression of these mirnas, but not control mirnas, results in translational repression of app mrna and significantly reduces app protein levels. these results are the first to demonstrate that levels of human app can be regulated by mirnas.",1
"annexin 1 (anxa1) is an endogenous anti-inflammatory protein implicated in cancer. anxa1 was previously shown to be regulated by hsa-mir-196a. however, whether anxa1 itself regulates microrna (mir) expression is unknown. therefore, we investigated the regulation of mir by anxa1 in mcf7 breast cancer cells. mcf7-ev (empty vector) and mcf7-v5 (anxa1-v5 expressing cells) were subjected to a mir microarray. microarray analysis revealed a number of mirnas which were dysregulated in mcf7-v5 cells. 2 novel mirnas (mir562 and mir26b*) were validated, cloned and functionally characterized. as anxa1 constitutively activates nf-κb activity to modulate breast cancer metastasis, we found that mir26b* and mir562 directly targeted the canonical nf-κb pathway by targeting the 3' utr and inhibiting expression of rel a (p65) and nf-κb1 (p105) respectively. mir562 inhibited wound healing, which was reversed when anxa1 was overexpressed. overexpression of either mir562 or mir26b* in mcf-7 cells enhanced endothelial tube formation when cocultured with human umbilical cord endothelial cells while conversely, treatment of mcf7 cells with either anti-mir562 or anti-mir26b* inhibited endothelial tube formation after co-culture. further analysis of mir562 revealed that mir562-transfected cell conditioned media enhances endothelial cell tube formation, indicating that mir562 increased angiogenic secreted factors from mcf-7 breast tumor cells. tnfα was increased upon overexpression of mir562, which was reversed when anxa1 was co-transfected in conclusion, this data suggests that anxa1-regulated mir26b* and mir562 may play a role in wound healing and tumor-induced endothelial cell tube formation by targeting nf-κb expression and point towards a potential therapeutic target for breast cancer.",1
"as a cleavage enzyme of precursor tnf-α, the high expression level of adam17 in endothelial cells is an important factor in atherosclerosis. in this study, we demonstrate that adam17 is the target of mir-152. we found that mir-152 could reduce tnf precursor cleavage and inhibit cell proliferation and migration by targeting adam17 in human umbilical vein endothelial cells (huvecs). furthermore, the expression pattern of mir-152 and corresponding target adam17 was opposite in huvecs under hypoxic conditions. the levels of circulating mir-152 in as patient sera were lower than those detected in the sera of normal individuals. our results indicate that mir-152 may be involved in the development of human atherosclerosis and could be used as diagnostic biomarker or therapeutic target in atherosclerosis.",1
"micrornas (mirnas) are genomically encoded small rnas used by organisms to regulate the expression of proteins generated from messenger rna transcripts. the in vivo requirement of specific mirnas in mammals through targeted deletion remains unknown, and reliable prediction of mrna targets is still problematic. here, we show that mirna biogenesis in the mouse heart is essential for cardiogenesis. furthermore, targeted deletion of the muscle-specific mirna, mir-1-2, revealed numerous functions in the heart, including regulation of cardiac morphogenesis, electrical conduction, and cell-cycle control. analyses of mir-1 complementary sequences in mrnas upregulated upon mir-1-2 deletion revealed an enrichment of mir-1 ""seed matches"" and a strong tendency for potential mir-1 binding sites to be located in physically accessible regions. these findings indicate that subtle alteration of mirna dosage can have profound consequences in mammals and demonstrate the utility of mammalian loss-of-function models in revealing physiologic mirna targets.",1
"the coat protein (cp) of alfalfa mosaic virus (amv) is required to initiate infection by the viral tripartite rna genome whereas infection by the tripartite brome mosaic virus (bmv) genome is independent of cp. amv cp stimulates translation of amv rna in vivo 50- to 100-fold. the 3' untranslated region (utr) of the amv subgenomic cp messenger rna 4 contains at least two cp binding sites. a cp binding site in the 3'-terminal 112 nucleotides of rna 4 was found to be required for efficient translation of the rna whereas an upstream binding site was not. binding of cp to the amv 3' utr induces a conformational change of the rna but this change alone was not sufficient to stimulate translation. cp mutant r17a is unable to bind to the 3' utr and translation in vivo of rna 4 encoding this mutant occurs at undetectable levels. replacement of the 3' utr of this mutant rna 4 by the 3' utr of bmv rna 4 restored translation of r17a-cp to wild-type levels. apparently, the bmv 3' utr stimulates translation independently of cp. amv cp mutant n199 is defective in the formation of cp dimers and did not stimulate translation of rna 4 in vivo although the mutant cp did bind to the 3' utr. the finding that n199-cp does not promote amv infection corroborates the notion that the requirement of cp in the inoculum reflects its role in translation of the viral rnas.",1
"objectives micrornas(mirnas) play important roles in tumor development and progression. the purposes of this study were to investigate the role of mir-31 in cervical cancer and clarified the regulation of arid1a by mir-31. methods quantitative rt-pcr was used to examine mir-31 expression in cervical cancer cell lines and patient specimens. the clinicopathological significance of mir-31 upregulation was further analyzed. the mtt, colony formation, apoptosis, cell cycle, wound healing and transwell invasion assays, and a xenograft model were performed. a luciferase reporter assay was conducted to confirm the target gene of mir-31, and the results were validated in cell lines and patient specimens. results mir-31 was significantly up-regulated in cervical cancer cell lines and clinical tissues. the high mir-31 level was significantly correlated with higher figo stage, node metastasis, vascular involvement and deep stromal invasion. patients with high expression of mir-31 had poorer overall survival than patients with low expression. mir-31 was an independent prognostic factor in cervical cancer in multivariate cox regression analysis. down-regulation of mir-31 impaired cell proliferation, colony formation, and cell migration and invasion in vitro, and inhibited xenograft tumor growth in vivo. arid1a was verified as a direct target of mir-31, which was further confirmed by the inverse expression of mir-31 and arid1a in patient specimens. conclusions the newly identified mir-31/arid1a pathway provides insight into cervical cancer progression, and may represent a novel therapeutic target.",1
"unlabelled the hepatitis b virus x protein (hbx) has been implicated as an oncogene in both epigenetic modifications and genetic regulation during hepatocarcinogenesis, but the underlying mechanisms are not entirely clear. long noncoding rnas (lncrnas), which regulate gene expression with little or no protein-coding capacity, are involved in diverse biological processes and in carcinogenesis. we asked whether hbx could promote hepatocellular carcinoma (hcc) by regulating the expression of lncrnas. in this study we investigated the alteration in expression of lncrnas induced by hbx using microarrays and real-time quantitative polymerase chain reaction (pcr). our results indicate that hbx transgenic mice have a specific profile of liver lncrnas compared with wildtype mice. we identified an lncrna, down-regulated expression by hbx (termed lncrna-dreh), which can inhibit hcc growth and metastasis in vitro and in vivo, act as a tumor suppressor in the development of hepatitis b virus (hbv)-hcc. lncrna-dreh could combine with the intermediate filament protein vimentin and repress its expression, and thus further change the normal cytoskeleton structure to inhibit tumor metastasis. we also identified a human ortholog rna of dreh (hdreh) and found that its expression level was frequently down-regulated in hbv-related hcc tissues in comparison with the adjacent noncancerous hepatic tissues, and its decrement significantly correlated with poor survival of hcc patients. conclusion these findings support a role of lncrna-dreh in tumor suppression and survival prediction in hcc patients. this discovery contributes to a better understanding of the importance of the deregulated lncrnas by hbx in hcc and provides a rationale for the potential development of lncrna-based targeted approaches for the treatment of hbv-related hcc.",1
"aging-associated dysfunction of the immune system contributes to the increase in pathophysiological processes that occur with age. numerous studies have shown that micrornas regulate immune responses, although their role in age-related macrophage dysfunction remains elusive. here, we found that mir-350-3p is expressed at lower levels in peritoneal macrophages from aged mice compared with young mice, and that lipopolysaccharide (lps) stimulation downregulates mir-350-3p expression to a greater extent in young macrophages compared with aged macrophages. consequently, lps-stimulated aged macrophages express more mir-350-3p than do similarly treated young macrophages. luciferase reporter assays showed that interleukin (il)-6 mrna is a mir-350-3p target in macrophages. furthermore, although lps induces less il-6 production by aged macrophages than by young macrophages, the aged cell response is rescued by production mir-350-3p inhibition. these findings suggest that mir-350-3p may contribute to age-related impairment of macrophage function and could be a novel target for the treatment of age-related inflammatory diseases.",1
"numerous noncoding transcripts of unknown function have recently been identified. in this study, we report a novel mechanism that relies on transcription of noncoding rna prt (pho1-repressing transcript) regulating expression of the pho1 gene. a product of this gene, pho1, is a major secreted phosphatase needed for uptake of extracellular phosphate in fission yeast. prt is produced from the promoter located upstream of the pho1 gene in response to phosphate, and its transcription leads to deposition of rnai-dependent h3k9me2 across the pho1 locus. in contrast, phosphate starvation leads to loss of h3k9me2 and pho1 induction. strikingly, deletion of clr4, a h3k9 methyltransferase, results in faster pho1 induction in response to phosphate starvation. we propose a new role for noncoding transcription in establishing transient heterochromatin to mediate an effective transcriptional response to environmental stimuli. rnai recruitment to prt depends on the rna-binding protein mmi1. importantly, we found that the exosome complex and mmi1 are required for transcription termination and the subsequent degradation of prt but not pho1 mrna. moreover, in mitotic cells, transcription termination of meiotic rnas also relies on this mechanism. we propose that exosome-dependent termination constitutes a specialized system that primes transcripts for degradation to ensure their efficient elimination.",1
"mononuclear cytotrophoblasts of the human placenta proliferate rapidly, subsequently fuse, and differentiate to form multinucleated syncytiotrophoblast with induction of aromatase (hcyp19a1) and chorionic gonadotropin (hcgβ) expression. using microarray analysis, we identified members of the mir-17~92 cluster and its paralogs, mir-106a~363 and mir-106b~25, that are significantly downregulated upon syncytiotrophoblast differentiation. interestingly, mir-19b and mir-106a directly targeted hcyp19a1 expression, while mir-19b also targeted human gcm1 (hgcm1), a transcription factor critical for mouse labyrinthine trophoblast development. overexpression of these micrornas (mirnas) impaired syncytiotrophoblast differentiation. hgcm1 knockdown decreased hcyp19a1 and hcgβ expression, substantiating its important role in human trophoblast differentiation. expression of the c-myc proto-oncogene was increased in proliferating cytotrophoblasts compared to that in differentiated syncytiotrophoblast. moreover, c-myc overexpression upregulated mir-17~92 and inhibited hcyp19a1 and hcgβ expression. binding of endogenous c-myc to genomic regions upstream of the mir-17~92 and mir-106a~363 clusters in cytotrophoblasts dramatically decreased upon syncytiotrophoblast differentiation. intriguingly, we observed higher levels of mir-106a and -19b and lower aromatase and hgcm1 expression in placentas from preeclamptic women than in placentas from gestation-matched normotensive women. our findings reveal that c-myc-regulated members of the mir-17~92 and mir-106a~363 clusters inhibit trophoblast differentiation by repressing hgcm1 and hcyp19a1 and suggest that aberrant regulation of these mirnas may contribute to the pathogenesis of preeclampsia.",1
"micrornas-221 and -222 are highly upregulated in several solid tumors, including melanomas. we demonstrate that the proto-oncogene ets-1, involved in the pathogenesis of cancers of different origin, is a transcriptional regulator of mir-222 by direct binding to its promoter region. differently from 293ft cells or early stage melanomas, where unphosphorylated ets-1 represses mir-222 transcription, in metastatic melanoma the constitutively thr-38 phosphorylated fraction of ets-1 induces mir-222. despite its stepwise decreased expression along with melanoma progression, the oncogenic activity of ets-1 relies on its ras/raf/erk-dependent phosphorylation status more than on its total amount. to close the loop, we demonstrate ets-1 as a direct target of mir-222, but not mir-221, showing the novel option of their uncoupled functions. in addition, a spatial redistribution of ets-1 protein from the nucleus to the cytoplasm is also evidenced in advanced melanoma cells. finally, in vivo studies confirmed the contribution of mir-222 to the increased invasive potential obtained by ets- silencing.",1
"osteoclast differentiation is regulated by transcriptional, post-transcriptional, and post-translational mechanisms. micrornas are fundamental post-transcriptional regulators of gene expression. the function of the mir-29 (a/b/c) family in cells of the osteoclast lineage is not well understood. in primary cultures of mouse bone marrow-derived macrophages, inhibition of mir-29a, -29b, or -29c diminished formation of trap (tartrate-resistant acid phosphatase-positive) multinucleated osteoclasts, and the osteoclasts were smaller. quantitative rt-pcr showed that all mir-29 family members increased during osteoclast differentiation, in concert with mrnas for the osteoclast markers trap (acp5) and cathepsin k. similar regulation was observed in the monocytic cell line raw264.7. in stably transduced raw264.7 cell lines expressing an inducible mir-29 competitive inhibitor (sponge construct), mir-29 knockdown impaired osteoclastic commitment and migration of pre-osteoclasts. however, mir-29 knockdown did not affect cell viability, actin ring formation, or apoptosis in mature osteoclasts. to better understand how mir-29 regulates osteoclast function, we validated mir-29 target genes using luciferase 3'-utr reporter assays and specific mir-29 inhibitors. we demonstrated that mir-29 negatively regulates rnas critical for cytoskeletal organization, including cdc42 (cell division control protein 42) and srgap2 (slit-robo rho gtpase-activating protein 2). moreover, mir-29 targets rnas associated with the macrophage lineage: gpr85 (g protein-coupled receptor 85), nfia (nuclear factor i/a), and cd93. in addition, calcr (calcitonin receptor), which regulates osteoclast survival and resorption, is a novel mir-29 target. thus, mir-29 is a positive regulator of osteoclast formation and targets rnas important for cytoskeletal organization, commitment, and osteoclast function. we hypothesize that mir-29 controls the tempo and amplitude of osteoclast differentiation.",1
"fine-tuned notch and hedgehog signalling pathways via attenuators and dampers have long been recognized as important mechanisms to ensure the proper size and differentiation of many organs and tissues. this notion is further supported by identification of mutations in these pathways in human cancer cells. however, although it is common that the notch and hedgehog pathways influence growth and patterning within the same organ through the establishment of organizing regions, the cross-talk between these two pathways and how the distinct organizing activities are integrated during growth is poorly understood. here, in an unbiased genetic screen in the drosophila melanogaster eye, we found that tumour-like growth was provoked by cooperation between the microrna mir-7 and the notch pathway. surprisingly, the molecular basis of this cooperation between mir-7 and notch converged on the silencing of hedgehog signalling. in mechanistic terms, mir-7 silenced the interference hedgehog (ihog) hedgehog receptor, while notch repressed expression of the brother of ihog (boi) hedgehog receptor. tumourigenesis was induced co-operatively following notch activation and reduced hedgehog signalling, either via overexpression of the microrna or through specific down-regulation of ihog, hedgehog, smoothened, or cubitus interruptus or via overexpression of the cubitus interruptus repressor form. conversely, increasing hedgehog signalling prevented eye overgrowth induced by the microrna and notch pathway. further, we show that blocking hh signal transduction in clones of cells mutant for smoothened also enhance the organizing activity and growth by delta-notch signalling in the wing primordium. together, these findings uncover a hitherto unsuspected tumour suppressor role for the hedgehog signalling and reveal an unanticipated cooperative antagonism between two pathways extensively used in growth control and cancer.",1
"unlabelled mirnas (mir) play a critical role in human cancers, including hepatocellular carcinoma. although mir-302b has been suggested to function as a tumor repressor in other cancers, its role in hepatocellular carcinoma is unknown. this study investigated the expression and functional role of mir-302b in human hepatocellular carcinoma. the expression level of mir-302b is dramatically decreased in clinical hepatocellular carcinoma specimens, as compared with their respective nonneoplastic counterparts, and in hepatocellular carcinoma cell lines. overexpression of mir-302b suppressed hepatocellular carcinoma cell proliferation and g1-s transition in vitro, whereas inhibition of mir-302b promoted hepatocellular carcinoma cell proliferation and g1-s transition. using a luciferase reporter assay, akt2 was determined to be a direct target of mir-302b. subsequent investigation revealed that mir-302b expression was inversely correlated with akt2 expression in hepatocellular carcinoma tissue samples. importantly, silencing akt2 recapitulated the cellular and molecular effects seen upon mir-302b overexpression, which included inhibiting hepatocellular carcinoma cell proliferation, suppressing g1 regulators (cyclin a, cyclin d1, cdk2) and increasing p27kip1 phosphorylation at ser10. restoration of akt2 counteracted the effects of mir-302b expression. moreover, mir-302b was able to repress tumor growth of hepatocellular carcinoma cells in vivo. implications taken together, mir-302b inhibits hcc cell proliferation and growth in vitro and in vivo by targeting akt2.",1
"background metagenomic sequence data are proving to be a vast resource for the discovery of biological components. yet analysis of this data to identify functional rnas lags behind efforts to characterize protein diversity. the genome of 'candidatus pelagibacter ubique' htcc 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. it is also small, contains little non-coding dna, and has strikingly low gc content. results to aid the discovery of rna motifs within the marine metagenome we exploited the genomic properties of 'cand. p. ubique' by targeting our search to long intergenic regions (igrs) with relatively high gc content. analysis of known rnas (rrna, trna, riboswitches etc.) shows that structured rnas are significantly enriched in such igrs. to identify additional candidate structured rnas, we examined other igrs with similar characteristics from 'cand. p. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. employing this strategy, we discovered four candidate structured rnas including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins s2 and s12, and the cytoplasmic protein component of the signal recognition particle. we also describe four additional potential rna motifs with few or no examples occurring outside the metagenomic data. conclusion this work begins the process of identifying functional rna motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.",1
"incidence of cutaneous squamous cell carcinomas (csccs) constantly increases in the caucasian population. developing preferentially on precancerous lesions such as actinic keratoses due to chronic sunlight exposure, csccs result from the malignant transformation of keratinocytes. although a resection of the primary tumor is usually curative, a subset of aggressive csccs shows a high risk of recurrence and metastases. the characterization of the molecular dysfunctions involved in cscc development should help to identify new relevant targets against these aggressive csccs. in that context, we have used small rna sequencing to identify 100 micrornas (mirnas) whose expression was altered during chemically induced mouse skin tumorigenesis. the decreased expression of the mir-193b/365a cluster during tumor progression suggests a tumor suppressor role. ectopic expression of these mirnas in tumor cells indeed inhibited their proliferation, clonogenic potential and migration, which were stimulated in normal keratinocytes when these mirnas were blocked with antisense oligonucleotides. a combination of in silico predictions and transcriptome analyses identified several target genes of interest. we validated kras and max as direct targets of mir-193b and mir-365a. repression of these targets using sirnas mimicked the effects of mir-193b and mir-365a, suggesting that these genes might mediate, at least in part, the tumor-suppressive action of these mirnas.",1
"defects in urothelial integrity resulting in leakage and activation of underlying sensory nerves are potential causative factors of bladder pain syndrome, a clinical syndrome of pelvic pain and urinary urgency/frequency in the absence of a specific cause. herein, we identified the microrna mir-199a-5p as an important regulator of intercellular junctions. on overexpression in urothelial cells, it impairs correct tight junction formation and leads to increased permeability. mir-199a-5p directly targets mrnas encoding lin7c, arhgap12, pals1, rnd1, and pvrl1 and attenuates their expression levels to a similar extent. using laser microdissection, we showed that mir-199a-5p is predominantly expressed in bladder smooth muscle but that it is also detected in mature bladder urothelium and primary urothelial cultures. in the urothelium, its expression can be up-regulated after activation of camp signaling pathways. while validating mir-199a-5p targets, we delineated novel functions of lin7c and arhgap12 in urothelial integrity and confirmed the essential role of pals1 in establishing and maintaining urothelial polarity and junction assembly. the present results point to a possible link between mir-199a-5p expression and the control of urothelial permeability in bladder pain syndrome. up-regulation of mir-199a-5p and concomitant down-regulation of its multiple targets might be detrimental to the establishment of a tight urothelial barrier, leading to chronic pain.",1
"mirnas are associated with various types of cancer due to their ability to affect expression of genes that modulate tumorigenesis. in this study, we explored the role of mir-141 in pancreatic cancer. the analysis of clinical characteristics showed that mir-141 was significantly downregulated in tissues and cell lines of pancreatic cancer. moreover, the decreased mir-141 level was significantly associated with tumor size and tnm stage, as well as lymph node and distant metastasis. meanwhile, both kaplan-meier and multivariate survival analysis showed decreased mir-141 were associated with overall survival. overexpression of mir-141 in pancreatic cancer cells inhibited cell proliferation, clonogenicity, and invasion; induced g1 arrest and apoptosis; and enhanced chemosensitivity. to understand how mir-141 mediates the phenotype of pancreatic cancer cells, a bioinformatics tool was used to identify map4k4 as a potential target of mir-141. the dual-luciferase reporter gene assay showed that mir-141 binds directly to the 3'-untranslated region (3'utr) of map4k4 to inhibit map4k4 expression. western blot and quantitative real-time pcr (qrt-pcr) analyses revealed that map4k4 expression was inversely correlated with mir-141 expression both in pancreatic cancer samples and cell lines. knockdown of map4k4 inhibited cell proliferation, clonogenicity, and invasion, induced g1 arrest and apoptosis, and enhanced chemosensitivity. in a nude mouse xenograft model, both overexpression of mir-141 and knockdown of map4k4 significantly repressed pancreatic cancer cell growth. therefore, we conclude that mir-141 targets map4k4, acts as a tumor suppressor in pancreatic cancer cells, and may serve as a novel therapeutic agent for mirna-based pancreatic cancer therapy.",1
"we investigated the expression of micrornas (mirnas) associated with replicative senescence in human primary keratinocytes. a cohort of mirnas up-regulated in senescence was identified by genome-wide mirna profiling, and their change in expression was validated in proliferative versus senescent cells. among these, mirna (mir)-138, -181a, -181b, and -130b expression increased with serial passages. mir-138, -181a, and -181b, but not mir-130b, overexpression in proliferating cells was sufficient per se to induce senescence, as evaluated by inhibition of brdu incorporation and quantification of senescence-activated β-galactosidase staining. we identified sirt1 as a direct target of mir-138, -181a, and -181b, whereas δnp63 expression was inhibited by mir-130b. we also found that δnp63α inhibits mir-138, -181a, -181b, and -130b expression by binding directly to p63-responsive elements located in close proximity to the genomic loci of these mirnas in primary keratinocytes. these findings suggest that changes in mirna expression, by modulating the levels of regulatory proteins such as p63 and sirt1, strongly contribute to induction of senescence in primary human keratinocytes, thus linking these two proteins. our data also indicate that suppression of mir-138, -181a, -181b, and -130b expression is part of a growth-promoting strategy of δnp63α in epidermal proliferating cells.",1
"amyloid precursor protein (app) and β-site amyloid precursor protein cleaving enzyme (bace-1) play important roles in the generation of alzheimer׳s disease (ad), a progressive neurodegenerative disorder. in the present study, microrna (mir) microarray was used to analyze the mir expression profiles in the hippocampi from app/ps1 transgenic and wild type mice. the mirs with significant alteration and putative targets on app or bace-1 were retrieved (mir-135a, -200b and -429). the deregulations of these mirs were confirmed in mice and further verified in ad patient samples by qpcr. primary mouse hippocampal neurons, sh-sy5y and hek293 cells were used to study the function of mirs on app and bace-1. we found that mir-135a, which was downregulated significantly in hippocampi from app/ps1 transgenic mice compared with the wild type control, directly interacted with the 3'-utr of bace-1 and repressed its expression and activity. on the other hand, mir-200b and -429, which were downregulated significantly in hippocampi from app/ps1 transgenic mice compared with the wild type control, targeted the 3'-utr of app and repressed its expression. furthermore, aβ42 could downregulate mir-200b expression which may generate a vicious cycle resulted in accumulating aβ42. the levels of mir-135a and -200b in the serum of dat group were significantly lower than that of control groups (p<0.05). the serum mir-200b level of mci group was higher than that of dat group (p<0.05) and lower than that of control group (p<0.05). we also found decreased mir-135a and -200b levels in the cerebrospinal fluid of dat group compared with the control group (p<0.05). in conclusion, these findings showed that mir-135a, -200b and -429 may take part in the progress of ad; mir-200b was of great potential as noninvasive and easily detected blood-based biomarkers of mci and dat patients.",1
"mir-122, a hepato-specific microrna (mirna), is frequently down-regulated in human hepatocellular carcinoma (hcc). in an effort to identify novel mir-122 targets, we performed an in silico analysis and detected a putative binding site in the 3'-untranslated region (3'-utr) of bcl-w, an anti-apoptotic bcl-2 family member. in the hcc-derived cell lines, hep3b and hepg2, we confirmed that mir-122 modulates bcl-w expression by directly targeting binding site within the 3'-utr. the cellular mrna and protein levels of bcl-w were repressed by elevated levels of mir-122, which subsequently led to reduction of cell viability and activation of caspase-3. thus, bcl-w is a direct target of mir-122 that functions as an endogenous apoptosis regulator in these hcc-derived cell lines.",1
"objective the generation of distinct cell types during the development of the pancreas depends on sequential changes in gene expression. we tested the hypothesis that micrornas (mirnas), which limit gene expression through posttranscriptional silencing, modulate the gene expression cascades involved in pancreas development. research design and methods mirnas were cloned and sequenced from developing pancreata, and expression of a subset of these genes was tested using locked nucleic acid in situ analyses. to assess the overall contribution of mirnas to pancreatic development, dicer1, an enzyme required for mirna processing, was conditionally deleted from the developing pancreas. results sequencing of small rnas identified over 125 mirnas, including 18 novel sequences, with distinct expression domains within the developing pancreas. to test the developmental contribution of these mirnas, we conditionally deleted the mirna processing enzyme dicer1 early in pancreas development. dicer-null animals displayed gross defects in all pancreatic lineages, although the endocrine cells, and especially the insulin-producing beta-cells, were most dramatically reduced. the endocrine defect was associated with an increase in the notch-signaling target hes1 and a reduction in the formation of endocrine cell progenitors expressing the hes1 target gene neurogenin3. conclusions the expression of a unique profile of mirnas is required during pancreas development and is necessary for beta-cell formation.",1
"drosophila myc (dmyc), as a broad-spectrum transcription factor, can regulate the expression of a large number of genes to control diverse cellular processes, such as cell cycle progression, cell growth, proliferation and apoptosis. however, it remains largely unknown about whether dmyc can be involved in drosophila innate immune response. here, we have identified dmyc to be a negative regulator of drosophila imd pathway via the loss- and gain-of-function screening. we demonstrate that dmyc inhibits drosophila imd immune response via directly activating mir-277 transcription, which further inhibit the expression of imd and tab2-ra/b. importantly, dmyc can improve the survival of flies upon infection, suggesting inhibiting drosophila imd pathway by dmyc is vital to restore immune homeostasis that is essential for survival. taken together, our study not only reports a new dmyc-mir-277-imd/tab2 axis involved in the negative regulation of drosophila imd pathway, and provides a new insight into the complex regulatory mechanism of drosophila innate immune homeostasis maintenance.",1
"in response to inflammatory stimulation, dendritic cells (dcs) have a remarkable pattern of differentiation (maturation) that exhibits specific mechanisms to control immunity. here, we show that in response to lipopolysaccharides (lps), several micrornas (mirnas) are regulated in human monocyte-derived dendritic cells. among these mirnas, mir-155 is highly up-regulated during maturation. using lna silencing combined to microarray technology, we have identified the toll-like receptor/interleukin-1 (tlr/il-1) inflammatory pathway as a general target of mir-155. we further demonstrate that mir-155 directly controls the level of tab2, an important signal transduction molecule. our observations suggest, therefore, that in mature human dcs, mir-155 is part of a negative feedback loop, which down-modulates inflammatory cytokine production in response to microbial stimuli.",1
"recent studies have revealed that microrna-29c (mir-29c) is involved in a variety of biological processes including carcinogenesis. here, we report that mir-29c was significantly downregulated in hepatitis b virus (hbv)-related hepatocellular carcinoma (hcc) cell lines as well as in clinical tissues compared with their corresponding controls. tumor necrosis factor alpha-induced protein 3 (tnfaip3), a key regulator in inflammation and immunity, was found to be inversely correlated with mir-29c levels and was identified as a target of mir-29c. overexpression of mir-29c in hepg2.2.15 cells effectively suppressed tnfaip3 expression and hbv dna replication as well as inhibited cell proliferation and induced apoptosis. we conclude that mir-29c may play an important role as a tumor suppressive microrna in the development and progression of hbv-related hcc by targeting tnfaip3. thus mir-29c and tnfaip3 represent key diagnostic markers and potential therapeutic targets for the prevention and treatment of hbv infection.",1
"micrornas (mirnas) are small non-coding rnas which regulate gene expression by base-pairing to the 3'-utr of the target mrna. recently, mirnas have been shown to regulate cancer metastasis, however, central molecular mechanisms of this ability still need to be investigated. epithelial to mesenchymal transition (emt), which is characterized especially by repression of e-cadherin expression and increased cell motility, is an essential component of cancer metastasis and progression. in the present study, we found that snai1, a known transcriptional repressor of e-cadherin and modulator of emt, is post-transcriptionally targeted by mirna-30a in non-small cell lung cancer (nsclc). consistent with this, microrna-30a expression was found inversely proportional to the invasive potential of various nsclc cell lines, correlating positively with e-cadherin (epithelial marker) and negatively with n-cadherin (mesenchymal marker) expression. forced re-introduction of mir-30a significantly altered cell morphology, in vitro invasion and migration of invasive cell lines, this being paralleled by a downregulation of snai1 and upregulation of e-cadherin expression. using a chicken embryonic metastasis assay, we found that mir-30a suppresses in vivo distant metastasis to the lungs and liver. finally, we screened the expression of mir-30a in 64 consecutively resected nsclc patients and found that, in 81% of the patients, expression of mir-30a was downregulated significantly (p < 0.0001) in tumors compared to corresponding normal tissues. these results suggest that mir-30a targets snai1, inhibits invasion and metastasis, and is downregulated in nsclc.",1
"macrophage apoptosis is a host innate defense mechanism against tuberculosis (tb). in this study, we found that percentage of apoptotic cells in peripheral blood monocytes from patients with active tb was lower than that from healthy controls (p<0.001). to understand whether micrornas can modulate apoptosis of monocytes, we investigated differentially expressed micrornas in patients with active tb. mir-582-5p was mainly expressed in monocytes and was upregulated in patients with active tb. the apoptotic percentage of thp-1 cells transfected with mir-582-5p mimics was significantly lower than those transfected with negative control of microrna mimics (p<0.001), suggesting that mir-582-5p could inhibit apoptosis of monocytes. to our knowledge, the role of mir-582-5p in regulating apoptosis of monocytes has not been reported so far. systematic bioinformatics analysis indicated that foxo1 might be a target gene for mir-582-5p and its 3'utr contains potential binding sites for mir-582-5p. to determine whether mir-582-5p could influence foxo1 expression, mir-582-5p mimics or negative control of microrna mimics were transfected into thp-1 cells. rt-pcr and western blot analysis showed that the mir-582-5p could suppress both foxo1 mrna and protein expression. co-transfection of mir-582-5p and foxo1 3'utr-luciferase reporter vector into cells demonstrated that significant decrease in luciferase activity was only found in reporter vector that contained a wild type sequence of foxo1 3'utr, suggesting that mir-582-5p could directly target foxo1. in conclusion, mir-582-5p inhibited apoptosis of monocytes by down-regulating foxo1 expression and might play an important role in regulating anti-m. tuberculosis directed immune responses.",1
"micrornas (mirnas) are a class of endogenous small noncoding rnas that regulate gene expression after transcription. aberrant expression of mirnas has been shown to be involved in tumorigenesis. we showed that mir-21 was one of the most frequently overexpressed mirna in human glioblastoma (gbm) cell lines. to explore whether mir-21 can serve as a therapeutic target for glioblastoma, we downregulated mir-21 with a specific antisense oligonucleotide and found that apoptosis was induced and cell-cycle progression was inhibited in vitro in u251 (pten mutant) and ln229 (pten wild-type) gbm cells; xenograft tumors from antisense-treated u251 cells were suppressed in vivo. antisense-mir-21-treated cells showed a decreased expression of egfr, activated akt, cyclin d, and bcl-2. although mir-21 is known to regulate pten and downregulation of mir-21 led to increased pten expression both endogenously and in a reporter gene assay, the gbm suppressor effect of antisense-mir-21 is most likely independent of pten regulation because u251 has mutant pten. microarray analysis showed that the knockdown of mir-21 significantly altered expression of 169 genes involved in nine cell-cycle and signaling pathways. taken together, our studies provide evidence that mir-21 may serve as a novel therapeutic target for malignant gliomas independent of pten status.",1
"small noncoding rnas (srna) can function as posttranscriptional activators of gene expression to regulate stress responses and metabolism. we here describe the mechanisms by which two srnas, glmy and glmz, activate the escherichia coli glms mrna, coding for an essential enzyme in amino-sugar metabolism. the two srnas, although being highly similar in sequence and structure, act in a hierarchical manner. glmz, together with the rna chaperone, hfq, directly activates glms mrna translation by an anti-antisense mechanism. in contrast, glmy acts upstream of glmz and positively regulates glms by antagonizing glmz rna inactivation. we also report the first example, to our knowledge, of mrna expression being controlled by the poly(a) status of a chromosomally encoded srna. we show that in wild-type cells, glmy rna is unstable due to 3' end polyadenylation; whereas in an e. coli pcnb mutant defective in rna polyadenylation, glmy is stabilized and accumulates, which in turn stabilizes glmz and causes glms overproduction. our study reveals hierarchical action of two well-conserved srnas in a complex regulatory cascade that controls the glms mrna. similar cascades of noncoding rna regulators may operate in other organisms.",1
"to clarify the role of micro (mi) rnas in gastric carcinogenesis, we studied the expression and function of mirnas in gastric carcinoma (gc) cells. initially, we performed microarray analysis using total rna from 3 human gc cell lines and noncancerous gastric tissue. among the downregulated mirnas in gc cells, mir-212 expression was decreased in all 8 gc cell lines examined and a significant decrease of mir-212 expression in human primary gc tissues was also observed in 6 of 11 cases. transfection of the precursor mir-212 molecule induced decreased growth of 3 gc cell lines. using 3 different databases, methyl-cpg-binding protein mecp2 was postulated to be a target of mir-212. as seen on reporter assaying, mir-212 repressed the construct with the mecp2 3'-utr. ectopic expression of mir-212 repressed expression of the mecp2 protein but not the mecp2 mrna level. these data suggest that downregulation of mir-212 may be related to gastric carcinogenesis through its target genes, such as mecp2.",1
"we aimed to determine the expression of microrna-203 (mir-203) in human lung cancer cell lines and to evaluate the effects of mir-203 by targeting survivin, on the lung cancer cell line 95-d to provide potential new strategies for treating lung cancer. the expression of mir-203 was detected using quantitative real-time pcr (qrt-pcr) in the in vitro cultured lung cancer cells a549, hcc827, nci-h1299, and 95-d as well as in normal human bronchial epithelial cells. following a 72-h transfection with the mir-203 precursor in 95-d lung cancer cells, the change in mir-203 expression was detected using qrt-pcr and the resulting effect on survivin protein expression was ascertained by western blot analysis. the influence of mir-203 on the viability of 95-d lung cancer cells was evaluated using 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (mtt) assay. the effect of mir-203 on 95-d cell proliferation was analyzed using flow cytometry. the consequences of mir-203 expression on 95-d cell apoptosis were analyzed by annexin v/propidium iodide double staining coupled with flow cytometry. the role of mir-203 in the invasive potential of 95-d cells was studied using a transwell chamber assay. a luciferase reporter gene system was used to verify that survivin is a target gene for mir-203. by qrt-pcr, the expression of mir-203 was lower in lung cancer cells than in normal bronchial epithelial cells (p < 0.01), and the expression of mir-203 in 95-d lung cancer cells was significantly higher after a 72-h transfection with the mir-203 precursor (p < 0.01). after a 72-h transfection with the mir-203 precursor, survivin protein levels in 95-d cells were significantly decreased (p < 0.01). cell viability, as assessed with an mtt assay, decreased following an increase in mir-203 expression (p < 0.05). the flow cytometry results indicated that after mir-203 expression increased, the cell proliferation index decreased (p < 0.05) and the number of apoptotic cells increased (p < 0.01). increased mir-203 expression led to a significant decrease in the number of cells that migrated through a transwell chamber membrane (p < 0.01). the luciferase reporter gene system demonstrated that the relative luciferase activity significantly decreased after transfection with the mir-203 precursor (p < 0.05). the expression of mir-203 is downregulated in lung cancer cells. mir-203 negatively regulates survivin protein expression and inhibits the proliferation and invasion of lung cancer cells. therapeutic strategies that enhance mir-203 expression or silence survivin could potentially benefit lung cancer patients.",1
"erbb2 overexpression occurs in numerous types of primary human tumors and alterations in microrna (mirna) expression have been associated with tumor suppression or tumorigenesis in human cancer, nevertheless, little is known about natural mirnas acting on erbb2. in this study, bioinformatical analysis of the 3'-utrs of erbb2 revealed the target elements for mir-548d-3p and mir-559. moreover, a predicted mirna/mrna interaction experimental validation showed that both mir-548d-3p and mir-559 can interact specifically with the 3'-utr of the erbb2 mrna. and mir-548d-3p plus mir-559 transfection showed a cooperative regulation of translationally repressing erbb2 mrna rather than by either mir-548d-3p or mir-559 alone. these results not only support the idea that different mirnas can simultaneously and cooperatively repress a given target mrna but also preliminarily validate the role of mir-548d-3p and mir-559 in regulating the erbb2 expression. these data provide molecular basis for the application of mirnas in erbb2-targeted therapy.",1
"background bacterial transcription attenuation occurs through a variety of cis-regulatory elements that control gene expression in response to a wide range of signals. the signal-sensing structures in attenuators are so diverse and rapidly evolving that only a small fraction have been properly annotated and characterized to date. here we apply a broad-spectrum detection tool in order to achieve a more complete view of the transcriptional attenuation complement of key bacterial species. results our protocol seeks gene families with an unusual frequency of 5' terminators found across multiple species. many of the detected attenuators are part of annotated elements, such as riboswitches or t-boxes, which often operate through transcriptional attenuation. however, a significant fraction of candidates were not previously characterized in spite of their unmistakable footprint. we further characterized some of these new elements using sequence and secondary structure analysis. we also present elements that may control the expression of several non-homologous genes, suggesting co-transcription and response to common signals. an important class of such elements, which we called mobile attenuators, is provided by 3' terminators of insertion sequences or prophages that may be exapted as 5' regulators when inserted directly upstream of a cellular gene. conclusions we show here that attenuators involve a complex landscape of signal-detection structures spanning the entire bacterial domain. we discuss possible scenarios through which these diverse 5' regulatory structures may arise or evolve.",1
"micro rnas (mirnas) are post-transcriptional modulators of gene expression that regulate the stability and translation of their target messenger rnas (mrnas). here we report that the levels of a human brain-enriched mirna-125b are up-regulated in interleukin-6 (il-6)-stressed normal human astrocytes (nha), a treatment known to induce astrogliosis. in vitro, anti-mirna-125b added exogenously to il-6-stressed nha cultures attenuated both glial cell proliferation and increased the expression of the cyclin-dependent kinase inhibitor 2a (cdkn2a), a mirna-125b target and negative regulator of cell growth. a strong positive correlation between mirna-125b abundance and the glial cell markers glial fibrillary acidic protein (gfap) and vimentin, and cdkn2a down-regulation was noted in advanced alzheimer's disease (ad) and in down's syndrome (ds) brain, chronic neurological disorders associated with astrogliosis. the results suggest that mirna-125b up-regulation contributes to astrogliosis and to defects in the cell cycle that are characteristic of degenerating brain tissues.",1
"long intergenic noncoding rnas (lincrnas) are important regulators of gene expression. although lincrnas are expressed in immune cells, their functions in immunity are largely unexplored. here, we identify an immunoregulatory lincrna, lincrna-eps, that is precisely regulated in macrophages to control the expression of immune response genes (irgs). transcriptome analysis of macrophages from lincrna-eps-deficient mice, combined with gain-of-function and rescue experiments, revealed a specific role for this lincrna in restraining irg expression. consistently, lincrna-eps-deficient mice manifest enhanced inflammation and lethality following endotoxin challenge in vivo. lincrna-eps localizes at regulatory regions of irgs to control nucleosome positioning and repress transcription. further, lincrna-eps mediates these effects by interacting with heterogeneous nuclear ribonucleoprotein l via a canaca motif located in its 3' end. together, these findings identify lincrna-eps as a repressor of inflammatory responses, highlighting the importance of lincrnas in the immune system.",1
"the approximately 1.2-kb 5'-noncoding region (5'-ncr) of mrna species encoding mouse kv1.4, a member of the shaker-related subfamily of voltage-gated potassium channels, was shown to mediate internal ribosome entry in cells derived from brain, heart, and skeletal muscle, tissues known to express kv1.4 mrna species. we also show that the upstream approximately 1.0 kb and the downstream approximately 0.2 kb of the kv1.4 5'-ncr independently mediated internal ribosome entry; however, separately, these sequences were less efficient in mediating internal ribosome entry than when together in the complete (and contiguous) 5'-ncr. using enzymatic structure probing, the 3'-most approximately 0.2 kb was predicted to form three distinct stem-loop structures (stem-loops x, y, and z) and two defined single-stranded regions (loops psi and omega) in the presence and absence of the upstream approximately 1.0 kb. although the systematic deletion of sequences within the 3'-most approximately 0.2 kb resulted in distinct changes in expression, enzymatic structure probing indicated that local rna folding was not completely altered. structure probing analysis strongly suggested an interaction between stem-loop x and a downstream polypyrimidine tract; however, opposing changes in activity were observed when sequences within these two regions were independently deleted. moreover, deletions correlating with positive as well as negative changes in expression altered rnase cleavage within stem-loop x, indicating that this structure may be an integral element. therefore, these findings indicate that kv1.4 expression is mediated through a complex interplay between many distinct rna regions.",1
"background comparative analysis of rna sequences is the basis for the detailed and accurate predictions of rna structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. underlying these accomplishments are very large, well-organized, and processed collections of rna sequences. this data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. this type of information can be fundamental for and have an influence on the study of phylogenetic relationships, rna structure, and the melding of these two fields. results we have prepared a large web site that disseminates our comparative sequence and structure models and data. the four major types of comparative information and systems available for the three ribosomal rnas (5s, 16s, and 23s rrna), transfer rna (trna), and two of the catalytic intron rnas (group i and group ii) are: (1) current comparative structure models; (2) nucleotide frequency and conservation information; (3) sequence and structure data; and (4) data access systems. conclusions this online rna sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our comparative rna web (crw) site in the future, more data and information will be added to these existing categories, new categories will be developed, and additional rnas will be studied and presented at the crw site.",1
"rna secondary structures play several important roles in the human immunodeficiency virus (hiv) life cycle. to assess whether rna secondary structure might affect the function of the hiv protease and reverse transcriptase genes, which are the main targets of anti-hiv drugs, we applied a series of different computational approaches to detect rna secondary structures, including thermodynamic rna folding predictions, synonymous variability analysis, and covariance analysis. each method independently revealed strong evidence of a novel rna secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, a, b, and c. first, rna folding calculations by mfold and rnafold both predicted the secondary structure with high confidence. moreover, the same structure was predicted in a diverse set of reference sequences in hiv-1 group m, indicating that it is conserved across this group. second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 hiv-1 subtype b sequences from clinical samples. third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems a and b. finally, this structure was validated experimentally using selective 2'-hydroxyl acylation and primer extension (shape). discovery of this novel secondary structure suggests many directions for further functional investigation.",1
"cd4(+) memory t cells include the th17 cell population, which has been shown to be implicated in autoimmune and inflammatory diseases. these memory t cells express higher il-23r and produce more il-17 compared with their naive counterparts. however, the molecular mechanisms that regulate il-23r expression in human t cells are not completely understood. micrornas play important roles in a wide range of biological events through posttranscriptional suppression of target mrnas. in this article, we provide evidence that a specific microrna, let-7f, inhibits il-23r expression in human cd4(+) memory t cells. endogenous expression of let-7f in memory t cells is significantly lower when compared with naive t cells, and let-7f blocks il-23r expression through its complementary target sequence within 3' untranslated region of target gene. furthermore, exogenous transfection of a let-7f mimic into memory t cells results in downregulation of il-23r and its downstream cytokine, il-17. our findings reveal a novel mechanism in regulating the il-23/il-23r pathway and subsequent downstream il-17 production, which may provide novel therapeutics for human inflammatory and autoimmune diseases.",1
"unlabelled micrornas (mirnas) are small noncoding rnas that regulate gene expression by interacting with the 3' untranslated region (3'-utr) of multiple mrnas. recent studies have linked mirnas to the development of cancer metastasis. in this study, we show that mir-194 is specifically expressed in the human gastrointestinal tract and kidney. moreover, mir-194 is highly expressed in hepatic epithelial cells, but not in kupffer cells or hepatic stellate cells, two types of mesenchymal cells in the liver. mir-194 expression was decreased in hepatocytes cultured in vitro, which had undergone a dedifferentiation process. furthermore, expression of mir-194 was low in liver mesenchymal-like cancer cell lines. the overexpression of mir-194 in liver mesenchymal-like cancer cells reduced the expression of the mesenchymal cell marker n-cadherin and suppressed invasion and migration of the mesenchymal-like cancer cells both in vitro and in vivo. we further demonstrated that mir-194 targeted the 3'-utrs of several genes that were involved in epithelial-mesenchymal transition and cancer metastasis. conclusion these results support a role of mir-194, which is specifically expressed in liver parenchymal cells, in preventing liver cancer cell metastasis.",1
"metastasis is a multistep process involving modification of morphology to suit migration, reduction of tumor cell adhesion to the extracellular matrix, increase of cell mobility, tumor cell resistance to anoikis, and other steps. micrornas are well-suited to regulate tumor metastasis due to their capacity to repress numerous target genes in a coordinated manner, thereby enabling their intervention at multiple steps of the invasion-metastasis cascade. in this study, we identified a microrna exemplifying these attributes, mir-124, whose expression was reduced in aggressive mda-mb-231 and sk-3rd breast cancer cells. down-regulation of mir-124 expression in highly aggressive breast cancer cells contributed in part to dna hypermethylation around the promoters of the three genes encoding mir-124. ectopic expression of mir-124 in mda-mb-231 cells suppressed metastasis-related traits including formation of spindle-like morphology, migratory capacity, adhesion to fibronectin, and anoikis. these findings indicate that mir-124 suppresses multiple steps of metastasis by diverse mechanisms in breast cancer cells and suggest a potential application of mir-124 in breast cancer treatment.",1
"rationale idiopathic pulmonary fibrosis (ipf) is a disease of progressive lung fibrosis with a high mortality rate. in organ repair and remodeling, epigenetic events are important. micrornas (mirnas) regulate gene expression post-transcriptionally and can target epigenetic molecules important in dna methylation. the mir-17~92 mirna cluster is critical for lung development and lung epithelial cell homeostasis and is predicted to target fibrotic genes and dna methyltransferase (dnmt)-1 expression. objectives we investigated the mir-17~92 cluster expression and its role in regulating dna methylation events in ipf lung tissue. methods expression and dna methylation patterns of mir-17~92 were determined in human ipf lung tissue and fibroblasts and fibrotic mouse lung tissue. the relationship between the mir-17~92 cluster and dnmt-1 expression was examined in vitro. using a murine model of pulmonary fibrosis, we examined the therapeutic potential of the demethylating agent, 5'-aza-2'-deoxycytidine. measurements and main results compared with control samples, mir-17~92 expression was reduced in lung biopsies and lung fibroblasts from patients with ipf, whereas dnmt-1 expression and methylation of the mir-17~92 promoter was increased. several mirnas from the mir-17~92 cluster targeted dnmt-1 expression resulting in a negative feedback loop. similarly, mir-17~92 expression was reduced in the lungs of bleomycin-treated mice. treatment with 5'-aza-2'-deoxycytidine in a murine bleomycin-induced pulmonary fibrosis model reduced fibrotic gene and dnmt-1 expression, enhanced mir-17~92 cluster expression, and attenuated pulmonary fibrosis. conclusions this study provides insight into the pathobiology of ipf and identifies a novel epigenetic feedback loop between mir-17~92 and dnmt-1 in lung fibrosis.",1
"transmissible gastroenteritis virus (tgev), belonging to the coronaviridae family, is the key cause of the fatal diarrhea of piglets and results in many pathological processes. micrornas (mirnas) play a key role in the regulation of virus-induced apoptosis. during the process of apoptosis induced by tgev infection in pk-15 cells, the mir-27b is notably down-regulated. thus, we speculate that mir-27b is involved in regulating the process of apoptosis in pk-15 cells. in this study we demonstrated that the over-expression of mir-27b led to the inhibition of tgev-induced apoptosis, reduction of bax protein level, and decrease of caspase-3 and -9 activities. conversely, silencing of mir-27b by mir-27b inhibitors enhanced apoptosis via up-regulating bax expression and promoting the activities of caspase-3 and -9 in tgev-infected cells. subsequently, the runt-related transcription factor 1 (runx1) is a candidate target of mir-27b predicted by bioinformatics search. we further identified that the mir-27b directly bound to the 3' utr of runx1 mrna and suppressed runx1 expression, which indicates runx1 is the direct target gene of mir-27b. the over-expression of runx1 increased apoptosis and knockdown runx1blocked apoptosis of viral-infected cells via regulating bax expression and the activities of caspase-3 and -9. our data reveal that mir-27b may repress the mitochondrial pathway of apoptosis by targeting runx1, indicating that tgev may induce apoptosis via down-regulating mir-27b and that mir-27b may act as a target for therapeutic intervention.",1
"rationale a strong risk factor for atherosclerosis- the leading cause of heart attacks and strokes- is the elevation of low-density lipoprotein cholesterol (ldl-c) in blood. the ldl receptor (ldlr) is the primary pathway for ldl-c removal from circulation, and their levels are increased by statins -the main treatment for high blood ldl-c. however, statins have low efficiency because they also increase pcsk9 which targets ldlr for degradation. since micrornas have recently emerged as key regulators of cholesterol homeostasis, our aim was to identify potential microrna-based therapeutics to decrease blood ldl-c and prevent atherosclerosis. methods and results we over expressed and knocked down mir-27a in hepg2 cells to assess its effect on the expression of key players in the ldlr pathway using pcr arrays, elisas, and western blots. we found that mir-27a decreases ldlr levels by 40% not only through a direct binding to its 3' untranslated region but also indirectly by inducing a 3-fold increase in pcsk9, which enhances ldlr degradation. interestingly, mir-27a also directly decreases lrp6 and ldlrap1, two other key players in the ldlr pathway that are required for efficient endocytosis of the ldlr-ldl-c complex in the liver. the inhibition of mir-27a using lock nucleic acids induced a 70% increase in ldlr levels and, therefore, it would be a more efficient treatment for hypercholesterolemia because of its desirable effects not only on ldlr but also on pcsk9. conclusion the results presented here provide evidence supporting the potential of mir-27a as a novel therapeutic target for the prevention of atherosclerosis.",1
"new genes can originate by the combination of sequences from unrelated genes or their duplicates to form a chimeric structure. these chimeric genes often evolve rapidly, suggesting that they undergo adaptive evolution and may therefore be involved in novel phenotypes. their functions, however, are rarely known. here, we describe the phenotypic effects of a chimeric gene, sphinx, that has recently evolved in drosophila melanogaster. we show that a knockout of this gene leads to increased male-male courtship in d. melanogaster, although it leaves other aspects of mating behavior unchanged. comparative studies of courtship behavior in other closely related drosophila species suggest that this mutant phenotype of male-male courtship is the ancestral condition because these related species show much higher levels of male-male courtship than d. melanogaster. d. melanogaster therefore seems to have evolved in its courtship behaviors by the recruitment of a new chimeric gene.",1
"a number of studies have implicated that micrornas (mirnas) play a critical role in the development of gestational diabetes mellitus (gdm). however, the role of mir-657 in gdm remains vague up to date. we aim to investigate the modifying effect of mir-657 on gdm, which will provide new insight into the pathogenesis of gdm and may help to identify new diagnostic or therapeutic targets for gdm. increased expression of mir-657 but decreased expression of interleukin-37 (il-37) was observed in patients with gdm. besides, negative association between mir-657 and il-37 was demonstrated in this study. mir-657 could targetedly regulate il-37 and enhance the proliferation of mononuclear macrophages. moreover, mir-657 promoted the generation of inflammatory cytokines (il-6 and tumor necrosis factor-α ) and activation of nuclear factor κb (nf-κb) in lipopolysaccharide-induced mononuclear macrophages, while its effect was significantly inhibited when exogenous recombinant il-37 was administrated into cells. accordingly, dysregulation of mir-657 contributes to the pathogenesis of gdm via il-37/nf-κb signaling axis.",1
"expression of the mannose receptor (mrc1/cd206) identifies macrophage subtypes, such as alternatively activated macrophages (aams) and m2-polarized tumor-associated macrophages (tams), which are endowed with tissue-remodeling, proangiogenic, and protumoral activity. however, the significance of mrc1 expression for tam's protumoral activity is unclear. here, we describe and characterize mir-511-3p, an intronic microrna (mirna) encoded by both mouse and human mrc1 genes. by using sensitive mirna reporter vectors, we demonstrate robust expression and bioactivity of mir-511-3p in mrc1(+) aams and tams. unexpectedly, enforced expression of mir-511-3p tuned down the protumoral gene signature of mrc1(+) tams and inhibited tumor growth. our findings suggest that transcriptional activation of mrc1 in tams evokes a genetic program orchestrated by mir-511-3p, which limits rather than enhances their protumoral functions. besides uncovering a role for mrc1 as gatekeeper of tam's protumoral genetic programs, these observations suggest that endogenous mirnas may operate to establish thresholds for inflammatory cell activation in tumors.",1
"human microrna (mir)-141 is a member of the mir‑200 family, which has been reported to be downregulated in gastric cancer, and involved in the proliferation of gastric cancer cells. however, little is currently known regarding its role in the migration of gastric cancer. the present study investigated the function of mir‑141 in gastric cancer cell migration, and evaluated the contribution of zinc finger e‑box‑binding homeobox 1 and 2 (zeb1/2) in mir‑141 mediated migration of gastric cancer cells. the expression levels of mir‑141 and its potential zeb1/2 targets were examined by quantitative polymerase chain reaction (qpcr) and western blotting, respectively. the migration of sgc‑7901 and hgc‑27 gastric cancer cells, which had been transfected with an mirna precursor, was examined by cell migration and wound healing assays. a luciferase activity assay was used to validate whether zeb1/2 was a direct target of mir‑141. the results demonstrated that overexpression of mir‑141 markedly inhibited the migration of gastric cancer cells in vitro. forced overexpression of mir‑141 significantly reduced the luciferase activity of the 3'‑untranslated region of zeb2 in gastric cancer cells. furthermore, the mrna and protein expression levels of zeb2 were reduced in cells overexpressing mir‑141, whereas the protein expression levels of e‑cadherin were increased. in gastric tumor samples the expression levels of zeb2 were inversely correlated with the expression of mir‑141. these results suggest that mir‑141 may be involved in the inhibition of gastric cancer cell migration, and that zeb2 is a target gene of mir-141.",1
"three muscle-specific micrornas, mir-206, -1, and -133, are induced during differentiation of c2c12 myoblasts in vitro. transfection of mir-206 promotes differentiation despite the presence of serum, whereas inhibition of the microrna by antisense oligonucleotide inhibits cell cycle withdrawal and differentiation, which are normally induced by serum deprivation. among the many mrnas that are down-regulated by mir-206, the p180 subunit of dna polymerase alpha and three other genes are shown to be direct targets. down-regulation of the polymerase inhibits dna synthesis, an important component of the differentiation program. the direct targets are decreased by mrna cleavage that is dependent on predicted microrna target sites. unlike small interfering rna-directed cleavage, however, the 5' ends of the cleavage fragments are distributed and not confined to the target sites, suggesting involvement of exonucleases in the degradation process. in addition, inhibitors of myogenic transcription factors, id1-3 and myor, are decreased upon mir-206 introduction, suggesting the presence of additional mechanisms by which micrornas enforce the differentiation program.",1
"background micrornas are a class of endogenous single strand non-coding rnas that are involved in many important physiological and pathological processes. the purpose of this study was to examine the expression levels of mir-497 in human breast cancer and its function in mda-mb-231 breast cancer cells. methods quantitative polymerase chain reaction was used to measure the expression levels of mir-497 in 40 breast cancer specimens and adjacent normal breast tissues. mtt assays, colony formation assays, wound healing assays, transwell assays and cell cycle assays were used to explore the potential function of mir-497 in mda-mb-231 breast cancer cells. dual-luciferase reporter assays were performed to analyze the regulation of putative target of mir-497, and western blot assays were used to validate the dual-luciferase results. results the expression of mir-497 in breast cancer specimens was lower than adjacent normal tissues (p conclusions mir-497 may act as a tumor suppressor gene in breast cancer. inhibited cellular growth, suppressed cellular migration and invasion, and g1 cell cycle arrest were observed upon overexpression of mir-497 in cells, possibly by targeting cyclin e1. these results indicate mir-497 could be considered a therapeutic target for the development of treatment for breast cancer.",1
"although some long noncoding rnas (lncrnas) have been shown to regulate gene expression in cis, it remains unclear whether lncrnas can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. here, we describe the genomically local and more distal functions of paupar, a vertebrate-conserved and central nervous system-expressed lncrna transcribed from a locus upstream of the gene encoding the pax6 transcription factor. knockdown of paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neural differentiation. paupar acts in a transcript-dependent manner both locally, to regulate pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with pax6 protein. paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by paupar transcript levels. our findings demonstrate that a lncrna can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.",1
"status epilepticus induces a cascade of protein expression changes contributing to the subsequent development of epilepsy. by identifying the cascade of molecular changes that contribute to the development of epilepsy we hope to be able to design therapeutics for preventing epilepsy. micrornas influence gene expression by altering mrna stability and/or translation and have been implicated in the pathology of multiple diseases. mir21 and its co-transcript mir21, micrornas produced from either the 5' or 3' ends of the same precursor rna strand, are increased in the hippocampus following status epilepticus. we have identified a mir21 binding site, in the 3' utr of neurotrophin-3 that inhibits translation. neurotrophin-3 mrna levels decrease in the hippocampus following se concurrent with the increase in mir21. mir21 levels in cultured hippocampal neurons inversely correlate with neurotrophin-3 mrna levels. treatment of hippocampal neuronal cultures with excess k(+)cl(-), a depolarizing agent mimicking the episode of status epilepticus, also results in an increase in mir21 and a decrease in neurotrophin-3 mrna. mir21 is a candidate for regulating neurotrophin-3 signaling in the hippocampus following status epilepticus.",1
"the tar hairpin of the hiv-1 rna genome is indispensable for trans-activation of the viral promoter and virus replication. the tar structure has been studied extensively, but most attention has been directed at the three-nucleotide bulge that constitutes the binding site of the viral tat protein. in contrast, the conformational properties of the apical loop have remained elusive. we performed biochemical studies and molecular dynamics simulations, which indicate that the tar loop is structured and stabilized by a cross-loop base pair between residues c30 and g34. mutational disruption of the cross-loop base pair results in reduced tat response of the ltr promoter, which can be rescued by compensatory mutations that restore the base pair. thus, tat-mediated transcriptional activation depends on the structure of the tar apical loop. the c30-g34 cross-loop base pair classes tar in a growing family of hairpins with a structured loop that was recently identified in ribosomal rna, trna, and several viral and cellular mrnas.",1
"micrornas (mirnas) modulate complex physiological and pathological processes by repressing expression of multiple components of cellular regulatory networks. here we demonstrate that mirnas encoded by the mir-23∼27∼24 gene clusters are enriched in endothelial cells and highly vascularized tissues. inhibition of mir-23 and mir-27 function by locked nucleic acid-modified anti-mirnas represses angiogenesis in vitro and postnatal retinal vascular development in vivo. moreover, mir-23 and mir-27 are required for pathological angiogenesis in a laser-induced choroidal neovascularization mouse model. mir-23 and mir-27 enhance angiogenesis by promoting angiogenic signaling through targeting sprouty2 and sema6a proteins, which exert antiangiogenic activity. manipulating mir-23/27 levels may have important therapeutic implications in neovascular age-related macular degeneration and other vascular disorders.",1
"micrornas regulate the expression of over 60% of protein coding genes by targeting their mrnas to ago2-containing complexes in the cytoplasm and promoting their translational inhibition and/or degradation. there is little evidence so far for microrna-mediated regulation of other classes of non-coding rnas. here we report that microrna-9 (mir-9) regulates the expression of the metastasis associated lung adenocarcinoma transcript 1 (malat-1), one of the most abundant and conserved long non-coding rnas. intriguingly, we find that mir-9 targets ago2-mediated regulation of malat1 in the nucleus. our findings reveal a novel direct regulatory link between two important classes of non-coding rnas, mirs and lncrnas, and advance our understanding of microrna functions.",1
"breast cancer metastasis suppressor 1 (brms1) is a predominantly nuclear protein that differentially regulates expression of multiple genes, leading to suppression of metastasis without blocking orthotopic tumor growth in multiple human and murine cancer cells of diverse origins. we hypothesized that mir-146 may be involved in the ability of brms1 to supress metastasis because mir-146 expression is altered by brms1 and because brms1 and mir-146 are both associated with decreased signaling through the nuclear factor-kappab pathway. brms1 significantly up-regulates mir-146a by 6- to 60-fold in metastatic mda-mb-231 and mda-mb-435 cells, respectively, and mir-146b by 40-fold in mda-mb-435 as measured by real-time quantitative reverse transcription-pcr. transduction of mir-146a or mir-146b into mda-mb-231 down-regulated expression of epidermal growth factor receptor, inhibited invasion and migration in vitro, and suppressed experimental lung metastasis by 69% and 84%, respectively (mean +/- se: empty vector = 39 +/- 6, mir-146a = 12 +/- 1, mir-146b = 6 +/- 1). these results further support the recent notion that modulating the levels of mir-146a or mir-146b could have a therapeutic potential to suppress breast cancer metastasis.",1
"favorable outcome after chemotherapy of glioblastomas cannot unequivocally be linked to promoter hypermethylation of the o6-methylguanine-dna methyltransferase (mgmt) gene encoding a dna repair enzyme associated with resistance to alkylating agents. this indicates that molecular mechanisms determining mgmt expression have not yet been fully elucidated. we here show that glioblastomas are capable to downregulate mgmt expression independently of promoter methylation by elongation of the 3'-utr of the mrna, rendering the alternatively polyadenylated transcript susceptible to mirna-mediated suppression. while the elongated transcript is poorly expressed in normal brain, its abundance in human glioblastoma specimens is inversely correlated with mgmt mrna expression. using a bioinformatically guided experimental approach, we identified mir-181d, mir-767-3p, and mir-648 as significant post-transcriptional regulators of mgmt in glioblastomas; the first two mirnas induce mgmt mrna degradation, the latter affects mgmt protein translation. a regression model including the two mirnas influencing mgmt mrna expression and the mgmt methylation status reliably predicts the cancer genome atlas mgmt expression data. responsivity of mgmt expressing t98g glioma cells to temozolomide was significantly enhanced after transfection of mir-181d, mir-767-3p, and mir-648. taken together, our results uncovered alternative polyadenylation of the mgmt 3'-utr and mirna targeting as new mechanisms of mgmt silencing.",1
"the plant snorna database ( provides information on small nucleolar rnas from arabidopsis and eighteen other plant species. information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. the arabidopsis information is divided into box c/d and box h/aca snornas, and within each of these groups, by target sites in rrna, snrna or unknown. alignments of orthologous genes and gene variants from different plant species are available for many snorna genes. plant snorna genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.",1
"generally, most mirnas that were up-regulated during differentiation promoted adipogenesis, but our research indicated that up-regulation of mir-145 in porcine preadipocytes did not promote but inhibit adipogenesis. in this study, mir-145 was significantly up-regulated during porcine dedifferentiated fat (dfat) cells differentiation. in mir-145 overexpressed dfat cells, adipogenesis was inhibited and triglycerides accumulation was decreased after hormone stimulation (p<0.05). furthermore, up-regulation of mir-145 expression repressed induction of mrna levels of adipogenic markers, such as ccaat/enhancer-binding protein α (c/ebpα), and peroxisome proliferator-activated receptor γ2 (pparγ2). these effects caused by mir-145 overexpression were mediated by insulin receptor substrate 1 (irs1) as a mechanism. these data suggested that induced mir-145 expression during differentiation could inhibit adipogenesis by targeting irs1, and mir-145 may be novel agent for adipose tissue engineering.",1
"micrornas comprise a broad class of small non-coding rnas that control expression of complementary target messenger rnas. dysregulation of micrornas by several mechanisms has been described in various disease states including cardiac disease. whereas previous studies of cardiac disease have focused on micrornas that are primarily expressed in cardiomyocytes, the role of micrornas expressed in other cell types of the heart is unclear. here we show that microrna-21 (mir-21, also known as mirn21) regulates the erk-map kinase signalling pathway in cardiac fibroblasts, which has impacts on global cardiac structure and function. mir-21 levels are increased selectively in fibroblasts of the failing heart, augmenting erk-map kinase activity through inhibition of sprouty homologue 1 (spry1). this mechanism regulates fibroblast survival and growth factor secretion, apparently controlling the extent of interstitial fibrosis and cardiac hypertrophy. in vivo silencing of mir-21 by a specific antagomir in a mouse pressure-overload-induced disease model reduces cardiac erk-map kinase activity, inhibits interstitial fibrosis and attenuates cardiac dysfunction. these findings reveal that micrornas can contribute to myocardial disease by an effect in cardiac fibroblasts. our results validate mir-21 as a disease target in heart failure and establish the therapeutic efficacy of microrna therapeutic intervention in a cardiovascular disease setting.",1
"abnormal proliferation of vascular smooth muscle cells (vsmcs) contributes to the development of cardiovascular diseases. studies have shown the great impact of micrornas (mirnas) on the cell proliferation of vsmcs. this study examined the effects of mir-137 on the cell proliferation and migration of vsmcs and also explored the underlying molecular mechanisms. the mrna and protein expression levels were determined by qrt-pcr and western blot assays, respectively. the cck-8 assay, wound healing assay and transwell migration assay were performed to measure cell proliferation and migration of vsmcs. the mir-137-targeted 3'untranslated region of insulin-like growth factor-binding protein-5 (igfbp-5) was confirmed by luciferase reporter assay. platelet-derived growth factor-bb (pdgf-bb) treatment enhanced cell proliferation and suppressed the expression of mir-137 in vsmcs. the gain-of-function and loss-of-function assays showed that overexpression of mir-137 suppressed the cell proliferation and migration, and also inhibited the expression of matrix genes of vsmcs; down-regulation of mir-137 had the opposite effects on vsmcs. bioinformatics analysis and luciferase report assay results showed that igfbp-5 was a direct target of mir-137, and mir-137 overexpression suppressed the igfbp-5 expression and down-regulation of mir-137 increased the igfbp-5 expression in vsmcs. pdgf-bb treatment also increased the igfbp-5 mrna expression. in addition, enforced expression of igfbp-5 reversed the inhibitory effects of mir-137 on cell proliferation and migration of vsmcs. more importantly, overexpression of mir-137 also suppressed the activity of mtor/stat3 signaling in vsmcs. taken together, the results suggest that mir-137 may suppress cell proliferation and migration of vsmcs via targeting igfbp-5 and modulating mtor/stat3 signaling pathway.",1
"background micrornas (mirnas) are small, noncoding rna molecules of 20 to 22 nucleotides that regulate gene expression by binding to their 3' untranslated region (3'utr). increasing data implicate altered mirna participation in the progress of cancer. we previously reported that cyp2j2 epoxygenase promotes human cancer phenotypes. but whether and how cyp2j2 is regulated by mirna is not understood. methods and results using bioinformatics analysis, we found potential target sites for mirna let-7b in 3'utr of human cyp2j2. luciferase and western blot assays revealed that cyp2j2 was regulated by let-7b. in addition, let-7b decreased the enzymatic activity of endogenous cyp2j2. furthermore, let-7b may diminish cell proliferation and promote cell apoptosis of tumor cells via posttranscriptional repression of cyp2j2. tumor xenografts were induced in nude mice by subcutaneous injection of mda-mb-435 cells. the let-7b expression vector, psilencer-let-7b, was injected through tail vein every 3 weeks. let-7b significantly inhibited the tumor phenotype by targeting cyp2j2. moreover, quantitative real-time polymerase chain reaction and western blotting were used to determine the expression levels of let-7b and cyp2j2 protein from 18 matched lung squamous cell cancer and adjacent normal lung tissues; the expression level of cyp2j2 was inversely proportional to that of let-7b. conclusions our results demonstrated that the decreased expression of let-7b could lead to the high expression of cyp2j2 protein in cancerous tissues. these findings suggest that mirna let-7b reduces cyp2j2 expression, which may contribute to inhibiting tumor phenotypes.",1
"insulin-like growth factor ii (igf-ii) is a fetal growth factor, which belongs to the family of insulin-like peptides. during fetal life, the igf-ii gene generates three mrnas with different 5' untranslated regions (utrs), but identical coding regions and 3' utrs. we have shown previously that igf-ii leader 3 mrna translation is regulated by a rapamycin-sensitive pathway, whereas leader 4 mrna is constitutively translated, but so far the significance of leader 2 mrna has been unclear. here, we show that leader 2 mrna is translated efficiently in an eif4e-independent manner. in a bicistronic vector system, the 411 nt leader 2 was capable of internal initiation via a phylogenetically conserved internal ribosome entry site (ires), located in the 3' half of the leader. the ires is composed of an approx. 120 nt ribosome recruitment element, followed by an 80 nt spacer region, which is scanned by the ribosomal pre-initiation complex. since cap-dependent translation is down-regulated during cell division, leader 2 might facilitate a continuous igf-ii production in rapidly dividing cells during development.",1
"a better understanding of the molecular mechanisms that govern human adipose tissue-derived mesenchymal stem cells (hascs) differentiation could improve hascs-based cell therapy and provide new insights into a number of diseases, including obesity. in this study, we examined the roles of microrna-21 (mir-21) in adipogenic differentiation of hascs. we found that mir-21 expression was transiently increased after induction of adipogenic differentiation, peaked at 3 days, and returned to the baseline level 8 days. lentiviral overexpression of mir-21 enhanced adipogenic differentiation. overexpression of mir-21 decreased both protein and mrna levels of tgfbr2. the expression of tgfbr2 was decreased during adipogenic differentiation of hascs in concordance with an increase in the level of mir-21. in contrast, inhibiting mir-21 with 2'-o-methyl-antisense microrna increased tgfbr2 protein levels in hascs, accompanied by decreased adipogenic differentiation. the activity of a luciferase construct containing the mir-21 target site from the tgfbr2 3'utr was lower in lv-mir21-infected hascs than in lv-milacz infected cells. tgf-beta-induced inhibition of adipogenic differentiation was significantly decreased in mir-21 overexpressing cells compared with control lentivirus-transduced cells. rna interference-mediated downregulation of smad3, but not of smad2, increased adipogenic differentiation. overexpression and inhibition of mir-21 altered smad3 phosphorylation without affecting total levels of smad3 protein. our data are the first to demonstrate that the role of mir-21 in the adipogenic differentiation of hascs is mediated through the modulation of tgf-beta signaling. this study improves our knowledge of the molecular mechanisms governing hascs differentiation, which may underlie the development of obesity or other metabolic diseases.",1
"growth and differentiation factor 5 (gdf5) has been implicated in chondrogenesis and joint formation, and an association of gdf5 and osteoarthritis (oa) has been reported recently. however, the in vivo function of gdf5 remains mostly unclarified. although various human gdf5 mutations and their phenotypic consequences have been described, only loss-of-function mutations that cause brachypodism (shortening and joint ankylosis of the digits) have been reported in mice. here, we report a new gdf5 allele derived from a large-scale n-ethyl-n-nitrosourea mutagenesis screen. this allele carries an amino acid substitution (w408r) in a highly conserved region of the active signaling domain of the gdf5 protein. the mutation is semi-dominant, showing brachypodism and ankylosis in heterozygotes and much more severe brachypodism, ankylosis of the knee joint and malformation with early-onset oa of the elbow joint in homozygotes. the mutant gdf5 protein is secreted and dimerizes normally, but inhibits the function of the wild-type gdf5 protein in a dominant-negative fashion. this study further highlights a critical role of gdf5 in joint formation and the development of oa, and this mouse should serve as a good model for oa.",1
"mirnas are a family of approximately 22-nuleotide-long noncoding rnas involved in the formation and progress of tumors. since traditional methods for the detection of mirnas expression have many disadvantages, we developed a simple method called polya rt pcr. with this method, we detected a series of mirnas and found that mir-126 is one of the mirnas underexpressed in breast cancer cells. flow cytometry analysis showed that mir-126 inhibited cell cycle progression from g1/g0 to s. further studies revealed that mir-126 targeted irs-1 at the translation level. knocking down of irs-1 suppresses cell growth in hek293 and breast cancer cell mcf-7, which recapitulates the effects of mir-126. in conclusion, we developed a simple method for high-throughput screening of mirnas and found that mir-126, a cell growth suppressor, targets irs-1.",1
"heparin binding epidermal growth factor (hbegf) is expressed in podocytes and was shown to play a role in glomerular physiology. microrna binding sites on the 3'utr of hbegf were predicted using mirwalk algorithm and followed by dna sequencing in 103 patients diagnosed with mild or severe glomerulopathy. a single nucleotide polymorphism, mirsnp c1936t (rs13385), was identified at the 3'utr of hbegf that corresponds to the second base of the hsa-mir-1207-5p seed region. when ab8/13 undifferentiated podocytes were transfected with mirna mimics of hsa-mir-1207-5p, the hbegf protein levels were reduced by about 50%. a dna fragment containing the mirsnp allele-1936c was cloned into the pmir-report luciferase vector and co-transfected with mirna mimics of hsa-mir-1207-5p into ab8/13 podocytes. in agreement with western blot data, this resulted in reduced luciferase expression demonstrating the ability of hsa-mir-1207-5p to directly regulate hbegf expression. on the contrary, in the presence of the mirsnp 1936t allele, this regulation was abolished. collectively, these results demonstrate that variant 1936t of this mirsnp prevents hsa-mir-1207-5p from down-regulating hbegf in podocytes. we hypothesized that this variant has a functional role as a genetic modifier. to this end, we showed that in a cohort of 78 patients diagnosed with cfhr5 nephropathy (also known as c3-glomerulopathy), inheritance of mirsnp 1936t allele was significantly increased in the group demonstrating progression to chronic renal failure on long follow-up. no similar association was detected in a cohort of patients with thin basement membrane nephropathy. this is the first report associating a mirsnp as genetic modifier to a monogenic renal disorder.",1
"a simple biochemical method to isolate mrnas pulled down with a transfected, biotinylated microrna was used to identify direct target genes of mir-34a, a tumor suppressor gene. the method reidentified most of the known mir-34a regulated genes expressed in k562 and hct116 cancer cell lines. transcripts for 982 genes were enriched in the pull-down with mir-34a in both cell lines. despite this large number, validation experiments suggested that ~90% of the genes identified in both cell lines can be directly regulated by mir-34a. thus mir-34a is capable of regulating hundreds of genes. the transcripts pulled down with mir-34a were highly enriched for their roles in growth factor signaling and cell cycle progression. these genes form a dense network of interacting gene products that regulate multiple signal transduction pathways that orchestrate the proliferative response to external growth stimuli. multiple candidate mir-34a-regulated genes participate in ras-raf-mapk signaling. ectopic mir-34a expression reduced basal erk and akt phosphorylation and enhanced sensitivity to serum growth factor withdrawal, while cells genetically deficient in mir-34a were less sensitive. fourteen new direct targets of mir-34a were experimentally validated, including genes that participate in growth factor signaling (araf and pik3r2) as well as genes that regulate cell cycle progression at various phases of the cell cycle (cyclins d3 and g2, mcm2 and mcm5, plk1 and smad4). thus mir-34a tempers the proliferative and pro-survival effect of growth factor stimulation by interfering with growth factor signal transduction and downstream pathways required for cell division.",1
"the wnt/β-catenin signaling is crucial for the proliferation and migration of breast cancer cells. however, the expression of microrna-224 (mir-224) in the different types of breast cancers and its role in the wnt/β-catenin signaling and the proliferation and migration of breast cancer cells are poorly understood. in this study, the levels of mir-224 in different types of breast cancer tissues and cell lines were examined by quantitative rt-pcr and the potential targets of mir-224 in the wnt/β-catenin signaling were investigated. the effects of altered mir-224 expression on the frequency of cd44+cd24- cancer stem-like cells (csc), proliferation and migration of mcf-7 and mda-mb-231 cells were examined by flow cytometry, mtt and transwell migration. we found that the levels of mir-224 expression in different types of breast cancer tissues and cell lines were associated inversely with aggressiveness of breast cancers. enhanced mir-224 expression significantly reduced the fizzled 5-regulated luciferase activity in 293t cells, fizzled 5 expression in mcf-7 and mda-mb-231 cells, the β-dependent luciferase activity in mcf-7 cells, and the nuclear translocation of β-catenin in mda-mb-231 cells. mir-224 inhibition significantly increased the percentages of csc in mcf-7 cells and enhanced proliferation and migration of mcf-7 cells. enhanced mir-224 expression inhibited proliferation and migration of mda-mb-231 cells, and the growth of implanted breast cancers in vivo. induction of frizzled 5 over-expression mitigated the mir-224-mediated inhibition of breast cancer cell proliferation. collectively, these data indicated that mir-224 down-regulated the wnt/β-catenin signaling possibly by binding to frizzled 5 and inhibited proliferation and migration of breast cancer cells.",1
"micrornas (mirnas) are a class of small endogenous gene regulators that play important roles in various developmental and pathological processes. however, little is known about the precise identity and functions of mir-26b in posterior capsule opacification (pco). in this study, we report that the expression of mir-26b is decreased in human pco-attached lens epithelial cells (lecs) and sra01/04 cells in the presence of tgf-β2. overexpression of mir-26b inhibited the proliferation of lecs based on mtt assays and brdu incorporation assays. in addition, the overexpression of mir-26b inhibited the migration ability of lecs, as shown by wound-healing and transwell migration assays. the overexpression of mir-26b increased the level of the lens epithelial marker e-cadherin and reduced the levels of mesenchymal-related proteins, such as fibronectin, a-sma, and type i collagen, in sra01/04 cells in the presence of tgf-β2. furthermore, the upregulation of e-cadherin and downregulation of mesenchymal-related proteins were induced in human pco-attached lecs transfected with mir-26b mimics. we further demonstrated that smad4 and cox-2 are targets of mir-26b in lecs using luciferase reporter assays. these data reveal that mir-26b can inhibit the proliferation, migration, and emt of lens epithelial cells, and restoration of mirna-26b may be a potential, novel therapeutic target for the prevention and treatment of posterior capsule opacification.",1
"background/aims micrornas (mirnas) play important roles in tumorigenesis. we investigated the roles and mechanisms of mir-138 in human non-small cell lung cancer (nsclc). methods the expression of mir-138 was first examined in nsclc cell lines and tumour tissues by real-time pcr the in vitro and in vivo functional effect of mir-138 was examined further. a luciferase reporter assay was conducted to confirm target association between mir-138 and the enhancer of zeste homolog 2 (ezh2). results mir-138 was frequently downregulated in nsclc cells and tissues. overexpression of mir-138 inhibited proliferation of nsclc cells in vitro and tumor growth in vivo. the ezh2 oncogene, which is often overexpressed in various human cancers and acts as an important regulator of cell growth and tumor invasion, was identified as a novel target of mir-138. mir-138 can bind to the 3' untranslated region (3' utr) of ezh2 and suppress the expression of ezh2 at both mrna and protein levels. furthermore, knockdown of ezh2 phenocopied the tumor suppressive effects of mir-138 in cell models, whereas ectopic expression of ezh2 rescued the suppressive effects of mir-138. conclusion these findings define a tumor suppressor function for mir-138 in nsclc and further suggest that mir-138 may represent a potential therapeutic target for nsclc patients.",1
"noncoding rna (ncrna) genes that produce functional rnas instead of encoding proteins seem to be somewhat more prevalent than previously thought. however, estimating their number and importance is difficult because systematic identification of ncrna genes remains challenging. here, we exploit a strong, surprising dna composition bias in genomes of some hyperthermophilic organisms: simply screening for gc-rich regions in the at-rich methanococcus jannaschii and pyrococcus furiosus genomes efficiently detects both known and new rna genes with a high degree of secondary structure. a separate screen based on comparative analysis also successfully identifies noncoding rna genes in p. furiosus. nine of the 30 new candidate genes predicted by these screens have been verified to produce discrete, apparently noncoding transcripts with sizes ranging from 97 to 277 nucleotides.",1
"angiogenesis, a key factor in ischemic heart disease, is rapidly initiated in response to hypoxic or ischemic conditions. micrornas (mirnas) are endogenously expressed small non-coding rnas that regulate gene expression at post-transcriptional level. the recent discovery of the involvement of these rnas in the control of angiogenesis renders them very attractive in the development of new approaches for restoring the angiogenic balance. in the present study, we explored that mir-483-5p, a microrna embedded in the intron of insulin-like growth factor 2 (igf2), acts as an endogenous angiogenesis-inhibiting factor. we identified that serum response factor (srf) is one of mir-483-5p target genes. these findings indicated that the mir-483-5p-srf pathway may offer a novel strategy for treatment with angiogenesis in ischemic heart disease patients.",1
"the efficacy of synaptic transmission depends, to a large extent, on postsynaptic receptor abundance. the molecular mechanisms controlling receptor abundance are poorly understood. we tested whether abundance of postsynaptic glutamate receptors (glurs) in drosophila neuromuscular junctions is controlled by micrornas, and provide evidence that it is. we show here that postsynaptic knockdown of dicer-1, the endoribonuclease necessary for microrna synthesis, leads to large increases in postsynaptic glur subunit messenger rna and protein. specifically, we measured increases in gluriia and gluriib but not gluriic. further, knockout of mir-284, a microrna predicted to bind to gluriia and gluriib but not gluriic, increases expression of gluriia and gluriib but not gluriic proportional to the number of predicted binding sites in each transcript. most of the de-repressed glur protein, however, does not appear to be incorporated into functional receptors, and only minor changes in synaptic strength are observed, which suggests that micrornas primarily regulate drosophila receptor subunit composition rather than overall receptor abundance or synaptic strength.",1
"the abnormal expression of several micrornas has a causal role in tumorigenesis with either antineoplastic or oncogenic functions. here we demonstrated that mir-126 and mir-126* play a tumor suppressor role in human melanoma through the direct or indirect repression of several key oncogenic molecules. the expression levels of mir-126&126* were elevated in normal melanocytes and primary melanoma cell lines, whereas they markedly declined in metastatic cells. indeed, the restored expression of mir-126&126* in two advanced melanoma cell lines was accompanied by a significant reduction of proliferation, invasion and chemotaxis in vitro as well as of growth and dissemination in vivo. in accordance, the reverse functional effects were obtained by knocking down mir-126&126* by transfecting antisense lna oligonucleotides in melanoma cells. looking for the effectors of these antineoplastic functions, we identified adam9 and mmp7, two metalloproteases playing a pivotal role in melanoma progression, as direct targets of mir-126&126*. in addition, as adam9 and mmp7 share a role in the proteolytic cleavage of the hb-egf precursor, we looked for the effectiveness of this regulatory pathway in melanoma, confirming the decrease of hb-egf activation as a consequence of mir-126&126*-dependent downmodulation of adam9 and mmp7. finally, gene profile analyses showed that mir-126&126* reexpression was sufficient to inactivate other key signaling pathways involved in the oncogenic transformation, as pi3k/akt and mapk, and to restore melanogenesis, as indicated by kit/mitf/tyr induction. in view of this mir-126&126* wide-ranging action, we believe that the replacement of these micrornas might be considered a promising therapeutic approach.",1
"aims this study aimed to investigate mir-106a expression in peripheral blood mononuclear cells (pbmcs) of chronic hepatitis b (chb) patients and to analyze the function of mir-106a. materials and methods mir-106a expression levels in pbmcs from 40 healthy controls and 56 chb patients were analyzed by quantitative real-time polymerase chain reaction (qrt-pcr). the luciferase activity assays were used to determine whether mir-106a binds to 3'utr of il-8. mir-106a mimics and inhibitors were transfected into healthy pbmcs. il-8 mrna and protein levels were detected and determined by qrt-pcr and elisa, respectively. results the qrt-pcr results suggested that the pbmc mir-106a levels were decreased in chb patients. il-8 was augmented in chb patients and was inversely correlated with mir-106a levels. the luciferase activity assays indicated that il-8 is a target of mir-106a. exogenous expression of mir-106a could significantly repress il-8 expression at both mrna and protein levels in pbmcs, whereas mir-106a inhibitor had the opposite effects. conclusions this study suggested that mir-106a is downregulated in pbmcs of chb patients and that mir-106a may play an important role in chb by targeting il-8.",1
"micrornas (mir) are small noncoding rna molecules that have recently emerged as critical regulators of gene expression and are often deregulated in cancer. in particular, mirs encoded by the mir-15a, mir-16-1 cluster seem to act as tumor suppressors. here, we evidence that the mir-15a, mir-16-1 cluster and related mir-15b, mir-16-2 cluster comprise mirs regulated by e2f1, a pivotal transcription factor that can induce both proliferation and cell death. e2f1 is a critical downstream target of the tumor suppressor retinoblastoma (rb). the rb pathway is often inactivated in human tumors resulting in deregulated e2f activity. we show that expression levels of the 4 mature mirs, mir-15a, mir-16-1 and mir-15b, mir-16-2, as well as their precursor pri-mirnas, are elevated upon activation of ectopic e2f1. moreover, activation of endogenous e2fs upregulates expression of these mirs and endogenous e2f1 binds their respective promoters. importantly, we corroborate that mir-15a/b inhibits expression of cyclin e, the latter a key direct transcriptional target of e2f pivotal for the g(1)/s transition, raising the possibility that e2f1, mir-15, and cyclin e constitute a feed-forward loop that modulates e2f activity and cell-cycle progression. in support of this, ectopic expression of mir-15 inhibits the g(1)/s transition, and, conversely, inhibition of mir-15 expression enhances e2f1-induced upregulation of cyclin e1 levels. furthermore, inhibition of both mir-15 and mir-16 enhances e2f1-induced g(1)/s transition. in summary, our data identify the mir-15 and mir-16 families as novel transcriptional targets of e2f, which, in turn, modulates e2f activity.",1
"objective macrophage foam cell formation is a key feature of atherosclerosis. recent studies have shown that specific micrornas (mirs) are regulated in modified low-density lipoprotein-treated macrophages, which can affect the cellular cholesterol homeostasis. undertaking a genome-wide screen of mirs regulated in primary macrophages by modified low-density lipoprotein, mir-302a emerged as a potential candidate that may play a key role in macrophage cholesterol homeostasis. approach and results the objective of this study was to assess the involvement of mir-302a in macrophage lipid homeostasis and if it can influence circulating lipid levels and atherosclerotic development when it is inhibited in a murine atherosclerosis model. we found that transfection of primary macrophages with either mir-302a or anti-mir-302a regulated the expression of atp-binding cassette (abc) transporter abca1 mrna and protein. luciferase reporter assays showed that mir-302a repressed the 3' untranslated regions (utr) activity of mouse abca1 by 48% and human abca1 by 45%. in addition, transfection of murine macrophages with mir-302a attenuated cholesterol efflux to apolipoprotein a-1 (apoa-1) by 38%. long-term in vivo administration of anti-mir-302a to mice with low-density lipoprotein receptor deficiency (ldlr(-/-)) fed an atherogenic diet led to an increase in abca1 in the liver and aorta as well as an increase in circulating plasma high-density lipoprotein levels by 35% compared with that of control mice. the anti-mir-302a-treated mice also displayed reduced atherosclerotic plaque size by ≈25% and a more stable plaque morphology with reduced signs of inflammation. conclusions these studies identify mir-302a as a novel modulator of cholesterol efflux and a potential therapeutic target for suppressing atherosclerosis.",1
"acute myocardial infarction (mi) due to coronary artery occlusion is accompanied by a pathological remodeling response that includes hypertrophic cardiac growth and fibrosis, which impair cardiac contractility. previously, we showed that cardiac hypertrophy and heart failure are accompanied by characteristic changes in the expression of a collection of specific micrornas (mirnas), which act as negative regulators of gene expression. here, we show that mi in mice and humans also results in the dysregulation of specific mirnas, which are similar to but distinct from those involved in hypertrophy and heart failure. among the mi-regulated mirnas are members of the mir-29 family, which are down-regulated in the region of the heart adjacent to the infarct. the mir-29 family targets a cadre of mrnas that encode proteins involved in fibrosis, including multiple collagens, fibrillins, and elastin. thus, down-regulation of mir-29 would be predicted to derepress the expression of these mrnas and enhance the fibrotic response. indeed, down-regulation of mir-29 with anti-mirs in vitro and in vivo induces the expression of collagens, whereas over-expression of mir-29 in fibroblasts reduces collagen expression. we conclude that mir-29 acts as a regulator of cardiac fibrosis and represents a potential therapeutic target for tissue fibrosis in general.",1
"a minor class of pre-mrna introns whose excision requires a spliceosome containing u11, u12, u4atac/u6atac, and u5 snrnps has been identified in plants, insects, and vertebrates. we have characterized single loci that specify the u6atac and u12 snrnas of drosophila melanogaster. p element-mediated disruptions of the u6atac and u12 genes cause lethality during the third instar larval and embryonic stages, respectively, and are rescued by u6atac and u12 transgenes. the p element disruption of u6atac results in excision defects of u12-type introns from several transcripts including an alternative u12-dependent spliced isoform of prospero, a homeodomain protein required for cns development. thus, we demonstrate the requirement for the u12 spliceosome in the development of a metazoan organism.",1
"micrornas (mirnas) play an important role in various stages of tumor progression. mir-494, which we had previously identified as a mirna induced by ionizing radiation (ir) in the glioma cell line u-251, was observed to enhance invasion of u-251 cells by activating mmp-2. the mir-494-induced invasive potential was accompanied by, and dependent on, epidermal growth factor receptor (egfr) upregulation and the activation of its downstream signaling constituents, akt and erk. the upregulation of egfr by mir-494 involved the suppression of lysosomal protein turnover. among the putative target proteins tested, p190b rhogap (p190b) was downregulated by mir-494, and its reduced expression was responsible for the increase in egfr expression. a reporter assay using a luciferase construct containing p190b 3'-untranslated region (3'utr) confirmed that p190b is a direct target of mir-494. downregulation of p190b by small interfering rna (sirna) transfection closely mimicked the outcomes of mir-494 transfection, and showed increased egfr expression, mmp-2 secretion, and invasion. ectopic expression of p190b suppressed the mir-494-induced egfr upregulation and invasion promotion, thereby suggesting that p190b depletion is critical for the invasion-promoting action of mir-494. collectively, our results suggest a novel function for mir-494 and its potential application as a target to control invasiveness in cancer therapy.",1
"inactivation of mismatch repair (mmr) is the cause of the common cancer predisposition disorder lynch syndrome (ls), also known as hereditary nonpolyposis colorectal cancer (hnpcc), as well as 10-40% of sporadic colorectal, endometrial, ovarian, gastric, and urothelial cancers. elevated mutation rates (mutator phenotype), including simple repeat instability are a signature of mmr defects. micrornas (mirs) have been implicated in the control of critical cellular pathways involved in development and cancer. here we show that overexpression of mir-155 significantly down-regulates the core mmr proteins, hmsh2, hmsh6, and hmlh1, inducing a mutator phenotype and msi. an inverse correlation between the expression of mir-155 and the expression of mlh1 or msh2 proteins was found in human colorectal cancer. finally, a number of msi tumors with unknown cause of mmr inactivation displayed mir-155 overexpression. these data provide support for mir-155 modulation of mmr as a mechanism of cancer pathogenesis.",1
"mirnas play a central role in numerous pathologies including multiple cancer types. mir-191 has predominantly been studied as an oncogene, but the role of mir-191 in the proliferation of primary cells is not well characterized, and the mir-191 targetome has not been experimentally profiled. here we utilized rna induced silencing complex immunoprecipitations as well as gene expression profiling to construct a genome wide mir-191 target profile. we show that mir-191 represses proliferation in primary human fibroblasts, identify multiple proto-oncogenes as novel mir-191 targets, including cdk9, notch2, and rps6ka3, and present evidence that mir-191 extensively mediates target expression through coding sequence (cds) pairing. our results provide a comprehensive genome wide mir-191 target profile, and demonstrate mir-191's regulation of primary human fibroblast proliferation.",1
"the tumor suppressor p53 is central to many cellular stress responses. although numerous protein factors that control p53 have been identified, the role of micrornas (mirnas) in regulating p53 remains unexplored. in a screen for mirnas that modulate p53 activity, we find that mir-29 family members (mir-29a, mir-29b and mir-29c) upregulate p53 levels and induce apoptosis in a p53-dependent manner. we further find that mir-29 family members directly suppress p85 alpha (the regulatory subunit of pi3 kinase) and cdc42 (a rho family gtpase), both of which negatively regulate p53. our findings provide new insights into the role of mirnas in the p53 pathway.",1
"scope obesity increases intracellular lipid accumulation in key tissues or organs, which often leads to metabolic dysfunction and insulin resistance. diets rich in saturated fatty acid (sfa) exacerbate obesity and hepatic steatosis, which accentuate the risk of insulin resistance and type 2 diabetes (t2dm). although micrornas (mirnas) play a critical role in the regulation of gene expression, the implication of obesity-induced mirnas in metabolic disorders particularly in the development of insulin resistance is largely unknown. here, we investigated the implication of mir-15b, which is induced by sfa palmitate or obesity, in hepatic insulin resistance. methods and results diet-induced obesity (dio) in mice developed hyperglycemia and insulin resistance, accompanying with a reduction of insulin receptor (insr) expression. palmitate impaired insulin signaling as well as a decrease of insr in hepatocytes. the expression of mir-15b was upregulated by dio or palmitate in hepatocytes. furthermore, the overexpression of mir-15b suppressed the protein expression of insr through targeting insr 3' untranslated region directly, resulting in an impairment of the insulin signaling and glycogen synthesis in hepatocytes. conclusion these results unveil a novel mechanism whereby mir-15b is linked causally to the pathogenesis of hepatic insulin resistance in sfa-induced obesity.",1
"the tfox (also called sxy) gene product is the central regulator of dna uptake in the naturally competent bacteria haemophilus influenzae and vibrio cholerae. however, the mechanisms regulating tfox gene expression in both organisms are poorly understood. our previous studies revealed that in v. cholerae, chitin disaccharide (glcnac)₂ is needed to activate the transcription and translation of v. cholerae tfox (tfox(vc)) to induce natural competence. in this study, we screened a multicopy library of v. cholerae dna fragments necessary for translational regulation of tfox(vc). a clone carrying the vc2078-vc2079 intergenic region, designated tfor, increased the expression of a tfox(vc)::lacz translational fusion constructed in escherichia coli. using a tfox(vc)::lacz reporter system in v. cholerae, we confirmed that tfor positively regulated tfox(vc) expression at the translational level. deletion of tfor abolished competence for exogenous dna even when (glcnac)₂ was provided. the introduction of a plasmid clone carrying the tfor(+) gene into the tfor deletion mutant complemented the competence deficiency. we also found that the tfor gene encodes a 102-nucleotide small rna (srna), which was transcriptionally activated in the presence of (glcnac)₂. finally, we showed that this srna activated translation from tfox(vc) mrna in a highly purified in vitro translation system. taking these results together, we propose that in the presence of (glcnac)₂, tfor srna is expressed to activate the translation of tfox(vc), which leads to the induction of natural competence.",1
"our pilot study using mirna arrays found that mirna-29c (mir-29c) is differentially expressed in the paired low-metastatic lung cancer cell line 95c compared to the high-metastatic lung cancer cell line 95d. bioinformatics analysis shows that integrin β1 and matrix metalloproteinase 2 (mmp2) could be important target genes of mir-29c. therefore, we hypothesized that mir-29c suppresses lung cancer cell adhesion to extracellular matrix (ecm) and metastasis by targeting integrin β1 and mmp2. the gain-of-function studies that raised mir-29c expression in 95d cells by using its mimics showed reductions in cell proliferation, adhesion to ecm, invasion and migration. in contrasts, loss-of-function studies that reduced mir-29c by using its inhibitor in 95c cells promoted proliferation, adhesion to ecm, invasion and migration. furthermore, the dual-luciferase reporter assay demonstrated that mir-29c inhibited the expression of the luciferase gene containing the 3'-utrs of integrin β1 and mmp2 mrna. western blotting indicated that mir-29c downregulated the expression of integrin β1 and mmp2 at the protein level. gelatin zymography analysis further confirmed that mir-29c decreased mmp2 enzyme activity. nude mice with xenograft models of lung cancer cells confirmed that mir-29c inhibited lung cancer metastasis in vivo, including bone and liver metastasis. taken together, our results demonstrate that mir-29c serves as a tumor metastasis suppressor, which suppresses lung cancer cell adhesion to ecm and metastasis by directly inhibiting integrin β1 and mmp2 expression and by further reducing mmp2 enzyme activity. the results show that mir-29c may be a novel therapeutic candidate target to slow lung cancer metastasis.",1
"identifying microrna (mirna)-regulated genes is key to understanding mirna function. however, many mirna recognition elements (mres) do not follow canonical ""seed"" base-pairing rules, making identification of bona fide targets challenging. here, we apply an unbiased sequencing-based systems approach to characterize mir-522, a member of the oncogenic primate-specific chromosome 19 mirna cluster, highly expressed in poorly differentiated cancers. to identify mirna targets, we sequenced full-length transcripts captured by a biotinylated mirna mimic. within these targets, mostly noncanonical mres were identified by sequencing rnase-resistant fragments. mir-522 overexpression reduced mrna, protein levels, and luciferase activity of >70% of a random list of candidate target genes and mres. bioinformatic analysis suggested that mir-522 regulates cell proliferation, detachment, migration, and epithelial-mesenchymal transition. mir-522 induces g1 cell-cycle arrest and causes cells to detach without anoikis, become invasive, and express mesenchymal genes. thus, our method provides a simple but effective technique for identifying mirna-regulated genes and biological function.",1
"pancreatic β cell dysfunction contributes to the pathogenesis of type 2 diabetes. mir-21 has been shown to be induced in the islets of glucose intolerant patients and type 2 diabetic mice. however, the role of mir-21 in the regulation of pancreatic β cell function remains largely elusive. in the current study, we identify the pathway by which mir-21 regulates glucose-stimulated insulin secretion utilizing mice lacking mir-21 in their β cells (mir-21βko). we find that mir-21βko mice develop glucose intolerance due to impaired glucose-stimulated insulin secretion. mechanistic studies reveal that mir-21 enhances glucose uptake and subsequently promotes insulin secretion by up-regulating glut2 expression in a mir-21-pdcd4-ap-1 dependent pathway. over-expression of glut2 in knockout islets results in rescue of the impaired glucose-stimulated insulin secretion. furthermore, we demonstrate that delivery of mir-21 into the pancreas of type 2 diabetic db/db male mice is able to promote glut2 expression and reduce blood glucose level. taking together, our results reveal that mir-21 in islet β cell promotes insulin secretion and support a role for mir-21 in the regulation of pancreatic β cell function in type 2 diabetes.",1
"unlabelled based on microarray data, we have previously shown a significant down-regulation of mir-29 in hepatocellular carcinoma (hcc) tissues. to date, the role of mir-29 deregulation in hepatocarcinogenesis and the signaling pathways by which mir-29 exerts its function and modulates the malignant phenotypes of hcc cells remain largely unknown. in this study, we confirmed that reduced expression of mir-29 was a frequent event in hcc tissues using both northern blot and real-time quantitative reverse-transcription polymerase chain reaction. more interestingly, we found that mir-29 down-regulation was significantly associated with worse disease-free survival of hcc patients. both gain- and loss-of-function studies revealed that mir-29 could sensitize hcc cells to apoptosis that was triggered by either serum starvation and hypoxia or chemotherapeutic drugs, which mimicked the tumor growth environment in vivo and the clinical treatment. moreover, introduction of mir-29 dramatically repressed the ability of hcc cells to form tumor in nude mice. subsequent investigation characterized two antiapoptotic molecules, bcl-2 and mcl-1, as direct targets of mir-29. furthermore, silencing of bcl-2 and mcl-1 phenocopied the proapoptotic effect of mir-29, whereas overexpression of these proteins attenuated the effect of mir-29. in addition, enhanced expression of mir-29 resulted in the loss of mitochondrial potential and the release of cytochrome c to cytoplasm, suggesting that mir-29 may promote apoptosis through a mitochondrial pathway that involves mcl-1 and bcl-2. conclusion our data highlight an important role of mir-29 in the regulation of apoptosis and in the molecular etiology of hcc, and implicate the potential application of mir-29 in prognosis prediction and in cancer therapy.",1
"cyanobacteria constitute a heterogeneous phylum of oxygen-producing, photosynthetic prokaryotes. they are susceptible to various stress conditions like heat, salt, or light stress, all inducing the cyanobacterial heat shock response (hsr). cyanobacterial small heat shock proteins (shsps) are known to preserve thylakoid membrane integrity under stress conditions, thereby protecting the photosynthesis machinery. in synechocystis sp pcc 6803, synthesis of the shsp hsp17 is regulated by an rna thermometer (rnat) in the 5'-untranslated region (5'-utr) of the hsp17 mrna. rnats are direct temperature sensors that control expression of many bacterial heat shock and virulence genes. they hinder translation at low temperatures by base pairing, thus blocking ribosome access to the mrna. to explore the temperature range in which rnats act, we studied various rnat candidates upstream of shsp genes from mesophilic and thermophilic cyanobacteria. the mesophilic cyanobacteria anabaena variabilis and nostoc sp chromosomally encode two shsps each. reporter gene studies suggested rnat-mediated post-transcriptional regulation of shsp expression in both organisms. detailed structural analysis of the two a. variabilis candidates revealed two novel rnat types. the first, avashort, regulates translation primarily by masking of the aug translational start codon. the second, featuring an extended initial hairpin, thus named avalong, presumably makes use of complex tertiary interaction. the 5'-utr of the small heat shock gene hspa in the thermophile thermosynechococcus elongatus is predicted to adopt an extended secondary structure. structure probing revealed that the ribosome binding site was blocked at temperatures below 55 °c. the results of this study demonstrate that cyanobacteria commonly use rnats to control expression of their small heat shock genes.",1
"this study shows that specific micrornas differentially regulated by δnp63α in cisplatin-sensitive and resistant squamous cell carcinoma (ssc) cells of larynx and tongue affect the expression of members of the necroptotic pathway cyld, ripk1, and mlkl. different degrees of protein interaction between necroptotic signaling intermediates were also observed in scc cells sensitive or resistant to cisplatin. modulation of ripk1 with mir-101-3p mimic or inhibitor, as well as with sirna, or chemical inhibitors was shown to affect sensitivity of scc cells to cisplatin. this is the first report showing the modulatory effect of δnp63α-responsive micrornas on the specific members of necroptotic pathway in scc tumor cells variably responding to platinum chemotherapy.",1
"micrornas (mirnas) regulate gene expression posttranscriptionally by interfering with a target mrna's translation, stability, or both. we sought to dissect the respective contributions of translational inhibition and mrna decay to microrna regulation. we identified direct targets of a specific mirna, mir-124, by virtue of their association with argonaute proteins, core components of mirna effector complexes, in response to mir-124 transfection in human tissue culture cells. in parallel, we assessed mrna levels and obtained translation profiles using a novel global approach to analyze polysomes separated on sucrose gradients. analysis of translation profiles for approximately 8,000 genes in these proliferative human cells revealed that basic features of translation are similar to those previously observed in rapidly growing saccharomyces cerevisiae. for approximately 600 mrnas specifically recruited to argonaute proteins by mir-124, we found reductions in both the mrna abundance and inferred translation rate spanning a large dynamic range. the changes in mrna levels of these mir-124 targets were larger than the changes in translation, with average decreases of 35% and 12%, respectively. further, there was no identifiable subgroup of mrna targets for which the translational response was dominant. both ribosome occupancy (the fraction of a given gene's transcripts associated with ribosomes) and ribosome density (the average number of ribosomes bound per unit length of coding sequence) were selectively reduced for hundreds of mir-124 targets by the presence of mir-124. changes in protein abundance inferred from the observed changes in mrna abundance and translation profiles closely matched changes directly determined by western analysis for 11 of 12 proteins, suggesting that our assays captured most of mir-124-mediated regulation. these results suggest that mirnas inhibit translation initiation or stimulate ribosome drop-off preferentially near the start site and are not consistent with inhibition of polypeptide elongation, or nascent polypeptide degradation contributing significantly to mirna-mediated regulation in proliferating hek293t cells. the observation of concordant changes in mrna abundance and translational rate for hundreds of mir-124 targets is consistent with a functional link between these two regulatory outcomes of mirna targeting, and the well-documented interrelationship between translation and mrna decay.",1
"background gastric cancer is the second most common cause of cancer-related death in the world. inflammatory signals originating from gastric cancer cells are important for recruiting inflammatory cells and regulation of metastasis of gastric cancer. several micrornas (mirna) have been shown to be involved in development and progression of gastric cancer. mirna-146a (mir-146a) is a modulator of inflammatory signals, but little is known about its importance in gastric cancer. we therefore wanted to identify targets of mir-146a in gastric cancer and examine its biological roles. results the expression of mir-146a was evaluated by quantitative pcr (qpcr) and found up-regulated in the gastrin knockout mice, a mouse model of gastric cancer, and in 73% of investigated human gastric adenocarcinomas. expression of mir-146a by gastric cancer cells was confirmed by in situ hybridization. global analysis of changes in mrna levels after mir-146a transfection identified two transcripts, caspase recruitment domain-containing protein 10 (card10) and cop9 signalosome complex subunit 8 (cops8), as new mir-146a targets. qpcr, western blotting and luciferase assays confirmed these transcripts as direct mir-146a targets. card10 and cops8 were shown to be part of the g protein-coupled receptor (gpcr) pathway of nuclear factor-kappab (nf-kappab) activation. lysophosphatidic acid (lpa) induces nf-kappab activation via this pathway and over-expression of mir-146a inhibited lpa-induced nf-kappab activation, reduced lpa-induced expression of tumor-promoting cytokines and growth factors and inhibited monocyte attraction. conclusions mir-146a expression is up-regulated in a majority of gastric cancers where it targets card10 and cops8, inhibiting gpcr-mediated activation of nf-kappab, thus reducing expression of nf-kappab-regulated tumor-promoting cytokines and growth factors. by targeting components of several nf-kappab-activating pathways, mir-146a is a key component in the regulation of nf-kappab activity.",1
"colorectal cancer (crc) transcriptional subtypes have been recently identified by gene expression profiling. here we describe an analytical pipeline, microrna master regulator analysis (mmra), developed to search for micrornas potentially driving crc subtypes. starting from a microrna-mrna tumour expression data set, mmra identifies candidate regulator micrornas by assessing their subtype-specific expression, target enrichment in subtype mrna signatures and network analysis-based contribution to subtype gene expression. when applied to a crc data set of 450 samples, assigned to subtypes by 3 different transcriptional classifiers, mmra identifies 24 candidate micrornas, in most cases downregulated in the stem/serrated/mesenchymal (ssm) poor prognosis subtype. functional validation in crc cell lines confirms downregulation of the ssm subtype by mir-194, mir-200b, mir-203 and mir-429, which share target genes and pathways mediating this effect. these results show that, by combining statistical tests, target prediction and network analysis, mmra effectively identifies micrornas functionally associated to cancer subtypes.",1
"androgen, which acts via the androgen receptor (ar), plays crucial roles in mammalian ovarian function. recent studies showed that androgen/ar signaling regulates follicle-stimulating hormone receptor (fshr) expression in follicles; however, the detailed mechanism underlying this regulation remained unknown. here, we demonstrate that ar and mir-126* cooperate to inhibit fshr expression and function in pig follicular granulosa cells (pgcs). in pgcs, overexpression of ar decreased, whereas knockdown increased, fshr mrna and protein expression; however, neither manipulation affected fshr promoter activity. using a dual-luciferase reporter assay, we found that the fshr gene is a direct target of mir-126*, which inhibits fshr expression and increases the rate of ar-induced apoptosis in pgcs. collectively, our data show for the first time that the ar/mir-126* axis exerts synergetic effects in the regulation of fshr expression and apoptosis in pgcs. our findings thus define a novel pathway, ar/mir-126*/fshr, that regulates mammalian gc functions.",1
"the origin of replication ( orir ) involved in the initiation of (-) strand enterovirus rna synthesis is a quasi-globular multi-domain rna structure which is maintained by a tertiary kissing interaction. the kissing interaction is formed by base pairing of complementary sequences within the predominant hairpin-loop structures of the enteroviral 3' untranslated region. in this report, we have fully characterised the kissing interaction. site-directed mutations which affected the different base pairs involved in the kissing interaction were generated in an infectious coxsackie b3 virus cdna clone. the kissing interaction appeared to consist of 6 bp. distortion of the interaction by mispairing of each of the base pairs involved in this higher order rna structure resulted in either temperature sensitive or lethal phenotypes. the nucleotide constitution of the base which gaps the major groove of the kissing domain was not relevant for virus growth. the reciprocal exchange of the complete sequence involved in the kissing resulted in a mutant virus with wild type virus growth characteristics arguing that the base pair constitution is of less importance for the initiation of (-) strand rna synthesis than the existence of the tertiary structure itself.",1
"background in our study, we investigated the expression and function of microrna-29 in myocardial microvascular endothelial cells (mmevc) in type 2 diabetic goto-kakizaki (gk) rats. methods mir-29 gene expression was compared, by qrt-pcr between diabetic gk rat mmevc and non-diabetic wistar rat mmevc. mir-29 was downregulated in gk mmevc and its effect on angiogenic properties of proliferation and migration was examined. potential downstream target gene of mir-29, insulin growth factor 1 (igf1), was assessed by dual-luciferase reporter assay, qrt-pcr and western blot in gk mmevc. igf1 was also downregulated by sirna in mir-29-downregulated gk mmevc. its effect on mir-29-associated angiogenic regulation on mmevc proliferation and migration was further investigated. results mir-29 was substantially upregulated in gk mmevc than in wistar mmevc. transfection of synthetic mir-29 inhibitor successfully downregulate endogenous mir-29 in gk mmevc, and subsequently promoted angiogenesis by increasing cell proliferation and migration. igf1 was confirmed to be downstream target gene of mir-29 in gk mmevc, with its gene and protein expressions both upregulated in mir-29-downregualted gk mmevc. conversely, sirna-mediated igf1 downregulation reversed the pro-angiogenic effect of mir-29 downregulation in gk mmevc, as it decreased cell proliferation and migration. conclusion our study suggests that mir-29 downregulation, through its inverse regulation on downstream target of igf1 gene, is a pro-angiogenic factor in mmevc in type 2 diabetic rats.",1
"in this study, phylogenetically conserved structural features of the ro rnp associated y rnas were investigated. the human, iguana, and frog y3 and y4 rna sequences have been determined previously and the respective rnas were subjected to enzymatic and chemical probing to obtain structural information. for all of the analyzed rnas, the probing data were used to compose secondary structures, which partly deviate from previously predicted structures. our results confirm the existence of two stem structures, which are also found at similar positions in hy1 and hy5 rna. for the remaining parts of hy3 and hy4 rna the secondary structures differ from those previously proposed based upon computer predictions. what might be more important is that certain parts of the rnas appear to be flexible, i.e., to adopt several conformations. another striking feature is that a characteristic pyrimidine-rich region, present in every y rna known, is single-stranded in all secondary structures. this may suggest that this region is readily available for base pairing inter-actions with other cellular nucleic acids, which might be important for the as yet unknown function of the rnas.",1
"avoiding excessive or insufficient immune responses and maintaining homeostasis are critical for animal survival. although many positive or negative modulators involved in immune responses have been identified, little has been reported to date concerning whether the long non-coding rna (lncrna) can regulate drosophila immunity response. in this study, we firstly discover that the overexpression of lncrna-cr11538 can inhibit the expressions of antimicrobial peptides drosomycin ( drs ) and metchnikowin ( mtk ) in vivo, thereby suppressing the toll signaling pathway. secondly, our results demonstrate that lncrna-cr11538 can interact with transcription factors dif/dorsal in the nucleus based on both subcellular localization and rip analyses. thirdly, our findings reveal that lncrna-cr11538 can decoy dif/dorsal away from the promoters of drs and mtk to repress their transcriptions by chip-qpcr and dual luciferase report experiments. fourthly, the dynamic expression changes of drs , dif , dorsal and lncrna-cr11538 in wild-type flies ( w 1118 ) at different time points after m. luteus stimulation disclose that lncrna-cr11538 can help drosophila restore immune homeostasis in the later period of immune response. overall, our study reveals a novel mechanism by which lncrna-cr11538 serves as a dif/dorsal decoy to downregulate antimicrobial peptide expressions for restoring drosophila toll immunity homeostasis, and provides a new insight into further studying the complex regulatory mechanism of animal innate immunity.",1
"microrna-200c (mir-200c) has been shown to suppress epithelial-mesenchymal transition (emt), which is attributed mainly to targeting of zeb1/zeb2, repressors of the cell-cell contact protein e-cadherin. here we demonstrated that modulation of mir-200c in breast cancer cells regulates cell migration, cell elongation, and transforming growth factor β (tgf-β)-induced stress fiber formation by impacting the reorganization of cytoskeleton that is independent of the zeb/e-cadherin axis. we identified fhod1 and ppm1f, direct regulators of the actin cytoskeleton, as novel targets of mir-200c. remarkably, expression levels of fhod1 and ppm1f were inversely correlated with the level of mir-200c in breast cancer cell lines, breast cancer patient samples, and 58 cancer cell lines of various origins. furthermore, individual knockdown/overexpression of these target genes phenocopied the effects of mir-200c overexpression/inhibition on cell elongation, stress fiber formation, migration, and invasion. mechanistically, targeting of fhod1 by mir-200c resulted in decreased expression and transcriptional activity of serum response factor (srf), mediated by interference with the translocation of the srf coactivator mycocardin-related transcription factor a (mrtf-a). this finally led to downregulation of the expression and phosphorylation of the srf target myosin light chain 2 (mlc2) gene, required for stress fiber formation and contractility. thus, mir-200c impacts on metastasis by regulating several emt-related processes, including a novel mechanism involving the direct targeting of actin-regulatory proteins.",1
"disruptions of normal hox gene expression can lead to severe morphological defects, revealing a link between the regulation of hox expression and pattern formation. here, we explore these links, focusing on the impact of microrna regulation on the expression of the drosophila hox gene ultrabithorax ( ubx ) during haltere development. through a combination of bioinformatic and transcriptomic analyses, we identify the mir-310/313 cluster ( mir-310c ) as a candidate regulator of ubx several experiments confirm this. first, mir-310c and ubx protein show complementary expression patterns in haltere imaginal discs; second, artificial activation of mir-310c expression in haltere discs leads to ubx -like phenotypes. third, expression of a fluorescent reporter bearing ubx 3'utr sequences is reduced when co-expressed with mir-310c fourth, deletion of mir-310c leads to ubx upregulation and changes the array of mechanosensory sensilla at the base of the haltere. fifth, an artificial increase of ubx levels within the mir-310c expression domain phenocopies the mechanosensory defects observed in mir-310c mutants. we propose that mir-310c -mediated repression delimits ubx fine-grain expression, contributing to the sculpting of complex morphologies in the drosophila haltere with implications for flight control. our work reveals a novel role of microrna regulation in the control of hox gene expression with impact on morphology.",1
"objective micrornas (mirnas) are recognised as important regulators of a variety of fundamental biologic processes. our study was undertaken to examine the role of microrna-203 (mir-203) in modulating nitric oxide (no) expression in female sprague-dawley rat mandibular condylar chondrocytes (mccs) via targeting transient receptor potential vanilloid 4 (trpv4) and to demonstrate the possible mechanism of no inhibition by chondroprotective factor 17β-oestradiol (e2). methods the expression of trpv4 in mandibular condylar cartilage tissue and mccs was detected by immunohistochemistry, immunofluorescence (if), rt-pcr and western blot, respectively. primary sd rat mccs were exposed to lipopolysaccharide (lps), plus ruthenium red, 4α-phorbol 12,13-didecanoate (4αpdd), over-expressed mir-203 or e2 (10(-9) to 10(-6)m), the cellular supernatants were used for no assay, mir-203 levels were measured by quantitative rt-pcr while trpv4 expression changes were analysed by western blot. the dual luciferase activity assay was performed to identify the target gene of mir-203. results trpv4 and mir-203 were stably expressed in mccs. the mccs' expression of no evoked by lps could be enhanced or depressed by ruthenium red or 4αpdd. the dual luciferase assay suggested that trpv4 was the direct target gene of mir-203. over-expression of mir-203 inhibited the expression of trpv4 and increased no expression in mccs. e2 inhibited no expression by inhibition of mir-203, which was concurrent with the up-regulation of trpv4 expression level in mccs. conclusion our findings first suggested that mir-203 could up-regulate no expression in female rat mccs via targeting trpv4. moreover, the inhibition of no by e2 might be at least in part through this mechanism.",1
"considering all small nucleolar rnas (snornas) enriched in the nucleolus, we generated a specialized cdna library of small nuclear rnas from schizosaccharomyces pombe and isolated, for the first time, 20 novel box h/aca snornas. thirteen of these were characterized as novel guides that were predicted to direct 19 pseudouridylations in 18 s and 25 s rrnas. the remaining seven snornas were considered as orphan guides that lack sequence complementarity to either rrnas or snrnas. we have experimentally demonstrated the function of the 10 novel snornas by gene deletion in the fission yeast. the snornas were shown to be dispensable for the viability of s. pombe, although an impact of snr94 depletion on yeast growth, especially at 23 degrees c, was revealed. a total of 30 pseudouridylation sites were precisely mapped in the s. pombe rrnas, showing a distinctive pseudouridylation pattern in the budding yeast. interestingly, the absence of pseudouridylation on u2347 in s. pombe 25 s rrna pointed out a critical role for psi2345 in conferring a growth advantage for yeast. in contrast to the intron-encoded box c/d sno-rnas in yeast, all box h/aca snornas appeared to be transcribed independently from intergenic regions between two protein-coding genes, except for snr35, which was nested in an open reading frame encoding for a hypothetical protein, although expressed from the opposite strand. remarkably, snr90 was cotranscribed with an intron-encoded box c/d snorna, and this is the first demonstration of a non-coding rna gene that encodes two different types of snornas by its exon and intron. a detailed comparison of the s. pombe snornas, with their functional homologues in diverse organisms, suggests a mechanism by which the snornas have evolved in coordination with rrnas to preserve the post-transcriptional modification sites among distant eukaryotes.",1
"background emerging evidence has shown that micrornas are involved in gastric cancer development and progression. here we examine the role of mir-133b in gastric cancer. methods quantitative real-time pcr analysis was performed in 140 patient gastric cancer tissues and 8 gastric cancer cell lines. the effects of mir-133b in gastric cancer cells metastasis were examined by scratch assay, transwell migration and matrigel invasion. in vivo effects of mir-133b were examined in an intraperitoneal mouse tumor model. targets of mir-133b were predicted by bioinformatics tools and validated by luciferase reporter analyses, western blot, and quantitative real-time pcr. results mir-133b was significantly downregulated in 70% (98/140) of gastric cancer patients. expression of mir-133b was negatively correlated with lymph node metastasis of gastric cancer in patients. similarly, the expression of mir-133b was significantly lower in seven tested gastric cancer cell lines than in the immortalized non-cancerous ges-1 gastric epithelial cells. overexpression of mir-133b markedly inhibited metastasis of gastric cancer cells in vitro and in vivo. moreover, the transcriptional factor gli1 was identified as a direct target for mir-133b. level of gli1 protein but not mrna was decreased by mir-133b. activity of luciferase with gli1 3'-untranslated region was markedly decreased by mir-133b in gastric cancer cells. gli1 target genes, opn and zeb2, were also inhibited by mir133b. conclusions mir-133b is frequently decreased in gastric cancer. overexpression of mir-133b inhibits cell metastasis in vitro and in vivo partly by directly suppressing expression of gli1 protein. these results suggested that mir-133b plays an important role in gastric cancer metastasis.",1
"the human 8q24 gene desert contains multiple enhancers that form tissue-specific long-range chromatin loops with the myc oncogene, but how chromatin looping at the myc locus is regulated remains poorly understood. here we demonstrate that a long noncoding rna (lncrna), ccat1-l, is transcribed specifically in human colorectal cancers from a locus 515 kb upstream of myc. this lncrna plays a role in myc transcriptional regulation and promotes long-range chromatin looping. importantly, the ccat1-l locus is located within a strong super-enhancer and is spatially close to myc. knockdown of ccat1-l reduced long-range interactions between the myc promoter and its enhancers. in addition, ccat1-l interacts with ctcf and modulates chromatin conformation at these loop regions. these results reveal an important role of a previously unannotated lncrna in gene regulation at the myc locus.",1
"endothelial cells (ecs) are critical for angiogenesis, and microrna plays important roles in this process. in this study, we investigated the function and mechanism of mir-302c in the process of endothelial-mesenchymal transition (endmt) in ecs. when mir-302c was overexpressed in huvecs, the motility of the huvecs was weakened; the expression levels of endmt markers were also changed: vascular endothelial (ve)-cadherin was up-regulated, whereas β-catenin, fsp1, and α-sma were down-regulated. further in vivo and in vitro experiments showed that the growth of hcc was inhibited when co-cultured or co-injected with huvecs overexpressing mir-302c. on the contrary, when mir-302c was suppressed in huvecs, the opposite results were observed. reporter assays showed that mir-302c inhibited metadherin (mtdh) expression through directly binding to its 3'utr. in addition, compared to ecs isolated from normal liver tissues of hcc patients, ecs isolated from tumor tissues expressed markedly low levels of mir-302c but high levels of mtdh. these results suggest that ec-specific mir-302c suppresses tumor growth in hcc through mtdh-mediated inhibition of endmt. mtdh and mir-302c might provide a new strategy for anti-angiogenic therapy in hcc.",1
"microrna (mirnas) are negative regulators of gene expression and can function as tumor suppressors or oncogenes. expression patterns of mirnas and their role in the pathogenesis of hepatocellular carcinoma (hcc) are still poorly understood. we profiled mirna expression in tissue samples (104 hcc, 90 adjacent cirrhotic livers, 21 normal livers) as well as in 35 hcc cell lines. a set of 12 mirnas (including mir-21, mir-221/222, mir-34a, mir-519a, mir-93, mir-96, and let-7c) was linked to disease progression from normal liver through cirrhosis to full-blown hcc. mir-221/222, the most up-regulated mirnas in tumor samples, are shown to target the cdk inhibitor p27 and to enhance cell growth in vitro. conversely, these activities can be efficiently inhibited by an antagomir specific for mir-221. in addition, we show, using a mouse model of liver cancer, that mir-221 overexpression stimulates growth of tumorigenic murine hepatic progenitor cells. finally, we identified dna damage-inducible transcript 4 (ddit4), a modulator of mtor pathway, as a bona fide target of mir-221. taken together, these data reveal an important contribution for mir-221 in hepatocarcinogenesis and suggest a role for ddit4 dysregulation in this process. thus, the use of synthetic inhibitors of mir-221 may prove to be a promising approach to liver cancer treatment.",1
"a critical question about signal transduction is how weak or transient activation of signaling pathways achieves a robust and long-term switch in gene expression. we report that a microrna is part of a mechanism that makes cells sensitive to signals in the drosophila eye. expression of mir-7 is activated in cells as they begin differentiating into photoreceptors. this is dependent on egf receptor (egfr) signaling that triggers erk-mediated degradation of the transcription factor yan. in nonstimulated cells, yan represses mir-7 transcription, whereas mir-7 rna represses yan protein expression in photoreceptors, by binding to sequences within its mrna 3'utr. we propose that reciprocal negative feedback between yan and mir-7 ensures mutually exclusive expression, with yan in progenitor cells and mir-7 in photoreceptor cells. expression is switched when egfr signaling transiently triggers yan degradation. this two-tiered mechanism explains how signal transduction activity can robustly generate a stable change in gene-expression patterns.",1
"for study of the pol gene expression of human t-cell leukemia virus type i (htlv-i), rna was transcribed in vitro from proviral dna and translated in rabbit reticulocyte lysates. this cell-free translation resulted in two major translation products representing the gag and gag-pro polyproteins. by contrast, the gag-pro-pol polyprotein could be readily observed only when translation was performed with mutant mrna in which the protease (pro) reading frame was aligned to gag to eliminate the frameshifting event in the gag-pro overlap. the results indicated that two independent ribosomal frameshifting events are required for expression of the htlv-i pol gene product. studies with mutant dnas facilitated the characterization of the primary structure of the htlv-i mrna responsible for the ribosomal frameshift in the pro-pol overlap and demonstrated that the frameshift occurs at the signal sequence uuuaaac. direct amino acid sequencing of the transframe protein localized the site of the frameshift to the asparagine codon aac.",1
"ischemia-reperfusion (i/r) injury of the kidney is a major cause of aki. micrornas (mirs) are powerful regulators of various diseases. we investigated the role of apoptosis-associated mir-24 in renal i/r injury. mir-24 was upregulated in the kidney after i/r injury of mice and in patients after kidney transplantation. cell-sorting experiments revealed a specific mir-24 enrichment in renal endothelial and tubular epithelial cells after i/r induction. in vitro, anoxia/hypoxia induced an enrichment of mir-24 in endothelial and tubular epithelial cells. transient overexpression of mir-24 alone induced apoptosis and altered functional parameters in these cells, whereas silencing of mir-24 ameliorated apoptotic responses and rescued functional parameters in hypoxic conditions. mir-24 effects were mediated through regulation of h2a histone family, member x, and heme oxygenase 1, which were experimentally validated as direct mir-24 targets through luciferase reporter assays. in vitro, adenoviral overexpression of mir-24 targets lacking mir-24 binding sites along with mir-24 precursors rescued various functional parameters in endothelial and tubular epithelial cells. in vivo, silencing of mir-24 in mice before i/r injury resulted in a significant improvement in survival and kidney function, a reduction of apoptosis, improved histologic tubular epithelial injury, and less infiltration of inflammatory cells. mir-24 also regulated heme oxygenase 1 and h2a histone family, member x, in vivo. overall, these results indicate mir-24 promotes renal ischemic injury by stimulating apoptosis in endothelial and tubular epithelial cell. therefore, mir-24 inhibition may be a promising future therapeutic option in the treatment of patients with ischemic aki.",1
"micrornas (mirnas) are processed from primary mirna transcripts (pri-mirnas), many of which are annotated as long noncoding rnas (lncrnas). we assessed whether mir205hg, the host gene for mir-205, has independent functions as an lncrna. comparing mice with targeted deletions of mir205hg and mir-205 revealed a functional role for the lncrna in the anterior pituitary. mice lacking mir205hg had a temporal reduction in pit1, growth hormone, and prolactin. this was mediated, in part, through the ability of this lncrna to bind and regulate the transcriptional activity of pit1 in conjunction with zbtb20. knockdown of mir205hg in lactotropes decreased the expression of pit1, zbtb20, prolactin, and growth hormone, while its overexpression enhanced the levels of these transcripts. the effects of mir205hg on the pituitary were independent of mir-205. the data support a role for mir205hg as an lncrna that regulates growth hormone and prolactin production in the anterior pituitary.",1
"the histone-modifying complexes prc2 and trxg/mll play pivotal roles in determining the activation state of genes controlling pluripotency, lineage commitment, and cell differentiation. long noncoding rnas (lncrnas) can bind to either complex, and some have been shown to act as modulators of prc2 or trxg/mll activity. here we show that the lateral mesoderm-specific lncrna fendrr is essential for proper heart and body wall development in the mouse. embryos lacking fendrr displayed upregulation of several transcription factors controlling lateral plate or cardiac mesoderm differentiation, accompanied by a drastic reduction in prc2 occupancy along with decreased h3k27 trimethylation and/or an increase in h3k4 trimethylation at their promoters. fendrr binds to both the prc2 and trxg/mll complexes, suggesting that it acts as modulator of chromatin signatures that define gene activity. thus, we identified an lncrna that plays an essential role in the regulatory networks controlling the fate of lateral mesoderm derivatives.",1
"the temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. mirnas affect cell function by regulating programmatic changes in protein expression levels. we show that the mir302/367 cluster is a target of the transcription factor gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. mir302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. gain- and loss-of-function studies show that altering mir302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. increased mir302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of mir302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. mir302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of rbl2 and cdkn1a, whereas apical-basal polarity is controlled by regulation of tiam1 and lis1. thus, mir302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity.",1
"tumor cells display features that are not found in healthy cells. how they become immortal and how their specific features can be exploited to combat tumorigenesis are key questions in tumor biology. here we describe the long non-coding rna cherub that is critically required for the development of brain tumors in drosophila but is dispensable for normal development. in mitotic drosophila neural stem cells, cherub localizes to the cell periphery and segregates into the differentiating daughter cell. during tumorigenesis, de-differentiation of cherub-high cells leads to the formation of tumorigenic stem cells that accumulate abnormally high cherub levels. we show that cherub establishes a molecular link between the rna-binding proteins staufen and syncrip. as syncrip is part of the molecular machinery specifying temporal identity in neural stem cells, we propose that tumor cells proliferate indefinitely, because cherub accumulation no longer allows them to complete their temporal neurogenesis program.",1
"this aim of this study was to explore the role of mirna-146a (mir-146a) and its target genes in endothelial cells. we demonstrated that lipopolysaccharide (lps) induced the upregulation of mir-146a in human umbilical vein endothelial cells (huvecs), and that the induction was blocked by silencing toll-like receptors, the adaptor molecule myd88, and the nonspecific nf-κb inhibitor bay 11-7082. in addition, knockdown of mir-146a by transfection of the locked nucleic acid antimir-146a significantly inhibited lps-induced cell migration and tube formation. a combined analysis of bioinformatics miranda algorithms and a whole genome expression microarray of immunoprecipitated ago2 ribonucleoprotein complexes identified 14 potential target genes. subsequent transfection with the mir-146a precursor pre-mir-146a into huvecs validated that card10 was the target gene of the mir-146a, both at the mrna and protein levels. silencing card10 inhibited p65 nuclear translocation in the cells receiving lps stimulation and increased angiogenesis. therefore, mir-146a may play a role in regulating the angiogenesis in huvecs by downregulating card10, which acts in a negative feedback regulation loop to inhibit the activation of nf-κb that normally impairs angiogenesis.",1
"atherosclerosis is a chronic inflammatory disease, starting with the accumulation of white blood cells and fatty materials in the arterial wall. abca1, a gene promotes phospholipid and cholesterol transfer from cells to poorly lapidated apoa1, is considered to be related to the pathogenesis of coronary atherosclerosis. meanwhile, disturbed mirnas were reported to be related to coronary atherosclerosis. to understand the relationship between mirna, abca1 and coronary atherosclerosis pathogenesis, we first screened the mirnas that may directly target 3'utr of abca1 and mir-33a was used as positive control. through dual luciferase assay and western blot, we confirmed that mir-93 and mir-17 repress abca1 expression through directly targeting 3'utr. the serum mir-33a, mir-93 and mir-17 levels in participants were detected by qrt-pcr and a significant reduction of mir-33a and mir-93 was found in the coronary patients. after statistical analysis we identified that a negative correlation was existed in the serum mir-93 and abca1 levels in coronary atherosclerosis patients. meanwhile, our results indicate that the serum mir-93 positively correlates with the serum cholesterol level. this research may give insight into understanding of coronary atherosclerosis pathogenesis and create an opportunity to the diagnosis of coronary atherosclerosis.",1
"the induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. here, we report that repression of a single rna binding polypyrimidine-tract-binding (ptb) protein, which occurs during normal brain development via the action of mir-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. besides its traditional role in regulated splicing, we show that ptb has a previously undocumented function in the regulation of microrna functions, suppressing or enhancing microrna targeting by competitive binding on target mrna or altering local rna secondary structure. a key event during neuronal induction is the relief of ptb-mediated blockage of microrna action on multiple components of the rest complex, thereby derepressing a large array of neuronal genes, including mir-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. this converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.",1
"a number of micrornas (mirnas), including mir-200 family, are aberrantly expressed in endometriosis and endometrial cancer. here we assessed the expression and functional aspects of mir-200c in endometrial tissues (n = 52) from normal endometrial biopsies (n = 15), endometrial tissues including those exposed to hormonal therapies (n = 20), and grade i-iii endometrial cancer (n = 17). mir-200c expression was elevated in normal endometrial biopsies from mid- and late-luteal phase, and in endometrial tumors as compared to endometrial tissues from peri- and postmenopausal period (p < .05) and its pattern of temporal expression displayed an inverse relationship with the expression of zebs. the expression of e-cadherin (cdh1) varied, but expressed at low levels, specifically in endometrial tissues and endometrial tumors. the endometrial expression of zebs and cdh1 in patients who were exposed to depo-provera and gonadotropin-releasing hormone agonist gnrha displayed a trend toward lower expression as compared to proliferative phase; however, treatment of ishikawa cells with 17β-estradiol, progesterone, and medroxy progesterone acetate had modest effects on the expression of mir-200c and zebs without affecting cdh1 expression. gain of function of mir-200c in ishikawa cells repressed zebs, as well as vegfa, flt1, ikkβ, and klf9 expression at transcriptional and translational levels through direct interaction with their respective 3'untranslated regions and increased the rate of their proliferation. these results indicated that endometrial mir-200c expression undergoes dynamic changes during transition from normal into cancerous states; possibly influenced by hormonal milieu and by targeting the expression of specific genes with key regulatory functions in cellular transformation, inflammation, and angiogenesis may influence these events during normal and disease progression.",1
"natural antisense transcripts (nats) are long non-coding rnas (lncrnas) that overlap coding genes in the opposite strand. nats roles have been related to gene regulation through different mechanisms, including post-transcriptional rna processing. with the aim to identify nats with potential regulatory function during fly development, we generated rna-seq data in drosophila developing tissues and found bsas, one of the most highly expressed lncrnas in the fly wing. bsas is antisense to bs/dsrf, a gene involved in wing development and neural processes. bsas plays a crucial role in the tissue specific regulation of the expression of the bs/dsrf isoforms. this regulation is essential for the correct determination of cell fate during drosophila development, as bsas knockouts show highly aberrant phenotypes. regulation of bs isoform usage by bsas is mediated by specific physical interactions between the promoters of these two genes, which suggests a regulatory mechanism involving the collision of rna polymerases transcribing in opposite directions. evolutionary analysis suggests that bsas nat emerged simultaneously to the long-short isoform structure of bs, preceding the emergence of wings in insects.",1
"activated microglia are capable of facilitating amyloid-β (aβ) accumulation via the release of inflammatory factors, thus resulting in the exacerbation of alzheimer's disease (ad). micrornas (mirs) participate in the activation of microglia, which is associated with ad. insulin-like growth factor 1 (igf1) is a neuroprotective, anti-inflammatory factor, which is able to accelerate clearance of aβ peptides. the present study aimed to investigate the precise role of mir‑206 and igf1 in lipopolysaccharide (lps)‑induced microglial inflammation. the expression levels of mir‑206 and igf1 were detected in 60 peripheral blood samples from patients with ad and matched age subjects using quantitative polymerase chain reaction. a dual luciferase reporter gene assay was used to indicate the relationship between mir‑206 and igf1. in addition, the role of mir‑206 was determined by gain and loss of function experiments in lps‑treated microglia. the results demonstrated that mir‑206 upregulation enhanced lps‑induced inflammation and aβ release in microglia by directly targeting the 3'-untranslated region of igf1. these effects were attenuated following treatment with exogenous igf1, thus indicating that the mir‑206/igf1 signaling pathway may be considered a novel therapeutic target for the treatment of ad‑associated microglial inflammation.",1
"the highly aggressive character of melanoma makes it an excellent model for probing the mechanisms underlying metastasis, which remains one of the most difficult challenges in treating cancer. we find that mir-182, member of a mirna cluster in a chromosomal locus (7q31-34) frequently amplified in melanoma, is commonly up-regulated in human melanoma cell lines and tissue samples; this up-regulation correlates with gene copy number in a subset of melanoma cell lines. moreover, mir-182 ectopic expression stimulates migration of melanoma cells in vitro and their metastatic potential in vivo, whereas mir-182 down-regulation impedes invasion and triggers apoptosis. we further show that mir-182 over-expression promotes migration and survival by directly repressing microphthalmia-associated transcription factor-m and foxo3, whereas enhanced expression of either microphthalmia-associated transcription factor-m or foxo3 blocks mir-182's proinvasive effects. in human tissues, expression of mir-182 increases with progression from primary to metastatic melanoma and inversely correlates with foxo3 and microphthalmia-associated transcription factor levels. our data provide a mechanism for invasion and survival in melanoma that could prove applicable to metastasis of other cancers and suggest that mirna silencing may be a worthwhile therapeutic strategy.",1
"systematic screening of differentially expressed genes among androgenetic, parthenogenetic, and normal embryos by means of fluorescent differential display revealed five imprinted genes. one of them, named rian, was expressed exclusively from the maternal allele and was closely linked to an imprinted gene, meg3(gtl2), mapped to the distal end of chromosome 12. the rian transcript did not have any apparent open reading frame, and its transcript was exclusively localized to the nucleus.",1
"pnd324 belongs to a family of closely related theta-type plasmids from lactococcus lactis. an antisense rna, termed countertranscript (ctrna), was identified which is complementary to the leader sequence of the mrna that encodes repb, a protein essential for plasmid replication. when the synthesis of ctrna was abolished by site-directed mutagenesis within its promoter region, the mutant replicon showed a 1.8-fold increase in copy number. similar ctrna promoter sequences are readily identifiable in 12 other published lactococcal theta-type plasmids, suggesting that they all encode a similar ctrna-mediated regulatory mechanism.",1
"mir-221 was reported to be upregulated and play roles in tumorigenesis of hepatitis c virus (hcv) associated hepatocellular carcinoma (hcc). however, the role of mir-221 in hcv infection remains unknown. in this study, it was found that mir-221 was upregulated in serum of hcv chronic hepatitis patients and huh7.5.1 cells infected with hcvcc. further studies indicated that mir-221 mimic could accentuate anti-hcv effect of ifn-α in hcvcc model, mir-221 mimic could further repressed 10% hcv rna expression and 35-42% hcv core or ns5a protein expression in hcvcc infected huh7.5.1 cells treated with 100iu/ml ifn-α, and mir-221 inhibitor resulted in the reverse effects. furthermore, two members of suppressor of cytokine signaling (socs) family, socs1 and socs3, which are well established inhibitory factors on ifn/jak/stat pathway, were identified as the targets of mir-221 and were involved in the effect of mir-221. in conclusion, mir-221 could accentuate ifn׳s anti-hcv effect by targeting socs1 and socs3.",1
"angiotensin ii (ang ii) is an important profibrotic factor, and the tumor-promoting microrna mir-21 was recently linked to fibrotic disorders. we aimed to investigate whether and how mir-21 mediates ang ii-induced renal fibrosis. in renal tubular epithelial cells, ang ii upregulated mir-21 and fibrosis-related indicators but decreased pparα expression. mir-21 overexpression promoted pparα downregulation, activated the tgf-β1/smad3 pathway and induced fibrogenesis, while mir-21 suppression exerted opposite effects. in ang ii-treated cells, reduced pparα expression, tgf-β1/smad3 pathway activation and fibrogenesis were all exacerbated by mir-21 upregulation but alleviated by mir-21 inhibition. the dual-luciferase assay confirmed pparα as the target of mir-21. pparα silencing alone could overactivate the tgf-β1/smad3 pathway in the presence or absence of ang ii. importantly, the regulatory effects of mir-21 knockdown and the angiotensin type 1 receptor blocker losartan alone or in combination on the pparα/tgf-β1/smad3 pathway in ang ii-treated cells were almost the same. more crucially, pparα restoration abolished the profibrotic effect of mir-21 overexpression. in addition, inhibiting mir-21 in ang ii-treated mice effectively ameliorated the abnormally activated pparα/tgf-β1/smad3 pathway, albuminuria, and renal fibrosis without lowering blood pressure. these results demonstrated that mir-21 extensively mediates ang ii-induced kidney fibrosis via amplifying the tgf-β1/smad3 pathway by targeting pparα.",1
"oxidative stress is involved in the etiology of diabetes-induced cardiac dysfunction while micrornas (mirnas) are known as regulators for genes involved in cardiac remodeling. however, a functional link between mirnas and diabetes-induced cardiac dysfunction remains to be investigated. here, we aimed to identify whether the expression levels of mirnas are associated with oxidative stress/diabetic heart and if proteins responsible from contractile activity during diabetes might be directly modulated by mirnas. diabetic cardiomyopathy developed with streptozotocin, is characterized with marked changes in sarcomere and mitochondria, depressed left ventricular developed pressure, and a massive oxidative stress that is particularly evident in the heart. mirna profiling was performed in freshly isolated left ventricular cells from diabetic rats. using microarray analysis, we identified marked changes in the expression of 43 mirnas (37 of them were downregulated while 6 mirnas were upregulated) out of examined total of 351 mirnas. among them, 6 mirnas were further validated by real-time pcr. the expression levels of mir-1, mir-499, mir-133a, and mir-133b were markedly depressed in the diabetic cardiomyocytes while mir-21 level increased and mir-16 level was unchanged. notably, normalization of cardiac function and oxidant/antioxidant level after n-acetylcysteine (nac)-treatment of diabetic rats resulted with a significant restoration in the expression levels of mir-499, mir-1, mir-133a, and mir-133b in the myocardium. since changes in the level of muscle-specific mir-1 has been implicated in cardiac diseases and its specific molecular targets involved in its action, in part, associated with oxidative stress are limited, we first examined the protein levels of some sr-associated proteins such as junctin and triadin. junctin but not triadin is markedly overexpressed in diabetic cardiomyocytes while its level was normalized in nac-treated diabetics. luciferase reporter assay showed that junctin is targetted by mir-1. taken together, our data demonstrates that intervention with an antioxidant treatment for 4-week leads to significant cardioprotection against diabetes-induced injury, controlling oxidant/antioxidant level, which may directly control the levels of some mirnas including mir-1 and its target protein junctin, which is involved in the development of diabetic cardiomyopathy.",1
"rationale females are predisposed to pulmonary arterial hypertension (pah); evidence suggests that serotonin, mutations in the bone morphogenetic protein receptor (bmpr) ii gene, and estrogens influence development of pah. the 5-hydroxytryptamine 1b receptor (5-ht1br) mediates human pulmonary artery smooth muscle cell (hpasmc) proliferation. objectives we aimed to determine whether selected micrornas (mirnas) expressed in pasmcs are influenced by sex, bmpr-ii mutations, and estrogens, and contribute to pasmc proliferation in pah. methods expression levels of mirnas targeting genes related to pah, estrogen, and serotonin were determined by quantitative rt-pcr in hpasmcs and mouse pasmcs harboring a heterozygous mutation in bmpr-ii (bmpr-ii(r899x+/-) pasmcs). mirna-96 targets 5-ht1br and was selected for further investigation. mirna target validation was confirmed by luciferase reporter assay. precursor mirna-96 was transfected into hpasmcs to examine effects on proliferation and 5-ht1br expression. the effect of a mirna-96 mimic on the development of hypoxic pulmonary hypertension in mice was also assessed. measurements and main results mirna-96 expression was reduced in bmpr-ii(r899x+/-) pasmcs from female mice and hpasmcs from female patients with pah; this was associated with increased 5-ht1br expression and serotonin-mediated proliferation. 5-ht1br was validated as a target for mirna-96. transfection of precursor mirna-96 into hpasmcs reduced 5-ht1br expression and inhibited serotonin-induced proliferation. restoration of mirna-96 expression in pulmonary arteries in vivo via administration of an mirna-96 mimic reduced the development of hypoxia-induced pulmonary hypertension in the mouse. conclusions increased 5-ht1br expression may be a consequence of decreased mirna-96 expression in female patient pasmcs, and this may contribute to the development of pah.",1
"aberrant expression of mitochondrial proteins impairs cardiac function and causes heart disease. the mechanism of regulation of mitochondria encoded protein expression during cardiac disease, however, remains underexplored. here, we show that multiple pathogenic cardiac stressors induce the expression of mir-574 guide and passenger strands (mir-574-5p/3p) in both humans and mice. mir-574 knockout mice exhibit severe cardiac disorder under different pathogenic cardiac stresses while mir-574-5p/3p mimics that are delivered systematically using nanoparticles reduce cardiac pathogenesis under disease insults. transcriptomic analysis of mir-574-null hearts uncovers family with sequence similarity 210 member a (fam210a) as a common target mrna of mir-574-5p and mir-574-3p. the interactome capture analysis suggests that fam210a interacts with mitochondrial translation elongation factor ef-tu. manipulating mir-574-5p/3p or fam210a expression changes the protein expression of mitochondrial-encoded electron transport chain (etc) genes but not nuclear-encoded mitochondrial etc genes in both human ac16 cardiomyocyte cells and mir-574-null murine hearts. together, we discovered that mir-574 regulates fam210a expression and modulates mitochondrial-encoded protein expression, which may influence cardiac remodeling in heart failure.",1
"implantation failure is a major cause of early embryonic loss. normally, the conceptus attachment is initiated at mesometrial side of the uterus and then spread to the anti-mesometrial side in pigs, however, the mechanisms that direct the mesometrial-biased attachment are largely unknown. in this study, the histological features of the entire uterine cross-section from gestational days 12 (pre-attachment stage) and 15 (post-attachment stage) were investigated and the differences in histological features between the mesometrial and anti-mesometrial side of the uterus were observed. then, transcriptomic and mirna analyses were performed on mesometrial and anti-mesometrial endometrium obtained from gestational days 12 and 15, respectively. differentially expressed genes (degs) and mirnas (de-mirs) that were common to both or unique to either of the two anatomical locations of uterus were identified, respectively, indicating that differences in molecular response to the implanting conceptus exist between the two anatomical locations. in addition, we detected degs and de-mirs between the two anatomical locations on the two gestational days, respectively. of these degs, a number of genes, such as chemokine and t cell surface marker genes, were found to be significantly up-regulated mesometrially. furthermore, we detected the interaction of cxcr4 , cxcl11 and mir-9 using dual luciferase reporter assay. taken together, this study revealed genes and pathways that might play the role of creating a receptive microenvironment at the mesometrial side, which is required to guide a proper positioning of conceptus in the uterus in pigs.",1
"the small rnas associated with the protein hfq constitute one of the largest classes of post-transcriptional regulators known to date. most previously investigated members of this class are encoded by conserved free-standing genes. here, deep sequencing of hfq-bound transcripts from multiple stages of growth of salmonella typhimurium revealed a plethora of new small rna species from within mrna loci, including dapz, which overlaps with the 3' region of the biosynthetic gene, dapb. synthesis of the dapz small rna is independent of dapb protein synthesis, and is controlled by hild, the master regulator of salmonella invasion genes. dapz carries a short g/u-rich domain similar to that of the globally acting gcvb small rna, and uses gcvb-like seed pairing to repress translation of the major abc transporters, dppa and oppa. this exemplifies double functional output from an mrna locus by the production of both a protein and an hfq-dependent trans-acting rna. our atlas of hfq targets suggests that the 3' regions of mrna genes constitute a rich reservoir that provides the hfq network with new regulatory small rnas.",1
"hyperlipidemia is a risk factor for various cardiovascular and metabolic disorders. overproduction of lipoproteins, a process that is dependent on microsomal triglyceride transfer protein (mtp), can contribute to hyperlipidemia. we show that microrna-30c (mir-30c) interacts with the 3' untranslated region of mtp mrna and induces its degradation, leading to reductions in mtp activity and in apolipoprotein b (apob) secretion. mir-30c also reduces lipid synthesis independently of mtp. hepatic overexpression of mir-30c reduced hyperlipidemia in western diet-fed mice by decreasing lipid synthesis and the secretion of triglyceride-rich apob-containing lipoproteins and decreased atherosclerosis in apoe(-/-) mice. furthermore, inhibition of hepatic mir-30c by anti-mir-30c increased hyperlipidemia and atherosclerosis. therefore, mir-30c coordinately reduces lipid biosynthesis and lipoprotein secretion, thereby regulating hepatic and plasma lipid concentrations. raising mir-30c levels might be useful in treating hyperlipidemias and associated disorders.",1
"long noncoding rnas (lncrnas) are thought to be prevalent regulators of gene expression, but the consequences of lncrna inactivation in vivo are mostly unknown. here, we show that targeted deletion of mouse hotair lncrna leads to derepression of hundreds of genes, resulting in homeotic transformation of the spine and malformation of metacarpal-carpal bones. rna sequencing and conditional inactivation reveal an ongoing requirement of hotair to repress hoxd genes and several imprinted loci such as dlk1-meg3 and igf2-h19 without affecting imprinting choice. hotair binds to both polycomb repressive complex 2, which methylates histone h3 at lysine 27 (h3k27), and lsd1 complex, which demethylates histone h3 at lysine 4 (h3k4) in vivo. hotair inactivation causes h3k4me3 gain and, to a lesser extent, h3k27me3 loss at target genes. these results reveal the function and mechanisms of hotair lncrna in enforcing a silent chromatin state at hox and additional genes.",1
"pt181 is the prototype of a family of staphylococcal plasmids that regulate their replication by means of antisense rnas (countertranscripts) that block expression of the plasmid-coded initiator protein. in this paper, we show that the pt181 countertranscripts induce premature termination (attenuation) of the initiator mrna by promoting the formation of a termination-causing hairpin just 5' to the initiator start codon. in the absence of the countertranscripts, an upstream sequence, the preemptor, pairs with the proximal arm of the terminator hairpin, preventing termination and permitting transcription of the initiator gene. this system thus differs from the classical attenuators in that attenuation is driven by antisense rnas rather than by trna-induced stalling of ribosomes.",1
"th17 cells and interleukin-17 (il-17) have been found to play an important role in the pathology of multiple sclerosis (ms) and its animal model, experimental autoimmune encephalomyelitis (eae). response to il-17, reactive astrocytes accompany with immune cells infiltration and axonal damage in ms/eae. however, the role and the regulatory mechanism of il-17-activated astrocytes in inflammation and in the eae process still remain largely unknown. here, we elucidated that mir-409-3p and mir-1896, as co-upregulated micrornas in activated astrocytes and in eae mice, targeted suppressor of cytokine signaling proteins 3 (socs3). overexpression of mir-409-3p or mir-1896 significantly reduced socs3 expression and increased phosphorylation of stat3 as well as induced the inflammatory cytokines production (il-1β, il-6, ip-10, mcp-1, and kc), cd4 + t cells migration and demyelination, in turn aggravating eae development. importantly, the effects of co-overexpression of mir-409-3p and mir-1896 in vitro or in vivo are strongly co-operative. in contrast, simultaneously silenced mir-409-3p and mir-1896 co-operatively ameliorates inflammation and demyelination in the central nervous system of eae mice. collectively, our findings highlight that mir-409-3p and mir-1896 co-ordinately promote the production of inflammatory cytokines in reactive astrocytes through the socs3/stat3 pathway and enhance reactive astrocyte-directed chemotaxis of cd4 + t cells, leading to aggravate pathogenesis in eae mice. co-inhibition of mir-409-3p and mir-1896 may be a therapeutic target for treating ms and neuroinflammation.",1
"a disintegrin and metalloproteinase 17 (adam17) is a metalloprotease that is overexpressed in many cancer types, including renal cancers. however, the regulatory mechanisms of adam17 in cancer development and progression are poorly understood. in the present work, we provide evidence using overexpression and inhibition of microrna 145 (mir-145) that mir-145 negatively regulates adam17 expression. furthermore, we show that adam17 negatively regulates mir-145 through tumor necrosis factor-α, resulting in a reciprocal negative feedback loop. in this study, the expression of adam17 and mir-145 correlated negatively in renal cancer tumor tissues and cell lines, suggesting an important regulatory mechanism. additionally, we showed that the regulation of adam17 is partly involved in the effects of mir-145 on proliferation and migration, whereas no involvement in chemosensitivity was observed. importantly, in the healthy kidney, mir-145 was detected in different cell types including tubular cells, which are considered the origin of renal cancer. in renal cancer cell lines, mir-145 expression was strongly suppressed by methylation. in summary, mir-145 is downregulated in renal cancer patients, which leads to the up-regulation of adam17 in renal cancer. importantly, mir-145 and adam17 are regulated in a reciprocal negative feedback loop.",1
"numerous micrornas (mirnas) are reported as differentially expressed in cancer, however the consequence of mirna deregulation in cancer is unknown for many mirnas. we report that two mirnas located on chromosome 17p13, mir-132 and mir-212, are over-expressed in pancreatic adenocarcinoma (pdac) tissues. both mirnas are predicted to target the retinoblastoma tumor suppressor, rb1. validation of this interaction was confirmed by luciferase reporter assay and western blot in a pancreatic cancer cell line transfected with pre-mir-212 and pre-mir-132 oligos. cell proliferation was enhanced in panc-1 cells transfected with pre-mir-132/-212 oligos. conversely, antisense oligos to mir-132/-212 reduced cell proliferation and caused a g(2)/m cell cycle arrest. the mrna of a number of e2f transcriptional targets were increased in cells over expressing mir-132/-212. exposing panc-1 cells to the β2 adrenergic receptor agonist, terbutaline, increased the mir-132 and mir-212 expression by 2- to 4-fold. we report that over-expression of mir-132 and mir-212 result in reduced prb protein in pancreatic cancer cells and that the increase in cell proliferation from over-expression of these mirnas is likely due to increased expression of several e2f target genes. the β2 adrenergic pathway may play an important role in this novel mechanism.",1
"it is widely accepted that long-term changes in synapse structure and function are mediated by rapid activity-dependent gene transcription and new protein synthesis. a growing amount of evidence suggests that the microrna (mirna) pathway plays an important role in coordinating these processes. despite recent advances in this field, there remains a critical need to identify specific activity-regulated mirnas as well as their key messenger rna (mrna) targets. to address these questions, we used the larval drosophila melanogaster neuromuscular junction (nmj) as a model synapse in which to identify novel mirna-mediated mechanisms that control activity-dependent synaptic growth. first, we developed a screen to identify mirnas differentially regulated in the larval cns following spaced synaptic stimulation. surprisingly, we identified five mirnas (mirs-1, -8, -289, -314, and -958) that were significantly downregulated by activity. neuronal misexpression of three mirnas (mirs-8, -289, and -958) suppressed activity-dependent synaptic growth suggesting that these mirnas control the translation of biologically relevant target mrnas. functional annotation cluster analysis revealed that putative targets of mirs-8 and -289 are significantly enriched in clusters involved in the control of neuronal processes including axon development, pathfinding, and growth. in support of this, mir-8 regulated the expression of a wingless 3'utr (wg 3' untranslated region) reporter in vitro. wg is an important presynaptic regulatory protein required for activity-dependent axon terminal growth at the fly nmj. in conclusion, our results are consistent with a model where key activity-regulated mirnas are required to coordinate the expression of genes involved in activity-dependent synaptogenesis.",1
"the establishment of dorsoventral polarity in the drosophila oocyte and future embryo is dependent on the efficient transport of k10 mrna from nurse cells into the oocyte. to investigate the cis-requirements of k10 mrna transport, we used a transgenic fly assay to analyze the expression patterns of a series of k10 deletion variants. such studies identify a 44 nucleotide sequence within the k10 3' untranslated region that is required and sufficient for k10 mrna transport and subsequent localization to the oocyte's anterior cortex. an inspection of the 44 nucleotide transport/localization sequence (tls) reveals a strong potential for the formation of a stem-loop secondary structure. nucleotide substitutions that interfere with the predicted base-pairing of the tls block mrna transport and anterior localization. conversely, mutations that alter the base composition of the tls while maintaining predicted base-pairing do not block mrna transport or anterior localization. we conclude that k10 mrna transport and anterior localization is mediated by a 44 nucleotide stem-loop structure. a similar putative stem-loop structure is found in the 3' untranslated region of the drosophila orb mrna, suggesting that the same factors mediate the transport and anterior localization of both k10 and orb mrnas. apart from orb, the k10 tls is not found in any other localized mrna, raising the possibility that the transport and localization of other mrnas, e.g., bicoid, oskar and gurken, are mediated by novel sets of cis- and trans-acting factors. moreover, we find that the k10 tls overrides the activity of oskar cis-regulatory elements that mediate the late stage movement of the mrna to the posterior pole. we propose the existence of a family of cis-regulatory elements that mediate mrna transport into the oocyte, only some of which are compatible with the elements that mediate late stage movements.",1
"background gout is considered one of the most painful acute conditions caused by deposition of monosodium urate (msu) crystals within joints. recent studies have shown that interleukin (il)-1β is a key inflammatory mediator in acute gouty arthritis (ga), and its level is regulated by micrornas (mirnas). however, the molecular mechanisms of the regulation remain unclear. methods a mirna microarray was used to analyze the mirna expression profiles in peripheral white blood cells (wbcs) of patients with ga. thp-1 cells were transfected with mirna mimics, stimulated by msu crystals, and then subjected to quantitative real-time polymerase chain reaction or western blot analysis. levels of il-1β, il-8, and tumor necrosis factor (tnf)-α in culture supernatants of thp-1 cells were measured by enzyme-linked immunosorbent assay. a luciferase reporter assay was conducted to confirm the interaction of mirna and il-1β 3'-untranslated regions (utrs). results combining bioinformatics and mirna expression profiles, we found five mirnas (hsa-mir-30c-1-3p, hsa-mir-488-3p, hsa-mir-550a-3p, hsa-mir-663a, and hsa-mir-920) that possibly target il-1β. then, we demonstrated that mir-488 and mir-920 were significantly decreased in the wbcs of patients with ga and that msu crystals could inhibit expression of mir-488 and mir-920. upregulation of mir-488 and mir-920 could suppress msu-induced il-1β protein expression in thp-1 cells, but no significant difference in il-1β messenger rna levels was observed. moreover, we found that mir-488 and mir-920 could directly target the 3'-utr of il-1β. overexpression of mir-488 and mir-920 could significantly inhibit the gene and protein expression of il-8 and tnf-α in msu-induced thp-1 cells. conclusions this study demonstrates the roles of mir-488 and mir-920 in regulating the production of proinflammatory cytokines in the pathogenesis of ga. these findings suggest that mir-488 and mir-920 could serve as potential therapeutic targets in the treatment of ga.",1
"micrornas (mirnas) are small noncoding rnas that have been linked to a number of disease-related signal transduction pathways. several studies indicate that they are also involved in nociception. it is not clear, however, which mirnas are important and which genes are modulated by mirna-associated mechanisms. this study focuses on the regulation and function of the central nervous system (cns)-specific mirna-124a in the spinal cord of mice in a formalin model of inflammatory nociception. mirna-124a is constitutively expressed in the spinal cord of mice, particularly in neurons of the dorsal horn. peripheral noxious stimulation with formalin led to significant down-regulation of its expression. knock-down of mirna-124a by intravenous administration of a specific mirna-124a inhibitor further increased the nociceptive behavior associated with an upregulation of the pain-relevant mirna-124a target mecp2 and proinflammatory marker genes. in contrast, administration of a mirna-124a mimic counteracted these effects and decreased nociception by down-regulation of the target gene. in conclusion, our results indicate that mirna-124a is involved in inflammatory nociception by regulation of relevant target proteins and might therefore constitute a novel target for anti-inflammatory therapy.",1
"aquaporin-1 (aqp1) is expressed in human and mouse hearts, but little is known about its cellular and subcellular localization and regulation. the aim of this study was to investigate the localization of aqp1 in the mouse heart and to determine the effects of ischemia and hypoxia on its expression. mouse myocardial cells were freshly isolated and split into cardiomyocyte and non-cardiomyocyte fractions. isolated, langendorff-perfused c57bl6 mouse hearts (n=46) were harvested with no intervention, subjected to 35min of ischemia or ischemia followed by 60min of reperfusion. eleven mouse hearts were perfusion-fixed for electron microscopy. forty c57bl6 mice were exposed to normobaric hypoxia for one or two weeks (n=12). needle biopsies of human left ventricular myocardium were sampled (n=30) during coronary artery bypass surgery before cardioplegia and after 30min of reperfusion. human umbilical vein endothelial cells (huvecs) were subjected to 4h of hypoxia with reoxygenation for either 4 or 24h. aqp1 expression was studied by electron microscopy with immunogold labeling, western blot, and qpcr. expression of mir-214 and mir-320 in huvecs with hypoxia was studied with qpcr. huvecs were then transfected with precursors and inhibitors of mir-214. aqp1 expression was confined to cardiac endothelial cells, with no signal in cardiomyocytes or cardiac fibroblasts. immunogold electron microscopy showed aqp1 expression in endothelial caveolae with equal distribution along the basal and apical membranes. ischemia and reperfusion tended to decrease aqp1 mrna expression in mouse hearts by 37±9% (p=0.06), while glycosylated aqp1 protein was reduced by 16±9% (p=0.03). no difference in expression was found between ischemia alone and ischemia-reperfusion. in human left ventricles aqp1 mrna expression was reduced following cardioplegia and reperfusion (p=0.008). hypoxia in mice reduced aqp1 mrna expression by 20±7% (p<0.0001), as well as both glycosylated (-47±10%, p=0.03) and glycan-free protein (-34±16%, p=0.05). hypoxia and reoxygenation in huvecs downregulated glycan-free aqp1 protein (-34±24%, p=0.04) and upregulated mir-214 (+287±52%, p<0.05). huvecs transfected with anti-mir-214 had increased glycosylated (1.5 fold) and glycan-free (2 fold) aqp1. aqp1 in mouse hearts is localized to endothelial cell membranes and caveolae. cardioplegia, ischemia and hypoxia decrease aqp1 mrna as well as total protein expression and glycosylation, possibly regulated by mir-214.",1
"micrornas (mirnas) regulate the proliferation and metastasis of cancer cells. here, we showed that mir-152 was downregulated in non-small-cell lung cancer (nsclc) tissues and cell lines. overexpression of mir-152 suppressed cell proliferation and colony formation and also limited migration and invasion. fibroblast growth factor 2 (fgf2) was confirmed as a direct target of mir-152. fgf2 knockdown suppressed cell proliferation, colony formation, migration and invasion, whereas fgf2 overexpression partially reversed the suppressive effect of mir-152. furthermore, the presence of mir-152 was inversely correlated with fgf2 in nsclc tissues. overall, this study demonstrated that mir-152 suppressed the proliferation and invasion of nsclc cells by downregulating fgf2. these findings provide novel insights with potential therapeutic applications for the treatment of nsclc.",1
"the expression of trans-acting small rnas in firmicutes has been poorly documented to date. this gap is being filled quickly in the genus staphylococcus, which is both a model firmicute and an important human pathogen. here we analyze rsaog, a novel small rna family specific to staphylococcus and highly transcribed. this well conserved element, first discovered in a computational screen, was precisely mapped in the genome by race mapping and the identification of a putative transcriptional promoter. the proposed secondary structure presents two highly conserved unpaired sequences, part of which can form a pseudoknot. we suggest a possible involvement of the remaining conserved single stranded region in trans regulatory interactions.",1
"while most mirna knockouts exhibit only subtle defects, a handful of mirnas are profoundly required for development or physiology. a particularly compelling locus is drosophila mir-279, which was reported as essential to restrict the emergence of co2-sensing neurons, to maintain circadian rhythm, and to regulate ovarian border cells. the mir-996 locus is located near mir-279 and bears a similar seed, but they otherwise have distinct, conserved, non-seed sequences, suggesting their evolutionary maintenance for separate functions. we generated single and double deletion mutants of the mir-279 and mir-996 hairpins, and cursory analysis suggested that mir-996 was dispensable. however, discrepancies in the strength of individual mir-279 deletion alleles led us to uncover that all extant mir-279 mutants are deficient for mature mir-996, even though they retain its genomic locus. we therefore engineered a panel of genomic rescue transgenes into the double deletion background, allowing a pure assessment of mir-279 and mir-996 requirements. surprisingly, detailed analyses of viability, olfactory neuron specification, and circadian rhythm indicate that mir-279 is completely dispensable. instead, an endogenous supply of either mir-279 or mir-996 suffices for normal development and behavior. sensor tests of nine key mir-279/996 targets showed their similar regulatory capacities, although transgenic gain-of-function experiments indicate partially distinct activities of these mirnas that may underlie that co-maintenance in genomes. altogether, we elucidate the unexpected genetics of this critical mirna operon, and provide a foundation for their further study. more importantly, these studies demonstrate that multiple, vital, loss-of-function phenotypes can be rescued by endogenous expression of divergent seed family members, highlighting the importance of this mirna region for in vivo function.",1
"epigenetic reprogramming is a critical process of pathological gene induction during cardiac hypertrophy and remodeling, but the underlying regulatory mechanisms remain to be elucidated. here we identified a heart-enriched long noncoding (lnc)rna, named cardiac-hypertrophy-associated epigenetic regulator (chaer), which is necessary for the development of cardiac hypertrophy. mechanistically, chaer directly interacts with the catalytic subunit of polycomb repressor complex 2 (prc2). this interaction, which is mediated by a 66-mer motif in chaer, interferes with prc2 targeting to genomic loci, thereby inhibiting histone h3 lysine 27 methylation at the promoter regions of genes involved in cardiac hypertrophy. the interaction between chaer and prc2 is transiently induced after hormone or stress stimulation in a process involving mammalian target of rapamycin complex 1, and this interaction is a prerequisite for epigenetic reprogramming and induction of genes involved in hypertrophy. inhibition of chaer expression in the heart before, but not after, the onset of pressure overload substantially attenuates cardiac hypertrophy and dysfunction. our study reveals that stress-induced pathological gene activation in the heart requires a previously uncharacterized lncrna-dependent epigenetic checkpoint.",1
"micrornas (mirnas) are associated with cytogenetics and molecular subtypes of acute myelogeneous leukemia (aml), but their impact on aml pathogenesis is poorly understood. we have previously shown that mir-29b expression is deregulated in primary aml blasts. in this work, we investigated the functional role of mir-29b in leukemogenesis. restoration of mir-29b in aml cell lines and primary samples induces apoptosis and dramatically reduces tumorigenicity in a xenograft leukemia model. transcriptome analysis after ectopic transfection of synthetic mir-29b into leukemia cells indicates that mir-29b target apoptosis, cell cycle, and proliferation pathways. a significant enrichment for apoptosis genes, including mcl-1, was found among the mrnas inversely correlated with mir-29b expression in 45 primary aml samples. together, the data support a tumor suppressor role for mir-29 and provide a rationale for the use of synthetic mir-29b oligonucleotides as a novel strategy to improve treatment response in aml.",1
"we have purified the yeast u5 and u6 pre-mrna splicing small nuclear ribonucleoproteins (snrnps) by affinity chromatography and analyzed the associated polypeptides by mass spectrometry. the yeast u5 snrnp is composed of the two variants of u5 snrna, six u5-specific proteins and the 7 proteins of the canonical sm core. the u6 snrnp is composed of the u6 snrna, prp24, and the 7 sm-like (lsm) proteins. surprisingly, the yeast dead-box helicase-like protein prp28 is stably associated with the u5 snrnp, yet is absent from the purified u4/u6 x u5 snrnp. a novel yeast u5 and four novel yeast u4/u6 x u5 snrnp polypeptides were characterized by genetic and biochemical means to demonstrate their involvement in the pre-mrna splicing reaction. we also show that, unlike the human tri-snrnp, the yeast tri-snrnp dissociated upon addition of atp or datp.",1
"the abnormal proliferation and apoptosis of human aortic vascular smooth muscle cells (havsmcs) play an important role in the pathogenesis of hypertension. recent study revealed that angiotensin ii (ang ii) could elicit havsmc dysfunction, to induce or aggravate hypertension. purinergic receptor p2y6, an inflammation-inducible g protein-coupled receptor, promoted ang ii-induced hypertension. in the present study, we revealed that ang ii induced havsmc proliferation and upregulated p2y6 protein levels. after knockdown of p2y6, the promotive effect of ang ii on havsmc proliferation was restored. micrornas (mirnas) involve in most biological processes. in this study, we scanned out seven candidate mirnas, which were predicted to contain binding site of p2y6's 3'-utr by online tools. among them, mir-185 was significantly downregulated by ang ii treatment. mir-185 reduced p2y6 protein levels by direct binding to the 3'utr of p2y6. mir-185 overexpression suppressed havsmc proliferation; p2y6 overexpression or ang ii treatment promoted havsmc proliferation, and restored the suppressive effect of mir-185 on havsmc proliferation. besides, mir-185/p2y6 axis also affected perk1/2 protein levels. taken together, the present study indicated that mir-185/p2y6 axis might inhibit ang ii-induced havsmc proliferation through mir-185 negatively regulating p2y6 expression and the downstream erk pathway; rescuing mir-185 expression to inhibit p2y6 may represent a therapeutic strategy against havsmc dysfunction and hypertension.",1
"objective to identify circulating micrornas that are differentially expressed in severe coronary heart disease with well or poorly developed collateral arteries and to investigate their mechanisms of action in vivo and in vitro. approach and results in our study, we identified a circulating microrna, mir-15b-5p, with low expression that, nevertheless, characterized patients with sufficient coronary collateral artery function. moreover, in murine hindlimb ischemia model, in situ hybridization identified that mir-15b-5p was specifically expressed in vascular endothelial cells of adductors in sham group and was remarkably downregulated after femoral artery ligation. overexpressed mir-15b-5p significantly inhibited arteriogenesis and angiogenesis in mice. in vitro, both under basal and vascular endothelial growth factor stimulation, loss-of-function or gain-of-function studies suggested that mir-15b-5p significantly promoted or depressed the migration and proliferation of endothelial cells. we identified akt3 (protein kinase b-3) as a direct target of mir-15b-5p. interestingly, akt3 deficiency by injection with chol-akt3-sirna obviously suppressed arteriogenesis and the recovery of blood perfusion after femoral ligation in mice. conclusions these results indicate that circulating mir-15b-5p is a suitable biomarker for discriminating between patients with well-developed or poorly developed collaterals. moreover, mir-15b-5p is a key regulator of arteriogenesis and angiogenesis, which may represent a potential therapeutic target for ischemic disease.",1
"microrna (mirna) expression in fetal human retinal pigment epithelium (hfrpe), retina, and choroid were pairwise compared to determine those mirnas that are enriched by 10-fold or more in each tissue compared with both of its neighbors. mirs-184, 187, 200a/200b, 204/211, and 221/222 are enriched in hfrpe by 10- to 754-fold compared with neuroretina or choroid (p<0.05). five of these mirnas are enriched in rpe compared with 20 tissues throughout the body and are 10- to 20,000-fold more highly expressed (p<0.005). mir-204 and 211 are the most highly expressed in the rpe. in addition, expression of mir-204/211 is significantly lower in the nci60 tumor cell line panel compared with that in 13 normal tissues, suggesting the progressive disruption of epithelial barriers and increased proliferation. we demonstrated that tgf-beta receptor 2 (tgf-betar2) and snail2 are direct targets of mir-204 and that a reduction in mir-204 expression leads to reduced expression of claudins 10, 16, and 19 (message/protein) consistent with our observation that anti-mir-204/211 decreased transepithelial resistance by 80% and reduced cell membrane voltage and conductance. the anti-mir-204-induced decrease in kir7.1 protein levels suggests a signaling pathway that connects tgf-betar2 and maintenance of potassium homeostasis. overall, these data indicate a critical role for mir-204/211 in maintaining epithelial barrier function and cell physiology.",1
"both fragile x syndrome and rett syndrome are commonly associated with autism spectrum disorders and involve defects in synaptic plasticity. microrna is implicated in synaptic plasticity because fragile x mental retardation protein was recently linked to the microrna pathway. dna methylation is also involved in synaptic plasticity since methyl cpg-binding protein 2 (mecp2) is mutated in patients with rett syndrome. here we report that expression of mir-184, a brain-specific microrna repressed by the binding of mecp2 to its promoter, is upregulated by the release of mecp2 after depolarization. the restricted release of mecp2 from the paternal allele results in paternal allele-specific expression of mir-184. our finding provides a clue to the link between the microrna and dna methylation pathways.",1
"telomerase is a large ribonucleoprotein complex minimally composed of a catalytic telomerase reverse transcriptase (tert) and an rna component (tr) that provides the template for telomeric dna synthesis. however, it remains unclear how tert and tr assemble into a functional telomerase. here we report the crystal structure of the conserved regions 4 and 5 (cr4/5) of tr in complex with the tr-binding domain (trbd) of tert from the teleost fish oryzias latipes. the structure shows that cr4/5 adopts an l-shaped three-way-junction conformation with its two arms clamping onto trbd. both the sequence and conformation of cr4/5 are required for the interaction. our structural and mutational analyses suggest that the observed cr4/5-trbd recognition is common to most eukaryotes, and cr4/5 in vertebrate tr might have a similar role in telomerase regulation as that of stem-loop iv in tetrahymena tr.",1
"the initiation, progression and transmission of most bacterial infections is dependent upon the ability of the invading pathogen to acquire iron from each of the varied environments encountered during the course of a natural infection. in total, 95% of iron within the human body is complexed within heme, making heme a potentially rich source of host-associated nutrient iron for invading bacteria. as heme is encountered only within the host, pathogenic bacteria often regulate synthesis of heme utilization factors such that production is maximal under host-associated environmental conditions. this study examines the regulated production of shua, an outer-membrane receptor required for the utilization of heme as a source of nutrient iron by shigella dysenteriae, a pathogenic bacterium that causes severe diarrheal diseases in humans. specifically, the impact of the distinct environmental temperatures encountered during infection within a host (37°c) and transmission between hosts (25°c) on shua expression is investigated. we show that shua expression is subject to temperature-dependent post-transcriptional regulation resulting in increased shua production at 37°c. the observed thermoregulation is mediated by nucleic acid sequences within the 5' untranslated region. in addition, we have identified similar nucleotide sequences within the 5' untranslated region of the orthologous chua transcript of enteropathogenic e. coli and have demonstrated that it also functions to confer temperature-dependent post-transcriptional regulation. in both function and predicted structure, the regulatory element within the shua and chua 5' untranslated regions closely resembles a fouru rna thermometer, a zipper-like rna structure that occludes the shine-dalgarno sequence at low temperatures. increased production of shua and chua in response to the host body temperature allows for maximal production of these heme acquisition factors within the environment where s. dysenteriae and pathogenic e. coli strains would encounter heme, a host-specific iron source.",1
"background: micrornas are important posttranscriptional regulators of gene expression. mir-203 is a mirna preferentially expressed in the skin, and an important regulator of keratinocyte differentiation. mir-203 has been implicated in skin diseases, in particular in psoriasis in which it is overexpressed, and in basal cell carcinoma where it acts as a tumor suppressor mirna. objectives: to identify novel targets for mir-203 that may be relevant in skin physiology and diseases. materials & methods: bioinformatics was used to identify putative mir-203 targets among genes expressed in keratinocytes. interleukin-8 (il-8) gene expression and concentration in keratinocyte medium was measured by quantitative real-time pcr and elisa, respectively. for mirna overexpression, resting or tnf-α-treated primary human keratinocytes were transfected with synthetic precursor of mir-203, or scramble mirna precursors using lipofectamine 2000. 3'utr luciferase reporter experiments were performed to prove the direct mirna:mrna interaction. site-specific mutagenesis was used to mutate the predicted mir-203 binding sites in the 3'utr of il-8 gene. results: bioinformatic analysis indentified two putative mir-203 binding sites in the 3'utr of il-8. mir-203 suppressed il-8 mrna and protein expression in primary human keratinocytes both under resting conditions and after tnf-α treatment. overexpression of mir-203 suppressed the luciferase activity of a reporter gene fused with the il-8 3'utr. the suppressive effect was abolished when the predicted binding sites of mir-203 on il-8 3'utr were mutated. conclusion: we identify il-8 as a novel target of mir-203 for posttranscriptional suppression. these findings may have relevance in diseases in which mir-203 and il-8 expression are deregulated.",1
"background micrornas (mirnas) have the potential to regulate diverse sets of mrna targets. in addition, mammalian genomes contain numerous natural antisense transcripts, most of which appear to be non-protein-coding rnas (ncrnas). we have recently identified and characterized a highly conserved non-coding antisense transcript for beta-secretase-1 (bace1), a critical enzyme in alzheimer's disease pathophysiology. the bace1-antisense transcript is markedly up-regulated in brain samples from alzheimer's disease patients and promotes the stability of the (sense) bace1 transcript. results we report here that bace1-antisense prevents mirna-induced repression of bace1 mrna by masking the binding site for mir-485-5p. indeed, mir-485-5p and bace1-antisense compete for binding within the same region in the open reading frame of the bace1 mrna. we observed opposing effects of bace1-antisense and mir-485-5p on bace1 protein in vitro and showed that locked nucleic acid-antimir mediated knockdown of mir-485-5p as well as bace1-antisense over-expression can prevent the mirna-induced bace1 suppression. we found that the expression of bace1-antisense as well as mir-485-5p are dysregulated in rna samples from alzheimer's disease subjects compared to control individuals. conclusions our data demonstrate an interface between two distinct groups of regulatory rnas in the computation of bace1 gene expression. moreover, bioinformatics analyses revealed a theoretical basis for many other potential interactions between natural antisense transcripts and mirnas at the binding sites of the latter.",1
"site-specific post-transcriptional conversion of uridines to pseudouridine in ribosomal rnas and small nuclear rnas (snrnas) is directed by guide rnas which possess the conserved box h and aca sequence elements and fold into the consensus 'hairpin-hinge-hairpin-tail' secondary structure. here, we describe an unusual mammalian pseudouridylation guide rna, called u93, that is composed of two tandemly arranged box h/aca rna domains. the u93 rna therefore carries two h and two aca box motifs, all of which are essential for accumulation of the full-length rna. the human u93 rna accumulates in cajal (coiled) bodies and it is predicted to function in pseudouridylation of the u2 spliceosomal snrna. our results lend further support to the notion that modification of the rna polymerase ii-transcribed spliceosomal snrnas takes place in cajal bodies.",1
"a simple method for intraoperative autotransfusion (atf) in open-heart surgery was tested in a prospective clinical trial. the patients were randomly assigned to a control group (33) or to the atf group (35). the intraoperative atf was combined with preoperative collection of blood and postoperative atf. the postoperative chest-tube drainage was reduced by 24.3%, the donor-blood requirement by 43.3% and the consumption of fresh-frozen plasma by 43.9% in the atf group as compared with the controls (all differences statistically significant). to investigate possible haematologic side effects of atf, measurements of haemoglobin, haematocrit, fibrinogen concentration, thrombin, prothrombin and partial thromboplastin time, antithrombin-iii and fibrinolytic activity were made in all patients preoperatively and on postoperative days 1 and 2. no statistical differences were then found between the controls and the atf group. microbiologic tests of blood sampled from the cardiotomy reservoir gave satisfactory results.",1
"ciliogenesis requires the removal of cp110 from the mother centriole; actin dynamics also influence ciliation, at least partly by affecting the centrosomal accumulation of ciliogenic membrane vesicles. how these distinct processes are properly regulated remains unknown. here we show that mir-129-3p, a microrna conserved in vertebrates, controlled cilia biogenesis in cultured cells by concomitantly downregulating cp110 and repressing branched f-actin formation. blocking mir-129-3p inhibited serum-starvation-induced ciliogenesis, whereas its overexpression potently induced ciliation in proliferating cells and also promoted cilia elongation. gene expression analysis further identified arp2, toca1, ablim1 and ablim3 as its targets in ciliation-related actin dynamics. moreover, mir-129-3p inhibition in zebrafish embryos suppressed ciliation in kupffer's vesicle and the pronephros, and induced developmental abnormalities including a curved body, pericardial oedema and defective left-right asymmetry. therefore, our results reveal a mechanism that orchestrates both the centriole-to-basal body transition and subsequent cilia assembly through microrna-mediated post-transcriptional regulation.",1
"microrna mir-376c was expressed in normal intrahepatic biliary epithelial cells (hibepic), but was significantly suppressed in the hucct1 intrahepatic cholangiocarcinoma (icc) cell line. the biological significance of the down-regulation of mir-376c in hucct1 cells is unknown. we hypothesized that mir-376c could function as a tumor suppressor in these cells. to test this hypothesis, we sought the targets of mir-376c, and characterized the effect of its down-regulation on hucct1 cells. we performed proteomic analysis of mir-376c-overexpressing hucct1 cells to identify candidate targets of mir-376c, and validated these targets by 3'-utr reporter assay. transwell migration assays were performed to study the migratory response of hucct1 cells to mir-376c overexpression. furthermore, microarrays were used to identify the signaling that were potentially involved in the mir-376c-modulated migration of hucct1. finally, we assessed epigenetic changes within the potential promoter region of the mir-376c gene in these cells. proteomic analysis and subsequent validation assays showed that growth factor receptor-bound protein 2 (grb2) was a direct target of mir-376c. the transwell migration assay revealed that mir-376c significantly reduced epidermal growth factor (egf)-dependent cell migration in hucct1 cells. dna microarray and subsequent pathway analysis showed that interleukin 1 beta and matrix metallopeptidase 9 were possible participants in egf-dependent migration of hucct1 cells. bisulfite sequencing showed higher methylation levels of cpg sites upstream of the mir-376c gene in hucct1 relative to hibepic cells. combined treatment with the dna-demethylating agent 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor trichostatin a significantly upregulated the expression of mir-376c in hucct1 cells. we revealed that epigenetic repression of mir-376c accelerated egf-dependent cell migration through its target grb2 in hucct1 cells. these findings suggest that mir-376c functions as a tumor suppressor. since metastasis is the major cause of death in icc, microrna manipulation could lead to the development of novel anti-cancer therapy strategies for icc.",1
"telomerase activation is a common feature of advanced human cancers and facilitates the malignant transformation of cultured human cells and in mice. these experimental observations are in accord with the presence of robust telomerase activity in more advanced stages of human colorectal carcinogenesis. however, the occurrence of colon carcinomas in telomerase rna (terc)-null, p53-mutant mice has revealed complex interactions between telomere dynamics, checkpoint responses and carcinogenesis. we therefore sought to determine whether telomere dysfunction exerts differential effects on cancer initiation versus progression of mouse and human intestinal neoplasia. in successive generations of apcmin terc-/- mice, progressive telomere dysfunction led to an increase in initiated lesions (microscopic adenomas), yet a significant decline in the multiplicity and size of macroscopic adenomas. that telomere dysfunction also contributes to human colorectal carcinogenesis is supported by the appearance of anaphase bridges (a correlate of telomere dysfunction) at the adenoma-early carcinoma transition, a transition recognized for marked chromosomal instability. together, these data are consistent with a model in which telomere dysfunction promotes the chromosomal instability that drives early carcinogenesis, while telomerase activation restores genomic stability to a level permissive for tumor progression. we propose that early and transient telomere dysfunction is a major mechanism underlying chromosomal instability of human cancer.",1
"mir-17∼92 is a polycistronic microrna (mir) cluster (consisting of mir-17, mir-18a, mir-19a, mir-19b, mir-20a, and mir-92a) which frequently is overexpressed in several solid and lymphoid malignancies. loss- and gain-of-function studies have revealed the role of mir-17∼92 in heart, lung, and b-cell development and in myc-induced b-cell lymphomas, respectively. recent studies indicate that overexpression of this locus leads to lymphoproliferation, but no experimental proof that dysregulation of this cluster causes b-cell lymphomas or leukemias is available. to determine whether mir-17∼92- overexpression induces lymphomagenesis/leukemogenesis, we generated a b-cell-specific transgenic mouse model with targeted overexpression of this cluster in b cells. the mir-17∼92 overexpression was driven by the eµ-enhancer and ig heavy-chain promoter, and a 3' gfp tag was added to the transgene to track the mir expression. expression analysis using northern blot and quantitative rt-pcr confirmed 2.5- to 25-fold overexpression of all six mirs in the transgenic mice spleens as compared with spleens from wild-type mice. eµ-mir-17∼92 mice developed b-cell malignancy by the age of 12-18 mo with a penetrance of ∼80% (49% splenic b-cell lymphoproliferative disease, 28% lymphoma). at this stage mice exhibited severe splenomegaly with abnormal b-cell-derived white pulp expansion and enlarged lymph nodes. interestingly, we found three classes of b-cell lymphomas/leukemias at varying grades of differentiation. these included expansion of cd19(+) and cd5(+) double-positive b cells similar to the aggressive form of human b-cell chronic lymphocytic leukemia, b220(+) cd43(+) b1-cell proliferation, and a cd19(+) aggressive diffuse large b-cell lymphoma-like disease, as assessed by flow cytometry and histopathological analysis.",1
"approximately 6 million people worldwide are suffering from severe visual impairments or blindness due to corneal diseases. corneal allogeneic transplantation is often required to restore vision; however, shortage in corneal grafts and immunorejections remain major challenges. the molecular basis of corneal diseases is poorly understood largely due to lack of appropriate cellular models. here, we described a robust differentiation of human-induced pluripotent stem cells (hipscs) derived from hair follicles or skin fibroblasts into corneal epithelial-like cells. we found that bmp4, coupled with corneal fibroblast-derived conditioned medium and collagen iv allowed efficient corneal epithelial commitment of hipscs in a manner that recapitulated corneal epithelial lineage development with high purity. organotypic reconstitution assays suggested the ability of these cells to stratify into a corneal-like epithelium. this model allowed us identifying mir-450b-5p as a molecular switch of pax6, a major regulator of eye development. mir-450b-5p and pax6 were reciprocally distributed at the presumptive epidermis and ocular surface, respectively. mir-450b-5p inhibited pax6 expression and corneal epithelial fate in vitro, altogether, suggesting that by repressing pax6, mir-450b-5p triggers epidermal specification of the ectoderm, while its absence allows ocular epithelial development. additionally, mir-184 was detectable in early eye development and corneal epithelial differentiation of hipscs. the knockdown of mir-184 resulted in a decrease in pax6 and k3, in line with recent findings showing that a point mutation in mir-184 leads to corneal dystrophy. altogether, these data indicate that hipscs are valuable for modeling corneal development and may pave the way for future cell-based therapy.",1
"micrornas play important roles in cell differentiation by acting as translational inhibitors of specific target genes. here we show that human granulocytic differentiation is controlled by a regulatory circuitry involving mir-223 and two transcriptional factors, nfi-a and c/ebpalpha. the two factors compete for binding to the mir-223 promoter: nfi-a maintains mir-223 at low levels, whereas its replacement by c/ebpalpha, following retinoic acid (ra)-induced differentiation, upregulates mir-223 expression. the competition by c/ebpalpha and the granulocytic differentiation are favored by a negative-feedback loop in which mir-223 represses nfi-a translation. in line with this, both rnai against nfi-a and ectopic expression of mir-223 in acute promyelocytic leukemia (apl) cells enhance differentiation, whereas mir-223 knockdown inhibits the differentiation response to ra. altogether, our data indicate that mir-223 plays a crucial role during granulopoiesis and point to the nfi-a repression as an important molecular pathway mediating gene reprogramming in this cell lineage.",1
"micrornas (mirnas: short non-coding rnas) are emerging as a class of potential novel tumor markers, as their dysregulation is being increasingly reported in various types of cancers. in the present study, we investigated the transcription status of mirna-148a (mir-148a) in human pancreatic ductal adenocarcinoma (pdac) and its role in the regulation of the dual specificity protein phosphatase cdc25b. we observed that mir-148a exhibited a significant 4-fold down-regulation in pdac as opposed to normal pancreatic ductal cells. in addition, we observed that stable lentiviral-mediated overexpression of mir-148a in the pancreatic cancer cell line imim-pc2, inhibited tumor cell growth and colony formation. furthermore, cdc25b was identified as a potential target of mir-148a by in silico analysis using pictar, targetscan and miranda in conjunction with gene ontology analysis. the proposed interaction between mir-148a and the 3' untranslated region (utr) of cdc25b was verified by in-vitro luciferase assays. we demonstrate that the activity of a luciferase reporter containing the 3'utr of cdc25b was repressed in the presence of mir-148a mimics, confirming that mir-148a targets the 3'utr of cdc25b. finally, cdc25b was down-regulated at the protein level in mir-148a overexpressing imim-pc2-cells, and in transiently transfected pancreatic cell lines (as detected by western blot analysis), as well as in patient tumor samples (as detected by immunohistochemistry). in summary, we identified cdc25b as a novel mir-148a target which may confer a proliferative advantage in pdac.",1
"dysregulation of cholesterol homeostasis is associated with various metabolic diseases, including atherosclerosis and type 2 diabetes. the sterol response element binding protein (srebp)-2 transcription factor induces the expression of genes involved in de novo cholesterol biosynthesis and low density lipoprotein (ldl) uptake, thus it plays a crucial role in maintaining cholesterol homeostasis. here, we found that overexpressing microrna (mir)-185 in hepg2 cells repressed srebp-2 expression and protein level. mir-185-directed inhibition caused decreased srebp-2-dependent gene expression, ldl uptake, and hmg-coa reductase activity. in addition, we found that mir-185 expression was tightly regulated by srebp-1c, through its binding to a single sterol response element in the mir-185 promoter. moreover, we found that mir-185 expression levels were elevated in mice fed a high-fat diet, and this increase correlated with an increase in total cholesterol level and a decrease in srebp-2 expression and protein. finally, we found that individuals with high cholesterol had a 5-fold increase in serum mir-185 expression compared with control individuals. thus, mir-185 controls cholesterol homeostasis through regulating srebp-2 expression and activity. in turn, srebp-1c regulates mir-185 expression through a complex cholesterol-responsive feedback loop. thus, a novel axis regulating cholesterol homeostasis exists that exploits mir-185-dependent regulation of srebp-2 and requires srebp-1c for function.",1
"microrna (mirna) regulation clearly impacts animal development, but the extent to which development-with its resulting diversity of cellular contexts-impacts mirna regulation is unclear. here, we compared cohorts of genes repressed by the same mirnas in different cell lines and tissues and found that target repertoires were largely unaffected, with secondary effects explaining most of the differential responses detected. outliers resulting from differential direct targeting were often attributable to alternative 3' utr isoform usage that modulated the presence of mirna sites. more inclusive examination of alternative 3' utr isoforms revealed that they influence ∼10% of predicted targets when comparing any two cell types. indeed, considering alternative 3' utr isoform usage improved prediction of targeting efficacy significantly beyond the improvements observed when considering constitutive isoform usage. thus, although mirna targeting is remarkably consistent in different cell types, considering the 3' utr landscape helps predict targeting efficacy and explain differential regulation that is observed.",1
"micrornas are noncoding regulators of gene expression, which act by repressing protein translation and/or degrading mrna. many have been shown to drive tumorigenesis in cancer, but functional studies to understand their mode of action are typically limited to single-target genes. in this study, we use synthetic biotinylated mirna to pull down endogenous targets of mir-182-5p. we identified more than 1000 genes as potential targets of mir-182-5p, most of which have a known function in pathways underlying tumor biology. specifically, functional enrichment analysis identified components of both the dna damage response pathway and cell cycle to be highly represented in this target cohort. experimental validation confirmed that mir-182-5p-mediated disruption of the homologous recombination (hr) pathway is a consequence of its ability to target multiple components in that pathway. although there is a strong enrichment for the cell cycle ontology, we do not see primary proliferative defects as a consequence of mir-182-5p overexpression. we highlight targets that could be responsible for mir-182-5p-mediated disruption of other biological processes attributed in the literature so far. finally, we show that mir-182-5p is highly expressed in a panel of human breast cancer samples, highlighting its role as a potential oncomir in breast cancer.",1
"micrornas (mirnas) are potent post-transcriptional regulators of protein coding genes. patterns of misexpression of mirnas in cancer suggest key functions of mirnas in tumorigenesis. however, current bioinformatics tools do not entirely support the identification and characterization of the mode of action of such mirnas. here, we used a novel functional genetic approach and identified mir-221 and mir-222 (mir-221&222) as potent regulators of p27(kip1), a cell cycle inhibitor and tumor suppressor. using mirna inhibitors, we demonstrate that certain cancer cell lines require high activity of mir-221&222 to maintain low p27(kip1) levels and continuous proliferation. interestingly, high levels of mir-221&222 appear in glioblastomas and correlate with low levels of p27(kip1) protein. thus, deregulated expression of mir-221&222 promotes cancerous growth by inhibiting the expression of p27(kip1).",1
"plants have evolved sophisticated defense systems to enhance drought tolerance. these include the microrna (mirna) group of small noncoding rnas that act as post-transcriptional regulators; however, details of the mechanisms by which they confer drought tolerance are not well understood. here, we show that osa-mir171f , a member of osa - mir171 gene family, is mainly expressed in response to drought stress and regulates the transcript levels of scarecrow-like6-i ( scl6-i ) and scl6-ii in rice ( oryza sativa ). the scl6 genes are known to be involved in shoot branching and flag leaf morphology. osa-mir171f- overexpressing ( osa - mir171f -oe) transgenic plants showed reduced drought symptoms compared with non-transgenic (nt) control plants under both field drought and polyethylene glycol (peg)-mediated dehydration stress conditions. transcriptome analysis of osa-mir171f -oe plants and osa-mir171f -knockout (k/o) lines generated by clustered regularly interspaced short palindromic repeats (crispr/cas9) revealed that osa -mature-mir171a-f ( osa -mir171) regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. this upregulation in the osa-mir171f- oe plants, which did not occur in nt control plants, was observed under both normal and drought conditions. our findings indicate that osa -mir171 plays a role in drought tolerance by regulating scl6-i and scl6-ii transcript levels.",1
"pro-inflammatory cytokine-induced activation of nuclear factor, nf-κb has an important role in leukocyte adhesion to, and subsequent migration across, brain endothelial cells (becs), which is crucial for the development of neuroinflammatory disorders such as multiple sclerosis (ms). in contrast, microrna-146a (mir-146a) has emerged as an anti-inflammatory molecule by inhibiting nf-κb activity in various cell types, but its effect in becs during neuroinflammation remains to be evaluated. here, we show that mir-146a was upregulated in microvessels of ms-active lesions and the spinal cord of mice with experimental autoimmune encephalomyelitis. in vitro, tnfα and ifnγ treatment of human cerebral microvascular endothelial cells (hcmec/d3) led to upregulation of mir-146a. brain endothelial overexpression of mir-146a diminished, whereas knockdown of mir-146a augmented cytokine-stimulated adhesion of t cells to hcmec/d3 cells, nuclear translocation of nf-κb, and expression of adhesion molecules in hcmec/d3 cells. furthermore, brain endothelial mir-146a modulates nf-κb activity upon cytokine activation through targeting two novel signaling transducers, rhoa and nuclear factor of activated t cells 5, as well as molecules previously identified, il-1 receptor-associated kinase 1, and tnf receptor-associated factor 6. we propose brain endothelial mir-146a as an endogenous nf-κb inhibitor in becs associated with decreased leukocyte adhesion during neuroinflammation.",1
"fat deposition is very important in pig production, and its mechanism is not clearly understood. micrornas (mirnas) play critical roles in fat deposition and energy metabolism. in the current study, we investigated the mrna and mirna transcriptome in the livers of landrace pigs with extreme backfat thickness to explore mirna-mrna regulatory networks related to lipid deposition and metabolism. a comparative analysis of liver mrna and mirna transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. we identified differentially expressed genes from rna-seq data using a cufflinks pipeline. seventy-one differentially expressed genes (degs), including twenty-eight well annotated on the porcine reference genome genes, were found. the upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (fasn), glucokinase (gck), phosphoglycerate dehydrogenase (phgdh), and apolipoprotein a4 (apoa4). cytochrome p450, family 2, subfamily j, polypeptide 34 (cyp2j34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. moreover, 13 differentially expressed mirnas were identified. seven mirnas were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. based on comprehensive analysis of the transcriptome of both mrnas and mirnas, an important regulatory network, in which six degs could be regulated by differentially expressed mirnas, was established for fat deposition. the negative correlate in the regulatory network including, mir-545-5p and gramd3, mir-338 and fasn, and mir-127, mir-146b, mir-34c, mir-144 and thbs1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. based on liver mrna and mirna transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed mirnas, and established an important mirna-mrna regulatory network. this study provides new insights into the molecular mechanisms that determine fat deposition in pigs.",1
"preeclampsia (pe) is a serious pregnancy‑specific pathologic complication, and represents a primary cause of mother and fetus mortality. abnormally expressed micrornas (mirnas) serve important regulatory roles in the development of pe. at present, the pathogenesis and molecular mechanism of pe remain unclear. the aim of the present study was to investigate the potential functions of mirna (mir)‑320a in the human extravillous trophoblast cell line htr‑8/svneo and to identify the molecular mechanisms underlying mir‑320a function. reverse transcription‑quantitative pcr was used in the present study to detect the levels of mir‑320a in the placentas of 57 pregnant patients with pe and 57 healthy pregnant patients. the effects of mir‑320a overexpression on the proliferation and invasion of htr‑8/svneo cells were determined using mtt and transwell invasion assays. western blot analysis and dual luciferase reporter assay were used to identify the genes targeted by mir‑320a. the present results suggested that mir‑320a expression level was decreased in placentas of patients with pe and the expression level of mir‑320a was found to be associated with the pathogenesis of pe (p<0.05). overexpression of mir‑320a using mir‑320a mimics significantly inhibited cell proliferation and invasion in htr‑8/svneo cells in vitro (p<0.05). furthermore, interleukin (il)‑4 was identified to be a direct target gene of mir‑320a. mir‑320a could repress il‑4 expression by binding to its 3' untranslated region (p<0.05). mechanistic studies suggested that il‑4 was a functional target gene of mir‑320a, and mir‑320a upregulation inhibited the proliferation and invasion of htr‑8/svneo cells by directly targeting il‑4 (p<0.05). collectively, to the best of our knowledge, the present study is the first to suggest that mir‑320a may be a downregulated mirna during pe, and il‑4 may act as a functional target gene of mir‑320a. the present study suggested that mir‑320a upregulation was involved in the development of pe by inhibiting the proliferation and invasion of trophoblast cells by targeting il‑4, indicating that the mir‑320a/il‑4 pathway may represent a novel therapeutic target for pe treatment.",1
"to understand the process of cardiac aging, it is of crucial importance to gain insight into the age-related changes in gene expression in the senescent failing heart. age-related cardiac remodeling is known to be accompanied by changes in extracellular matrix (ecm) gene and protein levels. small noncoding micrornas regulate gene expression in cardiac development and disease and have been implicated in the aging process and in the regulation of ecm proteins. however, their role in age-related cardiac remodeling and heart failure is unknown. in this study, we investigated the aging-associated microrna cluster 17-92, which targets the ecm proteins connective tissue growth factor (ctgf) and thrombospondin-1 (tsp-1). we employed aged mice with a failure-resistant (c57bl6) and failure-prone (c57bl6 × 129sv) genetic background and extrapolated our findings to human age-associated heart failure. in aging-associated heart failure, we linked an aging-induced increase in the ecm proteins ctgf and tsp-1 to a decreased expression of their targeting micrornas 18a, 19a, and 19b, all members of the mir-17-92 cluster. failure-resistant mice showed an opposite expression pattern for both the ecm proteins and the micrornas. we showed that these expression changes are specific for cardiomyocytes and are absent in cardiac fibroblasts. in cardiomyocytes, modulation of mir-18/19 changes the levels of ecm proteins ctgf and tsp-1 and collagens type 1 and 3. together, our data support a role for cardiomyocyte-derived mir-18/19 during cardiac aging, in the fine-tuning of cardiac ecm protein levels. during aging, decreased mir-18/19 and increased ctgf and tsp-1 levels identify the failure-prone heart.",1
"in mouse brain cdna libraries generated from small rna molecules we have identified a total of 201 different expressed rna sequences potentially encoding novel small non-messenger rna species (snmrnas). based on sequence and structural motifs, 113 of these rnas can be assigned to the c/d box or h/aca box subclass of small nucleolar rnas (snornas), known as guide rnas for rrna. while 30 rnas represent mouse homologues of previously identified human c/d or h/aca snornas, 83 correspond to entirely novel snornas: among these, for the first time, we identified four c/d box snornas and four h/aca box snornas predicted to direct modifications within u2, u4 or u6 small nuclear rnas (snrnas). furthermore, 25 snornas from either class lacked antisense elements for rrnas or snrnas: therefore, additional snorna targets have to be considered. surprisingly, six c/d box snornas and one h/aca box snorna were expressed exclusively in brain. of the 88 rnas not belonging to either snorna subclass, at least 26 are probably derived from truncated heterogeneous nuclear rnas (hnrnas) or mrnas: short interspersed repetitive elements (sines) are located on five rna sequences and may represent rare examples of transcribed sines: the remaining rna species could not as yet be assigned either to any snmrna class or to a part of a larger hnrna/mrna. it is likely that at least some of the latter will represent novel, unclassified snmrnas:",1
"microrna 130b (mir-130b) is significantly dysregulated in various human tumor types. in this study, using a microarray assay, we characterized the upregulation of mir-130b expression in colorectal cancer (crc) specimens. however, there is limited knowledge about the roles of aberrant mir-130b expression in crc. our studies in crc cells demonstrated that mir-130b significantly decreases cell migration and invasion, but it has no evidently effects on cell proliferation and apoptosis. in the overexpression mir-130b crc cells and the crc specimens, we observed a decreased level of integrin β1 protein, which is considered as a key molecule involved in cell motility. the targeting of the 3'-utr region of integrin β1 gene by mir-130b was revealed using a luciferase reporter assay. the regulation of integrin β1 by mir-130b was further shown using the mir-130b mimics and the inhibitor of mir-130b. the impaired motility of the mir-130b overexpression cells is recovered partly by the expression of integrin β1 lacking the 3'-utr. additionally, the knockdown of integrin β1 also gives rise to a decrease in cell migration and invasion, which is similar to the impeded motility due to overexpression of mir-130b in crc cells. furthermore, the inverse expressions of mir-130b and integrin β1 were observed in crc specimens. in summary, these data demonstrate that mir-130b downregulates its target-integrin β1, leading to the impaired migration and invasion of crc cells.",1
"pro-opiomelanocortin (pomc) is a common precursor of melanocortin-related peptides in the pituitary and primarily regulated by corticotropin- releasing factor (crf). our results show that mir-375 is highly expressed in the mouse pituitary gland and located specifically in the intermediate lobe of pituitary. the functional studies show that the forced inhibition of endogenous mir-375 in att-20 mouse pituitary tumor cells and in the intermediate lobe of the pituitary gland significantly increases pomc expression, whereas mir-375 overexpression down-regulates pomc expression and acth secretion stimulated by crf. this function of mir-375 is accomplished by its binding to the 3'-utr of mitogen-activated protein kinase kinase kinase-8. our results here have demonstrated that mir-375 acts as a negative regulating molecule mediating the signaling pathway of crf and affecting pomc expression by targeting mitogen-activated protein kinase kinase kinase-8, which subsequently down-regulates erk1/2 phosphorylation and nerve growth factor-induced clone b (ngfi-b) transcription activity. taken together, our results show that mir-375 is a novel negative regulator of pomc expression and related hormone secretion.",1
"deregulated micrornas (mirnas) and their roles in cancer development have attracted much attention. two mirnas, mir-15a and mir-16, which act as putative tumor suppressor by targeting the oncogene bcl2, have been implicated in cell cycle, apoptosis and proliferation. in this study, we investigated the possible role of mir-15a/16 in the angiogenesis of multiple myeloma (mm). using a stem-loop quantitative reverse transcription-pcr, we analyzed mir-15a/16 expressions in bone marrow samples from newly diagnosed mm patients and a panel of mm cell lines. mirna transfection, western blotting analysis and assay of luciferase activity were used to examine whether vascular endothelial growth factor (vegf) is the target of mir-15a/16. the functional roles of mir-15a/16 on tumorigenesis and angiogenesis were examined by in vitro angiogenesis models and in vivo tumor xenograft model. we showed that mir-15a and mir-16 were significantly underexpressed in primary mm cells as well as in mm cell lines. the aberrant expression of mir-15a/16 was detected especially in advanced stage mm. in human mm cell lines and normal plasma cells, expression of mir-15a/16 inversely correlated with the expression of vegf-a. western blotting combined with the luciferase reporter assay demonstrated that vegf-a was a direct target of mir-15a/16. ectopic overexpression of mir-15a/16 led to decreased pro-angiogenic activity of mm cells. finally, infection of lentivirus-mir-15a or lentivirus-mir-16 resulted in significant inhibition of tumor growth and angiogenesis in nude mice. this study suggest that mir-15a/16 could play a role in the tumorigenesis of mm at least in part by modulation of angiogenesis through targeting vegf-a.",1
"advanced breast cancer cells acquire metastatic properties in response to tgfβ. we show here that the expression of c-myb increases in tgfβ-treated er (+) breast cancer cells by protein stabilization, transcription activation and release from mir200-dependent down-regulation. in particular, we mapped 2 sites for mir200b, mir200c and mir429 binding in the 3' utr of the human c-myb gene. these micrornas decreased the expression of c-myb when transfected in mcf-7 cells. in addition, luciferase activity from a vector containing the 3' utr of the c-myb gene was inhibited by mir200s through a binding-dependent mechanism. sirna- and shrna-mediated down-regulation was used to investigate the role of c-myb for the effects induced by tgfβ in er(+) breast cancer mcf-7 and zr-75.1 cells. transfection with c-myb sirnas blocked the increase of slug (snai2) and bcl-2 expression and reversed the decrease in e-cadherin expression induced by tgf-β treatment. conversely, c-myb down-regulation decreased invasion and anchorage-independent growth of breast cancer cells expressing a constitutively active tgfβ receptor i. finally, apoptosis induced by etoposide increased in c-myb-silenced tgfβ-treated er(+) cell lines. in summary, exposure of er(+) breast cancer cells to tgfβ induces an increase of c-myb expression which is required for expression of emt-associated markers, in vitro invasion and anchorage-independent growth. furthermore, our findings suggest a potentially detrimental effect of tgfβ and c-myb co-expression in breast cancer.",1
"thyroid hormone (t(3)) signaling through the thyroid hormone receptor (trα1) regulates hepatoma cell growth and pathophysiology, but the underlying mechanisms are unclear at present. here, we have shown that the oncomir microrna-21 (mir-21) is activated by t(3) through a native t(3) response element in the primary mir-21 promoter. overexpression of mir-21 promoted hepatoma cell migration and invasion, similar to that observed with t(3) stimulation in hepatoma cells. in addition, anti-mir-21-induced suppression of cell migration was rescued by t(3). the rac-controlled regulator of invasion and metastasis, t-cell lymphoma invasion and metastasis 1 (tiam1), was identified as a mir-21 target additionally downregulated by t(3). attenuation and overexpression of mir-21 induced upregulation and downregulation of tiam1, respectively. tiam1 attenuation, in turn, enhanced migration and invasion via the upregulation of β-catenin, vimentin, and matrix metalloproteinase-2 in hepatoma cells. notably, correlations between trα1, mir-21, and tiam1 expression patterns in animal models paralleled those observed in vitro. in the clinic, we observed a positive correlation (p = 0.005) between the tumor/nontumor ratios of trα1 and mir-21 expression, whereas a negative correlation (p = 0.019) was seen between mir-21 and tiam1 expression in patients with hepatoma. our findings collectively indicate that mir-21 stimulation by t(3) and subsequent tiam1 suppression promotes hepatoma cell migration and invasion.",1
"microrna mir-221 is frequently over-expressed in a variety of human neoplasms. aim of this study was to identify new mir-221 gene targets to improve our understanding on the molecular tumor-promoting mechanisms affected by mir-221. gene expression profiling of mir-221-transfected-snu-398 cells was analyzed by the sylamer algorithm to verify the enrichment of mir-221 targets among down-modulated genes. this analysis revealed that enforced expression of mir-221 in snu-398 cells caused the down-regulation of 602 mrnas carrying sequences homologous to mir-221 seed sequence within their 3'utrs. pathways analysis performed on these genes revealed their prominent involvement in cell proliferation and apoptosis. activation of e2f, myc, nfkb, and β-catenin pathways was experimentally proven. some of the new mir-221 target genes, including rb1, wee1 (cell cycle inhibitors), apaf1 (pro-apoptotic), anxa1, ctcf (transcriptional repressor), were individually validated as mir-221 targets in snu-398, hepg2, and hek293 cell lines. by identifying a large set of mir-221 gene targets, this study improves our knowledge about mir-221 molecular mechanisms involved in tumorigenesis. the modulation of mrna level of 602 genes confirms the ability of mir-221 to promote cancer by affecting multiple oncogenic pathways.",1
"recently, a number of ribosome-associated non-coding rnas (rancrnas) have been discovered in all three domains of life. in our previous studies, we have described several types of rancrnas in saccharomyces cerevisiae, derived from many cellular rnas, including mrnas, rrnas, trnas and snornas. here, we present the evidence that the trna fragments from simple eukaryotic organism s. cerevisiae directly bind to the ribosomes. interestingly, rancrna-trfs in yeast are derived from both, 5'- and 3'-part of the trnas and both types of trfs associate with the ribosomes in vitro the location of trfs within the ribosomes is distinct from classical a- and p-trna binding sites. moreover, 3'-trfs bind to the distinct site than 5'-trfs. these interactions are stress dependent and as a consequence, provoke regulation of protein biosynthesis. we observe strong correlation between trf binding to the ribosomes and inhibition of protein biosynthesis in particular environmental conditions. these results implicate the existence of an ancient and conserved mechanism of translation regulation with the involvement of ribosome-associating trna-derived fragments.",1
"exosomal micrornas (mirnas) transferred between cells have been implicated in modulating the host immune response in microbial infections. in this study, we isolated exosomes from treponema pallidum (t. pallidum)-stimulated macrophages and detected differential exosomal mirna expression using both microarrays, and rt-qpcr. a total of 65 differentially expressed mirnas (35 upregulated and 30 downregulated) were identified. of all identified mirnas, mir-146a-5p was one of the most significantly changed mirnas with high expression in exosomes from t. pallidum-stimulated macrophages. furthermore, we isolated plasma exosomes from early syphilis patients and healthy controls, and confirmed mir-146a-5p upregulation in the former group. we also show that exosomal mir-146a-5p is efficiently transported into endothelial cells, reducing monocyte transendothelial migration and endothelial permeability by targeting junctional adhesion molecule c (jam-c). luciferase reporter assays confirmed binding of exosomal mir-146a-5p to the 3'untranslated region (3'utr) of jam-c. we then demonstrated that also exosomes derived from macrophages stimulated by t. pallidum expressed high levels of mir-146a-5p which could be delivered to endothelial cells, and decreased monocyte transendothelial migration by targeting jam-c. overall, this work provides novel insights into the mechanism by which t. pallidum hampers inflammatory reactions of the host via a blockade of leukocytes transendothelial migration and endothelial permeability.",1
"background and aim accumulating evidence supports the effects of mirna in lipid metabolism, providing a potential linkage between certain mirna and non-alcoholic fatty liver disease (nafld). we aimed to investigate the mirna expression pattern in a steatotic l02 cell model and explore the function of certain mirna target pairs. methods the cell model was established by culturing l02 cells with a high concentration of free fatty acid. micro-array and stem-loop reverse transcription polymerase chain reaction (rt-pcr) were utilized to detect dysregulated mirna, whereas computational algorithms were used for target prediction. real time rt-pcr, western blot, luciferase activity measurement, and other techniques were employed for target verification. results seventeen upregulated and 15 downregulated mirna were found in steatotic l02 cells, while mirna-10b was proven to regulate the steatosis level. peroxisome proliferator-activated receptor-alpha (ppar-alpha) was also found to participate in steatosis, as its protein level was decreased in steatotic l02 cells and its overexpression by transfection into the ppar-alpha-pcdna 3.1 vector could partially alleviate steatosis. we further found that ppar-alpha is the direct target of mirna-10b as it showed significantly changed protein expression, but a relatively unchanged mrna level in steatotic l02 cells transfected with pre-mirna-10b and anti-mirna-10b. moreover, the action of mirna-10b on ppar-alpha depends on the presence of a single mirna-10b binding site, as the activity of a luciferase reporter carrying the mutant ppar-alpha 3'-untranslated region was not reduced by the expression of mirna-10b. conclusion the established mirna profile of the steatotic l02 cell model and the novel effect of mirna-10b in regulating hepatocyte steatosis may provide a new explanation of the pathogenesis of nafld.",1
"cardiac ischemia is associated with arrhythmias; however, effective therapies are currently limited. the cardiac voltage-gated sodium channel α subunit (scn5a), encoding the nav1.5 current, plays a key role in the cardiac electrical conduction and arrhythmic risk. here, we show that hypoxia reduces nav1.5 through effects on a mir, mir-448. mir-448 expression is increased in ischemic cardiomyopathy. mir-448 has a conserved binding site in 3'-utr of scn5a. mir-448 binding to this site suppressed scn5a expression and sodium currents. hypoxia-induced hif-1α and nf-κb were major transcriptional regulators for mir448. moreover, hypoxia relieved mir448 transcriptional suppression by re1 silencing transcription factor. therefore, mir-448 inhibition reduced arrhythmic risk after myocardial infarction. here, we show that ischemia drove mir-448 expression, reduced nav1.5 current, and increased arrhythmic risk. arrhythmic risk was improved by preventing nav1.5 downregulation, suggesting a new approach to antiarrhythmic therapy.",1
"in marmoset t cells transformed by herpesvirus saimiri (hvs), a viral u-rich noncoding (nc) rna, hsur 1, specifically mediates degradation of host microrna-27 (mir-27). high-throughput sequencing of rna after crosslinking immunoprecipitation (hits-clip) identified mrnas targeted by mir-27 as enriched in the t cell receptor (tcr) signaling pathway, including grb2. accordingly, transfection of mir-27 into human t cells attenuates tcr-induced activation of mitogen-activated protein kinases (mapks) and induction of cd69. mir-27 also robustly regulates sema7a and ifn-γ, key modulators and effectors of t cell function. knockdown or ectopic expression of hsur 1 alters levels of these proteins in virally transformed cells. two other t-lymphotropic γ-herpesviruses, alhv-1 and ovhv-2, do not produce a noncoding rna to downregulate mir-27 but instead encode homologs of mir-27 target genes. thus, oncogenic γ-herpesviruses have evolved diverse strategies to converge on common targets in host t cells.",1
"intestinal ischemic injury is a significant clinical problem arising from diseases or as a complication of abdominal surgery. our previous study showed aquaporin 3 is involved in intestinal barrier impairment. here, we revealed that intestinal ischemia induced a time-dependent increase of mir-874 expression and a time-dependent decrease of aqp3 expression, and the level of mir-874 expression was inversely related to aqp3 protein expression. in addition, mir-874 promoted the paracellular permeability in vitro through targeting 3'utr of aqp3. two of the tight junction proteins, occludin and claudin-1, were found to be involved in mir-874-induced intestinal barrier dysfunction.",1
"asymmetrical cell division (acd) maintains the proper number of stem cells to ensure self-renewal. in cancer cells, the deregulation of acd disrupts the homeostasis of the stem cell pool and promotes tumour growth. however, this mechanism is unclear. here, we show a reduction of acd in spheroid-derived colorectal cancer stem cells (crcscs) compared with differentiated cancer cells. the epithelial-mesenchymal transition (emt) inducer snail is responsible for the acd-to-symmetrical cell division (scd) switch in crcscs. mechanistically, snail induces the expression of microrna-146a (mir-146a) through the β-catenin-tcf4 complex. mir-146a targets numb to stabilize β-catenin, which forms a feedback circuit to maintain wnt activity and directs scd. interference with the snail-mir-146a–β-catenin loop by inhibiting the mek or wnt activity reduces the symmetrical division of crcscs and attenuates tumorigenicity. in colorectal cancer patients, the snail(high)numb(low) profile is correlated with cetuximab resistance and a poorer prognosis. this study elucidates a unique mechanism of emt-induced crcsc expansion.",1
"persistently activated il-6/stat3 pathway promotes acquired resistance to targeted therapy with epidermal growth factor receptor-tyrosine kinase inhibitors (egfr-tkis) in non-small-cell lung cancer (nsclc) treatment. mir-206 has been verified to be dysregulated and plays as a negative regulator in lung cancer. however, whether mir-206 may overcome il6-induced gefitinib resistance in egfr-mutant lung cancer remains elusive. in this study, we investigated the role of mir-206 in il6-induced gefitinib-resistant egfr-mutated lung cancer cell lines. we showed that forced mir-206 expression restored gefitinib sensitivity in il6-induced gefitinib-resistant egfr-mutant lung cancer cells by inhibiting il6/jak1/stat3 pathway. specifically, mechanistic investigations revealed that mir-206 blocked il-6/stat3 signalling via directly targeting the 3'-utr of intracellular il-6 messenger rna. moreover, il-6 induced mir-206 down-regulation by reducing the cropping process of primary mir-206 (pri-mir-206) into the drosha/dgcr8 complex. taken together, our findings reveal a direct role of mir-206 in regulating il-6/stat3 pathway and contrarily activated il-6/stat3 signalling mediates the mir-206 maturation process in gefitinib-resistant egfr-mutant lung cancer cells.",1
"rationale transforming growth factor (tgf)-β was linked to abnormal vessel function and can mediate impairment of endothelial angiogenic responses. its effect on micrornas and downstream targets in this context is not known. objective to study the role of micrornas in tgf-β-mediated angiogenic activity. methods and results microrna profiling after tgf-β treatment of endothelial cells identified mir-30a-3p, along with other members of the mir-30 family, to be strongly silenced. supplementation of mir-30a-3p restored function in tgf-β-treated endothelial cells. we identified the epigenetic factor methyl-cpg-binding protein 2 (mecp2) to be a direct and functional target of mir-30a-3p. viral overexpression of mecp2 mimicked the effects of tgf-β, suggesting that derepression of mecp2 after tgf-β treatment may be responsible for impaired angiogenic responses. silencing of mecp2 rescued detrimental tgf-β effects on endothelial cells. microarray transcriptome analysis of mecp2-overexpressing endothelial cells identified several deregulated genes important for endothelial cell function including sirtuin1 (sirt1). in vivo experiments using endothelial cell-specific mecp2 null or sirt1 transgenic mice confirmed the involvement of mecp2/sirt1 in the regulation of angiogenic functions of endothelial cells. additional experiments identified that mecp2 inhibited endothelial angiogenic characteristics partly by epigenetic silencing of sirt1. conclusions tgf-β impairs endothelial angiogenic responses partly by downregulating mir-30a-3p and subsequent derepression of mecp2-mediated epigenetic silencing of sirt1.",1
"the microrna (mirna) genes mir-127 and mir-136 are located near two cpg islands in the imprinted mouse retrotransposon-like gene rtl1, a key gene involved in placenta formation. these mirnas appear to be involved in regulating the imprinting of rtl1. to obtain insights into the epigenetic reprogramming of cloned embryos, we compared the expression levels of mir-127 and mir-136 in fertilized mouse embryos, parthenotes, androgenotes and cloned embryos developing in vitro. we also examined the dna methylation status of the promoter regions of rtl1 and mir-127 in these embryos. our data showed that mir-127 and mir-136 were highly expressed in parthenotes, but rarely expressed in androgenotes. interestingly, the expression levels of mir-127 and mir-136 in parthenotes were almost twice that seen in the fertilized embryos, but were much lower in the cloned embryos. the rtl1 promoter region was hyper-methylated in blastocyst stage parthenotes (75.0%), moderately methylated (32.4%) in the fertilized embryos and methylated to a much lower extent (approximately 10%) in the cloned embryos. conversely, the promoter region of mir-127 was hypo-methylated in parthenogenetically activated embryos (0.4%), moderately methylated (30.0%) in fertilized embryos and heavily methylated in cloned blastocysts (63-70%). these data support a role for mir-127 and mir-136 in the epigenetic reprogramming of the rtl1 imprinting process. analysis of the aberrant epigenetic reprogramming of mir-127 and rtl1 in cloned embryos may help to explain the nuclear reprogramming procedures that occur in donor cells following somatic cell nuclear transfer (scnt).",1
"in eukaryotic cells, an mrna bearing a premature termination codon (ptc) or an abnormally long 3' untranslated region (utr) is often degraded by the nonsense-mediated mrna decay (nmd) pathway. despite the presence of a 5- to 7-kb 3' utr, unspliced retroviral rna escapes this degradation. we previously identified the rous sarcoma virus (rsv) stability element (rse), an rna element downstream of the gag natural translation termination codon that prevents degradation of the unspliced viral rna. insertion of this element downstream of a ptc in the rsv gag gene also inhibits nmd. using partial rnase digestion and selective 2'-hydroxyl acylation analyzed by primer extension (shape) chemistry, we determined the secondary structure of this element. incorporating rnase and shape data into structural prediction programs definitively shows that the rse contains an au-rich stretch of about 30 single-stranded nucleotides near the 5' end and two substantial stem-loop structures. the overall secondary structure of the rse appears to be conserved among 20 different avian retroviruses. the structural aspects of this element will serve as a tool in the future design of cis mutants in addressing the mechanism of stabilization.",1
"abnormal microrna expression is a common and important feature of human malignancies. matrix metalloproteinase 2 (mmp2), which has been reported in several cancers, plays important roles in cancer progression. however, the microrna regulatory mechanism on mmp2 expression remains unclear. in this study, we first detected mmp2 and microrna-29a (mir-29a) expression in oral squamous carcinoma (oscc) specimens, which showed that mmp2 was higher in oscc cancer tissues than adjacent tissues but that mir-29a was lower in oscc cancer tissues than adjacent tissues. then, we confirmed that mir-29a, which directly targeted 3'-utr of mmp2 gene, negatively regulated mmp2 expression by mir-29a transfection and luciferase reporter assay. exogenous overexpression of mir-29a inhibited oscc cell invasion and anti-apoptosis significantly in vitro. whereas, knockdown of mir-29a promoted oscc cell invasion and induced drug-resistance in vitro. this study suggests that mir-29a plays an inhibiting role in the progression of oscc, which may be a potentially therapeutic approach in the future.",1
"the steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microrna (mirna) gene expression. however, the complete regulatory network controlling the expression of these genes remains to be elucidated. in this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous argonaute 1 (ago1) protein, the core effector of the mirna pathway, in drosophila s2 cells. we found that regulatory interactions between mirnas and their cognate targets were substantially altered by ago1 in response to ecdysone signaling. additionally, during the larva-to-adult metamorphosis, mir-252-5p was up-regulated via the canonical ecdysone-signaling pathway. moreover, we provide evidence that mir-252-5p targets abelson interacting protein ( abi) to decrease the protein levels of cyclins a and b, controlling the cell cycle. overall, our data suggest a potential role for the ecdysone/mir-252-5p/abi regulatory axis partly in cell-cycle control during metamorphosis in drosophila.-lim, d.-h., lee, s., han, j. y., choi, m.-s., hong, j.-s., seong, y., kwon, y.-s., lee, y. s. ecdysone-responsive micror-252-5p controls the cell cycle by targeting abi in drosophila.",1
"micrornas (mirnas) are short non-coding rnas that play a central role in regulation of gene expression by binding to target genes. many mirnas were associated with the function of the central nervous system (cns) in health and disease. astrocytes are the cns most abundant glia cells, providing support by maintaining homeostasis and by regulating neuronal signaling, survival and synaptic plasticity. astrocytes play a key role in repair of brain insults, as part of local immune reactivity triggered by inflammatory or pathological conditions. thus, astrocyte activation, or astrogliosis, is an important outcome of the innate immune response, which can be elicited by endotoxins such as lipopolysaccharide (lps) and cytokines such as interferon-gamma (ifn-γ). the involvement of mirnas in inflammation and stress led us to hypothesize that astrogliosis is mediated by mirna function. in this study, we compared the mirna regulatory layer expressed in primary cultured astrocyte derived from rodents (mice) and primates (marmosets) brains upon exposure to lps and ifn-γ. we identified subsets of differentially expressed mirnas some of which are shared with other immunological related systems while others, surprisingly, are mouse and rat specific. of interest, these specific mirnas regulate genes involved in the tumor necrosis factor-alpha (tnf-α) signaling pathway, indicating a mirna-based species-specific regulation. our data suggests that mirna function is more significant in the mechanisms governing astrocyte activation in rodents compared to primates.",1
"formation of the bicoid morphogen gradient in early drosophila embryos requires the pre-localization of bicoid mrna to the anterior pole of the egg. the program of bcd mrna localization involves multiples steps and proceeds from oogenesis until early embryogenesis. this process requires cis-elements in the 3' utr of bcd mrna and successive and/or concomitant critical protein interactions. furthermore, numerous rna elements and binding proteins contribute to regulate bcd expression. in the present paper, we investigated the secondary structure of the full length 3' utr of the bcd mrna, using a variety of chemical and enzymatic structural probes. this rna probing analysis allowed us to give a detailed description of the 3' utr of the bcd mrna and its organization into five well-defined and independent domains (i-v). one prominent result that emerges from our data is the unexpected high degree of flexibility of the different domains relative to each others. this plasticity relies upon the open conformation of the central hinge region interconnecting domains ii, iii, and iv + v. otherwise, dimerization of the 3' utr, which participates to anchoring bcd mrna at the anterior pole of the embryo, only results in discrete and local change in domain iii. domain i that contains sites for trans-acting factors exhibiting single stranded rna binding specificity is mainly unstructured. by contrast, each core domains (ii-v) is highly organized and folds into helices interrupted by bulges and interior loops and closed by very exposed apical loops. these elements mostly built specific determinants for trans-acting factors. besides, these findings provide a valuable database for structure/function studies.",1
"methionine adenosyltransferase (mat) is the cellular enzyme that catalyzes the synthesis of s-adenosylmethionine (sam), the principal biological methyl donor and a key regulator of hepatocyte proliferation, death and differentiation. two genes, mat1a and mat2a, encode 2 distinct catalytic mat isoforms. a third gene, mat2b, encodes a mat2a regulatory subunit. in hepatocellular carcinoma (hcc), mat1a downregulation and mat2a upregulation occur, known as the mat1a:mat2a switch. the switch is accompanied with an increasing expression of mat2b, which results in decreased sam levels and facilitates cancer cell growth. berberine, an isoquinoline alkaloid isolated from many medicinal herbs such as coptis chinensis, has a wide range of pharmacological effects including anti-cancer effects. because drug-induced micrornas have recently emerged as key regulators in guiding their pharmacological effects, we examined whether microrna expression is differentially altered by berberine treatment in hcc. in this study, we used microrna microarrays to find that the expression level of mir-21-3p (previously named mir-21*) increased after berberine treatment in the hepg2 human hepatoma cell line. to predict the putative targets of mir-21-3p, we integrated the gene expression profiles of hepg2 cells after berberine treatment by comparing with a gene list generated from sequence-based microrna target prediction software. we then confirmed these predictions through transfection of microrna mimics and a 3' utr reporter assay. our findings provide the first evidence that mir-21-3p directly reduces the expression of mat2a and mat2b by targeting their 3' utrs. in addition, an overexpression of mir-21-3p increased intracellular sam contents, which have been proven to be a growth disadvantage for hepatoma cells. the overexpression of mir-21-3p suppresses growth and induces apoptosis in hepg2 cells. overall, our results demonstrate that mir-21-3p functions as a tumor suppressor by directly targeting both mat2a and mat2b, indicating its therapeutic potential in hcc.",1
"the cyp2c genes are extensively regulated at the transcriptional stage. the present study shows for the first time that cyp2cs are also regulated post-transcriptionally by micrornas (mirnas). by using online search engines, we found potential mirna response elements (mres) in the 3'-untranslated region (3'-utr) of the cyp2c mrnas. among these were a mre for the mirnas mir-103 and mir-107 in the 3'-utr of human cyp2c8. cyp2c8 protein levels (measured through immunoblot analyses) did not correlate with cyp2c8 mrna levels (measured through quantitative polymerase chain reaction analyses) in human liver samples. the translation efficiency (protein/mrna ratio) for cyp2c8 was inversely correlated with the expression of mir-103 and mir-107. when three copies of the putative mre from cyp2c8 were inserted downstream from a luciferase expression reporter, transfection with precursors for mir-103 or mir-107 decreased luciferase activity in primary hepatocytes, whereas transfection with antisense oligonucleotides (asos) for mir-103/mir-107 increased luciferase activity. as expected, there was no effect of the precursors or asos when three copies of the putative mre were inserted in the reverse orientation. when precursors for mir-103/mir-107 were transfected into primary human hepatocytes, cyp2c8 protein levels were decreased, whereas asos increased cyp2c8 protein levels. neither precursors nor asos affected cyp2c8 mrna levels, which indicated that the effect was post-transcriptional. putative mre motifs were also found in the 3'-utrs of cyp2c9 and cyp2c19, which suggested that the same mirnas could regulate translation of other members of the cyp2c family, although to a lesser degree than cyp2c8. these results clearly show that cyp2cs are regulated post-transcriptionally by mir-103 and mir-107.",1
"micrornas are single-stranded rna of 18-24 nt expressed endogenously that play important roles in cancer development. here, we show that expression of mir-378 enhances cell survival, reduces caspase-3 activity, and promotes tumor growth and angiogenesis. proteomic analysis indicates reduced expression of suppressor of fused (sufu), a potential target of mir-378, which was confirmed in vitro and in vivo. expression of a luciferase construct containing the target site in sufu was repressed when cotransfected with mir-378. transfection of a sufu construct reversed the effect of mir-378, suggesting an important role for mir-378 in tumor cell survival. we also discovered that mir-378 targets fus-1. expression of luciferase constructs harboring the target sites in fus-1 was repressed by mir-378. fus-1 constructs with or without its 3' utr were also generated. cotransfection experiments showed that the presence of mir-378 repressed fus-1 expression. suppression of fus-1 expression by sirna against fus-1 enhanced cell survival. transfection of the fus-1 construct reversed the function of mir-378 in cell survival. our results suggest that mir-378 transfection enhanced cell survival, tumor growth, and angiogenesis through repression of the expression of two tumor suppressors, sufu and fus-1.",1
"while mirnas are increasingly linked to various immune responses, whether they can be targeted for regulating in vivo inflammatory processes such as endotoxin-induced gram-negative sepsis is not known. production of cytokines by the dendritic cells (dcs) plays a critical role in response to endotoxin, lipopolysaccharide (lps). we profiled the mirna and mrna of cd11c⁺ dcs in an unbiased manner and found that at baseline, mir-142-3p was among the most highly expressed endogenous mirs while il-6 was among the most highly expressed mrna after lps stimulation. multiple computational algorithms predicted the il-6 3' untranslated region (utr) to be a target of mir-142-3p. studies using luciferase reporters carrying wild-type (wt) and mutant il-6 3'utr confirmed il-6 as a target for mir-142-3p. in vitro knockdown and overexpression studies demonstrated a critical and specific role for mir142-3p in regulating il-6 production by the dcs after lps stimulation. importantly, treatment of only wt but not the il-6-deficient (il-6(⁻/⁻)) mice with locked nucleic acid (lna)-modified phosphorothioate oligonucleotide complementary to mir 142-3p reduced endotoxin-induced mortality. these results demonstrate a critical role for mir-142-3p in regulating dc responses to lps and provide proof of concept for targeting mirs as a novel strategy for treatment of endotoxin-induced mortality.",1
"micrornas (mirs) are small noncoding rnas that regulate gene expression by binding to target messenger rnas (mrnas), leading to translational repression or degradation. here, we show that the mir-17approximately92 cluster is highly expressed in human endothelial cells and that mir-92a, a component of this cluster, controls the growth of new blood vessels (angiogenesis). forced overexpression of mir-92a in endothelial cells blocked angiogenesis in vitro and in vivo. in mouse models of limb ischemia and myocardial infarction, systemic administration of an antagomir designed to inhibit mir-92a led to enhanced blood vessel growth and functional recovery of damaged tissue. mir-92a appears to target mrnas corresponding to several proangiogenic proteins, including the integrin subunit alpha5. thus, mir-92a may serve as a valuable therapeutic target in the setting of ischemic disease.",1
"psoriasis is a chronic inflammatory skin disease that is mediated by complex crosstalk between immune cells and keratinocytes (kcs). emerging studies have showed a specific psoriatic micrornas signature, in which mir-21 is one of the most upregulated and dynamic mirnas. in this study, we focused our investigations on the passenger mir-21-3p strand, which is poorly studied in skin and in psoriasis pathogenesis. here, we showed the upregulation of mir-21-3p in an imq-induced psoriasiform mouse model. this upregulation was correlated with il-22 expression and functionality, both in vitro and in vivo, and it occurred via stat3 and nf-κb signaling. we identified a network of differentially expressed genes involved in abnormal proliferation control and immune regulatory genes implicated in the molecular pathogenesis of psoriasis in response to mir-21-3p overexpression in kcs. these results were confirmed by functional assays that validated the proliferative potential of mir-21-3p. all these findings highlight the importance of mir-21-3p, an underestimated mirna, in psoriasis and provide novel molecular targets for therapeutic purposes.",1
"systemic lupus erythematosus is a complex autoimmune disease caused by genetic and epigenetic alterations. dna methylation abnormalities play an important role in systemic lupus erythematosus disease processes. micrornas (mirnas) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. dysregulation of mirnas has been described in various disease states, including human lupus. whereas previous studies have shown mirnas can regulate dna methylation by targeting the dna methylation machinery, the role of mirnas in aberrant cd4+ t cell dna hypomethylation of lupus is unclear. in this study, by using high-throughput microrna profiling, we identified that two mirnas (mir-21 and mir-148a) overexpressed in cd4+ t cells from both patients with lupus and lupus-prone mrl/lpr mice, which promote cell hypomethylation by repressing dna methyltransferase 1 (dnmt1) expression. this in turn leads to the overexpression of autoimmune-associated methylation-sensitive genes, such as cd70 and lfa-1, via promoter demethylation. further experiments revealed that mir-21 indirectly downregulated dnmt1 expression by targeting an important autoimmune gene, rasgrp1, which mediated the ras-mapk pathway upstream of dnmt1; mir-148a directly downregulated dnmt1 expression by targeting the protein coding region of its transcript. additionally, inhibition of mir-21 and mir-148a expression in cd4+ t cells from patients with lupus could increase dnmt1 expression and attenuate dna hypomethylation. together, our data demonstrated a critical functional link between mirnas and the aberrant dna hypomethylation in lupus cd4+ t cells and could help to develop new therapeutic approaches.",1
"glioma is the most common and fatal primary brain tumor. thus far, therapeutic strategies to efficiently and specifically antagonize glioma are limited and poorly developed. here we report that glia-enriched mir-135a, a microrna that is dramatically downregulated in malignant glioma and correlated with the pathological grading, is capable of inducing mitochondria-dependent apoptosis of malignant glioma by regulating various genes including stat6, smad5 and bmpr2, as well as affecting the signaling pathway downstream. moreover, this lethal effect is selectively towards malignant glioma cells, but not neurons and glial cells, through a novel mechanism. our findings suggest an important role of mir-135a in glioma etiology and provide a potential candidate for malignant glioma therapy.",1
"the pathogenesis of ischemic diseases remains unclear. here we demonstrate the induction of microrna-668 (mir-668) in ischemic acute kidney injury (aki) in human patients, mice, and renal tubular cells. the induction was hif-1 dependent, as hif-1 deficiency in cells and kidney proximal tubules attenuated mir-668 expression. we further identified a functional hif-1 binding site in the mir-668 gene promoter. anti-mir-668 increased apoptosis in renal tubular cells and enhanced ischemic aki in mice, whereas mir-668 mimic was protective. mechanistically, anti-mir-668 induced mitochondrial fragmentation, whereas mir-668 blocked mitochondrial fragmentation during hypoxia. we analyzed mir-668 target genes through immunoprecipitation of microrna-induced silencing complexes followed by rna deep sequencing and identified 124 protein-coding genes as likely targets of mir-668. among these genes, only mitochondrial protein 18 kda (mtp18) has been implicated in mitochondrial dynamics. in renal cells and mouse kidneys, mir-668 mimic suppressed mtp18, whereas anti-mir-668 increased mtp18 expression. luciferase microrna target reporter assay further verified mtp18 as a direct target of mir-668. in renal tubular cells, knockdown of mtp18 suppressed mitochondrial fragmentation and apoptosis. together, the results suggest that mir-668 is induced via hif-1 in ischemic aki and that, upon induction, mir-668 represses mtp18 to preserve mitochondrial dynamics for renal tubular cell survival and kidney protection.",1
"micrornas are a family of regulatory molecules involved in many physiological processes, including differentiation and activation of cells of the immune system. we found that brain-specific mir-124 is expressed in microglia but not in peripheral monocytes or macrophages. when overexpressed in macrophages, mir-124 directly inhibited the transcription factor ccaat/enhancer-binding protein-α (c/ebp-α) and its downstream target pu.1, resulting in transformation of these cells from an activated phenotype into a quiescent cd45(low), major histocompatibility complex (mhc) class ii(low) phenotype resembling resting microglia. during experimental autoimmune encephalomyelitis (eae), mir-124 was downregulated in activated microglia. peripheral administration of mir-124 in eae caused systemic deactivation of macrophages, reduced activation of myelin-specific t cells and marked suppression of disease. conversely, knockdown of mir-124 in microglia and macrophages resulted in activation of these cells in vitro and in vivo. these findings identify mir-124 both as a key regulator of microglia quiescence in the central nervous system and as a previously unknown modulator of monocyte and macrophage activation.",1
"micrornas are small noncoding rnas, which regulate the expression of protein coding transcripts through mrna degradation or translational inhibition. numerous reports have highlighted the role of mirnas in regulating cell death pathways including the expression of genes involved in the induction of apoptosis. tumor necrosis factor alpha (tnf-α) is a proinflammatory cytokine which can send pro-death signals through its receptor tnfr1. diverse adaptor molecules including denn/madd adaptor protein have been shown to modulate tnf-α pro-death signaling via recruitment of map kinases to tnfr1 and activation of pro-survival nfκb signaling. herein, we investigated the role of microrna-181 (mir-181) in regulating denn/madd expression levels and its subsequent effects on tnf-α-induced cell death. using bioinformatics analyses followed by luciferase reporter assays we showed that mir-181 interacts with the 3' utr of denn/madd transcripts. mir-181 overexpression also led to decreased endogenous denn/madd mrna levels in l929 murine fibroblasts. flow cytometric analysis of mir-181 transfected cells showed this mirna accentuates mitochondrial membrane potential loss caused by tnf-α. these findings were associated with enhanced apoptosis of l929 cells following tnf-α treatment. overall, these data point to the potential role of mir-181 in regulating tnf-α pro-death signaling, which could be of importance from pathogenesis and therapeutic perspectives in inflammatory disorders associated with tissue degeneration and cell death.",1
"primary immune thrombocytopenia (itp) is an acquired autoimmune disease with many immune dysfunctions. micrornas (mirnas) are a class of non-coding rnas that post-transcriptionally regulate gene expression by messenger rna degradation or translational repression. accumulating evidence has demonstrated that mirnas play a vital role in the regulation of immunological functions and prevention of autoimmunity. however, whether mirnas are involved in the pathogenesis of itp is still unknown. to illustrate the role of mirnas in itp, the expression profile of mirnas from peripheral blood mononuclear cells (pbmcs) in itp patients was investigated by mirna microarray, and further validated by taqman real-time polymerase chain reaction. mir409-3p expression was decreased in pbmcs of active itp patients, but this recovered after effective therapy. ifng was identified and validated as one of the targeted genes of mir409-3p by bioinformatic prediction and reporter gene analysis. in addition, we found dgcr8 transcript was down-regulated in itp patients and positively correlated with mir409-3p. thus, in itp patients, decreased dgcr8 leads to down-regulation of mir409-3p, which in turn results in up-regulation of ifng (ifn-γ).",1
"there is growing evidence that micrornas are implicated in pulmonary arterial hypertension (pah), but underlying mechanisms remain elusive. here, we identified that mir-223 was significantly downregulated in chronically hypoxic mouse and rat lungs, as well as in pulmonary artery and pulmonary artery smooth muscle cells (pasmc) exposed to hypoxia. knockdown of mir-223 increased pasmc proliferation. in contrast, mir-223 overexpression abrogated cell proliferation, migration and stress fiber formation. administering mir-223 agomir in vivo antagonized hypoxia-induced increase in pulmonary artery pressure and distal arteriole muscularization. rhob, which was increased by hypoxia, was identified as one of the targets of mir-223. overexpressed mir-223 suppressed rhob and inhibited the consequent phosphorylation of myosin phosphatase target subunit (mypt1) and the expression of myosin light chain of myosin ii (mlc2), which was identified as another target of mir-223. furthermore, serum mir-223 levels were decreased in female patients with pah associated with congenital heart disease. our study provides the first evidence that mir-223 can regulate pasmc proliferation, migration, and actomyosin reorganization through its novel targets, rhob and mlc2, resulting in vascular remodeling and the development of pah. it also highlights mir-223 as a potential circulating biomarker and a small molecule drug for diagnosis and treatment of pah.",1
"objective cyclooxygenase-2 (cox-2) is a major prostaglandin e2 (pge2) synthetic enzyme and is involved in the pathogenesis of chronic inflammation and pain in osteoarthritis (oa). the objective of this study was to directly address whether microrna (mir)-558 can control the interleukin (il)-1β-mediated induction of cox-2 and catabolic effects in human articular chondrocytes. materials and methods total rna was extracted from the cartilage tissues of normal and oa donors or cultured human articular chondrocytes. the expression of mir-558 was quantified by taqman assay. to investigate the repressive effect of mir-558 on cox-2 expression, human chondrocytes and chondrogenic sw1353 cells were transfected with mature mir-558 or an antisense inhibitor (anti-mir-558). the expression of cox-2 protein was determined by western blot analysis and the involvement of mir-558 in il-1β-induced catabolic effects was examined by western blot analysis and enzyme-linked immunosorbent assay (elisa). direct interaction between mir-558 and the putative site in the 3'-untranslated region (utr) of cox-2 messenger rna (mrna) was validated by luciferase reporter assay. results normal human articular cartilage expressed mir-558, and its expression was significantly lower in oa cartilage. stimulation with il-1β led to a significant reduction in mir-558 expression in normal and oa chondrocytes. il-1β-induced activation of map kinase (mapk) and nuclear factor-κb (nf-κb) decreased mir-558 expression and induced cox-2 expression in chondrocytes. the overexpression of mir-558 directly suppressed the luciferase activity of a reporter construct containing the 3'-utr of human cox-2 mrna and significantly inhibited il-1β-induced upregulation of cox-2, while treatment with anti-mir-558 enhanced il-1β-induced cox-2 expression and reporter activity in chondrocytes. interestingly, il-1β-induced activation of nf-κb and expression of matrix metalloproteinase (mmp)-1 and mmp-13 was significantly inhibited by mir-558 overexpression. conclusion these findings demonstrated that cartilage homeostasis is influenced by mir-558, which directly targets cox-2 and regulates il-1β-stimulated catabolic effects in human chondrocytes.",1
"the zhongwei goat is an important and unique goat breed indigenous to china. it has a natural hair curling phenotype at birth, but the degree of curling gradually decreases with growth. the molecular mechanism underlying the dynamic changes in the wool curvature in zhongwei goats is poorly understood. micrornas (mirnas) play important roles in many biological processes, including hair growth and development. in this study, we selected skins from zhongwei goats at different ages (45 and 108 days) that exhibited different levels of hair curvature and performed mirna sequencing to explore the molecular mechanism of hair bending. in total, 28 significantly differentially expressed mirnas (de mirnas) were identified in the three groups of samples between the two developmental stages. an analysis of the target genes of the above-mentioned de mirnas by the gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway analyses indicated that the de mirnas were involved in signal pathways which were previously associated with hair bending and hair follicle development, such as the tgf-β/smad , pi3k-akt , jak-stat , and mapk pathways. a comprehensive analysis of the correlations between the mirna-seq results and issued transcriptional findings indicated that smad1 was a target gene of mir-26a and smad5 was a target gene of mir-130a. furthermore, goat dermal papilla cells were successfully isolated and purified to determine the role of mirnas in follicle development in vitro. the study results demonstrated that mir-130a and mir-26a had significant effects on the proliferation of dermal papilla cells. in addition, the detection results of mrna and protein levels indicate that the overexpression of mir-26a can promote the expression of related genes in the tgf-β/smad pathway, while mir-130a has the opposite substitution effect. the dual luciferase report test showed that mir-26a targeted the smad1 gene and reduced the expression of the smad1 protein in hair papillary cells. our results identified de micrornas which perhaps change at the time of hair straightening in zhongwei goats and explore the role of mir-26a and mir-130a in dermal papilla cells proliferation. the present study provided a theoretical basis to explore the mechanisms underlying the zhongwei hair growth and curly phenotype.",1
"to investigate the role of micrornas in regulating oligodendrocyte (ol) differentiation and myelination, we utilized transgenic mice in which microrna processing was disrupted in ol precursor cells (opcs) and ols by targeted deletion of dicer1. we found that inhibition of opc-ol mirna processing disrupts normal cns myelination and that opcs lacking mature mirnas fail to differentiate normally in vitro. we identified three mirnas (mir-219, mir-138, and mir-338) that are induced 10-100x during ol differentiation; the most strongly induced of these, mir-219, is necessary and sufficient to promote ol differentiation, and partially rescues ol differentiation defects caused by total mirna loss. mir-219 directly represses the expression of pdgfralpha, sox6, foxj3, and zfp238 proteins, all of which normally help to promote opc proliferation. together, these findings show that mir-219 plays a critical role in coupling differentiation to proliferation arrest in the ol lineage, enabling the rapid transition from proliferating opcs to myelinating ols.",1
"introduction micrornas (mirnas) are a class of small non-coding rnas (20 to 24 nucleotides) that post-transcriptionally modulate gene expression. a key oncomir in carcinogenesis is mir-21, which is consistently up-regulated in a wide range of cancers. however, few functional studies are available for mir-21, and few targets have been identified. in this study, we explored the role of mir-21 in human breast cancer cells and tissues, and searched for mir-21 targets. methods we used in vitro and in vivo assays to explore the role of mir-21 in the malignant progression of human breast cancer, using mir-21 knockdown. using lna silencing combined to microarray technology and target prediction, we screened for potential targets of mir-21 and validated direct targets by using luciferase reporter assay and western blot. two candidate target genes (eif4a2 and ankrd46) were selected for analysis of correlation with clinicopathological characteristics and prognosis using immunohistochemistry on cancer tissue microrrays. results anti-mir-21 inhibited growth and migration of mcf-7 and mda-mb-231 cells in vitro, and tumor growth in nude mice. knockdown of mir-21 significantly increased the expression of ankrd46 at both mrna and protein levels. luciferase assays using a reporter carrying a putative target site in the 3' untranslated region of ankrd46 revealed that mir-21 directly targeted ankrd46. mir-21 and eif4a2 protein were inversely expressed in breast cancers (rs = -0.283, p = 0.005, spearman's correlation analysis). conclusions knockdown of mir-21 in mcf-7 and mda-mb-231 cells inhibits in vitro and in vivo growth as well as in vitro migration. ankrd46 is newly identified as a direct target of mir-21 in bc. these results suggest that inhibitory strategies against mir-21 using peptide nucleic acids (pnas)-antimir-21 may provide potential therapeutic applications in breast cancer treatment.",1
"using a multidimensional genomic data set on glioblastoma from the cancer genome atlas, we identified hsa-mir-26a as a cooperating component of a frequently occurring amplicon that also contains cdk4 and centg1, two oncogenes that regulate the rb1 and pi3 kinase/akt pathways, respectively. by integrating dna copy number, mrna, microrna, and dna methylation data, we identified functionally relevant targets of mir-26a in glioblastoma, including pten, rb1, and map3k2/mekk2. we demonstrate that mir-26a alone can transform cells and it promotes glioblastoma cell growth in vitro and in the mouse brain by decreasing pten, rb1, and map3k2/mekk2 protein expression, thereby increasing akt activation, promoting proliferation, and decreasing c-jun n-terminal kinase-dependent apoptosis. overexpression of mir-26a in pten-competent and pten-deficient glioblastoma cells promoted tumor growth in vivo, and it further increased growth in cells overexpressing cdk4 or centg1. importantly, glioblastoma patients harboring this amplification displayed markedly decreased survival. thus, hsa-mir-26a, cdk4, and centg1 comprise a functionally integrated oncomir/oncogene dna cluster that promotes aggressiveness in human cancers by cooperatively targeting the rb1, pi3k/akt, and jnk pathways.",1
"purpose in a spontaneous mutant substrain of c57bl/10 mice, severely affected retinal ribbon-type synapses have been described. the retinopathy was accompanied by a substantial loss in the activities of the second-order neurons. rod photoreceptor responses were maintained with reduced amplitude, whereas cone activities were absent. this study was conducted to identify the genetic defect underlying this hitherto unknown autosomal recessive cone-rod dysfunction. methods genome-wide linkage analysis and screening of positional candidate genes were used to identify the causative mutation. tissue-specific transcriptional activity of the defective gene was determined by northern blot analysis and rt-pcr approaches. the number of cone photoreceptors was estimated by immunohistochemistry. results the mutation was localized to a 275-kb region of chromosome 6. within this candidate interval, a homozygous frameshift mutation (c.2367insc) was identified in the cacna2d4 gene of affected animals. this gene codes for an l-type calcium channel auxiliary subunit of the alpha2delta type. the mutation introduces a premature stop codon that truncates one third of the predicted cacna2d4 protein. a severe reduction in cacna2d4 transcript levels observed in mutant retinas probably results in the lack of cacna2d4 protein. the mutation leads to significant loss of rods, whereas the number of cone cells remains unaffected until 6 weeks of age. conclusions the cacna2d4 mutation underlies a novel channelopathy leading to cone-rod dysfunction in the visual system of mice and provides a new candidate gene for human retinal disorders including night blindness, retinitis pigmentosa, and cone-rod dystrophies.",1
"micrornas (mirs) represent a class of endogenous approximately 18-25 nucleotide rnas that regulate gene expression through translational repression by binding to a target mrna. these mirs regulate several biological functions, such as cell growth, cell differentiation, carcinogenesis, and so on. in a previous report, we have indicated that mir-141 and -200a act as preosteoblast differentiation modulators. in the present study, using microrna array and in silico analyses, we found that mir-208 is closely involved in preosteoblast differentiation by partially regulating the expression of ets1 (v-ets erythroblastosis virus e26 oncogene homolog 1), which transactivates osteopontin, runt-related transcription factor 2, parathyroid hormone-related protein, and type i procollagen. furthermore, the enforced expression of mature mir-208 in murine preosteoblast in mc3t3-e1 cells or primary osteoblast cells remarkably attenuated bmp-2-induced preosteoblast differentiation. in addition, we determined that ets1 is a target gene of mir-208 by using a sensor luciferase reporter assay. taken together, these results suggest that the down-regulation of mir-208 in bmp-2-stimulated osteoblast differentiation is an important part of the regulatory machinery involved in early osteogenesis.",1
"the wobble residue c34 of haloferax volcanii elongator trna(met) is 2'-o-methylated. neither a protein enzyme nor a guide rna for this modification has been described. in this study, we show that this methylation is guided by a box c/d rna targeting the intron-containing precursor of the trna. this guide rna is starkly different from its homologs. this unique rna of approximately 75 bases, named sr-tmet, is encoded in the genomes of h. volcanii and several other haloarchaea. a unique feature of sr-tmet is that the mature rna in h. volcanii is substantially larger than its predicted size, whereas those in other haloarchaea are as predicted. while the 5'-ends of all tested haloarchaeal sr-tmets are equivalent, h. volcanii sr-tmet possesses an additional 51-base extension at its 3' end. this extension is present in the precursor but not in the mature sr-tmet of halobacterium sp., suggesting differential 3'-end processing of sr-tmet in these two closely related organisms. archaeal box c/d rnas mostly contain a k-loop at the c'/d' motif. another unique feature of sr-tmet is that its c'/d' motif lacks either a conventional k-turn or a k-loop. instead, it contains two tandem, sheared g•a base pairs and a pyrimidine-pyrimidine pair in the non-canonical stem; the latter may form an alternative k-turn. gel shift assays indicate that the l7ae protein can form a stable complex with this unusual c'/d' motif, suggesting a novel rna structure for l7ae interaction.",1
"the aggregation of aβ42-peptides and the formation of drusen in age-related macular degeneration (amd) are due in part to the inability of homeostatic phagocytic mechanisms to clear self-aggregating aβ42-peptides from the extracellular space. the triggering receptor expressed in myeloid/microglial cells-2 (trem2), a trans-membrane-spanning, sensor-receptor of the immune-globulin/lectin-like gene superfamily is a critical component of aβ42-peptide clearance. here we report a significant deficit in trem2 in amd retina and in cytokine- or oxidatively-stressed microglial (mg) cells. rt-pcr, mirna-array, led-northern and western blot studies indicated up-regulation of a microglial-enriched nf-кb-sensitive mirna-34a coupled to a down-regulation of trem2 in the same samples. bioinformatics/transfection-luciferase reporter assays indicated that mirna-34a targets the 299 nucleotide trem2-mrna-3'utr, resulting in trem2 down-regulation. c8b4-microglial cells challenged with aβ42 were able to phagocytose these peptides, while mirna-34a down-regulated both trem2 and the ability of microglial-cells to phagocytose. treatment of tnfα-stressed mg cells with phenyl-butyl nitrone (pbn), caffeic-acid phenethyl ester (cape), the nf-kb - inhibitor/resveratrol analog cay10512 or curcumin abrogated these responses. incubation of anti-mirna-34a (am-34a) normalized mirna-34a abundance and restored trem2 back to homeostatic levels. these data support five novel observations: (i) that a ros- and nf-kb - sensitive, mirna-34a-mediated modulation of trem2 may in part regulate the phagocytic response; (ii) that gene products encoded on two different chromosomes (mirna-34a at chr1q36.22 and trem2 at chr6p21.1) orchestrate a phagocytic-aβ42-peptide clearance-system; (iii) that this nf-kb-mediated-mirna-34a-trem2 mechanism is inducible from outside of the cell; (iv) that when operating normally, this pathway can clear aβ42 peptide monomers from the extracellular medium; and (v) that anti-nf-kb and/or anti-mirna (am)-based therapeutic strategies may be useful against deficits in trem-2 receptor-based-sensing and -phagocytic signaling that promote pathogenic amyloidogenesis.",1
"targeting oncogenic micrornas (mirnas) is emerging as a promising strategy for cancer therapy. in this study, we provide proof of principle for the safety and efficacy of mirna targeting against metastatic tumors. we tested the impact of targeting mir-182, a pro-metastatic mirna frequently overexpressed in melanoma, the in vitro silencing of which represses invasion and induces apoptosis. specifically, we assessed the effect of anti-mir-182 oligonucleotides synthesized with 2' sugar modifications and a phosphorothioate backbone in a mouse model of melanoma liver metastasis. luciferase imaging showed that mice treated with anti-mir-182 had a lower burden of liver metastases compared with control. we confirmed that mir-182 levels were effectively downregulated in the tumors of anti-mir-treated mice compared with tumors of control-treated mice, both in the liver and in the spleen. this effect was accompanied by an upregulation of multiple mir-182 direct targets. transcriptional profiling of tumors treated with anti-mir-182 or with control oligonucleotides revealed an enrichment of genes controlling survival, adhesion and migration modulated in response to anti-mir-182 treatment. these data indicate that in vivo administration of anti-mirs allows for efficient mirna targeting and concomitant upregulation of mirna-controlled genes. our results demonstrate that the use of anti-mir-182 is a promising therapeutic strategy for metastatic melanoma and provide a solid basis for testing similar strategies in human metastatic tumors.",1
"the notch1 signaling pathway is a critical determinant of cell fate decisions and drives oncogenesis through mechanisms that are incompletely understood. using an established mouse model of t cell acute lymphoblastic leukemia (t-all), here we report that induction of intracellular notch1 (icn1) leads to repression of mir-451 and mir-709. icn1 decreases expression of these mirnas by inducing degradation of the e2a tumor suppressor, which transcriptionally activates the genes encoding mir-451 and mir-709. both mir-451 and mir-709 directly repress myc expression. in addition, mir-709 directly represses expression of the akt and ras-grf1 oncogenes. we also show that repression of mir-451 and mir-709 expression is required for initiation and maintenance of mouse t-all. mir-451 but not mir-709 is conserved in humans, and human t-alls with activating notch1 mutations have decreased mir-451 and increased myc levels compared with t-alls with wild-type notch1. thus, mir-451 and mir-709 function as potent suppressors of oncogenesis in notch1-induced mouse t-all, and mir-451 influences myc expression in human t-all bearing notch1 mutations.",1
"tumors secrete proangiogenic factors to induce the ingrowth of blood vessels from the stroma. these peptides bind to cell surface receptors on vascular endothelial cells (ecs), triggering signaling cascades that activate and repress batteries of downstream genes responsible for the angiogenic phenotype. to determine if micrornas (mirnas) affect regulation of the ec phenotype by gax, a homeobox gene and negative transcriptional regulator of the angiogenic phenotype, we tested the effect of mir-221 on gax expression. mir-221 strongly upregulated gax, suggesting that mir-221 downregulates a repressor of gax. we next expressed mir-221 in ecs and identified zeb2, a modulator of the epithelial-mesenchymal transition, as being strongly downregulated by mir-221. using mir-221 expression constructs and an inhibitor, we determined that zeb2 is upregulated by serum and downregulates gax, while the expression of mir-221 upregulates gax and downregulates zeb2. a mutant mir-221 fails to downregulate zeb2 or upregulate gax. finally, using chromatin immunoprecipitation, we identified two zeb2 binding sites that modulate the ability of zeb2 to downregulate gax promoter activity. we conclude that mir-221 upregulates gax primarily through its ability to downregulate the expression of zeb2. these observations suggest a strategy for inhibiting angiogenesis by either recapitulating mir-221 expression or inhibiting zeb2 activation.",1
"we have identified a cell cycle delay in saccharomyces cerevisiae rnase mrp mutants. mutants delay with large budded cells, dumbbell-shaped nuclei, and extended spindles characteristic of ""exit from mitosis"" mutants. in accord with this, a rnase mrp mutation can be suppressed by overexpressing the polo-like kinase cdc5 or by deleting the b-type cyclin clb1, without restoring the mrp-dependent rrna-processing step. in addition, we identified a series of genetic interactions between rnase mrp mutations and mutations in cdc5, cdc14, cdc15, clb2, and clb5. as in most ""exit from mitosis"" mutants, levels of the clb2 cyclin were increased. the buildup of clb2 protein is not the result of a defect in the release of the cdc14 phosphatase from the nucleolus, but rather the result of an increase in clb2 mrna levels. these results indicate a clear role of rnase mrp in cell cycle progression at the end of mitosis. conservation of this function in humans may explain many of the pleiotropic phenotypes of cartilage hair hypoplasia.",1
"telomerase is a cellular reverse transcriptase that elongates the single-stranded chromosome ends and oligonucleotides in vivo and in vitro. in saccharomyces cerevisiae, est2p (telomerase catalytic subunit) and tlc1 (telomerase rna template subunit) constitute the telomerase core complex. we co-overexpressed gst (glutathione s-transferase)-est2p and tlc1 in s. cerevisiae, and reconstituted the telomerase activity. the gst-est2p-tlc1 complex was partially purified by ammonium sulphate fractionation and affinity chromatography on glutathione beads, and the partially purified telomerase did not contain the other two subunits of the telomerase holoenzyme, est1p and est3p. the purified recombinant gst-est2p-tlc1 telomerase core complex could specifically add nucleotides on to the single-stranded tg(1-3) primer in a processive manner, but could not translocate to synthesize more than one telomeric repeat. the purified telomerase core complex exhibited different activities when primers were paired with the tlc1 template at different positions. the procedure of reconstitution and purification of telomerase core enzyme that we have developed now allows for further mechanistic studies of the functions of other subunits of the telomerase holoenzyme as well as other telomerase regulation proteins.",1
"micrornas are endogenous repressors of gene expression. we examined micrornas in the renal medulla of dahl salt-sensitive rats and consomic ss-13(bn) rats. salt-induced hypertension and renal injury in dahl salt-sensitive rats, particularly medullary interstitial fibrosis, have been shown previously to be substantially attenuated in ss-13(bn) rats. of 377 micrornas examined, 5 were found to be differentially expressed between dahl salt-sensitive rats and consomic ss-13(bn) rats receiving a high-salt diet. real-time pcr analysis demonstrated that high-salt diets induced substantial upregulation of mir-29b in the renal medulla of ss-13(bn) rats but not in ss rats. mir-29b was predicted to regulate 20 collagen genes, matrix metalloproteinase 2 (mmp2), integrin beta1 (itgb1), and other genes related to the extracellular matrix. expression of 9 collagen genes and mmp2 was upregulated by a high-salt diet in the renal medulla of ss rats, but not in ss-13(bn) rats, an expression pattern opposite to mir-29b. knockdown of mir-29b in the kidneys of ss-13(bn) rats resulted in upregulation of several collagen genes. mir-29b reduced expression levels of several collagen genes and itgb1 in cultured rat renal medullary epithelial cells. moreover, mir-29b suppressed the activity of luciferase when the reporter gene was linked to a 3'-untranslated segment of collagen genes col1a1, col3a1, col4a1, col5a1, col5a2, col5a3, col7a1, col8a1, mmp2, or itgb1 but not col12a1. the result demonstrated broad effects of mir-29b on a large number of collagens and genes related to the extracellular matrix and suggested involvement of mir-29b in the protection from renal medullary injury in ss-13(bn) rats.",1
"transcriptional regulation by micrornas (mirnas) involves complementary base-pairing at target sites on mrnas, yielding complex secondary structures. here we introduce an efficient computational approach and software (fasth) for genome-scale prediction of mirna target sites based on minimizing the free energy of duplex structure. we apply our approach to identify mirna target sites in the human and mouse transcriptomes. our results show that short sequence motifs in the 5' end of mirnas frequently match mrnas perfectly, not only at validated target sites but additionally at many other, energetically favourable sites. high-quality matching regions are abundant and occur at similar frequencies in all mrna regions, not only the 3'utr. about one-third of potential mirna target sites are reassigned to different mrna regions, or gained or lost altogether, among different transcript isoforms from the same gene. many potential mirna target sites predicted in human are not found in mouse, and vice-versa, but among those that do occur in orthologous human and mouse mrnas most are situated in corresponding mrna regions, i.e. these sites are themselves orthologous. using a luciferase assay in hek293 cells, we validate four of six predicted mirna-mrna interactions, with the mrna level reduced by an average of 73%. we demonstrate that a thermodynamically based computational approach to prediction of mirna binding sites on mrnas can be scaled to analyse complete mammalian transcriptome datasets. these results confirm and extend the scope of mirna-mediated species- and transcript-specific regulation in different cell types, tissues and developmental conditions.",1
"dysregulation of human trophoblast invasion and differentiation can result in preeclampsia (pe), a hypertensive disorder of pregnancy with significant morbidity and mortality for mother and offspring. mirna microarray analysis of rna from human cytotrophoblasts (cytt), before and after differentiation to syncytiotrophoblast (synt) in primary culture, revealed that members of mir-515 family-including mir-515-5p, mir-519e-5p, mir-519c-3p, and mir-518f, belonging to the primate- and placenta-specific chromosome 19 mirna cluster ( c19mc )-were significantly down-regulated upon human synt differentiation. the proto-oncogene, c-myc, which declines during synt differentiation, interacted with e-boxes upstream of pri-mir-515-1 and pri-mir-515-2 , encoding these mrnas, to enhance their expression. predicted targets of mir-515-5p, known to be critical for human synt differentiation, including hcyp19a1/aromatase p450, glial cells missing 1 (gcm1), frizzled 5 (fzd5), wnt2, sp1, and estrogen receptor-α (erα) mrna, were markedly up-regulated during synt differentiation. notably, overexpression of mir-515-5p in cultured primary human trophoblasts impaired synt differentiation and specifically decreased expression of hcyp19a1, gcm1, and fzd5, which were validated as its direct targets. interestingly, mir-515-5p levels were significantly increased in pe placentas, whereas mrna and protein levels of targets, hcyp19a1, gcm1, and fzd5, were significantly decreased, compared with placentas of normotensive women. thus, mir-515-5p may serve a key role in human trophoblast differentiation; its aberrant up-regulation may contribute to the pathogenesis of pe.",1
"telomerase is a ribonucleoprotein enzyme that maintains telomere length by adding telomeric sequence repeats onto chromosome ends. the essential rna component of telomerase provides the template for telomeric repeat synthesis. to determine the secondary structure of vertebrate telomerase rna, 32 new telomerase rna genes were cloned and sequenced from a variety of vertebrate species including 18 mammals, 2 birds, 1 reptile, 7 amphibians, and 4 fishes. using phylogenetic comparative analysis, we propose a secondary structure that contains four structural domains conserved in all vertebrates. ten helical regions of the rna are universally conserved while other regions vary significantly in length and sequence between different classes of vertebrates. the proposed vertebrate telomerase rna structure displays a strikingly similar topology to the previously determined ciliate telomerase rna structure, implying an evolutionary conservation of the global architecture of telomerase rna.",1
"background colorectal carcinoma (crc) is one of the leading causes of cancer-related mortality worldwide. micrornas (mirnas, mirs) play important roles in carcinogenesis. mir-126 has been shown to be down-regulated in crc. in this study, we identified the potential effects of mir-126 on some important biological properties of crc cells and clarified the regulation of insulin receptor substrate 1 (irs-1) and its possible signaling pathway by mir-126. methods the effect of mir-126 on irs-1, akt, and erk1/2 expression was assessed in the crc cell lines ht-29 and hct-116 with a mir-126 mimic or inhibitor to increase or decrease mir-126 expression. furthermore, the roles of mir-126 in regulation of the biological properties of crc cells were analyzed with mir-126 mimic or inhibitor-transfected cells. the 3'-untranslated region (3'-utr) of irs-1 regulated by mir-126 was analyzed by using a dual-luciferase reporter assay. results we found that irs-1 is the functional downstream target of mir-126 by directly targeting the 3'-utr of irs-1. endogenous mir-126 and exogenous mir-126 mimic inhibited irs-1 expression. furthermore, gain-of-function or loss-of-function studies showed that over-expression of mir-126 down-regulated irs-1, suppressed akt and erk1/2 activation, crc cells proliferation, migration, invasion, and caused cell cycle arrest, but had no effect on cell apoptosis. knockdown of mir-126 promoted these processes in hct-116 cells and promoted akt and erk1/2 activation by up-regulating the expression of the irs-1 protein. conclusions mir-126 may play roles in regulation of the biological behavior of crc cells, at least in part, by targeting irs-1 via akt and erk1/2 signaling pathways.",1
"background blood bank-stored human platelets are one of the life-saving transfusion products to prevent bleeding in multiple clinical settings. in ex vivo storage, platelets undergo apoptosis and it is highly desirable to prevent this process to preserve platelet quality. however, underlying mechanisms of apoptosis are not well understood in stored platelets. integrin beta 3 (itgb3) glycoprotein plays multiple roles in platelet physiological processes, and it was reported in other cell types that downregulation of itgb3 induces apoptosis. small noncoding regulatory rnas known as micrornas (mirnas), some of which are abundant in platelets such as mir-103b that belong to mir-103 family of mirnas, known to play key roles in platelet functions both in vivo and during storage; cellular mir-103 downregulates certain genes in other cell types and promotes apoptosis. however, whether mir-103b can target and downregulate itgb3 in stored platelets and such mirna regulation promotes apoptosis is not known. here, we tested this working hypothesis. objective our objective of this study is to validate the abundance of mir-103b in stored platelets and identify whether itgb3 is a target of mir-103b for the downregulation and this interaction promotes apoptosis. methods rt-qpcr validation of mir-103b was performed in 11 donor samples at 3 different storage time points. in-silico analysis was performed to identify predicted targets of the mir-103b. the mirna and messenger rna interactions were confirmed using different biochemical approaches such as qrt-pcr, western blotting and, suppression of luciferase reporter gene expression by ectopic expression of mir-103b in hela cells. final validation of the functional role of mir-103b in itgb3 downregulation and resulting induction of apoptosis was assessed in stored platelets by facs analysis following ectopic expression of mir-103b. results using the target scan vert algorithm, we identified several integrin subunit-encoding mrnas as potential targets of mir-103b. while itgb3 and itgb6 were found to have two targeting sites for mir-103b, since itgb3 is known to play a role in apoptosis, we chose this for further validation in this study. ectopic expression of mir-103b decreased the luciferase reporter activity in hela cells and decreased itgb3 mrna and protein levels in platelets, concomitant with an increase in apoptosis. conclusion the results demonstrate that in stored platelets, mir-103b is highly expressed and can interact with and downregulate itgb3 and promote apoptosis in stored platelets.",1
"macrophage (mφ) activation must be tightly controlled to preclude overzealous responses that cause self-damage. micrornas promote classical mφ activation by blocking antiinflammatory signals and transcription factors but also can prevent excessive tlr signaling. in contrast, the microrna profile associated with alternatively activated mφ and their role in regulating wound healing or antihelminthic responses has not been described. by using an in vivo model of alternative activation in which adult brugia malayi nematodes are implanted surgically in the peritoneal cavity of mice, we identified differential expression of mir-125b-5p, mir-146a-5p, mir-199b-5p, and mir-378-3p in helminth-induced mφ. in vitro experiments demonstrated that mir-378-3p was specifically induced by il-4 and revealed the il-4-receptor/pi3k/akt-signaling pathway as a target. chemical inhibition of this pathway showed that intact akt signaling is an important enhancement factor for alternative activation in vitro and in vivo and is essential for il-4-driven mφ proliferation in vivo. thus, identification of mir-378-3p as an il-4rα-induced microrna led to the discovery that akt regulates the newly discovered mechanism of il-4-driven macrophage proliferation. together, the data suggest that negative regulation of akt signaling via micrornas might play a central role in limiting mφ expansion and alternative activation during type 2 inflammatory settings.",1
"human pluripotent stem cells offer promise for use in cell-based therapies for brain injury and diseases. however, their cellular behavior is poorly understood. here we show that the expression of the brain-specific microrna-9 (mir-9) is turned on in human neural progenitor cells (hnpcs) derived from human embryonic stem cells. loss of mir-9 suppressed proliferation but promoted migration of hnpcs cultured in vitro. hnpcs without mir-9 activity also showed enhanced migration when transplanted into mouse embryonic brains or adult brains of a mouse model of stroke. these effects were not due to precocious differentiation of hnpcs. one of the key targets directly regulated by mir-9 encodes stathmin, which increases microtubule instability and whose expression in hnpcs correlates inversely with that of mir-9. partial inhibition of stathmin activity suppressed the effects of mir-9 loss on proliferation and migration of human or embryonic rat neural progenitors. these results identify mir-9 as a novel regulator that coordinates the proliferation and migration of hnpcs.",1
"mir-126 is an endothelial-specific microrna essential for governing vascular integrity and angiogenesis. its role in tumor angiogenesis of gastric cancer (gc) is unclear. this study aimed at determining the role of mir-126 in gc angiogenesis. down-regulation of mir-126 was found to inversely correlate with an increased microvessel density (mvd) and vascular endothelial growth factor a (vegf-a) expression in gastric cancer tissues. bioinformatics analysis and luciferase reporter assay revealed that mir-126 directly targeted the 3'-untranslated region (3'-utr) of vegf-a mrna. in addition, the restoration of mir-126 expression by lentivirus-mir-126 (lenti-mir-126) transfection obviously reduced the expression of vegf-a and the activition of its downstream genes, akt, mtor and erk1/2 in gastric cancer cell lines sgc-7901, mkn-28 and mkn-45. in contrast, the down-regulation of mir-126 expression by lentivirus-anti-mir-126 (lenti-anti-mir-126) transfection obviously up-regulated the expression of vegf-a and its downstream signaling pathways. in vivo xenograft mice model experiments clarified the down-regulation of vegf-a and mvd as well as inhibition of tumor growth by up-regulation of mir-126. overall, the results from our study suggested that mir-126 could suppress tumor growth and tumor angiogenesis of gc through vegf-a signaling, and it is a novel potential therapeutic target for gc.",1
"recent years have seen a massive expansion in our understanding of the biology of micrornas (mirnas) in cancer, through the identification of mirnas with aberrant expression in specific cancers and the functional validation of their critical target molecules and cellular effects. in parallel, targeted therapeutic agents to block signalling pathways critical to tumour growth and progression have been developed but have yielded disappointing clinical results. the discovery of mirnas that regulate erbb signalling in cancer cells brings new hope that in the future these oncogenic pathways can be more effectively inhibited to improve patient outcomes.",1
"recently, many studies have found that the mir-106b ~25 cluster plays an oncogenic role in tumor progression. however, the precise role of each micrornas (mirnas) in the cluster is not yet clear. in the present study, we examined the expression of mir-106b in glioma samples and a tissue microarray by real-time pcr and in situ hybridization (ish), respectively, finding that mir-106b is overexpressed in the majority of gliomas. meanwhile, the expression of mir-106b was positively correlated with tumor grade (p < 0.05). the transfection of a mir-106b anti-sense oligonucleotide (ason) into three human glioma cell lines (u251, ln229 and tj905) suppressed the proliferation of these cells. moreover, the growth of xenograft tumors in nude mice treated with mir-106b ason was significantly impaired. a bioinformatics analysis predicted that rbl2 may be the target of mir-106b, and dual-luciferase reporter assays identified rbl2, but not rb1 or rbl1, as a target of mir-106b. these results suggest that mir-106b facilitates glioma cell growth by promoting cell cycle progression through the negative regulation of rbl2.",1
"the epithelial-mesenchymal transition (emt) imparts metastatic competence on otherwise non-metastatic cancer cells through decreased inter-cellular adhesions, increased migratory capacity, stem cell properties and anoikis and chemotherapy resistance. in this study, we profiled changes in microrna expression during emt in conjunction with changes in dna methylation at microrna promoters to discover essential mediators of emt-imparted stemness properties. microrna-203 (mir-203) expression is repressed following emt induced by multiple different stimuli and in established claudin-low cell lines as well as the cd44hi/cd24lo stem cell-enriched fraction. expression of mir-203 in mesenchymal cells compromises migratory and invasive capacity in vitro, and tumor initiation and metastasis in vivo. unexpectedly, mir-203 expression affects the sphere-forming capacity of neighboring cells by indirectly enhancing expression of dkk1, a secreted inhibitor of wnt signaling and stemness resulting in suppression of β-catenin protein levels. our data suggest that restoring mir-203 expression levels may inhibit metastasis and combat deregulated wnt signaling.",1
"conversion of uridines into pseudouridines (psis) is the most frequent base modification in ribosomal rnas (rrnas). in eukaryotes, the pseudouridylation sites are specified by base-pairing with specific target sequences within h/aca small nucleolar rnas (snornas). the yeast rrnas harbor 44 psis, but, when this work began, 15 psis had completely unknown guide snornas. this suggested that many snornas remained to be discovered. to address this problem and further complete the snorna assignment to psi sites, we identified the complete set of rnas associated with the h/aca snornp specific proteins gar1p and nhp2p by coupling tap-tag purifications with genomic dna microarrays experiments. surprisingly, while we identified all the previously known h/aca snornas, we selected only three new snornas. this suggested that most of the missing psi guides were present in previously known snornas but had been overlooked. we confirmed this hypothesis by systematically investigating the role of previously known, as well as of the newly identified snornas, in specifying rrna psi sites and found all but one missing guide rnas. during the completion of this work, another study, based on bioinformatic predictions, also reported the identification of most missing guide rnas. altogether, all psi guides are now identified and we can tell that, in budding yeast, the 44 psis are guided by 28 snornas. finally, aside from snr30, an atypical small rna of heterogeneous length and at least one mrna, all gar1p and nhp2p associated rnas characterized by our work turned out to be snornas involved in rrna psi specification.",1
"micrornas are critical mediators of stem cell pluripotency, differentiation, and malignancy. limited information exists regarding microrna alterations that facilitate initiation and progression of human lung cancers. in this study, array techniques were used to evaluate microrna expression in normal human respiratory epithelia and lung cancer cells cultured in the presence or absence of cigarette smoke condensate (csc). under relevant exposure conditions, csc significantly repressed mir-487b. subsequent experiments demonstrated that mir-487b directly targeted suz12, bmi1, wnt5a, myc, and kras. repression of mir-487b correlated with overexpression of these targets in primary lung cancers and coincided with dna methylation, de novo nucleosome occupancy, and decreased h2az and tcf1 levels within the mir-487b genomic locus. deoxy-azacytidine derepressed mir-487b and attenuated csc-mediated silencing of mir-487b. constitutive expression of mir-487b abrogated wnt signaling, inhibited in vitro proliferation and invasion of lung cancer cells mediated by csc or overexpression of mir-487b targets, and decreased growth and metastatic potential of lung cancer cells in vivo. collectively, these findings indicate that mir-487b is a tumor suppressor microrna silenced by epigenetic mechanisms during tobacco-induced pulmonary carcinogenesis and suggest that dna demethylating agents may be useful for activating mir-487b for lung cancer therapy.",1
"most polycistronic genes are expressed in a single transcript, in which each cistron produces a fixed amount of protein. in this report, we show the first example of differential degradation of a polycistronic gene induced by a small regulatory rna (srna). our data show that the iron-responsive srna, ryhb, binds to the second cistron of the polycistronic mrna, iscrsua, which encodes the necessary machinery for biosynthesis of fe-s clusters, and promotes the cleavage of the downstream iscsua transcript. this cleavage gives rise to the remaining 5'-section of the transcript encoding iscr, a transcriptional regulator responsible for activation and repression of several genes depending on the cellular fe-s level. our data indicate that the iscr transcript is stable and that translation is active. the stability of the iscr transcript depends on a 111-nucleotide long non-translated rna section located between iscr and iscs, which forms a strong repetitive extragenic palindromic secondary structure and may protect against ribonucleases degradation. this novel regulation shows how srnas and mrna structures can work together to modulate the transcriptional response to a specific stress.",1
"mitochondria are complex organelles whose dysfunction underlies a broad spectrum of human diseases. identifying all of the proteins resident in this organelle and understanding how they integrate into pathways represent major challenges in cell biology. toward this goal, we performed mass spectrometry, gfp tagging, and machine learning to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. we link poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. using this approach, we predict 19 proteins to be important for the function of complex i (ci) of the electron transport chain. we validate a subset of these predictions using rnai, including c8orf38, which we further show harbors an inherited mutation in a lethal, infantile ci deficiency. our results have important implications for understanding ci function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria.",1
"background during goat embryonic morphogenesis and postnatal initiation of hair follicle (hf) regeneration, dermal papilla (dp) cells play a vital role in hair formation. growing evidence shows that micrornas (mirnas) participate in hf development and dp cell proliferation. however, the molecular mechanisms have not been thoroughly investigated. result in this study, we utilized mirna sequencing (mirna-seq) to identify differentially expressed mirnas at different hf cycling stages (anagen and telogen). mirna-seq has identified 411 annotated mirnas and 130 novel mirnas in which 29 mirnas were up-regulated and 32 mirnas were down-regulated in the anagen phase compared to the telogen phase. target gene prediction and functional enrichment analysis indicated some major biological pathways related to hair cycling, such as wnt signaling pathways, ecm-receptor interaction, vegf signaling pathway, biosynthesis of amino acids, metabolic pathways, ribosome and oxidative phosphorylation. also, we explored the function of chi-mir-30b-5p in regulating hair growth cycle. similar to the hf cycling, dp cells were isolated from skin and used to investigate mirna functions. the mtt and edu assays showed that the viability and proliferation of dp cells were inhibited or promoted after the transfection of chi-mir-30b-5p mimic or inhibitor, respectively. bioinformatics analysis revealed camkiiδ as a candidate target gene of chi-mir-30b-5p, and the dual-luciferase and western blot assay demonstrated that chi-mir-30b-5p bound to the 3'utr of camkiiδ and further inhibited its translation. conclusion chi-mir-30b-5p was found to be highly expressed in the telogen than that in the anagen phase and could inhibit the proliferation of dp cells by targeting camkiiδ. our study provides new information on the regulatory functions of mirnas during hf development.",1
"epithelial to mesenchymal transition (emt) facilitates tissue remodelling during embryonic development and is viewed as an essential early step in tumour metastasis. we found that all five members of the microrna-200 family (mir-200a, mir-200b, mir-200c, mir-141 and mir-429) and mir-205 were markedly downregulated in cells that had undergone emt in response to transforming growth factor (tgf)-beta or to ectopic expression of the protein tyrosine phosphatase pez. enforced expression of the mir-200 family alone was sufficient to prevent tgf-beta-induced emt. together, these micrornas cooperatively regulate expression of the e-cadherin transcriptional repressors zeb1 (also known as deltaef1) and sip1 (also known as zeb2), factors previously implicated in emt and tumour metastasis. inhibition of the micrornas was sufficient to induce emt in a process requiring upregulation of zeb1 and/or sip1. conversely, ectopic expression of these micrornas in mesenchymal cells initiated mesenchymal to epithelial transition (met). consistent with their role in regulating emt, expression of these micrornas was found to be lost in invasive breast cancer cell lines with mesenchymal phenotype. expression of the mir-200 family was also lost in regions of metaplastic breast cancer specimens lacking e-cadherin. these data suggest that downregulation of the micrornas may be an important step in tumour progression.",1
"drosophila gurken mrna is localized by dynein-mediated transport to a crescent near the oocyte nucleus, thus targeting the tgfalpha signal and forming the primary embryonic axes. here, we show that gurken and the i factor, a non-ltr retrotransposon, share a small consensus rna stem loop of defined secondary structure, which forms a conserved signal for dynein-mediated rna transport to the oocyte nucleus. furthermore, gurken and the i factor compete in vivo for the same localization machinery. i factor transposition leads to its mrna accumulating near and within the oocyte nucleus, thus causing perturbations in gurken and bicoid mrna localization and axis specification. these observations further our understanding of the close association of transposable elements with their host and provide an explanation for how i factor transposition causes female sterility. we propose that the transposition of other elements may exploit the host's rna transport signals and machinery.",1
"dendritic cells (dcs) are potent antigen-presenting cells derived from hematopoietic progenitor cells and circulating monocytes. to investigate the role of micrornas (mirnas) during dc differentiation, maturation, and function, we profiled mirna expression in human monocytes, immature dcs (imdcs), and mature dcs (mdcs). stage-specific, differential expression of 27 mirnas was found during monocyte differentiation into imdcs and mdcs. among them, decreased mir-221 and increased mir-155 expression correlated with p27(kip1) accumulation in dcs. silencing of mir-221 or overexpressing of mir-155 in dcs resulted in p27(kip1) protein increase and dc apoptosis. moreover, mdcs from mir-155(-/-) mice were less apoptotic than those from wild-type mice. silencing of mir-155 expression had little effect on dc maturation but reduced il-12p70 production, whereas mir-155 overexpression in mdcs enhanced il-12p70 production. kip1 ubiquitination-promoting complex 1, suppressor of cytokine signaling 1, and cd115 (m-csfr) were functional targets of mir-155. furthermore, we provide evidence that mir-155 indirectly regulated p27(kip1) protein level by targeting kip1 ubiquitination-promoting complex 1. thus, our study uncovered mirna signatures during monocyte differentiation into dcs and the new regulatory role of mir-221 and mir-155 in dc apoptosis and il-12p70 production.",1
"differentiation of periodontal ligament (pdl) cells occurs under specific induction; furthermore, nf-kappab signaling is important for regulation of bone differentiation. micrornas are small non-coding rnas that repress the translation of target genes and modulate cellular processes. mir-146a has been reported to modulate nf-kappab signaling. this study hypothesized that mir-146a has a regulatory role in pdl differentiation by affecting nf-kappab signaling. immortalized pdl (i-pdl) cell lines were established by exogenous telomerase expression. the genesis of alkaline phosphatase and the up-regulation of mir-146a were induced by ascorbic acid in the i-pdl cells and primary pdl cells. i-pdl cells with exogenous mir-146a expression showed attenuation of nf-kappab activity and exhibited higher differentiation relative to the controls. exogenous nf-kappab expression decreased the expression of differentiation markers, while the inactivation of endogenous nf-kappab increased alkaline phosphatase in i-pdl cells. this study concludes that mir-146a promotes the differentiation in pdl cells through the down-regulation of nf-kappab signaling.",1
"gain-of-function mutations in leucine-rich repeat kinase 2 (lrrk2) cause familial as well as sporadic parkinson's disease characterized by age-dependent degeneration of dopaminergic neurons. the molecular mechanism of lrrk2 action is not known. here we show that lrrk2 interacts with the microrna (mirna) pathway to regulate protein synthesis. drosophila e2f1 and dp messenger rnas are translationally repressed by let-7 and mir-184*, respectively. pathogenic lrrk2 antagonizes these mirnas, leading to the overproduction of e2f1/dp, previously implicated in cell cycle and survival control and shown here to be critical for lrrk2 pathogenesis. genetic deletion of let-7, antagomir-mediated blockage of let-7 and mir-184* action, transgenic expression of dp target protector, or replacement of endogenous dp with a dp transgene non-responsive to let-7 each had toxic effects similar to those of pathogenic lrrk2. conversely, increasing the level of let-7 or mir-184* attenuated pathogenic lrrk2 effects. lrrk2 associated with drosophila argonaute-1 (dago1) or human argonaute-2 (hago2) of the rna-induced silencing complex (risc). in aged fly brain, dago1 protein level was negatively regulated by lrrk2. further, pathogenic lrrk2 promoted the association of phospho-4e-bp1 with hago2. our results implicate deregulated synthesis of e2f1/dp caused by the mirna pathway impairment as a key event in lrrk2 pathogenesis and suggest novel mirna-based therapeutic strategies.",1
"nearly all members of a widespread family of bacterial transposable elements related to insertion sequence 3 (is3), therefore called the is3 family, very likely use programmed -1 ribosomal frameshifting to produce their transposase, a protein required for mobility. comparative analysis of the potential frameshift signals in this family suggested that most of the insertion sequences from the is51 group contain in their mrna an elaborate pseudoknot that could act as a recoding stimulator. it results from a specific intramolecular interaction between an apical loop and an internal loop from two stem-loop structures. directed mutagenesis, chemical probing, and gel mobility assays of the frameshift region of one element from the is51 group, is3411, provided clear evidences of the existence of the predicted structure. modeling was used to generate a three-dimensional molecular representation of the apical loop-internal loop complex. we could demonstrate that mutations affecting the stability of the structure reduce both frameshifting and transposition, thus establishing the biological importance of this new type of rna structure for the control of transposition level.",1
"acute lung injury (ali) is a common complication of sepsis to which patients often succumb due to poor effective pharmacological interventions. recent studies have focused on the potential application of circulating micrornas (mirs or mirnas) as novel prognostic and therapeutic biomarkers. the present study focuses mainly on mir-140, the role of which is poorly understood in the progression of ali. the results of the present study revealed that toll-like receptor 4 (tlr4) expression was upregulated the lungs of rats with ali. meanwhile, serum levels of tumor necrosis factor-α, interleukin (il)-6 and il-1β were significantly increased in rats with ali compared with normal control rats. these data indicated the successful establishment of lps-induced ali. furthermore, mir-140 was decreased in the peripheral blood of patients with ali compared with control subjects. receiver operator characteristic analysis indicated that mir-140 could be used to screen ali patients and distinguish them from healthy controls. mir-140 was demonstrated to be downregulated in the plasma and lungs of rats with ali compared with the normal control group. a dual luciferase reporter assay indicated that tlr4 was a target gene of mir-140. to investigate whether mir-140 exerted its role via tlr4, a specific tlr4-targeting small interfering rna was selected. it was revealed that tlr4 silencing was able to suppress the phosphorylation of nf-κb even in cells transfected with mir-140 inhibitor. in summary, reduced mir-140 expression and increased tlr4 signaling activation may serve a key role in the progression of ali.",1
"organ patterning during embryonic development requires precise temporal and spatial regulation of protein activity. micrornas (mirnas), small noncoding rnas that typically inhibit protein expression, are broadly important for proper development, but their individual functions during organogenesis are largely unknown. we report that mir-138 is expressed in specific domains in the zebrafish heart and is required to establish appropriate chamber-specific gene expression patterns. disruption of mir-138 function led to ventricular expansion of gene expression normally restricted to the atrio-ventricular valve region and, ultimately, to disrupted ventricular cardiomyocyte morphology and cardiac function. temporal-specific knockdown of mir-138 by antagomirs showed mir-138 function was required during a discrete developmental window, 24-34 h post-fertilization (hpf). mir-138 functioned partially by repressing the retinoic acid synthesis enzyme, aldehyde dehydrogenase-1a2, in the ventricle. this activity was complemented by mir-138-mediated ventricular repression of the gene encoding versican (cspg2), which was positively regulated by retinoic-acid signaling. our findings demonstrate that mir-138 helps establish discrete domains of gene expression during cardiac morphogenesis by targeting multiple members of a common pathway, and also establish the use of antagomirs in fish for temporal knockdown of mirna function.",1
"the present study aimed to investigate the expression of microrna (mirna) 26a in blood mononuclear cells and serum in neonatal sepsis, as well as its role in the disease pathogenesis. in total 28 cases of neonatal sepsis were included in the study. the mrna expression levels of mirna-26a and interleukin (il)-6 in the blood mononuclear cells and serum samples were detected by reverse transcription-quantitative polymerase chain reaction. the protein expression of il-6 was detected by western blot analysis and elisa. the in vitro septic environment was simulated by lipopolysaccharide (lps) in thp-1 cells, and the expression of mirna-26a and il-6 were determined. interaction between mirna-26a and il-6 was confirmed by a dual-luciferase reporter assay. compared with the control group, the mrna and protein expression levels of il-6 in the blood mononuclear cells and serum samples from the neonates with sepsis were significantly elevated, while the expression of mirna-26a was significantly decreased. in addition, similar results were observed in the lps-induced septic models in thp-1 cells. furthermore, the results of the dual-luciferase reporter assay demonstrated that il-6 was the direct target of mirna-26a. the expression of il-6 was significantly upregulated in the blood mononuclear cells and serum in neonatal sepsis, which may be associated with the downregulation of mirna-26a. mirna-26a may regulate the disease pathogenesis and immune responses.",1
"ribonuclease p (rnase p) is an essential enzyme required for 5'-maturation of trna. while an rna-free, protein-based form of rnase p exists in eukaryotes, the ribonucleoprotein (rnp) form is found in all domains of life. the catalytic component of the rnp is an rna known as rnase p rna (rpr). eukaryotic rpr genes are typically transcribed by rna polymerase iii (pol iii). here we showed that the rpr gene in drosophila, which is annotated in the intron of a pol ii-transcribed protein-coding gene, lacks signals for transcription by pol iii. using reporter gene constructs that include the rpr-coding intron from drosophila, we found that the intron contains all the sequences necessary for production of mature rpr but is dependent on the promoter of the recipient gene for expression. we also demonstrated that the intron-coded rpr copurifies with rnase p and is required for its activity. analysis of rpr genes in various animal genomes revealed a striking divide in the animal kingdom that separates insects and crustaceans into a single group in which rpr genes lack signals for independent transcription and are embedded in different protein-coding genes. our findings provide evidence for a genetic event that occurred approximately 500 million years ago in the arthropod lineage, which switched the control of the transcription of rpr from pol iii to pol ii.",1
"the postentry restriction of hiv-1 replication in monocytes can be relieved when they differentiate to dendritic cells (dcs) or macrophages. multiple mechanisms have been proposed to interpret the differentiation-dependent susceptibility of monocytes to hiv-1 infection, and the absence of host-cell-encoded essential factors for hiv-1 completing the life cycle may provide an explanation. we have analyzed the gene expression profile in monocytes by mrna microarray and compared it with that of differentiated dcs. we demonstrated that purine-rich element binding protein α (pur-α), a host-cell-encoded ubiquitous, sequence-specific dna- and rna-binding protein, showed inadequate expression in monocytes, and the translation of pur-α mrna was repressed by cell-expressed microrna (mirna). these pur-α-targeted mirnas modulated the differentiation-dependent susceptibility of monocytes/dcs to hiv-1 infection, because rescue of pur-α expression by transfection of mirna inhibitors relieved the restriction of hiv-1 infection in monocytes, and ectopic input of mirna mimics significantly reduced hiv-1 infection of monocyte-derived dcs (mddcs). collectively, our data emphasized that inadequate host factors contribute to hiv-1 restriction in monocytes, and cellular mirnas modulate differentiation-dependent susceptibility of host cells to hiv-1 infection. elaboration of hiv-1 restriction in host cells facilitates our understanding of viral pathogenesis and the search for a new antiviral strategy.",1
"to elucidate the key mirnas and the signalling pathways that are involved in porcine oocyte maturation, we performed a deep sequencing analysis of the mirnas of pig germinal vesicle (gv) oocytes and metaphase ii (mii) oocytes. seven differentially expressed (de) mirnas were identified and the expression levels of mir-21 and mir-27b-3p were further confirmed by qpcr analysis. the target genes of 7 de mirnas were predicted and subjected to pathway analysis. interestingly, fatty acid metabolism and fatty acid biosynthesis were the top two significantly enriched molecular functions during oocyte maturation. heat map, which was built with 7 de mirnas and the enriched the molecular functions, revealed that mir-21, mir-27b-3p, mir-10a-5p and mir-10b-5p were involved in fatty acid metabolism. in particular, the regulatory role of mir-27b-3p on peroxisome proliferator-activated receptor-γ (pparγ) was confirmed by their inversed expression patterns in gv and mii oocytes and luciferase report assays. in addition, we observed that pparγ agonist (rosiglitazone) treatment significantly enhanced porcine oocyte maturation rate and early embryo developmental competent. taken together, our results demonstrated that mir-27b and its target, pparγ, play the vital roles in pig oocyte maturation through regulating the fatty acid metabolism. these data increased our understanding of the regulatory gene networks in porcine oocyte maturation and development.",1
"systemic iron homeostasis is mainly controlled by the liver through synthesis of the peptide hormone hepcidin (encoded by hamp), the key regulator of duodenal iron absorption and macrophage iron release. here we show that the liver-specific microrna mir-122 is important for regulating hamp mrna expression and tissue iron levels. efficient and specific depletion of mir-122 by injection of a locked-nucleic-acid-modified (lna-modified) anti-mir into wt mice caused systemic iron deficiency, characterized by reduced plasma and liver iron levels, mildly impaired hematopoiesis, and increased extramedullary erythropoiesis in the spleen. moreover, mir-122 inhibition increased the amount of mrna transcribed by genes that control systemic iron levels, such as hemochromatosis (hfe), hemojuvelin (hjv), bone morphogenetic protein receptor type 1a (bmpr1a), and hamp. importantly, mir-122 directly targeted the 3′ untranslated region of 2 mrnas that encode activators of hepcidin expression, hfe and hjv. these data help to explain the increased hamp mrna levels and subsequent iron deficiency in mice with reduced mir-122 levels and establish a direct mechanistic link between mir-122 and the regulation of systemic iron metabolism.",1
"polycomb repressive complexes (prc1 and prc2)-mediated epigenetic regulation is critical for maintaining cellular homeostasis. members of polycomb group (pcg) proteins including ezh2, a prc2 component, are upregulated in various cancer types, implicating their role in tumorigenesis. here, we have identified several micrornas (mirnas) that are repressed by ezh2. these mirnas, in turn, regulate the expression of prc1 proteins bmi1 and ring2. we found that ectopic overexpression of ezh2-regulated mirnas attenuated cancer cell growth and invasiveness, and abrogated cancer stem cell properties. importantly, expression analysis revealed an inverse correlation between mirna and prc protein levels in cell culture and prostate cancer tissues. taken together, our data have uncovered a coordinate regulation of prc1 and prc2 activities that is mediated by mirnas.",1
"micrornas are small endogenous noncoding rnas, which post-transcriptionally regulate gene expression. in breast cancer, overexpression of the transmembrane heparan sulfate proteoglycan syndecan-1, a predicted target of the oncomir mir-10b, correlates with poor clinical outcome. to investigate the potential functional relationship of mir-10b and syndecan-1, mda-mb-231 and mcf-7 breast cancer cells were transiently transfected with pre-mir-10b, syndecan-1 sirna or control reagents, respectively. altered cell behavior was monitored by proliferation, migration and invasion chamber assays, and time-lapse video microscopy. mir-10b overexpression induced post-transcriptional downregulation of syndecan-1, as demonstrated by quantitative real-time pcr (qpcr), flow cytometry, and 3'utr luciferase assays, resulting in increased cancer cell migration and matrigel invasiveness. syndecan-1 silencing generated a copy of this phenotype. adhesion to fibronectin and laminin and basal cell proliferation was increased. syndecan-1 coimmunoprecipitated with focal adhesion kinase, which showed increased activation upon syndecan-1 depletion. affymetrix screening and confirmatory qpcr and western blotting analysis of syndecan-1-deficient cells revealed upregulation of atf-2, cox-2, cadherin-11, vinculin, actin γ 2, myl9, transgelin-1, rhoa/c, matrix metalloproteinase 2 (mmp2) and heparanase, and downregulation of aml1/runx1, e-cadherin, cldn1, p21waf/cip, cyclin-dependent kinase 6, tlr-4, pai1/2, collagen1alpha1, jhdm1d, mpp4, mmp9, matrilin-2 and anxa3/a10. video microscopy demonstrated massively increased rho kinase-dependent motility of syndecan-1-depleted cells, which displayed increased filopodia formation. we conclude that syndecan-1 is a novel target of the oncomir mir-10b. rho-gtpase-dependent modulation of cytoskeletal function and downregulation of e-cadherin expression are identified as relevant effectors of the mir-10b-syndecan-1 axis, which emerges as a promising target for the development of new therapeutic approaches for breast cancer.",1
"micrornas (mirnas) regulate mrna stability and translation through the action of the rnai-induced silencing complex. in this study, we systematically identified endogenous mirna target genes by using ago2 immunoprecipitation (ago2-ip) and microarray analyses in two breast cancer cell lines, mcf7 and mda-mb-231, representing luminal and basal-like breast cancer, respectively. the expression levels of ∼70% of the ago2-ip mrnas were increased by drosha or dicer1 knockdown. in addition, integrated analysis of mirna expression profiles, mrna-ago2 interaction, and the 3'-utr of mrnas revealed that >60% of the ago2-ip mrnas were putative targets of the 50 most abundantly expressed mirnas. together, these results suggested that the majority of the ago2-associated mrnas were bona fide mirna targets. functional enrichment analysis uncovered that the ago2-ip mrnas were involved in regulation of cell cycle, apoptosis, adhesion/migration/invasion, stress responses (e.g. dna damage and endoplasmic reticulum stress and hypoxia), and cell-cell communication (e.g. notch and ephrin signaling pathways). a role of mirnas in regulating cell migration/invasion and stress response was further defined by examining the impact of drosha knockdown on cell behaviors. we demonstrated that drosha knockdown enhanced cell migration and invasion, whereas it sensitized cells to cell death induced by suspension culture, glucose depletion, and unfolding protein stress. data from an orthotopic xenograft model showed that drosha knockdown resulted in reduced growth of primary tumors but enhanced lung metastasis. taken together, these results suggest that mirnas collectively function to promote survival of tumor cells under stress but suppress cell migration/invasion in breast cancer cells.",1
"recent studies have revealed the importance of multiple micrornas (mirnas) in promoting tumorigenesis, among which mir-17-92/oncomir-1 exhibits potent oncogenic activity. genomic amplification and elevated expression of mir-17-92 occur in several human b-cell lymphomas, and enforced mir-17-92 expression in mice cooperates with c-myc to promote the formation of b-cell lymphomas. unlike classic protein-coding oncogenes, mir-17-92 has an unconventional gene structure, where one primary transcript yields six individual mirnas. here, we functionally dissected the individual components of mir-17-92 by assaying their tumorigenic potential in vivo. using the emu-myc model of mouse b-cell lymphoma, we identified mir-19 as the key oncogenic component of mir-17-92, both necessary and sufficient for promoting c-myc-induced lymphomagenesis by repressing apoptosis. the oncogenic activity of mir-19 is at least in part due to its repression of the tumor suppressor pten. consistently, mir-19 activates the akt-mtor (mammalian target of rapamycin) pathway, thereby functionally antagonizing pten to promote cell survival. our findings reveal the essential role of mir-19 in mediating the oncogenic activity of mir-17-92, and implicate the functional diversity of mir-17-92 components as the molecular basis for its pleiotropic effects during tumorigenesis.",1
"background a growing body of evidence suggests that micrornas (mirnas) play an important role in cancer diagnosis and therapy. microrna-99a (mir-99a), a potential tumor suppressor, is downregulated in several human malignancies. the expression and function of mir-99a, however, have not been investigated in human renal cell carcinoma (rcc) so far. we therefore examined the expression of mir-99a in rcc cell lines and tissues, and assessed the impact of mir-99a on the tumorigenesis of rcc. methods mir-99a levels in 40 pairs of rcc and matched adjacent non-tumor tissues were assessed by real-time quantitative reverse transcription pcr (qrt-pcr). the rcc cell lines 786-o and os-rc-2 were transfected with mir-99a mimics to restore the expression of mir-99a. the effects of mir-99a were then assessed by cell proliferation, cell cycle, transwell, and colony formation assay. a murine xenograft model of rcc was used to confirm the effect of mir-99a on tumorigenicity in vivo. potential target genes were identified by western blotting and luciferase reporter assay. results we found that mir-99a was remarkably downregulated in rcc and low expression level of mir-99a was correlated with poor survival of rcc patients. restoration of mir-99a dramatically suppressed rcc cells growth, clonability, migration and invasion as well as induced g1-phase cell cycle arrest in vitro. moreover, intratumoral delivery of mir-99a could inhibit tumor growth in murine xenograft models of human rcc. in addition, we also fond that mammalian target of rapamycin (mtor) was a direct target of mir-99a in rcc cells. furthermore, sirna-mediated knockdown of mtor partially phenocopied the effect of mir-99a overexpression, suggesting that the tumor suppressive role of mir-99a may be mediated primarily through mtor regulation. conclusions collectively, these results demonstrate for the first time, to our knowledge, that deregulation of mir-99a is involved in the etiology of rcc partially via direct targeting mtor pathway, which suggests that mir-99a may offer an attractive new target for diagnostic and therapeutic intervention in rcc.",1
"aim to investigate the function and mechanism of mir-133a in gastric cancer (gc) and its relationship with clinicopathological characteristics of gc. methods a total of 105 gc patients who underwent surgical resection as primary treatment were selected for this study. real-time quantitative reverse transcriptase polymerase chain (qrt-pcr) was used to examine the expression levels of mir-133a in human gc and adjacent non-tumor tissues, as well as in gc cell lines (sgc-7901, bgc-823, mgc-803, and ags) and a human gastric mucosal epithelial cell line (ges-1). the biological role of mirna (mir)-133a was assessed in the gc cell lines using mtt, apoptosis, migration and invasion, and colony formation assays, and xenograft tumorigenesis. qrt-pcr and western blot analyses were used to evaluate the potential target gene expression of mir-133a. pearson's correlation was calculated to evaluate the correlation between mir-133a and insulin-like growth factor 1 receptor (igf1r) expression. the regulation of igf1r by mir-133a was verified using the luciferase reporter assay. results in 80% of the 105 gc patients, the mean expression of mir-133a was significantly downregulated in tumor tissues compared with adjacent normal tissues (1.215 ± 0.1477 vs 3.093 ± 0.4104, p conclusion this study suggests that mir-133a is downregulated in gc and functions as a tumor suppressor in vitro and in vivo partly by repressing igf1r.",1
"interactions of host cell factors with rna sequences and structures in the genomes of positive-strand rna viruses play various roles in the life cycles of these viruses. our understanding of the functional rna elements present in norovirus genomes to date has been limited largely to in vitro analysis. however, we recently used reverse genetics to identify evolutionarily conserved rna structures and sequences required for norovirus replication. we have now undertaken a more detailed analysis of rna structures present at the 3' extremity of the murine norovirus (mnv) genome. biochemical data indicate the presence of three stable stem-loops, including two in the untranslated region, and a single-stranded polypyrimidine tract of variable length between mnv isolates, within the terminal stem-loop structure. the well-characterized host cell pyrimidine binding proteins ptb and pcbp bound the 3'-untranslated region via an interaction with this variable sequence. viruses lacking the p(y) tract were viable both in cell culture and upon mouse infection, demonstrating that this interaction was not essential for virus replication. however, competition analysis with wild-type mnv in cell culture indicated that the loss of the p(y) tract was associated with a fitness cost. furthermore, a p(y)-deleted mutant showed a reduction in virulence in the stat1(-/-) mouse model, highlighting the role of rna structures in norovirus pathogenesis. this work highlights how, like with other positive-strand rna viruses, rna structures present at the termini of the norovirus genome play important roles in virus replication and virulence.",1
"background telomerase is a ribonucleoprotein complex whose rna moiety dictates the addition of specific simple sequences onto chromosomes ends. while relevant for certain human genetic diseases, the contribution of the essential telomerase rna to rnp assembly still remains unclear. phylogenetic analyses of vertebrate and ciliate telomerase rnas revealed conserved elements that potentially organize protein subunits for rnp function. in contrast, the yeast telomerase rna could not be fitted to any known structural model, and the limited number of known sequences from saccharomyces species did not permit the prediction of a yeast specific conserved structure. results we cloned and analyzed the complete telomerase rna loci (tlc1) from all known saccharomyces species belonging to the ""sensu stricto"" group. complementation analyses in s. cerevisiae and end mappings of mature rnas ensured the relevance of the cloned sequences. by using phylogenetic comparative analysis coupled with in vitro enzymatic probing, we derived a secondary structure prediction of the saccharomyces cerevisiae tlc1 rna. this conserved secondary structure prediction includes a central domain that is likely to orchestrate dna synthesis and at least two accessory domains important for rna stability and telomerase recruitment. the structure also reveals a potential tertiary interaction between two loops in the central core. conclusions the predicted secondary structure of the tlc1 rna of s. cerevisiae reveals a distinct folding pattern featuring well-separated but conserved functional elements. the predicted structure now allows for a detailed and rationally designed study to the structure-function relationships within the telomerase rnp-complex in a genetically tractable system.",1
"osteosarcoma is the most common primary tumor of the bone. it leads to many deaths because of its rapid proliferation and metastasis. recent studies have shown that micrornas are important gene regulators that are involved in various cancer-related processes. in this study, we found that mir-135b was down-regulated in both osteoscarcoma patient tumor tissues and osteoscarcoma cell lines in comparison to paired adjacent non-tumor bone tissue. we observed that a lower level of mir-135b was associated with metastasis. the ectopic expression of mir-135b markedly suppressed osteoscarcoma cell proliferation, migration, and invasion. conversely, the inhibition of mir-135b expression dramatically accelerated cell proliferation, migration, and invasion. the forced expression of mir-135b in osteosarcoma cells resulted in a significant reduction in the protein level of c-myc and repressed the activity of a luciferase reporter that contained the 3'-untranslated region of the c-myc mrna. these effects were abolished by the mutation of the predicted mir-135b-binding site, which indicates that c-myc may be a mir-135b target gene. moreover, the ectopic expression of c-myc partially reversed the inhibition of cell proliferation and invasion that was caused by mir-135b. these data therefore suggest that mir-135b may function as a tumor suppressor to regulate osteosarcoma cell proliferation and invasion through a mechanism that targets the c-myc oncogene. these findings indicate that mir-135b may play a role in the pathogenesis of osteosarcoma.",1
"despite progress in the determination of mir interactions, their regulatory role in cancer is only beginning to be unraveled. utilizing gene expression data from 27 glioblastoma samples we found that the mere knowledge of physical interactions between specific mrnas and mirs can be used to determine associated regulatory interactions, allowing us to identify 626 associated interactions, involving 128 mirs that putatively modulate the expression of 246 mrnas. experimentally determining the expression of mirs, we found an over-representation of over(under)-expressed mirs with various predicted mrna target sequences. such significantly associated mirs that putatively bind over-expressed genes strongly tend to have binding sites nearby the 3'utr of the corresponding mrnas, suggesting that the presence of the mirs near the translation stop site may be a factor in their regulatory ability. our analysis predicted a significant association between mir-128 and the protein kinase wee1, which we subsequently validated experimentally by showing that the over-expression of the naturally under-expressed mir-128 in glioma cells resulted in the inhibition of wee1 in glioblastoma cells.",1
"clustered regularly interspaced short palindromic repeats (crispr)/crispr-associated (cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using crispr rnas (crrnas) to guide the silencing of invading nucleic acids. we show here that in a subset of these systems, the mature crrna that is base-paired to trans-activating crrna (tracrrna) forms a two-rna structure that directs the crispr-associated protein cas9 to introduce double-stranded (ds) breaks in target dna. at sites complementary to the crrna-guide sequence, the cas9 hnh nuclease domain cleaves the complementary strand, whereas the cas9 ruvc-like domain cleaves the noncomplementary strand. the dual-tracrrna:crrna, when engineered as a single rna chimera, also directs sequence-specific cas9 dsdna cleavage. our study reveals a family of endonucleases that use dual-rnas for site-specific dna cleavage and highlights the potential to exploit the system for rna-programmable genome editing.",1
"huntington disease (hd) is a neurodegenerative disorder caused by expanded cag repeats in the exon1 of huntingtin gene (htt). the mutant htt affects the transcriptional profile of neurons by disrupting the activities of transcriptional machinery and alters expression of many genes. in this study, we identified dysregulated non-coding rnas (ncrnas) in medium spiny neurons of 4-week-old hd model mouse. also, we observed the intracellular localizations of abhd11os and neat1 ncrnas by viewrna in situ hybridization, which could provide more precise detection, suggesting that it is a useful method to investigate the expression changes of genes with low expression levels.",1
"chronic skin inflammation in atopic eczema is associated with elevated expression of proinflammatory genes and activation of innate immune responses in keratinocytes. micrornas (mirnas) are short, single-stranded rna molecules that silence genes via the degradation of target mrnas or inhibition of translation. recent studies have demonstrated that mir-124 is associated with regulation of inflammation factors in several diseases. the aim of this study was to investigate the role of mir-124 in skin inflammation of atopic eczema. we showed that mir-124 expression is decreased in chronic lesional skin of patients with atopic eczema, and could be strongly inhibited by ifn-γ and tnf-α. through western blot, real-time pcr and luciferase assays, we revealed that mir-124 inhibited the expression of p65, a member of nf-κb family which can regulate many factors involved in the immune response and inflammatory reactions, through direct targeting. further, upon ifn-γ or tnf-α stimulation, il8, ccl5 and ccl8 showed to be significantly upregulated by ifn-γ or tnf-α, downregulated by mir-124; the promotive effect of ifn-γ and tnf-α could be partially reversed by mir-124. the levels of il8, ccl5 and ccl8 could be significantly downregulated by p65 knockdown, upregulated by mir-124 inhibition; the suppressive effect of p65 knockdown could be partially reversed by mir-124. moreover, contrary to mir-124, p65, il8, ccl5 and ccl8 mrna expression was upregulated in chronic lesional skin of patients with atopic eczema, and all inversely correlated with mir-124. taken together, our data demonstrate that mir-124 controls nf-κb-dependent inflammatory responses in keratinocytes and chronic skin inflammation in atopic eczema; rescuing mir-124 expression presents a promising strategy for atopic eczema treatment.",1
"regulatory mechanisms of alx/fpr2, the lipoxin a4 receptor, expression have considerable relevance in inflammation resolution. because micrornas (mirs) are emerging as key players in inflammation resolution, here we examined microrna-mediated regulation of alx/fpr2 (lipoxin a4 receptor/formyl peptide receptor 2) expression. by matching data from bioinformatic algorithms, we found 27 mirs predicted to bind the 3'-utr of alx/fpr2. among these, we selected mir-181b because of its link with inflammation. using a luciferase reporter system, we assessed mir-181b binding to alx/fpr2 3'-utr. consistent with this, mir-181b overexpression in human macrophages significantly down-regulated alx/fpr2 protein levels (-25%), whereas mir-181b knockdown gave a significant increase in alx/fpr2 (+60%). mir-181b levels decreased during monocyte to macrophage differentiation (-50%), whereas alx/fpr2 expression increased significantly (+60%). mir-181b overexpression blunted lipoxin a4 (0.1-10 nm)- and resolvin d1 (0.01-10 nm)-stimulated phagocytic activity of macrophages. these results unravel novel regulatory mechanisms of alx/fpr2 expression and ligand-evoked macrophages proresolution responses mediated by mir-181b, thus uncovering novel components of the endogenous inflammation resolution circuits.",1
"micrornas (mirnas) are strongly implicated in cancer but their specific roles and functions in the major cancers have yet to be fully elucidated. in this study, we defined the oncogenic significance and function of mir-95, which we found to be elevated in colorectal cancer (crc) tissues by microarray analysis. evaluation of an expanded crc cohort revealed that mir-95 expression was up-regulated in nearly half of the tumors examined (42/87) compared with the corresponding noncancerous tissues. ectopic overexpression of mir-95 in human crc cell lines promoted cell growth in vitro and tumorigenicity in vivo, whereas rnai-mediated silencing of mir-95 decreased cell growth ratio. mechanistic studies revealed that mir-95 repressed the expression of reporter gene coupled to the 3'-untranslated region of sorting nexin 1 (snx1), whereas mir-95 silencing up-regulated snx1 expression. moreover, mir-95 expression levels correlated inversely with snx1 protein levels in human crc tissues. rnai-mediated knockdown of snx1 phenocopied the proliferation-promoting effect of mir-95, whereas overexpression of snx1 blocked mir-95-induced proliferation of crc cells. taken together, these results demonstrated that mir-95 increases proliferation by directly targeting snx1, defining mir-95 as a new oncogenic mirna in crc.",1
"attenuating the expression of immediate early (ie) proteins is essential for controlling the lytic replication of human cytomegalovirus (hcmv). the human micrornas (hsa-mirs), mir-200b-3p and mir-200c-3p, have been identified to bind the 3'-untranslated region (3'-utr) of the mrna encoding ie proteins. however, whether hsa-mirs can reduce ie72 expression and hcmv viral load or exhibit a crosstalk with the host cellular signaling machinery, most importantly the nf-κb cascade, has not been evaluated. in this study, argonaute-crosslinking and immunoprecipitation-seq revealed that mir-200b-3p and mir-200c-3p bind the 3'-utr of ul123 , which is a gene that encodes ie72. the binding of these mirnas to the 3'-utr of ul123 was verified in transfected cells stably expressing gfp. we used mir-200b-3p/mir-200c-3p mimics to counteract the downregulation of these mirna after acute hcmv infection. this resulted in reduced ie72/ie86 expression and hcmv vl during lytic infection. we determined that ie72/ie86 alone can inhibit the phosphorylation of rela/p65 at the ser 536 residue and that p-ser 536 rela/p65 binds to the major ie promoter/enhancer (miep). the upregulation of mir-200b-3p and mir-200c-3p resulted in the phosphorylation of rela/p65 at ser 536 through the downregulation of ie, and the binding of the resultant p-ser 536 rela/p65 to miep resulted in a decreased production of pro-inflammatory cytokines. overall, mir-200b-3p and mir-200c-3p-together with p-ser 536 rela/p65-can prevent lytic hcmv replication during acute and latent infection.",1
"u14 is a conserved small nucleolar rna (snorna) required for processing of yeast 18s rrna. the presence of two long sequences (13 and 14 nucleotides) with strong complementarity to 18s rrna suggests that u14 base-pairs with pre-rrna. evidence of direct binding was developed by showing that mutations in these u14 elements mimic u14 depletion and that function can be rescued by a compensatory sequence change in 18s rna. the u14 elements are functionally interdependent, indicating that both participate in binding. folding models predict that binding might occur through both rrna elements simultaneously. potential roles of u14 in rrna folding, maturation, and ribosome assembly are discussed. u14 is one of several snornas with long complementarities to rrna and the first snorna in this class shown to interact directly with rrna.",1
"background the 5' end of the rous sarcoma virus (rsv) rna around the primer-binding site forms a series of rna secondary stem/loop structures (u5-ir stem, tpsic interaction region, u5-leader stem) that are required for efficient initiation of reverse transcription. the u5-ir stem and loop also encode the u5 integrase (in) recognition sequence at the level of dna such that this region has overlapping biological functions in reverse transcription and integration. results we have investigated the ability of rsv to tolerate mutations in and around the u5 ir stem and loop. through the use of viral libraries with blocks of random sequence, we have screened for functional mutants in vivo, growing the virus libraries in turkey embryo fibroblasts. the library representing the u5-ir stem rapidly selects for clones that maintain the structure of the stem, and is subsequently overtaken by wild type sequence. in contrast, in the library representing the u5-ir loop, wild type sequence is found after five rounds of infection but it does not dominate the virus pool, indicating that the mutant sequences identified are able to replicate at or near wild type levels. conclusion these results indicate that the region of the rna genome in u5 adjacent to the pbs tolerates much sequence variation even though it is required for multiple biological functions in replication. the in vivo selection method utilized in this study was capable of detecting complex patterns of selection as well as identifying biologically relevant viral mutants.",1
"rationale platelets shed micrornas (mirnas). plasma mirnas change on platelet inhibition. it is unclear whether plasma mirna levels correlate with platelet function. objective to link small rnas to platelet reactivity. methods and results next-generation sequencing of small rnas in plasma revealed 2 peaks at 22 to 23 and 32 to 33 nucleotides corresponding to mirnas and yrnas, respectively. among yrnas, predominantly, fragments of rny4 and rny5 were detected. plasma mirnas and yrnas were measured in 125 patients with a history of acute coronary syndrome who had undergone detailed assessment of platelet function 30 days after the acute event. using quantitative real-time polymerase chain reactions, 92 mirnas were assessed in patients with acute coronary syndrome on different antiplatelet therapies. key platelet-related mirnas and yrnas were correlated with platelet function tests. mir-223 (rp=0.28; n=121; p=0.002), mir-126 (rp=0.22; n=121; p=0.016), and other abundant platelet mirnas and yrnas showed significant positive correlations with the vasodilator-stimulated phosphoprotein phosphorylation assay. yrnas, mir-126, and mir-223 were also among the small rnas showing the greatest dependency on platelets and strongly correlated with plasma levels of p-selectin, platelet factor 4, and platelet basic protein in the population-based bruneck study (n=669). a single-nucleotide polymorphism that facilitates processing of pri-mir-126 to mature mir-126 accounted for a rise in circulating platelet activation markers. inhibition of mir-126 in mice reduced platelet aggregation. mir-126 directly and indirectly affects adam9 and p2y12 receptor expression. conclusions levels of platelet-related plasma mirnas and yrnas correlate with platelet function tests in patients with acute coronary syndrome and platelet activation markers in the general population. alterations in mir-126 affect platelet reactivity.",1
"research has revealed that microrna (mir)‑4500 is downregulated in non‑small cell lung cancer (nsclc), and mir‑4500 suppresses tumor growth by targeting lin‑28 homolog b and nras proto‑oncogene, gtpase. in the present study, it was reported that signal transducer and activator of transcription 3 (stat3) may function as a novel target gene for mir‑4500 in nsclc. the experiments conducted in the present study confirmed that the mir‑4500 expression was decreased in nsclc tissues and cells compared with adjacent normal tissues and a normal lung cell line. mir‑4500 suppressed the cell proliferation, migration, invasion and promoted apoptosis of the human nsclc cell lines a549 and h1975. expression of stat3 was negatively correlated with mir‑4500 expression in vivo. a luciferase reporter assay suggested that mir‑4500 directly targeted the 3' untranslated region of stat3. the tumor inhibition effect of small interfering rna stat3 in a549 and h1975 lines may be partially impaired by a mir‑4500 inhibitor. the results of the present study suggests that mir‑4500 may be a tumor suppressor and a potential therapeutic target in nsclc.",1
"purpose recently, several micrornas (mirnas) were reported to be involved in the modulation of glioma development. the aim of our study was to determine the effect of mir-181d on the growth of glioma and to investigate whether this growth is modulated by targeting k-ras and bcl-2. methods real-time pcr was used to analyze the expression of mir-181d in human glioma samples and glioma cell lines. apoptosis, cell cycle, and proliferation (mtt) assays were performed to assess the phenotypic changes in glioma cells. immunohistochemistry was used to determine the expression of k-ras and bcl-2 in glioma tissues, and a luciferase reporter assay was carried out to confirm whether k-ras and bcl-2 are direct targets of mir-181d. western blotting was used to identify the potential signaling pathways affected glioma cell growth by mir-181d. in vivo, xenograft tumors were examined for an anti-glioma effect of mir-181d. results mir-181d was down-regulated in human glioma samples and up-regulated in transfected glioma cells. ectopic expression of mir-181d suppressed proliferation and triggered cell cycle arrest and apoptosis in glioma cell lines. k-ras and bcl-2 were identified as direct targets of mir-181d and were up-regulated in glioma samples. the results showed evidence linking the tumor suppressor activity of mir-181d in glioma cells with the k-ras-related pi3k/akt and mapk/erk pathways. furthermore, xenograft tumors from mir-181d-treated u251 cells were suppressed in vivo. conclusion mir-181d may act as a glioma suppressor by targeting k-ras and bcl-2.",1
"elastin production is characteristically turned off during the maturation of elastin-rich organs such as the aorta. micrornas (mirnas) are small regulatory rnas that down-regulate target mrnas by binding to mirna regulatory elements (mres) typically located in the 3' utr. here we show a striking up-regulation of mir-29 and mir-15 family mirnas during murine aortic development with commensurate down-regulation of targets including elastin and other extracellular matrix (ecm) genes. there were a total of 14 mres for mir-29 in the coding sequences (cds) and 3' utr of elastin, which was highly significant, and up to 22 mir-29 mres were found in the cds of multiple ecm genes including several collagens. this overrepresentation was conserved throughout mammalian evolution. luciferase reporter assays showed synergistic effects of mir-29 and mir-15 family mirnas on 3' utr and coding-sequence elastin constructs. our results demonstrate that multiple mir-29 and mir-15 family mres are characteristic for some ecm genes and suggest that mir-29 and mir-15 family mirnas are involved in the down-regulation of elastin in the adult aorta.",1
"microrna-132 is markedly downregulated in alzheimer's disease (ad) and related tauopathies, and its levels are closely associated with tau pathology in ad. whether and how mir-132 contributes to pathology in these neurodegenerative diseases remains unclear. here, we show that mir-132 and its paralogue mir-212 directly regulate the expression of neuronal nitric oxide synthase (nos1) through the primate-specific binding site. inhibition of mir-132 in primary human neurons and neural cells leads to increased nos1 levels and triggers excessive production of nitric oxide, followed by aberrant s-nitrosylation (sno) of specific proteins associated with neurodegeneration and tau pathology, such as cyclin-dependent kinase 5, dynamin-related protein 1, and glyceraldehyde-3-phosphate dehydrogenase. this, in turn, increases tau phosphorylation at disease associated ser396, ser404, and ser202 sites, and impairs neural viability. our findings indicate that downregulation of mir-132/212 disturbs the balance of s-nitrosylation and induces tau phosphorylation in a nos1-dependent way, and thereby may contribute to the pathogenesis of ad and other tauopathies.",1
"cellular senescence is a permanent cell cycle arrest triggered by different stimuli. we recently identified up-regulation of microrna (mir)-494 as a component of the genetic program leading to senescence of human diploid imr90 fibroblasts. here, we used 2-dimensional differential gel electrophoresis (2d-dige) coupled to mass spectrometry to profile protein expression changes induced by adoptive overexpression of mir-494 in imr90 cells. mir-494 induced robust perturbation of the imr90 proteome by significantly (p≤0.05) down-regulating a number of proteins. combination of mass spectrometry-based identification of down-regulated proteins and bioinformatic prediction of the mir-494 binding sites on the relevant mrnas identified 26 potential targets of mir-494. among them, computational analysis identified 7 potential evolution-conserved mir-494 targets. functional mir-494 binding sites were confirmed in 3'-untranslated regions (utrs) of 4 of them . their reduced expression correlated with mir-494 up-regulation in senescent cells. rna interference-mediated knockdown of hnrnpa3 and, to a lesser extent, rad23b mirrored the senescent phenotype induced by mir-494 overexpression, blunting cell proliferation and causing up-regulation of sa-β-galactosidase and dna damage. ectopic expression of hnrnpa3 or rad23b slowed the appearance of the senescent phenotype induced by mir-494. overall, these findings identify novel mir-494 direct targets that are involved in cellular senescence.",1
"the platelet-derived growth factor (pdgf) signaling pathway is a critical regulator of animal development and homeostasis. activation of the pdgf pathway leads to neointimal proliferative responses to artery injury; it promotes a switch of vascular smooth muscle cells (vsmc) to a less contractile phenotype by inhibiting the smc-specific gene expression and increasing the rate of proliferation and migration. the molecular mechanism for these pleiotropic effects of pdgfs has not been fully described. here, we identify the microrna-221 (mir-221), a small noncoding rna, as a modulator of the phenotypic change of vsmcs in response to pdgf signaling. we demonstrate that mir-221 is transcriptionally induced upon pdgf treatment in primary vsmcs, leading to down-regulation of the targets c-kit and p27kip1. down-regulation of p27kip1 by mir-221 is critical for pdgf-mediated induction of cell proliferation. additionally, decreased c-kit causes inhibition of smc-specific contractile gene transcription by reducing the expression of myocardin (myocd), a potent smc-specific nuclear coactivator. our study demonstrates that pdgf signaling, by modulating the expression of mir-221, regulates two critical determinants of the vsmc phenotype; they are smc gene expression and cell proliferation.",1
"background in many eukaryotes, micrornas (mirnas) bind to complementary sites in the 3'-untranslated regions (3'-utrs) of target messenger rnas (mrnas) and regulate their expression at the stage of translation. recent studies have revealed that many mirnas are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. we sought to elucidate a set of conserved mirna/target-gene pairs and to analyse the mechanism underlying mirna-mediated gene regulation in the early stage of bilaterian evolution. results initially, we extracted five evolutionarily conserved mirnas (let-7, mir-1, mir-124, mir-125/lin-4, and mir-34) among five diverse bilaterian animals. subsequently, we designed a procedure to predict evolutionarily conserved mirna/target-gene pairs by introducing orthologous gene information. as a result, we extracted 31 orthologous mirna/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous mirna/target-gene pairs that were verified experimentally. approximately 84% of the target genes were regulated by three mirnas (let-7, mir-1, and mir-124) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. we used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in hela cells. conclusions the application of our new method enables the identification of 31 mirna/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. the downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by mirnas; it was also an efficient tool for the elimination of false positives from the predicted candidates. in conclusion, our study identified potentially important mirna-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage mirna functions.",1
"background growing evidence indicates that mir-200c is involved in carcinogenesis and tumor progression in non-small-cell lung cancer (nsclc). however, its precise biological role remains largely elusive. methods the functions of mir-200c and usp25 in migration/invasion and lung metastasis formation were determined by transwell and tail vein injection assays, respectively. the potential regulatory targets of mir-200c were determined by prediction tools, correlation with target protein expression, and luciferase reporter assay. the mrna expression levels of mir-200c and usp25 were examined in nsclc cell lines and patient specimens using quantitative reverse transcription-pcr. the protein expression levels of usp25 were examined in nsclc cell lines and patient specimens using western blot and immunohistochemical staining. results we demonstrated that over-expression of mir-200c inhibited nsclc cells migration, invasion, epithelial-mesenchymal transition (emt) in vitro and lung metastasis formation in vivo. further studies revealed that usp25 was a downstream target of mir-200c in nsclc cells as mir-200c bound directly to the 3'-untranslated region of usp25, thus reducing both the messenger rna and protein levels of usp25. silencing of the usp25 gene recapitulated the effects of mir-200c over-expression. clinical analysis indicated that mir-200c was negatively correlated with clinical stage, lymph node metastasis in nsclc patients. moreover, usp25 protein and mrna level expressions were higher in nsclc patients, compared to healthy control, and correlated with clinical stage and lymphatic node metastasis. conclusions these findings indicate that mir-200c exerts tumor-suppressive effects for nsclc through the suppression of usp25 expression and suggests a new therapeutic application of mir-200c in the treatment of nsclc.",1
"various mirnas play critical roles in the development and progression of solid tumors. in this study, we describe the role of mir-204-5p in limiting growth and progression of breast cancer. in breast cancer tissues, mir-204-5p was significantly downregulated compared with normal breast tissues, and its expression levels were associated with increased survival outcome in patients with breast cancer. overexpression of mir-204-5p inhibited viability, proliferation, and migration capacity in human and murine breast cancer cells. in addition, mir-204-5p overexpression resulted in a significant alteration in metabolic properties of cancer cells and suppression of tumor growth and metastasis in mouse breast cancer models. the association between mir-204-5p expression and clinical outcomes of patients with breast cancer showed a nonlinear pattern that was reproduced in experimental assays of cancer cell behavior and metastatic capacities. transcriptome and proteomic analysis revealed that various cancer-related pathways including pi3k/akt and tumor-immune interactions were significantly associated with mir-204-5p expression. pik3cb, a major regulator of pi3k/akt pathway, was a direct target for mir-204-5p, and the association between pik3cb-related pi3k/akt signaling and mir-204-5p was most evident in the basal subtype. the sensitivity of breast cancer cells to various anticancer drugs including pik3cb inhibitors was significantly affected by mir-204-5p expression. in addition, mir-204-5p regulated expression of key cytokines in tumor cells and reprogrammed the immune microenvironment by shifting myeloid and lymphocyte populations. these data demonstrate both cell-autonomous and non-cell-autonomous impacts of tumor suppressor mir-204-5p in breast cancer progression and metastasis. significance: this study demonstrates that regulation of pi3k/akt signaling by mir-204-5p suppresses tumor metastasis and immune cell reprogramming in breast cancer.",1
"conformational change within the spliceosome is required between the first and second catalytic steps of pre-mrna splicing. a prior genetic screen for suppressors of an intron mutant that stalls between the two steps yielded both prp8 and non-prp8 alleles that suppressed second-step splicing defects. we have now identified the strongest non-prp8 suppressors as alleles of the ntc (prp19 complex) component, cef1. these cef1 alleles generally suppress second-step defects caused by a variety of intron mutations, mutations in u6 snrna, or deletion of the second-step protein factor prp17, and they can activate alternative 3' splice sites. genetic and functional interactions between cef1 and prp8 alleles suggest that they modulate the same event(s) in the first-to-second-step transition, most likely by stabilization of the second-step spliceosome; in contrast, alleles of u6 snrna that also alter this transition modulate a distinct event, most likely by stabilization of the first-step spliceosome. these results implicate a myb-like domain of cef1/cdc5 in interactions that modulate conformational states of the spliceosome and suggest that alteration of these events affects splice site use, resulting in alternative splicing-like patterns in yeast.",1
"current understanding of microrna (mirna) biology is limited, and antisense oligonucleotide (aso) inhibition of mirnas is a powerful technique for their functionalization. to uncover the role of the liver-specific mir-122 in the adult liver, we inhibited it in mice with a 2'-o-methoxyethyl phosphorothioate aso. mir-122 inhibition in normal mice resulted in reduced plasma cholesterol levels, increased hepatic fatty-acid oxidation, and a decrease in hepatic fatty-acid and cholesterol synthesis rates. activation of the central metabolic sensor ampk was also increased. mir-122 inhibition in a diet-induced obesity mouse model resulted in decreased plasma cholesterol levels and a significant improvement in liver steatosis, accompanied by reductions in several lipogenic genes. these results implicate mir-122 as a key regulator of cholesterol and fatty-acid metabolism in the adult liver and suggest that mir-122 may be an attractive therapeutic target for metabolic disease.",1
"an inducible program of inflammatory gene expression is central to antimicrobial defenses. this response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. we have identified a long noncoding rna (lncrna) that acts as a key regulator of this inflammatory response. pattern recognition receptors such as the toll-like receptors induce the expression of numerous lncrnas. one of these, lincrna-cox2, mediates both the activation and repression of distinct classes of immune genes. transcriptional repression of target genes is dependent on interactions of lincrna-cox2 with heterogeneous nuclear ribonucleoprotein a/b and a2/b1. collectively, these studies unveil a central role of lincrna-cox2 as a broad-acting regulatory component of the circuit that controls the inflammatory response.",1
"microrna-27a (mir-27a) is expressed in mcf-7 breast cancer cells, and antisense mir-27a (as-mir-27a) induces zbtb10, a specificity protein (sp) repressor. both as-mir-27a and overexpression of zbtb10 decreased sp1, sp3, and sp4 mrna and protein expression in mcf-7 cells, and this was also accompanied by decreased levels of estrogen receptor alpha (eralpha) mrna and protein. rna interference studies confirmed that basal expression of eralpha was dependent on sp1 but not sp3 or sp4 in mcf-7 cells. as-mir-27a and overexpression of zbtb10 inhibited 17beta-estradiol (e2)-induced transactivation in mcf-7 cells, and this was accompanied by decreased binding of sp and er proteins in cell lysates to oligonucleotides containing gc-rich motifs or estrogen-responsive elements, respectively. as-mir-27a and overexpression of zbtb10 arrested mcf-7 cells in g(0)/g(1) and inhibited e2-induced g(0)/g(1) to s phase progression. as-mir-27a induced only a minimal increase in myt-1, another mir-27a regulated gene, and this was not accompanied by myt-1-dependent g(2)/m arrest as observed previously in er-negative mda-mb-231 breast cancer cells. thus, mir-27a indirectly regulates e2-responsiveness in mcf-7 cells through suppression of zbtb10, thereby enhancing expression of eralpha.",1
"despite great progress for two decades in micrornas (mirnas), the direct regulation of host gene by intragenic (mostly intronic) mirna is conceptually plausible but evidence-limited. here, we report that intronic mir-932 could target its host gene via binding with coding sequence (cds) region rather than regular 3'utr. the conserved mir-932 is embedded in the fourth intron of drosophila neuroligin2 (dnlg2), which encodes a synaptic cell adhesion molecule, dnlg2. in silico analysis predicted two putative mir-932 target sites locate in the cds region of dnlg2 instead of regular 3'-utr mirna binding sites. employing luciferase reporter assay, we further proved that the mir-932 regulates expression of its host gene dnlg2 via the binding cds region of dnlg2. consistently, we observed mir-932 downregulated expression of dnlg2 in s2 cell, and the repression of dnlg2 by mir-932 at both protein and rna level. furthermore, we found cds-located site1 is dominant for regulating expression of host dnlg2 by mir-932. in addition to providing thorough examination of one intronic mirna targeting the cds region of its host gene, our genome-wide analysis indicated that nearly half of fruitfly and human intronic mirnas may target their own host gene at coding region. this study would be valuable in elucidating the regulation of intronic mirna on host gene, and provide new information about the biological context of their genomic arrangements and functions.",1
"micrornas (mirnas) are increasingly implicated in regulating cancer initiation and progression. in this study, two mirnas, mir-25 and -32, are identified as p53-repressed mirnas by p53-dependent negative regulation of their transcriptional regulators, e2f1 and myc. however, mir-25 and -32 result in p53 accumulation by directly targeting mdm2 and tsc1, which are negative regulators of p53 and the mtor (mammalian target of rapamycin) pathway, respectively, leading to inhibition of cellular proliferation through cell cycle arrest. thus, there is a recurrent autoregulatory circuit involving expression of p53, e2f1, and myc to regulate the expression of mir-25 and -32, which are mirnas that, in turn, control p53 accumulation. significantly, overexpression of transfected mir-25 and -32 in glioblastoma multiforme cells inhibited growth of the glioblastoma multiforme cells in mouse brain in vivo. the results define mir-25 and -32 as positive regulators of p53, underscoring their role in tumorigenesis in glioblastoma.",1
"during c. elegans development, the temporal pattern of many cell lineages is specified by graded activity of the heterochronic gene lin-14. here we demonstrate that a temporal gradient in lin-14 protein is generated posttranscriptionally by multiple elements in the lin-14 3'utr that are regulated by the heterochronic gene lin-4. the lin-14 3'utr is both necessary and sufficient to confer lin-4-mediated posttranscriptional temporal regulation. the function of the lin-14 3'utr is conserved between c. elegans and c. briggsae. among the conserved sequences are seven elements that are each complementary to the lin-4 rnas. a reporter gene bearing three of these elements shows partial temporal gradient activity. these data suggest a molecular mechanism for lin-14p temporal gradient formation: the lin-4 rnas base pair to sites in the lin-14 3'utr to form multiple rna duplexes that down-regulate lin-14 translation.",1
"micrornas (mirnas) have recently emerged as regulators of metastasis. we provide insight into the behavior of mir-221 in colorectal cancer (crc) metastasis by showing that mir-221 is significantly upregulated in metastatic crc cell lines and tissues. mir-221 overexpression enhances, whereas mir-221 depletion reduces crc cell migration and invasion in vitro and metastasis in vivo. we identify reck as a direct target of mir-221, reveal its expression to be inversely correlated with mir-221 in crc samples and show that its re-introduction reverses mir-221-induced crc invasiveness. collectively, mir-221 is an oncogenic mirna which may regulate crc migration and invasion through targeting reck.",1
"pancreatic cancer is an aggressive malignancy with an extremely poor prognosis. the human ether-a-go-go-related potassium channel (herg1) is a human rapid delayed rectifier, which is involved in many crucial cellular events. in this article, we find that herg1 expression is dramatically increased both in pancreatic cancer tissues and cell lines, and that increased herg1 expression is significantly related to the development of pancreatic cancer. herg1 silencing in pancreatic cancer-derived cell lines panc-1 and cfpac-1 strongly inhibits their malignant capacity in vitro as well as tumorigenicity and metastasis in nude mice. in addition, herg1 is identified as a direct target of mir-96, which is downregulated in pancreatic cancer tissues and cell lines. ectopic expression of mir-96 represses the herg1 expression in pancreatic cancer and significantly inhibits malignant behavior of pancreatic cancer cells in vitro and in vivo. collectively, our findings suggest that mir-96 acts as a tumor suppressor in pancreatic cancer and may therefore serve as a useful therapeutic target for the development of new anticancer therapy.",1
"hormone-sensitive prostate cancer typically progresses to castration resistant prostate cancer (crpc) after the androgen deprivation therapy. we investigated the impact of micrornas (mirs) in the transition of prostate cancer to crpc. mir-221/-222 was highly expressed in bone metastatic crpc tumor specimens. we previously demonstrated that transient overexpression of mir-221/-222 in lncap promoted the development of the crpc phenotype. in current study, we show that stably overexpressing mir-221 confers androgen independent (ai) cell growth in lncap by rescuing lncap cells from growth arrest at g1 phase due to the lack of androgen. overexpressing of mir-221 in lncap reduced the transcription of a subgroup of androgen-responsive genes without affecting the androgen receptor (ar) or ar-androgen integrity. by performing systematic biochemical and bioinformatical analyses, we identified two mir-221 targets, hectd2 and rab1a, which could mediate the development of crpc phenotype in multiple prostate cancer cell lines. downregulation of hectd2 significantly affected the androgen-induced and ar-mediated transcription, and downregulation of hectd2 or rab1a enhances ai cell growth. as a result of the elevated expression of mir-221, expression of many cell cycle genes was altered and pathways promoting epithelial to mesenchymal transition/tumor metastasis were activated. we hypothesize that a major biological consequence of upregulation of mir-221 is reprogramming of ar signaling, which in turn may mediate the transition to the crpc phenotype.",1
"a low-grade proinflammatory state contributes to the metabolic syndrome (ms). adiponectin (apn), which is reduced in the ms, has emerged as a master regulator of inflammation/immunity. we wanted to identify whether micrornas (mirnas) may mediate the antiinflammatory action of apn on adipose tissue (at). mirna expression profiling was performed in mice overexpressing apn specifically in at and in wild-type controls. the role of specific mirnas was analyzed by gain- or loss-of function approaches in 3t3-f442a (pre)-adipocytes and in de novo at formed from engineered 3t3-f442a preadipocytes transplanted in nude mice. mirna expression was compared in the omental at of lean and obese subjects. the expression of mir532-5p and mir1983 was down-regulated, whereas that of mir883b-5p and mir1934 was up-regulated in at of mice overexpressing apn specifically in at. we focused on mir883b-5p identified by computational analysis as being involved in inflammatory pathways. mir883b-5p overexpression down-regulated the lipopolysaccharide-binding protein (lbp) in 3t3-f442a cells, whereas mir883b-5p blockade had reverse effects. lbp aids in lipopolysaccharide binding to toll-like receptor-4. mir883b-5p blockade also abolished the protective effects of apn on proinflammatory adipokine induction. these data were recapitulated in the de novo at in which mir883b-5p silencing induced lbp production and tissue inflammation. eventually mir883b-5p expression was down-regulated in at of obese subjects. we identified several novel mirnas that are regulated by apn in at in vivo. mir883b-5p, which is up-regulated by apn represses lbp and toll-like receptor-4 signaling, acting therefore as a major mediator of the antiinflammatory action of apn. these novel mirnas may open new therapeutic perspectives for the ms.",1
"dysregulated micrornas (mirnas) have an important role in many malignant tumors. however, elucidating the roles of mirnas in cancer biology, especially in epithelial cancers, remains an ongoing process. in this study, we show that both mir-143 and mir-145, which belong to the same mirna cluster, can negatively modulate expression of their target gene, mdm2. the mir-143 and mir-145 is posttranscriptionally activated by upregulated p53, thereby generating a short mirnas-mdm2-p53 feedback loop. re-expression of these mirnas suppresses cellular growth and triggers the apoptosis of epithelial cancer, in vitro and in vivo, by enhancing p53 activity via mdm2 turnover. moreover, the mirna-dependent mdm2 turnover contributes to the equilibrium of repeated p53 pulses in response to dna damage stress. these findings suggest that mdm2 dysregulation caused by downregulation of mir-143 and mir-145 contributes to epithelial cancer development and has a key role in regulating cellular proliferation and apoptosis. re-expression of mir-143 and mir-145 may be a reasonable strategy for treatment of epithelial cancers.",1
"several essential biological progresses in mammals are regulated by circadian rhythms. though the molecular mechanisms of oscillating these circadian rhythms have been uncovered, the specific functions of the circadian genes are not very clear. it has been reported that knocking down circadian genes by microrna is a useful strategy to explore the function of the circadian rhythms. in this study, through a forward bioinformatics screening approach, we identified mir-29a/b/c as potent inhibitors for the human circadian gene hper1. we further found that mir-29a/b/c could directly target hper1 3'untranslated region (utr) and down-regulate hper1 at both mrna and protein expression levels in human a549 cells. thus, our findings suggested that the expression of hper1 is regulated by mir-29a/b/c, which may also provide a new clue for the function of hper1.",1
"members of the slit family of secreted ligands interact with roundabout (robo) receptors to provide guidance cues for many cell types. for example, slit/robo signaling elicits repulsion of axons during neural development, whereas in endothelial cells this pathway inhibits or promotes angiogenesis depending on the cellular context. here, we show that mir-218 is intronically encoded in slit2 and slit3 and that it suppresses robo1 and robo2 expression. our data indicate that mir-218 and multiple slit/robo signaling components are required for heart tube formation in zebrafish and that this network modulates the previously unappreciated function of vegf signaling in this process. these findings suggest a new paradigm for microrna-based control of ligand-receptor interactions and provide evidence for a novel signaling pathway regulating vertebrate heart tube assembly.",1
"micrornas (mirnas) are small non-coding rnas that negatively regulate gene expression at post-transcriptional level. mirna dysregulation plays a causal role in cancer progression. in this study, mir-208-3p was highly expressed and directly repressed arid2 expression. as a result, arid2 expression in hepatocellular carcinoma (hcc) was decreased. in vitro, mir-208-3p down-regulation and arid2 over-expression elicited similar inhibitory effects on hcc cell proliferation and invasion. in vivo test results revealed that mir-208-3p down-regulation inhibited hcc tumorigenesis in hep3b cells. moreover, arid2 was possibly a downstream element of transforming growth factor beta1 (tgfβ1)/mir-208-3p/arid2 regulatory pathway. these findings suggested that mir-208-3p up-regulation is associated with hcc cell progression and may provide a new target for liver cancer treatment.",1
"fragile x syndrome is the most common form of inherited mental retardation caused by loss of the fragile x mental retardation protein 1 (fmrp). the detailed molecular pathways underlying the pathogenesis of this disorder remain incompletely understood. here, we show that mir-124a, a nervous-system-specific mirna, is associated with the drosophila homolog of fmrp (dfmr1) in vivo. ectopic expression of wild-type but not mutant mir-124a precursors decreased dendritic branching of dendritic arborization sensory neurons, which was partially rescued by the loss of dfmr1 activity, suggesting that the biogenesis and/or function of mir-124a are partially dependent on dfmr1. indeed, in contrast with the complete loss of mature mir-124a in dicer-1 mutants, steady-state levels of endogenous or ectopically expressed mature mir-124a were partially reduced in dfmr1 mutants, whereas the level of pre-mir-124a increased. this effect could be explained in part by the reduced abundance of the dicer-1-ago1 complex in the absence of dfmr1. these findings suggest a modulatory role for dfmr1 to maintain proper levels of mirnas during neuronal development.",1
"the epstein-barr virus (ebv) is an oncogenic human herpes virus found in ∼15% of diffuse large b-cell lymphoma (dlbcl). ebv encodes mirnas and induces changes in the cellular mirna profile of infected cells. mirnas are small, non-coding rnas of ∼19-26 nt which suppress protein synthesis by inducing translational arrest or mrna degradation. here, we report a comprehensive mirna-profiling study and show that hsa-mir-424, -223, -199a-3p, -199a-5p, -27b, -378, -26b, -23a, -23b were upregulated and hsa-mir-155, -20b, -221, -151-3p, -222, -29b/c, -106a were downregulated more than 2-fold due to ebv-infection of dlbcl. all known ebv mirnas with the exception of the bhrf1 cluster as well as ebv-mir-bart15 and -20 were present. a computational analysis indicated potential targets such as c-myb, lats2, c-ski and siah1. we show that c-myb is targeted by mir-155 and mir-424, that the tumor suppressor siah1 is targeted by mir-424, and that c-ski is potentially regulated by mir-155. downregulation of siah1 protein in dlbcl was demonstrated by immunohistochemistry. the inhibition of siah1 is in line with the notion that ebv impedes various pro-apoptotic pathways during tumorigenesis. the down-modulation of the oncogenic c-myb protein, although counter-intuitive, might be explained by its tight regulation in developmental processes.",1
"several mrna aptamers have been identified in mesoplasma florum that have sequence and structural features resembling those of guanine and adenine riboswitches. two features distinguish these rnas from established purine-sensing riboswitches. all possess shortened hairpin-loop sequences expected to alter tertiary contacts known to be critical for aptamer folding. the rnas also carry nucleotide changes in the core of each aptamer that otherwise is strictly conserved in guanine and adenine riboswitches. some aptamers retain the ability to selectively bind guanine or adenine despite these mutations. however, one variant type exhibits selective and high-affinity binding of 2'-deoxyguanosine, which is consistent with its occurrence in the 5' untranslated region of an operon containing ribonucleotide reductase genes. the identification of riboswitch variants that bind nucleosides and reject nucleobases reveals that natural metabolite-sensing rna motifs can accrue mutations that expand the diversity of ligand detection in bacteria.",1
"nat10 is an essential enzyme that catalyzes n4-acetylcytidine (ac4c) in eukaryotic transfer rna and 18s ribosomal rna. recent studies suggested that rrna acetylation is dependent on snord13, a box c/d small nucleolar rna predicted to base-pair with 18s rrna via two antisense elements. however, the selectivity of snord13-dependent cytidine acetylation and its relationship to nat10's essential function remain to be defined. here, we demonstrate that snord13 is required for acetylation of a single cytidine of human and zebrafish 18s rrna. in-depth characterization revealed that snord13-dependent ac4c is dispensable for human cell growth, ribosome biogenesis, translation and development. this loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rrna acetylation 'machinery' that led to the characterization of many novel metazoan snord13 genes. this includes an atypical snord13-like rna in drosophila melanogaster which guides ac4c to 18s rrna helix 45 despite lacking one of the two rrna antisense elements. finally, we discover that caenorhabditis elegans 18s rrna is not acetylated despite the presence of an essential nat10 homolog. our findings shed light on the molecular mechanisms underlying snord13-mediated rrna acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rrna modification.",1
"micrornas (mirnas) were recently reported to play an important role in the pathogenesis of pulmonary arterial hypertension (pah), but it is not clear which mirnas are important or what pathways are involved in the process. because hypoxia is an important stimulus for human pulmonary artery smooth muscle cell (hpasmc) proliferation and pah, we performed mirna microarray assays in hypoxia-treated and control hpasmc. we found that mir-210 is the predominant mirna induced by hypoxia in hpasmc. induction of mir-210 was also observed in whole lungs of mice with chronic hypoxia-induced pah. we found that transcriptional induction of mir-210 in hpasmc is hypoxia-inducible factor-1α dependent. inhibition of mir-210 in hpasmc caused a significant decrease in cell number due to increased apoptosis. we found that mir-210 appears to mediate its antiapoptotic effects via the regulation of transcription factor e2f3, a direct target of mir-210. our results have identified mir-210 as a hypoxia-inducible mirna both in vitro and in vivo, which inhibits pulmonary vascular smooth muscle cell apoptosis in hypoxia by specifically repressing e2f3 expression.",1
"background the prognosis of non-small-cell lung cancer (nsclc) is poor yet mechanistic understanding and therapeutic options remain limited. we investigated the biological and clinical significance of microrna-130b and its relationship with apoptosis in nsclc. methods the level of microrna-130b in relationship with the expression of pparγ, vegf-a, bcl-2 and apoptosis were analyzed in 91 lung cancer patient samples using immunohistochemistry and terminal deoxynucleotidyl transferase dutp nick end labeling (tunel) assay on tissue microarrays. gain and loss-of-function studies were performed to investigate the effects of microrna-130b, peroxisome proliferator-activated receptor γ (pparγ) or vascular endothelial growth factor-a (vegf-a) on biological functions of lung cancer cells using in vitro and in vivo approaches. results microrna-130b up-regulation conferred unfavorable prognosis of lung cancer patients. notably, microrna-130b targeted pparγ and inhibiting microrna-130b markedly repressed proliferation, invasion and metastasis of lung cancer cells, leading to increased apoptosis. microrna-130b-dependent biologic effects were due to suppression of pparγ that in turn activated bcl-2, the key mediator of anti-apoptosis. administration of microrna-130b mimic to mouse xenografts promoted tumor growth. in vitro and in vivo, mir-130b enrichment associated with down-regulation of pparγ, up-regulation of vegf-a and bcl-2, and decreased apoptosis. conclusions the present study demonstrates that microrna-130b promotes lung cancer progression via pparγ/vegf-a/bcl-2-mediated suppression of apoptosis. targeting microrna-130b might have remarkable therapeutic potential for lung cancer therapy.",1
"many bacteria contain an ortholog of the ro autoantigen, a ring-shaped protein that binds noncoding rnas (ncrnas) called y rnas. in the only studied bacterium, deinococcus radiodurans, the ro ortholog rsr functions in heat-stress-induced ribosomal rna (rrna) maturation and starvation-induced rrna decay. however, the mechanism by which this conserved protein and its associated ncrnas act has been obscure. we report that rsr and the exoribonuclease polynucleotide phosphorylase (pnpase) form an rna degradation machine that is scaffolded by y rna. single-particle electron microscopy, followed by docking of atomic models into the reconstruction, suggests that rsr channels single-stranded rna into the pnpase cavity. biochemical assays reveal that rsr and y rna adapt pnpase for effective degradation of structured rnas. a ro ortholog and ncrna also associate with pnpase in salmonella typhimurium. our studies identify another ribonucleoprotein machine and demonstrate that ncrna, by tethering a protein cofactor, can alter the substrate specificity of an enzyme.",1
"mirnas associate with argonaute (ago) proteins to silence the expression of mrna targets by inhibiting translation and promoting deadenylation, decapping, and mrna degradation. a current model for silencing suggests that agos mediate these effects through the sequential recruitment of gw182 proteins, the ccr4-not deadenylase complex and the translational repressor and decapping activator ddx6. an alternative model posits that agos repress translation by interfering with eif4a function during 43s ribosomal scanning and that this mechanism is independent of gw182 and the ccr4-not complex in drosophila melanogaster here, we show that mirnas, agos, gw182, the ccr4-not complex, and ddx6/me31b repress and degrade polyadenylated mrna targets that are translated via scanning-independent mechanisms in both human and dm cells. this and additional observations indicate a common mechanism used by these proteins and mirnas to mediate silencing. this mechanism does not require eif4a function during ribosomal scanning.",1
"delta-like 4 (dll4), a membrane-bound ligand belonging to the notch signaling family, plays a fundamental role in vascular development and angiogenesis. we identified a conserved microrna family, mir-30, which targets dll4. overexpression of mir-30b in endothelial cells led to increased vessel number and length in an in vitro model of sprouting angiogenesis. microinjection of mir-30 mimics into zebrafish embryos resulted in suppression of dll4 and subsequent excessive sprouting of intersegmental vessels and reduction in dorsal aorta diameter. use of a target protector against the mir-30 site within the dll4 3'utr up-regulated dll4 and synergized with vegfa signaling knockdown to inhibit angiogenesis. furthermore, restoration of mir-30b or mir-30c expression during kaposi sarcoma herpesvirus (kshv) infection attenuated viral induction of dll4. together these results demonstrate that the highly conserved molecular targeting of dll4 by the mir-30 family regulates angiogenesis.",1
"micrornas (mirnas) regulate gene expression by guiding argonaute proteins to specific target mrna sequences. identification of bona fide mirna target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between mirna and target as well as the location of functional binding sites within mrnas. here we present the results of a comprehensive strategy aimed at isolating endogenous mrna target sequences bound by the argonaute protein alg-1 in c. elegans. using cross-linking and alg-1 immunoprecipitation coupled with high-throughput sequencing (clip-seq), we identified extensive alg-1 interactions with specific 3' untranslated region (utr) and coding exon sequences and discovered features that distinguish mirna complex binding sites in 3' utrs from those in other genic regions. furthermore, our analyses revealed a striking enrichment of argonaute binding sites in genes important for mirna function, suggesting an autoregulatory role that may confer robustness to the mirna pathway.",1
"the metastastic cascade is a complex process that is regulated at multiple levels in prostate cancer (pca). recent evidence suggests that micrornas (mirnas) are involved in pca metastasis and hold great promise as therapeutic targets. in this study, we found that mir-573 expression is significantly lower in metastatic tissues than matched primary pca. its downregulation is correlated with high gleason score and cancer-related mortality of pca patients (p = 0.041, kaplan-meier analysis). through gain- and loss-of function experiments, we demonstrated that mir-573 inhibits pca cell migration, invasion and tgf-β1-induced epithelial-mesenchymal transition (emt) in vitro and lung metastasis in vivo. mechanistically, mir573 directly targets the fibroblast growth factor receptor 1 (fgfr1) gene. knockdown of fgfr1 phenocopies the effects of mir-573 expression on pca cell invasion, whereas overexpression of fgfr1 partially attenuates the functions of mir-573. consequently, mir-573 modulates the activation of fgfr1-downstream signaling in response to fibroblast growth factor 2 (fgf2). importantly, we showed that gata3 directly increases mir-573 expression, and thus down-regulates fgfr1 expression, emt and invasion of pca cells in a mir-573-dependent manner, supporting the involvement of gata3, mir-573 and fgfr1 in controlling the emt process during pca metastasis. altogether, our findings demonstrate a novel mechanism by which mir-573 modulates emt and metastasis of pca cells, and suggest mir-573 as a potential biomarker and/or therapeutic target for pca management.",1
"chemotherapy has improved the survival of patients with gastric cancer by unknown mechanisms. in this study, we showed that cisplatin and docetaxel used in gastric cancer treatment increase the expression of mirna-29 (mir-29) family members and decrease the expression of their oncogenic targets, mediating a significant part of the efficacious benefits of these chemotherapeutic agents. in particular, patients with gastric cancer who experienced recurrences after chemotherapy tended to exhibit low levels of mir-29c expression in their tumors, suggesting that mir-29c activation may contribute to the chemotherapeutic efficacy. enforced expression of mir-29s in gastric cancer cells inhibited cell invasion in vitro and in vivo by directly targeting catenin-δ (ctnnd1). drug treatment suppressed gastric cancer cell invasion by restoring mir-29c-mediated suppression of catenin-δ and rhoa signaling. in parallel, drug treatment also activated several tumor-suppressive mirnas, thereby decreasing expression of their oncogenic effector targets. overall, our findings defined a global mechanism for understanding the efficacious effects of cytotoxic chemotherapy in gastric cancer.",1
"purpose to investigate expression, regulation, potential role and targets of mir-195 and mir-497 in breast cancer. experimental design the expression patterns of mir-195 and mir-497 were initially examined in breast cancer tissues and cell lines by northern blotting and quantitative real-time pcr. combined bisulfite restriction analysis and bisulfite sequencing were carried out to study the dna methylation status of mir-195 and mir-497 genes. breast cancer cells stably expressing mir-195 and mir-497 were established to study their role and targets. finally, normal, fibroadenoma and breast cancer tissues were employed to analyze the correlation between mir-195/497 levels and malignant stages of breast tumor tissues. results mir-195 and mir-497 were significantly downregulated in breast cancer. the methylation state of cpg islands upstream of the mir-195/497 gene was found to be responsible for the downregulation of both mirnas. forced expression of mir-195 or mir-497 suppressed breast cancer cell proliferation and invasion. raf-1 and ccnd1 were identified as novel direct targets of mir-195 and mir-497. mir-195/497 expression levels in clinical specimens were found to be correlated inversely with malignancy of breast cancer. conclusions our data imply that both mir-195 and mir-497 play important inhibitory roles in breast cancer malignancy and may be the potential therapeutic and diagnostic targets.",1
"precise regulation of the formation, maintenance, and remodeling of the vasculature is required for normal development, tissue response to injury, and tumor progression. how specific micrornas intersect with and modulate angiogenic signaling cascades is unknown. here, we identified micrornas that were enriched in endothelial cells derived from mouse embryonic stem (es) cells and in developing mouse embryos. we found that mir-126 regulated the response of endothelial cells to vegf. additionally, knockdown of mir-126 in zebrafish resulted in loss of vascular integrity and hemorrhage during embryonic development. mir-126 functioned in part by directly repressing negative regulators of the vegf pathway, including the sprouty-related protein spred1 and phosphoinositol-3 kinase regulatory subunit 2 (pik3r2/p85-beta). increased expression of spred1 or inhibition of vegf signaling in zebrafish resulted in defects similar to mir-126 knockdown. these findings illustrate that a single mirna can regulate vascular integrity and angiogenesis, providing a new target for modulating vascular formation and function.",1
"gastric cancer is the fourth most common malignancy in the world. although microrna-200 (mir-200) family members are thought to play roles in tumorigenesis, their functions in carcinogenesis are tumor specific, and the underlying mechanism of action still remains elusive. few studies to date have addressed the dysregulation and function of mir-200 family members in gastric cancer progression. here, we report that the mir-200 family members, mir-200c and mir-141, were significantly downregulated in gastric cancer specimens and gastric cancer cell lines. importantly, on clinical samples, the expression of mir-200c and mir-141 was inversely correlated with tnm stage, tumor invasion depth (t), tumor embolus and disease-free survival. wound-healing assay results showed that co-transfected mir-200c/141 could inhibit the migration and invasion capability of the gastric cell line sgc-7901. we also found that mir-200c and mir-141 directly targeted zinc finger e-box-binding homeobox 1/2 (zeb1/2) and upregulated e-cadherin expression. in specimens from gastric cancer patients, reduced expression of mir-200c/141 was associated with increased expression of zeb1 and/or zeb2. in addition, the downregulation of mir-200c and mir-141 was found to be due to a highly methylated cpg island located upstream of their genomic sequence and/or upregulated tgf-β signaling. treatment with the chemotherapeutic agent decitabine, a known dna methyltransferase inhibitor, increased mir-200c/141 expression and ameliorated decreased expression of mir-200c/141 induced by tgf-β in sgc-7901 cells. our study revealed that mir-200c/141 was downregulated by cpg island methylation and tgf-β signaling, which decreased zeb1/2 expression and increased e-cadherin expression to inhibit migration and invasion of gastric cancer cells and provides powerful evidence for the application of decitabine in gastric cancer treatment.",1
"neuron-enriched micrornas (mirnas), mir-9/9* and mir-124 (mir-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing antineurogenic genes. how these mirnas function after the repression of fibroblast genes for neuronal fate remains unclear. here, we identified targets of mir-9/9*-124 as reprogramming cells activate the neuronal program and reveal the role of mir-124 that directly promotes the expression of its target genes associated with neuronal development and function. the mode of mir-124 as a positive regulator is determined by the binding of both ago and a neuron-enriched rna-binding protein, elavl3, to target transcripts. although existing literature indicates that mirna-elavl family protein interaction can result in either target gene up-regulation or down-regulation in a context-dependent manner, we specifically identified neuronal elavl3 as the driver for mir-124 target gene up-regulation in neurons. in primary human neurons, repressing mir-124 and elavl3 led to the down-regulation of genes involved in neuronal function and process outgrowth and cellular phenotypes of reduced inward currents and neurite outgrowth. our results highlight the synergistic role between mir-124 and rna-binding proteins to promote target gene regulation and neuronal function.",1
"objective defects in angiogenesis/vasculogenesis or vessel repair are major complications of coronary artery disease (cad). endothelial progenitor cells (epcs) play a fundamental role in postnatal vascular repair and cad. the role of micrornas in cad pathogenesis and their potential as biomarkers remain to be elucidated. approach and results microrna-31 (mir-31) level in both the plasma and epcs of patients with cad is found lower. mir-31 regulates epc activities by targeting fat atypical cadherin 4 and thromboxane a2 receptor, which show increased expression in cad epcs. overexpressing mir-31 in cad epcs rescued their angiogenic and vasculogenic abilities both in vitro and in vivo. when exploring approaches to restore endogenous mir-31, we found that far-infrared treatment enhanced the expression of not only mir-31, but also mir-720 in cad epcs. mir-720, which was also decreased in epcs and the plasma of patients with cad, stimulated epc activity by targeting vasohibin 1. the mir720-vasohibin 1 pair was shown to be downstream of fat atypical cadherin 4, but not of thromboxane a2 receptor. fat atypical cadherin 4 inhibited mir-720 expression via repression of the planar cell polarity signaling gene four-jointed box 1 (fjx1), which was required for mir-720 expression through a hypoxia-inducible factor 1, α subunit-dependent mechanism. restoring mir-720 level strengthened activity of cad epcs. the mir-31-mir-720 pathway is shown critical to epc activation and that downregulation of this pathway contributes to cad pathogenesis. circulating levels of mir-31, mir-720, and vasohibin 1 have the potential to allow early diagnosis of cad and to act as prognosis biomarkers for cad and other epc-related diseases. conclusions manipulating the expression of the mir-31-mir-720 pathway in malfunction epcs should help develop novel therapeutic modalities.",1
"regulation of the transcription factor tcf8 (zeb1) by the microrna mir-200c and was first identified using a bioinformatic and relative quantitative pcr based approach.(1) using stable ectopic expression of mir-200c we then demonstrated loss of tcf8 (zeb1) mrna and restoration of its primary regulatory target, e-cadherin.(2) recently, other members of the mir-200 'family' and an additional unrelated microrna, mir-205, have been reported to be essential for the regulation of tcf8 (zeb1) and restoration of e-cadherin.(3-5) to investigate, we repeated our initial method(s) and generated individual stable cell-lines, expressing the mir-200 'family' members; mir-200c, mir-200b, mir-141 and the related mir-205. of these lines, mir-200b produced no mature transcript and mir-205 and mir-141 cells were either morphologically similar to controls or showed some slight changes respectively. however no reduction in tcf8/zeb1 mrna or restoration of e-cadherin could be detected in either line. in contrast, cells expressing mir-200c had a significantly altered morphology from mesenchymal to epithelial and restored expression of e-cadherin. these contrasting findings demonstrate that, as transient transfection is in essence an rnai experiment, results should be treated with caution when investigating micrornas and that an examination of micrornas with similar seed regions requires stable ectopic expression to accurately reflect the endogenous mechanism(s).",1
"the expression of eukaryotic antizyme genes requires +1 translational frameshifting. the frameshift in decoding most vertebrate antizyme mrnas is stimulated by an rna pseudoknot 3' of the frameshift site. although the frameshifting event itself is conserved in a wide variety of organisms from yeast to mammals, until recently no corresponding 3' rna pseudoknot was known in invertebrate antizyme mrnas. a pseudoknot, different in structure and origin from its vertebrate counterparts, is now shown to be encoded by the antizyme genes of distantly related invertebrates. identification of the 3' frameshifting stimulator in intermediate species or other invertebrates remains unresolved.",1
"micrornas (mirnas) are small noncoding endogenous rnas, typically 21-23 nucleotides long, that regulate gene expression, usually post-transcriptionally, by binding to the 3'-utr of target mrna, thus blocking translation. the expression of several mirnas is significantly altered during cardiac hypertrophy, myocardial ischemia, fibrosis, heart failure, and other cardiac myopathies. recent studies have implicated mirna-9 (mir-9) in myocardial hypertrophy. however, a detailed mechanism remains obscure. in this study, we have addressed the roles of mir-9 in muscle development and function using a genetically tractable model system, the indirect flight muscles (ifms) of drosophila melanogaster bioinformatics analysis identified 135 potential mir-9a targets, of which 27 genes were associated with drosophila muscle development. troponin-t (tnt) was identified as major structural gene target of mir-9a. we show that flies overexpressing mir-9a in the ifms have abnormal wing position and are flightless. these flies also exhibit a loss of muscle integrity and sarcomeric organization causing an abnormal muscle condition known as ""hypercontraction."" additionally, mir-9a overexpression resulted in the reduction of tnt protein levels while transcript levels were unaffected. furthermore, muscle abnormalities associated with mir-9a overexpression were completely rescued by overexpression of tnt transgenes which lacked the mir-9a binding site. these findings indicate that mir-9a interacts with the 3'-utr of the tnt mrna and downregulates the tnt protein levels by translational repression. the reduction in tnt levels leads to a cooperative downregulation of other thin filament structural proteins. our findings have implications for understanding the cellular pathophysiology of cardiomyopathies associated with mir-9 overexpression.",1
"micrornas (mirnas) represent a class of small non-coding rnas regulating gene expression by inducing rna degradation or interfering with translation. aberrant mirna expression has been described for several human malignancies. herein, we show that mir-145 is down-regulated in human cancer cell line mcf-7 when compared to normal human mammary epithelial cell line mcf10a. overexpression of mir-145 by plasmid inhibits mcf-7 cell growth and induces apoptosis. subsequently, rtkn is identified as a potential mir-145 target by bioinformatics. using reporter constructs, we show that the rtkn 3' untranslated region (3'utr) carries the directly binding site of mir-145. additionally, overexpression of mir-145 in mcf-7 reduces rtkn protein expression as well as mrna level. furthermore, down-regulation of rtkn by sirna can inhibit mcf-7 cell growth. taken together, we propose that loss of mir-145 may provide a selective growth advantage for mcf-7 by targeting rtkn.",1
"micrornas (mirnas) are increasingly implicated in regulating the malignant progression of cancer. here we show that mir-9, which is upregulated in breast cancer cells, directly targets cdh1, the e-cadherin-encoding messenger rna, leading to increased cell motility and invasiveness. mir-9-mediated e-cadherin downregulation results in the activation of beta-catenin signalling, which contributes to upregulated expression of the gene encoding vascular endothelial growth factor (vegf); this leads, in turn, to increased tumour angiogenesis. overexpression of mir-9 in otherwise non-metastatic breast tumour cells enables these cells to form pulmonary micrometastases in mice. conversely, inhibiting mir-9 by using a 'mirna sponge' in highly malignant cells inhibits metastasis formation. expression of mir-9 is activated by myc and mycn, both of which directly bind to the mir-9-3 locus. significantly, in human cancers, mir-9 levels correlate with mycn amplification, tumour grade and metastatic status. these findings uncover a regulatory and signalling pathway involving a metastasis-promoting mirna that is predicted to directly target expression of the key metastasis-suppressing protein e-cadherin.",1
"mutations in mitochondrial trna genes can produce alterations in trna structure resulting in defective mitochondrial protein synthesis and hence respiratory defects. such defects are often at the origin of neurodegenerative diseases in humans and can be easily studied in yeast since respiratory deficient mutants are viable. several nuclear encoded trna interactors have been shown to rescue the mitochondrial defects due to mutations in mitochondrial trnas. among these, we have identified the gene for the mitochondrial protein synthesis elongation factor ef-tu and the specific mt aminoacyl-trna synthetases. we also observed that the respiratory defects and the effect of the tuf1 over-expression were strongly strain dependent. the importance of the nuclear background in which the mitochondrial mutation is expressed was investigated by changing the nuclear context. finally, we demonstrated, using the rt-pcr method, the existence of significantly variable levels of the tuf1 transcript among strains with functional and dysfunctional mitochondria.",1
"micrornas are dysregulated in a setting of heart disease and have emerged as promising therapeutic targets. microrna-34 family members (mir-34a, -34b, and -34c) are up-regulated in the heart in response to stress. in this study, we assessed whether inhibition of the mir-34 family using an s.c.-delivered seed-targeting 8-mer locked nucleic acid (lna)-modified antimir (lna-antimir-34) can provide therapeutic benefit in mice with preexisting pathological cardiac remodeling and dysfunction due to myocardial infarction (mi) or pressure overload via transverse aortic constriction (tac). an additional cohort of mice subjected to mi was given lna-antimir-34a (15-mer) to inhibit mir-34a alone as a comparison for lna-antimir-34. lna-antimir-34 (8-mer) efficiently silenced all three mir-34 family members in both cardiac stress models and attenuated cardiac remodeling and atrial enlargement. in contrast, inhibition of mir-34a alone with lna-antimir-34a (15-mer) provided no benefit in the mi model. in mice subjected to pressure overload, lna-antimir-34 improved systolic function and attenuated lung congestion, associated with reduced cardiac fibrosis, increased angiogenesis, increased akt activity, decreased atrial natriuretic peptide gene expression, and maintenance of sarcoplasmic reticulum ca(2+) atpase gene expression. improved outcome in lna-antimir-34-treated mi and tac mice was accompanied by up-regulation of several direct mir-34 targets, including vascular endothelial growth factors, vinculin, protein o-fucosyltranferase 1, notch1, and semaphorin 4b. our results provide evidence that silencing of the entire mir-34 family can protect the heart against pathological cardiac remodeling and improve function. furthermore, these data underscore the utility of seed-targeting 8-mer lna-antimirs in the development of new therapeutic approaches for pharmacologic inhibition of disease-implicated mirna seed families.",1
"micrornas are known to contribute significantly to stem cell phenotype by post-transcriptionally regulating gene expression. most of our knowledge of micrornas comes from the study of canonical micrornas that require two sequential cleavages by the drosha/dgcr8 heterodimer and dicer to generate mature products. in contrast, non-canonical micrornas bypass the cleavage by the drosha/dgcr8 heterodimer within the nucleus but still require cytoplasmic cleavage by dicer. the function of non-canonical micrornas in embryonic stem cells (escs) remains obscure. it has been hypothesized that non-canonical micrornas have important roles in escs based upon the phenotypes of esc lines that lack these specific classes of micrornas; dicer-deficient escs lacking both canonical and non-canonical micrornas have much more severe proliferation defect than dgcr8-deficient escs lacking only canonical micrornas. using these cell lines, we identified two non-canonical micrornas, mir-320 and mir-702, that promote proliferation of dgcr8-deficient escs by releasing them from g1 arrest. this is accomplished by targeting the 3'-untranslated regions of the cell cycle inhibitors p57 and p21 and thereby inhibiting their expression. this is the first report of the crucial role of non-canonical micrornas in escs.",1
"the transformation of vascular smooth muscle cells into foam cells leading to increased plaque size and decreased stability is a key, yet understudied step in atherogenesis. we reported that interleukin-19 (il-19), a novel, anti-inflammatory cytokine, attenuates atherosclerosis by anti-inflammatory effects on vsmc. in this work we report that il-19 induces expression of mir133a, a muscle-specific mirna, in vsmc. although previously unreported, we report that mir133a can target and reduce mrna abundance, mrna stability, and protein expression of low density lipoprotein receptor adaptor protein 1, (ldlrap1), an adaptor protein which functions to internalize the ldl receptor. mutations in this gene lead to ldl receptor malfunction and cause the autosomal recessive hypercholesterolemia (arh) disorder in humans. herein we show that il-19 reduces lipid accumulation in vsmc, and ldlrap1 expression and oxldl uptake in a mir133a-dependent mechanism. we show that ldlrap1 is expressed in plaque and neointimal vsmc of mouse and human injured arteries. transfection of mir133a and ldlrap1 sirna into vsmc reduces their proliferation and uptake of oxldl. mir133a is significantly increased in plasma from hyperlipidemic compared with normolipidemic patients. expression of mir133a in il-19 stimulated vsmc represents a previously unrecognized link between vascular lipid metabolism and inflammation, and may represent a therapeutic opportunity to combat vascular inflammatory diseases.",1
"background alzheimer's disease (ad) results in cognitive impairment. the calcium voltage-gated channel subunit alpha-1 c cacna1c gene encodes an alpha-1 c subunit of l-type calcium channel (ltcc). the aim of this study was to investigate the role of micro-rna-137 (mir-137) and the cacna1c gene in appswe/ps1δe9 (app/ps1) double-transgenic ad mice and in human neuroblastoma sh-sy5y cells. material and methods six-month-old app/ps1 double-transgenic ad mice (n=6) and age-matched normal c57bl/6 mice (n=6) underwent a morris water maze (mwm) test, expression levels of amyloid-β (aβ), ltcc, the cacna1c gene, and mir-137 were measured in the rat hippocampus and cerebral cortex in both groups of mice. a luciferase assay was used to evaluate the effect of mir-137 on the expression of cacna1c in sh-sy5y human neuroblastoma sh-sy5y cells. western blotting was used to detect the cacna1c, phosphorylated-tau (p-tau), and aβ proteins. results in app/ps1 transgenic ad mice, spatial learning and memory was significantly reduced, levels of aβ1-40 and aβ1-42 were increased in the serum, hippocampus, and cerebral cortex, expression levels of mir-137 were reduced, expression of cacna1c protein was increased in the hippocampus and cerebral cortex, compared with normal control mice. mir-137 regulated the expression of the cacna1c gene. increased expression levels of p-tau (ser202, ser396, and ser404) induced by aβ1-42 were inhibited by mir-137 mimics in sh-sy5y human neuroblastoma cells in vitro. conclusions in a transgenic mouse model of ad, mir-137 and expression of the cacna1c gene inhibited the hyperphosphorylation of tau protein.",1
"rationale pericytes are key regulators of vascular maturation, but their value for cardiac repair remains unknown. objective we investigated the therapeutic activity and mechanistic targets of saphenous vein-derived pericyte progenitor cells (svps) in a mouse myocardial infarction (mi) model. methods and results svps have a low immunogenic profile and are resistant to hypoxia/starvation (h/s). transplantation of svps into the peri-infarct zone of immunodeficient cd1/foxn-1(nu/nu) or immunocompetent cd1 mice attenuated left ventricular dilatation and improved ejection fraction compared to vehicle. moreover, svps reduced myocardial scar, cardiomyocyte apoptosis and interstitial fibrosis, improved myocardial blood flow and neovascularization, and attenuated vascular permeability. svps secrete vascular endothelial growth factor a, angiopoietin-1, and chemokines and induce an endogenous angiocrine response by the host, through recruitment of vascular endothelial growth factor b expressing monocytes. the association of donor- and recipient-derived stimuli activates the proangiogenic and prosurvival akt/enos/bcl-2 signaling pathway. moreover, microrna-132 (mir-132) was constitutively expressed and secreted by svps and remarkably upregulated, together with its transcriptional activator cyclic amp response element-binding protein, on stimulation by h/s or vascular endothelial growth factor b. we next investigated if svp-secreted mir-132 acts as a paracrine activator of cardiac healing. in vitro studies showed that svp conditioned medium stimulates endothelial tube formation and reduces myofibroblast differentiation, through inhibition of ras-gtpase activating protein and methyl-cpg-binding protein 2, which are validated mir-132 targets. furthermore, mir-132 inhibition by antimir-132 decreased svp capacity to improve contractility, reparative angiogenesis, and interstitial fibrosis in infarcted hearts. conclusion svp transplantation produces long-term improvement of cardiac function through a novel paracrine mechanism involving the secretion of mir-132 and inhibition of its target genes.",1
"micrornas (mirna) are small noncoding rnas that regulate gene expression through translational repression or mrna cleavage. here, we found that cytochrome p450 (cyp), a superfamily of drug-metabolizing enzymes, is a target of mirna. human cyp1b1, which is highly expressed in estrogen target tissues, catalyzes the metabolic activation of various procarcinogens and the 4-hydroxylation of 17beta-estradiol. cyp1b1 protein is abundant in cancerous tissues. we identified a near-perfect matching sequence with mir-27b in the 3'-untranslated region of human cyp1b1. luciferase assays revealed that the reporter activity of the plasmid containing the mir-27b recognition element was decreased in mcf-7 cells (mir-27 positive) but not in jurkat cells (mir-27b negative). exogenously expressed mir-27b could decrease the luciferase activity in jurkat cells. in mcf-7 cells, the antisense oligoribonucleotide for mir-27b restored the luciferase activity and increased the protein level and enzymatic activity of endogenous cyp1b1. these results suggested that human cyp1b1 is post-transcriptionally regulated by mir-27b. the expression levels of mir-27b and cyp1b1 protein in breast cancerous and adjacent noncancerous tissues from 24 patients were evaluated. in most patients, the expression level of mir-27b was decreased in cancerous tissues, accompanied by a high level of cyp1b1 protein. a significant inverse association was observed between the expression levels of mir-27b and cyp1b1 protein. thus, the decreased expression of mir-27b would be one of causes of the high expression of cyp1b1 protein in cancerous tissues. this is the first study to show that mirnas regulate not only essential genes for physiologic events but also drug-metabolizing enzymes.",1
"epigenetic reprogramming in early germ cells is critical toward the establishment of totipotency, but investigations of the germline events are intractable. an objective cell culture-based system could provide mechanistic insight on how the key determinants of primordial germ cells (pgcs), including prdm14, induce reprogramming in germ cells to an epigenetic ground state. here we show a prdm14-klf2 synergistic effect that can accelerate and enhance reversion of mouse epiblast stem cells (episcs) to a naive pluripotent state, including x reactivation and dna demethylation. notably, prdm14 alone has little effect on episc reversion, but it enhances the competence for reprogramming and potentially pgc specification. reprogramming of episcs by the combinatorial effect of prdm14-klf2 involves key epigenetic changes, which might have an analogous role in pgcs. our study provides a paradigm toward a systematic analysis of how other key genes contribute to complex and dynamic events of reprogramming in the germline.",1
"diverse forms of injury and stress evoke a hypertrophic growth response in adult cardiac myocytes, which is characterized by an increase in cell size, enhanced protein synthesis, assembly of sarcomeres, and reactivation of fetal genes, often culminating in heart failure and sudden death. given the emerging roles of micrornas (mirnas) in modulation of cellular phenotypes, we searched for mirnas that were regulated during cardiac hypertrophy and heart failure. we describe >12 mirnas that are up- or down-regulated in cardiac tissue from mice in response to transverse aortic constriction or expression of activated calcineurin, stimuli that induce pathological cardiac remodeling. many of these mirnas were similarly regulated in failing human hearts. forced overexpression of stress-inducible mirnas was sufficient to induce hypertrophy in cultured cardiomyocytes. similarly, cardiac overexpression of mir-195, which was up-regulated during cardiac hypertrophy, resulted in pathological cardiac growth and heart failure in transgenic mice. these findings reveal an important role for specific mirnas in the control of hypertrophic growth and chamber remodeling of the heart in response to pathological signaling and point to mirnas as potential therapeutic targets in heart disease.",1
"purpose constitutive activation of nf-κb signaling plays vital roles in esophageal squamous cell carcinoma (escc) progression. the aim of this study was to evaluate the effect of mir-138 on nf-κb activation and escc progression. experimental design expression of mir-138 in escc cell lines, escc tissues, and 205 archived essc specimens was determined using real-time pcr analysis. anchorage-independent growth, chicken chorioallantoic membrane, transwell matrix invasion and annexin v-binding assays, and a xenograft tumor model were used to determine the role of mir-138 in escc progression. the effect of mir-138 on nf-κb activation was investigated using ikk in vitro kinase, electrophoretic mobility shift, lipid raft isolation, and luciferase reporter assays. results mir-138 was downregulated and inversely correlated with tumor progression and patient survival in esccs. downregulation of mir-138 enhanced, whereas upregulation of mir-138 reduced, the aggressive phenotype of escc cells both in vitro and in vivo. silencing mir-138 promoted k63-linked polyubiquitination of the nf-κb signaling intermediaries traf2 and rip1 and sustained nf-κb activation. furthermore, downregulation of mir-138 induced lipid raft formation via upregulating multiple components of lipid rafts, including flot1, flot2, and caveolin-1. importantly, the in vitro analysis was consistent with a significant inverse correlation between mir-138 expression and nf-κb hyperactivation in a cohort of human escc specimens. conclusion our results show that mir-138 functions as a tumor-suppressive mirna and that downregulation of mir-138 contributes to constitutive nf-κb activation and escc progression.",1
"background non-alcoholic fatty liver disease (nafld) is characterized by excessive lipid accumulation and imbalances in lipid metabolism in the liver. although nuclear receptors (nrs) play a crucial role in hepatic lipid metabolism, the underlying mechanisms of nr regulation in nafld remain largely unclear. methods using network analysis and rna-seq to determine the correlation between nrs and microrna in human nafld patients, we revealed that mir20b specifically targets ppara. mir20b mimic and anti- mir20b were administered to human hepg2 and huh-7 cells and mouse primary hepatocytes as well as high-fat diet (hfd)- or methionine-deficient diet (mcd)-fed mice to verify the specific function of mir20b in nafld. we tested the inhibition of the therapeutic effect of a pparα agonist, fenofibrate, by mir20b and the synergic effect of combination of fenofibrate with anti- mir20b in nafld mouse model. results we revealed that mir20b specifically targets ppara through mirna regulatory network analysis of nuclear receptor genes in nafld. the expression of mir20b was upregulated in free fatty acid (fa)-treated hepatocytes and the livers of both obesity-induced mice and nafld patients. overexpression of mir20b significantly increased hepatic lipid accumulation and triglyceride levels. furthermore, mir20b significantly reduced fa oxidation and mitochondrial biogenesis by targeting ppara . in mir20b -introduced mice, the effect of fenofibrate to ameliorate hepatic steatosis was significantly suppressed. finally, inhibition of mir20b significantly increased fa oxidation and uptake, resulting in improved insulin sensitivity and a decrease in nafld progression. moreover, combination of fenofibrate and anti- mir20b exhibited the synergic effect on improvement of nafld in mcd-fed mice. conclusions taken together, our results demonstrate that the novel mir20b targets ppara , plays a significant role in hepatic lipid metabolism, and present an opportunity for the development of novel therapeutics for nafld. funding this research was funded by korea mouse phenotyping project (2016m3a9d5a01952411), the national research foundation of korea (nrf) grant funded by the korea government (2020r1f1a1061267, 2018r1a5a1024340, nrf-2021r1i1a2041463, 2020r1i1a1a01074940, 2016m3c9a394589324), and the future-leading project research fund (1.210034.01) of unist.",1
"mir-186 has been reported to be implicated in tumorigenesis and chemoresistance in a few cancer types. however, its role in regulating chemoresistance has not been investigated in non-small cell lung cancer (nsclc). to examine the effects of mir-186 on chemosensitivity in nsclc, an mir-186 mimic and inhibitor were transfected, followed by celltiter-glo® assay in nsclc cell lines. western blot and luciferase assay were performed to investigate the direct targeting of mir-186. a xenograft mouse model was used to examine the in vivo chemosensitizing function of mir-186. we found that overexpression of mir-186 sensitized a549 and h1299 cells to paclitaxel, whereas inhibition of mir-186 conferred resistance in these cells. mapt was the direct target of mir-186 which was required for the regulatory role of mir-186 in chemoresistance. this chemosensitizing function was partially due to the induction of the p53 mediated apoptotic pathway. the mir-186 mimic enhanced the tumor growth inhibitory effects of paclitaxel in a549 xenografts. in addition, mir-186 was found to be down-regulated in nsclc patients who were chemoresistant and this down-regulation was associated with poor survival. taken together, our study demonstrated that mir-186 regulates the chemoresistance of nsclc cells by modulating the mapt expression level both in vitro and in vivo. mir-186 may represent a new therapeutic target for the improvement of the clinical outcome in nsclc.",1
"background and objectives differentiation and de-differentiation of vascular smooth muscle cells (vsmcs) are important events in atherosclerosis and restenosis after angioplasty. micrornas are considered a key regulator in cellular processes such as differentiation, proliferation, and apoptosis. here, we report the role of new mir-18a-5p microrna and its downstream target genes in vsmcs and in a carotid balloon injury model. materials and methods expression of mir-18a-5p and its candidate genes was examined in vsmcs and in a carotid artery injury model by quantitative reverse-transcription polymerase chain reaction (qrt-pcr) and microrna microarray analysis. vsmc differentiation marker genes including smooth muscle (sm) α-actin and sm22α were determined by western blot, qrt-pcr, and a sm22α promoter study. gene overexpression or knockdown was performed in vsmcs. results mir-18a-5p was upregulated in the rat carotid artery at the early time after balloon injury. transfection of the mir-18a-5p mimic promoted the vsmc differentiation markers sm α-actin and sm22α. in addition, mir-18a-5p expression was induced in differentiated vsmcs, whereas it decreased in de-differentiated vsmcs. we identified syndecan4 as a downstream target of mir-18-5p in vsmcs. overexpression of syndecan4 decreased smad2 expression, whereas knockdown of syndecan4 increased smad2 expression in vsmcs. finally, we showed that smad2 induced the expression of vsmc differentiation marker genes in vsmcs. conclusion these results indicate that mir-18a-5p is involved in vsmc differentiation by targeting syndecan4.",1
"there is a close correlation between endothelin-1 (et-1) and microrna-1 (mirna-1) expression in the heart, but whether et-1 expression is regulated by mirna-1 warrants further research. our results revealed multiple clues suggesting that mirna-1 may participate in inhibiting et-1 gene expression. the inhibitory effect of mirna-1 on recombinant luciferase reporter gene was mediated by the target sequence at the 127th nucleotide on et-1 3'utr. we further confirmed that mirna-1 could inhibit endogenous et-1 gene expression at the post-transcriptional level. our study provides a new perspective on the regulatory mechanism of et-1 gene.",1
"c-myc promoter binding protein (mbp-1) is a multi-functional protein known to regulate expression of targets involved in the malignant phenotype. we have previously demonstrated that exogenous expression of mbp-1 inhibits prostate tumor growth, although the mechanism of growth inhibition is not well understood. we hypothesized that mbp-1 may modulate microrna (mirna) expression for regulation of prostate cancer cell growth. in this study, we demonstrated that exogenous mbp-1 upregulates mir-29b by 5-9 fold in prostate cancer cells as measured by real-time quantitative reverse transcription-pcr. subsequent studies indicated that exogenous expression of mir-29b inhibited mcl-1, col1a1, and col4a1. further, a novel target with potential implications for invasion and metastasis, matrix metallopeptidase-2 (mmp-2), was identified and confirmed to be a mir-29b target in prostate cancer cells. together our results demonstrated that exogenous expression of mir-29b regulates prostate cancer cell growth by modulating anti-apoptotic and pro-metastatic matrix molecules, implicating therapeutic potential of mir-29b for prostate cancer inhibition.",1
"understanding the molecular mechanisms that regulate cellular proliferation and differentiation is a central theme of developmental biology. micrornas (mirnas) are a class of regulatory rnas of approximately 22 nucleotides that post-transcriptionally regulate gene expression. increasing evidence points to the potential role of mirnas in various biological processes. here we show that mirna-1 (mir-1) and mirna-133 (mir-133), which are clustered on the same chromosomal loci, are transcribed together in a tissue-specific manner during development. mir-1 and mir-133 have distinct roles in modulating skeletal muscle proliferation and differentiation in cultured myoblasts in vitro and in xenopus laevis embryos in vivo. mir-1 promotes myogenesis by targeting histone deacetylase 4 (hdac4), a transcriptional repressor of muscle gene expression. by contrast, mir-133 enhances myoblast proliferation by repressing serum response factor (srf). our results show that two mature mirnas, derived from the same mirna polycistron and transcribed together, can carry out distinct biological functions. together, our studies suggest a molecular mechanism in which mirnas participate in transcriptional circuits that control skeletal muscle gene expression and embryonic development.",1
"dysregulation of mirna expression is associated with multiple diseases, including cancers, in which small rnas can have either oncogenic or tumor suppressive functions. here we investigated the potential tumor suppressive function of mir-450a, one of the most significantly downregulated mirnas in ovarian cancer. rna-seq analysis of the ovarian cancer cell line a2780 revealed that overexpression of mir-450a suppressed multiple genes involved in the epithelial-to-mesenchymal transition (emt). overexpression of mir-450a reduced tumor migration and invasion and increased anoikis in a2780 and skov-3 cell lines and reduced tumor growth in an ovarian tumor xenographic model. combined ago-par-clip and rna-seq analysis identified a panel of potential mir-450a targets, of which many, including timmdc1, mt-nd2, aco2, and atp5b, regulate energetic metabolism. following glutamine withdrawal, mir-450a overexpression decreased mitochondrial membrane potential but increased glucose uptake and viability, characteristics of less invasive ovarian cancer cell lines. in summary, we propose that mir-450a acts as a tumor suppressor in ovarian cancer cells by modulating targets associated with glutaminolysis, which leads to decreased production of lipids, amino acids, and nucleic acids, as well as inhibition of signaling pathways associated with emt. significance: mir-450a limits the metastatic potential of ovarian cancer cells by targeting a set of mitochondrial mrnas to reduce glycolysis and glutaminolysis. graphical abstract:",1
"deregulation of e2f1 activity and resistance to tgfbeta are hallmarks of gastric cancer. micrornas (mirnas) are small noncoding rnas frequently misregulated in human malignancies. here we provide evidence that the mir-106b-25 cluster, upregulated in a subset of human gastric tumors, is activated by e2f1 in parallel with its host gene, mcm7. in turn, mir-106b and mir-93 regulate e2f1 expression, establishing a mirna-directed negative feedback loop. furthermore, upregulation of these mirnas impairs the tgfbeta tumor suppressor pathway, interfering with the expression of cdkn1a (p21(waf1/cip1)) and bcl2l11 (bim). together, these results suggest that the mir-106b-25 cluster is involved in e2f1 posttranscriptional regulation and may play a key role in the development of tgfbeta resistance in gastric cancer.",1
"background and aims micrornas (mirnas) are short noncoding rnas that regulate gene expression negatively. although a role for aberrant mirna expression in cancer has been postulated, the pathophysiologic role and relevance of aberrantly expressed mirna to tumor biology has not been established. methods we evaluated the expression of mirna in human hepatocellular cancer (hcc) by expression profiling, and defined a target gene and biologically functional effect of an up-regulated mirna. results mir-21 was noted to be highly overexpressed in hcc tumors and cell lines in expression profiling studies using a mirna microarray. inhibition of mir-21 in cultured hcc cells increased expression of the phosphatase and tensin homolog (pten) tumor suppressor, and decreased tumor cell proliferation, migration, and invasion. in contrast-enhanced mir-21 expression by transfection with precursor mir-21 increased tumor cell proliferation, migration, and invasion. moreover, an increase in cell migration was observed in normal human hepatocytes transfected with precursor mir-21. pten was shown to be a direct target of mir-21, and to contribute to mir-21 effects on cell invasion. modulation of mir-21 altered focal adhesion kinase phosphorylation and expression of matrix metalloproteases 2 and 9, both downstream mediators of pten involved in cell migration and invasion. conclusions aberrant expression of mir-21 can contribute to hcc growth and spread by modulating pten expression and pten-dependent pathways involved in mediating phenotypic characteristics of cancer cells such as cell growth, migration, and invasion.",1
"sfmbt2-hosted mir-466a-3p and its close relatives are often among the most significantly up-regulated or down-regulated mirnas in responses to numerous deleterious environmental stimuli. the exact roles of these mirnas in cellular stress responses, however, are not clear. here we showed that many sfmbt2-hosted mirnas were highly hypertonic stress responsive in vitro and in vivo. in renal medulla, water deprivation induced alterations in the expression of mir-466(a/b/c/e/p)-3p in a pattern similar to that of mir-200b-3p, a known regulator of osmoresponsive transcription factor nfat5. remarkably, exposure of mimcd3 cells to an arginine vasopressin analog time-dependently down-regulated the expression of mir-466(a/b/c/e/p)-3p and mir-200b-3p, which provides a novel regulatory mechanism for these osmoresponsive mirnas. in cultured mimcd3 cells we further demonstrated that mir-466a-3p and mir-466g were capable of targeting nfat5 by interacting with its 3'utr. in transgenic mice overexpressing mir-466a-3p, significant down-regulation of nfat5 and many other osmoregulation-related genes was observed in both the renal cortex and medulla. moreover, sustained transgenic over-expression of mir-466a-3p was found to be associated with polydipsia, polyuria and disturbed ion homeostasis and kidney morphology. since the mature sequence of mir-466a-3p is completely equivalent to that of mir-466e-3p and that the seed sequence of mir-466a-3p is completely equivalent to that of mir-297(a/b/c)-3p, mir-466d-3p, mir-467g and mir-669d-3p, and that mir-466a-3p differs from mir-466(b/c/p)-3p only in a 5' nucleotide, we propose that mir-466a-3p and many of its close relatives are important epigenetic regulators of renal nfat5 signaling, osmoregulation and urine concentration in mice.",1
"induction of the arf tumor suppressor (encoded by the alternate reading frame of the cdkn2a locus) following oncogene activation engages a p53-dependent transcriptional program that limits the expansion of incipient cancer cells. although the p19(arf) protein is not detected in most tissues of fetal or young adult mice, it is physiologically expressed in the fetal yolk sac, a tissue derived from the extraembryonic endoderm (exen). expression of the mouse p19(arf) protein marks late stages of exen differentiation in cultured embryoid bodies (ebs) derived from either embryonic stem cells or induced pluripotent stem cells. arf inactivation delays differentiation of the exen lineage within ebs, but not the formation of other germ cell lineages from pluripotent progenitors. arf is required for the timely induction of exen cells in response to ras/erk signaling and, in turn, acts through p53 to ensure the development, but not maintenance, of the exen lineage. remarkably, a significant temporal delay in exen differentiation detected during the maturation of arf-null ebs is rescued by enforced expression of mouse microrna-205 (mir-205), a microrna up-regulated by p19(arf) and p53 that controls exen cell migration and adhesion. the noncanonical and canonical roles of arf in exen development and tumor suppression, respectively, may be conceptually linked through mechanisms that govern cell attachment and migration.",1
"introduction mesenchymal stem cells (mscs) transplantation has been demonstrated to be an effective strategy for the treatment of cardiovascular disease. however, the low survival rate of mscs at local diseased tissue reduces the therapeutic efficacy. we therefore investigated the influence of microrna-378 (mir-378) transfection on mscs survival and vascularization under hypoxic-ischemic condition in vitro. methods mscs were isolated from bone marrow of sprague-dawley rats and cultured in vitro. the third passage of mscs were divided into the mir-378 group and control group. for the mir-378 group, cells were transfected with mir-378 mimic. both groups experienced exposure to hypoxia (1% o2) and serum deprivation for 24 hours, using normoxia (20% o2) as a negative control during the process. after 24 hours of reoxygenation (20% o2), cell proliferation and apoptosis were evaluated. expressions of apoptosis and angiogenesis related genes were detected. both groups were further co-cultured with human umbilical vein endothelial cells to promote vascular differentiation for another 6 hours. vascular density was assessed thereafter. results compared with the control group, mscs transfected with mir-378 showed more rapid growth. their proliferation rates were much higher at 72 h and 96 h under hypoxic condition (257.33% versus 246.67%, p conclusion mir-378 transfection could effectively promote mscs survival and vascularization under hypoxic-ischemic condition in vitro.",1
"micrornas (mirnas) are a versatile class of non-coding rnas involved in regulation of various biological processes. mirna-122 (mir-122) is specifically and abundantly expressed in human liver. in this study, we employed 3'-end biotinylated synthetic mir-122 to identify its targets based on affinity purification. quantitative rt-pcr analysis of the affinity purified rnas demonstrated a specific enrichment of several known mir-122 targets such as cat-1 (also called slc7a1), adam17 and bcl-w. using microarray analysis of affinity purified rnas, we also discovered many candidate target genes of mir-122. among these candidates, we confirmed that protein kinase, interferon-inducible double-stranded rna-dependent activator (prkra), a dicer-interacting protein, is a direct target gene of mir-122. mirna quantitative-rt-pcr results indicated that mir-122 and small interfering rna against prkra may facilitate the accumulation of newly synthesized mirnas but did not detectably affect endogenous mirnas levels. our findings will lead to further understanding of multiple functions of this hepato-specific mirna. we conclude that mir-122 could repress prkra expression and facilitate accumulation of newly synthesized mirnas.",1
"primary transcripts of certain microrna (mirna) genes are subject to rna editing that converts adenosine to inosine. however, the importance of mirna editing remains largely undetermined. here we report that tissue-specific adenosine-to-inosine editing of mir-376 cluster transcripts leads to predominant expression of edited mir-376 isoform rnas. one highly edited site is positioned in the middle of the 5'-proximal half ""seed"" region critical for the hybridization of mirnas to targets. we provide evidence that the edited mir-376 rna silences specifically a different set of genes. repression of phosphoribosyl pyrophosphate synthetase 1, a target of the edited mir-376 rna and an enzyme involved in the uric-acid synthesis pathway, contributes to tight and tissue-specific regulation of uric-acid levels, revealing a previously unknown role for rna editing in mirna-mediated gene silencing.",1
"long noncoding (lnc)rnas have recently emerged as key regulators of gene expression. here, we performed high-depth poly(a)(+) rna sequencing across multiple clonal populations of mouse embryonic stem cells (escs) and neural progenitor cells (npcs) to comprehensively identify differentially regulated lncrnas. we establish a biologically robust profile of lncrna expression in these two cell types and further confirm that the majority of these lncrnas are enriched in the nucleus. applying weighted gene coexpression network analysis, we define a group of lncrnas that are tightly associated with the pluripotent state of escs. among these, we show that acute depletion of platr14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of escs. furthermore, we demonstrate that firre, a lncrna highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in escs, controls a network of genes related to rna processing. together, we provide a comprehensive, up-to-date, and high resolution compilation of lncrna expression in escs and npcs and show that nuclear lncrnas are tightly integrated into the regulation of esc gene expression.",1
"context evidence suggests that a number of microrna (mirna) are aberrantly expressed in endometrial disorders with potential posttranscriptional regulation of their specific target genes, including ovarian steroid receptors. objectives our objective was to assess the endometrial expression of mir-98 and mir-181a and their respective target genes, progesterone (p4) receptor membrane component 1 (pgrmc1) and p4 receptor (pgr). design, setting, and patients we evaluated tissue expression and in vitro regulation at an academic university medical center in endometrial biopsies and endometrial tissues from follicular and luteal phases with and without exposure to hormonal therapies and grade i-iii endometrial cancer (n = 52). interventions interventions included endometrial biopsies and in vitro transfection. main outcome measures we evaluated expression and function of mir-98 and mir-181a. results aberrant expression of mir-98 and mir-181a is associated with endometrial transition from normal into cancerous states, which to some extent is influenced by hormonal milieu, and exhibited an inverse relationship with pgmrc1 and pgr expression, respectively. treatments of ishikawa cells with 17β-estradiol, p4, or medroxyprogesterone acetate had limited effects on mir-98, mir-181a, and pgrmc1 expression, whereas 17β-estradiol treatment increased pgr expression. in ishikawa cells, gain of function of mir-98 repressed pgrmc1 and cyp19a1, and mir-181a repressed pgr, ddx3x, and timp3 at mrna and protein levels through direct interactions with their respective 3'-untranslated regions and ccne1 through mir-181a-induced ddx3x repression, with mir-98 reducing the rate of cell proliferation as compared with controls. conclusion mir-98 and mir-181a through their regulatory functions on pgrmc1, pgr, cyp19a1, timp3, and ddx3x expression may influence a wide range of endometrial cellular activities during normal menstrual cycle and transition into disease states, including endometrial cancer.",1
"the p53 tumor suppressor protein is a critical regulator of the cellular response to cancer-initiating insults such as genotoxic stress. in this report, we demonstrate that micrornas (mirnas) are important components of the p53 transcriptional network. global mirna expression analyses identified a cohort of mirnas that exhibit p53-dependent upregulation following dna damage. one such mirna, mir-34a, is commonly deleted in human cancers and, as shown here, frequently absent in pancreatic cancer cells. characterization of the mir-34a primary transcript and promoter demonstrates that this mirna is directly transactivated by p53. expression of mir-34a causes dramatic reprogramming of gene expression and promotes apoptosis. much like the known set of p53-regulated genes, mir-34a-responsive genes are highly enriched for those that regulate cell-cycle progression, apoptosis, dna repair, and angiogenesis. therefore, it is likely that an important function of mir-34a is the modulation and fine-tuning of the gene expression program initiated by p53.",1
"hepatocellular carcinoma (hcc) is the most common primary tumor of liver and the fifth most common cancer in the world. lung is the most frequent site for extra hepatic metastasis from hepatocellular carcinoma, while the cause and mechanism of it is still poor understood. here, we identify that the expression of mir-195 is markedly impaired in the lung metastasis cell lines of hcc. the result of real-time pcr reveals the expression of mir-195 is significantly downregulated in 92 hcc tissues. low expression of mir-195 is associated with tumor size, portal vein thrombosis, tnm stage and patients survival. luciferase reporter and elisa assay prove that hematogenous metastasis related genes including fgf2 and vegfa are the target genes of mir-195. overexpression of mir-195 in hcc cell line bel-7402 markedly inhibits the capability of migration and invasion. taken together, our results suggest that mir-195, a tumor suppressor mirna, contributes to the lung metastasis of hcc by negatively regulating fgf2 and vegfa, providing key implications of mir-195 for the therapeutic intervention of hcc.",1
"micrornas (mirnas) suppress targeting gene expression through blocking translation or triggering mrna degradation and, in general, act in trans, through a partially complementary interaction with the 3' untranslated region (3' utr) or coding regions of a target gene. although it has been reported previously that some mirnas suppress their target genes on the opposite strand with a fully complementary sequence (i.e., natural antisense mirnas that act in cis), there is no report to systematically study such cis-antisense mirnas in different animal species. here we report that cis-antisense mirnas do exist in different animal species: 48 in caenorhabditis elegans, 17 in drosophila, 36 in mus musculus, and 52 in homo sapiens using a systematical bioinformatics approach. we show that most of these cis-antisense mirnas can efficiently reduce the expression levels of their target genes in human cells. we further investigate hsa-mir-3661, one of the predicted cis-antisense mirnas, in detail and demonstrate that this mirna directly targets the coding sequence of ppp2ca located on the opposite dna strand and inhibits the ppp2ca expression. taken together, these results indicate that cis-antisense mirnas are conservative and functional in animal species including humans.",1
"rmrp is a non-coding rna that is ubiquitously expressed in both humans and mice. rmrp mutations that lead to decreased rmrp levels are found in the pleiotropic syndrome cartilage hair hypoplasia. to assess the effects of deleting rmrp, we engineered a targeting vector that contains loxp sequences flanking rmrp and created hemizygous mice harboring this engineered allele (rmrp conditional). we found that insertion of this cassette suppressed rmrp expression, and we failed to obtain viable mice homozygous for the rmrp conditional allele. furthermore, we were unable to obtain viable homozygous rmrp null mice, indicating that rmrp is essential for early embryonic development.",1
"although the catalytic subunit of the schizosaccharomyces pombe telomerase holoenzyme was identified over ten years ago, the unusual heterogeneity of its telomeric dna made it difficult to identify its rna component. we used a new two-step immunoprecipitation and reverse transcription-pcr technique to identify the s. pombe telomerase rna, which we call ter1. ter1 rna was 1,213 nucleotides long, similar in size to the saccharomyces cerevisiae telomerase rna, tlc1. ter1 rna associated in vivo with the two known subunits of the s. pombe telomerase holoenzyme, est1p and trt1p, and neither association was dependent on the other holoenzyme component. we present a model to explain how telomerase introduces heterogeneity into s. pombe telomeres. the technique used here to identify ter1 should be generally applicable to other model organisms.",1
"several transcription factors (tfs) have been implicated in neuroectoderm (ne) development, and recently, the tf pax6 was shown to be critical for human ne specification. however, microrna networks regulating human ne development have been poorly documented. we hypothesized that micrornas activated by pax6 should promote ne development. using a genomics approach, we identified pax6 binding sites and active enhancers genome-wide in an in vitro model of human ne development that was based on neural differentiation of human embryonic stem cells (hesc). pax6 binding to active enhancers was found in the proximity of several micrornas, including hsa-mir-135b. mir-135b was activated during ne development, and ectopic expression of mir-135b in hesc promoted differentiation toward ne. mir-135b promotes neural conversion by targeting components of the tgf-β and bmp signaling pathways, thereby inhibiting differentiation into alternate developmental lineages. our results demonstrate a novel tf-mirna module that is activated during human neuroectoderm development and promotes the irreversible fate specification of human pluripotent cells toward the neural lineage.",1
"smy rnas are a family of approximately 70-90 nt small nuclear rnas found in nematodes. in c. elegans, smy rnas copurify in a small ribonucleoprotein (snrnp) complex related to the sl1 and sl2 snrnps that are involved in nematode mrna trans-splicing. here we describe a comprehensive computational analysis of smy rna homologs found in the currently available genome sequences. we identify homologs in all sequenced nematode genomes in class chromadorea. we are unable to identify homologs in a more distantly related nematode species, trichinella spiralis (class: dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. using comparative rna sequence analysis, we infer a conserved consensus smy rna secondary structure consisting of two stems flanking a consensus sm protein binding site. a representative seed alignment of the smy rna family, annotated with the inferred consensus secondary structure, has been deposited with the rfam rna families database.",1
"in drosophila, the transcription factor gcm/glide plays a key role in cell fate determination and cellular differentiation. in light of its crucial biological impact, major efforts have been put for analyzing its properties as master regulator, from both structural and functional points of view. however, the lack of efficient antibodies specific to the gcm/glide protein precluded thorough analyses of its regulation and activity in vivo. in order to relieve such restraints, we designed an epitope-tagging approach to ""flag""-recognize and analyze the functional protein both in vitro (exogenous gcm/glide) and in vivo (endogenous protein). we here (i) reveal a tight interconnection between the small rna and the gcm/glide pathways. ago1 and mir-1 are gcm/glide targets whereas mir-279 negatively controls gcm/glide expression (ii) identify a novel cell population, peritracheal cells, expressing and requiring gcm/glide. peritracheal cells are non-neuronal neurosecretory cells that are essential in ecdysis. in addition to emphasizing the importance of following the distribution and the activity of endogenous proteins in vivo, this study provides new insights and a novel frame to understand the gcm/glide biology.",1
"the functional association between intronic mirnas and their host genes is still largely unknown. we found that three gene loci, which produced mir-26a and mir-26b, were embedded within introns of genes coding for the proteins of carboxy-terminal domain rna polymerase ii polypeptide a small phosphatase (ctdsp) family, including ctdspl, ctdsp2 and ctdsp1. we conducted serum starvation-stimulation assays in primary fibroblasts and two-thirds partial-hepatectomies in mice, which revealed that mir-26a/b and ctdsp1/2/l were expressed concomitantly during the cell cycle process. specifically, they were increased in quiescent cells and decreased during cell proliferation. furthermore, both mir-26 and ctdsp family members were frequently downregulated in hepatocellular carcinoma (hcc) tissues. gain- and loss-of-function studies showed that mir-26a/b and ctdsp1/2/l synergistically decreased the phosphorylated form of prb (pprb), and blocked g1/s-phase progression. further investigation disclosed that mir-26a/b directly suppressed the expression of cdk6 and cyclin e1, which resulted in reduced phosphorylation of prb. moreover, c-myc, which is often upregulated in cancer cells, diminished the expression of both mir-26 and ctdsp family members, enhanced the pprb level and promoted the g1/s-phase transition. our findings highlight the functional association of mir-26a/b and their host genes and provide new insight into the regulatory network of the g1/s-phase transition.",1
"micrornas (mirnas) are generally recognized as regulating gene expression posttranscriptionally by inhibiting translation or inducing target mrna degradation. new mechanisms for mirnas to regulate gene expression also still attract much attention. more and more novel mirnas are discovered by the advanced sequencing technology, but yet their biological functions are largely unknown. up to now, the function of mir-466l, a mirna discovered in mouse embryonic stem cells, remains unclear. in this study, we report that mir-466l can upregulate both mrna and protein expression of il-10 in tlr-triggered macrophages. furthermore, we show that mir-466l can competitively bind to the il-10 3' untranslated region au-rich elements, which is a typical binding site for rna-binding protein (rbp). tristetraprolin is a well-known rbp, and mediates rapid degradation of il-10 mrna. mirna always mediates target mrna degradation or translation repression modestly; thus, the net effect of mir-466l's binding to il-10 au-rich elements is to prevent il-10 mrna degradation mediated by tristetraprolin, resulting in extended t(1/2) of il-10 mrna and elevated il-10 expression. thus, competitive binding with rbp to the same target mrna and subsequent stabilization of target mrna is an alternative mechanism for gene regulation by mirnas. also, a mechanism for regulation of il-10 by mirnas is outlined.",1
"objectives emerging micrornas (mirnas) are validated to take part in pathological processes, including numerous carcinomas. currently, we focused on the functional role of mir-383 and interleukin-17 (il-17) in hepatocellular carcinoma (hcc), and the underlying molecular mechanisms were also the emphases in our research. methods we used reverse transcription-quantitative polymerase chain reaction (rt-qpcr) to measure the expression levels of mir-383 in 45 paired tumor tissues and adjacent non-tumor tissues extracted from patients with hepatocellular carcinoma. these tissues were also stained for il-17 using immunohistochemical staining. western blot was performed to detect the protein expressions of following protein-coding genes, including p-stat3, stat3 and gapdh. a dual-luciferase activity was carried out to determine whether il-17 was the downstream gene of mir-383 in hepatocellular carcinoma development. the colony assay, cck8 assay, and apoptosis assay were used to explore the detailed regulatory effects of mir-383/il-17 axis in the cellular processes of hepatocellular carcinoma separately. results mir-383 was down-regulated significantly in tumor tissues, while il-17 was up-regulated. il-17 was certificated to act as the downstream gene of mir-383. furthermore, overexpression of mir-383 suppressed cell proliferation and promoted apoptosis in hepatocellular carcinoma. however, the raised il-17 attenuated the inhibition effect of mir-383 in hepatocellular carcinoma. in addition, we found that p-stat3 was repressed by mir-383, and the up-regulation of il-17 reversed the suppression effect in hepatocellular carcinoma. conclusions mir-383 may play a anti-tumor role in the pathogenesis of hepatocellular carcinoma by targeting il-17 through stat3 signaling pathway. mir-383/il-17 axis maybe a potent target for the clinical diagnosis and treatment of hepatocellular carcinoma.",1
"many aspects of social behavior are controlled by sex-specific pheromones. gender-appropriate production of the sexually dimorphic transcription factors doublesex and fruitless controls sexual differentiation and sexual behavior. mir-124 mutant males exhibited increased male-male courtship and reduced reproductive success with females. females showed a strong preference for wild-type males over mir-124 mutant males when given a choice of mates. these effects were traced to aberrant pheromone production. we identified the sex-specific splicing factor transformer as a functionally significant target of mir-124 in this context, suggesting a role for mir-124 in the control of male sexual differentiation and behavior, by limiting inappropriate expression of the female form of transformer. mir-124 is required to ensure fidelity of gender-appropriate pheromone production in males. use of a microrna provides a secondary means of controlling the cascade of sex-specific splicing events that controls sexual differentiation in drosophila. doi:",1
"we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna whose unique tertiary structure includes a sharp 90 degrees kink of the helix axis and several novel longer-range tertiary interactions. the tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. these unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m rna element are attractive targets for the design of anti-viral therapeutic agents. structural genomics has sought to deduce protein function based on three-dimensional homology. here we have extended this approach to rna by proposing potential functions for a rigorously conserved set of rna tertiary structural interactions that occur within the sars rna genome itself. based on tertiary structural comparisons, we propose the s2m rna binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for sars viral rna hijacking of host protein synthesis, both based upon observed s2m rna macromolecular mimicry of a relevant ribosomal rna fold.",1
"the pancreatic acinar-enriched mir-216a, mir-216b and mir-217 are encoded within the mir217hg. these mirnas have been purported to play a tumor suppressive role as their expression is reduced in both human and mouse pancreatic ductal adenocarcinoma (pdac). to examine this possibility, we generated individual, germline knockout (ko) mice of mir-216a, mir-216b or mir-217. unlike our previous study showing germline deletion of the mir217hg was embryonic lethal, crispr-cas9 deleted portions of the 5' seed region of the mirnas produced live births. to investigate possible phenotypes during pancreatic acinar ductal metaplasia (adm), pancreatic acini from wild type and ko mice were plated on collagen and allowed to transdifferentiate over 4 days. acini from each of the three mirna ko mice produced greater numbers of ducts compared to controls. evaluation of the gene expression during in vitro adm demonstrated an increase in krt19 and a reduction in acinar genes (carboxypeptidase a1, amylase2a) on day 4 of the transdifferentiation. recovery was delayed for the mir-216a and mir-216b kos following caerulein-induced acute pancreatitis. also predominate in the caerulein treated mir-216a and mir-216b ko mice was the presence of pancreatic duct glands (pdgs). to further establish a phenotype, mirna ko mice were crossed with el-kras g12d (ek) mice and followed up to 13 months of age. while all mice developed severe dysplasia and cystic papillary neoplasms, there existed no apparent phenotypic difference in the mirna ko/ek mice compared to ek mice. our data does not support a tumor suppressor role for mir-216a, mir-216b or mir-217 in pdac and emphasizes the need for phenotypic evaluation of mirnas in complex in vivo models beyond that performed using cell culture.",1
"h19 non-coding rna downregulation stimulates melanogenesis in melasma patients. however, its mechanism is unclear. in this study, the potential role of a h19 microrna, mir-675, in melanogenesis was examined. real-time pcr using cultured normal human skin keratinocytes, melanocytes, and fibroblasts with or without h19 knockdown showed accompanying changes between expression levels of h19 and those of mir-675 in keratinocytes. mir-675 was also detected in concentrated culture supernatants and showed expression levels parallel with those of cell lysates. in addition to rnase resistance, facs analysis showed anti-cd63-positive exosomes in culture supernatants, suggesting mir-675 could be released extracellularly and delivered to neighboring cells without degradation. in western blot analysis, the mir-675 mimic reduced the expression of microphthalmia-associated transcription factor (mitf) and phosphorylation of camp-responsive element-binding protein, extracellular signal-regulated kinase and apoptosis signal-regulating kinase, whereas these expressions were increased by the mir-675 inhibitor. although h19 was not a mir-675 target, luciferase reporter assay showed a direct binding of mir-675 to 3'-untranslated region of mitf. in addition, localized in vivo mir-675 overexpression in mouse using a cationic polymer transfection reagent showed reduced mrna expression levels of mitf, tyrosinase, tyrosine-related protein-1 (trp-1), and trp-2. collectively, the results suggest that mir-675 derived from keratinocytes could be involved in h19-stimulated melanogenesis using mitf as a target of mir-675.",1
"background micrornas (mirnas) have emerged as important gene regulators and are recognized as key players in tumorigenesis. mir-145 is reported to be down-regulated in several cancers, but knowledge of its targets in colon cancer remains limited. methodology/principal findings to investigate the role of mir-145 in colon cancer, we have employed a microarray based approach to identify mir-145 targets. based on seed site enrichment analyses and unbiased word analyses, we found a significant enrichment of mirna binding sites in the 3'-untranslated regions (utrs) of transcripts down-regulated upon mirna overexpression. gene ontology analysis showed an overrepresentation of genes involved in cell death, cellular growth and proliferation, cell cycle, gene expression and cancer. a number of the identified mirna targets have previously been implicated in cancer, including yes, fscn1, adam17, birc2, vangl1 as well as the transcription factor stat1. both yes and stat1 were verified as direct mir-145 targets. conclusions/significance the study identifies and validates new cancer-relevant direct targets of mir-145 in colon cancer cells and hereby adds important mechanistic understanding of the tumor-suppressive functions of mir-145.",1
"interleukin 6 (il-6) is a major pro-inflammatory cytokine and dysregulation of il-6 is relevant to many inflammatory diseases. endotoxin induced tolerance of il-6 is an important mechanism to avoid the excessive immune reaction. but to date, the molecular mechanisms of endotoxin tolerance of il-6 remain unclear. here we reported that il-6 secretion and microrna-181b (mir-181b) expression were inversely correlated following lps stimulation. we also demonstrated that mir-181b targeting the 3'-utr of il-6 transcripts and up-regulation of mir-181b was associated with nf-kb. we further demonstrated that up-regulation of mir-181b in response to lps was required for inducing il-6 tolerance in macrophage. our results suggested that the post-transcriptional control mediated by mir-181b could be involved in fine tuning the critical level of il-6 expression in endotoxin tolerance.",1
"the activation of a hemostatic system plays a critical role in the incidence of acute coronary events. hemostatic proteins may be regulated by micrornas (mirnas). microparticles (mps) are the major carrier of circulating mirnas. the aim of this study was to determine the potential role of mirnas in regulating gene expression involved in the hemostatic system in patients with unstable angina (ua). mirna expression profiles in the plasma from patients with ua (ua group, n=9) compared with individuals with clinical suspicion of coronary artery disease (cad) but negative angiography (control group, n=9) showed that among 36 differentially expressed mirnas, mir-19b was the most obvious one. using real-time pcr, 5 selected mirna levels in plasma (ua group, n=20; control group, n=30) and plasma mps (ua group n=6; control group n=6) were proved to be consistent with the mirna array. flow cytometry analysis indicated that the amounts of plasma endothelial microparticles (emps) were increased in ua patients (ua group, n=4) compared to controls (control group, n=4). in cultured endothelial cells (ecs), tnf-α increased mir-19b release and expression. tissue factor (tf) was predicted to be the target of mir-19b by bioinformatics analysis. luciferase reporter assays demonstrated that mir-19b binds to tf mrna. overexpression of mir-19b inhibited tf expression and procoagulant activity. this study indicates that in ua patients, the increase of mir-19b wrapped in emps due to endothelial dysfunction may partially contribute to the circulating mir-19b elevation and mir-19b may play an anti-thrombotic role by inhibiting the expression of tf in ecs.",1
"micrornas (mirnas) may function as oncogenes or tumor suppressors. here, we identified that mir-590-5p was up-regulated in human cervical cancer. over-expression of mir-590-5p promoted cervical cancer cell growth, cell cycle and invasion via growth curve, colony formation, facs and transwell assays in hela and c33a cell lines. subsequently, chl1 was identified as a potential mir-590-5p target by bioinformatics analysis. moreover, we showed that chl1 was negatively regulated by mir-590-5p at the posttranscriptional level, via a specific target site within the 3'utr by luciferase reporter assay. furthermore, the mrna and protein levels of chl1 in cervical cancer cells were downregulated by mir-590-5p. and we identified the cell phenotype altered by mir-590-5p can be rescued by over-expression of chl1. therefore, our findings suggest that mir-590-5p acts as an oncogene by targeting the chl1 gene and promotes cervical cancer proliferation. the findings of this study contribute to current understanding of the functions of mir-590-5p in cervical cancer.",1
"riboswitches are rnas that form complex, folded structures that selectively bind small molecules or ions. as with certain groups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand specificity. we developed a procedure to systematically analyze known riboswitch classes to find additional variants that have altered their ligand specificity. this approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. among the discoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2'-deoxyguanosine. in addition, we identified variants of the glycine riboswitch class that no longer recognize this amino acid, additional members of a rare flavin mononucleotide (fmn) variant class, and also variants of c-di-gmp-i and -ii riboswitches that might recognize different bacterial signaling molecules. these findings further reveal the diverse molecular sensing capabilities of rna, which highlights the potential for discovering a large number of additional natural riboswitch classes.",1
"aims/hypothesis we analysed the genomic organisation of mir-153, a microrna embedded in genes that encode two of the major type 1 diabetes autoantigens, islet-associated protein (ia)-2 and ia-2β. we also identified mir-153 target genes that correlated with ia-2β localisation and function. methods a bioinformatics approach was used to identify mir-153's genomic organisation. to analyse the co-regulation of mir-153 and ia-2β, quantitative pcr analysis of mir-153 and ia-2β (also known as ptprn2) was performed after a glucose stimulation assay in min6b cells and isolated murine pancreatic islets, and also in wild-type ia-2 (also known as ptprn), ia-2β single knockout and ia-2/ia-2β double knockout mouse brain and pancreatic islets. bioinformatics identification of mir-153 target genes and validation via luciferase reporter assays, western blotting and quantitative pcr were also carried out. results two copies of mir-153, mir-153-1 and mir-153-2, are localised in intron 19 of ia-2 and ia-2β, respectively. in rodents, only mir-153-2 is conserved. we demonstrated that expression of mir-153-2 and ia-2β in rodents is partially co-regulated as demonstrated by a strong reduction of mir-153 expression levels in ia-2β knockout and ia-2/ia-2β double knockout mice. mir-153 levels were unaffected in ia-2 knockout mice. in addition, glucose stimulation, which increases ia-2 and ia-2β expression, also significantly increased expression of mir-153. several predicted targets of mir-153 were reduced after glucose stimulation in vitro, correlating with the increase in mir-153 levels. conclusions/interpretation this study suggests the involvement of mir-153, ia-2β and mir-153 target genes in a regulatory network, which is potentially relevant to insulin and neurotransmitter release.",1
"micrornas are key regulators of gene expression, but the precise mechanisms underlying their interaction with their mrna targets are still poorly understood. here, we systematically investigate the role of target-site accessibility, as determined by base-pairing interactions within the mrna, in microrna target recognition. we experimentally show that mutations diminishing target accessibility substantially reduce microrna-mediated translational repression, with effects comparable to those of mutations that disrupt sequence complementarity. we devise a parameter-free model for microrna-target interaction that computes the difference between the free energy gained from the formation of the microrna-target duplex and the energetic cost of unpairing the target to make it accessible to the microrna. this model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions. our study thus demonstrates that target accessibility is a critical factor in microrna function.",1
"objective we sought to identify specific microrna (mirna) for systemic juvenile idiopathic arthritis (sjia) and to determine the involvement of these mirna in regulating the expression of cytokines. methods microarray profiling was performed to identify differentially expressed mirna in sjia plasma. levels of candidate mirna and mrna were assessed by real-time pcr, and cytokines were measured by elisa. dual-luciferase reporter assay was used to validate the direct interaction between mir-26a and interleukin 6 (il-6). results forty-eight mirna were differentially expressed in the plasma of patients with sjia compared with healthy controls (hc). five mirna were selected for further validation. the expression level of mir-26a was exclusively elevated in the plasma of patients with sjia as compared with 4 rheumatic diseases and 2 subtypes of jia (oligoarticular and polyarticular). the levels of il-6, il-1β, and tumor necrosis factor-α in the plasma of patients with sjia were increased, and only il-6 presented a positive correlation with mir-26a (r = 0.539, p conclusion this study demonstrates that mir-26a is expressed specifically and highly in sjia plasma and suggests that mir-26a may regulate the levels of cytokines in sjia. our findings highlight mir-26a as a potential biomarker for the diagnosis as well as differential diagnosis of sjia.",1
"p53 has attracted tremendous attention due to its master role in tumor development. activation of p53 in tumor cells has been the prime focus for cancer drug discovery. recent studies have shown that few mirnas can regulate p53 activity directly or indirectly. we herein demonstrate that mir-128 positively regulates p53 activity. our data suggest that mir-128 inhibits sirt1 expression directly through a mir-128-binding site within the 3' utr of sirt1. mir-128 inhibition of sirt1 led to an increase in acetylated p53 and its transcriptional targets. mir-128 decreased phospho-akt and phospho-foxo3a, increased acetylated foxo3a and promoted foxo3a translocation to the nucleus. we further demonstrated that mir-128 augments the antitumor effect of compounds that target the p53 pathway. furthermore, mir-128 induces apoptosis in wild (wt) p53 as well as in mutant p53-expressing cells in a p53-dependent and -independent manner via induction of puma. pretreatment with puma and bak sirnas abolished mir-128-induced apoptosis in hct116 p53+/+ and hct116 p53-/- cells. taken together, we present the first evidence of mir-128 to be a new component joining the p53 network. this study emphasizes that mir-128 is a novel mitochondria-targeted mirna that can be further evaluated as a chemotherapeutic agent for human cancers as it induces apoptosis irrespective of p53 status.",1
"background interleukin 16 is an immunomodulatory chemokine that signals through cd4 + t cells, monocytes, macrophages and dendritic cells. its expression in immune-related cells enhances the antimicrobial effect and inhibits hiv replication in macrophages. however, the role of il-16 in macrophage polarization is uncertain. mir-145 was reported to regulate il-10 expression by targeting histone deacetylase 11 and promotes alternatively activated macrophage (m2) polarization. mir-145 was also predicted to target il-16 mrna. we aimed to explore the roles of il-16 and mir-145 in macrophage polarization and antimicrobial functions. methods thp1 monocytes were employed in this study, and their cell activity when incubated with different concentrations of il-16 was evaluated using the cck-8 cell counting kit. to obtain polarized macrophages, thp-1 cells were induced by il-4 and il-13 following pma incubation (m2 polarized macrophages) or induced by ifn-gamma and lps (m1 classical macrophage activation). the influence of il-16 on macrophage phagocytosis was quantified by the amount of chicken red blood cell phagocytized. il-16, il-10 and mir-145 expression in thp1 monocytes and induced macrophages was quantified by quantitative pcr. the mir-145 and il-16 targeting relationship was verified by the dual luciferase reporter assay. the influence of il-16 and mir-145 on macrophage polarization was evaluated by m1 and m2 macrophage characterized marker gene expression. results the m0 macrophage subtype was induced by pma. the m1 and m2 subtypes of macrophage were successfully induced by m1- and m2-specific induction. m1 macrophages express higher levels of il-16 than m2 macrophages but express lower levels of il-10 and mir-145 than m2 cells. il-16 with a concentration up to 150 ng/ml has no influence on thp-1 cell proliferation but improves macrophage phagocytosis ability with the down-expression of il-10 and up-expression of pro-inflammatory cytokines such as il-1a and il-6. knockdown with its target sirna is beneficial for macrophage maintenance but reduces phagocytosis ability. mir-145 specifically targets the il-16 3'utr verified by the dual luciferase reporter assay. mir-145 downregulates il-16 expression and upregulates il-10 expression, thereby promoting m2 macrophage polarization. conclusion il-16 modulates macrophage polarization through regulating il-10, il-1a and il-6 expression. mir-145 is involved in m2 macrophage polarization by targeting il-16 and enhancing il-10 expression.",1
"dc-stamp is a key regulating molecule of osteoclastogenesis and osteoclast precursor (ocp) fusion. emerging lines of evidence showed that micrornas play crucial roles in bone metabolism and osteoclast differentiation, but no microrna has yet been reported to be directly related to ocps fusion. through a microarray, we found that the expression of mir-7b in raw264.7 cells was significantly decreased after induction with m-csf and rankl. the overexpression of mir-7b in raw264.7 cells attenuated the number of trap-positive cells number and the formation of multinucleated cells, whereas the inhibition of mir-7b enhanced osteoclastogenesis. through a dual luciferase reporter assay, we confirmed that mir-7b directly targets dc-stamp. other fusogenic molecules, such as cd47, atp6v0d2, and oc-stamp, were detected to be down-regulated in accordance with the inhibition of dc-stamp. because dc-stamp also participates in osteoclast differentiation through the itam-itim network, multiple osteoclast-specific genes in the itam-itim network were detected to identify how dc-stamp is involved in this process. the results showed that molecules associated with the itam-itim network, such as nfatc1 and oscar, which are crucial in osteoclastogenesis, were consistently altered due to dc-stamp inhibition. these findings suggest that mir-7b inhibits osteoclastogenesis and cell-cell fusion by directly targeting dc-stamp. in addition, the inhibition of dc-stamp and its downstream signals changed the expression of other fusogenic genes and key regulating genes, such as nfatc1, c-fos, akt, irf8, mapk1, and traf6. in conclusion, our findings indicate that mir-7b may be a potential therapeutic target for the treatment of osteoclast-related bone disorders.",1
"irreversible respiratory obstruction resulting from progressive airway damage, inflammation and fibrosis is a feature of several chronic respiratory diseases, including cystic fibrosis (cf), idiopathic pulmonary fibrosis (ipf) and chronic obstructive pulmonary disease (copd). the cytokine transforming growth factor β (tgf-β) has a pivotal role in promoting lung fibrosis and is implicated in respiratory disease severity. in the present study, we show that a previously uncharacterized mirna, mir-1343, reduces the expression of both tgf-β receptor 1 and 2 by directly targeting their 3'-utrs. after tgf-β exposure, elevated intracellular mir-1343 significantly decreases levels of activated tgf-β effector molecules, psmad2 (phosphorylated smad2) and psmad3 (phosphorylated smad3), when compared with a non-targeting control mirna. as a result, the abundance of fibrotic markers is reduced, cell migration into a scratch wound impaired and epithelial-to-mesenchymal transition (emt) repressed. mature mir-1343 is readily detected in human neutrophils and hl-60 cells and is activated in response to stress in a549 lung epithelial cells. mir-1343 may have direct therapeutic applications in fibrotic lung disease.",1
"introduction posttranscriptional control of mrna by microrna (mirna) has been implicated in the regulation of diverse biologic processes from directed differentiation of stem cells through organism development. we describe a unique pathway by which mirna regulates the specialized differentiation of cardiomyocyte (cm) subtypes. methods we differentiated human embryonic stem cells (hescs) to cardiac progenitor cells and functional cms, and characterized the regulated expression of specific mirnas that target transcriptional regulators of left/right ventricular-subtype specification. results from >900 known human mirnas in hesc-derived cardiac progenitor cells and functional cms, a subset of differentially expressed cardiac mirnas was identified, and in silico analysis predicted highly conserved binding sites in the 3'-untranslated regions (3'utrs) of hand-and-neural-crest-derivative-expressed (hand) genes 1 and 2 that are involved in left and right ventricular development. we studied the temporal and spatial expression patterns of four mirnas in differentiating hescs, and found that expression of mirna (mir)-363, mir-367, mir-181a, and mir-181c was specific for stage and site. further analysis showed that mir-363 overexpression resulted in downregulation of hand1 mrna and protein levels. a dual luciferase reporter assay demonstrated functional interaction of mir-363 with the full-length 3'utr of hand1. expression of anti-mir-363 in-vitro resulted in enrichment for hand1-expressing cm subtype populations. we also showed that bmp4 treatment induced the expression of hand2 with less effect on hand1, whereas mir-363 overexpression selectively inhibited hand1. conclusions these data show that mir-363 negatively regulates the expression of hand1 and suggest that suppression of mir-363 could provide a novel strategy for generating functional left-ventricular cms.",1
"microrna have been demonstrated to be deregulated in multiple myeloma. we have previously reported that mir-214 is down-regulated in multiple myeloma compared to in normal plasma cells. the functional role of mir-214 in myeloma pathogenesis was explored by transfecting myeloma cell lines with synthetic microrna followed by gene expression profiling. putative mir-214 targets were validated by luciferase reporter assay. ectopic expression of mir-214 reduced cell growth and induced apoptosis of myeloma cells. in order to identify the potential direct target genes of mir-214 which could be involved in the biological pathways regulated by this microrna, gene expression profiling of the h929 myeloma cell line transfected with precursor mir-214 was carried out. functional analysis revealed significant enrichment for dna replication, cell cycle phase and dna binding. mir-214 directly down-regulated the expression of psmd10, which encodes the oncoprotein gankyrin, and asf1b, a histone chaperone required for dna replication, by binding to their 3'-untranslated regions. in addition, gankyrin inhibition induced an increase of p53 mrna levels and subsequent up-regulation of cdkn1a (p21waf1/cip1) and bax transcripts, which are direct transcriptional targets of p53. in conclusion, mir-214 functions as a tumor suppressor in myeloma by positive regulation of p53 and inhibition of dna replication.",1
"we have partially purified ribonucleoproteins (rnps) from schizosaccharomyces pombe and yarrowia lipolytica with properties resembling those of mammalian signal recognition particle (srp). in both species of yeast we have identified a single major rna species in the size range of srp rna (256 nucleotides in s. pombe and 270 nucleotides in y. lipolytica) present in postribosomal salt extracts of the cytoplasm. the rnps containing these rnas sediment in sucrose gradients at 11 s and 10 s for s. pombe and y. lipolytica, respectively. analysis of genomic clones of these rnas has revealed that (i) they are encoded by single copy genes; (ii) they share two short conserved sequences that match the a and b boxes defined for polymerase iii promoters; (iii) they can be folded into secondary structures that closely match that defined by phylogenetic analysis of higher eukaryotic srp rnas; and (iv) they show primary sequence conservation in short regions predicted to be single stranded. both of the yeast rnas bind under stringent conditions to canine srp proteins. most importantly, rnase protection of the s. pombe rna by the individual canine srp proteins, p19 and p68/72, shows that the proteins recognize homologous elements of the mammalian and yeast rna. taken together these data suggest strongly that we have identified yeast srp homologues.",1
"the importance of understanding how interleukin-33 (il-33) is regulated (particularly by mirs) is critical in il-33 biology, and evidence of this in asthma pathology is limited. microrna profiling of cells isolated from bronchoalveolar lavage of 14 asthmatic patients and 11 healthy controls revealed mir-200b and mir-200c were significantly reduced in asthmatic patients compared with healthy controls. the reduction was validated in two independent models of allergen-induced allergic airway inflammation and further demonstrated to be inversely correlated with asthma severity, as well as increased il-33 production in asthmatic patients. in addition, the mir-200b and mir-200c binding sites in the 3' utr of il-33 mrna were identified by bioinformatics analysis and reporter gene assay. more importantly, introduction of mir-200b and mir-200c reduced, while inhibition of endogenous mir-200b and mir-200c increased, the induction of il-33 expression in lung epithelial cells. exogenous administration of mir-200b to lungs of mice with allergic inflammation resulted in a decrease in il-33 levels and resolution of airway inflammation phenotype. in conclusion, mir-200b and mir-200c by regulating the expression of il-33 have a role in bronchial asthma, and dysregulation of expression of mir-200b/c may be the underlying mechanism resulting in the asthmatic phenotype.",1
"heart failure is characterized by the transition from an initial compensatory response to decompensation, which can be partially mimicked by transverse aortic constriction (tac) in rodent models. numerous signaling molecules have been shown to be part of the compensatory program, but relatively little is known about the transition to decompensation that leads to heart failure. here, we show that tac potently decreases the rbfox2 protein in the mouse heart, and cardiac ablation of this critical splicing regulator generates many phenotypes resembling those associated with decompensation in the failing heart. global analysis reveals that rbfox2 regulates splicing of many genes implicated in heart function and disease. a subset of these genes undergoes developmental regulation during postnatal heart remodeling, which is reversed in tac-treated and rbfox2 knockout mice. these findings suggest that rbfox2 may be a critical stress sensor during pressure overload-induced heart failure.",1
"abnormal proliferation and phenotypic modulation of pulmonary artery smooth muscle cells (pasmc) contributes to the pathogenesis of numerous cardiovascular disorders, including pulmonary arterial hypertension (pah). the nuclear factor of activated t cells (nfat) signaling pathway is linked to pasmc proliferation and pah. micrornas (mirnas) are small non-coding rnas that function in diverse biological processes. to systemically identify the specific mirnas that regulate the nfat pathway, a human primary mirna library was applied for cell-based high throughput screening with the nfat luciferase reporter system. eight mirnas were found to modulate nfat activity efficiently. of them, mir-124 robustly inhibited nfat reporter activity and decreased both the dephosphorylation and the nuclear translocation of nfat. mir-124 also inhibited nfat-dependent transcription of il-2 in jurkat t cells. mir-124 exerted its effects by targeting multiple genes, including a known component of the nfat pathway, nfatc1, and two new regulators of nfat signaling, camta1 (calmodulin-binding transcription activator 1) and ptbp1 (polypyrimidine tract-binding protein 1). physiologically, mir-124 was down-regulated by hypoxia in human pasmc, consistent with the activation of nfat during this process. down-regulation of mir-124 was also observed in 3-week hypoxia-treated mouse lungs. furthermore, the overexpression of mir-124 not only inhibited human pasmc proliferation but also maintained its differentiated phenotype by repressing the nfat pathway. taken together, our data provide the first evidence that mir-124 acts as an inhibitor of the nfat pathway. down-regulation of mir-124 in hypoxia-treated pasmc and its antiproliferative and prodifferentiation effects imply a potential value for mir-124 in the treatment of pah.",1
"background rnas perform many functions in addition to supplying coding templates, such as binding proteins. rna-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding rnas expands the scope for studying such interactions. to find such rnas, we exploited a form of ribosomal regulation. ribosome biosynthesis must be tightly regulated to ensure that concentrations of rrnas and ribosomal proteins (r-proteins) match. one regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5' utr of an mrna whose genes encode r-proteins. when the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mrna, reducing gene expression and thus protein concentrations. to date, 35 types of r-leaders have been validated or predicted. results by analyzing additional conserved rna structures on a multi-genome scale, we identified 20 novel r-leader structures. surprisingly, these included new r-leaders in the highly studied organisms escherichia coli and bacillus subtilis. our results reveal several cases where multiple unrelated rna structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. that the predicted r-leaders function as rnas is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved rna secondary structure. the r-leader predictions are also consistent with the locations of experimentally determined transcription start sites. conclusions this work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of rna-protein interactions. these results provide a starting point for detailed experimental studies.",1
"micrornas are short regulatory rnas that negatively modulate protein expression at a post-transcriptional level and are deeply involved in the pathogenesis of several types of cancers. here we show that mir-221 and mir-222, encoded in tandem on chromosome x, are overexpressed in the pc3 cellular model of aggressive prostate carcinoma, as compared with lncap and 22rv1 cell line models of slowly growing carcinomas. in all cell lines tested, we show an inverse relationship between the expression of mir-221 and mir-222 and the cell cycle inhibitor p27(kip1). we recognize two target sites for the micrornas in the 3' untranslated region of p27 mrna, and we show that mir-221/222 ectopic overexpression directly results in p27 down-regulation in lncap cells. in those cells, we demonstrate that the ectopic overexpression of mir-221/222 strongly affects their growth potential by inducing a g(1) to s shift in the cell cycle and is sufficient to induce a powerful enhancement of their colony-forming potential in soft agar. consistently, mir-221 and mir-222 knock-down through antisense lna oligonucleotides increases p27(kip1) in pc3 cells and strongly reduces their clonogenicity in vitro. our results suggest that mir-221/222 can be regarded as a new family of oncogenes, directly targeting the tumor suppressor p27(kip1), and that their overexpression might be one of the factors contributing to the oncogenesis and progression of prostate carcinoma through p27(kip1) down-regulation.",1
"micrornas (mirnas) are small regulatory rnas that participate in posttranscriptional gene regulation in a sequence-specific manner. however, little is understood about the role(s) of mirnas in alzheimer's disease (ad). we used mirna expression microarrays on rna extracted from human brain tissue from the university of kentucky alzheimer's disease center brain bank with near-optimal clinicopathological correlation. cases were separated into four groups: elderly nondemented with negligible ad-type pathology, nondemented with incipient ad pathology, mild cognitive impairment (mci) with moderate ad pathology, and ad. among the ad-related mirna expression changes, mir-107 was exceptional because mir-107 levels decreased significantly even in patients with the earliest stages of pathology. in situ hybridization with cross-comparison to neuropathology demonstrated that particular cerebral cortical laminas involved by ad pathology exhibit diminished neuronal mir-107 expression. computational analysis predicted that the 3'-untranslated region (utr) of beta-site amyloid precursor protein-cleaving enzyme 1 (bace1) mrna is targeted multiply by mir-107. from the same rna material analyzed on mirna microarrays, mrna expression profiling was performed using affymetrix exon array microarrays on nondemented, mci, and ad patients. bace1 mrna levels tended to increase as mir-107 levels decreased in the progression of ad. cell culture reporter assays performed with a subset of the predicted mir-107 binding sites indicate the presence of at least one physiological mir-107 mirna recognition sequence in the 3'-utr of bace1 mrna. together, the coordinated application of mirna profiling, affymetrix microarrays, new bioinformatics predictions, in situ hybridization, and biochemical validation indicate that mir-107 may be involved in accelerated disease progression through regulation of bace1.",1
"growing evidence indicates that micrornas play numerous important roles. however, the roles of some micrornas involved in regulation of circadian rhythm and sleep are still not well understood. in this study, we show that the mir-276b is essential for maintaining both sleep and circadian rhythm by targeting tim, npfr1 and dopr1 genes, with mir-276b deleted mutant flies sleeping more, and vice versa in mir-276b overexpressing flies. through analysing its promoter, we found that mir-276b is responsive to clock and regulates circadian rhythm through the negative feedback loop of the clk/cyc-tim/per. furthermore, mir-276b is broadly expressed in the clock neurons and the central complexes such as the mushroom body and the fan-shape body of drosophila brain, in which up-regulation of mir-276b in tim, npfr1 and dopr1 expressing tissues significantly causes sleep decreases. this study clarifies that the mir-276b is very important for participating in regulation of circadian rhythm and sleep.",1
"background analysis using publicly available algorithms predicts that x-ray repair complementing defective repair in chinese hamster cells 2 (xrcc2), a key component in the homologous recombination repair pathway, is a potential target of micro-ribonucleic acid-7 (mir-7). some studies have shown that both mir-7 and xrcc2 are associated with cancer development. for this purpose, we searched for the possible relationship between mir-7 and xrcc2 in the development of colorectal cancer (crc). methods mir-7 expression was assessed in crc specimens and cell lines using real-time polymerase chain reaction (pcr). luciferase reporter assay was used to confirm the target associations. the effect of mir-7 on cell proliferation and apoptosis was confirmed in vitro by the methylthiazol tetrazolium (mtt) assay, colony formation assay, and flow cytometry. gene and protein expression were examined using real time pcr and western blotting, respectively. results mir-7 was downregulated in crc specimens and cell lines, and targeted the 3' untranslated region of xrcc2. mir-7 overexpression reduced cyclin d1 expression and increased p21, caspase-3, and bax expression, which subsequently inhibited crc cell proliferation and induced crc cell apoptosis. however, xrcc2 can repress the inhibitory effects of mir-7 on proliferation. conclusion our findings suggest that mir-7 plays a protective role by inhibiting proliferation and increasing apoptosis of crc cells. it may identify new targets for anti-cancer treatment.",1
"patterns of cell fates generated by morphogens are critically important for normal development; however, the mechanisms by which graded morphogen signals are converted into all-or-none cell fate responses are incompletely understood. in the drosophila ovary, high and sustained levels of the secreted morphogen unpaired (upd) specify the migratory border-cell population by activating the signal transducer and activator of transcription (stat). a lower or transient level of stat activity specifies a non-migratory population of follicle cells. here we identify mir-279 as a component of a feedback pathway that further dampens the response in cells with low levels of jak/stat activity. mir-279 directly repressed stat, and loss of mir-279 mimicked stat gain-of-function or loss of apontic (apt), a known feedback inhibitor of stat. apt was essential for mir-279 expression in non-migratory follicle cells, whereas another stat target, ken and barbie (ken), downregulated mir-279 in border cells. mathematical modelling and simulations of this regulatory circuit including mir-279, apt and ken supported key roles for mir-279 and apt in generating threshold responses to the upd gradient.",1
"pancreatic cancer is an exceptionally aggressive disease in great need of more effective therapeutic options. epithelial-mesenchymal transition (emt) plays a key role in cancer invasion and metastasis, and there is a gain of stem cell properties during emt. here we report increased expression of the putative pancreatic stem cell marker dcamkl-1 in an established kras transgenic mouse model of pancreatic cancer and in human pancreatic adenocarcinoma. colocalization of dcamkl-1 with vimentin, a marker of mesenchymal lineage, along with 14-3-3 σ was observed within premalignant panin lesions that arise in the mouse model. sirna-mediated knockdown of dcamkl-1 in human pancreatic cancer cells induced microrna mir-200a, an emt inhibitor, along with downregulation of emt-associated transcription factors zeb1, zeb2, snail, slug, and twist. furthermore, dcamkl-1 knockdown resulted in downregulation of c-myc and kras through a let-7a microrna-dependent mechanism, and downregulation of notch-1 through a mir-144 microrna-dependent mechanism. these findings illustrate direct regulatory links between dcamkl-1, micrornas, and emt in pancreatic cancer. moreover, they demonstrate a functional role for dcamkl-1 in pancreatic cancer. together, our results rationalize dcamkl-1 as a therapeutic target for eradicating pancreatic cancers.",1
"objective osteogenic differentiation plays a crucial role in maintaining general bone homeostasis. long non-coding rnas (lncrnas) and micrornas (mirnas) act as important regulators during the osteogenesis process. this study aimed to elucidate the mechanism of potassium voltage-gated channel subfamily q member 1 overlapping transcript 1 (kcnq1ot1) in osteogenic differentiation. materials and methods quantitative real-time polymerase chain reaction (qrt-pcr) was conducted to detect the expression of kcnq1ot1, osteonectin (ocn), osteopontin (opn), runt-related transcription factor 2 (runx2), mir-320a, mothers against dpp homolog 5 (smad5). protein levels of ocn, opn, runx2 and smad5 were measured by western blot assay. alkaline phosphatase (alp) activity detection assay was performed to examine the alp activity. the interactions among kcnq1ot1, mir-320a and smad5 were determined by dual-luciferase reporter assay. results kcnq1ot1, ocn, opn and runx2 expression were enhanced in human bone marrow-derived mesenchymal stem cells (hbmscs) treated with osteogenic medium (om). kcnq1ot1 positively regulated ocn, opn and runx2 expression and alp activity of hbmscs. furthermore, kcnq1ot1 directly bound to mir-320a, and kcnq1ot1 knockdown reduced ocn, opn and runx2 expression and alp activity by suppressing mir-320a expression. moreover, smad5 was a target of mir-320a, and mir-320a inhibition abated the effects of smad5 silencing in ocn, opn and runx2 expression and alp activity of hbmscs. also, kcnq1ot1 knockdown reduced ocn, opn and runx2 expression by targeting mir-320a/smad5 axis. conclusions kcnq1ot1 promoted osteogenic differentiation of hbmscs by regulating smad5 expression via sponging mir-320a.",1
"background nemo-like kinase (nlk) is an evolutionarily conserved protein kinase involved in wnt/beta-catenin signaling, which has been reported to be associated with gliomagenesis. in the present study, we aimed to identify a concrete mechanism of wnt/beta-catenin pathway regulation by micrornas (mirnas) in glioma. methods quantitative reverse-transcription polymerase chain reaction and in situ hybridization were conducted to detect the expression of mir-92b. the cell proliferation rate and cell cycle kinetics were detected using 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide (mtt) assay and flow cytometry, cell invasion and migration were evaluated using transwell assay and wound healing assay, and cell apoptosis was detected using annexin v staining. furthermore, the relevant molecules regulating proliferation and invasion were examined using western blot analysis, immunohistochemistry, and immunofluorescence staining. luciferase reporter assay was used to identify the direct regulation of nlk by mir-92b and beta-catenin/tcf4 activity. results we first showed that the expression of mir-92b was elevated in both glioma samples and glioma cells. furthermore, down-regulation of mir-92b triggered growth inhibition, induced apoptosis, and suppressed invasion of glioma in vitro and in vivo. luciferase assay and western blot analysis revealed that nlk is a direct target of mir-92b. restoring expression of nlk inhibited glioma proliferation and invasion. mechanistic investigation revealed that mir-92b deletion suppressed beta-catenin/tcf-4 transcription activity by targeting nlk. moreover, expression of nlk was inversely correlated with mir-92b in glioma samples and was predictive of patient survival in a retrospective analysis. conclusions our findings identify a role for mir-92b in glioma proliferation and invasion after activation of wnt/beta-catenin signaling via nlk.",1
"during liver regeneration, normally quiescent liver cells reenter the cell cycle, nonparenchymal and parenchymal cells divide, and proper liver architecture is restored. the gene expression programs regulating these transitions are not completely understood. micrornas are a newly discovered class of small regulatory rnas that silence messenger rnas by binding to their 3'-untranslated regions (utrs). a number of micrornas, including mir-21, have been shown to be involved in regulation of cell proliferation. we performed partial hepatectomies on mice and allowed the liver to regenerate for 1, 6, 12, 24, and 48 h and 4 and 7 days. we compared the expression of mir-21 in the posthepatectomy liver to the prehepatectomy liver by northern blot and found that mir-21 was upregulated during the early stages of liver regeneration. nf-kappab signaling is also activated very early during liver regeneration. it has been previously reported that nf-kappab upregulates the mir-21 precursor transcript. the predicted mir-21 target, pellino (peli1), is a ubiquitin ligase involved in activating nf-kappab signaling. we observed an inverse correlation between mir-21 and peli1 mrna levels during liver regeneration. mir-21 overexpression in cultured cells inhibited a peli1 3'-utr luciferase reporter. using nf-kappab reporter assays, we determined that mir-21 overexpression inhibits nf-kappab signaling. in conclusion, mir-21 expression was upregulated during early stages of liver regeneration. targeting of peli1 by mir-21 could potentially provide the basis for a negative feedback cycle regulating nf-kappab signaling.",1
"pulmonary hypertension (ph) is a progressive disorder whose cellular pathogenesis involves enhanced smooth muscle cell (smc) proliferation and resistance to apoptosis signals. existing evidence demonstrates that the tumor suppressor programmed cell death 4 (pdcd4) affects patterns of cell growth and repair responses in the systemic vasculature following experimental injury. in the current study, the regulation pdcd4 and its functional effects on growth and apoptosis susceptibility in pulmonary artery smooth muscle cells were explored. we previously demonstrated that pharmacological activation of the nuclear transcription factor peroxisome proliferator-activated receptor-γ (pparγ) attenuated hypoxia-induced proliferation of human pulmonary artery smooth muscle cells (hpasmcs) by inhibiting the expression and mitogenic functions of microrna-21 (mir-21). in the current study, we hypothesize that pparγ stimulates pdcd4 expression and hpasmc apoptosis by inhibiting mir-21. our findings demonstrate that pdcd4 is reduced in the mouse lung upon exposure to chronic hypoxia (10% o 2 for 3 wk) and in hypoxia-exposed hpasmcs (1% o 2 ). hpasmc apoptosis was reduced by hypoxia, by mir-21 overexpression, or by sirna-mediated pparγ and pdcd4 depletion. activation of pparγ inhibited mir-21 expression and resultant proliferation, while restoring pdcd4 levels and apoptosis to baseline. additionally, pharmacological activation of pparγ with rosiglitazone enhanced pdcd4 protein expression and apoptosis in a dose-dependent manner as demonstrated by increased annexin v detection by flow cytometry. collectively, these findings demonstrate that pparγ confers growth-inhibitory signals in hypoxia-exposed hpasmcs through suppression of mir-21 and the accompanying derepression of pdcd4 that augments hpasmc susceptibility to undergo apoptosis.",1
"tnf is a central actor during inflammation and a well-recognized drug target for inflammatory diseases. we found that the mouse strain spret/ei, known for extreme and dominant resistance against tnf-induced shock, displays weak expression of tnf receptor 1 protein (tnfr1) but normal mrna expression, a trait genetically linked to the major tnfr1 coding gene tnfrsf1a and to a locus harbouring the predicted tnfr1-regulating mir-511. this mirna is a genuine tnfr1 regulator in cells. in mice, overexpression of mir-511 down-regulates tnfr1 and protects against tnf, while anti-mir-511 up-regulates tnfr1 and sensitizes for tnf, breaking the resistance of spret/ei. we found that mir-511 inhibits endotoxemia and experimental hepatitis and that this mir is strongly induced by glucocorticoids and is a true tnfr1 modulator and thus an anti-inflammatory mir. since minimal reductions of tnfr1 have considerable effects on tnf sensitivity, we believe that at least part of the anti-inflammatory effects of glucocorti-coids are mediated by induction of this mir, resulting in reduced tnfr1 expression.",1
"there is increasing evidence supporting the role of members of the polycomb group (pcg) gene family in tumor development and progression. however, their precise role in tumorigenesis and mechanisms of their regulation remain to be elucidated. using nasopharyngeal carcinoma (npc) as a disease model, a comprehensive analysis was undertaken on the clinical significance of ezh2 expression, identification of the cellular processes regulated by ezh2, and the mechanisms of its deregulated expression. herein, we report ezh2 as being associated with a higher risk of relapse in npc patients (p = 0.002). genome-wide microarray and bioinformatics identified several vital cellular processes (such as differentiation, development, and apoptosis) to be regulated by ezh2, corroborated by in vitro lethality, and delayed tumor formation in vivo upon ezh2 depletion. the combination of global microrna (mir) profiling in primary npc specimens, and in silico analyses provided several candidate mirs that could regulate ezh2. using a luciferase-based assay, mir-26a, mir-101, and mir-98 were validated as bona fide regulators of ezh2 expression. in particular, mir-98 was underexpressed in relapsed patient samples, strongly suggesting an important role for the mir-98 and ezh2 axis in npc biology.",1
"dsra rna regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated h-ns protein, and translation, by promoting efficient translation of the stress sigma factor, rpos. these two activities of dsra can be separated by mutation: the first of three stem-loops of the 85 nucleotide rna is necessary for rpos translation but not for anti-h-ns action, while the second stem-loop is essential for antisilencing and less critical for rpos translation. the third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either dsra function. the sequence of the first stem-loop of dsra is complementary with the upstream leader portion of rpos messenger rna, suggesting that pairing of dsra with the rpos message might be important for translational regulation. mutations in the rpos leader and compensating mutations in dsra confirm that this predicted pairing is necessary for dsra stimulation of rpos translation. we propose that dsra pairing stimulates rpos translation by acting as an anti-antisense rna, freeing the translation initiation region from the cis-acting antisense rna and allowing increased translation.",1
"cholangiocarcinoma (cca), which is a poor prognosis malignancy that arises from the malignant transformation of cholangiocytes, is associated with chronic inflammation of the biliary epithelium. thus far, the molecular mechanisms of the origin and neoplastic processes of cca that are promoted by inflammation are still unclear and need to be fully elucidated. here using small rna sequencing to determine the microrna (mirna) expression profiles in cca, we found that let-7c, mir-99a and mir-125b, which are three mirnas of the same cluster, were downregulated in cca and targeted interleukin 6 (il-6), il-6r and type 1 insulin-like growth factor, which are important cytokines and receptors of the il-6/signal transducer and activator 3 (stat3) pathway and have key roles in inflammation and cca initiation. we also found that enforced expression of let-7c, mir-99a or mir-125b could reduce the activity of stat3 and further suppress cca tumorigenicity in vivo and inhibit the migration and invasion of cca cells in vitro. surprisingly, let-7c/mir-99a/mir-125b cluster also significantly decreased the ability of cca cells for cancer stem cell-like mammosphere generation by downregulating cd133 and cd44, which suggests the pivotal roles of let-7c, mir-99a and mir-125b in cca by regulating both inflammation and stem-like properties. our findings showed potential links between mirnas and inflammation, and provide a potential treatment strategy for developing an mirna-based therapy via il-6/stat3 targeting for cca.",1
"an infectious cdna clone of hepatitis e virus was mutated in order to prevent synthesis of either open reading frame 2 (orf2) protein or orf3 protein. huh-7 cells transfected with an orf2-null mutant produced orf3, and those transfected with an orf3-null mutant produced orf2. silent mutations introduced into a highly conserved nucleotide sequence in the orf3 coding region eliminated the synthesis of both orf2 and orf3 proteins, suggesting that it comprised a cis-reactive element. a mutant that was not able to produce orf3 protein did not produce a detectable infection in rhesus macaques. however, a mutant that encoded an orf3 protein lacking a phosphorylation site reported to be critical for function was able to replicate its genome in cell culture and to induce viremia and seroconversion in rhesus monkeys, suggesting that phosphorylation of orf3 protein was not necessary for genome replication or for production of infectious virions.",1
"cellular expression of mcl-1, an anti-apoptotic bcl-2 family member, is tightly regulated. recently, bcl-2 expression was shown to be regulated by micrornas, small endogenous rna molecules that regulate protein expression through sequence-specific interaction with messenger rna. by analogy, we reasoned that mcl-1 expression may also be regulated by micrornas. we chose human immortalized, but non-malignant, h69 cholangiocyte and malignant kmch cholangiocarcinoma cell lines for these studies, because mcl-1 is dysregulated in cells with the malignant phenotype. by in silico analysis, we identified a putative target site in the mcl-1 mrna for the mir-29 family, and found that mir-29b was highly expressed in cholangiocytes. interestingly, mir-29b was downregulated in malignant cells, consistent with mcl-1 protein upregulation. enforced mir-29b expression reduced mcl-1 protein expression in kmch cells. this effect was direct, as mir-29b negatively regulated the expression of an mcl-1 3' untranslated region (utr)-based reporter construct. enforced mir-29b expression reduced mcl-1 cellular protein levels and sensitized the cancer cells to tumor necrosis factor-related apoptosis-inducing ligand (trail) cytotoxicity. transfection of non-malignant cells (that express high levels of mir-29) with a locked-nucleic acid antagonist of mir-29b increased mcl-1 levels and reduced trail-mediated apoptosis. thus mir-29 is an endogenous regulator of mcl-1 protein expression, and thereby, apoptosis.",1
"little is known about the contribution of translational control to circadian rhythms. to address this issue and in particular translational control by micrornas (mirnas), we knocked down the mirna biogenesis pathway in drosophila circadian tissues. in combination with an increase in circadian-mediated transcription, this severely affected drosophila behavioral rhythms, indicating that mirnas function in circadian timekeeping. to identify mirna-mrna pairs important for this regulation, immunoprecipitation of ago1 followed by microarray analysis identified mrnas under mirna-mediated control. they included three core clock mrnas-clock (clk), vrille (vri), and clockworkorange (cwo). to identify mirnas involved in circadian timekeeping, we exploited circadian cell-specific inhibition of the mirna biogenesis pathway followed by tiling array analysis. this approach identified mirnas expressed in fly head circadian tissue. behavioral and molecular experiments show that one of these mirnas, the developmental regulator bantam, has a role in the core circadian pacemaker. s2 cell biochemical experiments indicate that bantam regulates the translation of clk through an association with three target sites located within the clk 3' untranslated region (utr). moreover, clk transgenes harboring mutated bantam sites in their 3' utrs rescue rhythms of clk mutant flies much less well than wild-type clk transgenes.",1
"dietary restriction (dr) extends healthy lifespan in diverse species. age and nutrient-related changes in the abundance of micrornas (mirnas) and their processing factors have been linked to organismal longevity. however, the mechanisms by which they modulate lifespan and the tissue-specific role of mirna-mediated networks in dr-dependent enhancement of lifespan remains largely unexplored. we show that two neuronally enriched and highly conserved micrornas, mir-125 and let-7 mediate the dr response in drosophila melanogaster . functional characterization of mir-125 demonstrates its role in neurons while its target chinmo acts both in neurons and the fat body to modulate fat metabolism and longevity. proteomic analysis revealed that chinmo exerts its dr effects by regulating the expression of fatp, cg2017, cg9577, cg17554, cg5009, cg8778, cg9527 , and fasn1 . our findings identify mir-125 as a conserved effector of the dr pathway and open the avenue for this small rna molecule and its downstream effectors to be considered as potential drug candidates for the treatment of late-onset diseases and biomarkers for healthy aging in humans.",1
"background micrornas (mirs) participate in many cardiac pathophysiological processes, including ischemia/reperfusion (i/r)-induced cardiac injury. recently, we and others observed that mir-494 was downregulated in murine i/r-injured and human infarcted hearts. however, the functional consequence of mir-494 in response to i/r remains unknown. methods and results we generated a mouse model with cardiac-specific overexpression of mir-494. transgenic hearts and wild-type hearts from multiple lines were subjected to global no-flow i/r with the langendorff system. transgenic hearts exhibited improved recovery of contractile performance over the reperfusion period. this improvement was accompanied by remarkable decreases in both lactate dehydrogenase release and the extent of apoptosis in transgenic hearts compared with wild-type hearts. in addition, myocardial infarction size was significantly reduced in transgenic hearts on i/r in vivo compared with wild-type hearts. similarly, short-term overexpression of mir-494 in cultured adult cardiomyocytes demonstrated an inhibition of caspase-3 activity and reduced cell death on simulated i/r. in vivo treatment with antisense oligonucleotide mir-494 increased i/r-triggered cardiac injury relative to the administration of mutant antisense oligonucleotide mir-494 and saline controls. we further identified that 3 proapoptotic proteins (pten, rock1, and camkiiδ) and 2 antiapoptotic proteins (fgfr2 and lif) were authentic targets for mir-494. importantly, the akt-mitochondrial signaling pathway was activated in mir-494-overexpressing myocytes. conclusions our findings suggest that although mir-494 targets both proapoptotic and antiapoptotic proteins, the ultimate consequence is activation of the akt pathway, leading to cardioprotective effects against i/r-induced injury. thus, mir-494 may constitute a new therapeutic agent for the treatment of ischemic heart disease.",1
"background recent profile studies of microrna (mirna) expression have documented a deregulation of mirna (mir-124) in hepatocellular carcinoma (hcc). objective to determine the status of mir-124 expression and its underlying mechanisms in the pathogenesis of hcc. methods the expression levels of mir-124 were first examined in hcc cell lines and tumour tissues by real-time pcr. the in vitro and in vivo functional effect of mir-124 was examined further. a luciferase reporter assay was conducted to confirm target associations. results the expression levels of mir-124 were frequently reduced in hcc cells and tissues, and low-level expression of mir-124 was significantly associated with a more aggressive and/or poor prognostic phenotype of patients with hcc (p conclusion these data highlight an important role for mir-124 in the regulation of invasion and metastasis in the molecular aetiology of hcc, and suggest a potential application of mir-124 in prognosis prediction and cancer treatment.",1
"aberrant micro rna (mirna) expression has been implicated in the pathogenesis of cancer. recent studies have shown that the mir-17-92 cluster is overexpressed in many types of cancer. the oncogenic function of mature mirnas encoded by the mir-17-92 cluster has been identified from the 5' arm of six precursors. however, the function of the mirnas produced from the 3' arm of these precursors remains unknown. the present study demonstrates that mir-17* is able to suppress critical primary mitochondrial antioxidant enzymes, such as manganese superoxide dismutase (mnsod), glutathione peroxidase-2 (gpx2) and thioredoxin reductase-2 (trxr2). transfection of mir-17* into prostate cancer pc-3 cells significantly reduces levels of the three antioxidant proteins and activity of the luciferase reporter under the control of mir-17* binding sequences located in the 3'-untranslated regions of the three target genes. disulfiram (dsf), a dithiolcarbomate drug shown to have an anticancer effect, induces the level of mature mir-17* and cell death in pca cells, which can be attenuated by transfection of antisense mir-17*. increasing mir-17* level in pc-3 cells by a tet-on based conditional expression system markedly suppresses its tumorigencity. these results suggest that mir-17* may suppress tumorigenicity of prostate cancer through inhibition of mitochondrial antioxidant enzymes.",1
"mdr1 is highly expressed in mdr a2780dx5 ovarian cancer cells, mdr sgc7901r gastric cancer cells and recurrent tumours. it pumps cytoplasmic agents out of cells, leading to decreased drug accumulation in cells and making cancer cells susceptible to multidrug resistance. here, we identified that mir-495 was predicted to target abcb1, which encodes protein mdr1. to reduce the drug efflux and reverse mdr in cancer cells, we overexpressed a mir-495 mimic in sgc7901r and a2780dx cells and in transplanted mdr ovarian tumours in vivo. the results indicated that the expression of mdr1 in the above cells or tumours was suppressed and that subsequently the drug accumulation in the mdr cells was decreased, cell death was increased, and tumour growth was inhibited after treatment with taxol-doxorubicin, demonstrating increased drug sensitivity. this study suggests that pre-treatment with mir-495 before chemotherapy could improve the curative effect on mdr1-based mdr cancer.",1
"the drosophila let-7-complex (let-7-c) is a polycistronic locus encoding three ancient micrornas: let-7, mir-100, and fly lin-4 (mir-125). we find that the let-7-c locus is principally expressed in the pupal and adult neuromusculature. let-7-c knockout flies appear normal externally but display defects in adult behaviors (e.g., flight, motility, and fertility) as well as clear juvenile features in their neuromusculature. we find that the function of let-7-c to ensure the appropriate remodeling of the abdominal neuromusculature during the larval-to-adult transition is carried out predominantly by let-7 alone. this heterochronic role of let-7 is likely just one of the ways in which let-7-c promotes adult behavior.",1
"adult stem cells support tissue homeostasis and repair throughout the life of an individual. during ageing, numerous intrinsic and extrinsic changes occur that result in altered stem-cell behaviour and reduced tissue maintenance and regeneration. in the drosophila testis, ageing results in a marked decrease in the self-renewal factor unpaired (upd), leading to a concomitant loss of germline stem cells. here we demonstrate that igf-ii messenger rna binding protein (imp) counteracts endogenous small interfering rnas to stabilize upd (also known as os) rna. however, similar to upd, imp expression decreases in the hub cells of older males, which is due to the targeting of imp by the heterochronic microrna let-7. in the absence of imp, upd mrna therefore becomes unprotected and susceptible to degradation. understanding the mechanistic basis for ageing-related changes in stem-cell behaviour will lead to the development of strategies to treat age-onset diseases and facilitate stem-cell-based therapies in older individuals.",1
"cholesteatoma is a destructive and abnormal skin growth consisting of keratinizing squamous epithelium in the middle ear. its molecular mechanisms remain poorly understood. here, we found that the nf-κb inflammatory signaling pathway was highly activated in cholesteatoma. nf-κb activation increased the expression of microrna-802 (mir-802) and chromatin immunoprecipitation assays showed that p65 could uniquely bind to mir-802 promoter. mir-802 overexpression promoted keratinocyte cell proliferation and cell cycle progression, while inhibition of mir-802 decreased these effects. from computational analysis and luciferase report assays, mir-802 directly repressed pten expression by targeting its 3'-utr. our results demonstrate that the nf-κb/mir-802/pten signaling pathway plays an important role in the development of cholesteatoma.",1
"cell fate decisions of pluripotent embryonic stem (es) cells are dictated by activation and repression of lineage-specific genes. numerous signaling and transcriptional networks progressively narrow and specify the potential of es cells. whether specific micrornas help refine and limit gene expression and, thereby, could be used to manipulate es cell differentiation has largely been unexplored. here, we show that two serum response factor (srf)-dependent muscle-specific micrornas, mir-1 and mir-133, promote mesoderm formation from es cells but have opposing functions during further differentiation into cardiac muscle progenitors. furthermore, mir-1 and mir-133 were potent repressors of nonmuscle gene expression and cell fate during mouse and human es cell differentiation. mir-1's effects were in part mediated by translational repression of the notch ligand delta-like 1 (dll-1). our findings indicate that muscle-specific mirnas reinforce the silencing of nonmuscle genes during cell lineage commitment and suggest that mirnas may have general utility in regulating cell-fate decisions from pluripotent es cells.",1
"type i interferon (ifn-i) production is efficiently induced to ensure a potent innate immune response to viral infection. how this response can be enhanced, however, remains to be explored. here, we identify a new cytoplasmic long non-coding rna (lncrna), lnclrrc55-as, that drives a positive feedback loop to promote interferon regulatory factor 3 (irf3) signaling and ifn-i production. we show that lnclrrc55-as is virus-induced in multiple cell types via the ifn-jak-stat pathway. lnclrrc55-as-deficient mice display a weakened antiviral immune response and are more susceptible to viral challenge. mechanistically, lnclrrc55-as binds phosphatase methylesterase 1 (pme-1), and promotes the interaction between pme-1 and the phosphatase pp2a, an inhibitor of irf3 signaling. lnclrrc55-as supports pme-1-mediated demethylation and inactivation of pp2a, thereby enhancing irf3 phosphorylation and signaling. loss of pme-1 phenocopies lnclrrc55-as deficiency, leading to diminished irf3 phosphorylation and ifn-i production. we have identified an ifn-induced lncrna as a positive regulator of ifn-i production, adding mechanistic insight into lncrna-mediated regulation of signaling in innate immunity and inflammation.",1
"genome-wide studies have identified thousands of long noncoding rnas (lncrnas) lacking protein-coding capacity. however, most lncrnas are expressed at a very low level, and in most cases there is no genetic evidence to support their in vivo function. malat1 (metastasis associated lung adenocarcinoma transcript 1) is among the most abundant and highly conserved lncrnas, and it exhibits an uncommon 3'-end processing mechanism. in addition, its specific nuclear localization, developmental regulation, and dysregulation in cancer are suggestive of it having a critical biological function. we have characterized a malat1 loss-of-function genetic model that indicates that malat1 is not essential for mouse pre- and postnatal development. furthermore, depletion of malat1 does not affect global gene expression, splicing factor level and phosphorylation status, or alternative pre-mrna splicing. however, among a small number of genes that were dysregulated in adult malat1 knockout mice, many were malat1 neighboring genes, thus indicating a potential cis-regulatory role of malat1 gene transcription.",1
"the c-myc oncoprotein regulates >15% of the human transcriptome and a limited number of micrornas (mirnas). here, we establish that in a human b-lymphoid cell line, myc-repressed, but not myc-stimulated, genes are significantly enriched for predicted binding sites of myc-regulated mirnas, primarily those comprising the myc-activated mir-17~92 cluster. notably, gene set enrichment analysis demonstrates that mir-17∼92 is a major regulator of b-cell receptor (bcr) pathway components. many of them are immunoreceptor tyrosine inhibitory motif (itim)-containing proteins, and itim proteins cd22 and fcgr2b were found to be direct targets of mir-17∼92. consistent with the propensity of itim proteins to recruit phosphatases, either myc or mir-17~92 expression was necessary to sustain phosphorylation of spleen tyrosine kinase (syk) and the b-cell linker protein (blnk) upon ligation of the bcr. further downstream, stimulation of the bcr response by mir-17-92 resulted in the enhanced calcium flux and elevated levels of myc itself. notably, inhibition of the mir-17~92 cluster in diffuse large b-cell lymphoma (dlbcl) cell lines diminished the bcr response as measured by syk and blnk phosphorylation. conversely, human dlbcls of the bcr subtype express higher myc and mir17hg transcript levels than other subtypes. hence, the myc-mir-17-92-bcr axis, frequently affected by genomic rearrangements, constitutes a novel lymphomagenic feed-forward loop.",1
"aims recent ability to derive endothelial cells (ecs) from induced pluripotent stem (ips) cells holds a great therapeutic potential for personalized medicine and stem cell therapy. we aimed that better understanding of the complex molecular signals that are evoked during ips cell differentiation toward ecs may allow specific targeting of their activities to enhance cell differentiation and promote tissue regeneration. methods and results in this study, we have generated mouse ips cells from fibroblasts using established protocol. when ips cells were cultivated on type iv mouse collagen-coated dishes in differentiation medium, cell differentiation toward vascular lineages were observed. to study the molecular mechanisms of ips cell differentiation, we found that mir-199b is involved in ec differentiation. a step-wise increase in expression of mir-199 was detected during ec differentiation. notably, mir-199b targeted the notch ligand jag1, resulting in vascular endothelial growth factor (vegf) transcriptional activation and secretion through the transcription factor stat3. upon shrna-mediated knockdown of the notch ligand jag1, the regulatory effect of mir-199b was ablated and there was robust induction of stat3 and vegf during ec differentiation. knockdown of jag1 also inhibited mir-199b-mediated inhibition of ips cell differentiation toward smooth muscle markers. using the in vitro tube formation assay and implanted matrigel plugs, in vivo, mir-199b also regulated vegf expression and angiogenesis. conclusions this study indicates a novel role for mir-199b as a regulator of the phenotypic switch during vascular cell differentiation derived from ips cells by regulating critical signaling angiogenic responses. stem cells 2015;33:1405-1418.",1
"background we recently showed that mir-494 was downregulated in gastric carcinoma (gc). the objectives of this study were to determine the role of mir-494 in gc malignancy and to identify its target genes. methods real-time polymerase chain reaction was employed to quantify the expression level of mir-494 and c-myc in gastric cancer tissues. bioinformatics was used to predict the downstream target genes of mir-494, which were confirmed by luciferase and rna immunoprecipitation assays. cell functional analyses and a xenograft mouse model were used to evaluate the role of mir-494 in malignancy. results mir-494 was downregulated in human gc tissues and in gc cells and was negatively correlated with c-myc expression. high level of c-myc or low level of mir-494 correlated with poor prognosis. the mir-494-binding site in the c-myc 3' untranslated region was predicted using targetscan and was confirmed by the luciferase assay. additionally, c-myc and mir-494 were enriched in coimmunoprecipitates with tagged argonaute2 proteins in cells overexpressing mir-494. furthermore, a mir-494 mimic significantly downregulated endogenous c-myc expression, which may contribute to the delayed g1/s transition, decreased synthesis phase bromodeoxyuridine incorporation, and impaired cell growth and colony formation; on the other hand, treatment with a mir-494 inhibitor displayed the opposite effects. reduced tumor burden and decreased cell proliferation were observed following the delivery of mir-494 into xenograft mice. conclusion mir-494 is downregulated in human gc and acts as an anti-oncogene by targeting c-myc. mir-494 plays a role in the pathogenesis of gastric cancer in a recessive fashion.",1
"maintenance of telomere integrity requires the dynamic interplay between telomerase, telomere-associated proteins and dna repair proteins. these interactions are vital to suppress dna damage responses and changes in chromosome dynamics that can result in aneuploidy or other transforming aberrations. the interaction between the dna repair protein ku and the rna component of telomerase (tlc1) in saccharomyces cerevisiae has been shown to be important for maintaining telomere length. here, we sought to determine whether this interaction was conserved in higher eukaryotes. although there is no sequence similarity between tlc1 and the rna component (htr) of human telomerase, we show that human ku70/80 interacts with htr both in vitro and in a cellular context. specifically, ku70/80 interacts with a 47 nt region of the 3' end of htr, which resembles the stem-loop region of the yeast ku70/80 binding domain on tlc1. furthermore, utilizing immunoprecipitation/rt-pcr experiments, we show that ku interacts with htr in cell lines deficient in the human telomerase reverse transcriptase protein (htert), suggesting that this interaction does not require htert. these data suggest that ku interacts directly with htr, independent of htert, providing evidence for the conservation of the interaction between ku and telomerase rna among various species and provide significant insight into how ku is involved in telomere maintenance in higher eukaryotes.",1
"micrornas (mirnas) play important roles in diverse biological processes and are emerging as key regulators of tumorigenesis and tumor progression. to explore the dysregulation of mirnas in breast cancer, a genome-wide expression profiling of 939 mirnas was performed in 50 breast cancer patients. a total of 35 mirnas were aberrantly expressed between breast cancer tissue and adjacent normal breast tissue and several novel mirnas were identified as potential oncogenes or tumor suppressor mirnas in breast tumorigenesis. mir-125b exhibited the largest decrease in expression. enforced mir-125b expression in mammary cells decreased cell proliferation by inducing g2/m cell cycle arrest and reduced anchorage-independent cell growth of cells of mammary origin. mir-125b was found to perform its tumor suppressor function via the direct targeting of the 3'-utrs of enpep, ck2-α, ccnj, and megf9 mrnas. silencing these mir-125b targets mimicked the biological effects of mir-125b overexpression, confirming that they are modulated by mir-125b. analysis of enpep, ck2-α, ccnj, and megf9 protein expression in breast cancer patients revealed that they were overexpressed in 56%, 40-56%, 20%, and 32% of the tumors, respectively. the expression of enpep and ck2-α was inversely correlated with mir-125b expression in breast tumors, indicating the relevance of these potential oncogenic proteins in breast cancer patients. our results support a prognostic role for ck2-α, whose expression may help clinicians predict breast tumor aggressiveness. in particular, our results show that restoration of mir-125b expression or knockdown of enpep, ck2-α, ccnj, or megf9 may provide novel approaches for the treatment of breast cancer.",1
"the overexpression of microrna-21 (mir-21) is linked to a number of human tumors including colorectal cancer, where it appears to regulate the expression of tumor suppressor genes including p21, phosphatase and tensin homolog, tgfβ receptor ii, and b-cell leukemia/lymphoma 2 -associated x protein. here we demonstrate that mir-21 targets and down-regulates the core mismatch repair (mmr) recognition protein complex, human muts homolog 2 (hmsh2) and 6 (hmsh6). colorectal tumors that express a high level of mir-21 display reduced hmsh2 protein expression. cells that overproduce mir-21 exhibit significantly reduced 5-fluorouracil (5-fu)-induced g2/m damage arrest and apoptosis that is characteristic of defects in the core mmr component. moreover, xenograft studies demonstrate that mir-21 overexpression dramatically reduces the therapeutic efficacy of 5-fu. these studies suggest that the down-regulation of the mmr mutator gene associated with mir-21 overexpression may be an important clinical indicator of therapeutic efficacy in colorectal cancer.",1
"unlabelled development of improved rna interference-based strategies is of utmost clinical importance. although sirna-mediated silencing of epha2, an ovarian cancer oncogene, results in reduction of tumor growth, we present evidence that additional inhibition of epha2 by a microrna (mirna) further ""boosts"" its antitumor effects. we identified mir-520d-3p as a tumor suppressor upstream of epha2, whose expression correlated with favorable outcomes in two independent patient cohorts comprising 647 patients. restoration of mir-520d-3p prominently decreased epha2 protein levels, and suppressed tumor growth and migration/invasion both in vitro and in vivo. dual inhibition of epha2 in vivo using 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (dopc) nanoliposomes loaded with mir-520d-3p and epha2 sirna showed synergistic antitumor efficiency and greater therapeutic efficacy than either monotherapy alone. this synergy is at least in part due to mir-520d-3p targeting ephb2, another eph receptor. our data emphasize the feasibility of combined mirna-sirna therapy, and will have broad implications for innovative gene silencing therapies for cancer and other diseases. significance this study addresses a new concept of rna inhibition therapy by combining mirna and sirna in nanoliposomal particles to target oncogenic pathways altered in ovarian cancer. combined targeting of the eph pathway using epha2-targeting sirna and the tumor suppressor mir-520d-3p exhibits remarkable therapeutic synergy and enhanced tumor suppression in vitro and in vivo compared with either monotherapy alone.",1
"xb130, a novel adaptor protein, promotes cell growth by controlling expression of many related genes. micrornas (mirnas), which are frequently mis-expressed in cancer cells, regulate expression of targeted genes. in this present study, we aimed to explore the oncogenic mechanism of xb130 through mirnas regulation. we analyzed mirna expression in xb130 short hairpin rna (shrna) stably transfected wro thyroid cancer cells by a mirna array assay, and 16 mirnas were up-regulated and 22 mirnas were down-regulated significantly in these cells, in comparison with non-transfected or negative control shrna transfected cells. we chose three of the up-regulated mirnas (mir-33a, mir-149 and mir-193a-3p) and validated them by real-time qrt-pcr. ectopic overexpression of xb130 suppressed these 3 mirnas in mro cells, a cell line with very low expression of xb130. furthermore, we transfected mir mimics of these 3 mirnas into wro cells. they negatively regulated expression of oncogenes (mir-33a: myc, mir-149: fosl1, mir-193a-3p: slc7a5), by targeting their 3' untranslated region, and reduced cell growth. our results suggest that xb130 could promote growth of cancer cells by regulating expression of tumor suppressive mirnas and their targeted genes.",1
"ginsenoside-rg1 (rg1) has been identified as potent proangiogenic agent, which plays an important role in wound healing promotion or treatment of ischemic injury. we previously reported that mir-214/enos pathway was involved in rg1-induced angiogenesis. following the same microrna microarray profiling data, we proposed mir-15b would be another microrna candidate involved in rg1-induced angiogenesis. using human umbilical vein endothelial cells (huvecs), it was showed that rg1 could reduce mir-15b expression rapidly and steadily, leading to a temporal induction of vascular endothelial growth factor receptor-2 (vegfr-2). the in vitro motility and tubulogenesis via vegfr-2 in rg1-treated huvecs were also demonstrated. besides, the reduction of vegfr-2 3'-utr reporter activity by mir-15b in the luciferase reporter gene assay clearly indicated that mir-15b could affect the vegfr-2 transcript through targeting its 3'-utr region. diminishing expression of endogenous mir-15b could increase vegfr-2 expression and huvecs migration and tubulogenesis; while over-expression of mir-15b was found to associate with the reduction of vegfr-2 expression as well as cellular migration and tubulogenesis. in vivo, artificial increment of mir-15b by injecting pre-mir-15b precursor into zebrafish embryos was also found to significantly suppress the subintestinal vessels formation. in conclusion, our results further demonstrated the involvement of micrornas in rg1-induced angiogenesis.",1
"upregulation of pin1 was shown to advance the functioning of several oncogenic pathways. it was recently shown that pin1 is potentially an excellent prognostic marker and can also serve as a novel therapeutic target for prostate cancer. however, the molecular mechanism of pin1 overexpression in prostate cancer is still unclear. in the present study, we showed that the mrna expression levels of pin1 were not correlated with pin1 protein levels in prostate cell lines which indicated that pin1 may be regulated at the post-transcriptional level. a key player in post-transcriptional regulation is represented by micrornas (mirnas) that negatively regulate expressions of protein-coding genes at the post-transcriptional level. a bioinformatics analysis revealed that mir-296-5p has a conserved binding site in the pin1 3'-untranslated region (utr). a luciferase reporter assay demonstrated that the seed region of mir-296-5p directly interacts with the 3'-utr of pin1 mrna. moreover, mir-296-5p expression was found to be inversely correlated with pin1 expression in prostate cancer cell lines and prostate cancer tissues. furthermore, restoration of mir-296-5p or the knockdown of pin1 had the same effect on the inhibition of the ability of cell proliferation and anchorage-independent growth of prostate cancer cell lines. our results support mir-296-5p playing a tumor-suppressive role by targeting pin1 and implicate potential effects of mir-296-5p on the prognosis and clinical application to prostate cancer therapy.",1
"rationale cardiomyocytes in adult mammalian hearts are terminally differentiated cells that have exited from the cell cycle and lost most of their proliferative capacity. death of mature cardiomyocytes in pathological cardiac conditions and the lack of regeneration capacity of adult hearts are primary causes of heart failure and mortality. however, how cardiomyocyte proliferation in postnatal and adult hearts becomes suppressed remains largely unknown. the mir-17-92 cluster was initially identified as a human oncogene that promotes cell proliferation. however, its role in the heart remains unknown. objective to test the hypothesis that mir-17-92 participates in the regulation of cardiomyocyte proliferation in postnatal and adult hearts. methods and results we deleted mir-17-92 cluster from embryonic and postnatal mouse hearts and demonstrated that mir-17-92 is required for cardiomyocyte proliferation in the heart. transgenic overexpression of mir-17-92 in cardiomyocytes is sufficient to induce cardiomyocyte proliferation in embryonic, postnatal, and adult hearts. moreover, overexpression of mir-17-92 in adult cardiomyocytes protects the heart from myocardial infarction-induced injury. similarly, we found that members of mir-17-92 cluster, mir-19 in particular, are required for and sufficient to induce cardiomyocyte proliferation in vitro. we identified phosphatase and tensin homolog, a tumor suppressor, as an mir-17-92 target to mediate the function of mir-17-92 in cardiomyocyte proliferation. conclusions our studies therefore identify mir-17-92 as a critical regulator of cardiomyocyte proliferation, and suggest this cluster of micrornas could become therapeutic targets for cardiac repair and heart regeneration.",1
"transcript-selective translational control of eukaryotic gene expression is often directed by a structural element in the 3' untranslated region (3'-utr) of the mrna. in the case of ceruloplasmin (cp), induced synthesis of the protein by gamma interferon (ifn-gamma) in u937 monocytic cells is halted by a delayed translational silencing mechanism requiring the binding of a cytosolic inhibitor to the cp 3'-utr. silencing requires the essential elements of mrna circularization, i.e., eukaryotic initiation factor 4g, poly(a)-binding protein, and poly(a) tail. we here determined the minimal silencing element in the cp 3'-utr by progressive deletions from both termini. a minimal, 29-nucleotide (nt) element was determined by gel shift assay to be sufficient for maximal binding of the ifn-gamma-activated inhibitor of translation (gait), an as-yet-unidentified protein or complex. the interaction was shown to be functional by an in vitro translation assay in which the gait element was used as a decoy to overcome translational silencing. mutation analysis showed that the gait element contained a 5-nt terminal loop, a weak 3-bp helix, an asymmetric internal bulge, and a proximal 6-bp helical stem. two invariant loop residues essential for binding activity were identified. ligation of the gait element immediately downstream of a luciferase reporter conferred the translational silencing response to the heterologous transcript in vitro and in vivo; a construct containing a nonbinding, mutated gait element was ineffective. translational silencing of cp, and possibly other transcripts, mediated by the gait element may contribute to the resolution of the local inflammatory response following cytokine activation of macrophages.",1
"growing evidence indicates that some tumor suppressive mirnas are subject to epigenetic modifications during carcinogenesis. here, we found that a large mirna cluster of c19mc was upregulated in hcc cells after combined treatment with dna methylation inhibitor and histone deacetylase inhibitor. mir-517a and mir-517c were strikingly different from the remaining 41 mirnas in c19mc. ectopic expression of mir-517a and mir-517c inhibited cell proliferation by blocking g2/m transition, whereas down-regulation of mir-517a and mir-517c facilitated cell growth. we further showed pyk2 is a target of mir-517a and mir-517c and both the mirnas are downregulated in hcc samples. these data collectively suggest that down-regulation of both mir-517a and mir-517c contribute to hcc development through regulating pyk2.",1
"kaposi's sarcoma-associated herpesvirus (kshv) infection was necessary but not sufficient for ks development without other cofactors. we have previously reported that herpes simplex virus (hsv)-1 was an important cofactor that reactivated kshv from latency by inducing the expression of kshv replication and transcription activator (rta), the lytic switch protein. here, we further investigated the possible cellular micrornas (mirnas) involved in regulation of rta during hsv-1-induced kshv replication. the differential profiles of mirnas expression between mock- and hsv-1-infected body cavity-based lymphoma (bcbl-1) cells were identified by mirna microarray analysis. bioinformatics and luciferase reporter analyses showed that two of the hsv-1-downregulated cellular mirnas, mir-498 and mir-320d, directly targeted the 3' untranslated region (utr) of kshv rta. as a result, overexpression of these two mirnas significantly inhibited hsv-1-induced kshv replication, whereas repression of these mirnas with specific suppressors enhanced hsv-1-mediated kshv replication. in addition, mir-498 or mir-320d alone, without hsv-1 infection, regulated kshv replication in bcbl-1 cells. finally, bioinformatics gene ontology (go) analysis indicated that targets of hsv-1-regulated mirnas were enriched for proteins, whose roles were involved in protein binding, enzyme activity, biological regulation, and several potential signaling pathways including transforming growth factor (tgf)-β were likely to participate in hsv-1-induced kshv replication. collectively, these novel findings demonstrated that host-encoded mir-498 and mir-320d regulated hsv-1 induction of kshv lytic replication by targeting rta, which provided further insights into the molecular mechanisms controlling kshv lytic replication.",1
"small nucleolar rnas (snornas) are required for ribose 2'-o-methylation of eukaryotic ribosomal rna. many of the genes for this snorna family have remained unidentified in saccharomyces cerevisiae, despite the availability of a complete genome sequence. probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snornas, snr50 to snr71. gene disruptions and other experimental characterization confirmed their methylation guide function. in total, 51 of the 55 ribose methylated sites in yeast ribosomal rna were assigned to 41 different guide snornas.",1
"noncoding rnas (ncrnas) perform essential cellular tasks and play key regulatory roles in all organisms. although several new ncrnas in yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. we demonstrate a powerful and versatile method for global identification of previously undescribed ncrnas by modulating an essential rna processing pathway through the depletion of a key ribonucleoprotein enzyme component, and monitoring differential transcriptional activities with genome tiling arrays during the time course of the ribonucleoprotein depletion. the entire saccharomyces cerevisiae genome was scanned during cell growth decay regulated by promoter-mediated depletion of rpp1, an essential and functionally conserved protein component of the rnase p enzyme. in addition to most verified genes and ncrnas, expression was detected in 98 antisense and intergenic regions, 74 that were further confirmed to contain previously undescribed rnas. a class of ncrnas, located antisense to coding regions of verified protein-coding genes, is discussed in this article. one member, hra1, is likely involved in 18s rrna maturation.",1
"global mature microrna (mirna) expression is downregulated in cancers, and impaired mirna processing enhances cancer cell proliferation. these findings indicate that the mirna system generally serves as a negative regulator during cancer progression. in this study, we investigated the role of the mirna system in cancer cell invasion by determining the effect of damaging mirna processing on invasion-essential urokinase-type plasminogen activator (upa) expression in breast cancer cells. short hairpin rnas specific for drosha, dgcr8, and dicer, key components of mirna processing machinery, were introduced into 2 breast cancer cell lines with high upa expression and 2 lines with poor upa expression. knockdown of drosha, dgcr8, or dicer led to even higher upa expression in cells with high upa expression, while it was unable to increase upa level in cells with poor upa expression, suggesting that the mirna system most likely impacts upa expression as a facilitator. in cells with high upa expression, knockdown of drosha, dgcr8, or dicer substantially increased in vitro invasion, and depleting upa abrogated enhanced invasion. these results thus link the augmented invasion conferred by impaired mirna processing to upregulated upa expression. upa mrna was a direct target of mir-193a/b and mir-181a, and a higher upa level in cells with impaired mirna processing resulted from less mature mir-193a/b and mir-181a processed from their respective primary mirnas. importantly, the levels of mature mir-193a, mir-193b, and mir-181a, but not their respective primary mirnas, were lower in high upa-expressing cells compared to cells with low upa expression, and this apparently attributed to lower drosha/dgcr8 expression in high upa-expressing cells. this study suggests that less efficient mirna processing can be a mechanism responsible for reduced levels of mature forms of tumor-suppressive mirnas frequently detected in cancers.",1
"the drosophila bithorax complex encodes three well-characterized homeodomain proteins that direct segment identity, as well as several noncoding rnas of unknown function. here, we analyze the iab-4 locus, which produces the micrornas iab-4-5p and iab-4-3p. iab-4 is analogous to mir-196 in vertebrate hox clusters. previous studies demonstrate that mir-196 interacts with the hoxb8 3' untranslated region. evidence is presented that mir-iab-4-5p directly inhibits ubx activity in vivo. ectopic expression of mir-iab-4-5p attenuates endogenous ubx protein accumulation and induces a classical homeotic mutant phenotype: the transformation of halteres into wings. these findings provide the first evidence for a noncoding homeotic gene and raise the possibility that other such genes occur within the bithorax complex. we also discuss the regulation of mir-iab-4 expression during development.",1
"age-related macular degeneration (amd) is the leading cause of severe vision impairment in western populations over 55 years. a growing number of gene variants have been identified which are strongly associated with an altered risk to develop amd. nevertheless, gene-based biomarkers which could be dysregulated at defined stages of amd may point toward key processes in disease mechanism and thus may support efforts to design novel treatment regimens for this blinding disorder. circulating micrornas (cmirnas) which are carried by nanosized exosomes or microvesicles in blood plasma or serum, have been recognized as valuable indicators for various age-related diseases. we therefore aimed to elucidate the role of cmirnas in amd by genome-wide mirna expression profiling and replication analyses in 147 controls and 129 neovascular amd patients. we identified three micrornas differentially secreted in neovascular (nv) amd (hsa-mir-301-3p, pcorrected = 5.6*10-5, hsa-mir-361-5p, pcorrected = 8.0*10-4 and hsa-mir-424-5p, pcorrected = 9.6*10-3). a combined profile of the three mirnas revealed an area under the curve (auc) value of 0.727 and was highly associated with nv amd (p = 1.2*10-8). to evaluate subtype-specificity, an additional 59 amd cases with pure unilateral or bilateral geographic atrophy (ga) were analyzed for micrornas hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p. while we found no significant differences between ga amd and controls neither individually nor for a combined micrornas profile, hsa-mir-424-5p levels remained significantly higher in ga amd when compared to nv (pcorrected<0.005). pathway enrichment analysis on genes predicted to be regulated by micrornas hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p, suggests canonical tgfβ, mtor and related pathways to be involved in nv amd. in addition, knockdown of hsa-mir-361-5p resulted in increased neovascularization in an in vitro angiogenesis assay.",1
"mammalian genomes encode thousands of long noncoding rnas (lncrnas), yet the biological functions of most of them remain unknown. a particularly rich repertoire of lncrnas found in mammalian brain and in the early embryo. we used rna-seq and computational analysis to prioritize lncrnas that may regulate commitment of pluripotent cells to a neuronal fate and perturbed their expression prior to neuronal differentiation. knockdown by rnai of two highly conserved and well-expressed lncrnas, reno1 (2810410l24rik) and lnc-nr2f1, decreased the expression of neuronal markers and led to massive changes in gene expression in the differentiated cells. we further show that the reno1 locus forms increasing spatial contacts during neurogenesis with its adjacent protein-coding gene bahcc1. loss of either reno1 or bahcc1 leads to an early arrest in neuronal commitment, failure to induce a neuronal gene expression program, and to global reduction in chromatin accessibility at regions that are marked by the h3k4me3 chromatin mark at the onset of differentiation. reno1 and bahcc1 thus form a previously uncharacterized circuit required for the early steps of neuronal commitment.",1
"coronary collateral circulation (ccc) functions as a natural bypass in the event of coronary obstruction, which markedly improves prognosis in patients with coronary artery disease (cad). micrornas (mirnas) have been implicated in multiple physiological and pathological processes, including angiogenesis involved in ccc growth. the roles that mirna-939 (mir-939) plays in angiogenesis remain largely unknown. we conducted this study to explore the expression of mir-939 in cad patients and its role in angiogenesis. for the first time, our results indicated that the expression of circulating mir-939 was down-regulated in patients with sufficient ccc compared with patients with poor ccc. overexpression of mir-939 in primary human umbilical vein endothelial cells (huvecs) significantly inhibited the proliferation, adhesion and tube formation, but promoted the migration of cells. in contrast, mir-939 knockdown exerted reverse effects. we further identified that γ-catenin was a novel target of mir-939 by translational repression, which could rescue the effects of mir-939 in huvecs. in summary, this study revealed that the expression of circulating mir-939 was down-regulated in cad patients with sufficient ccc. mir-939 abolished vascular integrity and repressed angiogenesis through directly targeting γ-catenin. it provided a potential biomarker and a therapeutic target for cad.",1
"a major stress response influenced by micrornas (mirnas) is senescence, a state of indefinite growth arrest triggered by sublethal cell damage. here, through bioinformatic analysis and experimental validation, we identified mir-340-5p as a novel mirna that foments cellular senescence. mir-340-5p was highly abundant in diverse senescence models, and mir-340-5p overexpression in proliferating cells rendered them senescent. among the target mrnas, mir-340-5p prominently reduced the levels of lbr mrna, encoding lamin b receptor (lbr). loss of lbr by ectopic overexpression of mir-340-5p derepressed heterochromatin in lamina-associated domains, promoting the expression of dna repetitive elements characteristic of senescence. importantly, overexpressing mir-340-5p enhanced cellular sensitivity to senolytic compounds, while antagonization of mir-340-5p reduced senescent cell markers and engendered resistance to senolytic-induced cell death. we propose that mir-340-5p can be exploited for removing senescent cells to restore tissue homeostasis and mitigate damage by senescent cells in pathologies of human aging.",1
"the molecular mechanisms that control innate immune cell trafficking during chronic infection and inflammation, such as in tuberculosis (tb), are incompletely understood. during active tb, myeloid cells infiltrate the lung and sustain local inflammation. while the chemoattractants that orchestrate these processes are increasingly recognized, the posttranscriptional events that dictate their availability are unclear. we identified microrna-223 (mir-223) as an upregulated small noncoding rna in blood and lung parenchyma of tb patients and during murine tb. deletion of mir-223 rendered tb-resistant mice highly susceptible to acute lung infection. the lethality of mir-223(–/–) mice was apparently not due to defects in antimycobacterial t cell responses. exacerbated tb in mir-223(–/–) animals could be partially reversed by neutralization of cxcl2, ccl3, and il-6, by mab depletion of neutrophils, and by genetic deletion of cxcr2. we found that mir-223 controlled lung recruitment of myeloid cells, and consequently, neutrophil-driven lethal inflammation. we conclude that mir-223 directly targets the chemoattractants cxcl2, ccl3, and il-6 in myeloid cells. our study not only reveals an essential role for a single mirna in tb, it also identifies new targets for, and assigns biological functions to, mir-223. by regulating leukocyte chemotaxis via chemoattractants, mir-223 is critical for the control of tb and potentially other chronic inflammatory diseases.",1
"carbon dioxide (co2) elicits different olfactory behaviors across species. in drosophila, neurons that detect co2 are located in the antenna, form connections in a ventral glomerulus in the antennal lobe, and mediate avoidance. by contrast, in the mosquito these neurons are in the maxillary palps (mps), connect to medial sites, and promote attraction. we found in drosophila that loss of a microrna, mir-279, leads to formation of co2 neurons in the mps. mir-279 acts through down-regulation of the transcription factor nerfin-1. the ectopic neurons are hybrid cells. they express co2 receptors and form connections characteristic of co2 neurons, while exhibiting wiring and receptor characteristics of mp olfactory receptor neurons (orns). we propose that this hybrid orn reveals a cellular intermediate in the evolution of species-specific behaviors elicited by co2.",1
"micrornas are an extensive family of approximately 22-nucleotide-long noncoding rnas expressed in a wide range of eukaryotes, including humans, and they are important in development and disease. we found that microrna mir-17-5p has extensive complementarity to the mrna of aib1 (named for ""amplified in breast cancer 1""). cell culture experiments showed that aib1 expression was downregulated by mir-17-5p, primarily through translational inhibition. expression of mir-17-5p was low in breast cancer cell lines. we also found that downregulation of aib1 by mir-17-5p resulted in decreased estrogen receptor-mediated, as well as estrogen receptor-independent, gene expression and decreased proliferation of breast cancer cells. mir-17-5p also completely abrogated the insulin-like growth factor 1-mediated, anchorage-independent growth of breast cancer cells. our results reveal that mir-17-5p has a role as a tumor suppressor in breast cancer cells.",1
"the role of trivalent arsenic (as(3+)) on the regulation of the recently identified noncoding small rnas, mainly micrornas, has not been explored so far. in the present study, we provide evidence showing that as(3+) is a potent inducer for the expression of mir-190 in human bronchial epithelial cells. the induction of mir-190 by as(3+) is concentration dependent and associated with the expression of the host gene of mir-190, talin 2, a gene encoding a high-molecular-weight cytoskeletal protein. the elevated level of mir-190 induced by as(3+) is capable of downregulating the translation of the ph domain leucine-rich repeat protein phosphatase (phlpp), a negative regulator of akt signaling. such a downregulation is occurred through direct interaction of the mir-190 with the 3'-utr region of the phlpp mrna, leading to a diminished phlpp protein expression and consequently, an enhanced akt activation and expression of vascular endothelial growth factor, an akt-regulated protein. overexpression of mir-190 itself is able to enhance proliferation and malignant transformation of the cells as determined by anchorage-independent growth of the cells in soft agar. accordingly, the data presented suggest that induction of mir-190 is one of the key mechanisms in as(3+)-induced carcinogenesis.",1
"background the epithelial-mesenchymal transition (emt) is a key developmental program that is often activated during cancer progression and may promote resistance to therapy. an analysis of patients (n = 71) profiled with both gene expression and a global microrna assessment (∼ 415 mirs) identified mir-147 as highly anti-correlated with an emt gene expression signature score and postulated to reverse emt (met). methods and findings mir-147 was transfected into colon cancer cells (hct116, sw480) as well as lung cancer cells (a-549). the cells were assessed for morphological changes, and evaluated for effects on invasion, motility, and the expression of key emt markers. resistance to chemotherapy was evaluated by treating cells with gefitinib, an egfr inhibitor. the downstream genes regulated by mir-147 were assayed using the affymetrix genechip u133 plus2.0 platform. mir-147 was identified to: 1. cause met primarily by increasing the expression of cdh1 and decreasing that of zeb1; 2. inhibit the invasion and motility of cells; 3. cause g1 arrest by up-regulating p27 and down-regulating cyclin d1. mir-147 also dramatically reversed the native drug resistance of the colon cancer cell line hct116 to gefitinib. mir-147 significantly repressed akt phosphorylation, and knockdown of akt with sirna induced met. the morphologic effects of mir-147 on cells appear to be attenuated by tgf-b1, promoting a plastic and reversible transition between met and emt. conclusion mir-147 induced cancer cells to undergo met and induced cell cycle arrest, suggesting a potential tumor suppressor role. mir-147 strikingly increased the sensitivity to egfr inhibitor, gefitinib in cell with native resistance. we conclude that mir-147 might have therapeutic potential given its ability to inhibit proliferation, induce met, as well as reverse drug sensitivity.",1
"intron-encoded u17 rna is a member of the h/aca box class of small nucleolar rnas (snornas) involved in ribosomal rna (rrna) maturation. u17 snorna shows typical characteristics of guide rnas, which specify sites of pseudouridylation on the precursor rrna (pre-rrna). however, in spite of the presence of h and aca boxes and short regions complementary to the pre-rrna, its secondary structure does not show any evident pseudouridylation pocket. moreover, its length is larger than the typical one of snornas and it shows a more complex secondary structure compared to the canonical hairpin-hinge-hairpin-tail architecture. greater knowledge of eukaryotic u17 snorna structure is needed to understand its precise function. comparative molecular studies of this snorna with different vertebrates is still limited to a few cases. with the aim of increasing our understanding of the u17 snorna secondary structure, we cloned the u17 snorna coding sequence from 10 additional vertebrate taxa. on the basis of structure homology derived from sequence comparison and thermodynamic prediction, we propose a vertebrate consensus secondary structure and novel conserved sequence boxes for u17 snorna. host gene localization of u17 coding sequence and its ability to serve as a guide sequence for rna/rna interaction has been evolutionarily traced from fish to mammals. it is interesting to note that turtle u17 snornas show a noncanonical aca box, mainly consisting in the gca box. microinjections in x. laevis oocytes of in vitro synthesized turtle transcripts containing the u17 rna sequence which have canonical aca, wild-type gca, and mutated cca and uca boxes resulted in efficient production of mature u17 snorna.",1
"background recently, involvement of the chemokine/receptor system ccl20/ccr6 in colorectal cancer (crc) progression was shown. here, we analyzed the functional interaction of mirna-518-5p (mir-518a-5p) with ccr6 and its impact on ccr6 expression in crc cells. methods mir-518a-5p was identified by computer software to potentially interact with ccr6. hence, functional implications of mir-518a-5p with the 3'utr of ccr6 were analyzed using the dual luciferase reporter assay system. confirmation of the predicted target site for mir-518a-5p was achieved by site-directed mutagenesis of the seed sequence in the 3'utr of ccr6 and subsequent application of the mutated seed sequence in a luciferase assay with mir-518a-5p mimics. accordingly, two crc cell lines (caco-2 and ht-29) were transfected with mir-518a-5p mirna mimics and gene and protein expression of ccr6 was monitored using qrt pcr and immunocytochemistry, respectively. results addition of mir-518a-5p led to significant down-regulation of luciferase activity (p conclusions we have shown that mir-518a-5p functionally interacts with ccr6 and that transfection of crc cells with mir-518a-5p leads to significant ccr6 down-regulation. consequently, ccr6 expression is regulated by mir-518a-5p in crc cells indicating that regulation of ccr6 expression by mir-518a-5p might be a regulatory mechanism involved in crc pathogenesis.",1
"mir-17-92 cluster has recently been reported as an oncogene in some tumors. however, the association of mir-18a, an important member of this cluster, with glioblastoma remains unknown. therefore, this study aims to investigate the expression of mir-18a in glioblastoma and its role in biological behavior of u87 and u251 human glioblastoma cell lines. quantitative rt-pcr results showed that mir-18a was highly expressed in glioblastoma tissues and u87 and u251 cell lines compared with that in human brain tissues and primary normal human astrocytes, and the expression levels were increased along with the rising pathological grades of glioblastoma. neogenin was identified as the target gene of mir-18a by dual-luciferase reporter assays. rt-pcr and western blot results showed that its expression levels were decreased along with the rising pathological grades of glioblastoma. inhibition of mir-18a expression was established by transfecting exogenous mir-18a inhibitor into u87 and u251 cells, and its effects on the biological behavior of glioblastoma cells were studied using cck-8 assay, transwell assay and flow cytometry. inhibition of mir-18a expression in u87 and u251 cells significantly up-regulated neogenin, and dramatically suppressed the abilities of cell proliferation, migration and invasion, induced cell cycle arrest and promoted cellular apoptosis. collectively, these results suggest that mir-18a may regulate biological behavior of human glioblastoma cells by targeting neogenin, and mir-18a can serve as a potential target in the treatment of glioblastoma.",1
"context chromosomal abnormalities (namely 13q, 17p, and 11q deletions) have prognostic implications and are recurrent in chronic lymphocytic leukemia (cll), suggesting that they are involved in a common pathogenetic pathway; however, the molecular mechanism through which chromosomal abnormalities affect the pathogenesis and outcome of cll is unknown. objective to determine whether the microrna mir-15a/mir-16-1 cluster (located at 13q), tumor protein p53 (tp53, located at 17p), and mir-34b/mir-34c cluster (located at 11q) are linked in a molecular pathway that explains the pathogenetic and prognostic implications (indolent vs aggressive form) of recurrent 13q, 17p, and 11q deletions in cll. design, setting, and patients cll research consortium institutions provided blood samples from untreated patients (n = 206) diagnosed with b-cell cll between january 2000 and april 2008. all samples were evaluated for the occurrence of cytogenetic abnormalities as well as the expression levels of the mir-15a/mir-16-1 cluster, mir-34b/mir-34c cluster, tp53, and zeta-chain (tcr)-associated protein kinase 70 kda (zap70), a surrogate prognostic marker of cll. the functional relationship between these genes was studied using in vitro gain- and loss-of-function experiments in cell lines and primary samples and was validated in a separate cohort of primary cll samples. main outcome measures cytogenetic abnormalities; expression levels of the mir-15a/mir-16-1 cluster, mir-34 family, tp53 gene, downstream effectors cyclin-dependent kinase inhibitor 1a (p21, cip1) (cdkn1a) and b-cell cll/lymphoma 2 binding component 3 (bbc3), and zap70 gene; genetic interactions detected by chromatin immunoprecipitation. results in clls with 13q deletions the mir-15a/mir-16-1 cluster directly targeted tp53 (mean luciferase activity for mir-15a vs scrambled control, 0.68 relative light units (rlu) ; p = .02; mean for mir-16 vs scrambled control, 0.62 rlu ; p = .02) and its downstream effectors. in leukemic cell lines and primary cll cells, tp53 stimulated the transcription of mir-15/mir-16-1 as well as mir-34b/mir-34c clusters, and the mir-34b/mir-34c cluster directly targeted the zap70 kinase (mean luciferase activity for mir-34a vs scrambled control, 0.33 rlu ; p = .02; mean for mir-34b vs scrambled control, 0.31 rlu ; p = .01; and mean for mir-34c vs scrambled control, 0.35 rlu ; p = .02). conclusions a microrna/tp53 feedback circuitry is associated with cll pathogenesis and outcome. this mechanism provides a novel pathogenetic model for the association of 13q deletions with the indolent form of cll that involves micrornas, tp53, and zap70.",1
"increasing evidence suggests that mir‑205 is frequently dysregulated in many types of human cancers, suggesting its important roles in the initiation and progression of cancer. however, the functions of mir‑205 in human endometrial endometrioid carcinoma (eec) are still unknown. in this study, we investigated the expression of mir‑205 in both normal endometrium and eec tissues using taqman pcr. compared to normal tissues, mir‑205 was significantly upregulated in eec (p<0.001). after transfection of mir‑205 inhibitors into ishikawa cells (or transfection of mir‑205 mimics into an3ca cells), we demonstrated that the cellular proliferation, migration and invasion properties were negatively regulated by mir‑205. moreover, by combination of microrna target prediction algorithms and luciferase reporter system, we identified estrogen-related receptor‑γ (esrrg) as a target of mir‑205. in conclusion, we demonstrated frequent upregulation of mir‑205 in eec. in gain‑of‑function and loss‑of‑function assays, inhibition of mir‑205 reduced cellular proliferation, migration and invasion; vice versa, increased levels of mir‑205 led to upregulated cellular proliferation, migration and invasion. nonetheless, we identified the esrrg gene to be a novel target, which could be helpful to elucidate mechanisms underlying the tumorigenesis of eec.",1
"cellular cholesterol levels are tightly regulated and represent a balance of cholesterol uptake, endogenous synthesis and efflux. although the classic transcriptional regulations of cholesterol metabolism by liver x receptors (lxrs) have been well studied, the potential effects of lxr-responsive micrornas (mirnas) still need to be unveiled. here, we describe that mir-26, an lxr-suppressed mirna, inhibits the expression of the atp-binding cassette transporter a1 (abca1) and adp-ribosylation factor-like 7 (arl7), two lxr target genes which play critical roles in cholesterol efflux. these findings have not only figured out an alternative mechanism for lxr regulation, but also provided a potential therapeutic target for cholesterol metabolic disorders.",1
"purpose the aim of this study was to explore the function of microrna-27b (mir-27b) in fibroblast-like synoviocytes (flss) stimulated by tumor necrosis factor α (tnf-α). materials and methods mrna expression of mir-27b in fls cells (mh7a) treated with or without tnf-α was determined by q-pcr. mir-27b mimics was transfected into mh7a cells to upregulate mir-27b expression. mtt assay and flow cytometry analysis were performed to investigate the effect of mir-27b on mh7a cell viability and apoptosis. the targets of mir-27b were predicted by targetscan. the direct regulation of mir-27b on il-1β expression was verified by luciferase assay. the protein expression levels of apoptosis-related proteins, il-1β, and nf-κb signaling-related proteins were detected by western blot. results we discovered that mir-27b expression was decreased in mh7a cells stimulated by tnf-α. upregulation of mir-27b by mir-27b mimics significantly inhibited the proliferation and promoted the apoptosis of tnf-α-stimulated mh7a cells. consistently, upregulation of mir-27 decreased the level of bcl-2 and increased bax and caspase-3 expression in mh7a cells stimulated by tnf-α. luciferase assay revealed that il-1β was indeed a target of mir-27b. by quantitative real-time pcr and western blot, we found that the expression of il-1β is negatively regulated by mir-27b. moreover, the nf-κb signaling pathway was significantly inhibited by mir-27b. conclusion taken together, our results illustrated that enhanced mir-27b expression results in the suppression of proliferation and the promotion of apoptosis in flss stimulated by tnf-α, partially by regulating il-1β expression and nf-κb signaling.",1
"background recently several micrornas (mirnas) have been found to be regulated by genistein in cancer cells. in this study, we focused on the gene regulatory effect of genistein on microrna and its target genes in prostate cancer (pc). methods initially, we investigated the effect of genistein on prostate cancer cells and identified that the expression of mirna-1260b was decreased by genistein. we performed functional analyses and investigated the relationship between mirna-1260b expression and prostate cancer patient outcomes. two target genes (sfrp1 and smad4) of mir-1260b were identified based on computer algorithm and 3'utr luciferase assay was carried out to determine direct mirna regulation of the genes. results genistein promoted apoptosis while inhibiting prostate cancer cell proliferation, invasion and tcf reporter activity in pc cells. mir-1260b was highly expressed in prostate cancer tissues and significantly downregulated by genistein in pc cells. after knocking down mir-1260b, cell proliferation, invasion, migration and tcf reporter activity were decreased in pc cells. western analysis and 3'utr luciferase assay showed that the two target genes (sfrp1 and smad4) were directly regulated by mir-1260b. the expression of sfrp1 and smad4 was significantly decreased in prostate cancer tissues. genistein also increased expression of these two genes via dna demethylation and histone modifications. conclusions our data suggest that genistein exerts its anti-tumour effect via downregulation of mir-1260b that targeted srrp1 and smad4 genes in prostate cancer cells. the expression of sfrp1 and smad4 was also modulated by genistein via dna methylation or histone modifications in pc cell lines.",1
"although micrornas (mirnas) are increasingly linked to various physiologic processes, including hematopoiesis, their function in the myeloid development is poorly understood. we detected up-regulation of mir-29a and mir-142-3p during myeloid differentiation in leukemia cell lines and cd34(+) hematopoietic stem/progenitor cells. by gain-of-function and loss-of-function experiments, we demonstrated that both mirnas promote the phorbol 12-myristate 13-acetate-induced monocytic and all-trans-retinoic acid-induced granulocytic differentiation of hl-60, thp-1, or nb4 cells. both the mirnas directly inhibited cyclin t2 gene, preventing the release of hypophosphorylated retinoblastoma and resulting in induction of monocytic differentiation. in addition, a target of mir-29a, cyclin-dependent kinase 6 gene, and a target of mir-142-3p, tgf-β-activated kinase 1/map3k7 binding protein 2 gene, are involved in the regulation of both monocytic and granulocytic differentiation. a significant decrease of mir-29a and 142-3p levels and an obvious increase in their target protein levels were also observed in blasts from acute myeloid leukemia. by lentivirus-mediated gene transfer, we demonstrated that enforced expression of either mir-29a or mir-142-3p in hematopoietic stem/progenitor cells from healthy controls and acute myeloid leukemia patients down-regulated expression of their targets and promoted myeloid differentiation. these findings confirm that mir-29a and mir-142-3p are key regulators of normal myeloid differentiation and their reduced expression is involved in acute myeloid leukemia development.",1
"the translational gtpases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. mutations that impair gtp hydrolysis by eukaryotic translation initiation factor 5b/initiation factor 2 (eif5b/if2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. a mutation in helix h5 of the 18s rrna in the 40s ribosomal subunit and intragenic mutations in domain ii of eif5b suppress the toxic effects associated with expression of the eif5b-h480i gtpase-deficient mutant in yeast by lowering the ribosome binding affinity of eif5b. hydroxyl radical mapping experiments reveal that the domain ii suppressors interface with the body of the 40s subunit in the vicinity of helix h5. as the helix h5 mutation also impairs elongation factor function, the rrna and eif5b suppressor mutations provide in vivo evidence supporting a functionally important docking of domain ii of the translational gtpases on the body of the small ribosomal subunit.",1
"mef2 is the key transcription factor for muscle development and differentiation in drosophila. it activates hundreds of downstream target genes, including itself. precise control of mef2 levels is essential for muscle development as different mef2 protein levels activate distinct sets of muscle genes, but how this is achieved remains unclear. here, we have identified a novel heart- and muscle-specific microrna, mir-92b, which is activated by mef2 and subsequently downregulates mef2 through binding to its 3'utr, forming a negative regulatory circuit that fine-tunes the level of mef2. deletion of mir-92b caused abnormally high mef2 expression, leading to muscle defects and lethality. blocking mir-92b function using microrna sponge techniques also increased mef2 levels and caused muscle defects similar to those seen with the mir-92b deletion. additionally, overexpression of mir-92b reduced mef2 levels and caused muscle defects similar to those seen in mef2 rnai, and mef2 overexpression led to reversal of these defects. our results suggest that the negative feedback circuit between mir-92b and mef2 efficiently maintains the stable expression of both components that is required for homeostasis during drosophila muscle development.",1
"background microrna-449a is a tumor suppressor that is down-regulated in multiple tumors types. however, the role of mir-449a in gastric cancer (gc) remains largely unknown. methods mir-449a expression was up-regulated using mir-449a mimics, and the role of mir-449a in gc was assessed using cell viability and apoptosis assays. mir-449a target genes were confirmed using luciferase activity, rt-pcr and western blot assays. results mir-449a was downregulated in gastric cancer cell lines and gastric cancer tissues. restoration of mir-449a expression inhibited gastric cancer cell proliferation and colony formation. significant g0/g1 arrest was observed in gastric cancer cells transfected with mir-449a mimics. furthermore, combination therapy with mir-449a with cisplatin displayed greater anti-tumor effects than treatment with cisplatin alone. we also identified e2f3 (e2f transcription factor 3), an important transcription factor involved in the proliferation and metastasis of tumor cells, as a direct target gene of mir-449a. furthermore, silencing e2f3 elicits similar a repressive effect as overexpression of mir-449a in gastric cancer cells, and e2f3 overexpression rescued the repressing effects of mir-449a mimics. conclusions this study indicates that the mir-449a/e2f3 axis plays an important role in proliferation and apoptosis in gastric cancer. therefore, mir-449a represents a novel target for gastric cancer therapy.",1
"glioblastoma multiforme (gbm)-initiating cells (gics) represent a tumor subpopulation with neural stem cell-like properties that is responsible for the development, progression and therapeutic resistance of human gbm. we have recently shown that blockade of nfκb pathway promotes terminal differentiation and senescence of gics both in vitro and in vivo, indicating that induction of differentiation may be a potential therapeutic strategy for gbm. micrornas have been implicated in the pathogenesis of gbm, but a high-throughput analysis of their role in gic differentiation has not been reported. we have established human gic cell lines that can be efficiently differentiated into cells expressing astrocytic and neuronal lineage markers. using this in vitro system, a microarray-based high-throughput analysis to determine global expression changes of micrornas during differentiation of gics was performed. a number of changes in the levels of micrornas were detected in differentiating gics, including over-expression of hsa-mir-21, hsa-mir-29a, hsa-mir-29b, hsa-mir-221 and hsa-mir-222, and down-regulation of hsa-mir-93 and hsa-mir-106a. functional studies showed that mir-21 over-expression in gics induced comparable cell differentiation features and targeted spry1 mrna, which encodes for a negative regulator of neural stem-cell differentiation. in addition, mir-221 and mir-222 inhibition in differentiated cells restored the expression of stem cell markers while reducing differentiation markers. finally, mir-29a and mir-29b targeted mcl1 mrna in gics and increased apoptosis. our study uncovers the microrna dynamic expression changes occurring during differentiation of gics, and identifies mir-21 and mir-221/222 as key regulators of this process.",1
"single nucleotide polymorphisms in the fkbp5 gene increase the expression of the fkbp51 protein and have been associated with increased risk for neuropsychiatric disorders such as major depression and post-traumatic stress disorder. moreover, levels of fkbp51 are increased with aging and in alzheimer disease, potentially contributing to disease pathogenesis. however, aside from its glucocorticoid responsiveness, little is known about what regulates fkbp5 in recent years, non-coding rnas, and in particular micrornas, have been shown to modulate disease-related genes and processes. the current study sought to investigate which mirnas could target and functionally regulate fkbp5 following in silico data mining and initial target expression validation, mir-511 was found to suppress fkbp5 mrna and protein levels. using luciferase p-mir-report constructs and rna pulldown assays, we confirmed that mir-511 bound directly to the 3'-utr of fkbp5, validating the predicted gene-microrna interaction. mir-511 suppressed glucocorticoid-induced up-regulation of fkbp51 in cells and primary neurons, demonstrating functional, disease-relevant control of the protein. consistent with a regulator of fkbp5, mir-511 expression in the mouse brain decreased with age but increased following chronic glucocorticoid treatment. analysis of the predicted target genes of mir-511 revealed that neurogenesis, neuronal development, and neuronal differentiation were likely controlled by these genes. accordingly, mir-511 increased neuronal differentiation in cells and enhanced neuronal development in primary neurons. collectively, these findings show that mir-511 is a functional regulator of fkbp5 and can contribute to neuronal differentiation.",1
"background the purpose of this study was to identify mirnas and genes involved in nasopharyngeal carcinoma (npc) radioresistance, and explore the underlying mechanisms in the development of radioresistance. methods we used microarrays to compare the differences of both mirna and mrna expression profiles in the radioresistant npc cne2-ir and radiosensitive npc cne2 cells, applied qrt-pcr to confirm the reliability of microarray data, adopted databases prediction and anticorrelated analysis of mirna and mrna expression to identify the mirna target genes, and employed bioinformatics tools to examine the functions and pathways in which mirna target genes are involved, and construct a mirna-target gene regulatory network. we further investigated the roles of mirna-23a and its target gene il-8 in the npc radioresistance. results the main findings were fourfold: (1) fifteen differential mirnas and 372 differential mrnas were identified, and the reliability of microarray data was validated for randomly selected eight mirnas and nine genes; (2) 174 mirna target were identified, and most of their functions and regulating pathways were related to tumor therapeutic resistance; (3) a posttranscriptional regulatory network including 375 mirna-target gene pairs was constructed, in which the ten genes were coregulated by the six mirnas; (4) il-8 was a direct target of mirna-23a, the expression levels of il-8 were elevated in the radioresistant npc tissues and showed inverse correlation with mirna-23a expression, and genetic upregulation of mirna-23a and antibody neutralization of secretory il-8 could reduce npc cells radioresistance. conclusions we identified fifteen differential mirnas and 372 differential mrnas in the radioresistant npc cells, constructed a posttranscriptional regulatory network including 375 mirna-target gene pairs, discovered the ten target genes coregulated by the six mirnas, and validated that downregulated mirna-23a was involved in npc radioresistance through directly targeting il-8. our data form a basis for further investigating the mechanisms of npc radioresistance.",1
"fulvestrant is a selective estrogen receptor downregulator (serd) and highly effective antagonist to hormone-sensitive breast cancers following failure of previous tamoxifen or aromatase inhibitor therapies. however, after prolonged fulvestrant therapy, acquired resistance eventually occurs in the majority of breast cancer patients, due to poorly understood mechanisms. to examine a possible role(s) of aberrantly expressed micrornas (mirnas) in acquired fulvestrant resistance, we compared antiestrogen-resistant and -sensitive breast cancer cells, revealing the overexpression of mir-221/222 in the serd-resistant cell lines. fulvestrant treatment of estradiol (e2)- and fulvestrant-sensitive mcf7 cells resulted in increased expression of endogenous mir-221/222. ectopic upregulation of mir-221/222 in estrogen receptor-α (erα)-positive cell lines counteracted the effects of e2 depletion or fulvestrant-induced cell death, thus also conferring hormone-independent growth and fulvestrant resistance. in cells with acquired resistance to fulvestrant, mir-221/222 expression was essential for cell growth and cell cycle progression. to identify possible mir-221/222 targets, mir-221- or mir-222- induced alterations in global gene expression profiles and target gene expression at distinct time points were determined, revealing that mir-221/222 overexpression resulted in deregulation of multiple oncogenic signaling pathways previously associated with drug resistance. activation of β-catenin by mir-221/222 contributed to estrogen-independent growth and fulvestrant resistance, whereas tgf-β-mediated growth inhibition was repressed by the two mirnas. this first in-depth investigation into the role of mir-221/222 in acquired fulvestrant resistance, a clinically important problem, demonstrates that these two 'oncomirs' may represent promising therapeutic targets for treating hormone-independent, serd-resistant breast cancer.",1
"multidimensional cancer genome analysis and validation has defined quaking (qki), a member of the signal transduction and activation of rna (star) family of rna-binding proteins, as a novel glioblastoma multiforme (gbm) tumor suppressor. here, we establish that p53 directly regulates qki gene expression, and qki protein associates with and leads to the stabilization of mir-20a; mir-20a, in turn, regulates tgfβr2 and the tgfβ signaling network. this pathway circuitry is substantiated by in silico epistasis analysis of its components in the human gbm tcga (the cancer genome atlas project) collection and by their gain- and loss-of-function interactions in in vitro and in vivo complementation studies. this p53-qki-mir-20a-tgfβ pathway expands our understanding of the p53 tumor suppression network in cancer and reveals a novel tumor suppression mechanism involving regulation of specific cancer-relevant micrornas.",1
"in the nematode caenorhabditis elegans, up to 15% of the genes are organized in operons. polycistronic precursor rnas are processed by trans-splicing at the 5' ends of genes by adding a specific trans-spliced leader. ten different spliced leaders are known in c. elegans that differ in sequence and abundance. the sl1 leader is most abundant and is spliced to the 5' ends of monocistronic genes and to upstream genes in operons. trans-splicing is common among nematodes and was observed in the genera panagrellus, ascaris, haemonchus, anisakis, and brugia. however, little is known about operons in nonrhabditid nematodes. dolichorhabditis cew1, another rhabditid nematode that is now called oscheius cew1, contains operons and sl2 trans-splicing. we have studied the presence of operons and trans-splicing in pristionchus pacificus, a species of the diplogastridae that has recently been developed as a satellite organism in evolutionary developmental biology. we provide evidence that p. pacificus contains operons and that downstream genes are trans-spliced to sl2. surprisingly, the one operon analyzed so far in p. pacificus is not conserved in c. elegans, suggesting unexpected genomic plasticity.",1
"cocaine addiction is characterized by a gradual loss of control over drug use, but the molecular mechanisms regulating vulnerability to this process remain unclear. here we report that microrna-212 (mir-212) is upregulated in the dorsal striatum of rats with a history of extended access to cocaine. striatal mir-212 decreases responsiveness to the motivational properties of cocaine by markedly amplifying the stimulatory effects of the drug on camp response element binding protein (creb) signalling. this action occurs through mir-212-enhanced raf1 activity, resulting in adenylyl cyclase sensitization and increased expression of the essential creb co-activator torc (transducer of regulated creb; also known as crtc). our findings indicate that striatal mir-212 signalling has a key role in determining vulnerability to cocaine addiction, reveal new molecular regulators that control the complex actions of cocaine in brain reward circuitries and provide an entirely new direction for the development of anti-addiction therapeutics based on the modulation of noncoding rnas.",1
"micrornas (mirnas) are 19-22-nucleotide noncoding rnas that post-transcriptionally regulate mrna targets. we have identified endogenous mirna binding sites in mouse embryonic stem cells (mescs), by performing photo-cross-linking immunoprecipitation using antibodies to argonaute (ago2) followed by deep sequencing of rnas (clip-seq). we also performed clip-seq in dicer⁻/⁻ mescs that lack mature mirnas, allowing us to define whether the association of ago2 with the identified sites was mirna dependent. a significantly enriched motif, gcacuu, was identified only in wild-type mescs in 3' untranslated and coding regions. this motif matches the seed of a mirna family that constitutes ~68% of the mesc mirna population. unexpectedly, a g-rich motif was enriched in sequences cross-linked to ago2 in both the presence and absence of mirnas. expression analysis and reporter assays confirmed that the seed-related motif confers mirna-directed regulation on host mrnas and that the g-rich motif can modulate this regulation.",1
"osteoporosis is a bone metabolic disease, characterized by loss of bone density leading to fractures. its incidence increases with age and affects patient quality of life. although osteoclasts play a significant role in osteoporosis, their underlying regulatory mechanisms remain unclear. in this study, we found that microrna (mir)-25-3p negatively regulates osteoclast function through nuclear factor i x (nfix). overexpression of nfix promoted osteoclast proliferation and increased the expression of the osteoclast differentiation and activity markers tartrate-resistant acid phosphatase and cathepsin k. mir-25-3p transfection inhibited nfix expression, which in turn inhibited osteoclast proliferation. collectively, our results suggest that mir-25-3p promotes osteoclast activity by regulating the expression of nfix. therefore, targeting mir-25-3p in osteoclasts could be a promising strategy for treating skeletal disorders involving reduced bone formation.",1
"the src family of protein kinases (sfk) plays key roles in regulating fundamental cellular processes, including cell growth, differentiation, cell shape, migration, and survival, and specialized cell signals in various malignancies. the pleiotropic functions of sfks in cancer make them promising targets for intervention. here, we sought to investigate the role of microrna-205 (mir-205) in inhibition of src-mediated oncogenic pathways in renal cancer. we report that expression of mir-205 was significantly suppressed in renal cancer cell lines and tumors when compared with normal tissues and a nonmalignant cell line and is correlated inversely with the expression of sfks. mir-205 significantly suppressed the luciferase activity of reporter plasmids containing the 3'-utr (untranslated region) sequences complementary to either src, lyn, or yes, which was abolished by mutations in these 3'-utr regions. overexpression of mir-205 in a498 cells reduced src, lyn, and yes expression, both at mrna and protein levels. proliferation of renal cancer cells was suppressed by mir-205, mediated by the phospho-src-regulated erk1/2 pathway. cell motility factor fak (focal adhesion kinase) and stat3 activation were also inhibited by mir-205. transient and stable overexpression of mir-205 in a498 cells resulted in induction of g₀/g₁ cell-cycle arrest and apoptosis, as indicated by decreased levels of cyclin d1 and c-myc, suppressed cell proliferation, colony formation, migration, and invasion in renal cancer cells. mir-205 also inhibited tumor cell growth in vivo. this is the first study showing that mir-205 inhibits proto-oncogenic sfks, indicating a therapeutic potential of mir-205 in the treatment of renal cancer.",1
"alterations of several microrna (mirna) have been linked to cancer development and its biology. to search for unique mirna that might play a role in the development of anaplastic thyroid carcinoma (atc), we examined the expression of multiple mirna and their functional effects on target genes in human thyroid carcinoma cell lines. we quantitatively evaluated the expression of multiple mirna in 10 atc and five papillary thyroid carcinoma (ptc) cell lines, as well as primary tumors from 11 thyroid carcinoma patients (three atc and eight ptc), using the stem-loop-mediated reverse transcription real-time polymerase chain reaction method. we also examined the target gene specificity of unique mirna that showed differences in expression between atc and ptc cell lines. one mirna, mir-138, was significantly downregulated in atc cell lines in comparison with ptc (p < 0.01). eleven mirna (including mir-138) potentially targeting the human telomerase reverse transcriptase (htert) gene were totally downregulated in both atc and ptc cell lines in comparison with normal thyroid tissues. a tendency for an inverse correlation between mir-138 and htert protein expression was observed in the thyroid cancer cell lines, although this failed to reach significance (r = -0.392, p = 0.148). we demonstrated that overexpression of mir-138 induced a reduction in htert protein expression, and confirmed target specificity between mir-138 and the htert 3'-untranslated region by luciferase reporter assay. these results suggest that loss of mir-138 expression may partially contribute to the gain of htert protein expression in atc, and that further multiple mirna targeting htert mrna might be involved in the development of thyroid carcinoma.",1
"b-cell chronic lymphocytic leukemia (b-cll), the most common leukemia in the western world, occurs in two forms, aggressive (showing for the most part high zap-70 expression and unmutated igh v(h)) and indolent (showing low zap-70 expression and mutated igh v(h)). we found that mir-29a is up-regulated in indolent human b-cll as compared with aggressive b-cll and normal cd19(+) b cells. to study the role of mir-29 in b-cll, we generated emu-mir-29 transgenic mice overexpressing mir-29 in mouse b cells. flow cytometric analysis revealed a markedly expanded cd5(+) population in the spleen of these mice starting at 2 mo of age, with 85% (34/40) of mir-29 transgenic mice exhibiting expanded cd5(+) b-cell populations, a characteristic of b-cll. on average, 50% of b cells in these transgenic mice were cd5 positive. at 2 y of age the mice showed significantly enlarged spleens and an increase in the cd5(+) b-cell population to approximately 100%. of 20 emu-mir-29 transgenic mice followed to 24-26 mo of age, 4 (20%) developed frank leukemia and died of the disease. these results suggest that dysregulation of mir-29 can contribute to the pathogenesis of indolent b-cll.",1
"the strength and duration of the nf-κb signaling response must be tightly modulated to avoid an inadequate or excessive immune response. relish, a core nf-κb transcription factor of the drosophila imd pathway, can control the expression of antimicrobial peptides, including dpt and atta, to defend against gram-negative bacterial infections, but whether relish may regulate mirna expression to participate in the immune response remains unclear. in this study, taking advantage of drosophila s2 cells and different overexpression/knockout/knockdown flies, we first found that relish could directly activate the expression of mir-308 to negatively regulate the immune response and promote the survival of drosophila during enterobacter cloacae infection. second, our results demonstrated that relish-mediated expression of mir-308 could suppress target gene tab2 to attenuate the drosophila imd pathway signal during the middle and late stages of the immune response. third, we detected the dynamic expression patterns of dpt, atta, relish, mir-308, and tab2 in wild-type flies after e. coli infection, which further revealed that the feedback regulatory loop of relish-mir-308-tab2 plays a crucial role in the immune response and homeostasis maintenance of the drosophila imd pathway. overall, our present study not only illustrates an important mechanism by which this relish-mir-308-tab2 regulatory axis can negatively control the drosophila immune response and participate in homeostasis maintenance but also provides new insights into the dynamic regulation of the nf-κb/mirna expression network of animal innate immunity.",1
"micrornas (mirnas) are small non-coding rnas and have been implicated in the pathology of various diseases, including cancer. here we report that the mirna profiles have been changed after knockdown of one of the most important oncogene c-myc or re-expression of a candidate tumor suppressor gene splunc1 in nasopharyngeal carcinoma (npc) cells. both c-myc knockdown and splunc1 re-expression can down-regulate microrna-141 (mir-141). mir-141 is up-regulated in npc specimens in comparison with normal nasopharyngeal epithelium. inhibition of mir-141 could affect cell cycle, apoptosis, cell growth, migration and invasion in npc cells. we found that brd3, ubap1 and pten are potential targets of mir-141, which had been confirmed following luciferase reporter assays and western blotting. brd3 and ubap1 are both involved in npc carcinogenesis as confirmed through our previous studies and pten is a crucial tumor suppressor in many tumor types. brd3 is involved in the regulation of the rb/e2f pathway. inhibition of mir-141 could affect some important molecules in the rb/e2f, jnk2 and akt pathways. it is well known that carcinogenesis of npc is involved in the networks of genetic and epigenetic alteration events. we propose that mir-141- and tumor-related genes c-myc, splunc1, brd3, ubap1 and pten may constitute a gene-mirna network to contribute to npc development.",1
"chromatin remodeling has emerged as a hallmark of gastric cancer, but the regulation of chromatin regulators other than genetic change is unknown. helicobacter pylori causes epigenetic dysregulation to promote gastric carcinogenesis, but the roles and functions of micrornas (mirna) in this multistage cascade are not fully explored. in this study, mirna expression in preneoplastic and neoplastic lesions in murine stomachs induced by h. pylori and n-methyl-n-nitrosourea (mnu) was profiled by mirna expression array. mir-490-3p exhibited progressive downregulation in gastritis, intestinal metaplasia, and adenocarcinoma during h. pylori and mnu-induced gastric carcinogenesis. significant downregulation of mir-490-3p was confirmed in human gastric cancer tissues in which its regulatory region was found to be hypermethylated. mir-490-3p exerted growth- and metastasis-suppressive effects on gastric cancer cells through directly targeting smarcd1, a switch/sucrose nonfermentable (swi/snf) chromatin remodeling complex subunit. knockdown of smarcd1 significantly attenuated the protumorigenic effects of mir-490-3p inhibitor, whereas enforced expression of smarcd1 promoted in vitro and in vivo oncogenic phenotypes of gastric cancer cells. smarcd1 was markedly upregulated in gastric cancer in which its high expression was associated with shortened patients' survival independent of tnm staging. in conclusion, hypermethylation-mediated silencing of mir-490-3p reactivates smarcd1 to confer malignant phenotypes, mechanistically linking h. pylori, chromatin remodeling, and gastric carcinogenesis.",1
"aims microrna-1 (mir-1) has been demonstrated as a tumor-suppressive mirna, which shows a down-regulated pattern in several human malignancies including hepatocellular carcinoma (hcc). however, the pathophysiologic roles of mir-1 and their mechanisms in hcc tumorigenesis are still not totally elucidated. main methods pre-mir-1 was cloned into psuper plasmid to overexpress the mir-1 in hepatoma cells. real-time pcr and western blot were applied to detect mir-1, et-1 mrna and protein levels respectively. dual luciferase reporter assay was conducted to investigate the binding site of mir-1 on 3'utr of et-1 mrna. proliferation of hepatoma cells was evaluated by mtt assay. key findings we observed that over-expression of mir-1 by mirna-expressing plasmid transfection in hepg2 and hep3b cells significantly reduced the proliferation of these cells. to explore the mechanism, we examined the potential target genes of mir-1 by bioinformatics. a potent mitogen, endothelin-1 (et-1), attracted our attention. elevated expression of et-1 but reduced mir-1 level was detected both in human liver cancer tissues and in hepatoma cell lines using western blot and mirna real-time pcr respectively. by the over-expression and inhibition of mir-1 in hepg2 and hep3b, we confirmed that mir-1 negatively regulated et-1 expression in hepatoma cells. a luciferase reporter assay showed that mir-1 regulation was established by pairing to a complementary binding site within the et-1 3'utr. finally, attenuated proliferation of hepatoma cells by over-expression of mir-1 could be partially restored by exogenous et-1 treatment. significance our findings demonstrate that mir-1 could inhibit et-1 expression to attenuate the proliferation of hepatoma cells.",1
"the satellite rna of bamboo mosaic virus (satbamv) contains on open reading frame for a 20-kda protein that is flanked by a 5'-untranslated region (utr) of 159 nucleotides (nt) and a 3'-utr of 129 nt. a secondary structure was predicted for the 5'-utr of satbamv rna, which folds into a large stem-loop (lsl) and a small stem-loop. enzymatic probing confirmed the existence of lsl (nt 8-138) in the 5'-utr. the essential cis-acting sequences in the 5'-utr required for satbamv rna replication were determined by deletion and substitution mutagenesis. their replication efficiencies were analyzed in nicotiana benthamiana protoplasts and chenopodium quinoa plants coinoculated with helper bamv rna. all deletion mutants abolished the replication of satbamv rna, whereas mutations introduced in most of the loop regions and stems showed either no replication or a decreased replication efficiency. mutations that affected the positive-strand satbamv rna accumulation also affected the accumulation of negative-strand rna; however, the accumulation of genomic and subgenomic rnas of bamv were not affected. moreover, covariation analyses of natural satbamv variants provide substantial evidence that the secondary structure in the 5'-utr of satbamv is necessary for efficient replication.",1
"micrornas (mirs) participate in most cellular functions by posttranscriptional regulation of gene expression albeit with little information regarding their role in ischemic preconditioning (ip) of stem cells. we report that ip of bone marrow-derived mesenchymal stem cells (mscs) with two cycles of 30-min ischemia/reoxygenation (i/r) supported their survival under subsequent longer exposure to anoxia and following engraftment in the infarcted heart. ip significantly reduced apoptosis in mscs through activation of akt (ser(473)) and erk1/2 (thr(202)/tyr(204)) and nuclear translocation of hypoxia-inducible factor-1alpha (hif-1alpha). we observed concomitant induction of mir-210 in the preconditioned mscs ((pc)mscs). inhibition of hif-1alpha or of mir-210 abrogated the cytoprotective effects of preconditioning. extrapolation of these data to in vivo studies in a rat model of acute myocardial infarction predominantly improved stem cell survival after engraftment with a role for mir-210. notably, multiple i/r cycles more effectively regulated the mir-210 and hence promoted msc survival compared with single-cycle hypoxia of an equal duration. real time pcr array for rat apoptotic genes, computational target gene analyses, and luciferase reporter assay identified flice-associated huge protein (flash)/caspase-8-associated protein-2 (casp8ap2) in (pc)mscs as the target gene of mir-210. induction of flash/casp8ap2 in mir-210 knocked-down (pc)mscs resulted in increased cell apoptosis. taken together, these data demonstrated that cytoprotection afforded by ip was regulated by mir-210 induction via flash/casp8ap2 suppression. these results highlighted that ip by multiple short episodes of i/r is a novel strategy to promote stem cell survival.",1
"since proprotein convertase subtilisin kexin 9 (pcsk9) discovery, a gene involved in ldl metabolism regulation and cardiovascular diseases (cvd), many therapeutic strategies have been introduced for direct targeting of pcsk9. the main goal of these strategies has been to reduce pcsk9 protein level either by application of antibodies or inhibition of its production. in this study, we have tried to discover micrornas (mirnas) which can target, and hence regulate, pcsk9 expression. using bioinformatics tools, we selected three micrornas with binding sites on 3'-utr of pcsk9. the expression level of these mirnas was examined in three different cell lines using real-time rt-pcr. we observed a reciprocal expression pattern between expression level of mir-191, mir-222, and mir-224 with that of pcsk9. accordingly, the expression levels were highest in huh7 cells which expressed the lowest level of pcsk9, compared to hepg2 and a549 cell lines. pcsk9 mrna level also showed a significant decline in hepg2 cells transfected with the vectors overexpressing the aforementioned mirnas. furthermore, the mirnas target sites were cloned in psicheck-2 vector, and a direct interaction of the mirnas and the pcsk9 3'-utr putative target sites was investigated by means of luciferase assay. our findings revealed that mir-191, mir-222, and mir-224 can directly interact with pcsk9 3'-utr and regulate its expression. in conclusion, our data introduces a role for mirnas to regulate pcsk9 expression.",1
"the scn5a gene encodes cardiac sodium channel nav1.5 and causes lethal ventricular arrhythmias/sudden death and atrial fibrillation (af) when mutated. micrornas (mirnas) are important post-transcriptional regulators of gene expression, and involved in the pathogenesis of many diseases. however, little is known about the regulation of scn5a by mirnas. here we reveal a novel post-transcriptional regulatory mechanism for expression and function of scn5a/nav1.5 via mir-192-5p. bioinformatic analysis revealed that the 3'-utr of human and rhesus scn5a, but not elephant, pig, rabbit, mouse, and rat scn5a, contained a target binding site for mir-192-5p and dual luciferase reporter assays showed that the site was critical for down-regulation of human scn5a. with western blot assays and electrophysiological studies, we demonstrated that mir-192-5p significantly reduced expression of scn5a and nav1.5 as well as peak sodium current density ina generated by nav1.5. notably, in situ hybridization, immunohistochemistry and real-time qpcr analyses showed that mir-192-5p was up-regulated in tissue samples from af patients, which was associated with down-regulation of scn5a/nav1.5. these results demonstrate an important post-transcriptional role of mir-192-5p in post-transcriptional regulation of nav1.5, reveal a novel role of mir-192-5p in cardiac physiology and disease, and provide a new target for novel mirna-based antiarrhythmic therapy for diseases with reduced ina.",1
"micrornas (mirs) are small noncoding rnas that regulate gene expression primarily through translational repression. in erythropoietic (e) culture of cord blood cd34+ progenitor cells, the level of mir 221 and 222 is gradually and sharply down-modulated. hypothetically, this decline could promote erythropoiesis by unblocking expression of key functional proteins. indeed, (i) bioinformatic analysis suggested that mir 221 and 222 target the 3' utr of kit mrna; (ii) the luciferase assay confirmed that both mirs directly interact with the kit mrna target site; and (iii) in e culture undergoing exponential cell growth, mir down-modulation is inversely related to increasing kit protein expression, whereas the kit mrna level is relatively stable. functional studies show that treatment of cd34+ progenitors with mir 221 and 222, via oligonucleotide transfection or lentiviral vector infection, causes impaired proliferation and accelerated differentiation of e cells, coupled with down-modulation of kit protein: this phenomenon, observed in e culture releasing endogenous kit ligand, is magnified in e culture supplemented with kit ligand. furthermore, transplantation experiments in nod-scid mice reveal that mir 221 and 222 treatment of cd34+ cells impairs their engraftment capacity and stem cell activity. finally, mir 221 and 222 gene transfer impairs proliferation of the kit+ tf-1 erythroleukemic cell line. altogether, our studies indicate that the decline of mir 221 and 222 during exponential e growth unblocks kit protein production at mrna level, thus leading to expansion of early erythroblasts. furthermore, the results on kit+ erythroleukemic cells suggest a potential role of these mirs in cancer therapy.",1
"micrornas (mirnas) target mrnas in human cells via complex mechanisms that are still incompletely understood. using anti-argonaute (anti-ago) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, 'rip-chip' experiments enable direct analyses of mirna targets. rip-chip studies (and parallel assessments of total input mrna) were performed in cultured h4 cells after transfection with mirnas corresponding to the mir-15/107 gene group (mir-103, mir-107, mir-16 and mir-195), and five control mirnas. three biological replicates were run for each condition with a total of 54 separate human affymetrix human gene 1.0 st array replicates. computational analyses queried for determinants of mirna:mrna binding. the analyses support four major findings: (i) rip-chip studies correlated with total input mrna profiling provides more comprehensive information than using either rip-chip or total mrna profiling alone after mirna transfections; (ii) new data confirm that mir-107 paralogs target coding sequence (cds) of mrna; (iii) biochemical and computational studies indicate that the 3' portion of mirnas plays a role in guiding mir-103/7 to the cds of targets; and (iv) there are major sequence-specific targeting differences between mirnas in terms of cds versus 3'-untranslated region targeting, and stable ago association versus mrna knockdown. future studies should take this important mirna-to-mirna variability into account.",1
"piwi-interacting rna (pirna) pathways control transposable elements (tes) and endogenous genes, playing important roles in animal gamete formation. however, the underlying pirna biogenesis mechanisms remain elusive. here, we show that endogenous protein coding sequences (cdss), which are normally used for translation, serve as origins of noncoding pirna biogenesis in drosophila melanogaster testes. the product, namely, cds-pirnas, formed silencing complexes with aubergine (aub) in germ cells. proximity proteome and functional analyses show that cds-pirnas and cluster/te-pirnas are distinct species occupying aub, the former loading selectively relies on chaperone cyclophilin 40. moreover, argonaute 2 (ago2) and dicer-2 activities were found critical for cds-pirna production. we provide evidence that ago2-bound short interfering rnas (sirnas) and micrornas (mirnas) specify precursors to be processed into pirnas. we further demonstrate that aub is crucial in spermatid differentiation, regulating chromatins through mrna cleavage. collectively, our data illustrate a unique strategy used by male germ line, expanding pirna repertoire for silencing of endogenous genes during spermatogenesis.",1
"rnase mrp is a ribonucleoprotein enzyme involved in processing precursor rrna in eukaryotes. to facilitate our structure-function analysis of rnase mrp from saccharomyces cerevisiae, we have determined the likely secondary structure of the rna component by a phylogenetic approach in which we sequenced all or part of the rnase mrp rnas from 17 additional species of the saccharomycetaceae family. the structure deduced from these sequences contains the helices previously suggested to be common to the rna subunit of rnase mrp and the related rna subunit of rnase p, an enzyme cleaving trna precursors. however, outside this common region, the structure of rnase mrp rna determined here differs from a previously proposed universal structure for rnase mrps. chemical and enzymatic structure probing analyses were consistent with our revised secondary structure. comparison of all known rnase mrp rna sequences revealed three regions with highly conserved nucleotides. two of these regions are part of a helix implicated in rna catalysis in rnase p, suggesting that rnase mrp may cleave rrna using a similar catalytic mechanism.",1
"background kawasaki disease (kd) is a childhood systemic vasculitis that exhibits a specific preference for the coronary arteries. the aetiology remains unknown and there are no especially diagnostic tests. micrornas (mirnas) are 18 to 23 nucleotides non-coding rnas that are negative regulator of gene expression and play a crucial role in the regulatory network of the genome. recently, circulating mirnas have been found presentation in human plasma and displayed some characteristics of the ideal biomarker. however, few researches explored differentially expressed mirnas in the plasma of kd patients. our study is to identify circulating mirnas in kd plasma which can serve as potential biomarkers of kd diagnosis. materials and methods the total of five pairs of acute kd and normal plasma samples were analyzed using abi mirnas tlda assay chip. differentially expression of mir-125a-5p in plasma were confirmed by quantitative real-time pcr (qrt-pcr) in independent cohort (acute kd = 30, convalescent kd = 30 and healthy control = 32). after bioinformatics prediction, mir-125a-5p vector and inhibitor were transfected into huvecs respectively, to observe mkk7 expression as a potential target gene. flow cytometry was used to analyze apoptosis. the mrna and protein levels of desired genes including mkk7, caspase-3, bax and bcl2 were detected by qrt-pcr and western blotting. results eighteen mirnas were differentially expressed in acute kd's plasma compared with healthy control. mir-125a-5p was significantly increased in plasma of kd patients (p = 0.000), but no variation between acute and convalescent kd (p = 0.357). moreover, the results from the gain and loss functions of mir-125a-5p in huvecs have shown that mir-125a-5p remarkably suppressed mkk7 expression, as a novel target gene. importantly, mir-125a-5p also induced apoptosis in huvecs through inhibition mkk7 levels to regulate bax/bcl2 pathway resulting to activate caspase-3. conclusion our study indicated that the circulating mir-125a-5p levels in kd's plasma have remarkably evaluated compared with healthy individuals. mir-125a-5p might play a role in the development of kd by regulating target gene mkk7 to induce apoptosis in vascular endothelial cells. therefore, our findings have suggested that detected mir-125a-5p levels in plasma could be used as a potential biomarker in early kd diagnosis.",1
"mirnas play important roles in many biological processes, including erythropoiesis. although several mirnas regulate erythroid differentiation, how the key erythroid regulator, gata-1, directly orchestrates differentiation through mirna pathways remains unclear. in this study, we identified mir-23a as a key regulator of erythropoiesis, which was upregulated both during erythroid differentiation and in gata-1 gain-of-function experiments, as determined by mirna expression profile analysis. in primary human cd34+ hematopoietic progenitor cells, mir-23a increased in a gata-1-dependent manner during erythroid differentiation. gain- or loss-of-function analysis of mir-23a in mice or zebrafish demonstrated that it was essential for normal morphology in terminally differentiated erythroid cells. furthermore, a protein tyrosine phosphatase, shp2, was identified as a downstream target of mir-23a that mediated its regulation of erythropoiesis. taken together, our data identify a key gata-1-mirna axis in erythroid differentiation.",1
"a genetic locus is described that specifies two saccharomyces cerevisiae small nuclear rnas (snrnas). the genes specifying the two snrnas are separated by only 67 base pairs and are transcribed in the same direction. the product rnas contain 128 and 190 nucleotides and are designated snr128 and snr190, respectively. these rnas resemble snrnas of other eucaryotes in nuclear localization and possession of a 5' trimethylguanosine cap. neither snrna is related in sequence to previously described vertebrate or yeast snrnas. both rnas exhibit properties consistent with nucleolar organization and hydrogen bonding to pre-rrna species, suggesting possible roles in ribosome biogenesis. the snr128 species cosediments with deproteinized 27s pre-rrna, whereas snr190 is associated with a 20s intermediate. gene disruption in vitro followed by replacement of the chromosomal alleles reveals that snr128 is essential, whereas snr190 is not.",1
"a reporter gene construct was used to study the regulation of connexin43 (cx43) expression, the major gap junction protein found in heart and uterus, in transfected cell lines. the construct had the firefly luciferase gene under the control of the cx43 promoter. inclusion of the 5'-untranslated region (utr) of the mrna in the construct increased luciferase expression by 70%. a bicistronic vector assay demonstrated that the cx43 5'-utr contains a strong internal ribosome entry site (ires). deletion analysis localized the ires element to the upstream portion of the 5'-utr.",1
"osteoblast differentiation is tightly regulated by several factors including micrornas (mirnas). in this paper, we report that pre-mir-15b is highly expressed in differentiated osteoblasts. the functional role of mir-15b in osteoblast differentiation was determined using mir-15b mimic/inhibitor and the expression of osteoblast differentiation marker genes such as alkaline phosphatase (alp), type i collagen genes was decreased by mir-15b inhibitor. runx2, a bone specific transcription factor is generally required for expression of osteoblast differentiation marker genes and in response to mir-15b inhibitor treatment, runx2 mrna expression was not changed; whereas its protein expression was decreased. even though smurf1 (smad specific e3 ubiquitin protein ligase 1), hdac4 (histone deacetylase 4), smad7, and crim1 were found to be few of mir-15b's putative target genes, there was increased expression of only smurf1 gene at mrna and protein levels by mir-15b inhibitor. mir-15b mimic treatment significantly increased and decreased expressions of runx2 and smurf1 proteins, respectively. we further identified that the smurf1 3'utr is directly targeted by mir-15b using the luciferase reporter gene system. this is well documented that smurf1 interacts with runx2 and degrades it by proteasomal pathway. hence, based on our results we suggest that mir-15b promotes osteoblast differentiation by indirectly protecting runx2 protein from smurf1 mediated degradation. thus, this study identified that mir-15b can act as a positive regulator for osteoblast differentiation.",1
"lin28 is a developmentally regulated rna binding protein which has recently emerged as key regulator in the biogenesis of the let-7 micro-rna family. while the expression of lin28b has been linked to advanced tumor stage, the precise molecular mechanism(s) by which lin28b drives disease progression is still being unraveled. herein, we generated a let-7-resistant lin28b orf, stably expressed in the fadu head and neck cancer (hnc) cell line. fadu-lin28b cells exhibited enhanced tumor growth in vitro and in vivo. global gene and micro-rna expression analyses revealed significant enrichment in several pathways involved in cell migration, chromatin remodeling, and cellular stress response. direct regulation of selected genes (hmga2, ccnd2, igf1r, and igf2bp2) via a let-7-lin28b mechanism was validated. notably, up-regulation of several genes in the igf pathway in lin28b-expressing cells was observed. functional studies revealed significant increase in the survival of lin28b-expressing cells when cultured under stress conditions, which was dependent on the presence of igf1. therefore, our data identified several novel gene targets for lin28b-let7, and revealed a novel mechanism by which lin28b promote tumorigenesis. concordantly, clinical examinations of lin28b, igf2bp2 and igf2 revealed a significant association between the expression of these genes with disease relapse, thereby corroborating the potential relevance for the lin28b/igf axis in hnc progression.",1
"many bacterial genes of related function are organized in operons and transcribed as polycistronic mrnas to ensure the coordinate expression of the individual cistrons. post-transcriptional modulation of such mrnas can alter the expression of downstream cistrons, resulting in discoordinate protein synthesis from an operon mrna. several factors, including small non-coding rnas (srnas), have been described that act collectively as repressors within polycistronic mrnas. we describe the first case of discoordinated operon expression in which a downstream cistron is activated at the post-transcriptional level. we report that glmy srna activates glms synthesis from the escherichia coli glmus mrna without altering glmu expression. the srna is shown to be structurally and functionally conserved in diverse enterobacteria; its transcription may be controlled by the alternative sigma factor, sigma(54). our data suggest that gram-negative bacteria evolved a mechanism of glms riboregulation that is distinct from the glms riboswitch mechanism of gram-positive bacteria.",1
"assembly of microrna ribonucleoproteins (mirnps) or rna-induced silencing complexes (riscs) is essential for the function of mirnas and initiates from processing of precursor mirnas (pre-mirnas) by dicer or by ago2. here, we report an in vitro mirnp/risc assembly assay programmed by pre-mirnas from mammalian cell lysates. combining in vivo studies in dicer knockout cells reconstituted with wild-type or catalytically inactive dicer, we find that the mirna loading complex (mirlc) is the primary machinery linking pre-mirna processing to mirna loading. we show that a mirna precursor deposit complex (mipdc) plays a crucial role in dicer-independent mirna biogenesis and promotes mirnp assembly of certain dicer-dependent mirnas. furthermore, we find that 5'-uridine, 3'-mid base pairing, and 5'-mid mismatches within pre-mirnas promote their assembly into mipdc. our studies provide a comprehensive view of mirnp/risc assembly pathways in mammals, and our assay provides a versatile platform for further mechanistic dissection of such pathways in mammals.",1
"the evolutionary relationships of the onychophorans (velvet worms) and the monophyly of the arthropods have generated considerable debate. cladistic analyses of 12s ribosomal rna sequences indicate that arthropods are monophyletic and include the onychophorans. maximum parsimony analyses and monophyly testing within arthropods indicate that myriapods (millipedes and centipedes) form a sister group to all other assemblages, whereas crustaceans (shrimps and lobsters) plus hexapods (insects and allied groups) form a well-supported monophyletic group. parsimony analysis further suggests that onychophorans form a sister group to chelicerates (spiders and scorpions) and crustaceans plus hexapods, but this relationship is not well supported by monophyly testing. these relationships conflict with current hypotheses of evolutionary pathways within arthropods.",1
"genetic instability is a hallmark of cancer; the hypoxic tumor microenvironment has been implicated as a cause of this phenomenon. micrornas (mir) are small nonprotein coding rnas that can regulate various cellular pathways. we report here that two mirs, mir-210 and mir-373, are up-regulated in a hypoxia-inducible factor-1alpha-dependent manner in hypoxic cells. bioinformatics analyses suggested that these mirs could regulate factors implicated in dna repair pathways. forced expression of mir-210 was found to suppress the levels of rad52, which is a key factor in homology-dependent repair (hdr); the forced expression of mir-373 led to a reduction in the nucleotide excision repair (ner) protein, rad23b, as well as in rad52. consistent with these results, both rad52 and rad23b were found to be down-regulated in hypoxia, but in both cases, the hypoxia-induced down-regulation could be partially reversed by antisense inhibition of mir-210 and mir-373. importantly, luciferase reporter assays indicated that mir-210 is capable of interacting with the 3' untranslated region (utr) of rad52 and that mir-373 can act on the 3' utr of rad23b. these results indicate that hypoxia-inducible mir-210 and mir-373 play roles in modulating the expression levels of key proteins involved in the hdr and ner pathways, providing new mechanistic insight into the effect of hypoxia on dna repair and genetic instability in cancer.",1
"osteoarthritis (oa) is a multifactorial degenerative pathology, whose progression is exacerbated by pro-inflammatory cytokines signaling. among the changes triggered in chondrocytes during inflammation, modified expression of tiny epigenetic regulators as micrornas was shown having deleterious implications for articular cartilage. aim of the present study was to identify differentially expressed micrornas in human oa cartilage and to determine their relevance to pathological progression. an oa model based on inflammatory stimulation of a chondrocytic human cell line was used to analyze micrornas deregulation, and results revealed mir-149 severely down-regulated by il1β and tnfα. real-time pcr analysis of mir-149 was exerted also in human primary chondrocytes isolated from cartilage of oa donors and postmortem from subjects with no known history of oa, confirming down-regulation in osteoarthritis. moving on a functional study, mir-149 regulatory effect on tumor necrosis factor alpha (tnfα), interleukin 1 beta (il1β) and interleukin 6 (il6) 3'utrs was evaluated by luciferase assays, and chondrocytes production of tnfα upon mir-149 transfection was measured by enzyme-linked immuno sorbent assay. we found that mir-149 is down-regulated in oa chondrocytes, and this decrease seems to be correlated to increased expression of pro-inflammatory cytokines such as tnfα, il1β and il6. oa is a multifactorial disease and we think that our results give new insights for understanding the complex mechanisms of osteoarthritic pathogenesis.",1
"background recent studies have shown that micrornas may regulate the abcb1 gene (atp-binding cassette, sub-family b , member 1). computational programs have predicted that the 3'-untranslated region (3'-utr) of abcb1 contains a potential mirna-binding site for mir-186. here, we investigated the role of mir-186 in sensitizing ovarian cancer cells to paclitaxel and cisplatin. results human ovarian carcinoma cell lines ovcar3, a2780, a2780/ddp, and a2780/taxol were exposed to paclitaxel or cisplatin with or without mir-186 transfection, and cell viability was determined by mtt assay. reverse transcriptase-polymerase chain reaction (rt-pcr) and western blot analysis were used to assess the mdr1, gst-π, and mrp1 expression levels. dual-luciferase reporter assay was used to reveal the correlation between mir-186 and abcb1. lower mir-186 while higher mdr1 and gst-π mrna expression levels were found in the a2780/taxol and a2780/ddp cells than in the a2780 cells. after mir-186 transfection, all the cell lines showed increased sensitivity to paclitaxel and cisplatin. mir-186 transfection induced apoptosis while anti-mir-186 transfection reduced apoptosis. the dual-luciferase reporter assay verified that that mir-186 combined with the 3'-untranslated region (utr) of abcb1. mdr1 and gst-π mrna and protein expression levels were downregulated after transfection with mir-186 but upregulated following anti-mir-186 transfection compared to the mock and negative control cancer cells; however, the mrp1 expression levels did not significantly differ among the groups. conclusion our results are the first to demonstrate that mir-186 may sensitize ovarian cancer cell to paclitaxel and cisplatin by targeting abcb1 and modulating the expression of gst-π.",1
"micrornas (mirnas) are posttranscriptional modulators of gene expression and play an important role in many developmental processes. we report here that expression of microrna-145 (mir-145) is low in self-renewing human embryonic stem cells (hescs) but highly upregulated during differentiation. we identify the pluripotency factors oct4, sox2, and klf4 as direct targets of mir-145 and show that endogenous mir-145 represses the 3' untranslated regions of oct4, sox2, and klf4. increased mir-145 expression inhibits hesc self-renewal, represses expression of pluripotency genes, and induces lineage-restricted differentiation. loss of mir-145 impairs differentiation and elevates oct4, sox2, and klf4. furthermore, we find that the mir-145 promoter is bound and repressed by oct4 in hescs. this work reveals a direct link between the core reprogramming factors and mir-145 and uncovers a double-negative feedback loop involving oct4, sox2, klf4, and mir-145.",1
"enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. furthermore, it has been suggested to play a general role in non-symbiotic plant development. although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or rna structures encoded in the enod40 genes. we utilized conserved rna structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. rna secondary structure predictions and comparative sequence analysis of enod40 rnas allowed us to determine the most conserved structural features, present in all known enod40 genes. remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural rnas such as rrnas, rnase p and srp rnas. surprisingly, the enod40 rna structural elements are much more stronger conserved than the encoded peptides. this finding suggests that some general functions of enod40 gene could be determined by the encoded rna structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.",1
"human brains retain discrete populations of micro rna (mirna) species that support homeostatic brain gene expression functions; however, specific mirna abundance is significantly altered in neurological disorders such as alzheimer disease (ad) when compared with age-matched controls. here we provide evidence in ad brains of a specific up-regulation of an nf-kappab-sensitive mirna-146a highly complementary to the 3'-untranslated region of complement factor h (cfh), an important repressor of the inflammatory response of the brain. up-regulation of mirna-146a coupled to down-regulation of cfh was observed in ad brain and in interleukin-1beta, abeta42, and/or oxidatively stressed human neural (hn) cells in primary culture. transfection of hn cells using an nf-kappab-containing pre-mirna-146a promoter-luciferase reporter construct in stressed hn cells showed significant up-regulation of luciferase activity that paralleled decreases in cfh gene expression. treatment of stressed hn cells with the nf-kappab inhibitor pyrollidine dithiocarbamate or the resveratrol analog cay10512 abrogated this response. incubation of an antisense oligonucleotide to mirna-146a (anti-mirna-146a; am-146a) was found to restore cfh expression levels. these data indicate that nf-kappab-sensitive mirna-146a-mediated modulation of cfh gene expression may in part regulate an inflammatory response in ad brain and in stressed hn cell models of ad and illustrate the potential for anti-mirnas as an effective therapeutic strategy against pathogenic inflammatory signaling.",1
"newborn neurons in the dentate gyrus of the adult hippocampus rely upon camp response element binding protein (creb) signaling for their differentiation into mature granule cells and their integration into the dentate network. among its many targets, the transcription factor creb activates expression of a gene locus that produces two micrornas, mir-132 and mir-212. in cultured cortical and hippocampal neurons, mir-132 functions downstream from creb to mediate activity-dependent dendritic growth and spine formation in response to a variety of signaling pathways. to investigate whether mir-132 and/or mir-212 contribute to the maturation of dendrites in newborn neurons in the adult hippocampus, we inserted loxp sites surrounding the mir-212/132 locus and specifically targeted its deletion by stereotactically injecting a retrovirus expressing cre recombinase. deletion of the mir-212/132 locus caused a dramatic decrease in dendrite length, arborization, and spine density. the mir-212/132 locus may express up to four distinct micrornas, mir-132 and -212 and their reverse strands mir-132* and -212*. using ratiometric microrna sensors, we determined that mir-132 is the predominantly active product in hippocampal neurons. we conclude that mir-132 is required for normal dendrite maturation in newborn neurons in the adult hippocampus and suggest that this microrna also may participate in other examples of creb-mediated signaling.",1
"hepatitis b virus x protein (hbx) plays important roles in the development of hepatocellular carcinoma (hcc). micrornas (mirnas) contribute to cancer development by acting as oncogenes or tumor suppressors. previously, we reported that hbx was able to promote the migration of hepatoma hepg2 cells. however, the regulation of mirnas in the development of hbv-related hcc is poorly understood. in the present study, we reported that mir-29a was a novel regulator of migration of hepatoma cells mediated by hbx. our data showed that the expression of mir-29a was dramatically increased in p21-hbx transgenic mice, hbx-transfected hepatoma hepg2-x (or h7402-x) cells and hepg2.2.15 cells that constitutively replicate hbv. however, our data showed that mir-29a was upregulated in 4 of the 11 clinical hcc samples. we found that the overexpression of mir-29a promoted the migration of hepg2 cells, while a specific mir-29a inhibitor could partially abolish the enhanced migration of hepg2-x cells. moreover, we identified pten was one of the target genes of mir-29a in hepg2 cells. the deletion of the mir-29a-binding site was able to abolish the role of mir-29a in suppression of luciferase activity of the pten 3'utr reporter. meanwhile, the overexpression of pten was able to reverse the promoted migration of hepg2 cells mediated by mir-29a. moreover, our data showed that the modulation of akt phosphorylation, a downstream factor of pten, was involved in the cell migration enhanced by mir-29a, suggesting that mir-29a is responsible for the cell migration through its target gene pten. thus, we conclude that mir-29a is involved in the regulation of migration of hepatoma cells mediated by hbx through pten in cell culture model.",1
"hepatitis c virus (hcv) uniquely requires the liver-specific microrna-122 for replication, yet global effects on endogenous mirna targets during infection are unexplored. here, high-throughput sequencing and crosslinking immunoprecipitation (hits-clip) experiments of human argonaute (ago) during hcv infection showed robust ago binding on the hcv 5'utr at known and predicted mir-122 sites. on the human transcriptome, we observed reduced ago binding and functional mrna de-repression of mir-122 targets during virus infection. this mir-122 ""sponge"" effect was relieved and redirected to mir-15 targets by swapping the mirna tropism of the virus. single-cell expression data from reporters containing mir-122 sites showed significant de-repression during hcv infection depending on expression level and site number. we describe a quantitative mathematical model of hcv-induced mir-122 sequestration and propose that such mir-122 inhibition by hcv rna may result in global de-repression of host mir-122 targets, providing an environment fertile for the long-term oncogenic potential of hcv.",1
"the lining of the adult heart contains epicardial mesothelial cells (emcs) that have the potential to undergo fibrogenic epithelial-to-mesenchymal transition (emt) during cardiac injury. emt of emcs has therefore been suggested to contribute to the heterogeneous fibroblast pool that mediates cardiac fibrosis. however, the molecular basis of this process is poorly understood. recently, micrornas (mirnas) have been shown to regulate a number of sub-cellular events in cardiac disease. hence, we hypothesized that mirnas regulate fibrogenic emt in the adult heart. indeed pro-fibrogenic stimuli, especially tgf-β, promoted emt progression in emc cultures, which resulted in differential expression of numerous mirnas, especially the pleiotropic mir-21. accordingly, ectopic expression of mir-21 substantially promoted the fibroblast-like phenotype arising from fibrogenic emt, whereas an antagonist that targeted mir-21 blocked this effect, as assessed on the e-cadherin/α-smooth muscle actin balance, cell viability, matrix activity, and cell motility, thus making mir-21 a relevant target of emc-derived fibrosis. several mrna targets of mir-21 was differentially regulated during fibrogenic emt of emcs and mir-21-dependent targeting of programmed cell death 4 (pdcd4) and sprouty homolog 1 (spry1) significantly contributed to the development of a fibroblastoid phenotype. however, pdcd4- and spry1-targeting was not entirely ascribable to all phenotypic effects from mir-21, underscoring the pleiotropic biological role of mir-21 and the increasing number of recognized mir-21 targets.",1
"cell competition is a homeostatic process in which proliferating cells compete for survival. elimination of otherwise normal healthy cells through competition is important during development and has recently been shown to contribute to maintaining tissue health during organismal aging. the mechanisms that allow for ongoing cell competition during adult life could, in principle, contribute to tumorigenesis. however, direct evidence supporting this hypothesis has been lacking. here, we provide evidence that cell competition drives tumor formation in a drosophila model of epithelial cancer. cells expressing egfr together with the conserved microrna mir-8 acquire the properties of supercompetitors. neoplastic transformation and metastasis depend on the ability of these cells to induce apoptosis and engulf nearby cells. mir-8 expression causes genome instability by downregulating expression of the septin family protein peanut. cytokinesis failure due to downregulation of peanut is required for tumorigenesis. this study provides evidence that the cellular mechanisms that drive cell competition during normal tissue growth can be co-opted to drive tumor formation and metastasis. analogous mechanisms for cytokinesis failure may lead to polyploid intermediates in tumorigenesis in mammalian cancer models.",1
"micrornas (mir) have considerable potential as therapeutic tools in cardiac diseases. alterations in atrial mir are involved in the development of atrial fibrillation (af), but the molecular mechanism underlying their contribution to atrial remodeling in chronic atrial fibrillation (caf) is only partially understood. here we used mir array to analyze the mir profile of atrial biopsies from sinus rhythm (sr) and caf patients. qrt-pcr identified a distinctive caf-mir signature and described conserved mir-208b upregulation in human and ovine af atrial tissue. we used bioinformatics analysis to predict genes and signaling pathways as putative mir-208b targets, which highlighted genes from the cardiac muscle gene program and from canonical wnt, gap-junction and ca 2+ signaling networks. results from analysis of mir-208b-overexpressing hl-1 atrial myocytes and from myocytes isolated from caf patients showed that aberrant mir-208b levels reduced the expression and function of l-type ca 2+ channel subunits (cacna1c and cacnb2) as well as the sarcoplasmic reticulum-ca 2+ pump serca2. these findings clearly pointed to caf-specific upregulated mir-208b as an important mediator in ca 2+ handling impairment during atrial remodeling.",1
"in this study we analyzed the microrna profile of cystic fibrosis (cf) bronchial epithelial ib3-1 cells infected with pseudomonas aeruginosa by microarray and quantitative rt-pcr, demonstrating that microrna 93 (mir-93), which is highly expressed in basal conditions, decreases during infection in parallel with increased expression of the il-8 gene. the down-regulation of mir-93 after p. aeruginosa infection was confirmed in other bronchial cell lines derived from subjects with and without cf, namely cufi-1 and nuli-1 cells. sequence analysis shows that the 3'-utr region of il-8 mrna is a potential target of mir-93 and that the consensus sequence is highly conserved throughout molecular evolution. the possible involvement of mir-93 in il-8 gene regulation was validated using three luciferase vectors, including one carrying the complete 3'-utr region of the il-8 mrna and one carrying the same region with a mutated mir-93 site. up-modulation of il-8 after p. aeruginosa infection was counteracted in ib3-1, cufi-1, and nuli-1 cells by pre-mir-93 transfection. in addition, il-8 was up-regulated in uninfected cells treated with antagomir-93. our results support the concept of a possible link between microrna expression and il-8 induction in bronchial epithelial cells infected with p. aeruginosa. specifically, the data presented here indicate that, in addition to nf-κb-dependent up-regulation of il-8 gene transcription, il-8 protein expression is posttranscriptionally regulated by interactions of the il-8 mrna with the inhibitory mir-93.",1
"microsomal triglyceride transfer protein (mttp) is an essential chaperone that assists in the assembly of apolipoprotein b-containing lipoproteins to transport lipids. we have shown that microrna (mir)-30c regulates mttp expression but other members of the same family do not. further, we showed that interactions between mir-30c seed sequence and the 3΄-untranslated region (utr) of the mttp mrna are critical for this regulation. the same seed sequence is shared by all the members of the mir-30 family. therefore, it is unclear why only mir-30c regulates mttp expression. bioinformatics analysis revealed that, mir-30c interacts with mttp mrna involving supplementary site, besides seed sequence, forming an intervening loop. here, we evaluated the importance of the supplementary site and the size of the intervening loop in mir-30c/mttp mrna interactions by cloning mttp 3΄-utr at the end of the luciferase gene and subjecting it to site-directed mutagenesis. reducing the number of base pairs at the supplementary site abolished the ability of mir-30c to reduce luciferase activity. however, increasing the number of base pairs at the supplementary site, seed sequence or in the intervening loop enhanced the efficacy of mir-30c in reducing luciferase activity. these studies demonstrated that the supplementary site of mir-30c is, but the intervening loop is not, critical for binding to the mttp mrna. to our knowledge, this is the first demonstration that mirs might require both seed and supplementary interactions to regulate target mrna specificity. further, this study suggests that more potent mir-30c mimics could be synthesized by increasing base pairing in the loop region.",1
"alterations in the levels of molecules which interact with the extracellular matrix, such as integrins, are associated with invasion of oral squamous cell carcinomas (oscc). the molecular mechanisms underlying dysregulation of integrin expression in oscc, however, remain unclear. here, we show that microrna-124, a small non-coding rna down-regulated in oscc, is able to downregulate expression of integrin beta-1 (itgb1) by interacting with its 3' untranslated region. over-expression of mir-124 attenuates endogenous itgb1 expression and reduces the adherence and motility of oscc cells, suggesting disruption of mir-124-mediated repression of itgb1 may be a key factor in oscc progression.",1
"translational control of apolipoprotein b (apob) mrna has been previously documented; however, the molecular mechanisms that govern translation of apob mrna are unknown. we investigated the role of the untranslated regions (utr) in the regulation of apob mrna translation first by analyzing apob utr sequences using m-fold, a program used to predict rna secondary structure. m-fold analysis revealed hairpin-like elements within the 5'utr and 3'utr of apob mrna with potential to form stable secondary structure. luciferase (luc) reporter assays were conducted to assess the biological activity of the putative rna motifs within the utr sequences by transiently transfecting hepg2 cells with chimeric mrnas containing the 5' and/or 3' apob utrs linked to a luc reporter gene. we observed statistically significant increases in luc activity for the 5'utrpgl3 and 5'/3'utrpgl3 constructs. luc mrna levels remained constant for all constructs, suggesting that increased luc activity was likely posttranscriptional in nature. when rna isolated from transfected cells was translated in vitro, parallel increases in translatable luc activity were observed. we also examined the role of utr sequences within the context of the apob coding sequence, using constructs containing the n-terminal 15% of apob (apob15). we observed a 40% and 25% increase in total protein mass with the 5'utr-apob15 construct and the 5'utr-apob15-3'utr, respectively, over the control construct with no apob utr, with only a slight stimulation observed for apob15 3'utr. radiolabeling analysis of apob15 synthetic rate showed a more striking 4.5-fold stimulation of protein synthesis by 5'utr while addition of both utrs caused a 3.1-fold stimulation over the control construct. deletion mutant analysis revealed that the stimulatory effect of the 5'utr on apob mrna translation may be dependent on specific hairpin elements formed within the 5'utr secondary structure. overall, our data suggest that putative 5'utr motifs are important for optimal translation of the apob message whereas the presence of the 3'utr appears to attenuate wild-type expression. potential cis-trans interactions of these motifs with putative rna binding proteins/translational factors are likely to govern apob mrna translation and protein synthesis and may play an important role in dysregulation of atherogenic lipoprotein production in dyslipidemic states.",1
"cerebral vascular endothelial cell (cec) degeneration significantly contributes to blood-brain barrier (bbb) breakdown and neuronal loss after cerebral ischemia. recently, emerging data suggest that peroxisome proliferator-activated receptor delta (ppardelta) activation has a potential neuroprotective role in ischemic stroke. here we report for the first time that ppardelta is significantly reduced in oxygen-glucose deprivation (ogd)-induced mouse cec death. interestingly, ppardelta overexpression can suppress ogd-induced caspase-3 activity, golgi fragmentation, and cec death through an increase of bcl-2 protein levels without change of bcl-2 mrna levels. to explore the molecular mechanisms, we have identified that upregulation of ppardelta can alleviate odg-activated microrna-15a (mir-15a) expression in cecs. moreover, we have demonstrated that bcl-2 is a translationally repressed target of mir-15a. intriguingly, gain- or loss-of-mir-15a function can significantly reduce or increase ogd-induced cec death, respectively. furthermore, we have identified that mir-15a is a transcriptional target of ppardelta. consistent with the in vitro findings, we found that intracerebroventricular infusion of a specific ppardelta agonist, gw 501516 (2--1,3-thiazol-5-yl]methylsulfanyl]phenoxy]acetic acid), significantly reduced ischemia-induced mir-15a expression, increased bcl-2 protein levels, and attenuated caspase-3 activity and subsequent dna fragmentation in isolated cerebral microvessels, leading to decreased bbb disruption and reduced cerebral infarction in mice after transient focal cerebral ischemia. together, these results suggest that ppardelta plays a vascular-protective role in ischemia-like insults via transcriptional repression of mir-15a, resulting in subsequent release of its posttranscriptional inhibition of bcl-2. thus, regulation of ppardelta-mediated mir-15a inhibition of bcl-2 could provide a novel therapeutic strategy for the treatment of stroke-related vascular dysfunction.",1
"the use of anthracyclines such as doxorubicin (dox) has improved outcome in cancer patients, yet associated risks of cardiomyopathy have limited their clinical application. dox-associated cardiotoxicity is frequently irreversible and typically progresses to heart failure (hf) but our understanding of molecular mechanisms underlying this and essential for development of cardioprotective strategies remains largely obscure. as micrornas (mirnas) have been shown to play potent regulatory roles in both cardiovascular disease and cancer, we investigated mirna changes in dox-induced hf and the alteration of cellular processes downstream. myocardial mirna profiling was performed after dox-induced injury, either via acute application to isolated cardiomyocytes or via chronic exposure in vivo, and compared with mirna profiles from remodeled hearts following myocardial infarction. the mir-30 family was downregulated in all three models. we describe here that mir-30 act regulating the β-adrenergic pathway, where preferential β1- and β2-adrenoceptor (β1ar and β2ar) direct inhibition is combined with giα-2 targeting for fine-tuning. importantly, we show that mir-30 also target the pro-apoptotic gene bnip3l/nix. in aggregate, we demonstrate that high mir-30 levels are protective against dox toxicity and correlate this in turn with lower reactive oxygen species generation. in addition, we identify gata-6 as a mediator of dox-associated reductions in mir-30 expression. in conclusion, we describe that dox causes acute and sustained mir-30 downregulation in cardiomyocytes via gata-6. mir-30 overexpression protects cardiac cells from dox-induced apoptosis, and its maintenance represents a potential cardioprotective and anti-tumorigenic strategy for anthracyclines.",1
"mir-29c is frequently dysregulated in many cancers; however, the roles of mir-29c in pancreatic cancer (pc) and underlying mechanisms remain poorly understood. in this study, we investigated the role of mir-29c in pc. using quantitative real-time polymerase chain reaction, we demonstrated that mir-29c was frequently downregulated in clinical pc tissues and cell lines. overexpression of mir-29c significantly inhibited the proliferation, migration, and invasion of pc cells in vitro, which demonstrated that mir-29c acts as a tumor suppressor in pc cells. further analysis revealed that itgb1 is one of the functional target genes of mir-29c, and knockdown of itgb1 inhibited the proliferation, migration, and invasion of pc cells, which was similar to the effects of overexpression of mir-29c. taken together, our results highlight the significance of mir-29c-itgb1 interaction in the development and progression of pc.",1
"bioinformatic analysis of the intergenic regions of staphylococcus aureus predicted multiple regulatory regions. from this analysis, we characterized 11 novel noncoding rnas (rsaa-k) that are expressed in several s. aureus strains under different experimental conditions. many of them accumulate in the late-exponential phase of growth. all ncrnas are stable and their expression is hfq-independent. the transcription of several of them is regulated by the alternative sigma b factor (rsaa, d and f) while the expression of rsae is agra-dependent. six of these ncrnas are specific to s. aureus, four are conserved in other staphylococci, and rsae is also present in bacillaceae. transcriptomic and proteomic analysis indicated that rsae regulates the synthesis of proteins involved in various metabolic pathways. phylogenetic analysis combined with rna structure probing, searches for rsae-mrna base pairing, and toeprinting assays indicate that a conserved and unpaired uccc sequence motif of rsae binds to target mrnas and prevents the formation of the ribosomal initiation complex. this study unexpectedly shows that most of the novel ncrnas carry the conserved c-rich motif, suggesting that they are members of a class of ncrnas that target mrnas by a shared mechanism.",1
"micrornas (mirnas) are a class of short non-coding, single-stranded rnas, which perform posttranscriptional regulatory functions as tumor suppressors or oncogenes. single nucleotide polymorphisms (snps) in micrornas (mirnas) genes are currently being identified for contributing to cancer risk, prognosis and survival. we investigated whether genetic variations of mirnas were associated with the risk and prognosis of renal cell carcinoma (rcc). we genotyped four common mirna snps (i.e. mir-146a rs2910164, mir-149 rs2292832, mir-196a2 rs11614913 and mir-499 rs3746444) to assess their associations with rcc risk in a two-stage case-control study (355 cases and 362 controls in discovery set, meanwhile 647 cases and 660 controls in validation set), as well as rcc survival in 311 patients. we found that the mir-196a2 snp rs11614913 was associated with rcc susceptibility in recessive model and with survival of rcc in dominant model (tc/cc versus tt, adjusted hazard ratio = 0.40, 95% ci = 0.18-0.89). meanwhile, the rs11614913 cc genotype was associated with the significantly decreased expression of mir-196a-5p in 26 renal cancer tissues (p = 0.018). moreover, luciferase reporter assays revealed the potential effect of rs11614913 snp on the binding of mir-196a-3p to its targets. these results suggested that the mir-196a2 rs11614913 may contribute to the genetic susceptibility and prognosis for rcc, which may act as a biomarker for rcc occurrence and prognosis.",1
"x-chromosome inactivation (xci) is an essential epigenetic process in female mammalian development. although cell-based studies suggest the potential importance of the ftx long non-protein-coding rna (lncrna) in xci, its physiological roles in vivo remain unclear. here we show that targeted deletion of x-linked mouse ftx lncrna causes eye abnormalities resembling human microphthalmia in a subset of females but rarely in males. this inheritance pattern cannot be explained by x-linked dominant or recessive inheritance, where males typically show a more severe phenotype than females. in ftx-deficient mice, some x-linked genes remain active on the inactive x, suggesting that defects in random xci in somatic cells cause a substantially female-specific phenotype. the expression level of xist, a master regulator of xci, is diminished in females homozygous or heterozygous for ftx deficiency. we propose that loss-of-ftx lncrna abolishes gene silencing on the inactive x chromosome, leading to a female microphthalmia-like phenotype.",1
"gene targeting by micrornas is important in health and disease. we developed a functional assay for identifying microrna targets and applied it to the k(+) channel k(ir)2.1 which is dysregulated in cardiac and vascular disorders. the 3'utr (untranslated region) was inserted downstream of the mcherry red fluorescent protein coding sequence in a mammalian expression plasmid. microrna sequences were inserted into the psm30 expression vector which provides enhanced green fluorescent protein as an indicator of microrna expression. hek (human embryonic kidney)-293 cells were co-transfected with the mcherry-3'utr plasmid and a psm30-based plasmid with a microrna insert. the principle of the assay is that functional targeting of the 3'utr by the microrna results in a decrease in the red/green fluorescence intensity ratio as determined by automated image analysis. the method was validated with mir-1, a known down-regulator of k(ir)2.1 expression, and was used to investigate the targeting of the k(ir)2.1 3'utr by mir-212. the red/green ratio was lower in mir-212-expressing cells compared with the non-targeting controls, an effect that was attenuated by mutating the predicted target site. mir-212 also reduced inward rectifier current and k(ir)2.1 protein in hela cells. this novel assay has several advantages over traditional luciferase-based assays including larger sample size, amenability to time course studies and adaptability to high-throughput screening.",1
"aim to investigate the expression of mir-29a in rat acute pancreatitis and its functional role in ar42j cell apoptosis. methods twelve sd rats were divided into a control group and an acute edematous pancreatitis (aep) group randomly. aep was induced by intraperitoneal injection of l-arginine (150 mg/kg) in the aep group and equal volume of 0.9% nacl was injected in the control group. the apoptosis of acinar cells in pancreatic tissue was determined by tunel assay. mirna chip assay was performed to examine the expression of mirnas in two groups. besides, to further explore the role of mir-29a in apoptosis in vitro, recombinant rat tnf-α (50 ng/ml) was administered to treat the rat pancreatic acinar cell line ar42j for inducing ar42j cell apoptosis. quantitative real-time pcr (qrt-pcr) was adopted to measure mir-29a expression. then, mirna mimic, mirna antisense oligonucleotide (amo) and control vector were used to transfect ar42j cells. the expression of mir-29a was confirmed by qrt-pcr and the apoptosis rate of ar42j cells was detected by flow cytometry analysis. western blot was used to detect the expression of activated caspase3. moreover, we used bioinformatics software and luciferase assay to test whether tnfrsf1a was the target gene of mir-29a. after transfection, qrt-pcr and western blot was used to detect the expression of tnfrsf1a in ar42j cells after transfection. results the expression of mir-29a was much higher in the aep group compared with the control group as displayed by the mirna chip assay. after inducing apoptosis of ar42j cells in vitro, the expression of mir-29a was significantly increased by 1.49 ± 0.04 times in comparison with the control group. as revealed by qrt-pcr assay, the expression of mir-29a was 2.68 ± 0.56 times higher in the mir-29a mimic group relative to the control vector group, accompanied with an obviously increased acinar cell apoptosis rate (42.83 ± 1.25 vs 24.97 ± 0.15, p conclusion mir-29a might promote the apoptosis of ar42j cells via up-regulating the expression of its target gene tnfrsf1a.",1
"peripheral and cns inflammation leads to aberrations in developmental and postnatal neurogenesis, yet little is known about the mechanism linking inflammation to neurogenic abnormalities. specific mirs regulate peripheral and cns inflammatory responses. mir-155 is the most significantly upregulated mir in primary murine microglia stimulated with lipopolysaccharide (lps), a proinflammatory toll-like receptor 4 ligand. here, we demonstrate that mir-155 is essential for robust il6 gene induction in microglia under lps stimulation in vitro. lps-stimulated microglia enhance astrogliogenesis of cocultured neural stem cells (nscs), whereas blockade of il6 or genetic ablation of microglial mir-155 restores neural differentiation. mir-155 knock-out mice show reversal of lps-induced neurogenic deficits and microglial activation in vivo. moreover, mice with transgenic elevated expression of mir-155 in nestin-positive neural and hematopoietic stem cells, including microglia, show increased cell proliferation and ectopically localized doublecortin-positive immature neurons and radial glia-like cells in the hippocampal dentate gyrus (dg) granular cell layer. microglia have proliferative and neurogenic effects on nscs, which are significantly altered by microglial mir-155 overexpression. in addition, mir-155 elevation leads to increased microglial numbers and amoeboid morphology in the dg. our study demonstrates that mir-155 is essential for inflammation-induced neurogenic deficits via microglial activation and induction of il6 and is sufficient for disrupting normal hippocampal development.",1
"long non-coding rnas (lncrnas) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. many lncrnas are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncrnas play important roles in cellular processes, neural development, and even in cognitive and behavioral processes. however, relatively little is known about their in vivo functions and underlying molecular mechanisms in the nervous system. here, we report a neural-specific drosophila lncrna, cask regulatory gene (crg), which participates in locomotor activity and climbing ability by positively regulating its neighboring gene cask (ca(2+)/calmodulin-dependent protein kinase). crg deficiency led to reduced locomotor activity and a defective climbing ability-phenotypes that are often seen in cask mutant. crg mutant also showed reduced cask expression level while cask over-expression could rescue the crg mutant phenotypes in reciprocal. at the molecular level, crg was required for the recruitment of rna polymerase ii to the cask promoter regions, which in turn enhanced cask expression. our work has revealed new functional roles of lncrnas and has provided insights to explore the pathogenesis of neurological diseases associated with movement disorders.",1
"the structure of hiv-1 psi-rna has been elucidated by a concerted approach combining structural probes with mass spectrometric detection (ms3d), which is not affected by the size and crystallization properties of target biomolecules. distance constraints from bifunctional cross-linkers provided the information required for assembling an all-atom model from the high-resolution coordinates of separate domains by triangulating their reciprocal placement in 3d space. the resulting structure revealed a compact cloverleaf morphology stabilized by a long-range tertiary interaction between the gnra tetraloop of stemloop 4 (sl4) and the upper stem of stemloop 1 (sl1). the preservation of discrete stemloop structures ruled out the possibility that major rearrangements might produce a putative supersite with enhanced affinity for the nucleocapsid (nc) domain of the viral gag polyprotein, which would drive genome recognition and packaging. the steric situation of single-stranded regions exposed on the cloverleaf structure offered a valid explanation for the stoichiometry exhibited by full-length psi-rna in the presence of nc. the participation of sl4 in a putative gnra loop-receptor interaction provided further indications of the plasticity of this region of genomic rna, which can also anneal with upstream sequences to stabilize alternative conformations of the 5' untranslated region (5'-utr). considering the ability to sustain specific nc binding, the multifaceted activities supported by the sl4 sequence suggest a mechanism by which gag could actively participate in regulating the vital functions mediated by 5'-utr. substantiated by the 3d structure of psi-rna, the central role played by sl4 in specific rna-rna and protein-rna interactions advances this domain as a primary target for possible therapeutic intervention.",1
"micrornas (mirnas) regulate gene expression at the post-transcriptional level and play important roles in tumor initiation and progression. recently, we examined the global mirna expression profile of esophageal squamous cell carcinoma (escc) and demonstrated that mir-92a was highly expressed in tumor tissues. in this study, we found that the up-regulation of mir-92a was significantly correlated with the status of lymph node metastasis and tnm stage in 107 escc patients. moreover, the up-regulation of mir-92a was associated with poor survival of escc patients and might be used as an independent prognostic factor. next, we investigated the role and mechanism of mir-92a in escc cells, and found that mir-92a modulated the migration and invasion but not apoptosis and proliferation of escc cells in vitro. we further demonstrated that mir-92a directly targeted the cdh1 3'-utr and repressed the expression of cdh1, a tumor metastasis suppressor. in addition, restoring of mir-92a-resistant cdh1 expression in mir-92a-overexpression cells recovered the pro-metastasis activity of mir-92a. taken together, we demonstrated that mir-92a promotes escc cell migration and invasion at least partially via suppression of cdh1 expression, and patients with up-regulated mir-92a are prone to lymph node metastasis and thus have poor prognosis.",1
"peroxisome proliferator-activated receptor δ (pparδ) is a critical regulator of energy metabolism in the heart. here, we propose a mechanism that integrates two deleterious characteristics of heart failure, hypoxia and a metabolic shift toward glycolysis, involving the microrna cluster mir-199a∼214 and pparδ. we demonstrate that under hemodynamic stress, cardiac hypoxia activates dnm3os, a noncoding transcript that harbors the microrna cluster mir-199a∼214, which shares pparδ as common target. to address the significance of mir-199a∼214 induction and concomitant pparδ repression, we performed antagomir-based silencing of both micrornas and subjected mice to biomechanical stress to induce heart failure. remarkably, antagomir-treated animals displayed improved cardiac function and restored mitochondrial fatty acid oxidation. taken together, our data suggest a mechanism whereby mir-199a∼214 actively represses cardiac pparδ expression, facilitating a metabolic shift from predominant reliance on fatty acid utilization in the healthy myocardium toward increased reliance on glucose metabolism at the onset of heart failure.",1
"background micrornas (mirnas) are short, non-coding rnas that post-transcriptionally silence gene expression by binding to target mrnas. previous studies have identified the mirna mir-8 as a pleiotropic regulator of drosophila development, controlling body size and neuronal survival by targeting multiple mrnas. in this study we demonstrate that mir-8 is also required for proper spatial patterning of pigment on the adult abdominal cuticle in females but not males. results female adult flies lacking mir-8 exhibit decreased pigmentation of the dorsal abdomen, with a pattern of pigmentation similar to wild type flies grown at higher temperatures. this pigmentation defect in mir-8 mutants is independent of the previously reported body size defect, and mir-8 acts directly in the developing cuticle to regulate pigmentation patterning. the decrease in pigmentation in mir-8 mutants was more pronounced in flies grown at higher temperatures. we also found that loss of mir-8 dramatically affected the ability to eclose at higher temperatures. conclusion loss of mir-8 increased the sensitivity of drosophila to higher temperatures for both pigmentation patterning and the ability to eclose. together, these data suggest that mir-8 acts as a buffer to stabilize gene expression patterns in the midst of environmental variation.",1
"in eukaryotes, gene expression requires splicing, which starts with the identification of exon-intron boundaries by the small, nuclear rna (snrnas) of the spliceosome, aided by associated proteins. in the mammalian genome, <1% of introns lack canonical exon-intron boundary sequences and cannot be spliced by the canonical splicing machinery. these introns are spliced by the minor spliceosome, consisting of unique snrnas (u11, u12, u4atac, and u6atac). the importance of the minor spliceosome is underscored by the disease microcephalic osteodysplastic primordial dwarfism type 1 (mopd1), which is caused by mutation in u4atac. thus, it is important to understand the expression and function of the minor spliceosome and its targets in mammalian development, for which we used the mouse as our model. here, we report enrichment of the minor snrnas in the developing head/central nervous system (cns) between e9.5 and e12.5, along with enrichment of these snrnas in differentiating retinal neurons. moreover, dynamic expression kinetics of minor intron-containing genes (migs) was observed across retinal development. david analysis of migs that were cotranscriptionally upregulated embryonically revealed enrichment for rna metabolism and cell cycle regulation. in contrast, migs that were cotranscriptionally upregulated postnatally revealed enrichment for protein localization/transport, vesicle-mediated transport, and calcium transport. finally, we used u12 morpholino to inactivate the minor spliceosome in the postnatal retina, which resulted in apoptosis of differentiating retinal neurons. taken together, our data suggest that the minor spliceosome may have distinct functions in embryonic versus postnatal development. importantly, we show that the minor spliceosome is crucial for the survival of terminally differentiating retinal neurons.",1
"brain insulin resistance is a key pathological feature contributing to obesity, diabetes, and neurodegenerative disorders, including alzheimer's disease (ad). besides the classic transcriptional mechanism mediated by hormones, posttranscriptional regulation has recently been shown to regulate a number of signaling pathways that could lead to metabolic diseases. here, we show that microrna 7 (mir-7), an abundant microrna in the brain, targets insulin receptor (insr), insulin receptor substrate 2 (irs-2), and insulin-degrading enzyme (ide), key regulators of insulin homeostatic functions in the central nervous system (cns) and the pathology of ad. in this study, we found that insulin and liver x receptor (lxr) activators promote the expression of the intronic mir-7-1 in vitro and in vivo , along with its host heterogeneous nuclear ribonucleoprotein k (hnrnpk) gene, encoding an rna binding protein (rbp) that is involved in insulin action at the posttranscriptional level. our data show that mir-7 expression is altered in the brains of diet-induced obese mice. moreover, we found that the levels of mir-7 are also elevated in brains of ad patients; this inversely correlates with the expression of its target genes irs-2 and ide. furthermore, overexpression of mir-7 increased the levels of extracellular aβ in neuronal cells and impaired the clearance of extracellular aβ by microglial cells. taken together, these results represent a novel branch of insulin action through the hnrnpk-mir-7 axis and highlight the possible implication of these posttranscriptional regulators in a range of diseases underlying metabolic dysregulation in the brain, from diabetes to alzheimer's disease.",1
"a chronic proinflammatory state precedes pathological change in arterial endothelial cells located within regions of susceptibility to atherosclerosis. the potential contributions of regulatory micrornas to this disequilibrium were investigated by artery site-specific profiling in normal adult swine. expression of endothelial microrna10a (mir-10a) was lower in the athero-susceptible regions of the inner aortic arch and aorto-renal branches than elsewhere. expression of homeobox a1 (hoxa1), a known mir-10a target, was up-regulated in the same locations. endothelial transcriptome microarray analysis of mir-10a knockdown in cultured human aortic endothelial cells (haec) identified ikappab/nf-kappab-mediated inflammation as the top category of up-regulated biological processes. phosphorylation of ikappabalpha, a prerequisite for ikappabalpha proteolysis and nf-kappab activation, was significantly up-regulated in mir-10a knockdown haec and was accompanied by increased nuclear expression of nf-kappab p65. the inflammatory biomarkers monocyte chemotactic protein 1 (mcp-1), il-6, il-8, vascular cell adhesion molecule 1 (vcam-1), and e-selectin were elevated following mir-10a knockdown. conversely, knockin of mir-10a (a conservative 25-fold increase) inhibited the basal expression of vcam-1 and e-selectin in haec. two key regulators of ikappabalpha degradation--mitogen-activated kinase kinase kinase 7 (map3k7; tak1) and beta-transducin repeat-containing gene (betatrc)--contain a highly conserved mir-10a binding site in the 3' utr. both molecules were up-regulated by mir-10a knockdown and suppressed by mir-10a knockin, and evidence of direct mir-10a binding to the 3' utr was demonstrated by luciferase assay. comparative expression studies of endothelium located in athero-susceptible aortic arch and athero-protected descending thoracic aorta identified significantly up-regulated map3k7, betatrc, phopho-ikappabalpha, and nuclear p65 expression suggesting that the differential expression of mir-10a contributes to the regulation of proinflammatory endothelial phenotypes in athero-susceptible regions in vivo.",1
"alzheimer's disease (ad) is a great threat for the health and life of elderly people. microrna-128 (mir-128) has been reported to be abnormally expressed in the brain of ad patients and associated with the pathogenesis of ad. our study aimed to have a deep insight into the roles and molecular basis of mir-128 in the development and progression of ad. the cognitive ability and exploratory behaviors were assessed by morris water maze and open-field tests, respectively. the concentrations of amyloid-β (aβ) 40, aβ 42, tumor necrosis factor (tnf)-α, interleukin (il)-1β and il-10 and activity of β-secretase and α-secretase were determined by corresponding elisa commercial kits. rt-qpcr assay was performed to detect mir-128 level and the mrna expression of peroxisome proliferator-activated receptor gamma (pparγ), ionized calcium-binding adaptor molecule 1 (iba1) and glial fibrillary acidic protein (gfap). western blot assay was conducted to determine protein expression of pparγ, amyloid precursor protein (app), β-app cleaving enzyme (bace1), sappα and sappβ. the effect of mir-128 and pparγ on amyloid plaque formation was assessed by immunohistochemistry assay. pparγ mean optical density was determined by immunofluorescence assay. the interaction between mir-128 and pparγ were validated by bioinformatics analysis and luciferase reporter assay. we found ad mice showed ad-like performance and an increased cerebral cortex aβ production. mir-128 expression was upregulated and pparγ expression was downregulated in cerebral cortex of ad mice. moreover, pparγ was a target of mir-128. additionally, mir-128 knockout or pparγ upregulation inhibited ad-like performances, amyloid plaque formation, aβ generation, app amyloidogenic processing and inflammatory responses in ad mice, while these effects of mir-128 knockout were abrogated by pparγ inhibitor. the results indicated mir-128 knockout weakened ad-like performances, and reduced aβ production and inflammatory responses by targeting pparγ in ad mice.",1
"micrornas (mirnas) serve as post-transcriptional regulators of gene expression, by guiding effector complexes (mirnps) to target rnas. although considerable progress has been made in computational methods to identify mirna targets, only a relatively limited assessment of their ability to function in vivo has been reported. here we describe an alternative approach to mirna target identification based on a biochemical method for purifying mirnp complexes with associated mirnas and bound mrna targets. microarray analysis revealed a high degree of enrichment for mirna complementary sites in the 3'utrs of the mirnp-associated mrnas. mrnas specifically associated with an individual mirna were identified by comparing the mirnp-associated mrnas from wild-type flies and mutant flies lacking mir-1, and their regulation by the mirna was validated. this approach provides a means to identify functional mirna targets based on their physical interaction in vivo.",1
"the metastatic cascade is a complex and extremely inefficient process with many potential barriers. understanding this process is of critical importance because the majority of cancer mortality is associated with metastatic disease. recently, it has become increasingly clear that micrornas (mirna) play important roles in tumorigenesis and metastasis, yet few studies have examined how germline variations may dysregulate mirnas, in turn affecting metastatic potential. to explore this possibility, the highly metastatic mmtv-pymt mice were crossed with 25 akxd (akr/j × dba/2j) recombinant inbred strains to produce f1 progeny with varying metastatic indices. when mammary tumors from the f1 progeny were analyzed by mirna microarray, mir-290 (containing mir-290-3p and mir-290-5p) was identified as a top candidate progression-associated mirna. the microarray results were validated in vivo when mir-290 upregulation in two independent breast cancer cell lines suppressed both primary tumor and metastatic growth. computational analysis identified breast cancer progression gene arid4b as a top target of mir-290-3p, which was confirmed by luciferase reporter assay. surprisingly, pathway analysis identified estrogen receptor (er) signaling as the top canonical pathway affected by mir-290 upregulation. further analysis showed that er levels were elevated in mir-290-expressing tumors and positively correlated with apoptosis. taken together, our results suggest mir-290 targets arid4b while simultaneously enhancing er signaling and increasing apoptosis, thereby suppressing breast cancer progression. this, to the best of our knowledge, is the first example of inherited differences in mirna expression playing a role in breast cancer progression.",1
"inner mongolia cashmere goats, as an important part of animal husbandry production, play an important role in animal fiber industry. in recent years, scientific research has made a lot of explorations on the molecular regulation mechanism of hair follicle cycle growth, but few studies have been reported on the development of cashmere hair in fetal period. this study was based on the completion of 21 skin samples of mrna and mirna sequencing in 7 fetal periods (45 days, 55 days,65 days,75 days,95 days,115 days and 135 days) of the inner mongolia cashmere goat. the target genes of mirna associated with the development of secondary hair follicles in the cashmere goats were selected through the combination analysis of mrna and mirna data. then the overexpression vector was constructed and the interaction between the mirna and the target gene was identified by dual-luciferase reporter gene system. the function and interaction relationship of chi-mir-199a-5p and tgf-β2 were verified by rt-qpcr and western blot at the level of the fibroblasts in inner mongolia cashmere goat. it provides a theoretical basis for further study of mirna and its target genes regulating the occurrence and development of skin hair follicles. as the result shows, the expression trends of 7 genes (bambi, smad1, ltbp1, ppp2r1b, id4, bmp8b and pitx2) and 7 mirna (chi-mir-17-5p, chi-mir-125b-3p, chi-mir-21-5p, chi-mir-143-5p and chi-mir-106b-5p) in the skin samples for the seven stages of the fetus were shown to be consistent with the sequencing results. the results of sequencing are reliable. the correlation coefficient of tgf-β2 and chi-mir-199a-5p in fetal 45d-135d expression is -0.84, showing a strong negative correlation, the target relationship was preliminarily judged. the results of double luciferase vector report showed that chi-mir-199a-5p significantly decreased the expression of luciferase in tgf-β2 3'utr, it is determined that there is a reciprocal relationship between them at a specific time. we transfected chi-mir199a-5p-fam mimics into fibroblasts cultured in vitro from inner mongolia cashmere goats. after transfection, the cells were harvested to extract total rna and protein. the mrna and protein expression levels of tgf-β2 in fibroblasts were detected by rt-qpcr and western blot. it was verified that chi-mir-199a-5p inhibited tgf-β2 expression at both mrna and protein translation levels in fibroblasts. at the same time, it was again proved that the tgf-β2 gene is a target gene of chi-mir199a-5p.",1
"rpm2p is a protein subunit of yeast mitochondrial rnase p and is also required for the maturation of rpm1r, the mitochondrially-encoded rna subunit of the enzyme. previous work demonstrated that an insertional disruption of rpm2, which produces the c-terminally truncated protein rpm2-deltacp, supports growth on glucose but cells lose some or all of their mitochondrial genome and become petite. these petites, even if they retain the rpm1 locus, lose their ability to process the 5'-ends of mitochondrial trna. we report here that if strains containing the truncated rpm2 allele are created and maintained on respiratory carbon sources they have wild-type mitochondrial genomes, and a significant portion of trna transcripts are processed. in contrast, precursor rpm1r transcripts accumulate and mature rpm1r is not made. these data show that one function of the deleted c-terminal region is in the maturation of rpm1r, and that this region and mature rpm1r are not absolutely required for rnase p activity. finally, we demonstrate that full activity can be restored if the n-terminal and c-terminal domains of rpm2p are supplied in trans.",1
"alzheimer's disease (ad) is a neurodegenerative disorder which mainly affects elderly population. micrornas (mirna) are small rna molecules that fine-tune gene expression at posttranscriptional level and exert important functions in ad. microrna-124 (mir-124) is a kind of mirna abundantly expressed in the central nervous system. it is highly conserved from caenorhabditis elegans to humans. however, its function in ad is still elusive. in this study, we found mir-124 was significantly down-regulated in ad flies. mir-124 mutant flies showed impaired climbing ability and shortened lifespan. in contrast, mir-124 expression rescued locomotive defects of ad flies. using microarray analysis to test gene expression profiles of mir-124 mutant flies, we found that notch signaling pathway was potentially targeted by mir-124. further experiments showed that mir-124 regulated notch ligand delta expression by acting on specific site of delta 3`utr. in addition, reduced delta expression by rna interference extended lifespan and ameliorated learning defects of ad drosophila. notch inhibitor dapt could also alleviate ad phenotypes, which confirmed our findings. in conclusion, our study indicates that mir-124 plays neuroprotective roles in ad drosophila by targeting delta in notch signaling pathway, which helps further our understanding of mirnas in the molecular pathology of ad.",1
"mirnas are important regulators of cellular senescence yet the extent of their involvement remains to be investigated. we sought to identify mirnas that are involved in cytokine-induced premature senescence (cips) in endothelial cells. cips was established in young human pulmonary microvascular endothelial cells (hmvec-ls) following treatment with a sublethal dose (20ng/ml) of tumor necrosis factor alpha (tnf-α) for 15days. in parallel, hmvec-ls were grown and routinely passaged until the onset of replicative senescence (rs). differential expression analysis following mirna microarray profiling revealed an overlapped of eight deregulated mirnas in both the mirna profiles of rs and tnf-α-induced premature senescence cells. amongst the deregulated mirnas were members of the mir 17-92 cluster which are known regulators of angiogenesis. the role of hsa-mir-20b in tnf-α-induced premature senescence, a paralog member of the mir 17-92 cluster, was further investigated. biotin-labeled hsa-mir-20b captured the enriched transcripts of retinoblastoma-like 1 (rbl1), indicating that rbl1 is a target of hsa-mir-20b. knockdown of hsa-mir-20b attenuated premature senescence in the tnf-α-treated hmvec-ls as evidenced by increased cell proliferation, increased rbl1 mrna expression level but decreased protein expression of p16 ink4a , a cellular senescence marker. these findings provide an early insight into the role of hsa-mir-20b in endothelial senescence.",1
"cancers often utilize micrornas to suppress tumor suppressor genes, thus facilitating their potential for growth and invasion. in the present study, we report the novel findings that mir-892b inhibits proliferation, migration and invasion of bladder cancer cells. the basal expression level of mir‑892b was significantly lower in 3 different bladder cancer cell lines than in normal human urothelial cells. transfection of mir-892b mimics to bladder cancer cells resulted in dose‑dependent growth arrest. flow cytometric analysis of the cell cycle showed that mir-892b-transfected bladder cancer cells were subject to arrest in the g1 phase, which was due to the downregulation of cyclin d1 and cdk6 followed by upregulation of p19arf. in addition, overexpression of mir-892b impeded the migration and invasion of ej cells. expression of mmp-9 in ej cells was blocked by transfection of mir-892b; the effect was regulated, at least in part, by activation of the sp-1 transcription factor. overall, we verified that mir-892b regulates the p19arf/cyclin d1/cdk6 and sp-1/mmp-9 signaling networks in bladder cancer cells and may provide a treatment option for advanced-stage bladder cancers.",1
"granulin (grn, or progranulin) is a protein involved in wound repair, inflammation, and neoplasia. grn has also been directly implicated in frontotemporal dementia and may contribute to alzheimer's disease pathogenesis. however, grn regulation expression is poorly understood. a high-throughput experimental microrna assay showed that grn is the strongest target for mir-107 in human h4 neuroglioma cells. mir-107 has been implicated in alzheimer's disease pathogenesis, and sequence elements in the open reading frame-rather than the 3' untranslated region-of grn mrna are recognized by mir-107 and are highly conserved among vertebrate species. to better understand the mechanism of this interaction, flag-tagged argonaute constructs were used following mir-107 transfection. grn mrna interacts preferentially with argonaute 2. in vitro and in vivo studies indicate that regulation of grn by mir-107 may be functionally important. glucose supplementation in cultured cells that leads to increased mir-107 levels also results in decreased grn expression, including changes in cell compartmentation and decreased secretion of grn protein. this effect was eliminated following mir-107 transfection. we also tested a mouse model where mir-107 has been shown to be down-regulated. in brain tissue subjacent to 1.0 mm depth controlled cortical impact, surviving hippocampal neurons show decreased mir-107 with augmentation of neuronal grn expression. these findings indicate that mir-107 contributes to grn expression regulation with implications for brain disorders.",1
"wnt signaling determines human stromal (mesenchymal) stem cell (hmsc) differentiation fate into the osteoblast or adipocyte lineage. micrornas (mirnas) are small rna molecules of 21-25 nucleotides that regulate many aspects of osteoblast biology. thus, we examined mirnas regulated by wnt signaling in hmsc. we identified mirna (mir)-141-3p as a wnt target which in turn inhibited wnt signaling. moreover, mir-141-3p inhibited hmsc proliferation by arresting cells at the g1 phase of the cell cycle. mir-141-3p inhibited osteoblast differentiation of hmsc as evidenced by reduced alkaline phosphatase activity, gene expression and in vitro mineralized matrix formation. bioinformatic studies, western blot analysis and 3'utr reporter assay demonstrated that cell division cycle 25a (cdc25a) is a direct target of mir-141-3p. sirna-mediated knock-down of cdc25a inhibited hmsc proliferation and osteoblast differentiation. in summary, mir-141-3p acts as a negative regulator of hmsc proliferation and osteoblast differentiation. targeting mir-141-3p could be used as an anabolic therapy of low bone mass diseases, e.g. osteoporosis.",1
"melanoma is the most aggressive skin cancer, and it is typically resistant or rapidly develops resistance to a variety of chemotherapeutic agents. micrornas (mirnas) play a part in the occurrence and development of malignant melanoma. in this study, we analyzed the mir-218 expression level in melanoma patients and cell lines and observed alterations in proliferation, cell cycle, migration, and invasion by increasing mir-218 expression in melanoma cell lines. we also performed bioinformatic analyses using targetscan and miranda and cloned both the wild-type and mutant versions of the human cancerous inhibitor of protein phosphatase 2a (cip2a) and b lymphoma mo-mlv insertion region 1 (bmi1) 3'-utr fragments into the pmirglo reporter vector. we then used the dual-luciferase assay system, quantitative real-time rt-pcr (qrt-pcr), and western blot analysis to determine that mir-218 targeted the 3'-utr of the oncogenes cip2a and bmi1 and thus regulated the biological process of melanoma. we further demonstrated that cip2a and bmi1 knockdown phenocopies mir-218 overexpression. in conclusion, our findings have shown that mir-218 is downregulated in melanoma. by targeting cip2a and bmi1, mir-218 regulates the proliferation, migration, and invasion of the melanoma cell lines a375 and sk-mel-2, indicating that mir-218 plays a pivotal role in melanoma development.",1
"while fmr1 is silenced in fragile x syndrome (fxs) patients carrying the full mutation, its expression is elevated (2-8 fold) in premutated individuals. these people may develop the fragile x-associated tremor/ataxia syndrome (fxtas), a late onset neurodegenerative disorder characterized by ataxia and parkinsonism. in addition, people carrying the premutation can be affected by a set of neurological and behavioral disorders during young age. problems of memory have been detected in these patients as well as in the mouse models for fxtas. to date little is known concerning the metabolism of fmr1 mrna, notwithstanding the importance of the finely tuned regulation of the expression of this gene. in the present study, we identified three micrornas that specifically target the 3' utr of fmr1 and can modulate its expression throughout the brain particularly at the synapse where their expression is very high. the expression level of mir-221 is reduced in synaptosomal preparations of young fxtas mice suggesting a general deregulation of transcripts located at the synapse of these mice. by transcriptome analysis, we show here a robust deregulation of the expression levels of genes involved in learning, memory and autistic behavior, parkinson disease and neurodegeneration. these findings suggest the presence of a synaptopathy in these animals. interestingly, many of those deregulated mrnas are target of the same micrornas that modulate the expression of fmr1 at the synapse.",1
"modulation of mrna translatability either by trans-acting factors (proteins or srnas) or by in cis-acting riboregulators is widespread in bacteria and controls relevant phenotypic traits. unfortunately, global identification of post-transcriptionally regulated genes is complicated by poor structural and functional conservation of regulatory elements and by the limitations of proteomic approaches in protein quantification. we devised a genetic system for the identification of post-transcriptionally regulated genes and we applied this system to search for pseudomonas aeruginosa rna thermometers, a class of regulatory rna that modulates gene translation in response to temperature changes. as p. aeruginosa is able to thrive in a broad range of environmental conditions, genes differentially expressed at 37 °c versus lower temperatures may be involved in infection and survival in the human host. we prepared a plasmid vector library with translational fusions of p. aeruginosa dna fragments (padna) inserted upstream of tip2, a short peptide able to inactivate the tet repressor (tetr) upon expression. the library was assayed in a streptomycin-resistant merodiploid rpsl(+)/rpsl31 escherichia coli strain in which the dominant rpsl(+) allele, which confers streptomycin sensitivity, was repressed by tetr. padna fragments conferring thermosensitive streptomycin resistance (i.e., expressing padna-tip2 fusions at 37°c, but not at 28°c) were sequenced. we identified four new putative thermosensors. two of them were validated with conventional reporter systems in e. coli and p. aeruginosa. interestingly, one regulates the expression of ptxs, a gene implicated in p. aeruginosa pathogenesis.",1
"malignant gliomas are the most aggressive forms of brain tumors, associated with high rates of morbidity and mortality. recurrence and tumorigenesis are attributed to a subpopulation of tumor-initiating glioma stem cells (gscs) that are intrinsically resistant to therapy. initiation and progression of gliomas have been linked to alterations in microrna expression. here, we report the identification of microrna-138 (mir-138) as a molecular signature of gscs and demonstrate a vital role for mir-138 in promoting growth and survival of bona fide tumor-initiating cells with self-renewal potential. sequence-specific functional inhibition of mir-138 prevents tumorsphere formation in vitro and impedes tumorigenesis in vivo. we delineate the components of the mir-138 regulatory network by loss-of-function analysis to identify specific regulators of apoptosis. finally, the higher expression of mir-138 in gscs compared to non-neoplastic tissue and association with tumor recurrence and survival highlights the clinical significance of mir-138 as a prognostic biomarker and a therapeutic target for treatment of malignant gliomas.",1
"despite their clinicopathologic heterogeneity, malignant germ cell tumors (gct) share molecular abnormalities that are likely to be functionally important. in this study, we investigated the potential significance of downregulation of the let-7 family of tumor suppressor micrornas in malignant gcts. microarray results from pediatric and adult samples (n = 45) showed that lin28, the negative regulator of let-7 biogenesis, was abundant in malignant gcts, regardless of patient age, tumor site, or histologic subtype. indeed, a strong negative correlation existed between lin28 and let-7 levels in specimens with matched datasets. low let-7 levels were biologically significant, as the sequence complementary to the 2 to 7 nt common let-7 seed ""gaggua"" was enriched in the 3' untranslated regions of mrnas upregulated in pediatric and adult malignant gcts, compared with normal gonads (a mixture of germ cells and somatic cells). we identified 27 mrna targets of let-7 that were upregulated in malignant gct cells, confirming significant negative correlations with let-7 levels. among 16 mrnas examined in a largely independent set of specimens by quantitative reverse transcription pcr, we defined negative-associations with let-7e levels for six oncogenes, including mycn, aurkb, ccnf, rrm2, mki67, and c12orf5 (when including normal control tissues). importantly, lin28 depletion in malignant gct cells restored let-7 levels and repressed all of these oncogenic let-7 mrna targets, with lin28 levels correlating with cell proliferation and mycn levels. conversely, ectopic expression of let-7e was sufficient to reduce proliferation and downregulate mycn, aurkb, and lin28, the latter via a double-negative feedback loop. we conclude that the lin28/let-7 pathway has a critical pathobiologic role in malignant gcts and therefore offers a promising target for therapeutic intervention.",1
"the present study was undertaken to investigate the regulation of p12(cdk2ap1) by mirnas. a conserved target site for mir-21 within the cdk2ap1-3'-utr at nt 349-370 was predicted by bioinformatics software and an inverse correlation of mir-21 and cdk2ap1 protein was observed. highly specific amplification and quantification of mir-21 was achieved using real-time rt-pcr. transfection of hacat cells with pre-mir-21 significantly suppressed a luciferase reporter including the cdk2ap1-3'-utr, whereas transfection of tca8113 with anti-mir-21 increased activity of this reporter. this was abolished when a construct mutated at the mir-21/nt 349-370 target site was used instead. anti-mir-21-transfected tca8113 cells showed an increase of cdk2ap1 protein and reduced proliferation and invasion. resected primary tumors and tumor-free surgical margins of 18 patients with head and neck squamous cell carcinomas demonstrated an inverse correlation between mir-21 and p12(cdk2ap1). this study shows that p12(cdk2ap1) is downregulated by mir-21 and that mir-21 promotes proliferation and invasion in cultured cells.",1
"the tata box represents one of the most prevalent core promoters where the pre-initiation complexes (pics) for gene transcription are assembled. this assembly is crucial for transcription initiation and well regulated. here we show that some cellular micrornas (mirnas) are associated with rna polymerase ii (pol ii) and tata box-binding protein (tbp) in human peripheral blood mononuclear cells (pbmcs). among them, let-7i sequence specifically binds to the tata-box motif of interleukin-2 (il-2) gene and elevates il-2 mrna and protein production in cd4(+) t-lymphocytes in vitro and in vivo. through direct interaction with the tata-box motif, let-7i facilitates the pic assembly and transcription initiation of il-2 promoter. several other cellular mirnas, such as mir-138, mir-92a or mir-181d, also enhance the promoter activities via binding to the tata-box motifs of insulin, calcitonin or c-myc, respectively. in agreement with the finding that an hiv-1-encoded mirna could enhance viral replication through targeting the viral promoter tata-box motif, our data demonstrate that the interaction with core transcription machinery is a novel mechanism for mirnas to regulate gene expression.",1
"introduction micrornas are small, noncoding rnas that suppress gene expression by binding to the 3' untranslated region (utr) and thereby repress translation or decrease messenger rna stability. inhibitor of differentiation 1 (id1) is a putative stem-cell gene involved in invasion and angiogenesis. we previously showed that id1 is regulated by src kinases, overexpressed in human lung adenocarcinoma, and targeted by src-dependent micrornas. the current study focused on the association between mir-381 and id1 in lung adenocarcinoma. methods an id1 3'utr-luciferase reporter assay was used to determine whether mir-381 directly targets id1. human lung cancer cell lines were stably transduced with a precursor of mir-381 to evaluate its role on id1 expression and to investigate changes in cell migration and invasion. the src tyrosine kinase inhibitors saracatinib and dasatinib were used to repress id1 expression. mir-381 expression was measured in 18 human lung adenocarcinomas and corresponding normal lung tissue by quantitative reverse-transcription polymerase chain reaction. results id1 is a direct target of mir-381 as shown by 3'utr luciferase reporter assays. mir-381 expression was negatively correlated with id1 expression in lung cancer cell lines. ectopic expression of mir-381 reduced id1 mrna and protein levels, and significantly decreased cell migration and invasion. furthermore, mir-381 was significantly downregulated in human lung adenocarcinomas, and low mir-381 expression levels correlated with poor prognosis. conclusion these results suggest that downregulation of mir-381 and thus induction of its target id1 may contribute to the metastatic potential of lung adenocarcinomas. further studies to explore potential therapeutic strategies, including src inhibitors, are ongoing.",1
"small rna molecules play key regulatory roles in many bacterial species. however, little mechanistic data exists for the action of small regulatory rnas in the human pathogen group a streptococcus (gas). here, we analysed the relationship between a putative gas srna and production of the secreted virulence factor streptokinase (ska). ska promotes gas dissemination by activating conversion of host plasminogen into the fibrin-degrading protease plasmin. homologues of the putative srna-encoding gene fibronectin/fibrinogen-binding/haemolytic-activity/streptokinase-regulator-x (fasx) were identified in four different pyogenic streptococcal species. however, despite 79% fasx nucleotide identity, a fasx allele from the animal pathogen streptococcus zooepidemicus failed to complement a gas fasx mutant. using a series of precisely constructed fasx alleles we discovered that fasx is a bona-fide srna that post-transcriptionally regulates ska production in gas. by base-pairing to the 5' end of ska mrna, fasx enhances ska transcript stability, resulting in a ∼10-fold increase in ska activity. our data provide new insights into the mechanisms used by small regulatory rnas to activate target mrnas, and enhances our understanding of the regulation of a key gas virulence factor.",1
"mrna transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. this is exemplified in drosophila, where oskar mrna transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. within the oocyte, a spliced oskar localization element (sole) targets oskar mrna for plus end-directed transport by kinesin-1 to the posterior pole. however, the signals mediating the initial minus end-directed, dynein-dependent transport of the mrna from nurse cells into the oocyte have remained unknown. here, we show that a 67-nt stem-loop in the oskar 3' utr promotes oskar mrna delivery to the developing oocyte and that it shares functional features with the fs(1)k10 oocyte localization signal. thus, two independent cis-acting signals, the oocyte entry signal (oes) and the sole, mediate sequential dynein- and kinesin-dependent phases of oskar mrna transport during oogenesis. the oes also promotes apical localization of injected rnas in blastoderm stage embryos, another dynein-mediated process. similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter rnas bearing the oskar oes are apically enriched, demonstrating that this element promotes mrna localization independently of cell type. our work sheds new light on how oskar mrna is trafficked during oogenesis and the rna features that mediate minus end-directed transport.",1
"colorectal cancer (crc) is one of the primary causes of cancer‑associated mortality worldwide. however, the potential molecular mechanism of crc progression remains unknown. long non‑coding rna small nucleolar rna host gene 20 (snhg20) has been demonstrated to be involved in the development and progression of a variety of tumors, including crc. however, the involvement of snhg20 in crc progression remains unclear. the aim of the present study was to investigate the functional role and molecular mechanism of snhg20 in crc progression. in the present study, snhg20 expression was found to be significantly upregulated in crc tissues and cell lines. association analysis indicated that high snhg20 expression was significantly association with greater tumor size (p=0.014), tumor invasion depth (p=0.019), positive lymph node status (p=0.022), distant metastasis (p=0.017) and advanced tumor node metastasis stage (p=0.038). loss‑of‑function experiments indicated that snhg20 knockdown could significantly suppress proliferation, migration and invasion in vitro . notably, snhg20 knockdown significantly inhibited tumor growth and lung metastasis in vivo . bioinformatics analysis and luciferase reporter assays confirmed that microrna (mir)‑495 was a direct target of snhg20. rescue assays indicated that mir‑495 inhibitor reversed the suppressive effects of snhg20 knockdown on crc progression. moreover, stat3 was identified as a downstream target of mir‑495 in crc. stat3 overexpression partially rescued the inhibitory effects of snhg20 knockdown on crc progression. taken together, the results revealed that snhg20 facilitated crc progression by regulating stat3 expression and by sponging mir‑495.",1
"telomerase-mediated telomeric dna synthesis is important for eukaryotic cell immortality. telomerase adds tracts of short telomeric repeats to dna substrates using a unique repeat addition form of processivity. it has been proposed that repeat addition processivity is partly regulated by a telomerase reverse transcriptase (tert)-dependent anchor site; however, anchor site-mediating residues have not been identified in any tert. we report the characterization of an n-terminal human tert (htert) rna interaction domain 1 (rid1) mutation that caused telomerase activity defects consistent with disruption of a template-proximal anchor site, including reduced processivity on short telomeric primers and reduced activity on substrates with nontelomeric 5' sequences, but not on primers with nontelomeric g-rich 5' sequences. this mutation was located within a subregion of rid1 previously implicated in biological telomerase functions unrelated to catalytic activity (n-dat domain). other n-dat and c-terminal dat (c-dat) mutants and a c-terminally tagged htert-ha variant were defective in elongating short telomeric primers, and catalytic phenotypes of dat variants were partially or completely rescued by increasing concentrations of dna primers. these observations imply that rid1 and the htert c terminus contribute to telomerase's affinity for its substrate, and that rid1 may form part of the human telomerase anchor site.",1
"in this study, we detected mir-206 expression in gastric cancer (gc) and further investigated its effects on gc cell growth in vitro and in vivo. mir-206 expression was found to be significantly decreased in 30 gc samples and gc cell lines by real time-pcr. restoration of mir-206 reduced cell growth and colony forming ability in gc cells with g0/g1 cell cycle arrest. further studies demonstrated that mir-206 could suppress gc cells proliferation at least partially through targeting the cyclind2 (ccnd2). therefore, we provided evidence that mir-206 was a potential tumor suppressor and may be used as a therapeutic target for gastric cancer.",1
"background expression of the tumor suppressor p16(ink4a) increases during aging and replicative senescence. methodology/principal findings here, we report that the microrna mir-24 suppresses p16 expression in human diploid fibroblasts and cervical carcinoma cells. increased p16 expression with replicative senescence was associated with decreased levels of mir-24, a microrna that was predicted to associate with the p16 mrna coding and 3'-untranslated regions. ectopic mir-24 overexpression reduced p16 protein but not p16 mrna levels. conversely, introduction of antisense (as)-mir-24 blocked mir-24 expression and markedly enhanced p16 protein levels, p16 translation, and the production of egfp-p16 reporter bearing the mir-24 target recognition sites. conclusions/significance together, our results suggest that mir-24 represses the initiation and elongation phases of p16 translation.",1
"background/aims micrornas (mirnas) play key roles in tumor metastasis. the aim of this study was to determine the regulation and function of mir-30a in colorectal carcinoma (crc) metastasis. methods the expression of mir-30a was detected in crc cell lines and samples by qrt-pcr. the anti-metastatic effect of mir-30a was determined by both in vitro and in vivo assays. a luciferase reporter assay was performed to determine target association between mir-30a and phosphoinositide 3-kinase catalytic subunit delta (pik3cd). results mir-30a was significantly downregulated in highly metastatic crc cell lines and metastatic tissues. overexpression of mir-30a suppressed crc cell migration and invasion in vitro and liver metastasis in vivo, whereas mir-30a deletion dramatically promoted cell migration and invasion. further studies revealed that pik3cd is a direct target of mir-30a as mir-30a bounds directly to the 3'-utr of pik3cd, subsequently reducing its expression. similar to the restoring mir-30a expression, pik3cd downregulation inhibited cell migration and invasion, whereas pik3cd overexpression rescued the suppressive effect of mir-30a. moreover, significant downregulation of mir-30a in metastatic crc tissues was found to be inversely correlated with pik3cd expression. mechanistic studies revealed that mir-30a down-regulated the expression of key components of the akt/mtor pathway, whereas pik3cd overexpression reversed this negative effect. conclusion our findings indicate that mir-30a might function as a metastasis suppressor in crc. mir-30a may be a potential therapeutic target to block crc metastasis.",1
"transforming growth factor (tgf)-β/smad signaling plays an important role in colon cancer development, progression and metastasis. in this study we demonstrated that the microrna-130a/301a/454 family is up-regulated in colon cancer tissues compared to paired adjacent normal mucosa, which share the same 3'-untranslational region (3'-utr) binding seed sequence and are predicated to target smad4. in colorectal cancer hct116 and sw480 cells, overexpression of mirna-130a/301a/454 mimics enhances cell proliferation and migration, while inhibitors of these mirnas affect cell survival. the biological function of mirna-130a/301a/454 on colon cancer cells is likely mediated by suppression of smad4, and the up-regulation of the mirnas is correlated with smad4 down-regulation in human colon cancers. collectively, these results suggest that mirna-130a/301a/454 are novel oncogenic mirnas contributing to colon tumorigenesis by regulating tgf-β/smad signaling, which may have potential application in cancer therapy.",1
"sm-like (lsm) proteins function in a variety of rna-processing events. in yeast, the lsm2-lsm8 complex binds and stabilizes the spliceosomal u6 snrna, whereas the lsm1-lsm7 complex functions in mrna decay. here we report that a third lsm complex, consisting of lsm2-lsm7 proteins, associates with snr5, a box h/aca snorna that functions to guide site-specific pseudouridylation of rrna. experiments in which the binding of lsm proteins to snr5 was reconstituted in vitro reveal that the 3' end of snr5 is critical for lsm protein recognition. glycerol gradient sedimentation and sequential immunoprecipitation experiments suggest that the lsm protein-snr5 complex is partly distinct from the complex formed by snr5 rna with the box h/aca proteins gar1p and nhp2p. consistent with a separate complex, lsm proteins are not required for the function of snr5 in pseudouridylation of rrna. we demonstrate that in addition to their known nuclear and cytoplasmic locations, lsm proteins are present in nucleoli. taken together with previous findings that a small fraction of pre-rnase p rna associates with lsm2-lsm7, our experiments suggest that an lsm2-lsm7 protein complex resides in nucleoli, contributing to the biogenesis or function of specific snornas.",1
"high-mobility group a1 (hmga1) is a non-histone chromatin protein that has the ability to regulate the transcriptional activity of many genes. overexpression of hmga1 is associated with malignant cellular behavior in a range of human cancers but the underlying mechanism is largely unknown. here we showed that in a cohort of non-small cell lung cancer (nsclc) tumors, hmga1 overexpression was immediately associated with enhanced expression of an oncogenic mirna, namely, mir-222. chromatin immunoprecipitation (chip) assay revealed that hmga1 directly binds to the proximal promoter of mir-222 in nsclc cells. we further showed that hmga1 silencing reduced mir-222 transcriptional activity, whereas forced hmga1 expression increased it, indicating that mir-222 is directly regulated by hmga1. based on in silico prediction, one of the putative targets of mir-222 is phosphatase 2a subunit b (ppp2r2a) which inhibits akt phosphorylation (p-akt). we demonstrated that mir-222 inhibited protein expression of ppp2r2a in nsclc cells by directly interacting with its 3'-utr region, leading to an obvious increase of p-akt. hmga1 silencing augmented ppp2r2a protein expression and inhibited akt signaling, resulting in significantly retarded cell growth response to igf-i. these results suggested that hmga1 is a positive regulator of mir-222, and hmga1 overexpression might contribute to dysregulation of akt signaling in nsclc.",1
"background increasing evidence has revealed that micrornas (mirna) played a pivotal role in regulating cancer cell proliferation and metastasis. the deregulation of mir-182 has been identified in colorectal cancer (crc). however, the role and mechanism of mir-182 in crc have not been completely understood yet. methods the expression levels of mir-182 in crc tissues and crc cell lines were examined by performing stem-loop quantitative rt-pcr. the stable over-expression mir-182 cell lines and control cell lines were constructed by lentivirus infection. subsequently, cck-8 assay, plate colony formation assay, cell migration, invasion assay and experimental animal models were performed to detect the biological functions of mir-182 in vitro and in vivo. a luciferase reporter assay was conducted to confirm target associations. western blot and immunohistochemical analysis were performed to examine the expression changes of molecular markers that are regulated by mir-182. results we found that mir-182 expression is increased in crc cells that originated from metastatic foci and human primary crc tissues with lymph node metastases. the ectopic expression of mir-182 enhanced cell proliferation, invasion, and migration in vitro. stable overexpression of mir-182 also facilitated tumor growth and metastasis in vivo too. further research showed that mir-182 could directly target the 3'untranslated region (3'utr) of satb2 mrna and subsequently repress both the mrna and protein expressions of satb2, which we identified in previous studies as a crc metastasis-associated protein. restoring satb2 expression could reverse the effects of mir-182 on crc cell proliferation and migration. investigations of possible mechanisms underlying these behaviors induced by mir-182 revealed that mir-182 induced epithelial-mesenchymal transition (emt) by modulating the expression of key cellular molecules in emt. conclusions our results illustrated that the up-regulation of mir-182 played a pivotal role in crc tumorigenesis and metastasis, which suggesting a potential implication of mir-182 in the molecular therapy for crc.",1
"background & aims hepatocellular carcinoma (hcc) is a heterogeneous tumor that develops via activation of multiple pathways and molecular alterations. it has been a challenge to identify molecular classes of hcc and design treatment strategies for each specific subtype. micrornas (mirnas) are involved in hcc pathogenesis, and their expression profiles have been used to classify cancers. we analyzed mirna expression in human hcc samples to identify molecular subclasses and oncogenic mirnas. methods we performed mirna profiling of 89 hcc samples using a ligation-mediated amplification method. subclasses were identified by unsupervised clustering analysis. we identified molecular features specific for each subclass using expression pattern (affymetrix u133 2.0; affymetrix, santa clara, ca), dna change (affymetrix sty mapping array), mutation (ctnnb1), and immunohistochemical (phosphor-protein kinase b, p-insulin growth factor-ir, p-s6, p-epidermal growth factor receptor, β-catenin) analyses. the roles of selected mirnas were investigated in cell lines and in an orthotopic model of hcc. results we identified 3 main clusters of hccs: the wingless-type mmtv integration site (32 of 89; 36%), interferon-related (29 of 89; 33%), and proliferation (28 of 89; 31%) subclasses. a subset of patients with tumors in the proliferation subclass (8 of 89; 9%) overexpressed a family of poorly characterized mirnas from chr19q13.42. expression of mir-517a and mir-520c (from ch19q13.42) increased proliferation, migration, and invasion of hcc cells in vitro. mir-517a promoted tumorigenesis and metastatic dissemination in vivo. conclusions we propose mirna-based classification of 3 subclasses of hcc. among the proliferation class, mir-517a is an oncogenic mirna that promotes tumor progression. there is rationale for developing therapies that target mir-517a for patients with hcc.",1
"telomeres are protein-dna structures found at the ends of linear chromosomes and are crucial for genome integrity. telomeric dna length is primarily maintained by the enzyme telomerase. cells lacking telomerase will undergo senescence when telomeres become critically short. in saccharomyces cerevisiae, a very small percentage of cells lacking telomerase can remain viable by lengthening telomeres via two distinct homologous recombination pathways. these ""survivor"" cells are classified as either type i or type ii, with each class of survivor possessing distinct telomeric dna structures and genetic requirements. to elucidate the regulatory pathways contributing to survivor generation, we knocked out the telomerase rna gene tlc1 in 280 telomere-length-maintenance (tlm) gene mutants and examined telomere structures in post-senescent survivors. we uncovered new functional roles for 10 genes that affect the emerging ratio of type i versus type ii survivors and 22 genes that are required for type ii survivor generation. we further verified that pif1 helicase was required for type i recombination and that the ino80 chromatin remodeling complex greatly affected the emerging frequency of type i survivors. finally, we found the rad6-mediated ubiquitination pathway and the keops complex were required for type ii recombination. our data provide an independent line of evidence supporting the idea that these genes play important roles in telomere dynamics.",1
"mirnas are small, non-coding rnas that regulate gene expression post-transcriptionally. we used small rna sequencing to identify tissue-specific mirnas in the adult brain, thorax, gut, and fat body of drosophila melanogaster one of the most brain-specific mirnas that we identified was mir-210, an evolutionarily highly conserved mirna implicated in the regulation of hypoxia in mammals. in drosophila , we show that mir-210 is specifically expressed in sensory organs, including photoreceptors. mir-210 knockout mutants are not sensitive toward hypoxia but show progressive degradation of photoreceptor cells, accompanied by decreased photoreceptor potential, demonstrating an important function of mir-210 in photoreceptor maintenance and survival.",1
"programmed ribosomal frameshifting is an essential mechanism used for the expression of orf1b in coronaviruses. comparative analysis of the frameshift region reveals a universal shift site u_uua_aac, followed by a predicted downstream rna structure in the form of either a pseudoknot or kissing stem loops. frameshifting in sars-cov has been characterized in cultured mammalian cells using a dual luciferase reporter system and mass spectrometry. mutagenic analysis of the sars-cov shift site and mass spectrometry of an affinity tagged frameshift product confirmed tandem trna slippage on the sequence u_uua_aac. analysis of the downstream pseudoknot stimulator of frameshifting in sars-cov shows that a proposed rna secondary structure in loop ii and two unpaired nucleotides at the stem i-stem ii junction in sars-cov are important for frameshift stimulation. these results demonstrate key sequences required for efficient frameshifting, and the utility of mass spectrometry to study ribosomal frameshifting.",1
"introduction micrornas (mirs) have been shown to play critical roles in the regulation of trophoblast and endothelial cell functions, and one significant finding concerning the mir-15/16 family is that most members of this family are highly expressed in endothelial cells and contribute to functions, such as tube formation. the interaction between trophoblast and endothelial cell play an important role in normal placentation process. therefore, the aims of this study were to investigate the expression of mir-15b in human placenta and to uncover the potential role of mir-15b as well as its target functional loop in trophoblast and endothelial cells. whether inflammation could modulate the expression of mir-15b and its down-stream target was further investigated. additionally, the potential link between mir-15b deregulation and preeclampsia was also explored in the placenta of patients diagnosed with preeclampsia. methods the expression of mir-15b was studied in the placental tissue of a normal pregnancy using in situ hybridization, and the effects of mir-15b on proliferation, invasion, and angiogenesis were further explored in vitro using htr-8/svneo and huvec cell line models. a lipopolysaccharides (lps) treatment model in htr-8/svneo cell was utilized to explore the mechanism of how lps treatment could lead to the activation of mir-15b expression. western blot was used to detect the expression of proteins related to mir-15b mediated pathway in preeclamptic placentas. results mir-15b inhibits trophoblast cell invasion and endothelial cell tube formation by suppressing the expression of argonaute 2 (ago2), a major mirna effecter protein. ago2 is specifically localized to human placenta cytotrophoblast and endothelial cells, and it plays important roles in trophoblast cell invasion and endothelial cell tube formation. lps treatment may lead to the overexpression of mir-15b and down-regulation of ago2, which may be involved in shallow trophoblast cell invasion associated with the pathogenesis of preeclampsia. chromatin immunoprecipitation assay indicates that increased occupancy of ago2 to mir-15b promoter is responsible for the increased expression of mir-15b under the condition of lps treatment. furthermore, preeclamptic placentas have decreased expression of ago2, but increased expression of mir-15b and tlr-4 compared to normal controls. discussion this is the first report about the function of ago2 in human trophoblast and endothelial cells in the placenta. the data indicates that the aberrant expression of mir-15b contributes to abnormal placentation by targeting ago2 mrna. this study provides insight into the potential role of the mir-15b and ago2 functional loop in the placentation process.",1
"understanding cell cycle regulation in postmitotic cardiomyocytes may lead to new therapeutic approaches to regenerate damaged cardiac tissue. we have demonstrated previously that micrornas encoded by the gtl2-dio3 noncoding rna locus function downstream of the mef2a transcription factor in skeletal muscle regeneration. we have also reported expression of these mirnas in the heart. here we investigated the role of two gtl2-dio3 mirnas, mir-410 and mir-495, in cardiac muscle. overexpression of mir-410 and mir-495 robustly stimulated cardiomyocyte dna synthesis and proliferation. interestingly, unlike our findings in skeletal muscle, these mirnas did not modulate the activity of the wnt signaling pathway. instead, these mirnas targeted cited2, a coactivator required for proper cardiac development. consistent with mir-410 and mir-495 overexpression, sirna knockdown of cited2 in neonatal cardiomyocytes resulted in robust proliferation. this phenotype was associated with reduced expression of cdkn1c/p57/kip2, a cell cycle inhibitor, and increased expression of vegfa, a growth factor with proliferation-promoting effects. therefore, mir-410 and mir-495 are among a growing number of mirnas that have the ability to potently stimulate neonatal cardiomyocyte proliferation.",1
"the nf-kb pathway is key to epithelial immune defense and has been implicated in secretion of antimicrobial peptides, release of cytokines/chemokines to mobilize immune effector cells, and activation of adaptive immunity. the expression of many inflammatory genes following infection involves the remodeling of the chromatin structure. we reported here that histone deacetylases (hdacs) and nf-kb signaling coordinate expression of cx3cl1 in epithelial cells following cryptosporidium parvum infection. upregulation of cx3cl1 was detected in cultured human biliary epithelial cells following infection. expression of mir-424 and mir-503 was downregulated, and was involved in the induction of cx3cl1 in infected cells. c. parvum infection suppressed transcription of the mir-424-503 gene in a nf-kb- and hdac-dependent manner. increased promoter recruitment of nf-kb p50 and hdacs, and decreased promoter h3 acetylation associated with the mir-424-503 gene were observed in infected cells. upregulation of cx3cl1 in biliary epithelial cells and increased infiltration of cx3cr1(+) cells were detected during c. parvum infection in vivo. induction of cx3cl1 and downregulation of mir-424 and mir-503 were also detected in epithelial cells in response to lps stimulation. the above results indicate that hdacs and nf-kb signaling coordinate epithelial expression of cx3cl1 to promote mucosal antimicrobial defense through suppression of the mir-424-503 gene.",1
"cellular senescence acts as a barrier to cancer progression, and micrornas (mirnas) are thought to be potential senescence regulators. however, whether senescence-associated mirnas (sa-mirnas) contribute to tumor suppression remains unknown. here, we report that mir-22, a novel sa-mirna, has an impact on tumorigenesis. mir-22 is up-regulated in human senescent fibroblasts and epithelial cells but down-regulated in various cancer cell lines. mir-22 overexpression induces growth suppression and acquisition of a senescent phenotype in human normal and cancer cells. mir-22 knockdown in presenescent fibroblasts decreased cell size, and cells became more compact. mir-22-induced senescence also decreases cell motility and inhibits cell invasion in vitro. synthetic mir-22 delivery suppresses tumor growth and metastasis in vivo by inducing cellular senescence in a mouse model of breast carcinoma. we confirmed that cdk6, sirt1, and sp1, genes involved in the senescence program, are direct targets of mir-22. our study provides the first evidence that mir-22 restores the cellular senescence program in cancer cells and acts as a tumor suppressor.",1
"although innate immunity mediated by toll signaling has been extensively studied in drosophila melanogaster, the role of mirnas in regulating the toll-mediated immune response remains largely unknown. in this study, following gram-positive bacterial challenge, we identified 93 differentially expressed mirnas via genome-wide mirna screening. these mirnas were regarded as immune response related (irr). eight mirnas were confirmed to be involved in the toll-mediated immune response upon gram-positive bacterial infection through genetic screening of 41 uas-mirna lines covering 60 mirnas of the 93 irr mirnas. interestingly, four out of these eight mirnas, mir-310, mir-311, mir-312 and mir-313, are clustered mirnas and belong to the mir-310 family. these mir-310 family members were shown to target and regulate the expression of drosomycin, an antimicrobial peptide produced by toll signaling. taken together, our study implies important regulatory roles of mirnas in the toll-mediated innate immune response of drosophila upon gram-positive bacterial infection.",1
"the gram-negative plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria (xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. to gain insight into the transcriptome of the xcv strain 85-10, we took a differential rna sequencing (drna-seq) approach. using a novel method to automatically generate comprehensive transcription start site (tss) maps we report 1421 putative tsss in the xcv genome. genes in xcv exhibit a poorly conserved -10 promoter element and no consensus shine-dalgarno sequence. moreover, 14% of all mrnas are leaderless and 13% of them have unusually long 5'-utrs. northern blot analyses confirmed 16 intergenic small rnas and seven cis-encoded antisense rnas in xcv. expression of eight intergenic transcripts was controlled by hrpg and hrpx, key regulators of the xcv type iii secretion system. more detailed characterization identified sx12 as a small rna that controls virulence of xcv by affecting the interaction of the pathogen and its host plants. the transcriptional landscape of xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative tsss and clade-specific small rnas.",1
"sulfatases are key enzymatic regulators of sulfate homeostasis with several biological functions including degradation of glycosaminoglycans (gags) and other macromolecules in lysosomes. in a severe lysosomal storage disorder, multiple sulfatase deficiency (msd), global sulfatase activity is deficient due to mutations in the sulfatase-modifying factor 1 (sumf1) gene, encoding the essential activator of all sulfatases. we identify a novel regulatory layer of sulfate metabolism mediated by a microrna. mir-95 depletes sumf1 protein levels and suppresses sulfatase activity, causing the disruption of proteoglycan catabolism and lysosomal function. this blocks autophagy-mediated degradation, causing cytoplasmic accumulation of autophagosomes and autophagic substrates. by targeting mir-95 in cells from msd patients, we can effectively increase residual sumf1 expression, allowing for reactivation of sulfatase activity and increased clearance of sulfated gags. the identification of this regulatory mechanism opens the opportunity for a unique therapeutic approach in msd patients where the need for exogenous enzyme replacement is circumvented.",1
"ribonuclease p (rnase p) is an essential endonuclease responsible for the 5'-end maturation of precursor trnas. bacterial rnase p also processes precursor 4.5s rna, tmrna, 30s preribosomal rna, and several reported protein-coding rnas. eukaryotic nuclear rnase p is far more complex than in the bacterial form, employing multiple essential protein subunits in addition to the catalytic rna subunit. rnomic studies have shown that rnase p binds other rnas in addition to trnas, but no non-trna substrates have previously been identified. additional substrates were identified by using a multipronged approach in the budding yeast saccharomyces cerevisiae. first, rnase p-dependant changes in rna abundance were examined on whole-genome microarrays by using strains containing temperature sensitive (ts) mutations in two of the essential rnase p subunits, pop1p and rpr1r. second, rnase p was rapidly affinity-purified, and copurified rnas were identified by using a genome-wide microarray. third, to identify rnas that do not change abundance when rnase p is depleted but accumulate as larger precursors, >80 potential small rna substrates were probed directly by northern blot analysis with rna from the rnase p ts mutants. numerous potential substrates were identified, of which we characterized the box c/d intron-encoded small nucleolar rnas (snornas), because these both copurify with rnase p and accumulate larger forms in the rnase p temperature-sensitive mutants. it was previously known that two pathways existed for excising these snornas, one using the pre-mrna splicing path and the other that was independent of splicing. rnase p appears to participate in the splicing-independent path for the box c/d intron-encoded snornas.",1
"rationale effective neovascularization is crucial for recovery after cardiovascular events. objective because micrornas regulate expression of up to several hundred target genes, we set out to identify micrornas that target genes in all pathways of the multifactorial neovascularization process. using we performed a reverse target prediction analysis on a set of 197 genes involved in neovascularization. we found enrichment of binding sites for 27 micrornas in a single microrna gene cluster. microarray analyses showed upregulation of 14q32 micrornas during neovascularization in mice after single femoral artery ligation. methods and results gene silencing oligonucleotides (gsos) were used to inhibit 4 14q32 micrornas, mir-329, mir-487b, mir-494, and mir-495, 1 day before double femoral artery ligation. blood flow recovery was followed by laser doppler perfusion imaging. all 4 gsos clearly improved blood flow recovery after ischemia. mice treated with gso-495 or gso-329 showed increased perfusion already after 3 days (30% perfusion versus 15% in control), and those treated with gso-329 showed a full recovery of perfusion after 7 days (versus 60% in control). increased collateral artery diameters (arteriogenesis) were observed in adductor muscles of gso-treated mice, as well as increased capillary densities (angiogenesis) in the ischemic soleus muscle. in vitro, treatment with gsos led to increased sprout formation and increased arterial endothelial cell proliferation, as well as to increased arterial myofibroblast proliferation. conclusions the 14q32 microrna gene cluster is highly involved in neovascularization. inhibition of 14q32 micrornas mir-329, mir-487b, mir-494, and mir-495 provides a promising tool for future therapeutic neovascularization.",1
"objective myocardin is a cardiac- and smooth muscle-specific transcription co-factor that potently activates the expression of downstream target genes. previously, we demonstrated that overexpression of myocardin inhibited the proliferation of smooth muscle cells (smcs). recently, myocardin was reported to induce the expression of microrna-1 (mir-1) in cardiomyocytes. in this study, we investigated whether myocardin induces mir-1 expression to mediate its inhibitory effects on smc proliferation. methods and results using tetracycline-regulated expression (t-rex) inducible system expressing myocardin in human vascular smcs, we found that overexpression of myocardin resulted in significant induction of mir-1 expression and inhibition of smc proliferation, which was reversed by mir-1 inhibitors. consistently, introduction of mir-1 into smcs inhibited their proliferation. we isolated spindle-shaped and epithelioid human smcs and demonstrated that spindle-shaped smcs were more differentiated and less proliferative. correspondingly, spindle-shaped smcs had significantly higher expression levels of both myocardin and mir-1 than epithelioid smcs. we identified pim-1, a serine/threonine kinase, as a target gene for mir-1 in smcs. western blot and luciferase reporter assays further confirmed that mir-1 targeted pim-1 directly. furthermore, neointimal lesions of mouse carotid arteries displayed downregulation of myocardin and mir-1 with upregulation of pim-1. conclusions our data demonstrate that mir-1 participates in myocardin-dependent of smc proliferation inhibition.",1
"radioresistance poses a major challenge in nasopharyngeal carcinoma (npc) treatment, but little is known about how mirna (mir) regulates this phenomenon. in this study, we investigated the function and mechanism of mir-203 in npc radioresistance, one of downregulated mirs in the radioresistant npc cells identified by our previous microarray analysis. we observed that mir-203 was frequently downregulated in the radioresistant npc tissues compared with radiosensitive npc tissues, and its decrement significantly correlated with npc radioresistance and poor patient survival, and was an independent predictor for reduced patient survival. in vitro radioresponse assays showed that mir-203 mimic markedly decreased npc cell radioresistance. in a mouse model, therapeutic administration of mir-203 agomir dramatically sensitized npc xenografts to irradiation. mechanistically, we confirmed that il8 was a direct target of mir-203, and found that reduced mir-203 promoted npc cell radioresistance by activating il8/akt signaling. moreover, the levels of il8 and phospho-akt were significantly increased in the radioresistant npc tissues compared with radiosensitive npc tissues, and negatively associated with mir-203 level. our data demonstrate that mir-203 is a critical determinant of npc radioresponse, and its decrement enhances npc radioresistance through targeting il8/akt signaling, highlighting the therapeutic potential of the mir-203/il8/akt signaling axis in npc radiosensitization.",1
"alzheimer's disease (ad) is a neurodegenerative disorder characterized by progressive loss of memory and other cognitive functions and presents an increasing clinical challenge in terms of diagnosis and treatment. brain-derived neurotrophic factor (bdnf) plays an important role in neuronal survival and proliferation. in the present study, the mrna and protein expression level of bdnf was detected in serum, and cerebrospinal fluid (csf) of patients with mild cognitive impairment (mci), dementia of alzheimer's type (dat), and hippocampus in app/ps1 mice. a significant decrease of bdnf mrna and protein expression was observed in serum and csf of patients and hippocampus in app/ps1 mice compared with the corresponding controls. mir-613, which is predicted to target the 3'-utr of bdnf, was also detected in patients and the mouse model. opposite to the alteration of bdnf, mir-613 expression in serum, csf and hippocampus were obviously increased compared to the controls. in conclusion, these findings showed that mir-613 may function in the development of ad and may provide new insights in diagnosis and treatment of ad.",1
"fenofibrate, a specific agonist of peroxisome proliferator-activated receptor-α (pparα), displays robust therapeutic effects on diabetic retinopathy (dr) in patients with type 2 diabetes. our recent studies have shown that pparα is downregulated in the diabetic retina, which contributes to the pathogenesis of dr. however, the mechanism for diabetes-induced downregulation of pparα remains unknown. we investigated the role of microrna-21 ( mir-21 ) in regulating pparα in dr. mir-21 was overexpressed, while pparα levels were decreased in the retina of db/db mice, a model of type 2 diabetes. such alterations were also observed in palmitate-treated retinal endothelial cells. mir-21 targeted pparα by inhibiting its mrna translation. knockout of mir-21 prevented the decrease of pparα, alleviated microvascular damage, ameliorated inflammation, and reduced cell apoptosis in the retina of db/db mice. intravitreal injection of mir-21 inhibitor attenuated pparα downregulation and ameliorated retinal inflammation in db/db mice. further, retinal mir-21 levels were increased, while pparα levels were decreased in oxygen-induced retinopathy (oir). knockout of mir-21 prevented pparα downregulation and ameliorated retinal neovascularization and inflammation in oir retinas. in conclusion, diabetes-induced overexpression of mir-21 in the retina is at least partly responsible for pparα downregulation in dr. targeting mir-21 may represent a novel therapeutic strategy for dr.",1
"lipopolysaccharide (lps) induces germ cell apoptosis, but its mechanism of action is not clear. one possibility is that lps regulates the expression of fas ligand (faslg) in sertoli cells, which will then influence germ cell apoptosis. in this study, lps reduced the viability of cultured, immature boar sertoli cells in a time- and dose-dependent manner; enhanced the production of pro-inflammatory cytokines including tumor necrosis factor α (tnfa), interleukin-1β (il1b), nitric oxide (no), and transforming growth factor-β (tgfb); and increased the expression of faslg in a dose-dependent manner. while 10 μg/ml lps enhanced the expression of faslg, reduced cell cycle progression, and impaired the ultrastructure of sertoli cells, this dose did not induce apoptosis. lps also had no effect on the activity or expression of matrix metalloproteinases 2 or 9 (mmp2 or mmp9). in contrast, the expression of ssc-mir-187 increased following lps challenge, and inhibition of ssc-mir-187 blocked lps-induced expression of faslg. our results therefore suggest that lps reduces the viability of and enhances faslg expression in cultured, immature boar sertoli cells through elevated secretion of tnfa, il1b, no, and tgfb as well as through the regulation of ssc-mir-187 potency.",1
"aim to predict the probable genomic packaging signal of sars-cov by bioinformatics analysis. the derived packaging signal may be used to design antisense rna and rna interfere (rnai) drugs treating sars. methods based on the studies about the genomic packaging signals of mhv and bcov, especially the information about primary and secondary structures, the putative genomic packaging signal of sars-cov were analyzed by using bioinformatic tools. multi-alignment for the genomic sequences was performed among sars-cov, mhv, bcov, pedv and hcov 229e. secondary structures of rna sequences were also predicted for the identification of the possible genomic packaging signals. meanwhile, the n and m proteins of all five viruses were analyzed to study the evolutionary relationship with genomic packaging signals. results the putative genomic packaging signal of sars-cov locates at the 3' end of orf1b near that of mhv and bcov, where is the most variable region of this gene. the rna secondary structure of sars-cov genomic packaging signal is very similar to that of mhv and bcov. the same result was also obtained in studying the genomic packaging signals of pedv and hcov 229e. further more, the genomic sequence multi-alignment indicated that the locations of packaging signals of sars-cov, pedv, and hcov overlaped each other. it seems that the mutation rate of packaging signal sequences is much higher than the n protein, while only subtle variations for the m protein. conclusions the probable genomic packaging signal of sars-cov is analogous to that of mhv and bcov, with the corresponding secondary rna structure locating at the similar region of orf1b. the positions where genomic packaging signals exist have suffered rounds of mutations, which may influence the primary structures of the n and m proteins consequently.",1
"the repabc replicons contain an operon encoding the initiator protein (repc) and partitioning proteins (repa and repb). the latter two proteins negatively regulate the transcription of the operon. in this article we have identified two novel regulatory elements, located within the conserved repb-repc intergenic sequence, which negatively modulate the expression of repc, in plasmid p42d of rhizobium etli. one of them is a small antisense rna and the other is a stem-loop structure in the repabc mrna that occludes the shine-dalgarno sequence of repc. according to in vivo and in vitro analyses, the small antisense rna (57-59 nt) resembles canonical negative regulators of replication because: (i) it is transcribed from a strong constitutive promoter (p2), (ii) the transcript overlaps untranslated region upstream of the repc coding sequences, (iii) the rna forms one secondary structure acting as a rho-independent terminator, (iv) the antisense rna is a strong trans-incompatibility factor and (v) its presence reduces the level of repc expression. surprisingly, both of these seemingly negative regulators are required for efficient plasmid replication.",1
"it is well recognized that there is sex-dimorphic expression of mrna and protein in the heart; however, the underlying mechanism is poorly understood. endothelial nitric oxide synthase (enos) is an important regulator of cardiac function, and the expression levels of enos differ between male and female hearts. the aim of this study was to examine whether expression of specific microrna (mirna, mir) in males and females contributes to changes in the expression of enos. mirna was extracted from the myocardium of male and female c57bl/6 mice and subjected to an affymetrix mirna array. decreased expression of mir-222 was discovered in females and confirmed by qrt-pcr from whole heart or isolated cardiomyocytes. the transcription factor v-ets erythroblastosis virus e26 oncogene homolog-1 (ets-1) was identified as a potential target of mir-222 using targetscan, and fivefold increased ets-1 protein expression in females was confirmed by western blot. targeting of ets-1 by mir-222 was determined in hek293 cells overexpressing luciferase under regulation of either the ets-1 3'-utr, a null 3'-utr control, or a scrambled ets-1 3'-utr and treated with a small molecule mir-222 mimic or inhibitor. additionally qrt-pcr confirmed that mrna levels of the ets-1 transcriptional target, enos, were 25% higher in females. compared with untreated myocyte controls, 50% inhibition of enos expression was achieved by treatment with a mir-222 mimic, compared with a 25% increase due to mir-222 inhibitor. our findings indicate that sex-dependent mir-222 regulation alters the expression of the cardiac regulatory protein enos.",1
"purpose to evaluate the role of mir-200b expression in the proliferation of human tenon's capsule fibroblasts (htfs) induced by transforming growth factor-beta 1 (tgf-β1). methods human tenon's capsule fibroblasts were treated with various doses of tgf-β1 for 24 hours. cell proliferation was quantified by the cell counting kit-8 (cck-8) assay, cell cycle analysis, 5-ethynyl-2-deoxyuridine (edu) assay, and analysis of cyclin e, cyclin d1, and proliferating cell nuclear antigen (pcna) expression. microrna-200b (mir-200b) was detected by quantitative reverse-transcriptase polymerase chain reaction (qrt-pcr), and its potential target genes were validated by the luciferase assay and western blot analysis. the effect of mir-200b on the proliferation of htfs was analyzed using both mir200b-mimic and inhibitor-transfected htfs and confirmed in p27/kip1 and rnd3 (the target of mir-200b) knockdown cells. results the proliferation of the tgf-β1-treated htfs increased significantly in a dose- and time-dependent manner. treatment with 5 ng/ml tgf-β1 caused an upregulation of mir-200b. the luciferase assay identified p27/kip1 and rnd3 as target genes for mirna-200b, which was confirmed by the expression of p27/kip1 and rnd3 and their downstream products (cycline and cyclind1) in the tgf-β1-treated cells. transforming growth factor-β1 and mir-200b mimics enhanced the proliferation of htfs; suppressed the expression of p27/kip1 and rnd3; and subsequently stimulated the expression of cycline, cyclind1, and pcna. the mir-200b inhibitor attenuated the effects of tgf-β1 on htfs. furthermore, knockdown of p27/kip1 and rnd3 resulted in an increase in cell proliferation and expression of the proliferation-related genes. conclusions microrna-200b acts as a stimulant for the proliferation of htfs by targeting p27/kip1 and rnd3.",1
"background brain size and patterning are dependent on dosage-sensitive morphogen signaling pathways - yet how these pathways are calibrated remains enigmatic. recent studies point to a new role for micrornas in tempering the spatio-temporal range of morphogen functions during development. here, we investigated the role of mir-135a, derived from the mir-135a-2 locus, in embryonic forebrain development. method 1. we characterized the expression of mir-135a, and its host gene rmst, by in situ hybridization (ish). 2. we conditionally ablated, or activated, beta-catenin in the dorsal forebrain to determine if this pathway was necessary and/or sufficient for rmst/mir-135a expression. 3. we performed bioinformatics analysis to unveil the most predicted pathways targeted by mir-135a. 4. we performed gain and loss of function experiments on mir-135a-2 and analyzed by ish the expression of key markers of cortical hem, choroid plexus, neocortex and hippocampus. results 1. mir-135a, embedded in the host long non-coding transcript rmst, is robustly expressed, and functional, in the medial wall of the embryonic dorsal forebrain, a wnt and tgfβ/bmp-rich domain. 2. canonical wnt/beta-catenin signaling is critical for the expression of rmst and mir-135a, and the cortical hem determinant lmx1a. 3. bioinformatics analyses reveal that the wnt and tgfβ/bmp cascades are among the top predicted pathways targeted by mir-135a. 4. analysis of mir-135a-2 null embryos showed that dorsal forebrain development appeared normal. in contrast, modest mir-135a-2 overexpression, in the early dorsal forebrain, resulted in a phenotype resembling that of mutants with wnt and tgfβ/bmp deficits - a smaller cortical hem and hippocampus primordium associated with a shorter neocortex as well as a less convoluted choroid plexus. interestingly, late overexpression of mir-135a-2 revealed no change. conclusions all together, our data suggests the existence of a wnt/mir-135a auto-regulatory loop, which could serve to limit the extent, the duration and/or intensity of the wnt and, possibly, the tgfβ/bmp pathways.",1
"rnase p rna is an ancient, nearly universal feature of life. as part of the ribonucleoprotein rnase p complex, the rna component catalyzes essential removal of 5' leaders in pre-trnas. in 2004, li and altman computationally identified the rnase p rna gene in all but three sequenced microbes: nanoarchaeum equitans, pyrobaculum aerophilum, and aquifex aeolicus (all hyperthermophiles) . a recent study concluded that n. equitans does not have or require rnase p activity because it lacks 5' trna leaders. the ""missing"" rnase p rnas in the other two species is perplexing given evidence or predictions that trnas are trimmed in both, prompting speculation that they may have developed novel alternatives to 5' pre-trna processing. using comparative genomics and improved computational methods, we have now identified a radically minimized form of the rnase p rna in five pyrobaculum species and the related crenarchaea caldivirga maquilingensis and vulcanisaeta distributa, all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. we confirmed 5' trna processing activity by high-throughput rna sequencing and in vitro biochemical assays. the pyrobaculum and caldivirga rnase p rnas are the smallest naturally occurring form yet discovered to function as trans-acting precursor trna-processing ribozymes. loss of the specificity domain in these rnas suggests altered substrate specificity and could be a useful model for finding other potential roles of rnase p. this study illustrates an effective combination of next-generation rna sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding rna gene.",1
"micrornas (mirnas) are small noncoding rnas that regulate gene expression by binding to sequences within the 3' utr of mrnas. because mirnas bind to short sequences with partial complementarity, target identification is challenging. to complement the existing target prediction algorithms, we devised a systematic ""reverse approach"" screening platform that allows the empirical prediction of mirna-target interactions. using drosophila cells, we screened the 3' untranslated regions (3' utrs) of the hedgehog pathway genes against a genome-wide mirna library and identified both predicted and many nonpredicted mirna-target interactions. we demonstrate that mir-14 is essential for maintaining the proper level of hedgehog signaling activity by regulating its physiological target, hedgehog. furthermore, elevated levels of mir-14 suppress hedgehog signaling activity by cotargeting its apparent nonphysiological targets, patched and smoothened. altogether, our systematic screening platform is a powerful approach to identifying both physiological and apparent nonphysiological targets of mirnas, which are relevant in both normal and diseased tissues.",1
"micrornas (mirs) have emerged as key biological effectors in human health and disease. these small noncoding rnas are incorporated into argonaute (ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. although mirs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of mir research remain limited by a paucity of empirical mir targeting data, particularly in human primary tissues. here, to improve our understanding of the diverse roles mirs play in cardiovascular function and disease, we applied high-throughput methods to globally profile mir:target interactions in human heart tissues. we deciphered ago2:rna interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (hits-clip) to generate the first transcriptome-wide map of mir targeting events in human myocardium, detecting 4000 cardiac ago2 binding sites across >2200 target transcripts. our initial exploration of this interactome revealed an abundance of mir target sites in gene coding regions, including several sites pointing to new mir-29 functions in regulating cardiomyocyte calcium, growth and metabolism. also, we uncovered several clinically-relevant interactions involving common genetic variants that alter mir targeting events in cardiomyopathy-associated genes. overall, these data provide a critical resource for bolstering translational mir research in heart, and likely beyond.",1
"pancreatic ductal adenocarcinoma (pdac) is a highly invasive cancer with a poor prognosis. although microrna (mirna) transcripts have a crucial role in carcinogenesis and development, little information is known regarding the aberrant dna methylation of mirnas in pdac. using methylated dna immunoprecipitation-chip analysis, we found that mir-615-5p was hypermethylated in its putative promoter region, which silenced its expression in pdac cell lines. in addition, the overexpression of mir-615-5p in pancreatic cancer cells suppressed cell proliferation, migration and invasion. insulin-like growth factor 2 (igf2) is an imprinted gene, and its abnormal expression contributes to tumor growth. here, we identified igf2 as a target of mir-615-5p using a luciferase reporter assay. igf2 upregulation in pdac tissues was not correlated with a loss of imprinting but was inversely correlated with mir-615-5p downregulation. in addition, mir-615-5p suppressed pancreatic cancer cell proliferation, migration and invasion by directly targeting igf2, and this effect could be reversed by co-transfection with igf2. furthermore, the stable overexpression of mir-615-5p inhibited tumor growth in vivo and was correlated with igf2 expression. using rna sequencing, we further identified mir-615-5p as potentially targeting other genes, such as the proto-oncogene junb, and interfering with the insulin signaling pathway. taken together, our results demonstrate that mir-615-5p was abnormally downregulated in pdac cells due to promoter hypermethylation, which limited its inhibition of igf2 and other target genes, thereby contributing to tumor growth, invasion and migration. these data demonstrate a novel and important role of mir-615-5p as a tumor suppressor in pdac.",1
"the healing process of fractured bone is affected by the multiple factors regulating the growth and differentiation of osteoblasts and bone mesenchymal stem cells (mscs), however, such markers and molecular events need to be orchestrated in details. this study investigated the effect of polyphenol(-)-epigallocatechin-3-gallate (egcg) on the hypoxia-induced apoptosis and osteogenic differentiation of human bone marrow-derived mscs, examined the mir-210 induction by egcg, explored the target inhibition of the expression of receptor tyrosine kinase ligand ephrin-a3 (efna3) by mir-210, and then determined the association of the mir-210 promotion with the hypoxia-induced apoptosis and osteogenic differentiation. results demonstrated that egcg treatment significantly inhibited the hypoxia-induced apoptosis in mscs and promoted the level of alkaline phosphatase (alp), bone morphogenetic protein 2 (bmp-2), propeptide of type i procollagen i (pinp) and runt-related transcription factor 2 (runx2) in mscs under either normoxia or hypoxia. moreover, the egcg treatment upregulated the mir-210 expression, in an association with efna3 downregulation; and the mir-210 upregulation significantly downregulated the expression of efna3 via the specific binding to the 3' utr of efna3. in addition, the manipulated mir-210 upregulation exerted amelioration on the hypoxia-induced apoptosis and on the hypoxia-reduced expression of alp, bmp-2, pinp and runx2 in mscs. in summary, our study indicated the protective role of egcg in response to hypoxia and promontory role to osteogenic differentiation in mscs via upregulating mir-210 and downregulating the expression of mir-210-targeted efna3. our study implies the protective role of egcg in the hypoxia-induced impairment in mscs.",1
"micrornas (mirs) function as key regulators of gene expression and their deregulation is associated with the carcinogenesis of various cancers. in the present study, we investigated the biological role and mechanism of mir-361-5p in colorectal carcinoma (crc) and gastric cancer (gc). we showed that microrna-361-5p (mir-361-5p) was down-regulated in crc and gc in comparison to the controls. meanwhile, the expression levels of mir-361-5p negatively correlated with lung metastasis and prognosis in clinical crc patients. overexpression of mir-361-5p markedly suppressed proliferation, migration and invasion of cancer cells. additionally, this phenotype could be partially rescued by the ectopic expression of staphylococcal nuclease domain containing-1 (snd1). snd1 was identified as a target of mir-361-5p using bioinformatics analysis and in vitro luciferase reporter assays. in turn, snd1 bound to pre-mir-361-5p and suppressed the expression of mir-361-5p, thus exerting a feedback loop. most interestingly, in vivo studies showed that restoration of mir-361-5p significantly inhibited tumor growth and especially the lung metastasis in nude mice. therefore, it could be concluded that mir-361-5p functions as a tumor-suppressive mirna through directly binding to snd1, highlighting its potential as a novel agent for the treatment of patients with crc and gc.",1
"burkitt lymphoma (bl) is a highly aggressive b-cell non-hodgkin lymphoma (b-nhl), which originates from germinal center (gc) b cells and harbors translocations deregulating v-myc avian myelocytomatosis viral oncogene homolog (myc). a comparative analysis of micrornas expressed in normal and malignant gc b cells identified microrna 28 (mir-28) as significantly down-regulated in bl, as well as in other gc-derived b-nhl. we show that reexpression of mir-28 impairs cell proliferation and clonogenic properties of bl cells by modulating several targets including mad2 mitotic arrest deficient-like 1, mad2l1, a component of the spindle checkpoint whose down-regulation is essential in mediating mir-28-induced proliferation arrest, and bcl2-associated athanogene, bag1, an activator of the erk pathway. we identify the oncogene myc as a negative regulator of mir-28 expression, suggesting that its deregulation by chromosomal translocation in bl leads to mir-28 suppression. in addition, we show that mir-28 can inhibit myc-induced transformation by directly targeting genes up-regulated by myc. overall, our data suggest that mir-28 acts as a tumor suppressor in bl and that its repression by myc contributes to b-cell lymphomagenesis.",1
"micrornas (mirs) play an important role in the development and remodeling of tissues through the regulation of large cohorts of extracellular matrix (ecm) genes. the purpose of the present study was to determine the response of mir-29 family expression to loading forces and their effects on ecm gene expression in periodontal ligament cells, the key effector cell population during orthodontic tooth movement. in a comparison between mirs from human periodontal ligament cells (pdlcs) and alveolar bone cells (abcs) from healthy human subjects, the abc cohort of mirs was substantially greater than the corresponding pdlc cohort. cyclic mechanical stretch forces at 12% deformation at 0.1hz for 24h decreased expression of mir-29 family member mirs about 0.5 fold while 2g/cm(2) compression force for 24h increased mir-29 family member expression in pdlcs 1.8-4 folds. cyclic stretch up-regulated major ecm genes in pdlcs, such as col1a1, col3a1 and col5a1, while the compression force resulted in a down-regulation of these ecm genes. direct interactions of mir-29 and col1a1, col3a1 and col5a1 were confirmed using a dual luciferase reporter gene assay. in addition, transient transfection of a mir-29b mimic in mouse pdlcs down-regulated col1a1, col3a1 and col5a1 while the transfection of mir-29b inhibitor up-regulated these genes compared to control transfection indicating that these target ecm genes directly responded to the altered level of mir-29b. these results provided a possible explanation for the effects of the mir-29 family on loaded pdlcs and their roles in extracellular matrix gene expression.",1
"micrornas (mirnas) inhibit the translation of target mrnas and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. this study focuses on mirnas that are expressed in the mouse cochlea and vestibule, the 2 inner ear compartments. a conditional knock-out mouse for dicer1 demonstrated that mirnas are crucial for postnatal survival of functional hair cells of the inner ear. we identified mirnas that have a role in the vertebrate developing inner ear by combining mirna transcriptome analysis, spatial and temporal expression patterns, and bioinformatics. microarrays revealed similar mirna profiles in newborn-mouse whole cochleae and vestibules, but different temporal and spatial expression patterns of six mirnas (mir-15a, mir-18a, mir-30b, mir-99a, mir-182, and mir-199a) may reflect their roles. two of these mirnas, mir-15a-1 and mir-18a, were also shown to be crucial for zebrafish inner ear development and morphogenesis. to suggest putative target mrnas whose translation may be inhibited by selected mirnas, we combined bioinformatics-based predictions and mrna expression data. finally, we present indirect evidence that slc12a2, cldn12, and bdnf mrnas may be targets for mir-15a. our data support the hypothesis that inner ear tissue differentiation and maintenance are regulated and controlled by conserved sets of cell-specific mirnas in both mouse and zebrafish.",1
"unrestricted somatic stem cells (usscs) represent an intrinsically multipotent cd45-negative fetal population from human cord blood. they show differentiation into neuronal cells of a dopaminergic phenotype, which express neuronal markers such as synaptophysin, neuronal-specific nuclear protein, and neurofilament and release the neurotransmitter dopamine accompanied by expression of dopaminergic key factors tyrosine hydroxylase and nurr1 (nr4a2). microrna expression analysis highlighted their importance in neural development but their specific functions remain poorly understood. here, downregulation of a set of 18 micrornas during neuronal lineage differentiation of unrestricted somatic stem cells, including members of the mir-17-92 family and additional micrornas such as mir-130a, -138, -218, and -335 as well as their target genes, is described. in silico target gene predictions for this microrna group uncovered a large set of proteins involved in neuronal differentiation and having a strong impact on differentiation-related pathways such as axon guidance and tgfβ, wnt, and mapk signaling. experimental target validations confirmed approximately 35% of predictions tested and revealed a group of proteins with specific impact on neuronal differentiation and function including neurobeachin, neurogenic differentiation 1, cysteine-rich motor neuron protein 1, neuropentraxin 1, and others. these proteins are combined targets for several subgroups from the set of 18 downregulated micrornas. this finding was further supported by the observed upregulation of a significant amount of predicted and validated target genes based on illumina beadstudio microarray data. confirming the functional relationship of a limited panel of micrornas and predicted target proteins reveals a clear network-like impact of the group of 18 downregulated micrornas on proteins involved in neuronal development and function.",1
"the insulin signalling pathway plays a crucial role in regulating the metabolism of sugars, fats and proteins in cells, thereby affecting the growth, metabolism, reproduction and ageing of organisms. however, little is known about the functions of long non-coding rnas (lncrnas) in the regulation of insulin receptors under stress conditions in insects. in this study, we showed that insulin receptor-associated lncrna (irar) regulates insulin receptor transcripts in response to nutritional stress in drosophila melanogaster. genome editing by crispr-cas9 showed reduced sensitivity of irar mutants to environmental nutritional changes. in contrast, the sensitivity of mutants overexpressing tubulin-gal4 > irar increased under low nutrition. the pupation and eclosion timings in irar mutants were significantly delayed with an increase in insulin concentration compared with that in the w1118 group. in addition, the expression pattern of irar was almost consistent with that of the four transcripts of the insulin receptor from the embryonic period to the adult period. rna immunoprecipitation assay showed the direct regulation of insulin receptor transcripts by irar to the through foxo binding under nutritional stress. to our knowledge, this is the first study that describes a model of lncrna-mediated development regulation through insulin receptor transcripts.",1
"the functional role of microrna-23a in tumorigenesis has been investigated; however, the exact mechanism of microrna-23a (mir-23a) in colorectal cancer development has not been fully explored. in the present study, we aimed to investigate the molecular functional role of mir-23a in colorectal carcinogenesis. quantitative real-time polymerase chain reaction was conducted to investigate the expression level of mir-23a in tissue samples and cell lines (hct116 and sw480). cck-8, colony formation and transwell assay were used to explore the role of mir-23a in cell proliferation and migration. dual luciferase reporter assay was used to identify the direct binding of mir-23a with its target, mark1. western blot analysis was used to analyze the expression level of mark1, as well as a confirmed mir-23a target gene, mtss1, in mir-23a-mimic and mir-23a-inhibit groups. rescue experiments were conducted by overexpression of mark1 in mir-23a-mimic-transfected cell lines. the results showed that mir-23a was highly expressed in colorectal cancer tissue and cell lines. mir-23a could promote proliferation and migration of colorectal cancer cell lines. mark1 was a direct target of mir-23a and the expression level of mark1 was down-regulated in mir-23a-mimic-transfected cell lines but up-regulated in mir-23a-inhibit-transfected cells. overexpression of mark1 could partly reverse the cancer-promoting function of mir-23a. our results suggested that mir-23a promotes colorectal cancer cell proliferation and migration by mediating the expression of mark1. mir-23a may be a potential therapeutic target for colorectal cancer treatment.",1
"micrornas (mirnas) regulate gene expression at post-transcriptional level and are key modulators of immune system, whose dysfunction contributes to the progression of neuroinflammatory diseaseas such as amyotrophic lateral sclerosis (als), the most widespread motor neuron disorder. als is a non-cell-autonomous disease targeting motor neurons and neighboring glia, with microgliosis directly contributing to neurodegeneration. as limited information exists on mirnas dysregulations in als, we examined this topic in primary microglia from superoxide dismutase 1-g93a mouse model. we compared mirnas transcriptional profiling of non-transgenic and als microglia in resting conditions and after inflammatory activation by p2x7 receptor agonist. we identified upregulation of selected immune-enriched mirnas, recognizing mir-22, mir-155, mir-125b and mir-146b among the most highly modulated. we proved that mir-365 and mir-125b interfere, respectively, with the interleukin-6 and stat3 pathway determining increased tumor necrosis factor alpha (tnfα) transcription. as tnfα directly upregulated mir-125b, and inhibitors of mir-365/mir-125b reduced tnfα transcription, we recognized the induction of mir-365 and mir-125b as a vicious gateway culminating in abnormal tnfα release. these results strengthen the impact of mirnas in modulating inflammatory genes linked to als and identify specific mirnas as pathogenetic mechanisms in the disease.",1
"prostate cancer is the second most frequent malignancy in men worldwide, and its incidence is increasing. therefore, it is urgently required to clarify the underlying mechanisms of prostate cancer. although the long non-coding rna linc00115 was identified as an oncogene in several cancers, the expression and function of linc00115 in prostate cancer have not been explored. our results showed that linc00115 was significantly up-regulated in prostate cancer tissues, which was significantly associated with a poor prognosis for prostate cancer patients. functional studies showed that knockdown linc00115 inhibited cell proliferation and invasion. in addition, linc00115 served as a competing endogenous rna (cerna) through sponging mir-212-5p to release frizzled family receptor 5 (fzd5) expression. the expression of mir-212-5p was noticeably low in tumour tissues, and fzd5 expression level was down-regulated with the knockdown of linc00115. knockdown linc00115 inhibited the wnt/β-catenin signalling pathway by inhibiting the expression of fzd5. rescue experiments further showed that linc00115 inhibits prostate cancer cell proliferation and invasion via targeting mir-212-5p/ fzd5/ wnt/β-catenin axis. the present study provided clues that linc00115 may be a promising novel therapeutic target for prostate cancer patients.",1
"gastric cancer (gc) is a biologically heterogeneous disease accompanying various genetic and epigenetic alterations, and the molecular mechanisms underlying this disease are complex and not completely understood. increasing evidence shows that abnormal microrna (mirna) expression is involved in gc tumorigenesis, but the role of specific mirnas involved in this disease remains elusive. mir-141 was previously reported to act as tumor suppressors or oncogenes in diverse cancers. however, their accurate expression, function and mechanism in gc are largely unclear. here we found that the expression of mir-141 was significantly reduced in gc compared with paired adjacent normal tissues and was significantly correlated with a more aggressive phenotype of gc in patients. ectopic expression of mir-141 mimics in gc cell lines resulted in reduced proliferation, invasion and migration, and inhibition of mir-141 in gc cell lines promoted cell proliferation, invasion and migration in vitro. we further demonstrated that mir-141 acted as tumor suppressors through targeting transcriptional co-activator with pdz-binding motif (taz) in gc. moreover, the inverse relationship between mir-141 and its target was verified in patients and xenograft mice. finally, overexpression of mir-141 suppressed tumor growth and pulmonary metastasis in nude mice. take together, we identified that mir-141 is a potent tumor suppressor in the stomach, and its growth inhibitory effects are, in part, mediated through its downstream target gene, taz. these findings implied that mir-141 might be employed as novel prognostic markers and therapeutic targets of gc.",1
"as the most common neurodegenerative disease, alzheimer's disease (ad) is characterized by memory, perception, and behavioral damage, which may ultimately lead to emotional fluctuation and even lethal delirium. increasing studies indicate that micrornas (mirnas) are associated with pathological features of ad. however, the role of mir-219-5p in ad progression is still unclear. in this study, the functions of mir-219-5p were analyzed in vitro and in vivo. mir-219-5p was notably overexpressed in brain tissues of patients with ad. the overexpression of mir-219-5p activated the phosphorylation of tau-ser198, tau-ser199, tau-ser201, and tau-ser422. we further showed that mir-219-5p could mediate a decrease in the protein levels of tau-tubulin kinase 1 (ttbk1) and glycogen synthase kinase 3β (gsk-3β) by directly binding to their 3'-untranslated region, thereby promoting the phosphorylation of tau in sh-sy5y cells. rescue experiments further revealed that the phosphorylation of tau-mediated by mir-219-5p was dependent on the inhibition of ttbk1 and gsk-3β. moreover, suppressing the expression of both ttbk1 and gsk-3β using mir-219-5p remarkably rescued ad-like symptoms in amyloid precursor protein/presenilin 1 mice. our findings indicate that the upregulation of ttbk1 and gsk-3β mediated by the loss of mir-219-5p is a possible mechanism that contributes to tau phosphorylation and ad progression.",1
"during neuronal development and maturation, micrornas (mirs) play diverse functions ranging from early patterning, proliferation and commitment to differentiation, survival, homeostasis, activity and plasticity of more mature and adult neurons. the role of mirs in the differentiation of olfactory receptor neurons (orns) is emerging from the conditional inactivation of dicer in immature orn, and the depletion of all mature mirs in this system. here, we identify specific mirs involved in olfactory development, by focusing on mice null for dlx5, a homeogene essential for both orn differentiation and axon guidance and connectivity. analysis of mir expression in dlx5(-/-) olfactory epithelium pointed to reduced levels of mir-9, mir-376a and four mirs of the -200 class in the absence of dlx5. to functionally examine the role of these mirs, we depleted mir-9 and mir-200 class in reporter zebrafish embryos and observed delayed orn differentiation, altered axonal trajectory/targeting, and altered genesis and position of olfactory-associated gnrh neurons, i.e. a phenotype known as kallmann syndrome in humans. mir-9 and mir-200-class negatively control foxg1 mrna, a fork-head transcription factor essential for development of the olfactory epithelium and of the forebrain, known to maintain progenitors in a stem state. increased levels of z-foxg1 mrna resulted in delayed orn differentiation and altered axon trajectory, in zebrafish embryos. this work describes for the first time the role of specific mir (-9 and -200) in olfactory/gnrh development, and uncovers a dlx5-foxg1 regulation whose alteration affects receptor neuron differentiation, axonal targeting, gnrh neuron development, the hallmarks of the kallmann syndrome.",1
"rnase p is an essential and ubiquitous endonuclease that mediates the maturation of the 5' ends of all precursor trna molecules. the holoenzyme from dictyostelium discoideum possesses rna and protein subunits essential for activity, but the exact composition of the ribonucleoprotein complex is still under investigation. bioinformatic analysis of d. discoideum genome identified seven open reading frames encoding candidate rnase p protein subunits. the gene named drpp30 encodes a protein with a predicted molecular mass of 40.7 kda that clusters with rpp1 and rpp30 rnase p protein subunits from saccharomyces cerevisiae and human respectively, which have significantly lower molecular masses. cloning and heterologous expression of drpp30 followed by immunochemical analysis of rnase p active fractions demonstrates its association with rnase p holoenzyme. furthermore, we show that drpp30 can bind d. discoideum rnase p rna and trna transcripts in vitro, giving a first insight of its possible role in d. discoideum rnase p function. homology modeling using as a template the archaeal ph1887p, and molecular dynamics simulations of the modeled structure suggest that drpp30 adopts a tim-barrel fold.",1
"background micrornas (mirnas) mediate a form of translational regulation in animals. hundreds of animal mirnas have been identified, but only a few of their targets are known. prediction of mirna targets for translational regulation is challenging, since the interaction with the target mrna usually occurs via incomplete and interrupted base pairing. moreover, the rules that govern such interactions are incompletely defined. results movingtargets is a software program that allows a researcher to predict a set of mirna targets that satisfy an adjustable set of biological constraints. we used movingtargets to identify a high-likelihood set of 83 mirna targets in drosophila, all of which adhere to strict biological constraints. we tested and verified 3 of these predictions in cultured cells, including a target for the drosophila let-7 homolog. in addition, we utilized the flexibility of movingtargets by relaxing the biological constraints to identify and validate mirnas targeting tramtrack, a gene also known to be subject to translational control dependent on the rna binding protein musashi. conclusion movingtargets is a flexible tool for the accurate prediction of mirna targets in drosophila. movingtargets can be used to conduct a genome-wide search of mirna targets using all drosophila mirnas and potential targets, or it can be used to conduct a focused search for mirnas targeting a specific gene. in addition, the values for a set of biological constraints used to define a mirna target are adjustable, allowing the software to incorporate the rules used to characterize a mirna target as these rules are experimentally determined and interpreted.",1
"endothelial cells are the key components of vascular intima and play pivotal roles in vasculogenesis, angiogenesis, and tumor growth. using northern blot and real-time pcr, we confirmed that mir-126 and its host gene egf-like domain 7 (egfl7) were widely expressed in rat tissues but strictly expressed in endothelial cells. in mammals, mir-126 gene is embedded in intron7 of egfl7. to explore the biogenesis of mir-126, plasmid egfl7(126)-pegfpc1 containing segment of exon7-intron7-exon8 of egfl7 was constructed and expressed in 293t. expression of spliced exon7-8 and excised mature mir-126 was detected by pcr and northern blot. knocking-down of endothelial endogenous mir-126 did not affect egfl7 expression at mrna or protein level. to investigate the possible roles of mir-126, pictar, mirbase, miranda, bibiserv, and targetscan were used to screen the targets. vegfa and pik3r2 were confirmed as the targets of mir-126 by luciferase reporter assay and western blot. interestingly, northern blot and western blot showed that mir-126 was down-regulated in breast tumors where the vegf/pi3k/akt signaling pathway was activated. introduction of mir-126 mimics into mcf-7 could effectively decrease vegf/pi3k/akt signaling activity. in summary, mir-126 was strictly expressed in endothelial cells and excised from egfl7 pre-mrna without affecting splicing and expression of its host gene. in addition, mir-126 could target both vegfa and pik3r2, and its expression was decreased in human breast cancer, implying that mir-126 may play a role in tumor genesis and growth by regulating the vegf/pi3k/akt signaling pathway.",1
"mir-24, upregulated during terminal differentiation of multiple lineages, inhibits cell-cycle progression. antagonizing mir-24 restores postmitotic cell proliferation and enhances fibroblast proliferation, whereas overexpressing mir-24 increases the g1 compartment. the 248 mrnas downregulated upon mir-24 overexpression are highly enriched for dna repair and cell-cycle regulatory genes that form a direct interaction network with prominent nodes at genes that enhance (myc, e2f2, ccnb1, and cdc2) or inhibit (p27kip1 and vhl) cell-cycle progression. mir-24 directly regulates myc and e2f2 and some genes that they transactivate. enhanced proliferation from antagonizing mir-24 is abrogated by knocking down e2f2, but not myc, and cell proliferation, inhibited by mir-24 overexpression, is rescued by mir-24-insensitive e2f2. therefore, e2f2 is a critical mir-24 target. the e2f2 3'utr lacks a predicted mir-24 recognition element. in fact, mir-24 regulates expression of e2f2, myc, aurkb, ccna2, cdc2, cdk4, and fen1 by recognizing seedless but highly complementary sequences.",1
"psoriasis is a chronic autoimmune skin disease driven by dysregulations at the cellular, genomic and genetic levels. micrornas are key mediators of gene expression regulation. however, how micrornas control the pathogenesis of psoriasis is still unclear. here, we reported a significant up-regulation of mir-378a-3p (mir-378a) in skin biopsies from active psoriatic lesions while it was down-regulated after treatment with methotrexate or narrow-band ultraviolet b phototherapy. using the keratinocyte in vitro model, we showed that mir-378a disturbed the cell cycle progression, causing cell cycle arrest at g1 phase. transcriptomic analysis of keratinocytes with mir-378a overexpression and depletion revealed several important biological mechanisms related to inflammation and tight junction. target mrna transcript assessed by luciferase assay identified bone morphogenetic protein 2 as a novel target gene of mir-378a. these findings offer a mechanistic model where mir-378a contributes to the pathogenesis of psoriasis.",1
"objective ptk2 has been reported to be involved in tumor progression, but its regulating mechanisms in cervical cancer (cc) remain to be elusive. mirna-520d-5p was demonstrated to regulate the expression of many genes and inhibit the development of human tumors. however, the functional mechanisms of mirna-520d-5p in the regulation of cervical cancer are not fully understood. methods rt-qpcr was employed to detect the expression levels of mir-520d-5p and ptk2. western blot was performed to detect the expression levels of proteins. dual-luciferase reporter assay was utilized to investigate the associations between mir-520d-5p and ptk2. cck-8 assay was carried out to measure cell proliferation. in addition, transwell assay and scratch assay were used for cell invasion and migration analysis. flow cytometry was used to detect cell apoptosis of cervical cancer. results the expression levels of ptk2 were elevated in cc tissues and cells lines. it was found that ptk2 was a target gene of mir-520d-5p. the expression of mir-520d-5p was down-regulated in cc tissues, which was negatively correlated with the expression of ptk2. mir-520d-5p inhibited the proliferation, migration, and invasion of cc cells. in addition, overexpression of mir-520d-5p resulted in apoptosis of cc cells. finally, we demonstrated that mir-520d-5p inhibited the activation of pi3k/akt signaling. conclusion mir-520d-5p suppressed the proliferation, invasion, and migration of cc cells via targeting ptk2.",1
"much of the genome is transcribed into long noncoding rnas (ncrnas). previous data suggested that bithoraxoid (bxd) ncrnas of the drosophila bithorax complex (bx-c) prevent silencing of ultrabithorax (ubx) and recruit activating proteins of the trithorax group (trxg) to their maintenance elements (mes). we found that, surprisingly, ubx and several bxd ncrnas are expressed in nonoverlapping patterns in both embryos and imaginal discs, suggesting that transcription of these ncrnas is associated with repression, not activation, of ubx. our data rule out sirna or mirna-based mechanisms for repression by bxd ncrnas. rather, ncrna transcription itself, acting in cis, represses ubx. the trithorax complex tac1 binds the ubx coding region in nuclei expressing ubx, and the bxd region in nuclei not expressing ubx. we propose that tac1 promotes the mosaic pattern of ubx expression by facilitating transcriptional elongation of bxd ncrnas, which represses ubx transcription.",1
"the genome of red clover necrotic mosaic virus (rcnmv) consists of rna1 and rna2, both lacking a cap structure and a poly(a)tail. rna1 has a translational enhancer element (3'te-dr1) in the 3' untranslated region (utr). in this study, we analyzed the roles of 5' and 3' utrs of rna1 in 3'te-dr1-mediated cap-independent translation in cowpea and tobacco by-2 protoplasts using a dual-luciferase (luc) reporter assay system. most mutations introduced into rna1 5' utr in reporter luc mrna abolished or greatly reduced cap-independent translation in by-2 protoplasts, whereas those mutations had no or much milder effects if any on translational activity in cowpea protoplasts. our results suggest that a stem-loop structure predicted in the 5' proximal region of rna1 plays important roles in both translation and rna stability. we also show that 3'te-dr1-mediated cap-independent translation relies on a ribosome-scanning mechanism in both protoplasts.",1
"the tgf-β pathway plays an important role in physiological and pathological angiogenesis. micrornas (mirnas) are a class of 18- to 25-nucleotide, small, noncoding rnas that function by regulating gene expression. a number of mirnas have been found to be regulated by the tgf-β pathway. however, the role of endothelial mirnas in the tgf-β-mediated control of angiogenesis is still largely unknown. here we investigated the regulation of endothelial microrna-29a (mir-29a) by tgf-β signaling and the potential role of mir-29a in angiogenesis. mir-29a was directly up-regulated by tgf-β/smad4 signaling in human and mice endothelial cells. in a chick chorioallantoic membrane assay, mir-29a overexpression promoted the formation of new blood vessels, and mir-29a suppression completely blocked tgf-β1-stimulated angiogenesis. consistently, mir-29a overexpression increased tube formation and migration in endothelial cultures. mechanistically, mir-29a directly targeted the phosphatase and tensin homolog (pten) in endothelial cells, leading to activation of the akt pathway. pten knockdown recapitulated the role of mir-29a in endothelial migration, whereas akt inhibition completely attenuated the stimulating role of mir-29a in angiogenesis. taken together, these results reveal a crucial role of a tgf-β-regulated mirna in promoting angiogenesis by targeting pten to stimulate akt activity.",1
"microrna (mirna) is small rna of 20 to 22 nucleotides in length and is stably present in plasma. regulating the expression of mirna taken into cells has been suggested as a general therapeutic approach. we identified the novel anti-inflammatory mirna hsa-mir-766-3p and investigated its biological function in human rheumatoid arthritis (ra) fibroblast-like synoviocyte mh7a cells. to verify the function of the mirna present in the plasma of ra patients, we performed a comprehensive analysis of the mirna expression during abatacept treatment and identified eight mirnas with significantly altered expression levels. among these eight mirnas, mir-766-3p was found to have a clear function. the expression of inflammatory genes in response to inflammatory stimuli was suppressed in mh7a transduced with mir-766-3p. we showed that mir-766-3p indirectly reduced the activation of nf-κb and clarified that this mechanism was partially involved in the reduction of the mineralocorticoid receptor expression. in addition, the inflammatory responses were suppressed in other types of cells. these results indicate the novel function of mir-766-3p, findings that may aid in the development of therapies to suppress inflammation, not only in ra but also in other diseases.",1
"non-small cell lung cancer (nsclc) is a serious threat for human health and life. natural killer (nk) cell-based immunotherapy is a promising anti-tumor strategy in various cancers including nsclc. emerging microrna (mirna) has been identified as vital regulators in nk cell-mediated immunosurveillance process. microrna-130a (mir-130a) level and signal transducers and activators of transcription 3 (stat3) mrna level was measured by rt-qpcr assay. stat3 protein level was determined by western blot assay. ifn-γ and tnf-α secretion was examined by corresponding elisa kits. nk cell cytotoxicity was assessed by lactate dehydrogenase (ldh) assay. the interaction between mir-130a and stat3 was explored by bioinformatics analysis, luciferase reporter assay and rna immunoprecipitation (rip) assay. we found that mir-130a level was notably reduced and stat3 expression was dramatically increased in primary nk cells isolated from nsclc patients. but, mir-130a was highly expressed and stat3 was low expressed in il-2-activated nk-92 cells. functional analysis revealed that mir-130a overexpression potentiated killing ability of nk cells against a549 cells. further investigations unveiled that stat3 was a target of mir-130a and stat3 overexpression abrogated mir-130a-induced improvement in killing activity of nk cells against nsclc cells. in conclusion, mir-130a improved the killing capacity of nk cells against nsclc cells by targeting stat3, laying a foundation for future studies on the roles and molecular basis of mir-130a in nk cell-based immunotherapy against various cancers.",1
"mutational inactivation of the gene wrn causes werner syndrome, an autosomal recessive disease characterized by premature aging, elevated genomic instability and increased cancer incidence. the capacity of enforced telomerase expression to rescue premature senescence of cultured cells from individuals with werner syndrome and the lack of a disease phenotype in wrn-deficient mice with long telomeres implicate telomere attrition in the pathogenesis of werner syndrome. here, we show that the varied and complex cellular phenotypes of werner syndrome are precipitated by exhaustion of telomere reserves in mice. in late-generation mice null with respect to both wrn and terc (encoding the telomerase rna component), telomere dysfunction elicits a classical werner-like premature aging syndrome typified by premature death, hair graying, alopecia, osteoporosis, type ii diabetes and cataracts. this mouse model also showed accelerated replicative senescence and accumulation of dna-damage foci in cultured cells, as well as increased chromosomal instability and cancer, particularly nonepithelial malignancies typical of werner syndrome. these genetic data indicate that the delayed manifestation of the complex pleiotropic of wrn deficiency relates to telomere shortening.",1
"ten aca yeast small nucleolar rnas (snornas) were shown to be required for site-specific synthesis of pseudouridine psi in ribosomal rna. a common secondary folding motif for the snornas and rrna target segments predicts that site selection involves: (1) base pairing of the snorna with complementary rrna elements flanking the site of modification, and (2) identification of a uridine located at a near-constant distance from the snorna aca box. the model is supported by mutations showing that: (1) reducing the complementarity between the snorna and rrna disrupts psi formation, and (2) altering the distance between the aca box and target uridine causes an adjacent uridine to be modified. this discovery implies that most snornas function in targeting nucleotide modification in rrna: ribose methylation for the box c/d snornas and psi formation for the aca snornas.",1
"transcriptional regulation of mirnas that control the pathogenesis of breast cancer remains largely unknown. here, we showed that ionizing radiation, a known breast carcinogen, triggered the differential expression of mir-20b in mammary tissues. we identified several gc-rich consensus binding motifs for the zinc finger transcription factor early growth response-1 (egr1) in mir-20b promoter. mir-20b was upregulated by ir and its upregulation correlated with egr1 expression in the breast cancer cell line hcc1806. therefore, we used hcc1806 cells as a model system to explore the role of egr1 in mir-20b transcription. sirna knockdown of egr1 attenuated mir-20b expression. luciferase assays showed that whereas egr1 stimulated luciferase activity driven by the wild-type mir-20b promoter, this induction was abolished in the mutant mir-20 promoter construct. we noted significant enrichment of egr1 at mir-20b promoter in hcc1806 cells compared with normal human mammary epithelial cells. suppression of mir-20b significantly inhibited hcc1806 cell proliferation and migration, and led to g0/g1 and s phase arrest. in vitro rna-pull down assays indicated that mir-20b targets numerous tumor suppressors, including pten and brca1, which were downregulated in hcc1806. conversely, suppression of mir-20b increased pten and brca1 levels. moreover, immunohistochemical and fish analyses showed that the mir-20b expression correlated significantly with egr1 levels in breast cancer tissues. our findings thus demonstrate for the first time that egr1 is a key player in the transcriptional control of mir-20b, and mir-20b may in turn function as an oncogene by contributing to breast tumorigenesis via tumor suppressor targeting.",1
"mus spretus mice are highly resistant to several types of cancer compared to mus musculus mice. to determine whether differences in microrna (mirna) expression account for some of the differences in observed skin cancer susceptibility between the strains, we performed mirna expression profiling of skin rna for over 300 mirnas. five mirnas, mir-1, mir-124a-3, mir-133a, mir-134, mir-206, were differentially expressed by array and/or qpcr. mir-1 was previously shown to have tumor suppressing abilities in multiple tumor types. we found mir-1 expression to be lower in mouse cutaneous squamous cell carcinomas (csccs) compared to normal skin. based on the literature and our expression data, we performed detailed studies on predicted mir-1 targets and evaluated the effect of mir-1 expression on two murine cscc cell lines, a5 and b9. following transfection of mir-1, we found decreased mrna expression of three validated mir-1 targets, met, twf1 and ets1 and one novel target bag4. decreased expression of ets1 was confirmed by western analysis and by 3' reporter luciferase assays containing wildtype and mutated ets1 3'utr. we evaluated the effect of mir-1 on multiple tumor phenotypes including apoptosis, proliferation, cell cycle and migration. in a5 cells, expression of mir-1 led to decreased proliferation compared to a control mir. mir-1 expression also led to increased apoptosis at later time points (72 and 96 h) and to a decrease in cells in s-phase. in summary, we identified five mirnas with differential expression between cancer resistant and cancer susceptible mice and found that mir-1, a candidate tumor suppressor, has targets with defined roles in tumorigenesis.",1
"the aim of the study is to explore the role of mir-194 in mediating the effect of high-k (hk) intake on romk channel. northern blot analysis showed that mir-194 was expressed in kidney and that hk intake increased while low-k intake decreased the expression of mir-194. real-time pcr analysis further demonstrated that hk intake increased the mir-194 expression in the cortical collecting duct. hk intake decreased the expression of intersectin 1 (itsn1) which enhanced with-no-lysine kinase (wnk)-induced endocytosis of romk. expression of mir-194 mimic decreased luciferase reporter gene activity in hek293 t cells transfected with itsn-1-3'utr containing the complementary seed sequence for mir-194. in contrast, transfection of mir-194 inhibitor increased the luciferase activity. this effect was absent in the cells transfected with mutated 3'utr of itsn1 in which the complimentary seed sequence was deleted. moreover, the inhibition of mir-194 expression increased the protein level of endogenous itsn1 in hek293t cells. expression of mir-194 mimic also decreased the translation of exogenous itsn1 in the cells transfected with the itsn1 containing 3'utr but not with 3'utr-free itsn1. expression of pre-mir-194 increased k currents and romk expression in the plasma membrane in romk-transfected cells. coexpression of itsn1 reversed the stimulatory effect of mir-194 on romk channels. this effect was reversed by coexpression of itsn1. we conclude that mir-194 regulates romk channel activity by modulating itsn1 expression thereby enhancing itsn1/wnk-dependent endocytosis. it is possible that mir-194 is involved in mediating the effect of a hk intake on romk channel activity.",1
"autophagy is an evolutionarily conserved mechanism of cellular self-digestion in which proteins and organelles are degraded through delivery to lysosomes. defects in this process are implicated in numerous human diseases including cancer. to further elucidate regulatory mechanisms of autophagy, we performed a functional screen in search of micrornas (mirnas), which regulate the autophagic flux in breast cancer cells. in this study, we identified the tumour suppressive mirna, mir-101, as a potent inhibitor of basal, etoposide- and rapamycin-induced autophagy. through transcriptome profiling, we identified three novel mir-101 targets, stmn1, rab5a and atg4d. sirna-mediated depletion of these genes phenocopied the effect of mir-101 overexpression, demonstrating their importance in autophagy regulation. importantly, overexpression of stmn1 could partially rescue cells from mir-101-mediated inhibition of autophagy, indicating a functional importance for this target. finally, we show that mir-101-mediated inhibition of autophagy can sensitize breast cancer cells to 4-hydroxytamoxifen (4-oht)-mediated cell death. collectively, these data establish a novel link between two highly important and rapidly growing research fields and present a new role for mir-101 as a key regulator of autophagy.",1
"intrinsic glomerular cells in a diabetic milieu have transcriptional activation of genes that influence the development of diabetic nephropathy. the cellular repertoire of micrornas can regulate translation of these expressed genes into proteins. fibronectin is a key matrix protein accumulated in excess in diabetic nephropathy. here, we exposed cultured human and mouse mesangial cells to high glucose and transforming growth factor-beta to simulate the diabetic milieu. in these conditions in vitro, as well as in mouse diabetic nephropathy models in vivo, microrna-377 was consistently up-regulated relative to controls. through a combination of computational and biological approaches, we identified relevant mir-377 target genes. although fibronectin was induced by mir-377, it was not a direct target of mir-377. however, mir-377 led to reduced expressions of p21-activated kinase and superoxide dismutase, which enhanced fibronectin protein production. thus, overexpression of mir-377 in diabetic nephropathy indirectly leads to increased fibronectin protein production; as such, mir-377 can have a critical role in the pathophysiology of this prevalent human disease.",1
"nutrition during early mammalian development permanently influences health of the adult, including increasing the risk of type 2 diabetes and coronary heart disease. however, the molecular mechanisms underlying such programming are poorly defined. here we demonstrate that programmed changes in mirna expression link early-life nutrition to long-term health. specifically, we show that mir-483-3p is upregulated in adipose tissue from low-birth-weight adult humans and prediabetic adult rats exposed to suboptimal nutrition in early life. we demonstrate that manipulation of mir-483-3p levels in vitro substantially modulates the capacity of adipocytes to differentiate and store lipids. we show that some of these effects are mediated by translational repression of growth/differentiation factor-3, a target of mir-483-3p. we propose that increased mir-483-3p expression in vivo, programmed by early-life nutrition, limits storage of lipids in adipose tissue, causing lipotoxicity and insulin resistance and thus increasing susceptibility to metabolic disease.",1
"the non-coding micrornas (mirna) have tissue- and disease-specific expression patterns. they down-regulate target mrnas, which likely impacts on most fundamental cellular processes. differential expression patterns of mirnas are currently being exploited for identification of biomarkers for early disease diagnosis, prediction of progression for melanoma and other cancers and as promising drug targets, since they can easily be inhibited or replaced in a given cellular context. before successfully manipulating mirnas in clinical settings, their precise expression levels, endogenous functions and thus their target genes have to be determined. mir-211, a melanocyte lineage-specific small non-coding mirna, is located in an intron of trpm1, a target gene of the microphtalmia-associated transcription factor (mitf). by transcriptionally up-regulating trpm1, mitf, which is critical for both melanocyte differentiation and survival and for melanoma progression, indirectly drives the expression of mir-211. expression of this mirna is often reduced in melanoma samples. here, we investigated functional roles of mir-211 by identifying and studying new target genes. we show that mitf-correlated mir-211 expression levels are mostly but not always reduced in a panel of 11 melanoma cell lines and in primary and metastatic melanoma compared to normal melanocytes and nevi, respectively. mir-211 itself only marginally impacted on cell invasion and migration, while perturbation of some new mir-211 target genes, such as ap1s2, sox11, igfbp5, and serinc3 significantly increased invasion. these results and the variable expression levels of mir-211 raise serious doubts on the value of mir-211 as a melanoma tumor-suppressing mirna and/or as a biomarker for melanoma.",1
"aim this study was to investigate the effects and mechanisms of mir-362-3p on regulation of gastric cancer (gc) cell metastasis potential. methods we detected mir-362-3p level in gc and adjacent normal tissues and investigated the relationship with clinicopathological factors. next, we analyzed the level of mir-362-3p expression and cd82 in different differentiated gc cells compared with a normal gastric mucosa cell by rt-pcr and western blot. dual-luciferase reporter assay and western blot confirmed a direct interaction between mir-362-3p and cd82 3'utr. after mir-362-3p and cd82 were silenced in gc cells, we compared the transfected gc cells migration and invasion capacity by transwell assay. in addition, we detected the effects on cells angiogenesis by tube formation assay. western blot was used to detect the impact of cd82 and mir-362-3p on epithelial-to-mesenchymal transition markers in treated gc cells. results level of mir-362-3p expression was much higher in gc cells than in normal gastric mucosa cell, and mir-362-3p expression negatively correlated with cd82 mrna expression in these cell lines. furthermore, mir-362-3p expression induced gc cell metastasis capacity by suppression of cd82 expression. level of mir-362-3p may mediate e-cadherin, n-cadherin, and vimentin expression in gc cells. conclusion this study illuminated that downregulation of mir-362-3p along with the upregulation of cd82 in gc cells resulted in the inhibition of gc migration and invasion. thus, our results suggested that mir-362-3p or cd82 can be exploited as a new potential target for control of gc in the future.",1
"through a computer search of the genome of the yeast saccharomyces cerevisiae, the coding sequences of seven different box c/d antisense small nucleolar rnas (snornas) with the structural hallmarks of guides for rrna ribose methylation have been detected clustered over a 1.4-kb tract in an inter-open reading frame region of chromosome xiii. the corresponding snornas have been positively identified in yeast cells. disruption of the nonessential snorna gene cluster specifically suppressed the seven cognate rrna ribose methylations but did not result in any growth delay under the conditions of yeast culture tested. the seven snornas are processed from a common polycistronic transcript synthesized from an independent promoter, similar to some plant snornas but in marked contrast with their vertebrate functional homologues processed from pre-mrna introns containing a single snorna. processing of the polycistronic precursor requires nucleases also involved in rrna processing, i.e., rnt1p and rat1p. after disruption of the rnt1 gene, the yeast ortholog of bacterial rnase iii, production of the seven mature snornas was abolished, while the polycistronic snorna precursor accumulated. in cells lacking functional rat1p, an exonuclease involved in the processing of both pre-rrna and intron-encoded snornas, several processing intermediates of the polycistronic precursor accumulated. this allowed for the mapping in the precursor of the presumptive rnt1p endonucleolytic cuts which provide entry sites for subsequent exonucleolytic trimming of the pre-snornas. in line with known properties of double-stranded rna-specific rnase iii, pairs of rnt1p cuts map next to each other on opposite strands of long double-helical stems in the secondary structure predicted for the polycistronic snorna precursor.",1
"the mrna encoding the drosophila zn-finger transcription factor nerfin-1, required for cns axon pathfinding events, is subject to post-transcriptional silencing. although nerfin-1 mrna is expressed in many neural precursor cells including all early delaminating cns neuroblasts, the encoded nerfin-1 protein is detected only in the nuclei of neural precursors that divide just once to generate neurons and then only transiently in nascent neurons. using a nerfin-1 promoter-controlled reporter transgene, replacement of the nerfin-1 3' utr with the viral sv-40 3' utr releases the neuroblast translational block and prolongs reporter protein expression in neurons. comparative genomics analysis reveals that the nerfin-1 mrna 3' utr contains multiple highly conserved sequence blocks that either harbor and/or overlap 21 predicted binding sites for 18 different micrornas. to determine the functional significance of these microrna-binding sites and less conserved microrna target sites, we have studied their ability to block or limit the expression of reporter protein in nerfin-1-expressing cells during embryonic development. our results indicate that no single microrna is sufficient to fully inhibit protein expression but rather multiple micrornas that target different binding sites are required to block ectopic protein expression in neural precursor cells and temporally restrict expression in neurons. taken together, these results suggest that multiple micrornas play a cooperative role in the post-transcriptional regulation of nerfin-1 mrna, and the high degree of microrna-binding site evolutionary conservation indicates that all members of the drosophila genus employ a similar strategy to regulate the onset and extinction dynamics of nerfin-1 expression.",1
"micrornas are small 19-25 nucleotides which have been shown to play important roles in the regulation of gene expression in many organisms. downregulation or accumulation of mirnas implies either tumor suppression or oncogenic activation. in this study, differentially expressed hsa-mir-195 in hepatocellular carcinoma (hcc) was identified and analyzed. the prediction was done using a consensus approach of tools. the validation steps were done at two different levels in silico and in vitro. fgf7, ghr, pcmt1, cited2, pex5, pex13, nova1, axin2, and tspyl2 were detected with high significant (p < 0.005). these genes are involved in important pathways in cancer like mapk signaling pathway, jak-stat signaling pathways, regulation of actin cytoskeleton, angiogenesis, wnt signaling pathway, and tgf-beta signaling pathway. in vitro target validation was done for protein-l-isoaspartate (d-aspartate) o-methyltransferase (pcmt1). the co-transfection of pmirglo-pcmt1 and pegp-mir-195 showed highly significant results. firefly luciferase was detected using lumiscensor and t test analysis was done. firefly luciferase expression was significantly decreased (p < 0.001) in comparison to the control. the low expression of firefly luciferase validates the method of target prediction that we used in this work by working on pcmt1 as a target for mir-195. furthermore, the rest of the predicted genes are suspected to be real targets for hsa-mir-195. these target genes control almost all the hallmarks of liver cancer which can be used as therapeutic targets in cancer treatment.",1
"background the involvement of micrornas (mirnas) in neuronal differentiation and synaptic plasticity suggests a role for mirnas in psychiatric disorders; association analyses and functional approaches were used to evaluate the implication of mirnas in the susceptibility for panic disorder. methods case-control studies for 712 single-nucleotide polymorphisms (snps) tagging 325 human mirna regions were performed in 203 spanish patients with panic disorder and 341 control subjects. a sample of 321 anxiety patients and 642 control subjects from finland and 102 panic disorder patients and 829 control subjects from estonia was used as a replica. reporter-gene assays and mirna overexpression experiments in neuroblastoma cells were used to functionally evaluate the spectrum of genes regulated by the associated mirnas. results two snps associated with panic disorder: rs6502892 tagging mir-22 (p conclusions this work represents the first report of a possible implication of mirnas in the etiology of panic disorder.",1
"transforming growth factor-β1 (tgfβ1)-induced differentiation into and the activation of myofibroblasts have been regarded as critical events in benign prostatic hyperplasia (bph); however, the underlying mechanisms of bph pathogenesis remain unclear. microarray profiling, string analysis, kyoto encyclopedia of genes and genomes (kegg) pathway annotation, and gene ontology (go) enrichment analysis were performed to confirm the candidate genes and long non-coding rna (lncrnas) related to bph. collagen type iii (col3a1) was significantly upregulated by tgfβ1 in prostate stromal cells (prscs) and might be involved in dnm3os function in myofibroblasts upon tgfβ1 stimulation. upon tgfβ1 stimulation, col3a1 protein was decreased by dnm3os silencing. mir-29a and mir-29b could directly bind to the dnm3os and col3a1 3' untranslated region (utr)s to negatively regulate their expression, and by serving as a competing endogenous rnas (cerna), dnm3os competed with col3a1 for mir-29a/29b binding, therefore counteracting mir-29a/29b-mediated col3a1 suppression. the effect of dnm3os silencing on ecm components and tgfβ1 downstream signaling was similar to that of the tgfβ1 inhibitor sb431542. mir-361 could target dnm3os and tgfβ1; dnm3os competed for mir-361 binding to counteract mir-361-mediated tgfβ1 suppression. in conclusion, we identified dnm3os as a specifically-upregulated lncrna upon tgfβ1 stimulation in prscs; by serving as a cerna for the mir-29a/29b cluster and mir-361, dnm3os eliminated mirna-mediated suppression of col3a1 and tgfβ1, thereby promoting tgfβ1-induced prsc transformation into myofibroblasts.",1
"the prevailing model of microrna function is that the ""seed region"" (nt 2-8) is sufficient to mediate target recognition and repression. however, numerous recent studies have challenged this model, either by demonstrating extensive 3' pairing between physically defined mirna-mrna pairs or by showing in caenorhabditis elegans that disrupted 3' pairing can result in impaired function in vivo. to test the importance of mirna 3' pairing in a mammalian system in vivo, we engineered a mutant murine mir-146a allele in which the 5' half of the mature microrna retains its wild-type sequence, but the 3' half's sequence has been altered to robustly disrupt predicted pairing to this latter region. mice homozygous or hemizygous for this mutant allele are phenotypically indistinguishable from wild-type controls and do not recapitulate any of the immunopathology previously described for mir-146a -null mice. our results indicate that 3' pairing is dispensable for the established myeloid function of this key mammalian microrna.",1
"abnormal proliferation and migration of vascular smooth muscle cells (vsmcs) is a critical process in various cardiovascular diseases such as coronary artery disease (cad), atherosclerosis, stroke, and hypertension. micrornas (mirnas) are small, short, and noncoding rnas that inhibit gene expression through binding to the 3'-utr (3' untranslated regions) of target gene mrnas. we showed that the expression of mir-448 was upregulated in vsmcs from coronary atherosclerotic plaques compared with normal coronary artery tissues. we also found that pdgf-bb promoted vsmcs proliferation and could induce mir-448 expression. ectopic mir-448 expression induced vsmcs proliferation. overexpression of mir-448 induced ki-67 mrna and protein expression. moreover, we identified mef2c was a direct target of mir-448 in vsmcs. overexpression of mir-448 promoted vsmcs migration. furthermore, overexpression of mef2c decreased mir-448-induced vsmcs proliferation and migration. these evidences suggested that mir-448 played an important role in the proliferation and migration of vsmcs.",1
"micrornas are involved in various biological processes by regulating the degradation or repressing the translation of target genes. in this study, the target genes of mir-29b were analyzed and predicted by bioinformatics. and lipoprotein lipase (lpl) and thymine dna glycosylase (tdg) were selected for further validation by dual luciferase reporter assay. in addition, we investigated the effects of mir-29b on triglyceride synthesis and mammary epithelial cell (mec) apoptosis. the result showed that luciferase activity was significantly lower in cells that mir-29b cotransfected with lpl and tdg gene reporter vectors (pmir-rb-report-lpl-wt, pmir-rb-report-tdg-wt) than in cells of mir-29b cotransfected with gene reporter vectors (pmir-rb-report-lpl-mut and pmir-rb-report-lpl-si; pmir-rb-report-tdg-mut and pmir-rb-report-tdg-si) (p < 0.05), indicating that target sites existed in 3'utr of lpl and tdg. furthermore, the expressions of mir-29b were negatively correlated with levels of mrna and protein of lpl and tdg gene using quantitative real-time polymerase chain reaction and western blot analysis, suggesting that mir-29b might play an important role in regulation of lpl and tdg gene expression. finally, mir-29b promoted triglyceride production and suppressed apoptosis in mecs, which might be attributed to the expressions of target genes lpl and tdg.",1
"micrornas (mirnas) bind to specific messenger rna targets to posttranscriptionally modulate their expression. understanding the regulatory relationships between mirnas and targets remains a major challenge. many mirnas reduce expression of their targets to inconsequential levels. it has also been proposed that mirnas might adjust target expression to an optimal level. here we analyze the consequences of mutating the conserved mirna mir-8 in drosophila. we identify atrophin as a direct target of mir-8. mir-8 mutant phenotypes are attributable to elevated atrophin activity, resulting in elevated apoptosis in the brain and in behavioral defects. reduction of atrophin levels in mir-8-expressing cells to below the level generated by mir-8 regulation is detrimental, providing evidence for a ""tuning target"" relationship between them. drosophila atrophin is related to the atrophin family of mammalian transcriptional regulators, implicated in the neurodegenerative disorder drpla. the regulatory relationship between mir-8 and atrophin orthologs is conserved in mammals.",1
"cancer progression has similarities with the process of epithelial-to-mesenchymal transition (emt) found during embryonic development, during which cells down-regulate e-cadherin and up-regulate vimentin expression. by evaluating the expression of 207 micrornas (mirnas) in the 60 cell lines of the drug screening panel maintained by the nation cancer institute, we identified the mir-200 mirna family as an extraordinary marker for cells that express e-cadherin but lack expression of vimentin. these findings were extended to primary ovarian cancer specimens. mir-200 was found to directly target the mrna of the e-cadherin transcriptional repressors zeb1 (tcf8/deltaef1) and zeb2 (smad-interacting protein 1 /zfxh1b). ectopic expression of mir-200 caused up-regulation of e-cadherin in cancer cell lines and reduced their motility. conversely, inhibition of mir-200 reduced e-cadherin expression, increased expression of vimentin, and induced emt. our data identify mir-200 as a powerful marker and determining factor of the epithelial phenotype of cancer cells.",1
"the 3' untranslated region (utr) of bamboo mosaic potexvirus (bamv) rna was identified to fold into a tertiary structure comprising a cloverleaf-like structure designated abc domain followed by a major stem-loop d, which in turn is followed by a pseudoknot e and a poly(a) tail. the coat protein accumulation level of the mutant, bamv40a/deltaabc, lacking abc domain was just 15% that of wild-type when inoculated into protoplasts of nicotiana benthamiana. this suggested that abc domain might play an important role in bamv rna replication. to define the precise role of each of the three stem-loops of abc domain in rna replication, three mutants bamv40a/deltaa, -/deltab, and -/deltac each lacking stem-loop a, b, and c, respectively, were created. our results showed that accumulation of viral products of mutants bamv40a/deltab and -/deltac were not as efficient as wild-type. on the contrary, level of accumulation of viral products of bamv/deltaa was similar to that of wild-type in protoplasts and inoculated leaves. interestingly, the accumulation of viral products was not as efficient as that of wild-type in systemic leaves, implying that stem-loop a is dispensable for replication, but signifies a role in systemic accumulation. using uv cross-linking and competition experiments, it was demonstrated that the e. coli expressed helicase domain of bamv orf1 can preferentially interact with the abc domain.",1
"accumulation of non-metabolizable glucose-phosphate in escherichia coli is growth inhibitory and induces a specific stress response. this is sensed and coordinated by a transcription factor sgrr that in turn activates expression of the primary effector of the stress response, a small regulatory rna, sgrs. this rna negatively regulates the translation and stability of the ptsg mrna, which encodes the major glucose transporter of e. coli. the effect of sgrs on ptsg mrna occurs through a base-pairing mechanism facilitated by the rna chaperone hfq. other host factors required for the regulation by sgrs include the endonuclease rnase e and components of the rna degradosome, particularly enolase, a glycolytic enzyme whose role in rna degradation is currently not understood. there are many unanswered questions regarding the physiology of glucose-phosphate stress, including the cellular signals and targets involved. however, it is clear that the small rna sgrs is required for adaptation to stress. the current model is that sgrs promotes recovery by stopping the synthesis of glucose transport proteins, which in turn limits the accumulation of toxic sugar-phosphates.",1
"prdm1/blimp-1, a master regulator for b cell terminal differentiation, is a putative tumor suppressor in diffuse large b cell lymphomas (dlbcl). inactivating mutations of prdm1 have been previously identified in a subset of nongerminal center b cell-like (gcb) dlbcl. we investigated the presence of alternative mechanisms of down-regulating prdm1 in a cohort of 25 primary dlbcl and six dlbcl cell lines. while some dlbcl, predominantly the gcb-type, showed low levels of both prdm1alpha mrna and protein, presumably as a result of direct transcription repression, discordant expressions between the two were identified in a subset of dlbcl without prdm1 mutations, the primarily non-gcb type, consistent with translational down-regulation. this subset of dlbcl exhibits relatively high prdm1alpha mrna levels but low levels of prdm1. data obtained from expression analysis, luciferase reporter assays, and transfection experiments support a role of targeting of prdm1 by microrna let-7 family in mediating this down-regulation. let-7, in particular let-7b, is overexpressed in dlbcl relative to normal gcb cells, suggesting that it is deregulated. thus, abnormal epigenetic down-regulation of prdm1 by let-7 and other micrornas may represent an alternative mechanism of reducing normal prdm1 function in a subset of dlbcl with relatively high prdm1alpha mrna expression and unmutated prdm1. these findings provide further evidence for an important role of impairment of terminal b cell differentiation in dlbcl pathogenesis.",1
"high glycolysis, well known as ""warburg effect,"" is frequently observed in a variety of cancers. whether the deregulation of mirnas contributes to the warburg effect remains largely unknown. because mirna regulates gene expression at both mrna and protein levels, we constructed a gene functional association network, which allows us to detect the gene activity instead of gene expression, to integratively analyze the microarray data for gene expression and mirna expression profiling and identify glycolysis-related gene-mirna pairs deregulated in cancer. hexokinase 2 (hk2), coding for the first rate-limiting enzyme of glycolysis, is among the top list of genes predicted and potentially regulated by multiple mirnas including mir-143. interestingly, mir-143 expression was inversely associated with hk2 protein level but not mrna level in human lung cancer samples. mir-143, down-regulated by mammalian target of rapamycin activation, reduces glucose metabolism and inhibits cancer cell proliferation and tumor formation through targeting hk2. collectively, we have not only established a novel methodology for gene-mirna pair prediction but also identified mir-143 as an essential regulator of cancer glycolysis via targeting hk2.",1
"previous studies in mice have reported five different micrornas (mirnas; mir-219-1/132/183/96/182) to be modulators of the endogenous circadian clock and have presented experimental evidence for some of the genes involved in the molecular clock machinery as target sites. moreover, disruption of circadian rhythms has long been implicated in the pathophysiology of major depression (md). we investigated these mirnas and some of their target sites at the sequence and functional levels as possible predisposing factors for susceptibility to md and related chronobiological subphenotypes. mutational screening was performed in a sample of 359 md patients and 341 control individuals. we found a significant association between the t allele of the rs76481776 polymorphism in the pre-mir-182 and late insomnia in md patients. previous studies have reported an association between insomnia and clock gene, a predicted mir-182 target site. a significant overexpression of mir-182 was detected by quantitative real-time polymerase chain reaction in cells transfected with the mutated form of the pre-mir-182 when compared with wild-type form. moreover, a significant reduction in luciferase activity of plasmids with 3' utr of adcy6, clock and dsip genes was shown when transfecting cells with the mutated form of pre-mir-182 compared with cells that did not express mir-182. these data indicate that abnormal processing of pre-mir-182 in patients carrying the t allele of the rs76481776 polymorphism may contribute to the dysregulation of circadian rhythms in md patients with insomnia, which could influence expression levels of the mature form of mir-182 and might increase downregulation in some of its target genes.",1
"the transcription factor spi-1 (pu.1) has a central role in regulating myeloid gene expression during hematopoietic development and its overexpression has been implicated in erythroleukemic transformation. thus regulation of spi-1 expression has broad significance for hematopoietic development. a comparison of human and murine cdna sequences demonstrates that the 5'-untranslated region (5'-utr) of spi-1 mrna is as highly conserved as the coding region (87% identical), suggesting that this sequence may be involved in regulating expression of this protein. the experiments presented in this manuscript provide evidence that the 5'-utr of spi-1 contains extensive secondary structure, including three stem-loops that precede the aug codon. analysis of the in vitro transcribed spi-1 5'-utr by partial nuclease digestion sensitivity is consistent with the existence of two of these stem-loops. the 5'-utr decreased translation of spi-1 transcripts in reticuloctye lysates 8- to 10-fold. a series of partial deletions of the 5'-utr identified the sequence corresponding to the stem-loop most proximal to the initiating aug codon as sufficient for inhibition of translation. however, the effect of the 5'-utr on translation in vivo was negligible and resulted in only a slight reduction in the number of ribosomes that became associated with the mrna. further, this sequence had no affect on expression of luciferase. the disparity between in vivo and in vitro effects, coupled with the observation that endogenous spi-1 mrna is wholly associated with polysomes in mel cells, suggests that additional cellular mechanisms contribute to regulation of spi-1 expression in these cells or that conservation of these sequences serves a function that is independent of translation.",1
"micrornas (mirnas), noncoding rnas 21-25 nucleotides in length, regulate gene expression primarily at the posttranscriptional level. growing evidence suggests that mirnas are aberrantly expressed in many human cancers, and that they play significant roles in carcinogenesis and cancer progression. a search for mirnas with a tumor-suppressive function in esophageal squamous cell carcinoma (escc) was performed using the mirna expression signatures obtained from escc clinical specimens. a subset of 15 mirnas was significantly downregulated in escc. a comparison of mirna signatures from escc and our previous report identified 4 mirnas that are downregulated in common (mir-145, mir-30a-3p, mir-133a and mir-133b), suggesting that these mirnas are candidate tumor suppressors. gain-of-function analysis revealed that 3 transfectants (mir-145, mir-133a and mir-133b) inhibit cell proliferation and cell invasion in escc cells. these mirnas (mir-145, mir-133a and mir-133b), which have conserved sequences in the 3'utr of fscn1 (actin-binding protein, fascin homolog 1), inhibited fscn1 expression. the signal from a luciferase reporter assay was significantly decreased at 2 mir-145 target sites and 1 mir-133a/b site, suggesting both mirnas directly regulate fscn1. an fscn1 loss-of-function assay found significant cell growth and invasion inhibition, implying an fscn1 is associated with escc carcinogenesis. the identification of tumor-suppressive mirnas, mir-145, mir-133a and mir-133b, directly control oncogenic fscn1 gene. these signal pathways of escc could provide new insights into potential mechanisms of escc carcinogenesis.",1
"the mutation frequency of turnip crinkle virus can increase 12-fold without inducing error catastrophe. lesions in a hairpin repressor frequently reverted and led to second-site alterations biased for specific mutations. these results suggest that the hairpin may also function as an rna chaperone to properly fold the rna-dependent rna polymerase.",1
"micrornas (mirnas) are regulators of differentiation and development of inner ear cells. mutations in mirnas lead to deafness in humans and mice. among inner ear pathologies, inflammation may lead to structural and neuronal defects and eventually to hearing loss and vestibular dysfunction. while the genetic factors of these pathways have not been defined, autoimmunity participates in these processes. we report that inflammatory stimuli in the inner ear induce activation of the innate immune system via mir-224 and pentraxin 3 (ptx3). mir-224 is a transcriptional target of nuclear factor κb, a key mediator of innate immunity. ptx3 is a regulator of the immune response. it is released in response to inflammation and regulated by nuclear factor κb. we show that mir-224 and ptx3 are expressed in the inner ear and we demonstrate that mir-224 targets ptx3. as a model of the innate immune response, we injected lipopolysaccharide into the scala tympani of mouse inner ears. this resulted in changes in the levels of mir-224 and ptx3, in addition to activation of the complement system, as measured by immune cell infiltration and activated c3. this suggests that while mir-224 regulates ptx3 under normal conditions, upon inflammation, both are recruited to offer a front line of defense in acting as responders to inflammation in the inner ear. mir-224 diminishes the innate immune response by down-regulating ptx3 expression, while ptx3 stimulates the innate immune response. an understanding of the molecular components of the inflammatory pathway may help develop therapeutics for reducing inflammation associated with inner ear injury.",1
"alzheimer's disease (ad) is a progressive neurodegenerative disease characterized by β-amyloid deposits and neurofibrillary tangles consisting of hyperphosphorylated tau protein. increasing evidence has revealed that micrornas (mirnas) are implicated in the pathogenesis of ad. however, the effect of mirnas on abnormal tau phosphorylation remains largely unclear so far. in this study, we investigated the role of mir-106b in tau phosphorylation and identified a new molecular mechanism of the hyperphosphorylation of tau. the results of qrt-pcr showed that the expression level of mir-106b was decreased, but fyn was increased in the temporal cortex of ad patients. overexpression of mir-106b inhibited aβ1-42-induced tau phosphorylation at tyr18 in sh-sy5y cells stably expressing tau (sh-sy5y/tau), whereas no changes were observed in tau phosphorylation at ser396/404. dual-luciferase reporter gene assay validated that fyn was a direct target gene of mir-106b. in addition, western blot analysis revealed that fyn protein expression was suppressed when sh-sy5y cells were transfected with mir-106b mimics. endogenous fyn expression was knockdown by transfection with a small interfering rna specific for fyn (si-fyn). the phosphorylation level of tau at tyr 18 was decreased in the si-fyn group compared with the negative control group, but the inhibitory effect of si-fyn on tau phosphorylation was attenuated when mir-106b expression was inhibited. taken together, these data suggest that mir-106b inhibits aβ1-42-induced tau phosphorylation at tyr18 by targeting fyn. our findings extend the knowledge about the regulation of tau phosphorylation and the regulatory mechanism of fyn gene expression.",1
"the study of human micrornas is seriously hampered by the lack of proper tools allowing genome-wide identification of mirna targets. we performed ribonucleoprotein immunoprecipitation-gene chip (rip-chip) using antibodies against wild-type human ago2 in untreated hodgkin lymphoma (hl) cell lines. ten to thirty percent of the gene transcripts from the genome were enriched in the ago2-ip fraction of untreated cells, representing the hl mirna-targetome. in silico analysis indicated that approximately 40% of these gene transcripts represent targets of the abundantly co-expressed mirnas. to identify targets of mir-17/20/93/106, rip-chip with anti-mir-17/20/93/106 treated cells was performed and 1189 gene transcripts were identified. these genes were analyzed for mir-17/20/93/106 target sites in the 5'-utrs, coding regions and 3'-utrs. fifty-one percent of them had mir-17/20/93/106 target sites in the 3'-utr while 19% of them were predicted mir-17/20/93/106 targets by targetscan. luciferase reporter assay confirmed targeting of mir-17/20/93/106 to the 3'-utrs of 8 out of 10 genes. in conclusion, we report a method which can establish the mirna-targetome in untreated human cells and identify mirna specific targets in a high throughput manner. this approach is applicable to identify mirna targets in any human tissue sample or purified cell population in an unbiased and physiologically relevant manner.",1
"most eukaryotic mrnas require the cap-binding complex elf4f for efficient initiation of translation, which occurs as a result of ribosomal scanning from the capped 5' end of the mrna to the initiation codon. a few cellular and viral mrnas are translated by a cap and end-independent mechanism known as internal ribosomal entry. the internal ribosome entry site (ires) of classical swine fever virus (csfv) is approximately 330 nt long, highly structured, and mediates internal initiation of translation with no requirement for elf4f by recruiting a ribosomal 43s preinitiation complex directly to the initiation codon. the key interaction in this process is the direct binding of ribosomal 40s subunits to the ires to form a stable binary complex in which the initiation codon is positioned precisely in the ribosomal p site. here, we report the results of analyses done using enzymatic footprinting and mutagenesis of the ires to identify structural components in it responsible for precise binding of the ribosome. residues flanking the initiation codon and extending from nt 363-391, a distance equivalent to the length of the 40s subunit mrna-binding cleft, were strongly protected from rnase cleavage, as were nucleotides in the adjacent pseudoknot and in the more distal subdomain iiid1. ribosomal binding and ires-mediated initiation were abrogated by disruption of helix 1b of the pseudoknot and very severely reduced by mutation of the protected residues in iiid1 and by disruption of domain iiia. these observations are consistent with a model for ires function in which binding of the region flanking the initiation codon to the decoding region of the ribosome is determined by multiple additional interactions between the 40s subunit and the ires.",1
"the insulin-like growth factor (igf)-1 signaling is relevant in regulating cell growth and cytokine secretions by glioblastomas. micrornas determine the cell fate in glioblastomas. however, relationships between igf-1 signaling and mirnas in glioblastoma pathogenesis are still unclear. our aim was to validate the igf-1-mediated mrna/mirna regulatory network in glioblastomas. using in silico analyses of mrna array and rna sequencing data from the cancer genome atlas (tcga), we identified 32 core enrichment genes that were highly associated with igf-1-promoted cytokine-cytokine receptor interactions. to investigate the igf-1-downregulated mirna signature, microarray-based approaches with igf-1-treated u87-mg cells and array data in tcga were used. four mirnas, including microrna (mir)-9-5p, mir-9-3p, mir-181d, and mir-130b, exhibited an inverse correlation with igf-1 levels. the mir-181d, that targeted the most igf-1-related cytokine genes, was significantly reduced in igf-1-treated glioma cells. statistical models incorporating both high-igf-1 and low-mir-181d statuses better predicted poor patient survival, and can be used as an independent prognostic factor in glioblastomas. the c-c chemokine receptor type 1 (ccr1) and interleukin (il)-1b demonstrated inverse correlations with mir-181d levels and associations with patient survival. mir-181d significantly attenuated igf-1-upregulated ccr1 and il-1b gene expressions. these findings demonstrate a distinct role for igf-1 signaling in glioma progression via mir-181d/cytokine networks.",1
"micrornas (mirnas) are deregulated in a variety of human cancers, including neuroblastoma, the most common extracranial tumor of childhood. we previously reported a signature of 42 mirnas to be highly predictive of neuroblastoma outcome. one mirna in this signature, mir-542, was downregulated in tumors from patients with adverse outcome. reanalysis of quantitative pcr and next-generation sequencing transcript data revealed that mir-542-5p as well as mir-542-3p expression is inversely correlated with poor prognosis in neuroblastoma patients. we, therefore, analyzed the function of mir-542 in neuroblastoma tumor biology. ectopic expression of mir-542-3p in neuroblastoma cell lines reduced cell viability and proliferation, induced apoptosis and downregulated survivin. survivin expression was also inversely correlated with mir-542-3p expression in primary neuroblastomas. reporter assays confirmed that mir-542-3p directly targeted survivin. downregulating survivin using sirna copied the phenotype of mir-542-3p expression in neuroblastoma cell lines, while cdna-mediated ectopic expression of survivin partially rescued the phenotype induced by mir-542-3p expression. treating nude mice bearing neuroblastoma xenografts with mir-542-3p-loaded nanoparticles repressed survivin expression, decreased cell proliferation and induced apoptosis in the respective xenograft tumors. we conclude that mir-542-3p exerts its tumor suppressive function in neuroblastoma, at least in part, by targeting survivin. expression of mir-542-3p could be a promising therapeutic strategy for treating aggressive neuroblastoma.",1
"micrornas (mirnas) are short noncoding rnas that regulate a broad spectrum of biological processes, including immune responses. although the contributions of mirnas to the function of immune cells are beginning to emerge, their specific roles remain largely unknown. il-33 plays an important role in macrophage activation for innate host defense and proinflammatory responses. in this study, we report that mir-487b can suppress the levels of mrna and protein for il-33 during the differentiation of bone marrow-derived macrophages (bmdms). this results in inhibition of il-33-induced expression of ag-presenting and costimulatory molecules and proinflammatory mediators. a luciferase assay showed that mir-487b binds to the il-33 3'-untranslated region. we also confirmed that il-33 directly promotes the activation of bmdms by increasing the expression of mhc class i, mhc class ii, cd80/cd86, and inducible no synthase (inos) in a dose-dependent manner. exposure of bmdms to the tlr4 ligand, lps, decreased mir-487b expression, increased il-33 transcript levels, and induced the production of proinflammatory mediators (e.g., inos, il-1β, il-6, and tnf-α). treatment with a specific inhibitor of mir-487b function also resulted in increased levels of il-33 mrna, which augmented lps-induced expression of these inflammatory mediators in macrophages. collectively, our results indicate that mir-487b plays a negative regulatory role in macrophages by controlling the levels of il-33 transcript and protein to fine-tune innate immune host defense and proinflammatory responses of these cells. thus, mir-487b plays an important role in the regulation of macrophage homeostasis and activation by targeting il-33 transcripts.",1
"yeast u2 small nuclear rna (snrna) contains three pseudouridines (psi35, psi42, and psi44). pus7p and pus1p catalyze the formation of psi35 and psi44, respectively, but the mechanism of psi42 formation remains unclear. using a u2 substrate containing a single (32)p radiolabel at position 42, we screened a gst-orf library for pseudouridylase activity. surprisingly, we found a psi42-specific pseudouridylase activity that coincided with nhp2p, a protein component of a box h/aca sno/scarnp (small nucleolar/cajal body-specific ribonucleoprotein). when isolated by tandem affinity purification (tap), the other protein components of the h/aca sno/scarnp also copurified with the pseudouridylase activity. micrococcal nuclease-treated tap preparations were devoid of pseudouridylase activity; however, activity was restored upon addition of rnas from tap preparations. pseudouridylation reconstitution using rnas from a box h/aca rna library identified snr81, a snorna known to guide rrna pseudouridylation, as the psi42-specific guide rna. using the snr81-deletion strain, nhp2p- or cbf5p-conditional depletion strain, and a cbf5 mutation strain, we further demonstrated that the pseudouridylase activity is dependent on snr81 snornp in vivo. our data indicate that snrna pseudouridylation can be catalyzed by both rna-dependent and rna-independent mechanisms.",1
"mgmt expression is a critical determinant for therapeutic resistance to dna alkylating agents. we previously demonstrated that mgmt expression is post-transcriptionally regulated by mir-181d and other mirnas. here, we performed a genome-wide screen to identify mgmt regulating mirnas. candidate mirnas were further tested for inverse correlation with mgmt expression in clinical specimens. we identified 15 candidate mirnas and characterized the top candidate, mir-603. transfection of mir-603 suppressed mgmt mrna/protein expression in vitro and in vivo; this effect was reversed by transfection with antimir-603. mir-603 affinity-precipitated with mgmt mrna and suppressed luciferase activity in an mgmt-3'utr-luciferase assay, suggesting direct interaction between mir-603 and mgmt 3'utr. mir-603 transfection enhanced the temozolomide (tmz) sensitivity of mgmt-expressing glioblastoma cell lines. importantly, mir-603 mediated mgmt suppression and tmz resistance were reversed by expression of an mgmt cdna. in a collection of 74 clinical glioblastoma specimens, both mir-603 and mir-181d levels inversely correlated with mgmt expression. moreover, a combined index of the two mirnas better reflected mgmt expression than each individually. these results suggest that mgmt is co-regulated by independent mirnas. characterization of these mirnas should contribute toward strategies for enhancing the efficacy of dna alkylating agents.",1
"instigated by the discovery of adult cardiac progenitor cells, cell replacement therapy has become a promising option for myocardial repair in the past decade. we have previously shown that human-derived cardiomyocyte progenitor cells (hcmpcs) can differentiate into cardiomyocyte-, endothelial-, and smooth muscle-like cells in vitro, and in vivo after transplantation in a mouse model of myocardial infarction, resulting in preservation of cardiac function. however, to allow successful repopulation of the injured myocardium, it is of key importance to restore myocardial perfusion by the formation of new vasculature. several studies have shown that micrornas regulate vascular differentiation of different stem/progenitor cells. here, we show that mir-1 is upregulated in hcmpcs during angiogenic differentiation. upregulation of mir-1 enhanced the formation of vascular tubes on matrigel and within a collagen matrix, and also increased hcmpc motility, as shown by planar and transwell migration assays. by western blot, qrt-pcr and luciferase reporter assays, mir-1 was found to directly target and inhibit the expression of sprouty-related evh1 domain-containing protein 1 (spred1). knocking down spred1 phenocopies the functional effect seen for mir-1 upregulation. using a systems biology approach, we found that in hcmpcs, mir-1 is proposed to control a network of genes predominantly involved in angiogenesis-related processes, including the spred1 pathway. our data shows that by upregulation of mir-1, the angiogenic differentiation of hcmpcs can be enhanced, which may be used as a new therapeutic approach to improve the efficiency of cell-based therapy for cardiac regeneration by enhancing the formation of new vasculature.",1
"in the current investigation, we analysed all the known small nucleolar rnas (snornas) in the deeply branching protozoan parasite giardia lamblia for potential micrornas (mirnas) that might be derived from them. two putative mirnas have since been identified by northern blot, primer extension, 3' race and co-immunoprecipitation with giardia argonaute (glago), and designated mir6 and mir10. giardia dicer (gldcr) is capable of processing the snornas into the corresponding mirnas in vitro. potential mir6 and mir10 binding sites in giardia genome were predicted bio-informatically. a mir6 binding site was found at the 3' untranslated regions (utr) of 44 variant surface protein (vsp) genes, whereas a mir10 binding site was identified at the 3' end of 159 vsp open-reading frames. thirty-three of these vsp genes turned out to contain binding sites for both mir6 and mir10. a reporter mrna tagged with the 3' end of vsp1267, which contains the target sites for both mirnas, was translationally repressed by both mirnas in giardia. episomal expression of an n-terminal c-myc tagged vsp1267 was found significantly repressed by introducing either mir6 or mir10 into the cells and the repressive effects were additive. when the 2'-o-methyl antisense oligos (asos) of either mir6 or mir10 was introduced, however, there was an enhancement of tagged vsp1267 expression suggesting an inhibition of the repressive effects of endogenous mir6 or mir10 by the asos. of the total 220 vsp genes in giardia, we have now found 178 of them carrying putative binding sites for all the mirnas that have been currently identified, suggesting that mirnas are likely the regulators of vsp expression in giardia.",1
"micrornas(mir) play an important role in cell growth, differentiation, proliferation and apoptosis, which can function either as oncogenes or as tumor suppressors in their effect on tumor growth. smad3 is often underexpressed in very diverse types of malignant tumors and has an important tumor suppressive function; however, the underlying mechanism in solid cancer including glioblastomas(gbm) is not fully explored. the aim of this study is to explore the role of mir-92b in regulation of smad3 in gbm. in our study, we found that mir-92b expression was significantly increased in gbm tissues compared with normal brain tissues by q-rt-pcr and in situ hybridization (p<0.01). however, expression of smad3 in gbm samples was significantly reduced compared with normal brain tissues by western blot and immunohistochemistry (p<0.05). using 3'utr luciferase reporter gene assay, we found that mir-92b directly affected smad3 expression in gbm cells by targeting the 3'-untranslated region. silencing of mir-92b was able to significantly inhibit the viability of gbm cells in three gbm cell lines through up-regulating the tgf-beta/smad3/p21 signaling pathway in vitro. furthermore, the tumor growth and the weight of u87 cells in the mir-92b inhibitor group were significantly inhibited when compared with that of the control group in vivo. our data demonstrated that mir-92b may be considered as a tumor oncogene to promote gbm cell proliferation, and thus may serve as a potentially useful target for development of mirna-based therapies in the future.",1
"objective hsa-mir-206, a microrna, was found to be able to switch subtypes by targeting er-α in breast cancer. however, there are few studies addressing the role of mir-206 in triple-negative breast cancer (tnbc). the purpose of this study was to evaluate the metastatic-regulatory ability of mir-206 in tnbc. materials and methods we treated two tnbc lines (mda-mb-231 and mda-mb-436) with mir-206 mimics, inhibitors and paired controls and examined the in vitro and in vivo functions of mir-206 via the degradation of connexin43 (cx43). a luciferase reporter assay was used to identify the binding site of gja1 (gap junctional intercellular communication) (cx43) and mir-206. furthermore, quantitative rt-pcr was used to evaluate mir-206 expression in 77 breast cancer samples to determine the association with lymph node status and cx43 expression. results up-regulation of mir-206 in tnbc contributed to a decreasing metastatic potential, as demonstrated by a reduction of cell viability and proliferation, decreased cell migration and invasion, lower expression levels of matrix metalloproteinase (mmp)-2, mmp-9 and a higher expression level of breast cancer metastatic suppressor (brms)-1. in vitro dual luciferase assays showed gja1 (cx43) is a target of mir-206. quantitative rt-pcr was conducted to evaluate mir-206 expression in 77 breast cancer samples to determine the associations between mir-206 levels and both lymph node status and cx43 expression. restoring cx43 expression positively regulated cell adhesion and gja1, which may facilitate metastasis. mir-206 significantly attenuated the proliferation and metastatic potential of cancer cells but did not inhibit tumor onset in a mouse xenograft model because of the dual function of cx43. conclusions our results suggest hsa-mir-206 may repress the tumor proliferation and invasion in breast cancer by targeting cx43.",1
"the sprouting of new blood vessels by angiogenesis is critical in vascular development and homeostasis. aberrant angiogenesis leads to enormous pathological conditions such as ischemia and cancer. micrornas (also known as mirnas or mirs) play key roles in regulation of a range of cellular processes by posttranscriptional suppression of their target genes. recently, new studies have indicated that mirnas are involved in certain angiogenic settings and signaling pathways use these non-coding rnas to promote or suppress angiogenic processes. herein, vegfr2 and fgfr1 were identified as mir-129-1 and mir-133 targets using bioinformatic algorithms, respectively. afterwards, using luciferase reporter assay and gene expression analysis at both mrna and protein levels, vegfr2 and fgfr1 were validated as mir-129-1 and mir-133 targets. in addition, we showed that mir-129-1 and mir-133 suppress angiogenesis properties such as proliferation rate, cell viability, and migration activity of human umbilical vein endothelial cells (huvec) in vitro. we conclude that these mirnas can suppress key factors of angiogenesis by directly targeting them. these results have important therapeutic implications for a variety of diseases involving deregulation of angiogenesis, including cancer.",1
"production of functional proteins requires multiple steps, including gene transcription and posttranslational processing. micrornas (mirnas) can regulate individual stages of these processes. despite the importance of the cystic fibrosis transmembrane conductance regulator (cftr) channel for epithelial anion transport, how its expression is regulated remains uncertain. we discovered that mirna-138 regulates cftr expression through its interactions with the transcriptional regulatory protein sin3a. treating airway epithelia with an mir-138 mimic increased cftr mrna and also enhanced cftr abundance and transepithelial cl(-) permeability independent of elevated mrna levels. an mir-138 anti-mir had the opposite effects. importantly, mir-138 altered the expression of many genes encoding proteins that associate with cftr and may influence its biosynthesis. the most common cftr mutation, δf508, causes protein misfolding, protein degradation, and cystic fibrosis. remarkably, manipulating the mir-138 regulatory network also improved biosynthesis of cftr-δf508 and restored cl(-) transport to cystic fibrosis airway epithelia. this mirna-regulated network directs gene expression from the chromosome to the cell membrane, indicating that an individual mirna can control a cellular process more broadly than recognized previously. this discovery also provides therapeutic avenues for restoring cftr function to cells affected by the most common cystic fibrosis mutation.",1
"ovarian cancer is commonly treated with cisplatin and paclitaxel combination chemotherapy; however, ovarian cancer cells often develop resistance to these drugs. increasingly, micrornas (mirnas) including mir-873 have been implicated in drug resistance in many cancers, but the role of mir-873 in ovarian cancer remains unknown. mtt cell viability assays revealed that the sensitivities of ovarian cancer lines to cisplatin and paclitaxel increased following transfection with mir-873 (p < 0.05). after predicting the mir-873 binding region in the 3'-untranslated region of abcb1, dual-luciferase reporter assay confirmed this prediction. rt-pcr and western blotting revealed that mdr1 expression was significantly downregulated after transfection with mir-873 and upregulated after transfection with anti-mir-873 at both mrna and protein levels compared to negative controls (p < 0.05). experiments in a mouse xenograft model confirmed that intratumoral administration of mir-873 could enhance the efficacy of cisplatin in inhibiting tumor growth in ovarian cancer in vivo (p < 0.05). abcb1 overexpression reduced sensitivities of ovarian cancer lines ovcar3 and a2780 to cisplatin and paclitaxel, which can be reversed by mir-873 mimic transfection (p < 0.05). in summary, we demonstrated that overexpression of mir-873 increased the sensitivity of ovarian cancer cells to cisplatin and paclitaxel by targeting mdr1 expression. our findings suggest that combination therapies with chemotherapy agents and mir-873 may suppress drug resistance in ovarian cancer.",1
"the proteins msl1, msl2, msl3, mle, and mof and noncoding rnas rox1 and rox2 form the drosophila dosage compensation complex (dcc), which specifically binds to the x chromosome of males. it is known that noncoding rna rox are primary component of the dcc in the process of assembly and spreading of the complex among the x chromosome of males. however, the role of this rna in maintaining the structure of the already assembled complex remains unclear. in this work, we have shown that the full-assembled dosage compensation complex dissociates rather weakly when treated with rnases: the mle helicase is effectively released from the complex, and the remaining protein components (msl1, msl2, and msl3) undergo partial disassembly and continue to be part of subcomplexes. the results confirm the importance of the noncoding rox2 rna not only in the processes of initiation of dcc assembly but also at the stage of maintaining the structure of the already assembled complex.",1
"innate immunity plays a crucial role in host defense against pathogen invasion and its strength and duration requires precise control. long non-coding rnas (lncrnas) have become important regulators of innate immunity, yet their roles in drosophila immune responses remain largely unknown. in this study, we identified that the overexpression of lncrna-cr11538 inhibits the expression of antimicrobial peptides (amps) dpt and atta in drosophila upon escherichia coli (e. coli) infection, and influences the survival rate of flies after e. cloacae infection. mechanically, lncrna-cr11538 decoys relish away from amps promoter region. we further revealed that relish can promote the transcription of lncrna-cr11538. after analyzing the dynamic expression profile of lncrna-cr11538 during imd immune response, we put forward a hypothesis that in the late stage of imd immune response, lncrna-cr11538 can be activated by relish and further decoy relish away from the amps promoter to suppress excessive immune signal and maintain immune homeostasis. this mechanism we proposed provides insights into the complex regulatory networks controlling immune responses in drosophila and suggests potential targets for therapeutic intervention in diseases involving dysregulated immune responses.",1
"microrna-19b (mir‑19b) is part of the mir‑17‑92 cluster which is associated with cardiac development. it has previously been reported that the overexpression of mir‑19b increases proliferation, inhibits apoptosis and promotes differentiation of embryonic carcinoma cells (p19 cells). the aim of the current study was to investigate the effects of mir‑19b knockdown on the proliferation, apoptosis, differentiation and regulation of the wnt/β‑catenin signaling pathway in p19 cells. p19 cells were transfected with an mir‑19b knockdown plasmid or an empty vector. mir‑19b knockdown or vector control stable cell lines were selected using puromycin. cell counting kit‑8 and flow cytometry were used to analyze the levels of cellular proliferation, cell cycle progression and the levels of apoptosis, respectively. caspase‑3 activity and mitochondrial function assays were also used to analyze apoptosis. an inverted microscope was used to observe the morphological changes of p19 cells during differentiation. reverse transcription‑quantitative polymerase chain reaction and western blot analysis were used to detect p19 cell differentiation markers and wnt/β‑catenin signaling pathway‑related genes and their corresponding proteins. the results demonstrated that mir‑19b knockdown inhibited the proliferation and apoptosis of p19 cells. however, the levels of expression of wnt and β‑catenin increased. mir‑19b knockdown activated the wnt/β‑catenin signaling pathway, which may regulate cardiomyocyte differentiation. the results of this study indicate that mir‑19b is a novel therapeutic target for cardiovascular diseases and provide insight into the mechanisms underlying congenital heart diseases.",1
"some gammaherpesviruses encode nuclear noncoding rnas (ncrnas) that assemble with host proteins. their conservation and abundance implies that they serve important functions for the virus. this paper focuses on our studies of three classes of nuclear noncoding herpesvirus rnas. (1) ebers 1 and 2 are expressed by epstein-barr virus in latent infection of human b lymphocytes. recent studies revealed three sites on eber1 that associate with ribosomal protein l22. in addition, heterokaryon assays have definitively shown that both ebers are confined to the nucleus, arguing that their contribution to viral latency is purely nuclear. (2) hsurs 1-7 are u rnas encoded by herpesvirus saimiri, which causes aggressive t-cell leukemias and lymphomas. comparison of monkey t cells transformed with wild-type or mutant virus lacking hsurs 1 and 2 revealed significant changes in host mrnas implicated in t-cell signaling. (3) pan is a 1-kb polyadenylated rna that accumulates in the nucleus of kaposi's sarcoma-associated herpesvirus lytically infected cells. a novel element, the ene, is essential for its high accumulation. recent results indicate that the ene functions to counteract poly(a)-dependent rna degradation, which we propose contributes to nuclear surveillance of mrna transcripts in mammalian cells. continuing studies of these viral rnas will provide insights into both cellular and viral gene expression.",1
"micrornas are important gene regulators that potentially play a profound role in tumorigenesis. increasing evidence indicates that mir-145 is a tumor suppressor capable of inhibiting breast and colon cancer cell growth both in vitro and in vivo. however, the biological function of mir-145 in non-small cell lung cancer (nsclc) is largely unknown. in colon cancer cells, c-myc is a confirmed direct target for mir-145. the aim of this work was to investigate the effect of mir-145 and c-myc on proliferation of nsclc cells, using the nsclc cell lines a549 and h23 as models. we determined the expression level of mir-145 in tumor tissues relative to adjacent non-tumor tissues, and in nsclc cell lines relative to non-malignant lung cells. downregulation of mir-145 was seen in tumor tissues and the two nsclc cell lines by real-time quantitative reverse transcription polymerase chain reaction. mtt and focus formation assays were conducted to measure cell proliferation rates. cell growth was inhibited and the g1/s transition was blocked by mir-145 in transfection assays of a549 and h23 cells. we further showed that c-myc was a direct target for mir-145. introduction of mir-145 dramatically suppressed the c-myc/eif4e pathway, which was demonstrated to be crucial for cell proliferation in nsclc cells. furthermore, we found that cdk4 was regulated by mir-145 in cell cycle control. taken together, our study results demonstrate that mir-145 inhibits proliferation of nsclc cells through c-myc. increasing mir-145 expression may provide a novel approach for the treatment of nsclc.",1
"rationale necrosis is one of the main forms of cardiomyocyte death in heart disease. recent studies have demonstrated that certain types of necrosis are regulated and programmed dependent on the activation of receptor-interacting serine/threonine-protein kinase (ripk) 1 and 3 which may be negatively regulated by fas-associated protein with death domain (fadd). in addition, micrornas and long noncoding rnas have been shown to play important roles in various biological processes recently. objective the purpose of this study was to test the hypothesis that microrna-103/107 and h19 can participate in the regulation of ripk1- and ripk3-dependent necrosis in fetal cardiomyocyte-derived h9c2 cells and myocardial infarction through targeting fadd. methods and results our results show that fadd participates in h2o2-induced necrosis by influencing the formation of ripk1 and ripk3 complexes in h9c2 cells. we further demonstrate that mir-103/107 target fadd directly. knockdown of mir-103/107 antagonizes necrosis in the cellular model and also myocardial infarction in a mouse ischemia/reperfusion model. the mir-103/107-fadd pathway does not participate in tumor necrosis factor-α-induced necrosis. in exploring the molecular mechanism by which mir-103/107 are regulated, we show that long noncoding rna h19 directly binds to mir-103/107 and regulates fadd expression and necrosis. conclusions our results reveal a novel myocardial necrosis regulation model, which is composed of h19, mir-103/107, and fadd. modulation of their levels may provide a new approach for preventing myocardial necrosis.",1
"micrornas (mirna) are crucial post-transcriptional regulators of gene expression and control cell differentiation and proliferation. however, little is known about their targeting of specific developmental pathways. hedgehog (hh) signalling controls cerebellar granule cell progenitor development and a subversion of this pathway leads to neoplastic transformation into medulloblastoma (mb). using a mirna high-throughput profile screening, we identify here a downregulated mirna signature in human mbs with high hh signalling. specifically, we identify mir-125b and mir-326 as suppressors of the pathway activator smoothened together with mir-324-5p, which also targets the downstream transcription factor gli1. downregulation of these mirnas allows high levels of hh-dependent gene expression leading to tumour cell proliferation. interestingly, the downregulation of mir-324-5p is genetically determined by mb-associated deletion of chromosome 17p. we also report that whereas mirna expression is downregulated in cerebellar neuronal progenitors, it increases alongside differentiation, thereby allowing cell maturation and growth inhibition. these findings identify a novel regulatory circuitry of the hh signalling and suggest that misregulation of specific mirnas, leading to its aberrant activation, sustain cancer development.",1
"b-cell chronic lymphocytic leukemia (b-cll) is the most common human leukemia in the world. deregulation of the tcl1 oncogene is a causal event in the pathogenesis of the aggressive form of this disease as was verified by using animal models. to study the mechanism of tcl1 regulation in cll, we carried out microrna expression profiling of three types of cll: indolent cll, aggressive cll, and aggressive cll showing 11q deletion. we identified distinct microrna signatures corresponding to each group of cll. we further determined that tcl1 expression is regulated by mir-29 and mir-181, two micrornas differentially expressed in cll. expression levels of mir-29 and mir-181 generally inversely correlated with tcl1 expression in the cll samples we examined. our results suggest that tcl1 expression in cll is, at least in part, regulated by mir-29 and mir-181 and that these micrornas may be candidates for therapeutic agents in clls overexpressing tcl1.",1
"a diminished capacity to maintain tissue homeostasis is a central physiological characteristic of ageing. as stem cells regulate tissue homeostasis, depletion of stem cell reserves and/or diminished stem cell function have been postulated to contribute to ageing. it has further been suggested that accumulated dna damage could be a principal mechanism underlying age-dependent stem cell decline. we have tested these hypotheses by examining haematopoietic stem cell reserves and function with age in mice deficient in several genomic maintenance pathways including nucleotide excision repair, telomere maintenance and non-homologous end-joining. here we show that although deficiencies in these pathways did not deplete stem cell reserves with age, stem cell functional capacity was severely affected under conditions of stress, leading to loss of reconstitution and proliferative potential, diminished self-renewal, increased apoptosis and, ultimately, functional exhaustion. moreover, we provide evidence that endogenous dna damage accumulates with age in wild-type stem cells. these data are consistent with dna damage accrual being a physiological mechanism of stem cell ageing that may contribute to the diminished capacity of aged tissues to return to homeostasis after exposure to acute stress or injury.",1
"micrornas (mirnas) are important regulatory molecules in most eukaryotes and identification of their target mrnas is essential for their functional analysis. whereas conventional methods rely on computational prediction and subsequent experimental validation of target rnas, we directly sequenced >28,000,000 signatures from the 5' ends of polyadenylated products of mirna-mediated mrna decay, isolated from inflorescence tissue of arabidopsis thaliana, to discover novel mirna-target rna pairs. within the set of approximately 27,000 transcripts included in the 8,000,000 nonredundant signatures, several previously predicted but nonvalidated targets of mirnas were found. like validated targets, most showed a single abundant signature at the mirna cleavage site, particularly in libraries from a mutant deficient in the 5'-to-3' exonuclease atxrn4. although mirnas in arabidopsis have been extensively investigated, working in reverse from the cleaved targets resulted in the identification and validation of novel mirnas. this versatile approach will affect the study of other aspects of rna processing beyond mirna-target rna pairs.",1
"the cryptic multicopy plasmid pga1 (4,826 bp) from corynebacterium glutamicum lp-6 belongs to the fifth group of rolling-circle-replicating plasmids. a determinant, which negatively controls pga1 replication, was localized in the leader region of the rep gene coding for the initiator of plasmid replication. this region, when cloned into the compatible vector pec6, was found to cause decrease of segregational stability of the pga1 derivative pkg48. a promoter and a single transcriptional start site were found in the rep leader region in orientation opposite to the rep gene. these results suggest that a small countertranscribed rna (ctrna) (ca. 89 nucleotides in length), which might inhibit translation of pga1 rep gene, is formed. analysis of predicted secondary structure of the pga1-encoded ctrna revealed features common with the known ctrnas in bacteria. inactivation of the promoter p-ctrna caused a dramatic increase of copies of the respective plasmid, which proved a negative role of the ctrna in control of pga1 copy number. a region between the promoters prep and p-ctrna with a potential to form secondary structures on both ctrna and rep mrna was found to cause low activity of the rep promoter even when promoter p-ctrna was deleted. thus, the sequence within the rep leader region itself seems to act, in addition to the ctrna, as a second regulatory element of a novel type, negatively influencing expression of the pga1 rep gene.",1
"background micrornas (mirnas) are a large group of post-transcriptional gene regulators that potentially play a critical role in tumorigenesis. increasing evidences indicate that mir-744 deregulated in numerous human cancers including hepatocellular carcinoma (hcc). however, its role in hcc carcinogenesis remains poorly defined. in this study, we investigated the roles of mir-744 in tumor growth of hcc. methods quantitative reverse-transcription polymerase chain reaction (qrt-pcr) was conducted to detect the expression of mir-744 and immunohistochemistry was performed to detect expression of c-myc in hcc specimens and adjacent normal tissues. the biological functions of mir-744 were determined by cell proliferation and cell cycle assay. furthermore, cell lines transfected with mir-744 mimics were analyzed in vitro. luciferase reporter assays was performed to confirm whether mir-744 regulated the expression of c-myc. results our results showed that the expression of mir-744 was frequently down-regulated in both hcc tissues and cells. furthermore, restoration of mir-744 in hcc cells was statistically correlated with decrease of cell growth and restored g1 accumulation. luciferase assay and western blot analysis revealed that c-myc is a direct target of mir-744. down-regulation of mir-744 and up-regulation of c-myc were detected in hcc specimens compared with adjacent normal tissues. moreover, restoration of mir-744 rescues c-myc induced hcc proliferation. conclusions our data suggest that mir-744 exerts its tumor suppressor function by targeting c-myc, leading to the inhibition of hcc cell growth. mir-744 may serve as a potentially useful target for the mirna-based therapies of hcc in the future.",1
"constitutive expression of telomerase in human cells prevents the onset of senescence and crisis by maintaining telomere homeostasis. however, accumulating evidence suggests that the human telomerase reverse transcriptase catalytic subunit (tert) contributes to cell physiology independently of its ability to elongate telomeres. here we show that tert interacts with the rna component of mitochondrial rna processing endoribonuclease (rmrp), a gene that is mutated in the inherited pleiotropic syndrome cartilage-hair hypoplasia. human tert and rmrp form a distinct ribonucleoprotein complex that has rna-dependent rna polymerase (rdrp) activity and produces double-stranded rnas that can be processed into small interfering rna in a dicer (also known as dicer1)-dependent manner. these observations identify a mammalian rdrp composed of tert in complex with rmrp.",1
"micrornas (mirnas) interfere with translation of specific target mrnas and are thought to thereby regulate many cellular processes. recent studies have suggested that mirnas might play a role in osteoblast differentiation and bone formation. here, we identify a new mirna (mir-2861) in primary mouse osteoblasts that promotes osteoblast differentiation by repressing histone deacetylase 5 (hdac5) expression at the post-transcriptional level. mir-2861 was found to be transcribed in st2 stromal cells during bone morphogenetic protein 2-induced (bmp2-induced) osteogenesis, and overexpression of mir-2861 enhanced bmp2-induced osteoblastogenesis, whereas inhibition of mir-2861 expression attenuated it. hdac5, an enhancer of runt-related transcription factor 2 (runx2) degradation, was confirmed to be a target of mir-2861. in vivo silencing of mir-2861 in mice reduced runx2 protein expression, inhibited bone formation, and decreased bone mass. importantly, mir-2861 was found to be conserved in humans, and a homozygous mutation in pre-mir-2861 that blocked expression of mir-2861 was shown to cause primary osteoporosis in 2 related adolescents. consistent with the mouse data, hdac5 levels were increased and runx2 levels decreased in bone samples from the 2 affected individuals. thus, our studies show that mir-2861 plays an important physiological role in osteoblast differentiation and contributes to osteoporosis via its effect on osteoblasts.",1
"microrna-149 (mir-149) is located within the first intron of the glypican-1 (gpc1) gene. gpc1 is a low affinity receptor for fibroblast growth factor (fgf2) that enhances fgf2 binding to its receptor (fgfr1), subsequently promoting fgf2-fgfr1 activation and signaling. using bioinformatic approaches, both gpc1 and fgfr1 were identified and subsequently validated as targets for mir-149 (both the mature strand, mir-149, and the passenger strand, mir-149*) in endothelial cells (ecs). as a consequence of their targeting activity towards gpc1 and fgfr1, both mir-149 and mir-149* regulated fgf2 signaling and fgf2-induced responses in ecs, namely proliferation, migration and cord formation. moreover, lentiviral overexpression of mir-149 reduced in vivo tumor-induced neovascularization. importantly, fgf2 transcriptionally stimulated the expression of mir-149 independently of its host gene, therefore assuring the steady state of fgf2-induced responses through the regulation of the gpc1-fgfr1 binary complex in ecs.",1
"colorectal cancer (crc) remains the most common malignancy worldwide. tgf-β1 is often overexpressed in late stages of colorectal carcinogenesis and promotes tumour growth and metastasis. several reports have verified that the loss of functional tgfbrii expression contributed to escape the tumour suppressor activity of tgf-β1 and that the epithelial-to-mesenchymal transition (emt) responded to tgf-β1 involved in tumour invasion and metastasis. however, the mechanisms by which tgf-β1 confers a growth advantage to tgfbrii-null colorectal cancer cells have not been elucidated. micrornas (mirnas) are post-transcriptional inhibitory regulators of gene expression that act by directly binding complementary mrna and are key determinants of cancer initiation and progression. in this study, we revealed a role for mir-200b in colorectal cancer. mir-200b was highly expressed in tgfbrii-null tumour tissues and colorectal cancer cell lines and positively correlated with cell proliferation in tumour tissues and cell lines. in contrast, decreasing the mir-200b level in tgfbrii-null cells suppressed cell proliferation and cell cycle progression. furthermore, in vivo studies also suggested a stimulating effect of mir-200b on tgfbrii-null cell-derived xenografts. cdkn1b (p27/kip1) and rnd3 (rhoe) have mir-200b binding sequences within their 3' untranslated regions and were confirmed to be direct targets of mir-200b using fluorescent reporter assays. meanwhile, cdkn1b (p27/kip1) played a role in mir-200b-stimulated tgfbr-null crc. this study suggests that mir-200b plays a tumour-promoting role by targeting cdkn1b (p27/kip1) in crcs.",1
"introduction increasing evidence indicates that micrornas (mirnas) play a critical role in the pathogenesis of inflammatory diseases. the aim of the study was to investigate the expression pattern and function of mirnas in cd4+ t cells from patients with rheumatoid arthritis (ra). methods the expression profile of mirnas in cd4+ t cells from synovial fluid (sf) and peripheral blood of 33 ra patients was determined by microarray assay and validated by qrt-pcr analysis. the correlation between altered expression of mirnas and cytokine levels was determined by linear regression analysis. the role of mir-146a overexpression in regulating t cell apoptosis was evaluated by flow cytometry. a genome-wide gene expression analysis was further performed to identify mir-146a-regulated genes in t cells. results mirna expression profile analysis revealed that mir-146a expression was significantly upregulated while mir-363 and mir-498 were downregulated in cd4+ t cells of ra patients. the level of mir-146a expression was positively correlated with levels of tumor necrosis factor-alpha (tnf-alpha), and in vitro studies showed tnf-alpha upregulated mir-146a expression in t cells. moreover, mir-146a overexpression was found to suppress jurkat t cell apoptosis. finally, transcriptome analysis of mir-146a overexpression in t cells identified fas associated factor 1 (faf1) as a mir-146a-regulated gene, which was critically involved in modulating t cell apoptosis. conclusions we have detected increased mir-146a in cd4+ t cells of ra patients and its close correlation with tnf-alpha levels. our findings that mir-146a overexpression suppresses t cell apoptosis indicate a role of mir-146a in ra pathogenesis and provide potential novel therapeutic targets.",1
"hepatocellular carcinoma (hcc) is the third leading cause of cancer‑associated mortality in the 21st century. microrna (mir)‑23b has been shown to be involved in the pathogenesis of many cancers, including breast and prostate cancer. however, the role of mir‑23b in hcc remains unclear. the present study revealed a negative correlation between mir‑23b expression in hcc tissues and progression of carcinomas. compared to normal tissues, mir‑23b expression was significantly downregulated in hcc tissues, whereas the expression of interleukin (il)‑11 and il‑11 receptor α (il‑11rα) was significantly upregulated, indicating that mir‑23b expression is negatively correlated with il‑11 and il‑11rα expression. in addition, mir‑23b inhibited proliferation and promoted apoptosis of smmc‑7721 cells. this effect was mediated by il‑11, which was found to be the direct target of mir‑23b in this study. these results indicated that mir‑23b regulates il‑11 and il‑11rα expression, and might act as an anti‑oncogenic agent in the progression of hcc by directly downregulating il‑11 expression.",1
"we investigated the role of micrornas (mirnas) in the pathogenesis of human hepatocellular carcinoma (hcc). a genome-wide mirna microarray was used to identify differentially expressed mirnas in hccs arisen on cirrhotic livers. thirty-five mirnas were identified. several of these mirnas were previously found deregulated in other human cancers, such as members of the let-7 family, mir-221, and mir-145. in addition, the hepato-specific mir-122a was found down-regulated in approximately 70% of hccs and in all hcc-derived cell lines. microarray data for let-7a, mir-221, and mir-122a were validated by northern blot and real-time pcr analysis. understanding the contribution of deregulated mirnas to cancer requires the identification of gene targets. here, we show that mir-122a can modulate cyclin g1 expression in hcc-derived cell lines and an inverse correlation between mir-122a and cyclin g1 expression exists in primary liver carcinomas. these results indicate that cyclin g1 is a target of mir-122a and expand our knowledge of the molecular alterations involved in hcc pathogenesis and of the role of mirnas in human cancer.",1
"micrornas (mirnas) have gradually been recognized as regulators of embryonic development; however, relatively few mirnas have been identified that regulate cardiac development. a series of recent papers have established an essential role for the mirna-17-92 (mir-17-92) cluster of mirnas in the development of the heart. previous research has shown that the friend of gata-2 (fog-2) is critical for cardiac development. to investigate the possibility that the mir-17-92 cluster regulates fog-2 expression and inhibits proliferation in mouse embryonic cardiomyocytes we initially used bioinformatics to analyze 3' untranslated regions (3'utr) of fog-2 to predict the potential of mir-17-92 to target it. we used luciferase assays to demonstrate that mir-17-5p and mir-20a of mir-17-92 interact with the predicted target sites in the 3'utr of fog-2. furthermore, rt-pcr and western blot were used to demonstrate the post-transcriptional regulation of fog-2 by mir-17-92 in embryonic cardiomyocytes from e12.5-day pregnant c57bl/6j mice. finally, edu cell assays together with the fog-2 rescue strategy were employed to evaluate the effect of proliferation on embryonic cardiomyocytes. we first found that the mir-17-5p and mir-20a of mir-17-92 directly target the 3'utr of fog-2 and post-transcriptionally repress the expression of fog-2. moreover, our findings demonstrated that over-expression of mir-17-92 may inhibit cell proliferation via post-transcriptional repression of fog-2 in embryonic cardiomyocytes. these results indicate that the mir-17-92 cluster regulates the expression of fog-2 protein and suggest that the mir-17-92 cluster might play an important role in heart development.",1
"unlabelled the hepatitis b virus (hbv) x protein has been implicated as a potential trigger of the epigenetic modifications of some genes during hepatocarcinogenesis, but the underlying mechanisms remain unknown. micrornas (mirnas), which are noncoding rnas that regulate gene expression, are involved in diverse biological functions and in carcinogenesis. in this study, we investigated whether some mirnas are aberrantly expressed and involved in the regulation of the abnormal dna methylation status in hbv-related hepatocellular carcinoma (hcc). our results showed that the expression of microrna-152 (mir-152) was frequently down-regulated in hbv-related hcc tissues in comparison with adjacent noncancerous hepatic tissues and was inversely correlated to dna methyltransferase 1 (dnmt1) messenger rna (mrna) expression in hbv-related hccs. the forced expression of mir-152 in liver cell lines resulted in a marked reduction of the expression of dnmt1 at both the mrna and protein levels by directly targeting the 3' untranslated regions of dnmt1. this in turn led to a decrease in global dna methylation, whereas inhibition of mir-152 caused global dna hypermethylation and increased the methylation levels of two tumor suppressor genes, glutathione s-transferase pi 1 (gstp1) and e-cadherin 1 (cdh1). conclusion our findings suggest that mir-152 is frequently down-regulated and regulates dnmt1 in hbv-related hcc. these findings support a tumor-suppressive role of mir-152 in the epigenetic aberration of hbv-related hcc and the potential development of mirna-based targeted approaches for the treatment of hbv-related hcc.",1
"aims/hypothesis the contribution of aberrantly expressed micrornas (mirnas) to diabetic nephropathy in vivo is poorly understood. methods integrated comparative mirna array profiling was used to examine the expression of serum mirnas in patients with diabetic nephropathy. the abundance of mirna-135a (mir-135a) was measured by real-time quantitative pcr in the serum and kidney tissues of patients with diabetic nephropathy. the luciferase assay combined with mutation and immunoblotting was used to screen and verify the bioinformatically predicted mirnas. ca(2+) entry or intracellular ca(2+) (i) was performed by imaging fura-2/am-loaded cells using a fluorescence microscopy system. the role of mir-135a in vivo was explored with locked nucleic acid antisense oligonucleotides. results mir-135a was markedly upregulated in serum and renal tissue from patients with diabetic nephropathy, as well from db/db mice, and this was associated with the development of microalbuminuria and renal fibrosis. furthermore, we identified transient receptor potential cation channel, subfamily c, member 1 (trpc1) as a target of mir-135a during renal injury. we demonstrated that overexpression of trpc1 was able to reverse the pathological effects of mir-135a on promoting proliferation of mesangial cells and increasing synthesis of extracellular matrix proteins. moreover, mir-135a attenuated store depletion-induced ca(2+) entry into cells by regulating trpc1. importantly, knockdown of mir-135a in diabetic kidneys restored levels of trpc1 and reduced synthesis of fibronectin and collagen i in vivo. suppressing trpc1 levels to prevent ca(2+) entry into cells may be a mechanism whereby mir-135a promotes renal fibrosis in diabetic kidney injury. conclusions/interpretation these findings suggest an important role for mir-135a in renal fibrosis and inhibition of mir-135a might be an effective therapy for diabetic nephropathy.",1
"background unlike mammals, zebrafish have the ability to regenerate damaged parts of their central nervous system (cns) and regain functionality of the affected area. a better understanding of the molecular mechanisms involved in zebrafish regeneration may therefore provide insight into how cns repair might be induced in mammals. although many studies have described differences in gene expression in zebrafish during cns regeneration, the regulatory mechanisms underpinning the differential expression of these genes have not been examined. results we used microarrays to analyse and integrate the mrna and microrna (mirna) expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration. bioinformatic analysis identified 3 mirnas and 657 mrnas that were differentially expressed after injury. we then combined inverse correlations between our mirna expression and mrna expression, and integrated these findings with target predictions from targetscan fish to identify putative mirna-gene target pairs. we focused on two over-expressed mirnas (mir-29b and mir-223), and functionally validated seven of their predicted gene targets using rt-qpcr and luciferase assays to confirm mirna-mrna binding. gene ontology analysis placed the mirna-regulated genes (eva1a, layna, nefmb, ina, si:ch211-51a6.2, smoc1, sb:cb252) in key biological processes that included cell survival/apoptosis, ecm-cytoskeleton signaling, and heparan sulfate proteoglycan binding, conclusion our results suggest a key role for mir-29b and mir-223 in zebrafish regeneration. the identification of mirna regulation in a zebrafish injury model provides a framework for future studies in which to investigate not only the cellular processes required for cns regeneration, but also how these mechanisms might be regulated to promote successful repair and return of function in the injured mammalian brain.",1
"aim to elucidate the role of microrna-20a-5p (mir-20a-5p) in the pathogenesis of vogt-koyanagi-harada (vkh) disease. methods quantitative real-time pcr was used to quantify mir-20a-5p expression in cd4 + t cells from patients with active vkh and normal controls. the promoter methylation status of mir-20a-5p was detected by bisulfite sequencing pcr. targets were evaluated by a luciferase reporter assay. the functional effects of mir-20a-5p on cd4 + t cells from patients with active vkh were assessed by upregulation or downregulation of its expression using liposomes. results the mir-20a-5p level was significantly decreased in cd4 + t cells from patients with active vkh as compared with normal controls. the two genes, oncostatin m (osm) and c-c motif chemokine ligand 1 (ccl1), were identified as targets of mir-20a-5p. the upregulation of mir-20a-5p significantly suppressed interleukin 17 (il-17) production in cd4 + t cells from patients with active vkh, whereas downregulation of mir-20a-5p exhibited an inverse effect. in addition, overexpression of osm and ccl1 could rescue the effect of the upregulation of mir-20a-5p. moreover, the level of mir-20a-5p was reduced in response to hypermethylation of the promoter. further study showed that mir-20a-5p suppressed the activity of the phosphoinositide 3-kinase-akt pathway. conclusions our findings indicate that downregulation of mir-20a-5p is caused by promoter hypermethylation. mir-20a-5p could also suppress the production of il-17 by targeting osm and ccl1 production in cd4 + t cells in patients with active vkh.",1
"vascular mimicry (vm) describes the phenomenon that tumor cells but not endothelial cells form vascular-like channels, which provide blood perfusion for tumor tissues. vm is associated with tumor growth, metastasis and worse survival of different cancers. the mechanisms of vm formation remain largely unknown. we showed that the conditioned medium of cancer-associated fibroblast (cm-caf) promoted tumor cells to form capillary-like structure in vitro. consistently, co-implantation of cafs with tumor cells significantly enhanced vm formation in mouse xenografts, and higher amount of cafs was found in vm + human hcc tissues compared to vm - ones. however, the cm-caf-promoted vm formation was attenuated when tgf-β or sdf1 signaling was abrogated. similar to cm-caf, recombinant tgf-β1 and sdf1 induced vm formation. we further disclosed that the caf-secreted tgf-β and sdf1 enhanced the expression of ve-cadherin, mmp2 and laminin5γ2 via tgf-βr1 and cxcr4 in tumor cells, thereby promoted vm formation. moreover, tumor cells with high activity of self-sustaining tgf-β signaling displayed strong capability of vm formation. subsequent investigations showed that mir-101, which was down-regulated in both tumor cells and cafs, suppressed the caf-promoted vm formation in vitro and in vivo. gain- and loss-of-function analyses revealed that mir-101 attenuated tgf-β signaling transduction by targeting tgf-βr1 and smad2 in tumor cells, and simultaneously abrogated sdf1 signaling by suppressing sdf1 expression in cafs and inhibiting ve-cadherin expression in tumor cells. our findings suggest that the mir-101-tgf-β/sdf1-ve-cadherin/mmp2/lamc2 networks regulate vm formation and represent the potential targets for cancer therapy.",1
"micrornas (mirnas) are short non-coding rnas that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3'untranslated regions (3'utrs) of mrnas. individual mirnas can regulate networks of hundreds of genes, yet for the majority of mirnas few, if any, targets are known. misexpression of mirnas is also a major contributor to cancer progression, thus there is a critical need to validate mirna targets in high-throughput to understand mirnas' contribution to tumorigenesis. here we introduce a novel high-throughput assay to detect mirna targets in 3'utrs, called luminescent identification of functional elements in 3'utrs (3'life). we demonstrate the feasibility of 3'life using a data set of 275 human 3'utrs and two cancer-relevant mirnas, let-7c and mir-10b, and compare our results to alternative methods to detect mirna targets throughout the genome. we identify a large number of novel gene targets for these mirnas, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. functional analysis of target genes reveals consistent roles for each mirna as either a tumor suppressor (let-7c) or oncogenic mirna (mir-10b), and preferentially target multiple genes within regulatory networks, suggesting 3'life is a rapid and sensitive method to detect mirna targets in high-throughput.",1
"most studies on tcf7l2 snp variants in the pathogenesis of type 2 diabetes (t2d) focus on a role of the encoded transcription factor tcf4 in β cells. here, a mouse genetics approach shows that removal of tcf4 from β cells does not affect their function, whereas manipulating tcf4 levels in the liver has major effects on metabolism. in tcf7l2(-/-) mice, the immediate postnatal surge in liver metabolism does not occur. consequently, pups die due to hypoglycemia. by combining chromatin immunoprecipitation with gene expression profiling, we identify a tcf4-controlled metabolic gene program that is acutely activated in the postnatal liver. in concordance, adult liver-specific tcf7l2 knockout mice show reduced hepatic glucose production during fasting and display improved glucose homeostasis when maintained on high-fat diet. furthermore, liver-specific tcf4 overexpression increases hepatic glucose production. these observations imply that tcf4 directly activates metabolic genes and that inhibition of wnt signaling may be beneficial in metabolic disease.",1
"the insect steroid hormone ecdysone and its receptor play important roles during development and metamorphosis and regulate adult physiology and life span. ecdysone signaling, via the ecdysone receptor (ecr), has been proposed to act in a positive autoregulatory loop to increase ecr levels and sensitize the animal to ecdysone pulses. here we present evidence that this involves ecr-dependent transcription of the ecr gene, and that the microrna mir-14 modulates this loop by limiting expression of its target ecr. ecdysone signaling, via ecr, down-regulates mir-14. this alleviates mir-14-mediated repression of ecr and amplifies the response. failure to limit ecr levels is responsible for the many of the defects observed in mir-14 mutants. mir-14 plays a key role in modulating the positive autoregulatory loop by which ecdysone sensitizes its own signaling pathway.",1
"eukaryotic cells contain many fibrillarin-associated small nucleolar rnas (snornas) that possess long complementarities to mature rrnas. characterization of 21 novel antisense snornas from human cells followed by genetic depletion and reconstitution studies on yeast u24 snorna provides evidence that this class of snornas is required for site-specific 2'-o-methylation of preribosomal rna (pre-rrna). antisense sno-rnas function through direct base-pairing interactions with pre-rrna. the antisense element, together with the d or d' box of the snorna, provide the information necessary to select the target nucleotide for the methyltransfer reaction. the conclusion that sno-rnas function in covalent modification of the sugar moieties of ribonucleotides demonstrates that eukaryotic small nuclear rnas have a more versatile cellular function than earlier anticipated.",1
"the communication between vascular endothelial cells (ecs) and pericytes in the microvasculature is fundamental for vascular growth and homeostasis; however, these processes are disrupted by diabetes. here we show that modulation of p75(ntr) expression in ecs exposed to high glucose activates transcription of mir-503, which negatively affects pericyte function. p75(ntr) activates nf-κb to bind the mir-503 promoter and upregulate mir-503 expression in ecs. nf-κb further induces activation of rho kinase and shedding of endothelial microparticles carrying mir-503, which transfer mir-503 from ecs to vascular pericytes. the integrin-mediated uptake of mir-503 in the recipient pericytes reduces expression of efnb2 and vegfa, resulting in impaired migration and proliferation. we confirm operation of the above mechanisms in mouse models of diabetes, in which ec-derived mir-503 reduces pericyte coverage of capillaries, increased permeability and impaired post-ischaemic angiogenesis in limb muscles. collectively, our data demonstrate that mir-503 regulates pericyte-endothelial crosstalk in microvascular diabetic complications.",1
"the goal of replenishing the cardiomyocyte (cm) population using regenerative therapies following myocardial infarction (mi) is hampered by the limited regeneration capacity of adult cms, partially due to their withdrawal from the cell cycle. here, we show that microrna-128 (mir-128) is upregulated in cms during the postnatal switch from proliferation to terminal differentiation. in neonatal mice, cardiac-specific overexpression of mir-128 impairs cm proliferation and cardiac function, while mir-128 deletion extends proliferation of postnatal cms by enhancing expression of the chromatin modifier suz12, which suppresses p27 (cyclin-dependent kinase inhibitor) expression and activates the positive cell cycle regulators cyclin e and cdk2. furthermore, deletion of mir-128 promotes cell cycle re-entry of adult cms, thereby reducing the levels of fibrosis, and attenuating cardiac dysfunction in response to mi. these results suggest that mir-128 serves as a critical regulator of endogenous cm proliferation, and might be a novel therapeutic target for heart repair.",1
"increasing evidence shows that abnormal micrornas (mirnas) expression is involved in tumorigenesis. they might be the novel biomarkers or therapeutic targets in disease treatment. mir-29 family was previously reported to act as tumor suppressors or oncogenes in diverse cancers. however, their accurate expression, function and mechanism in gastric cancer (gc) are not well known. here, we found that the expression of mir-29 family members was significantly reduced in gc compared with adjacent controls. among them, mir-29c had the most reduced percentage in gc and was associated with aggressive and progressive phenotypes of gc. we further demonstrated that mir-29 family acted as tumor suppressors through targeting ccnd2 and matrix metalloproteinase-2 genes in gc. moreover, the inverse relationship between mir-29 family and their targets was verified in patients and xenograft mice. finally, reintroduction of mir-29 family significantly inhibited tumor formation of gc cells in the xenograft mice. take together, our finding characterized the expression properties of mir-29 family, contributed to the function and molecular mechanism of mir-29 family in gc and implied that mir-29 family might be employed as novel prognostic markers and therapeutic targets of gc.",1
"background staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. the severity of these infections is highly variable and depends on multiple parameters including the genome content of the bacterium as well as the condition of the infected host. clinically and epidemiologically, s. aureus shows a particular capacity to survive and adapt to drastic environmental changes including the presence of numerous antimicrobial agents. mechanisms triggering this adaptation remain largely unknown despite important research efforts. most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense rna molecules. principal findings using high-throughput sequencing technology, we performed an inventory of the whole transcriptome of s. aureus strain n315. in addition to the annotated transcription units, we identified more than 195 small transcribed regions, in the chromosome and the plasmid of s. aureus strain n315. the coding strand of each transcript was identified and structural analysis enabled classification of all discovered transcripts. rna purified at four time-points during the growth phase of the bacterium allowed us to define the temporal expression of such transcripts. a selection of 26 transcripts of interest dispersed along the intergenic regions was assessed for expression changes in the presence of various stress conditions including ph, temperature, oxidative shocks and growth in a stringent medium. most of these transcripts showed expression patterns specific for the defined stress conditions that we tested. conclusions these rna molecules potentially represent important effectors of s. aureus adaptation and more generally could support some of the epidemiological characteristics of the bacterium.",1
"mcs4 rna is one of the small stable rnas found in mycoplasma capricolum. its function is unknown. the conformation of mcs4 rna (125 nucleotides in length) in solution was investigated using chemical and enzymatic probes. single and double-stranded regions were estimated by means of diethyl pyrocarbonate (depc) and by dimethyl sulfate (dms) modifications. ribonuclease v1 was also used to identify paired or stacked nucleotides. based on these data, a secondary structure model for mcs4 rna containing four stem structures was constructed.",1
"background & aims chronic inflammatory bowel diseases such as ulcerative colitis (uc) are associated with differential expression of genes involved in inflammation and tissue remodeling. micrornas (mirnas), which direct mrna degradation and translational inhibition, influence a number of disease processes. we examined whether mirnas are differentially expressed in uc tissues and are associated with expression of genes that regulate inflammation. methods mirna expression was assessed in patients with active uc, inactive uc, crohn's disease, irritable bowel syndrome, infectious colitis, and microscopic colitis, as well as in healthy subjects by microarray, quantitative reverse transcription-polymerase chain reaction and in situ hybridization analyses. colonic epithelial cell (ht29) expression of mirnas was assessed. regulation of gene expression by mirnas was assessed by luciferase reporter construct assays and transfection of specific mirna mimics. results active uc was associated with the differential expression of 11 mirnas; 3 were significantly decreased and 8 were significantly increased in uc tissues. in situ hybridization analysis indicated that mir-192, an mirna with decreased expression in active uc, was predominantly localized to colonic epithelial cells. macrophage inflammatory peptide (mip)-2 alpha, a chemokine expressed by epithelial cells, was identified as a target of mir-192. in colon epithelial cells, induction of mip-2 alpha expression by tumor necrosis factor-alpha was accompanied by a concomitant reduction in mir-192 expression and mir-192 was observed to regulate the expression of mip-2 alpha. conclusions these findings expand the known roles of mirnas, indicating that tissues from patients with uc, and possibly other chronic inflammatory diseases, have altered mirna expression patterns. these findings also demonstrate that mirnas regulate colonic epithelial cell-derived chemokine expression.",1
"micrornas are short non-coding endogenous rnas that are implicated in regulating various aspects of plants and animal development, however their functions in organogenesis are largely unknown. here we report that mir-9a belonging to the mir-9 family, regulates drosophila wing development through a functional target site in the 3' untranslated region of the drosophila lim only protein, dlmo. dlmo is a transcription cofactor, that directly inhibits the activity of apterous, the lim-hd factor required for the proper dorsal identity of the wings. deletions of the 3' untranslated region, including the mir-9a site, generate gain-of-function dlmo mutants (beadex) associated with high levels of dlmo mrna and protein. beadex mutants lack wing margins, a phenotype also observed in null mir-9a mutants. we found that mir-9a and dlmo are co-expressed in wing discs and interact genetically for controlling wing development. lack of mir-9a results in overexpression of dlmo, while gain-of-function mir-9a mutant suppresses dlmo expression. these data indicate that a function of mir-9a is to ensure the appropriate stoichiometry of dlmo during drosophila wing development. the mir-9a binding site is conserved in the human counterpart lmo2, the t-cell acute leukemia oncogene, suggesting that mir-9 might apply a similar strategy to maintain lmo2 expression under a detrimental threshold.",1
"microrna-223 plays an important role in the inflammatory response of macrophages. recent studies have identified that mir-223 was highly expressed in h. pylori infection macrophages, the significance of the elevation, however, has not yet been investigated. in this study, we analyzed the impact of elevated mir-233 to macrophage inflammatory response and possible mechanisms. we found that mir-223 not only could inhibit the expression of inflammatory cytokines including il-6, il-8, il-12 and tnf-α, but also was able to decrease the expression of cd40, cd68, cd80, and cd163. furthermore, proteins relating to inflammatory signal pathways, such as irak-1, nf-κb and mapk, in h. pylori infected macrophages were down-regulated. taken together, these results indicated that mir-223 may act as an inflammatory inhibitory factor in h. pylori infected macrophages by irak-1, nf-κb or mapk signal pathways. these findings contribute to the understanding of mir-223 in macrophages inflammatory responses induced by h. pylori.",1
"energy homeostasis depends on insulin signaling in metazoans. insulin levels reflect the nutritional status of the animal to control levels of circulating sugar and regulate storage of resources in the form of glycogen and fat. over the past several years, evidence has begun to accumulate that insulin production and secretion, as well as cellular responsiveness to insulin, are subject to regulation by micrornas. here we present evidence that mir-14 acts in the insulin-producing neurosecretory cells in the adult drosophila brain to control metabolism. mir-14 acts in these cells through its direct target, sugarbabe. sugarbabe encodes a predicted zinc finger protein that regulates insulin gene expression in the neurosecretory cells. regulation of sugarbabe levels by nutrients and by mir-14 combines to allow the fly to manage resource mobilization in a nutritionally variable environment.",1
"non-coding y rnas have recently been identified as essential novel factors for chromosomal dna replication in mammalian cell nuclei, but mechanistic details of their function have not been defined. here, we identify the execution point for y rna function during chromosomal dna replication in a mammalian cell-free system. we determined the effect of degradation of y3 rna on replication origin activation and on fork progression rates at single-molecule resolution by dna combing and nascent-strand analysis. degradation of y3 rna inhibits the establishment of new dna replication forks at the g1- to s-phase transition and during s phase. this inhibition is negated by addition of exogenous y1 rna. by contrast, progression rates of dna replication forks are not affected by degradation of y3 rna or supplementation with exogenous y1 rna. these data indicate that y rnas are required for the establishment, but not for the elongation, of chromosomal dna replication forks in mammalian cell nuclei. we conclude that the execution point for non-coding y rna function is the activation of chromosomal dna replication origins.",1
"purpose micrornas (mirnas) play a global role in regulating gene expression and have important tissue-specific functions. little is known about their role in the retina. the purpose of this study was to establish the retinal expression of those mirnas predicted to target genes involved in vision. methods mirnas potentially targeting important ""retinal"" genes, as defined by expression pattern and implication in disease, were predicted using a published algorithm (targetscan; envisioneering medical technologies, st. louis, mo). the presence of candidate mirnas in human and rat retinal rna was assessed by rt-pcr. cdna levels for each mirna were determined by quantitative pcr. the ability to discriminate between mirnas varying by a single nucleotide was assessed. the activity of mir-124 and mir-29 against predicted target sites in rdh10 and impdh1 was tested by cotransfection of mirna mimics and luciferase reporter plasmids. results sixty-seven mirnas were predicted to target one or more of the 320 retinal genes listed herein. all 11 candidate mirnas tested were expressed in the retina, including mir-7, mir-124, mir135a, and mir135b. relative levels of individual mirnas were similar between rats and humans. the rdh10 3'utr, which contains a predicted mir-124 target site, mediated the inhibition of luciferase activity by mir-124 mimics in cell culture. conclusions many mirnas likely to regulate genes important for retinal function are present in the retina. conservation of mirna retinal expression patterns from rats to humans supports evidence from other tissues that disruption of mirnas is a likely cause of a range of visual abnormalities.",1
"background micrornas are important regulators of gene expression, including those involving electrical remodeling in atrial fibrillation (af). recently, kcnn3, the gene that encodes the small-conductance calcium-activated potassium channel 3 (sk3), was found to be strongly associated with af. objectives to evaluate the changes in atrial myocardial micrornas in patients with permanent af and to determine the role of microrna on the regulation of cardiac sk3 expression. methods atrial tissue obtained during cardiac surgery from patients (4 sinus rhythm and 4 permanent af) was analyzed by using microrna arrays. potential targets of micrornas were predicted by using software programs. the effects of specific micrornas on target gene expression were evaluated in hl-1 cells from a continuously proliferating mouse hyperplastic atrial cardiomyocyte cell line. interactions between micrornas and targets were further evaluated by using luciferase reporter assay and by using argonaute pull-down assay. results twenty-one micrornas showed significant (>2-fold) changes in af. microrna 499 (mir-499) was upregulated by 2.33-fold (p conclusion atrial mir-499 is significantly upregulated in af, leading to sk3 downregulation and possibly contributing to the electrical remodeling in af.",1
"micrornas in the mir-106b family are overexpressed in multiple tumor types and are correlated with the expression of genes that regulate the cell cycle. consistent with these observations, mir-106b family gain of function promotes cell cycle progression, whereas loss of function reverses this phenotype. microarray profiling uncovers multiple targets of the family, including the cyclin-dependent kinase inhibitor p21/cdkn1a. we show that p21 is a direct target of mir-106b and that its silencing plays a key role in mir-106b-induced cell cycle phenotypes. we also show that mir-106b overrides a doxorubicin-induced dna damage checkpoint. thus, mir-106b family members contribute to tumor cell proliferation in part by regulating cell cycle progression and by modulating checkpoint functions.",1
"spermatogonial differentiation and meiotic initiation during spermatogenesis are tightly regulated by a number of genes, including those encoding enzymes for mirna biogenesis. however, whether and how single mirnas regulate these processes remain unclear. here, we report that mir-202, a member of the let-7 family, prevents precocious spermatogonial differentiation and meiotic initiation in spermatogenesis by regulating the timely expression of many genes, including those for key regulators such as stra8 and dmrt6. in mir-202 knockout (ko) mice, the undifferentiated spermatogonial pool is reduced, accompanied by age-dependent decline of fertility. in ko mice, sycp3, stra8 and dmrt6 are expressed earlier than in wild-type littermates, and dmrt6 mrna is a direct target of mir-202-5p. moreover, the precocious spermatogonial differentiation and meiotic initiation were also observed in ko spermatogonial stem cells when cultured and induced in vitro, and could be partially rescued by the knockdown of dmrt6. therefore, we have not only shown that mir-202 is a regulator of meiotic initiation but also identified a previously unknown module in the underlying regulatory network.",1
"the mir-200 family plays a crucial role in epithelial to mesenchymal transition via controlling cell migration and polarity. we hypothesized that mir-200b, one mir-200 family member, could regulate angiogenic responses via modulating endothelial cell migration. delivery of the mir-200b mimic in human microvascular endothelial cells (hmecs) suppressed the angiogenic response, whereas mir-200b-depleted hmecs exhibited elevated angiogenesis in vitro, as evidenced by matrigel® tube formation and cell migration. using in silico studies, mir target reporter assay, and western blot analysis revealed that v-ets erythroblastosis virus e26 oncogene homolog 1 (ets-1), a crucial angiogenesis-related transcription factor, serves as a novel direct target of mir-200b. knocking down endogenous ets-1 simulated an anti-angiogenic response of the mir-200b mimic-transfected cells. certain ets-1-associated genes, namely matrix metalloproteinase 1 and vascular endothelial growth factor receptor 2, were negatively regulated by mir-200b. overexpression of ets-1 rescued mir-200b-dependent impairment in angiogenic response and suppression of ets-1-associated gene expression. both hypoxia as well as hif-1α stabilization inhibited mir-200b expression and elevated ets-1 expression. experiments to identify how mir-200b modulates angiogenesis under a low oxygen environment illustrated that hypoxia-induced mir-200b down-regulation de-repressed ets-1 expression to promote angiogenesis. this study provides the first evidence that hypoxia-sensitive mir-200b is involved in induction of angiogenesis via directly targeting ets-1 in hmecs.",1
"micrornas (mirnas) are thought to modulate a variety of cellular events. several studies have revealed the functions of mir-223 in granulopoiesis. here we analysed mir-223 expression in various human tissues, blood and leukaemia cells, and focused on its role in k562 erythroid and megakaryocytic differentiation. mir-223 was detected not only in granulocytes but also in erythroid cells. in k562 cells, expression of mir-223 was down-regulated during haemin-induced erythroid differentiation but up-regulated during phorbol myristate acetate (pma)-induced megakaryocytic differentiation. the overexpression of mir-223 resulted in significant decrease of gamma-globin mrna and the fraction of benzidine-positive cells in k562 cells, suggesting a suppressive effect of mir-223 on erythroid differentiation. peaks corresponding to 4n cells in stable transfectants overexpressing mir-223 were higher than that in control k562 cells during megakaryocytic differentiation, indicating that mir-223 increases megakaryocytic differentiation. the expression of lim domain only 2 (lmo2) reporter was suppressed in nih-3t3 when the expression of mir-223 was enforced by both the luciferase and fluorescence system. furthermore, lmo2 mrna and protein levels were significantly decreased in stable k562 transfectants overexpressing mir-223. these results indicate that lmo2 is a direct target of mir-223. thus, our results suggest that mir-223 reversibly regulates erythroid and megakaryocytic differentiation of k562 cells via down-modulation of lmo2.",1
"introduction pace4 plays an important role in prostate cancer (pca) proliferation and aggression, which might provide a useful target against prostate cancer. in this study, we had strived to find some key mirnas to decrease malignancy and invasiveness of pca through regulating pace4 expression. methods clinically pathological analysis of immunohistochemistry/in situ hybridization was carried out to detect the relationship between pace4 expression/mirnas and the malignancy of prostate mass. prostate cell lines (du145, c4-2, and bph-1) were cultured for growth curve, immunocytochemistry analysis, colony formation, matrigel invasion, and transcriptional/translational expression assay of pace4-related signaling molecules for confirming the relationship. mirnas targeting pace4 were predicted, validated and further-corroborated using bio-software, real-time pcr, luciferase reporter assay and transfection of mirna mimics and inhibitor. results it was suggested that pace4 might reflect the pathological malignancy of prostate lesion from pathology analysis. moreover, du145 cells, the highest pace4-level and related tf expression indicated of the strongest malignancy and invasiveness. it was significantly found that mir-124 was presented with the biggest odd to target pace4-3'utr, the capability of decreasing pace expression and slowing down cell growth and cell invasion. conclusions it was clear that pace4 level was closely associated with malignancy and invasiveness of pca in vivo or in vitro mir-124, played a crucial role inhibiting pace4 transcription thus exhibiting obvious effects of antiproliferation and antiaggression of pca.",1
"the rapid specification and differentiation of the embryonic zebrafish gut is essential to provide contractility for the digestion of food. the role of micrornas in modulating gut epithelial or smooth muscle differentiation is currently not known. here we show that the microrna mir-145 is strongly expressed in zebrafish gut smooth muscle and regulates its development. modulation of mir-145 levels results in gut smooth muscle and epithelium maturation defects. loss of mir-145 results in defects of smooth muscle function as measured by decreased nitric oxide production but also leads to increased expression of the embryonic smooth muscle markers sm22alpha-b, nm-mhc-b, and smoothelin. defects in gut epithelial maturation are also present as observed by immature morphology and a complete loss of alkaline phosphatase expression. loss or gain of mir-145 function phenocopies defects observed with altered gata6 expression and accordingly, we show that mir-145 directly represses gata6, and that gata6 is a major mir-145 target in vitro and in vivo. mir-145 therefore plays a critical role in promoting the maturation of both layers of the gut during development through regulation of gata6.",1
"objective myocardin, a potent transcriptional coactivator of serum response factor, is involved in vascular development and promotes a contractile smooth muscle phenotype. myocardin levels are reduced during vascular injury, in association with phenotypic switching of smooth muscle cells (smcs). however, the direct role of myocardin in vascular disease is unclear. approach and results we show that re-expression of myocardin prevents the vascular injury response in murine carotid arteries, with reduced neointima formation due to decreased smc migration and proliferation. myocardin reduced smc migration by downregulating platelet-derived growth factor receptor-β (pdgfrb) expression. pdgfrb was regulated by myocardin-induced mir-24 and mir-29a expression, and antagonizing these micrornas restored smc migration. furthermore, using mir-24 and mir-29a mimics, we demonstrated that mir-29a directly regulates pdgfrb expression at the 3' untranslated region while mir-24 has an indirect effect on pdgfrb levels. myocardin heterozygous-null mice showed an augmented neointima formation with increased smc migration and proliferation, demonstrating that endogenous levels of myocardin are a critical regulator of vessel injury responses. conclusions our results extend the function of myocardin from a developmental role to a pivotal regulator of smc phenotype in response to injury, and this transcriptional coactivator may be an attractive target for novel therapeutic strategies in vascular disease.",1
"the steroid hormone ecdysone is the central regulator of insect metamorphosis, during which a growing, immature larva is remodeled, through pupal stages, to a reproductive adult. however, the underlying mechanisms of ecdysone-mediated metamorphosis remain to be fully elucidated. here, we identified metamorphosis-associated micrornas (mirnas) and their potential targets by cross-linking immunoprecipitation coupled with deep sequencing of endogenous argonaute 1 protein in drosophila. interestingly, mir-8-3p targeted five vha genes encoding distinct subunits of vacuolar h + -atpase (v-atpase), which has a vital role in the organellar acidification. the expression of ecdysone-responsive mir-8-3p is normally downregulated during drosophila metamorphosis, but temporary overexpression of mir-8-3p in the whole body at the end of larval development led to defects in metamorphosis and survival, hallmarks of aberrant ecdysone signaling. in addition, mir-8-3p was expressed in the prothoracic gland (pg), which produces and releases ecdysone in response to prothoracicotropic hormone (ptth). notably, overexpression of mir-8-3p or knockdown of its vha targets in the pg resulted in larger than normal, ecdysone-deficient larvae that failed to develop into the pupal stage but could be rescued by ecdysone feeding. moreover, these animals showed defective ptth signaling with a concomitant decrease in the expression of ecdysone biosynthetic genes. we also demonstrated that the regulatory network between the conserved mir-8-3p/mir-200 family and v-atpase was functional in human cells. consequently, our data indicate that the coordinated regulation of v-atpase subunits by mir-8-3p is involved in drosophila metamorphosis by controlling the ecdysone biosynthesis.",1
"enhancing brown fat activity and promoting white fat browning are attractive therapeutic strategies for treating obesity and associated metabolic disorders. to provide a comprehensive picture of the gene regulatory network in these processes, we conducted a series of transcriptome studies by rna sequencing (rna-seq) and quantified the mrna and long noncoding rna (lncrna) changes during white fat browning (chronic cold exposure, beta-adrenergic agonist treatment, and intense exercise) and brown fat activation or inactivation (acute cold exposure or thermoneutrality, respectively). mrna-lncrna coexpression networks revealed dynamically regulated lncrnas to be largely embedded in nutrient and energy metabolism pathways. we identified a brown adipose tissue-enriched lncrna, lncbate10, that was governed by the camp-camp response element-binding protein (creb) axis and required for a full brown fat differentiation and white fat browning program. mechanistically, lncbate10 can decoy celf1 from pgc1α, thereby protecting pgc1α mrna from repression by celf1. together, these studies provide a comprehensive data framework to interrogate the transcriptomic changes accompanying energy homeostasis transition in adipose tissue.",1
"aims micrornas (mirnas) play critical roles during the development of the cardiovascular system. blocking mirna biosynthesis in embryonic hearts through a conditional gene inactivation approach led to differential cardiac defects depending on the cre drivers used in different studies. the goal of this study is to reveal the cardiogenic pathway that is regulated by the mirna mechanism at midgestation, a stage that has not been evaluated in previous publications. methods and results we specifically inactivated dicer1, which is essential for generation of functional mature mirnas, in the myocardium by crossing ctnt-cre mice with dicer1(loxp) mice. ctnt-cre efficiently inactivates target genes in cardiomyocytes at midgestation. all mutants died between e14.5 and e16.5 with severe myocardial wall defects, including reduced cell proliferation, increased cell death, and spongy myocardial wall. expression of tgfβ type i receptor (tgfbr1), which encodes the type i receptor of tgfβ ligands, was up-regulated in mutant hearts. as expected, tgfβ activity was increased in dicer1-inactivated hearts. our further molecular analysis suggested that tgfbr1 is a direct target of three mirnas. reducing tgfβ activities using a pharmacological inhibitor on in vitro cultured hearts, or through an in vivo genetic approach, partially rescued the cardiac defects caused by dicer1 inactivation. conclusions we show for the first time that tgfβ signalling is directly regulated by the mirna mechanism during myocardial wall morphogenesis. increased tgfβ activity plays a major role in the cardiac defects caused by myocardial deletion of dicer1. thus, mirna-mediated regulation of tgfβ signalling is indispensable for normal cardiogenesis.",1
"micrornas (mirnas) are essential for podocyte homeostasis, and the mir-30 family may be responsible for this action. however, the exact roles and clinical relevance of mir-30s remain unknown. in this study, we examined the expression of the mir-30 family in the podocytes of patients with fsgs and found that all members are downregulated. treating cultured human podocytes with tgf-β, lps, or puromycin aminonucleoside (pan) also downregulated the mir-30 family. podocyte cytoskeletal damage and apoptosis caused by treatment with tgf-β or pan were ameliorated by exogenous mir-30 expression and aggravated by mir-30 knockdown. moreover, we found that mir-30s exert their protective roles by direct inhibition of notch1 and p53, which mediate podocyte injury. in rats, treatment with pan substantially downregulated podocyte mir-30s and induced proteinuria and podocyte injury; however, transfer of exogenous mir-30a to podocytes of pan-treated rats ameliorated proteinuria and podocyte injury and reduced notch1 activation. finally, we demonstrated that glucocorticoid treatment maintains mir-30 expression in cultured podocytes treated with tgf-β, lps, or pan and in the podocytes of pan-treated rats. glucocorticoid-sustained mir-30 expression associated with reduced notch1 activation and alleviated podocyte damage. taken together, these findings demonstrate that mir-30s protect podocytes by targeting notch1 and p53 and that the loss of mir-30s facilitates podocyte injury. in addition, sustained mir-30 expression may be a novel mechanism underlying the therapeutic effectiveness of glucocorticoids in treating podocytopathy.",1
"during the expression of a certain genes standard decoding is over-ridden in a site or mrna specific manner. this recoding occurs in response to special signals in mrna and probably occurs in all organisms. this review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria.",1
"amyloid precursor protein (app) and β-site app cleaving enzyme (bace-1) play important roles in the pathogenesis of alzheimer's disease (ad). in this study, using bioinformatics analysis, we demonstrate that mir-384 is a microrna (mirna or mir) predicted to potentially target the 3' untranslated regions (3'-utrs) of both app and bace-1. sh-sy5y cells were transfected with mir-384 mimic oligonucleotide, mir-384 inhibitor oligonucleotide, or a non-specific control sirna. we found that the overexpression of mir-384 suppressed the mrna and protein expression of both app and bace-1. the mir-384 inhibitor oligonucleotide induced the upregulation of app and bace-1. the activity of bace-1 was altered following the change in its protein expression. the binding sites of mir-384 on the 3'-utrs of app and bace-1 were identified by luciferase assay. furthermore, cells were treasted with amyloid-β (aβ)42. aβ42 downregulated mir-384 expression, leading to the continuous reduction in mir-384 expression. in addition, using a mouse model of ad, as well as patients with mild cognitive impairment (mci) and dementia of alzheimer's type (dat), we examined the levels of mir-384 in cerebral spinal fluid (csf) and serum. patients with mci and dat had lower blood mir-384 levels compared with the controls. in addition, patients with dat had lower blood mir-384 levels in blood compared with the mci group. we also found decreased mir-384 expression in the several cerebral spinal fluid (csf) of the patients with dat. negative correlations were observed between mir-384 and aβ42 in the serum and csf from patients with ad. in conclusion, these findings demonstrate that mir-384 may plays a role in the development of ad and may be a potential non-invasive biomarker for the diagnosis of ad.",1
"micrornas are important regulators in many cellular processes, including stem cell self-renewal. recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. however, their role in human embryonic stem (es) cells (hescs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. here, we performed comprehensive microrna profiling in hescs and in purified neural and mesenchymal derivatives. using a combination of ago cross-linking and microrna perturbation experiments, together with computational prediction, we identified the targets of the mir-302/367 cluster, the most abundant micrornas in hescs. functional studies identified novel roles of mir-302/367 in maintaining pluripotency and regulating hesc differentiation. we show that in addition to its role in tgf-β signaling, mir-302/367 promotes bone morphogenetic protein (bmp) signaling by targeting bmp inhibitors tob2, dazap2, and slain1. this study broadens our understanding of microrna function in hescs and is a valuable resource for future studies in this area.",1
"proper regulation of x-linked gene expression, termed dosage compensation, is required for the normal development of mammalian embryos. through the process of x chromosome inactivation (xci), somatic cells of mammalian females inactivate one of their two x chromosomes in order to balance x-linked gene dosage with their male counterparts. the process of xci is dependent upon the long non-coding rna xist, which is expressed from and coats the inactivated x chromosome (xi) in cis. during mouse embryogenesis, imprinted xci inactivates the paternally inherited x chromosome (xp) within the extra-embryonic lineages. consequently, females harboring a paternally derived xist mutation (x/x(xist-)) die owing to failure of imprinted xci and, presumably, poor trophoblast development. here, we investigate the consequence of two active x chromosomes in the extra-embryonic ectoderm (exe) of x/x(xist-) female embryos. at embryonic day (e) 6.5, we find that the x/x(xist-) exe lacks the transcriptional regulator cdx2, a factor required to maintain the exe in a progenitor state. in addition, spongiotrophoblast progenitors are not maintained. surprisingly, we observe evidence of an xi in a subpopulation of x/x(xist-) exe cells. we demonstrate further that trophectodermal stem cells derived from x/x(xist-) embryos completely reverse normal imprinted xci patterns. taken together, our data suggest that, much like in the cells of the epiblast, the initial imprint that establishes imprinted xci is probably erased in exe cells. conversely, unlike the epiblast, in which xci is not required for progenitor cell maintenance, we demonstrate that dosage compensation is indispensable for the maintenance of trophoblast progenitors.",1
"cell proliferation, cell death, and pattern formation are coordinated in animal development. although many proteins that control cell proliferation and apoptosis have been identified, the means by which these effectors are linked to the patterning machinery remain poorly understood. here, we report that the bantam gene of drosophila encodes a 21 nucleotide microrna that promotes tissue growth. bantam expression is temporally and spatially regulated in response to patterning cues. bantam microrna simultaneously stimulates cell proliferation and prevents apoptosis. we identify the pro-apoptotic gene hid as a target for regulation by bantam mirna, providing an explanation for bantam's anti-apoptotic activity.",1
"the basal-like subtype of breast cancer has an aggressive clinical behavior compared to that of the luminal subtype. we identified the micrornas (mirnas) mir-221 and mir-222 (mir-221/222) as basal-like subtype-specific mirnas and showed that expression of mir-221/222 decreased expression of epithelial-specific genes and increased expression of mesenchymal-specific genes, and increased cell migration and invasion in a manner characteristic of the epithelial-to-mesenchymal transition (emt). the transcription factor fosl1 (also known as fra-1), which is found in basal-like breast cancers but not in the luminal subtype, stimulated the transcription of mir-221/222, and the abundance of these mirnas decreased with inhibition of the epidermal growth factor receptor (egfr) or mek (mitogen-activated or extracellular signal-regulated protein kinase kinase), placing mir-221/222 downstream of the ras pathway. furthermore, mir-221/222-mediated reduction in e-cadherin abundance depended on their targeting the 3' untranslated region of the gata family transcriptional repressor trps1 (tricho-rhino-phalangeal syndrome type 1), which inhibited emt by decreasing zeb2 (zinc finger e-box-binding homeobox2) expression. we conclude that by promoting emt, mir-221/222 may contribute to the more aggressive clinical behavior of basal-like breast cancers.",1
"inflammation is linked clinically and epidemiologically to cancer, and nf-kappab appears to play a causative role, but the mechanisms are poorly understood. we show that transient activation of src oncoprotein can mediate an epigenetic switch from immortalized breast cells to a stably transformed line that forms self-renewing mammospheres that contain cancer stem cells. src activation triggers an inflammatory response mediated by nf-kappab that directly activates lin28 transcription and rapidly reduces let-7 microrna levels. let-7 directly inhibits il6 expression, resulting in higher levels of il6 than achieved by nf-kappab activation. il6-mediated activation of the stat3 transcription factor is necessary for transformation, and il6 activates nf-kappab, thereby completing a positive feedback loop. this regulatory circuit operates in other cancer cells lines, and its transcriptional signature is found in human cancer tissues. thus, inflammation activates a positive feedback loop that maintains the epigenetic transformed state for many generations in the absence of the inducing signal.",1
"appropriate innate immune responses are required to protect an organism against foreign pathogens, and the immune response must be tightly controlled. here, we report a new microrna (mirna) identified from a small rna library from the epididymis, termed mir-7578, that acts as a negative regulator of inflammatory responses. it was abundantly expressed in immune-related organs and induced by lipopolysaccharide in the lung and epididymis, as well as macrophages stimulated with diverse toll-like receptor ligands, in an nf-κb-dependent manner. mmu-mir-7578 inhibited the release of pro-inflammatory cytokines, including tnfα and il6, by regulating its target gene egr1, which encodes a transcription factor that activates tnfα and nf-κb expression. transgenic mice overexpressing mmu-mir-7578 displayed higher resistance to endotoxin shock and lower plasma levels of tnfα and il6, indicating that this mirna acted as a negative molecule of immune response. in sum, we report a previously uncharacterized lps-responsive mirna that controls inflammatory response in a feedback loop by fine-tuning a key transcription factor in vivo.",1
"recent studies indicate important roles for long noncoding rnas (lncrnas) as essential regulators of myogenesis and adult skeletal muscle regeneration. however, the specific roles of lncrnas in myogenic differentiation of adult skeletal muscle stem cells and myogenesis are still largely unknown. here we identify a lncrna that is specifically enriched in skeletal muscle (myogenesis-associated lncrna, in short, lnc-mg). in mice, conditional knockout of lnc-mg in skeletal muscle results in muscle atrophy and the loss of muscular endurance during exercise. alternatively, skeletal muscle-specific overexpression of lnc-mg promotes muscle hypertrophy. in vitro analysis of primary skeletal muscle cells shows that lnc-mg increases gradually during myogenic differentiation and its overexpression improves cell differentiation. mechanistically, lnc-mg promotes myogenesis, by functioning as a competing endogenous rna (cerna) for microrna-125b to control protein abundance of insulin-like growth factor 2. these findings identify lnc-mg as a novel noncoding regulator for muscle cell differentiation and skeletal muscle development.",1
"atrial natriuretic peptide (anp) has a central role in regulating blood pressure in humans. recently, microrna 425 (mir-425) was found to regulate anp production by binding to the mrna of nppa, the gene encoding anp. mrnas typically contain multiple predicted microrna (mirna)-binding sites, and binding of different mirnas may independently or coordinately regulate the expression of any given mrna. we used a multifaceted screening strategy that integrates bioinformatics, next-generation sequencing data, human genetic association data, and cellular models to identify additional functional nppa-targeting mirnas. two novel mirnas, mir-155 and mir-105, were found to modulate anp production in human cardiomyocytes and target genetic variants whose minor alleles are associated with higher human plasma anp levels. both mir-155 and mir-105 repressed nppa mrna in an allele-specific manner, with the minor allele of each respective variant conferring resistance to the mirna either by disruption of mirna base pairing or by creation of wobble base pairing. moreover, mir-155 enhanced the repressive effects of mir-425 on anp production in human cardiomyocytes. our study combines computational, genomic, and cellular tools to identify novel mirna regulators of anp production that could be targeted to raise anp levels, which may have applications for the treatment of hypertension or heart failure.",1
"p53 is a master tumour repressor that participates in vast regulatory networks, including feedback loops involving micrornas (mirnas) that regulate p53 and that themselves are direct p53 transcriptional targets. we show here that a group of polycistronic mirna-like non-coding rnas derived from small nucleolar rnas (sno-mirnas) are transcriptionally repressed by p53 through their host gene, snhg1. the most abundant of these, sno-mir-28, directly targets the p53-stabilizing gene, taf9b. collectively, p53, snhg1, sno-mir-28 and taf9b form a regulatory loop which affects p53 stability and downstream p53-regulated pathways. in addition, snhg1, snord28 and sno-mir-28 are all significantly upregulated in breast tumours and the overexpression of sno-mir-28 promotes breast epithelial cell proliferation. this research has broadened our knowledge of the crosstalk between small non-coding rna pathways and roles of sno-mirnas in p53 regulation.",1
"micrornas (mirnas) play a prominent role in gastric cancer (gc) initiation and progression. in this study, we found that mir-374a expression was up-regulated in human gc cell lines and tissues. inhibition of mir-374a suppressed gc cell proliferation, migration and invasion in vitro and slowed tumor growth in vivo. src kinase signaling inhibitor 1 (srcin1) was identified as a direct target of mir-374a. silencing of srcin1 significantly enhanced cell proliferation, migration and invasion, whereas srcin1 reintroduction partially abrogated the oncogenic effects of mir-374a. taken together, these findings suggest that mir-374a functions as a candidate oncogene in gc by directly targeting srcin1. mir-374a may therefore be useful as a promising therapeutic target for malignant gc.",1
"h5n1 influenza a virus (iav) causes severe respiratory diseases and high mortality rates in animals and humans. micrornas are being increasingly studied to evaluate their potential as therapeutic entities to combat viral infection. however, mechanistic studies delineating the roles of micrornas in regulating host-h5n1 virus interactions remain scarce. here, we performed microrna microarray analysis using a549 human lung epithelial cells infected with a highly pathogenic avian influenza virus. the microrna expression profile of infected cells identified a small number of micrornas being dysregulated upon h5n1 influenza a virus infection. of the differentially expressed micrornas, mir-136 was up-regulated 5-fold and exhibited potent antiviral activity in vitro against h5n1 influenza a virus, as well as vesicular stomatitis virus. on the one hand, 3'-untranslated region (utr) reporter analysis revealed a mir-136 binding site in the 3' utr of il-6. however, on the other hand, we subsequently determined that mir-136 meanwhile acts as an immune agonist of retinoic acid-inducible gene 1 (rig-i), thereby causing il-6 and ifn-β accumulation in a549 cells. overall, this study implicates the dual role of mirna-136 in the regulation of host antiviral innate immunity and suggests an important role for the microrna-activated pathway in viral infection via pattern recognition receptors.",1
"introduction increased expression of aggrecanase-1 (adamts-4) has emerged as an important factor in osteoarthritis (oa) and other joint diseases. this study aimed to determine whether the expression of adamts-4 in human chondrocytes is regulated by mirna. methods mirna targets were identified using bioinformatics. chondrocytes were isolated from knee cartilage and treated with interleukin-1 beta (il-1β). gene expression was quantified using taqman assays and protein production was determined by immunoblotting. luciferase reporter assay was used to verify interaction between mirna and target messenger rna (mrna). results in silico analysis predicted putative target sequence of mir-125b on adamts-4. mir-125b was expressed in both normal and oa chondrocytes, with significantly lower expression in oa chondrocytes than in normal chondrocytes. furthermore, il-1β-induced upregulation of adamts-4 was suppressed by overexpression of mir-125b in human oa chondrocytes. in the luciferase reporter assay, mutation of the putative mir-125b binding site in the adamts-4 3'utr abrogated the suppressive effect of mir125. conclusions our results indicate that mir-125b plays an important role in regulating the expression of adamts-4 in human chondrocytes and this identifies mir-125b as a novel therapeutic target in oa.",1
"oxidative stress is a causal factor and key promoter of a variety of cardiovascular diseases associated with apoptotic cell death by causing deregulation of related genes. though carvedilol, a β-adrenergic blocker, has been shown to produce cytoprotective effects against cardiomyocyte apoptosis, the mechanisms are not fully understood. the present study was designed to investigate whether the beneficial effects of carvedilol are related to micrornas which have emerged as critical players in cardiovascular pathophysiology via post-transcriptional regulation of protein-coding genes. in vivo, we demonstrated that carvedilol ameliorated impaired cardiac function of infarct rats and restored mir-133 expression. in vitro, carvedilol protected cardiomyocytes from h2o2 induced apoptosis detected by tunel staining and mtt assays, and increased mir-133 expression in cardiomyocytes. overexpression of mir-133, a recognized anti-apoptotic mirna, produced similar effects to carvedilol: reduction of reactive oxygen species (ros) and malondialdehyde (mda) content and increment of superoxide dismutase (sod) activity and glutathione peroxidase (gpx) level, so as to protect cardiomyocytes from apoptosis by downregulating caspase-9 and caspase-3 expression in the presence of h2o2. transfection with amo-133 (antisense inhibitor oligodeoxyribonucleotides) alone abolished the beneficial effects of carvedilol. caspase-9-specific inhibitor z-lehd-fmk, caspase-3-specific inhibitor z-devd-fmk, caspase-9 sirna and caspase-3 sirna were used to establish caspase-3 as a downstream target of mir-133. in conclusion, our data indicated that carvedilol protected cardiomyocytes by increasing mir-133 expression and suppressing caspase-9 and subsequent apoptotic pathways.",1
"objective this study explored the protective effects of the microrna-126 (mir-126)-mediated pi3k/akt/enos signaling pathway on human cardiac microvascular endothelial cells (hcmecs) against hypoxia/reoxygenation (h/r)-induced injury and the inflammatory response. methods untreated hcmecs were selected for the control group. after h/r treatment and cell transfection, the hcmecs were assigned to the h/r, mir-126 mimic, mimic-negative control (nc), mir-126 inhibitor, inhibitor-nc, wortmannin (an inhibitor of pi3k) and mir-126 mimic + wortmannin groups. super oxide dismutase (sod), nitric oxide (no), vascular endothelial growth factor (vegf) and reactive oxygen species (ros) were measured utilizing commercial kits. quantitative real-time polymerase chain reaction (qrt-pcr) and enzyme-linked immunosorbent assay (elisa) were performed to detect mir-126 expression and the mrna and protein expression of inflammatory factors. western blotting was used to determine the expression of key members in the pi3k/akt/enos signaling pathway. acck-8 assay and flow cytometry were employed to examine cell proliferation and apoptosis, respectively. the angiogenic ability in each group was detected by the lumen formation test. results compared to the control group, p/t-pi3k, p/t-akt and p/t-enos expression, no, vegf and sod levels, cell proliferation and in vitro lumen formation ability were decreased, while the ros content, interleukin (il)-6, il-10 and tumor necrosis factor (tnf)-α expression and cell apoptosis were significantly increased in the h/r, mimic-nc, mir-126 inhibitor, inhibitor-nc, wortmannin and mir-126 mimic + wortmannin groups. additionally, in comparison with the h/r group, the mir-126 mimic group had elevated p/t-pi3k, p/t-akt and p/t-enos expression, increased no, vegf and sod contents, and strengthened cell proliferation and lumen formation abilities but also exhibited decreased ros content, reduced il-6, il-10 and tnf-α expressions, and weakened cell apoptosis, while the mir-126 inhibitor and wortmannin group exhibited the opposite results. furthermore, decreased p/t-pi3k, p/t-akt and p/t-enos expressions, decreased no, vegf and sod contents, cell proliferation and lumen formation abilities, as well as increased ros content, increased il-6, il-10 and tnf-α expression, and increased cell apoptosis were observed in the mir-126 mimic + wortmannin group compared to themir-126 mimic group. conclusions these findings indicated that mir-126 protects hcmecs from h/r-induced injury and inflammatory response by activating the pi3k/akt/ enos signaling pathway.",1
"micrornas (mirnas) are endogenous, small, non-coding rnas, which are capable of silencing gene expression at the post-transcriptional level. in this study, we report that mir-205 is significantly underexpressed in breast tumor compared to the matched normal breast tissue. similarly, breast cancer cell lines, including mcf-7 and mda-mb-231, express a lower level mir-205 than the non-malignant mcf-10a cells. of interest, ectopic expression of mir-205 significantly inhibits cell proliferation and anchorage independent growth, as well as cell invasion. furthermore, mir-205 was shown to suppress lung metastasis in an animal model. finally, western blot combined with the luciferase reporter assays demonstrate that erbb3 and vascular endothelial growth factor a (vegf-a) are direct targets for mir-205, and this mir-205-mediated suppression is likely through the direct interaction with the putative mir-205 binding site in the 3'-untranslated region (3'-utr) of erbb3 and vegf-a. together, these results suggest that mir-205 is a tumor suppressor in breast cancer.",1
"our recent studies of the microrna (mirna) expression signature in prostate cancer (pca) indicated that mirna-218 (mir-218) was significantly downregulated in clinical specimens, suggesting that mir-218 might act as a tumor-suppressive mirna in pca. the aim of the present study was to investigate the functional significance of mir-218 in pca and to identify novel mir-218-regulated cancer pathways and target genes involved in pca oncogenesis and metastasis. restoration of mir-218 in pca cell lines (pc3 and du145) revealed that this mirna significantly inhibited cancer cell migration and invasion. gene expression data and in silico analysis demonstrated that lim and sh3 protein 1 (lasp1) is a potential target of mir-218 regulation. lasp1 is a cytoskeletal scaffold protein that plays critical roles in cytoskeletal organization and cell migration. luciferase reporter assays showed that mir-218 directly regulated expression of lasp1. moreover, downregulating the lasp1 gene significantly inhibited cell migration and invasion in cancer cells, and the expression of lasp1 was upregulated in cancer tissues. we conclude that loss of tumor-suppressive mir-218 enhanced cancer cell migration and invasion in pca through direct regulation of lasp1. our data on pathways regulated by tumor-suppressive mir-218 provide new insight into the potential mechanisms of pca oncogenesis and metastasis.",1
"acting through degradation of target mrna or inhibition of translation, micrornas (mirnas) regulate development, differentiation, and cellular response to diverse cues. we analyzed changes in mirna expression in human placental trophoblasts exposed to hypoxia, which may result from hypoperfusion and placental injury. using an mirna microarray screen, confirmed by northern blot analysis, we defined a set of seven mirnas (mir-93, mir-205, mir-224, mir-335, mir-424, mir-451, and mir-491) that are differentially regulated in primary trophoblasts exposed to hypoxia. we combined in silico prediction of mirna targets with gene expression profiling data to identify a series of potential targets for the mirnas, which were further analyzed using luciferase reporter assays. among experimentally confirmed targets, we found that the transcriptional coactivator med1, which plays an important role in placental development, is a target for mir-205. using gain- and loss-of-function assays, we confirmed that mir-205 interacts with a specific target in the 3'-utr sequence of med1 and silences med1 expression in human trophoblasts exposed to hypoxia, suggesting that mir-205 plays a role in trophoblast injury.",1
"regulatory t (treg) cells are critical in preventing aberrant immune responses. posttranscriptional control of gene expression by microrna (mirna) has recently emerged as an essential genetic element for treg cell function. here, we report that mice with treg cell-specific ablation of mir-142 (hereafter foxp3cremir-142fl/fl mice) developed a fatal systemic autoimmune disorder due to a breakdown in peripheral t-cell tolerance. foxp3cremir-142fl/fl mice displayed a significant decrease in the abundance and suppressive capacity of treg cells. expression profiling of mir-142-deficient treg cells revealed an up-regulation of multiple genes in the interferon gamma (ifnγ) signaling network. we identified several of these ifnγ-associated genes as direct mir-142-3p targets and observed excessive ifnγ production and signaling in mir-142-deficient treg cells. ifng ablation rescued the treg cell homeostatic defect and alleviated development of autoimmunity in foxp3cremir-142fl/fl mice. thus, our findings implicate mir-142 as an indispensable regulator of treg cell homeostasis that exerts its function by attenuating ifnγ responses.",1
"widespread death of transplanted mesenchymal stem cells (mscs) hampers the development of stem cell therapy for alzheimer disease (ad). cell pre-conditioning might help cope with this challenge. we tested whether let-7f-5p-modified mscs could prolong the survival of mscs after transplantation. when exposed to aβ 25-35 in vitro , mscs showed significant early apoptosis with decrease in the let-7f-5p levels and increased caspase-3 expression. upregulating microrna let-7f-5p in mscs alleviated aβ 25-35 -induced apoptosis by decreasing the caspase-3 levels. after computerized analysis and the luciferase reporter assay, we identified that caspases-3 was the target gene of let-7f-5p. in vivo , hematoxylin and eosin staining confirmed the success of mscs transplantation into the lateral ventricles, and the let-7f-5p upregulation group showed the lowest apoptotic rate of mscs detected by tunel immunohistochemistry analysis and immunofluorescence. similarly, bioluminescent imaging showed that let-7f-5p upregulation moderately prolonged the retention of mscs in brain. in summary, we identified the anti-apoptotic role of let-7f-5p in aβ 25-35 -induced cytotoxicity, as well as the protective effect of let-7f-5p on survival of grafted mscs by targeting caspase-3 in ad models. these findings show a promising approach of microrna-modified mscs transplantation as a therapy for neurodegenerative diseases.",1
"activated b cells reshape their primary antibody repertoire after antigen encounter by two molecular mechanisms: somatic hypermutation (shm) and class switch recombination (csr). shm and csr are initiated by activation-induced cytidine deaminase (aid) through the deamination of cytosine residues on the immunoglobulin loci, which leads to the generation of dna mutations or double-strand break intermediates. as a bystander effect, endogenous aid levels can also promote the generation of chromosome translocations, suggesting that the fine tuning of aid expression may be critical to restrict b cell lymphomagenesis. to determine whether micrornas (mirnas) play a role in the regulation of aid expression, we performed a functional screening of an mirna library and identified mirnas that regulate csr. one such mirna, mir-181b, impairs csr when expressed in activated b cells, and results in the down-regulation of aid mrna and protein levels. we found that the aid 3' untranslated region contains multiple putative binding sequences for mir-181b and that these sequences can be directly targeted by mir-181b. overall, our results provide evidence for a new regulatory mechanism that restricts aid activity and can therefore be relevant to prevent b cell malignant transformation.",1
"micrornas are a highly conserved class of noncoding rnas with important regulatory functions in proliferation, apoptosis, development, and differentiation. to discover novel regulatory pathways during megakaryocytic differentiation, we performed microrna expression profiling of in vitro-differentiated megakaryocytes derived from cd34(+) hematopoietic progenitors. the main finding was down-regulation of mir-10a, mir-126, mir-106, mir-10b, mir-17 and mir-20. hypothetically, the down-regulation of micrornas unblocks target genes involved in differentiation. we confirmed in vitro and in vivo that mir-130a targets the transcription factor mafb, which is involved in the activation of the gpiib promoter, a key protein for platelet physiology. in addition, we found that mir-10a expression in differentiated megakaryocytes is inverse to that of hoxa1, and we showed that hoxa1 is a direct target of mir-10a. finally, we compared the microrna expression of megakaryoblastic leukemic cell lines with that of in vitro differentiated megakaryocytes and cd34(+) progenitors. this analysis revealed up-regulation of mir-101, mir-126, mir-99a, mir-135, and mir-20. our data delineate the expression of micrornas during megakaryocytopoiesis and suggest a regulatory role of micrornas in this process by targeting megakaryocytic transcription factors.",1
"among the key properties that distinguish adult mammalian stem cells from their more differentiated progeny is the ability of stem cells to remain in a quiescent state for prolonged periods of time. however, the molecular pathways for the maintenance of stem-cell quiescence remain elusive. here we use adult mouse muscle stem cells (satellite cells) as a model system and show that the microrna (mirna) pathway is essential for the maintenance of the quiescent state. satellite cells that lack a functional mirna pathway spontaneously exit quiescence and enter the cell cycle. we identified quiescence-specific mirnas in the satellite-cell lineage by microarray analysis. among these, mirna-489 (mir-489) is highly expressed in quiescent satellite cells and is quickly downregulated during satellite-cell activation. further analysis revealed that mir-489 functions as a regulator of satellite-cell quiescence, as it post-transcriptionally suppresses the oncogene dek, the protein product of which localizes to the more differentiated daughter cell during asymmetric division of satellite cells and promotes the transient proliferative expansion of myogenic progenitors. our results provide evidence of the mirna pathway in general, and of a specific mirna, mir-489, in actively maintaining the quiescent state of an adult stem-cell population.",1
"the mammalian target of rapamycin (mtor) is a downstream integrator of essential pathways. mtor signaling is frequently dysregulated in a variety of human cancers, and in silico analysis has revealed two mir-144 binding sites in the mtor 3' untranslated region. we investigated the clinicopathologic magnitude of the mtor pathway regulating microrna, mir-144 in colorectal cancer (crc) cases. the regulation of mtor by mir-144 was examined with inhibitor mir-144-transfected cells. we also investigated changes in sensitivity to the mtor inhibitor, rapamycin, in inhibitor mir-144-transfected cells. quantitative rt-pcr was used to evaluate the clinicopathologic significance of mir-144 expression in 137 crc. furthermore, we assessed the correlation between crc prognosis and the expression of 16 genes in the akt/mtor pathway. in vitro assays showed that mtor is a direct target of mir-144, and downregulation of mir-144 facilitated proliferation of crc cell line, ht29. in addition, the viability of ht29 cells with downregulated mir-144 expression was significantly reduced with rapamycin treatment. low expression levels of mir-144 were associated with enhanced malignant potential such as venous invasion (p = 0.0013), liver metastasis (p = 0.08), liver recurrence (p = 0.0058) and poor prognosis (p = 0.0041). multivariate analysis indicated that low mir-144 expression was an independent prognostic factor for survival. among many genes consisting of the mtor pathway, only high expression of rictor was associated with poor prognosis of crc. mir-144 is a meaningful prognostic marker. downregulation of mir-144 leads to poor prognosis of crc patients via activation of the mtor signaling pathway.",1
"our previous studies have shown that microrna-383 (mir-383) is one of the most down-regulated mirna in tgf-β1-treated mouse ovarian granulosa cells (gc). however, the roles and mechanisms of mir-383 in gc function during follicular development remain unknown. in this study, we found that mir-383 was mainly expressed in gc and oocytes of mouse ovarian follicles. overexpression of mir-383 enhanced estradiol release from gc through targeting rna binding motif, single stranded interacting protein 1 (rbms1). mir-383 inhibited rbms1 by affecting its mrna stability, which subsequently suppressed the level of c-myc (a downstream target of rbms1). forced expression of rbms1 or c-myc attenuated mir-383-mediated steroidogenesis-promoting effects. knockdown of the transcription factor steroidogenic factor-1 (sf-1) significantly suppressed the expression of sarcoglycan zeta (sgcz) (mir-383 host gene), primary and mature mir-383 in gc, indicating that mir-383 was transcriptionally regulated by sf-1. luciferase and chromatin immunoprecipitation assays revealed that sf-1 specifically bound to the promoter region of sgcz and directly transactivated mir-383 in parallel with sgcz. in addition, sf-1 was involved in regulation of mir-383- and rbms1/c-myc-mediated estradiol release from gc. these results suggest that mir-383 functions to promote steroidogenesis by targeting rbms1, at least in part, through inactivation of c-myc. sf-1 acts as a positive regulator of mir-383 processing and function in gc. understanding of regulation of mirna biogenesis and function in estrogen production will potentiate the usefulness of mirna in the control of reproduction and treatment of some steroid-related disorders.",1
"regulatory rna structures are often members of families with multiple paralogous instances across the genome. family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. we have developed a comparative method, evofam, for genome-wide identification of families of regulatory rna structures, based on primary sequence and secondary structure similarity. we apply evofam to a 41-way genomic vertebrate alignment. genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural rna elements. known families identified include both noncoding rnas, e.g., mirnas and the recently identified malat1/men β lincrna family; and cis-regulatory structures, e.g., iron-responsive elements. we also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as go term enrichments. for some of these, detailed analysis has led to the formulation of specific functional hypotheses. examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-utr of mat2a, a key metabolic gene that produces the primary human methyl donor s-adenosylmethionine; the other involving a trna-like structure in the intron of the trna maturation gene pop1. we experimentally validate the predicted mat2a structures. finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., tnf, fos, and ctla4, which include known transcript destabilizing elements. our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding rnas.",1
"prostate cancer (pca) is one of the most prevalent malignant tumors. micrornas (mirnas) play an important role in cancer initiation, progression, and metastasis, and their roles in pca are becoming more apparent. in this study, we found that microrna-372 (mir-372) is downregulated in human pca and inhibits the proliferation activity, migration, and invasion of du145 cells. subsequently, p65 is confirmed as a target of mir-372, and knockdown of p65 expression similarly resulted in decreased proliferation activity, migration, and invasion. cdk8, mmp-9, and prostate-specific antigen were involved in both these processes. taken together, our results show evidence that mir-372 may function as a tumor suppressor gene by regulating p65 in pca and may provide a strategy for blocking pca metastasis.",1
"in humans, there is a strong correlation between sensitivity to substances of abuse and addiction risk. this differential tolerance to drugs has a strong genetic component. the identification of human genetic factors that alter drug tolerance has been a difficult task. for this reason and taking advantage of the fact that drosophila responds similarly to humans to many drugs, and that genetically it has a high degree of homology (sharing at least 70% of genes known to be involved in human genetic diseases), we looked for genes in drosophila that altered their nicotine sensitivity. we developed an instantaneous nicotine vaporization technique that exposed flies in a reproducible way. the amount of nicotine sufficient to ""knock out"" half of control flies for 30 minutes was determined and this parameter was defined as half recovery time (hrt). two fly lines, l4 and l70, whose hrt was significantly longer than control´s were identified. the l4 insertion is a loss of function allele of the transcriptional factor escargot (esg), whereas l70 insertion causes miss-expression of the microrna cluster mir-310-311-312-313 (mir-310c). in this work, we demonstrate that esg loss of function induces nicotine sensitivity possibly by altering development of sensory organs and neurons in the medial section of the thoracoabdominal ganglion. the ectopic expression of the mir-310c also induces nicotine sensitivity by lowering esg levels thus disrupting sensory organs and possibly to the modulation of other mir-310c targets.",1
"transfer rnas represent the largest, most ubiquitous class of non-protein coding rna genes found in all living organisms. the trnascan-se search tool has become the de facto standard for annotating trna genes in genomes, and the genomic trna database (gtrnadb) was created as a portal for interactive exploration of these gene predictions. since its published description in 2009, the gtrnadb has steadily grown in content, and remains the most commonly cited web-based source of trna gene information. in this update, we describe not only a major increase in the number of trna predictions (>367000) and genomes analyzed (>4370), but more importantly, the integration of new analytic and functional data to improve the quality and biological context of trna gene predictions. new information drawn from other sources includes trna modification data, epigenetic data, single nucleotide polymorphisms, gene expression and evolutionary conservation. a richer set of analytic data is also presented, including better trna functional prediction, non-canonical features, predicted structural impacts from sequence variants and minimum free energy structural predictions. views of trna genes in genomic context are provided via direct links to the ucsc genome browsers. the database can be searched by sequence or gene features, and is available at",1
"the rna molecules of the spliceosome are critical for specificity and catalysis during splicing of eukaryotic pre-mrna. in order to examine the evolution and phylogenetic distribution of these rnas, we analyzed 149 eukaryotic genomes representing a broad range of phylogenetic groups. rnas were predicted using high-sensitivity local alignment methods and profile hmms in combination with covariance models. the results provide the most comprehensive view so far of the phylogenetic distribution of spliceosomal rnas. rnas were predicted in many phylogenetic groups where these rna were not previously reported. examples are rnas of the major (u2-type) spliceosome in all fungal lineages, in lower metazoa and many protozoa. we also identified the minor (u12-type) spliceosomal u11 and u6atac rnas in acanthamoeba castellanii, where u12 spliceosomal rna as well as minor introns were reported recently. in addition, minor-spliceosome-specific rnas were identified in a number of phylogenetic groups where previously such rnas were not observed, including the nematode trichinella spiralis, the slime mold physarum polycephalum and the fungal lineages zygomycota and chytridiomycota. the detailed map of the distribution of the u12-type rna genes supports an early origin of the minor spliceosome and points to a number of occasions during evolution where it was lost.",1
"background b7-h3, an immunoregulatory protein, is overexpressed in several cancers and is often associated with metastasis and poor prognosis. here, our aim was to identify micrornas (mirnas) regulating b7-h3 and assess their potential prognostic implications in breast cancer. methods micrornas targeting b7-h3 were identified by transfecting two breast cancer cell lines with a library of 810 mirna mimics and quantifying changes of b7-h3 protein levels using protein lysate microarrays. for validations we used western immunoblotting and 3'-utr luciferase assays. clinical significance of the mirnas was assayed by analysing whether their expression levels correlated with outcome in two cohorts of breast cancer patients (142 and 81 patients). results we identified nearly 50 mirnas that downregulated b7-h3 protein levels. western immunoblotting validated the impact of the 20 most effective mirnas. thirteen mirnas (mir-214, mir-363*, mir-326, mir-940, mir-29c, mir-665, mir-34b*, mir-708, mir-601, mir-124a, mir-380-5p, mir-885-3p, and mir-593) targeted b7-h3 directly by binding to its 3'-utr region. finally, high expression of mir-29c was associated with a significant reduced risk of dying from breast cancer in both cohorts. conclusions we identified mirnas efficiently downregulating b7-h3 expression. the expression of mir-29c correlated with survival in breast cancer patients, suggesting a tumour suppressive role for this mirna.",1
"background studies have shown that the drug resistance of gastric cancer cells can be modulated by abnormal expression of micrornas (mirnas). we investigated the role of mir-503 in the development of cisplatin resistance in human gastric cancer cell lines. methods mir-503 expression was measured by quantitative real-time pcr. mtt (3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide) and clonogenic assays were used to examine changes in cell viability and the drug resistance phenotype of cancer cells associated with upregulation or downregulation of the mirna. a dual-luciferase activity assay was used to verify target genes of mir-503. immunohistochemistry, western blotting analysis, and a flow cytometric apoptosis assay were used to elucidate the mechanism by which mir-503 modulates drug resistance in cancer cells. results mir-503 was significantly downregulated in gastric cancer tissues and several gastric cancer cell lines. additionally, downregulation of mir-503 in the cisplatin (ddp)-resistant gastric cancer cell line sgc7901/ddp was concurrent with the upregulation of insulin-like growth factor-1 receptor (igf1r) and b-cell lymphoma 2 (bcl2) expression compared with the parental sgc7901 cell line. an in vitro drug sensitivity assay showed that overexpression of mir-503 sensitized sgc7901/ddp cells to cisplatin. the luciferase activity of reporters driven by igf1r and bcl2 3'-untranslated regions in sgc7901/ddp cells suggested that igf1r and bcl2 were both direct target genes of mir-503. enforced mir-503 expression in sgc7901/ddp cells reduced expression of the target proteins, inhibited proliferation, and sensitized the cells to ddp-induced apoptosis. conclusion our findings suggest that hsa-mir-503 modulates cisplatin resistance of human gastric cancer cells at least in part by targeting igf1r and bcl2.",1
"the plus-strand rna genome of tomato bushy stunt virus (tbsv) contains a 351-nucleotide (nt)-long 3'-untranslated region. we investigated the role of the 3'-proximal 130 nt of this sequence in viral rna accumulation within the context of a tbsv defective interfering (di) rna. sequence comparisons between different tombusviruses revealed that the 3' portion of the 130-nt sequence is highly conserved and deletion analysis confirmed that this segment is required for accumulation of di rnas in protoplasts. computer-aided sequence analysis and in vitro solution structure probing indicated that the conserved sequence consists of three stem-loop (sl) structures (5'-sl3-sl2-sl1-3'). the existence of sls 1 and 3 was also supported by comparative secondary structure analysis of sequenced tombusvirus genomes. formation of the stem regions in all three sls was found to be very important, and modification of the terminal loop sequences of sl1 and sl2, but not sl3, decreased di rna accumulation in vivo. for sl3, alterations to an internal loop resulted in significantly reduced di rna levels. collectively, these data indicate that all three sls are functionally relevant and contribute substantially to di rna accumulation. in addition, secondary structure analysis of other tombusvirus replicons and related virus genera revealed that a tbsv satellite rna and members of the closely related genus aureusvirus (family tombusviridae) share fundamental elements of this general structural arrangement. thus, this secondary structure model appears to extend beyond tombusvirus genomes. these conserved 3'-terminal rna elements likely function in vivo by promoting and/or regulating minus-strand synthesis.",1
"unlabelled tumor recurrence and metastases are the major obstacles to improving the prognosis of patients with hepatocellular carcinoma (hcc). to identify novel risk factors associated with hcc recurrence and metastases, we have established a panel of recurrence-associated micrornas (mirnas) by comparing mirna expression in recurrent and nonrecurrent human hcc tissue samples using microarrays (recurrence is defined as recurrent disease occurring within a 2-year time point of the original treatment). among the panel, expression of the mir-216a/217 cluster was consistently and significantly up-regulated in hcc tissue samples and cell lines associated with early tumor recurrence, poor disease-free survival, and an epithelial-mesenchymal transition (emt) phenotype. stable overexpression of mir-216a/217-induced emt increased the stem-like cell population, migration, and metastatic ability of epithelial hcc cells. phosphatase and tensin homolog (pten) and mothers against decapentaplegic homolog 7 (smad7) were subsequently identified as two functional targets of mir-216a/217, and both pten and smad7 were down-regulated in hcc. ectopic expression of pten or smad7 partially rescued mir-216a/217-mediated emt, cell migration, and stem-like properties of hcc cells. previously, smad7 was shown to be a transforming growth factor beta (tgf-β) type 1 receptor antagonist. here, we further demonstrated that overexpression of mir-216a/217 acted as a positive feedback regulator for the tgf-β pathway and the canonical pathway involved in the activation of phosphoinositide 3-kinase/protein kinase k (pi3k/akt) signaling in hcc cells. additionally, activation of the tgf-β- and pi3k/akt-signaling pathways in hcc cells resulted in an acquired resistance to sorafenib, whereas blocking activation of the tgf-β pathway overcame mir-216a/217-induced sorafenib resistance and prevented tumor metastases in hcc. conclusion overexpression of mir-216a/217 activates the pi3k/akt and tgf-β pathways by targeting pten and smad7, contributing to hepatocarcinogenesis and tumor recurrence in hcc.",1
"micrornas (mirnas) regulate mrna stability and protein expression, and certain mirnas have been demonstrated to act either as oncogenes or tumor suppressors. differential mirna expression signatures have been documented in many human cancers but the role of mirnas in endometrioid endometrial cancer (eec) remains poorly understood. this study identifies significantly dysregulated mirnas of eec cells, and characterizes their impact on the malignant phenotype. we studied the expression of 365 human mirnas using taqman low density arrays in eecs and normal endometriums. candidate differentially expressed mirnas were validated by quantitative real-time pcr. expression of highly dysregulated mirnas was examined in vitro through the effect of anti-/pre-mirna transfection on the malignant phenotype. we identified 16 significantly dysregulated mirnas in eec and 7 of these are novel findings with respect to eec. antagonizing the function of mir-7, mir-194 and mir-449b, or overexpressing mir-204, repressed migration, invasion and extracellular matrix-adhesion in hec1a endometrial cancer cells. foxc1 was determined as a target gene of mir-204, and two binding sites in the 3'-untranslated region were validated by dual luciferase reporter assay. foxc1 expression was inversely related to mir-204 expression in eec. functional analysis revealed the involvement of foxc1 in migration and invasion of hec1a cells. our results present dysfunctional mirnas in endometrial cancer and identify a crucial role for mir-204-foxc1 interaction in endometrial cancer progression. this mirna signature offers a potential biomarker for predicting eec outcomes, and targeting of these cancer progression- and metastasis-related mirnas offers a novel potential therapeutic strategy for the disease.",1
"micrornas (mirnas) comprise a novel class of endogenous, small, noncoding rnas that negatively regulate approximately 30% of genes in a cell via degradation or translational inhibition of their target mrnas. however, the effects of reactive oxygen species (ros) on mirna expression and the roles of mirnas in ros-mediated gene regulation and biological functions of vascular cells are unclear. using microarray analysis, we demonstrated that mirnas are aberrantly expressed in vascular smooth muscle cells (vsmcs) after treatment with hydrogen peroxide (h(2)o(2)). h(2)o(2)-mediated up-regulation of microrna-21 (mir-21) was further confirmed by quantitative real-time pcr. to determine the potential roles of mirnas in h(2)o(2)-mediated gene regulation and cellular effects, mir-21 expression was down-regulated by mir-21 inhibitor and up-regulated by pre-mir-21. h(2)o(2)-induced vsmc apoptosis and death were increased by mir-21 inhibitor and decreased by pre-mir-21. programmed cell death 4(pdcd4) was a direct target of mir-21 that was involved in mir-21-mediated effects on vsmcs. pre-mir-21-mediated protective effect on vsmc apoptosis and death was blocked via adenovirus-mediated overexpression of pdcd4 without the mir-21 binding site. moreover, activator protein 1 was a downstream signaling molecule of pdcd4 in mir-21-modulated vsmcs. the results suggest that mirnas in vsmcs are sensitive to h(2)o(2) stimulation. mirn-21 participates in h(2)o(2)-mediated gene regulation and cellular injury response through pdcd4 and the activator protein 1 pathway. mirnas might play a role in vascular diseases related to ros.",1
"endothelin-1 (et-1) plays a critical role in endothelial dysfunction and contributes to the pathogenesis of pulmonary hypertension (ph). we hypothesized that peroxisome proliferator-activated receptor γ (pparγ) stimulates micrornas that inhibit et-1 and pulmonary artery endothelial cell (paec) proliferation. the objective of this study was to clarify molecular mechanisms by which pparγ regulates et-1 expression in vitro and in vivo. in paecs isolated from patients with pulmonary arterial hypertension, microrna (mir)-98 expression was reduced, and et-1 protein levels and proliferation were increased. similarly, hypoxia reduced mir-98 and increased et-1 levels and paec proliferation in vitro. in vivo, hypoxia reduced mir-98 expression and increased et-1 and proliferating cell nuclear antigen (pcna) levels in mouse lung, derangements that were aggravated by treatment with the vascular endothelial growth factor receptor antagonist sugen5416. reporter assays confirmed that mir-98 binds directly to the et-1 3'-untranslated region. compared with littermate control mice, mir-98 levels were reduced and et-1 and pcna expression were increased in lungs from endothelial-targeted pparγ knockout mice, whereas mir-98 levels were increased and et-1 and pcna expression was reduced in lungs from endothelial-targeted pparγ-overexpression mice. gain or loss of pparγ function in paecs in vitro confirmed that alterations in pparγ were sufficient to regulate mir-98, et-1, and pcna expression. finally, pparγ activation with rosiglitazone regimens that attenuated hypoxia-induced ph in vivo and human paec proliferation in vitro restored mir-98 levels. the results of this study show that pparγ regulates mir-98 to modulate et-1 expression and paec proliferation. these results further clarify molecular mechanisms by which pparγ participates in ph pathogenesis and therapy.",1
"background micro-ribonucleic acids (mirnas) are crucial regulators in malignant tumors. mirna-29b (mir-29b) has been identified as a tumor suppressor in prostate cancer (pca). however, very few studies have investigated the effects of mir-29b in pca, especially the mechanism and its association with chemotherapy. our study aimed to explore the role and mechanism of mir-29b in pca. materials and methods the expression levels of mir-29b were detected in ten clinical pca specimens and four different pca cell lines through quantitative real-time polymerase chain reaction. after mir-29b mimics and inhibitors were successfully transfected into lncap, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was then used to investigate cell proliferation and cisplatin sensitivity of pca cells. cell cycle, cell apoptosis, and cell invasion were detected via flow cytometry, annexin v-fluorescein isothiocyanate labeling, and transwell assay, respectively. based on bioinformatic methods, western blot analysis, and dual-luciferase reporter assay, novel target genes of mir-29b were identified. results mir-29b was downregulated in pca tissues compared with matched adjacent nontumor tissues. in the androgen-independent pca cell line (lncap-ai), the expression of mir-29b was much lower than the androgen-dependent pca cell line (lncap). subsequent studies showed that forced expression of mir-29b inhibited cell proliferation and cell invasion and induced cell apoptosis in pca. upregulation of mir-29b also enhanced the chemosensitivity of pca cells to cisplatin. moreover, we identified dnmt3b and akt3 as novel target genes of mir-29b in pca. conclusion taken together, the results showed that mir-29b plays a tumor-suppressive role in pca. it inhibits cell biological behavior and enhances the chemotherapy effects of cisplatin through its involvement in epigenetic regulation and pi3k/akt pathway.",1
"micrornas (mirnas) regulate many cellular events during brain development by interacting with hundreds of mrna transcripts. however, mirnas operate nonuniformly upon the transcriptional profile with an as yet unknown logic. shortcomings in defining mirna-mrna networks include limited knowledge of in vivo mirna targets and their abundance in single cells. by combining multiple complementary approaches, high-throughput sequencing of rna isolated by cross-linking immunoprecipitation with an antibody to ago2 (ago2-hits-clip), single-cell profiling and computational analyses using bipartite and coexpression networks, we show that mirna-mrna interactions operate as functional modules that often correspond to cell-type identities and undergo dynamic transitions during brain development. these networks are highly dynamic during development and over the course of evolution. one such interaction is between radial-glia-enriched orc4 and mir-2115, a great-ape-specific mirna, which appears to control radial glia proliferation rates during human brain development.",1
"micrornas (mirna) are small regulatory rnas that control gene expression by translational suppression and destabilization of target mrnas. there is increasing evidence that mirnas regulate genes associated with fibrosis in organs, such as the heart, kidney, liver, and the lung. in a large-scale screening for mirnas potentially involved in bleomycin-induced fibrosis, we found expression of mir-29 family members significantly reduced in fibrotic lungs. analysis of normal lungs showed the presence of mir-29 in subsets of interstitial cells of the alveolar wall, pleura, and at the entrance of the alveolar duct, known sites of pulmonary fibrosis. mir-29 levels inversely correlated with the expression levels of profibrotic target genes and the severity of the fibrosis. to study the impact of mir-29 down-regulation in the lung interstitium, we characterized gene expression profiles of human fetal lung fibroblast imr-90 cells in which endogenous mir-29 was knocked down. this confirmed the derepression of reported mir-29 targets, including several collagens, but also revealed up-regulation of a large number of previously unrecognized extracellular matrix-associated and remodeling genes. moreover, we found that mir-29 is suppressed by transforming growth factor (tgf)-β1 in these cells, and that many fibrosis-associated genes up-regulated by tgf-β1 are derepressed by mir-29 knockdown. interestingly, a comparison of tgf-β1 and mir-29 targets revealed that mir-29 controls an additional subset of fibrosis-related genes, including laminins and integrins, independent of tgf-β1. together, these strongly suggest a role of mir-29 in the pathogenesis of pulmonary fibrosis. mir-29 may be a potential new therapeutic target for this disease.",1
"background melanoma is one of the fastest-rising types of cancer in north american. accumulating evidence suggests that anti-tumor immune tolerance plays a critical role in tumor development. methods b16 melanoma cells were injected into wild type and mir-17 overexpressing transgenic mice. tumor growth was monitored and tumor bearing mice were sacrificed by the end of the forth week. peripheral blood and spleen cells were subject to flow cytometry analysis and tumor samples were subject to immunohistochemistry staining. meanwhile, jurkat cells transfected with mock-control or mir-17 overexpressing plasmid were co-cultured with b16 cells. the influence of mir-17 on cell cycle, proliferation and survival was evaluated. results the melanoma tumors formed in mice overexpressing mir-17 were less than that in wild type mice. in addition, the mir-17 tumors were less invasive and less angiogenic. the percentage of cd8+ t cells was suppressed in mir-17 transgenic mice before melanoma cell injection. its level was significantly increased upon tumor grafting. more tumor infiltrating cd8+ cytotoxic t lymphocyte could be found in transgenic mice with tumor formation. luciferase assay and protein analysis indicated that stat3 was the target of mir-17. decreased levels of stat3 were associated with mir-17 over-expression. down-regulation of stat3 in jurkat cells promoted cell proliferation and mitosis. conclusions mir-17 inhibits melanoma growth by stimulating cd8+ t cells mediated host immune response, which is due to its regulation of stat3.",1
"micrornas (mirnas) are small rnas that participate in the regulation of genes associated with the differentiation and proliferation. in this study, 5 novel mirnas were identified from human mesenchymal stem cells and characterized using various analyses. to investigate the potential functions associated with the regulation of cell differentiation, the differences in mirna expression were examined in undifferentiated and differentiated human embryonic stem (es) cells using reverse transcription (rt)-pcr analysis. specifically, 3 mirnas exhibited decreased expression levels in human umbilical vein endothelial cells (huvecs) and endothelial cells derived from human es cells. putative target genes related to differentiation or maturation of endothelial cells were predicted by seed sequences of 2 novel mirnas and analyzed for their expression via mirna-mediated regulation using a luciferase assay. in huvecs, cdh5 gene expression was directly repressed by hsa-mir-6086. similarly, hsa-mir-6087 significantly downregulated endoglin expression. therefore, the roles of these 2 mirnas may be to directly suppress their target genes, popularly known as endothelial cell markers. taken together, our results demonstrate that several novel mirnas perform critical roles in human endothelial cell development.",1
"objective to use an in vitro model of chondrogenesis to identify micrornas (mirnas) with a functional role in cartilage homeostasis. methods the expression of mirnas was measured in the atdc5 cell model of chondrogenesis using microarray and was verified using quantitative reverse transcription-polymerase chain reaction. microrna expression was localized by in situ hybridization. predicted mirna target genes were validated using 3'-untranslated region-luc reporter plasmids containing either wild-type sequences or mutants of the mirna target sequence. signaling through the smad pathway was measured using a (caga)(12) -luc reporter. results the expression of several mirnas was regulated during chondrogenesis. these included 39 mirnas that are coexpressed with mirna-140 (mir-140), which is known to be involved in cartilage homeostasis and osteoarthritis (oa). of these mirnas, mir-455 resides within an intron of col27a1 that encodes a cartilage collagen. when human oa cartilage was compared with cartilage obtained from patients with femoral neck fractures, the expression of both mir-140-5p and mir-455-3p was increased in oa cartilage. in situ hybridization showed mir-455-3p expression in the developing limbs of chicks and mice and in human oa cartilage. the expression of mir-455-3p was regulated by transforming growth factor β (tgfβ) ligands, and mirna regulated tgfβ signaling. acvr2b, smad2, and chrdl1 were direct targets of mir-455-3p and may mediate its functional impact on tgfβ signaling. conclusion microrna-455 is expressed during chondrogenesis and in adult articular cartilage, where it can regulate tgfβ signaling, suppressing the smad2/3 pathway. diminished signaling through this pathway during the aging process and in oa chondrocytes is known to contribute to cartilage destruction. we propose that the increased expression of mir-455 in oa exacerbates this process and contributes to disease pathology.",1
"we found that gm15290 was one of the most upregulated lncrnas in the adipose of ob/ob mice through lncrna microarray analysis. then, manipulations of overexpression and silencing in mouse primary adipocytes showed that gm15290 positively regulated adipogenesis, manifested by increasing lipid deposition and upregulating adipogenic genes including pparγ, c/ebpα, and ap2. however, overexpression of mutant gm15290 (at the binding site of mir-27c) did not have an promoting effect on adipogenesis. additionally, gm15290 was found to potentially interact with mir-27b that had been identified as a pparγ targeting mirna, and we verified their interaction by luciferase activity and rna pull down assays. furthermore, inhibition of gm15290, by injection of the gm15290 sirna, decreased the body weight gain and mass of adipose tissues, including iwat and ewat, in mice fed with hfd. in conclusion, gm15290 sponges mir-27b to increase fat deposition and body weight in hfd-fed mice.",1
"aims accumulating evidence suggest that numerous micrornas (mirnas) play important roles in cell proliferation, apoptosis, and differentiation, as well as various diseases that accompany inflammatory responses. inflammation is known to be a major contributor to atherogenesis. previous studies provide promising evidence in support of the role of mirnas in cardiovascular disease. however, mechanistic data on these small molecules in atherosclerosis (as) are still missing. the present study aims to investigate the potential role of mirnas in as. methods and results the mirna transcriptase was verified by taqman real-time polymerase chain reaction assay. thoracic aorta samples were obtained from apolipoprotein e knockout mice, and plasma samples were from coronary artery disease (cad) patients. the results showed that the mir-155 level was the most significantly elevated both in as mice and cad patients relative to the normal control. the functional role of mir-155 in the atherosclerotic path physiological process was also observed in vivo and in vitro. the observations suggested that mir-155 is a part of a negative feedback loop, which down-modulates inflammatory cytokine production and decreases as progression. mir-155 was also found to mediate the inflammatory response and mitogen-activated protein kinase (mapk) pathway by targeting mitogen-activated protein kinase kinase kinase 10. conclusions mir-155 contributes to the prevention of as development and progression. it may also be involved in the posttranscriptional regulation of the inflammatory response and mapk pathway by targeting mitogen-activated protein kinase kinase kinase 10.",1
"overexpression of the oncomir mir-21 is associated with many cancers, including breast cancer. elevated levels of jagged-1 (jag1), a predicted mir-21 target, are implicated in estrogen receptor negative (er-) breast cancer. we demonstrate (by ablation of the mir-21 binding site in the jag1 3'utr) that mir-21 directly targets and represses jag1 levels in mcf-7 (er+) breast cancer cells. mir-21 targeting of jag1 in mda-mb-231 (er-) breast cancer cells is dependent on mir-21 dosage (levels). in both cell lines, mir-21 and jag1 expression levels were negatively correlated due to their regulatory relationship. in addition, 17beta-estradiol (e2) increases jag1 levels by limiting (via downregulating mir-21 levels) the repressive effects of mir-21 on the jag1 3'utr. our results reveal a regulatory interplay between mir-21, jag1 and e2 that is important for advancing understanding of how the oncogenic potential of mir-21 and jag1 manifests in different sub-types of breast cancer.",1
"micrornas (mirnas) play a vital role in the regulation of immunological functions and prevention of autoimmune disease. the abnormal expressions of several mirnas in patients with the acquired autoimmune disease, immune thrombocytopenia (itp), have been reported. however, the exact mechanism of mirnas in the pathogenesis of itp is currently not well understood. this study examined the mirna expression profile of peripheral blood mononuclear cells (pbmcs) in itp patients by mirna array and taqman real-time polymerase chain reaction. mir130a expression was found to be significantly decreased in pbmcs from patients with active chronic itp compared with that of normal controls. subsequently, dual-luciferase reporter gene analysis was used to validate that mir130a targeted the transforming growth factor-beta1 (tgfb1) and interleukin 18 (il18) genes. in addition, we also monitored the dynamic expression of mir130a and its targeted genes pre- and post-treatment of itp patients and determined that the expression of mir130a and tgfb1 was up-regulated, whereas il18 expression was down-regulated after effective treatment. in conclusion, this study suggests that reduced mir130a is involved in itp via targeting of tgfb1 and il18 expression.",1
"splicing of precursor messenger rna (pre-mrna) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snrnps), ntc (nineteen complex), ntc-related proteins (ntr), and a number of associated enzymes and cofactors. here, we report the three-dimensional structure of a schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. this spliceosome contains u2 and u5 snrnps, ntc, ntr, u6 small nuclear rna, and an rna intron lariat. the atomic model includes 10,574 amino acids from 37 proteins and four rna molecules, with a combined molecular mass of approximately 1.3 megadaltons. spp42 (prp8 in saccharomyces cerevisiae), the key protein component of the u5 snrnp, forms a central scaffold and anchors the catalytic center. both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mrna splicing. our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mrna splicing.",1
"despite advances in our understanding of breast cancer, patients with metastatic disease have poor prognoses. gata3 is a transcription factor that specifies and maintains mammary luminal epithelial cell fate, and its expression is lost in breast cancer, correlating with a worse prognosis in human patients. here, we show that gata3 promotes differentiation, suppresses metastasis and alters the tumour microenvironment in breast cancer by inducing microrna-29b (mir-29b) expression. accordingly, mir-29b is enriched in luminal breast cancers and loss of mir-29b, even in gata3-expressing cells, increases metastasis and promotes a mesenchymal phenotype. mechanistically, mir-29b inhibits metastasis by targeting a network of pro-metastatic regulators involved in angiogenesis, collagen remodelling and proteolysis, including vegfa, angptl4, pdgf, lox and mmp9, and targeting itga6, itgb1 and tgfb, thereby indirectly affecting differentiation and epithelial plasticity. the discovery that a gata3-mir-29b axis regulates the tumour microenvironment and inhibits metastasis opens up possibilities for therapeutic intervention in breast cancer.",1
"background our recent studies of microrna (mirna) expression signatures demonstrated that microrna-29s (mir-29s; mir-29a/b/c) were significantly downregulated in head and neck squamous cell carcinoma (hnscc) and were putative tumour-suppressive mirnas in human cancers. our aim in this study was to investigate the functional significance of mir-29s in cancer cells and to identify novel mir-29s-mediated cancer pathways and responsible genes in hnscc oncogenesis and metastasis. methods gain-of-function studies using mature mir-29s were performed to investigate cell proliferation, migration and invasion in two hnscc cell lines (sas and fadu). to identify mir-29s-mediated molecular pathways and targets, we utilised gene expression analysis and in silico database analysis. loss-of-function assays were performed to investigate the functional significance of mir-29s target genes. results restoration of mir-29s in sas and fadu cell lines revealed significant inhibition of cancer cell migration and invasion. gene expression data and in silico analysis demonstrated that mir-29s modulated the focal adhesion pathway. moreover, laminin γ2 (lamc2) and α6 integrin (itga6) genes were candidate targets of the regulation of mir-29s. luciferase reporter assays showed that mir-29s directly regulated lamc2 and itga6. silencing of lamc2 and itga6 genes significantly inhibited cell migration and invasion in cancer cells. conclusion downregulation of mir-29s was a frequent event in hnscc. the mir-29s acted as tumour suppressors and directly targeted laminin-integrin signalling. recognition of tumour-suppressive mirna-mediated cancer pathways provides new insights into the potential mechanisms of hnscc oncogenesis and metastasis and suggests novel therapeutic strategies for the disease.",1
"high-resolution structures of bacterial 70s ribosomes have provided atomic details about mrna and trna binding to the decoding center during elongation, but such information is lacking for preinitiation complexes (pics). we identified residues in yeast 18s rrna critical in vivo for recruiting methionyl trna(i)(met) to 40s subunits during initiation by isolating mutations that derepress gcn4 mrna translation. several such gcd(-) mutations alter the a928:u1389 base pair in helix 28 (h28) and allow pics to scan through the start codons of upstream orfs that normally repress gcn4 translation. the a928u substitution also impairs tc binding to pics in a reconstituted system in vitro. mutation of the bulge g926 in h28 and certain other residues corresponding to direct contacts with the p-site codon or trna in bacterial 70s complexes confer gcd(-) phenotypes that (like a928 substitutions) are suppressed by overexpressing trna(i)(met). hence, the nonconserved 928:1389 base pair in h28, plus conserved 18s rrna residues corresponding to p-site contacts in bacterial ribosomes, are critical for efficient met-trna(i)(met) binding and aug selection in eukaryotes.",1
"micrornas are small, highly conserved, non-coding rnas that regulate gene expression of target mrnas through cleavage or translational inhibition, and are widely involved in carcinogenesis and cancer development. in this study, the expression profile of microrna-133a (mir-133a) was examined in breast cancer cells and breast cancer tissues. the results showed that expression of mir-133a in both breast cancer cells and breast cancer tissues was significantly down-regulated. over-expression of mir-133a in tumor cells arrested the cell cycle by drastically decreasing the g2 /s phase and retarded the newly synthesized dna, suggesting a regulatory role for mir-133a in proliferation of breast cancer cells. bioinformatics prediction showed that epidermal growth factor receptor (egfr) is a potential target for mir-133a. a dual luciferase reporter gene assay showed that mir-133a bound to the 3' utr of egfr but not a mutated 3' utr, thereby down-regulating the protein expression level. accordingly, we found that expression of egfr protein decreased with increased expression of mir-133a in mcf-7 and mda-mb-231 cells. over-expression of mir-133a in breast cancer cells resulted in suppression of the level of phosphorylated akt protein (p-akt) and inhibition of p-akt nuclear translocation. these results demonstrate that mir-133a, which may act as a tumor suppressor in breast cancer, regulates the cell cycle and proliferation in tumorigenesis by targeting egfr through the downstream signal molecule akt. overall, these results show that mir-133a may be used as biomarker and/or therapeutic target for diagnosis and therapy of breast cancer.",1
"lpl (lipoprotein lipase) is a rate-limiting enzyme involved in the hydrolysis of triglycerides. previous studies have shown that microrna (mir)-467b regulates hepatic lpl expression and plays a role in the progression of steatosis or abnormal lipid retention in obese mice. macrophage-derived lpl has been shown to promote atherosclerosis. however, if mir-476b influences macrophage lpl expression and the subsequent effects are unknown. here, we utilized oxldl-treatment raw 264.7 macrophages that were transfected with mir-467b mimics or inhibitors to investigate the potential roles of macrophage mir-476b. we found that mir-467b significantly decreased lipid accumulation and il-6, il-1β, tnf-α and mcp-1 secretions. furthermore, our studies suggested an additional explanation for the regulatory mechanism of mir-467b on its functional target, lpl in raw 264.7 macrophages. thus, our findings indicate that mir-467b may regulate lipid accumulation and proinflammatory cytokine secretion in oxldl-stimulated raw 264.7 macrophages by targeting the lpl gene.",1
"accumulation of amyloid β (aβ) in the brain is a key pathological hallmark of alzheimer's disease (ad). because aging is the most prominent risk factor for ad, understanding the molecular changes during aging is likely to provide critical insights into ad pathogenesis. however, studies on the role of mirnas in aging and ad pathogenesis have only recently been initiated. identifying mirnas dysregulated by the aging process in the brain may lead to novel understanding of molecular mechanisms of ad pathogenesis. here, we identified that mir-186 levels are gradually decreased in cortices of mouse brains during aging. in addition, we demonstrated that mir-186 suppresses β-site amyloid precursor protein-cleaving enzyme 1 (bace1) expression by directly targeting the 3'utr of bace1 mrna in neuronal cells. in contrast, inhibition of endogenous mir-186 significantly increased bace1 levels in neuronal cells. importantly, mir-186 over-expression significantly decreased aβ level by suppressing bace1 expression in cells expressing human pathogenic mutant amyloid precursor protein. taken together, our data demonstrate that mir-186 is a potent negative regulator of bace1 in neuronal cells and it may be one of the molecular links between brain aging and the increased risk for ad during aging. we identified that mir-186 levels are gradually decreased in mouse cortices during aging. furthermore, we demonstrated that mir-186 is a novel negative regulator of beta-site amyloid precursor protein-cleaving enzyme 1 (bace1) expression in neuronal cells. therefore, we proposed that reduction in mir-186 levels during aging may lead to the up-regulation of bace1 in the brain, thereby increasing a risk for alzheimer's disease in aged individuals. read the editorial highlight for this article on page 308.",1
"irritable bowel syndrome (ibs) is a common disorder of unknown etiology. studies have found a close relation between ibs and micrornas (mirnas), but the study concerning the relationship between ibs and mir-181c-5p in ibs is still blank. thus, this study aims to explore the role of mir-181c-5p in ibs via interleukin 1α (il1a). initially, microarray analysis was used to retrieve the genes related to ibs and to predict mirnas regulating il1a gene. ibs model was then established with abdominal withdraw reflection (awr) and bristol stool grading in mice measured. afterwards, the functional role of mir-181c-5p in ibs was determined using the ectopic expression, depletion and reporter assay experiments, as well as mir-181c-5p and il1a expression detected. subsequently, expression of tumor necrosis factor-α (tnf-α), interleukin-2 (il-2), and il-6 were detected to further determine the effects of mir-181c-5p and il1a on inflammation in ibs. mir-181c-5p and il1a might be involved in ibs. mir-181c-5p was found to be decreased while il1a was increased in ibs rats. in addition, mir-181c-5p could target and inhibit expression of il1a, and ibs mice exhibited elevated awr and bristol stool grading, namely 6 to 7 points (70.4 ). moreover, with the overexpression of mir-181c-5p or silencing of il1a, the expression of tnf-α, il-2, and il-6 was decreased. collectively, this study suggested that overexpressed mir-181c-5p could silence il1a, thus inhibiting low-grade inflammation in ibs rats. mir-181c-5p/il1a is expected to serve as a novel target for the treatment of ibs.",1
"background high-throughput sequencing of rna isolated by crosslinking immunoprecipitation (hits-clip) allows for high resolution, genome-wide mapping of rna-binding proteins. this methodology is frequently used to validate predicted targets of microrna binding, as well as direct targets of other rna-binding proteins. hence, the accuracy and sensitivity of binding site identification is critical. results we found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. up to 45 % of peaks in publicly available hits-clip libraries are attributable to this mispriming artifact, and the majority of libraries have detectable levels of mispriming. we also found that standard techniques for validating microrna-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. conclusions here, we present a modification to the hits-clip protocol that effectively eliminates this artifact and improves the sensitivity and complexity of resulting libraries.",1
"preeclampsia is a pregnancy-specific syndrome manifested by the onset of hypertension and proteinuria after the 20th week of gestation. abnormal placenta development has been generally accepted as the initial cause of the disorder. recently, microrna-210 (mir-210) has been found to be upregulated in preeclamptic placentas compared with normal placentas, indicating a possible association of this small molecule with the placental pathology of preeclampsia. however, the function of mir-210 in the development of the placenta remains elusive. the aim of this study was to characterize the molecular mechanism of preeclampsia development by examining the role of mir-210. in this study, mir-210 and potassium channel modulatory factor 1 (kcmf1) expressions were compared in placentas from healthy pregnant individuals and patients with preeclampsia, and the role of mir-210 in trophoblast cell invasion via the downregulation of kcmf1 was investigated in the immortal trophoblast cell line htr8/svneo. the levels of kcmf1 were significantly lower in preeclamptic placenta tissues than in gestational week-matched normal placentas, which was inversely correlated with the level of mir-210. kcmf1 was validated as the direct target of mir-210 using real-time polymerase chain reaction, western blotting, and dual luciferase assay in htr8/svneo cells. mir-210 inhibited the invasion of trophoblast cells, and this inhibition was abrogated by the overexpression of kcmf1. the inflammatory factor tumor necrosis factor-α could upregulate mir-210 while suppressing kcmf1 expression in htr8/svneo cells. this is the first report on the function of kcmf1 in human placental trophoblast cells, and the data indicate that aberrant mir-210 expression may contribute to the occurrence of preeclampsia by interfering with kcmf1-mediated signaling in the human placenta.",1
"tumor metastasis is the dominant cause of death in cancer patients, including patients with oral tongue squamous cell carcinoma (tscc). previously, we reported that reduced mir-138 level is correlated with enhanced metastatic potential in tscc cells. here, we demonstrate that mir-138 suppresses tscc cell migration and invasion by regulating 2 key genes in the rho gtpase signaling pathway: rhoc and rock2. direct targeting of mir-138 to specific sequences located in the 3'-untranslated regions of both rhoc and rock2 mrnas was confirmed using luciferase reporter gene assays. ectopic transfection of mir-138 reduced the expression of both rhoc and rock2 in tscc cells. these reduced expressions, in consequence, led to the reorganization of the stress fibers and the subsequent cell morphology change to a round bleb-like shape as well as the suppression of cell migration and invasion. in contrast, knockdown of mir-138 in tscc cells enhanced the expression of rhoc and rock2, which resulted in an altered, elongated cell morphology, enhanced cell stress fiber formation and accelerated cell migration and invasion. taken together, our results suggest that mir-138 plays an important role in tscc cell migration and invasion by concurrently targeting rhoc and rock2, and mir-138 may serve as a novel therapeutic target for tscc patients at risk of metastatic disease.",1
"aims micrornas (mirnas) are crucial for the post-transcriptional control of protein-encoding genes and together with transcription factors (tfs) regulate gene expression; however, the regulatory activities of mirnas during cardiac development are only partially understood. in this study, we tested the hypothesis that integrative computational approaches could identify mirnas that experimentally could be shown to regulate cardiomyogenesis. methods and results we integrated expression profiles with bioinformatics analyses of mirna and tf regulatory programs to identify candidate mirnas involved with cardiac development. expression profiling showed that mir-200c, which is not normally detected in adult heart, is progressively down-regulated both during cardiac development and in vitro differentiation of human embryonic stem cells (hescs) to cardiomyocytes (cms). we employed computational methodologies to predict target genes of both mir-200c and five key cardiac tfs to identify co-regulated gene networks. the inferred cardiac networks revealed that the cooperative action of mir-200c with these five key tfs, including three (gata4, srf and tbx5) targeted by mir-200c, should modulate key processes and pathways necessary for cm development and function. experimentally, over-expression (oe) of mir-200c in hesc-cms reduced the mrna levels of gata4, srf and tbx5. cardiac expression of ca2+, k+ and na+ ion channel genes (cacna1c, kcnj2 and scn5a) were also significantly altered by knockdown or oe of mir-200c. luciferase reporter assays validated mir-200c binding sites on the 3' untranslated region of cacna1c. in hesc-cms, elevated mir-200c increased beating frequency, and repressed both ca2+ influx, mediated by the l-type ca2+ channel and ca2+ transients. conclusions our analyses demonstrate that mir-200c represses hesc-cm differentiation and maturation. the integrative computation and experimental approaches described here, when applied more broadly, will enhance our understanding of the interplays between mirnas and tfs in controlling cardiac development and disease processes.",1
"foxo1 is a master regulator of signaling pathways used by growth factors and hormones, including insulin. its activity is regulated by changes in subcellular localization coupled to post-translational modifications such as phosphorylation, ubiquitination, and acetylation. as micrornas have emerged as a newly identified means by which cells fine-tune gene expression, we hypothesized that they could regulate foxo1. since foxo1 plays a key role in the liver, we used immortalized neonatal mouse hepatocytes to analyze the effects of potential micrornas targeting foxo1. we found that mir-139 targets foxo1 mrna directly and reduces the level of the protein without affecting transcript levels. this decrease in foxo1 protein results in a decrease of its target genes, such as adqr1, adqr2 and mttp. our findings suggest a novel mode of foxo1 regulation by which mir-139 could maintain the protein level of foxo1 to preserve homeostatic regulation of its transcriptional activity in response to environmental stimuli.",1
"adhesion molecules expressed by activated endothelial cells play a key role in regulating leukocyte trafficking to sites of inflammation. resting endothelial cells normally do not express adhesion molecules, but cytokines activate endothelial cells to express adhesion molecules such as vascular cell adhesion molecule 1 (vcam-1), which mediate leukocyte adherence to endothelial cells. we now show that endothelial cells express microrna 126 (mir-126), which inhibits vcam-1 expression. transfection of endothelial cells with an oligonucleotide that decreases mir-126 permits an increase in tnf-alpha-stimulated vcam-1 expression. conversely, overexpression of the precursor to mir-126 increases mir-126 levels and decreases vcam-1 expression. additionally, decreasing endogenous mir-126 levels increases leukocyte adherence to endothelial cells. these data suggest that microrna can regulate adhesion molecule expression and may provide additional control of vascular inflammation.",1
"deregulations of microrna have been frequently observed in tongue squamous cell carcinoma (tscc), but their roles in tumorigenesis are not entirely clear. here, we reported the up-regulation of mir-24 in tscc. mir-24 up-regulation reduced the expression of rna-binding protein dead end 1 (dnd1). knockdown of mir-24 led to enhanced expression of dnd1. the direct targeting of mir-24 to the dnd1 mrna was predicted bioinformatically and confirmed by luciferase reporter gene assays. furthermore, the mir-24-mediated change in dnd1 expression suppressed the expression of cyclin-dependent kinase inhibitor 1b (cdkn1b), and also led to enhanced proliferation and reduced apoptosis in tscc cells.",1
"the maintenance of chromosome termini, or telomeres, requires the action of the enzyme telomerase, as conventional dna polymerases cannot fully replicate the ends of linear molecules. telomerase is expressed and telomere length is maintained in human germ cells and the great majority of primary human tumours. however, telomerase is not detectable in most normal somatic cells; this corresponds to the gradual telomere loss observed with each cell division. it has been proposed that telomere erosion eventually signals entry into senescence or cell crisis and that activation of telomerase is usually required for immortal cell proliferation. in addition to the human telomerase rna component (htr; ref. 11), tr1/tlp1 (refs 12, 13), a protein that is homologous to the p80 protein associated with the tetrahymena enzyme, has been identified in humans. more recently, the human telomerase reverse transcriptase (htrt; refs 15, 16), which is homologous to the reverse transcriptase (rt)-like proteins associated with the euplotes aediculatus (ea_p123), saccharomyces cerevisiae (est2p) and schizosaccharomyces pombe (5ptrt1) telomerases, has been reported to be a telomerase protein subunit. a catalytic function has been demonstrated for est2p in the rt-like class but not for p80 or its homologues. we now report that in vitro transcription and translation of htrt when co-synthesized or mixed with htr reconstitutes telomerase activity that exhibits enzymatic properties like those of the native enzyme. single amino-acid changes in conserved telomerase-specific and rt motifs reduce or abolish activity, providing direct evidence that htrt is the catalytic protein component of telomerase. normal human diploid cells transiently expressing htrt possessed telomerase activity, demonstrating that htrt is the limiting component necessary for restoration of telomerase activity in these cells. the ability to reconstitute telomerase permits further analysis of its biochemical and biological roles in cell aging and carcinogenesis.",1
"mutations in the human telomerase rna component (htr), the telomerase ribonucleoprotein component dyskerin (dkc1) and the poly(a) rnase (parn) can lead to reduced levels of htr and to dyskeratosis congenita (dc). however, the enzymes and mechanisms responsible for htr degradation are unknown. we demonstrate that defects in dyskerin binding lead to htr degradation by papd5-mediated oligoadenylation, which promotes 3'-to-5' degradation by exosc10, as well as decapping and 5'-to-3' decay by the cytoplasmic dcp2 and xrn1 enzymes. parn increased htr levels by deadenylating htr, thereby limiting its degradation by exosc10. telomerase activity and proper htr localization in dyskerin- or parn-deficient cells were rescued by knockdown of dcp2 and/or exosc10. prevention of htr rna decay also led to a rescue of localization of dc-associated htr mutants. these results suggest that inhibition of rna decay pathways might be a useful therapy for some telomere pathologies.",1
"we discovered a new small non-coding rna (srna) gene, vrra of vibrio cholerae o1 strain a1552. a vrra mutant overproduces ompa porin, and we demonstrate that the 140 nt vrra rna represses ompa translation by base-pairing with the 5' region of the mrna. the rna chaperone hfq is not stringently required for vrra action, but expression of the vrra gene requires the membrane stress sigma factor, sigma(e), suggesting that vrra acts on ompa in response to periplasmic protein folding stress. we also observed that ompa levels inversely correlated with the number of outer membrane vesicles (omvs), and that vrra increased omv production comparable to loss of ompa. vrra is the first srna known to control omv formation. moreover, a vrra mutant showed a fivefold increased ability to colonize the intestines of infant mice as compared with the wild type. there was increased expression of the main colonization factor of v. cholerae, the toxin co-regulated pili, in the vrra mutant as monitored by immunoblot detection of the tcpa protein. vrra overproduction caused a distinct reduction in the tcpa protein level. our findings suggest that vrra contributes to bacterial fitness in certain stressful environments, and modulates infection of the host intestinal tract.",1
"nk cells are innate immune lymphocytes important for early host defense against infectious pathogens and malignant transformation. micrornas (mirnas) are small rna molecules that regulate a wide variety of cellular processes, typically by specific complementary targeting of the 3'utr of mrnas. the dicer1 gene encodes a conserved enzyme essential for mirna processing, and dicer1 deficiency leads to a global defect in mirna biogenesis. in this study, we report a mouse model of lymphocyte-restricted dicer1 disruption to evaluate the role of dicer1-dependent mirnas in the development and function of nk cells. as expected, dicer1-deficient nk cells had decreased total mirna content. furthermore, mirna-deficient nk cells exhibited reduced survival and impaired maturation defined by cell surface phenotypic markers. however, dicer1-deficient nk cells exhibited enhanced degranulation and ifn-γ production in vitro in response to cytokines, tumor target cells, and activating nk cell receptor ligation. moreover, a similar phenotype of increased ifn-γ was evident during acute mcmv infection in vivo. mirs-15a/15b/16 were identified as abundant mirnas in nk cells that directly target the murine ifn-γ 3'utr, thereby providing a potential mechanism for enhanced ifn-γ production. these data suggest that the function of mirnas in nk cell biology is complex, with an important role in nk cell development, survival, or homeostasis, while tempering peripheral nk cell activation. further study of individual mirnas in an nk cell specific fashion will provide insight into these complex mirna regulatory effects in nk cell biology.",1
"objective we aimed at studying the role of the most deregulated mir-99a, identifying its downstream targets, and exploring the clinical potential of mir-99a and its target(s) in oral cancer. subjects and methods following confirmation of mir-99a deregulation in nine oral lines and 26 pairwise clinical specimens, mir-99a-manipulated oral cancer cells were subjected to cell proliferation, migration, invasion, and in vivo murine metastasis assays. we characterized putative mir-99a target(s) using luciferase reporter assays and genetic manipulation. the inverse relation of mir-99a and its target(s) was examined in clinical specimens using real-time pcr and western blot analysis. results mir-99a down-regulation was confirmed both in tested oral cancer cell lines and clinical specimens. ectopic mir-99a expression inhibited oral cancer cell migration and invasion. anti-mir-99a, silencing mir-99a functions, had the opposite effect. myotubularin-related protein 3 (mtmr3) with one evolutionarily conserved seed region in the 3'-untranslated region was a novel mir-99a target. depleting mtmr3 expression significantly reduced cell proliferation, migration, or invasion. there was an inverse expression of mir-99a and mtmr3 protein in oral cancer lines and clinical specimens. conclusion mir-99a repressed oral cancer cell migration and invasion partly through decreasing mtmr3 expression. mtmr3 may serve as a therapeutic target for oral cancer treatment.",1
"micrornas (mirnas) have been suggested to play a vital role in regulate tumor progression and invasion. however, the expression of mir-339-5p in colorectal cancer and its effects are not known. here, we report that mir-339-5p is a tumor suppressor by regulating expression of prl-1. in this study, we showed that downregulated mir-339-5p levels in colorectal cancer tissues and highly invasive crc cell lines. furthermore, enhancing the expression of mir-339-5p inhibited crc cell growth, migration and invasion in vitro and suppressed tumor growth in vivo. we then screened and identified a novel mir-339-5p target, phosphatases of regenerating liver-1 1 (prl-1), and it was further confirmed by luciferase assay. overexpression of mir-339-5p would also reduce the expression of prl-1 mrna and protein. the reduced prl-1 expression was associated with low expression of phosphorylated-extracellular signal-regulated kinase1/2 (p-erk1/2). conversely, reduction of mir-339-5p by inhibitors in cells stimulated these phenotypes. in conclusion, our results demonstrate that mir-339-5p functions as a tumor suppressor and plays a role in inhibiting growth and metastasis of crc cells through targeting prl-1 and regulating p-erk1/2 .these findings suggest that mir-339-5p may be useful as a new potential therapeutic target for crc.",1
"angiogenesis plays a crucial role during tumorigenesis and much progress has been recently made in elucidating the role of vegf and other growth factors in the regulation of angiogenesis. recently, micrornas (mirnas) have been shown to modulate a variety of physiogical and pathological processes. we identified a set of differentially expressed mirnas in microvascular endothelial cells co-cultured with tumour cells. unexpectedly, most mirnas were derived from tumour cells, packaged into microvesicles (mvs), and then directly delivered to endothelial cells. among these mirnas, we focused on mir-9 due to the strong morphological changes induced in cultured endothelial cells. we found that exogenous mir-9 effectively reduced socs5 levels, leading to activated jak-stat pathway. this signalling cascade promoted endothelial cell migration and tumour angiogenesis. remarkably, administration of anti-mir-9 or jak inhibitors suppressed mv-induced cell migration in vitro and decreased tumour burden in vivo. collectively, these observations suggest that tumour-secreted mirnas participate in intercellular communication and function as a novel pro-angiogenic mechanism.",1
"epstein-barr virus (ebv) is a ubiquitous human herpesvirus linked to a number of b cell cancers and lymphoproliferative disorders. during latent infection, ebv expresses 25 viral pre-micrornas (mirnas) and induces the expression of specific host mirnas, such as mir-155 and mir-21, which potentially play a role in viral oncogenesis. to date, only a limited number of ebv mirna targets have been identified; thus, the role of ebv mirnas in viral pathogenesis and/or lymphomagenesis is not well defined. here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (par-clip) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular mirna targetome in ebv strain b95-8-infected lymphoblastoid cell lines (lcls). we identified 7,827 mirna-interaction sites in 3,492 cellular 3'utrs. 531 of these sites contained seed matches to viral mirnas. 24 par-clip-identified mirna:3'utr interactions were confirmed by reporter assays. our results reveal that ebv mirnas predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. furthermore, targets of ebv mirnas are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. finally, we present evidence that myc-regulated host mirnas from the mir-17/92 cluster can regulate latent viral gene expression. this comprehensive survey of the mirna targetome in ebv-infected b cells represents a key step towards defining the functions of ebv-encoded mirnas, and potentially, identifying novel therapeutic targets for ebv-associated malignancies.",1
"4.5s rna is a group of rnas 90 to 94 nucleotides long (length polymorphism due to a varying number of ump residues at the 3' end) that form hydrogen bonds with poly(a)-terminated rnas isolated from mouse, hamster, or rat cells (w. r. jelinek and l. leinwand, cell 15:205-214, 1978; f. harada, n. kato, and h.-o. hoshino, nucleic acids res. 7:909-917, 1979). we have cloned a gene that encodes the 4.5s rna. it is repeated 850 (sigma = 54) times per haploid mouse genome and 690 (sigma = 59) times per haploid rat genome. most, if not all, of the repeats in both species are arrayed in tandem. the repeat unit is 4,245 base pairs long in mouse dna (the complete base sequence of one repeat unit is presented) and approximately 5,300 base pairs in rat dna. this accounts for approximately 3 x 10(6) base pairs of genomic dna in each species, or 0.1% of the genome. cultured murine erythroleukemia cells contain 13,000 molecules per cell of the 4.5s rna, which can be labeled to equilibrium in 90 min by uridine added to the culture medium. the 4.5s rna, therefore, has a short half-life. the 4.5s rna can be cross-linked in vivo by 4'-aminomethyl-4,5',8-trimethylpsoralen to murine erythroleukemia cell poly(a)-terminated cytoplasmic rna contained in ribonucleoprotein particles.",1
"the 5' untranslated region (5'utr) of the dengue virus (denv) genome contains two defined elements essential for viral replication. at the 5' end, a large stem-loop (sla) structure functions as the promoter for viral polymerase activity. next to the sla, there is a short stem-loop that contains a cyclization sequence known as the 5' upstream aug region (5'uar). here, we analyzed the secondary structure of the sla in solution and the structural requirements of this element for viral replication. using infectious denv clones, viral replicons, and in vitro polymerase assays, we defined two helical regions, a side stem-loop, a top loop, and a u bulge within sla as crucial elements for viral replication. the determinants for sla-polymerase recognition were found to be common in different denv serotypes. in addition, structural elements within the sla required for denv rna replication were also conserved among different mosquito- and tick-borne flavivirus genomes, suggesting possible common strategies for polymerase-promoter recognition in flaviviruses. furthermore, a conserved oligo(u) track present downstream of the sla was found to modulate rna synthesis in transfected cells. in vitro polymerase assays indicated that a sequence of at least 10 residues following the sla, upstream of the 5'uar, was necessary for efficient rna synthesis using the viral 3'utr as template.",1
"the rb-e2f pathway drives cell cycle progression and cell proliferation, and the molecular strategies safeguarding its activity are not fully understood. here we report that e2f1 directly transactivates mir-449a/b. mir-449a/b targets and inhibits oncogenic cdk6 and cdc25a, resulting in prb dephosphorylation and cell cycle arrest at g1 phase, revealing a negative feedback regulation of the prb-e2f1 pathway. moreover, mir-449a/b expression in cancer cells is epigenetically repressed through histone h3 lys27 trimethylation, and epigenetic drug treatment targeting histone methylation results in strong induction of mir-449a/b. our study reveals a tumor suppressor function of mir-449a/b through regulating rb/e2f1 activity, and suggests that escape from this regulation through an aberrant epigenetic event contributes to e2f1 deregulation and unrestricted proliferation in human cancer.",1
"during their biogenesis small nuclear rnas (snrnas) undergo multiple covalent modifications that require guide rnas to direct methylase and pseudouridylase enzymes to the appropriate nucleotides. because of their localization in the nuclear cajal body (cb), these guide rnas are known as small cb-specific rnas (scarnas). using a fluorescent primer extension technique, we mapped the modified nucleotides in drosophila u1, u2, u4, and u5 snrnas. by fluorescent in situ hybridization (fish) we showed that seven drosophila scarnas are concentrated in easily detectable cbs. we used two assays based on xenopus oocyte nuclei to demonstrate that three of these drosophila scarnas do, in fact, function as guide rnas. in flies null for the cb marker protein coilin, cbs are absent and there are no localized fish signals for the scarnas. nevertheless, biochemical experiments show that scarnas are present at normal levels and snrnas are properly modified. our experiments demonstrate that several scarnas are concentrated as expected in the cbs of wild-type drosophila, but they function equally well in the nucleoplasm of mutant flies that lack cbs. we propose that the snrna modification machinery is not limited to cbs, but is dispersed throughout the nucleoplasm of cells in general.",1
"sirtuin 1 (sirt1) is a nad-dependent deacetylase that is critically involved in diverse cellular processes including metabolic disease, cancer, and possibly aging. despite extensive studies on sirt1 function, how sirt1 levels are regulated remains relatively unknown. here, we report that the nuclear bile acid receptor farnesoid x receptor (fxr) inhibits microrna-34a (mir-34a) in the liver, which results in a positive regulation of sirt1 levels. activation of fxr by the synthetic agonist gw4064 decreases hepatic mir-34a levels in normal mice, and consistently, hepatic mir-34a levels are elevated in fxr-null mice. fxr induces expression of small heterodimer partner (shp), an orphan nuclear receptor and transcriptional corepressor, which in turn results in repression of p53, a key activator of the mir-34a gene, by inhibiting p53 occupancy at the promoter. mir-34a decreased sirt1 levels by binding to the 3'-untranslated region of sirt1 mrna, and adenovirus-mediated overexpression of mir-34a substantially decreased sirt1 protein levels in mouse liver. remarkably, mir-34a levels were elevated, and sirt1 protein levels were reduced in diet-induced obese mice, and fxr activation in these mice reversed the mir-34a and sirt1 levels, indicating an intriguing link among fxr activation, decreased mir-34a, and subsequently, increased sirt1 levels. our study demonstrates an unexpected role of the fxr/shp pathway in controlling sirt1 levels via mir-34a inhibition and that elevated mir-34a levels in obese mice contribute to decreased sirt1 levels. manipulation of this regulatory network may be useful for treating diseases of aging, such as metabolic disease and cancer.",1
"exoribonuclease-resistant rnas (xrrnas) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded rna structures. a recently discovered class of xrrna is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic rnas. the structure of one such xrrna from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrrna class. here, we present the crystal structure of a representative polerovirus xrrna that contains sequence elements that diverge from the previously solved structure. this new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. together, the structures of these xrrnas from dianthovirus and polerovirus genera support the idea that these plant virus xrrnas fold through a defined pathway that includes a programmed intermediate conformation. this work deepens our knowledge of the structure-function relationship of xrrnas and shows how evolution can craft similar rna folds from divergent sequences.",1
"increasing evidence support the critical roles of active stromal fibroblasts in breast cancer development and spread. however, the mediators and the mechanisms of regulation are still not well defined. we have shown here that the tumor suppressor p16(ink4a) protein inhibits the pro-carcinogenic effects of breast stromal fibroblasts through repressing the expression/secretion of il-6. indeed, p16(ink4a) suppresses il-6 at the mrna and protein levels. this effect is mediated trough mir-146b-5p, which inhibits il-6 expression through a specific sequence at the il-6 3'utr. in addition, we present clear evidence that mir-146b-5p inhibition is sufficient to transactivate breast stromal fibroblasts, which promote epithelial-to-mesenchymal-transition in breast cancer cells in a paracrine manner. by contrast, ectopic expression of mir-146b-5p in active fibroblasts abrogated their pro-carcinogenic effects. the physiological importance of mir-146b-5p inhibition was revealed by showing that the levels of pre-mir-146b-5p as well as its mature form are reduced in cancer-associated fibroblasts as compared with their normal adjacent counterparts from cancer-free tissues isolated from the same patients. interestingly, treatment of active breast stromal fibroblasts with curcumin increased the level of the p16(ink4a) coding cdkn2a mrna and mir-146b-5p and suppressed il-6, which confirms the repressive effect of these two tumor suppressor molecules on il-6, and shows the possible ""normalization"" of cancer-related active fibroblasts. these results show that mir-146b-5p has non-cell-autonomous tumor suppressor function through inhibition of il-6, suggesting that targeting this microrna in breast stromal fibroblasts could be of great therapeutic value.",1
"micrornas (mirnas) are small non-coding rnas that regulate mrna stability and translation through the action of the rnai-induced silencing complex (risc). our current understanding of mirna function is inferred largely from studies of the effects of mirnas on steady-state mrna levels and from seed match conservation and context in putative targets. here we have taken a more direct approach to these issues by comprehensively assessing the mirnas and mrnas that are physically associated with argonaute 2 (ago2), which is a core risc component. we transfected hek293t cells with epitope-tagged ago2, immunopurified ago2 together with any associated mirnas and mrnas, and quantitatively determined the levels of these rnas by microarray analyses. we found that ago2 immunopurified samples contained a representative repertoire of the cell's mirnas and a select subset of the cell's total mrnas. transfection of the mirnas mir-1 and mir-124 caused significant changes in the association of scores of mrnas with ago2. the mrnas whose association with ago2 increased upon mirna expression were much more likely to contain specific mirna seed matches and to have their overall mrna levels decrease in response to the mirna transfection than expected by chance. hundreds of mrnas were recruited to ago2 by each mirna via seed sequences in 3'-untranslated regions and coding sequences and a few mrnas appear to be targeted via seed sequences in 5'-untranslated regions. microarray analysis of ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of mirnas and for elucidating roles of mirnas in cellular regulation.",1
"objective to investigate the potential effect of mir-487b/il-33-st2 axis on the pathology of allergic rhinitis (ar) and the relevant mechanism. patients and methods the expression level of interleukin-33 (il-33), a homolog of sulfotransferase (st2), and mir-487b were detected in patients with or without allergic rhinitis. luciferase assay was performed to evaluate the interaction between mir-487b and il-33, and the effects of mir-487b/il-33-st2 axis on allergic rhinitis mice were determined by established allergic rhinitis model in mice by ovalbumin (ova). the levels of ova-specific immunoglobulin e (ig-e), proinflammatory cytokines (il-4, il-5, and il-13), and pathological alterations were detected. results the level of il-33 and its specific ligand st2 were found increased in allergic rhinitis patients while mir-487b expression level was markedly repressed. to confirm whether mir-487b has a regulation effect on il-33, we checked it in three publicly available algorithms, targetscan, mirdb, and microrna. we found that il-33 is a direct target of mir-487b, and luciferase assays confirmed our hypothesis, the subsequent experiments showed that up-regulation of mir-487b could inhibit expression of il-33 and st2, resulting in the decrease of the immunoglobulin e (ig-e), proinflammatory cytokines and mitigation of pathological alterations. conclusions our research discovered the suppressor function of mir-487b in allergic rhinitis and revealed that mir-487b/il-33-st2 axis may be a potential therapeutic target for the treatment of allergic rhinitis.",1
"head and neck paragangliomas, rare neoplasms of the paraganglia composed of nests of neurosecretory and glial cells embedded in vascular stroma, provide a remarkable example of organoid tumor architecture. to identify genes and pathways commonly deregulated in head and neck paraganglioma, we integrated high-density genome-wide copy number variation (cnv) analysis with microrna and immunomorphological studies. gene-centric cnv analysis of 24 cases identified a list of 104 genes most significantly targeted by tumor-associated alterations. the ""notch signaling pathway"" was the most significantly enriched term in the list (p = 0.002 after bonferroni or benjamini correction). expression of the relevant notch pathway proteins in sustentacular (glial), chief (neuroendocrine) and endothelial cells was confirmed by immunohistochemistry in 47 head and neck paraganglioma cases. there were no relationships between level and pattern of notch1/jag2 protein expression and germline mutation status in the sdh genes, implicated in paraganglioma predisposition, or the presence/absence of immunostaining for sdhb, a surrogate marker of sdh mutations. interestingly, notch upregulation was observed also in cases with no evidence of cnvs at notch signaling genes, suggesting altered epigenetic modulation of this pathway. to address this issue we performed microarray-based microrna expression analyses. notably 5 micrornas (mir-200a,b,c and mir-34b,c), including those most downregulated in the tumors, correlated to notch signaling and directly targeted notch1 in in vitro experiments using sh-sy5y neuroblastoma cells. furthermore, lentiviral transduction of mir-200s and mir-34s in patient-derived primary tympano-jugular paraganglioma cell cultures was associated with notch1 downregulation and increased levels of markers of cell toxicity and cell death. taken together, our results provide an integrated view of common molecular alterations associated with head and neck paraganglioma and reveal an essential role of notch pathway deregulation in this tumor type.",1
"background emerging evidence has suggested that dysregulation of mir-182-5p may contribute to tumor development and progression in several types of human cancers. however, its role in renal cell carcinoma (rcc) is still unknown. methods quantitative rt-pcr was used to quantify mir-182-5p expression in rcc clinical tissues. bisulfite sequencing pcr was used for dna methylation analysis. the cck-8, colony formation, flow cytometry, and a xenograft model were performed. immunohistochemistry was conducted using the peroxidase and dab methods. a mir-182-5p target was determined by luciferase reporter assays, quantitative rt-pcr, and western blotting. results mir-182-5p is frequently down-regulated in human rcc tissues. epigenetic modulation may be involved in the regulation of mir-182-5p expression. enforced expression of mir-182-5p in rcc cells significantly inhibited the proliferation and tumorigenicity in vitro and in vivo. additionally, overexpression of mir-182-5p induced g1-phase arrest via inhibition of akt/foxo3a signaling. moreover, flot1 was confirmed as a target of mir-182-5p. silencing flot1 by small interfering rnas phenocopied the effects of mir-182-5p overexpression, whereas restoration of flot1 in mir-182-5p -overexpressed rcc cells partly reversed the suppressive effects of mir-182-5p. conclusions these findings highlight an important role for mir-182-5p in the pathogenesis of rcc, and restoration of mir-182-5p could be considered as a potential therapeutic strategy for rcc therapy.",1
"background post-ischemic microglial activation may contribute to neuronal damage through the release of large amounts of pro-inflammatory cytokines and neurotoxic factors. the involvement of micrornas (mirnas) in the pathogenesis of disorders related to the brain and central nervous system has been previously studied, but it remains unknown whether the production of pro-inflammatory cytokines is regulated by mirnas. methods bv-2 and primary rat microglial cells were activated by exposure to oxygen-glucose deprivation (ogd). global cerebral ischemia was induced using the four-vessel occlusion (4-vo) model in rats. induction of pro-inflammatory and neurotoxic factors, such as tumor necrosis factor (tnf)-α, interleukin (il)-1β, and nitric oxide (no), were assessed by elisa, immunofluorescence, and the griess assay, respectively. the mirna expression profiles of ogd-activated bv-2 cells were subsequently compared with the profiles of resting cells in a mirna microarray. bv-2 and primary rat microglial cells were transfected with mir-181c to evaluate its effects on tnf-α production after ogd. in addition, a luciferase reporter assay was conducted to confirm whether tnf-α is a direct target of mir-181c. results ogd induced bv-2 microglial activation in vitro, as indicated by the overproduction of tnf-α, il-1β, and no. global cerebral ischemia/reperfusion injury induced microglial activation and the release of pro-inflammatory cytokines in the hippocampus. ogd also downregulated mir-181c expression and upregulated tnf-α expression. overproduction of tnf-α after ogd-induced microglial activation provoked neuronal apoptosis, whereas the ectopic expression of mir-181c partially protected neurons from cell death caused by ogd-activated microglia. rnainterference-mediated knockdown of tnf-α phenocopied the effect of mir-181c-mediated neuronal protection, whereas overexpression of tnf-α blocked the mir-181c-dependent suppression of apoptosis. further studies showed that mir-181c could directly target the 3'-untranslated region of tnf-α mrna, suppressing its mrna and protein expression. conclusions our data suggest a potential role for mir-181c in the regulation of tnf-α expression after ischemia/hypoxia and microglia-mediated neuronal injury.",1
"micrornas (mirnas) are small noncoding rnas that are involved in different biological processes by suppressing target gene expression. mirna microarray analysis revealed a significant decrease of mir-26a in prostate cancer tissues versus their normal counterparts, but the role of mir-26a is needed to investigate. in the present study, we found that mir-26a expression was lower in prostate cancer tissues compared with their normal controls, so did the prostate cancer cells. next, by lentivirus-mediated gain-of-function studies, it was showed that stable mir-26a inhibited cell proliferation, metastasis, and epithelial mesenchymal transition and induced g1 phase arrest in prostate cancer. it was predicted that wnt5a was a potential target gene of mir-26a by bioinformatics analysis. then, luciferase assay and western blot analysis identified that wnt5a was a new direct target gene of mir-26a and mir-26a inhibited prostate cancer progression via wnt5a. altogether, the findings suggested that mir-26a may function as a tumor suppressor in prostate cancer by targeting wnt5a.",1
"although molecular components of the circadian clock are known, mechanisms that transmit signals from the clock and produce rhythmic behavior are poorly understood. we find that the microrna mir-279 regulates the jak/stat pathway to drive rest:activity rhythms in drosophila. overexpression of microrna mir-279 or mir-279 deletion attenuates rest:activity rhythms. oscillations of the clock protein period are normal in pacemaker neurons lacking mir-279, suggesting that mir-279 acts downstream of the clock. we identify the jak/stat ligand, upd, as a target of mir-279 and show that knockdown of upd rescues the behavioral phenotype of mir-279 mutants. manipulations of the jak/stat pathway also disrupt circadian rhythms. in addition, central clock neurons project in the vicinity of upd-expressing neurons, providing a possible physical connection by which the central clock could regulate jak/stat signaling to control rest:activity rhythms.",1
"objective we investigated the regulation and involvement of micrornas (mirnas) in fat cell development and obesity. research design and methods using mirna microarrays, we profiled the expression of >370 mirnas during adipogenesis of preadipocyte 3t3-l1 cells and adipocytes from leptin deficient ob/ob and diet-induced obese mice. changes in key mirnas were validated by rt-pcr. we further assessed the contribution of the chronic inflammatory environment in obese adipose tissue to the dysregulated mirna expression by tumor necrosis factor (tnf)-alpha treatment of adipocytes. we functionally characterized two adipocyte-enriched mirnas, mir-103 and mir-143, by a gain-of-function approach. results similar mirnas were differentially regulated during in vitro and in vivo adipogenesis. importantly, mirnas that were induced during adipogenesis were downregulated in adipocytes from both types of obese mice and vice versa. these changes are likely associated with the chronic inflammatory environment, since they were mimicked by tnf-alpha treatment of differentiated adipocytes. ectopic expression of mir-103 or mir-143 in preadipocytes accelerated adipogenesis, as measured both by the upregulation of many adipogenesis markers and by an increase in triglyceride accumulation at an early stage of adipogenesis. conclusions our results provide the first experimental evidence for mir-103 function in adipose biology. the remarkable inverse regulatory pattern for many mirnas during adipogenesis and obesity has important implications for understanding adipose tissue dysfunction in obese mice and humans and the link between chronic inflammation and obesity with insulin resistance.",1
"recent lentiviral-based microrna (mirna) library screening has identified mirna-7 (mir-7) as an anti‑angiogenic mirna in human umbilical vein endothelial cells (huvecs). however, the underlying mechanism of mir-7 in the suppression of angiogenesis remains largely unknown. in the present study, we report that mir-7 inhibition promoted angiogenesis by upregulating vascular endothelial growth factor (vegf) and directly targeting krüppel-like factor 4 (klf4). downregulation of mir-7 promoted tube formation of huvecs, accompanied by upregulation of mrna and protein levels of both vegf and klf4. mir-7 directly targeted klf4 as demonstrated by luciferase reporter assay and mir-7 mimics decreased klf4. furthermore, bioinformatic analysis revealed the presence of multiple dna-binding elements of klf4 in the vegf promoter. chromatin immunoprecipitation (chip) demonstrated that the klf4 antibody specifically pulled down the vegf promoter in the huvecs. furthermore, ectopic overexpression of klf4 induced vegf mrna and protein levels. in addition, klf4 silencing inhibited the angiogenesis induced by the mir-7 inhibitor in the huvecs. our results demonstrated that klf4 is a direct target of mir-7 and a transcription activator of vegf. these findings indicate that the mir-7-klf4-vegf signaling axis plays an important role in the regulation of angiogenesis in huvecs, suggesting that mir-7 is a potential agent for the development of anti-angiogenic therapeutics in vascular diseases and solid tumors.",1
"background gastric cancer is the fourth most common cancer in the world and the second most prevalent cause of cancer related death. the development of gastric cancer is mainly associated with h. pylori infection leading to a focus in pathology studies on bacterial and environmental factors, and to a lesser extent on the mechanistic development of the tumour. micrornas are small non-coding rna molecules involved in post-transcriptional gene regulation. they are found to regulate genes involved in diverse biological functions and alterations in microrna expression have been linked to the pathogenesis of many malignancies. the current study is focused on identifying micrornas involved in gastric carcinogenesis and to explore their mechanistic relevance by characterizing their targets. results invitrogen ncode mirna microarrays identified mir-449 to be decreased in 1-year-old gastrin ko mice and in h. pylori infected gastric tissues compared to tissues from wild type animals. growth rate of gastric cell lines over-expressing mir-449 was inhibited by 60% compared to controls. facs cell cycle analysis of mir-449 over-expressing cells showed a significant increase in the sub-g1 fraction indicative of apoptosis. ß-gal assays indicated a senescent phenotype of gastric cell lines over-expressing mir-449. affymetrix 133v2 arrays identified gmnn, met, ccne2, sirt1 and cdk6 as mir-449 targets. luciferase assays were used to confirm gmnn, met, ccne2 and sirt1 as direct targets. we also show that mir-449 over-expression activated p53 and its downstream target p21 as well as the apoptosis markers cleaved casp3 and parp. importantly, qpcr analyses showed a loss of mir-449 expression in human clinical gastric tumours compared to normal tissues. conclusions in this study, we document a diminished expression of mir-449 in gastrin ko mice and further confirmed its loss in human gastric tumours. we investigated the function of mir-449 by identifying its direct targets. furthermore we show that mir-449 induces senescence and apoptosis by activating the p53 pathway.",1
"the prognosis of non-small cell lung cancer (nsclc) is poor, since it has often metastasized to distant organs by the time of diagnosis. therefore, biomarkers predicting metastasis are crucial. mirnas play important roles in the regulation of different tumor cell processes, including metastasis. we recently showed that mirna-214 is linked to a radioresistant phenotype of nsclc. mirna-214 has been linked to metastasis in other tumor types. therefore, we examined the role of mirna-214 in the metastatic potential of nsclc. we showed that downregulation of mirna-214 increased invasive potential, and conversely, overexpression of mirna-214 decreased invasiveness of nsclc cells in vitro. gene expression and bioinformatic analyses of nsclc cells with ablated mirna-214, identified a number of metastasis-related target genes, including pregnancy-associated plasma protein a (papp-a), alpha protein kinase 2 (alpk2), cyclin-dependent kinase 6 (cdk6) and tumor necrosis-factor alpha-induced protein 3 (tnfaip3). these were validated on mrna and protein level to be regulated by mirna-214. through immunoprecipitation we showed that only alpk2 is directly regulated by mirna-214. we also examined the protein expression of these four genes in nsclc tumors with respect to metastatic potential. these results showed that nsclc tumors express these proteins at moderate-high levels in the nucleus, cytoplasm and/or plasma membrane although with no significant correlation to the overall survival or the metastatic potential of the patients. however, we also showed that the membrane-localized papp-a had a higher expression level compared to the cytoplasm-localized. in conclusion, we show that low mirna-214 expression is linked to a higher invasive potential of nsclc cells.",1
"summary dna-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. studies with escherichia coli and bacillus subtilis pyr genes reveal a variety of regulatory mechanisms. transcription attenuation via utp-sensitive coupled transcription and translation regulates expression of the pyrbi and pyre operons in enteric bacteria, whereas nucleotide effects on binding of the pyrr protein to pyr mrna attenuation sites control pyr operon expression in most gram-positive bacteria. nucleotide-sensitive reiterative transcription underlies regulation of other pyr genes. with the e. coli pyrbi, carab, codba, and upp-uraa operons, utp-sensitive reiterative transcription within the initially transcribed region (itr) leads to nonproductive transcription initiation. ctp-sensitive reiterative transcription in the pyrg itrs of gram-positive bacteria, which involves the addition of g residues, results in the formation of an antiterminator rna hairpin and suppression of transcription attenuation. some mechanisms involve regulation of translation rather than transcription. expression of the pyrc and pyrd operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. in mycobacterium smegmatis and other bacteria, pyrr modulates translation of pyr genes by binding to their ribosome binding site. evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.",1
"myeloid-derived suppressor cells (mdsc) are one of the main cell populations that negatively regulate immune responses. however, the mechanism underlying the expansion of mdsc remains unclear. using mirna microarray and taqman probe-based quantitative rt-pcr assay, we identified microrna (mir)-155 and mir-21 as the two most upregulated mirnas during the induction of mdsc from the bone marrow cells by gm-csf and il-6. high levels of mir-155 and mir-21 also were detected in bone marrow and spleen mdsc isolated from tumor-bearing mice. our results also showed that tgf-β promoted the induction of mdsc through upregulating mir-155 and mir-21 expression. overexpression of mir-155 and mir-21 enhanced whereas depletion of mir-155 and mir-21 reduced the frequencies of cytokine-induced mdsc. subpopulation analysis indicated that mir-21 and mir-155 induced the expansion of both monocytic and granulocytic mdsc. furthermore, mir-155 and mir-21 showed a synergistic effect on mdsc induction via targeting ship-1 and phosphatase and tensin homolog, respectively, leading to stat3 activation. finally, dexamethasone treatment strongly enhanced mdsc expansion through upregulating mir-155 and mir-21 expression, and the effect of dexamethasone on mdsc induction was abolished by depleting cellular mir-155 and mir-21. these results demonstrate a novel mir-155/mir-21-based regulatory mechanism that modulates functional mdsc induction.",1
"members of the two expanding rna subclasses termed c/d and h/aca rnas guide the 2'-o-methylations and pseudouridylations, respectively, of rrna and spliceosomal rnas (snrnas). here, we report on the identification of 13 novel human intron-encoded small rnas (u94-u106) belonging to the two subclasses of modification guides. seven of them are predicted to direct 2'-o-methylations in rrna or snrnas, while the remainder represent novel orphan rna modification guides. from these, u100, which is exclusively detected in cajal bodies (cbs), is predicted to direct modification of a u6 snrna uridine, u(9), which to date has not been found to be pseudouridylated. hence, within cbs, u100 might function in the folding pathway or other aspects of u6 snrna metabolism rather than acting as a pseudouridylation guide. u106 c/d snorna might also possess an rna chaperone activity only since its two conserved antisense elements match two rrna sequences devoid of methylated nucleotides and located remarkably close to each other within the 18s rrna secondary structure. finally, we have identified a retrogene for u99 snorna located within an intron of the siat5 gene, supporting the notion that retro-transposition events might have played a substantial role in the mobility and diversification of snorna genes during evolution.",1
"the genomic rnas of flaviviruses such as dengue virus (den) have a 5' m7gpppn cap like those of cellular mrnas but lack a 3' poly(a) tail. we have studied the contributions to translational expression of 5'- and 3'-terminal regions of the den serotype 2 genome by using luciferase reporter mrnas transfected into vero cells. dcld rna contained the entire den 5' and 3' untranslated regions (utrs), as well as the first 36 codons of the capsid coding region fused to the luciferase reporter gene. capped dcld rna was as efficiently translated in vero cells as capped glgpa rna, a reporter with utrs from the highly expressed alpha-globin mrna and a 72-residue poly(a) tail. analogous reporter rnas with regulatory sequences from west nile and sindbis viruses were also strongly expressed. although capped dcld rna was expressed much more efficiently than its uncapped form, uncapped dcld rna was translated 6 to 12 times more efficiently than uncapped rnas with utrs from globin mrna. the 5' cap and den 3' utr were the main sources of the translational efficiency of dcld rna, and they acted synergistically in enhancing translation. the den 3' utr increased mrna stability, although this effect was considerably weaker than the enhancement of translational efficiency. the den 3' utr thus has translational regulatory properties similar to those of a poly(a) tail. its translation-enhancing effect was observed for rnas with globin or den 5' sequences, indicating no codependency between viral 5' and 3' sequences. deletion studies showed that translational enhancement provided by the den 3' utr is attributable to the cumulative contributions of several conserved elements, as well as a nonconserved domain adjacent to the stop codon. one of the conserved elements was the conserved sequence (cs) cs1 that is complementary to ccs1 present in the 5' end of the den polyprotein open reading frame. complementarity between cs1 and ccs1 was not required for efficient translation.",1
"the self-cleaving ribozyme of the hepatitis delta virus (hdv) is the only catalytic rna known to be required for the viability of a human pathogen. we obtained crystals of a 72-nucleotide, self-cleaved form of the genomic hdv ribozyme that diffract x-rays to 2.3 a resolution by engineering the rna to bind a small, basic protein without affecting ribozyme activity. the co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. the 5'-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.",1
"brown adipose tissue (bat) protects against obesity by promoting energy expenditure via uncoupled respiration. to uncover bat-specific long non-coding rnas (lncrnas), we used rna-seq to reconstruct de novo transcriptomes of mouse brown, inguinal white, and epididymal white fat and identified ∼1,500 lncrnas, including 127 bat-restricted loci induced during differentiation and often targeted by key regulators pparγ, c/ebpα, and c/ebpβ. one of them, lnc-bate1, is required for establishment and maintenance of bat identity and thermogenic capacity. lnc-bate1 inhibition impairs concurrent activation of brown fat and repression of white fat genes and is partially rescued by exogenous lnc-bate1 with mutated sirna-targeting sites, demonstrating a function in trans. we show that lnc-bate1 binds heterogeneous nuclear ribonucleoprotein u and that both are required for brown adipogenesis. our work provides an annotated catalog for the study of fat depot-selective lncrnas and establishes lnc-bate1 as a regulator of bat development and physiology.",1
"epitranscriptomics refers to posttranscriptional alterations on an mrna sequence that are dynamic and reproducible, and affect gene expression in a similar way to epigenetic modifications. however, the functional relevance of those modifications for the transcript, the cell, and the organism remain poorly understood. here, we focus on rna editing and show that apolipoprotein b mrna-editing enzyme, catalytic polypeptide-1 (apobec1), together with its cofactor rbm47, mediates robust editing in different tissues. the majority of editing events alter the sequence of the 3'utr of targeted transcripts, and we focus on one cell type (monocytes) and on a small set of highly edited transcripts within it to show that editing alters gene expression by modulating translation (but not rna stability or localization). we further show that specific cellular processes (phagocytosis and transendothelial migration) are enriched for transcripts that are targets of editing and that editing alters their function. finally, we survey bone marrow progenitors and demonstrate that common monocyte progenitor cells express high levels of apobec1 and are susceptible to loss of the editing enzyme. overall, apobec1-mediated transcriptome diversification is required for the fine-tuning of protein expression in monocytes, suggesting an epitranscriptomic mechanism for the proper maintenance of homeostasis in innate immune cells.",1
"objectives acute viral myocarditis (vm) is an important cause of sudden cardiac death and heart failure in healthy young person. its pathogenesis is based on an adverse immune response evoked by infection of the cardiac muscle by cardiotropic viruses especially coxackievirus b3 (cvb3). micrornas (mirnas) are short, noncoding rna sequences that regulate gene expression at the posttranscriptional level. recently, there are reports that disturbed mirnas expression is associated with vm but the mechanism is not well understood. materials and methods herein, we screened 15 selected mirnas in myocardial tissues of patients with acute cvb3 caused myocarditis and found the expression of mir-155 and mir-148a was up-regulated significantly. results predicted by using bioinformatics tools and confirmed by dual-luciferase assay and western blot, we confirmed that rela is a direct target gene of mir-155 and mir-148a. subsequent in vitro functional study indicated that mir-155 function as immune response negative feedback factor that reduced cardiac myoblast cytokines expression during cvb3 infection. further in vivo experiments indicated that mir-155 can improved mice survival rate when cvb3 infected. conclusions so, our study indicated that mir-155 is a potential therapeutic target for viral myocarditis.",1
"hulc is a long noncoding rna overexpressed in hepatocellular carcinoma (hcc), but its functional contributions in this setting have not been determined. in this study, we explored the hypothesis that hulc contributes to malignant development by supporting abnormal lipid metabolism in hepatoma cells. hulc modulated the deregulation of lipid metabolism in hcc by activating the acyl-coa synthetase subunit acsl1. immunohistochemical analysis of tissue microarrays revealed that approximately 77% (180/233) of hcc tissues were positive for acsl1. moreover, hulc mrna levels correlated positively with acsl1 levels in 60 hcc cases according to real-time pcr analysis. mechanistic investigations showed that hulc upregulated the transcriptional factor ppara, which activated the acsl1 promoter in hepatoma cells. hulc also suppressed mir-9 targeting of ppara mrna by eliciting methylation of cpg islands in the mir-9 promoter. we documented the ability of hulc to promote lipogenesis, thereby stimulating accumulation of intracellular triglycerides and cholesterol in vitro and in vivo. strikingly, acsl1 overexpression that generates cholesterol was sufficient to enhance the proliferation of hepatoma cells. further, cholesterol addition was sufficient to upregulate hulc expression through a positive feedback loop involving the retinoid receptor rxra, which activated the hulc promoter. overall, we concluded that hulc functions as an oncogene in hepatoma cells, acting mechanistically by deregulating lipid metabolism through a signaling pathway involving mir-9, ppara, and acsl1 that is reinforced by a feed-forward pathway involving cholesterol and rxra to drive hulc signaling.",1
"background accumulating evidence indicates that the long non-coding rna hotair plays a critical role in cancer progression and metastasis. however, the overall biological role and clinical significance of hotair in gastric carcinogenesis remains largely unknown. methods hotair expression was measured in 78 paired cancerous and noncancerous tissue samples by real-time pcr. the effects of hotair on gastric cancer cells were studied by overexpression and rna interference approaches in vitro and in vivo. insights of the mechanism of competitive endogenous rnas (cernas) were gained from bioinformatic analysis, luciferase assays and rna binding protein immunoprecipitation (rip). the positive hotair/her2 interaction was identified and verified by immunohistochemistry assay and bivariate correlation analysis. results hotair upregulation was associated with larger tumor size, advanced pathological stage and extensive metastasis, and also correlated with shorter overall survival of gastric cancer patients. furthermore, hotair overexpression promoted the proliferation, migration and invasion of gastric carcinoma cells, while hotair depletion inhibited both cell invasion and cell viability, and induced growth arrest in vitro and in vivo. in particular, hotair may act as a cerna, effectively becoming a sink for mir-331-3p, thereby modulating the derepression of her2 and imposing an additional level of post-transcriptional regulation. finally, the positive hotair/her2 correlation was significantly associated with advanced gastric cancers. conclusions hotair overexpression represents a biomarker of poor prognosis in gastric cancer, and may confer malignant phenotype to tumor cells. the cerna regulatory network involving hotair and the positive interaction between hotair and her2 may contribute to a better understanding of gastric cancer pathogenesis and facilitate the development of lncrna-directed diagnostics and therapeutics against this disease.",1
"endothelial senescence is thought to play a role in cardiovascular diseases such as atherosclerosis. we hypothesized that endothelial micrornas (mirnas) regulate endothelial survival and senescence. we found that mir-34a is highly expressed in primary endothelial cells. we observed that mir-34a expression increases in senescent human umbilical cord vein endothelial cells (huvec) and in heart and spleen of older mice. mir-34a over-expression induces endothelial cell senescence and also suppresses cell proliferation by inhibiting cell cycle progression. searching for how mir-34a affects senescence, we discovered that sirt1 is a target of mir-34a. over-expressing mir-34a inhibits sirt1 protein expression, and knocking down mir-34a enhances sirt1 expression. mir-34a triggers endothelial senescence in part through sirt1, since forced expression of sirt1 blocks the ability of mir-34a to induce senescence. our data suggest that mir-34a contributes to endothelial senescence through suppression of sirt1.",1
"wild-type p53-induced phosphatase 1 (wip1) was identified as an oncogene amplified and overexpressed in several human cancers. recent evidence suggested that wip1 is a critical inhibitor in the atm/atr-p53 dna damage signaling pathway. wip1 dephosphorylates several key dna damage-responsive proteins and reverses dna damage-induced cell cycle checkpoints. previous reports showed that wip1 was transcriptionally induced by p53 at the early stage of the dna damage response. to investigate the temporal and functional regulation of wip1, we identified a microrna, mir-16, that specifically targets the mrna of wip1 and thus negatively regulates the expression level of wip1. mir-16 itself is induced immediately after dna damage. therefore, the increase in wip1 protein level is significantly postponed compared with that of its mrna level, preventing a premature inactivation of atm/atr signaling and allowing a functional completion of the early dna damage response. to better understand mir-16 biological functions in the context of cancer cells, we examined its expression in mammary tumor stem cells and found it to be markedly downregulated in mammary tumor stem cells. overexpression of mir-16 or inhibition of wip1 suppresses the self-renewal and growth of mouse mammary tumor stem cells and sensitizes mcf-7 human breast cancer cells to the chemotherapeutic drug doxorubicin. together, our results suggest an important role of mir-16 in the regulation of wip1 phosphatase in the dna damage response and mammary tumorigenesis.",1
"a previous study reported that the mir-181a level in serum was significantly different between patients with methamphetamine-use disorder and healthy controls and that chronic methamphetamine use down-regulates the expression of mir-181a. bioinformatic analysis predicted that mir-181a might bind the 3'-utrs of the mrna transcripts of the human glutamate receptor genes gria2 and gabra1. in this study, we measured the expression of gria2 and gabra1 in patients with methamphetamine-use disorder. in addition, we examined whether mir-181a down-regulates gria2 and gabra1 in a cell-based assay. we further examined the effects of chronic methamphetamine exposure on the expression of mir-181a, gria2 and gabra1. the results demonstrated that serum gria2 is higher in patients with methamphetamine-use disorder than in healthy controls. dual luciferase reporter assays and a cell-based model of methamphetamine exposure also showed that mir-181a directly regulates expression of gria2. this study supports the evidence that mir-181a and the glutamate ampa receptor gene gria2 play a critical role in methamphetamine-use disorder.",1
"background recent research has suggested that the oncomir microrna 155 (mir-155) is up-regulated in hepatocellular carcinoma (hcc). in this study, the authors investigated the tumorigenic mechanism of this oncomir in the development of hcc. methods quantitative reverse transcriptase-polymerase chain reaction (rt-pcr) was conducted to analyze the expressions of mir-155 and its potential target genes in paired tumor tissues and adjacent tumor-free tissues and in disease-free liver tissue samples. the in silico predicted target genes of mir-155 were assessed by dual-luciferase reporting assay, real-time rt-pcr, and western blot analyses. u6 promoters that drive mir-155 precursor overexpression and mir-155 tough decoy knock-down constructs were used to study its affects on cell proliferation in vitro and on tumor formation in nude mice. results quantitative rt-pcr demonstrated a gradual ascension of mir-155 expression in cirrhotic liver tissues and in hcc tumor tissues compared with low expression levels in normal liver tissues. ectopic expression of mir-155 in hepg2 cells enhanced its tumorigenesis, whereas depletion of the endogenous mir-155 reversed these tumorigenic properties. ectopic expression of sex-determining region y box 6 (sox6) was able to reverse the growth-promoting property of mir-155. concordantly, the results demonstrated for the first time that sox6 is a direct target of mir-155. further analysis revealed that sox6 reduced cell growth by up-regulating p21waf1/cip1 expression in a p53-dependent manner. in addition, a decline in p21waf1/cip1 expression caused by mir-155 could be reversed by sox6 expression. conclusions the current data indicated that sox6 is a novel target of mir-155 and that mir-155 enhances liver cell tumorigenesis at least in part through the novel mir-155/sox6/p21waf1/cip1 axis. these findings suggest that mir-155 may be a potential target for hcc treatment.",1
"background mast cells (mcs) play a central role in allergic and inflammatory disorders by rapid degranulation and release of inflammatory mediators upon antigen-driven engagement of the fcεri. receptor-mediated mc responses are controlled by the activation of different isoforms of phosphoinositide-3-kinase (pi3k) and the downstream signaling processes. recent evidence suggests that mirnas are important molecular players regulating the pi3k/akt pathway. methods the role of mir-155 in the regulation of mc functions in vivo was studied in the passive cutaneous anaphylaxis (pca) mc-dependent model. wt and mir-155(-/-) mice were injected intradermally with anti-dnp-ige and intravenously with the antigen dnp-hsa. ear swelling was assessed to evaluate the anaphylactic response. all investigations, to characterize mir-155 specific activities in mcs, were conducted comparing wt and mir-155(-/-) bone marrow-derived mcs (bmmcs). results we report that mir-155(-/-) mice display enhanced anaphylaxis reactions. although mir-155(-/-) bmmcs show normal development, proliferation, and survival, mir-155 deficiency enhances fcεri-mediated degranulation and release of tnf-α, il-13, and il-6. interestingly, the level of akt phosphorylation on both of its regulatory residues thr308 and ser473 was increased in mir-155(-/-) compared to wt bmmcs. gene expression profiling showed that mir-155(-/-) bmmcs exhibited significantly increased expression of the adapter pi3kγ subunits pik3r5 (p101) and pik3r6 (p84, p87(pikap) ). furthermore, selective blockade of the pi3kγ pathway inhibited degranulation in mir-155(-/-) bmmcs. conclusions thus, we suggest that mir-155 plays a critical role in fcεri-mediated mc responses by modulating components of the pi3kγ pathway. this newly identified mechanism of mirna-controlled mc activation may affect the initiation and maintenance of allergic disorders.",1
"microrna-125b (mir-125b) has been reported to be upregulated in several kinds of leukemia, suggesting that mir-125b plays a role in leukemia development. in this study, it was shown that mir-125b expression level decreased in response to 1α, 25-dihydroxy-vitamin d3 (1,25d 3 ) in a dose- and time-dependent manner and mir-125b blocked 1,25d 3 -induced monocytic differentiation of u937 cells. in addition, mir-125b decreased mrna expression of myelomonocytic differentiation markers, including cd11c, cd18 and cd64 and arrested the cell cycle at the s phase in u937 and hl60 cells. fes was identified as a novel direct target of mir-125b and mir-125b could also reduce the expression levels of pu.1 and macrophage colony-stimulating factor receptor (mcsfr). furthermore, fes was found to be involved in monocytic differentiation via upregulation of pu.1 and mcsfr and fes sirna could also inhibit 1,25d 3 -induced monocytic differentiation of u937 and hl60 cells and decrease mrna expression of cd11c, cd18 and cd64. importantly, the inhibition of fes sirna on 1,25d 3 -induced monocytic differentiation could be rescued by transfection with mir-125b inhibitor. our data highlights an important role of mir-125b in aml progression, implying the potential application of mir-125b in aml therapy.",1
"nasopharyngeal carcinoma (npc), a highly metastatic and invasive malignant tumor originating from the nasopharynx, is widely prevalent in southeast asia, the middle east and north africa. although viral, dietary and genetic factors have been implicated in npc, the molecular basis of its pathogenesis is not well defined. based on a recent microrna (mirna) microarray study showing mir-200 downregulation in npc, we further investigated the role of mir-200a in npc carcinogenesis. we found that the endogenous mir-200a expression level increases with the degree of differentiation in a panel of npc cell lines, namely undifferentiated c666-1, high-differentiated cne-1, and low-differentiated cne-2 and hne1 cells. by a series of gain-of-function and loss-of-function studies, we showed that over-expression of mir-200a inhibits c666-1 cell growth, migration and invasion, whereas its knock-down stimulates these processes in cne-1 cells. in addition, we further identified zeb2 and ctnnb1 as the functional downstream targets of mir-200a. interestingly, knock-down of zeb2 solely impeded npc cell migration and invasion, whereas ctnnb1 suppression only inhibited npc cell growth, suggesting that the inhibitory effects of mir-200a on npc cell growth, migration and invasion are mediated by distinct targets and pathways. our results reveal the important role of mir-200a as a regulatory factor of npc carcinogenesis and a potential candidate for mirna-based therapy against npc.",1
"the amyloid precursor protein (app) and its proteolytic product amyloid beta (abeta) are associated with both familial and sporadic forms of alzheimer disease (ad). aberrant expression and function of micrornas has been observed in ad. here, we show that in rat hippocampal neurons cultured in vitro, the down-regulation of argonaute-2, a key component of the rna-induced silencing complex, produced an increase in app levels. using site-directed mutagenesis, a microrna responsive element (re) for mir-101 was identified in the 3'-untranslated region (utr) of app. the inhibition of endogenous mir-101 increased app levels, whereas lentiviral-mediated mir-101 overexpression significantly reduced app and abeta load in hippocampal neurons. in addition, mir-101 contributed to the regulation of app in response to the proinflammatory cytokine interleukin-1beta (il-lbeta). thus, mir-101 is a negative regulator of app expression and affects the accumulation of abeta, suggesting a possible role for mir-101 in neuropathological conditions.",1
"the interactions of numerous regulatory small rnas (srnas) with target mrnas have been characterized, but how srnas can regulate multiple, structurally unrelated mrnas is less understood. here we show that salmonella gcvb srna directly acts on seven target mrnas that commonly encode periplasmic substrate-binding proteins of abc uptake systems for amino acids and peptides. alignment of gcvb homologs of distantly related bacteria revealed a conserved g/u-rich element that is strictly required for gcvb target recognition. analysis of target gene fusion regulation in vivo, and in vitro structure probing and translation assays showed that gcvb represses its target mrnas by binding to extended c/a-rich regions, which may also serve as translational enhancer elements. in some cases (oppa, dppa), gcvb repression can be explained by masking the ribosome-binding site (rbs) to prevent 30s subunit binding. however, gcvb can also effectively repress translation by binding to target mrnas at upstream sites, outside the rbs. specifically, gcvb represses glti mrna translation at the c/a-rich target site located at positions -57 to -45 relative to the start codon. taken together, our study suggests highly conserved regions in srnas and mrna regions distant from shine-dalgarno sequences as important elements for the identification of srna targets.",1
"aim multi-drug resistance poses a critical bottleneck in chemotherapy. given the up-regulation of mtor pathway in many chemoresistant cancers, we examined whether sirolimus (rapamycin), a first generation mtor inhibitor, might induce human osteosarcoma (os) cell apoptosis and increase the sensitivity of os cells to anticancer drugs in vitro. methods human os cell line mg63/adm was treated with sirolimus alone or in combination with doxorubicin (adm), gemcitabine (gem) or methotrexate (mtx). cell proliferation and apoptosis were detected using cck-8 assay and flow cytometry, respectively. mirnas in the cells were analyzed with mirna microarray. the targets of mir-34b were determined based on targetscan analysis and luciferase reporter assays. the expression of relevant mrna and proteins was measured using qrt-pcr and western blotting. mir-34, pak1 and abcb1 levels in 40 tissue samples of os patients were analyzed using qrt-pcr and in situ hybridization assays. results sirolimus (1-100 nmol/l) dose-dependently suppressed the cell proliferation (ic50=23.97 nmol/l) and induced apoptosis. sirolimus (10 nmol/l) significantly sensitized the cells to anticancer drugs, leading to decreased ic50 values of adm, gem and mtx (from 25.48, 621.41 and 21.72 μmol/l to 4.93, 73.92 and 6.77 μmol/l, respectively). treatment of with sirolimus increased mir-34b levels by a factor of 7.5 in the cells. upregulation of mir-34b also induced apoptosis and increased the sensitivity of the cells to the anticancer drugs, whereas transfection with mir-34b-amo, an inhibitor of mir-34b, reversed the anti-proliferation effect of sirolimus. two key regulators of cell cycle, apoptosis and multiple drug resistance, pak1 and abcb1, were demonstrated to be the direct targets of mir-34b. in 40 tissue samples of os patients, significantly higher mir-34 ish score and lower pak5 and abcb1 scores were detected in the chemo-sensitive group. conclusion sirolimus increases the sensitivity of human os cells to anticancer drugs in vitro by up-regulating mir-34b interacting with pak1 and abcb1. a low mir-34 level is an indicator of poor prognosis in os patients.",1
"micrornas are endogenous approximately 23-nucleotide rnas that can pair to sites in the messenger rnas of protein-coding genes to downregulate the expression from these messages. micrornas are known to influence the evolution and stability of many mrnas, but their global impact on protein output had not been examined. here we use quantitative mass spectrometry to measure the response of thousands of proteins after introducing micrornas into cultured cells and after deleting mir-223 in mouse neutrophils. the identities of the responsive proteins indicate that targeting is primarily through seed-matched sites located within favourable predicted contexts in 3' untranslated regions. hundreds of genes were directly repressed, albeit each to a modest degree, by individual micrornas. although some targets were repressed without detectable changes in mrna levels, those translationally repressed by more than a third also displayed detectable mrna destabilization, and, for the more highly repressed targets, mrna destabilization usually comprised the major component of repression. the impact of micrornas on the proteome indicated that for most interactions micrornas act as rheostats to make fine-scale adjustments to protein output.",1
"reciprocal relationship usually exists between osteoblastogenesis and adipogenesis, with factors stimulating one of these processes at the same time inhibiting the other. in the present study, mir-30e was found to be involved in the reciprocal regulation of osteoblast and adipocyte differentiation. our data indicated that mir-30e was induced in primarily cultured mouse bone marrow stromal cell, mesenchymal cell line c3h10t1/2 and preadipocyte 3t3-l1 after adipogenic treatment. conversely, it was reduced in mouse stromal line st2 and preosteoblast mc3t3-e1 after osteogenic treatment. enforced expression of mir-30e in 3t3-l1 significantly suppressed the growth of the cells and induced the preadipocytes to differentiate into mature adipocytes, along with increased expression of adipocyte-specific transcription factors peroxisome proliferator-activated receptor-γ (pparγ), ccaat/enhancer binding protein-α (c/ebpα) and c/ebpβ, and the marker gene ap2. in contrast, inhibition of the endogenous mir-30e enhanced the cell growth and repressed preadipocytes to differentiate. conversely, supplementing mir-30e activity blocked, whereas knocking down mir-30e enforced the preosteoblast mc3t3-e1 to fully differentiate. furthermore, mir-30e overexpression stimulated adipocyte formation and inhibited osteoblast differentiation from marrow stromal cells. low-density lipoprotein receptor-related protein 6 (lrp6), one of the critical coreceptor for wnts, was shown to be a direct target of mir-30e by using the luciferase assay. knockdown of lrp6 in 3t3-l1 cells downregulated β-catenin/t-cell factor (tcf) transcriptional activity and dramatically potentiated the differentiation of the cells into mature adipocytes. taken together, the present work suggests that the expression of mir-30e is indispensable for maintaining the balance of adipocytes and osteoblasts by targeting the canonical wnt/β-catenin signaling.",1
"micrornas (mirnas) attenuate gene expression by pairing to the 3'utr of target transcripts inducing rna cleavage or translational inhibition. overexpression of microrna-155 (mir-155), measured either at the primary (bic gene) or mature transcript level, was recently described in diffuse large b-cell lymphomas (dlbcl). these studies have been limited in size, however, and have not attempted to link mir-155 expression to that of putative target genes. to start to address these issues, we examined a collection of 22 well-characterized dlbcl cell lines. the expression of mir-155 is heterogeneous in these cell lines and associates with nf-kappab activity. we found that the expression of the primary mir-155 transcript reliably reflects that of the functional mature mir-155. because many gene array platforms include probe sets for the primary mir-155 sequences, these findings allowed us to confidently examine large array-based expression datasets of primary dlbcls in the context of mir-155 levels. our investigation revealed that mir-155 expression segregates with specific molecular subgroups of dlbcl and it is highest in activated b-cell (abc)-type lymphomas. these tumors are characterized by constitutive activation of nf-kappab signals, which supports the data derived from our cell lines. more importantly, using supervised learning algorithms, we identified a robust gene signature driven by the differential expression of mir-155. these profiles contained several gene markers, including predicted targets, consistently downregulated in tumors expressing high levels of mir-155. our data start to unveil the genome-wide effects of mir-155 expression in dlbcl and indicate the utility of this strategy in the identification and validation of mirna target genes.",1
"it has been proposed that the inflammatory response of monocytes/macrophages induced by oxidized low-density lipoprotein (oxldl) is a key event in the pathogenesis of atherosclerosis. microrna-155 (mir-155) is an important regulator of the immune system and has been shown to be involved in acute inflammatory response. however, the function of mir-155 in oxldl-stimulated inflammation and atherosclerosis remains unclear. here, we show that the exposure of human thp-1 macrophages to oxldl led to a marked up-regulation of mir-155 in a dose-dependent manner. silencing of endogenous mir-155 in thp-1 cells using locked nucleic acid-modified antisense oligonucleotides significantly enhanced oxldl-induced lipid uptake, up-regulated the expression of scavenger receptors (lectinlike oxidized ldl receptor-1, cluster of differentiation 36 , and cd68), and promoted the release of several cytokines including interleukin (il)-6, -8, and tumor necrosis factor α (tnf-α). luciferase reporter assay showed that targeting mir-155 promoted nuclear factor-kappa b (nf-κb) nuclear translocation and potentiated the nf-κb-driven transcription activity. moreover, mir-155 knockdown resulted in a marked increase in the protein amount of myeloid differentiation primary response gene 88 (myd88), an important adapter protein used by toll-like receptors to activate the nf-κb pathway. our data demonstrate that mir-155 serves as a negative feedback regulator in oxldl-stimulated thp-1 inflammatory responses and lipid uptake and thus might have potential therapeutic implications in atherosclerosis.",1
"self-cleaving ribozymes are catalytic rnas that cut themselves at a specific inter-nucleotide linkage. they serve as a model of rna catalysis, and as an important tool in biotechnology. for most of the nine known structural classes of self-cleaving ribozymes, at least hundreds of examples are known, and some are present in multiple domains of life. by contrast, only four unique examples of the hairpin ribozyme class are known, despite its discovery in 1986. we bioinformatically predicted 941 unique hairpin ribozymes of a different permuted form from the four previously known hairpin ribozymes, and experimentally confirmed several diverse predictions. these results profoundly expand the number of natural hairpin ribozymes, enabling biochemical analysis based on natural sequences, and suggest that a distinct permuted form is more biologically relevant. moreover, all novel hairpins were discovered in metatranscriptomes. they apparently reside in rna molecules that vary both in size-from 381 to 5170 nucleotides-and in protein content. the rna molecules likely replicate as circular single-stranded rnas, and potentially provide a dramatic increase in diversity of such rnas. moreover, these organisms have eluded previous attempts to isolate rna viruses from metatranscriptomes-suggesting a significant untapped universe of viruses or other organisms hidden within metatranscriptome sequences.",1
"drosophila dicer-1 produces micrornas (mirnas) from pre-mirna, whereas dicer-2 generates small interfering rnas (sirnas) from long dsrna. alternative splicing of the loquacious (loqs) mrna generates three distinct dicer partner proteins. to understand the function of each, we constructed flies expressing loqs-pa, loqs-pb, or loqs-pd. loqs-pd promotes both endo- and exo-sirna production by dicer-2. loqs-pa or loqs-pb is required for viability, but the proteins are not fully redundant: a specific subset of mirnas requires loqs-pb. surprisingly, loqs-pb tunes where dicer-1 cleaves pre-mir-307a, generating a longer mirna isoform with a distinct seed sequence and target specificity. the longer form of mir-307a represses glycerol kinase and taranis mrna expression. the mammalian dicer-partner trbp, a loqs-pb homolog, similarly tunes where dicer cleaves pre-mir-132. thus, dicer-binding partner proteins change the choice of cleavage site by dicer, producing mirnas with target specificities different from those made by dicer alone or dicer bound to alternative protein partners.",1
"the invasive behavior of glioblastoma multiforme (gbm) cells is one of the most important reasons for the poor prognosis of this cancer. for invasion, tumor cells must acquire an ability to digest the extracellular matrix and infiltrate the normal tissue bordering the tumor. preventing this by altering effector molecules can significantly improve a patient's prognosis. accumulating evidence suggests that mirnas are involved in multiple biological functions, including cell invasion, by altering the expression of multiple target genes. the expression levels of mir-218 correlate with the invasive potential of gbm cells. in this study, we found that mir-218 expression was low in glioma tissues, especially in gbm. the data showed an inverse correlation in 60 gbm tissues between the levels of mir-218 and mmp mrnas (mmp-2, -7 and -9). additionally, ectopic expression of mir-218 suppressed the invasion of gbm cells whereas inhibition of mir-218 expression enhanced the invasive ability. numerous members of the mmp family are downstream effectors of the wnt/lef1 pathway. target prediction databases and luciferase data showed that lef1 is a new direct target of mir-218. importantly, western blot assays demonstrated that mir-218 can reduce protein levels of lef1 and mmp-9. we, therefore, hypothesize that mir-218 directly targets lef1, resulting in reduced synthesis of mmp-9. results suggest that mir-218 is involved in the invasive behavior of gbm cells and by targeting lef1 and blocking the invasive axis, mir-218-lef1-mmps, it may be useful for developing potential clinical strategies.",1
"the nucleolus, the site of pre-ribosomal rna (pre-rrna) synthesis and processing in eukaryotic cells, contains a number of small nucleolar rnas (snornas). yeast u3 snorna is required for the processing of 18s rrna from larger precursors and contains a region complementary to the pre-rrna. substitution mutations in the pre-rrna which disrupt this base pairing potential are lethal and prevent synthesis of 18s rrna. these mutant pre-rrnas show defects in processing which closely resemble the effects of genetic depletion of components of the u3 snornp. co-expression of u3 snornas which carry compensatory mutations allows the mutant pre-rrnas to support viability and synthesize 18s rrna at high levels. pre-rrna processing steps which are blocked by the external transcribed spacer region mutations are largely restored by expression of the compensatory u3 mutants. pre-rrna processing therefore requires direct base pairing between snorna and the substrate. base pairing with the substrate is thus a common feature of small rnas involved in mrna and rrna maturation.",1
"the wnt/β-catenin signaling pathway is crucial for human organ development and is involved in tumor progression of many cancers. accumulating evidence suggests that the expression of β-catenin is, in part, regulated by specific micrornas (mirnas). the purpose of this study was to determine the expression of a recently identified epithelial to mesenchymal transition (emt)-associated tumor suppressor microrna (mir)-200a, in cancer cells. we also aimed to identify specific mir-200a target genes and to investigate the antitumor effects of mir-200a on the wnt/β-catenin signaling pathway. we employed top/fop flash luciferase assays to identify the effect of mir-200a on the wnt/β-catenin pathway and we confirmed our observations using fluorescence microscopy. to determine target genes of mir-200a, a 3' untranslated region (3' utr) luciferase assay was performed. cell viability, invasion and wound healing assays were carried out for functional analysis after mirna transfection. we further investigated the role of mir-200a in emt by western blot analysis. we found fluctuation in the expression of mir-200a that was accompanied by changes in the expression of members of the wnt/β-catenin signaling pathway. we also determined that mir-200a can directly interact with the 3' utr of ctnnb1 (the gene that encodes β-catenin) to suppress wnt/β-catenin signaling. mir-200a could also influence the biological activities of sgc790 and u251 cells. our results demonstrate that mir-200a is a new tumor suppressor that can regulate the activity of the wnt/β-catenin signaling pathway via two mechanisms. mir-200a is a candidate target for tumor treatment via its regulation of the wnt/β-catenin signaling pathway.",1
"methyl donors play critical roles in nutritional programming through epigenetic regulation of gene expression. here we fed gestational sows with control or betaine-supplemented diets (3g/kg) throughout the pregnancy to explore the effects of maternal methyl-donor nutrient on neonatal expression of hepatic lipogenic genes. betaine-exposed piglets demonstrated significantly lower liver triglyceride content associated with down-regulated hepatic expression of lipogenic genes acetyl-coa carboxylase (acc), fatty acid synthase (fas), stearoyl-coa desaturase (scd) and sterol regulatory element-binding protein-1c. moreover, s-adenosyl methionine to s-adenosyl homocysteine ratio was elevated in the liver of betaine-exposed piglets, which was accompanied by dna hypermethylation on fas and scd gene promoters and more enriched repression histone mark h3k27me3 on scd gene promoter. furthermore, glucocorticoid receptor (gr) binding to scd gene promoter was diminished along with reduced serum cortisol and liver gr protein content in betaine-exposed piglets. gr-mediated scd gene regulation was confirmed in hepg2 cells in vitro. dexamethasone (dex) drastically increased the luciferase activity of porcine scd promoter, while the deletion of gr response element on scd promoter significantly attenuated dex-mediated scd transactivation. in addition, mir-let-7e, mir-1285 and mir-124a, which respectively target porcine scd, acc and gr, were significantly up-regulated in the liver of betaine-exposed piglets, being in accordance with decreased protein content of these three genes. taken together, our results suggest that maternal dietary betaine supplementation during gestation attenuates hepatic lipogenesis in neonatal piglets via epigenetic and gr-mediated mechanisms.",1
"micrornas are a class of non-coding rnas including approximately 22 nucleotides in length and play a pivotal role in post-transcriptional gene regulation. currently, the role of mirnas in the pathophysiology of ischemic stroke has been the subject of recent investigations. in particular, antagomirs to microrna (mirna) let-7f have been found to be neuroprotective in vivo, although the detailed function of let-7f during cerebral ischemia has not been fully illustrated. ndrg3 is an n-myc downstream-regulated gene (ndrg) family member that has been observed in the nuclei in most brain cells. recently, a ndrg3-mediated lactate signaling, in which stabilized ndrg3 protein can promote angiogenesis and cell growth by activating the raf-erk pathway in hypoxia was discovered. in this study, we preliminarily explored the change in the expression of the ndrg3 protein which indicated that ndrg3 protein is an oxygen-regulated protein in neurons in rat cerebral ischemia in vivo and in vitro. we further identified let-7f as an upstream regulator of ndrg3 by the lentiviral transfection of rat cortical neurons and the dual luciferase analysis of human genes. in addition, a dual-color fluorescence in situ hybridization assay showed that when the expression of let-7f was elevated, the expression of ndrg3 mrna was accordingly reduced in rat cerebral ischemia. taken together, our results identify a new regulatory mechanism of let-7f on ndrg3 expression in the hypoxic response of cerebral ischemia and raise the possibility that the let-7f/ndrg3 pathway may serve as a potential target for the treatment of ischemic stroke.",1
"recurrent spontaneous abortion (rsa) is a common health problem that affects women of reproductive age. recent studies have indicated that micrornas are important factors in miscarriage. this study investigated the role of mir-16 in regulating vascular endothelial growth factor (vegf) expression and the pathogenesis of rsa. in this report, clinical samples revealed that mir-16 expression was significantly elevated in the villi and decidua of rsa patients. in vitro, mir-16 upregulation inhibited human umbilical vein endothelial cell proliferation, migration and tube formation. conversely, the downregulation of mir-16 reversed these effects. in vivo, we demonstrated that abnormal mir-16 levels affect the weights of the placenta and embryo and the number of progeny and microvascular density, as well as cause recurrent abortions by controlling vegf expression in pregnant mice. vegf, a potential target gene of mir-16, was inversely correlated with mir-16 expression in the decidua of clinical samples. furthermore, the luciferase reporter system demonstrated that mir-16 was found to directly downregulate the expression of vegf by binding a specific sequence of its 3'-untranslated region (3'utr). collectively, these data strongly suggest that mir-16 regulates placental angiogenesis and development by targeting vegf expression and is involved in the pathogenesis of rsa.",1
"rationale formation and remodeling of the vasculature during development and disease involve a highly conserved and precisely regulated network of attractants and repellants. various signaling pathways control the behavior of endothelial cells, but their posttranscriptional dose titration by micrornas is poorly understood. objective to identify micrornas that regulate angiogenesis. methods and results we show that the highly conserved microrna family encoding mir-10 regulates the behavior of endothelial cells during angiogenesis by positively titrating proangiogenic signaling. knockdown of mir-10 led to premature truncation of intersegmental vessel growth in the trunk of zebrafish larvae, whereas overexpression of mir-10 promoted angiogenic behavior in zebrafish and cultured human umbilical venous endothelial cells. we found that mir-10 functions, in part, by directly regulating the level of fms-related tyrosine kinase 1 (flt1), a cell-surface protein that sequesters vascular endothelial growth factor, and its soluble splice variant sflt1. the increase in flt1/sflt1 protein levels upon mir-10 knockdown in zebrafish and in human umbilical venous endothelial cells inhibited the angiogenic behavior of endothelial cells largely by antagonizing vascular endothelial growth factor receptor 2 signaling. conclusions our study provides insights into how flt1 and vascular endothelial growth factor receptor 2 signaling is titrated in a microrna-mediated manner and establishes mir-10 as a potential new target for the selective modulation of angiogenesis.",1
"epithelial-to-mesenchymal transition (emt) plays an important role in renal interstitial fibrosis (rif) with diabetic nephropathy (dn). smad7 (a inhibitory smad), a downstream signaling molecules of tgf-β1, represses the emt. the physiological function of mir-21 is closely linked to emt and rif. however, it remained unclear whether mir-21 over-expression affected tgf-β1-induced emt by regulating smad7 in dn. in this study, real-time rt-pcr, cell transfection, luciferase reporter gene assays, western blot and confocal microscope were used, respectively. here, we found that mir-21 expression was upregulated by tgf-β1 in time- and concentration -dependent manner. moreover, mir-21 over-expression enhanced tgf-β1-induced emt(upregulation of a-sma and downregulation of e-cadherin) by directly down-regulating smad7/p-smad7 and indirectly up-regulating smad3/p-smad3, accompanied by the decrease of ccr and the increase of col-iv, fn, the content of collagen fibers, rtbm, rtiaw and acr. meantime, the sirna experiment showed that smad7 can directly regulate a-sma and e-cadherin expression. more importantly, mir-21 inhibitor can not only inhibit emt and fibrosis but also ameliorate renal structure and function. in conclusion, our results demonstrated that mir-21 overexpression can contribute to tgf-β1-induced emt by inhibiting target smad7, and that targeting mir-21 may be a better alternative to directly suppress tgf-β1-mediated fibrosis in dn.",1
"the non-coding 3'-untranslated region (utr) plays an important role in the regulation of microrna (mirna) functions, since it can bind and inactivate multiple mirnas. here, we show the 3'-utr of cd44 is able to antagonize cytoplasmic mirnas, and result in the increased translation of cd44 and downstream target mrna, cdc42. a series of cell function assays in the human breast cancer cell line, mt-1, have shown that the cd44 3'-utr inhibits proliferation, colony formation and tumor growth. furthermore, it modulated endothelial cell activities, favored angiogenesis, induced tumor cell apoptosis and increased sensitivity to docetaxel. these results are due to the interaction of the cd44 3'-utr with multiple mirnas. computational algorithms have predicted three mirnas, mir-216a, mir-330 and mir-608, can bind to both the cd44 and cdc42 3'-utrs. this was confirmed with luciferase assays, western blotting and immunohistochemical staining and correlated with a series of sirna assays. thus, the non-coding cd44 3'-utr serves as a competitor for mirna binding and subsequently inactivates mirna functions, by freeing the target mrnas from being repressed.",1
"several functions have been attributed to protein binding within the 3'untranslated region (3'utr) of mrna, including mrna localization, stability, and translational repression. vimentin is an intermediate filament protein whose 3'untranslated sequence is highly conserved between species. in order to identify sequences that might play a role in vimentin mrna function, we synthesized32p-labeled rna from different regions of vimentin's 3'utr and assayed for protein binding with hela extracts using band shift assays. sequences required for binding are contained within a region 61-114 nucleotides downstream of the stop codon, a region which is highly conserved from xenopus to man. as judged by competition assays, binding is specific. solution probing studies of 32p-labeled rna with various nucleases and lead support a complex stem and loop structure for this region. finally, uv cross-linking of the rna-protein complex identifies an rna binding protein of 46 kda. fractionation of a hela extract on a sizing column suggests that in addition to the 46 kda protein, larger complexes containing additional protein(s) can be identified. vimentin mrna has been shown to be localized to the perinuclear region of the cytoplasm, possibly at sites of intermediate filament assembly. to date, all sequences required for localization of various mrnas have been confined to the 3'utr. therefore, we hypothesize that this region and associated protein(s) might be important for vimentin mrna function such as in localization.",1
"micrornas (mirnas) are involved in the pathogenesis of intrahepatic cholangiocarcinoma (icc). however, the role of microrna-31 (mir-31) in icc has yet to be elucidated. in this study, we demonstrated that the expression of mir-31 was significantly upregulated in icc tissues and the human icc cell line hccc-9810, when compared with that in normal adjacent tissues. bioinformatic analysis and a dual-luciferase reporter assay revealed ras p21 gtpase activating protein 1 (rasa1) to be a direct target of mir-31 in hccc-9810 cells. further investigation showed that the protein expression level of rasa1 was significantly decreased in icc tissues, suggesting an inverse correlation between mir-31 and rasa1 expression during the tumorigenesis of icc. moreover, the forced downregulation of mir-31 by its inhibitor in hccc-9810 cells significantly inhibited cell proliferation and promoted cell apoptosis. however, when the cells were cotransfected with mir-31 inhibitor and rasa1-specific small interfering rna (sirna), these changes were attenuated. further analysis of the molecular mechanism showed that the activity of the ras-mitogen-activated protein kinase (mapk) signaling pathway was significantly decreased in mir-31-downregulated hccc-8910 cells, while cotransfection with mir-31 inhibitor and rasa1-specific sirna attenuated this effect. these results indicate that the downregulation of rasa1 by mir-31 promoted cellular proliferation and inhibited cellular apoptosis, partially by upregulating the activity of the ras-mapk signaling pathway in icc. in conclusion, the present study revealed important regulatory functions of mir-31 and rasa1 in icc, indicating that mir-31 and rasa1 may become promising diagnostic and/or therapeutic targets for icc.",1
"proteasome inhibition represents a promising strategy of cancer pharmacotherapy, but resistant tumor cells often emerge. here we show that the microrna-101 (mir-101) targets the proteasome maturation protein pomp, leading to impaired proteasome assembly and activity, and resulting in accumulation of p53 and cyclin-dependent kinase inhibitors, cell cycle arrest, and apoptosis. mir-101-resistant pomp restores proper turnover of proteasome substrates and re-enables tumor cell growth. in erα-positive breast cancers, mir-101 and pomp levels are inversely correlated, and high mir-101 expression or low pomp expression associates with prolonged survival. mechanistically, mir-101 expression or pomp knockdown attenuated estrogen-driven transcription. finally, suppressing pomp is sufficient to overcome tumor cell resistance to the proteasome inhibitor bortezomib. taken together, proteasome activity can not only be manipulated through drugs, but is also subject to endogenous regulation through mir-101, which targets proteasome biogenesis to control overall protein turnover and tumor cell proliferation.",1
"metastatic progression of cancer is a complex and clinically daunting process. we previously identified a set of human micrornas (mirnas) that robustly suppress breast cancer metastasis to lung and bone and which display expression levels that predict human metastasis. although these findings revealed mirnas as suppressors of cell-autonomous metastatic phenotypes, the roles of non-coding rnas in non-cell-autonomous cancer progression processes remain unknown. here we reveal that endogenous mir-126, an mirna silenced in a variety of common human cancers, non-cell-autonomously regulates endothelial cell recruitment to metastatic breast cancer cells, in vitro and in vivo. it suppresses metastatic endothelial recruitment, metastatic angiogenesis and metastatic colonization through coordinate targeting of igfbp2, pitpnc1 and mertk--novel pro-angiogenic genes and biomarkers of human metastasis. insulin-like growth factor binding protein 2 (igfbp2) secreted by metastatic cells recruits endothelia by modulating igf1-mediated activation of the igf type-i receptor on endothelial cells; whereas c-mer tyrosine kinase (mertk) receptor cleaved from metastatic cells promotes endothelial recruitment by competitively antagonizing the binding of its ligand gas6 to endothelial mertk receptors. co-injection of endothelial cells with breast cancer cells non-cell-autonomously rescues their mir-126-induced metastatic defect, revealing a novel and important role for endothelial interactions in metastatic initiation. through loss-of-function and epistasis experiments, we delineate an mirna regulatory network's individual components as novel and cell-extrinsic regulators of endothelial recruitment, angiogenesis and metastatic colonization. we also identify the igfbp2/igf1/igf1r and gas6/mertk signalling pathways as regulators of cancer-mediated endothelial recruitment. our work further reveals endothelial recruitment and endothelial interactions in the tumour microenvironment to be critical features of metastatic breast cancer.",1
"micrornas are endogenous small regulatory rnas that modulate myriad biological processes by repressing target gene expression in a sequence-specific manner. here we show that the conserved mirna mir-34 regulates innate immunity and ecdysone signaling in drosophila. mir-34 over-expression activates antibacterial innate immunity signaling both in cultured cells and in vivo, and flies over-expressing mir-34 display improved survival and pathogen clearance upon gram-negative bacterial infection; whereas mir-34 knockout animals are defective in antibacterial defense. in particular, mir-34 achieves its immune-stimulatory function, at least in part, by repressing the two novel target genes dlg1 and eip75b. in addition, our study reveals a mutual repression between mir-34 expression and ecdysone signaling, and identifies mir-34 as a node in the intricate interplay between ecdysone signaling and innate immunity. lastly, we identify cis-regulatory genomic elements and trans-acting transcription factors required for optimal ecdysone-mediated repression of mir-34. taken together, our study enriches the repertoire of immune-modulating mirnas in animals, and provides new insights into the interplay between steroid hormone signaling and innate immunity.",1
"objective abnormal vascular smooth muscle cell (vsmc) proliferation is involved in the development of vascular diseases. however, the mechanisms by which insulin exerts this effect are not completely known. we hypothesize that micrornas might be involved in insulin-induced vsmc proliferation. methods vsmc proliferation was determined by -thymidine incorporation; micrornas were determined by microrna chips and real-time pcr; and p21expression was determined by immunoblotting. results in this study, we found that insulin increased vsmc proliferation and mir-208 expression. overexpression of mir-208 increased basal and insulin-mediated vsmc proliferation. although a mir-208 inhibitor, by itself, had no effect on vsmc proliferation, it reduced the insulin-mediated cell proliferation. moreover, mir-208 increased the transformation of cell cycle from g0/g1 phase to the s phase. bioinformatics analysis found that p21, a member of the cyclin-dependent kinase (cdk)-inhibitory protein family, may be the target of mir-208. insulin decreased p21 expression in vsmcs; transfection of mir-208 also decreased p21 protein expression. in the presence of mir-208 inhibitor, the inhibitory effect of insulin on p21 expression in vsmcs was partially blocked. the interaction between mir-208 and p21 was direct. using a luciferase reporter with entire wild-type p21 3'utr or a mutant p21 3'utr in hek293 cells, we found that mir-208 decreased but neither mir-208 mimic nor the mutant p21 3'utr had any significant effect on the luciferase activity. conclusion this study indicates that mirnas, mir-208, in particular, are involved in the insulin-induced vsmc proliferation via downregulation of its potential target, p21, a key member of cdk-inhibitory protein family.",1
"in response to environmental stresses, toxoplasma gondii induces a global translational repression which allows for the remodeling of its transcriptome. while some transcripts are preferentially translated, another subset is translationally repressed and maintained in bradyzoites. although little is known of how transcripts are targeted for sustained translational repression, the targeting probably operates through an rna-centric mechanism relying on the recognition of cis-acting elements. in this study, we sought to determine if the targeting of transcripts through recognizable cis-acting elements could be responsible for the transcript-specific sustained translational repression displayed by toxoplasma bradyzoites. we examined the utrs of a translationally repressed gene, lactate dehydrogenase 1, and found a 40 nucleotide regulatory element in its 5'utr. this element specifically induces translational repression in otherwise constitutively expressed transcripts. mutational studies revealed that the formation of a small 16 nucleotide regulatory rna hairpin is essential for this activity. we suggest that this hairpin may act as the nucleation site for the binding of an as yet to be identified trans-acting factor that allows for the transcript to be targeted for translational repression removal from the active translational pool. to our knowledge, this is the first report characterizing a specific cis-acting element contributing to post-transcriptional gene regulation in toxoplasma and suggests the presence of a pathway by which the parasites can recognize, identify and specifically target transcripts for sustained translational repression under stressful conditions.",1
"background lipoprotein lipase (lpl) is a key enzyme in triglyceride (tg) metabolism. lpl gene single nucleotide polymorphisms (snps) are associated with tg concentrations however the functionality of many of these snps remains poorly understood. micrornas (mir) exert post-transcriptional down-regulation and their target sequence on the 3'utr may be altered by snps. we therefore investigated whether lpl 3'utr snps could modulate plasma tg concentration through the alteration of mir binding-sites. methods and results we performed genetic association studies of lpl 3'utr snps with tg concentrations in 271 type 2 diabetic patients and in general population samples (2997 individuals). a specific lpl haplotype (hap4) was associated with lower plasma tg concentration (tg-0.18, ic95% mmol/l or logtg-0.13, ic95% , p = 4.77·10(-8)) in the meta-analysis. hap4 comprises seven 3'utr snp minor alleles and p.ser474ter (rs328) a well-documented nonsense mutation associated with low tg concentration although by an unknown mechanism so far. bio-informatic studies identified several putative mirna binding-sites on the wild-type hap1 haplotype, lost on hap4. functional validation performed in hek-293t cells using luciferase expression constructs with various lpl 3'utr allele combinations demonstrated a binding of mir-29, mir-1277 and mir-410 on hap1, lost on hap4. this loss of specific mir binding-site in presence of hap4 was independent of the allelic variation of p.ser474ter (rs328). conclusions we report the regulation of lpl by the mir-29, mir-1277 and mir-410 that is lost in presence of hap4, a specific lpl tg-lowering haplotype. consequently p.ser474ter association with tg concentration could be at least partially explained by its strong linkage disequilibrium with these functional 3'utr snps.",1
"emerging evidence indicates that the lncrnas/microrna/mrna axis plays important roles in a variety of diseases. this study was aimed to investigate the potential roles and underlying molecular mechanisms of lncrna h19 and h19-derived mir-675 in regulating hepatitis b virus (hbv)-associated liver injury. mrna and mir-675 levels were determined by quantitative real-time pcr (qrt-pcr), protein levels were determined by western blot, cell viability was measured by the mtt assay, cell apoptosis was measured by flow cytometry, inflammatory cytokine production was determined by elisa, oxidative stress and energy metabolism were assessed by commercial kits, and the target relationship between pparα and mir-675 was confirmed by the dual-luciferase reporter assay. the results showed that the expression of lncrna h19 and mir-675 was up-regulated in patients with chronic hepatitis b (n = 20). inhibition of lncrna h19 or mir-675 in l02 cells increased cell viability, suppressed hepatitis b x protein (hbx)-induced cell apoptosis, inflammatory cytokine production, and oxidative stress, and remodelled energy metabolism. furthermore, pparα was found to be a target gene of mir-675. the expression of pparα was down-regulated in patients with chronic hepatitis b, and there was a negative correlation between the expression of lncrna h19 and pparα, or between mir-675 and pparα. moreover, by knocking down the expression of pparα, the actions (apoptosis, inflammatory factors, oxidative stress, and energy metabolism) of lncrna h19 or mir-675 inhibition in hbx-induced l02 cells were at least partially reversed. in addition, hbx-induced elevated levels of p-akt ser473 , p-akt thr308 and p-mtor ser2448 were down-regulated by lncrna h19 or mir-675 inhibition. furthermore, pparα knockdown partly reversed the down-regulated effects of h19 or mir-675 inhibition. taken together, these data indicate that the lncrna h19/mir-675/pparα axis regulates liver cell injury and energy metabolism remodelling induced by hbx, which may be related to the modulation of akt/mtor signalling.",1
"following earlier reports on modulation of poly(q) toxicity in drosophila by the developmentally active and stress-inducible noncoding hsromega gene, we investigated possible mediators of this modulation. rnai-mediated downregulation of the large nuclear hsromega-n transcript, which organizes the nucleoplasmic omega speckles, suppressed the enhancement of poly(q) toxicity brought about by reduced availability of the heterogeneous nuclear ribonucleoprotein (hnrnp) hrb87f and of the transcriptional regulator, camp response element binding (creb) binding protein (cbp). levels of cbp rna and protein were reciprocally affected by hsromega transcript levels in eye disc cells. our data suggest that cbp and hnrnps like hrb57a and hrb87f physically interact with each other. in addition, downregulation of hsromega transcripts partially rescued eye damage following compromised proteasome activity, while overexpression of hsromega and/or poly(q) proteins disrupted the proteasomal activity. rescue of poly(q) toxicity by hsromega-rnai required normal proteasomal function. we suggest that hsromega-rnai suppresses poly(q) toxicity by elevating cellular levels of cbp, by enhancing proteasome-mediated clearance of the pathogenic poly(q) aggregates, and by inhibiting induced apoptosis. the direct and indirect interactions of the hsromega transcripts with a variety of regulatory proteins like hnrnps, cbp, proteasome, drosophila inhibitor of apoptosis protein 1 (diap1), etc., reinforce the view that the noncoding hsromega rna functions as a ""hub"" in cellular networks to maintain homeostasis by coordinating the functional availability of crucial cellular regulatory proteins.",1
"epithelial-mesenchymal transition (emt) has recently been recognized as a key element of cell invasion, migration, metastasis, and drug resistance in several types of cancer, including non-small cell lung cancer (nsclc). our aim was to clarify microrna (mirna)-related mechanisms underlying emt followed by acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitor (egfr-tki) in nsclc. mirna expression profiles were examined before and after transforming growth factor β1 (tgf-β1) exposure in four human adenocarcinoma cell lines with or without emt. correlation between expressions of emt-related mirnas and resistance to egfr-tki gefitinib was evaluated. mirna array and real-time quantitative reverse transcription pcr (qrt-pcr) revealed that tgf-β1 significantly induced overexpression of mir-134, mir-487b, and mir-655, which belong to the same cluster located on chromosome 14q32, in lung adenocarcinoma cells with emt. magi2 (membrane-associated guanylate kinase, ww, and pdz domain-containing protein 2), a predicted target of these mirnas and a scaffold protein required for pten, was diminished in a549 cells with emt after the tgf-β1 stimulation. overexpression of mir-134 and mir-487b promoted the emt phenomenon and affected the drug resistance to gefitinib, whereas knockdown of these mirnas inhibited the emt process and reversed tgf-β1-induced resistance to gefitinib. our study demonstrated that the mir-134/487b/655 cluster contributed to the tgf-β1-induced emt phenomenon and affected the resistance to gefitinib by directly targeting magi2, in which suppression subsequently caused loss of pten stability in lung cancer cells. the mir-134/mir-487b/mir-655 cluster may be a new therapeutic target in patients with advanced lung adenocarcinoma, depending on the emt phenomenon.",1
"nasopharayngeal carcinoma (npc) is an epstein-barr virus-associated malignancy most common in east asia and africa. here we report frequent downregulation of the microrna mir-218 in primary npc tissues and cell lines where it plays a critical role in npc progression. suppression of mir-218 was associated with epigenetic silencing of slit2 and slit3, ligands of robo receptors that have been previously implicated in tumor angiogenesis. exogenous expression of mir-218 caused significant toxicity in npc cells in vitro and delayed tumor growth in vivo. we used an integrated trimodality approach to identify targets of mir-218 in npc, cervical, and breast cell lines. direct interaction between mir-218 and the 3'-untranslated regions (utr) of mrnas encoding robo1, survivin (birc5), and connexin43 (gja1) was validated in a luciferase-based transcription reporter assay. mechanistic investigations revealed a negative feedback loop wherein mir-218 regulates npc cell migration via the slit-robo pathway. pleotropic effects of mir-218 on npc survival and migration were rescued by enforced expression of mir-218-resistant, engineered isoforms of survivin and robo1, respectively. in clinical specimens of npc (n=71), robo1 overexpression was significantly associated with worse overall (p=0.04, hr=2.4) and nodal relapse-free survival (p=0.008, hr=6.0). our findings define an integrative tumor suppressor function for mir-218 in npc and further suggest that restoring mir-218 expression in npc might be useful for its clinical management.",1
"the mir-106b-25 microrna (mirna) cluster is a candidate oncogene in human prostate cancer. here, we report that mirnas encoded by mir-106b-25 are upregulated in both primary tumors and distant metastasis. moreover, increased tumor mir-106b expression was associated with disease recurrence and the combination of high mir-106b and low casp7 (caspase-7) expressions in primary tumors was an independent predictor of early disease recurrence (adjusted hazard ratio=4.1; 95% confidence interval: 1.6-12.3). to identify yet unknown oncogenic functions of mir-106b, we overexpressed it in lncap human prostate cancer cells to examine mir-106b-induced global expression changes among protein-coding genes. the approach revealed that casp7 is a direct target of mir-106b, which was confirmed by western blot analysis and a 3'-untranslated region reporter assay. moreover, selected phenotypes induced by mir-106b knockdown in du145 human prostate cancer cells did not develop when both mir-106b and casp7 expression were inhibited. further analyses showed that casp7 is downregulated in primary prostate tumors and metastatic lesions across multiple data sets and is by itself associated with disease recurrence and disease-specific survival. using bioinformatics, we also observed that mir-106b-25 may specifically influence focal adhesion-related pathways. this observation was experimentally examined using mir-106b-25-transduced 22rv1 human prostate cancer cells. after infection with a mir-106b-25 lentiviral expression construct, 22rv1 cells showed increased adhesion to basement membrane- and bone matrix-related filaments and enhanced soft agar growth. in summary, mir-106b-25 was found to be associated with prostate cancer progression and disease outcome and may do so by altering apoptosis- and focal adhesion-related pathways.",1
"bone tissue arises from mesenchymal cells induced into the osteoblast lineage by essential transcription factors and signaling cascades. micrornas regulate biological processes by binding to mrna 3'-untranslated region (utr) sequences to attenuate protein synthesis. here we performed microrna profiling and identified mirs that are up-regulated through stages of osteoblast differentiation. among these are the mir-29, mir-let-7, and mir-26 families that target many collagens and extracellular matrix proteins. we find that mir-29b supports osteoblast differentiation through several mechanisms. mir-29b decreased and anti-mir-29b increased activity of col1a1, col5a3, and col4a2 3'-utr sequences in reporter assays, as well as endogenous gene expression. these results support a mechanism for regulating collagen protein accumulation during the mineralization stage when mir-29b reaches peak levels. we propose that this mechanism prevents fibrosis and facilitates mineral deposition. our studies further demonstrate that mir-29b promotes osteogenesis by directly down-regulating known inhibitors of osteoblast differentiation, hdac4, tgfbeta3, acvr2a, ctnnbip1, and dusp2 proteins through binding to target 3'-utr sequences in their mrnas. thus, mir-29b is a key regulator of development of the osteoblast phenotype by targeting anti-osteogenic factors and modulating bone extracellular matrix proteins.",1
"objective in this study, we attempted to uncover the functional impact of microrna-22 (mir-22) and its target gene in smooth muscle cell (smc) differentiation and delineate the molecular mechanism involved. approach and results mir-22 was found to be significantly upregulated during smc differentiation from embryonic stem cells and adventitia stem/progenitor cells. enforced expression of mir-22 by its mimic, while knockdown of mir-22 by its antagomir, promotes or inhibits smc differentiation from embryonic stem cells and adventitia stem/progenitor cells, respectively. expectedly, mir-22 overexpression in stem cells promoted smc differentiation in vivo. methyl cpg-binding protein 2 (mecp2) was predicted as one of the top targets of mir-22. interestingly, the gene expression levels of mecp2 were significantly decreased during smc differentiation, and mecp2 was dramatically decreased in mir-22 overexpressing cells but significantly increased when mir-22 was knockdown in the differentiating stem cells. importantly, luciferase assay showed that mir-22 substantially inhibited wild-type, but not mutant mecp2-3' untranslated region-luciferase activity. in addition, modulation of mecp2 expression levels affects multiple smc-specific gene expression in differentiated embryonic stem cells. mechanistically, our data showed that mecp2 could transcriptionally repress smc gene expression through modulating various smc transcription factors, as well as several proven smc differentiation regulators. evidence also revealed that enrichment of h3k9 trimethylation around the promoter regions of the smc differentiation regulators genes were significantly increased by mecp2 overexpression. finally, mir-22 was upregulated by platelet-derived growth factor-bb and transforming growth factor-β through a transcriptional mechanism during smc differentiation. conclusions mir-22 plays an important role in smc differentiation, and epigenetic regulation through mecp2 is required for mir-22 mediated smc differentiation.",1
"box h/aca small nucleolar ribonucleoprotein particles (h/aca snornps) play key roles in the synthesis of eukaryotic ribosomes. how box h/aca snornps are assembled remains unknown. here we show that yeast nhp2p, a core component of these particles, directly binds rna. in vitro, nhp2p interacts with high affinity with rnas containing irregular stem-loop structures but shows weak affinity for poly(a), poly(c) or for double-stranded rnas. the central region of nhp2p is believed to function as an rna-binding domain, since it is related to motifs found in various rna-binding proteins. removal of two amino acids that shortens a putative beta-strand element within nhp2p central domain impairs the ability of the protein to interact with h/aca snornas in cell extracts. in vivo, this deletion prevents cell viability and leads to a strong defect in the accumulation of h/aca snornas and gar1p. these data suggest that proper direct binding of nhp2p to h/aca snornas is required for the assembly of h/aca snornps and hence for the stability of some of their components. in addition, we show that converting a highly conserved glycine residue (g(59)) within nhp2p central domain to glutamate significantly reduces cell growth at 30 and 37 degrees c. remarkably, this modification affects the steady-state levels of h/aca snornas and the strength of nhp2p association with these rnas to varying degrees, depending on the nature of the h/aca snorna. finally, we show that the modified nhp2p protein whose interaction with h/aca snornas is impaired cannot accumulate in the nucleolus, suggesting that only the assembled h/aca snornp particles can be efficiently retained in the nucleolus.",1
"the lymphatics have emerged as critical players in the progression and resolution of inflammation. the goal of this study was to identify specific micrornas (mirnas) that regulate lymphatic inflammatory processes. rat mesenteric lymphatic endothelial cells (lecs) were exposed to the proinflammatory cytokine tumor necrosis factor-α for 2, 24, and 96 h, and mirna profiling was carried out by real-time pcr arrays. our data demonstrate a specific set of mirnas that are differentially expressed (>1.8-fold and/or p < 0.05) in lecs in response to tumor necrosis factor-α and are involved in inflammation, angiogenesis, endothelial-mesenchymal transition, and cell proliferation and senescence. we further characterized the expression of mirna 9 (mir-9) that was induced in lecs and in inflamed rat mesenteric lymphatics. our results showed that mir-9 overexpression significantly repressed nf-κb expression and, thereby, suppressed inflammation but promoted lec tube formation, as well as expression of the prolymphangiogenic molecules endothelial nitric oxide synthase and vegf receptor type 3. lec viability and proliferation and endothelial-mesenchymal transition were also significantly induced by mir-9. this study provides the first evidence of a distinct profile of mirnas associated with lecs during inflammation. it also identifies the critical dual role of mir-9 in fine-tuning the balance between lymphatic inflammatory and lymphangiogenic pathways.",1
"the effects and potential mechanisms of the vascular endothelial cell (ec)-enriched microrna-15a (mir-15a) on angiogenesis remain unclear. here, we show a novel finding that ec-selective mir-15a transgenic overexpression leads to reduced blood vessel formation and local blood flow perfusion in mouse hindlimbs at 1-3 weeks after hindlimb ischemia. mechanistically, gain- or loss-of-mir-15a function by lentiviral infection in ecs significantly reduces or increases tube formation, cell migration, and cell differentiation, respectively. by fgf2 and vegf 3'-utr luciferase reporter assays, real-time pcr, and immunoassays, we further identified that the mir-15a directly targets fgf2 and vegf to facilitate its anti-angiogenic effects. our data suggest that the mir-15a in ecs can significantly suppress cell-autonomous angiogenesis through direct inhibition of endogenous endothelial fgf2 and vegf activities. pharmacological modulation of mir-15a function may provide a new therapeutic strategy to intervene against angiogenesis in a variety of pathological conditions.",1
"background increasing evidence has indicated that micrornas (mirnas) are strongly implicated in the initiation and progression of glioblastoma multiforme (gbm). here, we identified a novel tumor suppressive mirna, mir-377, and investigated its role and therapeutic effect for gbm. methods mirna global screening was performed on gbm patient samples and adjacent nontumor brain tissues. the expression of mir-377 was detected by real-time reverse-transcription pcr. the effects of mir-377 on gbm cell proliferation, cell cycle progression, invasion, and orthotopic tumorigenicity were investigated the therapeutic effect of mir-377 mimic was explored in a subcutaneous gbm model. western blot and luciferase reporter assay were used to identify the direct and functional target of mir-377. results mir-377 was markedly downregulated in human gbm tissues and cell lines. overexpression of mir-377 dramatically inhibited cell growth both in culture and in orthotopic xenograft tumor models, blocked g1/s transition, and suppressed cell invasion in gbm cells. importantly, introduction of mir-377 could strongly inhibit tumor growth in a subcutaneous gbm model. subsequent investigation revealed that specificity protein 1 (sp1) was a direct and functional target of mir-377 in gbm cells. silencing of sp1 recapitulated the antiproliferative and anti-invasive effects of mir-377, whereas restoring the sp1 expression antagonized the tumor-suppressive function of mir-377. finally, analysis of mir-377 and sp1 levels in human gbm tissues revealed that mir-377 is inversely correlated with sp1 expression. conclusion these findings reveal that mir-377/sp1 signaling that may be required for gbm development and may consequently serve as a therapeutic target for the treatment of gbm.",1
"u7 small nuclear rna (snrna) sequences have been described only for a handful of animal species in the past. here we describe a computational search for functional u7 snrna genes throughout vertebrates including the upstream sequence elements characteristic for snrnas transcribed by polymerase ii. based on the results of this search, we discuss the high variability of u7 snrnas in both sequence and structure, and report on an attempt to find u7 snrna sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. these results cast doubt on putative u7 homologs in even more distant organisms that are reported in the most recent release of the rfam database.",1
"the dlk1-gtl2 imprinting locus is located on mouse distal chromosome 12 and consists of multiple maternally expressed non-coding rnas and several paternally expressed protein-coding genes. the imprinting of this locus plays a crucial role in embryonic development and postnatal growth. at least one cis-element, the intergenic differentially methylated region (ig-dmr) is required for expression of maternally expressed genes and repression of silenced paternally expressed genes. the mechanism by which the ig-dmr functions is largely unknown. however, it has been suggested that the unmethylated ig-dmr acts as a positive regulator activating expression of non-coding rnas. gtl2 is the first non-coding rna gene downstream of the ig-dmr. although its in vivo function in the mouse is largely unknown, its human ortholog meg3 has been linked to tumor suppression in human tumor-derived cell lines. we generated a knockout mouse model, in which the first five exons and adjacent promoter region of the gtl2 gene were deleted. maternal deletion of gtl2 resulted in perinatal death and skeletal muscle defects, indicating that gtl2 plays an important role in embryonic development. the maternal deletion also completely abolished expression of downstream maternally expressed genes, activated expression of silenced paternally expressed genes and resulted in methylation of the ig-dmr. by contrast, the paternal inherited deletion did not have this effect. these data strongly indicate that activation of gtl2 and its downstream maternal genes play an essential role in regulating dlk1-gtl2 imprinting, possibly by maintaining active status of the ig-dmr.",1
"micrornas (mirnas) are endogenous noncoding rnas that down-regulate gene expression by promoting cleavage or translational arrest of target mrnas. while most mirnas are transcribed from their own dedicated genes, some map to introns of 'host' transcripts, the biological significance of which remains unknown. here, we show that prostate cells are naturally devoid of egf-like domain 7 (egfl7) transcripts and hence also deficient in a mirna, mir-126*, generated from splicing and processing of its ninth intron. use of recombinant and synthetic mirnas or a specific antagomir established a role of mir-126* in silencing prostein in non-endothelial cells. we mapped two mir-126*-binding sites in the 3'utr of the prostein mrna required for translational repression. transfection of synthetic mir-126* into prostate cancer lncap cells strongly reduced the translation of prostein. interestingly, loss of prostein correlated with reduction of lncap cell migration and invasion. thus, the robust expression of prostein protein in the prostate cells results from a combination of transcriptional activation of the prostein gene and absence of intronic mirna-126* due to the prostate-specific repression of the egfl7 gene. we conclude that intronic mirnas from tissue-specific transcripts, or their natural absence, make cardinal contributions to cellular gene expression and phenotype. these findings also open the door to tissue-specific mirna therapy.",1
"micrornas (mirnas) have emerged as a major regulator in neurological diseases, and understanding their molecular mechanism in modulating cerebral ischemic injury may provide potential therapeutic targets for ischemic stroke. however, as one of 19 differentially expressed mirnas in mouse brain with middle cerebral artery occlusion (mcao), the role of mir-134 in ischemic injury is not well understood. in this study, the mir-134 expression level was manipulated both in oxygen-glucose deprivation (ogd)-treated n2a neuroblastoma cells in vitro and mouse brain with mcao-induced ischemic stroke in vivo, and its possible targets of heat shock protein a5 (hspa5) and hspa12b were determined by bioinformatics analysis and dual luciferase assay. the results showed that overexpression of mir-134 exacerbated cell death and apoptosis both in vitro and in vivo. conversely, downregulating mir-134 levels reduced cell death and apoptosis. furthermore, non-expression of mir-134 enhanced hspa12b protein levels in ogd-treated n2a cells as well as in the ischemic region. it could attenuate brain infarction size and neural cell damage, and improve neurological outcomes in mice with ischemic stroke, whereas upregulation of mir-134 had the opposite effect. in addition, hspa12b was validated to be a target of mir-134 and its short interfering rnas (sirnas) could block mir-134 inhibitor-induced neuroprotection in ogd-treated n2a cells. in conclusion, downregulation of mir-134 could induce neuroprotection against ischemic injury in vitro and in vivo by negatively upregulating hspa12b protein expression.",1
"purpose abnormal expression of mirnas is closely related to a variety of human cancers. the purpose of this study is to identify new tumor suppressor mirna and elucidate its physiological function and mechanism in renal cell carcinoma (rcc). methods the expression of mir-145 in 45 rcc and adjacent normal tissues was performed by quantitative rt-pcr. cell proliferation, migration, invasion, apoptosis and cycle assays were carried out for functional analysis after mir-145 transfection. two target genes of mir-145 were identified by luciferase reporter assay. the altered expression of 84 epithelial to mesenchymal transition (emt)-related genes after mir-145 transfection was detected by rt(2) profiler emt pcr array. results the expression of mir-145 was downregulated in rcc compared to their normal adjacent tissues. restoring mir-145 expression in rcc cell lines dramatically suppressed cell proliferation, migration and invasion, and induced cell apoptosis and g2-phase arrest. we further validated those mir-145 targets two oncogenes, angpt2 and nedd9 in rcc. in addition, mir-145 was found to regulate numerous genes involved in the emt. conclusions these findings demonstrate that mir-145 functions as tumor suppressor in rcc, suggesting that mir-145 may be a potential therapeutic target for rcc.",1
"the abnormal phenotypic transformation of vascular smooth muscle cells (smcs) causes various proliferative vascular diseases. micrornas (mirnas or mirs) have been established to play important roles in smc biology and phenotypic modulation. this study revealed that the expression of mir‑182 was markedly altered during rat vascular smc phenotypic transformation in vitro. we aimed to investigate the role of mir‑182 in the vascular smc phenotypic switch and to determine the potential molecular mechanisms involved. the expression of mir‑182 gene was significantly downregulated in cultured smcs during dedifferentiation from a contractile to a synthetic phenotype. conversely, the upregulation of mir‑182 increased the expression of smc-specific contractile genes, such as α-smooth muscle actin, smooth muscle 22α and calponin. additionally, mir‑182 overexpression potently inhibited smc proliferation and migration under both basal conditions and under platelet-derived growth factor-bb stimulation. furthermore, we identified fibroblast growth factor 9 (fgf9) as the target gene of mir‑182 for the phenotypic modulation of smcs mediated through platelet-derived growth factor receptor β (pdgfrβ) signaling. these data suggest that mir‑182 may be a novel smc phenotypic marker and a modulator that may be used to prevent smc dedifferentiation via fgf9/pdgfrβ signaling.",1
"angiopoietin‑1 (ang‑1), a ligand of the endothelial cell‑specific tie2 surface receptor, acts in a complementary and coordinated manner with vascular endothelial growth factor during the process of angiogenesis. ang‑1 can be used as a clinically informative biomarker of disease severity and outcome in severe sepsis. the epithelium‑specific ets transcription factor 1 can activate ang‑1 transcription in the setting of inflammation; however, relatively little is known about the regulation of ang‑1 by micrornas (mirs). it was observed that lipopolysaccharide (lps) significantly increased ang‑1 mrna and protein expression in ea.hy926 cells. ang‑1 was identified as a potential target gene of mir‑204 and mir‑211. overexpression of mir‑204/211 partially reversed the lps‑induced ang‑1 expression in ea.hy926 cells. furthermore, overexpression of mir‑204/211 significantly reduced the activity of a luciferase reporter gene containing the wild‑type ang‑1 3'‑untranslated region (utr), but did not influence the activity of a luciferase reporter gene containing the ang‑1 3'‑utr with a mutated mir‑204/211 binding site, confirming that mir‑204/211 can bind to the ang‑1 3'‑utr and post‑transcriptionally regulate ang‑1. additionally, lps enhanced the stability of ang‑1 mrna by reducing the abundance of mir‑204/211. overexpression of mir‑204/211 reduced the migration of ea.hy926 cells in vitro. the present study demonstrated that ang‑1 is a novel direct target gene of mir‑204 and mir‑211; in addition, lps was able to inhibit this effect by reducing the expression of mir‑204 and mir‑211.",1
"non-coding y rnas and stem-bulge rnas are homologous small rnas in vertebrates and nematodes, respectively. they share a conserved function in the replication of chromosomal dna in these two groups of organisms. however, functional homologues have not been found in insects, despite their common early evolutionary history. here, we describe the identification and functional characterization of two sbrnas in drosophila melanogaster, termed dm1 and dm2. the genes coding for these two rnas were identified by a computational search in the genome of d. melanogaster for conserved sequence motifs present in nematode sbrnas. the predicted secondary structures of dm1 and dm2 partially resemble nematode sbrnas and show stability in molecular dynamics simulations. both rnas are phylogenetically closer related to nematode sbrnas than to vertebrate y rnas. dm1, but not dm2 sbrna is abundantly expressed in d. melanogaster s2 cells and adult flies. only dm1, but not dm2 sbrna can functionally replace y rnas in a human cell-free dna replication initiation system. therefore, dm1 is the first functional sbrna described in insects, allowing future investigations into the physiological roles of sbrnas in the genetically tractable model organism d. melanogaster.",1
"discovering the genetic and cellular mechanisms that drive cardiac morphogenesis remains a fundamental goal, as three-dimensional architecture greatly impacts functional capacity. during development, accurately contoured chambers balloon from a primitive tube in a process characterized by regional changes in myocardial cell size and shape. how these localized changes are achieved remains elusive. here, we show in zebrafish that microrna-143 (mir-143) is required for chamber morphogenesis through direct repression of adducin3 (add3), which encodes an f-actin capping protein. knockdown of mir-143 or disruption of the mir-143-add3 interaction inhibits ventricular cardiomyocyte f-actin remodeling, which blocks their normal growth and elongation and leads to ventricular collapse and decreased contractility. using mosaic analyses, we find that mir-143 and add3 act cell-autonomously to control f-actin dynamics and cell morphology. as proper chamber emergence relies on precise control of cytoskeletal polymerization, add3 represents an attractive target to be fine-tuned by both uniform signals, such as mir-143, and undiscovered localized signals. together, our data uncover the mir-143-add3 genetic pathway as essential for cardiac chamber formation and function through active adjustment of myocardial cell morphology.",1
"aberrant expression of micrornas (mirnas) has been implicated in cancer initiation and progression. however, little is known about the potential role of mirnas in glioma tumorigenesis. in this study, we found that mirna-106b-5p was significantly upregulated in glioma tumor samples and cell lines compared with normal brain tissues, and its expression level correlated with the pathological grading. overexpression of mir-106b-5p in glioma tumor cells significantly promoted cell proliferation, although inhibited cell apoptosis in vitro and in vivo. in contrast, knockdown of mir-106b-5p significantly inhibited cell proliferation, although enhanced cell apoptosis. mechanistic study revealed that two target genes, retinoblastoma-like 1 (rbl1) and rbl2, were involved in mir-106b-5p's regulation of cell proliferation and one target gene, caspase-8 (casp8), mediated mir-106b-5p's regulation of apoptosis. we also investigated the function of the three targets in glioma tumorigenesis by rna interference manipulation and demonstrated that knockdown of these target genes led to cell proliferation enhancement or cell apoptosis inhibition in vitro. more interestingly, the expression levels of these targets were significantly downregulated in glioma samples and knockdown of these targets in glioma cells inhibited the xenograft tumor formation in vivo. moreover, we verified the regulation function of mir-106b-5p and its targets on cell proliferation and apoptosis of the primary cultured astrocytes isolated from glioma tumor samples and healthy controls. collectively, our findings show the critical roles of mir-106b-5p and its targets, rbl1, rbl2 and casp8, in glioma tumorigenesis and provide potential candidates for malignant glioma therapy.",1
"in an effort to understand the potential role of micrornas (mirnas) in mammary-gland stem or progenitor cells, mirna microarrays were performed on subpopulations of the mouse mammary epithelial cell (mec) line comma-dbetageo. this cell line contains a heterogeneous subpopulation of progenitors characterized by the expression of stem cell antigen 1 (sca-1; encoded by ly6a). microarray analysis indicated that the sca-1 subpopulations have distinct mirna expression profiles. functional studies were performed on mir-205, which was highly expressed in the sca-1-positive (sca-1(+)) cells. when mir-205 was overexpressed in vitro, the comma-dbetageo cells underwent several significant morphological and molecular changes. mir-205 overexpression led to an expansion of the progenitor-cell population, decreased cell size and increased cellular proliferation. in addition, the colony-forming potential of the two sca-1 subpopulations was increased. target prediction for mir-205 indicated that it might regulate the expression of the tumor-suppressor protein pten. overexpression studies using reporter constructs confirmed that pten expression is regulated by mir-205. in addition to pten, several other putative and previously validated mir-205 targets were identified by microarray analysis, including the previously reported mir-205 targets zeb1 and zeb2. additionally, in normal mouse mecs, high expression of mir-205 was observed in stem-cell-enriched cell populations isolated by facs using established cell-surface markers.",1
"in drosophila melanogaster, the male-specific lethal (msl) complex plays a key role in dosage compensation by stimulating expression of male x-chromosome genes. it consists of msl proteins and two long noncoding rnas, rox1 and rox2, that are required for spreading of the complex on the chromosome and are redundant in the sense that loss of either does not affect male viability. however, despite rapid evolution, both rox species are present in diverse drosophilidae species, raising doubts about their full functional redundancy. thus, we have investigated consequences of deleting rox1 and/or rox2 to probe their specific roles and redundancies in d. melanogaster. we have created a new mutant allele of rox2 and show that rox1 and rox2 have partly separable functions in dosage compensation. in larvae, rox1 is the most abundant variant and the only variant present in the msl complex when the complex is transmitted (physically associated with the x-chromosome) in mitosis. loss of rox1 results in reduced expression of the genes on the x-chromosome, while loss of rox2 leads to msl-independent upregulation of genes with male-biased testis-specific transcription. in rox1 rox2 mutant, gene expression is strongly reduced in a manner that is not related to proximity to high-affinity sites. our results suggest that high tolerance of mis-expression of the x-chromosome has evolved. we propose that this may be a common property of sex-chromosomes, that dosage compensation is a stochastic process and its precision for each individual gene is regulated by the density of high-affinity sites in the locus.",1
"lung cancer remains the leading cause of cancer-related death worldwide, and non-small cell lung cancer (nsclc) accounts for approximately 80% of lung cancer cases. recently, micrornas (mirnas) have been consistently demonstrated to be involved in nsclc and to act as either tumor oncogenes or tumor suppressors. in this study, we identified a specific binding site for mir-218-5p in the 3'-untranslated region of the epidermal growth factor receptor (egfr). we further experimentally validated mir-218-5p as a direct regulator of egfr. we also identified an inverse correlation between mir-218-5p and egfr protein levels in nsclc tissue samples. moreover, we demonstrated that mir-218-5p plays a critical role in suppressing the proliferation and migration of lung cancer cells probably by binding to egfr. finally, we examined the function of mir-218-5p in vivo and revealed that mir-218-5p exerts an anti-tumor effect by negatively regulating egfr in a xenograft mouse model. taken together, the results of this study highlight an important role for mir-218-5p in the regulation of egfr in nsclc and may open new avenues for future lung cancer therapies.",1
"in mammals, follicular atresia can be partially triggered by granulosa cell apoptosis. however, very little is known about the functions of mirnas in granulosa cell apoptosis. we previously reported that hsa-mir-23a (mir-23a) and hsa-mir-27a (mir-27a) were highly expressed in the plasma of patients with premature ovarian failure, but the action of these two mirnas in follicular development was unclear. in this study, we explored the roles of mir-23a and mir-27a in the granulosa cells of women undergoing in vitro fertilization/embryo transfer. using hoechst staining, we found that mir-23a and mir-27a promoted apoptosis in human granulosa cells. in addition, the western blotting results suggested that the mir-23a/mir-27a-mediated apoptosis occurred via the fasl-fas pathway. based on the results of a luciferase-reporter assay and quantitative rt-pcr and western blotting analyses, we found that smad5 is a target gene of both mir-23a and mir-27a. furthermore, knocking down smad5 expression increased the rate of apoptosis, as well as the levels of fas, fasl, cleaved caspase-8, and cleaved caspase-3 protein. taken together, these data suggest that mir-23a and mir-27a target smad5 and regulate apoptosis in human granulosa cells via the fasl-fas pathway. these findings provide an improved understanding of the mechanisms underlying granulosa cell apoptosis, which could potentially be used for future clinical applications.",1
"objective : to investigate the role of lncrna anril in the modulation of myocardial cell apoptosis in acute myocardial infarction (ami). methods : ami mice model was established, and lncrna anril, il-33 and st2 expressions were detected by quantitative real-time polymerase chain reaction (qrt-pcr) or western blot. the apoptosis of myocardial cells was detected by tunel assay. rna pull-down and rna immunoprecipitation (rip) assays were used to confirm the interaction between lncrna anril and usp17. results : compared with sham group, lncrna anril and st2 expression levels were up-regulated, and the apoptosis of myocardial cells was increased in heart tissues of ami group. compared with normoxia group, the apoptosis of mouse myocardial cell hl-1 and primary murine myocardial cells was increased, and lncrna anril and st2 expression levels were up-regulated in hypoxia group. we also found up-regulation of il-33 in ami group and hypoxia group. besides, lncrna anril affected deubiquitinase usp17-mediated degradation of il-33. interfering lncrna anril reduced the apoptosis of myocardial cells through il-33/st2 pathway. in vivo experiments found that interfering lncrna anril relieved myocardial cell apoptosis and improved heart function in ami mice. conclusion : lncrna anril regulated myocardial cell apoptosis through il-33/st2 pathway.",1
"we isolated a mouse genomic clone that hybridized with small rna present in the cytoplasm of the brain. the rna was about 150 nucleotides long. this rna seemed to be specific to the brain, since it was not found in the liver or kidney. the clone dna contained a sequence homologous to 82-nucleotide ""identifier"" core sequence of cdna clones of rat. the sequence contained a split promoter for rna polymerase iii and was flanked by a 12-nucleotide direct repeat (ataaataattta).",1
"introduction endothelium dysfunction plays a critical role in atherosclerosis. micrornas are endogenous non-coding rnas that suppress gene expression by binding to the 3' untranslated regions of target genes. mir-495 can regulate the proliferation and apoptosis of cancer cells, however, the roles of mir-495 in endothelial cells (ecs) remain unclear. therefore, this study aims to investigate the roles and mechanisms of mir-495 on ecs proliferation and apoptosis. materials and methods mir-495 and ccl2 expressions were examined using quantitative rt-pcr, elisa assay and western blot. bioinformatics analysis and luciferase reporter assay were used to examine the regulatory relationship between mir-495 and ccl2. cck8 assay, brdu incorporation assay and flow cytometry were used to analyze the roles of mir-495 and ccl2 on the proliferation of human umbilical vein endothelial cells (huvecs). the effects of mir-495 and ccl2 on huvecs apoptosis were examined by tunnel staining and western blot. results mir-495 was down-regulated in patients with coronary artery disease compared with healthy controls. ccl2 was a novel target gene of mir-495. mir-495 significantly promoted huvecs proliferation by altering cell cycle distribution, and it also inhibited huvecs apoptosis by affecting the expression of cleaved caspase 3. effects of mir-495 on huvecs proliferation and apoptosis were significantly reversed by overexpression of ccl2. conclusions mir-495 could affect huvecs proliferation and apoptosis by directly targeting ccl2. this is the first report to disclose the roles and mechanisms of mir-495 on huvecs proliferation and apoptosis, which may provide a theoretical basis for clarifying the mechanisms of atherosclerosis.",1
"micrornas have been implicated in regulating diverse cellular pathways. emerging evidence indicate that the mir-17-92 cluster may have a causal role in breast cancer tumorigenesis as a novel class of oncogenes, but the role of these mirnas in breast cancer invasion and migration remains unexplored. the aims of this study were to verify the effect of mir-17-5p (an important member of the mir-17-92 cluster) on the invasive and migratory ability of breast cancer cells. the matching of mir-17-5p and hmg box-containing protein 1 (hbp1) was predicted by targetscan and confirmed by dna constructs and luciferase target assay. the expression levels of mir-17-5p and its candidate target-hbp1 in mcf7 and mda-mb-231 breast cancer cells were measured by real-time pcr and western blotting. effects of mir-17-5p in cell cycle progression, proliferation, invasion and migration were evaluated by flow cytometry assay, 3-(4,-dimethy -lthiazol-2-yl)-2,-diphenyl -tetrazoliumbromide assay, soft-agar colony formation assay, and transwell invasive and migratory assay, respectively. the results showed that mir-17-5p was highly expressed in high-invasive mda-mb-231 breast cancer cells but not in low-invasive mcf-7 breast cancer cells. over-expression of mir-17-5p in mcf-7 cells rendered them the invasive and migratory abilities by targeting hbp1/β-catenin pathway. on the other hand, down-regulation of endogenous mir-17-5p suppressed the migration and invasion of mda-mb-231 cells in vitro. these findings suggest that mir-17-5p plays an important role in breast cancer cell invasion and migration by suppressing hbp1 and subsequent activation of wnt/β-catenin.",1
"small non-coding rnas (micrornas) are important regulators of gene expression that modulate many physiological processes; however, their role in regulating intracellular transport remains largely unknown. intriguingly, we found that the dynamin (dnm) genes, a gtpase family of proteins responsible for endocytosis in eukaryotic cells, encode the conserved mir-199a and mir-199b family of mirnas within their intronic sequences. here, we demonstrate that mir-199a and mir-199b regulate endocytic transport by controlling the expression of important mediators of endocytosis such as clathrin heavy chain (cltc), rab5a, low-density lipoprotein receptor (ldlr) and caveolin-1 (cav-1). importantly, mir-199a-5p and mir-199b-5p overexpression markedly inhibits cltc, rab5a, ldlr and cav-1 expression, thus preventing receptor-mediated endocytosis in human cell lines (huh7 and hela). of note, mir-199a-5p inhibition increases target gene expression and receptor-mediated endocytosis. taken together, our work identifies a new mechanism by which micrornas regulate intracellular trafficking. in particular, we demonstrate that the dnm, mir-199a-5p and mir-199b-5p genes act as a bifunctional locus that regulates endocytosis, thus adding an unexpected layer of complexity in the regulation of intracellular trafficking.",1
"following a search of sequence data bases for intronic sequences exhibiting structural features typical of snornas, we have positively identified by northern assays and sequence analysis another intron-encoded snorna, termed u21. u21 rna is a 93 nt. long, metabolically stable rna, present at about 10(4) molecules per hela cell. it is encoded in intron 5 of the ribosomal protein l5 gene, both in chicken and in the two mammals studied so far, human and mouse. u21 rna is devoid of a 5'-trimethyl-cap and is likely to result from processing of intronic rna. the nucleolar localization of u21 has been established by fluorescence microscopy after in situ hybridization with digoxigenin-labeled oligonucleotide probes. like most other snornas u21 contains the box c and box d motifs and is precipitated by anti-fibrillarin antibodies. by the presence of a typical 5'-3' terminal stem, u21 appears more particularly related to u14, u15, u16 and u20 intron-encoded snornas. remarkably, u21 contains a long stretch (13 nt.) of complementarity to a highly conserved sequence in 28s rrna. sequence comparisons between chicken and mammals, together with northern hybridizations with antisense oligonucleotides on cellular rnas from more distant vertebrates, point to the preferential preservation of this segment of u21 sequence during evolution. accordingly, this complementarity, which overlaps the complementarity of 28s rrna to another snorna, u18, could reflect an important role of u21 snorna in the biogenesis of large ribosomal subunit.",1
"unlabelled by comparing the expression profiles of micrornas (mirnas) in different hepatocellular carcinoma (hcc) subtypes, we identified mir-140-5p as an hcc-related mirna. we found that mir-140-5p was significantly decreased in hcc tissues and all of six liver cancer cell lines examined and its expression levels were correlated with multiple nodules, vein invasion, capsular formation, and differentiation, as well as overall and disease-free survival of hcc. we also found that mir-140-5p suppressed hcc cell proliferation and hcc metastasis. multipathway reporter arrays suggested that mir-140-5p inhibited transforming growth factor β (tgf-β) and mitogen-activated protein kinase / extracellular signal-regulated kinase (mapk/erk) signaling. tgfb receptor 1 (tgfbr1) and fibroblast growth factor 9 (fgf9) were then characterized as the direct targets for mir-140-5p after it was found that ectopic mir-140-5p expression suppressed tgfbr1 and fgf9 expression. silencing tgfbr1 and fgf9 by small interfering rna (sirna) resembled the phenotype resulting from ectopic mir-140-5p expression, while overexpression of tgfbr1 and fgf9 attenuated the effect of mir-140-5p on hcc growth and metastasis. conclusion these data elucidated a tumor suppressor role for mir-140-5p in hcc development and progression with therapeutic potential. our correlation studies in clinical hcc samples further suggest that mir-140-5p could be a valuable biomarker for hcc prognosis.",1
"human immunodeficiency virus type 1 (hiv-1) utilizes a distinctive form of gene regulation as part of its life cycle, termed programmed -1 ribosomal frameshifting, to produce the required ratio of the gag and gag-pol polyproteins. we carried out a sequence comparison of 1,000 hiv-1 sequences at the slippery site (uuuuuua) and found that the site is invariant, which is somewhat surprising for a virus known for its variability. this prompted us to prepare a series of mutations to examine their effect upon frameshifting and viral infectivity. among the series of mutations were changes of the hiv-1 slippery site to those effectively utilized by other viruses, because such mutations would be anticipated to have a relatively mild effect upon frameshifting. the results demonstrate that any change to the slippery site reduced frameshifting levels and also dramatically inhibited infectivity. because ribosomal frameshifting is essential for hiv-1 replication and it is surprisingly resistant to mutation, modulation of hiv-1 frameshifting efficiency potentially represents an important target for the development of novel antiviral therapeutics.",1
"little is known so far about rna regulators of photosynthesis in plants, algae, or cyanobacteria. the small rna psrr1 (formerly syr1) has been discovered in synechocystis sp pcc 6803 and appears to be widely conserved within the cyanobacterial phylum. expression of psrr1 is induced shortly after a shift from moderate to high-light conditions. artificial overexpression of psrr1 led to a bleaching phenotype under moderate light growth conditions. advanced computational target prediction suggested that several photosynthesis-related mrnas could be controlled by psrr1, a finding supported by the results of transcriptome profiling experiments upon pulsed overexpression of this small rna in synechocystis sp pcc 6803. we confirmed the interaction between psrr1 and the ribosome binding regions of the psal, psaj, chln, and cpca mrnas by mutational analysis in a heterologous reporter system. focusing on psal as a specific target, we show that the psal mrna is processed by rnase e only in the presence of psrr1. furthermore, we provide evidence for a posttranscriptional regulation of psal by psrr1 in the wild type at various environmental conditions and analyzed the consequences of psrr1-based regulation on photosystem i. in summary, computational and experimental data consistently establish the small rna psrr1 as a regulatory factor controlling photosynthetic functions.",1
"background the transcription factor gata2 orchestrates the expression of many endothelial-specific genes, illustrating its crucial importance for endothelial cell function. the capacity of this transcription factor in orchestrating endothelial-important micrornas (mirnas/mir) is unknown. methods endothelial gata2 was functionally analyzed in human endothelial cells in vitro. endogenous short interfering rna-mediated knockdown and lentiviral-based overexpression were applied to decipher the capacity of gata2 in regulating cell viability and capillary formation. next, the gata2-dependent mir transcriptome was identified by using a profiling approach on the basis of quantitative real-time polymerase chain reaction. transcriptional control of mir promoters was assessed via chromatin immunoprecipitation, luciferase promoter assays, and bisulfite sequencing analysis of sites in proximity. selected mirs were modulated in combination with gata2 to identify signaling pathways at the angiogenic cytokine level via proteome profiler and enzyme-linked immunosorbent assays. downstream mir targets were identified via bioinformatic target prediction and luciferase reporter gene assays. in vitro findings were translated to a mouse model of carotid injury in an endothelial gata2 knockout background. nanoparticle-mediated delivery of proangiogenic mir-126 was tested in the reendothelialization model. results gata2 gain- and loss-of-function experiments in human umbilical vein endothelial cells identified a key role of gata2 as master regulator of multiple endothelial functions via mirna-dependent mechanisms. global mirnanome-screening identified several gata2-regulated mirnas including mir-126 and mir-221. specifically, proangiogenic mir-126 was regulated by gata2 transcriptionally and targeted antiangiogenic spred1 and foxo3a contributing to gata2-mediated formation of normal vascular structures, whereas gata2 deficiency led to vascular abnormalities. in contrast to gata2 deficiency, supplementation with mir-126 normalized vascular function and expression profiles of cytokines contributing to proangiogenic paracrine effects. gata2 silencing resulted in endothelial dna hypomethylation leading to induced expression of antiangiogenic mir-221 by gata2-dependent demethylation of a putative cpg island in the mir-221 promoter. mechanistically, a reverted gata2 phenotype by endogenous suppression of mir-221 was mediated through direct proangiogenic mir-221 target genes icam1 and ets1. in a mouse model of carotid injury, gata2 was reduced, and systemic supplementation of mir-126-coupled nanoparticles enhanced mir-126 availability in the carotid artery and improved reendothelialization of injured carotid arteries in vivo. conclusions gata2-mediated regulation of mir-126 and mir-221 has an important impact on endothelial biology. hence, modulation of gata2 and its targets mir-126 and mir-221 is a promising therapeutic strategy for treatment of many vascular diseases.",1
"rationale in response to mechanical and pathological stress, adult mammalian hearts often undergo mal-remodeling, a process commonly characterized as pathological hypertrophy, which is associated with upregulation of fetal genes, increased fibrosis, and reduction of cardiac dysfunction. the molecular pathways that regulate this process are not fully understood. objective to explore the function of microrna-155 (mir-155) in cardiac hypertrophy and remodeling. methods and results our previous work identified mir-155 as a critical microrna that repressed the expression and function of the myocyte enhancer factor 2a. in this study, we found that mir-155 is expressed in cardiomyocytes and that its expression is reduced in pressure overload-induced hypertrophic hearts. in mouse models of cardiac hypertrophy, mir-155 null hearts suppressed cardiac hypertrophy and cardiac remodeling in response to 2 independent pathological stressors, transverse aortic restriction and an activated calcineurin transgene. most importantly, loss of mir-155 prevents the progress of heart failure and substantially extends the survival of calcineurin transgenic mice. the function of mir-155 in hypertrophy is confirmed in isolated cardiomyocytes. we identified jumonji, at rich interactive domain 2 (jarid2) as an mir-155 target in the heart. mir-155 directly represses jarid2, whose expression is increased in mir-155 null hearts. inhibition of endogenous jarid2 partially rescues the effect of mir-155 loss in isolated cardiomyocytes. conclusions our studies uncover mir-155 as an inducer of pathological cardiomyocyte hypertrophy and suggest that inhibition of endogenous mir-155 might have clinical potential to suppress cardiac hypertrophy and heart failure.",1
"aims aberrant expression of micrornas (mirnas) results in alterations of various biological processes (e.g., cell cycle, cell differentiation, and apoptosis) and cell transformation. altered mirnas expression was associated with lung carcinogenesis and tumor progression. this study aimed to investigate the function and underlying molecular events of mir-517a-3p on regulation of lung cancer cell proliferation and invasion. main methods transfected mir-517a-3p mimics or inhibitors into 95d and 95c cells respectively, the effects of mir-517a-3p on lung cancer cell proliferation, migration, and invasion were detected. bioinformatics software forecasted potential target genes of mir-517a-3p and dual luciferase reporter gene system and western blot verified whether mir-517a-3p regulates foxj3 expression directly. key findings mir-517a-3p was differentially expressed in lung cancer 95d and 95c cell lines that have different metastatic potential. manipulation of mir-517a-3p expression changed lung cancer cell proliferation, migration and invasion capacity. mir-517a-3p directly regulated foxj3 expression by binding to foxj3 promoter. significance this study demonstrated that mir-517a-3p promoted lung cancer cell proliferation and invasion by targeting of foxj3 expression.",1
"micrornas (mirnas) are small rnas that regulate gene expression posttranscriptionally and are critical for many cellular pathways. recent evidence has shown that aberrant mirna expression profiles and unique mirna signaling pathways are present in many cancers. here, we demonstrate that mir-29b is markedly lower expressed in cml patient samples. bioinformatics analysis reveals a conserved target site for mir-29b in the 3'-untranslated region (utr) of abl1. mir-29b significantly suppresses the activity of a luciferase reporter containing abl1-3'utr and this activity is not observed in cells transfected with mutated abl1-3'utr. enforced expression of mir-29b in k562 cells inhibits cell growth and colony formation ability thereby inducing apoptosis through cleavage of procaspase 3 and parp. furthermore, k562 cells transfected with a sirna targeting abl1 show similar growth and apoptosis phenotypes as cells overexpression of mir-29b. collectively, our results suggest that mir-29b may function as a tumor suppressor by targeting abl1 and bcr/abl1.",1
"mir-125b-1 maps at 11q24, a chromosomal region close to the epicenter of 11q23 deletions in chronic lymphocytic leukemias (clls). our results establish that both aggressive and indolent cll patients show reduced expression of mir-125b. overexpression of mir-125b in cll-derived cell lines resulted in the repression of many transcripts encoding enzymes implicated in cell metabolism. metabolomics analyses showed that mir-125b overexpression modulated glucose, glutathione, lipid, and glycerolipid metabolism. changes on the same metabolic pathways also were observed in clls. we furthermore analyzed the expression of some of mir-125b-target transcripts that are potentially involved in the aforementioned metabolic pathways and defined a mir-125b-dependent cll metabolism-related transcript signature. thus, mir-125b acts as a master regulator for the adaptation of cell metabolism to a transformed state. mir-125b and mir-125b-dependent metabolites therefore warrant further investigation as possible novel therapeutic approaches for patients with cll.",1
"micrornas (mirnas) are small non-coding rnas that regulate gene expression primarily at the post-transcriptional level and play critical roles in a variety of physiological and pathological processes. in this report, mir-141 was identified to repress hbv expression by screening a small mirna expressing library and synthetic mir-141 mimics could also significantly suppress hbv expression and replication in hepg2 cells. bioinformatic analysis and experiment assays indicate that peroxisome proliferator-activated receptor alpha (ppara) was the target of hsa-mir-141 during this process. furthermore, knockdown of ppara by small interfering rna (sirna) inhibited hbv replication similar to levels observed for mir-141. promoter functional analysis indicated that repression of hbv replication by mir-141 mimics or sirna was mediated by interfering with the hbv promoter functions, consistent with previous studies demonstrating that ppara regulated hbv gene expression through interactions with hbv promoter regulatory elements. our results suggest that mir-141 suppressed hbv replication by reducing hbv promoter activities by down-regulating ppara. this study provides new insights into the molecular mechanisms associated with hbv-host interactions. furthermore, this information may facilitate the development of novel anti-hbv therapeutic strategies.",1
"micrornas are important coordinators of circadian regulation that mediate the fine-tuning of gene expression. although many studies have shown the effects of individual mirnas on the circadian clock, the global functional mirna-mrna interaction network involved in the circadian system remains poorly understood. here, we used clear (covalent ligation of endogenous argonaute-bound rnas)-clip (cross-linking and immuno-precipitation) to explore the regulatory functions of mirnas in the circadian system by comparing the mirna-mrna interactions between drosophila wild-type strain w 1118 and a mutant of the key circadian transcriptional regulator clock (clk jrk ). this experimental approach unambiguously identified tens of thousands of mirna-mrna interactions in both the head and body. the mirna-mrna interactome showed dramatic changes in the clk jrk flies. particularly, among ~300 mirna-mrna circadian relevant interactions, multiple interactions involving core clock genes pdp1, tim, and vri displayed distinct changes as a result of the clk mutation. based on the clear-clip analysis, we found a novel regulation of the circadian rhythm and sleep by the mir-375-timeless interaction. the results indicated that clk disruption abolished normal rhythmic expression of mir-375 and the functional regulation occurred in the l-lnv neurons, where mir-375 modulated the circadian rhythm and sleep via targeting timeless. this work provides the first global view of mirna regulation in the circadian rhythm.",1
"micrornas (mirnas), a class of small non-coding rnas, have emerged as novel and potent regulators of adipogenesis. however, few mirnas have been fully investigated in porcine adipogenesis, given the fact that pig is not only an apropos model of human obesity research, but also a staple meat source of human diet. in this study, we showed that mirna-199a-5p is highly expressed in porcine subcutaneous fat deposits compared to several other tissue types and organs measured alongside. overexpression of mir-199a-5p in porcine preadipocytes significantly promoted cell proliferation while attenuating the lipid deposition in porcine adipocytes. by target gene prediction and experimental validation, we demonstrated that caveolin-1 (cav-1) may be a bona fide target of mir-199a-5p in porcine adipocytes, accounting for some of mir-199a-5p's functions. taken together, our data established a role of mir-199a-5p in porcine preadipocyte proliferation and differentiation, which is at least partially played by downregulating cav-1.",1
"finding a suitable cell source for endothelial cells (ecs) for cardiovascular regeneration is a challenging issue for regenerative medicine. in this paper, we describe a novel mechanism regulating induced pluripotent stem cells (ipsc) differentiation into ecs, with a particular focus on mirnas and their targets. we first established a protocol using collagen iv and vegf to drive the functional differentiation of ipscs into ecs and compared the mirna signature of differentiated and undifferentiated cells. among the mirnas overrepresented in differentiated cells, we focused on microrna-21 (mir-21) and studied its role in ipsc differentiation. overexpression of mir-21 in predifferentiated ipscs induced ec marker up-regulation and in vitro and in vivo capillary formation; accordingly, inhibition of mir-21 produced the opposite effects. importantly, mir-21 overexpression increased tgf-β2 mrna and secreted protein level, consistent with the strong up-regulation of tgf-β2 during ipsc differentiation. indeed, treatment of ipscs with tgfβ-2 induced ec marker expression and in vitro tube formation. inhibition of smad3, a downstream effector of tgfβ-2, strongly decreased ve-cadherin expression. furthermore, tgfβ-2 neutralization and knockdown inhibited mir-21-induced ec marker expression. finally, we confirmed the pten/akt pathway as a direct target of mir-21, and we showed that pten knockdown is required for mir-21-mediated endothelial differentiation. in conclusion, we elucidated a novel signaling pathway that promotes the differentiation of ipsc into functional ecs suitable for regenerative medicine applications.",1
"objectives chikungunya virus causes chronic infection with manifestations of joint pain. human synovial fibroblasts get infected with chikv and could lead to pro-inflammatory responses. micrornas have potentials to regulate the gene expression of various anti-viral and pro-inflammatory genes. the study aims to investigate the role of mir-146a in modulation of inflammatory responses of human synovial fibroblasts by chikungunya virus. methods to study the role of mir-146a in chikv pathogenesis in human synovial cells and underlying inflammatory manifestations, we performed chikv infection in primary human synovial fibroblasts. western blotting, real-time pcr, luciferase reporter assay, overexpression and knockdown of cellular mir-146a strategies have been employed to validate the role of mir-146a in regulation of pro-inflammatory nf-κb pathway. results chikv infection induced the expression of cellular mir-146a, which resulted into down-regulation of traf6, irak1, irak2 and increased replication of chikv in human synovial fibroblasts. exogenous expression of mir-146a in human synovial fibroblasts led to decreased expression of traf6, irak1, irak2 and decreased replication of chikv. inhibition of cellular mir-146a by anti-mir-146a restored the expression levels of traf6, irak1 and irak2. downregulation of traf6, irak1 and irak2 led to downstream decreased nf-κb activation through negative feedback loop. conclusion this study demonstrated the mechanism of exploitation of cellular mir-146a by chikv in modulating the host antiviral immune response in primary human synovial fibroblasts.",1
"micrornas (mirnas) act in concert with argonaute (ago) proteins to repress target messenger rnas. after ago loading, mirnas generally exhibit slow turnover. an important exception occurs when mirnas encounter highly complementary targets, which can trigger a process called target-directed mirna degradation (tdmd). during tdmd, mirnas undergo tailing and trimming, suggesting that this is an important step in the decay mechanism. we identified a cullin-ring ubiquitin ligase (crl), containing the substrate adaptor zswim8, that mediates tdmd. the zswim8 crl interacts with ago proteins, promotes tdmd in a tailing and trimming-independent manner, and regulates mirna expression in multiple cell types. these findings suggest a model in which the zswim8 ubiquitin ligase mediates tdmd by directing proteasomal decay of mirna-containing complexes engaged with highly complementary targets.",1
"microrna (mirna) is essential for the process of gene posttranscriptional regulation in skeletal muscle of many species, such as mice, cattle and so on. however, a little number of mirnas have been reported in the muscle development of chinese native pig breeds. in this study, the longissimus dorsi transcripts of chinese native rongchang pig at weaning and slaughter time points were analysed for mirna-seq. the results showed that 19 novel and 186 known mirnas involved in the rongchang pig skeletal muscle development were identified. based on these findings, we further confirmed that porcine mir-127, mir-299 and mir-432-5p were obviously down-expressed in adult pig (287 days of age), while mir-7134-3p and 664-5p were significantly up-expressed in weaning pig (35 days of age). in other words, these mirnas could be the potential molecular markers and play vital roles in the muscle development process. moreover, we found mir-127 could inhibit the proliferation and myogenesis of porcine satellite cells in longissimus dorsi muscle. our findings will provide deep insight into mirna function for pork quality research with chinese indigenous pig breeds.",1
"prostate cancer is one of the most common malignant cancers in men. recent studies have shown that microrna-21 (mir-21) is overexpressed in various types of cancers including prostate cancer. studies on glioma, colon cancer cells, hepatocellular cancer cells and breast cancer cells have indicated that mir-21 is involved in tumor growth, invasion and metastasis. however, the roles of mir-21 in prostate cancer are poorly understood. in this study, the effects of mir-21 on prostate cancer cell proliferation, apoptosis, and invasion were examined. in addition, the targets of mir-21 were identified by a reported risc-coimmunoprecipitation-based biochemical method. inactivation of mir-21 by antisense oligonucleotides in androgen-independent prostate cancer cell lines du145 and pc-3 resulted in sensitivity to apoptosis and inhibition of cell motility and invasion, whereas cell proliferation were not affected. we identified myristoylated alanine-rich protein kinase c substrate (marcks), which plays key roles in cell motility, as a new target in prostate cancer cells. our data suggested that mir-21 could promote apoptosis resistance, motility, and invasion in prostate cancer cells and these effects of mir-21 may be partly due to its regulation of pdcd4, tpm1, and marcks. gene therapy using mir-21 inhibition strategy may therefore be useful as a prostate cancer therapy.",1
"an increasing number of micrornas have been found to be involved in tumorigenesis, including melanoma tumorigenesis. mir-204-5p is down-regulated and functions as a tumor suppressor in many human malignant tumors. mir-204-5p expression is also decreased in melanoma tissues, but its biological roles and molecular mechanisms in malignant melanoma remain unclear. in this study, the aberrant down-regulation of mir-204-5p was detected in melanoma, especially in metastatic melanoma. mir-204-5p also served as a protective factor for the prognosis of melanoma patients. we determined that mir-204-5p suppresses cell proliferation, migration and invasion, and promotes cell apoptosis in melanoma. matrix metalloproteinases-9 and b-cell lymphoma-2 are the functional targets of mir-204-5p, through which it plays an important biological role in malignant melanoma. the effect of mir-204-5p on malignant melanoma is verified using a xenograft model. we also determined that mir-204-5p increases 5-fluorouracil and cisplatin (ddp) chemosensitivity in malignant melanoma cells. this finding elucidates new functions and mechanisms for mir-204-5p in melanoma development, and provides potential therapeutic targets for the treatment of melanoma.",1
"clostridium difficile is an emergent pathogen, and the most common cause of nosocomial diarrhea. in an effort to understand the role of small noncoding rnas (srnas) in c. difficile physiology and pathogenesis, we used an in silico approach to identify 511 srna candidates in both intergenic and coding regions. in parallel, rna-seq and differential 5'-end rna-seq were used for global identification of c. difficile srnas and their transcriptional start sites at three different growth conditions (exponential growth phase, stationary phase, and starvation). this global experimental approach identified 251 putative regulatory srnas including 94 potential trans riboregulators located in intergenic regions, 91 cis-antisense rnas, and 66 riboswitches. expression of 35 srnas was confirmed by gene-specific experimental approaches. some srnas, including an antisense rna that may be involved in control of c. difficile autolytic activity, showed growth phase-dependent expression profiles. expression of each of 16 predicted c-di-gmp-responsive riboswitches was observed, and experimental evidence for their regulatory role in coordinated control of motility and biofilm formation was obtained. finally, we detected abundant srnas encoded by multiple c. difficile crispr loci. these rnas may be important for c. difficile survival in bacteriophage-rich gut communities. altogether, this first experimental genome-wide identification of c. difficile srnas provides a firm basis for future rnome characterization and identification of molecular mechanisms of srna-based regulation of gene expression in this emergent enteropathogen.",1
"yeast contains at least 24 snrnas, many of which are dispensable for viability. we recently demonstrated that a small subset of these rnas has a functional binding site for the sm antigen, a hallmark of metazoan snrnas involved in mrna processing. here we show that one of these snrnas, snr7, is required for growth. to determine the biochemical basis of lethality in cells lacking snr7, we engineered the conditional synthesis of snr7 by fusing the snrna coding sequences to the yeast gal1 control region. cells depleted for the snr7 gene product by growth on glucose for five generations show marked accumulation of unspliced mrna precursors from the four intron-containing genes tested. in some cases, intron-exon 2 lariats also accumulate. we have identified a 70 nucleotide domain within snr7 with limited sequence-specific but striking structural homology to the mammalian snrna u5. we conclude that mrna splicing in yeast requires the function of a u5-like snrna.",1
"background gonadal differentiation in the mammalian fetus involves a complex dose-dependent genetic network. initiation and progression of fetal ovarian and testicular pathways are accompanied by dynamic expression patterns of thousands of genes. we postulate these expression patterns are regulated by small non-coding rnas called micrornas (mirnas). the aim of this study was to identify the expression of mirnas in mammalian fetal gonads using sheep as a model. methods we determined the expression of 128 mirnas by real time pcr in early-gestational (gestational day (gd) 42) and mid-gestational (gd75) sheep ovaries and testes. expression data were further examined and validated by bioinformatic analysis. results expression analysis revealed significant differences between ovaries and testes among 24 mirnas at gd42, and 43 mirnas at gd75. bioinformatic analysis revealed that a number of differentially expressed mirnas are predicted to target genes known to be important in mammalian gonadal development, including esr1, cyp19a1, and sox9. in situ hybridization revealed mir-22 localization within fetal testicular cords. as estrogen signaling is important in human and sheep ovarian development, these data indicate that mir-22 is involved in repressing estrogen signaling within fetal testes. conclusions based on our results we postulate that gene expression networks underlying fetal gonadal development are regulated by mirnas.",1
"vibrio cholerae is the waterborne bacterium responsible for worldwide outbreaks of the acute, potentially fatal cholera diarrhea. the primary factors this human pathogen uses to cause the disease are controlled by a complex regulatory program linking extracellular signaling inputs to changes in expression of several critical virulence genes. recently it has been uncovered that many non-coding regulatory srnas are important components of the v. cholerae virulence regulon. most of these srnas appear to require the rna-binding protein, hfq, to interact with and alter the expression of target genes, while a few srnas appear to function by an hfq-independent mechanism. direct base-pairing between the srnas and putative target mrnas has been shown in a few cases but the extent of each srnas regulon is not fully known. genetic and biochemical methods, coupled with computational and genomics approaches, are being used to validate known srnas and also to identify many additional putative srnas that may play a role in the pathogenic lifestyle of v. cholerae.",1
"the polycomb-group protein, ezh2, is required for epigenetic gene silencing in the adult heart by unknown mechanism. we investigated the role of ezh2 and non-coding rnas in a mouse model of pressure overload using transverse aortic constriction (tac) attenuated by the prototypical histone deacetylase inhibitor, trichostatin a (tsa). chromatin immunoprecipitation of tac and tac+tsa hearts suggests interaction of ezh2 and primary microrna-208b (pri-mir-208b) in the regulation of hypertrophic gene expression. rnai silencing of pri-mir-208b and ezh2 validate pri-mir-208b-mediated transcriptional silencing of genes implicated in cardiac hypertrophy including the suppression of the bi-directional promoter (bdp) of the cardiac myosin heavy chain genes. in tac mouse heart, tsa attenuated ezh2 binding to bdp and restored antisense β-mhc and α-mhc gene expression. rna-chromatin immunoprecipitation experiments in tac hearts also show increased pri-mir-208b dependent-chromatin binding. these results are the first description by which primary mir interactions serve to integrate chromatin modifications and the transcriptional response to distinct signaling cues in the heart. these studies provide a framework for mhc expression and regulation of genes implicated in pathological remodeling of ventricular hypertrophy.",1
"micrornas (mirnas) play essential roles in cardiogenesis. the altered expression of mirnas can result in cardiac malformations by inducing abnormalities in the behavior of cardiac cells. however, the role of mir-10a in the regulation of cardiomyocyte progenitor cells (cmpcs) remains undetermined. in the present study, we found that up- or down-regulation of mir-10a inhibited or promoted the proliferation of human cmpcs, respectively, without affecting their differentiation toward cardiomyocytes. mir-10a bound to gata6 directly and reduced gata6 expression. over-expression of gata6 greatly attenuated the mir-10a-mediated inhibitory effect on the proliferation of human cmpcs. thus, our results indicate that mir-10a could effectively modulate the proliferation of human cmpcs by targeting gata6. the finding provides novel insights into the potency of mir-10a during heart development.",1
"objective to evaluate microrna let7i in ischemic stroke and its regulation of leukocytes. methods a total of 212 patients were studied: 106 with acute ischemic stroke and 106 controls matched for risk factors. rna from circulating leukocytes was isolated from blood collected in paxgene tubes. let7i microrna expression was assessed using taqman quantitative reverse transcription pcr. to assess let7i regulation of gene expression in stroke, messenger rna (mrna) from leukocytes was measured by whole-genome human transcriptome array affymetrix microarray. given micrornas act to destabilize and degrade their target mrna, mrnas that inversely correlated with let7i were identified. to demonstrate let7i posttranscriptional regulation of target genes, a 3' untranslated region luciferase assay was performed. target protein expression was assessed using elisa. results let7i was decreased in patients with acute ischemic stroke (fold change -1.70, p conclusions let7i is decreased in circulating leukocytes of patients with acute ischemic stroke. mechanisms by which let7i regulates inflammatory response post stroke include targeting cd86, cxcl8, and hmgb1.",1
"the cellular microrna mir-155 has been shown to be involved in lymphocyte activation and is expressed in epstein-barr virus (ebv)-infected cells displaying type iii latency gene expression but not type i latency gene expression. we show here that the elevated levels of mir-155 in type iii latency cells is due to ebv gene expression and not epigenetic differences in cell lines tested, and we show that expression in ebv-infected cells requires a conserved ap-1 element in the mir-155 promoter. gene expression analysis was carried out in a type i latency cell line transduced with an mir-155-expressing retrovirus. this analysis identified both mir-155-suppressed and -induced cellular mrnas and suggested that in addition to direct targeting of 3' untranslated regions (utrs), mir-155 alters gene expression in part through the alteration of signal transduction pathways. 3' utr reporter analysis of predicted mir-155 target genes identified the transcriptional regulatory genes encoding bach1, zic3, hivep2, cebpb, znf652, arid2, and smad5 as mir-155 targets. western blot analysis of the most highly suppressed of these, bach1, showed lower expression in cells transduced with a mir-155 retrovirus. inspection of the promoters from genes regulated in ebv-infected cells and in cells infected with an mir-155 retrovirus identified potential binding sequences for bach1 and zic3. together, these experiments suggest that the induction of mir-155 by ebv contributes to ebv-mediated signaling in part through the modulation of transcriptional regulatory factors.",1
"the mir-17 family of micrornas has recently been recognized for its importance during lung development. the transgenic overexpression of the entire mir-17-92 cluster in the lung epithelium led to elevated cellular proliferation and inhibition of differentiation, while targeted deletion of mir-17-92 and mir-106b-25 clusters showed embryonic or early post-natal lethality. herein we demonstrate that mir-17 and its paralogs, mir-20a, and mir-106b, are highly expressed during the pseudoglandular stage and identify their critical functional role during embryonic lung development. simultaneous downregulation of these three mirnas in explants of isolated lung epithelium altered fgf10 induced budding morphogenesis, an effect that was rescued by synthetic mir-17. e-cadherin levels were reduced, and its distribution was altered by mir-17, mir-20a and mir-106b downregulation, while conversely, beta-catenin activity was augmented, and expression of its downstream targets, including bmp4 as well as fgfr2b, increased. finally, we identified stat3 and mapk14 as key direct targets of mir-17, mir-20a, and mir-106b and showed that simultaneous overexpression of stat3 and mapk14 mimics the alteration of e-cadherin distribution observed after mir-17, mir-20a, and mir-106b downregulation. we conclude that the mir-17 family of mirna modulates fgf10-fgfr2b downstream signaling by specifically targeting stat3 and mapk14, hence regulating e-cadherin expression, which in turn modulates epithelial bud morphogenesis in response to fgf10 signaling.",1
"microrna-155 (mir-155) has been implicated as a central regulator of the immune system. we have previously reported that mir-155 negatively regulates helicobacter pylori (h. pylori)-induced inflammation, but the molecular mechanism of mir-155 regulating the inflammation is not fully clear. here, we identified myeloid differentiation protein 88 (myd88) as a target gene of mir-155, and found that mir-155 decreased myd88 expression at the protein but not the mrna message level, suggesting that the mir-155-mediated inhibition is a post-transcriptional event. furthermore, the overexpression of mir-155 led to significantly reduced il-8 production induced by h. pylori infection. thus, we have demonstrated that mir-155 can negatively regulate inflammation by targeting a key adaptor molecule myd88 in inflammatory pathways.",1
"mutations in rrp6 result in the accumulation of aberrant polyadenylated transcripts from small nucleolar rna genes. we exploited this observation to search for novel noncoding rna genes in the yeast genome. when rna from rrp6delta yeast is compared with wild-type on whole-genome microarrays, numerous intergenic loci exhibit an increased mutant/wild type signal ratio. among these loci, we found one encoding a new c/d box small nucleolar rna, as well as a surprising number that gave rise to heterogeneous trf4p-polyadenylated rnas with lengths of approximately 250-500 nt. this class of rnas is not easily detected in wild-type cells and appears associated with promoters. fine mapping of several such transcripts shows they originate near known promoter elements but do not usually extend far enough to act as mrnas, and may regulate the transcription of downstream mrnas. rather than being uninformative transcriptional ""noise,"" we hypothesize that these transcripts reflect important features of rna polymerase activity at the promoter. this activity is normally undetectable in wild-type cells because the transcripts are somehow distinguished from true mrnas and are degraded in an rrp6p-dependent fashion in the nucleus.",1
"accumulation of amyloid β-peptide (aβ) in the brain of alzheimer disease (ad) patients is believed to be the main pathological feature of the disease. meanwhile, mir-98-5p dysregulation was found in ad. however, whether mir-98-5p is involved in the accumulation of aβ in ad, the underlying molecule mechanism remains unclear. in the present study, we confirmed that mir-98-5p negatively regulated sorting nexin 6 (snx6) expression by targeting the 3'-utr of snx6 mrna. downregulation of mir-98-5p alleviated aβ-induced viability inhibition and decreased apoptosis in sk-n-sh and sh-sy5y cells by upregulating snx6 expression. furthermore, downregulation of mir-98-5p decreased snx6-dependent levels of aβ40, aβ42, β-site app-cleaving enzyme 1 (bace1), soluble amyloid precursor protein β (sappβ), and membrane-associated app β-carboxyl terminal fragment (βctf) in sk-n-sh and hek293 cells. our findings demonstrate that mir-98-5p modulates snx6 expression and thus plays a critical role in accumulation of aβ. therefore, mir-98-5p may be a novel therapeutic target for ad.",1
"micrornas (mirnas) are a class of small noncoding rnas that negatively regulate protein expression by binding protein-coding mrnas and repressing translation. accumulating evidence suggests that mirnas are involved in cancer development and progression, acting as either tumor suppressors or oncogenes. intriguingly, it has been shown that mir-133b was significantly downregulated in several types of cancers. however, its role and relevance in gastric cancer are still largely unknown. we showed that mir-133b was downregulated in human gastric cancer tissues and cell lines compared with nontumor counterparts by quantitative rt-pcr analysis. overexpression of mir-133b could inhibit cell proliferation and colony formation of the gastric cancer cell lines mkn-45 and sgc-7901. bioinformatics analysis indicated two putative mir-133b binding sites in the 3'-untranslated region of fibroblast growth factor receptor 1 (fgfr1) mrna. in dual-luciferase reporter assay, mir-133b reduced the luciferase activity of luc-fgfr1-wt, and mutation of mir-133b binding sites abolished the inhibitory effect of mir-133b. in this study, we found that mir-133b reduced the protein but not the mrna levels of endogenous fgfr1. furthermore, fgfr1 expression was upregulated in gastric cancer tissues and inversely correlated with mir-133b expression. finally, knockdown of fgfr1 inhibited the growth of mkn-45 cells in a dose-dependent manner and overexpression of fgfr1 promoted the growth of ges-1 cells. these results indicate that mir-133b targets fgfr1 and inhibits gastric cancer cell growth, suggesting that it may serve as a tumor suppressive target in gastric cancer therapy.",1
"stem cells and cancer cells maintain telomere length mostly through telomerase. telomerase activity is high in male germ line and stem cells, but is low or absent in mature oocytes and cleavage stage embryos, and then high again in blastocysts. how early embryos reset telomere length remains poorly understood. here, we show that oocytes actually have shorter telomeres than somatic cells, but their telomeres lengthen remarkably during early cleavage development. moreover, parthenogenetically activated oocytes also lengthen their telomeres, thus the capacity to elongate telomeres must reside within oocytes themselves. notably, telomeres also elongate in the early cleavage embryos of telomerase-null mice, demonstrating that telomerase is unlikely to be responsible for the abrupt lengthening of telomeres in these cells. coincident with telomere lengthening, extensive telomere sister-chromatid exchange (t-sce) and colocalization of the dna recombination proteins rad50 and trf1 were observed in early cleavage embryos. both t-sce and dna recombination proteins decrease in blastocyst stage embryos, whereas telomerase activity increases and telomeres elongate only slowly. we suggest that telomeres lengthen during the early cleavage cycles following fertilization through a recombination-based mechanism, and that from the blastocyst stage onwards, telomerase only maintains the telomere length established by this alternative mechanism.",1
"t cell sensitivity to antigen is intrinsically regulated during maturation to ensure proper development of immunity and tolerance, but how this is accomplished remains elusive. here we show that increasing mir-181a expression in mature t cells augments the sensitivity to peptide antigens, while inhibiting mir-181a expression in the immature t cells reduces sensitivity and impairs both positive and negative selection. moreover, quantitative regulation of t cell sensitivity by mir-181a enables mature t cells to recognize antagonists-the inhibitory peptide antigens-as agonists. these effects are in part achieved by the downregulation of multiple phosphatases, which leads to elevated steady-state levels of phosphorylated intermediates and a reduction of the t cell receptor signaling threshold. importantly, higher mir-181a expression correlates with greater t cell sensitivity in immature t cells, suggesting that mir-181a acts as an intrinsic antigen sensitivity ""rheostat"" during t cell development.",1
"bacteria of the genus bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. among them, the species bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. here, we use differential rna sequencing (drna-seq) to generate a single-nucleotide resolution transcriptome map of b. thetaiotaomicron grown under defined laboratory conditions. an online browser, called 'theta-base' ( ), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding rna elements. among the latter is gibs, a conserved, 145 nt-long small rna that is highly expressed in the presence of n-acetyl-d-glucosamine as sole carbon source. we use computational predictions and experimental data to determine the secondary structure of gibs and identify its target genes. our results indicate that sensing of n-acetyl-d-glucosamine induces gibs expression, which in turn modifies the transcript levels of metabolic enzymes.",1
"micrornas (mirnas) are small non-coding rnas that regulate gene expression at the post-transcriptional level. their roles in regulating the responses of schwann cells (scs) to injury stimuli remain unexplored. here we report dynamic alteration of mirna expression following rat sciatic nerve injury using microarray analysis. we harvested the proximal nerve stumps and identified 77 mirnas that showed significant changes at four time points after nerve transection. subsequently, we analyzed the expression pattern of mirna, selected one significant profile, and then integrated putative mirna targets with differentially expressed mrna yielding 274 potential targets. the 274 targets were mainly involved in cell proliferation, cell locomotion and cellular homeostasis that were known to play important roles in modulating cell phenotype. the upregulation of the mir-221 and mir-222 cluster (mir-221/222) was found to correlate with the injury-induced sc phenotypic modulation. enhanced expression of mir-221/222 could promote sc proliferation and migration in vitro, whereas silencing their expression resulted in a reduced proliferation and migration. further studies revealed that longevity assurance homologue 2 (lass2) was a direct target of mir-221/222 in scs because mir-221/222 bound directly to the 3'-untranslated region of lass2, thus reducing both mrna and protein levels of lass2. silencing of lass2 recapitulated the effects of mir-221/222 mimics, whereas enforced knockdown of lass2 reversed the suppressive effects of mir-221/222 inhibitors. our findings indicate that injury promotes sc proliferation and migration through the regulation of mir-221/222 by targeting lass2, and provide new insights into the role of mirnas in nerve regeneration.",1
"ssb-1, the yeast single-strand rna-binding protein, is demonstrated to be a yeast nucleolar-specific, silver-binding protein. in double-label immunofluorescence microscopy experiments antibodies to two other nucleolar proteins, rna pol i 190-kd and fibrillarin, were used to reveal the site of rrna transcription; i.e., the fibrillar region of the nucleolus. ssb-1 colocalized with fibrillarin in a double-label immunofluorescence mapping experiment to the yeast nucleolus. ssb-1 is located, though, over a wider region of the nucleolus than the transcription site marker. immunoprecipitations of yeast cell extracts with the ssb-1 antibody reveal that in 150 mm nacl ssb-1 is bound to two small nuclear rnas (snrnas). these yeast snrnas are snr10 and snr11, with snr10 being predominant. since snr10 has been implicated in pre-rrna processing, the association of ssb-1 and snr10 into a nucleolar snrnp particle indicates ssb-1 involvement in rrna processing as well. also, another yeast protein, ssb-36-kd, isolated by single-strand dna chromatography, is shown to bind silver under the conditions used for nucleolar-specific staining. it is, most likely, another yeast nucleolar protein.",1
"primary effusion lymphoma (pel) is caused by kaposi's sarcoma-associated herpesvirus (kshv) and frequently also harbors epstein-barr virus (ebv). the expression of kshv- and ebv-encoded micrornas (mirnas) in pels suggests a role for these mirnas in latency and lymphomagenesis. using par-clip, a technology which allows the direct and transcriptome-wide identification of mirna targets, we delineate the target sites for all viral and cellular mirnas expressed in pel cell lines. the resulting data set revealed that kshv mirnas directly target more than 2000 cellular mrnas, including many involved in pathways relevant to kshv pathogenesis. moreover, 58% of these mrnas are also targeted by ebv mirnas, via distinct binding sites. in addition to a known viral analog of cellular mir-155, we show that kshv encodes a viral mirna that mimics cellular mir-142-3p function. in summary, this study identifies an extensive list of kshv mirna targets, which are likely to influence viral replication and pathogenesis.",1
"in the 3' non-coding region of the genomes of infectious bronchitis virus, an avian coronavirus and the picornavirus equine rhinovirus serotype 2, there is a motif with remarkable similarity, both in sequence and folding, to the second rna stem-loop from the 3' end of the genomes of human astroviruses. this motif was also found in astroviruses of sheep, pig and turkey, suggesting that it is a common feature of all astroviruses. the conserved nature of the motif indicates that there has been strong selection for its preservation. there is significant homology between the regions flanking this motif in infectious bronchitis virus and a continuous rna sequence at the same distance from the 3' poly(a) tail in some related mammalian coronaviruses. these observations suggest that the presence of the motif in these three viral families is the result of at least two separate rna recombination events.",1
"loss of drosophila mir-9a induces a subtle increase in sensory bristles, but a substantial loss of wing tissue. here, we establish that the latter phenotype is largely due to ectopic apoptosis in the dorsal wing primordium, and we could rescue wing development in the absence of this microrna by dorsal-specific inhibition of apoptosis. such apoptosis was a consequence of de-repressing drosophila lim-only (dlmo), which encodes a transcriptional regulator of wing and neural development. we observed cell-autonomous elevation of endogenous dlmo and a gfp-dlmo 3'utr sensor in mir-9a mutant wing clones, and heterozygosity for dlmo rescued the apoptosis and wing defects of mir-9a mutants. we also provide evidence that dlmo, in addition to senseless, contributes to the bristle defects of the mir-9a mutant. unexpectedly, the upregulation of dlmo, loss of cut, and adult wing margin defects seen with mir-9a mutant clones were not recapitulated by clonal loss of the mirna biogenesis factors dicer-1 or pasha, even though these mutant conditions similarly de-repressed mir-9a and dlmo sensor transgenes. therefore, the failure to observe a phenotype upon conditional knockout of a mirna processing factor does not reliably indicate the lack of critical roles of mirnas in a given setting.",1
"we have performed a computational comparative analysis of six small non-coding rna (srna) families in α-proteobacteria. members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont s. meliloti by a combined bioinformatics screen followed by experimental verification. consensus secondary structures inferred from covariance models for each srna family evidenced in some cases conserved motifs putatively relevant to the function of trans-encoded base-pairing srnas i.e., hfq-binding signatures and exposed anti shine-dalgarno sequences. two particular family models, namely αr15 and αr35, shared own sub-structural modules with the rfam model suhb (rf00519) and the uncharacterized srna family αr35b, respectively. a third srna family, termed αr45, has homology to the cis-acting regulatory element spef (rf00518). however, new experimental data further confirmed that the s. meliloti αr45 representative is an hfq-binding srna processed from or expressed independently of spef, thus refining the rfam spef model annotation. all the six families have members in phylogenetically related plant-interacting bacteria and animal pathogens of the order of the rhizobiales, some occurring with high levels of paralogy in individual genomes. in silico and experimental evidences predict differential regulation of paralogous srnas in s. meliloti 1021. the distribution patterns of these srna families suggest major contributions of vertical inheritance and extensive ancestral duplication events to the evolution of srnas in plant-interacting bacteria.",1
"this study aims to investigate the role of long noncoding rna snhg20 in the progression of nonalcoholic fatty liver disease (nalfd) to hepatocellular carcinoma (hcc), and to elucidate whether polarization of kupffer cells (kcs, liver macrophages) was involved in this process. mouse nalfd was induced by 16 weeks of high-fat diet (hfd) feeding. mouse nalfd-hcc was induced by 36 weeks of hfd feeding (from 1 week to 36 weeks) and 20 weeks of diethyl nitrosamine (den) administration (from 17 weeks to 36 weeks). the lv-shrna- and lv-sh-snhg20-infected raw264.7 cells were injected into the nalfd mice followed by den treatment to evaluate the role of snhg20 in regulating the progression of nalfd to hcc in mice. the proportion of m1 and m2 macrophages was determined by flow cytometry. the levels of m1-related inducible nitric oxide synthase (inos) and tumor necrosis factor-α and m2-related arg-1 and interleukin (il)-10 were also examined. snhg20 expression was decreased in nalfd but increased in nalfd-hcc, both in human and experimental mouse livers. furthermore, human and mouse nalfd-hcc kcs displayed decreased m1/m2 ratio compared with nalfd kcs. moreover, snhg20 overexpression induced m2 polarization through activating stat6, whereas snhg20 silencing suppressed m1 polarization in raw264.7 macrophages and delayed the progression of nalfd to hcc in mice. snhg20 may facilitate the progression of nalfd to hcc via inducing liver kcs m2 polarization via stat6 activation.",1
"vsmcs respond to changes in the local environment by adjusting their phenotype from contractile to synthetic, a phenomenon known as phenotypic modulation or switching. failure of vsmcs to acquire and maintain the contractile phenotype plays a key role in a number of major human diseases, including arteriosclerosis. although several regulatory circuits that control differentiation of smcs have been identified, the decisive mechanisms that govern phenotypic modulation remain unknown. here, we demonstrate that the mouse mir-143/145 cluster, expression of which is confined to smcs during development, is required for vsmc acquisition of the contractile phenotype. vsmcs from mir-143/145-deficient mice were locked in the synthetic state, which incapacitated their contractile abilities and favored neointimal lesion development. unbiased high-throughput, quantitative, mass spectrometry-based proteomics using reference mice labeled with stable isotopes allowed identification of mir-143/145 targets; these included angiotensin-converting enzyme (ace), which might affect both the synthetic phenotype and contractile functions of vsmcs. pharmacological inhibition of either ace or the at1 receptor partially reversed vascular dysfunction and normalized gene expression in mir-143/145-deficient mice. we conclude that manipulation of mir-143/145 expression may offer a new approach for influencing vascular repair and attenuating arteriosclerotic pathogenesis.",1
"acute myeloid leukemia (aml) involves a block in terminal differentiation of the myeloid lineage and uncontrolled proliferation of a progenitor state. using phorbol myristate acetate (pma), it is possible to overcome this block in thp-1 cells (an m5-aml containing the mll-mllt3 fusion), resulting in differentiation to an adherent monocytic phenotype. as part of fantom4, we used microarrays to identify 23 micrornas that are regulated by pma. we identify four pma-induced micrornas (mir-155, mir-222, mir-424 and mir-503) that when overexpressed cause cell-cycle arrest and partial differentiation and when used in combination induce additional changes not seen by any individual microrna. we further characterize these pro-differentiative micrornas and show that mir-155 and mir-222 induce g2 arrest and apoptosis, respectively. we find mir-424 and mir-503 are derived from a polycistronic precursor mir-424-503 that is under repression by the mll-mllt3 leukemogenic fusion. both of these micrornas directly target cell-cycle regulators and induce g1 cell-cycle arrest when overexpressed in thp-1. we also find that the pro-differentiative mir-424 and mir-503 downregulate the anti-differentiative mir-9 by targeting a site in its primary transcript. our study highlights the combinatorial effects of multiple micrornas within cellular systems.",1
"the ten-eleven-translocation 2 (tet2) gene, which oxidates 5-methylcytosine in dna to 5-hydroxylmethylcytosine (5hmc), is a key tumor suppressor frequently mutated in hematopoietic malignancies. however, the molecular regulation of tet2 expression is poorly understood. we show that tet2 is under extensive microrna (mirna) regulation, and such tet2 targeting is an important pathogenic mechanism in hematopoietic malignancies. using a high-throughput 3' utr activity screen, we identify >30 mirnas that inhibit tet2 expression and cellular 5hmc. forced expression of tet2-targeting mirnas in vivo disrupts normal hematopoiesis, leading to hematopoietic expansion and/or myeloid differentiation bias, whereas coexpression of tet2 corrects these phenotypes. importantly, several tet2-targeting mirnas, including mir-125b, mir-29b, mir-29c, mir-101, and mir-7, are preferentially overexpressed in tet2-wild-type acute myeloid leukemia. our results demonstrate the extensive roles of mirnas in functionally regulating tet2 and cellular 5hmc and reveal mirnas with previously unrecognized oncogenic potential. our work suggests that tet2-targeting mirnas might be exploited in cancer diagnosis.",1
"the spliceosomal small nuclear rnas (snrnas) are modified post-transcriptionally by introduction of pseudouridines and 2'-o-methyl modifications, which are mediated by box h/aca and box c/d guide rnas, respectively. because of their concentration in the nuclear cajal body (cb), these guide rnas are known as small cb-specific (sca) rnas. in the cell, scarnas are associated with the wd-repeat protein wdr79. we used coimmunoprecipitation with wdr79 to recover seven new scarnas from drosophila cell lysates. we demonstrated concentration of these new scarnas in the cb by in situ hybridization, and we verified experimentally that they can modify their putative target rnas. surprisingly, one of the new scarnas targets u6 snrna, whose modification is generally assumed to occur in the nucleolus, not in the cb. two other scarnas have dual guide functions, one for an snrna and one for 28s rrna. again, the modification of 28s rrna is assumed to take place in the nucleolus. these findings suggest that canonical scarnas may have functions in addition to their established role in modifying u1, u2, u4, and u5 snrnas. we discuss the likelihood that processing by scarnas is not limited to the cb.",1
"innate immunity is the first and essential line for resisting pathogens, and the immune intensity and duration need to be strictly regulated to balance excessive or insufficient immune response. micrornas (mirnas) are crucial regulators of immune response in drosophila, yet how immune-related mirnas are regulated remains poorly understood. herein, we elucidated that the involvement of mir-317 in nf-κb transcription factor relish mediated drosophila imd pathway in response to gram-negative (g-) bacteria stimulation. remarkably, the dynamic expression profiling for immune response indicated that relish simultaneously enhances the expression of the effector antimicrobial peptide dpt as well as mir-317 post-infection. upregulation of mir-317 could further down-regulate the expression of pgrp-lc, thereby forming a feedback in drosophila imd pathway to prevent over-activation and restore immune homeostasis. taken together, our study not only uncovers a novel relish/mir-317/pgrp-lc regulatory axis to attenuate drosophila imd immune response and facilitate immune homeostasis restoration, but also provides vital insights into the complex mechanisms of animal innate immune regulation.",1
"spatially restricted synthesis of nanos protein in the drosophila embryo is essential for anterior-posterior patterning. nanos translation is restricted to the posterior of the embryo by translational repression of nanos mrna throughout the bulk cytoplasm and selective activation of posteriorly localized nanos mrna. a 90-nucleotide translational control element (tce) mediates translational repression. we show that tce function requires formation of a bipartite secondary structure that is recognized by smaug repressor and at least one additional factor. we also demonstrate that translational activation requires the interaction of localization factors with sequences that overlap tce structural motifs. the identification of separate but overlapping recognition motifs for translational repressors and localization factors provides a molecular mechanism for the switch between translational repression and activation.",1
"a human imprinted domain at 14q32 contains two co-expressed and reciprocally imprinted genes, dlk1 and gtl2, which are expressed from the paternally and maternally inherited alleles, respectively. we have previously shown that another imprinted locus, on human 15q11-q13, contains a large number of tandemly repeated c/d small nucleolar rna genes (or c/d snornas) only expressed from the paternal allele. here we show that the region downstream from the gtl2 gene is also characterized by a transcription unit spanning many repeated intron-encoded c/d snorna genes, most of them arranged into two tandem arrays of 31 and 9 copies. intriguingly, these snornas depart from previously reported rrna or snrna methylation guides by their tissue-specific expression and by their lack of complementarity to rrna or snrna within their sequences. analysis of the orthologous region in the mouse shows that the previously reported maternally expressed rian gene, located downstream of gtl2 on the distal 12 chromosome, encodes at least nine c/d snornas. through a systematic search in rodents, we could identify other c/d snorna genes in this domain. all snornas identified on mouse distal 12 are brain-specific and only expressed from the maternally inherited allele. the human imprinted 14q32 domain therefore shares common genomic features with the imprinted 15q11-q13 loci. this link between tandemly repeated c/d snorna genes and genomic imprinting suggests a role for these snornas and/or their host non-coding rna genes in the evolution and/or mechanism of the epigenetic imprinting process.",1
"objective tuberculosis (tb), a major public health problem worldwide, is induced by mycobacterium tuberculosis (m.tb) infection. macrophages serve as the cellular home in immunoreaction against m.tb infection, which is tightly adjusted by host micrornas (mirnas) expression. the purpose of this research was to investigate the function mechanism of mir-708-5p in mycobacterial vitality and immunoreaction in human macrophages (htp-1 and u937 cells) after m.tb infection. materials and methods colony-forming unit (cfu) assay was used to measure mycobacterial survival. the interferon-γ (ifn-γ), interleukin-6 (il-6), il-1β, and tumor necrosis factor-α (tnf-α) expression in cell supernatants were detected by enzyme-linked immunosorbent assay (elisa). the relationship between mir-708-5p and toll-like receptor 4 (tlr4) was predicted and revealed by targetscan and dual-luciferase reporter assay. results our results suggested that the mir-708-5p level was increased in a concentration-dependent and time-dependent manner in m.tb-infected human macrophages. compared with the control group, mir-708-5p mimic enhanced the intracellular mycobacterial survival during m.tb infection, while mir-708-5p downregulation suppressed the mycobacteria survival. moreover, the secretion of the pro-inflammatory factors, including ifn-γ, il-6, il-1β, and tnf-α significantly enhanced in m.tb-induced macrophages, while mir-708-5p mimic reduced these inflammatory cytokines. conversely, mir-708-5p inhibitor dramatically promoted the accumulation of the inflammatory factors in macrophages after m.tb treatment. in addition, evidence indicated that tlr4 was a direct and functional target of mir-708-5p. mir-708-5p negatively regulated the tlr4 level in macrophages. conclusions the findings indicated that mir-708-5p level was upregulated in macrophages after m.tb infection. and mir-708-5p could regulate mycobacterial vitality and inflammatory response to m.tb infection in human macrophages by targeting tlr4.",1
"allergic inflammation is the foundation of allergic rhinitis and asthma. although micrornas are implicated in the pathogenesis of various diseases, information regarding the functional role of micrornas in allergic diseases is limited. herein, we reported that microrna-302e (mir-302e) serves as an important regulator of allergic inflammation in human mast cell line, hmc-1 cells. our results showed that mir-302e is the dominant member of mir-302 family expressed in hmc-1 cells. moreover, the expression of mir-302e was significantly decreased in response to phorbol 12-myristate 13-acetate (pma) and calcium ionophore a23187 or ovalbumin (ova) stimulation. overexpression of mir-302e blocked pma/a23187 or ova induced the increase in inflammatory cytokines levels, such as il-1β, il-6, tumor necrosis factor (tnf)-α and thymic stromal lymphopoietin, while mir-302 inhibition further promoted the release of these cytokines. mechanistically, we found that mir-302e is a novel mirna that targets rela, a gene known to be involved in regulating inflammation, through binding to the 3'-utr of rela mrna. ectopic mir-302e remarkably suppressed the luciferase activity and expression of rela, whereas down-regulation of mir-302e increased rela luciferase activity and expression. pharmacological inhibition of nf-κb reversed the augmented effect of mir-302e down-regulation on inflammatory cytokines level. taken together, the present study demonstrates mir-302e limits allergic inflammation through inhibition of nf-κb activation, suggesting mir-302e may play an anti-inflammatory role in allergic diseases and function as a novel therapeutic target for the treatment of these diseases.",1
"adaptive changes to oxygen availability are critical for cell survival and tissue homeostasis. prolonged oxygen deprivation due to reduced blood flow to cardiac or peripheral tissues can lead to myocardial infarction and peripheral vascular disease, respectively. mammalian cells respond to hypoxia by modulating oxygen-sensing transducers that stabilize the transcription factor hypoxia-inducible factor 1α (hif-1α), which transactivates genes governing angiogenesis and metabolic pathways. oxygen-dependent changes in hif-1α levels are regulated by proline hydroxylation and proteasomal degradation. here we provide evidence for what we believe is a novel mechanism regulating hif-1α levels in isolated human ecs during hypoxia. hypoxia differentially increased microrna-424 (mir-424) levels in ecs. mir-424 targeted cullin 2 (cul2), a scaffolding protein critical to the assembly of the ubiquitin ligase system, thereby stabilizing hif-α isoforms. hypoxia-induced mir-424 was regulated by pu.1-dependent transactivation. pu.1 levels were increased in hypoxic endothelium by runx-1 and c/ebpα. furthermore, mir-424 promoted angiogenesis in vitro and in mice, which was blocked by a specific morpholino. the rodent homolog of human mir-424, mu-mir-322, was significantly upregulated in parallel with hif-1α in experimental models of ischemia. these results suggest that mir-322/424 plays an important physiological role in post-ischemic vascular remodeling and angiogenesis.",1
"the ms2 coat protein binds specifically to an rna hairpin formed within the viral genome. by soaking different rna fragments into crystals of ms2 coat protein capsids it is possible to determine the x-ray structure of the rna-protein complexes formed. here we present the structure to 2.85 a resolution of a complex between a chemically modified rna hairpin variant and the ms2 coat protein. this rna variant has a substitution at the -5 base position, which has been shown previously to be pyrimidine-specific and is a uracil in the wild-type rna. the modified rna hairpin contains a pyridin-4-one base (4one) at this position that lacks the exocyclic 2-oxygen eliminating the possibility of forming a hydrogen bond to asparagine a87 in the protein. the 4one complex structure shows an unprecedented major conformational change in the loop region of the rna, whereas there is almost no change in the conformation of the protein.",1
"aberrant cholangiocyte reactions in response to inflammatory stimuli are important pathogenic factors for the persistent biliary inflammation in patients with cholangiopathies. overexpression of intercellular cell adhesion molecule-1 (icam-1) in cholangiocytes is a common pathological feature in inflammatory cholangiopathies and can promote cholangiocyte interactions with effector lymphocytes in the portal region. in this study, we tested the involvement of mirna-mediated posttranscriptional regulation in ifn-gamma-induced icam-1 expression in cholangiocytes. using both immortalized and nonimmortalized human cholangiocyte cell lines, we found that ifn-gamma activated icam-1 transcription and increased icam-1 protein expression. inhibition of icam-1 transcription could only partially block ifn-gamma-induced icam-1 expression at the protein level. in silico target prediction analysis revealed complementarity of mir-221 to the 3'-untranslated region of icam-1 mrna. targeting of icam-1 3'-untranslated region by mir-221 resulted in translational repression in cholangiocytes but not icam-1 mrna degradation. functional inhibition of mir-221 with anti-mir-221 induced icam-1 protein expression. moreover, ifn-gamma stimulation decreased mir-221 expression in cholangiocytes in a signal transducer and activator of transcription 1-dependent manner. transfection of mir-221 precursor abolished ifn-gamma-stimulated icam-1 protein expression. in addition, mir-221-mediated expression of icam-1 on cholangiocytes showed a significant influence on the adherence of cocultured t cells. these findings indicate that both transcriptional and mirna-mediated posttranscriptional mechanisms are involved in ifn-gamma-induced icam-1 expression in human cholangiocytes, suggesting an important role for mirnas in the regulation of cholangiocyte inflammatory responses.",1
"splicing of u12-dependent introns requires the function of u11, u12, u6atac, u4atac, and u5 snrnas. recent studies have suggested that u6atac and u12 snrnas interact extensively with each other, as well as with the pre-mrna by watson-crick base pairing. the overall structure and many of the sequences are very similar to the highly conserved analogous regions of u6 and u2 snrnas. we have identified the homologs of u6atac and u12 snrnas in the plant arabidopsis thaliana. these snrnas are significantly diverged from human, showing overall identities of 65% for u6atac and 55% for u12 snrna. however, there is almost complete conservation of the sequences and structures that are implicated in splicing. the sequence of plant u6atac snrna shows complete conservation of the nucleotides that base pair to the 5' splice site sequences of u12-dependent introns in human. the immediately adjacent agaga sequence, which is found in human u6atac and all u6 snrnas, is also conserved. high conservation is also observed in the sequences of u6atac and u12 that are believed to base pair with each other. the intramolecular u6atac stem-loop structure immediately adjacent to the u12 interaction region differs from the human sequence in 9 out of 21 positions. most of these differences are in base pairing regions with compensatory changes occurring across the stem. to show that this stem-loop was functional, it was transplanted into a human suppressor u6atac snrna expression construct. this chimeric snrna was inactive in vivo but could be rescued by coexpression of a u4atac snrna expression construct containing compensatory mutations that restored base pairing to the chimeric u6atac snrna. these data show that base pairing of u4atac snrna to u6atac snrna has a required role in vivo and that the plant u6atac intramolecular stem-loop is the functional analog of the human sequence.",1
"the mir-317 has been revealed to involve in the reproductive response and the larval ovary morphogenesis of drosophila. however, whether the mir-317 can also regulate drosophila innate immune responses, which remains unclear to date. here we have verified that mir-317 can directly target the 3'utr of dif-rc to down-regulate the expression levels of amp drs to negatively control drosophila toll immune response in vivo and vitro. specially, the dif is an important transcription factor of toll pathway with four transcripts (dif-ra, dif-rb, dif-rc and dif-rd). our results show that mir-317 only targets to dif-rc, but not dif-ra/b/d, implying that mirnas can regulate different isoforms of an alternative splicing gene to fine tune immune responses and maintain homeostasis in post-transcriptional level. furthermore, we have demonstrated that the mir-317 sponge can restore the expression levels of drs and dif-rc at mrna and protein levels. remarkably, during gram-positive bacterial infection, the overexpressed mir-317 flies have poor survival outcome, whereas the knockout mir-317 flies have favorable survival compared to the control group, respectively, suggesting that the mir-317 might play a key role in drosophila survival. taken together, our current works not only reveal an innate immune function and a novel regulation pattern of mir-317, but also provide a new insight into the underlying molecular mechanisms of immunity disorder influencing on drosophila survival.",1
"intragenic micrornas (mirnas), located mostly in the introns of protein-coding genes, are often co-expressed with their host mrnas. however, their functional interaction in development is largely unknown. here we show that in drosophila, mir-92a and mir-92b are embedded in the intron and 3'utr of jigr1, respectively, and co-expressed with some jigr1 isoforms. mir-92a and mir-92b are highly expressed in neuroblasts of larval brain where jigr1 expression is low. genetic deletion of both mir-92a and mir-92b demonstrates an essential cell-autonomous role for these mirnas in maintaining neuroblast self-renewal through inhibiting premature differentiation. we also show that mir-92a and mir-92b directly target jigr1 in vivo and that some phenotypes due to the absence of these mirnas are partially rescued by reducing the level of jigr1. these results reveal a novel function of the mir-92 family in drosophila neuroblasts and provide another example that local negative feedback regulation of host genes by intragenic mirnas is essential for animal development.",1
"the cancer-associated loss of microrna (mirna) expression leads to a proliferative advantage and aggressive behavior through largely unknown mechanisms. here, we exploit a model system that recapitulates physiological terminal differentiation and its reversal upon oncogene expression to analyze coordinated mrna/mirna responses. the cell cycle reentry of myotubes, forced by the e1a oncogene, was associated with a pattern of mrna/mirna modulation that was largely reciprocal to that induced during the differentiation of myoblasts into myotubes. the e1a-induced mrna response was preponderantly retinoblastoma protein (rb)-dependent. conversely, the mirna response was mostly rb-independent and exerted through tissue-specific factors and myc. a subset of these mirnas (mir-1, mir-34, mir-22, mir-365, mir-29, mir-145, and let-7) was shown to coordinately target rb-dependent cell cycle and dna replication mrnas. thus, a dual level of regulation-transcriptional regulation via rb-e2f and posttranscriptional regulation via mirnas-confers robustness to cell cycle control and provides a molecular basis to understand the role of mirna subversion in cancer.",1
"recent comparative studies have indicated distinct expression profiles of short, non-coding micrornas (mirnas) in various types of cancer, including oral squamous cell carcinoma (oscc). in this study, we employed a hybrid approach using drosophila melanogaster as well as oscc cell lines to validate putative targets of oral cancer-related mirnas both in vivo and in vitro. following overexpression of drosophila mir-31, we found a significant decrease in the size of the imaginal wing discs and downregulation of a subset of putative targets, including wntless ( wls ), an important regulator of the wnt signaling pathway. parallel experiments performed in oscc cells have also confirmed a similar mir-31-dependent regulation of human wls that was not initially predicted as targets of human mir-31. furthermore, we found subsequent downregulation of cyclin d1 and c-myc , two of the main transcriptional targets of wnt signaling, suggesting a potential role of mir-31 in regulating the cell cycle and proliferation of oscc cells. taken together, our drosophila -based in vivo system in conjunction with the human in vitro platform will thus provide a novel insight into a mammal-to- drosophila -to-mammal approach to validate putative targets of human mirna and to better understand the mirna-target relationships that play an important role in the pathophysiology of oral cancer.",1
"the epithelium of the intestinal mucosa is a rapidly self-renewing tissue in the body, and defects in the renewal process occur commonly in various disorders. micrornas (mirnas) posttranscriptionally regulate gene expression and are implicated in many aspects of cellular physiology. here we investigate the role of mirna-29b (mir-29b) in the regulation of normal intestinal mucosal growth and further validate its target mrnas. mirna expression profiling studies reveal that growth inhibition of the small intestinal mucosa is associated with increased expression of numerous mirnas, including mir-29b. the simple systemic delivery of locked nucleic acid-modified, anti-mir-29b-reduced endogenous mir-29b levels in the small intestinal mucosa increases cyclin-dependent kinase 2 (cdk2) expression and stimulates mucosal growth. in contrast, overexpression of the mir-29b precursor in intestinal epithelial cells represses cdk2 expression and results in growth arrest in g1 phase. mir-29b represses cdk2 translation through direct interaction with the cdk2 mrna via its 3'-untranslated region (3'-utr), whereas point mutation of mir-29b binding site in the cdk2 3'-utr prevents mir-29b-induced repression of cdk2 translation. these results indicate that mir-29b inhibits intestinal mucosal growth by repressing cdk2 translation.",1
"micrornas (mirs) function primarily as post-transcriptional negative regulators of gene expression through binding to their mrna targets. reliable prediction of a mir's targets is a considerable bioinformatic challenge of great importance for inferring the mir's function. sequence-based prediction algorithms have high false-positive rates, are not in agreement, and are not biological context specific. here we introduce cosmic (context-specific microrna analysis), an algorithm that combines sequence-based prediction with mir and mrna expression data. cosmic differs from existing methods--it identifies mirs that play active roles in the specific biological system of interest and predicts with less false positives their functional targets. we applied cosmic to search for mirs that regulate the migratory response of human mammary cells to epidermal growth factor (egf) stimulation. several such mirs, whose putative targets were significantly enriched by migration processes were identified. we tested three of these mirs experimentally, and showed that they indeed affected the migratory phenotype; we also tested three negative controls. in comparison to other algorithms cosmic indeed filters out false positives and allows improved identification of context-specific targets. cosmic can greatly facilitate mir research in general and, in particular, advance our understanding of individual mirs' function in a specific context.",1
"mammalian skeletal muscles comprise different types of muscle fibers, and this muscle fiber heterogeneity is generally characterized by the expression of myosin heavy chain (myhc) isoforms. a switch in myhc expression leads to muscle fiber-type transition under various physiological and pathological conditions, but the underlying regulator coordinating the switch of myhc expression remains largely unknown. experiments reported in this study revealed the presence of a skeletal muscle-specific antisense transcript generated from the intergenic region between porcine myhc iia and iix and is referred to here as myhc iia/x-as. we found that myhc iia/x-as is identified as a long noncoding rna (lncrna) that is strictly expressed in skeletal muscles and is predominantly distributed in the cytoplasm. genetic analysis disclosed that myhc iia/x-as stimulates cell cycle exit of skeletal satellite cells and their fusion into myotubes. moreover, we observed that myhc iia/x-as is more enriched in fast-twitch muscle and represses slow-type gene expression and thereby maintains the fast phenotype. furthermore, we found that myhc iia/x-as acts as a competing endogenous rna that sponges microrna-130b (mir-130b) and thereby maintains myhc iix expression and the fast fiber type. we also noted that mir-130b was proved to down-regulate myhc iix by directly targeting its 3'-utr. together, the results of our study uncovered a novel pathway, which revealed that lncrna derived from the skeletal myhc cluster could modulate local myhc expression in trans , highlighting the role of lncrnas in muscle fiber-type switching.",1
"small regulatory rnas (srnas) from bacterial chromosomes became the focus of research over the past five years. however, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense rnas. here, we present a detailed in vitro analysis of sr1, a srna of bacillus subtilis that is involved in regulation of arginine catabolism by basepairing with its target, ahrc mrna. the secondary structures of sr1 species of different lengths and of the sr1/ahrc rna complex were determined and functional segments required for complex formation narrowed down. the initial contact between sr1 and its target was shown to involve the 5' part of the sr1 terminator stem and a region 100 bp downstream from the ahrc transcriptional start site. toeprinting studies and secondary structure probing of the ahrc/sr1 complex indicated that sr1 inhibits translation initiation by inducing structural changes downstream from the ahrc rbs. furthermore, it was demonstrated that hfq, which binds both sr1 and ahrc rna was not required to promote ahrc/sr1 complex formation but to enable the translation of ahrc mrna. the intracellular concentrations of sr1 were calculated under different growth conditions.",1
"bone morphogenetic protein 4 (bmp4) plays an important role in maintaining embryonic stem cells (escs) in the undifferentiated state and in the regulation of lineage commitment. we recently identified a transmembrane protein, named dies1, the suppression of which by rna interference blocks mouse esc differentiation by interfering with the bmp4 signaling. we asked whether modulation of dies1 levels could be a physiological mechanism to regulate esc pluripotency and/or differentiation. we demonstrated that mir-125a targets dies1 and regulates its expression in escs. the overexpression of mir-125a impairs differentiation, and this effect is specifically mediated by dies1 down-regulation and accompanied by a decrease of bmp4 signaling. we also found that dies1 is associated with bmp4 receptor complex and that bmp4 activates the transcription of mir-125a gene. therefore, a feedback loop exists that sets esc sensitivity to bmp4. the analysis of this regulatory mechanism revealed that mir-125a overexpression and the consequent inhibition of the bmp4 signaling arrest the cells in the epiblast stem cell (episc) status, due to the concomitant activation of the nodal/activin pathway.",1
"reactive oxygen species (ros)-induced cardiac cell injury via expression changes of multiple genes plays a critical role in the pathogenesis of numerous heart diseases. micrornas (mirnas) comprise a novel class of endogenous, small, noncoding rnas that negatively regulate about 30% of the genes in a cell via degradation or translational inhibition of their target mrnas. currently, the effects of ros on mirna expression and the roles of mirnas in ros-mediated injury on cardiac myocytes are uncertain. using quantitative real-time rt-pcr (qrt-pcr), we demonstrated that microrna-21 (mir-21) was upregulated in cardiac myocytes after treatment with hydrogen peroxide (h(2)o(2)). to determine the potential roles of mirnas in h(2)o(2)-mediated gene regulation and cellular injury, mir-21 expression was downregulated by mir-21 inhibitor and upregulated by pre-mir-21. h(2)o(2)-induced cardiac cell death and apoptosis were increased by mir-21 inhibitor and was decreased by pre-mir-21. programmed cell death 4 (pdcd4) that was regulated by mir-21 and was a direct target of mir-21 in cardiac myocytes. pre-mir-21-mediated protective effect on cardiac myocyte injury was inhibited in h(2)o(2)-treated cardiac cells via adenovirus-mediated overexpression of pdcd4 without mir-21 binding site. moreover, activator protein 1 (ap-1) was a downstream signaling molecule of pdcd4 that was involved in mir-21-mediated effect on cardiac myocytes. the results suggest that mir-21 is sensitive to h(2)o(2) stimulation. mir-21 participates in h(2)o(2)-mediated gene regulation and functional modulation in cardiac myocytes. mir-21 might play an essential role in heart diseases related to ros such as cardiac hypertrophy, heart failure, myocardial infarction, and myocardial ischemia/reperfusion injury.",1
"background patients with diabetic cardiomyopathy are often associated with increasing risk of heart failure. in this work, we used animal model to characterize the angiogenic effect of microrna-193-5p, mir-193-5p in type 2 diabetic goto-kakizaki (gk) rats' myocardial microvascular endothelial cells, mmec(gk). methods mir-193-5p in mmec(gk) was compared to its expression in wistar rat mmec. in mmec(gk), mir-193-5p was downregulated through viral infection. its angiogenic effects on mmec(gk) migration and proliferation were assessed by transwell and mtt assays, respectively. downstream target of mir-193-5p, insulin growth factor 2 (igf2), was assessed by dual-luciferase activity, qrt-pcr and western blot assays, respectively. in mir-193-5p-downregulated mmec(gk), igf2 was further de-regulated to assess its mechanism in mir-193-5p-downreuglation induced angiogenic regulation. results mir-193-5p is overexpressed in mmec(gk). its downregulation has significantly angiogenic effect by inducing migration and proliferation in mmec(gk). igf2 was demonstrated to be directly regulated by mir-193-5p in mmec(gk). in addition, igf2 inhibition in mir-193-5p-downregulated mmec(gk)'s severely hindered cell migration and proliferation. conclusion mir-193-5p is an active angiogenic factor in diabetic cardiomyopathy, possibly through inverse regulation on its downstream igf2 gene.",1
"objectives to explore the mechanism of mir-21 involved in the development of renal cell carcinoma. methods cell proliferation and apoptosis were measured after repression of mir-21 expression by antisense oligonucleotides. mir-21 targets were scanned using target prediction programs. after reduction of mir-21, fas ligand and metalloproteinase inhibitor 3 (timp3) expression and luciferase activity were detected by western blot and luciferase reporter assay. the effect of timp3 on mir-21-induced cell survival was determined by transfection with timp3 lacking 3' untranslated region and mir-21. results the reduction of mir-21 by antisense oligonucleotides inhibited cell proliferation and induced cell apoptosis by activation of caspase pathway in renal cell carcinoma cells. moreover, bioinformatics analysis revealed that mir-21 has the potential to regulate multiple apoptosis-related genes. the reduction of mir-21 inhibited fas ligand and timp3 expression by targeting the binding site within the 3' untranslated region. finally, the introduction of timp3 cdna without 3' untranslated region abrogated mir-21-induced cell survival. conclusions together, these findings indicate that mir-21 plays a key role in regulating cell apoptosis by targeting multiple genes in renal cell carcinoma.",1
"the noncoding rna mir-125b has been described to reduce erbb2 protein expression as well as proliferation and migration of cancer cell lines. as additional target of mir-125b, we identified the c-raf-1 mrna by sequence analysis. we designed a short hairpin-looped oligodeoxynucleotide (odn) targeted to the same 3' untranslated region of c-raf-1 mrna as mir-125b. the fully complementary odn antisense strand is linked to a second strand constituting a partially double-stranded structure of the odn. transfection of the c-raf-1-specific odn (odn-raf) in a breast cancer cell line reduced the protein levels of c-raf, erbb2, and their downstream effector cyclin d1 similar to mir-125b. mir-125b as well as odn-raf showed no effect on the c-raf-1 mrna level in contrast to small interfering rna. unlike mir-125b, odn-raf induced a cytopathic effect. this may be explained by the structural properties of odn-raf, which can form g-tetrads. thus, the short hairpin-looped odn-raf, targeting the same region of c-raf-1 as mir-125b, is a multifunctional molecule reducing the expression of oncoproteins and stimulating cell death. both features may be useful to interfere with tumor growth.",1
"we have previously examined the transcription and splicing of open reading frames (orfs) 71 (k13), 72, and 73 of kaposi's sarcoma-associated herpesvirus (kshv) in the primary effusion lymphoma cell line bcp-1 (latently infected with kshv) (45). the three genes encoded by these orfs (for vflip, vcyclin, and latency-associated nuclear antigen ) are transcribed from a common transcription start site in bcp-1 cells during both latency and the lytic cycles. the resulting transcript is spliced to yield a 5.32-kb message encoding lana, vcyclin, and vflip and a 1.7-kb bicistronic message encoding vcyclin and vflip. to investigate whether the vflip protein could be expressed from this vcyclin/vflip message, we utilized a bicistronic luciferase reporter system. the genes for renilla and firefly luciferases (which utilize different substrates) were cloned in tandem downstream from a t7 rna polymerase promoter. fragments of dna immediately upstream from the initiating codon of vflip were cloned between the two luciferase genes. the relative expression of the two luciferases, one directed by the putative internal ribosome entry site (ires) sequences and the other by cap-dependent ribosome scanning, was used to compare the activities of the different dna fragments. a minimum fragment of 233 bp within the coding region of vcyclin was found to direct efficient expression of the downstream cistron (firefly luciferase). the activity of this ires was orientation dependent and unaffected by methods used to inhibit cap-dependent translation. this is the first demonstration of an ires element encoded by a dna virus and may represent a novel mechanism through which kshv controls protein expression.",1
"transforming growth factor (tgf)-β is one of the main fibrogenic cytokines that drives the pathophysiology of progressive renal scarring. micrornas (mirnas) are endogenous non-coding rnas that post-transcriptionally regulate gene expression. we examined the role of tgf-β-induced expression of mir-21, mirnas in cell culture models and mirna expression in relevant models of renal disease. in vitro, tgf-β changed expression of mir-21, mir-214, and mir-145 in rat mesangial cells (crl-2753) and mir-214, mir-21, mir-30c, mir-200b, and mir-200c during induction of epithelial-mesenchymal transition in rat tubular epithelial cells (nrk52e). mir-214 expression was robustly modulated in both cell types, whereas in tubular epithelial cells mir-21 was increased and mir-200b and mir-200c were decreased by 58% and 48%, respectively, in response to tgf-β. tgf-β receptor-1 was found to be a target of mir-200b/c and was down-regulated after overexpression of mir-200c. to assess the differential expression of these mirnas in vivo, we used the anti-thy1.1 mesangial glomerulonephritis model and the unilateral ureteral obstruction model in which tgf-β plays a role and also a genetic model of hypertension, the stroke-prone spontaneously hypertensive rat with and without salt loading. the expressions of mir-214 and mir-21 were significantly increased in all in vivo models, showing a possible mirna signature of renal damage despite differing causes.",1
"interleukin 10 (il-10) is a potent anti-inflammatory cytokine that is crucial for dampening the inflammatory response after pathogen invasion, and was found to be produced by macrophages after exposure to lipopolysaccharide (lps). it remains unclear whether microrna-mediated regulatory mechanism is involved in lps-induced il-10 production. here we reported that mir-98 expression in macrophages significantly decreased following lps stimulation. we also found that mir-98 targets the 3'untranslated region of il-10 transcript. overexpression of mir-98 inhibited tlr4-triggered il-10 production and promoted cox-2 expression. we further demonstrated that mir-98 significantly mitigated the induction of endotoxin tolerance, suggesting that mir-98-mediated posttranscriptional control could potentially be involved in fine tuning the critical level of il-10 production in endotoxin tolerance.",1
"it is obvious that the majority of cellular transcripts are long noncoding rnas (lncrnas). although studies suggested that lncrnas participate in many biological processes through diverse mechanisms, however, little is known about their effects on epidermal mechanoreceptors. here, we identified one novel drosophila lncrna, scutellar macrochaetes regulatory gene (smrg), which regulates scutellar macrochaetes that act as mechanoreceptors by antagonizing the proneural gene scute (sc), through the repressor enhancer-of-split mβ (e(spl)mβ). smrg deficiency induced supernumerary scutellar macrochaetes and simultaneously a high sc rna level in the adult thorax. genetically, sc overexpression enhanced this supernumerary phenotype, while heterozygous sc mutant rescued this phenotype, both of which were mediated by e(spl)mβ. at the molecular level, smrg recruited e(spl)mβ to the sc promoter region, which in turn suppressed sc expression. our work presents a novel function of lncrna and offers insights into the molecular mechanism underlying mechanoreceptor development.",1
"inositol 1,4,5'-triphosphate receptor ii (ip(3)rii) calcium channel expression is increased in both hypertrophic failing human myocardium and experimentally induced models of the disease. the ectopic calcium released from these receptors induces pro-hypertrophic gene expression and may promote arrhythmias. here, we show that ip(3)rii expression was constitutively restrained by the muscle-specific mirna, mir-133a. during the hypertrophic response to pressure overload or neurohormonal stimuli, mir-133a down-regulation permitted ip(3)rii levels to increase, instigating pro-hypertrophic calcium signaling and concomitant pathological remodeling. using a combination of in vivo and in vitro approaches, we demonstrated that ip(3)-induced calcium release (iicr) initiated the hypertrophy-associated decrease in mir-133a. in this manner, hypertrophic stimuli that engage iicr set a feed-forward mechanism in motion whereby iicr decreased mir-133a expression, further augmenting ip(3)rii levels and therefore pro-hypertrophic calcium release. consequently, iicr can be considered as both an initiating event and a driving force for pathological remodeling.",1
"hedgehog (hh) proteins act as morphogens in a variety of developmental contexts to control cell fates and growth in a concentration-dependent manner. therefore, secretion, distribution, and reception of hh proteins must be tightly regulated and deregulation of these processes contributes to numerous human diseases. brother of ihog (boi) and its close relative ihog (interference hedgehog) are cell surface proteins that act as hh co-receptors required for hh signaling response and cell-surface maintenance of hh protein. micrornas (mirnas) are a group of widely expressed 21-23 nucleotides non-coding rnas that repress gene function through interactions with target mrnas. here, we have identified a novel mirna, mir-932, as an important regulator for boi. we show that overexpression of mir-932 in the wing disc can enhance hh signaling strength, but reduce its signaling range, a phenotype similar to that of boi knockdown. in both in vivo sensor assay and in vitro luciferase assay, mir-932 can suppress boi by directly binding to its 3'utr. meanwhile, down-regulation of mir-932 by sponge elevates the protein level of boi, confirming that mir-932 is an in vivo regulator of boi expression. further, we demonstrate that mir-932 can block hh signaling when co-expressed with ihog-rnai. moreover, we find that other predicted mirnas of boi fail to suppress it as strong as mir-932. taken together, our data demonstrate that mir-932 can modulate hh activity by specifically targeting boi in drosophila, illustrating the important roles of mirnas in fine regulation of the hh signaling pathway.",1
"background/aims micrornas (mirnas) are a class of small noncoding rna molecules that play important roles in carcinogenesis and tumor progression. we investigated the roles and mechanisms of mir-200b in human nasopharyngeal carcinoma (npc). methods we used quantitative real-time polymerase chain reaction (qrt-pcr) analyses to measure levels of mir-200b and notch1 in npc specimens and cell lines. human npc cell lines stably expressing mir-200b or control were used to analyze the tumour-suppressive effect of mir-200b. luciferase reporter assays were used to determine the association between mir-200b and the notch1 3' untranslated region. results we found that mir-200b is significantly downregulated in npc tissues and cell lines. gain-of-function and loss-of-function studies demonstrated that mir-200b suppresses npc cell growth, migration and invasion in vitro. importantly, overexpression of mir-200b effectively repressed tumor growth in nude mouse models. integrated analysis identified notch1 as a direct and functional target of mir-200b. overexpression of notch1 reversed the inhibitory effect of mir-200b on npc cell growth and invasion. conclusion these results indicate that mir-200b exerts tumor-suppressive effects in npc carcinogenesis through the suppression of notch1 expression and suggest a therapeutic application of mir-200b in npc.",1
"background in eukaryotic cells, each molecule of h/aca small nucleolar rna (snorna) assembles with four evolutionarily conserved core proteins to compose a specific ribonucleoprotein particle. one of the four core components has pseudouridine synthase activity and catalyzes the conversion of a selected uridine to pseudouridine. members of the pseudouridine synthase family are highly conserved. in addition to catalyzing pseudouridylation of target rnas, they carry out a variety of essential functions related to ribosome biogenesis and, in mammals, to telomere maintenance. to investigate further the molecular mechanisms underlying the expression of pseudouridine synthase genes, we analyzed the transcriptional activity of the drosophila member of this family in great detail. results the drosophila gene for pseudouridine synthase, minifly/nop60b (mfl), encodes two novel mrnas ending at a downstream poly(a) site. one species is characterized only by an extended 3'-untranslated region (3'utr), while a minor mrna encodes a variant protein that represents the first example of an alternative subform described for any member of the family to date. the rare spliced variant is detected mainly in females and is predicted to have distinct functional properties. we also report that a cluster comprising four isoforms of a c/d box snorna and two highly related copies of a small ncrna gene of unknown function is intron-encoded at the gene-variable 3'utrs. because this arrangement, the alternative 3' ends allow mfl not only to produce two distinct protein subforms, but also to release different ncrnas. intriguingly, accumulation of all these intron-encoded rnas was found to be sex-biased and quantitatively modulated throughout development and, within the ovaries, the ncrnas of unknown function were found not ubiquitously expressed. conclusion our results expand the repertoire of coding/non-coding transcripts derived from the gene encoding drosophila pseudouridine synthase. this gene exhibits a complex and interlaced organization, and its genetic information may be expressed as different protein subforms and/or ncrnas that may potentially contribute to its biological functions.",1
"results of overexpression or downregulation of a microrna (mirna) on its target mrna expression are often validated by reverse-transcription and quantitative pcr analysis using an appropriate housekeeping gene as an internal control. the possible direct or indirect effects of a mirna on the expression of housekeeping genes are often overlooked. among many housekeeping genes, expressions of glyceraldehyde-3-phosphate dehydrogenase (gapdh) and β-actin have been used extensively for normalization of gene expression data. here, we show that gapdh and β-actin are direct targets of mir-644a. our data demonstrate the unsuitability of gapdh and β-actin as internal controls in mir-644a functional studies and emphasize the need to carefully consider the choice of a reference gene in mirna experiments.",1
"aberrant activation of the pi3k/akt/mtor pathway contributes to the proliferation of malignant cells, and may confer resistance to chemotherapy in various malignancies, including acute myeloid leukemia (aml). chemoresistance is the major reason for relapse in aml. rad001 (everolimus) has been used at d1 and d7 of an induction chemotherapy regimen for aml, which has acceptable toxicity and may improve conventional chemotherapeutic treatment. dual inhibitors of pi3k and mtor overcome some of the intrinsic disadvantages of rapamycin and its derivatives. in this study, we evaluated the effects of bez235, a pi3k/mtor dual inhibitor, on the multidrug-resistant aml cell lines hl-60/vcr and k562/adr in vitro. bez235 dose-dependently inhibited the viability of hl-60/vcr and k562/adr cells with the ic 50 values of 66.69 and 71.44 nmol/l, respectively. bez235 (25-100 nmol/l) dose-dependently inhibited the migration of the two aml cell lines, and it also significantly sensitized the two aml cell lines to vcr and adr. after treatment with bez235, the mir-1-3p levels were markedly increased in hl-60/vcr cells. using targetscan analysis and luciferase assays, we showed that mir-1-3p targeted bag4, edn1 and abcb1, the key regulators of cell apoptosis, migration and multidrug resistance, and significantly decreased their levels in the two aml cell lines. transfection of hl-60/vcr and k562/adr cells with mir-1-3p-amo to inhibit mir-1-3p could reverse the anti-proliferation effects of bez235. in conclusion, the pi3k/mtor dual inhibitor bez235 effectively chemosensitizes aml cells via increasing mir-1-3p and subsequently down-regulating bag4, edn1 and abcb1.",1
"a cloverleaf structure at the 5' terminus of poliovirus rna binds viral and cellular proteins. to examine the role of the cloverleaf in poliovirus replication, we determined how cloverleaf mutations affected the stability, translation and replication of poliovirus rna in hela s10 translation-replication reactions. mutations within the cloverleaf destabilized viral rna in these reactions. adding a 5' 7-methyl guanosine cap fully restored the stability of the mutant rnas and had no effect on their translation. these results indicate that the 5' cloverleaf normally protects uncapped poliovirus rna from rapid degradation by cellular nucleases. preinitiation rna replication complexes formed with the capped mutant rnas were used to measure negative-strand synthesis. although the mutant rnas were stable and functional mrnas, they were not active templates for negative-strand rna synthesis. therefore, the 5' cloverleaf is a multifunctional cis-acting replication element required for the initiation of negative-strand rna synthesis. we propose a replication model in which the 5' and 3' ends of viral rna interact to form a circular ribonucleoprotein complex that regulates the stability, translation and replication of poliovirus rna.",1
"ribonuclease p is responsible for the 5'-maturation of trna precursors. ribonuclease p is a ribonucleoprotein, and in bacteria (and some archaea) the rna subunit alone is catalytically active in vitro, i.e. it is a ribozyme. the ribonuclease p database is a compilation of ribonuclease p sequences, sequence alignments, secondary structures, three-dimensional models and accessory information, available via the world wide web at the following url: .html",1
"the 7sk small nuclear rna (snrna) is a key player in the regulation of polymerase (pol) ii transcription. the 7sk rna was long believed to be specific to vertebrates where it is highly conserved. homologs in basal deuterostomes and a few lophotrochozoan species were only recently reported. on longer timescales, 7sk evolves rapidly with only few conserved sequence and structure motifs. previous attempts to identify the drosophila homolog thus have remained unsuccessful despite considerable efforts. here we report on the discovery of arthropod 7sk rnas using a novel search strategy based on pol iii promoters, as well as the subsequent verification of its expression. our results demonstrate that a 7sk snrna featuring 2 highly structured conserved domains was present already in the bilaterian ancestor.",1
"arhi is an imprinted tumor suppressor gene and is downregulated in various malignancies. however, arhi expression, function, and mechanisms of action in prostate cancer have not been reported. here, we report that arhi mrna and protein levels were downregulated in prostate cancer tissues compared with adjacent normal tissues. overexpression of arhi inhibited cell proliferation, colony formation, invasion, and induced apoptosis. further studies on a new mechanism of arhi downregulation showed a significant inverse relationship between arhi and mir-221 and 222, which were upregulated in prostate cancer cell lines. transfection of mir-221 and 222 inhibitors into pc-3 cells caused a significant induction of arhi expression. a direct interaction of mir-221 or 222 with a target site on the 3'utr of arhi was confirmed by a dual luciferase pmir-report assay. finally, we also found that genistein upregulates arhi by downregulating mir-221 and 222 in pc-3 cells. in conclusion, arhi is a tumor suppressor gene downregulated in prostate cancer, and overexpression of arhi can inhibit cell proliferation, colony formation, and invasion. this study demonstrates for the first time that prostate cancer cells have decreased level of arhi which could be caused by direct targeting of 3'utr of arhi by mir221/222. genistein, a potential nontoxic chemopreventive agent, restores expression of arhi and may be an important dietary therapeutic agent for treating prostate cancer.",1
"rationale the rationale was to utilize a bioinformatics approach to identify mirna binding sites in genes with single nucleotide mutations (snps) to discover pathways in heart failure (hf). objective the objective was to focus on the genes containing mirna binding sites with mirnas that were significantly altered in end-stage hf and in response to a left ventricular assist device (lvad). methods and results bedtools v2.14.3 was used to discriminate snps within predicted 3'utr mirna binding sites. a member of the mir-15/107 family, mir-16, was decreased in the circulation of end-stage hf patients and increased in response to a lvad (p conclusions we provide evidence that mir-16 decreases in the circulation of end-stage hf patients and increases with a lvad. modeling studies suggest that mir-16 binds to and decreases expression of vps4a. overexpression of vps4a decreases cell number. together, these experiments suggest that mir-16 and vps4a expression are altered in end-stage hf and in response to unloading with a lvad. this signaling pathway may lead to reduced circulating cell number in hf.",1
"due to the poor prognosis of pancreatic cancer, novel diagnostic modalities for early diagnosis and new therapeutic strategy are urgently needed. recently, microrna-21 (mir-21) was reported to be strongly overexpressed in pancreatic cancer as well as in other solid cancers. we investigated the functional roles of mir-21, which have not been fully elucidated in pancreatic cancer. mir-21 expression was assessed in pancreatic cancer cell lines (14 cancer cell lines, primary cultures of normal pancreatic epithelial cells and fibroblasts, and a human normal pancreatic ductal epithelial cell line) and pancreatic tissue samples (25 cancer tissues and 25 normal tissues) by quantitative real-time reverse transcription-pcr amplification. moreover, we investigated the proliferation, invasion, and chemoresistance of pancreatic cancer cells transfected with mir-21 precursor or inhibitor. mir-21 was markedly overexpressed in pancreatic cancer cells compared with nonmalignant cells, and mir-21 in cancer tissues was much higher than in nonmalignant tissues. the cancer cells transfected with the mir-21 precursor showed significantly increased proliferation, matrigel invasion, and chemoresistance for gemcitabine compared with the control cells. in contrast, inhibition of mir-21 decreased proliferation, matrigel invasion, and chemoresistance for gemcitabine. moreover, mir-21 positively correlated with the mrna expression of invasion-related genes, matrix metalloproteinase-2 and -9, and vascular endothelial growth factor. these data suggest that mir-21 expression is increased in pancreatic cancer cells and that mir-21 contributes to the cell proliferation, invasion, and chemoresistance of pancreatic cancer.",1
"ageing is the predominant risk factor for cardiovascular diseases and contributes to a significantly worse outcome in patients with acute myocardial infarction. micrornas (mirnas) have emerged as crucial regulators of cardiovascular function and some mirnas have key roles in ageing. we propose that altered expression of mirnas in the heart during ageing contributes to the age-dependent decline in cardiac function. here we show that mir-34a is induced in the ageing heart and that in vivo silencing or genetic deletion of mir-34a reduces age-associated cardiomyocyte cell death. moreover, mir-34a inhibition reduces cell death and fibrosis following acute myocardial infarction and improves recovery of myocardial function. mechanistically, we identified pnuts (also known as ppp1r10) as a novel direct mir-34a target, which reduces telomere shortening, dna damage responses and cardiomyocyte apoptosis, and improves functional recovery after acute myocardial infarction. together, these results identify age-induced expression of mir-34a and inhibition of its target pnuts as a key mechanism that regulates cardiac contractile function during ageing and after acute myocardial infarction, by inducing dna damage responses and telomere attrition.",1
"micrornas (mirnas) are a group of short, noncoding, regulatory rna molecules the dysregulation of which contributes to the pathogenesis of myocarditis. argonaute proteins are essential components of mirna-induced silencing complex and play important roles during mirna biogenesis and function. however, the expression pattern of four ago family members has not yet been detected in the coxsackievirus b3 (cvb3)-induced myocarditis tissue samples. in this study, we detected the expression of four agos in the cvb3-infected mouse heart tissues and found that ago1 and ago3 up-regulated significantly at 4 and 8h after cvb3 infection. further in vitro research indicated that up-regulated ago1 and ago3 are related to the down-regulated tnfaip3, which is a negative regulator of nf-κb pathway. subsequently, we confirmed that tnfaip3 is a direct target of mir-19a/b, and during cvb3 infection, the expression of mir-19a/b and mir-125a/b is not significantly changed. tnfaip3 level is mainly reduced by up-regulated ago1 and ago3. this research sheds light on the relationship between overexpressed ago proteins and cvb3-induced myocarditis, and this provides potential therapeutic target for viral myocarditis.",1
"cytokine secretion and degranulation represent key components of cd8(+) t-cell cytotoxicity. while transcriptional blockade of ifn-γ and inhibition of degranulation by tgf-β are well established, we wondered whether tgf-β could also induce immune-regulatory mirnas in human cd8(+) t cells. we used mirna microarrays and high-throughput sequencing in combination with qrt-pcr and found that tgf-β promotes expression of the mir-23a cluster in human cd8(+) t cells. likewise, tgf-β up-regulated expression of the cluster in cd8(+) t cells from wild-type mice, but not in cells from mice with tissue-specific expression of a dominant-negative tgf-β type ii receptor. reporter gene assays including site mutations confirmed that mir-23a specifically targets the 3'utr of cd107a/lamp1 mrna, whereas the further mirnas expressed in this cluster-namely, mir-27a and -24-target the 3'utr of ifn-γ mrna. upon modulation of the mir-23a cluster by the respective mirna antagomirs and mimics, we observed significant changes in ifn-γ expression, but only slight effects on cd107a/lamp1 expression. still, overexpression of the cluster attenuated the cytotoxic activity of antigen-specific cd8(+) t cells. these functional data thus reveal that the mir-23a cluster not only is induced by tgf-β, but also exerts a suppressive effect on cd8(+) t-cell effector functions, even in the absence of tgf-β signaling.",1
"background in animals, micrornas (mirnas) regulate the protein synthesis of their target messenger rnas (mrnas) by either translational repression or deadenylation. mirnas are frequently found to be co-expressed in different tissues and cell types, while some form polycistronic clusters on genomes. interactions between targets of co-expressed mirnas (including mirna clusters) have not yet been systematically investigated. results here we integrated information from predicted and experimentally verified mirna targets to characterize protein complex networks regulated by human mirnas. we found striking evidence that individual mirnas or co-expressed mirnas frequently target several components of protein complexes. we experimentally verified that the mir-141-200c cluster targets different components of the ctbp/zeb complex, suggesting a potential orchestrated regulation in epithelial to mesenchymal transition. conclusions our findings indicate a coordinate posttranscriptional regulation of protein complexes by mirnas. these provide a sound basis for designing experiments to study mirna function at a systems level.",1
"the two major families of small nucleolar rnas (snornas), box c/d and box h/aca, are generated in the nucleoplasm and transported to the nucleolus where they function in rrna processing and modification. we have investigated the sequences involved in the intranuclear transport of box h/aca snornas by assaying the localization of injected fluorescent rnas in xenopus oocyte nuclear spreads. our analysis of u17, u64 and u65 has revealed that disruption of either of the conserved sequence elements, box h or box aca, eliminates nucleolar localization. in addition, the stem present at the base of the 3' hairpin is required for efficient nucleolar localization of u65. fragments or rearrangements of u65 that consist of box h and box aca flanking either the 5' or 3' hairpin are targeted to the nucleolus. the targeting is dependent on the presence of the box sequences, but not on their orientation. our results indicate that in each of the two major families of snornas, a motif composed of the signature conserved sequences and an adjacent structural element that tethers the sequence elements directs the nucleolar localization of the rnas. we demonstrate that telomerase rna is also targeted to the nucleolus by a box aca-dependent mechanism.",1
"mirnas are small rnas directing many developmental processes by posttranscriptional regulation of protein-coding genes. we uncovered a new role for mir-1-1/133a-2 and mir-1-2/133a-1 clusters in the specification of embryonic cardiomyocytes allowing transition from an immature state characterized by expression of smooth muscle (sm) genes to a more mature fetal phenotype. concomitant knockout of mir-1-1/133a-2 and mir-1-2/133a-1 released suppression of the transcriptional co-activator myocardin, a major regulator of sm gene expression, but not of its binding partner srf. overexpression of myocardin in the embryonic heart essentially recapitulated the mir-1/133a mutant phenotype at the molecular level, arresting embryonic cardiomyocytes in an immature state. interestingly, the majority of postulated mir-1/133a targets was not altered in double mutant mice, indicating that the ability of mir-1/133a to suppress target molecules strongly depends on the cellular context. finally, we show that myocardin positively regulates expression of mir-1/133a, thus constituting a negative feedback loop that is essential for early cardiac development.",1
"micrornas (mirnas) are small noncoding rnas that regulate vast networks of genes that share mirna target sequences. to examine the physiologic effects of an individual mirna-mrna interaction in vivo, we generated mice that carry a mutation in the putative microrna-155 (mir-155) binding site in the 3'-untranslated region of activation-induced cytidine deaminase (aid), designated aicda(155) mice. aid is required for immunoglobulin gene diversification in b lymphocytes, but it also promotes chromosomal translocations. aicda(155) caused an increase in steady-state aicda mrna and protein amounts by increasing the half-life of the mrna, resulting in a high degree of myc-igh translocations. a similar but more pronounced translocation phenotype was also found in mir-155-deficient mice. our experiments indicate that mir-155 can act as a tumor suppressor by reducing potentially oncogenic translocations generated by aid.",1
"fibrosis pathophysiology is critically regulated by smad 2- and smad 3-mediated transforming growth factor-β (tgf-β) signaling. disintegrin metalloproteases (adam) can manipulate the signaling environment, however, the role and regulation of adams in renal fibrosis remain unclear. tgf-β stimulation of renal cells results in a significant up-regulation of adams 10, 17, 12, and 19. the selective smad2/3 inhibitor sb 525334 reversed these tgf-β-induced changes. in vivo, using ureteral obstruction to model renal fibrosis, we observed increased adams gene expression that was blocked by oral administration of sb 525334. similar increases in adam gene expression also occurred in preclinical models of hypertension-induced renal damage and glomerulonephritis. mirnas are a recently discovered second level of regulation of gene expression. analysis of 3' untranslated regions of adam12 and adam19 mrnas showed multiple binding sites for mir-29a, mir-29b, and mir-29c. we show that mir-29 family expression is decreased after unilateral ureter obstruction and this significant decrease in mir-29 family expression was observed consistently in preclinical models of renal dysfunction and correlated with an increase in adam12 and adam19 expression. exogenous overexpression of the mir-29 family blocked tgf-β-mediated up-regulation of adam12 and adam19 gene expression. this study shows that adams are involved in renal fibrosis and are regulated by canonical tgf-β signaling and mir-29. therefore, both adams and the mir-29 family represent therapeutic targets for renal fibrosis.",1
"background the let-7 family of micrornas has been considered as tumor suppressors in various cancers; however, the role of let-7c in oral squamous cell carcinoma has not been determined yet. methods in this study, phenotypical behaviors and the radio/chemoresistance were examined subsequent to overexpression of let-7c. in addition, the expression of let-7c in cancer stem cells (cscs) was evaluated and the effect of let-7c on stemness characteristics was assessed. also, luciferase activity assays were performed to test whether interleukin (il)-8 was a putative target of let-7c. results our results confirmed that the expression of let-7c in cscs was reduced, while overexpression of let-7c attenuated the oncogenicity. moreover, ectopic expression of let-7c in cscs downregulated the stemness hallmarks and the radio/chemoresistance. expression and secretion of il-8 in oral cscs were both reduced following overexpression of let-7c. besides, the inhibitory effect of let-7c on various stemness phenotypes was reverted by il-8, indicating that lower expression of let-7c may confer higher cancer stemness through a failure to downregulate il-8. conclusion these findings revealed the significance of let-7c in the contribution of oral cancer stemness and radio/chemoresistance. targeting let-7c and its downstream il-8 may be beneficial to prevent cancer recurrence and metastasis of oral squamous cell carcinoma.",1
"micrornas (mirnas) are endogenous approximately 22-nucleotide rnas, some of which are known to play important regulatory roles in animals by targeting the messages of protein-coding genes for translational repression. we find that mir-196, a mirna encoded at three paralogous locations in the a, b, and c mammalian hox clusters, has extensive, evolutionarily conserved complementarity to messages of hoxb8, hoxc8, and hoxd8. rna fragments diagnostic of mir-196-directed cleavage of hoxb8 were detected in mouse embryos. cell culture experiments demonstrated down-regulation of hoxb8, hoxc8, hoxd8, and hoxa7 and supported the cleavage mechanism for mir-196-directed repression of hoxb8. these results point to a mirna-mediated mechanism for the posttranscriptional restriction of hox gene expression during vertebrate development and demonstrate that metazoan mirnas can repress expression of their natural targets through mrna cleavage in addition to inhibiting productive translation.",1
"micrornas (mirnas) have emerged as critical regulators of many cellular responses, through the action of mirna-induced silencing complex (mirisc)- or mirna ribonucleoprotein complex (mirnp)-mediated gene repression. here we studied the role of mirnas in the development of dendritic cells (dcs), an important immune cell type that is divided into conventional dc (cdc) and plasmacytoid dc (pdc) subsets. we found that mir-22 was highly expressed in mouse cd11c(+) cd11b(+) b220(-) cdcs compared to pdcs, and was induced in dc progenitor cell cultures with gm-csf, which stimulate cd11c(+) cd11b(+) b220(-) cdc differentiation. enforced overexpression of mir-22 during dc development enhanced cd11c(+) cd11b(+) b220(-) cdc generation at the expense of pdcs, while mir-22 knockdown demonstrated opposite effects. moreover, overexpression and knockdown of mir-22 showed significant effects on the mrna abundance of irf8, which encodes the transcription factor irf8 that plays essential roles in dc development. luciferase reporter assays confirmed that mir-22 binds directly to the 3'utr of the mouse irf8 mrna. collectively, these results suggest that mir-22 targets irf8 mrna for posttranscriptional repression and controls dc subset differentiation.",1
"micrornas (mirnas) are noncoding, around 22-nucleotide-long rnas that exert significant modulatory roles in gene expression throughout the genome. as such, mirnas take part in and modulate almost all biological processes like cell growth, development, and immunity. we previously showed that mir-8 mirna plays a role in maintaining immune homeostasis in drosophila. here, we further discovered that targeting of multiple coding genes by mir-8 contributes to the maintenance of immune homeostasis. toll and dorsal, respectively the receptor and transcription factor in the toll immune pathway, were found to be mir-8 targets, as shown by reporter assays and mir-8 null flies. moreover, u-shaped (ush), a previously verified mir-8 target, was seen to mediate mir-8 regulation of immune homeostasis. consistently, overexpression of either dorsal or ush in the fat body led to increased drosomycin expression, mimicking that induced by deletion of mir-8. furthermore, mutation in toll immune pathway or ush rescues the abnormal expression of drosomycin and lethality in mir-8 mutant. thus, mir-8 regulates drosophila immune homeostasis by targeting multiple immune genes, thereby contributing to survival.",1
"the toll signaling pathway is highly conserved from insects to mammals. drosophila is a model species that is commonly used to study innate immunity. although many studies have assessed protein-coding genes that regulate the toll pathway, it is unclear whether long noncoding rnas (lncrnas) play regulatory roles in the toll pathway. here, we evaluated the expression of the lncrna cr46018 in drosophila. our results showed that this lncrna was significantly overexpressed after infection of drosophila with micrococcus luteus. a cr46018-overexpressing drosophila strain was then constructed; we expected that cr46018 overexpression would enhance the expression of various antimicrobial peptides downstream of the toll pathway, regardless of infection with m. luteus. rna-seq analysis of cr46018-overexpressing drosophila after infection with m. luteus showed that upregulated genes were mainly enriched in toll and imd signaling pathways. moreover, bioinformatics predictions and rna-immunoprecipitation experiments showed that cr46018 interacted with the transcription factors dif and dorsal to enhance the toll pathway. during gram-positive bacterial infection, flies overexpressing cr46018 showed favorable survival compared with flies in the control group. overall, our current work not only reveals a new immune regulatory factor, lncrna-cr46018, and explores its potential regulatory model, but also provides a new perspective for the effect of immune disorders on the survival of drosophila melanogaster.",1
"background our previous studies show that microrna-92a (mir-92a) is overexpressed in colorectal cancer (crc) and is thought to be correlated with the development of the cancer. however, its biological role in crc remains poorly understood. aims the aim of the study was to determine the role of mir-92a and to elucidate its regulatory mechanism in crc. methods the expression levels of mir-92a and phosphatase and tensin homologue (pten) were detected by qrt-pcr and western blot. mtt, migration and invasion assays were used to examine the proliferation, migration and invasion of pre-mir-92a transfected sw480 cells, and a mouse model was used to investigate tumorigenesis. in addition, the regulation of pten by mir-92a was evaluated by qrt-pcr, western blot and luciferase reporter assays. results the expression of mir-92a was significantly up-regulated in the tissues of crc patients with lymph node metastasis. the ectopic expression of mir-92a enhanced crc cell proliferation, migration and invasion. similar results were found in xenograft assay performed in nude mice. up-regulation of mir-92a induced emt in crc cells. there was an inverse correlation between the levels of mir-92a and pten in crc tissues. the overexpression of mir-92a in crc cells decreased pten expression at the translational level, and decreased pten-driven luciferase-reporter activity. conclusions our results demonstrated that mir-92a induced emt and regulated cell growth, migration and invasion in the sw480 cells, at least partially, via suppression of pten expression. mir-92a may serve as a novel therapeutic target in colorectal cancer.",1
"α6β4 integrin is an adhesion molecule for laminin receptors involved in tumor progression. we present a link between β4 integrin expression and mir-221/222 in the most prevalent human mammary tumor: luminal invasive carcinomas (lum-ics). using human primary tumors that display different β4 integrin expression and grade, we show that mir-221/222 expression inversely correlates with tumor proliferating index, ki67. interestingly, most high-grade tumors express β4 integrin and low mir-221/222 levels. we ectopically transfected mir-221/222 into a human-derived mammary tumor cell line that recapitulates the luminal subtype to investigate whether mir-221/222 regulates β4 expression. we demonstrate that mir-221/222 overexpression results in β4 expression downregulation, breast cancer cell proliferation, and invasion inhibition. the role of mir-221/222 in driving β4 integrin expression is also confirmed via mutating the mir-221/222 seed sequence for β4 integrin 3'utr. furthermore, we show that these 2 mirnas are also key breast cancer cell proliferation and invasion regulators, via the post-transcriptional regulation of signal transducer and activator of transcription 5a (stat5a) and of a disintegrin and metalloprotease-17 (adam-17). we further confirm these data by silencing adam-17, using a dominant-negative or an activated stat5a form. mir-221/222-driven β4 integrin, stat5a, and adam-17 did not occur in mcf-10a cells, denoted ""normal"" breast epithelial cells, indicating that the mechanism is cancer cell-specific. these results provide the first evidence of a post-transcriptional mechanism that regulates β4 integrin, stat5a, and adam-17 expression, thus controlling breast cancer cell proliferation and invasion. pre-mir-221/222 use in the aggressive luminal subtype may be a powerful therapeutic anti-cancer strategy.",1
"micrornas are important regulators of gene expression and have been suggested to play a key role in tumorigenesis. in this study, we show that mir-145 is significantly downregulated in glioma cell lines compared to normal brain tissue and negatively regulates tumorigenesis. restoration of mir-145 in glioma cells significantly reduced in vitro proliferation, migration and invasion. also, overexpression of mir-145 reduced adam17 and egfr expression. in addition, we tested the hypothesis that the mir-145-mediated suppression of cell proliferation, migration and invasion is, at least in part, due to silencing of adam17 and egfr gene expression. using luciferase reporters carrying the 3'-untranslated region of adam17 combined with western blotting, we identified adam17 as a direct target of mir-145. collectively, these results suggest that as a tumor suppressor, mir-145 inhibits not only tumor proliferation, but also cell migration and invasion, and warrants further investigation.",1
"in many bacteria, iron homeostasis is controlled primarily by the ferric uptake regulator (fur), a transcriptional repressor. however, some genes, including those involved in iron storage, are positively regulated by fur. a fur-repressed regulatory small rna (srna), ryhb, has been identified in escherichia coli, and it has been demonstrated that negative regulation of genes by this srna is responsible for the positive regulation of some genes by fur. no ryhb sequence homologs were found in pseudomonas aeruginosa, despite the identification of genes positively regulated by its fur homolog. a bioinformatics approach identified two tandem srnas in p. aeruginosa that were candidates for functional homologs of ryhb. these srnas (prrf1 and prrf2) are >95% identical to each other, and a functional fur box precedes each. their expression is induced under iron limitation. deletion of both srnas is required to affect the iron-dependent regulation of an array of genes, including those involved in resistance to oxidative stress, iron storage, and intermediary metabolism. as in e. coli, induction of the prrf srnas leads to the rapid loss of mrnas for sodb (superoxide dismutase), sdh (succinate dehydrogenase), and a gene encoding a bacterioferritin. thus, the prrf srnas are the functional homologs of ryhb srna. at least one gene, bfrb, is positively regulated by fur and fe(2+), even in the absence of the prrf srnas. this work suggests that the role of srnas in bacterial iron homeostasis may be broad, and approaches similar to those described here may identify these srnas in other organisms.",1
"ribozymes are thought to have played a pivotal role in the early evolution of life, but relatively few have been identified in modern organisms. we performed an in vitro selection aimed at isolating self-cleaving rnas from the human genome. the selection yielded several ribozymes, one of which is a conserved mammalian sequence that resides in an intron of the cpeb3 gene, which belongs to a family of genes regulating messenger rna polyadenylation. the cpeb3 ribozyme is structurally and biochemically related to the human hepatitis delta virus (hdv) ribozymes. the occurrence of this ribozyme exclusively in mammals suggests that it may have evolved as recently as 200 million years ago. we postulate that hdv arose from the human transcriptome.",1
"mammalian micrornas are emerging as key regulators of the development and function of the immune system. here, we report a strong but transient induction of mir-155 in mouse bone marrow after injection of bacterial lipopolysaccharide (lps) correlated with granulocyte/monocyte (gm) expansion. demonstrating the sufficiency of mir-155 to drive gm expansion, enforced expression in mouse bone marrow cells caused gm proliferation in a manner reminiscent of lps treatment. however, the mir-155-induced gm populations displayed pathological features characteristic of myeloid neoplasia. of possible relevance to human disease, mir-155 was found to be overexpressed in the bone marrow of patients with certain subtypes of acute myeloid leukemia (aml). furthermore, mir-155 repressed a subset of genes implicated in hematopoietic development and disease. these data implicate mir-155 as a contributor to physiological gm expansion during inflammation and to certain pathological features associated with aml, emphasizing the importance of proper mir-155 regulation in developing myeloid cells during times of inflammatory stress.",1
"noncoding rnas have recently emerged as important regulators of mrna translation and turnover . nevertheless, we largely ignore how their function integrates with protein-mediated translational regulation. we focus on bicoid, a key patterning molecule in drosophila, which inhibits the translation of caudal in the anterior part of the embryo . previous work showed that bicoid recruits the cap-binding protein d4ehp on the caudal mrna to repress translation . here we show that mir-2 family micrornas are essential cofactors in the repression of caudal. using an in vivo sensor, we demonstrate that bicoid acts through a 63 nt response element in the caudal 3' utr that includes a single mir-2 target site. mutating that site abolishes bicoid-mediated repression, and this effect can be partly reversed by expressing a microrna with compensatory changes that restore binding to the mutated target. four predicted bicoid splice isoforms are capable of caudal repression, including two that lack the d4ehp interaction domain; all four isoforms require the microrna target for repression. the synergy between bicoid and micrornas appears to have evolved recently in the context of the drosophilid caudal bre. the discovery that micrornas play an essential role in bicoid-mediated translational repression opens up new perspectives on bicoid's function and evolution.",1
"micrornas (mirnas) have been demonstrated to be critical in regulating tumor development and progression. the present study investigated the expression of mir‑588 using reverse transcription‑quantitative polymerase chain reaction analysis in 85 cases of lung squamous cell carcinoma (scc), and observed the correlation between the expression of mir‑588 with clinical pathologic features. the results indicated that the expression of mir‑588 was predominantly lower in the tumor samples, compared with non‑tumorous samples, and was negatively associated with tumor stages and lymph node invasion. the present study also examined the significance of the expression of mir‑588 in scc using gain‑ and loss‑of‑function analyses. it was found that mir‑588 inhibited tumor cell migration and invasion. in addition, it was revealed that the overexpression of mir‑588 in scc cells reduced the mrna and protein levels of progranulin (grn), whereas mir‑588 silencing increased the expression of grn. a luciferase activity assay showed that mir‑588 was able to directly bind to the 3'untranslated region of grn and regulate its expression. furthermore, it was found that the expression of grn was inversely correlated with the expression of mir‑588 in 85 paired scc samples. these results indicated that grn was involved in the mir-588-mediated suppressive functions in the progression of scc.",1
"wnt/β-catenin signaling underlies the pathogenesis of a broad range of human cancers, including the deadly plasma cell cancer multiple myeloma. in this study, we report that downregulation of the tumor suppressor microrna mir-30-5p is a frequent pathogenetic event in multiple myeloma. evidence was developed that mir-30-5p downregulation occurs as a result of interaction between multiple myeloma cells and bone marrow stromal cells, which in turn enhances expression of bcl9, a transcriptional coactivator of the wnt signaling pathway known to promote multiple myeloma cell proliferation, survival, migration, drug resistance, and formation of multiple myeloma cancer stem cells. the potential for clinical translation of strategies to re-express mir-30-5p as a therapeutic approach was further encouraged by the capacity of mir-30c and mir-30 mix to reduce tumor burden and metastatic potential in vivo in three murine xenograft models of human multiple myeloma without adversely affecting associated bone disease. together, our findings offer a preclinical rationale to explore mir-30-5p delivery as an effective therapeutic strategy to eradicate multiple myeloma cells in vivo.",1
"streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. during the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and rna regulators acting in response to various environmental signals. here, we focus on the class of small rna regulators (srnas) and present the first complete analysis of srna sequencing data in s. pyogenes. in the sf370 clinical isolate (m1 serotype), we identified 197 and 428 putative regulatory rnas by visual inspection and bioinformatics screening of the sequencing data, respectively. only 35 from the 197 candidates identified by visual screening were assigned a predicted function (t-boxes, ribosomal protein leaders, characterized riboswitches or srnas), indicating how little is known about srna regulation in s. pyogenes. by comparing our list of predicted srnas with previous s. pyogenes srna screens using bioinformatics or microarrays, 92 novel srnas were revealed, including antisense rnas that are for the first time shown to be expressed in this pathogen. we experimentally validated the expression of 30 novel srnas and antisense rnas. we show that the expression profile of 9 srnas including 2 predicted regulatory elements is affected by the endoribonucleases rnase iii and/or rnase y, highlighting the critical role of these enzymes in srna regulation.",1
"many studies have shown decreased cortical muscarinic m1 receptors (chrm1) in schizophrenia (sz), with one study showing sz can be separated into two populations based on a marked loss of chrm1 (-75%) in -25% of people (def-sz) with the disorder. to better understand the mechanism contributing to the loss of chrm1 in def-sz, we measured specific markers of gene expression in the cortex of people with sz as a whole, people differentiated into def-sz and people with sz that do not have a deficit in cortical chrm1 (non-def-sz) and health controls. we now report that cortical chrm1 gene promoter methylation and chrm1 mrna are decrease in sz, def-sz and non-def-sz but levels of the micro rna (mir)-107, a chrm1 targeting mir, are increased only in def-sz. we also report in vitro data strongly supporting the notion that mir-107 levels regulate chrm1 expression. these data suggest there is a reversal of the expected inverse relationship between gene promoter methylation and chrm1 mrna in people with sz and that a breakdown in gene promoter methylation control of chrm1 expression is contributing to the global pathophysiology of the syndrome. in addition, our data argues that increased levels of at least one mir, mir-107, is contributing to the marked loss of cortical chrm1 in def-sz and this may be a differentiating pathophysiology. these latter data continue to support the hypothesis that micrornas (mirna) have a role in the underlying neurobiology of sz but argue they are differentially affected in subsets of people within that syndrome.",1
"the importance of micrornas (mirnas) in human malignancies has been well recognized. here, we report that the expression of microrna-210 (mir-210) is down-regulated in human esophageal squamous cell carcinoma and derived cell lines. marked decreases in the level of mir-210 were observed especially in poorly differentiated carcinomas. we found that mir-210 inhibits cancer cell survival and proliferation by inducing cell death and cell cycle arrest in g(1)/g(0) and g(2)/m. finally, we identified fibroblast growth factor receptor-like 1 (fgfrl1) as a target of mir-210 in esophageal squamous cell carcinoma and demonstrated that fgfrl1 accelerates cancer cell proliferation by preventing cell cycle arrest in g(1)/g(0). taken together, our findings show an important role for mir-210 as a tumor-suppressive microrna with effects on cancer cell proliferation.",1
"to identify micrornas (mirnas) associated with estrogen receptor (esr1) status, we profiled luminal a, esr1+ breast cancer cell lines versus triple negative (tn), which lack erα, progesterone receptor and her2/neu. although two thirds of the differentially expressed mirnas are higher in esr1+ breast cancer cells, some mirnas, such as mir-222/221 and mir-29a, are dramatically higher in esr1- cells (∼100- and 16-fold higher, respectively). mir-222/221 (which target esr1 itself) and mir-29a are predicted to target the 3' utr of dicer1. addition of these mirnas to esr1+ cells reduces dicer protein, whereas antagonizing mir-222 in esr1- cells increases dicer protein. we demonstrate via luciferase reporter assays that these mirnas directly target the dicer1 3' utr. in contrast, mir-200c, which promotes an epithelial phenotype, is 58-fold higher in the more well-differentiated erα+ cells, and restoration of mir-200c to erα- cells causes increased dicer protein, resulting in increased levels of other mature mirnas typically low in esr1- cells. together, our findings explain why dicer is low in erα negative breast cancers, since such cells express high mir-221/222 and mir-29a levels (which repress dicer) and low mir-200c (which positively affect dicer levels). furthermore, we find that mir-7, which is more abundant in erα+ cells and is estrogen regulated, targets growth factor receptors and signaling intermediates such as egfr, igf1r, and irs-2. in summary, mirnas differentially expressed in erα+ versus erα- breast cancers actively control some of the most distinguishing characteristics of the luminal a and tn subtypes, such as erα itself, dicer, and growth factor receptor levels.",1
"microrna (mirna)-mediated gene regulation plays a key role in brain development and function. but there are few cases in which the roles of individual mirnas have been elucidated in behaving animals. we report a mir-276a::dopr regulatory module in drosophila that functions in distinct circuits for naive odor responses and conditioned odor memory. drosophila olfactory aversive memory involves convergence of the odors (conditioned stimulus) and the electric shock (unconditioned stimulus) in mushroom body (mb) neurons. dopamine receptor dopr mediates the unconditioned stimulus inputs onto mb. distinct dopaminergic neurons also innervate ellipsoid body (eb), where dopr function modulates arousal to external stimuli. we demonstrate that mir-276a is required in mb neurons for memory formation and in eb for naive responses to odors. both roles of mir-276a are mediated by tuning dopr expression. the dual role of this mir-276a::dopr genetic module in these two neural circuits highlights the importance of mirna-mediated gene regulation within distinct circuits underlying both naive behavioral responses and memory.",1
"the vascular endothelial (ve)-cadherin functions as an endothelial barrier protein controlling endothelial permeability and leukocyte transmigration. developmental studies indicate that ve-cadherin also plays a vital role in angiogenesis. microrna-22 plays important roles in cardiovascular diseases including cardiac hypertrophy and heart failure. we identified that mir-22 interacts with ve-cadherin mrna. overexpression of mir-22 in endothelial cells increases the synthesis of proinflammatory cytokines. injection of mir-22 results in increased myeloperoxidase activity in the mouse lungs. moreover, mir-22 injection into the fluorescent-labeled transgenic zebrafish tg(fli1:egfp) embryos caused defective vascular development in the dorsal and intersegmental vessels, and vascular markers were significantly suppressed in these embryos. our studies demonstrate that the conserved targeting of ve-cadherin by mir-22 regulates endothelial inflammation, tissue injury, and angiogenesis.",1
"listeria monocytogenes is a foodborne pathogen that crosses the intestinal barrier and disseminates within the host. here, we report a unique comprehensive analysis of the impact of two lactobacillus species, lactobacillus paracasei cncm i-3689 and lactobacillus casei bl23, on l. monocytogenes and orally acquired listeriosis in a gnotobiotic humanized mouse model. we first assessed the effect of treatment with each lactobacillus on l. monocytogenes counts in host tissues and showed that each decreases l. monocytogenes systemic dissemination in orally inoculated mice. a whole genome intestinal transcriptomic analysis revealed that each lactobacillus changes expression of a specific subset of genes during infection, with ifn-stimulated genes (isgs) being the most affected by both lactobacilli. we also examined microrna (mir) expression and showed that three mirs (mir-192, mir-200b, and mir-215) are repressed during l. monocytogenes infection. treatment with each lactobacillus increased mir-192 expression, whereas only l. casei association increased mir-200b and mir-215 expression. finally, we showed that treatment with each lactobacillus significantly reshaped the l. monocytogenes transcriptome and up-regulated transcription of l. monocytogenes genes encoding enzymes allowing utilization of intestinal carbon and nitrogen sources in particular genes involved in propanediol and ethanolamine catabolism and cobalamin biosynthesis. altogether, these data reveal that the modulation of l. monocytogenes infection by treatment with lactobacilli correlates with a decrease in host gene expression, in particular isgs, mir regulation, and a dramatic reshaping of l. monocytogenes transcriptome.",1
"circular rnas (circrnas) in animals are an enigmatic class of rna with unknown function. to explore circrnas systematically, we sequenced and computationally analysed human, mouse and nematode rna. we detected thousands of well-expressed, stable circrnas, often showing tissue/developmental-stage-specific expression. sequence analysis indicated important regulatory functions for circrnas. we found that a human circrna, antisense to the cerebellar degeneration-related protein 1 transcript (cdr1as), is densely bound by microrna (mirna) effector complexes and harbours 63 conserved binding sites for the ancient mirna mir-7. further analyses indicated that cdr1as functions to bind mir-7 in neuronal tissues. human cdr1as expression in zebrafish impaired midbrain development, similar to knocking down mir-7, suggesting that cdr1as is a mirna antagonist with a mirna-binding capacity ten times higher than any other known transcript. together, our data provide evidence that circrnas form a large class of post-transcriptional regulators. numerous circrnas form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.",1
"long noncoding rnas (lncrnas), a recently discovered class of cellular rnas, play important roles in the regulation of many cellular developmental processes. although lncrnas have been systematically identified in various systems, most of them have not been functionally characterized in vivo in animal models. in this study, we identified 128 testis-specific drosophila lncrnas and knocked out 105 of them using an optimized three-component crispr/cas9 system. among the lncrna knockouts, 33 (31%) exhibited a partial or complete loss of male fertility, accompanied by visual developmental defects in late spermatogenesis. in addition, six knockouts were fully or partially rescued by transgenes in a trans configuration, indicating that those lncrnas primarily work in trans furthermore, gene expression profiles for five lncrna mutants revealed that testis-specific lncrnas regulate global gene expression, orchestrating late male germ cell differentiation. compared with coding genes, the testis-specific lncrnas evolved much faster. moreover, lncrnas of greater functional importance exhibited higher sequence conservation, suggesting that they are under constant evolutionary selection. collectively, our results reveal critical functions of rapidly evolving testis-specific lncrnas in late drosophila spermatogenesis.",1
"studies investigating the pathogenic role of the microtubule associated protein tau (mapt) gene in parkinson's disease (pd) have indicated that dna methylation of the promoter region is aberrant in disease, leading to dysregulated mapt expression. we examined two potential regulators of mapt gene expression in respect to pd, a promoter-associated long non-coding rna mapt-as1, and dna methyltransferases (dnmts), enzymes responsible for new and maintenance of dna methylation. we assessed the relationship between expression levels of mapt and the candidate mapt-as1, dnmt1, dnmt3a and dnmt3b transcripts in four brain regions with varying degrees of cell loss and pathology (putamen, anterior cingulate cortex, visual cortex and cerebellum) in n = 10 pd and n = 10 controls. we found a significant decrease in mapt-as1 expression in pd (p = 7.154 x 10-6). the transcript levels of both mapt-as1 (p = 2.569 x 10-4) and dnmt1 (p = 0.001) correlated with those of mapt across the four brain regions, but not with each other. overexpression of mapt-as1 decreased mapt promoter activity by ∼2.2 to 4.3 fold in an in vitro luciferase assay performed in two cell lines (p ≤ 2.678 x 10-4). knock-down expression of mapt-as1 led to a 1.3 to 6.3 fold increase in methylation of the endogenous mapt promoter (p ≤ 0.011) and a 1.2 to 1.5 fold increased expression of the 4-repeat mapt isoform transcript (p ≤ 0.013). in conclusion, mapt-as1 and dnmt1 have been identified as potential epigenetic regulators of mapt expression in pd across four different brain regions. our data also suggest that increased mapt expression could be associated with disease state, but not with pd neuropathology severity.",1
"unlabelled hepatocellular carcinoma (hcc) remains a significant clinical challenge with few therapeutic options available to cancer patients. microrna 21-5p (mir-21) has been shown to be upregulated in hcc, but the contribution of this oncomir to the maintenance of tumorigenic phenotype in liver cancer remains poorly understood. we have developed potent and specific single-stranded oligonucleotide inhibitors of mir-21 (anti-mirnas) and used them to interrogate dependency on mir-21 in a panel of liver cancer cell lines. treatment with anti-mir-21, but not with a mismatch control anti-mirna, resulted in significant derepression of direct targets of mir-21 and led to loss of viability in the majority of hcc cell lines tested. robust induction of caspase activity, apoptosis, and necrosis was noted in anti-mir-21-treated hcc cells. furthermore, ablation of mir-21 activity resulted in inhibition of hcc cell migration and suppression of clonogenic growth. to better understand the consequences of mir-21 suppression, global gene expression profiling was performed on anti-mir-21-treated liver cancer cells, which revealed striking enrichment in mir-21 target genes and deregulation of multiple growth-promoting pathways. finally, in vivo dependency on mir-21 was observed in two separate hcc tumor xenograft models. in summary, these data establish a clear role for mir-21 in the maintenance of tumorigenic phenotype in hcc in vitro and in vivo. implications mir-21 is important for the maintenance of the tumorigenic phenotype of hcc and represents a target for pharmacologic intervention.",1
"mir-210 is a key player of cell response to hypoxia, modulating cell survival, vegf-driven endothelial cell migration, and the ability of endothelial cells to form capillary-like structures. a crucial step in understanding microrna (mirna) function is the identification of their targets. however, only few mir-210 targets have been identified to date. here, we describe an integrated strategy for large-scale identification of new mir-210 targets by combining transcriptomics and proteomics with bioinformatic approaches. to experimentally validate candidate targets, the rna-induced silencing complex (risc) loaded with mir-210 was purified by immunoprecipitation along with its mrna targets. the complex was significantly enriched in mrnas of 31 candidate targets, such as bdnf, gpd1l, iscu, ncam, and the non-coding rna xist. a subset of the newly identified targets was further confirmed by 3'-untranslated region (utr) reporter assays, and hypoxia induced down-modulation of their expression was rescued blocking mir-210, providing support for the approach validity. in the case of 9 targets, such as ptpn1 and p4hb, mir-210 seed-pairing sequences localized in the coding sequence or in the 5'-utr, in line with recent data extending mirna targeting beyond the ""classic"" 3'-utr recognition. finally, gene ontology analysis of the targets highlights known mir-210 impact on cell cycle regulation and differentiation, and predicts a new role of this mirna in rna processing, dna binding, development, membrane trafficking, and amino acid catabolism. given the complexity of mirna actions, we view such a multiprong approach as useful to adequately describe the multiple pathways regulated by mir-210 during physiopathological processes.",1
"rna thermometers regulate expression of some genes involved in virulence of pathogenic bacteria such as yersinia , neisseria , and salmonella they often function through temperature-dependent conformational changes that alter accessibility of the ribosome-binding site. the 5'-untranslated region (utr) of the htra mrna from salmonella enterica contains a very short rna thermometer. we have systematically characterized the structure and dynamics of this thermometer at single-nucleotide resolution using shape (selective 2'-hydroxyl acylation analyzed by primer extension) assays. our results confirm that the htra thermometer adopts the predicted hairpin conformation at low temperatures, with conformational change occurring over a physiological temperature regime. detailed shape melting curves for individual nucleotides suggest that the thermometer unfolds in a cooperative fashion, with nucleotides from both upper and lower portions of the stem gaining flexibility at a common transition temperature. intriguingly, analysis of an extended htra 5' utr sequence revealed not only the presence of the rna thermometer, but also an additional, stable upstream structure. we generated and analyzed point mutants of the htra thermometer, revealing elements that modulate its stability, allowing the hairpin to melt under the slightly elevated temperatures experienced during the infection of a warm-blooded host. this work sheds light on structure-function relationships in htra and related thermometers, and it also illustrates the utility of shape assays for detailed study of rna thermometer systems.",1
"the fin-to-limb transition represents one of the major vertebrate morphological innovations associated with the transition from aquatic to terrestrial life and is an attractive model for gaining insights into the mechanisms of morphological diversity between species. one of the characteristic features of limbs is the presence of digits at their extremities. although most tetrapods have limbs with five digits (pentadactyl limbs), palaeontological data indicate that digits emerged in lobed fins of early tetrapods, which were polydactylous. how the transition to pentadactyl limbs occurred remains unclear. here we show that the mutually exclusive expression of the mouse genes hoxa11 and hoxa13, which were previously proposed to be involved in the origin of the tetrapod limb, is required for the pentadactyl state. we further demonstrate that the exclusion of hoxa11 from the hoxa13 domain relies on an enhancer that drives antisense transcription at the hoxa11 locus after activation by hoxa13 and hoxd13. finally, we show that the enhancer that drives antisense transcription of the mouse hoxa11 gene is absent in zebrafish, which, together with the largely overlapping expression of hoxa11 and hoxa13 genes reported in fish, suggests that this enhancer emerged in the course of the fin-to-limb transition. on the basis of the polydactyly that we observed after expression of hoxa11 in distal limbs, we propose that the evolution of hoxa11 regulation contributed to the transition from polydactyl limbs in stem-group tetrapods to pentadactyl limbs in extant tetrapods.",1
"micrornas are small non-coding rna molecules that can regulate gene expression by interacting with multiple mrnas and inducing either translation suppression or degradation of mrna. recently, several mirnas were identified as either promoters or suppressors of metastasis. however, it is unclear in which step(s) of the multistep metastatic cascade these mirnas play a defined functional role. to study the functional importance of mirnas in epithelial-mesenchymal transition (emt), a process thought to initiate metastasis by enhancing the motility of tumor cells, we used a well established in vitro emt assay: transforming growth factor-beta-induced emt in nmumg murine mammary epithelial cells. we found that members of the mir-200 family, organized as two clusters in the genome, were repressed during emt. overexpression of each mirna individually or as clusters in nmumg cells hindered emt by enhancing e-cadherin expression through direct targeting of zeb1 and zeb2, which encode transcriptional repressors of e-cadherin. in the 4to7 mouse carcinoma cell line, which expresses low levels of endogenous e-cadherin and displays a mesenchymal phenotype, ectopic expression of the mir-200 family mirnas significantly increased e-cadherin expression and altered cell morphology to an epithelial phenotype. furthermore, ectopic expression of each mir-200 mirna cluster significantly reduced the in vitro motility of 4to7 cells in migration assays. these results suggested that loss of expression of the mir-200 family members may play a critical role in the repression of e-cadherin by zeb1 and zeb2 during emt, thereby enhancing migration and invasion during cancer progression.",1
"the mir-17-92 cluster encodes 7 mirnas inside a single polycistronic transcript, and is known as a group of oncogenic mirnas that contribute to tumorigenesis in several cancers. however, their direct targets remain unclear, and it has been suggested that a single mirna is capable of reducing the production of hundreds of proteins. the majority of reports on the identification of mirna targets are based on computational approaches or the detection of altered mrna levels, despite the fact that most mirnas are thought to regulate their targets primarily by translational inhibition in higher organisms. in this study, we examined the target profiles of mir-19a, mir-20a and mir-92-1 in mcf-7 breast cancer cells by a quantitative proteomic strategy to identify their direct targets. a total of 123 proteins were significantly increased after the endogenous mir-19a, mir-20a and mir-92-1 were knocked down, and were identified as potential targets by two-dimensional electrophoresis and a mass spectrometric analysis. among the upregulated proteins, four (ppp2r2a, arhgap1, impdh1 and npepl1) were shown to have mir-19a or mir-20a binding sites on their mrnas. the luciferase activity of the plasmids with each binding site was observed to decrease, and an increased luciferase activity was observed in the presence of the specific anti-mirna-lna. a western blot analysis showed the expression levels of impdh1 and npepl1 to increase after treatment with anti-mir-19a, while the expression levels of ppp2r2a and arhgap1 did not change. the expression levels of impdh1 and npepl1 did not significantly change by anti-mir-19a-lna at the mrna level. these results suggest that the impdh1 and npepl1 genes are direct targets of mir-19a in breast cancer, while the exogenous expression of these genes is not associated with the growth suppression of mcf-7 cells. furthermore, our proteomic approaches were shown to be valuable for identifying direct mirna targets.",1
"the tyrosine kinase c-src is upregulated in various human cancers, but the molecular mechanisms underlying c-src-mediated tumor growth remain unclear. here we examined the involvement of micrornas in the c-src-mediated tumor growth. microarray profiling revealed that c-src activation downregulates a limited set of micrornas, including mir-99a, which targets oncogenic mammalian target of rapamycin (mtor) and fibroblast growth factor receptor 3 (fgfr3). re-expression of mir-99a suppressed tumor growth of c-src-transformed cells, and this effect was restored by the overexpression of mtor. the downregulation of mir-99a was also observed in epidermal growth factor- and ras-transformed cells, and it was suppressed by inhibiting the mitogen-activated protein kinase (mapk) pathway. furthermore, mir-99a downregulation is associated with mtor/fgfr3 upregulation in various human lung cancer cells/tissues. the tumorigenicity of these cells was suppressed by the introduction of mir-99a. these findings suggest that the mir-99a-mtor/fgfr3 pathway is crucial for controlling tumor growth in a wide range of human cancers that harbor upregulation of the src-related oncogenic pathways.",1
"the rfn element is a highly conserved domain that is found frequently in the 5'-untranslated regions of prokaryotic mrnas that encode for flavin mononucleotide (fmn) biosynthesis and transport proteins. we report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds fmn in the absence of proteins. our results also indicate that in bacillus subtilis, the riboswitch most likely controls gene expression by causing premature transcription termination of the ribdeaht operon and precluding access to the ribosome-binding site of ypaa mrna. sequence and structural analyses indicate that the rfn element is a natural fmn-binding aptamer, the allosteric character of which is harnessed to control gene expression.",1
"micrornas have been linked to different cancer-related processes. the microrna mir-21 appears to function as an anti-apoptosis factor in glioblastomas. however, the functional target genes of mir-21 are largely unknown in glioblastomas. in this study, bioinformatics analysis was used to identify mir-21 target sites in various genes. luciferase activity assay showed that a number of genes involved in apoptosis, pdcd4, mtap, and sox5, carry putative mir-21 binding sites. expression of pdcd4 protein correlates inversely with expression of mir-21 in a number of human glioblastoma cell lines such as t98g, a172, u87, and u251. inhibition of mir-21 increases endogenous levels of pdcd4 in cell line t98g and over-expression mir-21 inhibits pdcd4-dependent apoptosis. together, these results indicate that mir-21 expression plays a key role in regulating cellular processes in glioblastomas and may serve as a target for effective therapies.",1
"animal micrornas (mirnas) are short rnas that function as posttranscriptional regulators of gene expression by binding to the target mrnas. noting that some mirnas are highly conserved in evolution, we explored the possibility of evolutionary conservation of their targets. we identified human orthologues of experimentally verified let-7 mirna target genes in caenorhabditis elegans and used the luciferase reporter system to examine whether these human genes are still the targets of let-7 mirna. we found that in some cases, the mirna-target relationship has indeed been conserved in human. interestingly, human trim71, an orthologue of c. elegans let-7-target lin-41 gene, can be repressed by hsa-let-7a and hsa-let-7c. this repression was abolished when both predicted let-7 target sites of trim71 were mutated. moreover, the zebrafish lin-41 orthologue was also repressed by let-7 to a similar degree as was trim71. when the expression of zebrafish lin-41 orthologue was silenced by microinjection of rna interference or morpholino into zebrafish zygotes, retarded embryonic development was observed, providing direct evidence for an essential role of lin-41 in zebrafish development. taken together, our results suggest that the regulation of trim71 expression by let-7 has been evolutionarily conserved and that trim71 likely plays an important role in development.",1
"pregnancy-induced noncoding rna (pinc) and retinoblastoma-associated protein 46 (rbap46) are upregulated in alveolar cells of the mammary gland during pregnancy and persist in alveolar cells that remain in the regressed lobules following involution. the cells that survive involution are thought to function as alveolar progenitor cells that rapidly differentiate into milk-producing cells in subsequent pregnancies, but it is unknown whether pinc and rbap46 are involved in maintaining this progenitor population. here, we show that, in the post-pubertal mouse mammary gland, mpinc is enriched in luminal and alveolar progenitors. mpinc levels increase throughout pregnancy and then decline in early lactation, when alveolar cells undergo terminal differentiation. accordingly, mpinc expression is significantly decreased when hc11 mammary epithelial cells are induced to differentiate and produce milk proteins. this reduction in mpinc levels may be necessary for lactation, as overexpression of mpinc in hc11 cells blocks lactogenic differentiation, while knockdown of mpinc enhances differentiation. finally, we demonstrate that mpinc interacts with rbap46, as well as other members of the polycomb repressive complex 2 (prc2), and identify potential targets of mpinc that are differentially expressed following modulation of mpinc expression levels. taken together, our data suggest that mpinc inhibits terminal differentiation of alveolar cells during pregnancy to prevent abundant milk production and secretion until parturition. additionally, a prc2 complex that includes mpinc and rbap46 may confer epigenetic modifications that maintain a population of mammary epithelial cells committed to the alveolar fate in the involuted gland.",1
"the h/aca motif of human telomerase rna (htr) directs specific pathways of endogenous telomerase holoenzyme assembly, function, and regulation. similarities between htr and other h/aca rnas have been established, but differences have not been explored even though unique features of htr h/aca rnp assembly give rise to telomerase deficiency in human disease. here, we define htr h/aca rna and rnp architecture using rna accumulation, rnp affinity purification, and primer extension activity assays. first, we evaluate alternative folding models for the htr h/aca motif 5' hairpin. second, we demonstrate an unanticipated and surprisingly general asymmetry of 5' and 3' hairpin requirements for h/aca rna accumulation. third, we establish that htr assembles not one but two sets of all four of the h/aca rnp core proteins, dyskerin, nop10, nhp2, and gar1. fourth, we address a difference in predicted specificities of htr association with the holoenzyme subunit wdr79/tcab1. together, these results complete the analysis of htr elements required for active rnp biogenesis and define the interaction specificities and stoichiometries of all functionally essential human telomerase holoenzyme subunits. this study uncovers unexpected similarities but also differences between telomerase and other h/aca rnps that allow a unique specificity of telomerase biogenesis and regulation.",1
"despite a general repression of translation under hypoxia, cells selectively upregulate a set of hypoxia-inducible genes. results from deep sequencing revealed that let-7 and mir-103/107 are hypoxia-responsive micrornas (hrms) that are strongly induced in vascular endothelial cells. in silico bioinformatics and in vitro validation showed that these hrms are induced by hif1α and target argonaute 1 (ago1), which anchors the microrna-induced silencing complex (mirisc). hrm targeting of ago1 resulted in the translational desuppression of vegf mrna. inhibition of hrm or overexpression of ago1 without the 3' untranslated region decreased hypoxia-induced angiogenesis. conversely, ago1 knockdown increased angiogenesis under normoxia in vivo. in addition, data from tumor xenografts and human cancer specimens indicate that ago1-mediated translational desuppression of vegf may be associated with tumor angiogenesis and poor prognosis. these findings provide evidence for an angiogenic pathway involving hrms that target ago1 and suggest that this pathway may be a suitable target for anti- or proangiogenesis strategies.",1
"micrornas (mirnas) play important roles in the the gene regulation of carcinogenesis including breast cancer. mir‑519d has been studied in various types of cancer, but its role in breast cancer remains unclear. in the present study, we investigated the expression and biological function of mir-519d in breast cancer. using quantitative rt-pcr (rt-qpcr) analysis, we analyzed the expression of mir-519d in breast cancer tissues and cell lines. it was shown that mir-519d expression was decreased in cancer tissues and cell lines compared with their controls. overexpression of mir-519d inhibited cell proliferation and invasion, and induced apoptosis of breast cancer cells. signal transducer and activator of transcription 3 (stat3) was predicted as a target gene of mir-519d and it was verified by the luciferase reporter assay. additionally, stat3 mrna and protein expression levels were downregulated in the cells with mir-519d overexpression as determined by rt-qpcr and western blotting. taken together, the results indicated that mir-519d functions as a tumor suppressor in breast cancer by suppressing stat3 expression.",1
"aim mir-145 is a candidate tumor suppressor mirna. however, it is unknown whether mir-145 is involved in the invasion of hepatocellular carcinoma (hcc). therefore, we aimed to explore the effect and mechanism of mir-145 in the control of hcc cell invasion. methods hcc cell invasion was evaluated by transwell assays after transfection with pre-mir-145 or anti-mir-145. a luciferase reporter assay was used to determine whether a disintegrin and metalloprotease 17 (adam17) were a target of mir-145. the levels of mir-145 and adam17 mrna were detected by a real-time polymerase chain reaction assay, and the level of adam17 protein was measured by western blot analysis. pearson's correlation test was used to assess the correlation between adam17 mrna expression and mir-145 expression in 20 hcc tissue samples. results mir-145 was significantly downregulated in hcc tissues and cell lines. the loss of mir-145 expression was associated with the tumor-node-metastasis stage, vascular invasion and intrahepatic metastasis. the overexpression of mir-145 was able to suppress tumor mhcc-97h cell invasion, whereas the knockdown of mir-145 expression induced smmc-7721 cell invasion. we demonstrated that mir-145 bound directly to the 3'-untranslated region of adam17 and inhibited the expression of adam17. the knockdown of adam17 in smmc-7721 cells could partially reverse the effects of anti-mir-145. mir-145 expression was inversely associated with adam17 expression in 20 hcc tissue specimens. conclusion our findings indicate that mir-145 could inhibit hcc cell invasion by regulating the expression of adam17.",1
"growing evidence indicates that changes in microrna (mirna) expression in cancer induced by chemical carcinogens play an important role in cancer development and progression by regulating related genes. however, the mechanisms underlying mirna involvement in hepatocarcinogenesis induced by polycyclic aromatic hydrocarbons (pahs) remain unclear. thus, the identification of aberrant mirna expression during pah-induced cancer cell migration will lead to a better understanding of the substantial role of mirnas in cancer progression. in the present study, mirna expression profiling showed significant upregulation of mir-181a, -181b, and -181d in human hepatocellular carcinoma cells (hepg2 line) exposed to benzoanthracene (ba) and benzofluoranthene (bf). mapk phosphatase-5 (mkp-5), a validated mir-181 target that deactivates mapks, was markedly suppressed while phosphorylation of p38 mapk was increased after ba and bf exposure. the migration of hepg2 cells, observed using the scratch wound-healing assay, also increased in a dose-dependent manner. depletion of mir-181 family members by mirna inhibitors enhanced the expression of mkp-5 and suppressed the phosphorylation of p38 mapk. furthermore, the depletion of the mir-181 family inhibited cancer cell migration. based on these results, we conclude that the mir-181 family plays a critical role in pah-induced hepatocarcinogenesis by targeting mkp-5, resulting in the regulation of p38 mapk activation.",1
"micrornas (mirnas) are noncoding rnas that regulate gene expression at the post-transcriptional level and are involved in the regulation of the formation, maintenance, and function of skeletal muscle. using mirna sequencing and bioinformatics analysis, we previously found that the mirna mir-664-5p is significantly differentially expressed in longissimus dorsi muscles of rongchang pigs. however, the molecular mechanism by which mir-664-5p regulates myogenesis remains unclear. in this study, using flow cytometry, 5-ethynyl-2'-deoxyuridine staining, and cell count and immunofluorescent assays, we found that cell-transfected mir-664-5p mimics greatly promoted proliferation of c2c12 mouse myoblasts by increasing the proportion of cells in the s- and g 2 -phases and up-regulating the expression of cell cycle genes. moreover, mir-664-5p inhibited myoblast differentiation by down-regulating myogenic gene expression. in contrast, mir-664-5p inhibitor repressed myoblast proliferation and promoted myoblast differentiation. mechanistically, using dual-luciferase reporter gene experiments, we demonstrated that mir-664-5p directly targets the 3'-utr of serum response factor ( srf ) and wnt1 mrnas. we also observed that mir-664-5p inhibits both mrna and protein levels of srf and wnt1 during myoblast proliferation and myogenic differentiation, respectively. furthermore, the activating effect of mir-664-5p on myoblast proliferation was attenuated by srf overexpression, and mir-664-5p repressed myogenic differentiation by diminishing the accumulation of nuclear β-catenin. of note, mir-664-5p's inhibitory effect on myogenic differentiation was abrogated by treatment with wnt1 protein, the key activator of the wnt/β-catenin signaling pathway. collectively, our findings suggest that mir-664-5p controls srf and canonical wnt/β-catenin signaling pathways in myogenesis.",1
"mammalian reproduction requires that males and females produce functional haploid germ cells through complex cellular differentiation processes known as spermatogenesis and oogenesis, respectively. while numerous studies have functionally characterized protein-coding genes and small noncoding rnas (micrornas and pirnas) that are essential for gametogenesis, the roles of regulatory long noncoding rnas (lncrnas) are yet to be fully characterized. previously, we and others have demonstrated that intergenic regions of the mammalian genome encode thousands of long noncoding rnas, and many studies have now demonstrated their critical roles in key biological processes. thus, we postulated that some lncrnas may also impact mammalian spermatogenesis and fertility. in this study, we identified a dynamic expression pattern of lncrnas during murine spermatogenesis. importantly, we identified a subset of lncrnas and very few mrnas that appear to escape meiotic sex chromosome inactivation, an epigenetic process that leads to the silencing of the x- and y-chromosomes at the pachytene stage of meiosis. further, some of these lncrnas and mrnas show a strong testis expression pattern suggesting that they may play key roles in spermatogenesis. lastly, we generated a mouse knockout of one x-linked lncrna, tslrn1 (testis-specific long noncoding rna 1), and found that males carrying a tslrn1 deletion displayed normal fertility but a significant reduction in spermatozoa. our findings demonstrate that dysregulation of specific mammalian lncrnas is a novel mechanism of low sperm count or infertility, thus potentially providing new biomarkers and therapeutic strategies.",1
"micrornas (mirnas) are a class of small non-coding rnas that repress the expression of their target genes post-transcriptionally. mirnas participate in the regulation of a variety of biological processes, including development and diseases. however, the functional role and molecular mechanism by which mirnas regulate skeletal muscle development and differentiation are not fully understood. in this report, we identified mir-23a as a key regulator of skeletal muscle differentiation. using bioinformatics analyses, mir-23a is predicted to target multiple adult fast myosin heavy chain (myh) genes, including myh 1, 2 and 4. luciferase reporter assays show that mir-23a directly targets the 3' untranslated regions (utrs) of these mrnas. interestingly, the expression level of mature mir-23a is inversely correlated with myogenic progression in mouse skeletal muscle. both gain- and loss-of-function studies using c2c12 myoblasts demonstrate that mir-23a inhibits myogenic differentiation. these findings therefore reveal a novel role of mir-23a in regulating myogenic differentiation via inhibiting the expression of fast myosin heavy chain isoforms.",1
"genomic imprinting is the phenomenon whereby a subset of genes is differentially expressed according to parental origin. imprinted genes tend to occur in clusters, and micrornas are associated with the majority of well-defined clusters of imprinted genes. we show here that two micrornas, mir-296 and mir-298, are part of the imprinted gnas/gnas clusters in both mice and humans. both micrornas show imprinted expression and are expressed from the paternally derived allele, but not the maternal allele. they arise from a long, noncoding antisense transcript, nespas, with a promoter more than 27 kb away. nespas had been shown previously to act in cis to regulate imprinted gene expression within the gnas cluster. using microarrays and luciferase assays, ikbke, involved in many signaling pathways, and tmed9, a protein transporter, were verified as new targets of mir-296. thus, nespas has two clear functions: as a cis-acting regulator within an imprinted gene cluster and as a precursor of micrornas that modulate gene expression in trans. furthermore, imprinted micrornas, including mir-296 and mir-298, impose a parental specific modulation of gene expression of their target genes.",1
"objective calcific aortic valve disease is an active process involving a wide range of pathologic changes. valve interstitial cells are the most prevalent cells in the heart valve and maintain normal valve structure and function. micrornas (mirnas) are essential posttranscriptional modulators of gene expression, and mirna-30b is a known repressor of bone morphogenetic protein 2-mediated osteogenesis. we hypothesized that mirna-30b is a multifunctional regulator of aortic valve interstitial cells during calcification. methods to determine the role of mirna-30b in calcific aortic valve disease, we evaluated mirna expression in human calcific aortic valve leaflets obtained intraoperatively. furthermore, human valve interstitial cells were evaluated with regard to mirna-30b expression and osteogenesis by quantitative real-time polymerase chain reaction, western blotting, flow cytometry, and alkaline phosphatase assays. results in this study, we demonstrated that mirna-30b attenuates bone morphogenetic protein 2-induced osteoblast differentiation by targeting runx2, smad1, and caspase-3. transfection of a mimic of mirna-30b led to decreases in alkaline phosphatase activity and expressions of runx2, smad1, and caspase-3. furthermore, dual luciferase reporter assays confirmed that runx2, smad1, and caspase-3 are direct targets of mirna-30b. conclusions we demonstrated a remarkable role of mirna-30b in calcific aortic valve disease as a regulator of human aortic valvular calcification and apoptosis through direct targeting of runx2, smad1, and caspase-3. targeting of mirna-30b could serve as a novel therapeutic strategy to limit progressive calcification in aortic stenosis.",1
"microrna-200c (mir200c) is emerging as an important regulator of tumourigenicity and cancer metastasis with a strong capacity for inducing epithelial-mesenchymal transitions. however, the role of mir200c in head and neck squamous cell carcinoma (hnscc) and hnscc-associated cancer stem cells (hnscc-cscs) is unknown. in this study, the expression of mir200c in the regional metastatic lymph node of hnscc tissues was significantly decreased, but bmi1 expression was increased as compared to parental tumours. importantly, site-directed mutagenesis with a luciferase reporter assay showed that mir200c targeted the 3' utr of bmi1 in hnscc cells. isolated hnscc-derived aldh1(+) /cd44(+) cells displayed csc-like tumour initiating and radio-resistant properties. the expression levels of mir200c were significantly down-regulated while bmi1 was increased in hnscc-aldh1(+) /cd44(+) compared to the other subsets of hnscc cells. furthermore, increased mir200c expression or knockdown of bmi1 could significantly inhibit the malignant csc-like properties of aldh1(+) /cd44(+) cells. mir200c over-expression further down-regulated the expressions of zeb1, snail and n-cadherin, but up-regulated e-cadherin expression in aldh1(+) /cd44(+) cells. finally, a xenotransplantion study confirmed that over-expression of mir200c or bmi1 knockdown effectively inhibited the lung metastatic ability and prolonged the survival rate of aldh1(+) /cd44(+) -transplanted mice. in summary, mir200c negatively modulates the expression of bmi1 but also significantly inhibits the metastatic capability of epithelial-mesenchymal transitions in malignant hnscc by reducing the expression of bmi1/zeb1. restoration of mir200c in hnscc and cscs may be a promising therapeutic approach.",1
"placental cell growth depends on an adaptable combination of an endogenous developmental program and the exogenous influence of maternal growth factors, both of which may be influenced by microrna (mir)-dependent effects on gene expression. we have previously shown that global mir suppression in placenta accelerates proliferation and enhances levels of growth factor signaling mediators in cytotrophoblast. this study aimed to identify mirs involved in regulating placental growth. an initial array revealed 58 mir species whose expression differs between first trimester, when cytotrophoblast proliferation is rapid, and term, by which time proliferation has slowed. in silico analysis defined potential growth-regulatory mirs; among these, hsa-mir-145, hsa-mir-377, and hsa-let-7a were predicted to target known placental growth genes and were higher at term than in the first trimester, so they were selected for further analysis. overexpression of mir-377 and let-7a, but not mir-145, in first trimester placental explants significantly reduced basal cytotrophoblast proliferation and expression of erk and myc. pcr arrays, in silico analysis, western blotting, and 3'-utr luciferase reporter assays revealed targets of mir-145 within the insulin-like growth factor axis. analysis of proliferation in placental explants overexpressing mir-145 demonstrated its role as a mediator of insulin-like growth factor-induced trophoblast proliferation. these findings identify mir-377 and let-7a in regulation of endogenous cell growth and mir-145 in the placental response to maternal stimulation and will aid the development of therapeutic strategies for problem pregnancies.",1
"several micrornas (mirna) have been implicated in h. pylori related gastric cancer (gc). however, the molecular mechanism of mirnas in gc has not been fully understood. in this study, we reported that mir-203 is significantly down-regulated in h. pylori positive tissues and cells and in tumor tissues with important functional consequences. ectopic expression of mir-203 dramatically suppressed cell proliferation and invasion. we found that mir-203 strongly reduced the expression of cask oncogene in gc cells. similar to the restoring mir-203 expression, cask down-regulation inhibited cell growth and invasion, whereas cask over-expression rescued the suppressive effect of mir-203. these results can also be found in nude mice. in clinical specimens, cask was over-expressed in tumors and h. pylori positive tissues and its mrna levels were inversely correlated with mir-203 expression. taken together, our results indicated that mir-203 functions as a growth-suppressive mirna in h. pylori related gc, and that its suppressive effects are mediated mainly by repressing cask expression.",1
"the existence of vast regulatory networks mediated by micrornas (mirnas) suggests broad potential for mirna dysfunction to contribute to disease. however, relatively few mirna-target interactions are likely to make detectable contributions to phenotype, and effective strategies to identify these few interactions are currently wanting. we hypothesized that signaling cascades represent critical points of susceptibility to mirna dysfunction, and we developed a strategy to test this theory by using quantitative cell-based screens. here we report a screen for mirnas that affect the wingless (wg) pathway, a conserved pathway that regulates growth and tissue specification. this process identified ectopic mir-315 as a potent and specific activator of wg signaling, an activity that we corroborated in transgenic animals. this mir-315 activity was mediated by direct inhibition of axin and notum, which encode essential, negatively acting components of the wg pathway. genetic interaction tests substantiated both of these genes as key functional targets of mir-315. the ability of ectopic mir-315 to activate wg signaling was not a trivial consequence of predicted mirna-target relationships because other mirnas with conserved sites in the axin 3' utr neither activated wg outputs nor inhibited an axin sensor. in summary, activity-based screening can selectively identify mirnas whose deregulation can lead to interpretable phenotypic consequences.",1
"congenital heart disease (chd) is a devastating anomaly that affects ∼1% of live births. defects of the outflow tract (oft) make up a large percentage of human chd. we investigated bmp signaling in mouse oft development by conditionally deleting both bmp4 and bmp7 in the second heart field (shf). shf bmp4/7 deficiency resulted in defective epithelial to mesenchymal transition (emt) and reduced cardiac neural crest ingress, with resultant persistent truncus arteriosus. using a candidate gene approach, we found that vegfa was upregulated in the bmp4/7 mutant hearts. to determine if vegfa is a downstream bmp effector during emt, we examined whether vegfa is transcriptionally regulated by the bmp receptor-regulated smad. our findings indicate that smad directly binds to vegfa chromatin and represses vegfa transcriptional activity. we also found that vegfa is a direct target for the mir-17-92 cluster, which is also regulated by bmp signaling in the shf. deletion of mir-17-92 reveals similar phenotypes to bmp4/7 shf deletion. to directly address the function of vegfa repression in bmp-mediated emt, we performed ex vivo explant cultures from bmp4/7 and mir-17-92 mutant hearts. emt was defective in explants from the bmp4/7 double conditional knockout (dcko; mef2c-cre;bmp4/7(f/f)) and mir-17-92 null. by antagonizing vegfa activity in explants, emt was rescued in bmp4/7 dcko and mir-17-92 null culture. moreover, overexpression of mir-17-92 partially suppressed the emt defect in bmp4/7 mutant embryos. our study reveals that vegfa levels in the oft are tightly controlled by smad- and microrna-dependent pathways to modulate oft development.",1
"the regulation of pyrg expression in a group of low gc gram-positive bacteria was previously shown to be mediated by a novel form of transcription attenuation in which low levels of intracellular ctp induce reiterative addition of g residues at position +4 in the 5' end of the pyrg mrna, which is encoded as pppgggc. . . . the poly(g) sequences formed under these conditions act to prevent attenuation by base pairing with the c- and u-rich 5' strand of a downstream terminator stem-loop located in the pyrg leader. in this work we document the reconstitution of this regulatory system in vitro using only the native pyrg dna template, rna polymerase and appropriate concentrations of ribonucleotides. ctp-regulated reiterative transcription producing 5'-poly(g) tracts and regulation of transcription termination at the pyrg attenuator by ctp were demonstrated. mutations in the native pyrg template that altered reiterative transcription and attenuation in vivo resulted in alternations in expression in the in vitro transcription system that were predicted by the mechanism described above. these findings provide strong experimental support for the proposed reiterative transcription/antitermination mechanism and confirm that no trans-acting regulatory protein is required for pyrg regulation.",1
"we have identified a highly conserved rna motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (moco) biosynthesis enzymes, and proteins that utilize moco as a coenzyme. bioinformatics searches have identified 176 representatives in gamma-proteobacteria, delta-proteobacteria, clostridia, actinobacteria, deinococcus-thermus species and dnas from environmental samples. using genetic assays, we demonstrate that a moco rna in escherichia coli associated with the moco biosynthetic operon controls gene expression in response to moco production. in addition, we provide evidence indicating that this conserved rna discriminates against closely related analogues of moco. these results, together with extensive phylogenetic conservation and typical gene control structures near some examples, indicate that representatives of this structured rna represent a novel class of riboswitches that sense moco. furthermore, we identify variants of this rna that are likely to be triggered by the related tungsten cofactor (tuco), which carries tungsten in place of molybdenum as the metal constituent.",1
"pulmonary hypertension (ph) is a serious disorder that causes significant morbidity and mortality. the pathogenesis of ph involves complex derangements in multiple pathways including reductions in peroxisome proliferator-activated receptor gamma (pparγ). hypoxia, a common ph stimulus, reduces pparγ in experimental models. in contrast, activating pparγ attenuates hypoxia-induced ph and endothelin 1 (et-1) expression. to further explore mechanisms of hypoxia-induced ph and reductions in pparγ, we examined the effects of hypoxia on selected microrna (mirna or mir) levels that might reduce pparγ expression leading to increased et-1 expression and ph. our results demonstrate that exposure to hypoxia (10% o2) for 3-weeks increased levels of mir-27a and et-1 in the lungs of c57bl/6 mice and reduced pparγ levels. hypoxia-induced increases in mir-27a were attenuated in mice treated with the pparγ ligand, rosiglitazone (rsg, 10 mg/kg/d) by gavage for the final 10 d of exposure. in parallel studies, human pulmonary artery endothelial cells (hpaecs) were exposed to control (21% o2) or hypoxic (1% o2) conditions for 72 h. hypoxia increased hpaec proliferation, mir-27a and et-1 expression, and reduced pparγ expression. these alterations were attenuated by treatment with rsg (10 µm) during the last 24 h of hypoxia exposure. overexpression of mir-27a or pparγ knockdown increased hpaec proliferation and et-1 expression and decreased pparγ levels, whereas these effects were reversed by mir-27a inhibition. further, compared to lungs from littermate control mice, mir-27a levels were upregulated in lungs from endothelial-targeted pparγ knockout (epparγ ko) mice. knockdown of either sp1 or egr1 was sufficient to significantly attenuate mir-27a expression in hpaecs. collectively, these studies provide novel evidence that mir-27a and pparγ mediate mutually repressive actions in hypoxic pulmonary vasculature and that targeting pparγ may represent a novel therapeutic approach in ph to attenuate proliferative mediators that stimulate proliferation of pulmonary vascular cells.",1
"microrna-mediated post-transcriptional regulations are increasingly recognized as important components of the circadian rhythm. here we identify microrna let-7, part of the drosophila let-7-complex, as a regulator of circadian rhythms mediated by a circadian regulatory cycle. overexpression of let-7 in clock neurons lengthens circadian period and its deletion attenuates the morning activity peak as well as molecular oscillation. let-7 regulates the circadian rhythm via repression of clockwork orange (cwo). conversely, upregulated cwo in cwo-expressing cells can rescue the phenotype of let-7-complex overexpression. moreover, circadian prothoracicotropic hormone (ptth) and clock-regulated 20-oh ecdysteroid signalling contribute to the circadian expression of let-7 through the 20-oh ecdysteroid receptor. thus, we find a regulatory cycle involving ptth, a direct target of clock, and ptth-driven mirna let-7.",1
"background lipoprotein lipase (lpl) expressed in macrophages plays an important role in promoting the development of atherosclerosis or atherogenesis. microrna-182 (mir-182) is involved in the regulation of lipid metabolism and inflammation. however, it remains unclear how mir-182 regulates lpl and atherogenesis.methods and results:using bioinformatics analyses and a dual-luciferase reporter assay, we identified histone deacetylase 9 (hdac9) as a target gene of mir-182. moreover, mir-182 upregulated lpl expression by directly targetinghdac9in thp-1 macrophages. hematoxylin-eosin (h&e), oil red o and masson's trichrome staining showed that apolipoprotein e (apoe)-knockout (ko) mice treated with mir-182 exhibited more severe atherosclerotic plaques. treatment with mir-182 increased cd68 and lpl expression in atherosclerotic lesions in apoe-ko mice, as indicated by double immunofluorescence staining in the aortic sinus. increased mir-182-induced increases in lpl expression in apoe-ko mice was confirmed by real-time quantitative polymerase chain reaction and western blotting analyses. treatment with mir-182 also increased plasma concentrations of proinflammatory cytokines and lipids in apoe-ko mice. conclusions the results of the present study suggest that mir-182 upregulates lpl expression, promotes lipid accumulation in atherosclerotic lesions, and increases proinflammatory cytokine secretion, likely through targetinghdac9, leading to an acceleration of atherogenesis in apoe-ko mice.",1
"p300, a transcriptional co-activator with histone acetyl transferase (hat) activity, plays an essential role in the pathogenesis of cardiomyocyte hypertrophy in response to multiple pro-hypertrophic stimuli including hyperglycemia. however, the precise mechanisms by which p300 expression is regulated remain unclear. the purpose of this study was to investigate the role of mir-150, a potential p300-targeting microrna (mirna), in the post-transcriptional control of p300 expression and cardiomyocyte hypertrophy induced by high glucose. we observed that the expression of mir-150 was significantly reduced, whereas the expression of p300 was strongly elevated, concomitant with cardiomyocyte hypertrophy, in the hearts of diabetic rats compared with normal controls. similar alterations were observed in neonatal rat cardiomyocytes that had been exposed to high levels of glucose. mir-150 mimics inhibited p300 3'-utr luciferase reporter activity, as well as endogenous p300 expression. in addition, mir-150 mimics prevented glucose-induced cardiomyocyte hypertrophy. co-transfection with a p300 expression vector and mir-150 mimics reversed the protective effect of mir-150 on cardiomyocyte hypertrophy. we further showed that the high glucose-mediated activation of pkcβ(2) in turn mediated the down-regulation of mir-150 expression. these data demonstrated a novel upstream role for mir-150 in p300-mediated cardiomyocyte hypertrophy and revealed a previously uncharacterized mirnas and hats cross-talk mechanism for the hypertrophic phenotype induced by high glucose.",1
"many biological and behavioural processes of animals are governed by an endogenous circadian clock, which is dependent on transcriptional regulation. here we address post-transcriptional regulation and the role of mirnas in drosophila circadian rhythms. at least six mirnas show cycling expression levels within the pigment dispersing factor (pdf) cell-pacemaker neurons; only mir-92a peaks during the night. in vivo calcium monitoring, dynamics of pdf projections, arclight, gcamp6 imaging and sleep assays indicate that mir-92a suppresses neuronal excitability. in addition, mir-92a levels within pdf cells respond to light pulses and also affect the phase shift response. translating ribosome affinity purification (trap) and in vitro luciferase reporter assay indicate that mir-92a suppresses expression of sirt2, which is homologous to human sir2 and sirt3. sirt2 rnai also phenocopies mir-92a overexpression. these experiments indicate that sirt2 is a functional mir-92a target and that mir-92a modulates pdf neuronal excitability via suppressing sirt2 levels in a rhythmic manner.",1
"the tyrt operon of e. coli and several other trna operons of e. coli show striking structural features: they contain repeated sequence units including a 19bp motif resembling the 3' end of the corresponding mature trna. a novel rna, encoded by the repeated sequence of the tyrt operon, was identified. the rna, characterized by primer extension and nuclease-s1 analysis, contained 171 nucleotides and terminated with the 19bp motif of the cca-end of trna(1tyr). the rna, designated as rtt rna, is probably released from the primary transcript of tyrt during trna processing, it includes the coding capacity for the arginine rich peptide tpr. predictions of secondary folding resulted a rather stable rna structure with a free energy of -44.3kcal/mol. a weak ribosome binding site was found, preceding the second possible aug initiator codon for tpr. the comparison of rtt rna with putative transcripts from the repeated sequences associated with related trna genes showed common features with respect to primary structure, arrangement and secondary folding. in e. coli cultures the lag-phase during growth, caused by transient glycine or by isoleucine limitation, was found to be overcome or markedly shortened in the presence of rtt rna. these and previously reported results suggest a modulatory effect of rtt rna on stringent response.",1
"the identification of specific functional roles for the numerous long noncoding (nc)rnas found in eukaryotic transcriptomes is currently a matter of intense study amid speculation that these ncrnas have key regulatory roles. we have identified a pair of cis-interfering ncrnas in yeast that contribute to the control of variegated gene expression at the flo11 locus by implementing a regulatory circuit that toggles between two stable states. these capped, polyadenylated ncrnas are transcribed across the large intergenic region upstream of the flo11 orf. as with mammalian long intervening (li)ncrnas, these yeast ncrnas (icr1 and pwr1) are themselves regulated by transcription factors (sfl1 and flo8) and chromatin remodelers (rpd3l) that are key elements in phenotypic transitions in yeast. the mechanism that we describe explains the unanticipated role of a histone deacetylase complex in activating gene expression, because rpd3l mutants force the ncrna circuit into a state that silences the expression of the adjacent variegating gene.",1
"recently, more than 1000 large intergenic noncoding rnas (lincrnas) have been reported. these rnas are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. here, we report the identification of lincrnas that are regulated by p53. one of these lincrnas (lincrna-p21) serves as a repressor in p53-dependent transcriptional responses. inhibition of lincrna-p21 affects the expression of hundreds of gene targets enriched for genes normally repressed by p53. the observed transcriptional repression by lincrna-p21 is mediated through the physical association with hnrnp-k. this interaction is required for proper genomic localization of hnrnp-k at repressed genes and regulation of p53 mediates apoptosis. we propose a model whereby transcription factors activate lincrnas that serve as key repressors by physically associating with repressive complexes and modulate their localization to sets of previously active genes.",1
"bacteria regularly encounter widely varying metal concentrations in their surrounding environment. as metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. a suite of metal-sensing regulatory (""metalloregulatory"") proteins orchestrate these responses by allosterically coupling the selective binding of target metals to the activity of dna-binding domains. however, we report here the discovery, validation, and structural details of a widespread class of riboswitch rnas, whose members selectively and tightly bind the low-abundance transition metals, ni(2+) and co(2+). these riboswitches bind metal cooperatively, and with affinities in the low micromolar range. the structure of a co(2+)-bound rna reveals a network of molecular contacts that explains how it achieves cooperative binding between adjacent sites. these findings reveal that bacteria have evolved to utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins, for detecting and responding to toxic levels of heavy metals.",1
"micrornas (mirnas) are endogenous small non-coding rnas that play central roles in diverse pathological processes. in this study, we investigated the effect of microrna-182 (mir-182) on the development of posterior uveal melanomas. initially, we demonstrated that mir-182 expression was dependent on p53 induction in uveal melanoma cells. interestingly, transient transfection of mir-182 into cultured uveal melanoma cells led to a significant decrease in cell growth, migration, and invasiveness. cells transfected with mir-182 demonstrated cell cycle g1 arrest and increased apoptotic activity. using bioinformatics, we identified three potential targets of mir-182, namely mitf, bcl2 and cyclin d2. mir-182 was shown to have activity on mrna expression by targeting the 3' untranslated region of mitf, bcl2 and cyclin d2. subsequent western blot analysis confirmed the downregulation of mitf, bcl2 and cyclin d2 protein expression. the expression of oncogene c-met and its downstream akt and erk1/2 pathways was also downregulated by mir-182. concordant with the findings that mir-182 was decreased in uveal melanoma tissue samples, overexpression of mir-182 also suppressed the in vivo growth of uveal melanoma cells. our results demonstrated that mir-182, a p53 dependent mirna, suppressed the expression of mitf, bcl2, cyclin d2 and functioned as a potent tumor suppressor in uveal melanoma cells.",1
"whole-genome microrna and gene expression analyses were used to monitor changes during retinoic acid induced differentiation of neuroblasts in vitro. interestingly, the entire mir-17 family was over-represented among the down-regulated mirna. the implications of these changes are considerable, as target gene prediction suggests that the mir-17 family is involved in the regulation of the mitogen-activated protein kinase (mapk) signaling pathway, synaptic plasticity and other markers of neuronal differentiation. significantly, many of the target responses predicted by changes in mirna expression were supported by the observed changes in gene expression. as expected, markers of neuronal differentiation such as anti-apoptotic protein b-cell lymphoma 2 (bcl2), myocyte enhancer factor-2d (mef2d) and zipper protein kinase (map3k12; aka zpk/muk/dlk) were each up-regulated in response to differentiation. the expression of these genes was also reduced in response to mir-17 and mir-20a transfection, and more specifically they were also shown to contain functional mirna recognition elements for members of the mir-17 family by reporter gene assay. this suggests that the mir-17 family have an integral role in fine-tuning the pathways involved in the regulation of neuronal differentiation.",1
"the paternally expressed imprinted retrotransposon-like 1 (rtl1) is a retrotransposon-derived gene that has evolved a function in eutherian placentation. seven mirnas, including mir-127, are processed from a maternally expressed antisense rtl1 transcript (rtl1as) and regulate rtl1 levels through rnai-mediated post-transcriptional degradation. to determine the relative functional role of rtl1as mirnas in rtl1 dosage, we generated a mouse specifically deleted for mir-127. the mir-127 knockout mice exhibit placentomegaly with specific defects within the labyrinthine zone involved in maternal-fetal nutrient transfer. although fetal weight is unaltered, specific rtl1 transcripts and protein levels are increased in both the fetus and placenta. phenotypic analysis of single (δmir-127/rtl1 or mir-127/δrtl1) and double (δmir-127/δrtl1) heterozygous mir-127- and rtl1-deficient mice indicate that rtl1 is the main target gene of mir-127 in placental development. our results demonstrate that mir-127 is an essential regulator of rtl1, mediated by a trans-homologue interaction between reciprocally imprinted genes on the maternally and paternally inherited chromosomes.",1
"the 72nt 3' non-translated region (ntr) of potato virus x (pvx) rna is identical in all sequenced pvx strains and contains sequences that are conserved among all potexviruses. computer folding of the 3' ntr sequence predicted three stem-loop structures (sl1, sl2, and sl3 in the 3' to 5' direction), which generally were supported by solution structure analyses. the importance of these sequence and/or structural elements to pvx rna accumulation was further analyzed by inoculation of nicotiana tabacum (nt-1) protoplasts with pvx transcripts containing mutations in the 3' ntr. analyses of rna accumulation by s(1) nuclease protection indicated that multiple sequence elements throughout the 3' ntr were important for minus-strand rna accumulation. formation of sl3 was required for accumulation of minus-strand rna, whereas sl1 and sl2 formation were less important. however, sequences within all of these predicted structures were required for minus-strand rna accumulation, including a conserved hexanucleotide sequence element in the loop of sl3, and the cu nucleotide in a u-rich sequence within sl2. in contrast, 13 nucleotides that were predicted to reside in sl1 could be deleted without any significant reduction in minus or plus-strand rna levels. potential polyadenylation signals (near upstream elements; nues) in the 3' ntr of pvx rna were more important for plus-strand rna accumulation than for minus-strand rna accumulation. in addition, one of these nues overlapped with other sequence required for optimal minus-strand rna levels. these data indicate that the pvx 3' ntr contains multiple, overlapping elements that influence accumulation of both minus and plus-strand rna.",1
"defective interfering (di) rnas of tomato bushy stunt virus (tbsv), a plus-sense rna virus, comprise four conserved noncontiguous regions (i through iv) derived from the viral genome. region iii, a 70-nucleotide-long sequence corresponding to a genomic segment located 378 nucleotides upstream of the 3' terminus of the genome, has been found to enhance di rna accumulation by approximately 10-fold in an orientation-independent manner (d. ray and k. a. white, virology 256:162-171, 1999). in this study, a more detailed structure-function analysis of region iii was conducted. rna secondary-structure analyses indicated that region iii contains stem-loop structures in both plus and minus strands. through deletion analyses of a di rna, a primary determinant of region iii activity was mapped to the 5'-proximal 35-nucleotide segment. compensatory-type mutational analyses showed that a stem-loop structure in the minus strand of this subregion was required for enhanced di rna replication. the same stem-loop structure was also found to function in a position-independent manner in a di rna (albeit at reduced levels) and to be important for efficient accumulation within the context of the tbsv genome. taken together, these observations suggest that the 5'-proximal segment of region iii is a modular rna replication element that functions primarily through the formation of an rna hairpin structure in the minus strand.",1
"the epidermal growth factor receptor (egfr) is frequently overexpressed in cancer and is an important therapeutic target. aberrant expression and function of micrornas have been associated with tumorigenesis. bioinformatic predictions suggest that the human egfr mrna 3'-untranslated region contains three microrna-7 (mir-7) target sites, which are not conserved across mammals. we found that mir-7 down-regulates egfr mrna and protein expression in cancer cell lines (lung, breast, and glioblastoma) via two of the three sites, inducing cell cycle arrest and cell death. because mir-7 was shown to decrease egfr mrna expression, we used microarray analysis to identify additional mrna targets of mir-7. these included raf1 and multiple other genes involved in egfr signaling and tumorigenesis. furthermore, mir-7 attenuated activation of protein kinase b (akt) and extracellular signal-regulated kinase 1/2, two critical effectors of egfr signaling, in different cancer cell lines. these data establish an important role for mir-7 in controlling mrna expression and indicate that mir-7 has the ability to coordinately regulate egfr signaling in multiple human cancer cell types.",1
"we have identified a highly conserved rna motif that occurs upstream of genes involved in s-adenosyl-l-methionine (sam) recycling in many gram-positive and gram-negative species of bacteria. the phylogenetic distribution and the conserved structural features of representatives of this motif are indicative of riboswitch function. riboswitches are widespread metabolite-sensing gene control elements that are typically found in the 5' untranslated regions (utrs) of bacterial mrnas. we experimentally verified that examples of this rna motif specifically recognize s-adenosylhomocysteine (sah) in protein-free in vitro assays, and confirmed that these rnas strongly discriminate against sam and other closely related analogs. a representative sah motif was found to activate expression of a downstream gene in vivo when the metabolite is bound. these observations confirm that sah motif rnas are distinct ligand-binding aptamers for a riboswitch class that selectively binds sah and controls genes essential for recycling expended sam coenzymes.",1
"in heart failure (hf), arrhythmogenic spontaneous sarcoplasmic reticulum (sr) ca(2+) release and afterdepolarizations in cardiac myocytes have been linked to abnormally high activity of ryanodine receptors (ryr2s) associated with enhanced phosphorylation of the channel. however, the specific molecular mechanisms underlying ryr2 hyperphosphorylation in hf remain poorly understood. the objective of the current study was to test the hypothesis that the enhanced expression of muscle-specific micrornas (mirnas) underlies the hf-related alterations in ryr2 phosphorylation in ventricular myocytes by targeting phosphatase activity localized to the ryr2. we studied hearts isolated from canines with chronic hf exhibiting increased left ventricular (lv) dimensions and decreased lv contractility. qrt-pcr revealed that the levels of mir-1 and mir-133, the most abundant muscle-specific mirnas, were significantly increased in hf myocytes compared with controls (2- and 1.6-fold, respectively). western blot analyses demonstrated that expression levels of the protein phosphatase 2a (pp2a) catalytic and regulatory subunits, which are putative targets of mir-133 and mir-1, were decreased in hf cells. pp2a catalytic subunit mrnas were validated as targets of mir-133 by using luciferase reporter assays. pharmacological inhibition of phosphatase activity increased the frequency of diastolic ca(2+) waves and afterdepolarizations in control myocytes. the decreased pp2a activity observed in hf was accompanied by enhanced ca(2+)/calmodulin-dependent protein kinase (camkii)-mediated phosphorylation of ryr2 at sites ser-2814 and ser-2030 and increased frequency of diastolic ca(2+) waves and afterdepolarizations in hf myocytes compared with controls. in hf myocytes, camkii inhibitory peptide normalized the frequency of pro-arrhythmic spontaneous diastolic ca(2+) waves. these findings suggest that altered levels of major muscle-specific mirnas contribute to abnormal ryr2 function in hf by depressing phosphatase activity localized to the channel, which in turn, leads to the excessive phosphorylation of ryr2s, abnormal ca(2+) cycling, and increased propensity to arrhythmogenesis.",1
"the rna structure of the 3' untranslated region (utr) of the r2 retrotransposable element is recognized by the r2-encoded reverse transcriptase in a reaction called target primed reverse transcription (tprt). to provide insight into structure-function relationships important for tprt, we have created alignments that reveal the secondary structure for 22 drosophila and five silkmoth 3' utr r2 sequences. in addition, free energy minimization has been used to predict the secondary structure for the 3' utr r2 rna of forficula auricularia. the predicted structures for bombyx mori and f. auricularia are consistent with chemical modification data obtained with beta-ethoxy-alpha-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. the structures appear to have common helices that are likely important for function.",1
"p27(kip1) regulates cell proliferation by binding to and modulating the activity of cyclin-dependent kinases. the cdk inhibitor is haploinsufficient for tumor suppression and reduced p27 activity is fundamental for the development of many human malignancies. consistently, reduced p27 protein provides independent prognostic information in various tumors including breast, prostate, colon and gastric carcinomas. in normal cells, p27 protein increases in growth arrest but also oscillates during cell cycle progression. expression of p27 is regulated through mechanisms including transcription, translation and ubiquitin-mediated degradation. each of these pathways may contribute to deregulation of p27 in hyperproliferative diseases. p27 translation increases in proliferating cells during g(1) phase and declines as cells enter s phase. to investigate the mechanisms of p27 translational control, we analyzed fragments of the p27 transcript for their contribution to cell cycle regulated translation. we found that an element in the p27 5'-utr can render reporter translation cell cycle sensitive with maximal translation in g1-arrested cells. this novel element of 114 nt contains a g/c-rich hairpin domain that is predicted to form multiple stable stemloops and also overlaps with a small upstream orf (uorf). both structures contribute to cell cycle-regulated translation. the uorf can be translated in vitro and its sequence and position are highly conserved in mice and chickens. interestingly, the precise sequence or the length of the uorf-encoded peptide are not important for p27 translation, consistent with the idea that ribosomal recruitment to its initiation codon rather than the translation product itself contributes to the regulation.",1
"human mesenchymal stem cells (hmscs) have self-renewal and differentiation capabilities but the regulatory mechanisms of msc fate determination remain poorly understood. here, we aimed to identify micrornas enriched in hmscs that modulate differentiation commitments. microarray analysis revealed that mir-140-5p is commonly enriched in undifferentiated hmscs from various tissue sources. moreover, bioinformatic analysis and luciferase reporter assay validated that mir-140-5p directly represses bone morphogenic protein 2 (bmp2). furthermore, blocking mir-140-5p in hmscs increased the expression of bmp signaling components and critical regulators of osteogenic differentiation. we propose that mir-140-5p functionally inhibits osteogenic lineage commitment in undifferentiated hmscs.",1
"micrornas (mirnas) are post-transcriptional regulators of gene expression that play important roles in nervous system development and physiology. however, our understanding of the strategies by which mirnas control synapse development is limited. we find that the highly conserved mirna mir-8 regulates the morphology of presynaptic arbors at the drosophila neuromuscular junction (nmj) through a postsynaptic mechanism. developmental analysis shows that mir-8 is required for presynaptic expansion that occurs in response to larval growth of the postsynaptic muscle targets. with an in vivo sensor, we confirm our hypothesis that the founding member of the conserved ena/vasp (enabled/vasodilator activated protein) family is regulated by mir-8 through a conserved site in the ena 3' untranslated region (utr). synaptic marker analysis and localization studies suggest that ena functions within the subsynaptic reticulum (ssr) surrounding presynaptic terminals. transgenic lines that express forms of a conserved mammalian ena ortholog further suggest that this localization and function of postsynaptic ena/vasp family protein is dependent on conserved c-terminal domains known to mediate actin binding and assembly while antagonizing actin-capping proteins. ultrastructural analysis demonstrates that mir-8 is required for ssr morphogenesis. as predicted by our model, we find that ena is both sufficient and necessary to account for mir-8-mediated regulation of ssr architecture, consistent with its localization in this compartment. finally, electrophysiological analysis shows that mir-8 is important for spontaneous neurotransmitter release frequency and quantal content. however, unlike the structural phenotypes, increased expression of ena fails to mimic the functional defects observed in mir-8-null animals. together, these findings suggest that mir-8 limits the expansion of presynaptic terminals during larval synapse development through regulation of postsynaptic actin assembly that is independent of changes in synapse physiology.",1
"transposable elements (tes) account for nearly one-half of the sequence content in the human genome, and de novo germline transposition into regulatory or coding sequences of protein-coding genes can cause heritable disorders. tes are prevalent in and around protein-coding genes, providing an opportunity to impart regulation. computational studies reveal that microrna (mirna) genes and mirna target sites reside within te sequences, but there is little experimental evidence supporting a role for tes in the birth of mirnas, or as platform for gene regulation by mirnas. in this work, we validate mirnas and target sites derived from te families prevalent in the human genome, including the ancient long interspersed nuclear element 2 (line2/l2), mammalian-wide interspersed repeat (mir) retrotransposons and the primate-specific alu family. we show that genes with 3' untranslated region (3' utr) mir elements are enriched for let-7 targets and that these sites are conserved and responsive to let-7 expression. we also demonstrate that 3' utr-embedded alus are a source of mir-24 and mir-122 target sites and that a subset of active genomic alus provide for de novo target site creation. finally, we report that although the creation of mirna genes by alu elements is relatively uncommon relative to their overall genomic abundance, alu-derived mir-1285-1 is efficiently processed from its genomic locus and regulates genes with target sites contained within homologous elements. taken together, our data provide additional evidence for tes as a source for mirnas and mirna target sites, with instances of conservation through the course of mammalian evolution.",1
"background discrete rna structures such as cis-acting replication elements (cre) in the coding region of rna virus genomes create characteristic suppression of synonymous site variability (sssv). different phylogenetic methods have been developed to predict secondary structures in rna viruses, for high-resolution thermodynamic scanning and for detecting sssv. these approaches have been successfully in predicting cis-acting signals in different members of the family picornaviridae and caliciviridae. in order to gain insight into the identification of cis-acting signals in viruses whose mechanisms of replication are currently unknown, we performed a phylogenetic analysis of complete genome sequences from 49 human norovirus (nov) strains. findings the complete coding sequences of nov orf1 were obtained from the ddbj database and aligned. shannon entropy calculations and rnaalifold consensus rna structure prediction identified a discrete, conserved, invariant sequence region with a characteristic aaacg cre motif at positions 240 through 291 of the rna dependant rna polymerase (rdrp) sequence (relative to strain ). this sequence region has a high probability to conform a stem-loop. conclusion a new predicted stem-loop has been identified near the 5' end of the rdrp of human nov genome. this is the same location recently reported for hepatovirus cre stem-loop.",1
"micrornas (mirnas) play pivotal roles in osteoblast differentiation. however, the mechanisms of mirnas regulating osteoblast mineralization still need further investigation. here, we performed mirna profiling and identified that mir-93 was the most significantly downregulated mirna during osteoblast mineralization. overexpression of mir-93 in cultured primary mouse osteoblasts attenuated osteoblast mineralization. expression of the sp7 transcription factor 7 (sp7, osterix), a zinc finger transcription factor and critical regulator of osteoblast mineralization, was found to be inversely correlated with mir-93. then sp7 was confirmed to be a target of mir-93. overexpression of mir-93 in cultured osteoblasts reduced sp7 protein expression without affecting its mrna level. luciferase reporter assay showed that mir-93 directly targeted sp7 by specifically binding to the target coding sequence region (cds) of sp7. experiments such as electrophoretic mobility shift assay (emsa), chromatin immunoprecipitation (chip), and promoter luciferase reporter assay confirmed that sp7 bound to the promoter of mir-93. furthermore, overexpression of sp7 reduced mir-93 transcription, whereas blocking the expression of sp7 promoted mir-93 transcription. our study showed that mir-93 was an important regulator in osteoblast mineralization and mir-93 carried out its function through a novel mir-93/sp7 regulatory feedback loop. our findings provide new insights into the roles of mirnas in osteoblast mineralization.",1
"exosomes, nano-vesicles naturally released from living cells, have been well recognized to play critical roles in mediating cell-to-cell communication. given that diabetic hearts exhibit insufficient angiogenesis, it is significant to test whether diabetic cardiomyocyte-derived exosomes possess any capacity in regulating angiogenesis. in this study, we first observed that both proliferation and migration of mouse cardiac endothelial cells (mcecs) were inhibited when co-cultured with cardiomyocytes isolated from adult goto-kakizaki (gk) rats, a commonly used animal model of type 2 diabetes. however, gk-myocyte-mediated anti-angiogenic effects were negated upon addition of gw4869, an inhibitor of exosome formation/release, into the co-cultures. next, exosomes were purified from the myocyte culture supernatants by differential centrifugation. while exosomes derived from gk myocytes (gk-exosomes) displayed similar size and molecular markers (cd63 and cd81) to those originated from the control wistar rat myocytes (wt-exosomes), their regulatory role in angiogenesis is opposite. we observed that the mcec proliferation, migration and tube-like formation were inhibited by gk-exosomes, but were promoted by wt-exosomes. mechanistically, we found that gk-exosomes encapsulated higher levels of mir-320 and lower levels of mir-126 compared to wt-exosomes. furthermore, gk-exosomes were effectively taken up by mcecs and delivered mir-320. in addition, transportation of mir-320 from myocytes to mcecs could be blocked by gw4869. importantly, the exosomal mir-320 functionally down-regulated its target genes (igf-1, hsp20 and ets2) in recipient mcecs, and overexpression of mir-320 inhibited mcec migration and tube formation. gk exosome-mediated inhibitory effects on angiogenesis were removed by knockdown of mir-320. together, these data indicate that cardiomyocytes exert an anti-angiogenic function in type 2 diabetic rats through exosomal transfer of mir-320 into endothelial cells. thus, our study provides a novel mechanism underlying diabetes mellitus-induced myocardial vascular deficiency which may be caused by secretion of anti-angiogenic exosomes from cardiomyocyes.",1
"expression of the cystic fibrosis transmembrane conductance regulator (cftr) is altered in individuals with the δf508 cftr mutation. we previously reported differential expression of microrna (mirna) in cf airway epithelium; however, the role of mirna in regulation of cftr expression here remains unexplored. in this study, we investigated the role of upregulated mirnas in cftr regulation in vivo in bronchial brushings from individuals homozygous or heterozygous for δf508 cftr, validated our observations in vitro, and assessed the impact of defective chloride ion conductance, genotype, and colonization status on mirna expression. mirna target prediction was performed in silico, and expression of mirna and target genes were measured by quantitative real-time pcr and/or western blotting. overexpression and inhibition studies were performed with pre-mirs or antimirs, respectively, and a luciferase reporter gene was used to elucidate direct mirna-target interactions. mir-145, mir-223, and mir-494 were upregulated in cf versus non-cf bronchial brushings and cell lines; in δf508 cftr homozygotes versus heterozygotes; in subjects positive for p. aeruginosa; and in cells treated with a cftr inhibitor or il-1β. reciprocal downregulation or upregulation of cftr gene and/or protein expression was observed after mirna manipulation and direct mirna-target relationships demonstrated via a reporter system containing a wild type or mutated full-length cftr 3' untranslated region. increased expression of mir-145, mir-223, and mir-494 in vivo in bronchial epithelium of individuals carrying the δf508 cftr mutation correlates with decreased cftr expression. defective cftr function, pseudomonas colonization, and inflammation may affect mirna expression and contribute to the regulation of δf508 cftr.",1
"bcr-abl negative myeloproliferative neoplasms (mpns; polycythemia vera, essential thrombocythemia, primary myelofibrosis) are malignant diseases arising from a multipotent hematopoietic progenitor, frequently altered by jak2 v617f or other jak/stat activating mutations. the thrombopoietin receptor (tpor, mpl) is one of the major dimeric cytokine receptors that use jak2 in the myeloid lineage, and was found to be down-modulated in certain mpn patients. we searched for negative regulators of mpl expression. here we report that mir-28 targets the 3' untranslated (3'utr) region of mpl, inhibiting its translation, as well as other proteins potentially involved in megakaryocyte differentiation, such as e2f6. expression of mir-28 in cd34-derived megakaryocytes inhibited terminal differentiation. mir-28 was found to be overexpressed in platelets of a fraction of mpn patients, while it was expressed at constant low levels in platelets from healthy subjects. constitutive activation of stat5 leading to autonomous growth of hematopoietic cell lines was associated with increased mir-28 expression. we discuss how down-modulating mpl and other targets of mir-28, and of related mir-708 and mir-151, could contribute to mpn pathogenicity.",1
"telomerase is a ribonucleoprotein with an intrinsic telomerase rna (ter) component. within yeasts, ter is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate ters. to better understand the evolution of fungal telomerase, we identified 74 ters from pezizomycotina and taphrinomycotina subphyla, sister clades to budding yeasts. we initially identified ter from neurospora crassa using a novel deep-sequencing-based approach, and homologous ter sequences from available fungal genome databases by computational searches. remarkably, ters from these non-yeast fungi have many attributes in common with vertebrate ters. comparative phylogenetic analysis of highly conserved regions within pezizomycotina ters revealed two core domains nearly identical in secondary structure to the pseudoknot and cr4/5 within vertebrate ters. we then analyzed n. crassa and schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two rna core domains in both systems can reconstitute activity in trans as two separate rna fragments. furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted n. crassa telomerase synthesizes ttaggg repeats with high processivity, a common attribute of vertebrate telomerase. overall, this study reveals the common ancestral cores of vertebrate and fungal ters, and provides insights into the molecular evolution of fungal ter structure and function.",1
"both cell-intrinsic and extrinsic pathways govern axon regeneration, but only a limited number of factors have been identified and it is not clear to what extent axon regeneration is evolutionarily conserved. whether dendrites also regenerate is unknown. here we report that, like the axons of mammalian sensory neurons, the axons of certain drosophila dendritic arborization (da) neurons are capable of substantial regeneration in the periphery but not in the cns, and activating the akt pathway enhances axon regeneration in the cns. moreover, those da neurons capable of axon regeneration also display dendrite regeneration, which is cell type-specific, developmentally regulated, and associated with microtubule polarity reversal. dendrite regeneration is restrained via inhibition of the akt pathway in da neurons by the epithelial cell-derived microrna bantam but is facilitated by cell-autonomous activation of the akt pathway. our study begins to reveal mechanisms for dendrite regeneration, which depends on both extrinsic and intrinsic factors, including the pten-akt pathway that is also important for axon regeneration. we thus established an important new model system--the fly da neuron regeneration model that resembles the mammalian injury model--with which to study and gain novel insights into the regeneration machinery.",1
"in addition to the devastating symptoms of dementia, alzheimer's disease (ad) is characterized by accumulation of the processing products of the amyloid-β (aβ) peptide precursor protein (app). app's non-pathogenic functions include regulating intracellular iron (fe) homeostasis. micrornas are small (~ 20 nucleotides) rna species that instill specificity to the rna-induced silencing complex (risc). in most cases, risc inhibits mrna translation through the 3'-untranslated region (utr) sequence. by contrast, we report a novel activity of mir-346: specifically, that it targets the app mrna 5'-utr to upregulate app translation and aβ production. this upregulation is reduced but not eliminated by knockdown of argonaute 2. the target site for mir-346 overlaps with active sites for an iron-responsive element (ire) and an interleukin-1 (il-1) acute box element. ires interact with iron response protein1 (irp1), an iron-dependent translational repressor. in primary human brain cultures, mir-346 activity required chelation of fe. in addition, mir-346 levels are altered in late-braak stage ad. thus, mir-346 plays a role in upregulation of app in the cns and participates in maintaining app regulation of fe, which is disrupted in late stages of ad. further work will be necessary to integrate other metals, and il-1 into the fe-mir-346 activity network. we, thus, propose a ""fear"" (fe, app, rna) nexus in the app 5'-utr that includes an overlapping mir-346-binding site and the app ire. when a ""healthy fear"" exists, activities of mir-346 and irp/fe interact to maintain app homeostasis. disruption of an element that targets the fear nexus would lead to pathogenic disruption of app translation and protein production.",1
"microrna 520c and 373 (mir-520c and mir-373) have been characterized as oncogenes and play critical roles in cancer cell metastasis. however, the relationship between these two micrornas and matrix metalloproteinases (mmps), which are important in cancer cell metastasis, remains unknown. here, we report new evidence in which mir-520c and mir-373 effects in human fibrosarcoma ht1080 cells are associated with mmp9 activity, and this upregulation of mmp9 is not only at the activity and protein levels, but also at that of its mrna. our experimental data demonstrate that these effects occur not by direct binding to the mmp9 promoter, but by mir-520c and mir-373 directly targeting the 3'-untranslational region (utr) of mrnas of mtor and sirt1 (negative regulators of expression of mmp9 via inactivating the ras/raf/mek/erk signaling pathway and transcription factor nf-κb activity); and thus suppressing translation levels of sirt1 and mtor. moreover, inhibition of key kinases of the ras/raf/mek/erk signaling pathway and western blots for selected proteins further identified mir-520c and mir-373 as activating this signaling pathway and nf-κb. in conclusion, mir-520c and mir-373 increased the expression of mmp9 by directly targeting the 3'-utrs of mrnas of mtor and sirt1 and suppressing their translation; resulting in activation of the ras/raf/mek/erk signaling pathway and nf-κb; and, finally, increasing the mrna, protein, and activity of mmp9 and enhancing cell migration and cell growth in 3d type i collagen gels.",1
"background increasing evidence showed that mirnas serve as modulators of human cancer, either as oncogene or tumor suppressors. cisplatin resistance is the most common cause of chemotherapy failure in gastric cancer (gc). however, the roles of mirnas in cisplatin resistance of gc remain largely unknown. the aim of the study was to identify a novel mirna/gene pathway that regulates the sensitivity of gc cells to cisplatin. methods in this study, we chose mir-223 by qrt-pcr analysis, the most significantly up-regulated mirna in gc, to investigate its formation of ddp-resistant phenotype of gc cells and possible molecular mechanisms. results we found that mir-223 was most significantly up-regulated mirna in ddp-resistant gc cells compared with parental gc cells. besides, its expression was also significantly up-regulated in gc tissues. fbxw7 was identified as the direct and functional target gene of mir-223. overexpression of fbxw7 could mimic the effect of mir-223 down-regulation and silencing of fbxw7 could partially reverse the effect of mir-223 down-regulation on ddp resistance of ddp-resistant gc cells. besides, mir-223 and fbxw7 could affect the g1/s transition of cell cycle by altering some certain cell cycle regulators. furthermore, mir-223 was found to be significantly up-regulated in h. pylori infected tissues and cells, suggesting that h. pylori infection may lead to gc development and ddp resistance. conclusions our findings revealed the roles of mir-223/fbxw7 signaling in the ddp resistance of gc cells and targeting it will be a potential strategic approach for reversing the ddp resistance in human gc.",1
"background mor1 is the main transcript of μ-opioid receptor (mor) gene, which represents a mandatory molecule for the analgesic effects of opioids and plays an important role in the pathology of inflammatory pain. micrornas (mir) are non-coding molecules that primarily modulate gene expression at the post-transcriptional level in various pathophysiological conditions. based on in silico analysis, an exact match to the seed sequence of mir-134 was found in 3'-untranslated region of mor1. given the important roles of mor1 in pain modulation, the purpose of this study is to investigate whether mir-134 can regulate the mor1 following allodynia. methods using freund's adjuvant (cfa)-induced chronic inflammatory pain model, we investigated the expression profiles of mir-134 and mor1 in rat dorsal root ganglia (drg) using quantitative real-time polymerase chain reaction, in situ hybridization and immunohistochemistry, respectively. the relationship of mir-134 and mor1 expressions was analysed by linear regression. luciferase assay was used to examine whether mor1 was the target of mir-134. results our results showed that mir-134 expression level was inversely related to mor1 expression. down-regulation of mir-134 and up-regulation of mor1 in the same tissues after inflammatory pain were observed. functional experiments showed that mor1 expression in sh-sy5y cells was up-regulated after inhibition of mir-134, indicating that mor1 was a target of mir-134. conclusions our present data suggested a model that mir-134 participated in cfa-induced inflammatory pain by balancing the expression of mor1 in drgs, which implied that mir-134 may be a potential therapeutic target for the treatment of neuropathic pain including inflammation.",1
"brain-derived neurotrophic factor (bdnf) is a secreted protein of the neurotrophin family that regulates brain development, synaptogenesis, memory and learning, as well as development of peripheral organs, such as angiogenesis in the heart and postnatal growth and repair of skeletal muscle. however, while precise regulation of bdnf levels is an important determinant in defining the biological outcome, the role of micrornas (mirs) in modulating bdnf expression has not been extensively analyzed. using in silico approaches, reporter systems, and analysis of endogenous bdnf, we show that mir-1, mir-10b, mir-155, and mir-191 directly repress bdnf through binding to their predicted sites in bdnf 3'utr. we find that the overexpression of mir-1 and mir-10b suppresses endogenous bdnf protein levels and that silencing endogenous mir-10b increases bdnf mrna and protein levels. furthermore, we show that mir-1/206 binding sites within bdnf 3'utr are used in differentiated myotubes but not in undifferentiated myoblasts. finally, our data from two cell lines suggest that endogenous mir-1/206 and mir-10 family mirs act cooperatively in suppressing bdnf through their predicted sites in bdnf 3'utr. in conclusion, our results highlight mir-1, mir-10b, mir-155, and mir-191 as novel regulators of bdnf long and short 3'utr isoforms, supporting future research in different physiological and pathological contexts.",1
"the flavivirus genome is a positive-stranded approximately 11-kb rna including 5' and 3' noncoding regions (ncr) of approximately 100 and 400 to 600 nucleotides (nt), respectively. the 3' ncr contains adjacent, thermodynamically stable, conserved short and long stem-and-loop structures (the 3'-sl), formed by the 3'-terminal approximately 100 nt. the nucleotide sequences within the 3'-sl are not well conserved among species. we examined the requirement for the 3'-sl in the context of dengue virus type 2 (den2) replication by mutagenesis of an infectious cdna copy of a den2 genome. genomic full-length rna was transcribed in vitro and used to transfect monkey kidney cells. a substitution mutation, in which the 3'-terminal 93 nt constituting the wild-type (wt) den2 3'-sl sequence were replaced by the 96-nt sequence of the west nile virus (wn) 3'-sl, was sublethal for virus replication. an analysis of the growth phenotypes of additional mutant viruses derived from rnas containing den2-wn chimeric 3'-sl structures suggested that the wt den2 nucleotide sequence forming the bottom half of the long stem and loop in the 3'-sl was required for viability. one 7-bp substitution mutation in this domain resulted in a mutant virus that grew well in monkey kidney cells but was severely restricted in cultured mosquito cells. in contrast, transpositions of and/or substitutions in the wt den2 nucleotide sequence in the top half of the long stem and in the short stem and loop were relatively well tolerated, provided the stem-loop secondary structure was conserved.",1
"x chromosome inactivation (xci) in female placental mammals is a vital mechanism for dosage compensation between x-linked and autosomal genes. xci starts with activation of xist and silencing of the negative regulator tsix, followed by cis spreading of xist rna over the future inactive x chromosome (xi). here, we show that xci does not require physical contact between the two x chromosomes (x-pairing) but is regulated by trans-acting diffusible factors. we found that the x-encoded trans-acting and dose-dependent xci-activator rnf12 acts in concert with the cis-regulatory region containing jpx, ftx, and xpr to activate xist and to overcome repression by tsix. rnf12 acts at two subsequent steps; two active copies of rnf12 drive initiation of xci, and one copy needs to remain active to maintain xci toward establishment of the xi. this two-step mechanism ensures that xci is very robust and fine-tuned, preventing xci of both x chromosomes.",1
"the peroxisome proliferators-activated receptor (ppar)γ pathway is involved in cancer, but it appears to have both tumor suppressor and oncogenic functions. in neuroblastoma cells, mir-27b targets the 3' untranslated region of pparγ and inhibits its mrna and protein expression. mir-27b overexpression or pparγ inhibition blocks cell growth in vitro and tumor growth in mouse xenografts. pparγ activates expression of the ph regulator nhe1, which is associated with tumor progression. lastly, mir-27b through pparγ regulates nuclear factor-κb activity and transcription of inflammatory target genes. thus, in neuroblastoma, mir-27b functions as a tumor suppressor by inhibiting the tumor-promoting function of pparγ, which triggers an increased inflammatory response. in contrast, in breast cancer cells, pparγ inhibits nhe1 expression and the inflammatory response, and it functions as a tumor suppressor. we suggest that the ability of pparγ to promote or suppress tumor formation is linked to cell type-specific differences in regulation of nhe1 and other target genes.",1
"skeletal myoblast fusion in vitro requires the expression of connexin43 (cx43) gap junction channels. however, gap junctions are rapidly downregulated after the initiation of myoblast fusion in vitro and in vivo. in this study we show that this downregulation is accomplished by two related micrornas, mir-206 and mir-1, that inhibit the expression of cx43 protein during myoblast differentiation without altering cx43 mrna levels. cx43 mrna contains two binding sites for mir-206/mir-1 in its 3'-untranslated region, both of which are required for efficient downregulation. while it has been demonstrated before that mir-1 is involved in myogenesis, in this work we show that mir-206 is also upregulated during perinatal skeletal muscle development in mice in vivo and that both mir-1 and mir-206 downregulate cx43 expression during myoblast fusion in vitro. proper development of singly innervated muscle fibers requires muscle contraction and nmj terminal selection and it is hypothesized that prolonged electrical coupling via gap junctions may be detrimental to this process. this work details the mechanism by which initial downregulation of cx43 occurs during myogenesis and highlights the tight control mechanisms that are utilized for the regulation of gap junctions during differentiation and development.",1
"in addition to establishing dendritic coverage of the receptive field, neurons need to adjust their dendritic arbors to match changes of the receptive field. here, we show that dendrite arborization (da) sensory neurons establish dendritic coverage of the body wall early in drosophila larval development and then grow in precise proportion to their substrate, the underlying body wall epithelium, as the larva more than triples in length. this phenomenon, referred to as scaling growth of dendrites, requires the function of the microrna (mirna) bantam (ban) in the epithelial cells rather than the da neurons themselves. we further show that ban in epithelial cells dampens akt kinase activity in adjacent neurons to influence dendrite growth. this signaling between epithelial cells and neurons receiving sensory input from the body wall synchronizes their growth to ensure proper dendritic coverage of the receptive field.",1
"development of the vascular disease pulmonary hypertension (ph) involves disparate molecular pathways that span multiple cell types. micrornas (mirnas) may coordinately regulate ph progression, but the integrative functions of mirnas in this process have been challenging to define with conventional approaches. here, analysis of the molecular network architecture specific to ph predicted that the mir-130/301 family is a master regulator of cellular proliferation in ph via regulation of subordinate mirna pathways with unexpected connections to one another. in validation of this model, diseased pulmonary vessels and plasma from mammalian models and human ph subjects exhibited upregulation of mir-130/301 expression. evaluation of pulmonary arterial endothelial cells and smooth muscle cells revealed that mir-130/301 targeted pparγ with distinct consequences. in endothelial cells, mir-130/301 modulated apelin-mir-424/503-fgf2 signaling, while in smooth muscle cells, mir-130/301 modulated stat3-mir-204 signaling to promote ph-associated phenotypes. in murine models, induction of mir-130/301 promoted pathogenic ph-associated effects, while mir-130/301 inhibition prevented ph pathogenesis. together, these results provide insight into the systems-level regulation of mirna-disease gene networks in ph with broad implications for mirna-based therapeutics in this disease. furthermore, these findings provide critical validation for the evolving application of network theory to the discovery of the mirna-based origins of ph and other diseases.",1
"we aimed to analyse the relative abundance of mir-505 in age-related macular degeneration (amd) and elucidate its underlying mechanisms. relative expression of mir-505 was analysed by real-time polymerase chain reaction (pcr). macrophage polarization was characterized by measurement of molecular markers including ym-1, arg-1, tnf-α and inos via both real-time pcr and western blot. vascular endothelial growth factor (vegf) content was determined by enzyme-linked immunosorbent assay. choroidal neovascularization (cnv) formation was evaluated by choroidal flat mount technique. the regulatory action of mir-505-5p on 3'utr of transmembrane protein 229b (tmem229b) was interrogated by luciferase reporter assay. mir-505 was aberrantly upregulated in both amd and laser-induced choroidal neovascularization mouse model. administration with mir-505 specific inhibitor suppressed m2 polarization in cnv mice as indicated by decreasing both ym-1 and arg-1. meanwhile, vegf expression and cnv formation were greatly suppressed by mir-505 inhibition as well. the similar phenotype was consolidated in prostaglandin e2 (pge2)-stimulated bone marrow-derived macrophages. at the molecular level, mir-505-5p directly targeted and negatively regulated tmem229b expression, while forced ectopic expression of tmem229b significantly rescued mir-505-imposed m2 polarization. our data have uncovered the critical contribution of mir-505 in amd, which is predominantly mediated by downregulation of tmem229b.",1
"lineage progression in osteoblasts and chondrocytes is stringently controlled by the cell-fate-determining transcription factor runx2. in this study, we directly addressed whether micrornas (mirnas) can control the osteogenic activity of runx2 and affect osteoblast maturation. a panel of 11 runx2-targeting mirnas (mir-23a, mir-30c, mir-34c, mir-133a, mir-135a, mir-137, mir-204, mir-205, mir-217, mir-218, and mir-338) is expressed in a lineage-related pattern in mesenchymal cell types. during both osteogenic and chondrogenic differentiation, these mirnas, in general, are inversely expressed relative to runx2. based on 3'utr luciferase reporter, immunoblot, and mrna stability assays, each mirna directly attenuates runx2 protein accumulation. runx2-targeting mirnas differentially inhibit runx2 protein expression in osteoblasts and chondrocytes and display different efficacies. thus, cellular context contributes to mirna-mediated regulation of runx2. all runx2-targeting mirnas (except mir-218) significantly impede osteoblast differentiation, and their effects can be reversed by the corresponding anti-mirnas. these findings demonstrate that osteoblastogenesis is limited by an elaborate network of functionally tested mirnas that directly target the osteogenic master regulator runx2.",1
"novel strategies against treatment-resistant tumor cells remain a challenging but promising therapeutic approach. despite accumulated evidence suggesting the presence of highly malignant cell populations within tumors, the unsolved issues such as in vivo targeting and clinical relevance remain. here, we report a preclinical trial based on the identified molecular mechanisms underlying osteosarcoma-initiating cells and their clinical relevance. we identified key micrornas (mirnas) that were deregulated in a highly malignant cd133(high) population and found that mir-133a regulated the cell invasion that characterizes a lethal tumor phenotype. silencing of mir-133a with locked nucleic acid (lna) reduced cell invasion of this cell population, and systemic administration of lna along with chemotherapy suppressed lung metastasis and prolonged the survival of osteosarcoma-bearing mice. furthermore, in a clinical study, high expression levels of cd133 and mir-133a were significantly correlated with poor prognosis, whereas high expression levels of the four mir-133a target genes were correlated with good prognosis. overall, silencing of mir-133a with concurrent chemotherapy would represent a novel strategy that targets multiple regulatory pathways associated with metastasis of the malignant cell population within osteosarcoma.",1
"lung surfactant secretion is a highly regulated process. our previous studies have shown that vamp-2 is essential for surfactant secretion. in the present study we investigated the role of mir-206 in surfactant secretion through vamp-2. vamp-2 was confirmed to be a target of mir-206 by 3'-untranslational region (3'-utr) luciferase assay. mutations in the predicated mir-206 binding sites reduced the binding of mir-206 to the 3'-utr of vamp-2. mir-206 decreased the expression of vamp-2 protein and decreased the lung surfactant secretion in alveolar type ii cells. in conclusion, mir-206 regulates lung surfactant secretion by limiting the availability of vamp-2 protein.",1
"the purposes of this study were to determine the expression profile of raf kinase inhibitor protein (rkip) in human gastric cancer cells and its effect on the biological characteristics of sgc-7901 cell lines, to examine the modulatory effect of microrna-224 (mir-224) on rkip. the research will provide novel strategies for gastric cancer treatment in the future. quantitative real-time reverse transcription pcr (qrt-pcr) was employed to determine the expression profile of rkip in gastric cancer cell lines (sgc-7901, mgc80-3, and mkn45). a eukaryotic expression vector, pcdna3.1-rkip, was constructed and transfected into sgc-7901 cells. changes in rkip protein expression were examined by western blot assays, and the effect of rkip overexpression on scg-7901 cell viability was determined by 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-diphenytetrazoliumromide (mtt) assays. the effect of rkip overexpression on sgc-7901 cell proliferation and apoptosis was analyzed by flow cytometry and that on the migration of sgc-7901 cells was investigated by transwell migration assays. rkip was identified to be a regulatory target gene of mir-224 using a luciferase reporter gene system, and the effect of mir-224 on intracellular rkip protein expression was examined by western blot assays. the regulatory effect of mir-224 on the biological characteristics of rkip was investigated by mtt, flow cytometry, and transwell invasion chamber assays. the expression of rkip in gastric cancer cells was decreased significantly in comparison to that of normal gastric mucosal epithelial cells (ges-1) (p < 0.01), as demonstrated by qrt-pcr assays. compared with the control group, the up-regulation of rkip intracellular expression was observed in sgc-7901 cells after transfection of pcdna3.1-rkip for 48 h (p < 0.01). there were significant decreases in cell viability and the s-phase fraction (p < 0.05), concomitant with a significant increase in apoptosis (p < 0.01), as well as a significant reduction in cells migrating through transwell chambers (p < 0.05), as shown by mtt, flow cytometry, and transwell invasion chamber assays. a significant decrease in luciferase activities in cells transfected with a mir-224 mimic was observed compared with that of the control group (p < 0.05), as suggested by the luciferase reporter gene system. as shown by western blot assays, there was a significant decrease in rkip expression in sgc-7901 cells transfected with the mir-224 mimic for 48 h compared with the control group (p < 0.05). as shown by mtt, flow cytometry, and transwell invasion chamber assays, the changes in biological characteristics induced by rkip overexpression could be suppressed in sgc-7901 cells after transfection of the mir-224 mimic. in conclusion, the down-regulation of rkip expression was observed in human gastric cell lines, and mir-224 could negatively regulate the expression and biological characteristics of rkip, contributing to suppress the proliferation and invasion of gastric cells.",1
"bacterial small rnas perform numerous regulatory roles, including acting as antitoxic components in toxin-antitoxin systems. in type iii toxin-antitoxin systems, small processed rnas directly antagonize their toxin protein partners, and in the systems characterized the toxin and antitoxin components together form a trimeric assembly. in the present study, we sought to define how the rna antitoxin, toxi, inhibits its potentially lethal protein partner, toxn. we show through cross-inhibition experiments with the toxin systems from pectobacterium atrosepticum (toxin(pa)) and bacillus thuringiensis (toxin(bt)) that toxi rnas are highly selective enzyme inhibitors. both systems have an ""addictive"" plasmid maintenance phenotype. we demonstrate that toxi(pa) can inhibit toxn(pa) in vitro both in its processed form and as a repetitive precursor rna, and this inhibition is linked to the self-assembly of the trimeric complex. inhibition and self-assembly are both mediated entirely by the toxi(pa) rna, with no requirement for cellular factors or exogenous energy. finally, we explain the origins of toxi antitoxin selectivity through our crystal structure of the toxin(bt) complex. our results show how a processed rna pseudoknot can inhibit a deleterious protein with exquisite molecular specificity and how these self-contained and addictive rna-protein pairs can confer different adaptive benefits in their bacterial hosts.",1
"metazoan replication-dependent histone mrnas are not polyadenylated, and instead terminate in a conserved stem-loop structure generated by an endonucleolytic cleavage involving the u7 snrnp, which interacts with histone pre-mrnas through base-pairing between u7 snrna and a purine-rich sequence in the pre-mrna located downstream of the cleavage site. here we generate null mutations of the single drosophila u7 gene and demonstrate that u7 snrna is required in vivo for processing all replication-associated histone pre-mrnas. mutation of u7 results in the production of poly a+ histone mrna in both proliferating and endocycling cells because of read-through to cryptic polyadenylation sites found downstream of each drosophila histone gene. a similar molecular phenotype also results from mutation of slbp, which encodes the protein that binds the histone mrna 3' stem-loop. u7 null mutants develop into sterile males and females, and these females display defects during oogenesis similar to germ line clones of slbp null cells. in contrast to u7 mutants, slbp null mutations cause lethality. this may reflect a later onset of the histone pre-mrna processing defect in u7 mutants compared to slbp mutants, due to maternal stores of u7 snrna. a double mutant combination of a viable, hypomorphic slbp allele and a viable u7 null allele is lethal, and these double mutants express polyadenylated histone mrnas earlier in development than either single mutant. these data suggest that slbp and u7 snrnp cooperate in the production of histone mrna in vivo, and that disruption of histone pre-mrna processing is detrimental to development.",1
"recent studies have suggested that mir-590 may play critical roles in cardiovascular disease. this study was designed to determine the effects of mir-590 on lipoprotein lipase (lpl) expression and development of atherosclerosis in apolipoprotein e knockout (apoe-/-) mice and explore the potential mechanisms. en face analysis of the whole aorta revealed that mir-590 significantly decreased aortic atherosclerotic plaque size and lipid content in apoe-/- mice. double immunofluorescence staining in cross-sections of the proximal aorta showed that mir-590 agomir reduced cd68 and lpl expression in macrophages in atherosclerotic lesions. mir-590 agomir down-regulated lpl mrna and protein expression as analyzed by rt-qpcr and western blotting analyses, respectively. consistently, mir-590 decreased the expression of cd36 and scavenger receptor a1 (sra1) mrna and protein. high-performance liquid chromatography (hplc)analysis confirmed that treatment with mir-590 agomir reduced lipid levels either in plasma orinabdominal cavity macrophages of apoe-/- mice. elisa analysis showed that mir-590 agomir decreased plasma levels of pro-inflammatory cytokines, such as tumor necrosis factor-alpha (tnf-α), monocyte chemotactic protein-1 (mcp-1), interleukin-1β (il-1β)and interleukin-6 (il-6). in contrast, treatment with mir-590 antagomir prevented or reversed these effects. taken together, these results reveal a novel mechanism of mir-590 effects, and may provide new insights into the development of strategies for attenuating lipid accumulation and pro-inflammatory cytokine secretion.",1
"rationale many processes in endothelial cells including angiogenic responses are regulated by micrornas. however, there is limited information available about their complex cross-talk in regulating certain endothelial functions. aim the objective of this study is to identify endothelial functions of the pro-hypertrophic mir-212/132 cluster and its cross-talk with other micrornas during development and disease. methods and results we here show that anti-angiogenic stimulation by transforming growth factor-beta activates the microrna-212/132 cluster by derepression of their transcriptional co-activator camp response element-binding protein (creb)-binding protein (cbp) which is a novel target of a previously identified pro-angiogenic mirna mir-30a-3p in endothelial cells. surprisingly, despite having the same seed-sequence, mir-212 and mir-132 exerted differential effects on endothelial transcriptome regulation and cellular functions with stronger endothelial inhibitory effects caused by mir-212. these differences could be attributed to additional auxiliary binding of mir-212 to its targets. in vivo, deletion of the mir-212/132 cluster increased endothelial vasodilatory function, improved angiogenic responses during postnatal development and in adult mice. conclusion our results identify (i) a novel mirna-cross-talk involving mir-30a-3p and mir-212, which led to suppression of important endothelial genes such as gab1 and sirt1 finally culminating in impaired endothelial function; and (ii) micrornas may have different biological roles despite having the same seed sequence.",1
"aims atp-binding cassette transporter a1 (abca1) mediates the efflux of cholesterol and phospholipids to lipid-poor apolipoproteins, which then form nascent hdl, a key step in the mechanism of reverse cholesterol transport (rct). while a series of micrornas (mirnas) have been identified as potent post-transcriptional regulators of lipid metabolism, their effects on abca1 function and associated mechanisms remain unclear. methods and results abca1 was identified as a potential target of mir-144-3p, based on the results of bioinformatic analysis and the luciferase reporter assay, and downregulated after transfection of cells with mir-144-3p mimics, as observed with real-time pcr and western blot. moreover, mir-144-3p mimics (agomir) enhanced the expression of inflammatory factors, including il-1β, il-6 and tnf-α, in vivo and in vitro, inhibited cholesterol efflux in thp-1 macrophage-derived foam cells, decreased hdl-c circulation and impaired rct in vivo, resulting in accelerated pathological progression of atherosclerosis in apoe-/- mice. clinical studies additionally revealed a positive correlation of circulating mir-144-3p with serum ck, ck-mb, ldh and ast in subjects with ami. conclusions our findings clearly indicate that mir-144-3p is essential for the regulation of cholesterol homeostasis and inflammatory reactions, supporting its utility as a potential therapeutic target of atherosclerosis and a promising diagnostic biomarker of ami.",1
": circadian clocks drive rhythmic physiology and behavior to allow adaption to daily environmental changes. in drosophila , the small ventral lateral neurons (slnvs) are primary pacemakers that control circadian rhythms. circadian changes are observed in the dorsal axonal projections of the slnvs, but their physiological importance and the underlying mechanism are unclear. here, we identified mir-263b as an important regulator of circadian rhythms and structural plasticity of slnvs in drosophila . depletion of mir-263b ( mir-263b ko ) in flies dramatically impaired locomotor rhythms under constant darkness. indeed, mir-263b is required for the structural plasticity of slnvs. mir-263b regulates circadian rhythms through inhibition of expression of the lim-only protein beadex (bx). consistently, overexpression of bx or loss-of-function mutation ( bx hdpr26 ) phenocopied mir-263b ko and mir-263b overexpression in behavior and molecular characteristics. in addition, mutating the mir-263b binding sites in the bx 3' utr using crispr/cas9 recapitulated the circadian phenotypes of mir-263b ko flies. together, these results establish mir-263b as an important regulator of circadian locomotor behavior and structural plasticity.",1
"the role of the microrna mir-93-5p on the secretome profile and the expression levels of vascular endothelial growth factor (vegf) and interleukin-8 (il-8) was investigated in the neuroblastoma sk-n-as cell line by bio-plex analysis and rt-qpcr. the results indicate that vegf and il-8 are the major mir-93-5p molecular targets. this conclusion was based on in vitro transfection with pre-mir-93-5p and anti-mir-93-5p; these treatments inversely modulated both vegf and il-8 gene expression and protein release in the neuroblastoma sk-n-as cell line. computational analysis showed the presence of mir-93-5p consensus sequences in the 3'utr region of both vegf and il-8 mrnas, predicting possible interaction with mir-93-5p and confirming a potential regulatory role of this microrna.",1
"mir-33 is an intronic microrna within the gene encoding the srebp2 transcription factor. like its host gene, mir-33 has been shown to be an important regulator of lipid metabolism. inhibition of mir-33 has been shown to promote cholesterol efflux in macrophages by targeting the cholesterol transporter abca1, thus reducing atherosclerotic plaque burden. inhibition of mir-33 has also been shown to improve high-density lipoprotein (hdl) biogenesis in the liver and increase circulating hdl-c levels in both rodents and nonhuman primates. however, evaluating the extent to which these changes in hdl metabolism contribute to atherogenesis has been hindered by the obesity and metabolic dysfunction observed in whole-body mir-33-knockout mice. to determine the impact of hepatic mir-33 deficiency on obesity, metabolic function, and atherosclerosis, we have generated a conditional knockout mouse model that lacks mir-33 only in the liver. characterization of this model demonstrates that loss of mir-33 in the liver does not lead to increased body weight or adiposity. hepatic mir-33 deficiency actually improves regulation of glucose homeostasis and impedes the development of fibrosis and inflammation. we further demonstrate that hepatic mir-33 deficiency increases circulating hdl-c levels and reverse cholesterol transport capacity in mice fed a chow diet, but these changes are not sufficient to reduce atherosclerotic plaque size under hyperlipidemic conditions. by elucidating the role of mir-33 in the liver and the impact of hepatic mir-33 deficiency on obesity and atherosclerosis, this work will help inform ongoing efforts to develop novel targeted therapies against cardiometabolic diseases.",1
"objective diabetes mellitus accelerates proatherogenic and proinflammatory phenotype of vascular smooth muscle cell (vsmc) associated with vascular complications. evidence shows that micrornas (mirnas) play key roles in vsmc functions, but their role under diabetic conditions is unclear. we profiled mirnas in vsmc from diabetic mice and examined their role in vsmc dysfunction. approach and results high throughput small rna-sequencing identified 135 differentially expressed mirnas in vsmc from type 2 diabetic db/db mice (db/dbvsmc) versus nondiabetic db/+ mice. several of these mirnas were known to regulate vsmc functions. we further focused on mir-504, because it was highly upregulated in db/dbvsmc, and its function in vsmc is unknown. mir-504 and its host gene fgf13 were significantly increased in db/dbvsmc and in aortas from db/db mice. bioinformatics analysis predicted that mir-504 targets including signaling adaptor grb10 and transcription factor egr2 could regulate growth factor signaling. we experimentally validated grb10 and egr2 as novel targets of mir-504. overexpression of mir-504 in vsmc inhibited contractile genes and enhanced extracellular signal-regulated kinase 1/2 activation, proliferation, and migration. these effects were blocked by mir-504 inhibitors. grb10 knockdown mimicked mir-504 functions and increased inflammatory genes. egr2 knockdown-inhibited anti-inflammatory socs1 and increased proinflammatory genes. furthermore, high glucose and palmitic acid upregulated mir-504 and inflammatory genes, but downregulated grb10. conclusions diabetes mellitus misregulates several mirnas including mir-504 that can promote vsmc dysfunction. because changes in many of these mirnas are sustained in diabetic vsmc even after in vitro culture, they may be involved in metabolic memory of vascular complications. targeting such mechanisms could offer novel therapeutic strategies for diabetic complications.",1
"dosage compensation modifies the chromatin of x-linked genes to assure equivalent expression in sexes with unequal x chromosome dosage. in drosophila dosage compensation is achieved by increasing expression from the male x chromosome. the ribonucleoprotein dosage compensation complex (dcc) binds hundreds of sites along the x chromosome and modifies chromatin to facilitate transcription. loss of rox rna, an essential component of the dcc, reduces expression from x-linked genes. surprisingly, loss of rox rna also reduces expression from genes situated in proximal heterochromatin and on the small, heterochromatic fourth chromosome. mutation of some, but not all, of the genes encoding dcc proteins produces a similar effect. reduction of rox function suppresses position effect variegation (pev), revealing functional alteration in heterochromatin. the effects of rox mutations on heterochromatic gene expression and pev are limited to males. a sex-limited role for the rox rnas in autosomal gene expression was unexpected. we propose that this reflects a difference in the heterochromatin of males and females, which serves to accommodate the heterochromatic y chromosome present in the male nucleus. rox transcripts may thus participate in two distinct regulatory systems that have evolved in response to highly differentiated sex chromosomes: compensation of x-linked gene dosage and modulation of heterochromatin.",1
"the insulin receptor substrate-1 (irs-1), a docking protein for both the type 1 insulin-like growth factor receptor (igf-ir) and the insulin receptor, is known to send a mitogenic, anti-apoptotic, and anti-differentiation signal. several micro rnas (mirs) are suggested by the data base as possible candidates for targeting irs-1. we show here that one of the mirs predicted by the data base, mir145, whether transfected as a synthetic oligonucleotide or expressed from a plasmid, causes down-regulation of irs-1 in human colon cancer cells. irs-1 mrna is not decreased by mir145, while it is down-regulated by an sirna targeting irs-1. targeting of the irs-1 3'-untranslated region (utr) by mir145 was confirmed using a reporter gene (luciferase) expressing the mir145 binding sites of the irs-1 3'-utr. in agreement with the role of irs-1 in cell proliferation, we show that treatment of human colon cancer cells with mir145 causes growth arrest comparable to the use of an sirna against irs-1. taken together, these results identify mir145 as a micro rna that down-regulates the irs-1 protein, and inhibits the growth of human cancer cells.",1
"we have cloned and sequenced the yeast snr19 gene and show here that snr19 is the yeast homolog of metazoan u1 snrna. sn r19 is 569 nucleotides long, strikingly larger than its metazoan counterpart. the two molecules resemble each other closely in the predicted secondary structure of their first 50 nucleotides. primary sequence homology is restricted to some of their single-stranded regions, including 11 consecutive nucleotides at the 5' end of the two molecules, the region that interacts with pre-mrna 5' splice junctions. snr19 is spliceosome-associated and required for in vitro pre-mrna splicing. we also note that 8 sequences in snr19 have extensive complementarity to snr20, the large yeast u2 rna, suggesting that yeast u1 may interact with yeast u2 by base-pairing.",1
"cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local rna secondary structure. these structures are expected to be significantly more ordered than those anticipated at random because of evolutionary constraints and intrinsic structural properties. in this study, we introduce a computing method to calculate two quantitative measures, nrd and stscr, for estimating the uniqueness of an rna secondary structure. nrd is a normalized score based on evaluating how different a natural rna structure is from those predicted for its randomly shuffled variants. the lower the score nrd the more well ordered is the natural rna structure. the statistical significance of nrd compared with that computed from structural comparisons among large numbers of randomly permuted sequences is represented by a standardized score, stscr: we tested the method on the trans-activation response element and rev response element of hiv-1 mrna, internal ribosome entry sequence of hepatitis c virus, tetrahymena thermophila rrna intron, 100 trnas and 14 rnase p rnas. our data indicate that functional rna structures have high stscr, while other structures have low stscr. we conclude that rna functional molecules and/or cis-acting elements with structure dependent functions possess well ordered conformations and they are uniquely folded as measured by this technique.",1
"micrornas (mirnas), a class of short non-coding rnas that regulate the expression of mrna targets, are important regulators of cellular senescence and aging. we questioned which mirnas are involved in age-related degeneration of the organ of corti (oc), the auditory sensory epithelium that transduces mechanical stimuli to electrical activity in the inner ear. degeneration of the oc is generally accepted as the main cause of age-related hearing loss (arhl), a progressive loss of hearing in individuals as they grow older. to determine which mirnas are involved in the onset and progression of arhl, mirna gene expression in the oc of two mouse strains, c57bl/6j and cba/j, was compared at three different ages using genechip mirna microarray and was validated by real-time pcr. we showed that 111 and 71 mirnas exhibited differential expression in the c57 and cba mice, respectively, and that downregulated mirnas substantially outnumbered upregulated mirnas during aging. mirnas that had approximately 2-fold upregulation included members of mir-29 family and mir-34 family, which are known regulators of pro-apoptotic pathways. in contrast, mirnas that were downregulated by about 2-fold were members of the mir-181 family and mir-183 family, which are known to be important for proliferation and differentiation, respectively. the shift of mirna expression favoring apoptosis occurred earlier than detectable hearing threshold elevation and hair cell loss. our study suggests that changes in mirna expression precede morphological and functional changes, and that upregulation of pro-apoptotic mirnas and downregulation of mirnas promoting proliferation and differentiation are both involved in age-related degeneration of the oc.",1
"purpose to investigate the role of mir-29b on the changes in expression of genes involved in the synthesis and deposition of extracellular matrix (ecm) induced by chronic oxidative stress in human trabecular meshwork cells (htm). methods changes in gene expression induced by mir-29b in htm cells were evaluated by gene array analysis using affymetrix u133a2 arrays and confirmed by quantitative-pcr. pathway analysis was conducted using metacore. targeting of mir-29b to the 3'-untranslated region of three novel putative targets was evaluated using the psicheck luciferase system. chronic oxidative stress was induced by incubation at 40% oxygen for 4-5 days, using cultures incubated at 5% oxygen as controls. changes in expression in microrna or gene expression were analyzed by q-pcr. cell viability was measured by lactate dehydrogenase release. results transfection of htm cells with mir-29b mimic resulted in downregulation of multiple ecm components, including collagens (col1a1, col1a2, col4a1, col5a1, col5a2, col3a1) lamc1, and fbn as well as several genes involved in ecm deposition and remodeling, such as sparc/osteonectin. three additional genes, bmp1, adam12, and nkiras2, were identified as direct targets of mir-29b. chronic oxidative stress induced a significant downregulation of mir-29b in two htm cell lines that was associated with increased expression of several ecm genes known to be regulated by mir-29b. the increase in expression of these genes was inhibited by transfection with mir-29b mimic. mir-29b increased cell viability under both chronic oxidative stress and physiologic oxygen concentrations. conclusions mir-29b negatively regulates the expression of multiple genes involved in the synthesis and deposition of ecm in trabecular meshwork (tm) cells. downregulation of mir-29b might contribute to increased expression of several ecm genes under chronic oxidative stress conditions. the balance between the activation of ecm production induced by oxidative stress and the protective effects of mir-29b could be a relevant factor in understanding how oxidative damage may lead to increased deposition of ecm in the tm and contribute to the elevation of intra-ocular pressure in glaucoma.",1
"structured noncoding rnas (ncrnas) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. few ncrna classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. we previously developed a computational pipeline that enables the near-comprehensive identification of structured ncrnas expressed from individual bacterial genomes. the regions between protein coding genes are first sorted based on length and the fraction of guanosine and cytidine nucleotides. long, gc-rich intergenic regions are then examined for sequence and structural similarity to other bacterial genomes. herein, we describe the implementation of this pipeline on 50 bacterial genomes from varied phyla. more than 4700 candidate intergenic regions with the desired characteristics were identified, which yielded 44 novel riboswitch candidates and numerous other putative ncrna motifs. although experimental validation studies have yet to be conducted, this rate of riboswitch candidate discovery is consistent with predictions that many hundreds of novel riboswitch classes remain to be discovered among the bacterial species whose genomes have already been sequenced. thus, many thousands of additional novel ncrna classes likely remain to be discovered in the bacterial domain of life.",1
"background although few micrornas (mirnas) have been involved in the regulation of post-ischemic cardiac fibrosis, the exact effect and underlying mechanism of mirnas in cardiac fibrosis remains unclear. here, we sought to investigate whether microrna-34 (mir-34) plays a role in the pathogenic development of myocardial fibrosis. methods the myocardial infarction (mi) mice model was induced and cardiac fibroblasts were cultured. histological analyses, quantitative real-time polymerase chain reaction and western blotting analysis were used. results we found that the mir-34 cluster, especially mir-34a, was upregulated in the mi heart. in vivo, inhibition of mir-34a reduces the severity of experimental cardiac fibrosis in mice. tgf-β1 increased mir-34a expression in cardiac fibroblasts. overexpressing mir-34a levels increased the profibrogenic activity of tgf-β1 in cardiac fibroblast, whereas inhibition mir-34a levels weakened the activity. finally, we showed that mir-34a's underlying mechanism during cardiac fibrosis occurs through the targeting of smad4 expression. conclusions our findings provide evidence that mir-34a plays a critical role in the progression of cardiac tissue fibrosis by directly targeting smad4, which suggests that mir-34a may be new marker for cardiac fibrosis progression and that inhibition of mir-34a may be a promising strategy in the treatment of cardiac fibrosis.",1
"mir-181c is a newly identified negative regulator of immune cell activation. in this study, we aimed to investigate the expression and functional role of mir-181c in myasthenia gravis (mg). mir-181c showed significant downregulation in peripheral blood mononuclear cells (pbmcs) from mg patients compared with healthy controls, with lower expression in generalized patients than in ocular ones. mg patients also had increased serum il-7 and il-17 levels. additionally, serum il-7 level presents a positive correlation with the serum il-17 level. mir-181c levels were negatively correlated with serum levels of il-7 and il-17 in either generalized patients or ocular patients. a luciferase reporter assay revealed that mir-181c could directly bind to the 3'-utr of interleukin-7. forced expression of mir-181c led to decreased il-7 and il-17 release in cultured pbmcs, while depletion of mir-181c increased the secretion of these two proinflammatory cytokines. the results from our study suggested for the first time that mir-181c was able to negatively regulate the production of proinflammatory cytokines il-7 and il-17 in mg patients, and it is a novel potential therapeutic target for mg.",1
"the regulation of toll-like receptor (tlr) signaling in a tumor microenvironment is poorly understood despite its importance in cancer biology. to address this problem, tlr7-responses of chronic lymphocytic leukemia (cll) cells were studied in the presence and absence of a human stromal cell-line derived from a leukemic spleen. cll cells alone produced high levels of tumor necrosis factor (tnf)-α and proliferated in response to tlr7-agonists. a signal transducer and activator of transcription 3 -activating stromal factor, identified as interleukin (il)-6, was found to upregulate microrna (mir)-17 and mir-19a, target tlr7 and tnfa messenger rna, and induce a state of tolerance to tlr7-agonists in cll cells. overexpression of the mir-17-92 cluster tolerized cll cells directly and mir-17 and mir-19a antagomirs restored tlr7-signaling. inhibition of il-6 signaling with antibodies or small-molecule janus kinase inhibitors reversed tolerization and increased tlr7-stimulated cll cell numbers in vitro and in nod-scidγc (null) mice. these results suggest il-6 can act as tumor suppressor in cll by inhibiting tlr-signaling.",1
"uncontrolled cell proliferation and cytoskeletal remodeling are responsible for tumor development and ultimately metastasis. a number of studies have implicated micrornas in the regulation of cancer cell invasion and migration. here, we show that mir-23b regulates focal adhesion, cell spreading, cell-cell junctions and the formation of lamellipodia in breast cancer (bc), implicating a central role for it in cytoskeletal dynamics. inhibition of mir-23b, using a specific sponge construct, leads to an increase of cell migration and metastatic spread in vivo, indicating it as a metastatic suppressor microrna. clinically, low mir-23b expression correlates with the development of metastases in bc patients. mechanistically, mir-23b is able to directly inhibit a number of genes implicated in cytoskeletal remodeling in bc cells. through intracellular signal transduction, growth factors activate the transcription factor ap-1, and we show that this in turn reduces mir-23b levels by direct binding to its promoter, releasing the pro-invasive genes from translational inhibition. in aggregate, mir-23b expression invokes a sophisticated interaction network that co-ordinates a wide range of cellular responses required to alter the cytoskeleton during cancer cell motility.",1
"micrornas (mirnas) are short non-coding rnas that negatively modulate gene expression at the post-transcriptional level and are known to be involved in the cross-talk between the host and virus. using a standard plaque assay and real-time pcr method, we found that ectopic expression of mir-101 could significantly suppress herpes simplex virus-1 (hsv-1) replication, and that blocking endogenous mir-101 could increase viral progeny without affecting cell viability. bioinformatics analysis indicates the 3' untranslated region (utr) of mitochondrial atp synthase subunit beta (atp5b) has a putative binding site for mir-101. mir-101 can directly bind to atp5b 3'utr and negatively regulate atp5b expression. using a rna interference technique, knockdown of atp5b significantly inhibited hsv-1 replication, indicating that atp5b functions as a pro-viral factor. the ectopic expression of atp5b lacking the 3'utr could override the suppressive effect of mir-101 on hsv-1 replication. a concordant inverse correlation between mir-101 and atp5b was observed in hsv-1-infected hela cells. up-regulation of mir-101 expression may play a role in repressing productive hsv-1 replication by targeting atp5b. exploring the role of host-encoded mirna in the regulation of viral infection would enable us to better understand the intricate networks of host-pathogen interactions.",1
"multiciliated cells lining the surface of some vertebrate epithelia are essential for various physiological processes, such as airway cleansing. however, the mechanisms governing motile cilia biosynthesis remain poorly elucidated. we identify mir-449 micrornas as evolutionarily conserved key regulators of vertebrate multiciliogenesis. in human airway epithelium and xenopus laevis embryonic epidermis, mir-449 micrornas strongly accumulated in multiciliated cells. in both models, we show that mir-449 micrornas promote centriole multiplication and multiciliogenesis by directly repressing the delta/notch pathway. we established notch1 and its ligand delta-like 1(dll1) as mir-449 bona fide targets. human dll1 and notch1 protein levels were lower in multiciliated cells than in surrounding cells, decreased after mir-449 overexpression and increased after mir-449 inhibition. in frog, mir-449 silencing led to increased dll1 expression. consistently, overexpression of dll1 mrna lacking mir-449 target sites repressed multiciliogenesis, whereas both dll1 and notch1 knockdown rescued multiciliogenesis in mir-449-deficient cells. antisense-mediated protection of mir-449-binding sites of endogenous human notch1 or frog dll1 strongly repressed multiciliogenesis. our results unravel a conserved mechanism whereby notch signalling must undergo mir-449-mediated inhibition to permit differentiation of ciliated cell progenitors.",1
"accumulating evidence has shown that micrornas are involved in multiple processes in cancer development and progression. recently, mir-22 has been identified as a tumor-suppressing microrna in many human cancers. however, the specific function of mir-22 in gastric cancer is unclear at this point. in this study, we first measured mir-22 expression level in 30 pairs of gastric cancer and matched normal tissues, two normal and six gastric cancer cell lines by real-time quantitative rt-pcr. we found that the expression of mir-22 in gastric cancer tissues and cell lines was much lower than that in normal control, respectively. transfection of mir-22 expression plasmid could significantly inhibit the cell migration and invasion in sgc-7901 and ncl-n87 gastric cancer cell lines. moreover, we also showed that sp1 was negatively regulated by mir-22 at the posttranscriptional level, via a specific target site within the 3'utr by luciferase reporter assay. the expression of sp1 was inversely correlated with mir-22 expression in gastric cancer tissues, and knockdown of sp1 by sirna inhibited cell malignant behaviors. thus, our findings suggest that mir-22 acts as tumor suppressor by targeting the sp1 gene and inhibiting gastric cancer cell migration and invasion. the findings of this study contribute to current understanding of the functions of mir-22 in gastric cancer.",1
"nontypeable haemophilus influenzae (nthi) are gram-negative commensal bacteria that reside in the nasopharynx. nthi can also cause multiple upper and lower respiratory tract diseases that include sinusitis, conjunctivitis, bronchitis, and otitis media. in numerous bacterial species the ferric uptake regulator (fur) acts as a global regulator of iron homeostasis by negatively regulating the expression of iron uptake systems. however in nthi strain 86-028np and numerous other bacterial species there are multiple instances where fur positively affects gene expression. it is known that many instances of positive regulation by fur occur indirectly through a small rna intermediate. however, no examples of small rnas have been described in nthi. therefore we used rna-seq analysis to analyze the transcriptome of nthi strain 86-028nprpsl and an isogenic 86-028nprpslδfur strain to identify fur-regulated intergenic transcripts. from this analysis we identified hrrf, the first small rna described in any haemophilus species. orthologues of this small rna exist only among other pasteurellaceae. our analysis showed that hrrf is maximally expressed when iron levels are low. additionally, fur was shown to bind upstream of the hrrf promoter. rna-seq analysis was used to identify targets of hrrf which include genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid biosynthesis. the stability of hrrf is not dependent on the rna chaperone hfq. this study is the first step in an effort to investigate the role small rnas play in altering gene expression in response to iron limitation in nthi.",1
"aims micrornas (mirnas) are an abundant group of small non-coding rnas that have been implicated in tumorigenesis. they regulate expression of target genes by complementary base pairing. the purposes of this study were to delineate mir-106b expression in medulloblastoma (mb) and to explore its functional contributions to mb pathogenesis. methods we analysed expression of mir-106b in 32 mb samples by quantitative rt-pcr. we applied gain- and loss-of-function strategies to delineate the functional roles of mir-106b in mb. luciferase reporter assay was conducted to confirm target gene of mir-106b. results expression of mir-106b was overexpressed in mb, and was significantly associated with its host gene mcm7 (p = 0.020). transfection of mir-106b inhibitor in mb cell lines markedly reduced cell proliferation, migration and invasion potential, and tumour sphere formation. cell cycle analysis indicated that mir-106b inhibition induced g1 arrest and apoptosis. the cell cycle regulators, p21 and cyclin d1, and apoptotic marker cleaved parp were differentially expressed in mir-106b inhibitor-transfected cells. pten was identified as a direct target gene of mir-106b. luciferase reporter assay confirmed mir-106b directly interacted with the 3' utr of pten. we found mir-106b directly targeted pten at transcriptional and translational levels. immunohistochemistry revealed a trend between pten and mir-106b in mb tumours (p = 0.07). conclusions these data suggested the upregulation of mir-106b in mb and the involvement of mir-106b in mb biology.",1
"the polyprotein of cocksfoot mottle virus (cfmv) is encoded by two overlapping open reading frames (orfs). the putative replicase of cfmv is produced as a part of the polyprotein from orf2b by the -1 ribosomal frameshifting mechanism. the signals leading to -1 ribosomal frameshifting directed by cfmv rna are the slippery heptamer uuuaaac and a stem-loop structure starting seven nucleotides downstream from the heptamer. we studied the effect of different parts of the cfmv genome on the -1 ribosomal frameshifting efficiency using a wheat germ extract transcription/translation system. a point mutation in the slippery heptamer and a mutation deleting the stem-loop structure prevented frameshifting. seventy nucleotides of cfmv sequence, including the slippery sequence and the stem-loop structure, was found to act as a minimal region for frameshifting. interestingly, a termination codon introduced into the -1-frame 27 nucleotides downstream of the stem-loop structure increased frameshift efficiency threefold, while a similarly located termination codon in the 0-frame had no effect. even fourfold to fivefold efficiencies were observed when the polyprotein encoding orfs were fused together, which led simultaneously to the formation of a termination codon downstream of the frameshift signal. possible reasons underlying these observations are discussed.",1
"objectives microrna (mirna) machinery regulates cancer cell behavior, and has been implicated in patients' clinical status and prognosis. we found that microrna-29b (mir-29b) increased significantly in advanced migratory cells. however, mir-29b controls the migration ability, and its regulatory mechanism in oral squamous cell carcinoma (oscc) remains unknown. materials and methods we triggered mir-29b expression in oscc patients and cell lines by conducting real-time quantitative pcr. we determined the functions of mir-29b in the migration of oscc cells by using gain- and loss-of-function approaches. we elevated the target genes of mir29b through software predictions and a luciferase report assay. we used an orthotopic oscc animal model to investigate the effects of mir29b on oscc cell metastasis in vivo. results the clinical data revealed that mir-29b expression was correlated with lymph node metastasis and an advanced tumor stage in 98 oscc patients. furthermore, multivariate analysis revealed that mir-29b expression was significantly correlated with recurrence, and indicated poor survival. mir-29b promoted oscc cell migration and downregulated cx3cl1, a cell-cell adhesion regulator, which plays an essential role in mir-29b-regulated oscc cell migration machinery. furthermore, we found that cx3cl1 expression was correlated with lymph node metastasis and an early tumor stage in oscc patients, and negatively correlated with mir-29b expression. conclusion mir-29b acts as an oncomir, promoting cell migration through cx3cl1 suppression, and could be a potential therapeutic target for preventing oscc progression.",1
"we report the characterization of early pre-ribosomal particles. twelve tap-tagged components each showed nucleolar localization, sedimented at approximately 90s on sucrose gradients, and coprecipitated both the 35s pre-rrna and the u3 snorna. thirty-five non-ribosomal proteins were coprecipitated, including proteins associated with u3 (nop56p, nop58p, sof1p, rrp9, dhr1p, imp3p, imp4p, and mpp10p) and other factors required for 18s rrna synthesis (nop14p, bms1p, and krr1p). mutations in components of the 90s pre-ribosomes impaired 40s subunit assembly and export. strikingly, few components of recently characterized pre-60s ribosomes were identified in the 90s pre-ribosomes. we conclude that the 40s synthesis machinery predominately associates with the 35s pre-rrna factors, whereas factors required for 60s subunit synthesis largely bind later, showing an unexpected dichotomy in binding.",1
"mammalian long intergenic noncoding rnas (lincrnas) are best known for modulating transcription. here we report a posttranscriptional function for lincrna-p21 as a modulator of translation. association of the rna-binding protein hur with lincrna-p21 favored the recruitment of let-7/ago2 to lincrna-p21, leading to lower lincrna-p21 stability. under reduced hur levels, lincrna-p21 accumulated in human cervical carcinoma hela cells, increasing its association with junb and ctnnb1 mrnas and selectively lowering their translation. with elevated hur, lincrna-p21 levels declined, which in turn derepressed junb and β-catenin translation and increased the levels of these proteins. we propose that hur controls translation of a subset of target mrnas by influencing lincrna-p21 levels. our findings uncover a role for lincrna as a posttranscriptional inhibitor of translation.",1
"the tumor suppressor p21 acts as a cell cycle inhibitor and has also been shown to regulate gene expression by functioning as a transcription corepressor. here, we identified p21-regulated micrornas (mirnas) by sequencing small rnas from isogenic p21(+/+) and p21(-/-) cells. three abundant mirna clusters, mir-200b-200a-429, mir-200c-141, and mir-183-96-182, were downregulated in p21-deficient cells. consistent with the known function of the mir-200 family and p21 in inhibition of the epithelial-mesenchymal transition (emt), we observed emt upon loss of p21 in multiple model systems. to explore a role of the mir-183-96-182 cluster in emt, we identified its genome-wide targets and found that mir-183 and mir-96 repressed common targets, including slug, zeb1, itgb1, and klf4. reintroduction of mir-200, mir-183, or mir-96 in p21(-/-) cells inhibited emt, cell migration, and invasion. conversely, antagonizing mir-200 and mir-183-96-182 cluster mirnas in p21(+/+) cells increased invasion and elevated the levels of vim, zeb1, and slug mrnas. furthermore, we found that p21 forms a complex with zeb1 at the mir-183-96-182 cluster promoter to inhibit transcriptional repression of this cluster by zeb1, suggesting a reciprocal feedback loop.",1
"human cardiomyocyte progenitor cells (hcmpcs) are cardiac progenitor cells that are unique for their efficient differentiation into beating cardiomyocytes without requiring co-culture with neonatal cardiomyocytes. hcmpcs have shown great potential in preserving the function of infarcted mouse myocardium. mirna-204 has been reported to be up-regulated in differentiated hcmpcs, however, its biological significance is unclear. in this study, hcmpc proliferation, viability, apoptosis and necrosis were determined using the elisa kit (colorimetric brdu detection), cell counting kit-8, and annexin v and propidium iodide staining, respectively. mirna-204 inhibition promoted hcmpc proliferation without affecting cell viability and the level of apoptosis and necrosis, indicating that mirna-204 might be required for hcmpc differentiation. quantitative reverse transcriptase-polymerase chain reactions were used to detect the expression profile of cardiac genes, including mef2c, gata-4, nkx-2.5, tropt, βmhc, and cactin. cardiac α-actin staining was used to quantify the degree of differentiation. mirna-204 inhibition significantly down-regulated tropt, βmhc, and cactin and reduced differentiation by 47.81% after 2 weeks of differentiation induction. interestingly, mirna-204 mimics (30 nm) did not promote hcmpc proliferation and differentiation. the bioinformatic tool gomir identified the activating transcription factor 2 (atf-2) as a potential target, which was confirmed by western blot and a luciferase reporter assay. atf-2 overexpression promoted hcmpc proliferation, further demonstrating the role played by atf-2 as a target gene of mirna-204. therefore, mirna-204 is required for hcmpc differentiation and atf-2 is a target gene of mirna-204 in hcmpcs. this study indicates that mirna-204 is among the regulators that drive hcmpc proliferation and differentiation, and mirna-204 might be used to influence cell fate.",1
"downregulated expression of k + channels and decreased k + currents in pulmonary artery smooth muscle cells (pasmc) have been implicated in the development of sustained pulmonary vasoconstriction and vascular remodeling in patients with idiopathic pulmonary arterial hypertension (ipah). however, it is unclear exactly how k + channels are downregulated in ipah-pasmc. micrornas (mirnas) are small non-coding rnas that are capable of posttranscriptionally regulating gene expression by binding to the 3'-untranslated regions of their targeted mrnas. here, we report that specific mirnas are responsible for the decreased k + channel expression and function in ipah-pasmc. we identified 3 mirnas (mir-29b, mir-138, and mir-222) that were highly expressed in ipah-pasmc in comparison to normal pasmc (>2.5-fold difference). selectively upregulated mirnas are correlated with the decreased expression and attenuated activity of k + channels. overexpression of mir-29b, mir-138, or mir-222 in normal pasmc significantly decreased whole cell k + currents and downregulated voltage-gated k + channel 1.5 (k v 1.5/kcna5) in normal pasmc. inhibition of mir-29b in ipah-pasmc completely recovered k + channel function and k v 1.5 expression, while mir-138 and mir-222 had a partial or no effect. luciferase assays further revealed that k v 1.5 is a direct target of mir-29b. additionally, overexpression of mir-29b in normal pasmc decreased large-conductance ca 2+ -activated k + (bk ca ) channel currents and downregulated bk ca channel β1 subunit (bk ca β1 or kcnmb1) expression, while inhibition of mir-29b in ipah-pasmc increased bk ca channel activity and bk ca β1 levels. these data indicate upregulated mir-29b contributes at least partially to the attenuated function and expression of k v and bk ca channels in pasmc from patients with ipah.",1
"breast cancer is often fatal during its metastatic dissemination. to unravel the role of micrornas (mirs) during malignancy, we analyzed mir expression in 77 primary breast carcinomas and identified 16 relapse-associated mirs that correlate with survival and/or distinguish tumor subtypes in different datasets. among them, mir-148b, down-regulated in aggressive breast tumors, was found to be a major coordinator of malignancy. in fact, it is able to oppose various steps of tumor progression when overexpressed in cell lines by influencing invasion, survival to anoikis, extravasation, lung metastasis formation, and chemotherapy response. mir-148b controls malignancy by coordinating a novel pathway involving over 130 genes and, in particular, it directly targets players of the integrin signaling, such as itga5, rock1, pik3ca/p110α, and nras, as well as csf1, a growth factor for stroma cells. our findings reveal the importance of the identified 16 mirs for disease outcome predictions and suggest a critical role for mir-148b in the control of breast cancer progression.",1
"micrornas are a class of small rnas that regulate the expression of target mrnas by inhibiting translation or destabilizing target mrnas. mir-126 is a microrna that is highly enriched in endothelial cells. mir-126 has been found to promote angiogenesis and inhibit vascular inflammation in endothelial cells by repressing three target genes sprouty-related evh1 domain-containing protein 1 (spred1), phosphoinositol-3 kinase regulatory subunit 2 (pik3r2), and vascular cell adhesion molecule 1 (vcam1). our previous study showed that the expression of mir-126 was downregulated after spinal cord injury (sci). therefore, we wanted to examine whether upregulation of mir-126 could promote angiogenesis, inhibit inflammation, and exert a positive effect on recovery after contusion sci. in this study, we found that increased levels of mir-126 promoted angiogenesis, and inhibited leukocyte extravasation into the injured spinal cord, which was concurrent with downregulation of mrna and protein expression of three validated mir-126 target genes, spred1, pik3r2, and vcam1. moreover, a dose-dependent effect of mir-126 was observed in rescuing tissue damage and improving the functional deficit after sci. thus, the present study indicated that mir-126 played an important role in angiogenesis and inflammation after sci.",1
"emerging evidences suggest that necrosis is programmed and is one of the main forms of cell death in the pathological process in cardiac diseases. long noncoding rnas (lncrnas) are emerging as new players in gene regulation. however, it is not yet clear whether lncrnas can regulate necrosis in cardiomyocytes. here, we report that a long noncoding rna, named necrosis-related factor (nrf), regulates cardiomyocytes necrosis by targeting mir-873 and ripk1 (receptor-interacting serine/threonine-protein kinase 1)/ripk3 (receptor-interacting serine/threonine-protein kinase 3). our results show that ripk1 and ripk3 participate in h2o2-induced cardiomyocytes necrosis. mir-873 suppresses the translation of ripk1/ripk3 and inhibits ripk1/ripk3-mediated necrotic cell death in cardiomyocytes. mir-873 reduces myocardial infarct size upon ischemia/reperfusion (i/r) injury in the animal model. in exploring the molecular mechanism by which mir-873 expression is regulated, we identify nrf as an endogenous sponge rna and repress mir-873 expression. nrf directly binds to mir-873 and regulates ripk1/ripk3 expression and necrosis. knockdown of nrf antagonizes necrosis in cardiomyocytes and reduces necrosis and myocardial infarction upon i/r injury. further, we identify that p53 transcriptionally activates nrf expression. p53 regulates cardiomyocytes necrosis and myocardial i/r injury through nrf and mir-873.our results identify a novel mechanism involving nrf and mir-873 in regulating programmed necrosis in the heart and suggest a potential therapeutic avenue for cardiovascular diseases.",1
"5s rrnas are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. nevertheless, a clearly identifiable, mitochondrion-encoded 5s rrna is present in acanthamoeba castellanii, a member of amoebozoa. during a search for additional mitochondrial 5s rrnas, we detected small abundant rnas in other members of amoebozoa, namely, in the lobose amoeba hartmannella vermiformis and in the myxomycete slime mold physarum polycephalum. these rnas are encoded by mitochondrial dna (mtdna), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5s rrnas. further, in the mtdna of another slime mold, didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the physarum small rna. a mtdna-encoded small rna previously identified in dictyostelium discoideum is here shown to share several characteristics with known 5s rrnas. again, we detected genes encoding potential homologs of this rna in the mtdna of three other species of the genus dictyostelium as well as in a related genus, polysphondylium. taken together, our results indicate a widespread occurrence of small, abundant, mtdna-encoded rnas with 5s rrna-like structures that are associated with the mitoribosome in various amoebozoan taxa. our working hypothesis is that these novel small abundant rnas represent radically divergent mitochondrial 5s rrna homologs. we posit that currently unrecognized 5s-like rnas may exist in other mitochondrial systems in which a conventional 5s rrna cannot be identified.",1
"micrornas, a large family of small regulatory rnas, are posttranscriptional gene regulators that bind mrna in a sequence-specific manner, thereby controlling diverse aspects of cell function, including immune reaction. in this study, we screened and identified a group of differentially expressed mirnas in naive and activated cd4(+) t cells. among the mirnas studied, mir-181c was proven to have the potential to regulate cd4(+) t cell activation. mir-181c was downregulated in the process of cd4(+) t cell activation, and transfection of mir-181c mimics partially repressed the activation of both jurkat cells and human peripheral blood mononuclear cells (pbmc) cd4(+) t cells. we further showed that mir-181c can bind to the il-2 3' utr and repress its expression by inhibiting translation. moreover, mir-181c mimics reduced activated cd4(+) t cell proliferation. taken together, our results show that mir-181c serves as a negative regulator that modulates the activation of cd4(+) t cells.",1
"long non-coding (lnc) rnas can regulate gene expression and protein functions. however, the proportion of lncrnas with biological activities among the thousands expressed in mammalian cells is controversial. we studied lockd (lncrna downstream of cdkn1b), a 434-nt polyadenylated lncrna originating 4 kb 3' to the cdkn1b gene. deletion of the 25-kb lockd locus reduced cdkn1b transcription by approximately 70% in an erythroid cell line. in contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the lockd transcription start site reduced the entire lncrna transcript level by >90% with no effect on cdkn1b transcription. the lockd promoter contains a dnase-hypersensitive site, binds numerous transcription factors, and physically associates with the cdkn1b promoter in chromosomal conformation capture studies. therefore, the lockd gene positively regulates cdkn1b transcription through an enhancer-like cis element, whereas the lncrna itself is dispensable, which may be the case for other lncrnas.",1
"the microrna mir-451 is downregulated in gliomas, this has been suggested by several different research groups and is consistent with our data. our previous study also confirmed that mir-451 has a repressive role in glioma by inhibiting cell growth, proliferation and by inducing cell apoptosis. in the present study, we identified a target gene of mir-451 in human glioma and investigated the mechanism for the glioma suppressive effect of mir-451 functions. expression of mir-451 in gliomas was identified by quantitative real-time pcr and fluorescence in situ hybridization. human glioma cell lines (u251, u87, ln229 and a172) were transfected with mir-451 mimics to restore mir-451 expression. the tumor suppressive effects of mir-451 were further verified by subcutaneous assays in nude mice, in addition to our previous in vitro data. a candidate target gene was tested by western blotting and luciferase reporter assays. some pi3k/akt pathway factors were tested by western blotting. we found that mir-451 expression was downregulated in glioma samples and was inversely correlated with who grades of gliomas. in vivo assays confirmed that mir-451 had tumor suppressive traits. cab39-3'utr luciferase reporter assay confirmed cab39 as a direct target gene of mir-451. significant alterations in the expression of pi3k/akt pathway factors were observed by western blot assays. we conclude that mir-451 represses glioma in vitro and in vivo, likely through targeting cab39 directly and inhibiting the pi3k/akt pathway indirectly.",1
"steroid-induced osteonecrosis of femoral head (onfh) is a serious complication of glucocorticoid (gc) use. we investigated the differential expression of mirs in the mesenchymal stem cells (mscs) of patients with onfh, and aimed to explain the relationship between gc use and the development of msc dysfunction in onfh. cells were collected from bone marrow of patients with onfh. samples were assigned to either gcs group or control group at 1:1 matched with control. we then used mirna microarray analysis and real-time pcr to identify the differentially expressed mirs. we also induced normal mscs with gcs to verify the differential expression above. subsequently, we selected some of the mirs for further studies, including mirna target and pathway prediction, and functional analysis. we discovered that mir-708 was upregulated in onfh patients and gc-treated mscs. smad3 was identified as a direct target gene of mir-708, and functional analysis demonstrated that mir-708 could markedly suppress osteogenic differentiation and adipogenesis differentiation of mscs. inhibition of mir-708 rescued the suppressive effect of gc on osteonecrosis. therefore, we determined that gc use resulted in overexpression of mir-708 in mscs, and thus, targeting mir-708 may serve as a novel therapeutic biomarker for the prevention and treatment of onfh.",1
"the human est1a/smg6 polypeptide physically interacts with the chromosome end replication enzyme telomerase. in an attempt to better understand hest1a function, we have started to dissect the molecular interactions between hest1a and telomerase. here, we demonstrate that the interaction between hest1a and telomerase is mediated by protein-rna and protein-protein contacts. we identify a domain within hest1a that binds the telomerase rna moiety htr while full-length hest1a establishes in addition rnase-resistant and htr-independent protein-protein contacts with the human telomerase reverse transcriptase polypeptide (tert). conversely, within htert, we identify a hest1a interaction domain, which comprises htr-binding activity and rna-independent hest1a-binding activity. purified, recombinant hest1a binds the telomerase rna moiety (htr) with high affinity (apparent overall k(d) = 25 nm) but low specificity. we propose that hest1a assembles specifically with telomerase in the context of the htr-htert ribonucleoprotein, through the high affinity of hest1a for htr and specific protein-protein contacts with htert.",1
"the hippo signaling pathway governs organ size via coordinating cell proliferation and apoptosis, and its dysregulation causes congenital diseases and cancers. the homeostasis of hippo pathway is achieved through multiple post translational modifications. through drosophila genetic screening, we found that mirnas were also involved in hippo pathway regulation. here, we showed that overexpression of mir-7 resulted in small wings, which were neutralized by mir-7-sponge (mir-7-sp) co-expression. mechanistically, mir-7 inhibited the expression of hippo pathway target genes. epistatic analyses revealed that mir-7 modulated hippo pathway through the transcriptional cofactor yorkie (yki). consistently, overexpression of mir-7 decreased yki protein. we further found a seed sequence of mir-7 in the yki 3'-utr region. in addition, we discovered that mir-7 was a transcriptional target of yki. thus, a negative feedback loop existed for fine tuning hippo pathway activity. taken together, our findings uncovered a novel mechanism by which yki was silenced by mir-7 for hippo pathway regulation.",1
"neurodegeneration associated with amyloid β (aβ) peptide accumulation, synaptic loss, and memory impairment are pathophysiological features of alzheimer's disease (ad). numerous micrornas regulate amyloid precursor protein (app) expression and metabolism. we previously reported that mir-101 is a negative regulator of app expression in cultured hippocampal neurons. in this study, a search for predicted app metabolism-associated mir-101 targets led to the identification of a conserved mir-101 binding site within the 3' untranslated region (utr) of the mrna encoding ran-binding protein 9 (ranbp9). ranbp9 increases app processing by β-amyloid converting enzyme 1 (bace1), secretion of soluble appβ (sappβ), and generation of aβ. mir-101 significantly reduced reporter gene expression when co-transfected with a ranbp9 3'-utr reporter construct, while site-directed mutagenesis of the predicted mir-101 target site eliminated the reporter response. to investigate the effect of stable inhibition of mir-101 both in vitro and in vivo, a microrna sponge was developed to bind mir-101 and derepress its targets. four tandem bulged mir-101 responsive elements (res), located downstream of the enhanced green fluorescence protein (egfp) open reading frame and driven by the synapsin promoter, were placed in a lentiviral vector to create the plsyn-mir-101 sponge. delivery of the sponge to primary hippocampal neurons significantly increased both app and ranbp9 expression, as well as sappβ levels in the conditioned medium. importantly, silencing of endogenous ranbp9 reduced sappβ levels in mir-101 sponge-containing hippocampal cultures, indicating that mir-101 inhibition may increase amyloidogenic processing of app by ranbp9. lastly, the impact of mir-101 on its targets was demonstrated in vivo by intrahippocampal injection of the plsyn-mir-101 sponge into c57bl6 mice. this study thus provides the basis for studying the consequences of long-term mir-101 inhibition on the pathology of ad.",1
"a change in intracellular free calcium (ca(2+)) is a common signaling mechanism of reperfusion-induced cardiomyocyte death. calcium/calmodulin dependent protein kinase ii (camkii) is a critical regulator of ca(2+) signaling and mediates signaling pathways responsible for functions in the heart including hypertrophy, apoptosis, arrhythmia, and heart disease. micrornas (mirna) are involved in the regulation of cell response, including survival, proliferation, apoptosis, and development. however, the roles of mirnas in ca(2+)-mediated apoptosis of cardiomyocytes are uncertain. here, we determined the potential role of mirna in the regulation of camkii dependent apoptosis and explored its underlying mechanism. to determine the potential roles of mirnas in h2o2-mediated ca(2+) overload, we selected and tested 6 putative mirnas that targeted camkiiδ, and showed that mir-145 represses camkiiδ protein expression and ca(2+) overload. we confirmed camkiiδ as a direct downstream target of mir-145. furthermore, mir-145 regulates ca(2+)-related signals and ameliorates apoptosis. this study demonstrates that mir-145 regulates reactive oxygen species (ros)-induced ca(2+) overload in cardiomyocytes. thus, mir-145 affects ros-mediated gene regulation and cellular injury responses.",1
"introduction mir-146a is one of the first identified mirnas expressed differentially in osteoarthritis (oa) cartilage. however, the role it plays in oa pathogenesis is not clear. the aim of this study is to identify a molecular target of mir-146a, thereby elucidating its function in chondrocytes during oa pathogenesis. methods primary chondrocytes from sprague-dawley rats were treated with il-1β before the expression levels of mir-146a, smad4 and vascular endothelial growth factor (vegf) were quantified by real-time pcr and/or western blotting. the effect of mir-146a on cellular response to transforming growth factor (tgf)-β1 was quantified by a luciferase reporter harboring tgf-β1 responsive elements and by extracellular signal-regulated kinase assay. the effect of mir-146a on apoptosis was quantified by the tunel assay. oa pathogenesis was surgically induced with joint instability in rats, evaluated by histopathological analysis with safranin o staining, and the expression levels of mir-146a, smad4, and vegf were quantified using real-time pcr and/or immunohistochemistry. results il-1β treatment of chondrocytes increased the expression levels of mir-146a and vegf and decreased the levels of smad4 in a time-dependent manner. mir-146a upregulated vegf expression and downregulated smad4 expression in chondrocytes, while a mir-146a inhibitor acted in a converse manner. smad4, a common mediator of the tgf-β pathway, is identified as a direct target of mir-146a by harboring a mir-146a binding sequence in the 3'-utr region of its mrna. mutation of the binding sequence significantly relieved the inhibition of the smad4 reporter activity by mir-146a. furthermore, mir-146a upregulation of vegf is mediated by smad4. expression of mir-146a led to a reduction of cellular responsiveness to tgf-β and an increase of apoptosis rate in chondrocytes. in vivo, cartilage from surgically induced oa rats displayed higher levels of mir-146a and vegf compared with the sham group. in contrast, smad4 expression level was lower in the oa group than the sham group. conclusion il-1β responsive mir-146a is overexpressed in an experimentally induced oa model, accompanied by upregulation of vegf and downregulation of smad4 in vivo. mir-146a may contribute to oa pathogenesis by increasing vegf levels and by impairing the tgf-β signaling pathway through targeted inhibition of smad4 in cartilage.",1
"pregnane x receptor (pxr) is a major transcription factor regulating the inducible expression of a variety of transporters and drug-metabolizing enzymes, including cyp3a4 (cytochrome p450 3a4). we first found that the pxr mrna level was not correlated with the pxr protein level in a panel of 25 human livers, indicating the involvement of post-transcriptional regulation. notably, a potential mir-148a recognition element was identified in the 3'-untranslated region of human pxr mrna. we investigated whether pxr might be regulated by mir-148a. a reporter assay revealed that mir-148a could recognize the mir-148a recognition element of pxr mrna. the pxr protein level was decreased by the overexpression of mir-148a, whereas it was increased by inhibition of mir-148a. the mir-148a-dependent decrease of pxr protein attenuated the induction cyp3a4 mrna. furthermore, the translational efficiency of pxr (pxr protein/pxr mrna ratio) was inversely correlated with the expression levels of mir-148a in a panel of 25 human livers, supporting the mir-148a-dependent regulation of pxr in human livers. eventually, the pxr protein level was significantly correlated with the cyp3a4 mrna and protein levels. in conclusion, we found that mir-148a post-transcriptionally regulated human pxr, resulting in the modulation of the inducible and/or constitutive levels of cyp3a4 in human liver. this study will provide new insight into the unsolved mechanism of the large interindividual variability of cyp3a4 expression.",1
"micrornas (mirnas) typically direct degradation of their mrna targets. however, some targets have unusual mirna-binding sites that direct degradation of cognate mirnas. although this target-directed mirna degradation (tdmd) is thought to shape the levels of numerous mirnas, relatively few sites that endogenously direct degradation have been identified. here, we identify six sites, five in mrnas and one in a noncoding rna named marge, which serve this purpose in drosophila cells or embryos. these six sites direct mirna degradation without collateral target degradation, helping explain the effectiveness of this mirna-degradation pathway. mutations that disrupt this pathway are lethal, with many flies dying as embryos. concomitant derepression of mir-3 and its paralog mir-309 appears responsible for some of this lethality, whereas the loss of marge-directed degradation of mir-310 mirnas causes defects in embryonic cuticle development. thus, tdmd is implicated in the viability of an animal and is required for its proper development.",1
"accumulating evidence suggests that micrornas (mirnas) are over- or under-expressed in tumors, and abnormalities in mirna expression may contribute to carcinogenesis. mir-383 was previously identified as one of the under-expressed mirnas in medulloblastoma (mb) by mirna expression profiling. quantitative reverse transcription polymerase chain reaction (rt-pcr)-based mirna assays showed an enrichment of mir-383 in normal brain. based on these data, we speculated that mir-383 is important in mb pathogenesis. in this study, we demonstrated significant downregulation of mir-383 in 23/29 (79%) mb samples and 7/7 (100%) mb cells lines. ectopic expression of mir-383 in mb cells led to suppression of cell growth, cell accumulation at sub-g1 phase and alteration of apoptosis-related proteins. by transcriptomic analysis and computational algorithms, we identified peroxiredoxin 3 (prdx3) as a target gene of mir-383. luciferase reporter assay confirmed that mir-383 negatively regulated prdx3 by interaction between mir-383 and complementary sequences in the 3' utr of prdx3. mir-383 repressed prdx3 at transcriptional and translational levels as revealed by quantitative rt-pcr and western blot analysis. furthermore, depletion of prdx3 by sirnas resulted in similar effects as observed in mir-383-transfected cells. in conclusion, mir-383 acts as a regulator controlling cell growth of mb, at least in part, through targeting prdx3.",1
"microrna-mediated regulation of gene expression appears to be involved in a variety of cellular processes, including development, differentiation, proliferation, and apoptosis. mir-146a is thought to be involved in the regulation of the innate immune response, and its expression is increased in tissues associated with chronic inflammation. among the predicted gene targets for mir-146a, the chemokine ccl8/mcp-2 is a ligand for the ccr5 chemokine receptor and a potent inhibitor of cd4/ccr5-mediated hiv-1 entry and replication. in the present study, we have analyzed changes in the expression of mir-146a in primary human fetal microglial cells upon infection with hiv-1 and found increased expression of mir-146a. we further show that ccl8/mcp-2 is a target for mir-146a in hiv-1 infected microglia, as overexpression of mir-146a prevented hiv-induced secretion of mcp-2 chemokine. the clinical relevance of our findings was evaluated in hiv-encephalitis (hive) brain samples in which decreased levels of mcp-2 and increased levels of mir-146a were observed, suggesting a role for mir-146a in the maintenance of hiv-mediated chronic inflammation of the brain.",1
"the werner and bloom syndromes are caused by loss-of-function mutations in wrn and blm, respectively, which encode the recq family dna helicases wrn and blm, respectively. persons with werner syndrome displays premature aging of the skin, vasculature, reproductive system, and bone, and those with bloom syndrome display more limited features of aging, including premature menopause; both syndromes involve genome instability and increased cancer. the proteins participate in recombinational repair of stalled replication forks or dna breaks, but the precise functions of the proteins that prevent rapid aging are unknown. accumulating evidence points to telomeres as targets of wrn and blm, but the importance in vivo of the proteins in telomere biology has not been tested. we show that wrn and blm mutations each accentuate pathology in later-generation mice lacking the telomerase rna template terc, including acceleration of phenotypes characteristic of latest-generation terc mutants. furthermore, pathology not observed in terc mutants but similar to that observed in werner syndrome and bloom syndrome, such as bone loss, was observed. the pathology was accompanied by enhanced telomere dysfunction, including end-to-end chromosome fusions and greater loss of telomere repeat dna compared with terc mutants. these findings indicate that telomere dysfunction may contribute to the pathogenesis of werner syndrome and bloom syndrome.",1
"the role of microrna-1 (mir-1) has been studied in cardiac and skeletal muscle differentiation. however, it remains unexplored in vascular smooth muscle cells (smcs) differentiation. the aim of this study was to uncover novel targets of and shed light on the function of mir-1 in the context of embryonic stem cell (esc) differentiation of smcs in vitro. mir-1 expression is steadily increased during differentiation of mouse esc to smcs. loss-of-function approaches using mir-1 inhibitors uncovered that mir-1 is required for smc lineage differentiation in esc-derived smc cultures, as evidenced by downregulation of smc-specific markers and decrease of derived smc population. in addition, bioinformatics analysis unveiled a mir-1 binding site on the kruppel-like factor 4 (klf4) 3' untranslated region (3'utr), in a region that is highly conserved across species. consistently, mir-1 mimic reduced klf4 3'utr luciferase activity, which can be rescued by mutating the mir-1 binding site on the klf4 3'utr in the reporter construct. additionally, repression of the mir-1 expression by mir-1 inhibitor can reverse klf4 downregulation during esc-smc differentiation, which subsequently inhibits smc differentiation. we conclude that mir-1 plays a critical role in the determination of smc fate during retinoid acid-induced esc/smc differentiation, which may indicate that mir-1 has a role to promote smc differentiation.",1
"background hypoxia in cancers results in the upregulation of hypoxia inducible factor 1 (hif-1) and a microrna, hsa-mir-210 (mir-210) which is associated with a poor prognosis. methods and findings in human cancer cell lines and tumours, we found that mir-210 targets the mitochondrial iron sulfur scaffold protein iscu, required for assembly of iron-sulfur clusters, cofactors for key enzymes involved in the krebs cycle, electron transport, and iron metabolism. down regulation of iscu was the major cause of induction of reactive oxygen species (ros) in hypoxia. iscu suppression reduced mitochondrial complex 1 activity and aconitase activity, caused a shift to glycolysis in normoxia and enhanced cell survival. cancers with low iscu had a worse prognosis. conclusions induction of these major hallmarks of cancer show that a single microrna, mir-210, mediates a new mechanism of adaptation to hypoxia, by regulating mitochondrial function via iron-sulfur cluster metabolism and free radical generation.",1
"nematodes are the only group of organisms in which both cis- and trans-splicing of nuclear mrnas are known to occur. most caenorhabditis elegans introns are exceptionally short, often only 50 bases long. the consensus donor and acceptor splice site sequences found in other animals are used for both cis- and trans-splicing. in order to identify the machinery required for these splicing events, we have characterized the c. elegans snrnas. they are similar in sequence and structure to those characterized in other organisms, and several sequence variations discovered in the nematode snrnas provide support for previously proposed structure models. the c. elegans snrnas are encoded by gene families. we report here the sequences of many of these genes. we find a highly conserved sequence, the proximal sequence element (pse), about 65 bp upstream of all 21 snrna genes thus far sequenced, including the sl rna genes, which specify the snrnas that provide the 5' exons in trans-splicing. the sequence of the c. elegans pse is distinct from pse's from other organisms.",1
"invasion and metastasis are major contributors to cancer-caused death in patients suffered from esophageal squamous cell carcinoma (escc). to explore the micrornas involved in regulating invasion-metastasis cascade of escc, we established two pairs of sublines (30-u/d and 180-u/d) with distinct motility capacity from two escc cell lines (kyse30 and kyse180). screening of the differentially expressed micrornas identified that microrna-92b-3p (mir-92b) could dramatically inhibit invasion and metastasis of escc cells in vitro and in vivo. subsequent studies showed that mir-92b exerted its inhibitory function through suppressing the expression of integrin αv (itgav), which further reduced phosphrylated fak and impaired rac1 activation. moreover, higher expression of mir-92b in escc tissues correlated inversely with lymph node metastasis and indicated better prognosis. together, these results for the first time describe how mir-92b suppresses the motility of escc cells and provide a promise for diagnosis or therapy of escc invasion and metastasis.",1
"notch pathway plays critical role in stem cell maintenance and angiogenesis, as well as cell fate decisions of cancer. however, concrete mechanisms of notch pathway regulation in glioma were not well known, especially mediated by micrornas. in this study, we identified a brain-specific mirna, mir-524-5p, which was associated with the pathological grade and overall survival of gliomas. restorated expression of mir-524-5p in glioma suppressed cell proliferation and invasion both in vitro and in vivo. using bioinformatics and biological approaches, we found that jagged-1 and hes-1, two key components of notch pathway, were direct targets of mir-524-5p. knocking down of jagged-1 or hes-1 partially phenocopied mir-524-5p re-expression, whereas forced expression of jagged-1 or hes-1 reversed the effects of mir-524-5p on proliferation and invasion of glioma. moreover, mir-524-5p levels in glioma samples were inversely correlated with jagged-1 and hes-1 and their overexpressions were associated with poor survival. thus, we have identified that mir-524-5p behaves as a tumor suppressor by negatively targeting jagged-1 and hes-1 and provides an additional option to inhibit this oncogene in gliomas.",1
"background drug-eluting stents reduce the incidence of in-stent restenosis, but they result in delayed arterial healing and are associated with a chronic inflammatory response and hypersensitivity reactions. identifying novel interventions to enhance wound healing and reduce the inflammatory response may improve long-term clinical outcomes. micro-ribonucleic acids (mirnas) are noncoding small ribonucleic acids that play a prominent role in the initiation and resolution of inflammation after vascular injury. objectives this study sought to identify mirna regulation and function after implantation of bare-metal and drug-eluting stents. methods pig, mouse, and in vitro models were used to investigate the role of mirna in in-stent restenosis. results we documented a subset of inflammatory mirnas activated after stenting in pigs, including the mir-21 stem loop mirnas. genetic ablation of the mir-21 stem loop attenuated neointimal formation in mice post-stenting. this occurred via enhanced levels of anti-inflammatory m2 macrophages coupled with an impaired sensitivity of smooth muscle cells to respond to vascular activation. conclusions mir-21 plays a prominent role in promoting vascular inflammation and remodeling after stent injury. mirna-mediated modulation of the inflammatory response post-stenting may have therapeutic potential to accelerate wound healing and enhance the clinical efficacy of stenting.",1
"epithelial tumor cells that have undergone epithelial-to-mesenchymal transition (emt) are typically prone to metastasis and drug resistance and contribute to a poor clinical outcome. the transcription factor zeb1 is a known driver of emt, and mediators of zeb1 represent potential therapeutic targets for metastasis suppression. here, we have shown that phosphatidylinositol 3-kinase-targeted (pi3k-targeted) therapy suppresses metastasis in a mouse model of kras/tp53-mutant lung adenocarcinoma that develops metastatic disease due to high expression of zeb1. in lung adenocarcinoma cells from kras/tp53-mutant animals and human lung cancer cell lines, zeb1 activated pi3k by derepressing mir-200 targets, including amphiregulin (areg), betacellulin (btc), and the transcription factor gata6, which stimulated an egfr/erbb2 autocrine loop. additionally, zeb1-dependent derepression of the mir-200 and mir-183 target friend of gata 2 (fog2) enhanced gata3-induced expression of the p110α catalytic subunit of pi3k. knockdown of fog2, p110α, and rheb ameliorated invasive and metastatic propensities of tumor cells. surprisingly, fog2 was not required for mesenchymal differentiation, suggesting that mesenchymal differentiation and invasion are distinct and separable processes. together, these results indicate that zeb1 sensitizes lung adenocarcinoma cells to metastasis suppression by pi3k-targeted therapy and suggest that treatments to selectively modify the metastatic behavior of mesenchymal tumor cells are feasible and may be of clinical value.",1
"background valvular heart disease is a leading cause of cardiovascular mortality, especially in china. more than a half of valvular heart diseases are caused by acute rheumatic fever. microrna is involved in many physiological and pathological processes. however, the mirna profile of the rheumatic valvular heart disease is unknown. this research is to discuss micrornas and their target gene pathways involved in rheumatic heart valve disease. methods serum mirna from one healthy individual and four rheumatic heart disease patients were sequenced. specific differentially expressed mirnas were quantified by q-pcr in 40 patients, with 20 low-to-moderate rheumatic mitral valve stenosis patients and 20 severe mitral valve stenosis patients. the target relationship between certain mirna and predicted target genes were analysis by luciferase reporter assay. the il-1β and il1r1 expression levels were analyzed by immunohistochemistry and western blot in the mitral valve from surgery of mitral valve replacement. results the results showed that 13 and 91 mirnas were commonly upregulated or downregulated in all four patients. nine mirnas, 1 upregulated and 8 downregulated, that had a similar fold change in all 4 patients were selected for quantitative pcr verification. the results showed similar results from mirna sequencing. within these 9 tested mirnas, hsa-mir-205-3p and hsa-mir-3909 showed a low degree of dispersion between the members of each group. hsa mir-205-3p and hsa-mir-3909 were predicted to target the 3'utr of il-1β and il1r1 respectively. this was verified by luciferase reporter assays. immunohistochemistry and western blot results showed that the mitral valve from rheumatic valve heart disease showed higher levels of il- 1β and il1r1 expression compared with congenital heart valve disease. this suggested a difference between rheumatic heart valve disease and other types of heart valve diseases, with more inflammatory responses in the former. conclusion in the present study, by next generation sequencing of mirnas, it was revealed that interleukin 1β and interleukin 1 receptor 1 was involved in rheumatic heart diseases. and this is useful for diagnosis and understanding of mechanism of rheumatic heart disease.",1
"in nuclear pre-messenger rna splicing, introns are excised by the spliceosome, a dynamic machine composed of both proteins and small nuclear rnas (snrnas). over thirty years ago, after the discovery of self-splicing group ii intron rnas, the snrnas were proposed to catalyse splicing. however, no definitive evidence for a role of either rna or protein in catalysis by the spliceosome has been reported so far. by using metal rescue strategies in spliceosomes from budding yeast, here we show that the u6 snrna catalyses both of the two splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction. notably, all of the u6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group ii intron rna. these findings indicate that group ii introns and the spliceosome share common catalytic mechanisms and probably common evolutionary origins. our results demonstrate that rna mediates catalysis within the spliceosome.",1
"hepatitis b virus (hbv) x protein (hbx) plays a key role in the initiation and progression of hbv infection‑induced hepatocellular carcinoma (hcc). oncogenic microrna-21 (mir-21) can be modulated by hbx protein in hcc. however, critical regulator genes in the pathway of hbx-induced mir-21 in hcc remain unclear. this study aimed to investigate the role of hbx-induced mir-21 in the apoptosis of hcc cells. in the study, interleukin-12 (il-12) was demonstrated as a direct target of mir-21 by dual‑luciferase report assay, and mir-21 was highly expressed in hcc cells (hepg2 and hepg2 2.2.15) compared to l02 cells, but il-12 was weakly expressed as detected by real-time quantitative pcr (rt-qpcr). furthermore, mir-21 mimics, inhibitor, hbx-targeted sirna, and the hbx overexpression vector (phbx) were used to observe the regulatory effects of hbx-induced mir-21 via il-12, and cell apoptosis was assessed. the results showed that overexpression of hbx resulted in the inhibition of il-12. a high level of mir-21 resulted in a significant increase in proliferation and a decrease in il-12 expression. inhibition of mir-21 resulted in a significant increase in apoptosis and increased il-12 expression. the results suggest that hcc cell apoptosis was suppressed at least partially through hbx-induced mir-21 by targeting il-12.",1
"hypoxia-induced pulmonary hypertension, which is characterized by vascular remodeling of blood vessels, is an important complication in copd. in this study, we found that the expression of mir-214 was differentially expressed by screening 13 candidate mirnas in pulmonary artery smooth muscle cells (pasmcs). additionally, using luciferase assay in pasmcs, we found that phosphatase-and-tensin homolog (pten) was a target of mir-214. furthermore, the expression of pten was found to be substantially downregulated in pasmcs from copd patients with pulmonary hypertension (ph) compared with normal controls by using real-time polymerase chain reaction (pcr), immunohistochemistry, and western blot. in addition, we transfected pasmcs with mir-214 mimics, using real-time pcr and western blotting, to confirm the mirna/mrna relationship. furthermore, the introduction of mir-214 significantly promoted the proliferation of pasmcs by suppressing apoptosis of the cells, which was mediated by the downregulation of pten. exposure to hypoxia significantly increased the expression of mir-214 and decreased the expression of pten in pasmcs, and its proliferation was significantly promoted. such effects could be significantly attenuated by the introduction of mir-214 inhibitors, which significantly downregulated mir-214 expression and upregulated the expression of pten. in conclusion, hypoxia-induced upregulation of mir-214 was found to promote ph development by targeting pten in pasmcs, and mir-214 could be a promising diagnostic tool and novel therapeutic target in the management of hypoxia-induced ph in copd.",1
"several members of the let-7 microrna family are downregulated in ovarian and other cancers. they are thought to act as tumor suppressors by lowering growth-promoting and anti-apoptotic proteins. in order to measure cellular let-7 levels systematically, we have developed a highly sensitive let-7 reporter assay system based on the expression of a chimeric mrna that contains the luciferase coding region and a 3'-untranslated region (utr) bearing two let-7-binding sites. in cells expressing the reporter construct, termed pmirglo-let7, luciferase activity was high when let-7 was absent, while luciferase activity was low when let-7 levels were elevated. the ovarian cancer cell lines bg-1 and uci-101 were transfected with the let-7 reporter and surveyed with a library of kinase inhibitors in order to identify pathways affecting let-7 activity. among the inhibitors causing changes in endogenous let-7 abundance, the lowering of glycogen synthase kinase 3 (gsk-3)β function specifically increased let-7 levels and lowered luciferase activity. similarly, silencing gsk-3β increased both mature and primary-let-7 levels in bg-1 cells, and decreased bg-1 cell survival. further studies identified p53 as a downstream effector of the gsk-3β-mediated repression of let-7 biosynthesis. our studies highlight gsk-3β as a novel therapeutic target in ovarian tumorigenesis.",1
"notch signalling is crucial for the correct development and growth of numerous organs and tissues, and when subverted it can cause cancer. loss of mir-8/200 micrornas (mirnas) is commonly observed in advanced tumours and correlates with their invasion and acquisition of stem-like properties. here, we show that this mirna family controls notch signalling activation in drosophila and human cells. in an overexpression screen, we identified the drosophila mir-8 as a potent inhibitor of notch-induced overgrowth and tumour metastasis. gain and loss of mir-8 provoked developmental defects reminiscent of impaired notch signalling and we demonstrated that mir-8 directly inhibits notch ligand serrate. likewise, mir-200c and mir-141 directly inhibited jagged1, impeding proliferation of human metastatic prostate cancer cells. it has been suggested that jagged1 may also be important for metastases. although in metastatic cancer cells, jagged1 modestly regulated zeb1, the mir-200c's target in invasion, studies in drosophila revealed that only concurrent overexpression of notch and zfh1/zeb1 induced tumour metastases. together, these data define a new way to attenuate or boost notch signalling that may have clinical interest.",1
"the pcf10-encoded negative regulators prgx and qa (prgq antisense) rna inhibit pcf10 transfer by blocking prgq transcription extension past a potential transcription terminator sequence irs1. to identify potential target sites for negative regulation, we isolated and analysed 13 cis-acting mutations in the prgxq region. determination of the 3' end of qa rna showed that eight mutations mapped in the region encoding qa rna. four mutations were in the qa promoter region and one was in irs1. three mutations in qa greatly reduced the intracellular level of this rna but did not affect that of prgx. however, both qa rna and prgx protein were reduced in three qa promoter region mutants and the expression of prgq transcripts extending 3' from irs1 became constitutive. qa rna could mediate its negative regulatory activity in the absence of prgx, and this activity was not abolished by ccf10, the peptide pheromone that induces pcf10 transfer. rna analysis showed that qa rna abolished transcription readthrough. based on the experimental data as well as computer analysis of predicted secondary structures of prgq mrna in the presence or absence of qa, we concluded that qa rna is a pheromone-insensitive effector of prgq mrna termination or degradation at irs1. in cells lacking a qa target sequence, expression of prgx repressed transcription from the prgq promoter, and this repression was relieved by addition of exogenous ccf10. thus, even though the synthesis of these negative regulators is coupled, they each act independently on separate targets to regulate expression of conjugation functions.",1
"fibrodysplasia ossificans progressiva (fop) is a rare congenital disorder of skeletal malformations and progressive extraskeletal ossification. there is still no effective treatment for fop. all fop individuals harbor conserved point mutations in acvr1 gene that are thought to cause acvr1 constitutive activation and activate bmp signal pathway. the constitutively active acvr1 is also found to be able to cause endothelial-to-mesenchymal transition (endmt) in endothelial cells, which may cause the formation of fop lesions. micrornas (mirnas) play an essential role in regulating cell differentiation. here, we verified that mir-148a directly targeted the 3' utr of acvr1 mrna by reporter gene assays and mutational analysis at the mirna binding sites, and inhibited acvr1 both at the protein level and mrna level. further, we verified that mir-148a could inhibit the mrna expression of the inhibitor of dna binding (id) gene family thereby suppressing the bmp signaling pathway. this study suggests mir-148a is an important mediator of acvr1, thus offering a new potential target for the development of therapeutic agents against fop.",1
"aging is a multifactorial process that affects most of the biological functions of the organism and increases susceptibility to disease and death. recent studies with animal models of accelerated aging have unveiled some mechanisms that also operate in physiological aging. however, little is known about the role of micrornas (mirnas) in this process. to address this question, we have analysed mirna levels in zmpste24-deficient mice, a model of hutchinson-gilford progeria syndrome. we have found that expression of the mir-29 family of mirnas is markedly upregulated in zmpste24(-/-) progeroid mice as well as during normal aging in mouse. functional analysis revealed that this transcriptional activation of mir-29 is triggered in response to dna damage and occurs in a p53-dependent manner since p53(-/-) murine fibroblasts do not increase mir-29 expression upon doxorubicin treatment. we have also found that mir-29 represses ppm1d phosphatase, which in turn enhances p53 activity. based on these results, we propose the existence of a novel regulatory circuitry involving mir-29, ppm1d and p53, which is activated in aging and in response to dna damage.",1
"micrornas (mirnas) are a class of endogenous, non-coding small rnas that regulate the expression of target genes. previous studies have suggested that mirnas are key regulators in cardiovascular systems. this study investigated the role of mir-873 in h9c2 cardiomyocytes by targeting glioma-associated oncogene 1 (gli1). mir-873 was significantly up-regulated in serum samples from congenital heart disease (chd) patients compared with those from normal individuals. furthermore, mir-873 over-expression suppressed h9c2 proliferation and induced cell cycle arrest. bioinformatic algorithms revealed a predicted target site for mir-873 in the 3'-untranslated region (3'utr) of gli1, which was verified using a dual-luciferase reporter assay. qpcr and western blot analysis also showed that mir-873 negatively regulated gli1 mrna and protein expression in h9c2 cells. conversely, gli1 over-expression partially reversed the growth-inhibitory effect of mir-873. to summarize, our data suggest that mir-873 is a novel mirna that regulates h9c2 cell proliferation via targeting gli1, and mir-873 may serve as a new potential biomarker diagnosis in chd in the future.",1
"eukaryotic cells contain a large number of small nucleolar rnas (snornas). a major family of snornas features a consensus aca motif positioned 3 nucleotides from the 3' end of the rna. in this study we have characterized nine novel human aca snornas (u64-u72). structural probing of u64 rna followed by systematic computer modeling of all known box aca snornas revealed that this class of snornas is defined by a phylogenetically conserved secondary structure. the aca snornas fold into two hairpin structures connected by a single-stranded hinge region and followed by a short 3' tail. the hinge region carries an evolutionarily conserved sequence motif, called box h (consensus, ananna). the h box, probably in concert with the flanking helix structures and the aca box characterized previously, plays an essential role in the accumulation of human u64 intronic snorna. the correct processing of a yeast aca snorna, snr36, in mammalian cells demonstrated that the cis- and trans-acting elements required for processing and accumulation of aca snornas are evolutionarily conserved. the notion that aca snornas share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., gar1) suggests that these rnas possess closely related nucleolar functions.",1
"obesity has emerged as a global health problem with more than 1.1 billion adults to be classified as overweight or obese, and is associated with type 2 diabetes, cardiovascular disease, and several cancers. since obesity is characterized by an increased size and/or number of adipocytes, elucidating the molecular events governing adipogenesis is of utmost importance. recent findings indicate that micrornas (mirnas) - small non-protein-coding rnas that function as post-transcriptional gene regulators - are involved in the regulatory network of adipogenesis. whereas only a single human mirna is known so far to be functional in adipogenesis as pro-adipogenic, several mouse mirnas have been identified very recently as adipogenic regulators, thereby stimulating demand for studying the functional role of mirnas during adipogenesis in human. here, we demonstrate that mir-27b abundance decreased during adipogenesis of human multipotent adipose-derived stem (hmads) cells. overexpression of mir-27b blunted induction of ppargamma and c/ebpalpha, two key regulators of adipogenesis, during early onset of adipogenesis and repressed adipogenic marker gene expression and triglyceride accumulation at late stages. ppargamma has a predicted and highly conserved binding site in its 3'utr and was indeed confirmed to be a direct target of mir-27b. thus, these results suggest that the anti-adipogenic effect of mir-27b in hmads cells is due, at least in part, to suppression of ppargamma.",1
"flow shear stress plays important roles in modulating differentiation of endothelial progenitor cells (epcs). micrornas are crucial for diverse cellular processes, but the expressions and functions of micrornas in epcs responding to mechanical stimuli remain unclear. we sought to determine the effects of microrna-34a (mir-34a) and a novel target forkhead box j2 (foxj2) on shear stress-induced epc differentiation. human umbilical cord blood-derived epcs were exposed to laminar shear stress of 15dyn/cm(2) with parallel plate flow chamber system. real time rt-pcr showed that shear stress significantly increased mir-34a expression, which was accompanied by the endothelial differentiation of epcs. whereas foxj2, a putative target of mir-34a predicted by multiple algorithms, was suppressed in this process. dual luciferase reporter assays, as well as mir-34a mimics and inhibitor treatment were used to confirm the interplay between mir-34a and foxj2. our results revealed an inverse correlation of mir-34a and foxj2 expressions implicated in the endothelial differentiation of epcs. mir-34a contributed to this process by up-regulating the expressions of endothelial cell markers, and down-regulating smooth muscular cell markers. in addition, foxj2 overexpression attenuated endothelial differentiation of epcs, while foxj2 sirna had the opposite effect. these data suggested a unique mechanism that shear stress induces the expression of mir-34a, which targets to foxj2 and promotes endothelial differentiation of epcs. the results provide new insights into mir-34a/foxj2 on shear stress-induced epc differentiation.",1
"micrornas (mirnas) play key roles in modulating a variety of cellular processes through repression of mrna targets. in a screen for mirnas regulated by myocardin-related transcription factor-a (mrtf-a), a coactivator of serum response factor (srf), we discovered a muscle-enriched mirna, mir-486, controlled by an alternative promoter within intron 40 of the ankyrin-1 gene. transcription of mir-486 is directly controlled by srf and mrtf-a, as well as by myod. among the most strongly predicted targets of mir-486 are phosphatase and tensin homolog (pten) and foxo1a, which negatively affect phosphoinositide-3-kinase (pi3k)/akt signaling. accordingly, pten and foxo1a protein levels are reduced by mir-486 overexpression, which, in turn, enhances pi3k/akt signaling. similarly, we show that mrtf-a promotes pi3k/akt signaling by up-regulating mir-486 expression. conversely, inhibition of mir-486 expression enhances the expression of pten and foxo1a and dampens signaling through the pi3k/akt-signaling pathway. our findings implicate mir-486 as a downstream mediator of the actions of srf/mrtf-a and myod in muscle cells and as a potential modulator of pi3k/akt signaling.",1
"the 5' end of the mason-pfizer monkey virus (mpmv) genomic rna has been predicted to fold into a complex stem/loop structure that is thought to play a role in specific rna encapsidation. in this study, we used a set of mutations that either abrogated or recreated the first four stem loops predicted within the 5' untranslated region (5' utr) for effects on rna packaging. test of these mutations in our biological assay revealed that only stem loop 1 (sl1) was important for the packaging potential of mpmv, while mutations in none of the other stem loops affected packaging significantly. interestingly, it was the primary sequence of sl1 rna and not its secondary structure that affected packaging since compensatory mutations that reformed sl1 were unable to restore the packaging efficiency of the retroviral vector. additionally, our mutational analysis reveals that stem loop 4, predicted to be the major packaging determinant of mpmv, does not seem to have a significant role in packaging. finally, results of the biological effects of the structural mutations are discussed in relation to their effects on the folding potential of the various stem loops.",1
"the regulatory transcriptional factor patz1 is abnormally up-regulated in diabetic endothelial cells (ecs) where it acts as an anti-angiogenic factor via modulation of fatty acid-binding protein 4 (fabp4) signaling. the aim of the present work was to elucidate the upstream molecular events regulating patz1 expression in diabetic angiogenesis. the bioinformatics search for micrornas (mirnas) able to potentially target patz1 led to the identification of several mirnas. among them we focused on the mir-24 since the multiple targets of mir-24, which have so far been identified in beta cells, cardiomyocytes and macrophages, are all involved in diabetic complications. mir-24 expression was significantly impaired in the ecs isolated from diabetic hearts. functionally, endothelial migration was profoundly inhibited by mir-24 suppression in ctrl ecs, whereas mir-24 overexpression by mimics treatment effectively restored the migration rate in diabetic ecs. mechanistically, mir-24 directly targeted the 3'untranslated region (3'utr) of patz1, and mir-24 accumulation potentiated endothelial migration by reducing the mrna stability of patz1. together, these results suggest a novel mechanism regulating endothelial patz1 expression based on the down-regulation of mir-24 expression caused by hyperglycemia. interfering with patz1 expression via mirnas or mirna mimics could potentially represent a new way to target endothelial patz1-dependent signaling of vascular dysfunction in diabetes.",1
"friedreich's ataxia (frda) is a severe neurodegenerative disease caused by gaa repeat expansion within the first intron of the frataxin gene. it has been suggested that the repeat is responsible for the disease severity due to impaired transcription thereby reducing expression of the protein. however, genotype-phenotype correlation is imperfect, and the influence of other gene regions of the frataxin gene is unknown. we hypothesized that frda patients may harbor specific regulatory variants in the 3'-utr. we sequenced the 3'-utr region of the frataxin gene in a cohort of 57 frda individuals and 58 controls. seven single nucleotide polymorphisms (snps) out of 19 were polymorphic in our case-control sample. these snps defined several haplotypes with one reaching 89% of homozygosity in patients versus 24% in controls. in another cohort of 47 frda reunionese patients, 94% patients were found to be homozygous for this haplotype. we found that this frda 3'-utr conferred a 1.2-fold decrease in the expression of a reporter gene versus the alternative haplotype configuration. we established that differential targeting by mirna could account for this functional variability. we specifically demonstrated the involvement of mir-124 (i.e hsa-mir-124-3p) in the down-regulation of frda-3'-utr. our results suggest for the first time that post-transcriptional regulation of frataxin occurs through the 3'-utr and involves mirna targeting. we propose that the involvement of mirnas in a frda-specific regulation of frataxin may provide a rationale to increase residual levels of frataxin through mirna-inhibitory molecules.",1
"metazoan replication-dependent histone mrnas are not polyadenylated, and instead terminate in a conserved stem-loop structure generated by an endonucleolytic cleavage of the pre-mrna involving u7 snrnp. u7 snrnp contains two like-sm proteins, lsm10 and lsm11, which replace smd1 and smd2 in the canonical heptameric sm protein ring that binds spliceosomal snrnas. here we show that mutations in either the drosophila lsm10 or the lsm11 gene disrupt normal histone pre-mrna processing, resulting in production of poly(a)+ histone mrna as a result of transcriptional read-through to cryptic polyadenylation sites present downstream from each histone gene. this molecular phenotype is indistinguishable from that which we previously described for mutations in u7 snrna. lsm10 protein fails to accumulate in lsm11 mutants, suggesting that a pool of lsm10-lsm11 dimers provides precursors for u7 snrnp assembly. unexpectedly, u7 snrna was detected in lsm11 and lsm1 mutants and could be precipitated with anti-trimethylguanosine antibodies, suggesting that it assembles into a snrnp particle in the absence of lsm10 and lsm11. however, this u7 snrna could not be detected at the histone locus body, suggesting that lsm10 and lsm11 are necessary for u7 snrnp localization. in contrast to u7 snrna null mutants, which are viable, lsm10 and lsm11 mutants do not survive to adulthood. because we cannot detect differences in the histone mrna phenotype between lsm10 or lsm11 and u7 mutants, we propose that the different terminal developmental phenotypes result from the participation of lsm10 and lsm11 in an essential function that is distinct from histone pre-mrna processing and that is independent of u7 snrna.",1
"aberrant expression of mir-196a has been frequently reported in different cancers including pancreatic cancer. however, its function in pancreatic cancer has not been fully elucidated. here, we investigated the expression pattern and the biological role of mir-196a in pancreatic cancer cell lines, as well as its interaction with a metastasis-related gene, nuclear factor-kappa-b-inhibitor alpha (nfkbia). we demonstrated that mir-196a was up-regulated in human pancreatic cancer cell lines compared with immortalized pancreatic ductal epithelial cells by means of micrornas microarray and qrt-pcr. furthermore, down-regulation of mir-196a in panc-1 suppressed its proliferation and migration with an increase in g0/g1 transition and decreased expression of cyclin d1 and cdk4/6. meanwhile, an increased expression in e-cadherin and decreased expression in n-cadherin and vimentin were also observed. we identified a novel mir-196a target, nfkbia, and down-regulation of mir-196a enhanced the expression of nfkbia protein. luciferase assay confirmed that nfkbia was a direct and specific target of mir-196a. silencing nfkbia in panc-1 cells enhanced its proliferation and migration. taken together, our findings indicate that mir-196a is highly expressed in pancreatic cancer cell lines, and may play a crucial role in pancreatic cancer proliferation and migration, possibly through its downstream target, nfkbia. thus, mir-196a may serve as a potential therapeutic target for pancreatic cancer.",1
"micrornas are small non-coding rnas that may also function as oncogenes and tumor-suppressor genes, as the abnormal expression of micrornas is associated with various human tumors. however, the effect of mir-335 on the lung cancer cells remains unclear. the aim of the paper was to study the expression of mir335 in non-small cell lung cancer (nsclc) and mir335's relation to the metastasis, invasion, and apoptosis in lung cancer cells a549 and h1299. qrt-pcr was used to identify the mir-335 expression. the effects of mir-335 on cell proliferation, apoptosis, and invasion were further analyzed. luciferase reporter assay and western blot were to verify bcl-w and sp1 as potential major target genes of mir-335. finally, the effect of bcl-w on mir-335-induced cell survival was determined. our results showed that mir-335 expression was significantly lower in nsclc tissue, which was significantly associated with lymph node metastasis. in contrast to cells in blank and negative control groups, incidence of apoptosis was significantly higher (p < 0.05) and the number of cells migrating through matrigel was significantly lower (p < 0.05) in mir-335 mimics transfected group. western blot and luciferase reporter assay demonstrated that mir-335 could bind to the putative binding sites in bcl-w (or sp1) mrna 3'-untranslated region to visibly lower the expression of bcl-w (or sp1). the introduction of bcl-w cdna without 3'-untranslated region abrogated mir-335-induced cell survival. these results indicated that upregulation of mir-335 can simultaneously suppress the invasiveness and promote apoptosis of lung cancer cell a549 and h1299 by targeting bcl-w and sp1. therefore, mir-335 may be a potential therapeutic target in nsclc treatment.",1
"microrna-122 (mir-122), which accounts for 70% of the liver's total mirnas, plays a pivotal role in the liver. however, its intrinsic physiological roles remain largely undetermined. we demonstrated that mice lacking the gene encoding mir-122a (mir122a) are viable but develop temporally controlled steatohepatitis, fibrosis, and hepatocellular carcinoma (hcc). these mice exhibited a striking disparity in hcc incidence based on sex, with a male-to-female ratio of 3.9:1, which recapitulates the disease incidence in humans. impaired expression of microsomal triglyceride transfer protein (mttp) contributed to steatosis, which was reversed by in vivo restoration of mttp expression. we found that hepatic fibrosis onset can be partially attributed to the action of a mir-122a target, the klf6 transcript. in addition, mir122a(-/-) livers exhibited disruptions in a range of pathways, many of which closely resemble the disruptions found in human hcc. importantly, the reexpression of mir-122a reduced disease manifestation and tumor incidence in mir122a(-/-) mice. this study demonstrates that mice with a targeted deletion of the mir122a gene possess several key phenotypes of human liver diseases, which provides a rationale for the development of a unique therapy for the treatment of chronic liver disease and hcc.",1
"micrornas (mirnas) are endogenous small noncoding rnas that regulate gene expression with functional links to tumorigenesis. hepatocellular carcinoma (hcc) is the most common type of liver cancer, and it is heterogeneous in clinical outcomes and biological activities. recently, we have identified a subset of highly invasive epithelial cell adhesion molecule (epcam)(+) hcc cells from alpha-fetoprotein (afp)(+) tumors with cancer stem/progenitor cell features, that is, the abilities to self-renew, differentiate, and initiate aggressive tumors in vivo. here, using a global microarray-based mirna profiling approach followed by validation with quantitative reverse transcription polymerase chain reaction, we have demonstrated that conserved mir-181 family members were up-regulated in epcam(+)afp(+) hccs and in epcam(+) hcc cells isolated from afp(+) tumors. moreover, mir-181 family members were highly expressed in embryonic livers and in isolated hepatic stem cells. importantly, inhibition of mir-181 led to a reduction in epcam(+) hcc cell quantity and tumor initiating ability, whereas exogenous mir-181 expression in hcc cells resulted in an enrichment of epcam(+) hcc cells. we have found that mir-181 could directly target hepatic transcriptional regulators of differentiation (for example, caudal type homeobox transcription factor 2 and gata binding protein 6 ) and an inhibitor of wnt/beta-catenin signaling (nemo-like kinase ). taken together, our results define a novel regulatory link between mir-181s and human epcam(+) liver cancer stem/progenitor cells and imply that molecular targeting of mir-181 may eradicate hcc.",1
"micrornas (mirnas) are short non-coding rnas, which negatively regulate gene expression. post‑transcriptional regulation by mirnas is important for organism development. in addition, endothelial cells are key regulators of angiogenesis. by using the 3-(4,5-dimethylthiazol-2-yl)‑2,5‑diphenyltetrazolium bromide (mtt), migration and gelatin sponge-chorioallantoic membrane assays, it was demonstrated that when mir-137 was overexpressed, cell viability and migration decreased. in addition, it was observed that blocking endogenous mir-137 increased cell viability and migration. bioinformatics analysis indicated that the 3'‑untranslated region (3'utr) of the ephrin type-a receptor 7 (epha7) has a putative binding site for mir-137. mir-137 is able to directly bind to the epha7 3'utr and negatively regulate the expression of epha7. mir-137 is also able to decrease the growth and migration of human umbilical vein endothelial cells (huvecs). the identification of the function of mir-137 and its target gene epha7 in huvecs may provide novel insights into the mechanisms of angiogenesis.",1
"unlabelled micrornas (mirna) posttranscriptionally regulate gene expression and are important in tumorigenesis. previous deep sequencing identified the mirna profile of prostate carcinoma versus nonmalignant prostate tissue. here, we generated mirna expression profiles of prostate carcinoma by deep sequencing, with increasing tumor stage relative to corresponding nonmalignant and healthy prostate tissue, and detected clearly changed mirna expression patterns. the mirna profiles of the healthy and nonmalignant tissues were consistent with our previous findings, indicating a high fidelity of the method employed. in the tumors, quantitative real-time pcr (qrt-pcr) analysis of 40 paired samples of prostate carcinoma versus normal tissue revealed significant upregulation of mir-20a, mir-148a, mir-200b, and mir-375 and downregulation of mir-143 and mir-145. hereby, mir-375 increased from normal to organ-confined tumors (pt2 pn0), slightly decreased in tumors with extracapsular growth (pt3 pn0), but was then expressed again at higher levels in lymph node metastasizing (pn1) tumors. the sequencing data for mir-375 were confirmed by northern blotting and qrt-pcr. the regulation for other selected mirnas could, however, not be confirmed by qrt-pcr in individual tumor stages. mir-200b, in addition to mir-200c and mir-375 reduced the expression of sec23a. interestingly, mir-375, found by sequencing in pt2 upregulated by us and others in tumor versus normal tissue, and mir-15a, found by sequencing in pt2 and pt3 and in the metastasizing tumors, target the phosphatases phlpp1 and phlpp2, respectively. phlpp1 and phlpp2 dephosphorylate members of the akt family of signal transducers, thereby inhibiting cell growth. coexpression of mir-15a and mir-375 resulted in downregulation of phlpp1/2 and strongly increased prostate carcinoma cell growth. implications these genomic data reveal relevant mirnas in prostate cancer that may have biomarker and therapeutic potential.",1
"japanese encephalitis, west nile, usutu and murray valley encephalitis viruses form a tight subgroup within the larger flavivirus genus. these viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the ns2a protein. such peaks are generally indicative of functionally important non-coding sequence elements. the second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. the pseudoknot is preceded by a conserved slippery heptanucleotide (y ccu uuu), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. we hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. since cleavage at the ns1-ns2a boundary is known to require synthesis of ns2a in cis, the resulting transframe fusion protein is predicted to be ns1-ns2a(n-term)-foo. we hypothesize that this may explain the origin of the previously identified ns1 'extension' protein in jev-group flaviviruses, known as ns1'.",1
"therapeutic inhibition of the mir-34 family (mir-34a,-b,-c), or mir-34a alone, have emerged as promising strategies for the treatment of cardiac pathology. however, before advancing these approaches further for potential entry into the clinic, a more comprehensive assessment of the therapeutic potential of inhibiting mir-34a is required for two key reasons. first, mir-34a has ∼40% fewer predicted targets than the mir-34 family. hence, in cardiac stress settings in which inhibition of mir-34a provides adequate protection, this approach is likely to result in less potential off-target effects. secondly, silencing of mir-34a alone may be insufficient in settings of established cardiac pathology. we recently demonstrated that inhibition of the mir-34 family, but not mir-34a alone, provided benefit in a chronic model of myocardial infarction. inhibition of mir-34 also attenuated cardiac remodeling and improved heart function following pressure overload, however, silencing of mir-34a alone was not examined. the aim of this study was to assess whether inhibition of mir-34a could attenuate cardiac remodeling in a mouse model with pre-existing pathological hypertrophy. mice were subjected to pressure overload via constriction of the transverse aorta for four weeks and echocardiography was performed to confirm left ventricular hypertrophy and systolic dysfunction. after four weeks of pressure overload (before treatment), two distinct groups of animals became apparent: (1) mice with moderate pathology (fractional shortening decreased ∼20%) and (2) mice with severe pathology (fractional shortening decreased ∼37%). mice were administered locked nucleic acid (lna)-antimir-34a or lna-control with an eight week follow-up. inhibition of mir-34a in mice with moderate cardiac pathology attenuated atrial enlargement and maintained cardiac function, but had no significant effect on fetal gene expression or cardiac fibrosis. inhibition of mir-34a in mice with severe pathology provided no therapeutic benefit. thus, therapies that inhibit mir-34a alone may have limited potential in settings of established cardiac pathology.",1
"emerging evidence indicates that the mir-23a/24-2/27a cluster may possess a causal role in mammary tumorigenesis and function as a novel class of oncogenes. however, the regulatory mechanism of the mir-23a/24-2/27a cluster in mammary carcinoma cell invasion and migration is still largely unknown. we observed that the expression levels of mir-23a, mir-24-2 and mir-27a were significantly higher in breast cancer with lymph node metastasis, compared with that from patients without lymph node metastasis or normal tissue. forced expression of the mir-23a/24-2/27a cluster promoted mammary carcinoma cell migration, invasion, and hepatic metastasis, through targeting sprouty2 (spry2) and consequent activation of p44/42 mapk. epidermal growth factor induced the expression of the transcription factor c-myc, which promoted the expression of mature mir-23a, mir-24-2, and mir-27a and subsequently decreased expression of spry2 and activated p44/42 mapk to promote mammary carcinoma cell migration and invasion. we therefore suggest a novel link between epidermal growth factor and the mir-23a/24-2/27a cluster via the regulation of c-myc, providing the potential for the mir-23a/24-2/27a cluster to be used as biomarker in the diagnosis and/or treatment of breast cancer.",1
"the intestinal epithelium is remarkably robust despite perturbations and demand uncertainty. here, we investigate the basis of such robustness using novel tracing methods that allow simultaneously capturing the dynamics of stem and committed progenitor cells (called enteroblasts) and intestinal cell turnover with spatiotemporal resolution. we found that intestinal stem cells (iscs) divide ""ahead"" of demand during drosophila midgut homeostasis. their newborn enteroblasts, on the other hand, take on a highly polarized shape, acquire invasive properties and motility. they extend long membrane protrusions that make cell-cell contact with mature cells, while exercising a capacity to delay their final differentiation until a local demand materializes. this cellular plasticity is mechanistically linked to the epithelial-mesenchymal transition (emt) programme mediated by escargot, a snail family gene. activation of the conserved microrna mir-8/mir-200 in ""pausing"" enteroblasts in response to a local cell loss promotes timely terminal differentiation via a reverse met by antagonizing escargot. our findings unveil that robust intestinal renewal relies on hitherto unrecognized plasticity in enteroblasts and reveal their active role in sensing and/or responding to local demand.",1
"background pulmonary arterial hypertension (pah) is a fatal disease characterized by impaired regulation of pulmonary artery vascular growth and remodeling. aberrant expression of mir-17 has been shown to be involved in the pathogenesis of pah, but its underlying molecular mechanism has not been elucidated. material and methods mitofusin 2 (mfn2) expression was determined by qrt-pcr. the protein expression levels of mfn2, proliferating cell nuclear antigen (pcna), and pro-apoptotic protein cleaved caspase-3 were measured using western blot analysis. cell proliferation and apoptosis were assessed by celltiter-glo reagent and flow cytometry, respectively. caspase-3/7 activity was measured using an apo-one homogeneous caspase-3/7 assay kit. the regulation of mir-17 on mfn2 expression was assessed using luciferase reporter assay system. results mir-17 expression was upregulated in human pulmonary artery smooth muscle cells (hpasmcs) treated with hypoxia and lung tissues of pah patients. inhibition of mir-17 suppressed hypoxia-induced proliferation and promoted apoptosis in hpasmcs. mir-17 inhibited mfn2 expression by binding to its 3'-utr. decreased cell viability and increased apoptosis and caspase-3 activity were observed in the anti-mir-17 + sinc group compared with the anti-mir-nc + sinc group. the expression of cleaved caspase-3 was upregulated and the expression of pcna was downregulated in the anti-mir-17 + sinc group. moreover, these alterations were attenuated by knockdown of mfn2. conclusions mir-17 regulates proliferation and apoptosis in hpasmcs through mfn2 modulation. we found that mir-17 acts as a potential regulator of proliferation and apoptosis of hpasmcs, and that it might be developed as a promising new strategy for the treatment of pah.",1
"the drosophila toll signaling pathway mainly responds to gram-positive (g + ) bacteria or fungal infection, which is highly conserved with mammalian tlr signaling pathway. although many positive and negative regulators involved in the immune response of the toll pathway have been identified in drosophila , the roles of long noncoding rnas (lncrnas) in drosophila toll immune responses are poorly understood to date. in this study, our results demonstrate that lncrna-cr33942 is mainly expressed in the nucleus and upregulated after micrococcus luteus infection. especially, lncrna-cr33942 not only modulates differential expressions of multiple antimicrobial peptide genes but also affects the drosophila survival rate during response to g + bacterial infection based on the transiently overexpressing and the knockdown lncrna-cr33942 assays in vivo. mechanically, lncrna-cr33942 interacts with the nf-κb transcription factors dorsal-related immunity factor/dorsal to promote the transcriptions of antimicrobial peptides drosomycin and metchnikowin , thus enhancing drosophila toll immune responses. taken together, this study identifies lncrna-cr33942 as a positive regulator of drosophila innate immune response to g + bacterial infection to facilitate toll signaling via interacting with dorsal-related immunity factor/dorsal. it would be helpful to reveal the roles of lncrnas in toll immune response in drosophila and provide insights into animal innate immunity.",1
"multiple conserved mechanisms sense nutritional conditions and coordinate metabolic changes in the whole organism. we unravel a role for the drosophila homolog of p53 (dp53) in the fat body (fb; a functional analog of vertebrate adipose and hepatic tissues) in starvation adaptation. under nutrient deprivation, fb-specific depletion of dp53 accelerates consumption of major energy stores and reduces survival rates of adult flies. we show that dp53 is regulated by the microrna (mirna) machinery and mir-305 in a nutrition-dependent manner. in well-fed animals, tor signaling contributes to mir-305-mediated inhibition of dp53. nutrient deprivation reduces the levels of mirna machinery components and leads to dp53 derepression. our results uncover an organism-wide role for dp53 in nutrient sensing and metabolic adaptation and open up avenues toward understanding the molecular mechanisms underlying p53 activation under nutrient deprivation.",1
"the 3' untranslated region (3' utr) between the 3' end of env and the long terminal repeat is well conserved among avian retroviruses and is essential for efficient replication. deletion of the dr1 element within the 3' utr has been reported to have various effects, including reduced levels of unspliced rna in the cytoplasm, decreased stability of unspliced rna, decreased particle production, and decreased genomic rna packaging. to probe the role of specific sequences within dr1 in virus replication, site-directed mutagenesis was utilized to perturb parts of the predicted secondary structure of dr1. seven of thirteen mutations had no significant effect; the others resulted in an approximately 10- to 20-fold reduction in replication. these mutants were further characterized and found to impair cytoplasmic accumulation of unspliced rna only slightly. furthermore, no decreases were observed in the stability of the unspliced rna or in the production of virus particles. genomic rna packaging, however, was reduced by about 10-fold. similar amounts of particles were produced by cells containing the mutant and wild-type dna, and all particles contained similar levels of reverse transcriptase activity. the results suggest that the region of the dr1 disrupted by the mutations plays a role in genomic rna packaging, although that packaging may not be the only role for dr1.",1
"background rhd is an autoimmune disease that arises following infection by s. pyogenes and imposes a heavy burden on public health. material and methods we detected 11 selected mirnas expressed in the cardiac tissues of 11 rhd patients and 11 controls. by employing dual-luciferase assay and western blot, we identified the relationship between tlr2 and mir-101 and mir-101. we used elisa to test the concentration of tnf-α, il-1β, and il-6. results in cardiac tissue of rhd patients, mir-101 was significantly down-regulated (p=0.011). ectopically expressed mir-101 repressed the luciferase activity by 27% through targeting tlr2 3'utr. combined with the results of western blot, we confirmed that tlr2 is a direct target gene of mir-101. mir-101 knock-down is related to over-stimulated immune response in pgn-activated thp-1 cells. we detected a significantly higher concentration of tnf-α (p=0.0017), il-1β (p=0.015), and il-6 (p=0.014) in serum samples. tlr2 had a higher expression in patients in the protein level rather than the mrna level, indicating that post-transcriptional regulation factors play a crucial role in regulating tlr2 expression. conclusions the present study confirmed that mir-101 targets tlr2 3'utr and represses tlr2 expression. this work also found an association between down-regulated mir-101 and rheumatic heart disease.",1
"cholesterol 7alpha-hydroxylase (cyp7a1) plays a critical role in regulation of bile acid synthesis in the liver. cyp7a1 mrnas have very short half-lives, and bile acids destabilize cyp7a1 mrna via the 3'-untranslated region (3'-utr). however, the underlying mechanism of translational regulation of cyp7a1 mrna remains unknown. screening of a human micro rna (mirna) microarray has identified five differentially expressed mirnas in human primary hepatocytes treated with chenodeoxycholic acid, gw4064, or fibroblast growth factor (fgf)19. these compounds also significantly induced the expression of mir-122a, a liver-specific and the predominant mirna in human hepatocytes. the putative recognition sequences for mir-122a and mir-422a were localized in the 3'-utr of human cyp7a1 mrna. the mir-122a and mir-422a mimics inhibited, whereas their inhibitors stimulated cyp7a1 mrna expression. these mirnas specifically inhibited the activity of the cyp7a1-3'-utr reporter plasmids, and mutations of mirna binding sites in 3'-utr abrogated mirna inhibition of reporter activity. these results suggest that mir-122a and mir-422a may destabilize cyp7a1 mrna to inhibit cyp7a1 expression. however, these mirnas did not play a role in mediating fgf19 inhibition of cyp7a1 transcription. under certain conditions, mirna may reduce cyp7a1 mrna stability to inhibit bile acid synthesis, and the mir-122a antagomirs may stimulate bile acid synthesis to reduce serum cholesterol and triglycerides.",1
"understanding how p53 activates certain gene programs and not others is critical. here, we identify low-density lipoprotein receptor-related protein 1 (lrp1), a transmembrane endocytic receptor, as a p53 target gene. we show that, although lrp1 transcript expression is upregulated in response to both sub-lethal and lethal doses of p53-activating stress, lrp1 protein is only upregulated in response to sub-lethal stress. interestingly, lethal doses of p53-activating stress inhibit lrp1 de novo translation through an mirna-based translational repression mechanism. we show that the p53-regulated mirnas mir-103 and mir-107 are significantly upregulated by lethal doses of stress, resulting in suppression of lrp1 translation and cell death. our results define a negative feedback loop involving the p53-regulated coding gene lrp1 and p53-regulated mirna genes. these findings provide mechanistic insight into the selective expression of p53 target genes in response to different stress intensities to elicit either cell survival or cell death.",1
"interleukin-6 (il-6) is overexpressed and contributes to tumor cell growth in cholangiocarcinoma. enforced il-6 production can alter the expression of specific micrornas (mirnas) involved in tumor growth, and moreover can modulate expression of methylation-dependent genes. thus, we assessed the methylation-dependent regulation of mirna expression in human malignant cholangiocytes stably transfected to overexpress il-6. the expression of the methyltransferases dna methyltransferase enzyme-1 and hasj4442 was increased by il-6 overexpression, but was decreased by the methylation inhibitor 5-aza-2'-deoxycytidine (5-aza-cdr). expression profiling identified seven mirnas that were significantly downregulated by il-6 overexpression ( 2-fold) by 5-aza-cdr. one of these, mir-370, is embedded in a cpg island. although 5-aza-cdr increased mir-370 expression by 2.1-fold in malignant cells, the expression in nonmalignant cells was unchanged. the oncogene mitogen-activated protein kinase kinase kinase 8 (map3k8) was identified as a target of mir-370, and its expression was decreased by 5-aza-cdr in cholangiocarcinoma cells. overexpression of il-6 reduced mir-370 expression and reinstated map3k8 expression in vitro as well as in tumor cell xenografts in vivo. thus, il-6 may contribute to tumor growth by modulation of expression of selected mirnas, such as mir-370. these studies define a mechanism by which inflammation-associated cytokines can epigenetically modulate gene expression and directly contribute to tumor biology.",1
"the full repertoire of regulatory interactions utilized by human cells to control expression of amyloid-β precursor protein (app) is still undefined. we investigated here the contribution of microrna (mirna) to this regulatory network. several bioinformatic algorithms predicted mir-101 target sites within the app 3'-untranslated region (3'-utr). using reporter assays, we confirmed that, in human cell cultures, mir-101 significantly reduced the expression of a reporter under control of app 3'-utr. mutation of predicted site 1, but not site 2, eliminated this reporter response. delivery of mir-101 directly to human hela cells significantly reduced app levels and this effect was eliminated by co-transfection with a mir-101 antisense inhibitor. delivery of a specific target protector designed to blockade the interaction between mir-101 and its functional target site within app 3'-utr enhanced app levels in hela. therefore, endogenous mir-101 regulates expression of app in human cells via a specific site located within its 3'-utr. finally, we demonstrate that, across a series of human cell lines, highest expression of mir-101 levels was observed in model nt2 neurons.",1
"recent reports suggest that the adult epicardium is a source of cardiac progenitor cells having the ability to undergo epithelial-to-mesenchymal transition (emt) and predominantly differentiate into myofibroblasts, thereby contributing to fibrosis of the stressed myocardium. islet-1 (isl1) is a widely applied marker of progenitor cells, including the epicardial mesothelial cells (emcs). however, little is known of the general biological function of islet-1, let alone its role in emt of emcs. using rat-derived adult emc cultures we therefore investigated the role of isl1 expression in both non-stimulated emcs and during tgf-β-induced emt. we found that isl1 had a dual role by promoting mesenchymal features in non-stimulated emcs, while a loss of isl1 associated with emt acted as a negative modulator of emt progression as assessed on phenotype. we furthermore found that the loss of isl1 expression during emt was, in addition to transcriptional regulation by β-catenin, mediated through direct targeting by microrna-31 (mir-31). through manipulations of mir-31 bioactivity in emcs, we thus report that mir-31 is a negative modulator of cardiac fibrogenic emt, primarily via targeting isl1. our data show that isl1 is a key regulatory molecule in adult cardiac emt.",1
"the synthesis of ribosomes is one of the major metabolic pathways in all cells. in addition to around 75 individual ribosomal proteins and 4 ribosomal rnas, synthesis of a functional eukaryotic ribosome requires a remarkable number of trans-acting factors. here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast saccharomyces cerevisiae. these will underscore the unexpected complexity of eukaryotic ribosome synthesis.",1
"elongation and elevation of palatal shelves, mainly caused by proliferation and extra-cellular matrix synthesis of palatal mesenchymal cells (pmcs), are essential for normal palatal development. transforming growth factor beta (tgfb) pathway could induce proliferation inhibition and collagen synthesis in pmcs. recent studies found that mirna-17-92 (mir-17-92) cluster, including mir-17, mir-18a, mir-19a, mir-20a, mir-19b, and mir-92a, expressed in the 1st bronchial arch of mouse embryos during the period of palatal shelf elongation and elevation, and directly targeted tgfb pathway in cancer cell lines. whether mir-17-92 cluster expresses and targets tgfb pathway in pmcs has not yet been studied. using quantitative real-time rt-pcr, we found that mir-17-92 expressed in pmcs and decreased from embryonic day (e) 12 to e14 in palatal shelves. mtt assay and western blot showed that mir-17-92 inhibited tgfb1 induced proliferation inhibition and collagen synthesis in pmcs by decreasing tgfbr2, smad2, and smad4 protein level. further luciferase assay showed that mir-17 and mir-20a directly targeted 3′utr of tgfbr2, and that mir-18a directly targeted 3′utr of smad2 and smad4. we thus conclude that mir-17-92 cluster could inhibit tgfb pathway induced proliferation inhibition and collagen synthesis in pmcs by directly targeting tgfbr2, smad2, and smad4.",1
"the nucleoli of eukaryotic cells are the sites of ribosomal rna transcription and processing and of ribosomal subunit assembly. they contain multiple small nucleolar rnas (snornas), several of which are essential for rrna maturation. the u3, u8 and u13 snorna genes are transcribed independently, whereas u14-u24, as well as e3, are located within introns of protein-coding genes, most of whose functions are linked to translation. these snornas are co-transcribed with their host pre-mrnas and released by processing from excised introns. here we show that, in addition to u22, seven novel fibrillarin-associated snornas, named u25-u31, are encoded within different introns of the unusually compact mammalian u22 host gene (uhg). all seven rnas exhibit extensive (12-15 nucleotides) complementarity to different segments of the mature rrnas, followed by a c/auga ('u-turn') sequence. the spliced uhg rna, although it is associated with polysomes, has little potential for protein coding, is short-lived, and is poorly conserved between human and mouse. thus, the introns rather than the exons specify the functional products of uhg.",1
"micrornas (mirnas) are noncoding rnas with specific regulatory role in gene expression. recent reports suggested their involvement in human malignancies. currently, there is no information concerning mirna expression and functions in squamous cell carcinoma (scc) of tongue. in this study, we evaluated the expression patterns of 156 mature mirnas in tongue scc using taqman-based microrna assays. of these 156 mirnas, mir-133a and mir-133b were significantly reduced in tongue scc cells in comparison with the paired normal epithelial cells. tongue scc cell lines transfected with mir-133a and mir-133b precursors displayed reduction in proliferation rate. in addition, the number of apoptotic cells was increased in response to the introduction of precursors. computational target gene prediction suggested that both mir-133a and mir-133b are targeting transcript of pyruvate kinase type m2 (pkm2), a potential oncogene in solid cancers. in tongue scc cell lines, pkm2 expression was reduced in response to mir-133a and mir-133b precursors transfection. immunohistochemical staining results of tongue scc tissues suggested that pkm2 was overexpressed in tongue scc and was associated with the downregulation of mir-133a and mir-133b. our results suggested that aberrant reduction of mir-133a and mir-133b was associated with the dysregulation of pkm2 in scc of tongue.",1
"tmrna employs both trna-like and mrna-like properties as it rescues stalled bacterial ribosomes, while targeting the defective mrna and incomplete nascent protein for degradation. we describe variation of the tmrna gene (ssra) and how it informs tmrna structure and function. endosymbiont tmrnas tend to lose secondary structure and length in the mrna-like region as nucleotide composition drifts with that of the whole genome. a dramatic gene structure variation is circular permutation, which produces two-piece tmrnas in three bacterial lineages; new sequences blur these lineages. we present evidence that sinorhizobium two-piece tmrna retains the 5'-triphosphate of transcriptional initiation and predict a new structure at the 5' end of cyanobacterial two-piece tmrna precursor. ssra is a target for some mobile dnas and a passenger on others. it has been found interrupted (but not functionally disrupted) by mobile elements such as group i introns, genomic islands and palindromic elements. the alphaproteobacterial permuted genes are significantly less frequently interrupted by genomic islands than are their standard counterparts, yet are a hotspot for insertion or swapping of rickettsial palindromic elements, in contrast to other rickettsial loci that show steady decay of a single ancestral element. bacteriophages, plasmids and genomic islands can carry tmrna genes; we describe a native bacterial ssra disrupted by insertion of a genomic island that carries its own ssra, a genome encoding both one- and two-piece tmrna, and a phage encoding a tmrna variant lacking the mrna-like function, which may counteract host tmrna during infection.",1
"micrornas, a class of 22-nucleotide non-coding rnas, modulate gene expression by associating with the 3'-untranslated regions (3'-utrs) of messenger rnas (mrnas). although multiple mirnas are known to be regulated during angiogenesis, their individual roles in blood vessel development are still not fully understood. herein, we investigate the role of mir-29c in regulating cell cycle and angiogenic phenotype of endothelial cells. the results showed that igf-1 is highly expressed and down-regulated by mir-29c in human umbilical vein endothelial cells (huvec). consistent with this preliminary finding, introduction of exogenous mir-29c or mir-29c inhibitor alters cell cycle progression, proliferation and tube formation of huvec, respectively. furthermore, by using luciferase reporter assay, we find that the expression of igf-1, a suppressor transcription factor, is directly regulated by mir-29c through 3'-utr. in addition, we show that the selective inhibition of pi3k/akt pathway prior to mir-29c stimulation prevents the expression of angiogenesis suppressor mirnas that are family and cluster specific. as a conclusion, we find that mir-29c plays a significant role in regulating cell cycle, proliferation and angiogenic properties of huvecs. this function is likely mediated through igf-1 proteins at the post-transcriptional level. as a novel molecular target, mir-29c may have a potential value in the treatment of angiogenesis-associated diseases, such as cardiovascular diseases and cancers.",1
"having a better grasp of the molecular mechanisms underlying carcinogenesis and progression in osteosarcoma would be helpful to find novel therapeutic targets. different types of cancers have presented abnormal expression of mirna-101 (mir-101). nevertheless, we still could not figure out what expression of mir-101 in human osteosarcoma is and its biological function. thus, we conducted the present study to identify its expression, function, and molecular mechanism in osteosarcoma. we detected the expression of mir-101 in osteosarcoma samples and cell lines. the effects of mir-101 on osteosarcoma cells' proliferation and invasion were evaluated. luciferase reporter assay was applied to identify the direct target of mir-101. compared with adjacent normal specimens and normal bone cell line by using qpcr, the expression levels of mir-101 in osteosarcoma specimens and human osteosarcoma cell lines distinctly decreased. according to function assays, we found that overexpression of mir-101 significantly inhibited the cell proliferation and invasion in osteosarcoma cells. moreover, we confirmed that zinc finger e-box binding homeobox 2 (zeb2) was a direct target of mir-101. in addition, overexpression of zeb2 could rescue the inhibition effect of proliferation and invasion induced by mir-101 in osteosarcoma cells. mir-101 has been proved to be down-regulated in osteosarcoma and has the ability to suppress osteosarcoma cell proliferation and invasion by directly targetting zeb2.",1
"terminal differentiation of distinct cell types requires the transcriptional activation of differentiation-specific genes and the suppression of genes associated with the precursor cell. for example, the expression of utrophin (utrn) is suppressed during skeletal muscle differentiation, and it is replaced at the sarcolemma by the related dystrophin protein. the myod transcription factor directly activates the expression of a large number of skeletal muscle genes, but also suppresses the expression of many genes. to characterize a mechanism of myod-mediated suppression of gene expression, we investigated two genes that are suppressed in fibroblasts converted to skeletal muscle by myod, follistatin-like 1 (fstl1) and utrn. myod directly activates the expression of a muscle-specific microrna (mirna), mir-206, which targets sequences in the fstl1 and utrn rna, and these sequences are sufficient to suppress gene expression in the presence of mir-206. these findings demonstrate that myod, in addition to activating muscle-specific genes, induces mirnas that repress gene expression during skeletal muscle differentiation.",1
"adult organisms must sense and adapt to environmental fluctuations. in high-turnover tissues such as the intestine, these adaptive responses require rapid changes in gene expression that, in turn, likely involve posttranscriptional gene control. however, intestinal-tissue-specific microrna (mirna)-mediated regulatory pathways remain unexplored. here, we report the role of an intestinal-specific mirna, mir-958 , that non-cell autonomously regulates stem cell numbers during tissue homeostasis and regeneration in the drosophila adult midgut. we identify its downstream target cabut , the drosophila ortholog of mammalian klf10/11 transcription factors, which mediates this mir-958 function by promoting paracrine enterocyte-to-stem-cell bone morphogenetic protein (bmp) signaling. we also show that mature mir-958 levels transiently decrease in response to stress and that this decrease is required for proper stem cell expansion during tissue regeneration. in summary, we have identified a posttranscriptional mechanism that modulates bmp signaling activity within drosophila adult intestinal tissue during both normal homeostasis and tissue regeneration to regulate intestinal stem cell numbers.",1
"background micrornas (mirnas) are a class of small non-coding rnas that play important roles in carcinogenesis. in the present study, we investigated the effect of mir-212 on pancreatic ductal adenocarcinoma (pdac) and its target protein. methods quantitative real-time pcr(qrt-pcr) was performed to detect the expression of mir-212 in pdac tissues and pancreatic cancer cell lines. mir-212 mimic, mir-212 inhibitor and negative control were transfected into pancreatic cancer cells and the effect of mir-212 up-regulation and down-regulation on the proliferation, migration and invasion of cells were investigated. furthermore, the mrna and protein levels of patched-1(ptch1) were measured. meanwhile, luciferase assays were performed to validate ptch1 as mir-212 target in pdac. results mir-212 was up-regulated in pdac tissues and cells.using both gain-of function and loss-of function experiments, a pro-oncogenic function of mir-212 was demonstrated in pdac. moreover, up-regulated of ptch1 could attenuate the effect induced by mir-212. conclusion these data suggest that mir-212 could facilitate pdac progression and metastasis through targeting ptch1, implicating a novel mechanism for the progression of pdac.",1
"in a previous study, we reported that microrna (mirna) precursors are expressed in synaptic fractions within adult mouse forebrain, where they are enriched at post-synaptic densities (psds). however, because that study employed qrt-pcr primers that recognize the hairpin region, it was not able to distinguish between primary microrna gene transcripts (pri-mirs) and small hairpin precursors (pre-mirs). here, using primer sets that selectively measure regions upstream, downstream and flanking the hairpin, we demonstrate that pri-mirs are present in synaptic fractions (enriched several-fold relative to total tissue homogenate) and are especially enriched in isolated psds. drosha and dgcr8 proteins are also expressed in synaptic fractions and psds, and are tightly associated with pri-mirs as assessed by coimmunoprecipitation under stringent conditions. pri-mirs, drosha, and dgcr8 are highly enriched in fractions that contain mrna transport particles, and cytosolic drosha is associated with kinesin heavy chain; these findings suggest that pri-mirs are transported to synaptic regions in a manner similar to mrnas. this study supports the notion that mirna biogenesis occurs locally near synapses in a regulated fashion.",1
"the transcription factor myb has a key role in hematopoietic progenitor cells (hpcs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. we previously demonstrated that myb controls erythroid versus megakaryocyte lineage decision by transactivating klf1 and lmo2 expression. to further unravel the molecular mechanisms through which myb affects lineage fate decision, we performed the integrative analysis of mirna and mrna changes in myb-silenced human primary cd34+ hpcs. among the mirnas with the highest number of predicted targets, we focused our studies on hsa-mir-486-3p by demonstrating that myb controls mir-486-3p expression through the transactivation of its host gene, ankyrin-1 (ank1) and that mir-486-3p affects hpcs commitment. indeed, overexpression and knockdown experiments demonstrated that mir-486-3p supports the erythropoiesis while restraining the megakaryopoiesis. of note, mir-486-3p also favors granulocyte differentiation while repressing the macrophage differentiation. to shed some light on the molecular mechanisms through which mir-486-3p affects hpcs lineage commitment, we profiled the gene expression changes upon mir-486-3p overexpression in cd34+ cells. among the genes downregulated in mir-486-3p-overexpressing hpcs and computationally predicted to be mir-486-3p targets, we identified maf as a mir-486-3p target by 3'utr luciferase reporter assay. noteworthy, maf overexpression was able to partially reverse the effects of mir-486-3p overexpression on erythroid versus megakaryocyte lineage choice. moreover, the myb/maf co-silencing constrained the skewing of erythroid versus megakaryocyte lineage commitment in myb-silenced cd34+ cells, by restraining the expansion of megakaryocyte lineage while partially rescuing the impairment of erythropoiesis. therefore, our data collectively demonstrate that myb favors erythropoiesis and restrains megakaryopoiesis through the transactivation of mir-486-3p expression and the subsequent downregulation of maf. as a whole, our study uncovers the myb/mir-486-3p/maf axis as a new mechanism underlying the myb-driven control of erythroid versus megakaryocyte lineage fate decision.",1
"genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes dna methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. genes subject to imprinting are often organised in clusters associated with large non-coding rnas (ncrnas), some of which have cis-regulatory functions. here we have undertaken a detailed allelic expression analysis of an imprinted domain on mouse proximal chromosome 10 comprising the paternally expressed plagl1 gene. we identified three novel plagl1 transcripts, only one of which contains protein-coding exons. in addition, we characterised two unspliced ncrnas, hymai, the mouse orthologue of hymai, and plagl1it (plagl1 intronic transcript), a transcript located in intron 5 of plagl1. imprinted expression of these novel ncrnas requires dnmt3l-mediated maternal dna methylation, which is also indispensable for establishing the correct chromatin profile at the plagl1 dmr. significantly, the two ncrnas are retained in the nucleus, consistent with a potential regulatory function at the imprinted domain. analysis with catrapid, a protein-ncrna association prediction algorithm, suggests that hymai and plagl1it rnas both have potentially high affinity for trithorax chromatin regulators. the two ncrnas could therefore help to protect the paternal allele from dna methylation by attracting trithorax proteins that mediate h3 lysine-4 methylation.",1
"non-coding micrornas (mirnas) have been proposed to play diverse roles in cancer biology, including epithelial-mesenchymal transition (emt) crucial for cancer progression. previous comparative studies revealed distinct expression profiles of mirnas relevant to tumorigenesis and progression of oral cancer. with putative targets of these mirnas mostly validated in vitro , it remains unclear whether similar mirna-target relationships exist in vivo . in this study, we employed a hybrid approach, utilizing both drosophila melanogaster and human oral cancer cells, to validate projected mirna-target relationships relevant to emt. notably, overexpression of dme-mir-133 resulted in significant tissue growth in drosophila larval wing discs. the rt-pcr analysis successfully validated a subset of its putative targets, including pde1c . subsequent experiments performed in oral cancer cells confirmed conserved targeting of human pde1c by hsa-mir-133 . furthermore, the elevated level of mir-133 and its targeting of pde1c was positively correlated with enhanced migrative ability of oral cancer cells treated with lps, along with the molecular signature of a facilitated emt process induced by lps and tgf-β. the analysis on the rnaseq data also revealed a negative correlation between the expression level of hsa-mir-133 and the survival of oral cancer patients. taken together, our mammal-to- drosophila -to-mammal approach successfully validates targeting of pde1c by mir-133 both in vivo and in vitro , underlying the promoted emt phenotypes and potentially influencing the prognosis of oral cancer patients. this hybrid approach will further aid to widen our scope in investigation of intractable human malignancies, including oral cancer.",1
"micrornas (mirnas) are increasingly reported to have important roles in diverse biological and pathological processes. changes in abundance of muscle-specific microrna, mir-1, have been implicated in cardiac disease, including arrhythmia and heart failure. however, the specific molecular targets and cellular mechanisms involved in the mir-1 function in the heart are only beginning to emerge. in this study, we investigated mir-1 expression and its potential role in the mouse model of viral myocarditis (vmc). the expression levels of mir-1 and its target gene connexin 43 (cx43) were measured by real-time pcr and western blotting, respectively. the mir-1 expression levels were significantly increased in cardiac myocytes from vmc mice in comparison with control samples (relative expression: 10 ± 2.5 vs. 31 ± 7.6, p < 0.05). among the target genes of mir-1, the expression cx43 protein was significantly reduced in such mice while there was no significant difference in the its mrna levels. our results revealed an inverse correlation between mir-1 levels and cx43 protein expression in vmc samples. using a bioinformatics-based approach, we found two identical potential binding sites were found in mouse mir-1 and cx43 3'- untranslated region, this confirms a possible regulatory role of mir-1. in cultured, mirna transfected myocardial cells, we show overexpression of mir-1 accompanied by a decrease in cx43 protein's expression. there was only a slight (not statistically significant) drop in cx43 mrna levels. our results indicate that mir-1 is involved in vmc via post-transcriptional repression of cx43, and might constitute potentially valuable data for the development of a new approach in the treatment of this disease.",1
"background/aims this study was developed to investigate a potential therapeutic method for myocardial ischemia/reperfusion injury involving the promotion of mir-24-3p expression. methods microarray analysis was used to screen differentially expressed genes in a myocardial ischemia/reperfusion (i/r) injury mouse model. gene set enrichment analysis was utilized to determine vital signaling pathways. targeting verification was conducted with a luciferase reporter assay. myocardial i/r injury was developed in mice, and the expression levels of ripk1 and mir-24-3p were investigated by qrt-pcr and western blot. hemodynamic parameters and the activity of serum myocardial enzymes were measured to evaluate cardiac function. infarct area was observed through he and ttc staining. myocardial cell apoptosis was examined by tunel staining and caspase-3 activity analysis. results ripk1 was an upregulated mrna found by microarray analysis and a verified target of the downregulated mirna mir-24-3p. the upregulation of ripk1 (1.8-fold) and the downregulation of mir-24-3p (0.3-fold) were confirmed in i/r mice. ripk1 led to impaired cardiac function indexes, increased infarct area and cell apoptosis, while mir-24-3p could reverse the injury by regulating ripk1. the tnf signaling pathway was proven to be involved in myocardial i/r injury through the detection of the dysregulation of related proteins. conclusion in conclusion, ripk1 was upregulated and mir-24-3p was downregulated in a myocardial i/r injury mouse model. ripk1 could aggravate myocardial i/r injury via the tnf signaling pathway, while mir-24-3p could suppress ripk1 and therefore exert cardioprotective effects in myocardial i/r injury.",1
"background micrornas (mirnas) are regulatory molecules that play an important role in many physiological processes, including cell growth, differentiation, and apoptosis. in addition to modulating normal cellular functions, it has also been reported that mirnas are involved in the development of many pathologies, including cardiovascular diseases, cancer, inflammation, and neurodegeneration. methods for the sensitive detection and measurement of specific mirnas and their cellular targets are essential for both basic research endeavours, as well as diagnostic efforts aimed at understanding the role of mirnas in disease processes. findings in this study, we describe a novel, imaging cytometry-based protocol that allows for simultaneous visualisation and quantification of mirnas and their putative targets. we validated this methodology in a neuronal cell line by examining the relationship of the mirna mir-124 and its known target, cyclin dependent kinase 6 (cdk6). we found that ectopic overexpression of mir-124 resulted in the downregulation of cdk6, decreased cellular proliferation, and induced cellular morphological changes. conclusions this method is suitable for analysing the expression and cellular localisation of mirnas and target proteins in small cell subsets within a heterogeneous cell suspension. we believe that our cytometry-based methodology will be easily adaptable to mirna studies in many areas of biomedical research including neuroscience, stem cell biology, immunology, and oncology.",1
"osteogenic differentiation of human mesenchymal stem cells (hmscs) is regulated by multiple transcription factors and signaling molecules. however, the molecular mechanisms underlying this process remain to be fully elucidated. micrornas (mirnas) act as key regulators in various biological processes by mediating mrna degradation or translational inhibition of target genes. in this study, we report that mir-346 plays critical roles in regulating osteogenic differentiation of hbmscs. the expression of endogenous mir-346 was increased during osteogenic differentiation of hbmscs. overexpression of mir-346 significantly promoted osteogenic differentiation, whereas mir-346 depletion suppressed this process. further studies confirmed that mir-346 directly targeted the 3'-utr of the glycogen synthase kinase-3β (gsk-3β) gene so as to suppress the expression of gsk-3β protein. similar to mir-346 overexpression, gsk-3β depletion promoted osteogenic differentiation, whereas gsk-3β overexpression reversed the promotional effect of mir-346. we further found that mir-346 overexpression activated the wnt/β-catenin pathway and increased the expression of several downstream genes including cyclind1, c-myc, tcf-1 and lef-1. depletion of β-catenin almost completely blocked the positive role of mir-346 on osteogenic differentiation. taken together, our data indicate that mir-346 positively regulates hbmsc osteogenic differentiation by targeting gsk-3β and activating the wnt/β-catenin pathway.",1
"background micrornas (mirnas) are identified as crucial gene regulators in response to myocardial infarction (mi). however, the overall relationships between mirnas and the gene targets which contribute to the cellular phenotypes in mi are not fully elucidated. to make a better understanding towards functional roles of mirnas in mi, useful information was mined through bioinformatic techniques. method mi-related mirnas were retrieved from publications, and pictar, targetscans, and miranda programs were used to predict their gene targets. gene ontology (go) and pathway analyses of gene targets were applied to uncover functional roles of mirnas. the mirna-gene networks were illustrated by pajek tool. finally, validation experiments were performed towards two important mirnas in the networks. result up to 119 mi-related mirnas were retrieved from publications. go and pathway analyses for their predicted gene targets demonstrated that these dysregulated mirnas were enriched in cardiovascular-related phenotypes. through illustrating mirna-gene networks, overall relationships between mirnas and gene targets were detected especially in processes of apoptosis and angiogenesis. moreover, experimental data supported bioinformatic predictions that mir-106b served as an anti-apoptotic modulator through inhibition of p21 expression and mir-15b displayed anti-angiogenesis activity. conclusion the mirnas played essential roles in pathological processes of mi. further, mir-106b and mir-15b maybe mediated as robust regulators in apoptosis or angiogenesis following mi, respectively.",1
"pancreatic cancer is one of the most common types of cancers in the whole world with a poor prognosis. finding out how the cancer form and develop is the most important way to cure this cancer. mirnas, 21-22 nucleotides regulatory small non-coding rnas, have been found to be critical involved in the growth of pancreatic cancer. in this study, we found that mir-92a was up regulated in three kinds of human pancreatic cancer cell lines. there is a correlation between mir-92a and malignant degree of human pancreatic cancer cell lines. then we found that mir-92a was essential for promoting cell proliferation in human pancreatic cancer. inhibition of the function of mir-92a repressed the proliferation of pancreatic cancer cells. further, we found that mir-92a enhanced the activation of jnk signalling pathway by directly targeting the jnk signalling inhibitor dusp10. dusp10 is responsible for mir-92a induced jnk signalling and cell proliferation. altogether, our study showed a mir-92a/dusp10/jnk signalling pathway that plays an important role in regulating the proliferation of pancreatic cancer cells.",1
"micrornas (mirnas) are a class of small non-coding rnas that, in general, negatively regulate gene expression. they have been identified in various tumor types, showing that different sets of mirnas are usually deregulated in different cancers. some mirna genes harboring cpg islands undergo methylation-mediated silencing, a characteristic of many tumor suppressor genes. to identify such mirnas in hepatocellular carcinoma (hcc), we first examined the methylation status of 43 loci containing cpg islands around 39 mature mirna genes in a panel of hcc cell lines and non-cancerous liver tissues as controls. among 11 mirna genes frequently methylated in hcc cell lines but not in non-cancerous liver tissues, three mirna genes, i.e. mir-124, mir-203 and mir-375, were selected as silenced mirnas through cpg-island methylation by comparing methylation and expression status and evaluating restored expression after treatment with 5-aza-2'-deoxycytidine. in primary tumors of hcc with paired non-tumorous liver tissues, only mir-124 and mir-203 showed frequent tumor-specific methylation, and their expression status was inversely correlated with methylation status. ectopic expression of mir-124 or mir-203 in hcc cells lacking their expression inhibited cell growth, with direct downregulation of possible targets, cyclin-dependent kinase 6 (cdk6), vimentin (vim), set and mynd domain containing 3 (smyd3) and iq motif containing gtpase activating protein 1 (iqgap1) or atp-binding cassette, subfamily e, member 1 (abce1), respectively. our results suggest that mir-124 and mir-203 are novel tumor-suppressive mirnas for hcc epigenetically silenced and activating multiple targets during hepatocarcinogenesis.",1
"background this study was aimed to investigate the role and specific molecular mechanism of hif1a-as2/mir-665/il6 axis in regulating osteogenic differentiation of adipose-derived stem cells (ascs) via the pi3k/akt signaling pathway. methods rnas' expression profile in normal/osteogenic differentiation-induced ascs (osteogenic group) was from the gene expression omnibus database. the analysis was carried out using bioconductor of r. gene set enrichment analysis and kyoto encyclopedia of genes and genomes dataset were applied to identify up- and downregulated signaling pathways. co-expression network of specific lncrnas and mrnas was structured by cytoscape, while binding sites amongst lncrna, mrna, and mirna were predicted by targetscan and miranda. ascs were derived from human adipose tissue and were authenticated by flow cytometry. asc cell function was surveyed by alizarin red and alkaline phosphatase (alp) staining. molecular mechanism of hif1a-as2/mir-665/il6 axis was investigated by rnai, cell transfection, western blot, and qrt-pcr. rna target relationships were validated by dual-luciferase assay. results hif1a-as2 and il6 were highly expressed while mir-665 was lowly expressed in induced ascs. hif1a-as2 and il6 improved the expression level of osteoblast markers runx2, osterix, and osteocalcin and also accelerated the formation of calcium nodule and alp activity, yet mir-665 had opposite effects. hif1a-as2 directly targeted mir-665, whereas mir-665 repressed il6 expression. moreover, the hif1a-as2/mir-665/il6 regulating axis activated the pi3k/akt signaling pathway. conclusions lncrna hif1a-as2 could sponge mir-665 and hence upregulate il6, activate the pi3k/akt signaling pathway, and ultimately promote asc osteogenic differentiation.",1
"many positive stand rna viral genomes lack the poly(a) tail that is characteristic of cellular mrnas and that promotes translation in cis. the 3' untranslated regions (utrs) of such genomes are expected to provide similar translation-enhancing properties as a poly(a) tail, yet the great variety of 3' sequences suggests that this is accomplished in a range of ways. we have identified a translational enhancer present in the 3' utr of turnip yellow mosaic virus (tymv) rna using luciferase reporter rnas with generic 5' sequences transfected into plant cells. the 3' terminal 109 nucleotides comprising the trna-like structure (tls) and an upstream pseudoknot (upsk) act in synergy with a 5'-cap to enhance translation, with a minor contribution in stabilizing the rna. maximum enhancement requires that the rna be capable of aminoacylation, but either the native valine or engineered methionine is acceptable. mutations that decrease the affinity for translation elongation factor eef1a (but also diminish aminoacylation efficiency) strongly decrease translational enhancement, suggesting that eef1a is mechanistically involved. the upsk seems to act as an important, though nonspecific, spacer element ensuring proper presentation of a functional tls. our studies have uncovered a novel type of translational enhancer and a new role for a plant viral tls.",1
"mir-181a has been presumed to target the 3'-untranslated regions (3'-utr) of il1a based on software predictions. mir-181a and il1a have opposite expression levels in monocytes and macrophages in the inflammatory state. this led us to suspect that mir-181a has an important function in regulating inflammatory response by targeting il1a. fluorescence reporter assays showed that mir-181a effectively binds to the 3'-utr of il1a. the anti-inflammatory functions of mir-181a were investigated in lipopolysaccharides (lps)-induced raw264.7 and phorbol 12-myristate 13-acetate (pma)/lps-induced thp-1 cells. we found that mir-181a mimics significantly lowered il1a expression levels in these cells and, interestingly, mir-181a inhibitors reversed this decrease. in addition, mir-181a mimics significantly inhibited increase in the levels of inflammatory factors (il1b, il6, and tnfa) in these cells. furthermore, mir-181a mimics and inhibitors decreased and increased, respectively, production of reactive oxygen species in pma/lps-induced thp-1 cells. these results indicate that mir-181a regulates inflammatory responses by directly targeting the 3'-utr of il1a and down-regulating il1a levels. interestingly, we found that mir-181a inhibited production of inflammatory factors even in il1a-induced thp-1 cells, suggesting that the anti-inflammatory effects of mir-181a possibly involves other targets in addition to il1a. thus, we provide the first evidence for anti-inflammatory effects of mir-181a mediated at least in part by down-regulating il1a.",1
"background chemoresistance hinders the curative cancer chemotherapy. micrornas (mirnas) are key players in diverse biological processes including the chemoresistance of cancers. methods a rna-seq-based mir-omic analysis of osteosarcoma (os) cells was performed to detect the levels of mir-34a-5p. bioinformatics analysis revealed that agtr1 is one of the target genes of mir-34a-5p. the mrna and protein levels of agtr1 were detected in both the mir-34a-5p-mimic transfected g-292 and mir-34a-5p-antagomir transfected sjsa-1 cells. the involvement of agtr1 with os chemoresistance was validated by the experiments with sirna-mediated repression or overexpression of the agtr1 gene. results we showed that mir-34a-5p promotes the multi- chemoresistance of os. the angiotensin ii type 1 receptor (agtr1) gene, is one of the targets of mir-34a-5p in os and thus negatively correlates with os chemoresistance by systematic investigations of a multi-drug sensitive (g-292) and resistant (sjsa-1) os cell lines. down-regulation of the agtr1 expression by sirna passivates g-292 cells and suppresses cell apoptosis, while over-expression of agtr1 sensitizes sjsa-1 cells and thus promotes the drug-triggered cell death. conclusions the mir-34a-5p and its target gene agtr1 are the potential targets for an effective chemotherapy of os. our results also provide novel insights into the effective chemotherapy for os patients.",1
"human gastric cancers contain a population of gastric cancer stem cells (gcscs) that can undergo self-renewal and multipotent differentiation. gcscs can be enriched with epcam+/cd44+ gastric cancer cells. however, the underlying mechanisms controlling the balance of gcsc self-renewal and differentiation remain to be explored. because mirnas can regulate cancer cell fates, we compared mirna expression in tumorspheric cancer cells enriched with gcscs and more differentiated cells. we found that the mir-17-92 cluster members mir-19b, mir-20a and mir-92a were gradually reduced during the differentiation of gcscs. therefore, we speculated that mir-17-92 members might regulate the self-renewal ability of gcscs. by downregulating mir-19b, mir-20a and mir-92a in epcam+/cd44+ gcscs, or overexpressing them in epcam-/cd44- non-gcsc populations, we found that mir-19b, mir-20a and mir-92a could sustain the self-renewal function of gcscs. furthermore, we found that mir-19b, mir-20a and mir-92a could also promote the proliferation of gastric cancer cells. mir-17-92 targeted the e2f1 and hipk1 proteins, which suppressed wnt-β-catenin signaling. a real-time pcr analysis of mir-19b, mir-20a and mir-92a expression in 97 gastric cancer specimens suggested that mir-92a could be used as an independent prognostic factor in gastric cancer. this study showed that several members of the mir-17-92 cluster, mir-19b, mir-20a and mir-92a, might play important roles in the development of gastric cancer stem cells and that mir-92a has the potential to be used as a predictive prognostic marker in gastric cancer.",1
"despite the growing number of genome-wide association studies, the involvement of polymorphisms in microrna target sites (polymirts) in alzheimer's disease (ad) remains poorly investigated. recently, we have shown that ad-associated single-nucleotide polymorphisms (snps) present in the 3' untranslated region (3'utr) of amyloid precursor protein (app) could directly affect mirna function. in theory, loss of microrna (mirna) function could lead to risk for ad by increasing app expression and aβ peptide production. in this study, we tested the hypothesis that nicastrin, a γ-secretase subunit involved in aβ generation, could be regulated by mirnas, and consequently affected by 3'utr polymorphisms. bioinformatic analysis identified 22 putative mirna binding sites located in or near nicastrin 3'utr polymorphisms. from these mirna candidates, six were previously shown to be expressed in human brain. we identified mir-24, mir-186, and mir-455 as regulators of nicastrin expression, both in vitro and under physiological conditions in human cells, which resulted in altered aβ secretion. using luciferase-based assays, we further demonstrated that rs113810300 and rs141849450 snps affected mirna-mediated repression of nicastrin. notably, rs141849450 completely abolished the mir-455-mediated repression of nicastrin. finally, the rs141849450 variant was identified in 1 out of 511 ad cases but not in 631 controls. these observations set the stage for future studies exploring the role of mirnas and 3'utr polymorphisms in ad.",1
"nuage is a germline-unique perinuclear structure conserved throughout the animal kingdom. maelstrom (mael) is an unusual nuage component, as it is also found in the nucleus. mael contains a high mobility group box, known to mediate dna binding. we show that mael nuclear function is required for proper differentiation in the drosophila germline stem cell (gsc) lineage. in mael mutant testes, transit-amplifying cysts fail to differentiate into primary spermatocytes, instead breaking down into ectopic gscs and smaller cysts, due to a depletion of bag-of-marbles (bam) protein. mael regulates bam via repression of mir-7. mael binds the mir-7 promoter and is required for the local accumulation of hp1 and h3k9me3. mir-7 targets bam directly at its 3'utr, and a reduction in mir-7 expression can rescue germline differentiation defects found in mael mutants by alleviating bam repression. we propose that mael ensures proper differentiation in the gsc lineage by repressing mir-7.",1
"micrornas (mirnas) represent a class of small non-coding rnas that regulate gene expression at the post-transcriptional levels. recent studies show that mirnas may function as oncogenes or tumor suppressor genes. in this study, we demonstrated that mir-518b was down-regulated in esophageal squamous cell carcinoma (escc) tissues and correlated with metastasis and survival. mir-518b suppressed the proliferation by inducing apoptosis and repressed the invasion in escc cells, but had no effect on the cell cycle. furthermore, rap1b was revealed to be directly regulated by mir-518b. these findings indicate that mir-518b may function as a tumor suppressor by targeting rap1b in the development of escc and has important clinical and prognostic value.",1
"maternally inherited noncoding rnas (ncrnas) can regulate zygotic gene expression across generations . recently, many stable intronic sequence rnas (sisrnas), which are byproducts of pre-mrna splicing, were found to be maternally deposited and persist till zygotic transcription in xenopus and drosophila . in various organisms, sisrnas can be in linear or circular conformations, and they have been suggested to regulate host gene expression . it is unknown whether maternally deposited sisrnas can regulate zygotic gene expression in the embryos. here, we show that a maternally inherited sisrna (sisr-4) from the deadpan locus is important for embryonic development in drosophila. mothers, but not fathers, mutant for sisr-4 produce embryos that fail to hatch. during embryogenesis, sisr-4 promotes transcription of its host gene (deadpan), which is essential for development. interestingly, sisr-4 functions by activating an enhancer present in the intron where sisr-4 is encoded. we propose that a maternal sisrna triggers expression of its host gene via a positive feedback loop during embryogenesis.",1
"a growing number of studies have suggested micrornas (mirnas) are involved in the modulation of myocardial ischemia-reperfusion (mi/r) injury; however, the role of endogenous mirnas targeting endothelial cells (ecs) and its interaction with icam-1 in the setting of mi/r remain poorly understood. our microarray results showed that mir-146a, mir-146b-5p, mir-155*, mir-155, mir-497, and mir-451 were significantly upregulated, whereas, mir-141 and mir-564 were significantly downregulated in the ecs challenged with tnf-α for 6 h. real-time pcr analyses additionally validated that the expression levels of mir-146a, mir-155*, and mir-141 were consistent with the microarray results. then, icam-1 was identified as a novel target of mir-141 by target scan software and the reporter gene system. further functional experiments showed that elevated levels of mir-141 inhibited icam-1 expression and diminished leukocytes adhesion to ecs in vitro. in an in vivo murine model of mi/r injury, pretreatment with mir-141 mimics through the tail vein downregulated the expression level of icam-1 in heart and attenuated mi/r injury as evidenced by decreased infarct size and decline of serum cardial troponin i (ctni) and lactate dehydrogenase (ldh) concentration. the cardioprotective effects of mir-141 mimics may be attributed to the decreased infiltration of cd11b(+) cells and f4/80(+) macrophages into ischemic myocardium tissue. in conclusion, our results demonstrate that mir-141, as a novel repressor of icam-1, is involved in the attenuation of mi/r injury via antithetical regulation of icam-1 and inflammatory cells infiltration. thus mir-141 may constitute a new therapeutic target in the setting of ischemic heart disease.",1
"the hippo pathway is an evolutionarily conserved regulator of organ growth and tumorigenesis. in drosophila , oncogenic ras v12 cooperates with loss-of-cell polarity to promote hippo pathway-dependent tumor growth. to identify additional factors that modulate this signaling, we performed a genetic screen utilizing the drosophila ras v12 /lgl -/- in vivo tumor model and identified rox8, a rna-binding protein (rbp), as a positive regulator of the hippo pathway. we found that rox8 overexpression suppresses whereas rox8 depletion potentiates hippo-dependent tissue overgrowth, accompanied by altered yki protein level and target gene expression. mechanistically, rox8 directly binds to a target site located in the yki 3' utr, recruits and stabilizes the targeting of mir-8-loaded risc, which accelerates the decay of yki messenger rna (mrna). moreover, tiar, the human ortholog of rox8, is able to promote the degradation of yki mrna when introduced into drosophila and destabilizes yap mrna in human cells. thus, our study provides in vivo evidence that the hippo pathway is posttranscriptionally regulated by the collaborative action of rbp and microrna (mirna), which may provide an approach for modulating hippo pathway-mediated tumorigenesis.",1
"rationale circulating proangiogenic cells (pacs) support postischemic neovascularization. cardiovascular disease and diabetes mellitus impair pac regenerative capacities via molecular mechanisms that are not fully known. we hypothesize a role for micrornas (mirs). circulating mirs are currently investigated as potential diagnostic and prognostic biomarkers. objective the objectives were the following: (1) to profile mir expression in pacs from critical limb ischemia (cli) patients; (2) to demonstrate that mir-15a and mir-16 regulate pac functions; and (3) to characterize circulating mir-15a and mir-16 and to investigate their potential biomarker value. methods and results twenty-eight mirs potentially able to modulate angiogenesis were measured in pacs from cli patients with and without diabetes mellitus and controls. mir-15a and mir-16 were further analyzed. cli-pacs expressed higher level of mature mir-15a and mir-16 and of the primary transcript pri-mir-15a/16-1. mir-15a/16 overexpression impaired healthy pac survival and migration. conversely, mir-15a/16 inhibition improved cli-pac-defective migration. vascular endothelial growth factor-a and akt-3 were validated as direct targets of the 2 mirs, and their protein levels were reduced in mir-15a/16-overexpressing healthy pacs and in cli-pacs. transplantation of healthy pacs ex vivo-engineered with anti-mir-15a/16 improved postischemic blood flow recovery and muscular arteriole density in immunodeficient mice. mir-15a and mir-16 were present in human blood, including conjugated to argonaute-2 and in exosomes. both mirs were increased in the serum of cli patients and positively correlated with amputation after restenosis at 12 months postrevascularization of cli type 2 diabetes mellitus patients. serum mir-15a additionally correlated with restenosis at follow-up. conclusions ex vivo mir-15a/16 inhibition enhances pac therapeutic potential, and circulating mir-15a and mir-16 deserves further investigation as a prognostic biomarker in cli patients undergoing revascularization.",1
"formation of the drosophila adult abdomen involves a process of tissue replacement in which larval epidermal cells are replaced by adult cells. the progenitors of the adult epidermis are specified during embryogenesis and, unlike the imaginal discs that make up the thoracic and head segments, they remain quiescent during larval development. during pupal development, the abdominal histoblast cells proliferate and migrate to replace the larval epidermis. here, we provide evidence that the microrna, mir-965, acts via string and wingless to control histoblast proliferation and migration. ecdysone signaling downregulates mir-965 at the onset of pupariation, linking activation of the histoblast nests to the hormonal control of metamorphosis. replacement of the larval epidermis by adult epidermal progenitors involves regulation of both cell-intrinsic events and cell communication. by regulating both cell proliferation and cell migration, mir-965 contributes to the robustness of this morphogenetic system.",1
"background and aims microrna-34a (mir-34a) as a tumor suppressor has been reported in many other studies. however, its role in modulating the sensitivity of breast cancer cells to adriamycin (adr) remains unclear. the aim of this study is to evaluate the role of mir-34a in the sensitivity of breast cancer cells to adr. methods the role of mir-34a in breast cancer cells was detected using mtt assay, flow cytometry assay, real-time pcr and western blot, etc. the association of mir-34a and notch1 was analyzed by dual-luciferase reporter assay and notch1-sirna technology. real-time pcr assay was performed to test the expression of mir-34a and notch1 in 38 selective breast cancer tissue samples. results ectopic overexpression of mir-34a could sensitize mcf-7 breast cancer cells to adr. mir-34a mimic could inhibit the luciferase activity of the construct containing wild-type 3' utr of notch1 in mcf-7/adr cells. notch1-sirna could partially reverse the effect of mir-34a inhibitor in inducing chemoresistance of mcf-7 cells to adr. further, there was an inverse association between notch1 and mir-34a expression in breast cancer. conclusion dysregulation of mir-34a plays critical roles in the acquired adr resistance of breast cancer, at least in part via targeting notch1.",1
"though tumor suppressor p53 and the canonical wnt cascade have been extensively studied for the last 30 years, due to their important physiological roles, the two signaling pathways have been largely considered independent. recently, the mir-34 family was found to directly link p53 and wnt, revealing the tight connection between loss of tumor suppressor function and activation of oncogenic signaling. these observations demonstrate that mir-34, known to be directly downstream of p53, targets a set of highly conserved sites in the utr of wnt and emt genes, specifically wnt1, wnt3, lrp6, axin2, β-catenin, lef1 and snail, resulting in suppression of tcf/lef transcriptional activity and the emt program. the loss of p53 function increases wnt activities and promotes the snail-dependent emt program at multiple levels in a mir-34/utr-specific manner. the tcf/lef transcriptional signature was closely associated with functionality of p53 and mir-34 in clinical samples, suggesting the pervasive impact of mir-34 loss on the oncogenic pathway in human cancer. here, we review recent findings on cerna in light of novel data to elucidate the physiological relevance of the p53-mir-34-wnt network, which encompasses sets of genes and directions of signaling. as loss of wt-p53 or hyperactivation of wnt is critical in maintaining cancer stem cell properties and in establishing the metastatic program, these observations indicate a mechanism of mir-mediated quasi-sufficiency which connects tumor suppressor and oncogenic signaling pathways, supporting a continuum model of human cancer.",1
"the kcnq1 imprinting control region (icr) located in intron 10 of the kcnq1 gene is unmethylated on the paternal chromosome and methylated on the maternal chromosome and has been implicated in the manifestation of parent-of-origin-specific expression of six neighboring genes. the unmethylated kcnq1 icr harbors bidirectional silencer activity and drives expression of an antisense rna, kcnq1ot1, which overlaps the kcnq1 coding region. to elucidate whether the kcnq1ot1 rna plays a role in the bidirectional silencing activity of the kcnq1 icr, we have characterized factor binding sites by genomic footprinting and tested the functional consequence of various deletions of these binding sites in an episome-based system. deletion of the elements necessary for kcnq1ot1 promoter function resulted in the loss of silencing activity. furthermore, interruption of kcnq1ot1 rna production by the insertion of a polyadenylation sequence downstream of the promoter also caused a loss of both silencing activity and methylation spreading. thus, the antisense rna plays a key role in the silencing function of the icr. double-stranded rna (dsrna)-mediated rna interference is unlikely to be involved, as the icr is active irrespective of the simultaneous production of dsrna from the genes it silences.",1
"the repressive effect of the 3'-untranslated region (3'-utr) in human connective tissue growth factor/ hypertrophic chondrocyte specific 24 (ctgf/hcs24) mrna on gene expression had been demonstrated in our previous study. here, we identified a minimal rna element in the 3'-utr, which acts as a cis-acting element of structure-anchored repression (caesar). deletion analyses of the 3'-utr led us to minimize the element of 84 bases at the junction of the coding region and the 3'-utr. the minimized rna segment is predicted, and actually capable of forming a stable secondary structure in vitro. mutational analyses disclosed a significant relationship between the predicted structure and repressive effect. the utility of caesar as a post-transcriptional regulatory element was represented by the fact that steady-state mrna levels were not affected by caesar linked in cis, while protein levels from such a chimeric gene were markedly reduced. of note, the caesar sequence exerted no effect, when it was placed upstream of the promoter. finally, rna gel electromobility-shift analyses demonstrated a nuclear factor that interacts with the folded caesar. taken together, it was uncovered that caesar of ctgf is a novel post-transcriptional structured rna regulatory element, probably acting through direct interactions with a nuclear factor as observed in retroviral rna elements with certain proteins.",1
"background nf-κb signaling pathway plays an important role in gastric carcinogenesis. the basic expression and functional role of nfkb1 and rela (components of canonical nf-κb pathway) in gastric cancer (gc) have not been well elucidated. in this study, the role of nfkb1 and rela in gastric tumorigenesis will be investigated and their regulation by micrornas (mirnas) will be deeply explored. methods the mrna and protein expression of nfkb1 and rela were investigated by qrt-pcr and western blot in gc cell lines and primary tumors. the functional roles of nfkb1 and rela in gc were demonstrated by mtt proliferation assay, monolayer colony formation, cell invasion and migration, cell cycle analysis and in vivo study through sirna mediated knockdown. identification of nfkb1 as a direct target of tumor suppressor mirna mir-508-3p was achieved by expression regulation assays together with dual luciferase activity experiments. results nfkb1 and rela were up-regulated in gc cell lines and primary tumors compared with normal gastric epithelium cells and their upregulation correlation with poor survival in gc. sirna mediated knockdown of nfkb1 or rela exhibited anti-oncogenic effect both in vitro and in vivo. nfkb1 was further revealed to be a direct target of mir-508-3p in gastric tumorigenesis and their expression showed negative correlation in primary gc samples. mir-508-3p was down-regulated in gc cells compared with normal gastric epithelium samples and its ectopic expression in gc cell lines also exerts tumor suppressor function. nfkb1 re-expression was found to partly abolish the tumor-suppressive effect of mir-508-3p in gc. conclusion all these findings supports that canonical nf-κb signaling pathway is activated in gc at least by the inactivation of mir-508-3p and this might have therapeutic potential in gc treatment.",1
"ring box protein1 (rbx1), an essential component of scf e3 ubiquitin ligases, plays an important role in gastric cancer. in the study, mir-194 and rbx1 expression was evaluated in 76 pairs of gastric tumor and non-tumor tissue samples by qrt-pcr, and clinicopathological characteristics were analyzed. cck8, transwell assay, wound healing assay, and flow cytometry assay were performed to evaluate the effect of mir-194 on gastric cancer (gc) cellular proliferation, invasion, migration, apoptosis, and cell cycle, respectively. luciferase reporter assays and western blotting were used to evaluate whether rbx1 is a direct target of mir-194. the kaplan-meier method and log-rank test were used to evaluate the correlation between mir-194 or rbx1 expression and patient survival. then, we found that mir-194 was significantly downregulated and rbx1 upregulated in gc tissues; both of which showed significant association with tumor size, location, invasion, and tumor node metastasis. cell proliferation, invasion, and migration were significantly restricted with mir-194 overexpression. mir-194 downregulated rbx1 protein expression, and luciferase assays showed that binding sites in the rbx1 3'utr were required for mir-194-mediated repression of rbx1, indicating that rbx1 was a direct target of mir-194. transfection of rbx1 without the 3'utr restored the mir-194-inhibiting migration function. mir-194 overexpression or rbx1 lowexpression was associated with prolonged survival of gc patients. in conclusion, upregulation of mir-194 can inhibit proliferation, migration, and invasion of gc cells, possibly by targeting rbx1. aberrant expression of mir-194 and rbx1 is correlated to gc patient survival time.",1
"mir-140-5p is down-regulated in patients with pulmonary arterial hypertension (pah) and experimental models of pah, and inhibits hypoxia-mediated pulmonary artery smooth muscle cell (pasmc) proliferation in vitro. delivery of synthetic mir-140-5p prevents and treats established, experimental pah. dna methyltransferase 1 (dnmt1) is up-regulated in pah associated human pasmcs (hpasmcs), which promotes the development of pah by hypermethylation of cpg islands within the promoter for superoxide dismutase 2 (sod2) and down-regulating sod2 expression. we searched for mir-140-5p targets using targetscan, pictar and miranda tools, and found that dnmt1 is a potential target of mir-140-5p. based on these findings, we speculated that mir-140-5p might target dnmt1 and regulate sod2 expression to regulate hypoxia-mediated hpasmc proliferation, apoptosis and differentiation. we detected the expression of mir-140-5p, dnmt1 and sod2 by quantitative real-time polymerase chain reaction (qrt-pcr) and western blot assays, respectively, and found down-regulation of mir-140-5p and sod2 and up-regulation of dnmt1 exist in pah tissues and hypoxia-mediated hpasmcs. cell proliferation, apoptosis and differentiation detection showed that mir-140-5p inhibits proliferation and promotes apoptosis and differentiation of hpasmcs in hypoxia, while the effect of dnmt1 on hypoxia-mediated hpasmcs is reversed. luciferase assay confirmed that mir-140-5p targets dnmt1 directly. an inverse correlation is also found between mir-140-5p and dnmt1 in hpasmcs. in addition, we further investigated whether mir-140-5p and dnmt1 regulate hpasmc proliferation, apoptosis and differentiation by regulating sod2 expression, and the results confirmed our speculation. taken together, these results indicated that mir-140-5p at least partly targets dnmt1 and regulates sod2 expression to inhibit proliferation and promote apoptosis and differentiation of hpasmcs in hypoxia.",1
"objectives this study sought to identify proteins from the cardiomyocyte (cm) secretome that are directly targeted by the muscle-specific microrna-1 (mir-1), and thus reflect the pathophysiological state of the cm. background micrornas play critical regulatory roles during myocardial remodeling and progression to heart failure. however, it remains unknown whether secreted microrna-targeted proteins can be used as indicators of myocardial microrna expression and function. methods a proteomic analysis based on multidimensional protein identification technology was performed on supernatants from cultured cms overexpressing mir-1. biochemical assays and an inducible cardiac-specific transgenic mouse model overexpressing mir-1 were used to demonstrate that heart-type fatty acid-binding protein-3 (fabp3) is a target of mir-1. levels of mir-1 and fabp3 in cardiac tissue and plasma samples from mouse models as well as human patients were quantified by quantitative reverse-transcription polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. the study included wild-type mice subjected to ventricular pressure overload or fasting, as well as patients diagnosed with ventricular hypertrophy due to valvular aortic stenosis, acromegaly, or growth hormone deficiency, conditions associated with altered mir-1 expression. results an inverse relationship between myocardial expression of mir-1 and circulating levels of fabp3 was found both in vitro and in vivo under various pathological conditions. conclusions assessment of fabp3 plasma levels in human patients might be used for indirectly measuring cardiac mir-1 activity.",1
"the porcine brain closely resembles the human brain in aspects such as development and morphology. temporal mirna profiling in the developing embryonic porcine cortex revealed a distinct set of mirnas, including mir-34c and mir-204, which exhibited a highly specific expression profile across the time of cortical folding. these mirnas were found to target doublecortin (dcx), known to be involved in neuron migration during cortical folding of gyrencephalic brains. in vivo modulation of mirna expression in mouse embryos confirmed that mir-34c and mir-204 can control neuronal migration and cortical morphogenesis, presumably by posttranscriptional regulation of dcx.",1
"atherosclerosis, a hyperlipidemia-induced chronic inflammatory process of the arterial wall, develops preferentially at sites where disturbed laminar flow compromises endothelial cell (ec) function. here we show that endothelial mir-126-5p maintains a proliferative reserve in ecs through suppression of the notch1 inhibitor delta-like 1 homolog (dlk1) and thereby prevents atherosclerotic lesion formation. endothelial recovery after denudation was impaired in mir126(-/-) mice because lack of mir-126-5p, but not mir-126-3p, reduced ec proliferation by derepressing dlk1. at nonpredilection sites, high mir-126-5p levels in endothelial cells confer a proliferative reserve that compensates for the antiproliferative effects of hyperlipidemia, such that atherosclerosis was exacerbated in mir126(-/-) mice. in contrast, downregulation of mir-126-5p by disturbed flow abrogated ec proliferation at predilection sites in response to hyperlipidemic stress through upregulation of dlk1 expression. administration of mir-126-5p rescued ec proliferation at predilection sites and limited atherosclerosis, introducing a potential therapeutic approach.",1
"in drosophila, heterozygosity in the pro-apoptotic gene hid significantly reduces apoptosis that is induced by ionizing radiation (ir). therefore, mechanisms that regulate hid levels can potentially contribute to life-or-death decision of an irradiated cell. 3'utr of hid mrna contains 5 potential binding sites for bantam microrna. ectopic expression of ban attenuated apoptosis that results from ectopic expression of hid but the significance of this regulation under physiological conditions remained to be investigated. we report here that ban is needed to limit ir-induced apoptosis in larval imaginal discs. using tubulin-egfp ban sensors with ban consensus sequences in the 3'utr, we find that egfp decreases following ir, indicating that ir activates ban. likewise, a tubulin-egfp reporter with hid-3'utr is repressed in irradiated discs and this repression requires ban consensus sites in the hid 3'utr. ban mutant larvae show increased sensitivity to killing by ir, which is suppressed by a mutation in hid. these results can fit into a model in which ir activates ban and ban represses hid to limit ir-induced apoptosis. mirnas have been shown previously to be induced by radiation but this is the first report that a mirna is functionally important for radiation responses.",1
"microrna-26a (mir-26a) is a tumor suppressor that is reduced in hepatocellular carcinoma (hcc). increasing evidence indicates that the liver is a hormone-responsive organ like the breast. the purpose of this study was to investigate whether mir-26a, regulated by a human α-fetoprotein (hafp) and human telomerase reverse transcriptase (htert) dual promoter, could be specifically expressed in liver tumor cells to suppress their growth and to clarify whether estrogen receptor-α (erα) is regulated by mir-26a and involved in the hcc process. our data show that mir-26a expression driven by a hafp-tert dual promoter was tumor-specific and decreased the viability of tumor cells by regulating erα, progesterone receptor (pr) and p53 except for cyclin d2 or cyclin e2 in vitro and in vivo. our data also show that estradiol (e2) promotes the growth of liver cancer cells similar to breast cancer cells partly via the e2-erα pathway and that mir-26a significantly down regulates erα and prevents the stimulation of hepatoma cell growth by e2. these data suggest that erα, which is regulated by mir-26a, is important for liver tumor cell growth. moreover, hafp-tert dual promoter-mediated mir-26a expression could specifically exert potential antitumor activity and provide a novel targeting approach for cancer therapy.",1
"local anesthetic may cause neurotoxicity in developing neurons. in this study, we examined the molecular mechanisms of microrna-210 (mir-210) in regulating bupivacaine-induced dorsal root ganglia (drg) neurotoxicity in vitro. young mouse (p30) drg explants were cultured in vitro and treated with 5 mm bupivacaine to induce neurotoxicity. qrt-pcr was used to evaluate the expression profiles of mirnas within 24 h after bupivacaine treatment. mir-210 was downregulated in drg, and its effects on bupivacaine-induced neurotoxicity were evaluated by apoptosis and neurite growth assays, respectively. putative downstream target of mir-210 in drg, bdnf, was evaluated by dual-luciferase assay, qrt-pcr, and western blot, respectively. bdnf was then knocked down by sirna to assess its associated effects in regulating drg neurotoxicity. within the initial 24 h after bupivacaine treatment, various patterns of mirna expression were observed, whereas mir-210 was constantly upregulated. application of mir-210 inhibitor efficiently downregulated endogenous mir-210, protected apoptosis and neurite retraction in bupivacaine damaged drg neurons. using dual-luciferase assay, qrt-pcr, and western blot, bdnf was confirmed to the downstream target of mir-210 in drg. sirna-mediated bdnf downregulation reversed the effect of mir-210 downregulation in drg neurotoxicity. mir-210, through the regulation of bdnf, plays important role in anesthetics-induced drg neurotoxicity.",1
"although mitochondrial import of nuclear dna-encoded rnas is widely occurring, their functions in the organelles are not always understood. mitochondrial function(s) of trna(lys)(cuu), trk1, targeted into saccharomyces cerevisiae mitochondria was mysterious, since mitochondrial dna-encoded trna(lys)(uuu), trk3, was hypothesized to decode both lysine codons, aaa and aag. mitochondrial targeting of trk1 depends on the precursor of mitochondrial lysyl-trna synthetase, pre-msk1p. here we show that substitution of pre-msk1p by its ashbya gossypii ortholog results in a strain in which trk3 is aminoacylated, while trk1 is not imported. at elevated temperature, drop of trk1 import inhibits mitochondrial translation of mrnas containing aag codons, which coincides with the impaired 2-thiolation of trk3 anticodon wobble nucleotide. restoration of trk1 import cures the translational defect, suggesting the role of trk1 in conditional adaptation of mitochondrial protein synthesis. in contrast with the known ways of organellar translation control, this mechanism exploits the rna import pathway.",1
"gastric cancer tissue-derived msc-like cells (gc-msc) share similar characteristics to bone marrow msc (bm-msc); however, the phenotypical and functional differences and the molecular mechanism of transition between the two cell types remain unclear. compared to bm-msc, gc-msc exhibited the classic phenotype of reactive stroma cells, a stronger gastric cancer promoting capacity and lower expression of mir-155-5p. inhibition of mir-155-5p by transfecting mirna inhibitor induced a phenotypical and functional transition of bm-msc into gc-msc-like cells, and the reverse experiment deprived gc-msc of tumor-promoting phenotype and function. nf-kappa b p65 (nf-κb p65) and inhibitor of nf-kappa b kinase subunit epsilon (ikbke/ikkε) were identified as targets of mir-155-5p and important for mirna inhibitor activating nf-κb p65 in the transition. inactivation of nf-κb by pyrrolidine dithiocarbamic acid (pdtc) significantly blocked the effect of mir-155-5p inhibitor on bm-msc. ikbke, nf-κb p65 and phospho-nf-κb p65 proteins were highly enriched in msc-like cells of gastric cancer tissues, and the latter two were correlated with the pathological progression of gastric cancer. in gc-msc, the expression of mir-155-5p was downregulated and nf-κb p65 protein was increased and activated. nf-κb inactivation by pdtc or knockdown of its downstream cytokines reversed the phenotype and function of gc-msc. taken together, our findings revealed that mir-155-5p downregulation induces bm-msc to acquire a gc-msc-like phenotype and function depending on nf-κb p65 activation, which suggests a novel mechanism underlying the cancer associated msc remodeling in the tumor microenvironment and offers an effective target and approach for gastric cancer therapy.",1
"in response to stress, the heart undergoes extensive cardiac remodeling that results in cardiac fibrosis and pathological growth of cardiomyocytes (hypertrophy), which contribute to heart failure. alterations in microrna (mirna) levels are associated with dysfunctional gene expression profiles associated with many cardiovascular disease conditions; however, mirnas have emerged recently as paracrine signaling mediators. thus, we investigated a potential paracrine mirna crosstalk between cardiac fibroblasts and cardiomyocytes and found that cardiac fibroblasts secrete mirna-enriched exosomes. surprisingly, evaluation of the mirna content of cardiac fibroblast-derived exosomes revealed a relatively high abundance of many mirna passenger strands (""star"" mirnas), which normally undergo intracellular degradation. using confocal imaging and coculture assays, we identified fibroblast exosomal-derived mir-21_3p (mir-21*) as a potent paracrine-acting rna molecule that induces cardiomyocyte hypertrophy. proteome profiling identified sorbin and sh3 domain-containing protein 2 (sorbs2) and pdz and lim domain 5 (pdlim5) as mir-21* targets, and silencing sorbs2 or pdlim5 in cardiomyocytes induced hypertrophy. pharmacological inhibition of mir-21* in a mouse model of ang ii-induced cardiac hypertrophy attenuated pathology. these findings demonstrate that cardiac fibroblasts secrete star mirna-enriched exosomes and identify fibroblast-derived mir-21* as a paracrine signaling mediator of cardiomyocyte hypertrophy that has potential as a therapeutic target.",1
"progress in understanding the biology of multiple myeloma (mm), a plasma cell malignancy, has been slow. the discovery of micrornas (mirnas), a class of small noncoding rnas targeting multiple mrnas, has revealed a new level of gene expression regulation. to determine whether mirnas play a role in the malignant transformation of plasma cells (pcs), we have used both mirna microarrays and quantitative real time pcr to profile mirna expression in mm-derived cell lines (n = 49) and cd138+ bone marrow pcs from subjects with mm (n = 16), monoclonal gammopathy of undetermined significance (mgus) (n = 6), and normal donors (n = 6). we identified overexpression of mir-21, mir-106b approximately 25 cluster, mir-181a and b in mm and mgus samples with respect to healthy pcs. selective up-regulation of mir-32 and mir-17 approximately 92 cluster was identified in mm subjects and cell lines but not in mgus subjects or healthy pcs. furthermore, two mirnas, mir-19a and 19b, that are part of the mir-17 approximately 92 cluster, were shown to down regulate expression of socs-1, a gene frequently silenced in mm that plays a critical role as inhibitor of il-6 growth signaling. we also identified p300-cbp-associated factor, a gene involved in p53 regulation, as a bona fide target of the mir106b approximately 25 cluster, mir-181a and b, and mir-32. xenograft studies using human mm cell lines treated with mir-19a and b, and mir-181a and b antagonists resulted in significant suppression of tumor growth in nude mice. in summary, we have described a mm mirna signature, which includes mirnas that modulate the expression of proteins critical to myeloma pathogenesis.",1
"the levels of circulating micrornas (mirnas) in mice with experimental sepsis induced by cecal ligation and puncture (clp) were determined using whole blood samples obtained from c57bl/6 mice at 4, 8, and 24 h after clp; mirna expression analysis was performed in these samples using an mirna array. microarray analysis revealed upregulation of 10 mirna targets (mir-16, mir-17, mir-20a, mir-20b, mir-26a, mir-26b, mir-106a, mir-106b, mir-195, and mir-451). the expression of these mirna targets in the whole blood, serum, and white blood cells (wbcs) of clp mice was quantified using quantitative real-time pcr; these values were compared to those in sham-operated c57bl/6 mice, and the results indicated that these mirna targets were significantly up-regulated in the whole blood and serum but not in the wbcs. in addition, the levels of these 10 mirna targets in the serum of tlr2-/-, tlr4-/-, and nf-κb-/- mice at 8 h after clp did not decrease significantly., which indicated that the transcription of these mirnas was not directly mediated by the tlr2/nf-κb or tlr4/nf-κb pathway, and pathways induced by exposure to the gram-positive or gram-negative bacteria. immunoprecipitation with the argonaute 2 ribonucleoprotein complex revealed significantly increased expression of the 10 mirna targets in the serum of mice after clp, and the levels of 6 (mir-16, mir-17, mir-20a, mir-20b, mir-26a, and mir-26b) of these 10 mirna targets increased significantly in exosomes isolated using exoquick precipitation solution. in this study, we identified circulating mirnas that were up-regulated after clp and determined the increase in the levels of these mirnas, and our results suggest that circulating ago2 complexes and exosomes may be responsible for the stability of mirnas in the serum.",1
"exposure to low-dose irradiation causes transiently elevated expression of the long ncrna particle (gene particle, promoter of mat2a-antisense radiation-induced circulating lncrna). particle affords both a cytosolic scaffold for the tumor suppressor methionine adenosyltransferase (mat2a) and a nuclear genetic platform for transcriptional repression. in situ hybridization discloses that particle and mat2a associate together following irradiation. bromouridine tracing and presence in exosomes indicate intercellular transport, and this is supported by ex vivo data from radiotherapy-treated patients. surface plasmon resonance indicates that particle forms a dna-lncrna triplex upstream of a mat2a promoter cpg island. we show that particle represses mat2a via methylation and demonstrate that the radiation-induced particle interacts with the transcription-repressive complex proteins g9a and suz12 (subunit of prc2). the interplay of particle with mat2a implicates this lncrna in intercellular communication and as a recruitment platform for gene-silencing machineries through triplex formation in response to irradiation.",1
"long noncoding rnas (lncrnas) play important roles in diverse biological processes; however, few have been identified that regulate immune cell differentiation and function. here, we identified lnc-dc, which was exclusively expressed in human conventional dendritic cells (dcs). knockdown of lnc-dc impaired dc differentiation from human monocytes in vitro and from mouse bone marrow cells in vivo and reduced capacity of dcs to stimulate t cell activation. lnc-dc mediated these effects by activating the transcription factor stat3 (signal transducer and activator of transcription 3). lnc-dc bound directly to stat3 in the cytoplasm, which promoted stat3 phosphorylation on tyrosine-705 by preventing stat3 binding to and dephosphorylation by shp1. our work identifies a lncrna that regulates dc differentiation and also broadens the known mechanisms of lncrna action.",1
"phenotypic similarities have long been recognized between subpopulations of glioma and neural stem cells. many of these similar properties, including the robust abilities to self-renew, migrate, and invade, are hallmarks of glioma cells that render them extremely aggressive. however, the molecular mechanisms underlying this character, particularly in glioma stem-like cells that drive this disease, remain poorly understood. here, we report the results of a differential mirna expression screen that compared glioma and neural stem cells, where we found that mir-204 was markedly downregulated in both types of cells. mechanistic investigations revealed that mir-204 simultaneously suppressed self-renewal, stem cell-associated phenotype, and migration of glioma cells by targeting the stemness-governing transcriptional factor sox4 and the migration-promoting receptor ephb2. restoring mir-204 expression in glioma cells suppressed tumorigenesis and invasiveness in vivo and increased overall host survival. further evaluation revealed that the mir-204 promoter was hypermethylated and that attenuating promoter methylation was sufficient to upregulate mir-204 in glioma cells. together, our findings reveal mir-204 as a pivotal regulator of the development of stem cell-like phenotypes and cell motility in malignant glioma cells.",1
"we have cloned and characterized cdna copies of larval and adult drosophila 7sl rna. the drosophila 7sl sequence shares 66.3% homology with that of human 7sl rna. the homology is not evenly distributed along the sequence, but is concentrated in blocks in the central part of the molecule. we have analysed the secondary structure of drosophila and human 7sl rna free in solution by digestion with single and double strand specific nucleases. similar experiments with the 7sl rna bound to proteins within the signal recognition particle show essentially the same digestion pattern. a model of the secondary structure common to drosophila and human 7sl rna is presented.",1
"micrornas are established as crucial modulators of skeletal myogenesis, but our knowledge about their identity and targets remains limited. in this study, we have identified microrna-146b (mir-146b) as a novel regulator of skeletal myoblast differentiation. following up on a previous microrna profiling study, we establish that the expression of mir-146b is up-regulated during myoblast differentiation in vitro and muscle regeneration in vivo. inhibition of mir-146b led to reduced myoblast differentiation, whereas overexpression of mir-146b enhanced differentiation. computational prediction combined with gene expression information has revealed candidates for mir-146b targets in muscles. among them, the expression of smad4, notch1, and hmga2 are significantly suppressed by mir-146b overexpression in myocytes. in addition, expression levels of smad4, notch1 and hmga2 are decreased during myoblast differentiation and muscle regeneration, inversely correlating to the levels of mir-146b. importantly, inhibition of endogenous mir-146b prevents the down-regulation of smad4, notch1 and hmga2 during differentiation. furthermore, mir-146b directly targets the microrna response elements (mres) in the 3'utr of those genes as assessed by reporter assays. reporters with the seed regions of mres mutated are insensitive to mir-146b, further confirming the specificity of targeting. in conclusion, mir-146b is a positive regulator of myogenic differentiation, possibly acting through multiple targets.",1
"background and aims micrornas (mirnas) are small noncoding rnas that regulate cognate mrnas post-transcriptionally. mirnas have been implicated in regulating gene expression in embryonic developmental processes, including proliferation and differentiation. the liver is a multifunctional organ, which undergoes rapid changes during the developmental period and relies on tightly-regulated gene expression. little is known regarding the complex expression patterns of both mrnas and mirnas during the early stages of human liver development, and the role of mirnas in the regulation of this process has not been studied. the aim of this work was to study the impact of mirnas on gene expression during early human liver development. methods global gene and mirna expression were profiled in adult and in 9-12w human embryonic livers, using high-density microarrays and quantitative rt-pcr. results embryonic liver samples exhibited a gene expression profile that differentiated upon progression in the developmental process, and revealed multiple regulated genes. mirna expression profiling revealed four major expression patterns that correlated with the known function of regulated mirnas. comparison of the expression of the most regulated mirnas to that of their putative targets using a novel algorithm revealed a significant anti-correlation for several mirnas, and identified the most active mirnas in embryonic and in adult liver. furthermore, our algorithm facilitated the identification of tgfbeta-r1 as a novel target gene of let-7. conclusions our results uncover multiple regulated mirnas and genes throughout human liver development, and our algorithm assists in identification of novel mirna targets with potential roles in liver development.",1
"mechanical stress is a well-acknowledged positive regulatory factor for osteogenic differentiation of adipose- derived mesenchymal stem cells (adscs). however, the molecular mechanisms associated with micro-rnas (mirnas) whereby adscs respond to mechanical stimuli remain elusive. we investigated the mechanism of mechanotransduction from the mirna perspective in the osteogenic differentiation of adscs under tensile stress. microarray analysis showed that mir-154-5p was remarkably downregulated when adscs were subjected to mechanical tension. bioinformatics analysis with luciferase reporter assays demonstrated that wnt11 3'utr was a new direct target of mir-154-5p. under tensile stress, lentivirus-mediated gain- or loss-of-function studies revealed that forced expression of mir-154-5p inhibited osteogenic differentiation of adscs, whereas inhibition of endogenous mir-154-5p with its antisense oligonucleotide (aso-154-5p) obviously promoted osteogenic differentiation. furthermore, mir-154-5p overexpression decreased activity of the non-canonical wnt/pcp (rhoa-rock) pathway, as indicated by lower expression of wnt11, active rhoa and rockii in mir-154-5p-treated adscs. by contrast, mir-154-5p inhibition activated the wnt/pcp signals. taken together, these results demonstrate that, under tensile stress, mir-154-5p negatively regulates adscs osteogenic differentiation through the wnt/pcp pathway by directly targeting wnt11. this novel regulatory pathway provides new insights into the molecular mechanism of mechanotransduction in osteogenic differentiation of adscs.",1
"il-10 is a potent anti-inflammatory molecule that, in phagocytes, negatively targets cytokine expression at transcriptional and posttranscriptional levels. posttranscriptional checkpoints also represent the specific target of a recently discovered, evolutionary conserved class of small silencing rnas known as ""micrornas"" (mirnas), which display the peculiar function of negatively regulating mrna processing, stability, and translation. in this study, we report that activation of primary human monocytes up-regulates the expression of mir-187 both in vitro and in vivo. accordingly, we identify mir-187 as an il-10-dependent mirna playing a role in il-10-mediated suppression of tnf-α, il-6, and the p40 subunit of il-12 (il-12p40) produced by primary human monocytes following activation of toll-like receptor 4 (tlr4). ectopic expression of mir-187 consistently and selectively reduces tnfα, il-6, and il-12p40 produced by lps-activated monocytes. conversely, the production of lps-induced tnf-α, il-6, and il-12p40 is increased significantly when mir-187 expression is silenced. our data demonstrate that mir-187 directly targets tnf-α mrna stability and translation and indirectly decreases il-6 and il-12p40 expression via down-modulation of iκbζ, a master regulator of the transcription of these latter two cytokines. these results uncover an mirna-mediated pathway controlling cytokine expression and demonstrate a central role of mir-187 in the physiological regulation of il-10-driven anti-inflammatory responses.",1
"we have previously reported that the human acat1 gene produces a chimeric mrna through the interchromosomal processing of two discontinuous rnas transcribed from chromosomes 1 and 7. the chimeric mrna uses aug(1397-1399) and ggc(1274-1276) as translation initiation codons to produce normal 50-kda acat1 and a novel enzymatically active 56-kda isoform, respectively, with the latter being authentically present in human cells, including human monocyte-derived macrophages. in this work, we report that rna secondary structures located in the vicinity of the ggc(1274-1276) codon are required for production of the 56-kda isoform. the effects of the three predicted stem-loops (nt 1255-1268, 1286-1342 and 1355-1384) were tested individually by transfecting expression plasmids into cells that contained the wild-type, deleted or mutant stem-loop sequences linked to a partial acat1 aug open reading frame (orf) or to the orfs of other genes. the expression patterns were monitored by western blot analyses. we found that the upstream stem-loop(1255-1268) from chromosome 7 and downstream stem-loop(1286-1342) from chromosome 1 were needed for production of the 56-kda isoform, whereas the last stem-loop(1355-1384) from chromosome 1 was dispensable. the results of experiments using both monocistronic and bicistronic vectors with a stable hairpin showed that translation initiation from the ggc(1274-1276) codon was mediated by an internal ribosome entry site (ires). further experiments revealed that translation initiation from the ggc(1274-1276) codon requires the upstream au-constituted rna secondary structure and the downstream gc-rich structure. this mechanistic work provides further support for the biological significance of the chimeric nature of the human acat1 transcript.",1
"nsclc (non-small cell lung cancer) often exhibits resistance to paclitaxel treatment. identifying the elements regulating paclitaxel response will advance efforts to overcome such resistance in nsclc therapy. using in vitro approaches, we demonstrated that over-expression of the microrna mir-337-3p sensitizes nci-h1155 cells to paclitaxel, and that mir-337-3p mimic has a general effect on paclitaxel response in nsclc cell lines, which may provide a novel adjuvant strategy to paclitaxel in the treatment of lung cancer. by combining in vitro and in silico approaches, we identified stat3 and rap1a as direct targets that mediate the effect of mir-337-3p on paclitaxel sensitivity. further investigation showed that mir-337-3p mimic also sensitizes cells to docetaxel, another member of the taxane family, and that stat3 levels are significantly correlated with taxane resistance in lung cancer cell lines, suggesting that endogenous stat3 expression is a determinant of intrinsic taxane resistance in lung cancer. the identification of a mir-337-3p as a modulator of cellular response to taxanes, and stat3 and rap1a as regulatory targets which mediate that response, defines a novel regulatory pathway modulating paclitaxel sensitivity in lung cancer cells, which may provide novel adjuvant strategies along with paclitaxel in the treatment of lung cancer and may also provide biomarkers for predicting paclitaxel response in nsclc.",1
"the microrna (mirna) locus mir-144/451 is abundantly expressed in erythrocyte precursors, facilitating their terminal maturation and protecting against oxidant stress. however, the full repertoire of erythroid mir-144/451 target messenger rnas (mrnas) and associated cellular pathways is unknown. in general, the numbers of mrnas predicted to be targeted by an mirna vary greatly from hundreds to thousands, and are dependent on experimental approaches. to comprehensively and accurately identify erythroid mir-144/451 target mrnas, we compared gene knockout and wild-type fetal liver erythroblasts by rna sequencing, quantitative proteomics, and rna immunoprecipitation of argonaute (ago), a component of the rna-induced silencing complex that binds mirnas complexed to their target mrnas. argonaute bound ∼1400 erythroblast mrnas in a mir-144/451-dependent manner, accounting for one-third of all ago-bound mrnas. however, only ∼100 mrnas were stabilized after mir-144/451 loss. thus, mir-144 and mir-451 deregulate cox10 , facilitates the assembly of mitochondrial electron transport complex iv. loss of mir-144/451 caused increased cox10 mrna and protein, accumulation of complex iv, and increased mitochondrial membrane potential with no change in mitochondrial mass. thus, mir-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting the production of cox10.",1
"head and neck squamous cell carcinoma (hnscc) cells exposed to cisplatin (cis) displayed a dramatic atm-dependent phosphorylation of δnp63α that leads to the transcriptional regulation of downstream mrnas. here, we report that phospho (p)-δnp63α transcriptionally deregulates mirna expression after cis treatment. several p-δnp63α-dependent microrna species (mirnas) were deregulated in hnscc cells upon cis exposure, including mir-181a, mir-519a, and mir-374a (downregulated) and mir-630 (upregulated). deregulation of mirna expression led to subsequent modulation of mrna expression of several targets (tp53-s46, hipk2, atm, cdkn1a and 1b, casp3, parp1 and 2, ddit1 and 4, bcl2 and bcl2l2, tp73, yes1, and yap1) that are involved in the apoptotic process. our data support the notion that mirnas are critical downstream targets of p-δnp63α and mediate key pathways implicated in the response of cancer cells to chemotherapeutic drugs.",1
"gene silencing mediated by either micrornas (mirnas) or adenylate/uridylate-rich elements mediated mrna degradation (amd) is a powerful way to post-transcriptionally modulate gene expression. we and others have reported that the rna-binding protein ksrp favors the biogenesis of select mirnas (including let-7 family) and activates amd promoting the decay of inherently labile mrnas. different layers of interplay between mirna- and amd-mediated gene silencing have been proposed in cultured cells, but the relationship between the two pathways in living organisms is still elusive. we conditionally deleted dicer in mouse pituitary from embryonic day (e) 9.5 through cre-mediated recombination. in situ hybridization, immunohistochemistry, and quantitative reverse transcriptase-pcr revealed that dicer is essential for pituitary morphogenesis and correct expression of hormones. strikingly, αgsu (alpha glycoprotein subunit, common to three pituitary hormones) was absent in dicer-deleted pituitaries. αgsu mrna is unstable and its half-life increases during pituitary development. a transcriptome-wide analysis of microdissected e12.5 pituitaries revealed a significant increment of ksrp expression in conditional dicer-deleted mice. we found that ksrp directly binds to αgsu mrna, promoting its rapid decay; and, during pituitary development, αgsu expression displays an inverse temporal relationship to ksrp. further, let-7b/c downregulated ksrp expression, promoting the degradation of its mrna by directly binding to the 3'utr. therefore, we propose a model in which let-7b/c and ksrp operate within a negative feedback loop. starting from e12.5, ksrp induces the maturation of let-7b/c that, in turn, post-transcriptionally downregulates the expression of ksrp itself. this event leads to stabilization of αgsu mrna, which ultimately enhances the steady-state expression levels. we have identified a post-transcriptional regulatory network active during mouse pituitary development in which the expression of the hormone αgsu is increased by let7b/c through downregulation of ksrp. our study unveils a functional crosstalk between mirna- and amd-dependent gene regulation during mammalian organogenesis events.",1
"for human prostate cancer, the chromosome 8p21 locus, which contains nkx3.1 and the microrna (mir)-3622 family (mir-3622a/b), is a frequently deleted region. thus, mir-3622 is proposed as a suppressor for prostate cancer, but its role remains debatable. in the present study, we found that expression of mir-3622a was lower, whereas expression of mir-3622b-3p was higher in human prostate cancer tissues than in normal prostate tissues. mir-3622a-3p inhibited cell migration and invasion of human prostate cancer cells, whereas mir-3622b-3p facilitated cell proliferation, migration, and invasion. to address the opposing roles of mir-3622 family members in various human prostate cancer cell lines, we knocked out (ko) endogenous mir-3622, including both mir-3622a/b. our results showed that mir-3622 ko reduced cell proliferation, migration, and invasion in vitro and tumor growth and metastasis in vivo. functional analyses revealed that mir-3622 regulated the p53-downstream gene network, including aifm2, c-myc, and p21, to control apoptosis and the cell cycle. furthermore, using crispr interference, mirna/mrna immunoprecipitation assays, and dual-luciferase assays, we established that aifm2, a direct target of mir-3622b-3p, is responsible for mir-3622 ko-induced apoptosis. we identified an mir-3622-aifm2 axis that contributes to oncogenic function during tumor progression. in addition, mir-3622 ko inhibited the epithelial-mesenchymal transition involved in prostate cancer metastasis via upregulation of vimentin. the results show that mir-3622b-3p is upregulated in human prostate cancers and has an oncogenic function in tumor progression and metastasis via repression of p53 signaling, especially through an mir-3622-aifm2 axis. in contrast, for human prostate cancer, deletion of the mir-3622 locus at 8p21 reduced the oncogenic effects on tumor progression and metastasis.",1
"in liver, most metabolic pathways are under circadian control, and hundreds of protein-encoding genes are thus transcribed in a cyclic fashion. here we show that rhythmic transcription extends to the locus specifying mir-122, a highly abundant, hepatocyte-specific microrna. genetic loss-of-function and gain-of-function experiments have identified the orphan nuclear receptor rev-erbalpha as the major circadian regulator of mir-122 transcription. although due to its long half-life mature mir-122 accumulates at nearly constant rates throughout the day, this mirna is tightly associated with control mechanisms governing circadian gene expression. thus, the knockdown of mir-122 expression via an antisense oligonucleotide (aso) strategy resulted in the up- and down-regulation of hundreds of mrnas, of which a disproportionately high fraction accumulates in a circadian fashion. mir-122 has previously been linked to the regulation of cholesterol and lipid metabolism. the transcripts associated with these pathways indeed show the strongest time point-specific changes upon mir-122 depletion. the identification of pparbeta/delta and the peroxisome proliferator-activated receptor alpha (pparalpha) coactivator smarcd1/baf60a as novel mir-122 targets suggests an involvement of the circadian metabolic regulators of the ppar family in mir-122-mediated metabolic control.",1
"rationale the rapid induction and orchestration of new blood vessels are critical for tissue repair in response to injury, such as myocardial infarction, and for physiological angiogenic responses, such as embryonic development and exercise. objective we aimed to identify and characterize micrornas (mir) that regulate pathological and physiological angiogenesis. methods and results we show that mir-26a regulates pathological and physiological angiogenesis by targeting endothelial cell (ec) bone morphogenic protein/smad1 signaling in vitro and in vivo. mir-26a expression is increased in a model of acute myocardial infarction in mice and in human subjects with acute coronary syndromes. ectopic expression of mir-26a markedly induced ec cycle arrest and inhibited ec migration, sprouting angiogenesis, and network tube formation in matrigel, whereas blockade of mir-26a had the opposite effects. mechanistic studies demonstrate that mir-26a inhibits the bone morphogenic protein/smad1 signaling pathway in ecs by binding to the smad1 3'-untranslated region, an effect that decreased expression of id1 and increased p21(waf/cip) and p27. in zebrafish, mir-26a overexpression inhibited formation of the caudal vein plexus, a bone morphogenic protein-responsive process, an effect rescued by ectopic smad1 expression. in mice, mir-26a overexpression inhibited ec smad1 expression and exercise-induced angiogenesis. furthermore, systemic intravenous administration of an mir-26a inhibitor, locked nucleic acid-anti-mir-26a, increased smad1 expression and rapidly induced robust angiogenesis within 2 days, an effect associated with reduced myocardial infarct size and improved heart function. conclusions these findings establish mir-26a as a regulator of bone morphogenic protein/smad1-mediated ec angiogenic responses, and that manipulating mir-26a expression could provide a new target for rapid angiogenic therapy in ischemic disease states.",1
"in drosophila, formation of the germline progenitors, the pole cells, is induced by polar plasm localized in the posterior pole region of early embryos. the polar plasm contains polar granules, which act as a repository for the factors required for pole cell formation. it has been postulated that the factors are stored as mrna and are later translated on polysomes attached to the surface of polar granules. here, the identification of mitochondrial small ribosomal rna (mtsrrna) as a new component of polar granules is described. the mtsrrna was enriched in the polar plasm of the embryos immediately after oviposition and remained in the polar plasm throughout the cleavage stage until pole cell formation. in situ hybridization at an ultrastructural level revealed that mtsrrna was enriched on the surface of polar granules in cleavage embryos. furthermore, the localization of mtsrrna in the polar plasm depended on the normal function of oskar, vasa and tudor genes, which are all required for pole cell formation. the temporal and spatial distribution of mtsrrna is essentially identical to that of mitochondrial large ribosomal rna (mtlrrna), which has been shown to be required for pole cell formation. taken together, it is speculated that mtsrrna and mtlrrna are part of the translation machinery localized to polar granules, which is essential for pole cell formation.",1
"parkinson disease (pd) is a common neurodegenerative disorder caused by environmental and genetic factors. we have previously shown linkage of pd to chromosome 8p. subsequently, fibroblast growth factor 20 (fgf20) at 8p21.3-22 was identified as a risk factor in several association studies. to identify the risk-conferring polymorphism in fgf20, we performed genetic and functional analysis of single-nucleotide polymorphisms within the gene. in a sample of 729 nuclear families with 1089 affected and 1165 unaffected individuals, the strongest evidence of association came from rs12720208 in the 3' untranslated region of fgf20. we show in several functional assays that the risk allele for rs12720208 disrupts a binding site for microrna-433, increasing translation of fgf20 in vitro and in vivo. in a cell-based system and in pd brains, this increase in translation of fgf20 is correlated with increased alpha-synuclein expression, which has previously been shown to cause pd through both overexpression and point mutations. we suggest a novel mechanism of action for pd risk in which the modulation of the susceptibility gene's translation by common variations interfere with the regulation mechanisms of microrna. we propose this is likely to be a common mechanism of genetic modulation of individual susceptibility to complex disease.",1
"endothelial progenitor cells (epcs) play an important role in angiogenesis, which is essential for numerous physiological processes as well as tumor growth. several micrornas (mirnas) have been reported to be involved in angiogenesis. mir-34a, recently reported as a tumor suppressor, has been found to target silent information regulator 1 (sirt1), leading to cell cycle arrest or apoptosis. however, the role of mir-34a in epc-mediated angiogenesis was unknown. the present study tested the hypothesis that mir-34a inhibits epc-mediated angiogenesis by inducing senescence via suppressing sirt1. bone marrow-derived epcs from adult male sprague-dawley rats were used. results of flow cytometry showed that epcs after 7 days of culture expressed both stem cell markers cd34 and cd133 and endothelial cell markers vegfr-2 (flk-1) and ve-cadherin. mir-34a was expressed in normal epcs, and overexpression of mir-34a via its mimic transfection significantly increased its expression and impaired in vitro epc angiogenesis. mir-34a overexpression led to a significantly increased epc senescence, paralleled with an approximately 40% sirt1 reduction. furthermore, knockdown of sirt1 by its sirna resulted in diminished epc angiogenesis and increased senescence. finally, overexpression of mir-34a increased the level of sirt1 effector-acetylated forkhead box o transcription factors 1 (foxo1), an effect mimicked in epcs following sirt1 knockdown. in conclusion, mir-34a impairs epc-mediated angiogenesis by induction of senescence via inhibiting sirt1.",1
"long-term potentiation (ltp) is a form of synaptic plasticity that results in enhanced synaptic strength. it is associated with the formation and enlargement of dendritic spines-tiny protrusions accommodating excitatory synapses. both ltp and spine remodelling are crucial for brain development, cognition and the pathophysiology of neurological disorders. the role of micrornas (mirnas) in the maintenance of ltp, however, is not well understood. using next-generation sequencing to profile mirna transcriptomes, we demonstrate that mir-26a and mir-384-5p specifically affect the maintenance, but not induction, of ltp and different stages of spine enlargement by regulating the expression of rsk3. using bioinformatics, we also examine the global effects of mirna transcriptome changes during ltp on gene expression and cellular activities. this study reveals a novel mirna-mediated mechanism for gene-specific regulation of translation in ltp, identifies two mirnas required for long-lasting synaptic and spine plasticity and presents a catalogue of candidate 'ltp mirnas'.",1
"purpose aberrant expression of mirnas is crucial in several tissues tumorigenesis including thyroid. recent studies demonstrated that mir-650 plays different role depending on the cancer type. herein, we investigated the role of mir-650 in thyroid carcinoma. methods the expression of mir-650 was analyzed in human thyroid tissues by q-rt-pcr. anaplastic (8505c, cal62, sw1736) and papillary (tpc-1) thyroid cancer cell lines were used to dissect the role of mir-650 on malignant hallmarks of transformation. label-free proteomic analysis was exploited to unravel the targets of mir-650, while luciferase reporter assay and functional experiments were performed to confirm a selected target. spearman's rank correlation test was used to assess the association between mir-650 and its target in human thyroid cancer tissues. results mir-650 is over-expressed in anaplastic (atc) thyroid carcinoma where it enhances cell migration and invasion. proteomic label-free and bioinformatics analysis revealed that the serine-threonine protein phosphatase 2 catalytic subunit alpha (ppp2ca) is a target of mir-650; these finding were confirmed by luciferase assay. restoration of ppp2ca mrna, deprived of its 3'utr, is able to revert the malignant phenotype induced by mir-650 in hek-293 cells. importantly, ppp2ca is down-regulated in atc tissues and is inversely correlated with mir-650. conclusions mir-650 displayed oncogenic activity in atc cells through targeting ppp2ca phosphatase. these results suggest that mir-650/ppp2ca axis could be modulated to interfere with motile ability of thyroid carcinoma cells.",1
"background excessive collagen synthesis and deposit during skin wound healing results in scar formation. micrornas (mirnas) are endogenous noncoding rna regulators that mediate diverse biological functions through repressing target genes and hold great potentials for clinical therapeutic applications. the aim of the present study was to identify mirnas as post-transcriptional regulators of collagen 1 in skin fibroblasts. methods mirna candidates that potentially target collagen 1 were predicted by computational algorithms pictar and targetscan. the expression changes of collagen subunits 1α1 and 1α2 were measured by real-time reverse transcription-polymerase chain reaction and western blot after the primary skin fibroblasts were transfected with mir-29b mimics or inhibitor, respectively. a luciferase reporter assay was performed to further determine whether both collagen 1 subunits were probably direct targets of mir-29b. results computational predictions identified several mirnas as possible regulators for collagen 1 synthesis, including mir-29b. enforced overexpression of mir-29b resulted in remarkable decrease of collagen 1α1 and 1α2, whereas knockdown of endogenous mir-29b induced pronounced increase of collagen 1α1 and 1α2 at both the messenger rna and the protein levels. the luciferase activities were significantly inhibited when cells were cotransfected with reporter constructs and mir-29 mimics in vitro. moreover, mir-29b transcriptional abundance inversely related to the levels of both collagen 1 subunits in skin scar as compared with normal skin. conclusions our data indicate that mir-29b is a potent post-transcriptional repressor of collagen 1 in skin fibroblasts and its deregulation might be implicated in scar formation, suggesting that mir-29b might represent a potential therapeutic target for scar reduction.",1
"tumor growth is modulated by crosstalk between cancer cells and the tumor microenvironment. recent advances have shown that mirna dysfunction in tumor cells can modulate the tumor microenvironment to indirectly determine their progression. however, this process is poorly understood in testicular germ cell tumors (tgcts). we reported here that mir-125b was repressed in tgct samples by epigenetic modifications rather than genetic alternations. furthermore, mir-125b overexpression significantly alleviated the tumor growth in two nccit human embryonic carcinoma xenograft models in vivo, whereas mir-125b did not stimulate autonomous tumor cell growth in vitro. notably, forced expression of mir-125b in nccit embryonic carcinoma cells decreased the abundance of host tumor-associated macrophages (tams) within tumor microenvironment. selective deletion of host macrophages by clodronate abolished the anti-tumoral ability of mir-125b in xenograft models. by rna profiling, western blot and luciferase reporter assay, we further observed that mir-125b directly regulated tumor cell-derived chemokine csf1 and cx3cl1, which are known to control the recruitment of tams to tumor sites. lastly, we found that one set of mirnas, which are under the regulation of mir-125b, might convergently target csf1/cx3cl1 in nccit cells using mirna profiling. these findings uncover the anticancer effect of mir-125b via mediating tumor-stroma crosstalk in xenograft models of tgcts and raise the possibility of targeting mir-125b as mirna therapeutics.",1
"hoxa9 and meis1 have essential oncogenic roles in mixed lineage leukaemia (mll)-rearranged leukaemia. here we show that they are direct targets of mirna-196b, a microrna (mirna) located adjacent to and co-expressed with hoxa9, in mll-rearranged leukaemic cells. forced expression of mir-196b significantly delays mll-fusion-mediated leukemogenesis in primary bone marrow transplantation through suppressing hoxa9/meis1 expression. however, ectopic expression of mir-196b results in more aggressive leukaemic phenotypes and causes much faster leukemogenesis in secondary transplantation than mll fusion alone, likely through the further repression of fas expression, a proapoptotic gene downregulated in mll-rearranged leukaemia. overexpression of fas significantly inhibits leukemogenesis and reverses mir-196b-mediated phenotypes. targeting hoxa9/meis1 and fas by mir-196b is probably also important for normal haematopoiesis. thus, our results uncover a previously unappreciated mirna-regulation mechanism by which a single mirna may target both oncogenes and tumour suppressors, simultaneously, or, sequentially, in tumourigenesis and normal development per cell differentiation, indicating that mirna regulation is much more complex than previously thought.",1
"obesity is characterized by excessive adipose tissue mass and associated with type 2 diabetes and cardiovascular diseases. to fight obesity and its sequels, elucidating molecular events that govern adipocyte differentiation and function is of key importance. micrornas (mirnas) are a novel class of non-coding, regulatory rnas that have been shown to regulate crucial cellular processes, including differentiation. several studies have already assigned mirnas to distinct functions in murine adipocyte differentiation but only a few studies did so for humans. here, we investigated the function of mir-30c in human adipogenesis. mir-30c expression was increased during adipogenesis of human multipotent adipose-derived stem (hmads) cells, and mir-30c overexpression enforced adipocyte marker gene induction and triglyceride accumulation. mirna target prediction revealed two putative direct targets of mir-30c, pai-1 (serpine1) and alk2 (acvr1, actri), both inversely regulated to mir-30c during adipogenesis and responsive to mir-30c overexpression. luciferase reporter assays confirmed pai-1 and alk2 as direct mir-30c targets. moreover, reciprocal expression between mir-30c and pai-1 could also be demonstrated in white adipose tissue of obesity mouse models, suggesting a potential physiological role of mir-30c for pai-1 regulation in the obese state. validating pai-1 and alk-2 as mir-30c mediators in adipogenesis revealed that not single silencing of pai-1 or alk2, but only co-silencing of both phenocopied the pro-adipogenic mir-30c effect. thus, mir-30c can target two, so far not interconnected genes in distinct pathways, supporting the idea that mirnas might coordinate larger regulatory networks than previously anticipated.",1
"astrocytes are important mediators of inflammatory processes in the brain and seem to play an important role in several neurological disorders, including epilepsy. recent studies show that astrocytes produce several micrornas, which may function as crucial regulators of inflammatory pathways and could be used as therapeutic target. we aim to study which mirnas are produced by astrocytes during il-1β mediated inflammatory conditions in vitro, as well as their functional role and to validate these findings in human epileptogenic brain tissue. sequencing was used to assess mirna and mrna expression in il-1β-stimulated human fetal astrocyte cultures. mirnas were overexpressed in cell cultures using mirna mimics. expression of mirnas in resected brain tissue from patients with tuberous sclerosis complex or temporal lobe epilepsy with hippocampal sclerosis was examined using in situ hybridization. two differentially expressed mirnas were found: mir146a and mir147b, which were associated with increased expression of genes related to the immune/inflammatory response. as previously reported for mir146a, overexpression of mir147b reduced the expression of the pro-inflammatory mediators il-6 and cox-2 after il-1β stimulation in both astrocyte and tuberous sclerosis complex cell cultures. mir146a and mir147b overexpression decreased proliferation of astrocytes and promoted neuronal differentiation of human neural stem cells. similarly to previous evidence for mir146a, mir147b was increased expressed in astrocytes in epileptogenic brain. due to their anti-inflammatory effects, ability to restore aberrant astrocytic proliferation and promote neuronal differentiation, mir146a and mir147b deserve further investigation as potential therapeutic targets in neurological disorders associated with inflammation, such as epilepsy.",1
"as the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. central to cell function are rna-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snornas, rnase p, and telomerase, among others. in this article we identify by comparative genomics and validate by rna analysis numerous previously unknown structural rnas encoded by the plasmodium falciparum genome, including the telomerase rna, u3, 31 snornas, as well as previously predicted spliceosomal snrnas, srp rna, mrp rna, and rnase p rna. furthermore, we identify six new rna coding genes of unknown function. to investigate the relationships of the rna coding genes to other genomic features in related parasites, we developed a genome browser for p. falciparum ( additional experiments provide evidence supporting the prediction that snornas guide methylation of a specific position on u4 snrna, as well as predicting an snrna promoter element particular to plasmodium sp. these findings should allow detailed structural comparisons between the rna components of the gene expression machinery of the parasite and its vertebrate hosts.",1
"micrornas (mirnas) are small non-coding rnas that post-transcriptionally repress the expression of target genes. many mirnas have been implicated in a number of diseases, including cancers. the mir-17-92 mirna cluster is known as a body of oncogenic mirnas, and has been shown to be overexpressed in several cancers, including lung cancer. although the overexpression of mir-17-92 is clearly implicated in the development of lung cancer, only a few direct targets for the mir-17-92 cluster have been identified thus far. in this study, we examined mir-17-92 target profiles in sbc-3 small-cell lung cancer cells using a quantitative proteomic strategy to identify direct targets of the mir-17-92 cluster. by knocking down the expression of endogenous mir-19a, mir-20a and mir-92-1, which are contained in the cluster, 112 up-regulated proteins were detected and also identified as potential targets of these mirnas. among these candidate targets, we validated one direct target, rab14. in conclusion, these findings suggest that proteomic approaches are valuable for identifying direct mirna targets, and we were able to identify a novel direct target for the mir-92-1 using our proteomic strategy.",1
"micrornas (mirnas) play important roles in pulmonary artery hypertension (pah). recently, it has been reported that mir-199a-5p participates in the progression of chronic obstructive pulmonary disease, ventricular hypertrophy and heart failure. however, the roles of mir-199a-5p in pah are still unclear. in the present study, mir-199a-5p was investigated in pah rat models and in human pulmonary artery smooth muscle cells (hpasmcs) and endothelial cells (hpaecs). the expression of mir-199a-5p was significantly increased following pah induction, and anti-mir-199a-5p could increase the nitric oxide (no) level and decrease the pah-induced upregulation of pulmonary artery pressure and right ventricular hypertrophy. moreover, in hpasmcs and hpaecs, mir-199a-5p overexpression could inhibit the level of no and promote the concentration of ca(2+), but anti-mir-199a-5p showed opposite results. further analysis demonstrated that mir-199a-5p attenuated the expression of smad3. importantly, smad3 was confirmed to be the target gene of mir-199a-5p using dual-luciferase reporter assay. mechanism analyses revealed that the downregulation of no and the upregulation of ca(2+) caused by mir-199a-5p were all reversed by smad3 overexpression in hpasmcs and hpaecs. moreover, in pah model, smad3, p-smad3 and smad4 were all downregulated in lung tissues, and sis3 (smad3 inhibitor) could reverse the effects of anti-mir-199a-5p in pah rats. our date suggest that mir-199a-5p may function as a regulator of pah by targeting smad3, indicating a novel therapeutic strategy for patients with pah.",1
"through in vivo selection of human cancer cell populations, we uncover a convergent and cooperative mirna network that drives melanoma metastasis. we identify mir-1908, mir-199a-5p, and mir-199a-3p as endogenous promoters of metastatic invasion, angiogenesis, and colonization in melanoma. these mirnas convergently target apolipoprotein e (apoe) and the heat shock factor dnaja4. cancer-secreted apoe suppresses invasion and metastatic endothelial recruitment (mer) by engaging melanoma cell lrp1 and endothelial cell lrp8 receptors, respectively, while dnaja4 promotes apoe expression. expression levels of these mirnas and apoe correlate with human metastatic progression outcomes. treatment of cells with locked nucleic acids (lnas) targeting these mirnas inhibits metastasis to multiple organs, and therapeutic delivery of these lnas strongly suppresses melanoma metastasis. we thus identify mirnas with dual cell-intrinsic/cell-extrinsic roles in cancer, reveal convergent cooperativity in a metastatic mirna network, identify apoe as an anti-angiogenic and metastasis-suppressive factor, and uncover multiple prognostic mirnas with synergistic combinatorial therapeutic potential in melanoma.",1
"the targeted small-molecule drug azd6244 is an allosteric, atp-noncompetitive inhibitor of mek1/2 that has shown activity against several malignant tumors. here, we report that azd6244 repressed cell growth and induced apoptosis and g1-phase arrest in the breast cancer cell lines mda-mb-231 and hcc1937. using microrna (mirna) arrays and quantitative rt-pcr, we found that mir-203 was up-regulated after azd6244 treatment. in accordance with bioinformatics and luciferase activity analyses, cul1 was found to be the direct target of mir-203. furthermore, mir-203 inhibition and cul1 overexpression reversed the cytotoxicity of azd6244 on the mda-mb-231 and hcc1937 cells. collectively, our data indicate that mir-203 mediates the azd6244-induced cytotoxicity of breast cancer cells and that the mek/erk/mir-203/cul1 signaling pathway may participate in this process.",1
"progressive cardiac hypertrophy owing to pathological stimuli, such as pressure overload, is frequently associated with the development of heart failure, a major cause of morbidity and mortality worldwide. growing evidence has shown that mirnas are extensively involved in the pathogenesis of cardiac hypertrophy. in the present study, we examined the hypothesis that the mir-19a/b family acts as a key regulator of cardiac hypertrophy and apoptosis. forced overexpression of mir-19a/b was sufficient to induce hypertrophy in rat neonatal cardiomyocytes. luciferase assays revealed that mir-19a/b directly target the anti-hypertrophic genes atrogin-1 and murf-1 (muscle ring-finger protein-1). the endogenous expressions of the target genes were down-regulated by mir-19a/b. pro-hypertrophic calcineurin/nfat (nuclear factor of activated t-cells) signalling was elevated markedly in the presence of mir-19b, and the calcineurin inhibitor csa (cyclosporin a) and the pkc (protein kinase c) inhibitor gf10923x significantly attenuated the mir-19b-mediated increase in cell size and expression of hypertrophic markers. furthermore, mir-19b led to increased cell survival through up-regulation of the nfat target gene encoding α-crystallin-b and repression of the pro-apoptotic gene bim (bcl-2-interacting mediator of cell death) under er (endoplasmic reticulum) stress conditions. taken together, the results of the present study demonstrate that the mir-19a/b family regulates phenotypes of cardiomyocytes via suppression of multiple direct target genes.",1
"substantial evidence indicates that the human ether-a-go-go-related gene potassium channel (herg, kv11.1, kcnh2) is overexpressed in human glioblastoma multiforme (gbm) specimens and plays an essential role in the malignant proliferation of glioma cells. however, its upstream regulator in glioma cells is not fully elucidated. the present study was designed to determine whether the expression of herg gene is regulated by mir-133b or mir-34a, thereby contributing to the anti-proliferation effect of arsenic trioxide (ato) in u251 human glioma cells. real-time polymerase chain reactions (qrt-pcr) and western blot results demonstrated that herg mrna and protein levels were dramatically upregulated in clinical gbm specimens. conversely, both mir-133b and mir-34a were markedly downregulated in clinical gbm specimens by qrt-pcr. the herg gene was a direct target of mir-133b and mir-34a by bioinformatics analyses and luciferase reporter assays. moreover, ato, which is an emerging chemotherapy drug for glioma disease, remarkably elevated the level of mir-133b, but not mir-34a in u251 glioma cells. the level of mir-133b upstream transactivator serum response factor (srf) was also suppressed by ato. the transfection of anti-mir-133b oligonucleotide (amo-133b) remarkably prevented the decrease of herg protein by 5 μm ato treatment for 24 h in u251 cells, whereas anti-mir-34a oligonucleotide (amo-34a) did not exhibit recuperated effect. finally, the transient overexpression by mir-133b mimics and treatment with the herg channel-specific blocker e4031 markedly facilitated the ato inhibition of proliferation of and induced apoptosis in u251 cells, whereas amo-mir-133b attenuated these changes. our study provided the evidence for the pathological role of mir-133b and mir-34a in the development of gbm and thus expanded our understanding of the herg gene expression and ato chemotherapeutic roles of mirnas. targeting mir-133b/herg pathway may be a new strategy for chemotherapy of malignant gliomas.",1
"the signaling pathways associated with the toll-like receptors (tlrs) and nuclear factor-kappab (nf-κb) are essential to pro-inflammatory cytokine and chemokine expression, as well as initiating innate epithelial immune responses. the tlr/nf-κb signaling pathways must be stringently controlled through an intricate network of positive and negative regulatory elements. micrornas (mirnas) are non-coding small rnas that regulate the stability and/or translation of protein-coding mrnas. herein we report that mir-16 promotes nf-κb-regulated transactivation of the il-8 gene by suppression of the silencing mediator for retinoid and thyroid hormone receptor (smrt). lps stimulation activated mir-16 gene transcription in human monocytes (u937) and biliary epithelial cells (h69) through mapk-dependent mechanisms. transfection of cells with the mir-16 precursor promoted lps-induced production of il-8, il-6, and il-1α, without a significant effect on their rna stability. instead, an increase in nf-κb-regulated transactivation of the il-8 gene was confirmed in cells following transfection of mir-16 precursor. importantly, mir-16 targeted the 3'-untranslated region of smrt and caused translational suppression of smrt. lps decreased smrt expression via upregulation of mir-16. moreover, functional manipulation of smrt altered nf-κb-regulated transactivation of lps-induced il-8 expression. these data suggest that mir-16 targets smrt and modulates nf-κb-regulated transactivation of the il-8 gene.",1
"in a number of bacterial pathogens, the production of virulence factors is induced at 37 °c; this effect is often regulated by mrna structures formed in the 5' untranslated region (utr) that block translation initiation of genes at environmental temperatures. at 37 °c, the rna structures become unstable and ribosomes gain access to their binding sites in the mrnas. pseudomonas aeruginosa is an important opportunistic pathogen and the expression of many of its virulence-associated traits is regulated by the quorum-sensing (qs) response, but the effect of temperature on virulence-factor expression is not well-understood. the aim of this work is the characterization of the molecular mechanism involved in thermoregulation of qs-dependent virulence-factor production. we demonstrate that traits that are dependent on the qs transcriptional regulator rhlr have a higher expression at 37 °c, correlating with a higher rhlr concentration as measured by western blot. we also determined, using gene fusions and point mutations, that rhlr thermoregulation is a posttranscriptional effect dependent on an rna thermometer of the rose (repression of heat-shock gene expression) family. this rna element regulates the expression of the rhlab operon, involved in rhamnolipid production, and of the downstream rhlr gene. we also identified a second functional thermometer in the 5' utr of the lasi gene. we confirmed that these rna thermometers are the main mechanism of thermoregulation of qs-dependent gene expression in p. aeruginosa using quantitative real-time pcr. this is the first description, to our knowledge, of a rose element regulating the expression of virulence traits and of an rna thermometer controlling multiple genes in an operon through a polar effect.",1
"aims the present study was designed to decipher molecular mechanisms underlying nicotine's promoting atrial fibrillation (af) by inducing atrial structural remodelling. methods and results the canine model of af was successfully established by nicotine administration and rapid pacing. the atrial fibroblasts isolated from healthy dogs were treated with nicotine. the role of micrornas (mirnas) on the expression and regulation of transforming growth factor-beta1 (tgf-beta1), tgf-beta receptor type ii (tgf-betarii), and collagen production was evaluated in vivo and in vitro. administration of nicotine for 30 days increased af vulnerability by approximately eight- to 15-fold in dogs. nicotine stimulated remarkable collagen production and atrial fibrosis both in vitro in cultured canine atrial fibroblasts and in vivo in atrial tissues. nicotine produced significant upregulation of expression of tgf-beta1 and tgf-betarii at the protein level, and a 60-70% decrease in the levels of mirnas mir-133 and mir-590. this downregulation of mir-133 and mir-590 partly accounts for the upregulation of tgf-beta1 and tgf-betarii, because our data established tgf-beta1 and tgf-betarii as targets for mir-133 and mir-590 repression. transfection of mir-133 or mir-590 into cultured atrial fibroblasts decreased tgf-beta1 and tgf-betarii levels and collagen content. these effects were abolished by the antisense oligonucleotides against mir-133 or mir-590. the effects of nicotine were prevented by an alpha7 nicotinic acetylcholine receptor antagonist. conclusion we conclude that the profibrotic response to nicotine in canine atrium is critically dependent upon downregulation of mir-133 and mir-590.",1
"our previous study indicated that microrna 145 (mir-145) and its predicated target, erythropoietin-producing hepatoma (eph) receptor a4 (epha4), was closely associated with ischemic stroke. in this study, we aimed to further explore their function in a model of oxygen-glucose deprivation (ogd). the expression of mir-145 in the blood of 44 patients with ischemic stroke and 37 normal controls was detected by qrt-pcr. after transfection with either the wild- or mutant-type pgl3-promoter epha4 3'utr into the mir-145 mimic and mir-145 inhibitor, a dual-luciferase reporter assay was performed to explore the interaction between mir-145 and epha4. qrt-pcr and western blot were performed to further explore the effects of mir-145 on epha4 expression after an mir-145 mimic, an mir-145 inhibitor or lv-sh-epha4 was transfected into cerebral cortical neurons. the expression of mir-145 was significantly upregulated in the blood of patients with ischemic stroke compared to that of normal controls. dual-luciferase reporter assay, qrt-pcr and western blot results indicated that mir-145 indeed targets epha4 through its 3'-utr and regulates the expression level of epha4 at both the mrna and protein levels. moreover, the ogd model was successfully constructed, and mir-145 exerted a protective effects in cell viability in the ogd model by downregulating epha4. the expression of loc105376244 could be regulated by the mir-145-epha4 interaction. mir-145 exerted a protective effects in cell viability in the ogd model by downregulating epha4, which suggested their potential roles in ischemic stroke and requires further research.",1
"the eel long interspersed element (line) unal2 and its partner short interspersed element (sine) share a conserved 3' tail containing a stem-loop that is critical for their retrotransposition. presumably, the first step of retrotransposition is the recognition of their 3' tails by unal2-encoded reverse transcriptase. the solution structure of a 17-nucleotide rna derived from the 3' tail of unal2 was determined by nmr. the ggaua loop forms a specific structure in which the uridine is exposed to solvent with the third and fifth adenosines stacked. a sharp turn in the phosphodiester backbone occurs between the second guanosine and third adenosine. when the uridine is mutated (but not deleted), all mutants form the loop structure, indicating that the loop structure requires an exposed fourth residue. the retrotransposition assay in hela cells revealed that retrotransposition requires the second guanosine, although any nucleoside functions at the fourth position, suggesting that unal2 reverse transcriptase specifically recognizes the 5' side of the ggana loop.",1
"dysfunction and reduction of circulating endothelial progenitor cell (epc) is correlated with the onset of cardiovascular disorders including coronary artery disease (cad). vegf is a known mitogen for epc to migrate out of bone marrow to possess angiogenic activities, and the plasma levels of vegf are inversely correlated to the progression of cad. circulating micrornas (mirnas) in patient body fluids have recently been considered to hold the potential of being novel disease biomarkers and drug targets. however, how mirnas and vegf cooperate to regulate cad progression is still unclear. through the small rna sequencing (smrna-seq), we deciphered the mirnome patterns of epcs with different angiogenic activities, hypothesizing that mirnas targeting vegf must be more abundant in epcs with lower angiogenic activities. candidates of anti-vegf mirnas, including mir-361-5p and mir-484, were enriched in not only diseased epcs but also the plasma of cad patients. however, we found out only mir-361-5p, but not mir-484, was able to suppress vegf expression and epc activities. reporter assays confirmed the direct binding and repression of mir-361-5p to the 3'-utr of vegf mrna. knock down of mir-361-5p not only restored vegf levels and angiogenic activities of diseased epcs in vitro, but further promoted blood flow recovery in ischemic limbs of mice. collectively, we discovered a mir-361-5p/vegf-dependent regulation that could help to develop new therapeutic modalities not only for ischemia-related diseases but also for tumor angiogenesis.",1
"several mirnas have been implicated in the development and progression of osteosarcoma (os). in this study, we found that mir-16 is downregulated in os cell lines and tissues. overexpression of mir-16 suppresses os cell proliferation and tumor growth in nude mice. furthermore, we confirmed that igf1r is a direct target of mir-16. mechanistic investigation revealed that mir-16 overexpression inhibits the raf1-mek1/2-erk1/2 pathway. in clinical specimens, igf1r levels inversely correlate with mir-16 expression. our results provide significant clues regarding the role of mir-16 as a tumor suppressor by targeting igf1r in os.",1
"sustained endoplasmic reticulum (er) stress has been linked to cell death and the pathogenesis of many liver diseases, including toxic liver, cholestasis, and infectious liver disease. the cellular pathways that attenuate hepatic er stress have been the focus of many recent studies, but the role of micrornas (mirna) in this process remains unknown. here, we report that one of the most abundant mirnas in hepatocytes, mir-199a-5p, was elevated in both bile acid- and thapsigargin (tg)-stimulated cultured hepatocytes, as well as in the liver of bile duct-ligated mice. we identify the misfolded protein chaperone grp78, as well as the unfolded protein response transducers endoplasmic reticulum to nucleus signaling 1 and activating transcription factor 6 as direct targets of mir-199a-5p, and show that endogenous mir-199a-5p represses the 3' untranslated regions (utrs) of their mrnas. through gain-of-function and loss of function approaches, we demonstrate that the elevated mir-199-5p disrupts sustained er stress and prevents hepatocytes from undergoing bile acid- or tg-induced cell death. furthermore, we reveal that the transcription factor ap-1 is a strong positive regulator of mir-199a-5p. in brief, our study demonstrates that ap-1/mir-199a-5p and er stress mediators form a feedback loop, which shields hepatocytes from sustained er stress and protects the liver from injury. on the basis of these findings, we also suggest that the mirna mir-199a-5p is a potential target for clinical approaches aiming to protect hepatocytes in liver disease.",1
"anaplastic astrocytoma (aa) is a grade iii glioma that often occurs in middle-aged patients and presents a uniformly poor prognosis. a small subpopulation of cancer stem cells (cscs) possessing a self-renewing capacity is reported to be responsible for tumor recurrence and therapeutic resistance. an accumulating amount of micrornas (mirna) were found aberrantly expressed in human cancers and regulate cscs. efforts have been made to couple mirnas with nonviral gene delivery approaches to target specific genes in cancer cells. however, the efficiency of delivery of mirnas to aa-derived cscs is still an applicability hurdle. the present study aimed to investigate the effectiveness and applicability of nonviral vector-mediated delivery of let-7a with regard to eradication of aa and aa-derived csc cells. herein, our mirna/mrna microarray and rt-pcr analysis showed that the expression of let-7a, a tumor-suppressive mirna, is inversely correlated with the levels of hmga2 and sox2 in the aa side population (sp(+)) cells. luciferase reporter assay showed that let-7a directly targets the 3'-utrs of hmga2 in aa-sp(+) cells. knockdown of hmga2 significantly suppressed the protein expression of sox2 in aa-sp(+) cells, whereas overexpression of hmga2 upregulated sox2 expression in aa-sp(-). nuclear localization signal (nls) peptides can facilitate nuclear targeting of dna and are used to improve gene delivery. using polyurethane-short branch polyethylenimine (pu-pei) as a therapeutic delivery vehicle, we conjugated nls with let-7 and successfully delivered it to aa-sp(+) cells, resulting in significantly suppressed expression of hmga2 and sox2, tumorigenicity, and csc-like abilities. this treatment facilitated the differentiation of aa-sp(+) cells into non-sp cscs. furthermore, pu-pei-mediated delivery of nls-conjugated let-7a in aa-sp(+) cells suppressed the expression of drug-resistant and antiapoptotic genes, and increased cell sensitivity to radiation. finally, the in vivo delivery of pu-pei-nls-let-7a significantly suppressed the tumorigenesis of aa-sp(+) cells and synergistically improved the survival rate of orthotopically aa-sp(+)-transplanted immunocompromised mice when combined with radiotherapy. therefore, pu-pei-nls-let-7a is a potential novel therapeutic approach for aa.",1
"suppression of annexin a1 (anxa1), a mediator of apoptosis and inhibitor of cell proliferation, is well documented in various cancers but the underlying mechanism remains unknown. we investigated whether decreased anxa1 expression was mediated by micrornas (mirnas), which are small, non-coding rnas that negatively regulate gene expression. using sanger mirbase, we identified mir-584, mir-196a and mir-196b as potential mirnas targeting anxa1. only mirna-196a showed significant inverse correlation with anxa1 mrna levels in 12 cancer cell lines of esophageal, breast and endometrial origin (pearson's correlation -0.66, p=0.019), identifying this as the candidate mirna targeting anxa1. inverse correlation was also observed in 10 esophageal adenocarcinomas (pearson's correlation -0.64, p=0.047). analysis of paired normal/tumor tissues from additional 10 patients revealed an increase in mir-196a in the cancers (p=0.003), accompanied by a decrease in anxa1 mrna (p=0.004). increasing mir-196a levels in cells by mir-196a mimics resulted in decreased anxa1 mrna and protein. in addition, mir-196a mimics inhibited luciferase expression in luciferase plasmid reporter that included predicted mir-196a recognition sequence from anxa1 3'-untranslated region confirming that mir-196a directly targets anxa1. mir-196a promoted cell proliferation, anchorage-independent growth and suppressed apoptosis, suggesting its oncogenic potential. this study demonstrated a novel mechanism of post-transcriptional regulation of anxa1 expression and identified mir-196a as a marker of esophageal cancer.",1
"the human 7sk ribonucleoprotein (rnp) has been analyzed to determine its rna secondary structure and protein constituents. hela cell 7sk rna alone and within its rnp have been probed by chemical modification and enzymatic cleavage, and sites of modification or cleavage have been mapped by primer extension. the resulting secondary structure suggests that structural determinants necessary for capping (a 5' stem followed by the sequence aupuupuc) and nuclear migration (the sequence aupuupuc) of 7sk rna may be similar to those for u6 small nuclear rna (snrna). it also supports existence of a 3' stem structure which could serve to self-prime cdna synthesis during pseudogene formation. oligonucleotide-directed rnase h digestion indicated regions of 7sk rna capable of base pairing with other nucleic acids. antisense 2'-o-methyl rna oligonucleotides were used to affinity select the 7sk rnp from an in vivo 35s-labeled cell sonic extract and identify eight associated proteins of 83, 48, 45, 43, 42, 21, 18, and 13 kda. 7sk rna has extensive sequence complementarity to u4 snrna, within the u4/u6 base pairing domain, and also to u11 snrna. the possibility that the 7sk rnp is an unrecognized component of the pre-mrna processing machinery is discussed.",1
"we developed a simple, direct and cost-effective approach to search for the most likely target genes of a known microrna (mirna) in vitro. we term this method 'labeled mirna pull-down (lamp)' assay system. briefly, the pre-mirna is labeled with digoxigenin (dig), mixed with cell extracts and immunoprecipitated by anti-dig antiserum. when the dig-labeled mirna and bound mrna complex are obtained, the total cdnas are then subcloned and sequenced, or rt-pcr-amplified, to search for the putative target genes of a known mirna. after successfully identifying the known target genes of caenorhabditis elegans mirnas lin-4 and let-7 and zebrafish let-7, we applied lamp to find the unknown target gene of zebrafish mir-1, which resulted in the identification of hand2. we then confirmed hand2 as a novel target gene of mir-1 by whole-mount in situ hybridization and luciferase reporter gene assay. we further validated this target gene by microarray analysis, and the results showed that hand2 is the top-scoring among 302 predicted putative target genes. we concluded that lamp is an experimental approach for high-throughput identification of the target gene of known mirnas from both c. elegans and zebrafish, yielding fewer false positive results than those produced by using only the bioinformatics approach.",1
"micrornas (mirnas) are a recently discovered class of endogenous, small, noncoding rnas that regulate about 30% of the encoding genes of the human genome. however, the role of mirnas in vascular disease is currently completely unknown. using microarray analysis, we demonstrated for the first time that mirnas are aberrantly expressed in the vascular walls after balloon injury. the aberrantly expressed mirnas were further confirmed by northern blot and quantitative real-time polymerase chain reaction. modulating an aberrantly overexpressed mirna, mir-21, via antisense-mediated depletion (knock-down) had a significant negative effect on neointimal lesion formation. in vitro, the expression level of mir-21 in dedifferentiated vascular smooth muscle cells was significantly higher than that in fresh isolated differentiated cells. depletion of mir-21 resulted in decreased cell proliferation and increased cell apoptosis in a dose-dependent manner. mir-21-mediated cellular effects were further confirmed in vivo in balloon-injured rat carotid arteries. western blot analysis demonstrated that pten and bcl-2 were involved in mir-21-mediated cellular effects. the results suggest that mirnas are novel regulatory rnas for neointimal lesion formation. mirnas may be a new therapeutic target for proliferative vascular diseases such as atherosclerosis, postangioplasty restenosis, transplantation arteriopathy, and stroke.",1
"levels of p27(kip1), a key negative regulator of the cell cycle, are often decreased in cancer. in most cancers, levels of p27(kip1) mrna are unchanged and increased proteolysis of the p27(kip1) protein is thought to be the primary mechanism for its downregulation. here we show that p27(kip1) protein levels are also downregulated by micrornas in cancer cells. we used rna interference to reduce dicer levels in human glioblastoma cell lines and found that this caused an increase in p27(kip1) levels and a decrease in cell proliferation. when the coding sequence for the 3'utr of the p27(kip1) mrna was inserted downstream of a luciferase reporter gene, dicer depletion also enhanced expression of the reporter gene product. the microrna target site software targetscan predicts that the 3'utr of p27(kip1) mrna contains multiple sites for micrornas. these include two sites for microrna 221 and 222, which have been shown to be upregulated in glioblastoma relative to adjacent normal brain tissue. the genes for microrna 221 and microrna 222 occupy adjacent sites on the x chromosome; their expression appears to be coregulated and they also appear to have the same target specificity. antagonism of either microrna 221 or 222 in glioblastoma cells also caused an increase in p27(kip1) levels and enhanced expression of the luciferase reporter gene fused to the p27(kip1) 3'utr. these data show that p27(kip1) is a direct target for micrornas 221 and 222, and suggest a role for these micrornas in promoting the aggressive growth of human glioblastoma.",1
"the catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. we previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. in the present study, we found that the catsper1 promoter has in vitro transcriptional activity in either orientation in gc-1 spg mouse spermatogonial cells. the results also showed that this promoter regulates the expression of a new divergent catsper1 gene named catsper1au (catsper1 antisense upstream transcript). catsper1au is expressed in adult male mouse testis and liver tissues but not in female mouse liver or ovary tissues. in the testis, catsper1au is expressed in embryos at 11.5 days post-coitum and from newborns to adults. this gene is also expressed in 1- to 3-week postnatal hearts and in 1-week to adult stage livers. the analysis of the 1402 bp whole genome sequence revealed that catsper1au is an intronless and polyadenylated lncrna, located in the nuclei of sertoli and spermatogenic cells from adult testis. these data indicate that catsper1au is divergently expressed from the catsper1 promoter and could regulate gene expression during spermatogenesis.",1
"over the last few decades, the epithelial-to-mesenchymal transition (emt) has been identified as being involved in a number of aspects of physiological processes and various pathological events, including embryonic development and renal fibrosis. transforming growth factor‑β receptor 2 (tgfβr2) is a widely studied gene, which fulfils a vital role in the tgfβ signaling pathway and exerts a crucial function in the progression of emt. previous studies demonstrated that the dysregulation of micrornas (mirnas) is considered to be associated with the emt process. however, the precise functional involvement of mirnas in emt remains to be fully elucidated. in the present study, the level of mir‑590 was decreased in an emt model in vitro and in vivo. furthermore, the overexpression of mir‑590 inhibited emt by upregulating the epithelial marker, e‑cadherin, and downregulating the mesenchymal markers, laminin, α‑smooth muscle actin (α‑sma) and collagen, in the human kidney 2 (hk2) cell line. furthermore, tgfβr2 was negatively regulated by mir‑590. in addition, performing a knockdown of tgfβr2 with small‑interfering rna had an effect similar to mir‑590 on emt in the hk2 cell line, whereas the transfection of pcmv‑tag2b‑tgfβr2 reversed the effect of mir‑590 on emt in hk2 cells. taken together, the present study demonstrated that mir-590 is a novel emt-suppressive microrna, which targets tgfβr2.",1
"objective to characterize downstream effectors of p300 acetyltransferase in the myocardium. background acetyltransferase p300 is a central driver of the hypertrophic response to increased workload, but its biological targets and downstream effectors are incompletely known. methods and results mice expressing a myocyte-restricted transgene encoding acetyltransferase p300, previously shown to develop spontaneous hypertrophy, were observed to undergo robust compensatory blood vessel growth together with increased angiogenic gene expression. chromatin immunoprecipitation demonstrated binding of p300 to the enhancers of the angiogenic regulators angpt1 and egln3. interestingly, p300 overexpression in vivo was also associated with relative upregulation of several members of the anti-angiogenic mir-17∼92 cluster in vivo. confirming this finding, both mir-17-3p and mir-20a were upregulated in neonatal rat ventricular myocytes following adenoviral transduction of p300. relative expression of most members of the 17∼92 cluster was similar in all 4 cardiac chambers and in other organs, however, significant downregulation of mir-17-3p and mir-20a occurred between 1 and 8 months of age in both wt and tg mice. the decline in expression of these micrornas was associated with increased expression of vegfa, a validated mir-20a target. in addition, mir-20a was demonstrated to directly repress p300 expression through a consensus binding site in the p300 3'utr. in vivo transduction of p300 resulted in repression both of p300 and of p300-induced angiogenic transcripts. conclusion p300 drives an angiogenic transcription program during hypertrophy that is fine-tuned in part through direct repression of p300 by mir-20a.",1
"telomerase uses an internal rna moiety as template for the synthesis of telomere repeats. in saccharomyces cerevisiae, the telomerase holoenzyme contains the telomerase reverse transcriptase subunit est2p, the telomerase rna moiety tlc1, the telomerase associated proteins est1p and est3p, and sm proteins. here we assess telomerase assembly by determining the localization of telomerase components. we found that est1p, est2p and tlc1 can migrate independently of each other to the nucleus. with limiting amounts of tlc1, overexpressed est1p and est2p accumulated in the nucleolus, whereas enzymatically active est2p-tlc1 complexes are distributed over the entire nucleus. the distribution to the nucleoplasm depended on the specific interaction between est2p and tlc1 but was independent of est1p and est3p. altogether, our results suggest a role of the nucleolus in telomerase biogenesis. we also describe experiments that support a transient cytoplasmic localization of tlc1 rna.",1
"the role of long noncoding rna (lncrna) in adult hearts is unknown; also unclear is how lncrna modulates nucleosome remodelling. an estimated 70% of mouse genes undergo antisense transcription, including myosin heavy chain 7 (myh7), which encodes molecular motor proteins for heart contraction. here we identify a cluster of lncrna transcripts from myh7 loci and demonstrate a new lncrna-chromatin mechanism for heart failure. in mice, these transcripts, which we named myosin heavy-chain-associated rna transcripts (myheart, or mhrt), are cardiac-specific and abundant in adult hearts. pathological stress activates the brg1-hdac-parp chromatin repressor complex to inhibit mhrt transcription in the heart. such stress-induced mhrt repression is essential for cardiomyopathy to develop: restoring mhrt to the pre-stress level protects the heart from hypertrophy and failure. mhrt antagonizes the function of brg1, a chromatin-remodelling factor that is activated by stress to trigger aberrant gene expression and cardiac myopathy. mhrt prevents brg1 from recognizing its genomic dna targets, thus inhibiting chromatin targeting and gene regulation by brg1. it does so by binding to the helicase domain of brg1, a domain that is crucial for tethering brg1 to chromatinized dna targets. brg1 helicase has dual nucleic-acid-binding specificities: it is capable of binding lncrna (mhrt) and chromatinized--but not naked--dna. this dual-binding feature of helicase enables a competitive inhibition mechanism by which mhrt sequesters brg1 from its genomic dna targets to prevent chromatin remodelling. a mhrt-brg1 feedback circuit is thus crucial for heart function. human mhrt also originates from myh7 loci and is repressed in various types of myopathic hearts, suggesting a conserved lncrna mechanism in human cardiomyopathy. our studies identify a cardioprotective lncrna, define a new targeting mechanism for atp-dependent chromatin-remodelling factors, and establish a new paradigm for lncrna-chromatin interaction.",1
"based on our microrna (mirna) expression signature analysis of maxillary sinus squamous cell carcinoma (msscc), we found that mir-1 and mir-133a were significantly reduced in tumor tissues. quantitative real-time rt-pcr revealed that the expression levels of mir-1 and mir-133a were significantly downregulated in clinical msscc tumor tissues compared with normal tissues. we focused on the functional significance of mir-1 and mir-133a in cancer cells and identification of the novel cancer networks regulated by these mirnas in msscc. restoration of downregulated mirnas (mir-1 or mir-133a) in cancer cells revealed that both mirnas significantly inhibited cancer cell proliferation and induced cell apoptosis. molecular target identification of these mirnas showed that transgelin 2 (tagln2) and purine nucleoside phosphorylase (pnp) were regulated by mir-1 and mir-133a. both tagln2 and pnp mrna expression levels were significantly upregulated in clinical msscc tumor tissues. silencing studies of target genes demonstrated that both genes inhibited cancer cell proliferation. the identification of novel mir-1/mir-133a-regulated cancer pathways could provide new insights into potential molecular mechanisms of msscc oncogenesis.",1
"we investigated the regulation of the transcription factor runx1 by microrna (mir)-27 and the resulting effects upon the differentiation of myeloblasts into granulocytes. when 32d.cl3 cell differentiation was induced using granulocyte colony-stimulating factor (csf3), runx1 transcription was moderately downregulated, while runx1 protein levels were completely inhibited, suggesting an involvement of post-transcriptional regulation. simultaneously, levels of mir-27 and its precursor increased substantially. reporter assays revealed that mir-27 targets the 3'utr of the runx1 transcript. furthermore, introduction of pre-mir-27 alone into 32d.cl3 cells resulted in downregulation of runx1 protein, thereby allowing the cell differentiation even in the absence of csf3. conversely, transduction of anti-mir-27 caused upregulation of runx1 protein, thereby antagonizing the csf3-mediated granulocyte differentiation. finally, the csf3-induced transcription factor c/ebpalpha enhanced transcription of a host gene of mir-27, c9orf3, via activation of its promoter. thus, mir-27 enhances differentiation of myeloblasts into granulocytes via post-transcriptional downregulation of runx1.",1
"calcium signaling is a central regulator of cardiomyocyte growth and function. calmodulin is a critical mediator of calcium signals. because the amount of calmodulin within cardiomyocytes is limiting, the precise control of calmodulin expression is important for the regulation of calcium signaling. in this study, we show for the first time that calmodulin levels are regulated posttranscriptionally in heart failure. the cardiomyocyte-restricted microrna mir-1 inhibited the translation of calmodulin-encoding mrnas via highly conserved target sites within their 3' untranslated regions. in keeping with its effect on calmodulin expression, mir-1 downregulated calcium-calmodulin signaling through calcineurin to nfat. mir-1 also negatively regulated the expression of mef2a and gata4, key transcription factors that mediate calcium-dependent changes in gene expression. consistent with the downregulation of these hypertrophy-associated genes, mir-1 attenuated cardiomyocyte hypertrophy in cultured neonatal rat cardiomyocytes and in the intact adult heart. our data indicate that mir-1 regulates cardiomyocyte growth responses by negatively regulating the calcium signaling components calmodulin, mef2a, and gata4.",1
"noncoding rnas (ncrnas) play increasingly appreciated gene-regulatory roles. here, we describe a regulatory network centered on four ncrnas-a long ncrna, a circular rna, and two micrornas-using gene editing in mice to probe the molecular consequences of disrupting key components of this network. the long ncrna cyrano uses an extensively paired site to mir-7 to trigger destruction of this microrna. cyrano-directed mir-7 degradation is much more effective than previously described examples of target-directed microrna degradation, which come primarily from studies of artificial and viral rnas. by reducing mir-7 levels, cyrano prevents repression of mir-7-targeted mrnas and enables accumulation of cdr1as, a circular rna known to regulate neuronal activity. without cyrano, excess mir-7 causes cytoplasmic destruction of cdr1as in neurons, in part through enhanced slicing of cdr1as by a second mirna, mir-671. thus, several types of ncrnas can collaborate to establish a sophisticated regulatory network.",1
"glioblastoma is the most common primary central nervous system malignancy and its unique invasiveness hinders effective treatment. its high invasiveness may be controlled partly by micrornas (mirnas, mirs) and their target genes. in the present study, we found that increased mir-223 expression and reduced pax6 expression coexisted in glioblastoma as detected by quantitative pcr or tissue microarrays. we confirmed that mir-223 directly targets pax6 through binding to its 3'-utr using dual luciferase reporter assay. in u251 and u373 glioblastoma cells, overexpression of mir-223 decreased pax6 mrna and protein expression; however, inhibition of mir-223 increased pax6 mrna and protein expression. moreover, overexpression of mir-223 led to effects similar to those of pax6 knockdown: increased cell viability, increased percentage of cells in the g1 phase and increased cell invasiveness parallel with increased mmp2, mmp9 and vegfa expression. in addition, inhibition of mir-223 resulted in effects similar to those of pax6 overexpression: decreased cell viability, decreased percentage of cells in the g1 phase and decreased cell invasiveness parallel with reduced mmp2, mmp9 and vegfa expression. the data presented here suggest that mir-223 promotes the growth and invasion of u251 and u373 glioblastoma cells by targeting pax6, which serves as a tumor suppressor in glioblastoma exerting the functions of inhibition of cell cycle transition, and the expression of mmp2, mmp9 and vegfa. in conclusion, the present study supports mir-223 and pax6 as novel therapeutic targets for glioblastoma.",1
"non-coding (nc)rnas are important players in most biological processes. although small rnas such as micrornas and small interfering rnas have emerged as exceptionally important regulators of gene expression, great numbers of larger ncrnas have also been identified. many of these are abundant and differentially expressed but their functions have in most cases not been elucidated. the social amoeba dictyostelium discoideum contain the ncrnas commonly found in eukaryotes. in addition, we previously reported the identification of two novel classes of 42-65 nt long stem-loop forming rnas, class i and class ii rnas, with unknown function. in this study we have further characterized these abundant ncrnas, which are down regulated during development. we have confirmed expression of 29 class i rnas and experimentally verified the formation of the computationally predicted short conserved stem structure. furthermore, we have for the first time created knockout strains for several small ncrna genes in d. discoideum and found that deletion of one of the class i rnas, ddr-21, results in aberrant development. in addition we have shown that this class i rna forms a complex with one or several proteins but do not appear to be associated with ribosomes or polysomes. in a pull down assay, several proteins interacting with ddr-21 were identified, one of these has two rna recognition motifs (rrms). the purified rrm containing protein was demonstrated to bind directly and specifically to ddr-21.",1
"the dlk1-gtl2 imprinted domain, encompassing the callipyge (clpg) locus in sheep, has recently been shown to harbor a large number of maternally expressed mirna genes . two of these (mir127 and mir136) are processed from a transcript (antipeg11) that is antisense to rtl1/peg11, a paternally expressed intronless gene with homology to the gag and pol polyproteins of sushi-like retroelements . we herein demonstrate that several additional mirnas are processed from antipeg11 and that these regulate rtl1/peg11 in trans by guiding risc-mediated cleavage of its mrna. this is the first demonstration of mirna-mediated rnai involving imprinted genes in mammals.",1
"recently, the epithelial-to-mesenchymal transition (emt) has been demonstrated to contribute to normal and disease processes including cancer progression. to explore emt-suppressive micrornas (mirnas), we established a cell-based reporter system using a stable clone derived from a pancreatic cancer cell line, panc1, transfected with a reporter construct containing a promoter sequence of cdh1/e-cadherin in the 5' upstream region of the zsgreen1 reporter gene. then, we performed function-based screening with 470 synthetic double-stranded rnas (dsrnas) mimicking human mature mirnas using the system and identified mir-655 as a novel emt-suppressive mirna. overexpression of mir-655 not only induced the upregulation of e-cadherin and downregulation of typical emt-inducers but also suppressed migration and invasion of mesenchymal-like cancer cells accompanied by a morphological shift toward the epithelial phenotype. in addition, we found a significant correlation between mir-655 expression and a better prognosis in esophageal squamous cell carcinoma (escc). moreover, zeb1 and tgfbr2, which are essential components of the tgf-b signaling pathway, were identified as direct targets of mir-655, suggesting that the activation of the tgf-b-zeb1-e-cadherin axis by aberrant downregulation of mir-655 may accelerate cancer progression.",1
"the production of blood cells depends on a rare hematopoietic stem-cell (hsc) population, but the molecular mechanisms underlying hsc biology remain incompletely understood. here, we identify a subset of micrornas (mirnas) that is enriched in hscs compared with other bone-marrow cells. an in vivo gain-of-function screen found that three of these mirnas conferred a competitive advantage to engrafting hematopoietic cells, whereas other hsc mirnas attenuated production of blood cells. overexpression of the most advantageous mirna, mir-125b, caused a dose-dependent myeloproliferative disorder that progressed to a lethal myeloid leukemia in mice and also enhanced hematopoietic engraftment in human immune system mice. our study identifies an evolutionarily conserved subset of mirnas that is expressed in hscs and functions to modulate hematopoietic output.",1
"animal micrornas (mirnas) regulate gene expression through base pairing to their targets within the 3' untranslated region (utr) of protein-coding genes. single-nucleotide polymorphisms (snps) located within such target sites can affect mirna regulation. we mapped annotated snps onto a collection of experimentally supported human mirna targets. of the 143 experimentally supported human target sites, 9 contain 12 snps. we further experimentally investigated one of these target sites for hsa-mir-155, within the 3' utr of the human agtr1 gene that contains snp rs5186. using reporter silencing assays, we show that hsa-mir-155 down-regulates the expression of only the 1166a, and not the 1166c, allele of rs5186. remarkably, the 1166c allele has been associated with hypertension in many studies. thus, the 1166c allele may be functionally associated with hypertension by abrogating regulation by hsa-mir-155, thereby elevating agtr1 levels. since hsa-mir-155 is on chromosome 21, we hypothesize that the observed lower blood pressure in trisomy 21 is partially caused by the overexpression of hsa-mir-155 leading to allele-specific underexpression of agtr1. indeed, we have shown in fibroblasts from monozygotic twins discordant for trisomy 21 that levels of agtr1 protein are lower in trisomy 21.",1
"long noncoding rnas (lncrnas) play important roles in the regulation of genes involved in cell proliferation. we have previously sought to more globally understand the differences of lncrna expression between human fetal heart and adult heart to identify some functional lncrnas which involve in the process of heart repair. we found that a highly conserved long noncoding rna nr_045363 was mainly expressed in cardiomyocytes and rarely in non-cardiomyocytes. nr_045363 overexpression in 7-day-old mice heart could improve cardiac function and stimulate cardiomyocyte proliferation after myocardial infarction. furthermore, nr_045363 knockdown inhibited proliferation of primary embryonic cardiomyocytes, while nr_045363 overexpression enhanced dna synthesis and cytokinesis in neonatal cardiomyocytes in vitro. mechanistic analysis revealed that nr_045363 promoted cardiomyocyte proliferation through interaction with mir-216a, which regulated the jak2-stat3 pathway. our results showed that nr_045363 is a potent lncrna modulator essential for cardiomyocyte proliferation.",1
"micrornas (mirnas) regulate gene expression through translational repression and/or messenger rna (mrna) deadenylation and decay. because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. we have investigated the kinetics of these events in mirna-mediated gene silencing by using a drosophila s2 cell-based controllable expression system and show that mrnas with both natural and engineered 3' untranslated regions with mirna target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. we next used a natural translational elongation stall to show that mirna-mediated silencing inhibits translation at an early step, potentially translation initiation.",1
"introduction micrornas are small non-coding rnas that are involved in the post-transcriptional negative regulation of mrnas. microrna 510 (mir-510) was initially shown to have a potential oncogenic role in breast cancer by the observation of its elevated levels in human breast tumor samples when compared to matched non-tumor samples. few targets have been identified for mir-510. however, as micrornas function through the negative regulation of their direct targets, the identification of those targets is critical for the understanding of their functional role in breast cancer. methods breast cancer cell lines were transfected with pre-mir-510 or antisense mir-510 and western blotting and quantitative real time pcr were performed. functional assays performed included cell growth, migration, invasion, colony formation, cytotoxicity and in vivo tumor growth. we performed a pcr assay to identify novel direct targets of mir-510. the study focused on peroxiredoxin 1 (prdx1) as it was identified through our screen and was bioinformatically predicted to contain a mir-510 seed site in its 3' untranslated region (3'utr). luciferase reporter assays and site-directed mutagenesis were performed to confirm prdx1 as a direct target. the student's two-sided, paired t-test was used and a p-value less than 0.05 was considered significant. results we show that mir-510 overexpression in non-transformed and breast cancer cells can increase their cell growth, migration, invasion and colony formation in vitro. we also observed increased tumor growth when mir-510 was overexpressed in vivo. we identified prdx1 through a novel pcr screen and confirmed it as a direct target using luciferase reporter assays. the reintroduction of prdx1 into breast cancer cell lines without its regulatory 3'utr confirmed that mir-510 was mediating its migratory phenotype at least in part through the negative regulation of prdx1. furthermore, the pi3k/akt pathway was identified as a positive regulator of mir-510 both in vitro and in vivo. conclusions in this study, we provide evidence to support a role for mir-510 as a novel oncomir. we show that mir-510 directly binds to the 3'utr of prdx1 and blocks its protein expression, thereby suppressing migration of human breast cancer cells. taken together, these data support a pivotal role for mir-510 in breast cancer progression and suggest it as a potential therapeutic target in breast cancer patients.",1
"microrna-21 (mir-21) is highly up-regulated during hypertrophic and cancerous cell growth. in contrast, we found that it declines in cardiac myocytes upon exposure to hypoxia. thus, the objective was to explore its role during hypoxia. we show that mir-21 not only regulates phosphatase and tensin homologue deleted on chromosome 10 (pten), but also targets fas ligand (fasl). during prolonged hypoxia, down-regulation of mir-21 proved necessary and sufficient for enhancing expression of both proteins. we demonstrate here for the first time that mir-21 is positively regulated via an akt-dependent pathway, which is depressed during prolonged hypoxia. accordingly, hypoxia-induced down-regulation of mir-21 and up-regulation of fasl and pten were reversed by activated akt and reproduced by a dominant negative mutant, wortmannin, or pten. moreover, the antiapoptotic function of akt partly required mir-21, which was sufficient for inhibition of caspase-8 activity and mitochondrial damage. in consensus, overexpression of mir-21 in a transgenic mouse heart resulted in suppression of ischemia-induced up-regulation of pten and fasl expression, an increase in phospho-akt, a smaller infarct size, and ameliorated heart failure. thus, we have identified a unique aspect of the function of akt by which it inhibits apoptosis through mir-21-dependent suppression of fasl.",1
"microrna-365 (mir-365) plays crucial roles in regulating cell proliferation, apoptosis and differentiation in various cell types. however, its function in vascular smooth muscle cells (vsmcs) is largely unknown. in our study, we found mir-365 was highly expressed in adult rat carotid arteries, but was significantly decreased in rat carotid arteries after balloon injury, a process involving neointima formation and vsmc proliferation. in vitro, the mir-365 significantly inhibited cell proliferation of isolated primary rat aortic vsmcs. furthermore, we identified that cyclin d1 was a direct target of mir-365 in vsmcs. the mir-365 suppressed cyclin d1 expression on both mrna and protein level. luciferase reporter assay demonstrated that mir-365 inhibited cyclin d1 through targeting its 3'utr. importantly, cyclin d1 overexpression rescued the inhibitory effect of mir-365 on vsmcs proliferation. taken together, by our studies, we identified a new microrna, mir-365, involving in the pathological process of vascular injury, which inhibits vsmc proliferation through targeting cyclind1.",1
"a key step in angiogenesis is the upregulation of growth factor receptors on endothelial cells. here, we demonstrate that a small regulatory microrna, mir-296, has a major role in this process. glioma cells and angiogenic growth factors elevate the level of mir-296 in primary human brain microvascular endothelial cells in culture. the mir-296 level is also elevated in primary tumor endothelial cells isolated from human brain tumors compared to normal brain endothelial cells. growth factor-induced mir-296 contributes significantly to angiogenesis by directly targeting the hepatocyte growth factor-regulated tyrosine kinase substrate (hgs) mrna, leading to decreased levels of hgs and thereby reducing hgs-mediated degradation of the growth factor receptors vegfr2 and pdgfrbeta. furthermore, inhibition of mir-296 with antagomirs reduces angiogenesis in tumor xenografts in vivo.",1
"a multitude of proteins and small nucleolar rnas transiently associate with eukaryotic ribosomal rnas to direct their modification and processing and the assembly of ribosomal proteins. utp22 and rrp7, two interacting proteins with no recognizable domain, are components of the 90s preribosome or the small subunit processome that conducts early processing of 18s rrna. here, we determine the cocrystal structure of utp22 and rrp7 complex at 1.97 å resolution and the nmr structure of a c-terminal fragment of rrp7, which is not visible in the crystal structure. the structure reveals that utp22 surprisingly resembles a dimeric class i trna cca-adding enzyme yet with degenerate active sites, raising an interesting evolutionary connection between trna and rrna processing machineries. rrp7 binds extensively to utp22 using a deviant rna recognition motif and an extended linker. functional sites on the two proteins were identified by structure-based mutagenesis in yeast. we show that rrp7 contains a flexible rna-binding c-terminal tail that is essential for association with preribosomes. rna-protein crosslinking shows that rrp7 binds at the central domain of 18s rrna and shares a neighborhood with two processing h/aca snornas snr30 and snr10. depletion of snr30 prevents the stable assembly of rrp7 into preribosomes. our results provide insight into the evolutionary origin and functional context of utp22 and rrp7.",1
"rna, including long noncoding rna (lncrna), is known to be an abundant and important structural component of the nuclear matrix. however, the molecular identities, functional roles and localization dynamics of lncrnas that influence nuclear architecture remain poorly understood. here, we describe one lncrna, firre, that interacts with the nuclear-matrix factor hnrnpu through a 156-bp repeating sequence and localizes across an ~5-mb domain on the x chromosome. we further observed firre localization across five distinct trans-chromosomal loci, which reside in spatial proximity to the firre genomic locus on the x chromosome. both genetic deletion of the firre locus and knockdown of hnrnpu resulted in loss of colocalization of these trans-chromosomal interacting loci. thus, our data suggest a model in which lncrnas such as firre can interface with and modulate nuclear architecture across chromosomes.",1
"recently, the inhibition of epithelial-mesenchymal-transition (emt) by p53 has been described as a new mode of tumor suppression which presumably prevents metastasis. here we report that activation of p53 down-regulates the emt-inducing transcription factor snail via induction of the mir-34a/b/c genes. suppression of mir-34a/b/c caused up-regulation of snail and cells displayed emt markers and related features, as enhanced migration and invasion. ectopic mir-34a induced mesenchymal-epithelial-transition (met) and down-regulation of snail, which was mediated by a conserved mir-34a/b/c seed-matching sequence in the snail 3'-utr. mir-34a also down-regulated slug and zeb1, as well as the stemness factors bmi1, cd44, cd133, olfm4 and c-myc. conversely, the transcription factors snail and zeb1 bound to e-boxes in the mir-34a/b/c promoters, thereby repressing mir-34a and mir-34b/c expression. since ectopic mir-34a prevented tgf-β-induced emt, the repression of mir-34 genes by snail and related factors is part of the emt program. in conclusion, the frequent inactivation of p53 and/or mir-34a/b/c found in cancer may shift the equilibrium of these reciprocal regulations towards the mesenchymal state and thereby lock cells in a metastatic state.",1
"in recent years, micrornas (mirnas) have been proved to be closely related to the tumorigenesis and progression. an increasing number of researches have shown that micrornas function as oncogenes or tumor suppressor genes in human malignant tumors. this study aims to explore the effects of microrna-383 (mir-383) on malignant biological function of human gliomas. we detected the expression of mir-383 in glioma tissues and normal brain tissues by quantitative real-time pcr. anchorage-independent growth assays, and flow cytometry were used to evaluate the functions of mir-383 that involves in cell growth and cell cycle. western blotting assay was used to examine protein expression levels of cyclin d1 (ccnd1), a cell cycle-associated oncogene which has a predicted binding site of mir-383 within its 3'-untranslated region (3'-utr), and luciferase activity assay was used to evaluate the 3'-utr activity of ccnd1. in this study, we found that mir-383 expression level was lower in gliomas than normal brain tissues. overexpression of mir-383 in u251 and u87 cells showed a significant inhibitory effect on cell growth, which accompanied with cell cycle g0/g1 arrest as well as downregulation of ccnd1 expression. moreover, ccnd1 was verified to be one of the direct targets of mir-383. in summary, this study suggested that mir-383 plays the role of tumor suppressor by targeting ccnd1 in glioma cells, and may be useful for developing a new therapeutic strategy for gliomas.",1
"the β-catenin/wnt signaling pathway is activated in many cancers and its constitutive activation has a central role in colorectal cancer pathogenesis. recent studies have highlighted the role of micrornas as novel regulators of gene expression including that of signaling intermediates from the wnt signaling pathway. the purpose of our study was to determine the role of mir-29b in the regulation of wnt signaling in human colorectal cancer cells. topflash/fopflash reporter assays, gene expression studies by quantitative rt-pcr and western blot analysis were used to study the effect of ectopic expression of mir-29b on canonical wnt signaling. mir-29b antagonized transactivation of β-catenin target genes by downregulating coactivators of β-catenin (tcf7l2, snail, and bcl9l) in sw480 cells. mir-29b targeted the 3'utr of bcl9l and decreased its expression with a consequent decrease in nuclear translocation of β-catenin. ectopic expression of mir-29b inhibited anchorage independent cell growth, promoted reversal of epithelial to mesenchymal transition and reduced the ability of conditioned medium from sw480 cells to induce in vitro tube formation in endothelial cells. these results have unraveled a novel role of mir-29b in wnt signaling in human colorectal cancer cells with implications in the treatment of colorectal cancer.",1
"mirnas are endogenously expressed 18- to 25-nucleotide rnas that regulate gene expression through translational repression by binding to a target mrna. recently, it has been indicated that mirnas are closely related to osteogenesis. our previous data suggested that mir-30 family members might be important regulators during the biomineralization process. however, whether and how they modulate osteogenic differentiation have not been explored. in this study, we demonstrated that mir-30 family members negatively regulate bmp-2-induced osteoblast differentiation by targeting smad1 and runx2. evidentially, overexpression of mir-30 family members led to a decrease of alkaline phosphatase activity, whereas knockdown of them increased the activity. then bioinformatic analysis identified potential target sites of the mir-30 family located in the 3' untranslated regions of smad1 and runx2. western blot analysis and quantitative rt-pcr assays demonstrated that mir-30 family members inhibit smad1 gene expression on the basis of repressing its translation. furthermore, dual-luciferase reporter assays confirmed that smad1 is a direct target of mir-30 family members. rescue experiments that overexpress smad1 and runx2 significantly eliminated the inhibitory effect of mir-30 on osteogenic differentiation and provided strong evidence that mir-30 mediates the inhibition of osteogenesis by targeting smad1 and runx2. also, the inhibitory effects of the mir-30 family were validated in mouse bone marrow mesenchymal stem cells. therefore, our study uncovered that mir-30 family members are key negative regulators of bmp-2-mediated osteogenic differentiation.",1
"heart diseases such as myocardial infarction (mi) can damage individual cardiomyocytes, leading to the activation of cell death programs. the most scrutinized type of cell death in the heart is apoptosis, and one of the key events during the propagation of apoptotic signaling is the formation of apoptosomes, which relay apoptotic signals by activating caspase-9. as one of the major components of apoptosomes, apoptotic protease activating factor 1 (apaf-1) facilitates the formation of apoptosomes containing cytochrome c (cyto-c) and deoxyadenosine triphosphate (datp). thus, it may be possible to suppress the activation of the apoptotic program by down-regulating the expression of apaf-1 using mirnas. to validate this hypothesis, we selected a number of candidate mirnas that were expected to target apaf-1 based on mirna target prediction databases. among these candidate mirnas, we empirically identified mir-17 as a novel apaf-1-targeting mirna. the delivery of exogenous mir-17 suppressed apaf-1 expression and consequently attenuated formation of the apoptosome complex containing caspase-9, as demonstrated by co-immunoprecipitation and immunocytochemistry. furthermore, mir-17 suppressed the cleavage of procaspase-9 and the subsequent activation of caspase-3, which is downstream of activated caspase-9. cell viability tests also indicated that mir-17 pretreatment significantly prevented the norepinephrine-induced apoptosis of cardiomyocytes, suggesting that down-regulation of apoptosome formation may be an effective strategy to prevent cellular apoptosis. these results demonstrate the potential of mir-17 as an effective anti-apoptotic agent.",1
"background mirnas are critical post-transcriptional regulators of gene expression and key mediators of tumourigenesis. mir-501-5p is newly identified to be involved in the tumor progression, but its biological role and mechanism remain largely unknown. this study is aimed to study the role of mir-501-5p in the progression of gastric cancer. methods real-time pcr analysis was used to determine mir-501-5p expression in gastric cancer cell lines, clinical tissues and 112 clinicopathologically characterized gastric cancer specimens. the role of mir-501-5p in maintaining gastric cancer stem cell like phenotype was examined by tumor-sphere formation assay and expression of stem cell markers. luciferase reporter assay, cellular fractionation and western blot analysis were used to determined that mir-501-5p activated the wnt/β-catenin signaling by directly targeting dkk1, nkd1 and gsk3β. results herein, our results revealed that mir-501-5p was markedly upregulated in gastric cancer cell lines and clinical tissues. high mir-501-5p levels predicted poor overall survival in gastric cancer patients. gain-of-function and loss-of-function studies showed that ectopic expression of mir-501-5p enhanced the cancer stem cell-like phenotype in gastric cancer cells. notably,wnt/β-catenin signaling was hyperactivated in gastric cancer cells that overexpress mir-501-5p, and mediated mir-501-5p-induced cancer stem cell-like phenotype. furthermore, mir-501-5p directly targeted and suppressed multiple repressors of the wnt/β-catenin signaling cascade, including dkk1, nkd1 and gsk3β. these results demonstrate that mir-501-5p maintains constitutively activated wnt/β-catenin signaling by directly targeting dkk1, nkd1 and gsk3β, which promotes gastric cancer stem cell like phenotype. conclusions taken together, our findings reveal a new regulatory mechanism of mir-501-5p and suggest that mir-501-5p might be a potential target in gastric cancer therapy.",1
"the effect of wnt/β-catenin signalling in the response to acute myocardial infarction (ami) remains controversial. the membrane receptor adaptor protein disabled-2 (dab2) is a tumour suppressor protein and has a critical role in stem cell specification. we recently demonstrated that down-regulation of dab2 regulates cardiac protein expression and wnt/β-catenin activity in mesenchymal stem cells (msc) in response to transforming growth factor-β(1) (tgf-β(1)). although dab2 expression has been shown to have effects in stem cells and tumour suppression, the molecular mechanisms regulating this expression are still undefined. we identified putative binding sites for mir-145 in the 3'-utr of dab2. in msc in culture, we observed that tgf-β(1) treatment led to rapid and sustained up-regulation of pri-mir-145. through gain and loss of function studies we demonstrate that mir-145 up-regulation was required for the down-regulation of dab2 and increased β-catenin activity in response to tgf-β(1). to begin to define how dab2 might regulate wnt/β-catenin in the heart following ami, we quantified myocardial dab2 as a function of time after left anterior descending ligation. there was no significant dab2 expression in sham-operated myocardium. following ami, dab2 levels were rapidly up-regulated in cardiac myocytes in the infarct border zone. the increase in cardiac myocyte dab2 expression correlated with the rapid and sustained down-regulation of myocardial pri-mir-145 expression following ami. our data demonstrate a novel and critical role for mir-145 expression as a regulator of dab2 expression and β-catenin activity in response to tgf-β(1) and hypoxia.",1
"background whereas many causes and mechanisms of neurodegenerative diseases have been identified, very few therapeutic strategies have emerged in parallel. one possible explanation is that successful treatment strategy may require simultaneous targeting of more than one molecule of pathway. a new therapeutic approach to have emerged recently is the engagement of micrornas (mirnas), which affords the opportunity to target multiple cellular pathways simultaneously using a single sequence. methodology/principal findings we identified mir-22 as a potentially neuroprotective mirna based on its predicted regulation of several targets implicated in huntington's disease (histone deacetylase 4 (hdac4), rest corepresor 1 (rcor1) and regulator of g-protein signaling 2 (rgs2)) and its diminished expression in huntington's and alzheimer's disease brains. we then tested the hypothesis that increasing cellular levels of mirna-22 would achieve neuroprotection in in vitro models of neurodegeneration. as predicted, overexpression of mir-22 inhibited neurodegeneration in primary striatal and cortical cultures exposed to a mutated human huntingtin fragment (htt171-82q). overexpression of mir-22 also decreased neurodegeneration in primary neuronal cultures exposed to 3-nitropropionic acid (3-np), a mitochondrial complex ii/iii inhibitor. in addition, mir-22 improved neuronal viability in an in vitro model of brain aging. the mechanisms underlying the effects of mir-22 included a reduction in caspase activation, consistent with mir-22's targeting the pro-apoptotic activities of mitogen-activated protein kinase 14/p38 (mapk14/p38) and tumor protein p53-inducible nuclear protein 1 (tp53inp1). moreover, hd-specific effects comprised not only targeting hdac4, rcor1 and rgs2 mrnas, but also decreasing focal accumulation of mutant htt-positive foci, which occurred via an unknown mechanism. conclusions these data show that mir-22 has multipartite anti-neurodegenerative activities including the inhibition of apoptosis and the targeting of mrnas implicated in the etiology of hd. these results motivate additional studies to evaluate the feasibility and therapeutic efficacy of manipulating mir-22 in vivo.",1
"purpose our goal was to identify circulating micro rna (mirna) levels that could distinguish patients with low-stage pancreatic cancer from healthy and disease controls. experimental design we measured 735 mirnas in pancreatic cancer case and control sera by qrtpcr using taqman microrna arrays. after array analysis, we selected 18 mirna candidates for validation in an independent set of cases and control samples. results of the significantly elevated circulating mirnas in patients with pancreatic cancer compared with controls, mir-1290 had the best diagnostic performance: receiver operating characteristic (roc) analysis on mir-1290 serum level yielded curve areas (auc) of 0.96 , 0.81 (0.71-0.91), and 0.80 (0.67-0.93), for subjects with pancreatic cancer (n = 41) relative to healthy controls (n = 19), subjects with chronic pancreatitis (n = 35), and pancreatic neuroendocrine tumors (n = 18), respectively. serum mir-1290 levels were also significantly higher than healthy controls among patients with intraductal papillary mucinous neoplasm (ipmn; n = 20; auc = 0.76, 0.61-0.91). serum mir-1290 levels distinguished patients with low-stage pancreatic cancer from controls better than ca19-9 levels, and like ca19-9, higher mir-1290 levels predicted poorer outcome among patients undergoing pancreaticoduodenectomy. greater numbers of mir-1290 transcripts were detected by fish in primary pancreatic cancer and ipmn than normal pancreatic duct cells. mir-1290 influenced in vitro pancreatic cancer cell proliferation and invasive ability. several other circulating mirnas distinguished sera of patients with pancreatic cancer from those of healthy controls with aucs >0.7, including mir-24, mir-134, mir-146a, mir-378, mir-484, mir-628-3p, and mir-1825. conclusions the detection of elevated circulating mir-1290 has the potential to improve the early detection of pancreatic cancer.",1
"although interaction with dna repair proteins has demonstrated that rassf1a is a tumour suppressor gene, much attention has been directed in recent years towards its roles in regulating the cell cycle. however, the precise mechanism remains unclear. uncovering how rassf1a participates in regulating the cell cycle is critical to exploring effective therapeutic targets for gastric cancer. here we show that rassf1a could regulate 14 mirnas' expression in the typical human gastric cancer line sgc-7901, of which mir-711 was upregulated the most. moreover, for sgc-7901 cells, mir-711 was found to downregulate cdk4 expression, and to arrest the cell cycle in the g1 phase. our results suggest that rassf1a inhibits the proliferation of gastric cancer cells by upregulating the expression of mir-711, which arrested gastric cancer cells in the g1 phase by downregulating expression of cdk4. this finding might provide us with a novel therapeutic target for gastric cancer by increasing rassf1a expression via mir-711 regulation.",1
"background in eukaryotes, mir-16 is an important microrna (mirna) that is involved in numerous biological processes. however, it is not fully understood how mir-16 executes its physiological functions. in the present study, we aimed to identify novel mir-16 targets and study their biological functions. methods candidate target genes of mir-16 were screened by microarray analysis of mrna levels in several cancer cell lines with enhanced mir-16. three bioinformatics algorithms, including targetscan, pictar, and miranda, were used in combination to calculate the mir-16 targets. the expression levels of mir-16 and target mrna were examined by relative quantification rt-pcr, and the expression levels of target protein were detected by western blot. luciferase reporter plasmids were constructed to confirm direct targeting. the effect of mir-16 and target gene on cell viability was evaluated using mtt assays. the effects of mir-16 and target gene on apoptosis and cell cycle distribution were evaluated by flow cytometry analysis. results by overexpressing mir-16 in several cancer cell lines and measuring global mrna levels using microarray analysis, we identified 27 genes that may be regulated by mir-16. after the bioinformatics filtering process, 18 genes were selected as candidate mir-16 targets. furthermore, we experimentally validated three of these candidates, map7 (microtubule-associated protein 7), prdm4 (pr domain containing 4) and cds2 (cdp-diacylglycerol synthase 2), as direct targets of mir-16. finally, we demonstrated that mir-16 targeting map7 played a critical role in regulating proliferation but not apoptosis and cell cycle progression in cancer cells. conclusion in summary, the present study identifies several novel mir-16 targets and illustrates a novel function of mir-16 targeting map7 in modulating proliferation in cancer cells.",1
"unlabelled in staphylococcus aureus, hundreds of small regulatory or small rnas (srnas) have been identified, yet this class of molecule remains poorly understood and severely understudied. srna genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. to facilitate improved detection and analysis of srnas in s. aureus, we generated updated genbank files for three commonly used s. aureus strains (mrsa252, nctc 8325, and usa300), in which we added annotations for >260 previously identified srnas. these files, the first to include genome-wide annotation of srnas in s. aureus, were then used as a foundation to identify novel srnas in the community-associated methicillin-resistant strain usa300. this analysis led to the discovery of 39 previously unidentified srnas. investigating the genomic loci of the newly identified srnas revealed a surprising degree of inconsistency in genome annotation in s. aureus, which may be hindering the analysis and functional exploration of these elements. finally, using our newly created annotation files as a reference, we perform a global analysis of srna gene expression in s. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated srna in human serum. this study provides an invaluable resource to the s. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential srna expression in pathophysiologically relevant conditions. importance despite a large number of studies identifying regulatory or small rna (srna) genes in staphylococcus aureus, their annotation is notably lacking in available genome files. in addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same srna being identified multiple times and bearing multiple names. in this work, we have consolidated and curated known srna genes from the literature and mapped them to their position on the s. aureus genome, creating new genome annotation files. these files can now be used by the scientific community at large in experiments to search for previously undiscovered srna genes and to monitor srna gene expression by transcriptome sequencing (rna-seq). we demonstrate this application, identifying 39 new srnas and studying their expression during s. aureus growth in human serum.",1
"genetic amplification, mutation, and translocation are known to play a causal role in the upregulation of an oncogene in cancer cells. here, we report an emerging role of microrna, the epigenetic deregulation of which may also lead to this oncogenic activation. sox4, an oncogene belonging to the sry-related high mobility group box family, was found to be overexpressed (p < 0.005) in endometrial tumors (n = 74) compared with uninvolved controls (n = 20). this gene is computationally predicted to be the target of a microrna, mir-129-2. when compared with the matched endometria, the expression of mir-129-2 was lost in 27 of 31 primary endometrial tumors that also showed a concomitant gain of sox4 expression (p < 0.001). this inverse relationship is associated with hypermethylation of the mir-129-2 cpg island, which was observed in endometrial cancer cell lines (n = 6) and 68% of 117 endometrioid endometrial tumors analyzed. reactivation of mir-129-2 in cancer cells by pharmacologic induction of histone acetylation and dna demethylation resulted in decreased sox4 expression. in addition, restoration of mir-129-2 by cell transfection led to decreased sox4 expression and reduced proliferation of cancer cells. further analysis found a significant correlation of hypermethylated mir-129-2 with microsatellite instability and mlh1 methylation status (p < 0.001) and poor overall survival (p < 0.039) in patients. therefore, these results imply that the aberrant expression of sox4 is, in part, caused by epigenetic repression of mir-129-2 in endometrial cancer. unlike the notion that promoter hypomethylation may upregulate an oncogene, we present a new paradigm in which hypermethylation-mediated silencing of a microrna derepresses its oncogenic target in cancer cells.",1
"background diabetic nephropathy (dn) is one of the most significant long-term complications of diabetes mellitus (dm), and it is a primary risk factor for end-stage renal disease. micrornas (mirnas) play important roles in regulating the expression of genes, including interleukin-6r (il-6r), which has been reported to be involved in the development of dndn. the aim of this study was to identify the dysregulation of mirna and its target responsible for the development of dn in dm. material and methods we collected the kidney tissues from patients with dn (n=36) and control patients (n=28), and performed real-time pcr and western blot analysis to determine the expression of il-6r. computational analysis and luciferase assay were used to identify the mirna that regulates il-6r. to explore the association between rs12976445 polymorphism and risk of dn, we enrolled 594 dm patients with (n=282) or without dn (n=312), and studied the association between a variant in mir-125a and risk of dn in dm. results the expression of il-6r was barely detected in the control groups, while in the dn group, the il-6r was clearly detectable. next, mir-125a was identified as a regulator of il-6r by using informatics analysis and luciferase assay. a single-nucleotide polymorphism (rs12976445) in pri-mir-125a has been shown to compromise the mature processing of mir-125a, and we showed that the expression levels of mir-125a was comparable between individuals carrying tt and ct, and when combined into 1 group, the mir-125a expression was approximately 3 times lower than in the cc group. we found significant differences regarding rs12976445 genotype distribution between the dn and the control (or=1.45, 95% c.i.=1.02-2.08, p conclusions we identified mir-125a as a direct regulator of il-6r, and the genotype of rs12976445 might be a novel predictor of the development of dn in dm.",1
"micrornas (mirs) regulate gene expression at the posttranscriptional level and play crucial roles in vascular integrity. as such, they may have a role in modifying abdominal aortic aneurysm (aaa) expansion, the pathophysiological mechanisms of which remain incompletely explored. here, we investigate the role of mirs in 2 murine models of experimental aaa: the porcine pancreatic elastase (ppe) infusion model in c57bl/6 mice and the angii infusion model in apoe-/- mice. aaa development was accompanied by decreased aortic expression of mir-29b, along with increased expression of known mir-29b targets, col1a1, col3a1, col5a1, and eln, in both models. in vivo administration of locked nucleic acid anti-mir-29b greatly increased collagen expression, leading to an early fibrotic response in the abdominal aortic wall and resulting in a significant reduction in aaa progression over time in both models. in contrast, overexpression of mir-29b using a lentiviral vector led to augmented aaa expansion and significant increase of aortic rupture rate. cell culture studies identified aortic fibroblasts as the likely vascular cell type mediating the profibrotic effects of mir-29b modulation. a similar pattern of reduced mir-29b expression and increased target gene expression was observed in human aaa tissue samples compared with that in organ donor controls. these data suggest that therapeutic manipulation of mir-29b and its target genes holds promise for limiting aaa disease progression and protecting from rupture.",1
"tight control over the segregation of endoderm, mesoderm, and ectoderm is essential for normal embryonic development of all species, yet how neighboring embryonic blastomeres can contribute to different germ layers has never been fully explained. we postulated that micrornas, which fine-tune many biological processes, might modulate the response of embryonic blastomeres to growth factors and other signals that govern germ layer fate. a systematic screen of a whole-genome microrna library revealed that the let-7 and mir-18 families increase mesoderm at the expense of endoderm in mouse embryonic stem cells. both families are expressed in ectoderm and mesoderm, but not endoderm, as these tissues become distinct during mouse and frog embryogenesis. blocking let-7 function in vivo dramatically affected cell fate, diverting presumptive mesoderm and ectoderm into endoderm. sirna knockdown of computationally predicted targets followed by mutational analyses revealed that let-7 and mir-18 down-regulate acvr1b and smad2, respectively, to attenuate nodal responsiveness and bias blastomeres to ectoderm and mesoderm fates. these findings suggest a crucial role for the let-7 and mir-18 families in germ layer specification and reveal a remarkable conservation of function from amphibians to mammals.",1
"red clover necrotic mosaic virus (rcnmv) is a positive-strand rna virus with a bipartite genome. rna1 encodes n-terminally overlapping replication proteins, p27 and p88. rna2 is replicated efficiently by the replication proteins supplied in trans, whereas rna1 needs p88 preferentially in cis for its replication. cis-acting elements required for rna2 replication have been mapped to the 3' terminal stem-loop structure conserved between rna1 and rna2, and to the protein-coding region including the trans-activator. here, we have identified a y-shaped rna structure with three-way rna junctions predicted in the 3' untranslated region of rna2 as a novel element required for negative-strand synthesis using an in vitro translation/replication system. we also show that, in addition to the 3' terminal core promoter, several rna elements including the trans-activator are also required for negative-strand synthesis. functional roles and structural requirements of these cis-acting elements in rcnmv rna replication are discussed.",1
"micrornas (mirnas), single-stranded non-coding rnas, influence myriad biological processes that can contribute to cancer. although tumor-suppressive and oncogenic functions have been characterized for some mirnas, the majority of micrornas have not been investigated for their ability to promote and modulate tumorigenesis. here, we established that the mir-191/425 cluster is transcriptionally dependent on the host gene, dalrd3, and that the hormone 17β-estradiol (estrogen or e2) controls expression of both mir-191/425 and dalrd3. mir-191/425 locus characterization revealed that the recruitment of estrogen receptor α (erα) to the regulatory region of the mir-191/425-dalrd3 unit resulted in the accumulation of mir-191 and mir-425 and subsequent decrease in dalrd3 expression levels. we demonstrated that mir-191 protects erα positive breast cancer cells from hormone starvation-induced apoptosis through the suppression of tumor-suppressor egr1. furthermore, enforced expression of the mir-191/425 cluster in aggressive breast cancer cells altered global gene expression profiles and enabled us to identify important tumor promoting genes, including satb1, ccnd2, and fscn1, as targets of mir-191 and mir-425. finally, in vitro and in vivo experiments demonstrated that mir-191 and mir-425 reduced proliferation, impaired tumorigenesis and metastasis, and increased expression of epithelial markers in aggressive breast cancer cells. our data provide compelling evidence for the transcriptional regulation of the mir-191/425 cluster and for its context-specific biological determinants in breast cancers. importantly, we demonstrated that the mir-191/425 cluster, by reducing the expression of an extensive network of genes, has a fundamental impact on cancer initiation and progression of breast cancer cells.",1
"metastasis is a multistep process that involves the deregulation of oncogenes and tumor suppressors beyond changes required for primary tumor formation. rhob is known to have tumor suppressor activity, and its knockdown is associated with more aggressive tumors as well as changes in cell shape, migration, and adhesion. this study shows that oncogenic microrna, mir-21, represses rhob expression by directly targeting the 3' untranslated region. loss of mir-21 is associated with an elevation of rhob in hepatocellular carcinoma cell lines huh-7 and hepg2 and in the metastatic breast cancer cell line mda-mb-231. using in vitro models of distinct stages of metastasis, we showed that loss of mir-21 also causes a reduction in migration, invasion, and cell elongation. the reduction in migration and cell elongation can be mimicked by overexpression of rhob. furthermore, changes in mir-21 expression lead to alterations in matrix metalloproteinase-9 activity. therefore, we conclude that mir-21 promotes multiple components of the metastatic phenotype in vitro by regulating several important tumor suppressors, including rhob.",1
"osteoarthritis is a common cause of functional deterioration in older adults and is an immense burden on the aging population. altered chondrogenesis is the most important pathophysiological process involved in the development of osteoarthritis. however, the molecular mechanism underlying the regulation of chondrogenesis in patients with osteoarthritis requires further elucidation, particularly with respect to the role of micrornas. mir-21 expression in cartilage specimens was examined in 10 patients with knee osteoarthritis and 10 traumatic amputees. the effect of mir-21 on chondrogenesis was also investigated in a chondrocyte cell line. the effect of mir-21 on the expression of growth differentiation factor 5 (gdf-5) was further assessed by luciferase reporter assay and western blot. we found that endogenous mir-21 is upregulated in osteoarthritis patients, and overexpression of mir-21 could attenuate the process of chondrogenesis. furthermore, we identified gdf-5 as the direct target of mir-21 during the regulation of chondrogenesis. our data suggest that mir-21 has an important role in the pathogenesis of osteoarthritis and is a potential therapeutic target.",1
"aim to profile expression of micrornas (mirnas) in gastric cancer cells and investigate the effect of mir-374b-5p on gastric cancer cell invasion and metastasis. methods an mirna microarray assay was performed to identify mirnas differentially expressed in gastric cancer cell lines (mgc-803 and sgc-7901) compared with a normal gastric epithelial cell line. upregulation of mir-374b-5p was newly identified and confirmed via quantitative real-time reverse transcription-pcr (qrt-pcr). mgc-803 cells were transfected with a synthesized anti-mir-374b-5p sequence or a control vector using lipofectamine reagent, or treated with transfection reagent alone or phosphate-buffered saline as controls. rate of transfection was verified after 48 h by qrt-pcr. cells were then subjected to transwell migration, wound scratch and cell counting kit-8 assays. a bioinformatic analysis to identify mir-374b-5p target genes was performed using miranda, pictar and targetscan software. a dual luciferase reporter assay was performed to evaluate the influence of mir-374b-5p on target gene activation, and qrt-pcr and western blot were used to evaluate the levels of target mrna and protein following transfection with mir-374b-5p antisense oligonucleotides. results the microarray profiling revealed downregulation of 14 (fold change 1.50; p conclusion these findings indicate that upregulation of mir-374b-5p contributes to gastric cancer cell metastasis and invasion through inhibition of reck expression.",1
"hepatocellular carcinoma (hcc) can be derived from malignant transformed adult hepatic progenitor cells. however, the regulatory factors and molecular mechanisms underlying the process are not well defined. our previous microrna (mirna) microarray analysis revealed a significant decrease of mir-200a level in f344 rat hcc side population (sp) fraction cells versus their normal counterparts. in the present study, we further investigated the effect of mir-200a on hepatic oval cell (hoc) phenotypes. we first confirmed downregulated mir-200a levels in rat hepatoma cells compared with wb-f344 cells. next, by lentivirus-mediated loss-of-function studies, we showed that stable knockdown of mir-200a confers a mesenchymal phenotype to wb-f344 cells, including an elongated cell morphology, enhanced cell migration ability and expression of epithelial mesenchymal transition (emt)-representative markers. concomitantly, several cancer stem cell (csc)-like traits appeared in these cells, which exhibit enhanced spheroid-forming capacity, express putative hepatic csc markers and display superior resistance to chemotherapeutic drugs in vitro. furthermore, bioinformatics analysis, luciferase assays and western blot analysis identified β-catenin (ctnnb1) as a direct and functional target of mir-200a. knockdown of mir-200a partially activated wnt/β-catenin signaling, and silencing of β-catenin functionally attenuated anti-mir-200a effects in vitro in wb-f344 cells. at length, in vivo xenograft assay demonstrated the acquisition of tumorigenicity of wb-f344 cells after mir-200a siliencing. collectively, our findings indicate that mir-200a may function as an important regulatory factor in neoplastic transition of hocs by targeting the β-catenin pathway.",1
"micrornas (mirnas) fine tune gene expression to regulate many aspects of nervous system physiology. here, we show that mir-92a suppresses memory consolidation that occurs in the αβ and γ mushroom body neurons (mbns) of drosophila , making mir-92a a memory suppressor mirna. bioinformatics analyses suggested that mrnas encoding kinesin heavy chain 73 (khc73), a protein that belongs to kinesin-3 family of anterograde motor proteins, may be a functional target of mir-92a. behavioral studies that employed expression of khc73 with and without its 3' untranslated region (utr) containing mir-92a target sites, luciferase assays in hek cells with reporters containing wild-type and mutant target sequences in the khc73 3'utr, and immunohistochemistry experiments involving khc73 expression with and without the wild-type khc73 3'utr, all point to the conclusion that khc73 is a major target of mir-92a in its functional role as a mirna memory suppressor gene.",1
"mirtrons are non-canonical mirnas arising by splicing and debranching from short introns. a plethora of introns have been inferred by computational analyses as potential mirtrons. yet, few have been experimentally validated and their functions, particularly in relation to their host genes, remain poorly understood. here, we found that drosophila larvae lacking either the mirtron mir-1010 or its binding site in the nicotinic acetylcholine receptor β2 (nacrβ2) 3'utr fail to grow properly and pupariate. increase of cortical nacrβ2 mediated by neural activity elevates the level of intracellular ca 2+ , which in turn activates camkii and, further downstream, the transcription factor adf-1. we show that mir-1010 downregulates nacrβ2. we reveal that adf-1 initiates the expression of skip, the host gene of mir-1010. preventing synaptic potentials from overshooting their optimal range requires both skip to temper synaptic potentials (incoherent feedforward loop) and mir-1010 to reduce nacrβ2 mrna levels (negative feedback loop). our results demonstrate how a mirtron, in coordination with its host gene, contributes to maintaining appropriate receptor levels, which in turn may play a role in maintaining homeostasis.",1
"granulocyte colony-stimulating factor (g-csf) mrna contains two distinct types of cis-acting mrna destabilizing elements in the 3'-untranslated region. in addition to several copies of the au-rich element the g-csf mrna also contains a destabilizing region that includes several predicted stem-loop structures. we report here that the destabilizing activity resides in a single stem-loop structure within this region. a consensus sequence for the active structure has been derived by site-directed mutagenesis, revealing that a three-base loop of sequence yau and unpaired bases either side of the stem contribute to the activity. the helical nature of the stem is essential and the stem must be less than 11 bp in length, but the destabilizing activity is relatively insensitive to the sequence within the helix. the stem-loop increases the rate of mrna deadenylation, most likely by enhancing the processivity of the deadenylation reaction. a protein that binds the stem-loop, but not an inactive mutant form, has been detected in cytoplasmic lysates.",1
"microrna-9 (mir-9) presents to exert distinct and even opposite functions in different kinds of tumors through targeting different cellular genes. however, its role in cervical adenocarcinoma remains uncertain. here, we report that mir-9 is down-regulated in cervical adenocarcinoma due to its frequent promoter-hypermethylation and exerts its tumor suppressor role through inhibiting several novel target genes, including interleukin-6 (il-6). the promoters of mir-9 precursors (mir-9-1, -2, and -3) were hypermethylated in cervical adenocarcinoma tissues. demethylation treatment of hela dramatically increased the expression of mature mir-9. both in vitro and in vivo functional experiments confirmed that mir-9 can inhibit the proliferation, migration, and malignant transformation abilities of hela cells. bioinformatics methods and array-based rna expression profiles were used to screen the downstream target genes of mir-9. dual-luciferase reporting assay, real-time qpcr, and elisa or western blot confirmed four genes (ckap2, hspc159, il-6, and tc10) to be novel direct target genes of mir-9. pathway annotation analysis of the differently expressed genes (degs) induced by ectopic mir-9 expression revealed the enrichment in jak/stat3 pathway, which is one of the downstream pathways of il-6. ectopic expression of mir-9 in hela inhibited jak/stat3 signaling activity. moreover, such effect could be partially reversed by the addition of exogenous il-6. in conclusion, our results here present a tumor suppressor potential of mir-9 in cervical adenocarcinoma for the first time and suggest that mir-9 could repress tumorigenesis through inhibiting the activity of il-6/jak/stat3 pathway.",1
"slt11p is a new splicing factor identified on the basis of synthetic lethality with a mutation in the 5' end of u2 snrna, a region that is involved in intermolecular u2/u6 helix ii interaction. slt11p is required for spliceosome assembly. our genetic results suggest that slt11p is involved in the base-pairing interaction of u2/u6 helix ii in vivo. we showed that the recombinant protein binds to rnas with some degree of structural specificity. slt11p also anneals rna and binds to the resulting duplexes, which contain two separated helical regions. these rna structures are reminiscent of u2/u6 helix ii, which is formed concomitantly with u4/u6 stem ii, and suggest that slt11p facilitates the cooperative formation of helix ii in association with stem ii in the spliceosome. we show that slt11p and slu7p, a second-step factor, interact with each other both in vivo and in vitro and that the binding of slu7p to slt11p impairs the rna-binding activity of the latter. these results suggest that the function of slt11p is regulated by slu7p in the spliceosome.",1
"within the family of rtks (receptor tyrosine kinases), pdgfr (platelet-derived growth factor receptor) has been implicated in carcinogenesis and tumour development. mirnas (micrornas), which can target the mrnas (messenger rnas) of cancer-associated genes, are abnormally expressed in various cancers. in this study, our aim was to identify the mirnas that target pdgfr-α/β and to study the functions of these mirnas. mir-34a was predicted to target pdgfr, and luciferase reporter assays showed that mir-34a could directly target pdgfr. meanwhile, we found that mir-34a was down-regulated in gastric cancer tissues and was associated with metastasis. our findings showed that mir-34a could inhibit gastric cancer cell migration, invasion and proliferation, but these tumourigenic properties were only partially restored when pdgfr-α/β was overexpressed. in subsequent experiments, we found that the overexpression of both pdgfr and met could completely restore the gastric cancer tumourigenic properties. moreover, the cancer-associated cell signalling pathway was studied, and we found that mir-34a could inhibit akt phosphorylation, which was restored by the overexpression of both pdgfr and met. in conclusion, mir-34a may act as a potential tumour suppressor in gastric cancer and is associated with the mechanisms of gastric cancer metastasis; mir-34a can inhibit gastric cancer tumourigenesis by targeting pdgfr and met through the pi3k (phosphoinositide 3-kinase)/akt pathway.",1
"blood-brain barrier (bbb) dysfunction is a hallmark of neurological conditions such as multiple sclerosis (ms) and stroke. however, the molecular mechanisms underlying neurovascular dysfunction during bbb breakdown remain elusive. micrornas (mirnas) have recently emerged as key regulators of pathogenic responses, although their role in central nervous system (cns) microvascular disorders is largely unknown. we have identified mir-155 as a critical mirna in neuroinflammation at the bbb. mir-155 is expressed at the neurovascular unit of individuals with ms and of mice with experimental autoimmune encephalomyelitis (eae). in mice, loss of mir-155 reduced cns extravasation of systemic tracers, both in eae and in an acute systemic inflammation model induced by lipopolysaccharide. in cultured human brain endothelium, mir-155 was strongly and rapidly upregulated by inflammatory cytokines. mir-155 up-regulation mimicked cytokine-induced alterations in junctional organization and permeability, whereas inhibition of endogenous mir-155 partially prevented a cytokine-induced increase in permeability. furthermore, mir-155 modulated brain endothelial barrier function by targeting not only cell-cell complex molecules such as annexin-2 and claudin-1, but also focal adhesion components such as dock-1 and syntenin-1. we propose that brain endothelial mir-155 is a negative regulator of bbb function that may constitute a novel therapeutic target for cns neuroinflammatory disorders.",1
"atrial fibrillation (af) is a highly prevalent arrhythmia with pronounced morbidity and mortality. inward-rectifier k+ current (ik1) is believed to be an important regulator of reentrant-spiral dynamics and a major component of af-related electrical remodeling. microrna-26 (mir-26) is predicted to target the gene encoding kir2.1, kcnj2. we found that mir-26 was downregulated in atrial samples from af animals and patients and this downregulation was accompanied by upregulation of ik1/kir2.1 protein. mir-26 overexpression suppressed expression of kcnj2/kir2.1. in contrast, mir-26 knockdown, inhibition, or binding-site mutation enhanced kcnj2/kir2.1 expression, establishing kcnj2 as a mir-26 target. knockdown of endogenous mir-26 promoted af in mice, whereas adenovirus-mediated expression of mir-26 reduced af vulnerability. kcnj2-specific mir-masks eliminated mir-26-mediated reductions in kcnj2, abolishing mir-26's protective effects, while coinjection of a kcnj2-specific mir-mimic prevented mir-26 knockdown-associated af in mice. nuclear factor of activated t cells (nfat), a known actor in af-associated remodeling, was found to negatively regulate mir-26 transcription. our results demonstrate that mir-26 controls the expression of kcnj2 and suggest that this downregulation may promote af.",1
"recent studies have established mir-34a as a key effector of the p53 signaling pathway and have implicated its role in multiple cancer types. here, we establish that mir-34a induces apoptosis, g2 arrest, and senescence in medulloblastoma and renders these cells more sensitive to chemotherapeutic agents. these effects are mediated in part by the direct post-transcriptional repression of the oncogenic mage-a gene family. we demonstrate that mir-34a directly targets the 3' untranslated regions of mage-a genes and decreases mage-a protein levels. this decrease in mage-a results in a concomitant increase in p53 and its associated transcriptional targets, p21/waf1/cip1 and, importantly, mir-34a. this establishes a positive feedback mechanism where mir-34a is not only induced by p53 but increases p53 mrna and protein levels through the modulation of mage-a genes. additionally, the forced expression of mir-34a or the knockdown of mage-a genes by small interfering rna similarly sensitizes medulloblastoma cells to several classes of chemotherapeutic agents, including mitomycin c and cisplatin. finally, the analysis of mrna and micro-rna transcriptional profiles of a series of primary medulloblastomas identifies a subset of tumors with low mir-34a expression and correspondingly high mage-a expression, suggesting the coordinate regulation of these genes. our work establishes a role for mir-34a in modulating responsiveness to chemotherapy in medulloblastoma and presents a novel positive feedback mechanism involving mir-34a and p53, via direct targeting of mage-a.",1
"early heart development takes place through a complex series of steps, including the induction of cardiac mesoderm, formation of the cardiovascular progenitor cells and the commitment of cardiovascular lineage cells, such as cardiomyocytes (cms), smooth muscle cells (smcs) and endothelial cells (ecs). recently, micrornas, a family of endogenous, small non-coding rnas, have been identified as critical regulators in cardiogenesis and cardiovascular disease. previous studies demonstrated that microrna-1 (mir-1) could promote cardiac differentiation from mouse and human embryonic stem (es) cells. however, the underlying mechanism remained largely unclear. we performed microrna deep sequencing among human es cells, es cell derived-multipotent cardiovascular progenitors (mcps), and mcp-specified cms, ecs, and smcs. a specific enrichment of mir-1 was found in cms, not in smcs or ecs, implying a key role of mir-1 in determining cardiovascular commitment from mcps. when overexpressed in human induced pluripotent stem cells, mir-1 enhanced the expression of key cardiac transcriptional factors and sarcomeric genes. importantly, we found mir-1 promoted cm differentiation and suppressed ec commitment from mcps by modulating the activities of wnt and fgf signaling pathways. fzd7 and frs2 were confirmed as mir-1 targets using luciferase reporter assay and western blot. overall, this study reveals a fate-switching role of mir-1 at early human cardiovascular commitment stage via suppressing both wnt and fgf signaling pathways.",1
"znf143 is a ubiquitously expressed transcription factor conserved in all vertebrates, regulating genes involved in primary metabolism and cell growth. it is therefore crucial to tightly maintain the adequate level of this factor in the cell. although znf143 expression is auto-regulated at the transcriptional level, nothing is known about the post-transcriptional events influencing its expression. in this work, performed in mammalian cells, we show that znf143 expresses different 3'-untranslated regions (3'-utr) as a result of alternative polyadenylation. these 3'utr isoforms have a diverse impact on the znf143 transcript fate. indeed, we show that the longest isoform, unlike the short one, contains a destabilizing au-rich element and is targeted by the mirna 590-3p. additionally we observed a correlation between znf143 downregulation and mir-590-3p up-regulation in retinoic acid treated teratocarcinoma cells. this strongly suggests that znf143 post-transcriptional regulation depends on the long 3'utr isoform during teratocarcinoma cells differentiation. finally we evidenced that the alternative polyadenylation site usage is independent of the previously identified znf143 transcriptional auto-regulation.",1
"coronary artery disease (cad) is associated with high mortality and occurs via endothelial injury. endothelial progenitor cells (epcs) restore the integrity of the endothelium and protect it from atherosclerosis. in this study, we compared the expression of micrornas (mirnas) in epcs in atherosclerosis patients and normal controls. we found that mir-221 expression was significantly up-regulated in patients compared with controls. we predicted and identified p21/cdc42/rac1-activated kinase 1 (pak1) as a novel target of mir-221 in epcs. we also demonstrated that mir-221 targeted a putative binding site in the 3'utr of pak1, and absence of this site was inversely associated with mir-221 expression in epcs. we confirmed this relationship using a luciferase reporter assay. furthermore, overexpression of mir-221 in epcs significantly decreased epc proliferation, in accordance with the inhibitory effects induced by decreased pak1. overall, these findings demonstrate that mir-221 affects the mek/erk pathway by targeting pak1 to inhibit the proliferation of epcs.",1
"tau inclusions are a prominent feature of many neurodegenerative diseases including alzheimer's disease. their accumulation in neurons as ubiquitinated filaments suggests a failure in the degradation limb of the tau pathway. the components of a tau protein triage system consisting of chip/hsp70 and other chaperones have begun to emerge. however, the site of triage and the master regulatory elements are unknown. here, we report an elegant mechanism of tau degradation involving the cochaperone bag2. the bag2/hsp70 complex is tethered to the microtubule and this complex can capture and deliver tau to the proteasome for ubiquitin-independent degradation. this complex preferentially degrades sarkosyl insoluble tau and phosphorylated tau. bag2 levels in cells are under the physiological control of the microrna mir-128a, which can tune paired helical filament tau levels in neurons. thus, we propose that ubiquitinated tau inclusions arise due to shunting of tau degradation toward a less efficient ubiquitin-dependent pathway.",1
"objective increased deposition of extracellular matrix (ecm) within the kidney is driven by profibrotic mediators including transforming growth factor-beta (tgf-beta) and connective tissue growth factor (ctgf). we investigated whether some of their effects may be mediated through changes in expression of certain micrornas (mirnas). research design and methods proximal tubular cells, primary rat mesangial cells, and human podocytes were analyzed for changes in the expression of key genes, ecm proteins, and mirna after exposure to tgf-beta (1-10 ng/microl). tubular cells were also infected with ctgf-adenovirus. kidneys from diabetic apoe mice were also analyzed for changes in gene expression and mirna levels. results tgf-beta treatment was associated with morphologic and phenotypic changes typical of epithelial-mesenchymal transition (emt) including increased fibrogenesis in all renal cell types and decreased e-cadherin expression in tubular cells. tgf-beta treatment also modulated the expression of certain mirnas, including decreased expression of mir-192/215 in tubular cells, mesangial cells, which are also decreased in diabetic kidney. ectopic expression of mir-192/215 increased e-cadherin levels via repressed translation of zeb2 mrna, in the presence and absence of tgf-beta, as demonstrated by a zeb2 3'-untranslated region luciferase reporter assay. however, ectopic expression of mir-192/215 did not affect the expression of matrix proteins or their induction by tgf-beta. in contrast, ctgf increased mir-192/215 levels, causing a decrease in zeb2, and consequently increased e-cadherin mrna. conclusions these data demonstrate the linking role of mirna-192/215 and zeb2 in tgf-beta/ctgf-mediated changes in e-cadherin expression. these changes appear to occur independently of augmentation of matrix protein synthesis, suggesting that a multistep emt program is not necessary for fibrogenesis to occur.",1
"background/aims endothelial colony-forming cells (ecfcs) have the potential to be used in regenerative medicine. dysfunction of ecfcs is correlated with the onset of cardiovascular disorders, especially coronary artery disease (cad). binding of vascular endothelial growth factor a (vegfa) to vascular endothelial growth factor receptor-2 (vegfr2) triggers cell motility and angiogenesis of ecfcs, which are crucial to vascular repair. methods to identify the mirna-vegfr2-dependent regulation of ecfc functions, ecfcs isolated from peripheral blood of disease-free and cad individuals were subjected to small rna sequencing for identification of anti-vegfr2 mirnas. the angiogenic activities of the mirnas were determined in both in vitro and in vivo mice models. results three mirnas, namely mir-410-3p, mir-497-5p, and mir-2355-5p, were identified to be upregulated in cad-ecfcs, and vegfr2 was their common target gene. knockdown of these mirnas not only restored the expression of vegfr2 and increased angiogenic activities of cad-ecfcs in vitro, but also promoted blood flow recovery in ischemic limbs in vivo. mir-410-3p, mir-497-5p, and mir-2355-5p could serve as potential biomarkers for cad detection as they are highly expressed in the plasma of cad patients. conclusions this modulation could help develop new therapeutic modalities for cardiovascular diseases and other vascular dysregulated diseases, especially tumor angiogenesis.",1
"alternative pre-mrna splicing determines many changes in gene expression during development. two regulators known to control splicing patterns during neuron and muscle differentiation are the polypyrimidine tract-binding protein (ptb) and its neuronal homolog nptb. these proteins repress certain exons in early myoblasts, but upon differentiation of mature myotubes ptb/nptb expression is reduced, leading to increased inclusion of their target exons. we show here that the repression of nptb expression during myoblast differentiation results from its targeting by the muscle-restricted microrna mir-133. during differentiation of c2c12 myoblasts, nptb protein but not mrna expression is strongly reduced, concurrent with the up-regulation of mir-133 and the induction of splicing for several ptb-repressed exons. introduction of synthetic mir-133 into undifferentiated c2c12 cells leads to a decrease in endogenous nptb expression. both the mir-133 and the coexpressed mir-1/206 micrornas are extremely conserved across animal species, and ptb proteins are predicted targets for these mirnas in drosophila, mice, and humans. there are two potential mir-133-responsive elements (mre) within the nptb 3' untranslated region (utr), and a luciferase reporter carrying this 3' utr is repressed by mir-133 in an mre-dependent manner. transfection of locked nucleic acid (lna) oligonucleotides designed to block the function of mir-133 and mir-1/206 increases expression of nptb and decreases the inclusion of ptb dependent exons. these results indicate that mir-133 directly down-regulates a key splicing factor during muscle development and establishes a role for micrornas in the control of a developmentally dynamic splicing program.",1
"a long noncoding rna, kcnq1ot1, regulates the expression of both ubiquitously and tissue-specific imprinted genes within the kcnq1 domain. however, the functional sequences of the kcnq1ot1 rna that mediate lineage-specific imprinting are unknown. here, we have generated a knockout mouse with a deletion encompassing an 890-bp silencing domain (delta890) downstream of the kcnq1ot1 promoter. maternal transmission of the delta890 allele has no effect on imprinting, whereas paternal inheritance of the deletion leads to selective relaxation of the imprinting of ubiquitously imprinted genes to a variable extent in a tissue-specific manner. interestingly, the deletion affects dna methylation at somatically acquired differentially methylated regions (dmrs), but does not affect the histone modifications of the ubiquitously imprinted genes. importantly, we found that kcnq1ot1 recruits dnmt1 to somatic dmrs by interacting with dnmt1, and that this interaction was significantly reduced in the delta890 mice. thus, the ubiquitous and placental-specific imprinting of genes within the kcnq1 domain might be mediated by distinct mechanisms, and kcnq1ot1 rna might mediate the silencing of ubiquitously imprinted genes by maintaining allele-specific methylation through its interactions with dnmt1.",1
"gastric cancer remains the third leading cause of cancer-related mortality worldwide, and invasion and metastasis of gastric cancer represent the major reason for its poor prognosis. in this study, we found that loss of the receptor for activated c-kinase 1 (rack1) promoted the metastasis of gastric cancer by enhancing the autocrine expression of il8 in vitro and in vivo. microrna (mirna; mir) array identified that rack1 modulated the expression of a series of mirnas, including the mir-302 cluster, and rack1 modulated the il8 expression and tumor invasion through mirna-302c. moreover, upregulation of il8 in turn decreased the level of mirna-302c and induced il8 expression in a feedback manner. tissue microarray also indicated that rack1 was correlated with invasion/metastasis phenotype, il8 expression, as well as 5-year survival in clinical cases of gastric cancer. together, our results imply that loss of rack1 in gastric cancer links epigenetics to inflammatory cytokines to promote tumor metastasis.",1
"methylation of ribose sugars at the 2'-oh group is one of the major chemical modifications in rrna, and is catalyzed by snorna directed c/d box snornps. previous biochemical and computational analyses of the c/d box snornas have identified and mapped a large number of 2'-oh ribose methylations in rrnas. in the present study, we systematically analyzed ribose methylations of 18s rrna in saccharomyces cerevisiae, using mung bean nuclease protection assay and rp-hplc. unexpectedly, we identified a hitherto unknown ribose methylation at position g562 in the helix 18 of 5' central domain of yeast 18s rrna. furthermore, we identified snr40 as being responsible to guide snornp complex to catalyze g562 ribose methylation, which makes it only second snorna known so far to target three ribose methylation sites: gm562, gm1271 in 18s rrna, and um898 in 25s rrna. our sequence and mutational analysis of snr40 revealed that snr40 uses the same d' box and methylation guide sequence for both gm562 and gm1271 methylation. with the identification of gm562 and its corresponding snorna, complete set of ribose methylations of 18s rrna and their corresponding snornas have finally been established opening great prospects to understand the physiological function of these modifications.",1
"amyloid precursor protein (app) is a transmembrane glycoprotein proteolytically processed to release amyloid beta, a pathological hallmark of alzheimer's disease. app is expressed throughout the developing and mature brain; however, the primary function of this protein is unknown. we previously demonstrated that app deficiency enhances neurogenesis, but the mechanisms underlying this process are not known. here we show that app regulates the expression of micrornas in the cortex and in neural progenitors, specifically repressing mir-574-5p. we also show that overexpression of mir-574-5p promotes neurogenesis, but reduces the neural progenitor pool. in contrast, the reduced expression of mir-574-5p inhibits neurogenesis and stimulates proliferation in vitro and in utero. we further demonstrate that the inhibition of mir-574-5p in app-knockout mice rescues the phenotypes associated with app deficiency in neurogenesis. taken together, these results reveal a mechanism in which app regulates the neurogenesis through mirna-mediated post-transcriptional regulation.",1
"endogenous small rnas (mirnas) regulate gene expression by mechanisms conserved across metazoans. while the number of verified human mirnas is still expanding, only few have been functionally annotated. to perform genetic screens for novel functions of mirnas, we developed a library of vectors expressing the majority of cloned human mirnas and created corresponding dna barcode arrays. in a screen for mirnas that cooperate with oncogenes in cellular transformation, we identified mir-372 and mir-373, each permitting proliferation and tumorigenesis of primary human cells that harbor both oncogenic ras and active wild-type p53. these mirnas neutralize p53-mediated cdk inhibition, possibly through direct inhibition of the expression of the tumor-suppressor lats2. we provide evidence that these mirnas are potential novel oncogenes participating in the development of human testicular germ cell tumors by numbing the p53 pathway, thus allowing tumorigenic growth in the presence of wild-type p53.",1
"the human prion gene contains five copies of a 24 nt repeat that is highly conserved among species. an analysis of folding free energies of the human prion mrna, in particular in the repeat region, suggested biased codon selection and the presence of rna patterns. in particular, pseudoknots, similar to the one predicted by wills in the human prion mrna, were identified in the repeat region of all available prion mrnas available in genbank, but not those of birds and the red slider turtle. an alignment of these mrnas, which share low sequence homology, shows several co-variations that maintain the pseudoknot pattern. the presence of pseudoknots in yeast sup35p and rnq1 suggests acquisition in the prokaryotic era. computer generated three-dimensional structures of the human prion pseudoknot highlight protein and rna interaction domains, which suggest a possible effect in prion protein translation. the role of pseudoknots in prion diseases is discussed as individuals with extra copies of the 24 nt repeat develop the familial form of creutzfeldt-jakob disease.",1
"small non-coding rnas have emerged as key modulators of viral infection. however, with the exception of hepatitis c virus, which requires the liver-specific microrna (mirna)-122, the interactions of rna viruses with host mirnas remain poorly characterized. here, we used crosslinking immunoprecipitation (clip) of the argonaute (ago) proteins to characterize strengths and specificities of mirna interactions in the context of 15 different rna virus infections, including several clinically relevant pathogens. notably, replication of pestiviruses, a major threat to milk and meat industries, critically depended on the interaction of cellular mir-17 and let-7 with the viral 3' utr. unlike canonical mirna interactions, mir-17 and let-7 binding enhanced pestivirus translation and rna stability. mir-17 sequestration by pestiviruses conferred reduced ago binding and functional de-repression of cellular mir-17 targets, thereby altering the host transcriptome. these findings generalize the concept of rna virus dependence on cellular mirnas and connect virus-induced mirna sequestration to host transcriptome regulation.",1
"the life of aerobes is dependent on iron and oxygen for efficient bioenergetics. due to potential risks associated with iron/oxygen chemistry, iron acquisition, concentration, storage, utilization, and efflux are tightly regulated in the cell. a central role in regulating iron/oxygen chemistry in animals is played by mrna translation or turnover via the iron responsive element (ire)/iron regulatory protein (irp) system. the ire family is composed of three-dimensional rna structures located in 3' or 5' untranslated regions of mrna. to date, there are 11 different ire mrnas in the family, regulated through translation initiation or mrna stability. iron or oxidant stimuli induce a set of graded responses related to mrna-specific ire substructures, indicated by differential responses to iron in vivo and binding irps in vitro. molecular effects of phosphorylation, iron and oxygen remain to be added to the structural information of the ire-rna and irp repressor in the regulatory complex.",1
"objective to investigate mir-155 in the sod1 mouse model and human sporadic and familial amyotrophic lateral sclerosis (als). methods nanostring microrna, microglia and immune gene profiles, protein mass spectrometry, and rna-seq analyses were measured in spinal cord microglia, splenic monocytes, and spinal cord tissue from sod1 mice and in spinal cord tissue of familial and sporadic als. mir-155 was targeted by genetic ablation or by peripheral or centrally administered anti-mir-155 inhibitor in sod1 mice. results in sod1 mice, we found loss of the molecular signature that characterizes homeostatic microglia and increased expression of mir-155. there was loss of the microglial molecules p2ry12, tmem119, olfml3, transcription factors egr1, atf3, jun, fos, and mafb, and the upstream regulators csf1r, tgfb1, and tgfbr1, which are essential for microglial survival. microglia biological functions were suppressed including phagocytosis. genetic ablation of mir-155 increased survival in sod1 mice by 51 days in females and 27 days in males and restored the abnormal microglia and monocyte molecular signatures. disease severity in sod1 males was associated with early upregulation of inflammatory genes, including apoe in microglia. treatment of adult microglia with apolipoprotein e suppressed the m0-homeostatic unique microglia signature and induced an m1-like phenotype. mir-155 expression was increased in the spinal cord of both familial and sporadic als. dysregulated proteins that we identified in human als spinal cord were restored in sod1(g93a) /mir-155(-/-) mice. intraventricular anti-mir-155 treatment derepressed microglial mir-155 targeted genes, and peripheral anti-mir-155 treatment prolonged survival. interpretation we found overexpression of mir-155 in the sod1 mouse and in both sporadic and familial human als. targeting mir-155 in sod1 mice restores dysfunctional microglia and ameliorates disease. these findings identify mir-155 as a therapeutic target for the treatment of als.",1
"interleukin-6 (il-6) is a pleiotropic cytokine that plays a central role in host defense. il-6 expression can be regulated at both a transcriptional and a post-transcriptional level. we used a combination of bioinformatics and experimental techniques to demonstrate that the mir-365 is a direct negative regulator of il-6. overexpression of mir-365 mimics decreased activity of a luciferase reporter containing the il-6 3'-utr and led to repression of il-6 protein. in contrast, ectopic expression of a mir-365 inhibitor elevated il-6 expression. the negative regulation of mir-365 was strictly dependent on a microrna binding element in the 3'-utr of il-6 mrna. deletion mutant analysis of the mir-365 promoter showed that two transcription factors, sp1 and nf-κb, are essential for the transcriptional regulation of mir-365. we also demonstrate that the mapk/erk pathway contributes to the regulation of mir-365. furthermore, mir-365 exhibited a greater negative regulatory effect on il-6 than hsa-let-7a, a previously identified microrna negatively regulating il-6. taken together, our results show that mir-365 is a novel negative regulator of il-6.",1
"micrornas (mirnas) represent an abundant class of non-coding rnas that negatively regulate gene expression, primarily at the post-transcriptional level. mirna genes are frequently located in proximity to fragile chromosomal sites associated with cancers and amplification of a mirna cluster has been correlated with the etiology of lymphomas and solid tumors. the oncogenic potential of a mirna polycistron has recently been demonstrated in vivo. here, we show that misexpression of the drosophila mirna mirvana/mir-278 in the developing eye causes massive overgrowth, in part due to inhibition of apoptosis. a single base substitution affecting the mature mirna blocks the gain-of-function phenotype but is not associated with a detectable reduction-of-function phenotype when homozygous. this result demonstrates that misexpressed mirnas may acquire novel functions that cause unscheduled proliferation in vivo and thus exemplifies the potential of mirnas to promote tumor formation.",1
"background/aims hirschsprung's disease (hscr) is a genetic disorder of neural crest development. in this study, we investigated whether and how mir-200a and mir-141, belonging to mir-200 family, were involved in the pathogenesis of hscr. methods quantitative real time pcr and western blot were used to detect the levels of mirna, mrnas, and proteins in colon tissues from 88 hscr patients and 75 controls. the direct regulation of specific mrna by mirnas was validated by dual-luciferase reporter assay and rna interference in cell lines. transwell assays, cck8 assay, and flow cytometry were inplemented to measure viability and activities of human 293t and sh-sy5y cells, respectively. results aberrant suppression of mir-200a was observed in colon tissues of hscr patients. a decreased level of mir-200a and mir-141 correlated with increased levels of pten mrna and protein. the dual-luciferase reporter gene assay demonstrated that mir-200a and mir-141 binded directly to 3'utr of pten and resulting in the inhibition of pten. the reductions in mir-200a and mir-141 inhibited migration and proliferation of 293t and sh-sy5y cells through up-regulating the expression of pten. moreover, knocking-down of pten rescued the extent of suppressed cell migration and proliferation induced by mir-200a and mir-141. conclusions the mir-200 family may play a crucial role in the pathogenesis of hscr by co-regulating pten.",1
"unbalanced tumor necrosis factor (tnf)-α production is associated with pathogenesis of a variety of human diseases. however, the molecular pathways maintaining tnf-α homeostasis remain elusive. here, we report that nf-κb/p65-dicer-mirs axis negatively regulates tnf-α production. we demonstrated that nf-κb bound to dicer promoter and transcriptionally regulated dicer expression. in addition, the nf-κb/dicer signaling suppresses tnf-α expression by generating mature forms of mir-125b and mir-130a which negatively regulate tnf-α mrna. furthermore, we showed that the hepatocyte-specific depletion of dicer in mice resulted in tnf-α overproduction and sensitized the mice to endotoxin, which could be corrected by administration of mir-125b mimics. these data suggest that nf-κb/p65-dicer-mirs axis involved in maintaining of tnf-α homeostasis, and injection of mir-125b as a potential therapeutic method for septic shock.",1
"stem cell niches act as signaling platforms that regulate stem cell self-renewal and sustain stem cells throughout life; however, the specific developmental events controlling their assembly are not well understood. here, we show that during drosophila ovarian germline stem cell niche formation, the status of notch signaling in the cell can be reprogrammed. this is controlled via steroid-induced mir-125 , which targets a negative regulator of notch signaling, tom. thus, mir-125 acts as a spatiotemporal coordinator between paracrine notch and endocrine steroid signaling. moreover, a dual security mechanism for notch signaling activation exists to ensure the robustness of niche assembly. particularly, stem cell niche cells can be specified either via lateral inhibition, in which a niche cell precursor acquires notch signal-sending status randomly, or via peripheral induction, whereby delta is produced by a specific cell. when one mechanism is perturbed due to mutations, developmental defects or environmental stress, the remaining mechanism ensures that the niche is formed, perhaps abnormally, but still functional. this guarantees that the germline stem cells will have their residence, thereby securing progressive oogenesis and, thus, organism reproduction.",1
"activity of human natural killer (nk) cells against cancer cells is deeply suppressed by tgf-β1, an immunomodulatory cytokine that is released and activated in the tumor microenvironment. moreover, our previous data showed that tgf-β1 modifies the chemokine receptor repertoire of nk cells. in particular, it decreases the expression of cx 3 cr1 that drives these effectors toward peripheral tissues, including tumor sites. to identify possible mechanisms mediating chemokine receptors modulation, we analyzed the microrna profile of tgf-β1-treated primary nk cells. the analysis pointed out mir-27a-5p as a possible modulator of cx 3 cr1. we demonstrated the functional interaction of mir-27a-5p with the 3' untranslated region (3'utr) of cx 3 cr1 mrna by two different experimental approaches: by the use of a luciferase assay based on a reporter construct containing the cx 3 cr1 3'utr and by transfection of primary nk cells with a mir-27a-5p inhibitor. we also showed that the tgf-β1-mediated increase of mir-27a-5p expression is a consequence of mir-23a-27a-24-2 cluster induction. moreover, we demonstrated that mir-27a-5p downregulates the surface expression of cx 3 cr1. finally, we showed that neuroblastoma cells induced in resting nk cells a downregulation of the cx 3 cr1 expression that was paralleled by a significant increase of mir-27a-5p expression. therefore, the present study highlights mir-27a-5p as a pivotal tgf-β1-induced regulator of cx 3 cr1 expression.",1
"fibroblast-like synoviocytes (fls) play an important role in the pathogenesis of rheumatoid arthritis (ra) through participating in joint tissue inflammation and joint damage. micrornas are a kind of small non-coding rnas that can regulate gene expression in the transcription level to affect cell behaviors. this study intended to investigate the expression of mir-19 in fls from ra patients and related mechanism. a total of 126 ra patients were selected in this study. mir-19 expression in fls was detected by qrt-pcr. toll like receptor 2 (tlr2) protein expression was tested by western blot. mir-19 target genes were confirmed by bioinformatics analysis and luciferase reporter assay. the impact of mir-19 on the expression of tlr2, interleukin 6 (il-6), and matrix metalloproteinase 3 (mmp-3) in fls were analyzed by cell transfection and western blot. mir-19 expression in fls from ra patients was significantly downregulated compared with control (p < 0.05), while tlr2 level was increased (p < 0.05). bioinformatics analysis and luciferase reporter assay confirmed that tlr2 was the target gene of mir-19. transfection of mir-19 mimic or mir-19 inhibitor obviously suppressed or increased tlr2 expression, and reduced or promoted release of cytokines il-6 and mmp-3 in fls, respectively. in conclusion, mir-19 expression was downregulated in fls from ra patients, leading to increased tlr2 expression and enhanced cytokines release.",1
"previously we have shown that microrna mir-382 can facilitate loss of renal epithelial characteristics in cultured cells. this study examined the in vivo role of mir-382 in the development of renal interstitial fibrosis in a mouse model. unilateral ureteral obstruction was used to induce renal interstitial fibrosis in mice. with 3 days of unilateral ureteral obstruction, expression of mir-382 in the obstructed kidney was increased severalfold compared with sham-operated controls. intravenous delivery of locked nucleic acid-modified anti-mir-382 blocked the increase in mir-382 expression and significantly reduced inner medullary fibrosis. expression of predicted mir-382 target kallikrein 5, a proteolytic enzyme capable of degrading several extracellular matrix proteins, was reduced with unilateral ureteral obstruction. anti-mir-382 treatment prevented the reduction of kallikrein 5 in the inner medulla. furthermore, the protective effect of the anti-mir-382 treatment against fibrosis was abolished by renal knockdown of kallikrein 5. targeting of kallikrein 5 by mir-382 was confirmed by 3'-untranslated region luciferase assay. these data support a completely novel mechanism in which mir-382 targets kallikrein 5 and contributes to the development of renal inner medullary interstitial fibrosis. the study provided the first demonstration of an in vivo functional role of mir-382 in any species and any organ system.",1
"drosophila melanogaster is widely used as a model system to study innate immunity and signaling pathways related to innate immunity, including the toll signaling pathway. although this pathway is well studied, the precise mechanisms of posttranscriptional regulation of key components of the toll signaling pathway by micrornas (mirnas) remain obscure. in this study, we used an in silico strategy in combination with the gal80 ts -gal4 driver system to identify microrna-958 (mir-958) as a candidate toll pathway regulating mirna in drosophila we report that overexpression of mir-958 significantly reduces the expression of drosomycin, a key antimicrobial peptide involved in toll signaling and the innate immune response. we further demonstrate in vitro and in vivo that mir-958 targets the toll and dif genes, key components of the toll signaling pathway, to negatively regulate drosomycin expression. in addition, a mir-958 sponge rescued the expression of toll and dif, resulting in increased expression of drosomycin. these results, not only revealed a novel function and modulation pattern of mir-958, but also provided a new insight into the underlying molecular mechanisms of toll signaling in regulation of innate immunity.",1
"acute pancreatitis (ap) is an inflammatory, complicated pancreatic disease, carrying significant morbidity and mortality. however, the molecular and cellular mechanisms involved in ap pathogenesis remain to be elucidated. here, we explore the role of foxf1 adjacent non-coding developmental regulatory rna (fendrr) in ap progression. caerulein with or without lps- induced or taurolithocholic acid 3-sulfate (tlc-s)-induced ap mouse models and cell models were performed for the validation of fendrr expression in vivo and in vitro, respectively. histopathological examinations of pancreatic tissues were performed to evaluate the severity of ap. transmission electron microscopy was utilized to visualize the autophagic vacuoles. sirna specifically targeting fendrr was further applied. flow cytometry was employed to assess cell apoptosis. elisa, immunoflureoscence, and western blotting analysis were also performed to determine the levels of inflammatory cytokines and autophagy activity. rna immunoprecipitation (rip) and chromatin immunoprecipitation (chip) assays were carried out to reveal the epigenetic regulation of fendrr on atg7. additionally, silencing fendrr was also verified in ap mouse models. higher fendrr and impaired autophagy were displayed in both ap mouse models and cell models. fendrr knockdown dramatically attenuated caerulein- or tlc-s-induced ar42j cells apoptosis and autophagy suppression. further mechanistic experiments implied that the action of fendrr is moderately attributable to its repression of atg7 via direct interaction with the epigenetic repressor prc2. moreover, the silencing of fendrr significantly induced the promotion of atg7, thus alleviating the development of ap in vivo. our study highlights fendrr as a novel target that may contribute to ap progression, suggesting a therapeutic target for ap treatment.",1
"caveolin-1 is the principal component of caveolae, and it is implicated in endocytosis, cholesterol homeostasis, signal transduction and tumorigenesis. micrornas play key regulatory roles in many cellular processes. however, the molecular mechanism by which porcine caveolin-1 is regulated by micrornas remains unclear. in the present study, we found that mir-124 could directly target caveolin-1 in porcine kidney epithelial cells (pk15). a luciferase reporter assay revealed that mir-124 directly bound to cav1 mrna. ectopic expression of mir-124 decreased porcine cav1 expression at both the mrna and protein levels. furthermore, we used transmission electron microscopy to count caveolae in the cytosolic space next to the membrane and we found that the overexpression of mir-124 in pk15 cells reduced the density of the caveolae. our results suggested that mir-124 reduced caveolar density by targeting caveolin-1 in pk15 cells; therefore, mir-124 could play an important role in the caveolae-mediated endocytosis of pathogens and signal transduction.",1
"abnormal proliferation of vascular smooth muscle cells (vsmcs) contributes to the development of cardiovascular diseases. studies have showed the great impact of micrornas (mirnas) on the cell proliferation in vsmcs. this study examined the in vitro functional roles of mir-665 in the vsmcs and explored the underlying molecular mechanisms. the mrna and protein expression levels were determined by qrt-pcr and western blot assays, respectively. cck-8, transwell invasion and wound healing assays were performed to measure vsmcs proliferation, invasion and migration, respectively. the mir-665 targeted-3'utr of fibroblast growth factor 9 (fgf9) and myocyte enhancer factor 2d (mef2d) was confirmed by luciferase reporter assay. platelet-derived growth factor-bb (pdgf-bb) and 20% serum promoted cell proliferation and suppressed the expression of mir-665 in vsmcs. in vitro functional assays demonstrated that mir-665 inhibited vsmcs proliferation, invasion and migration. bioinformatics analysis showed that fgf9 and mef2d were found to be downstream targets of mir-665. luciferase report assay confirmed that fgf9 and mef2d 3'utrs are direct targets of mir-665, and mir-665 overexpression suppressed both the mrna and protein expression levels of fgf9 and mef2d. furthermore, rescue experiments showed that enforced expression of fgf9 or mef2d attenuated the inhibitory effects of mir-665 on vsmcs proliferation. more importantly, overexpression of mir-665 also suppressed the mrna and protein expression levels of β-catenin, c-myc and cyclin d1. in summary, mir-665 suppressed the vsmcs proliferation, invasion and migration via targeting fgf9 and mef2d, and the in vitro effects of mir-665 on vsmcs may be associated with modulation of wnt/β-catenin signaling activities.",1
"unlabelled the overexpression of microrna-221 (mir-221) is reported in several human cancers including hepatocellular carcinoma, and its targeting by tailored treatments has been proposed. the evidence supporting the role of mir-221 in cancer is growing and has been mainly focused on the discovery of mir-221 targets as well as on its possible therapeutic exploitations. however, the mechanism sustaining mir-221 aberrant expression remains to be elucidated. in this study, mdm2 (e3 ubiquitin-protein ligase homolog), a known p53 (tp53) modulator, is identified as a direct target of mir-221, and a feed-forward loop is described that sustains mir-221 aberrant expression. interestingly, mir-221 can activate the p53/mdm2 axis by inhibiting mdm2 and, in turn, p53 activation contributes to mir-221 enhanced expression. moreover, by modulating the p53 axis, mir-221 impacts cell-cycle progression and apoptotic response to doxorubicin in hepatocellular carcinoma-derived cell lines. finally, cpg island methylation status was assessed as a causative event associated with mir-221 upregulation in hepatocellular carcinoma cells and primary tumor specimens. in hepatocellular carcinoma-derived cell lines, pharmacologically induced dna hypomethylation potentiated a significant increase in mir-221 expression. these data were confirmed in clinical specimens of hepatocellular carcinoma in which elevated mir-221 expression was associated with the simultaneous presence of wild-type p53 and dna hypomethylation. implications these findings reveal a novel mir-221-sustained regulatory loop that determines a p53-context-specific response to doxorubicin treatment in hepatocellular carcinoma.",1
"exposure of endothelial cells (ecs) to agents such as oxidized glycerophospholipids (oxgps) and cytokines, known to accumulate in atherosclerotic lesions, perturbs the expression of hundreds of genes in ecs involved in inflammatory and other biological processes. we hypothesized that micrornas (mirnas) are involved in regulating the inflammatory response in human aortic endothelial cells (haecs) in response to oxgps and interleukin 1β (il-1β). using next-generation sequencing and rt-quantitative pcr, we characterized the profile of expressed mirnas in haecs pre- and postexposure to oxgps. using this data, we identified mir-21-3p and mir-27a-5p to be induced 3- to 4-fold in response to oxgp and il-1β treatment compared with control treatment. transient overexpression of mir-21-3p and mir-27a-5p resulted in the downregulation of 1,253 genes with 922 genes overlapping between the two mirnas. gene ontology functional enrichment analysis predicted that the two mirnas were involved in the regulation of nuclear factor κb (nf-κb) signaling. overexpression of these two mirnas leads to changes in p65 nuclear translocation. using 3' untranslated region luciferase assay, we identified 20 genes within the nf-κb signaling cascade as putative targets of mirs-21-3p and -27a-5p, implicating these two mirnas as modulators of nf-κb signaling in ecs.",1
"objectives there have been no previous reports concerning functions of mir-103a in gastric cancer (gc) cells. thus the aim of the study was to investigate its expression and role in development of this tumour. materials and methods real-time rt-pcr was performed to detect expression of mir-103a in gc cell lines and clinical cancer specimens. to further understand its role, we restored expression of mir-103a in mgc-803 cell line by transfection with mir-103a mimics or inhibitors. effects of mir-103a on cell proliferation, migration and invasion on targets were also determined. results mir-103a was down-regulated in both gc cell lines and clinical cancer specimens. meanwhile, its level was closely associated with pm or ptnm stage of gc. overexpression of mir-103a markedly suppressed proliferation, migration, and invasion of gc cells, while its inhibition significantly accelerated cell proliferation, migration and invasion. moreover, c-myb was identified to be a functional downstream target of mir-103a, ectopic expression of which partially reversed suppression of cell proliferation and invasion. conclusions thus our observations suggest that mir-103a functioned as a tumour suppressor by targeting c-myb. these findings indicate that mir-103a might play a significant role in pathogenesis of gc.",1
"kaposi's sarcoma (ks) tumors are derived from endothelial cells and express kaposi's sarcoma-associated herpesvirus (kshv) micrornas (mirnas). although mirna targets have been identified in b cell lymphoma-derived cells and epithelial cells, little has been done to characterize the kshv mirna targetome in endothelial cells. a recent innovation in the identification of mirna targetomes, cross-linking, ligation, and sequencing of hybrids (clash), unambiguously identifies mirnas and their targets by ligating the two species while both species are still bound within the rna-induced silencing complex (risc). we developed a streamlined quick clash (qclash) protocol that requires a lower cell input than the original method and therefore has the potential to be used on patient biopsy samples. additionally, we developed a fast-growing, kshv-negative endothelial cell line derived from telomerase-immortalized vein endothelial long-term culture (tive-ltc) cells. qclash was performed on uninfected cells and cells infected with either wild-type kshv or a mutant virus lacking mir-k12-11/11*. more than 1,400 cellular targets of kshv mirnas were identified. many of the targets identified by qclash lacked a canonical seed sequence match. additionally, most target regions in mrnas originated from the coding dna sequence (cds) rather than the 3' untranslated region (utr). this set of genes includes some that were previously identified in b cells and some new genes that warrant further study. pathway analysis of endothelial cell targets showed enrichment in cell cycle control, apoptosis, and glycolysis pathways, among others. characterization of these new targets and the functional consequences of their repression will be important in furthering our understanding of the role of kshv mirnas in oncogenesis. importance ks lesions consist of endothelial cells latently infected with kshv. cells that make up these lesions express kshv mirnas. identification of the targets of kshv mirnas will help us understand their role in viral oncogenesis. the cross-linking and sequencing of hybrids (clash) protocol is a method for unambiguously identifying mirna targetomes. we developed a streamlined version of clash, called quick clash (qclash). qclash requires a lower initial input of cells than for its parent protocol. additionally, a new fast-growing kshv-negative endothelial cell line, named tive-ex-ltc cells, was established. qclash was performed on tive-ex-ltc cells latently infected with wild-type (wt) kshv or a mutant virus lacking mir-k12-11/11*. a number of novel targets of kshv mirnas were identified, including targets of mir-k12-11, the ortholog of the cellular oncogenic mirna (oncomir) mir-155. many of the mirna targets were involved in processes related to oncogenesis, such as glycolysis, apoptosis, and cell cycle control.",1
"background lung cancer is the leading cause of cancer-related mortality worldwide, with near 1.4 million deaths each year. nsclc accounts for nearly 85% of all case of lung cancer. mirnas play important roles in regulation of gene expression at the post-transcriptional level. mirnas profiles may predict prognosis and disease recurrence in early-stage nsclc. our previous study proved that over-expression of ubiquitin specific peptidase 14 (usp14), a deubiquitinating enzyme, was associated with favorable prognosis in nsclc patients and promoted tumor cells proliferation. here, we tried to identify which mirnas targeted usp14, and the roles of these mirnas in nsclc. methods mir-4782-3p and its potential targeted genes were identified by bioinformatics algorithm. dual luciferase reporter assay system was used to analyze the interaction between mir-4782-3p and targeted genes. cell proliferation was assayed by mtt and bdu assay. mirnas and mrna expression were assayed by qrt-pcr. usp14 protein level was assayed by western blot. the role of mir-4782-3p in patients survival was revealed by kaplan-meier plot of overall survival. results up-expression of mir-4782-3p in nsclc cells decreased the usp14 expression. down-expression of mir-4782-3p increased usp14 expression. in nsclc specimen, negative correlation between usp14 mrna level and mir-4782-3p level was identified. higher mir-4782-3p expression is associated with longer survival. usp14, zeb2, xiap overexpression reversed the inhibitory effect of mir-4782-3p. conclusions high expression of mir-4782-3p was associated with favorable prognosis in nsclc patients. mir-4782-3p inhibited cell proliferation in nsclc by targeting usp14, zeb2 and xiap.",1
"slc26a3 is a cl(-)/hco3(-) exchanger involved in electroneutral nacl absorption in the mammalian intestine. altered dra expression levels are associated with infectious and inflammatory diarrheal diseases. therefore, it is critical to understand the regulation of dra expression. micrornas (mirnas) are endogenous, small rnas that regulate protein expression via blocking the translation and/or promoting mrna degradation. to investigate potential modulation of dra expression by mirna, five different in silico algorithms were used to predict the mirnas that target dra. of these mirnas, mir-494 was shown to have a highly conserved putative binding site in the dra 3'-untranslated region (3'-utr) compared with other dra-targeting mirnas in vertebrates. transfection with pmirglo dual luciferase vector containing dra 3'-utr (pmirglo-3'-utr dra) resulted in a significant decrease in relative luciferase activity compared with empty vector. cotransfection of the dra 3'-utr luciferase vector with a mir-494 mimic further decreased luciferase activity compared with cells transfected with negative control. the transfection of a mir-494 mimic into caco-2 and t-84 cells significantly increased the expression of mir-494 and concomitantly decreased the dra protein expression. mutation of the seed sequences for mir-494 in 3'-utr of dra abrogated the effect of mir-494 on 3'-utr. these data demonstrate a novel regulatory mechanism of dra expression via mir-494 and indicate that targeting this microrna may serve to be a potential therapeutic strategy for diarrheal diseases.",1
"leprosy provides a model to investigate mechanisms of immune regulation in humans, given that the disease forms a spectrum of clinical presentations that correlate with host immune responses. here we identified 13 mirnas that were differentially expressed in the lesions of subjects with progressive lepromatous (l-lep) versus the self-limited tuberculoid (t-lep) disease. bioinformatic analysis revealed a significant enrichment of l-lep-specific mirnas that preferentially target key immune genes downregulated in l-lep versus t-lep lesions. the most differentially expressed mirna in l-lep lesions, hsa-mir-21, was upregulated in mycobacterium leprae-infected monocytes. by directly downregulating toll-like receptor 2/1 heterodimer (tlr2/1)-induced cyp27b1 and il1b expression as well as indirectly upregulating interleukin-10 (il-10), hsa-mir-21 inhibited expression of the genes encoding two vitamin d-dependent antimicrobial peptides, camp and defb4a. conversely, knockdown of hsa-mir-21 in m. leprae-infected monocytes enhanced expression of camp and defb4a and restored tlr2/1-mediated antimicrobial activity against m. leprae. therefore, the ability of m. leprae to upregulate hsa-mir-21 targets multiple genes associated with the immunologically localized disease form, providing an effective mechanism to escape from the vitamin d-dependent antimicrobial pathway.",1
"the microrna-183/96/182 cluster is highly expressed in the retina and other sensory organs. to uncover its in vivo functions in the retina, we generated a knockout mouse model, designated ""mir-183c(gt/gt),"" using a gene-trap embryonic stem cell clone. we provide evidence that inactivation of the cluster results in early-onset and progressive synaptic defects of the photoreceptors, leading to abnormalities of scotopic and photopic electroretinograms with decreased b-wave amplitude as the primary defect and progressive retinal degeneration. in addition, inactivation of the mir-183/96/182 cluster resulted in global changes in retinal gene expression, with enrichment of genes important for synaptogenesis, synaptic transmission, photoreceptor morphogenesis, and phototransduction, suggesting that the mir-183/96/182 cluster plays important roles in postnatal functional differentiation and synaptic connectivity of photoreceptors.",1
"lung cancer is the most common cause of death from cancer worldwide and recent studies have revealed that micrornas play critical roles to regulate lung carcinogenesis. here we present evidence to show the role of mir-198 in lung cancer development. our results showed that ectopic expression of mir-198 inhibits the viability and induces the apoptosis of human non-small cell lung cancer cells a549 and nci-h460, while mir-198 inhibition resulted in opposite changes. in nude mice mir-198 inhibits a549 growth of tumor graft. we further demonstrated that mir-198 directly targets fibroblast growth factor receptor 1 (fgfr1) in lung cancer cells. restoring fgfr1 expression blocked the inhibitory function of mir-198, while fgfr1 inhibition achieved the similar phenotypes of mir-198 overexpression. hence, our data delineates the molecular pathway by which mir-198 inhibits lung cancer cellular proliferation and induces apoptosis, and may have important implication for the treatment of lung carcinogenesis.",1
"we had previously proposed that the post-transcriptional regulation through microrna as a mechanism for incomplete penetrance and variable expressivity, leads to lack of correlation between genotype and phenotype. here we report the validation of mirna-target interactions we predicted earlier and demonstrate the regulation of endogenous jag1 by hsa-mir-214 and hsa-mir-124, and tgfbr2 by hsa-mir-34b*, through luciferase activity of reporter constructs and also the expression levels of the endogenous genes. using these targets, we have modeled the diploid state for mirna target site with heterozygosity for the snp and demonstrate the differential targeting of an otherwise identical 3'utr. we show that snp rs8708 (a > g) at the target site of hsa-mir-214 can relieve the repression while an snp rs11466532 (c > t) enhances the repression of reporter expression by hsa-mir-34b*. we discuss the results in the light of its implications in the context of penetrance of dominant mutations in mirna targeted genes, using jag1 as an example. these observations imply that disease causing mutations in jag1 linked to the snp rs8708g will be poorly targeted by hsa-mir-214 when present against a normal allele of jag1 with rs8708a and will show penetrance of jag1 mutations as alagille syndrome, while mutant jag1 linked to rs8708a against rs8708g on the normal allele will show either no disease or much attenuated symptoms and hence exhibit incomplete penetrance.",1
"members of the microrna-29 (mir-29) family directly target the dna methyltransferases, dnmt3a and dnmt3b. disturbances in the expression levels of mir-29 have been linked to tumorigenesis and tumor aggressiveness. members of the mir-29 family are currently thought to repress dna methylation and suppress tumorigenesis by protecting against de novo methylation. here, we report that members of the mir-29 family repress the activities of dna methyltransferases and dna demethylases, which have opposing roles in control of dna methylation status. members of the mir-29 family directly inhibited dna methyltransferases and two major factors involved in dna demethylation, namely tet methylcytosine dioxygenase 1 (tet1) and thymine dna glycosylase (tdg). overexpression of mir-29 upregulated the global dna methylation level in some cancer cells and downregulated dna methylation in other cancer cells, suggesting that mir-29 suppresses tumorigenesis by protecting against changes in the existing dna methylation status rather than by preventing de novo methylation of dna.",1
"background non-coding rnas (ncrna) are regulators of gene expression in all domains of life. they control growth and differentiation, virulence, motility and various stress responses. the identification of ncrnas can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. the small ncrna yfr1 has previously been found in the prochlorococcus/synechococcus group of marine cyanobacteria. results here we show that screening available genome sequences based on an rna motif and followed by experimental analysis works successfully in detecting this rna in all lineages of cyanobacteria. yfr1 is an abundant ncrna between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of prochlorococcus, mit 9211 and ss120, in which it must have been lost secondarily. yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16-20 nucleotides containing the ultraconserved undecanucleotide 5'-acuccucacac-3'. conclusion starting with an ncrna previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of e. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. the integration of rna motif prediction into computational pipelines for the detection of ncrnas in bacteria appears as a promising step to improve the quality of such predictions.",1
"there are two secondary structure models for the eukaryotic selenocysteine (sec) trna(sec). one model, the 9/4 structure, was experimentally tested and possesses acceptor and t-stems with 9 and 4 bp, respectively . the other one, the 7/5 secondary structure with a bulge in the t-stem, was derived from theoretical calculation [ioudovitch and steinberg, 19991. in this report, we show more experimental results supporting the 9/4 secondary structure. several trna(sec) mutants, whose secondary structure can adopt only the 9/4 structure, were active for serylation and selenylation. some mutants that cannot base-pair between positions 26 and 44 to provide the 6 bp anticodon stem were still active, inconsistent with the model by steinberg. we also show that the orientation of the v-arm directly or indirectly influences the selenylation activity, and that the rigid 6 bp d-stem is important. finally, we conclude that all trna(sec) possess the 13 bp domain ii made by the stacking of the colinear aa and t-stems, whether they present the 9/4 structure in eukarya and archaea or the 8/5 structure in bacteria.",1
"atherosclerosis is an inflammatory process due to oxidized low-density lipoprotein (oxldl) accumulation in macrophages. we investigated the involvement of micrornas in oxldl accumulation and inflammatory response in macrophages. the expression of mir-146a decreases under oxldl stimulation. mir-146a significantly reduces intracellular ldl cholesterol content and secretion of interleukin 6, interleukin 8, chemokine (c-c motif) ligand 2 and matrix metallopeptidase 9. toll-like receptor 4 (tlr4) is a relevant target of mir-146a, and mir-146a inhibits the activation of tlr4-dependent intracellular signaling pathways involved in cytoskeleton rearrangement, lipid uptake, and inflammatory cytokine secretion. these results indicate that mir-146a contributes to the regulation of both oxldl accumulation and inflammatory response by negatively regulating tlr4 and thereby inhibiting the activation of tlr4-dependent signaling pathways. over-expression of mir-146a may be useful in the prevention and treatment of atherosclerosis.",1
"aims we set about to investigate the potential role of microrna-155-5p (mir-155-5p) in the development of immune thrombocytopenia (itp), an idiopathic deficiency of blood platelets. main methods initially, rt-qpcr and western blot analyses were carried out to determine the expression of mir-155-5p and socs1 in peripheral blood mononuclear cells (pbmcs) and macrophages from itp patients. we undertook gain- and loss- function methods by transfection of macrophages and pbmcs with treated plasmids. the expression patterns of platelet-related factors were measured by elisa, and the expressions of pd1, pdl1, and macrophage m2 marker cd206 and cd86 were also measured. the relationship between mir-155-5p and socs1 was determined using the dual-luciferase reporter gene assay. we also established an itp mouse model to explore the roles of mir-155-5p and socs1 in vivo. key findings mir-155-5p was up-regulated, while socs1 was down-regulated in pbmcs and macrophages from itp patients. socs1 was indicated as a target of mir-155-5p. inhibition of mir-155-5p or up-regulation of socs1 facilitated macrophage m2 polarization as demonstrated by an increased m2/m1 ratio and suppressed expression of platelet-related factors. furthermore, silencing of socs1 promoted itp progression through blocking the pd1/pdl1 pathway, whilst upregulation of mir-155-5p remarkably increased the platelet abundance and suppressed socs1 expression in itp model mice. significance silencing of mir-155-5p could promote pd1/pdl1 pathway-mediated macrophage m2 polarization and prevent itp via up-regulation of socs1, thus relieving itp.",1
"development in multicellular organisms includes both small incremental changes and major switches of cell differentiation and proliferation status. during drosophila oogenesis, the follicular epithelial cells undergo two major developmental switches that cause global changes in the cell-cycle program. one, the switch from the endoreplication cycle to a gene-amplification phase, during which special genomic regions undergo repeated site-specific replication, is attributed to notch downregulation, ecdysone signaling activation and upregulation of the zinc-finger protein tramtrack69 (ttk69). here, we report that the microrna mir-7 exerts an additional layer of regulation in this developmental switch by regulating ttk69 transcripts. mir-7 recognizes the 3' utr of ttk69 transcripts and regulates ttk69 expression in a dose-dependent manner. overexpression of mir-7 effectively blocks the switch from the endocycle to gene amplification through its regulation of ttk69. mir-7 and ttk69 also coordinate other cell differentiation events, such as vitelline membrane protein expression, that lead to the formation of the mature egg. our studies reveal the important role mir-7 plays in developmental decision-making in association with signal-transduction pathways.",1
"adenosine deaminases-acting-on-rna (adar) proteins induce adenosine-to-inosine editing in double-stranded rna molecules. this editing generates rna diversity at the post-transcriptional level, and it has been implicated in the control of cell differentiation and development. the editing of microrna (mirna) precursors, along with tudor-sn (snd1) activity, could lead to the elimination of selected mirnas and reprogram mirna activity. here, we report the dynamics of adenosine-to-inosine editing in mirna precursors and their selected elimination during mouse preimplantation development. adar1p110 and snd1 were found to be strongly but differentially expressed in oocytes and zygotes with respect to later pre-implantation stages. when the biogenesis of mir-151 was assessed, the majority of mir-151 precursors was edited and subsequently eliminated during early development. deep sequencing of this and other mirnas confirmed that, in general, edited precursors were selectively eliminated at early post-zygotic stages. moreover, in oocytes and throughout the zygote-to-blastocyst stages, tudor-sn accumulated in newly discovered aggregates termed 't bodies'. these results provide new insight into how editing and tudor-sn-mediated elimination of mirna precursors is regulated during early development.",1
"deregulation of micro-rnas (mirnas) is emerging as a major aspect of cancer etiology because their capacity to direct the translation and stability of targeted transcripts can dramatically influence cellular physiology. to explore the potential of exogenously applied mirnas to suppress oncogenic proteins, the erbb oncogene family was chosen with a bioinformatics search identifying targeting seed sequences for mir-125a and mir-125b within the 3'-untranslated regions of both erbb2 and erbb3. using the human breast cancer cell line skbr3 as a model for erbb2 and erbb3 dependence, infection of these cells with retroviral constructs expressing either mir-125a or mir-125b resulted in suppression of erbb2 and erbb3 at both the transcript and protein level. luciferase constructs containing the 3' 3'-untranslated regions of erbb2 and erbb3 demonstrated approximately 35% less activity in mir-125a- and mir-125b-expressing cells relative to controls. additionally, phosphorylation of erk1/2 and akt was suppressed in skbr3 cells overexpressing either mir-125a or mir-125b. consistent with suppression of both erbb2 and erbb3 signaling, mir-125a-or mir-125b-overexpressing skbr3 cells were impaired in their anchorage-dependent growth and exhibited reduced migration and invasion capacities. parallel studies performed on mcf10a cells demonstrated that mir-125a or mir-125b overexpression produced only marginal influences on the growth and migration of these non-transformed human mammary epithelial cells. these results illustrate the feasibility of using mirnas as a therapeutic strategy to suppress oncogene expression and function.",1
"background a characteristic of both clinical and experimental atrial fibrillation (af) is atrial electric remodeling associated with profound reduction of l-type ca(2+) current and shortening of the action potential duration. the possibility that micrornas (mirnas) may be involved in this process has not been tested. accordingly, we assessed the potential role of mirnas in regulating experimental af. methods and results the mirna transcriptome was analyzed by microarray and verified by real-time reverse-transcription polymerase chain reaction with left atrial samples from dogs with af established by right atrial tachypacing for 8 weeks and from human atrial samples from af patients with rheumatic heart disease. mir-223, mir-328, and mir-664 were found to be upregulated by >2 fold, whereas mir-101, mir-320, and mir-499 were downregulated by at least 50%. in particular, mir-328 level was elevated by 3.9-fold in af dogs and 3.5-fold in af patients relative to non-af subjects. computational prediction identified cacna1c and cacnb1, which encode cardiac l-type ca(2+) channel α1c- and β1 subunits, respectively, as potential targets for mir-328. forced expression of mir-328 through adenovirus infection in canine atrium and transgenic approach in mice recapitulated the phenotypes of af, exemplified by enhanced af vulnerability, diminished l-type ca(2+) current, and shortened atrial action potential duration. normalization of mir-328 level with antagomir reversed the conditions, and genetic knockdown of endogenous mir-328 dampened af vulnerability. cacna1c and cacnb1 as the cognate target genes for mir-328 were confirmed by western blot and luciferase activity assay showing the reciprocal relationship between the levels of mir-328 and l-type ca(2+) channel protein subunits. conclusions mir-328 contributes to the adverse atrial electric remodeling in af through targeting l-type ca(2+) channel genes. the study therefore uncovered a novel molecular mechanism for af and indicated mir-328 as a potential therapeutic target for af.",1
"micrornas play an important role in myocardial diseases. mir-133a regulates cardiac hypertrophy, while mir-29b is involved in cardiac fibrosis. the aim of this study was to evaluate whether mir-133a and mir-29b play a role in myocardial fibrosis caused by angiotensin ii (ang ii)-dependent hypertension. sprague-dawley rats were treated for 4 weeks with ang ii (200 ng/kg/min) or ang ii + irbesartan (50 mg/kg/day in drinking water), or saline by osmotic minipumps. at the end of the experimental period, cardiac mir-133a and mir-29b expression was measured by real-time pcr, and myocardial fibrosis was evaluated by morphometric analysis. a computer-based prediction algorithm led to the identification of collagen 1a1 (col1a1) as a putative target of mir-133a. a reporter plasmid bearing the 3'-untranslated regions (utrs) of col1a1 mrna was constructed and luciferase assay was performed. mir-133a suppressed the activity of luciferase when the reporter gene was linked to a 3'-utr segment of col1a1 (p < 0.01). mutation of mir-133a binding sites in the 3'-utr of col1a1 mrna abolished mir-133a-mediated repression of reporter gene activity, showing that col1a1 is a real target of mir-133a. in vivo, ang ii caused an increase in systolic blood pressure (p < 0.0001, tail cuff) and myocardial fibrosis in presence of a decrease in mir-133a (p < 0.01) and mir-29b (p < 0.01), and an increase in col1a1 expression (p < 0.01). these effects were abolished by ang ii administration + irbesartan. these data demonstrate a relationship between mir-133a and col1a1, suggesting that myocardial fibrosis occurring in ang ii-dependent hypertension is regulated by the down-regulation of mir-133a and mir-29b through the modulation of col1a1 expression.",1
"circulating endothelial colony forming cells (ecfcs) contribute to vascular repair where they are a target for therapy. since ecfc proliferative potential is increased in cord versus peripheral blood and to define regulatory factors controlling this proliferation, we compared the mirna profiles of cord blood and peripheral blood ecfc-derived cells. of the top 25 differentially regulated mirnas selected, 22 were more highly expressed in peripheral blood ecfc-derived cells. after validating candidate mirnas by q-rt-pcr, we selected mir-193a-3p for further investigation. the mir-193a-3p mimic reduced cord blood ecfc-derived cell proliferation, migration and vascular tubule formation, while the mir-193a-3p inhibitor significantly enhanced these parameters in peripheral blood ecfc-derived cells. using in silico mirna target database analyses combined with proteome arrays and luciferase reporter assays of mir-193a-3p mimic treated cord blood ecfc-derived cells, we identified 2 novel mir-193a-3p targets, the high mobility group box-1 (hmgb1) and the hypoxia upregulated-1 (hyou1) gene products. hmgb1 silencing in cord blood ecfc-derived cells confirmed its role in regulating vascular function. thus, we show, for the first time, that mir-193a-3p negatively regulates human ecfc vasculo/angiogenesis and propose that antagonising mir-193a-3p in less proliferative and less angiogenic ecfc-derived cells will enhance their vasculo/angiogenic function.",1
"background micrornas (mirnas) regulate expression of many cancer-related genes through posttranscriptional repression of their mrnas. in this study we investigate the proto-oncogene mycn as a target for mirna regulation. methods a luciferase reporter assay was used to investigate software-predicted mirna target sites in the 3'-untranslated region (3'utr) of mycn. the mirnas were overexpressed in cell lines by transfection of mirna mimics or mirna-expressing plasmids. mutation of the target sites was used to validate mycn 3'utr as a direct target of several mirnas. to measure mirna-mediated suppression of endogenous n-myc protein, inhibition of proliferation and inhibition of clonogenic growth, mirnas were overexpressed in a mycn-amplified neuroblastoma cell line. results the results from this study show that mycn is targeted by several mirnas. in addition to the previously shown mir-34a/c, we experimentally validate mir-449, mir-19a/b, mir-29a/b/c, mir-101 and let-7e/mir-202 as direct mycn-targeting mirnas. these mirnas were able to suppress endogenous n-myc protein in a mycn-amplified neuroblastoma cell line. the let-7e and mir-202 were strong negative regulators of mycn expression. the mir-101 and the let-7 family mirnas let-7e and mir-202 inhibited proliferation and clonogenic growth when overexpressed in kelly cells. conclusion the tumour-suppressor mirnas let-7 and mir-101 target mycn and inhibit proliferation and clonogenic growth of mycn-amplified neuroblastoma cells.",1
"approximately 100 genes undergo genomic imprinting. mutations in fewer than 10 imprinted genetic loci, including gnas, are associated with complex human diseases that differ phenotypically based on the parent transmitting the mutation. besides the ubiquitously expressed gsalpha, which is of broad biological importance, gnas gives rise to an antisense transcript and to several gsalpha variants that are transcribed from the nonmethylated parental allele. we previously identified two almost identical gnas microdeletions extending from exon nesp55 to antisense (as) exon 3 (delnesp55/delas3-4). when inherited maternally, both deletions are associated with erasure of all maternal gnas methylation imprints and autosomal-dominant pseudohypoparathyroidism type ib, a disorder characterized by parathyroid hormone-resistant hypocalcemia and hyperphosphatemia. as for other imprinting disorders, the mechanisms resulting in abnormal gnas methylation are largely unknown, in part because of a paucity of suitable animal models. we now showed in mice that deletion of the region equivalent to delnesp55/delas3-4 on the paternal allele (deltanesp55(p)) leads to healthy animals without gnas methylation changes. in contrast, mice carrying the deletion on the maternal allele (deltanesp55(m)) showed loss of all maternal gnas methylation imprints, leading in kidney to increased 1a transcription and decreased gsalpha mrna levels, and to associated hypocalcemia, hyperphosphatemia, and secondary hyperparathyroidism. besides representing a murine autosomal-dominant pseudohypoparathyroidism type ib model and one of only few animal models for imprinted human disorders, our findings suggest that the nesp55 differentially methylated region is an additional principal imprinting control region, which directs gnas methylation and thereby affects expression of all maternal gnas-derived transcripts.",1
"the regulation of hif-1alpha is considered to be realized by pvhl-mediated ubiquitin-26s proteasome pathway at a post-transcriptional level. the discovery of a class of small noncoding rnas, called micrornas, implies alternative mechanism of regulation of hif-1alpha. here, we show that mir-20b plays an important role in fine-tuning the adaptation of tumor cells to oxygen concentration. the inhibition of mir-20b increased the protein levels of hif-1alpha and vegf in normoxic tumor cells; the increase of mir-20b in hypoxic tumor cells, nevertheless, decreased the protein levels of hif-1alpha and vegf. by using luciferase reporter vector system, we confirmed that mir-20b directly targeted the 3'utr of hif1a and vegfa. on the other hand, the forced overexpression of hif-1alpha in normoxic tumor cells downregulated mir-20b expression. however, hif-1alpha knockdown in hypoxic tumor cells caused the increase of mir-20b. the differential expression of mir-20b has important biological significance in tumor cells, either enhancing the growth or favoring the survival of tumor cells upon the oxygen supply. thus, we identify a novel molecular regulation mechanism through which mir-20b regulates hif-1alpha and vegf and is regulated by hif-1alpha so to keep tumor cells adapting to different oxygen concentrations.",1
"the nogo-b receptor (ngbr) is necessary for not only nogo-b-mediated angiogenesis but also vascular endothelial growth factor (vegf) -induced angiogenesis. however, the molecular mechanisms underlying the regulatory role of the vegf-ngbr axis in angiogenesis are not fully understood. here, we report that mir-26a serves as a critical regulator of vegf-mediated angiogenesis through directly targeting ngbr in endothelial cells (ecs). stimulation of ecs by vegf increased the expression of ngbr and decreased the expression of mir-26a. in addition, mir-26a decreased the vegf-induced migration and proliferation of ecs. moreover, mir-26a overexpression in ecs decreased the vegf-induced phosphorylation of the endothelial nitric oxide synthase (enos) and the production of nitric oxide, which is important for angiogenesis. overall, our data suggest that mir-26a plays a key role in vegf-mediated angiogenesis through the modulation of enos activity, which is mediated by its ability to regulate ngbr expression by directly targeting the ngbr 3'-utr. .",1
"the e2f family of transcription factors regulates the expression of both genes associated with cell proliferation and genes that regulate cell death. the net outcome is dependent on cellular context and tissue environment. the mir-11 gene is located in the last intron of the drosophila e2f1 homolog gene de2f1, and its expression parallels that of de2f1. here, we investigated the role of mir-11 and found that mir-11 specifically modulated the proapoptotic function of its host gene, de2f1. a mir-11 mutant was highly sensitive to de2f1-dependent, dna damage-induced apoptosis. consistently, coexpression of mir-11 in transgenic animals suppressed de2f1-induced apoptosis in multiple tissues, while exerting no effect on de2f1-driven cell proliferation. importantly, mir-11 repressed the expression of the proapoptotic genes reaper (rpr) and head involution defective (hid), which are directly regulated by de2f1 upon dna damage. in addition to rpr and hid, we identified a novel set of cell death genes that was also directly regulated by de2f1 and mir-11. thus, our data support a model in which the coexpression of mir-11 limits the proapoptotic function of its host gene, de2f1, upon dna damage by directly modulating a de2f1-dependent apoptotic transcriptional program.",1
"several micrornas have been implicated in human breast cancer but none to date have been validated or utilized consistently in clinical management. microrna-301 (mir-301) overexpression has been implicated as a negative prognostic indicator in lymph node negative (lnn) invasive ductal breast cancer, but its potential functional impact has not been determined. here we report that in breast cancer cells, mir-301 attenuation decreased cell proliferation, clonogenicity, migration, invasion, tamoxifen resistance, tumor growth, and microvessel density, establishing an important oncogenic role for this gene. algorithm-based and experimental strategies identified foxf2, bbc3, pten, and col2a1 as candidate mir-301 targets, all of which were verified as direct targets through luciferase reporter assays. we noted that mir-301 is located in an intron of the ska2 gene which is responsible for kinetochore assembly, and both genes were found to be coexpressed in primary breast cancer samples. in summary, our findings define mir-301 as a crucial oncogene in human breast cancer that acts through multiple pathways and mechanisms to promote nodal or distant relapses.",1
"background mitochondrial dysfunction induces insulin resistance in myocytes via a reduction of insulin receptor substrate-1 (irs-1) expression. however, the effect of mitochondrial dysfunction on insulin sensitivity is not understood well in hepatocytes. although research has implicated the translational repression of target genes by endogenous non-coding micrornas (mirna) in the pathogenesis of various diseases, the identity and role of the mirnas that are involved in the development of insulin resistance also remain largely unknown. methodology to determine whether mitochondrial dysfunction induced by genetic or metabolic inhibition causes insulin resistance in hepatocytes, we analyzed the expression and insulin-stimulated phosphorylation of insulin signaling intermediates in sk-hep1 hepatocytes. we used qrt-pcr to measure cellular levels of selected mirnas that are thought to target irs-1 3' untranslated regions (3'utr). using overexpression of mir-126, we determined whether irs-1-targeting mirna causes insulin resistance in hepatocytes. principal findings mitochondrial dysfunction resulting from genetic (mitochondrial dna depletion) or metabolic inhibition (rotenone or antimycin a) induced insulin resistance in hepatocytes via a reduction in the expression of irs-1 protein. in addition, we observed a significant up-regulation of several mirnas presumed to target irs-1 3'utr in hepatocytes with mitochondrial dysfunction. using reporter gene assay we confirmed that mir-126 directly targeted to irs-1 3'utr. furthermore, the overexpression of mir-126 in hepatocytes caused a substantial reduction in irs-1 protein expression, and a consequent impairment in insulin signaling. conclusions/significance we demonstrated that mir-126 was actively involved in the development of insulin resistance induced by mitochondrial dysfunction. these data provide novel insights into the molecular basis of insulin resistance, and implicate mirna in the development of metabolic disease.",1
"the family dicistroviridae (order picornavirales) includes species that infect insects and other arthropods. these viruses have a linear positive-sense ssrna genome of approximately 8-10 kb, which contains two long orfs. the 5' orf encodes the nonstructural polyprotein while the 3' orf encodes the structural polyprotein. the dicistroviruses are noteworthy for the intergenic internal ribosome entry site (igr-ires) that mediates efficient translation initation on the 3' orf without the requirement for initiator met-trna. acute bee paralysis virus, israel acute paralysis virus of bees and kashmir bee virus form a distinct subgroup within the dicistroviridae family. in this brief report, we describe the bioinformatic discovery of a new, apparently coding, orf in these viruses. the orf overlaps the 5' end of the structural polyprotein coding sequence in the +1 reading frame. we also identify a potential 14-18 bp rna stem-loop structure 5'-adjacent to the igr-ires. we discuss potential translation initiation mechanisms for the novel orf in the context of the igr-ires and 5'-adjacent stem-loop.",1
"objective endothelial transcription factors krüppel-like factor 4 (klf4) and klf2 are implicated in protection against atherogenesis. steady-state microrna (mir) regulation of klfs in vivo is accessible by screening region-specific endothelial mirs and their targets. methods and results a subset of differentially expressed endothelial mirs was identified in atherosusceptible versus protected regions of normal swine aorta. in silico analyses predicted highly conserved binding sites in the 3'-untranslated region (3'utr) of klf4 for 5 mirs of the subset (mir-26a, -26b, -29a, -92a, and -103) and a single binding site for a mir-92a complex in the 3'utr of klf2. of these, only mir-92a knockdown and knock-in resulted in responses of klf4 and klf2 expression in human arterial endothelial cells. dual luciferase reporter assays demonstrated functional interactions of mir-92a with full-length 3'utr sequences of both klfs and with the specific binding elements therein. two evolutionarily conserved mir-92a sites in klf4 3'utr and 1 site in klf2 3'utr were functionally validated. knockdown of mir-92a in vitro resulted in partial rescue from cytokine-induced proinflammatory marker expression (monocyte chemotactic protein 1, vascular cell adhesion molecule-1, e-selectin, and endothelial nitric oxide synthase) that was attributable to enhanced klf4 expression. leukocyte-human arterial endothelial cell adhesion experiments supported this conclusion. in swine aortic arch endothelium, a site of atherosusceptibility where mir-92a expression was elevated, both klfs were expressed at low levels relative to protected thoracic aorta. conclusions mir-92a coregulates klf4 and klf2 expression in arterial endothelium and contributes to phenotype heterogeneity associated with regional atherosusceptibility and protection in vivo.",1
"the foxo1 transcription factor orchestrates the regulation of genes involved in the apoptotic response, cell cycle checkpoints, and cellular metabolism. foxo1 is a putative tumor suppressor, and the expression of this gene is dysregulated in some cancers, including prostate and endometrial cancers. however, the molecular mechanism resulting in aberrant expression of human foxo1 in cancer cells is poorly understood. we show here that foxo1 mrna is down-regulated in breast tumor samples as compared with normal breast tissue. silencing of the microrna processing enzymes, drosha and dicer, led to an increase in foxo1 expression. we also identified functional and specific microrna target sites in the foxo1 3'-untranslated region for mir-27a, mir-96, and mir-182, micrornas that have previously been linked to oncogenic transformation. the three micrornas, mir-27a, mir-96 and mir-182, were observed to be highly expressed in mcf-7 breast cancer cells, in which the level of foxo1 protein is very low. antisense inhibitors to each of these micrornas led to a significant increase in endogenous foxo1 expression and to a decrease in cell number in a manner that was blocked by foxo1 sirna. overexpression of foxo1 resulted in decreased cell viability because of inhibition of cell cycle traverse and induction of cell death. we have identified a novel mechanism of foxo1 regulation, and targeting of foxo1 by micrornas may contribute to transformation or maintenance of an oncogenic state in breast cancer cells.",1
"translationally competent mrnas form a closed loop via interaction of initiation factors with the 5' cap and poly(a) tail. however, many viral mrnas lack a cap and/or a poly(a) tail. we show that an uncapped, nonpolyadenylated plant viral mrna forms a closed loop by direct base-pairing (kissing) of a stem loop in the 3' untranslated region (utr) with a stem loop in the 5' utr. this allows a sequence in the 3' utr to confer translation initiation at the 5'-proximal aug. this base-pairing is also required for replication. unlike other cap-independent translation mechanisms, the ribosome enters at the 5' end of the mrna. this remarkably long-distance base-pairing reveals a novel mechanism of cap-independent translation and means by which mrna utrs can communicate.",1
"to exert regulatory function, mirnas guide argonaute (ago) proteins to partially complementary sites on target rnas. crosslinking and immunoprecipitation (clip) assays are state-of-the-art to map ago binding sites, but assigning the targeting mirna to these sites relies on bioinformatics predictions and is therefore indirect. to directly and unambiguously identify mirna:target site interactions, we modified our clip methodology in c. elegans to experimentally ligate mirnas to their target sites. unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. our in vivo data set and reanalysis of published mammalian ago-clip data for mirna-chimeras yielded ∼17,000 mirna:target site interactions. analysis of interactions and extensive experimental validation of chimera-discovered targets of viral mirnas suggest that our strategy identifies canonical, noncanonical, and nonconserved mirna:targets. about 80% of mirna interactions have perfect or partial seed complementarity. in summary, analysis of mirna:target chimeras enables the systematic, context-specific, in vivo discovery of mirna binding.",1
"pattern formation during epithelial development requires the coordination of multiple signaling pathways. here, we investigate the functions of an ovary-enriched mirna, mir-318, in epithelial development during drosophila oogenesis. mir-318 maternal loss-of-function mutants were female-sterile and laid eggs with abnormal morphology. removal of mir-318 disrupted the dorsal-anterior follicle cell patterning, resulting in abnormal dorsal appendages. mir-318 mutant females also produced thin and fragile eggshells due to impaired chorion gene amplification. we provide evidence that the ecdysone signaling pathway activates expression of mir-318 and that mir-318 cooperates with tramtrack69 to control the switch from endocycling to chorion gene amplification during differentiation of the follicular epithelium. the multiple functions of mir-318 in oogenesis illustrate the importance of mirnas in maintaining cell fate and in promoting the developmental transition in the female follicular epithelium.",1
"micrornas (mirnas) are short non-coding rnas that regulate gene expression by targeting mrnas, inhibiting the expression of the associated proteins. although a role for aberrant mirna expression in cancer has been postulated, the pathophysiologic role and relevance of aberrantly expressed mirnas in tumor biology has not been established. we evaluated the expression pattern of mirnas in human breast cancer cells by qpcr, finding out an up-regulated mirna mir-29b and studying its biological effect by migration assay. we defined a target gene pten by bioinformatics approach and western blot. in breast cancer cell line mda-mb-231 cell, which migrate faster than mcf-7, we observed that mir-29b was highly over-expressed. inhibition of mir-29b in cultured cells increased the expression of the phosphatase and tensin homolog (pten) tumor suppressor, promoting apoptosis, decreasing migration, and decreasing invasion. in contrast, enhanced mir-29b expression by transfection with pre-mir-29b decreased the expression of pten and impaired apoptosis, increasing tumor cell migration and invasion. moreover, pten was shown to be a direct target of mir-29b and was also shown to contribute to the mir-29b-mediated effects on cell invasion. modulation of mir-29b altered the role of pten involved in cell migration and invasion. aberrant expression of mir-29b, which modulates pten expression, can contribute to migration, invasion, and anti-apoptosis.",1
"with ∼30 000 deaths annually in the united states, prostate cancer (pca) is a major oncologic disease. here we show that the micrornas mir-130a, mir-203 and mir-205 jointly interfere with the two major oncogenic pathways in prostate carcinoma and are downregulated in cancer tissue. using transcriptomics we show that the micrornas repress several gene products known to be overexpressed in this cancer. argonaute 2 (ago2) co-immunoprecipitation, reporter assays and western blot analysis demonstrate that the micrornas directly target several components of the mitogen-activated protein kinase (mapk) and androgen receptor (ar) signaling pathways, among those several ar coregulators and hras (harvey rat sarcoma viral oncogene homolog), and repress signaling activity. both pathways are central for the development of the primary tumor and in particular the progression to its incurable castration-resistant form. reconstitution of the micrornas in lncap pca cells induce morphological changes, which resemble the effect of androgen deprivation, and jointly impair tumor cell growth by induction of apoptosis and cell cycle arrest. we therefore propose that these micrornas jointly act as tumor suppressors in prostate carcinoma and might interfere with progression to castration resistance.",1
"purpose the aim of this study was to find a novel molecular network involved in renal cell carcinoma (rcc) development through investigating the functions of mir-1 and mir-133a and their target genes. methods we checked the expression levels of mir-1 and mir-133a in rcc cell lines and specimens (n=40) using real time rt-pcr. mir-1 and mir-133a transfectants were subjected to a gain-of-function study to identify the functions of the mirnas. to find the target genes of the mirnas, we analysed the gene expression profile of their transfectants and performed a luciferase reporter assay. mrna expression levels of the candidate target gene in the clinical specimens were examined, and loss-of-function studies were performed. results the expression levels of mir-1 and mir-133a were significantly suppressed in rcc cell lines and specimens. ectopic restoration of mir-1 and mir-133a showed significant inhibition of cell proliferation and invasion, and moreover, revealed induction of apoptosis and cell cycle arrest. the luciferase assay revealed transgelin-2 (tagln2), selected as a target gene for mir-1 and mir-133a on the basis of the gene expression profile, to be directly regulated by both mir-1 and mir-133a. the loss-of-function studies showed significant inhibitions of cell proliferation and invasion in the si-tagln2 transfectant. the expression level of tagln2 mrna was significantly up-regulated in the rcc specimens; in addition, there was a statistically significant inverse correlation between tagln2 and mir-1 and mir-133a expression. conclusions our data indicate that up-regulation of the oncogenic tagln2 was due to down-regulation of tumour-suppressive mir-1 and mir-133a in human rcc.",1
"osteogenic differentiation of mesenchymal stem cells (mscs) is a complex process, which is regulated by various factors including micrornas. our preliminary data showed that the expression of endogenous mir-20a was increased during the course of osteogenic differentiation. simultaneously, the expression of osteoblast markers and regulators bmp2, bmp4, runx2, osx, ocn and opn was also elevated whereas adipocyte markers pparγ and osteoblast antagonist, bambi and crim1, were downregulated, thereby suggesting that mir-20a plays an important role in regulating osteoblast differentiation. to validate this hypothesis, we tested its effects on osteogenic differentiation by introducing mir-20a mimics and lentiviral-mir20a-expression vectors into hmscs. we showed that mir-20a promoted osteogenic differentiation by the upregulation of bmp/runx2 signaling. we performed bioinformatics analysis and predicted that pparγ, bambi and crim1 would be potential targets of mir-20a. pparγ is a negative regulator of bmp/runx2 signaling whereas bambi or crim1 are antagonists of the bmp pathway. furthermore, we confirmed that all these molecules were indeed the targets of mir-20a by luciferase reporter, quantitative rt-pcr and western blot assays. similarly to mir-20a overexpression, the osteogenesis was enhanced by the silence of pparγ, bambi or crim1 by specific sirnas. taken together, for the first time, we demonstrated that mir-20a promoted the osteogenesis of hmscs in a co-regulatory pattern by targeting pparγ, bambi and crim1, the negative regulators of bmp signaling.",1
"growth control relies on extrinsic and intrinsic mechanisms that regulate and coordinate the size and pattern of organisms. this control is crucial for a homeostatic development and healthy physiology. the gene networks acting in this process are large and complex: factors involved in growth control are also important in diverse biological processes and these networks include multiple regulators that interact and respond to intra- and extra-cellular inputs that may ultimately converge in the control of the cell cycle. in this work we have studied the function of the drosophila abrupt gene, coding for a btb-zf protein and previously reported to be required for wing vein pattern, in the control of haltere and wing growth. we have found that inactivation of abrupt reduces the size of the wing and haltere. we also found that the microrna mir-306 controls abrupt expression and that mir-306 and abrupt genetically interact to control wing size. moreover, the reduced appendage size due to abrupt inactivation is rescued by overexpression of cyclin-e and by inactivation of dacapo. these findings define a mir-306-abrupt regulatory axis that controls wing and haltere size, whereby mir-306 maintains appropriate levels of abrupt expression which, in turn, regulates the cell cycle. thus, our results uncover a novel function of abrupt in the regulation of the size of drosophila appendages during development and contribute to the understanding of the coordination between growth and pattern as well as to the understanding of abrupt oncogenic function in flies.",1
"caloric restriction (cr) has been shown to cause tumor regression in models of triple-negative breast cancer (tnbc), and the regression is augmented when coupled with ionizing radiation (ir). in this study, we sought to determine if the molecular interaction between cr and ir could be mediated by microrna (mir). mir arrays revealed 3 mirs in the mir-17~92 cluster as most significantly down regulated when cr is combined with ir. in vivo, cr and ir down regulated mir-17/20 in 2 tnbc models. to elucidate the mechanism by which this cluster regulates the response to cr, cdna arrays were performed and the top 5 statistically significant gene ontology terms with high fold changes were all associated with extracellular matrix (ecm) and metastases. in silico analysis revealed 4 potential targets of the mir-17~92 cluster related to ecm: collagen 4 alpha 3, laminin alpha 3, and metallopeptidase inhibitors 2 and 3, which were confirmed by luciferase assays. the overexpression or silencing of mir-17/20a demonstrated that those mirs directly affected the ecm proteins. furthermore, we found that cr-mediated inhibition of mir-17/20a can regulate the expression of ecm proteins. functionally, we demonstrate that cr decreases the metastatic potential of cells which further demonstrates the importance of the ecm. in conclusion, cr can be used as a potential treatment for cancer because it may alter many molecular targets concurrently and decrease metastatic potential for tnbc.",1
"transcriptome profiling studies have recently uncovered a large number of noncoding rna transcripts (ncrnas) in eukaryotic organisms, and there is growing interest in their role in the cell. for example, in haploid saccharomyces cerevisiae cells, the expression of an overlapping antisense ncrna, referred to here as rme2 (regulator of meiosis 2), prevents ime4 expression. in diploid cells, the a1-α2 complex represses the transcription of rme2, allowing ime4 to be induced during meiosis. in this study we show that antisense transcription across the ime4 promoter region does not block transcription factors from binding and is not required for repression. mutational analyses found that sequences within the ime4 open reading frame (orf) are required for the repression mediated by rme2 transcription. these results support a model where transcription of rme2 blocks the elongation of the full-length ime4 transcript but not its initiation. we have found that another antisense transcript, called rme3, represses zip2 in a cell-type-specific manner. these results suggest that regulated antisense transcription may be a widespread mechanism for the control of gene expression and may account for the roles of some of the previously uncharacterized ncrnas in yeast.",1
"micrornas have been proposed as novel regulators of vascular inflammation and dysfunction. this study aimed to evaluate the role of mir-149 in regulating the expression of key molecules associated with tnfα-induced endothelial activation. mir-149 was selected by in silico analysis and microrna target prediction. endothelial dysfunction was induced by tnfα treatment in eahy926 endothelial cells and huvec. mir-149 level was evaluated by quantitative real time-polymerase chain reaction (rt-qpcr). metalloproteinase-9 (mmp-9) was measured by zymography, inducible nitric oxide synthase (inos) by immunoblotting, interleukin-6 (il-6) and interleukin-8 (il-8) by elisa. mir-149 regulatory effect was evaluated by gain-of-function technique upon mir-149 mimics transfection. tnfα down-modulated mir-149 level in eahy926 and huvec. this effect was significantly abolished in eahy926 by treatment with p38mapk inhibitor. mir-149 mimic transfection counteracted the tnfα-induced expression of mmp-9, inos and il-6. no effect was detected on il-8 expression. our results suggest that mir-149 represents an important new regulator of endothelial function through negative regulation of molecules associated with tnfα-induced endothelial dysfunction.",1
"the u5 snrna loop 1 interacts with the 5' exon before the first step of pre-mrna splicing and with the 5' and 3' exons following the first step. these u5-exon interactions are proposed to hold the exons in the correct orientation for the second step of splicing. reconstitution of u5 snrnps in vitro indicated that u5 loop 1-5' exon interactions are not necessary for the first catalytic step of splicing but are critical for the second step in yeast spliceosomes. we systematically made deletion and insertion mutations in loop 1 then monitored splicing activity and loop-exon interactions by cross-linking. single nucleotide deletions or insertions in loop 1 permitted both steps of splicing. larger insertions or deletions allowed the first step but progressively inhibited the second step. analysis of selected loop 1 insertions and deletions by cross-linking revealed that inhibition of the second catalytic step resulted from misalignment of the 5' and 3' exons. these data indicate that the size of loop 1 is critical for proper alignment of the exons for the second catalytic step of splicing and that the 3' exon is positioned on loop 1 independently of the 5' exon.",1
"regulation of hematopoietic stem cell proliferation, lineage commitment, and differentiation in adult vertebrates requires extrinsic signals provided by cells in the marrow microenvironment (me) located within the bone marrow. both secreted and cell-surface bound factors critical to this regulation have been identified, yet control of their expression by cells within the me has not been addressed. herein we hypothesize that micrornas (mirnas) contribute to their controlled expression. mirnas are small noncoding rnas that bind to target mrnas and downregulate gene expression by either initiating mrna degradation or preventing peptide translation. testing the role of mirnas in downregulating gene expression has been difficult since conventional techniques used to define mirna-mrna interactions are indirect and have high false-positive and negative rates. in this report, a genome-wide biochemical technique (high-throughput sequencing of rna isolated by cross-linking immunoprecipitation or hits-clip) was used to generate unbiased genome-wide maps of mirna-mrna interactions in two critical cellular components of the marrow me: marrow stromal cells and bone marrow endothelial cells. analysis of these datasets identified mirnas as direct regulators of jag1, wnt5a, mmp2, and vegfa; four factors that are important to me function. our results show the feasibility and utility of unbiased genome-wide biochemical techniques in dissecting the role of mirnas in regulation of complex tissues such as the marrow me.",1
"background micrornas are regulators of gene expression, which act mainly by decreasing mrna levels of their multiple targets. deregulated microrna expression has been shown for acute myeloid leukemia, a disease also characterized by altered gene expression associated with distinct genomic aberrations such as nucleophosmin (npm1) mutations. to shed further light on the role of deregulated microrna and gene expression in cytogenetically normal acute myeloid leukemia with npm1 mutation we performed an integrative analysis of microrna and mrna expression data sets. design and methods both microrna and gene expression profiles were investigated in samples from a cohort of adult cytogenetically normal acute myeloid leukemia patients (n=43; median age 46 years, range 23-60 years) with known npm1 mutation status (n=23 mutated, n=20 wild-type) and the data were integratively analyzed. putative microrna-mrna interactions were validated by quantitative reverse transcriptase polymerase chain reaction, western blotting and luciferase reporter assays. for selected micrornas, sensitivity of microrna-overexpressing cells to cytarabine treatment was tested by facs viability and cell proliferation assays. results our integrative approach of analyzing both microrna- and gene expression profiles in parallel resulted in a refined list of putative target genes affected by npm1 mutation-associated microrna deregulation. of 177 putative microrna - target mrna interactions we identified and validated 77 novel candidates with known or potential involvement in leukemogenesis, such as irf2-mir-20a, kit-mir-20a and mn1-mir-15a. furthermore, our data showed that deregulated expression of tumor suppressor micrornas, such as mir-29a and mir-30c, might contribute to sensitivity to cytarabine, which is observed in npm1 mutated acute myeloid leukemia. conclusions overall, our observations highlight that integrative data analysis approaches can improve insights into leukemia biology, and lead to the identification of novel microrna - target gene interactions of potential relevance for acute myeloid leukemia treatment.",1
"many proteins are expressed dynamically during different stages of cellular life and the accuracy of protein amounts is critical for cell endurance. therefore, cells should have a perceptive system that notifies about fluctuations in the amounts of certain components and an executive system that efficiently restores their precise levels. at least one mechanism that evolution has employed for this task is regulation of 3'-utr length for microrna targeting. here we show that in drosophila the microrna complex mir-310s acts as an executive mechanism to buffer levels of the muscular dystrophy-associated extracellular matrix receptor dystroglycan via its alternative 3'-utr. mir-310s gene expression fluctuates depending on dystroglycan amounts and nitric oxide signalling, which perceives dystroglycan levels and regulates microrna gene expression. aberrant levels of dystroglycan or deficiencies in mir-310s and nitric oxide signalling result in cobblestone brain appearance, resembling human lissencephaly type ii phenotype.",1
"tamoxifen is an endocrine therapy which is administered to up to 70% of all breast cancer patients with oestrogen receptor alpha (erα) expression. despite the initial response, most patients eventually acquire resistance to the drug. micrornas (mirnas) are a class of small non-coding rnas which have the ability to post-transcriptionally regulate genes. although the role of a few mirnas has been described in tamoxifen resistance at the single gene/target level, little is known about how concerted actions of mirnas targeting biological networks contribute to resistance. here we identified the mirna cluster, c19mc, which harbours around 50 mature mirnas, to be up-regulated in resistant cells, with mirna-519a being the most highly up-regulated. we could demonstrate that mirna-519a regulates tamoxifen resistance using gain- and loss-of-function testing. by combining functional enrichment analysis and prediction algorithms, we identified three central tumour-suppressor genes (tsgs) in pi3k signalling and the cell cycle network as direct target genes of mir-519a. combined expression of these target genes correlated with disease-specific survival in a cohort of tamoxifen-treated patients. we identified mirna-519a as a novel oncomir in er+ breast cancer cells as it increased cell viability and cell cycle progression as well as resistance to tamoxifen-induced apoptosis. finally, we could show that elevated mirna-519a levels were inversely correlated with the target genes' expression and that higher expression of this mirna correlated with poorer survival in er+ breast cancer patients. hence we have identified mirna-519a as a novel oncomir, co-regulating a network of tsgs in breast cancer and conferring resistance to tamoxifen. using inhibitors of such mirnas may serve as a novel therapeutic approach to combat resistance to therapy as well as proliferation and evasion of apoptosis in breast cancer.",1
"pseudouridine, the most abundant modified nucleoside in rna, is synthesized by posttranscriptional isomerization of uridines. in eukaryotic rnas, site-specific synthesis of pseudouridines is directed primarily by box h/aca guide rnas. in this study, we have identified 61 novel putative pseudouridylation guide rnas by construction and characterization of a cdna library of human box h/aca rnas. the majority of the new box h/aca rnas are predicted to direct pseudouridine synthesis in rrnas and spliceosomal small nuclear rnas. we can attribute rna-directed modification to 79 of the 97 pseudouridylation sites present in the human 18s, 5.8s, and 28s rrnas and to 11 of the 21 pseudouridines reported for the u1, u2, u4, u5, and u6 spliceosomal rnas. we have also identified 12 novel box h/aca rnas which lack apparent target pseudouridines in rrnas and small nuclear rnas. these putative guide rnas likely function in the pseudouridylation of some other types of cellular rnas, suggesting that rna-guided pseudouridylation is more general than assumed before. the genomic organization of the new box h/aca rna genes indicates that in human cells, all box h/aca pseudouridylation guide rnas are processed from introns of pre-mrna transcripts which either encode a protein product or lack protein-coding capacity.",1
"background & aims little is known about functions of microrna (mir) passenger strands (mir*) or their roles in tumor development or progression. we screened for mirs and mir* with levels that were altered in metastatic colorectal cancer (crc) cells and human tumor samples and investigated their targets and effects on cell function and tumor progression in mice. methods we performed array-based profile analysis to identify mirs with levels that were increased more than 2-fold in metastatic (sw620) crc cells compared with nonmetastatic (sw480) cells. quantitative polymerase chain reaction and in situ hybridization analyses were used to measure mirna levels in crc cell lines and human tumor samples. we used mirna duplex mimics or inhibitors to increase and decrease levels of mirna in crc cells and assessed their activities and ability to form metastatic xenograft tumors in nude mice. results levels of mir-221* and mir-224 were reduced in metastatic compared with nonmetastatic crc cells; levels in human tumor samples correlated inversely with tumor stage and metastasis to lymph nodes as well as patient survival times. sw480 cells transfected with mir-221* or mir-224 inhibitors had increased motility in vitro compared with sw480 control cells and formed larger, more metastatic tumors when injected into mice. sw620 cells transfected with mir-221* or mir-224 mimics had reduced migration and motility in vitro and formed smaller tumors with fewer metastases in mice compared with control sw620 cells. we identified the 3' untranslated region of mbd2 messenger rna as a target of mir-221* and mir-224. mbd2 silences the gene encoding maspin, a suppressor of metastasis. in crc cells, we found that mir-221* and mir-224 increase the expression of maspin through mbd2 down-regulation. conclusions in metastatic crc cells, reduced levels of mir-221* and mir-224 increase levels of mbd2, thereby decreasing expression of the metastasis suppressor maspin. increased activities of mir-221* and mir-224 reduce growth and metastasis of crc xenograft tumors in mice; these mirs might be developed as therapeutic reagents or biomarkers of crc progression.",1
"a mature mirna generally suppresses hundreds of mrna targets. to evaluate the selective effect of synthetic oligonucleotide decoys on hsa-mir-223 activity, reporters containing 3' untranslated regions (utr) of igf1r, foxo1, polr3g, foxo3, cdc27, fbxw7 and paxip1 mrnas were constructed for the luciferase assay. the oligonucleotide decoys were designed and synthesized according to mature mir-223 sequence and its target mrna sequence. quantitative rt-pcr & western analysis were used to measure mir-223-targeted mrna expression, interestingly, apart from the antisense oligonucleotide, decoy nucleotides which were complementary to the 5', central or 3' region of mature mir-223 suppressed mir-223 targeting the 3'utr of igf1r, foxo1, foxo3, cdc27, polr3g, and fbxw7 mrnas and rescued the expression of these genes to varying degrees from mir-223 suppression at both mrna and protein levels. all decoys had no effect on paxip1 which was not targeted by mir-223. the decoy 1 that was based on the sequence of igf1r 3'utr rescued the expression of igf1r more significantly than other decoy nucleotides except the antisense decoy 4. decoy 1 also rescued the expression of foxo3 and polr3g of which their 3'utrs have similar binding sites for mir-223 with igf1r 3'utr. however decoy 1 failed to recover sp1, cdc27 and fbxw7 expression. these data support that the sequence-specific decoy oligonucleotides might represent exogenous competing rna which selectively inhibits microrna targeting.",1
"insulin-like growth factor 2 (igf2), a developmentally regulated and maternally imprinted gene, is frequently overexpressed in pediatric cancers. although loss of imprinting (loi) at fetal promoters contributes to increased igf2 in tumors, the magnitude of igf2 expression suggests the involvement of additional regulatory mechanisms. a microrna (mirna) screen of primary wilms' tumors identified specific overexpression of mir-483-5p, which is embedded within the igf2 gene. unexpectedly, the igf2 mrna itself is transcriptionally up-regulated by mir-483-5p. a nuclear pool of mir-483-5p binds directly to the 5' untranslated region (utr) of fetal igf2 mrna, enhancing the association of the rna helicase dhx9 to the igf2 transcript and promoting igf2 transcription. ectopic expression of mir-483-5p in igf2-dependent sarcoma cells is correlated with increased tumorigenesis in vivo. together, these observations suggest a functional positive feedback loop of an intronic mirna on transcription of its host gene.",1
"background/aims this study aimed to investigate the microrna (mirna) expression profiles in peripheral blood mononuclear cell (pbmc) of hepatitis b virus (hbv)-infected patients with different clinical manifestations and to analyze the function of mir-197. methods pbmc mirna expression profiles in 51 healthy controls, 70 chronic asymptomatic carriers, 107 chronic hepatitis b patients, and 76 hbv-related acute on chronic liver failure patients were analyzed by quantitative real-time polymerase chain reaction (qrt-pcr). mir-197 mimic and inhibitor were transfected in thp-1 cells. qrt-pcr and elisa for interleukin (il)-18 mrna and protein levels were performed, respectively. results the microarray analysis revealed that 17 pbmc mirna expression profiles (12 mirnas downregulated and five mirnas upregulated) differed significantly in hbv-induced liver disease patients presenting with various symptoms. the qrt-pcr results suggested that the pbmc mir-197 levels regularly decreased as the severity of liver disease symptoms became aggravated. il-18, a key regulator in inflammation and immunity, was inversely correlated with mir-197 levels. bioinformatic analysis indicated that il-18 was a target of mir-197. exogenous expression of mir-197 could significantly repress il-18 expression at both the mrna and protein levels in thp-1 cells. conclusions we concluded that multiple pbmc mirnas had differential expression profiles during hbv infection and that mir-197 may play an important role in the reactivation of liver inflammation by targeting il-18.",1
"beta-site amyloid precursor protein cleaving enzyme 1 (bace1) is conceived as a potential target for therapies against alzheimer disease (ad). micrornas (mirnas) are small non-coding rnas that negatively regulate gene expression in a sequence-specific manner. although mirnas have been increasingly recognized as important modulators in sporadic ad. in order to confirm whether mir-15b correlates with the bace1 upregulation in sporadic ad, we firstly evaluated the expression of mir-15b and bace1 in sporadic ad brain tissues and analyzed the correlation of mir-15b with bace1. then we determined the regulation of mir-15b in sh-sy5y cells on the bace1 expression. and finally we determined the targeting to 3' utr of bace1 by mir-15b by a luciferase reporter. downregulation of mir-15b alleviated aβ-induced viability inhibition and decreased apoptosis in sh-sy5y cells. our results demonstrated that mir-15b play an important role in the cellular ad phenotype and might be involved in the pathogenesis of ad.",1
"peroxisome proliferator-activated receptor gamma (ppargamma) gained considerable interest as a therapeutic target during chronic inflammatory diseases. remarkably, the pathogenesis of diseases such as multiple sclerosis or alzheimer is associated with impaired ppargamma expression. considering that regulation of ppargamma expression during inflammation is largely unknown, we were interested in elucidating underlying mechanisms. to this end, we initiated an inflammatory response by exposing primary human macrophages to lipopolysaccharide (lps) and observed a rapid decline of ppargamma1 expression. because promoter activities were not affected by lps, we focused on mrna stability and noticed a decreased mrna half-life. as rna stability is often regulated via 3'-untranslated regions (utrs), we analyzed the impact of the ppargamma-3'-utr by reporter assays using specific constructs. lps significantly reduced luciferase activity of the pgl3-ppargamma-3'-utr, suggesting that ppargamma1 mrna is destabilized. deletion or mutation of a potential microrna-27a/b (mir-27a/b) binding site within the 3'-utr restored luciferase activity. moreover, inhibition of mir-27b, which was induced upon lps exposure, partially reversed ppargamma1 mrna decay, whereas mir-27b overexpression decreased ppargamma1 mrna content. in addition, lps further reduced this decay. the functional relevance of mir-27b-dependent ppargamma1 decrease was proven by inhibition or overexpression of mir-27b, which affected lps-induced expression of the pro-inflammatory cytokines tumor necrosis factor alpha (tnfalpha) and interleukin (il)-6. we provide evidence that lps-induced mir-27b contributes to destabilization of ppargamma1 mrna. understanding molecular mechanisms decreasing ppargamma might help to better appreciate inflammatory diseases.",1
"acute cellular rejection (acr) is the adverse response of the recipient's immune system against the allogeneic graft. using human surveillance endomyocardial biopsies (embs) manifesting acr and murine allogeneic grafts, we profiled implicated micrornas (mirs) and mrnas. mir profiling showed that mir-21, -142-3p, -142-5p, -146a, -146b, -155, -222, -223, and -494 increased during acr in humans and mice, whereas mir-149-5p decreased. mrna profiling revealed 70 common differentially regulated transcripts, all involved in immune signaling and immune-related diseases. interestingly, 33 of 70 transcripts function downstream of il-6 and its transcription factor spleen focus forming virus proviral integration oncogene (spi1), an established target of mir-155, the most upregulated mir in human embs manifesting rejection. in a mouse model of cardiac transplantation, mir-155 absence and pharmacological inhibition attenuated acr, demonstrating the causal involvement and therapeutic potential of mirs. finally, we corroborated our mir signature in acute cellular renal allograft rejection, suggesting a nonorgan specific signature of acute rejection. we concluded that mir and mrna profiling in human and murine acr revealed the shared significant dysregulation of immune genes. inflammatory mirs, for example mir-155, and transcripts, in particular those related to the il-6 pathway, are promising therapeutic targets to prevent acute allograft rejection.",1
"many studies are uncovering functional roles for long noncoding rnas (lncrnas), yet few have been tested for in vivo relevance through genetic ablation in animal models. to investigate the functional relevance of lncrnas in various physiological conditions, we have developed a collection of 18 lncrna knockout strains in which the locus is maintained transcriptionally active. initial characterization revealed peri- and postnatal lethal phenotypes in three mutant strains (fendrr, peril, and mdgt), the latter two exhibiting incomplete penetrance and growth defects in survivors. we also report growth defects for two additional mutant strains (linc-brn1b and linc-pint). further analysis revealed defects in lung, gastrointestinal tract, and heart in fendrr(-/-) neonates, whereas linc-brn1b(-/-) mutants displayed distinct abnormalities in the generation of upper layer ii-iv neurons in the neocortex. this study demonstrates that lncrnas play critical roles in vivo and provides a framework and impetus for future larger-scale functional investigation into the roles of lncrna molecules. doi:",1
"gene dosage effects of amyloid precursor protein (app) can cause familial ad. recent evidence suggest that microrna (mirna) pathways, implicated in gene transcriptional control, could be involved in the development of sporadic alzheimer's disease (ad). we therefore investigated whether mirnas could participate in the regulation of app gene expression. we show that mirnas belonging to the mir-20a family (that is, mir-20a, mir-17-5p and mir-106b) could regulate app expression in vitro and at the endogenous level in neuronal cell lines. a tight correlation between these mirnas and app was found during brain development and in differentiating neurons. we thus identify mirnas as novel endogenous regulators of app expression, suggesting that variations in mirna expression could contribute to changes in app expression in the brain during development and disease. this possibility is further corroborated by the observation that a statistically significant decrease in mir-106b expression was found in sporadic ad patients.",1
"longevity is influenced by genetic and environmental factors, but the underlying mechanisms remain elusive. here, we functionally characterise a drosophila small nucleolar rna (snorna), named jouvence whose loss of function reduces lifespan. the genomic region of jouvence rescues the longevity in mutant, while its overexpression in wild-type increases lifespan. jouvence is required in enterocytes. in mutant, the epithelium of the gut presents more hyperplasia, while the overexpression of jouvence prevents it. molecularly, the mutant lack pseudouridylation on 18s and 28s-rrna, a function rescued by targeted expression of jouvence in the gut. a transcriptomic analysis performed from the gut reveals that several genes are either up- or down-regulated, while restoring the mrna level of two genes (ninad or cg6296) rescue the longevity. since snornas are structurally and functionally well conserved throughout evolution, we identified putative jouvence orthologue in mammals including humans, suggesting that its function in longevity could be conserved.",1
"regulation of mitochondrial dna (mtdna) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. we have previously shown that mitochondrial transcription termination factor 3 (mterf3) is a key regulator that represses mtdna transcription in the mouse, but its molecular mode of action has remained elusive. based on the hypothesis that key regulatory mechanisms for mtdna expression are conserved in metazoans, we analyzed mterf3 knockout and knockdown flies. we demonstrate here that decreased expression of mterf3 not only leads to activation of mtdna transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. this novel function of mterf3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for mterf3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtdna gene expression.",1
"purpose we sought to determine the role and retinal cellular location of microrna-124 (mir-124) in a neuroinflammatory model of retinal degeneration. further, we explored the anti-inflammatory relationship of mir-124 with a predicted messenger rna (mrna) binding partner, chemokine (c-c motif) ligand 2 (ccl2), which is crucially involved in inflammatory cell recruitment in the damaged retina. methods human amd donor eyes and photo-oxidative damaged (pd) mice were labeled for mir-124 expression using in situ hybridization. pdgfra-cre rfp mice were used for müller cell isolation from whole retinas. mio-m1 immortalized cells and rat primary müller cells were used for in vitro analysis of mir-124 expression and its relationship with ccl2. therapeutic efficacy was tested with intravitreal administration of mir-124 mimic in mice, with electroretinography used to determine retinal function. iba1 immunohistochemistry and photoreceptor row counts were used for assessment of inflammation and cell death. results mir-124 expression was correlated with progressive retinal damage, inflammation, and cell death in human amd and pd mice. in addition, mir-124 expression was inversely correlated to ccl2 expression in mice following pd. mir-124 was localized to both neuronal-like photoreceptors and glial (müller) cells in the retina, with a redistribution from neurons to glia occurring as a consequence of pd. finally, intravitreal administration of mir-124 mimics decreased retinal inflammation and photoreceptor cell death, and improved retinal function. conclusions this study has provided an understanding of the mechanism behind mir-124 in the degenerating retina and demonstrates the usefulness of mir-124 mimics for the modulation of retinal degenerations.",1
"micrornas (mirnas) are small non-coding rnas that participate in the spatiotemporal regulation of messenger rna and protein synthesis. aberrant mirna expression leads to developmental abnormalities and diseases, such as cardiovascular disorders and cancer; however, the stimuli and processes regulating mirna biogenesis are largely unknown. the transforming growth factor beta (tgf-beta) and bone morphogenetic protein (bmp) family of growth factors orchestrates fundamental biological processes in development and in the homeostasis of adult tissues, including the vasculature. here we show that induction of a contractile phenotype in human vascular smooth muscle cells by tgf-beta and bmps is mediated by mir-21. mir-21 downregulates pdcd4 (programmed cell death 4), which in turn acts as a negative regulator of smooth muscle contractile genes. surprisingly, tgf-beta and bmp signalling promotes a rapid increase in expression of mature mir-21 through a post-transcriptional step, promoting the processing of primary transcripts of mir-21 (pri-mir-21) into precursor mir-21 (pre-mir-21) by the drosha (also known as rnasen) complex. tgf-beta- and bmp-specific smad signal transducers are recruited to pri-mir-21 in a complex with the rna helicase p68 (also known as ddx5), a component of the drosha microprocessor complex. the shared cofactor smad4 is not required for this process. thus, regulation of mirna biogenesis by ligand-specific smad proteins is critical for control of the vascular smooth muscle cell phenotype and potentially for smad4-independent responses mediated by the tgf-beta and bmp signalling pathways.",1
"micrornas (mirnas) are approximately 22-nucleotide endogenous rnas that often repress the expression of complementary messenger rnas. in animals, mirnas derive from characteristic hairpins in primary transcripts through two sequential rnase iii-mediated cleavages; drosha cleaves near the base of the stem to liberate a approximately 60-nucleotide pre-mirna hairpin, then dicer cleaves near the loop to generate a mirna:mirna* duplex. from that duplex, the mature mirna is incorporated into the silencing complex. here we identify an alternative pathway for mirna biogenesis, in which certain debranched introns mimic the structural features of pre-mirnas to enter the mirna-processing pathway without drosha-mediated cleavage. we call these pre-mirnas/introns 'mirtrons', and have identified 14 mirtrons in drosophila melanogaster and another four in caenorhabditis elegans (including the reclassification of mir-62). some of these have been selectively maintained during evolution with patterns of sequence conservation suggesting important regulatory functions in the animal. the abundance of introns comparable in size to pre-mirnas appears to have created a context favourable for the emergence of mirtrons in flies and nematodes. this suggests that other lineages with many similarly sized introns probably also have mirtrons, and that the mirtron pathway could have provided an early avenue for the emergence of mirnas before the advent of drosha.",1
"micrornas (mirnas) are small non-coding rnas that participate in a large variety of biological processes. in this paper, the spatiotemporal expression pattern of mir-370 was characterized during mouse embryonic development, and was found to be stage- and tissue-specifically expressed. in addition, through luciferase reporter assays and western blot analyses, dna methyltransferase 3a (dnmt3a) was identified as a directly regulated target of mir-370. altogether, our results indicate that mir-370 may play important roles in the morphogenesis of diverse organs, especially brain and adrenal glands, by mediating dnmt3a expression during mouse development.",1
"background & aims the function of microrna (mirna) in liver development is unknown. to address this issue, we characterized mirna expression in the embryonic mouse liver, performed functional mirna analysis in zebrafish larvae, and identified novel hepatic mirna targets. methods hepatic rna isolated from mice at embryonic days 15.5, 18.5, and postnatal day 2 was hybridized to a mouse mirna microarray. the microarray results were confirmed by northern blot hybridization and quantitative reverse-transcription polymerase chain reaction. the spatial distribution of selected mirnas was determined by in situ hybridization. functional analysis of mir-30a was performed in zebrafish using antisense-mediated mirna knockdown. targets of mir-30a were identified by microarray analysis of gene expression following knockdown in cultured cells. results a set of 38 differentially expressed fetal hepatic mirnas was identified. several of these mirnas were found to exhibit distinct temporal and spatial patterns of expression in hepatocytes, cholangiocytes, and nonepithelial cells within the liver. two (mir-30a and mir-30c) are the first examples of ductal plate and bile duct-specific hepatic mirnas. knockdown of mir-30a in the zebrafish larva results in defective biliary morphogenesis. several newly identified targets of mir-30a are known regulators of liver development and function. conclusions we have identified mirnas whose spatial and temporal patterns of expression are suggestive of functional roles in hepatic development and/or function. one of these, the biliary mirna mir-30a, is required for biliary development in zebrafish. this is the first demonstration of a functional role for mirna in hepatic organogenesis.",1
"purpose wilms' tumor is a childhood cancer of the kidney with an incidence of approximately 1 in 10,000. cooccurrence of wilms' tumor with 2q37 deletion syndrome, an uncommon constitutional chromosome abnormality, has been reported previously in three children. given these are independently rare clinical entities, we hypothesized that 2q37 harbors a tumor suppressor gene important in wilms' tumor pathogenesis. experimental design to test this, we performed loss of heterozygosity analysis in a panel of 226 sporadic wilms' tumor samples and mutation analysis of candidate genes. results loss of heterozygosity was present in at least 4% of cases. two tumors harbored homozygous deletions at 2q37.1, supporting the presence of a tumor suppressor gene that follows a classic two-hit model. however, no other evidence of second mutations was found, suggesting that heterozygous deletion alone may be sufficient to promote tumorigenesis in concert with other genomic abnormalities. we show that mir-562, a microrna within the candidate region, is expressed only in kidney and colon and regulates eya1, a critical gene for renal development. mir-562 expression is reduced in wilms' tumor and may contribute to tumorigenesis by deregulating eya1. two other candidate regions were localized at 2q37.3 and 2qter, but available data from patients with constitutional deletions suggest that these probably do not confer a high risk for wilms' tumor. conclusions our data support the presence of a tumor suppressor gene at 2q37.1 and suggest that, in individuals with constitutional 2q37 deletions, any increased risk for developing wilms' tumor likely correlates with deletions encompassing 2q37.1.",1
"somatic reprogramming induced by defined transcription factors is a low-efficiency process that is enhanced by p53 deficiency. so far, p21 is the only p53 target shown to contribute to p53 repression of ipsc (induced pluripotent stem cell) generation, indicating that additional p53 targets may regulate this process. here, we demonstrate that mir-34 micrornas (mirnas), particularly mir-34a, exhibit p53-dependent induction during reprogramming. mir34a deficiency in mice significantly increased reprogramming efficiency and kinetics, with mir-34a and p21 cooperatively regulating somatic reprogramming downstream of p53. unlike p53 deficiency, which enhances reprogramming at the expense of ipsc pluripotency, genetic ablation of mir34a promoted ipsc generation without compromising self-renewal or differentiation. suppression of reprogramming by mir-34a was due, at least in part, to repression of pluripotency genes, including nanog, sox2 and mycn (also known as n-myc). this post-transcriptional gene repression by mir-34a also regulated ipsc differentiation kinetics. mir-34b and c similarly repressed reprogramming; and all three mir-34 mirnas acted cooperatively in this process. taken together, our findings identified mir-34 mirnas as p53 targets that play an essential role in restraining somatic reprogramming.",1
"alteration of gene expression tightly regulates lipogenesis. stearoyl-coa desaturase-1 (scd-1), a key enzyme in lipogenesis, catalyzes the conversion of sfa to mufa, and inhibition of its activity impairs lipid synthesis. as posttranscriptional regulators, micrornas are involved in many pathways of lipid metabolism; however, their effect on scd-1 has not been reported. in this study, mir-125b was identified as a potential regulator of scd-1 using bioinformatics analysis. here, we validated scd-1 as the target of mir-125b using a dual luciferase assay. during adipogenesis, a synthetic mimic or inhibitor was used to overexpress or reduce the expression of mir-125b in porcine adipocytes. overexpression of mir-125b reduced the accumulation of lipid droplets and triglycerides concentration and repressed scd-1 protein expression and mufa composition. the inhibitor had the reverse effect. small interfering rna against tested in adipocytes further proved the direct correlation between mir-125b and scd-1. moreover, in vivo experiments in mice showed that injection of mir-125b expression vector decreased the hepatic triglycerides concentration relative to saline. this study indicated that mir-125b regulates lipogenesis by targeting scd-1; therefore, mir-125b might be applied in therapy of lipid metabolism disorders.",1
"objectives micrornas are potent regulators of gene expression and may serve as disease markers. this study aimed to identify the plasma microrna signature in hypertensive patients, which may help better understand the mechanisms underlying the pathogenesis of hypertension and target organ impairment. methods and results plasma samples from three independent cohorts were analyzed to identify circulating microrna candidates associated with hypertension in patients. the results revealed that the plasma level of hsa-mir-505, a previously reported tumor suppressive microrna, was significantly elevated in hypertensive patients. further studies were carried out in endothelial cells to elucidate the functional significance of the enhanced level of hsa-mir-505. the results showed that hsa-mir-505 expression markedly impaired the migration and tube formation of all three types of endothelial cells examined. moreover, gene expression analyses and luciferase reporter assay revealed that fgf18, a proangiogenic factor, is a target directly regulated by hsa-mir-505 in endothelial cells, which may in part underlie the function of hsa-mir-505 in angiogenic processes. conclusions our findings indicate that hsa-mir-505 is a novel circulating signature of hypertension, which may play a role in angiogenesis. our results provide mechanistic insights into hypertension-associated pathogenesis and point hsa-mir-505 as a potential target for intervention of hypertension.",1
"rationale myocardial infarction (mi) is a leading cause of death worldwide. because endogenous cardiac repair mechanisms are not sufficient for meaningful tissue regeneration, mi results in loss of cardiac tissue and detrimental remodeling events. micrornas (mirnas) are small, noncoding rnas that regulate gene expression in a sequence dependent manner. our previous data indicate that mirnas are dysregulated in response to ischemic injury of the heart and actively contribute to cardiac remodeling after mi. objective this study was designed to determine whether mirnas are dysregulated on ischemic damage in porcine cardiac tissues and whether locked nucleic acid (lna)-modified anti-mir chemistries can target cardiac expressed mirnas to therapeutically inhibit mir-15 on ischemic injury. methods and results our data indicate that the mir-15 family, which includes 6 closely related mirnas, is regulated in the infarcted region of the heart in response to ischemia-reperfusion injury in mice and pigs. lna-modified chemistries can effectively silence mir-15 family members in vitro and render cardiomyocytes resistant to hypoxia-induced cardiomyocyte cell death. correspondingly, systemic delivery of mir-15 anti-mirs dose-dependently represses mir-15 in cardiac tissue of both mice and pigs, whereas therapeutic targeting of mir-15 in mice reduces infarct size and cardiac remodeling and enhances cardiac function in response to mi. conclusions oligonucleotide-based therapies using lna-modified chemistries for modulating cardiac mirnas in the setting of heart disease are efficacious and validate mir-15 as a potential therapeutic target for the manipulation of cardiac remodeling and function in the setting of ischemic injury.",1
"long noncoding rnas (lncrnas) are emerging as important regulators of developmental pathways. however, their roles in human cardiac precursor cell (cpc) remain unexplored. to characterize the long noncoding transcriptome during human cpc cardiac differentiation, we profiled the lncrna transcriptome in cpcs isolated from the human fetal heart and identified 570 lncrnas that were modulated during cardiac differentiation. many of these were associated with active cardiac enhancer and super enhancers (se) with their expression being correlated with proximal cardiac genes. one of the most upregulated lncrnas was a se-associated lncrna that was named carmen, (car)diac (m)esoderm (e)nhancer-associated (n)oncoding rna. carmen exhibits rna-dependent enhancing activity and is upstream of the cardiac mesoderm-specifying gene regulatory network. interestingly, carmen interacts with suz12 and ezh2, two components of the polycomb repressive complex 2 (prc2). we demonstrate that carmen knockdown inhibits cardiac specification and differentiation in cardiac precursor cells independently of mir-143 and -145 expression, two micrornas located proximal to the enhancer sequences. importantly, carmen expression was activated during pathological remodeling in the mouse and human hearts, and was necessary for maintaining cardiac identity in differentiated cardiomyocytes. this study demonstrates therefore that carmen is a crucial regulator of cardiac cell differentiation and homeostasis.",1
"age-related macular degeneration (amd), the leading cause of blindness in the elderly, is a complex disease that results from multiple genetic and environmental factors. micrornas (mirnas) are small noncoding rnas that post-transcriptionally regulate target mrnas and are frequently implicated in human diseases. here, we investigated the association of genetic variants in mirnas and mirna-binding sites within gene 3'-untranslated regions (3'utrs) with amd using data from the largest amd genome-wide association study. first, we identified three variants in mirnas significantly associated with amd. these include rs2168518:g>a in the mir-4513 seed sequence, rs41292412:c>t in pre-mir-122/mir-3591, and rs4351242:c>t in the terminal-loop of pre-mir-3135b. we demonstrated that these variants reduce expression levels of the mature mirnas in vitro and pointed the target genes that may mediate downstream effects of these mirnas in amd. second, we identified 54 variants (in 31 genes) in mirna-binding sites associated with amd. based on stringent prioritization criteria, we highlighted the variants that are more likely to have an impact on the mirna-target interactions. further, we selected rs4151672:c>t within the cfb 3'utr and experimentally showed that while mir-210-5p downregulates expression of cfb, the variant decreases mir-210-5p-mediated repression of cfb. together, our findings support the notion that mirnas may play a role in amd.",1
"in this study, to search for novel preeclampsia (pe) biomarkers, we focused on microrna expression and function in the human placenta complicated with pe. by comprehensive analyses of microrna expression, we identified 22 micrornas significantly upregulated in preeclamptic placentas, 5 of which were predicted in silico to commonly target the mrna encoding hydroxysteroid (17-β) dehydrogenase 1 (hsd17b1), a steroidogenetic enzyme expressed predominantly in the placenta. in vivo hsd17b1 expression, at both the mrna and protein levels, was significantly decreased in preeclamptic placentas. of these micrornas, mir-210 and mir-518c were experimentally validated to target hsd17b1 by luciferase assay, real-time pcr, and elisa. furthermore, we found that plasma hsd17b1 protein levels in preeclamptic pregnant women reflected the decrease of its placental expression. moreover, a prospective cohort study of plasma hsd17b1 revealed a significant reduction of plasma hsd17b1 levels in pregnant women at 20 to 23 and 27 to 30 weeks of gestation before pe onset compared with those with normal pregnancies. the sensitivities/specificities for predicting pe at 20 to 23 and 27 to 30 weeks of gestation were 0.75/0.67 (cutoff value=21.9 ng/ml) and 0.88/0.51 (cutoff value=30.5 ng/ml), and the odds ratios were 6.09 (95% ci: 2.35-15.77) and 7.83 (95% ci: 1.70-36.14), respectively. we conclude that hsd17b1 is dysregulated by mir-210 and mir-518c that are aberrantly expressed in preeclamptic placenta and that reducing plasma level of hsd17b1 precedes the onset of pe and is a potential prognostic factor for pe.",1
"the epstein-barr virus (ebv) is an oncogenic human herpes virus involved in the pathogenesis of nasal nk/t-cell lymphoma. ebv encodes micrornas (mirnas) and induces changes in the host cellular mirna profile. mirnas are short non-coding rnas of about 19-25 nt length that regulate gene expression by post-transcriptional mechanisms and are frequently deregulated in human malignancies including cancer. the microrna profiles of ebv-positive nk/t-cell lymphoma, non-infected t-cell lymphoma and normal thymus were established by deep sequencing of small rna libraries. the comparison of the ebv-positive nk/t-cell vs. ebv-negative t-cell lymphoma revealed 15 up- und 16 down-regulated mirnas. in contrast, the majority of mirnas was repressed in the lymphomas compared to normal tissue. we also identified 10 novel mirnas from known precursors and two so far unknown mirnas. the sequencing results were confirmed for selected mirnas by quantitative real-time pcr (qrt-pcr). we show that the proinflammatory cytokine interleukin 1 alpha (il1a) is a target for mir-142-3p and the oncogenic bcl6 for mir-205. mir-142-3p is down-regulated in the ebv-positive vs. ebv-negative lymphomas. mir-205 was undetectable in ebv-negative lymphoma and strongly down-regulated in ebv-positive nk/t-cell lymphoma as compared to thymus. the targets were confirmed by reporter assays and by down-regulation of the proteins by ectopic expression of the cognate mirnas. taken together, our findings demonstrate the relevance of deregulated mirnas for the post-transcriptional gene regulation in nasal nk/t-cell lymphomas.",1
"genistein has been shown to inhibit cancers both in vitro and in vivo, by altering the expression of several micrornas (mirnas). in this study, we focused on tumor suppressor mirnas regulated by genistein and investigated their function in prostate cancer (pca) and target pathways. using mirna microarray analysis and real-time rt-pcr we observed that mir-574-3p was significantly up-regulated in pca cells treated with genistein compared with vehicle control. the expression of mir-574-3p was significantly lower in pca cell lines and clinical pca tissues compared with normal prostate cells (rwpe-1) and adjacent normal tissues. low expression level of mir-574-3p was correlated with advanced tumor stage and higher gleason score in pca specimens. re-expression of mir-574-3p in pca cells significantly inhibited cell proliferation, migration and invasion in vitro and in vivo. mir-574-3p restoration induced apoptosis through reducing bcl-xl and activating caspase-9 and caspase-3. using genecodis software analysis, several pathways affected by mir-574-3p were identified, such as 'pathways in cancer', 'jak-stat signaling pathway', and 'wnt signaling pathway'. luciferase reporter assays demonstrated that mir-574-3p directly binds to the 3' utr of several target genes (such as rac1, egfr and ep300) that are components of 'pathways in cancer'. quantitative real-time pcr and western analysis showed that the mrna and protein expression levels of the three target genes in pca cells were markedly down-regulated with mir-574-3p. loss-of-function studies demonstrated that the three target genes significantly affect cell proliferation, migration and invasion in pca cell lines. our results show that genistein up-regulates tumor suppressor mir-574-3p expression targeting several cell signaling pathways. these findings enhance understanding of how genistein regulates with mirna in pca.",1
"arsenic trioxide (as2o3) has been widely used in the treatment of acute promyelocytic leukemia and has been observed to exhibit therapeutic effects in various types of solid tumor. in a previous study by this group, it was shown that as2o3 induces the apoptosis of mcf-7 breast cancer cells through inhibition of the human ether-à-go-go-related gene (herg) channel. the present study was designed to further investigate the effect of as2o3 on breast cancer cells and to examine the mechanism underlying the regulation of herg expression. the present study confirmed that as2o3 inhibited tumor growth in vivo, following mcf-7 cell implantation into nude mice. using computational prediction , it was identified that microrna (mir)-328 had a binding site in the 3'-untranslated region of herg mrna. a luciferase activity assay demonstrated that herg is a target gene of mir-328. further investigation using western blot analysis and reverse transcription-quantitative polymerase chain reaction revealed that as2o3 downregulated herg expression via upregulation of mir-328 expression in mcf-7 cells. in conclusion, as2o3 was observed to inhibit breast cancer cell growth, at least in part, through the mir-328/herg pathway.",1
"micrornas are well known to mediate translational repression and mrna degradation in the cytoplasm. various micrornas have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. here, we report that mir-1, a microrna specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. we show that this positive effect requires specific mir:mrna base-pairing and ago2, but not its functional partner gw182, which is excluded from the mitochondria. we provide evidence for the direct action of ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (clip-seq), functional rescue with mitochondria-targeted ago2, and selective inhibition of the microrna machinery in the cytoplasm. these findings unveil a positive function of microrna in mitochondrial translation and suggest a highly coordinated myogenic program via mir-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.",1
"increasing evidence has suggested that dysregulation of certain micrornas (mirnas) may contribute to tumorigenesis. microrna-125b (mir-125b) was implicated to have close relationship with cell proliferation and differentiation, and downregulation of mir-125b was observed in various types of cancers. however, the biological function of mir-125b in bladder tumorigenesis is still unknown. in our study, we showed that the expression of mir-125b was significantly decreased in bladder cancer tissues and four bladder cancer cell lines. moreover, mir-125b could suppress bladder cancer cells to form colonies in vitro and to develop tumors in nude mice. e2f3, which was critical for g1/s transition and was overexpressed in most of poor-differentiated bladder cancers, was identified as a target of mir-125b by luciferase assay. the e2f3 mrna and protein expression levels were detected in bladder cancer tissues and cell lines, and interestingly, inverse correlations between mir-125b and e2f3 protein level were found in bladder cancer tissues and four e2f3 nonamplified cell lines. introduction of mir-125b could reduce the expression of e2f3 protein but not the e2f3 mrna. in addition, we observed that transfection of mir-125b could inhibit the expression of cyclin a2, one of the e2fs-responsive genes involved in g1/s transition. these results suggest that mir-125b may regulate g1/s transition through the e2f3-cyclin a2 signaling pathway. taken together, mir-125b may act as a tumor suppressor in bladder urothelium, and downregulation of mir-125b may contribute to the tumorigenesis of bladder cancer.",1
"analysis of global microrna (mirna) expression in postmortem cortical grey matter from the superior temporal gyrus, revealed significant up-regulation of mir-181b expression in schizophrenia. this finding was supported by quantitative real-time rt-pcr analysis of mirna expression in a cohort of 21 matched pairs of schizophrenia and non-psychiatric controls. the implications of this finding are substantial, as this mirna is predicted to regulate many target genes with potential significance to the development of schizophrenia. they include the calcium sensor gene visinin-like 1 (vsnl1) and the ionotropic ampa glutamate receptor subunit (gria2), which were found to be down-regulated in the same cortical tissue from the schizophrenia group. both of these genes were also suppressed in mir-181b transfected cells and shown to contain functional mir-181b mirna recognition elements by reporter gene assay. this study suggests altered mirna levels could be a significant factor in the dysregulation of cortical gene expression in schizophrenia.",1
"micrornas (mirnas) have critical roles in regulating cancer cell survival, proliferation and sensitivity to chemotherapy. the potential application of using mirnas to predict chemotherapeutic response to cancer treatment is highly promising. however, the underlying mechanisms of chemotherapy response control by mirnas remain to be fully identified and their prognostic value has not been fully evaluated. here we show a strong correlation between mir-205 expression and chemosensitivtiy to tac (docetaxol, doxorubicin plus cyclophosphamide), a widely-used neoadjuvant chemotherapy (nac) regimen, for breast cancer patients. high level of mir-205 predicted better response to tac regimen nac in breast cancer patients. we found mir-205 downregulated in both mcf-7/a02 and caldox cells, two drug-resistant derivatives of mcf-7 and cal51 cells, and its ectopic expression led to an increase in apoptosis resensitization of both drug-resistant cell lines to doxorubicin and taxol. we further show that mir-205 directly binds vegfa and fgf2 mrna 3'-utrs and confirm that mir-205 levels are negatively correlated with vegfa and fgf2 mrna expression in breast cancer patients. adding vegfa and fgf2 exogenously to chemosensitive breast cancer cells and chemoresistant cells with mir-205 overexpression led to drug resistance. consistently, low vegfa and fgf2 expression correlated with better response to nac in breast cancer patients. in addition, inhibition of tumor growth and resensitization to doxorubicin were also observed in mouse tumor xenografts from cells overexpressing mir-205. taken together, our data suggest that mir-205 enhances chemosensitivity of breast cancer cells to tac chemotherapy by suppressing both vegfa and fgf2, leading to evasion of apoptosis. mir-205 may serve as a predictive biomarker and a potential therapeutic target in breast cancer treatment.",1
"mouse embryonic stem (es) cells express a unique set of micrornas (mirnas), the mir-290-295 cluster. to elucidate the role of these mirnas and how they integrate into the es cell regulatory network requires identification of their direct regulatory targets. the difficulty, however, arises from the limited complementarity of metazoan mirnas to their targets, with the interaction requiring as few as six nucleotides of the mirna seed sequence. to identify mir-294 targets, we used dicer1-null es cells, which lack all endogenous mature mirnas, and introduced just mir-294 into these es cells. we then employed two approaches to discover mir-294 targets in mouse es cells: transcriptome profiling using microarrays and a biochemical approach to isolate mrna targets associated with the argonaute2 (ago2) protein of the risc (rna induced silencing complex) effector, followed by rna-sequencing. in the absence of dicer1, the risc complexes are largely devoid of mature mirnas and should therefore contain only transfected mir-294 and its base-paired targets. our data suggest that mir-294 may promote pluripotency by regulating a subset of c-myc target genes and upregulating pluripotency-associated genes such as lin28.",1
"introduction deep venous thrombosis (dvt) is one of the common peripheral vascular diseases. the recruitment and migration of bone marrow-derived endothelial progenitor cells (epcs) to the sites of venous thrombus are necessary in the process of thrombus organization and recanalization. our objective was to investigate the functional role of mir-150 in rat epcs and its potential application in deep venous thrombosis. materials and methods rat epcs were cultured and transfected with mir-150 mimics and inhibitor. wound healing assay, transwell migration assay and matrigel tube formation assay were performed to elucidate the effect of mir-150 of rat epcs. lentiviral construct expressing mir-150 was transfected into epcs and the epcs were injected to rat models of dvt. the rats were sacrificed on the day of 7 and 14 after the transplantation and the histological study was performed. luciferase reporter assay and western blot were performed to evaluate rat mir-150 regulates the expression of c-myb. results mir-150 significantly promoted the migration and tube formation ability of epcs in vitro and enhanced epcs' homing, organization and resolution ability in vivo. overexpression of mir-150 significantly reduced the protein level of c-myb and repressed the activity of a luciferase reporter containing both of the two predicted mir-150 binding sites in c-myb 3'-utr, indicating that c-myb may be a mir-150 target gene. conclusion mir-150 enhanced the migration, tube formation, homing, thrombus recanalization and resolution ability of rat epcs. restoring mir-150 in epcs revealed potential application in dvt therapy.",1
"cutaneous melanoma is an aggressive form of human skin cancer characterized by high metastatic potential and poor prognosis. to better understand the role of micrornas (mirnas) in melanoma, the expression of 470 mirnas was profiled in tissue samples from benign nevi and metastatic melanomas. we identified 31 mirnas that were differentially expressed (13 up-regulated and 18 down-regulated) in metastatic melanomas relative to benign nevi. notably, mir-193b was significantly down-regulated in the melanoma tissues examined. to understand the role of mir-193b in melanoma, functional studies were undertaken. overexpression of mir-193b in melanoma cell lines repressed cell proliferation. gene expression profiling identified 314 genes down-regulated by overexpression of mir-193b in malme-3m cells. eighteen of these down-regulated genes, including cyclin d1 (ccnd1), were also identified as putative mir-193b targets by targetscan. overexpression of mir-193b in malme-3m cells down-regulated ccnd1 mrna and protein by > or = 50%. a luciferase reporter assay confirmed that mir-193b directly regulates ccnd1 by binding to the 3'untranslated region of ccnd1 mrna. these studies indicate that mir-193b represses cell proliferation and regulates ccnd1 expression and suggest that dysregulation of mir-193b may play an important role in melanoma development.",1
"comparative sequence analyses of bacterial genomes are revealing many structured rna motifs that function as metabolite-binding riboswitches. we have identified an rna motif frequently positioned in the 5' utrs of folate transport and biosynthesis genes in firmicute genomes. biochemical experiments confirm that representatives of this new-found rna class selectively bind derivatives of the vitamin folate, including di- and tetrahydrofolate coenzymes. in addition, representatives of this aptamer class occasionally reside upstream of rna structures that are predicted to control translation initiation in response to ligand binding. these findings expand the number of coenzymes that are directly sensed by rna and reveal possible riboswitch-controlled regulons that respond to changes in single-carbon metabolism.",1
"the heart responds to diverse forms of stress by hypertrophic growth accompanied by fibrosis and eventual diminution of contractility, which results from down-regulation of alpha-myosin heavy chain (alphamhc) and up-regulation of betamhc, the primary contractile proteins of the heart. we found that a cardiac-specific microrna (mir-208) encoded by an intron of the alphamhc gene is required for cardiomyocyte hypertrophy, fibrosis, and expression of betamhc in response to stress and hypothyroidism. thus, the alphamhc gene, in addition to encoding a major cardiac contractile protein, regulates cardiac growth and gene expression in response to stress and hormonal signaling through mir-208.",1
"identifying the genetic mechanisms underlying phenotypic change is essential to understanding how gene regulatory networks and ultimately the genotype-to-phenotype map evolve. it is recognized that micrornas (mirnas) have the potential to facilitate evolutionary change ; however, there are no known examples of natural morphological variation caused by evolutionary changes in mirna expression. therefore, the contribution of mirnas to evolutionary change remains unknown . drosophila melanogaster subgroup species display a portion of trichome-free cuticle on the femur of the second leg called the ""naked valley."" it was previously shown that ultrabithorax (ubx) is involved in naked valley variation between d. melanogaster and d. simulans . however, naked valley size also varies among populations of d. melanogaster, ranging from 1,000 up to 30,000 μm(2). we investigated the genetic basis of intraspecific differences in the naked valley in d. melanogaster and found that neither ubx nor shavenbaby (svb) contributes to this morphological difference. instead, we show that changes in mir-92a expression underlie the evolution of naked valley size in d. melanogaster through repression of shavenoid (sha) . therefore, our results reveal a novel mechanism for morphological evolution and suggest that modulation of the expression of mirnas potentially plays a prominent role in generating organismal diversity.",1
"the exploration of the non-protein-coding rna (ncrna) transcriptome is currently focused on profiling of microrna expression and detection of novel ncrna transcription units. however, recent studies suggest that rna processing can be a multi-layer process leading to the generation of ncrnas of diverse functions from a single primary transcript. up to date no methodology has been presented to distinguish stable functional rna species from rapidly degraded side products of nucleases. thus the correct assessment of widespread rna processing events is one of the major obstacles in transcriptome research. here, we present a novel automated computational pipeline, named apart, providing a complete workflow for the reliable detection of rna processing products from next-generation-sequencing data. the major features include efficient handling of non-unique reads, detection of novel stable ncrna transcripts and processing products and annotation of known transcripts based on multiple sources of information. to disclose the potential of apart, we have analyzed a cdna library derived from small ribosome-associated rnas in saccharomyces cerevisiae. by employing the apart pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable rna molecules differentially processed from well known ncrnas, like rrnas, trnas or snornas, in a stress-dependent manner.",1
"steroid hormones and their nuclear receptors drive developmental transitions in diverse organisms, including mammals. in this study, we show that the drosophila steroid hormone 20-hydroxyecdysone (20e) and its nuclear receptor directly activate transcription of the evolutionarily conserved let-7-complex (let-7-c) locus, which encodes the co-transcribed micrornas mir-100, let-7 and mir-125. these small rnas post-transcriptionally regulate the expression of target genes, and are required for the remodeling of the drosophila neuromusculature during the larval-to-adult transition. deletion of three 20e responsive elements located in the let-7-c locus results in reduced levels of let-7-c micrornas, leading to neuromuscular and behavioral defects in adults. given the evolutionary conservation of let-7-c microrna sequences and temporal expression profiles, these findings indicate that steroid hormone-coupled control of let-7-c micrornas is part of an ancestral pathway controlling the transition from larval-to-reproductive animal forms.",1
"polycomb proteins play essential roles in stem cell renewal and human disease. recent studies of hox genes and x inactivation have provided evidence for rna cofactors in polycomb repressive complex 2 (prc2). here we develop a rip-seq method to capture the prc2 transcriptome and identify a genome-wide pool of >9000 prc2-interacting rnas in embryonic stem cells. the transcriptome includes antisense, intergenic, and promoter-associated transcripts, as well as many unannotated rnas. a large number of transcripts occur within imprinted regions, oncogene and tumor suppressor loci, and stem cell-related bivalent domains. we provide evidence for direct rna-protein interactions, most likely via the ezh2 subunit. we also identify gtl2 rna as a prc2 cofactor that directs prc2 to the reciprocally imprinted dlk1 coding gene. thus, polycomb proteins interact with a genome-wide family of rnas, some of which may be used as biomarkers and therapeutic targets for human disease.",1
"background combinatorial gene regulation by multiple micrornas (mirnas) is widespread and closely spaced target sites often act cooperatively to achieve stronger repression (""neighborhood"" mirna cotargeting). while mirna cotarget sites are suggested to be more conserved and implicated in developmental control, the pathological significance of mirna cotargeting remains elusive. results here, we report the pathogenic impacts of combinatorial mirna regulation on inflammation in systemic lupus erythematosus (sle). in the sle mouse model, we identified the downregulation of two mirnas, mir-128 and mir-148a, by tlr7 stimulation in plasmacytoid dendritic cells. functional analyses using human cell lines demonstrated that mir-128 and mir-148a additively target klf4 via extensively overlapping target sites (""seed overlap"" mirna cotargeting) and suppress the inflammatory responses. at the transcriptome level, ""seed overlap"" mirna cotargeting increases susceptibility to downregulation by two mirnas, consistent with additive but not cooperative recruitment of two mirnas. systematic characterization further revealed that extensive ""seed overlap"" is a prevalent feature among broadly conserved mirnas. highly conserved target sites of broadly conserved mirnas are largely divided into two classes-those conserved among eutherian mammals and from human to coelacanth, and the latter, including klf4-cotargeting sites, has a stronger association with both ""seed overlap"" and ""neighborhood"" mirna cotargeting. furthermore, a deeply conserved mirna target class has a higher probability of haplo-insufficient genes. conclusions our study collectively suggests the complexity of distinct modes of mirna cotargeting and the importance of their perturbations in human diseases.",1
"micrornas (mirnas) may represent new therapeutic targets for bone and joint diseases. we hypothesized that several cartilage-specific proteins are targeted by a single mirna and used bioinformatics to identify a mirna that can modulate extracellular matrix (ecm) homeostasis in cartilage. bioinformatic analysis of mirna binding sequences in the 3'-untranslated region (3'-utr) of target genes was performed to identify a mirna that could bind to the 3'-utr of cartilage matrix-related genes. mirna expression was studied by quantitative pcr of microdissected growth plate cartilage and binding to the 3'-utr sequences was analyzed by luciferase interaction studies. levels of proteins encoded by target genes in cultures of mir-26a mimic- or inhibitor-transfected chondrocytes were determined by facs or immunoblot analysis. the complementary binding sequence of mir-26a and mir-26b was found in the 3'-utr of the prehypertrophic/hypertrophic-specific genes cd200, col10a1 as well as col9a1 and ctgf. both mirnas were expressed in cartilage and only mir-26a was downregulated in hypertrophic growth plate cartilage. mir-26a could interact with the 3'-utr of cd200 and col10a1 in luciferase binding studies, but not with col9a1 and ctgf. however, protein expression of target genes and the ecm adaptor genes matrilin-3 and comp was significantly altered in mir-26a mimic- or inhibitor-transfected chondrocytes, whereas the abundance of the cell surface receptor for insulin was not changed. in conclusion, mir-26a suppresses hypertrophic and ecm adaptor protein production. dysregulation of mir-26a expression could contribute to ecm changes in cartilage diseases and this mirna may therefore act as a therapeutic target.",1
"micrornas (mirnas), which are noncoding rnas that regulate gene expression, are involved in tumor metastasis. in this study, we describe the down-regulation and function of mir-139 in colorectal cancer (crc) metastasis. mir-139 was found underexpressed in 34 crc tissues compared to their corresponding nontumor tissues. decreased mir-139 in crc tissue was associated with disease progression and metastasis. re-expression of mir-139 did not inhibit crc cell growth but suppresses crc cell metastasis and invasion in vitro and in vivo. mir-139 might suppress crc cells invasion and metastasis by targeting type i insulin-like growth factor receptor (igf-ir). we also found mir-139 directed migration inactivation of human crc cells involves down-regulation of matrix metalloproteinase 2 (mmp-2). the igf-ir/mek/erk signaling was inhibited by mir-139 overexpression and then resulted in mmp-2 promoter suppression. taken together, our results provide evidence that mir-139 might function as a metastasis suppressor in crc. targeting mir-139 may provide a strategy for blocking crc metastasis.",1
"background micrornas play important roles in the development and progression of various cancers. recent studies have shown that mir-638 was downregulated in several tumors; however, its role in gastric cancer (gc) has not been investigated in detail. aims the purpose of this study was to determine the role of mir-638 and to elucidate its regulatory mechanism in gc. methods the expression levels of mir-638 and specificity protein 2 (sp2) were detected by real-time pcr and western blotting in gc. after pcdna6.2-gw/emgfp-mir-638 vector, mir-638 inhibitor and sp2-sirna transfection, the ags cell proliferation was investigated by mtt assay and cell cycle, and apoptosis was detected using the annexin v/pi. in addition, the regulation of sp2 by mir-638 was evaluated by real-time rt-pcr, western blot and luciferase reporter assays; cyclin d1 expression was measured by western blotting. results the expression of mir-638 is dramatically down-regulated and sp2 expression is remarkably up-regulated in gc tissues. luciferase assays revealed that mir-638 inhibited sp2 expression by targeting the 3'-utr of sp2 mrna. overexpression of mir-638 and sp2-sirna reduced sp2 expression at both the mrna and protein levels in vitro, and inhibition of mir-638 increased sp2 expression. moreover, we found that mir-638 overexpression and sp2-sirna markedly suppressed cell proliferation with decreasing expression of cyclin d1 and inducing g1-phase cell-cycle arrest in vitro; inhibition of mir-638 significantly promoted cell proliferation by increasing expression of cyclin d1 and leading more cells into the s and g2/m phase. conclusions our results demonstrated that mir-638 suppressed gc cell proliferation by targeting sp2 with influence on the expression of cyclin d1. we suggest that mir-638 might be a candidate predictor or an anticancer therapeutic target for gc patients.",1
"micrornas (mirnas) regulate gene expression by repressing translation or directing sequence-specific degradation of complementary mrna. here, we report that expression of mir-205 is significantly suppressed in melanoma specimens when compared with nevi and is correlated inversely with melanoma progression. mirna target databases predicted e2f1 and e2f5 as putative targets. the expression levels of e2f1 and e2f5 were correlated inversely with that of mir-205 in melanoma cell lines. mir-205 significantly suppressed the luciferase activity of reporter plasmids containing the 3'-utr sequences complementary to either e2f1 or e2f5. overexpression of mir-205 in melanoma cells reduced e2f1 and e2f5 protein levels. the proliferative capacity of melanoma cells was suppressed by mir-205 and mediated by e2f-regulated akt phosphorylation. mir-205 overexpression resulted in induction of apoptosis, as evidenced by increased cleaved caspase-3, poly-(adp-ribose) polymerase, and cytochrome c release. stable overexpression of mir-205 suppressed melanoma cell proliferation, colony formation, and tumor cell growth in vivo and induced a senescence phenotype accompanied by elevated expression of p16ink4a and other markers for senescence. e2f1 overexpression in mir-205-expressing cells partially reversed the effects on melanoma cell growth and senescence. these results demonstrate a novel role for mir-205 as a tumor suppressor in melanoma.",1
"vascular injury triggers dedifferentiation and cytoskeletal remodeling of smooth muscle cells (smcs), culminating in vessel occlusion. serum response factor (srf) and its coactivator, myocardin, play a central role in the control of smooth muscle phenotypes by regulating the expression of cytoskeletal genes. we show that srf and myocardin regulate a cardiovascular-specific microrna (mirna) cluster encoding mir-143 and mir-145. to assess the functions of these mirnas in vivo, we systematically deleted them singly and in combination in mice. mice lacking both mir-143 and mir-145 are viable and do not display overt abnormalities in smooth muscle differentiation, although they show a significant reduction in blood pressure due to reduced vascular tone. remarkably, however, neointima formation in response to vascular injury is profoundly impeded in mice lacking these mirnas, due to disarray of actin stress fibers and diminished migratory activity of smcs. these abnormalities reflect the regulation of a cadre of modulators of srf activity and actin dynamics by mir-143 and mir-145. thus, mir-143 and mir-145 act as integral components of the regulatory network whereby srf controls cytoskeletal remodeling and phenotypic switching of smcs during vascular disease.",1
"the box h/aca rna gene family is one of the largest non-protein-coding gene families in eukaryotes and archaea. recently, we developed snogps, a computational screening program for h/aca snornas, and applied it to saccharomyces cerevisiae. we report here results of extending our method to screen for h/aca rnas in multiple large genomes of related species, and apply it to the human, mouse, and rat genomes. because of the 250-fold larger search space compared to s. cerevisiae, significant enhancements to our algorithms were required. complementing extensive cloning experiments performed by others, our findings include the detection and experimental verification of seven new mammalian h/aca rnas and the prediction of 23 new h/aca rna pseudouridine guide assignments. these assignments include four for h/aca rnas previously classified as orphan h/aca rnas with no known targets. we also determined systematic syntenic conservation among human and mouse h/aca rnas. with this work, 82 of 97 ribosomal rna pseudouridines and 18 of 32 spliceosomal rna pseudouridines in mammals have been linked to h/aca guide rnas.",1
"in the human brain, micrornas (mirnas) from the microrna-376 (mir-376) cluster undergo programmed ""seed"" sequence modifications by adenosine-to-inosine (a-to-i) editing. emerging evidence suggests a link between impaired a-to-i editing and cancer, particularly in high-grade gliomas. we hypothesized that disruption of a-to-i editing alters expression of genes regulating glioma tumor phenotypes. by sequencing the mir-376 cluster, we show that the overall mirna editing frequencies were reduced in human gliomas. specifically in high-grade gliomas, mir-376a* accumulated entirely in an unedited form. clinically, a significant correlation was found between accumulation of unedited mir-376a* and the extent of invasive tumor spread as measured by magnetic resonance imaging of patient brains. using both in vitro and orthotopic xenograft mouse models, we demonstrated that the unedited mir-376a* promoted glioma cell migration and invasion, while the edited mir-376a* suppressed these features. the effects of the unedited mir-376a* were mediated by its sequence-dependent ability to target rap2a and concomitant inability to target amfr. thus, the tumor-dependent introduction of a single base difference in the mir-376a* sequence dramatically alters the selection of its target genes and redirects its function from inhibiting to promoting glioma cell invasion. these findings uncover a new mechanism of mirna deregulation and identify unedited mir-376a* as a potential therapeutic target in glioblastoma cells.",1
"background aberrant microrna expression is implicated in cancer initiation and progression. we sought to identify dysregulated mirnas in conjunctival mucosa-associated lymphoid tissue (malt) lymphoma, and investigated their biological significance. methods the profiles of mirnas in conjunctival malt lymphoma and normal adjacent tissues were investigated by microrna microarray of four pairs of surgically removed conjunctival malt lymphoma tissues and matched controls. the results of microarray were further confirmed in 14 paired conjunctival malt lymphoma samples (including the former four pairs) using quantitative rt-pcr. the functional effect of mir-200 was examined further. a luciferase reporter assay was performed to confirm the predicted target. results the microarray results revealed upregulated mir-150/155, and downregulated mir-184, mir-200a, b, c, and mir-205. these findings were confirmed by quantitative rt-pcr. targetscan analysis suggested cyclin e2 as potential target of mir-200a, b, c. luciferase reporter assay using vectors containing the 3'utr of cyclin e2 showed that mir-200a, b, c could suppress luciferase activities. rt-pcr and immunoblotting studies revealed that overexpression of mir-200a, b, c reduced the mrna and protein levels of cyclin e2 respectively. conclusions we demonstrated that mirnas were dysregulated in conjunctival malt lymphoma, and dysregulation of the mir-200 family could be involved in the pathogenesis and progression of the disease.",1
"micrornas (mirnas) are noncoding small rnas that play important roles in a variety of physiological and pathological events. in this study, we performed large-scale profiling of eif2c2-bound mirnas in 3 human granulosa-derived cell lines (ie, kgn, hsogt, and gc1a) by high-throughput sequencing and found that mir-21 accounted for more than 80% of eif2c2-bound mirnas, suggesting that it was enriched in the rna-induced silencing complex (risc) and played a functional role in human granulosa cell (gc) lines. we also found high expression levels of mir-21 in primary human gcs. assuming that mir-21 target mrnas are enriched in risc, we performed cdna cloning of eif2c2-bound mrnas in kgn cells. we identified col4a1 mrna as a mir-21 target in the gc lines. these data suggest that mir-21 is involved in the regulation of the synthesis of col4a1, a component of the basement membrane surrounding the gc layer and granulosa-embedded extracellular structure.",1
"objective vascular precursor cells with angiogenic potentials are important for tissue repair, which is impaired in diabetes mellitus. micrornas are recently discovered key regulators of gene expression, but their role in vascular precursor cell-mediated angiogenesis in diabetes mellitus is unknown. we tested the hypothesis that the microrna mir-27b rescues impaired bone marrow-derived angiogenic cell (bmac) function in vitro and in vivo in type 2 diabetic mice. approach and results bmacs from adult male type 2 diabetic db/db and from normal littermate db/+ mice were used. mir-27b expression was decreased in db/db bmacs. mir-27b mimic improved db/db bmac function, including proliferation, adhesion, tube formation, and delayed apoptosis, but it did not affect migration. elevated thrombospondin-1 (tsp-1) protein in db/db bmacs was suppressed on mir-27b mimic transfection. inhibition of mir-27b in db/+ bmacs reduced angiogenesis, which was reversed by tsp-1 small interfering rna (sirna). mir-27b suppressed the pro-oxidant protein p66(shc) and mitochondrial oxidative stress, contributing to its protection of bmac function. mir-27b also suppressed semaphorin 6a to improve bmac function in diabetes mellitus. luciferase binding assay suggested that mir-27b directly targeted tsp-1, tsp-2, p66(shc), and semaphorin 6a. mir-27b improved topical cell therapy of diabetic bmacs on diabetic skin wound closure, with a concomitant augmentation of wound perfusion and capillary formation. normal bmac therapy with mir-27b inhibition demonstrated reduced efficacy in wound closure, perfusion, and capillary formation. local mir-27b delivery partly improved wound healing in diabetic mice. conclusions mir-27b rescues impaired bmac angiogenesis via tsp-1 suppression, semaphorin 6a expression, and p66shc-dependent mitochondrial oxidative stress and improves bmac therapy in wound healing in type 2 diabetic mice.",1
"glioblastoma multiforme (gbm) is one of the most deadly types of cancer. to date, the best clinical approach for treatment is based on administration of temozolomide (tmz) in combination with radiotherapy. much evidence suggests that the intracellular level of the alkylating enzyme o(6)-methylguanine-dna methyltransferase (mgmt) impacts response to tmz in gbm patients. mgmt expression is regulated by the methylation of its promoter. however, evidence indicates that this is not the only regulatory mechanism present. here, we describe a hitherto unknown microrna-mediated mechanism of mgmt expression regulation. we show that mir-221 and mir-222 are upregulated in gmb patients and that these paralogues target mgmt mrna, inducing greater tmz-mediated cell death. however, mir-221/mir-222 also increase dna damage and, thus, chromosomal rearrangements. indeed, mir-221 overexpression in glioma cells led to an increase in markers of dna damage, an effect rescued by re-expression of mgmt. thus, chronic mir-221/222-mediated mgmt downregulation may render cells unable to repair genetic damage. this, associated also to mir-221/222 oncogenic potential, may poor gbm prognosis.",1
"background signal transducer and activator of transcription 3 (stat3) activation is frequently found in human lung cancer and is associated with increased metastasis and reduced survival. how stat3 enhances invasiveness is unclear. methods the expression of micrornas and target genes was measured by real-time rt-pcr. protein level was studied by western blotting. luciferase reporter assay was used to confirm the direct targeting of micrornas. gelatin zymography was used to study matrix metalloproteinase (mmp) activity. transwell assay was used to investigate cell migration and invasion. results enforced expression of stat3 decreases the endogenous mmp inhibitor reck protein but not mrna level in h460 cells. conversely, stat3 inhibitor s3i-201 increases reck protein in stat3-activating h1299 cells. we demonstrate that stat3 upregulates mir-92a to repress reck via post-transcriptional inhibition. the reck 3'-untranslated region (3'utr) reporter activity assay suggests that reck is a direct repression target of mir-92a. delivery of pre-mir-92a reduces reck protein level whereas transfection of anti-mir-92a restores stat3-induced downregulation of reck. anti-mir-92a attenuates mmp activity, migration and invasion of h1299 cells and stat3-overexpressing h460 cells, suggesting mir-92a is critical for stat3-induced invasiveness. conclusion the stat3-induced mir-92a promotes cancer invasion by suppressing reck and targeting of the stat3/mir-92a axis may be helpful for cancer treatment.",1
"to remodel functional neuronal connectivity, neurons often alter dendrite arbors through elimination and subsequent regeneration of dendritic branches. however, the intrinsic mechanisms underlying this developmentally programmed dendrite regeneration and whether it shares common machinery with injury-induced regeneration remain largely unknown. drosophila class iv dendrite arborization (c4da) sensory neurons regenerate adult-specific dendrites after eliminating larval dendrites during metamorphosis. here we show that the microrna mir-87 is a critical regulator of dendrite regeneration in drosophila. mir-87 knockout impairs dendrite regeneration after developmentally-programmed pruning, whereas mir-87 overexpression in c4da neurons leads to precocious initiation of dendrite regeneration. genetic analyses indicate that the transcriptional repressor tramtrack69 (ttk69) is a functional target for mir-87-mediated repression as ttk69 expression is increased in mir-87 knockout neurons and reducing ttk69 expression restores dendrite regeneration to mutants lacking mir-87 function. we further show that mir-87 is required for dendrite regeneration after acute injury in the larval stage, providing a mechanistic link between developmentally programmed and injury-induced dendrite regeneration. these findings thus indicate that mir-87 promotes dendrite regrowth during regeneration at least in part through suppressing ttk69 in drosophila sensory neurons and suggest that developmental and injury-induced dendrite regeneration share a common intrinsic mechanism to reactivate dendrite growth.",1
"micrornas (mirnas) are genomically encoded small rnas that hybridize with messenger rnas, resulting in degradation or translational inhibition of targeted transcripts. the potential for mirnas to regulate cell-lineage determination or differentiation from pluripotent progenitor or stem cells is unknown. here, we show that microrna1 (mir-1) is an ancient muscle-specific gene conserved in sequence and expression in drosophila. drosophila mir-1 (dmir-1) is regulated through a serum response factor-like binding site in cardiac progenitor cells. loss- and gain-of-function studies demonstrated a role for dmir-1 in modulating cardiogenesis and in maintenance of muscle-gene expression. we provide in vivo evidence that dmir-1 targets transcripts encoding the notch ligand delta, providing a potential mechanism for the expansion of cardiac and muscle progenitor cells and failure of progenitor cell differentiation in some dmir-1 mutants. these findings demonstrate that dmir-1 may ""fine-tune"" critical steps involved in differentiation of cardiac and somatic muscle progenitors and targets a pathway required for progenitor cell specification and asymmetric cell division.",1
"previous studies have investigated the role of micrornas (mirs) in heart development to reveal the mirna mechanism of action in congenital heart disease (chd) in children. the present study aimed to investigate the role of mir‑1 in heart development in p19 cells. the mrna level for mir‑1 in p19 cells was detected before or after cardiomyocyte differentiation, using reverse transcription‑quantitative polymerase chain reaction analysis. expression of cardiomyocyte differentiation markers was also analyzed. the effect of mir‑1 overexpression on the viability and apoptosis of differentiated p19 cells was assessed using mtt and annexin v‑fitc assays, respectively. furthermore, the effects of mir-1 on expression of markers of cell proliferation and apoptosis were also analyzed in differentiated p19 cells using western blotting. the results demonstrated that p19 cells were successfully differentiated into cardiomyocytes, and that endogenous mir‑1 expression was significantly decreased in differentiated p19 cells compared with undifferentiated p19 cells. overexpression of mir‑1 resulted in increased viability in differentiated p19 cells and decreased apoptosis, compared with the normal control. in addition, expression of heart and neural crest derivatives expressed transcript 2 (hand2) was increased in differentiated cells with mir‑1 overexpressed compared with normal cells, while caspase‑3 cleavage was decreased by mir‑1 overexpression. in conclusion, the present study suggested that mir-1 upregulation may be important in regulating cell proliferation and apoptosis in p19 differentiated cardiomyocytes by increasing hand2 expression and suppressing caspase‑3 cleavage. the present study aimed to provide a theoretical basis for the explanation of the mechanism of chd and investigate mir‑1 as a potential therapeutic target for its clinical treatment.",1
"deposition of collagen iv in proximal tubule cells (ptcs) plays an important role during diabetic nephropathy, but the mechanism underlying excessive production of collagen iv remains poorly understood. in this study, we examined the mirna profile of hk-2 cells and found that high glucose/tgf-beta1 induced significant down-regulation of mir-29a. we then showed that mir-29a negatively regulated collagen iv by directly targeting the 3'utrs of col4a1 and col4a2. these results suggest that mir-29a acts as a repressor to fine-tune collagen expression and that the reduction of mir-29a caused by high glucose may increase the risk of excess collagen deposition in ptcs.",1
"one mechanism by which endogenous micrornas (mirnas) function is to suppress translation of target mrnas. computational identification of target mrnas is hampered by the partial complementarity between mirnas and their targets and the lack of in vivo approaches to identify targets. here, we identify mrnas that are regulated by specific endogenous mirna by detecting shifts in individual mrna abundance in polyribosome profiles following mirna knockdown via sirna. we have identified human genes whose mrnas were found at significantly increased levels in the heavy polyribosome fractions following mirna mir-30a-3p knockdown. if antibody was available, targets showed an increase in protein levels following the mirna knockdown and a decrease following the mirna overexpression. although all identified transcripts have sequences that partially complement mir-30a-3p, none was identified by commonly used computational means. these data suggest that the functional interaction between mirnas and mrna targets is more complex than previously realized and describe an approach to refine predictive algorithms.",1
"aims kv7.4, a voltage-dependent potassium channel expressed throughout the vasculature, controls arterial contraction and is compromised in hypertension by an unknown mechanism. micrornas (mirs) are post-transcriptional regulators of protein production and are altered in disease states such as hypertension. we investigated whether mirs regulate kv7.4 expression. methods and results in renal and mesenteric arteries (mas) of the spontaneously hypertensive rat (shr), kv7.4 protein decreased compared with the normotensive (nt) rat without a decrease in kcnq4 mrna, inferring that kv7.4 abundance was determined by post-transcriptional regulation. in silico analysis of the 3' utr of kcnq4 revealed seed sequences for mir26a, mir133a, mir200b, mir153, mir214, mir218, and let-7d with quantitative polymerase chain reaction showing mir153 increased in those arteries from shrs that exhibited decreased kv7.4 levels. luciferase reporter assays indicated a direct targeting effect of mir153 on the 3' utr of kcnq4. introduction of high levels of mir153 to mas increased vascular wall thickening and reduced kv7.4 expression/kv7 channel function compared with vessels receiving a non-targeting mir, providing a proof of concept of kv7.4 regulation by mir153. conclusion this study is the first to define a role for aberrant mir153 contributing to the hypertensive state through targeting of kcnq4 in an animal model of hypertension, raising the possibility of the use of mir153-related therapies in vascular disease.",1
"unlabelled metabolic changes are common features of many cancer cells and are frequently associated with the clinical outcome of patients with various cancers, including hepatocellular carcinoma (hcc). thus, aberrant metabolic pathways in cancer cells are attractive targets for cancer therapy. however, our understanding of cancer-specific regulatory mechanisms of cell metabolism is still very limited. we found that tat-activating regulatory dna-binding protein (tardbp) is a novel regulator of glycolysis in hcc cells. tardbp regulates expression of the platelet isoform of phosphofructokinase (pfkp), the rate-limiting enzyme of glycolysis that catalyzes the irreversible conversion of fructose-6-phosphate to fructose-1,6-bisphosphate. silencing of tardbp expression in multiple hcc cell lines leads to impaired glucose metabolism and inhibition of in vitro and in vivo growth of hcc cells. notably, the microrna 520 (mir-520) family is an intermediate regulator of tardbp-mediated regulation of glycolysis. mechanistically, tardbp suppressed expression of the mir-520 family, which, in turn, inhibited expression of pfkp. we further showed that expression of tardbp is significantly associated with the overall survival of patients with hcc. conclusion our study provides new mechanistic insights into the regulation of glycolysis in hcc cells and reveals tardbp as a potential therapeutic target for hcc.",1
"the drosophila wing primordium is subdivided into a dorsal (d) and a ventral (v) compartment by the activity of the lim-homeodomain protein apterous in d cells. cell interactions between d and v cells induce the activation of notch at the dv boundary. notch is required for the maintenance of the compartment boundary and the growth of the wing primordium. beadex, a gain-of-function allele of dlmo, results in increased levels of dlmo protein, which interferes with the activity of apterous and results in defects in dv axis formation. we performed a gain-of-function enhancer-promoter (ep) screen to search for suppressors of beadex when overexpressed in d cells. we identified 53 lines corresponding to 35 genes. loci encoding for micro-rnas and proteins involved in chromatin organization, transcriptional control, and vesicle trafficking were characterized in the context of dlmo activity and dv boundary formation. our results indicate that a gain-of-function genetic screen in a sensitized background, as opposed to classical loss-of-function-based screenings, is a very efficient way to identify redundant genes involved in a developmental process.",1
"to metastasize, a tumor cell must acquire abilities such as the capacity to colonize new tissue and evade immune surveillance. recent evidence suggests that micrornas can promote the evolution of malignant behaviors by regulating multiple targets. we performed a microrna analysis of human melanoma, a highly invasive cancer, and found that mir-30b/30d upregulation correlates with stage, metastatic potential, shorter time to recurrence, and reduced overall survival. ectopic expression of mir-30b/30d promoted the metastatic behavior of melanoma cells by directly targeting the galnac transferase galnt7, resulted in increased synthesis of the immunosuppressive cytokine il-10, and reduced immune cell activation and recruitment. these data support a key role of mir-30b/30d and galnac transferases in metastasis, by simultaneously promoting cellular invasion and immunosuppression.",1
"neuraminidase (na), a structural protein of the h9n2 avian influenza virus (h9n2 aiv), can facilitate viral invasion of the upper airway by cleaving the sialic acid moieties on mucin. dendritic cells (dcs) are major antigen-presenting cells whose immune functions, such as presenting antigens and activating lymphocytes, can be regulated by micrornas. here, we studied the molecular mechanism of mirna-induced repression of immune responses in mouse dcs. first, we screened for and verified the mirnas induced by na. then, we showed that, consistent with the h9n2 virus treatment, the viral na up-regulated the expression of mir-155, mir-674, and mir-499 in dcs; however, unlike h9n2 virus treatment, the presence of na was associated with reduced expression of mir-181b1. our results suggest that na significantly increased dc surface markers cd80 and mhcii and enhanced the ability of activating lymphocytes and secreting cytokines compared with ha, np and m2. meanwhile, we found that mir-674 and mir-155 over-expression increased all surface markers of dc. nevertheless, by inhibiting the expression of mir-674 and mir-155, na lost the ability to promote dc maturation. furthermore, we predicted and demonstrated that pgm2l1, aldh18a1, camk1d, and mbnl3 were the target genes of mir-674. among them, mbnl3 interference strongly blocked the mature dcs. collectively, our data shed new light on the roles of and mechanisms involved in the repression of dcs by mirnas, which may contribute to efforts to develop a prophylaxis for the influenza virus.",1
"translational autocontrol of the expression of the ribosomal protein s15 proceeds through the transitory formation of a pseudoknot. a synopsis of the known data is used to propose a molecular model of the mechanism involved and for the role of the pseudoknot. this latter structure is able to recruit 30s ribosomal subunits to initiate translation, but also to bind s15 and to stop translation by trapping the ribosome on its loading site. information on the s15 protein recognition of the messenger rna site was deduced from mutational analyses and chemical probing. a comparison of this messenger site with the s15 ribosomal binding site was conducted by analysing hydroxyl radical footprintings of these two sites. the existence of two subsites in 16s rna suggests that the ribosomal protein s15 might present either two different binding sites or at least one common subsite. clues for the presence of a common site between the messenger and 16s rna are given which cannot rule out that recognition specificity is linked to a few other determinants. whether these determinants are different or not remains an open question.",1
"the formation of hyperphosphorylated intracellular tau tangles in the brain is a hallmark of alzheimer's disease (ad). tau hyperphosphorylation destabilizes microtubules, promoting neurodegeneration in ad patients. to identify suppressors of tau-mediated ad, we perform a screen using a microrna (mir) library in drosophila and identify the mir-9 family as suppressors of human tau overexpression phenotypes. cg11070, a mir-9a target gene, and its mammalian orthologue ube4b, an e3/e4 ubiquitin ligase, alleviate eye neurodegeneration, synaptic bouton defects, and crawling phenotypes in drosophila human tau overexpression models. total and phosphorylated tau levels also decrease upon cg11070 or ube4b overexpression. in mammalian neuroblastoma cells, overexpression of ube4b and stub1, which encodes the e3 ligase chip, increases the ubiquitination and degradation of tau. in the tau-bifc mouse model, ube4b and stub1 overexpression also increase oligomeric tau degradation. inhibitor assays of the autophagy and proteasome systems reveal that the autophagy-lysosome system is the major pathway for tau degradation in this context. these results demonstrate that ube4b, a mir-9 target gene, promotes autophagy-mediated tau degradation together with stub1, and is thus an innovative therapeutic approach for ad.",1
"pancreatic cancer is one of the devastating human cancers responsible for tremendous human mortality. current study was undertaken to explore the therapeutic potential of microrna-374 in human pancreatic cancer. the results showed that microrna-374 exhibited lower expression in pancreatic cancer cells and tissues. overexpression of microrna-374 in cancer cells resulted in significant decrease in the cell viability. the inhibition of the cell viability was mainly due to the induction of apoptosis as evident from the dapi and ao/eb staining. annexin v/pi staining also showed that the overexpression of microrna-374 enhanced the percentage of apoptotic cells. the western blot analysis showed that microrna-374 overexpression increases bax and decreased the bcl-2 expression. the cleaved parp and cleaved caspase-3 expression was also considerably increased upon mir-374 overexpression. the targetscan analysis together with the dual luciferase assay showed that microrna-374 targets jam-2 by binding to mrna at 3'-utr. the qrt-pcr analysis showed that jam-2 was significantly upregulated in the pancreatic cancer cell lines and tissues. moreover, overexpression of mir-374 suppressed the expression of jam-2. additionally, suppression of jam-2 also inhibited the viability of the pancreatic cancer cells. in vivo studies in xenografted mice models showed that microrna-374 expression is effective in suppressing the growth and volume of pancreatic tumors. in conclusion, microrna-374 is downregulated in pancreatic cancers and may exhibit therapeutic implications in the pancreatic cancer treatment.",1
"background increasing evidences have documented that micrornas (mirnas) act as oncogenes or tumor suppressors in gastric cancer (gc). in this study, we aimed to investigate the expression of mir-133b in a large number of gc samples and elucidate its role in gc carcinogenesis and the detailed mechanism. methods we used taqman probe stem-loop real-time pcr to accurately measure the levels of mir-133b in 100 pairs of gastric cancer tissues and the adjacent non-neoplastic tissues. mir-133b mimics were overexpressed in gc cell lines, mir-133b inhibitors were also introduced in ges cells to investigate its role on regulating cell proliferation, cell migration and cell invasion. the target of mir-133b was identified by luciferase reporter assay and western blot. fascin actin-bundling protein 1 (fscn1) sirna was used to achieve the knockdown of fscn1 in gc cells and to investigate its role on modulating gc cell proliferation and invasion. results mir-133b was significantly down-regulated in gc cell lines and in gc tissues compared with adjacent normal tissues. moreover, lower-level of mir-133b was also associated with venous invasion and a more aggressive tumor phenotype. re-introduction of mir-133b in gc cells can inhibit cell proliferation, cell migration and invasion. in contrary, knockdown of mir-133b in ges cells can promote cell proliferation and invasion. further investigation indicated that mir-133b targeted fscn1 in gc cells and knockdown of fscn1 can also inhibit gc cell growth and invasion. conclusion our findings demonstrated that mir-133b was significantly down-regulated in gc tissues and exerted its tumor suppressor role in gc cells. the investigation of the detailed mechanism showed that mir-133b directly targeted fscn1 which functioned as an oncogenic gene in gc cells. these results suggested that mir-133b can be developed as a new diagnostic marker or therapeutic target for gc.",1
"myocardin is regarded as a key mediator for the change of smooth muscle phenotype. the gap junction protein connexin 43 (cx43) has been shown to be involved in vascular smooth muscle cells (vsmcs) proliferation and the development of atherosclerosis. however, the role of myocardin on gap junction of cell communication and the relation between myocardin and cx43 in vsmc phenotypic switch has not been investigated. the goal of the present study is to investigate the molecular mechanism by which myocardin affects cx43-regulated vsmc proliferation. data presented in this study demonstrated that inhibition of the cx43 activation process impaired vsmc proliferation. on the other hand, overexpression mir-206 inhibited vsmc proliferation. in additon, mir-206 silences the expression of cx43 via targeting cx43 3' untranslated regions. importantly, myocardin can significantly promote the expression of mir-206. cx43 regulates vsmcs' proliferation and metastasis through mir-206, which could be promoted by myocardin and used as a marker for diagnosis and a target for therapeutic intervention. thus myocardin affected the gap junction by inhibited cx43 and myocardin-mir-206-cx43 formed a loop to regulate vsmc phenotypic switch.",1
"introduction mesenchymal stem cells (mscs) have therapeutic potential for the repair of myocardial injury. the efficacy of msc therapy for myocardial regeneration mainly depends on the survival of cells after transplantation into the infarcted heart. in the transplanted regions, reactive oxygen species (ros) can cause cell death, and this process depends on caspase activation and autophagosome formation. methods a software targetscan was utilized to search for micrornas (mirnas) that target caspase-3 mrna. six candidate mirnas including let-7b were selected and transfected into human mscs in vitro. expression of mek-ekr signal pathways and autophagy-related genes were detected. using ischemia/reperfusion model (i/r), the effect of mscs enriched with let-7b was determined after transplantation into infarcted heart area. miller catheter was used to evaluate cardiac function. results here, we report that let-7b targets caspase-3 to regulate apoptosis and autophagy in mscs exposed to ros. let-7b-transfected mscs (let-7b-mscs) showed high expression of survival-related proteins, including p-mek, p-erk and bcl-2, leading to a decrease in annexin v/pi- and tunel-positive cells under ros-rich conditions. moreover, autophagy-related genes, including atg5, atg7, atg12 and beclin-1, were significantly downregulated in let-7b-mscs. using a rat model of acute myocardial infarction, we found that intramyocardial injection of let-7b-mscs markedly enhanced left ventricular (lv) function and microvessel density, in accordance with a reduced infarct size and the expression of caspase-3. conclusions taken together, these data indicate that let-7b may protect mscs implanted into infarcted myocardium from apoptosis and autophagy by directly targeting caspase-3 signaling.",1
"tumor necrosis factor superfamily-15 (tnfsf15; vegi; tl1a) is a negative modulator of angiogenesis for blood vessel homeostasis and is produced by endothelial cells in a mature vasculature. it is known to be downregulated by vascular endothelial growth factor (vegf), a major regulator of neovascularization but the mechanism of this interaction is unclear. here we report that vegf is able to stimulate the production of two micrornas, mir-20a and mir-31, which directly target the 3'-utr of tnfsf15. additionally, we show that two vegf-stimulated cell growth signals, erk and akt, are responsible for promoting the expression of mir-20a and mir-31. treatment of human umbilical vein endothelial cells (huvecs) with akt inhibitor ly294002 results in diminished mir-20a and mir-31 production, while erk inhibitor u0126 prevented vegf-stimulated expression of mir-20a but not that of mir-31. furthermore, inactivation of either erk or akt signals restores tnfsf15 gene expression. in an angiogenesis assay, elevated mir-20a or mir-31 levels in huvecs leads to enhancement of capillary-like tubule formation in vitro , whereas lowered mir-20a and mir-31 levels results in an inhibition. these findings are consistent with the view that mir-20a and mir-31 mediate vegf-induced downregulation of tnfsf15. targeting these microrna molecules may therefore provide an effective approach to inhibit angiogenesis.",1
"micrornas (mirnas) are posttranscriptional regulators of gene expression that may act as buffering agents to stabilize gene-regulatory networks. here, we identify two mirnas that are maternally required for normal embryonic primordial germ cell development in drosophila melanogaster. embryos derived from mir-969 and mir-9c mutant mothers had, on average, reduced germ cell numbers. intriguingly, this reduction correlated with an increase in the variance of this quantitative phenotypic trait. analysis of an independent set of maternal mutant genotypes suggests that reduction of germ cell number need not lead to increased variance. our observations are consistent with the hypothesis that mir-969 and mir-9c contribute to stabilizing the processes that control germ number, supporting phenotypic robustness.",1
"background micrornas have the potential as diagnostic biomarkers and therapeutic targets in autoimmune diseases. however, very limited studies have evaluated the expression of microrna profile in thyroid gland related to hashimoto's thyroiditis (ht). methods microrna microarray expression profiling was performed and validated by quantitative rt-pcr. the expression pattern of mir-142-5p was detected using locked nucleic acid-in situ hybridization. the target gene was predicted and validated using mirna targets prediction database, gene expression analysis, quantitative rt-pcr, western blot, and luciferase assay. the potential mechanisms of mir-142-5p were studied using immunohistochemistry, immunofluorescence, and quantitative assay of thyrocyte permeability. results thirty-nine micrornas were differentially expressed in ht (fold change ≥2, p conclusions our findings indicate a previously unrecognized mechanism that mir-142-5p, targeting cldn1, plays an important role in ht pathogenesis.",1
"interleukin-34 (il-34) is a recently discovered cytokine that promotes tissue macrophage maturation and differentiation. we previously found that 1α,25-dihydroxyvitamin d3 up-regulated il-34 expression in sh-sy5y neural cells. however, whether microrna regulates il-34 expression is not completely clear. by using on-line targetscan and miranda software, we found that there was only one conserved microrna-31 (mir-31) binding site in the 3' untranslated region (3'utr) of il-34 mrna. intriguingly, using qpcr we demonstrated that mir-31 levels were negatively correlated to il-34 mrna levels in different cell lines. by examining the effect of mir-31 on il-34 3' utr reporter luciferase activity and on il-34 mrna and argonaute risc catalytic component 2 (ago2) binding, it was found that mir-31 bound directly to il-34 3'utr and regulated the post-transcriptional expression of il-34 in mgc-803 cells. moreover, a mir-31 mimic significantly reduced il-34 expression levels while a mir-31 inhibitor up-regulated il-34 expression in kyse-45 and ht-29 cells. taken together, these results show that mir-31 negatively regulates il-34 expression by directly binding to the il-34 3' utr in vitro.",1
"purpose peroxisome proliferator-activated receptor α (pparα) is an important transcriptional factor that regulates genes encoding endo/xenobiotic enzymes and lipid metabolizing enzymes. in this study, we investigated whether micrornas (mirnas) are involved in the regulation of pparα in human liver. methods precursor or antisense oligonucleotide for mir-21 or mir-27b was transfected into huh7 cells; expression of pparα and acyl-coa synthetase m2b was determined by western blot and real-time rt-pcr. luciferase assay was performed to identify the functional mirna recognition element (mre). expression levels of pparα, mir-21, and mir-27b in a panel of 24 human livers were determined. results the overexpression and inhibition of mir-21 or mir-27b in huh7 cells significantly decreased and increased the pparα protein level, respectively, but not pparα mrna level. the mirna-dependent regulation of pparα affected the expression of its downstream gene. luciferase assay identified a functional mre for mir-21 in the 3'-untranslated region of pparα. in human livers, the pparα protein levels were not correlated with pparα mrna, but inversely correlated with the mir-21 levels, suggesting a substantial impact of mir-21, although the contribution of mir-27b could not be ruled out. conclusions we found that pparα in human liver is regulated by mirnas.",1
"the polycomb repressive complexes prc1 and prc2 play a central role in developmental gene regulation in multicellular organisms. prc1 and prc2 modify chromatin by catalysing histone h2a lysine 119 ubiquitylation (h2ak119u1), and h3 lysine 27 methylation (h3k27me3), respectively. reciprocal crosstalk between these modifications is critical for the formation of stable polycomb domains at target gene loci. while the molecular mechanism for recognition of h3k27me3 by prc1 is well defined, the interaction of prc2 with h2ak119u1 is poorly understood. here we demonstrate a critical role for the prc2 cofactor jarid2 in mediating the interaction of prc2 with h2ak119u1. we identify a ubiquitin interaction motif at the amino-terminus of jarid2, and demonstrate that this domain facilitates prc2 localization to h2ak119u1 both in vivo and in vitro. our findings ascribe a critical function to jarid2 and define a key mechanism that links prc1 and prc2 in the establishment of polycomb domains.",1
"micrornas (mirnas) are small non-coding rnas that, by targeting certain messenger rnas (mrnas) for translational repression or cleavage, can regulate the expression of these genes. in addition, mirnas may also function as oncogenes and tumor-suppressor genes, as the abnormal expression of mirnas is associated with various human tumors. however, the effects of the expression of mir-124 in breast cancer remain unclear. the present study was conducted to study the expression of mir-124 in breast cancer, paying particular attention to mir-124's relation to the proliferation, invasion, and apoptosis in breast cancer cell mcf-7 and mda-mb-231. real-time quantitative rt-pcr (qrt-pcr) was performed to identify mir-124 that was down-regulated in breast cancer tissues. we also showed e26 transformation specific-1 (ets-1) and mir-124 expression levels in breast cancer tissues that were associated with lymph node metastases. with transfected synthetic mir-124 agomir into mcf-7 and mda-mb-231, a significant reduction (p < 0.05) in mcf-7 and mda-mb-231 cell proliferation and colony forming potential was observed after treatment with mir-124. apoptosis and migration rates were found to be significantly higher in two breast-derived cell lines transfected with a mir-124 agomir (p < 0.05). luciferase reporter assay and western blot were used to verify ets-1 as a potential major target gene of mir-124, and the result showed that mir-124 can bind to putative binding sites within the ets-1 mrna 3' untranslated region (utr) to reduce its expression. based on these findings, we propose that mir-124 and ets-1 may serve as a therapeutic agent in breast cancer.",1
"dendritic cell (dc) maturation is a tightly regulated process that requires coordinated and timed developmental cues. here we investigate whether micrornas are involved in this process. we identify micrornas in mouse gm-csf-generated, monocyte-related dc (gm-dc) that are differentially expressed during both spontaneous and lps-induced maturation and characterize m-csf receptor (m-csfr), encoded by the csf1r gene, as a key target for microrna-mediated regulation in the final step toward mature dc. microrna-22, -34a, and -155 are up-regulated in mature mhcii(hi) cd86(hi) dc and mediate csf1r mrna and protein down-regulation. experimental inhibition of csf1r-targeting micrornas in vitro results not only in sustained high level m-csfr protein expression but also in impaired dc maturation upon stimulation by lps. accordingly, over-expression of csf1r in gm-dc inhibits terminal differentiation. taken together, these results show that developmentally regulated micrornas control csf1r expression, supplementing previously identified mechanisms that regulate its transcription and protein surface expression. furthermore, our data indicate a novel function for csf1r in mouse monocyte-derived dc, showing that down-regulation of m-csfr expression is essential for final dc maturation.",1
"the objectives of this study were to detect the expressions of microrna-218 (mir-218) in human gastrointestinal stromal tumor (gist) tissues and cells and explore its effects on the biological features of gist-t1 cells and the expression of its target gene kit, so as to provide new insights for gist treatment. using quantitative real-time polymerase chain reaction (qrt-pcr), we detected the expressions of mir-218 in the tissues and adjacent tissues of gist and in the gist cell lines including gist882, gist430, gist48, and gist-t1. forty-eight hours after the mir-218 mimic was transfected into the gist-t1 cells, the expression of mir-218 in the gist-t1 cells was detected by qrt-pcr. the effect of mir-218 on the gist-t1 cell viability was detected using mtt. the effect of mir-218 on the proliferation and apoptosis of gist-t1 cell was analyzed using flow cytometry. transwell invasion chamber was applied to detect the effect of mir-218 on the invasion of gist-t1 cells. kit was identified to be a target gene of mir-218 by the luciferase reporter enzyme system, and the effect of mir-218 on the expression of kit protein in cells was determined using western blotting. as shown by qrt-pcr, compared with that in the gist adjacent tissue, the expressions of mir-218 in the tumor tissue and gist cell lines were significantly decreased (p < 0.0001). compared with the control group, the expression of mir-218 increased significantly in gist-t1 cells transfected with mir-218 mimic for 48 h (p < 0.01). mtt showed that the cell viability decreased significantly after the overexpression of mir-218 in the gist-t1 cells (p < 0.01). flow cytometry showed that the cell proliferation index significantly declined after the overexpression of mir-218 (p < 0.01); meanwhile, the apoptosis of cells also significantly increased (p < 0.01). detection using the transwell invasion chamber showed that the number of cells passing through the transwell chamber significantly dropped after the enhanced expression of mir-218 (p < 0.01). luciferase reporter gene assay showed that, compared with the control group, the relative luciferase activity significantly declined in the mir-218 mimic transfection group (p < 0.01). compared with the control group, the expression of kit protein in the gist-t1 cells transfected with mir-218 mimic for 48 h significantly decreased (p < 0.01). in conclusion, the expression of mir-218 decreases in human gist tissue and cell lines. mir-218 can negatively regulate the expression of kit protein and inhibit the proliferation and invasion of gist cells. treatment based on the enhanced expression of mir-218 may be a promising strategy for gist.",1
"pre-messenger rna splicing is a two-step process by which introns are removed and exons joined together. in yeast, the u5 snrna loop 1 interacts with the 5' exon before the first step of splicing and with the 5' and 3' exons before the second step. in vitro studies revealed that yeast u5 loop 1 is not required for the first step of splicing but is essential for holding the 5' and 3' exons for ligation during the second step. it is critical, therefore, that loop 1 contacts the 5' exon before the first step of splicing to hold this exon following cleavage from the pre-mrna. at present it is not known how u5 loop 1 is positioned on the 5' exon prior to the first step of splicing. to address this question, we have used site-specific photoactivated crosslinking in yeast spliceosomes to investigate the interaction of u5 loop 1 with the pre-mrna prior to the first step of splicing. we have found that the highly conserved uridines in loop 1 make atp-dependent contacts with an approximately 8-nt region at the 5' splice site that includes the invariant gu. these interactions are dependent on functional u2 and u6 snrnas. our results support a model where u5 snrna loop 1 interacts with the 5' exon in two steps during its targeting to the 5' splice site.",1
"immunoparalysis is an important pathological mechanism in sepsis. however, an effective small molecule therapy is lacking. here, we show that ouabain, a na(+),k(+)-atpase ligand, can reverse immunoparalysis in vitro, in vivo, and in clinical samples. notably, the effect of ouabain was critically dependent on tnf-α expression. however, ouabain had opposing effects on the stability of tnf-α mrna: ouabain triggered mir-181 transcription, which promoted tnf-α mrna degradation and induced immunoparalysis, and ouabain triggered the nuclear export of human antigen r (hur), which stabilized tnf-α mrna and suppressed immuno-paralysis. interestingly, because the mir-181 binding site is located within the hur binding site in the 3'-untranslated region of tnf-α, in ouabain-treated cells, hur competed with mir-181 for binding to tnf-α mrna and recruited tnf-α mrna to stress granules, thereby stabilizing tnf-α mrna and reversing immunoparalysis. ouabain also induced gm-csf and interferon-γ expression in a hur-dependent manner. hence, the fine-tuning of tnf-α mrna stability by hur and mir181 plays a crucial role in immunoparalysis, and na(+),k(+)-atpase ligands are promising agents for immunoparalysis therapy.",1
"cancer stem cells (cscs), or tumor-initiating cells, are involved in tumor progression and metastasis. micrornas (mirnas) regulate both normal stem cells and cscs, and dysregulation of mirnas has been implicated in tumorigenesis. cscs in many tumors--including cancers of the breast, pancreas, head and neck, colon, small intestine, liver, stomach, bladder and ovary--have been identified using the adhesion molecule cd44, either individually or in combination with other marker(s). prostate cscs with enhanced clonogenic and tumor-initiating and metastatic capacities are enriched in the cd44(+) cell population, but whether mirnas regulate cd44(+) prostate cancer cells and prostate cancer metastasis remains unclear. here we show, through expression analysis, that mir-34a, a p53 target, was underexpressed in cd44(+) prostate cancer cells purified from xenograft and primary tumors. enforced expression of mir-34a in bulk or purified cd44(+) prostate cancer cells inhibited clonogenic expansion, tumor regeneration, and metastasis. in contrast, expression of mir-34a antagomirs in cd44(-) prostate cancer cells promoted tumor development and metastasis. systemically delivered mir-34a inhibited prostate cancer metastasis and extended survival of tumor-bearing mice. we identified and validated cd44 as a direct and functional target of mir-34a and found that cd44 knockdown phenocopied mir-34a overexpression in inhibiting prostate cancer regeneration and metastasis. our study shows that mir-34a is a key negative regulator of cd44(+) prostate cancer cells and establishes a strong rationale for developing mir-34a as a novel therapeutic agent against prostate cscs.",1
"cross-linking and immunoprecipitation (clip) is increasingly used to map transcriptome-wide binding sites of rna-binding proteins. we developed a method for clip data analysis, and applied it to compare clip with photoactivatable ribonucleoside-enhanced clip (par-clip) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. we found only small differences in accuracies of these methods in identifying binding sites of hur, which binds low-complexity sequences, and argonaute 2, which has a complex binding specificity. we found that cross-link-induced mutations led to single-nucleotide resolution for both par-clip and clip. our results confirm the expectation from original clip publications that rna-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the clip procedure, and we show that extensive digestion with sequence-specific rnases strongly biases the recovered binding sites. this bias can be substantially reduced by milder nuclease digestion conditions.",1
"wnt signaling plays many important roles in animal development. this evolutionarily conserved signaling pathway is highly regulated at all levels. to identify regulators of the wnt/wingless (wg) pathway, we performed a genetic screen in drosophila. we identified the microrna mir-8 as an inhibitor of wg signaling. expression of mir-8 potently antagonizes wg signaling in vivo, in part by directly targeting wntless, a gene required for wg secretion. in addition, mir-8 inhibits the pathway downstream of the wg signal by repressing tcf protein levels. another positive regulator of the pathway, cg32767, is also targeted by mir-8. our data suggest that mir-8 potently antagonizes the wg pathway at multiple levels, from secretion of the ligand to transcription of target genes. in addition, mammalian homologues of mir-8 promote adipogenesis of marrow stromal cells by inhibiting wnt signaling. these findings indicate that mir-8 family members play an evolutionarily conserved role in regulating the wnt signaling pathway.",1
"heat shock in drosophila results in repression of most normal (non-heat shock) mrna translation and the preferential translation of the heat shock mrnas. the sequence elements that confer preferential translation have been localized to the 5'-untranslated region (5'-utr) for hsp22 and hsp70 mrnas (in drosophila). hsp90 mrna is unique among the heat shock mrnas in having extensive secondary structure in its 5'-utr and being abundantly represented in the non-heat shocked cell. in this study, we show that hsp90 mrna translation is inefficient at normal growth temperature, and substantially activated by heat shock. its preferential translation is not based on an ires-mediated translation pathway, because overexpression of eif4e-bp inhibits its translation (and the translation of hsp70 mrna). the ability of hsp90 mrna to be preferentially translated is conferred by its 5'-utr, but, in contrast to hsp22 and -70, is primarily influenced by nucleotides close to the aug initiation codon. we present a model to account for hsp90 mrna translation, incorporating results indicating that heat shock inhibits eif4f activity, and that hsp90 mrna translation is sensitive to eif4f inactivation.",1
"we analyzed the effects of suppressor mutations in the u1 snrna (snr19) gene from saccharomyces cerevisiae on the splicing of mutant pre-mrna substrates. the results indicate that pairing between u1 snrna and the highly conserved position 5 (gtatgt) of the intron occurs early in spliceosome assembly in vitro. this pairing is important for efficient splicing both in vitro and in vivo. however, pairing at position 5 does not appear to influence 5' splice site selection in vivo, indicating that the previously described u1 snrna:5' splice junction base pairing interaction is not sufficient to define the 5' cleavage site.",1
"micrornas are a kind of small non-coding rnas that play important roles in various biological processes such as cell proliferation, differentiation, and apoptosis. cellular responses to uv-induced apoptosis have been suggested to be regulated by micrornas at the posttranscriptional level, while the detailed mechanisms underlying this process remain unclear. our aim in this study was to investigate the effects of mir-1246 in uvb-induced apoptosis and to identify the functional targets of mir-1246 in keratinocyte hacat cells. the expression of mir-1246 and apoptotic genes in hacat cells experiencing uvb stress was determined using quantitative real-time pcr. mir-1246 functions in uvb-induced apoptosis were quantified via fluorescence-activated cell sorter analysis of mir-1246 mimic or inhibitor-transfected cells. additionally, the regulatory relationship between rtkn2 and mir-1246 was identified by western blot and luciferase reporter assays. mir-1246 was upregulated accompanying with uvb-irradiated apoptosis in hacat cells. overexpression of mir-1246 promoted uvb-induced apoptosis, while knockdown of mir-1246, using a specific inhibitor, resulted in a significant reduction in uvb-elicited apoptosis. we further demonstrate that mir-1246 negatively regulated the expression of rtkn2 through binding to the 3'-untranslated region of rtkn2 at the posttranscriptional level. moreover, rtkn2 was observed to be resistant to uvb-induced apoptosis and rtkn2 antagonized the pro-apoptotic effects of mir-1246 during uvb-induced apoptosis in hacat cells. these findings suggested that mir-1246 promotes uvb-induced apoptosis by downregulating rtkn2 expression and that uvb-upregulated mir-1246 released rtkn2-dependent resistance to uvb-induced apoptosis by targeting rtkn2 post-transcriptionally in keratinocyte cells.",1
"background loss of transient outward k(+) current (ito) is well documented in cardiac hypertrophy and failure both in animal models and in humans. electrical remodeling contributes to prolonged action potential duration and increased incidence of arrhythmias. furthermore, there is a growing body of evidence linking microrna (mir) dysregulation to the progression of both conditions. in this study, we examined the mechanistic basis underlying mir dysregulation in electrical remodeling and revealed a novel interaction with the adrenergic signaling pathway. methods and results we first used a tissue-specific knockout model of dicer1 in cardiomyocytes to reveal the overall regulatory effect of mirs on the ionic currents and action potentials. we then validated the inducible camp early repressor as a target of mir-1 and took advantage of a clinically relevant model of post myocardial infarction and mir delivery to probe the mechanistic basis of mir dysregulation in electrical remodeling. these experiments revealed the role of inducible camp early repressor as a repressor of mir-1 and ito, leading to prolonged action potential duration post myocardial infarction. in addition, delivery of mir-1 and mir-133a suppressed inducible camp early repressor expression and prevented both electrical remodeling and hypertrophy. conclusions taken together, our results illuminate the mechanistic links between mirs, adrenergic signaling, and electrical remodeling. they also serve as a proof-of-concept for the therapeutic potential of mir delivery post myocardial infarction.",1
"low-density lipoprotein receptor-related protein 1 (lrp1) is a multifunctional endocytic receptor that plays critical roles in the pathogenesis of several human diseases including tumor metastasis and alzheimer's disease. however, mechanisms that regulate lrp1 expression under physiological and pathophysiological conditions are not unclear. in human cell lines, we found that mir-205 down-regulates the expression of lrp1 by targeting sequences in the 3'utr of lrp1 mrna. this effect was abolished by deleting the mir-205 seed site in the 3'utr of lrp1. the ectopic expression of mir-205 also significantly mitigated migration of both u87 and sk-lu-1 cells. these results, for the first time, demonstrate that expression of human lrp1 is regulated in part by a specific mirna, leading to decreased tumor cell migration.",1
"small ribozymes have been regarded as living fossils of a prebiotic rna world that would have remained in the genomes of modern organisms. in this study, we report the ultraconserved occurrence of hammerhead ribozymes in amniota genomes (reptiles, birds and mammals, including humans), similar to those described previously in amphibians and platyhelminth parasites. the ribozymes mapped to intronic regions of different genes, such as the tumour suppressor reck in birds and mammals, a mammalian tumour antigen and the dystrobrevin beta in lizards and birds. in vitro characterization confirmed a high self-cleavage activity, whereas analysis of reck-expressed sequence tags revealed fusion events between the in vivo self-cleaved intron and u5 or u6 small nuclear rna fragments. together, these results suggest a conserved role for these ribozymes in messenger rna biogenesis.",1
"background micrornas (mirnas) are endogenous noncoding rnas of approximately 22 nucleotides in length that mediate post-transcriptional gene silencing by annealing to sequences in the 3'-untranslated region of target mrnas. methods in this study, we analyzed 25 candidate mirnas selected based on microarray data for cardiac tissue from individuals with congenital heart defects (chds) and from healthy control tissue. results this study identified specific changes in the mir-1-1 and mir-181c levels in human cardiac samples from individuals with ventricular septal defects (vsds) relative to the levels in healthy control tissue. increased levels of gja1 and sox9 were associated with the decreased expression of mir-1-1 in vsd patients, and increased mir-181c expression was correlated with downregulated bmpr2 levels. in addition, the results revealed that mir-1-1 and mir-181c directly regulate the expression of these predicted targets. conclusions mir-1-1 and mir-181c are associated with the pathogenesis of vsds.",1
"myotonic dystrophy type 1 (dm1) originates from alleles of the dmpk gene with hundreds of extra ctg repeats in the 3' untranslated region (3' utr). cug repeat rnas accumulate in foci that sequester muscleblind-like (mbnl) proteins away from their functional target transcripts. endogenous upregulation of mbnl proteins is, thus, a potential therapeutic approach to dm1. here we identify two mirnas, dme-mir-277 and dme-mir-304, that differentially regulate muscleblind rna isoforms in mirna sensor constructs. we also show that their sequestration by sponge constructs derepresses endogenous muscleblind not only in a wild type background but also in a dm1 drosophila model expressing non-coding cug trinucleotide repeats throughout the musculature. enhanced muscleblind expression resulted in significant rescue of pathological phenotypes, including reversal of several mis-splicing events and reduced muscle atrophy in dm1 adult flies. rescued flies had improved muscle function in climbing and flight assays, and had longer lifespan compared to disease controls. these studies provide proof of concept for a similar potentially therapeutic approach to dm1 in humans.",1
"chemotherapeutic drug resistance remains a major obstacle to the successful treatment of colon cancer. here, we show that 77 differentially expressed mirnas were identified in sw1116/hcpt versus sw1116, and over-expressed mir-506 in sw1116/hcpt cells was validated. then it was indicated that pparα is a common target of mir-506 by using a luciferase reporter assay. our results also demonstrated that cytotoxic ability of hcpt requires the concomitant presence of pparα, and that loss of pparα expression imparts resistance to hcpts anti-tumor effects. all together, our studies indicate that mir-506 over-expression in established hcpt-resistant colon cancer cell line confers resistance to hcpt by inhibiting pparα expression, then providing a rationale for the development of mirna-based strategies for reversing resistance in hcpt-resistant colon cancer cells.",1
"in this study we performed a systematic evaluation of functional mirna-mrna interactions associated with the invasiveness of breast cancer cells using a combination of integrated mirna and mrna expression profiling, bioinformatics prediction, and functional assays. analysis of the mirna expression identified 11 mirnas that were differentially expressed, including 7 down-regulated (mir-200c, mir-205, mir-203, mir-141, mir-34a, mir-183, and mir-375) and 4 up-regulated mirnas (mir-146a, mir-138, mir-125b1 and mir-100), in invasive cell lines when compared to normal and less invasive cell lines. transfection of mir-200c, mir-205, and mir-375 mimics into mda-mb-231 cells led to the inhibition of in vitro cell migration and invasion. the integrated analysis of mirna and mrna expression identified 35 known and novel target genes of mir-200c, mir-205, and mir-375, including cfl2, lamc1, timp2, zeb1, cdh11, prkca, ptprj, ptprm, ldhb, and sec23a. surprisingly, the majority of these genes (27 genes) were target genes of mir-200c, suggesting that mir-200c plays a pivotal role in regulating the invasiveness of breast cancer cells. we characterized one of the target genes of mir-200c, cfl2, and demonstrated that cfl2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous mir-200c. tissue microarray analysis further revealed that cfl2 expression in primary breast cancer tissue correlated with tumor grade. the results obtained from this study may improve our understanding of the role of these candidate mirnas and their target genes in relation to breast cancer invasiveness and ultimately lead to the identification of novel biomarkers associated with prognosis.",1
"background in the process of hepatic fibrosis, hepatic stellate cells (hscs) can be activated by many inflammatory cytokines. the transforming growth factor-β1 (tgf-β1) is one of the main profibrogenic mediators. recently, some studies have also shown that micrornas (mirnas) play essential roles in the progress of liver fibrosis by being involved in the differentiation, fat metabolism and ecm production of hscs. methods the expression of mir-454 in lx-2 cells treated with tgf-β1 and in the fibrotic livers with schistosoma japonicum infection was detected by qrt-pcr. the role of mir-454 on lx-2 cells was then analyzed by western blot, flow cytometry and luciferase assay. results the results showed that the expression of mir-454 was down-regulated in the tgf-β1-treated lx-2 cells and mir-454 could inhibit the activation of hscs by directly targeting smad4. however, we found that mir-454 had no effect on cell cycle and cell proliferation in tgf-β1-treated lx-2. besides these, mir-454 was found to be regulated in the process of schistosoma japonicum infection. conclusions all the results suggested that mir-454 could provide a novel therapeutic approach for treating liver fibrosis, especially the liver fibrosis induced by schistosoma japonicum.",1
"micrornas (mirnas) are small non-coding rnas that regulate expression by translational repression or messenger rna (mrna) degradation. although numerous bioinformatic prediction models exist to identify mirna-mrna interactions, experimental validation of bona fide interactions can be difficult and laborious. few methods can comprehensively identify mirnas that target a single mrna. we have developed an experimental approach to search for mirnas targeting any mrna using a capture affinity assay involving a biotinylated dna anti-sense oligonucleotide. this method identifies mirnas targeting the full length of the mrna. the method was tested using three separate mrna targets: alpha-1 antitrypsin (aat) mrna, interleukin-8 mrna and secretory leucoprotease inhibitor mrna. aat mrna-specific and total mirnas from three different cell lines (monocytic thp-1, bronchial epithelial 16hbe14o- and liver hepg2 cells) were profiled, and validation studies revealed that aat mrna-specific mirnas functionally target the aat mrna in a cell-specific manner, providing the first evidence of innate mirnas selectively targeting and modulating aat mrna expression. interleukin-8 and secretory leucoprotease inhibitor mrnas and their cognate mirnas were also successfully captured using this approach. this is a simple and an efficient method to potentially identify mirnas targeting sequences within the full length of a given mrna transcript.",1
"the transforming growth factor-β (tgf-β) signalling pathway participates in various biological processes. dysregulation of smad4, a central cellular transducer of tgf-β signalling, is implicated in a wide range of human diseases and developmental disorders. however, the mechanisms underlying smad4 dysregulation are not fully understood. using a functional screening approach based on luciferase reporter assays, we identified 39 micrornas (mirnas) as potential regulators of smad4 from an expression library of 388 human mirnas. the screening was supported by bioinformatic analysis, as 24 of 39 identified mirnas were also predicted to target smad4. mir-199a, one of the identified mirnas, was inversely correlated with smad4 expression in various human cancer cell lines and gastric cancer tissues, and repressed smad4 expression and blocked canonical tgf-β transcriptional responses in cell lines. these effects were dependent on the presence of a conserved, but not perfect seed paired, mir-199a-binding site in the smad4 3'-untranslated region (utr). overexpression of mir-199a significantly inhibited the ability of tgf-β to induce gastric cancer cell growth arrest and apoptosis in vitro, and promoted anchorage-independent growth in soft agar, suggesting that mir-199a plays an oncogenic role in human gastric tumourigenesis. in conclusion, our functional screening uncovers multiple mirnas that regulate the cellular responsiveness to tgf-β signalling and reveals important roles of mir-199a in gastric cancer by directly targeting smad4.",1
"cell-cycle quiescence is a common feature of early germline development in many animal species. in drosophila germline progenitors (pole cells), both g2/m and g1/s transitions are blocked. g2/m transition is repressed by maternal nanos through suppression of cyclin b production. however, the molecular mechanism underlying blockage of g1/s transition remains elusive. we found that repression of mir-10404 expression is required to block g1/s transition in pole cells. expression of mir-10404, a microrna encoded within the internal transcribed spacer 1 of rdna, is repressed in early pole cells by maternal polar granule component. this repression delays the degradation of maternal dacapo mrna, which encodes an inhibitor of g1/s transition. moreover, derepression of g1/s transition in pole cells causes defects in their maintenance and their migration into the gonads. our observations reveal the mechanism inhibiting g1/s transition in pole cells and its requirement for proper germline development.",1
"myotonic dystrophy type 1 (dm1) is a multisystemic genetic disorder caused by the ctg repeat expansion in the 3'-untranslated region of dmpk gene. heart dysfunctions occur in ∼80% of dm1 patients and are the second leading cause of dm1-related deaths. herein, we report that upregulation of a non-muscle splice isoform of rna-binding protein rbfox2 in dm1 heart tissue-due to altered splicing factor and microrna activities-induces cardiac conduction defects in dm1 individuals. mice engineered to express the non-muscle rbfox2 40 isoform in heart via tetracycline-inducible transgenesis, or crispr/cas9-mediated genome editing, reproduced dm1-related cardiac conduction delay and spontaneous episodes of arrhythmia. further, by integrating rna binding with cardiac transcriptome datasets from dm1 patients and mice expressing the non-muscle rbfox2 isoform, we identified rbfox2 40 -driven splicing defects in voltage-gated sodium and potassium channels, which alter their electrophysiological properties. thus, our results uncover a trans-dominant role for an aberrantly expressed rbfox2 40 isoform in dm1 cardiac pathogenesis.",1
"human cyp2e1 is one of the pharmacologically and toxicologically important cytochrome p450 isoforms. earlier studies have reported that the cyp2e1 expression is extensively regulated by post-transcriptional and post-translational mechanisms, but the molecular basis remains unclear. in the present study, we examined the possibility that microrna may be involved in the post-transcriptional regulation of human cyp2e1. in silico analysis identified a potential recognition element of mir-378 (mre378) in the 3'-untranslated region (utr) of human cyp2e1 mrna. luciferase assays using hek293 cells revealed that the reporter activity of the plasmid containing the mre378 was decreased by co-transfection of precursor mir-378, indicating that mir-378 functionally recognized the mre378. we established two hek293 cell lines stably expressing human cyp2e1 including or excluding 3'-utr. when the precursor mir-378 was transfected into the cells expressing human cyp2e1 including 3'-utr, the cyp2e1 protein level and chlorzoxazone 6-hydroxylase activity were significantly decreased, but were not in the cells expressing cyp2e1 excluding 3'-utr. in both cell lines, the cyp2e1 mrna levels were decreased by overexpression of mir-378, but mir-378 did not affect the stability of cyp2e1 mrna. in a panel of 25 human livers, no positive correlation was observed between the cyp2e1 protein and cyp2e1 mrna levels, supporting the post-transcriptional regulation. interestingly, the mir-378 levels were inversely correlated with the cyp2e1 protein levels and the translational efficiency of cyp2e1. in conclusion, we found that human cyp2e1 expression is regulated by mir-378, mainly via translational repression. this study could provide new insight into the unsolved mechanism of the post-transcriptional regulation of cyp2e1.",1
"the dna damage response activates several pathways that stall the cell cycle and allow dna repair. these consist of the well-characterized atr (ataxia telangiectasia and rad-3 related)/chk1 and atm (ataxia telangiectasia mutated)/chk2 pathways in addition to a newly identified atm/atr/p38mapk/mk2 checkpoint. crucial to maintaining the integrity of the genome is the s-phase checkpoint that functions to prevent dna replication until damaged dna is repaired. inappropriate expression of the proto-oncogene c-myc is known to cause dna damage. one mechanism by which c-myc induces dna damage is through binding directly to components of the prereplicative complex thereby promoting dna synthesis, resulting in replication-associated dna damage and checkpoint activation due to inappropriate origin firing. here we show that following etoposide-induced dna damage translation of c-myc is repressed by mir-34c via a highly conserved target-site within the 3(') utr. while mir-34c is induced by p53 following dna damage, we show that in cells lacking p53 this is achieved by an alternative pathway which involves p38 mapk signalling to mk2. the data presented here suggest that a major physiological target of mir-34c is c-myc. inhibition of mir-34c activity prevents s-phase arrest in response to dna damage leading to increased dna synthesis, dna damage, and checkpoint activation in addition to that induced by etoposide alone, which are all reversed by subsequent c-myc depletion. these data demonstrate that mir-34c is a critical regulator of the c-myc expression following dna damage acting downstream of p38 mapk/mk2 and suggest that mir-34c serves to remove c-myc to prevent inappropriate replication which may otherwise lead to genomic instability.",1
"skeletal muscle stem cells are regulated by pax3/7. during development, pax3 is required for the maintenance of these cells in the somite and their migration to sites of myogenesis; high levels of pax3 interfere with muscle cell differentiation, both in the embryo and in the adult. quantitative fine-tuning of pax3 is critical, and micrornas provide a potential mechanism. we identify microrna-27b (mir-27b), which directly targets the 3'-utr of pax3 mrna, as such a regulator. mir-27b is expressed in the differentiating skeletal muscle of the embryonic myotome and in activated satellite cells of adult muscle. in vivo overexpression of a mir-27b transgene in pax3-positive cells in the embryo leads to down-regulation of pax3, resulting in interference with progenitor cell migration and in premature differentiation. in a complementary experiment, mir-27b inhibitors were transfected into cultures of adult muscle satellite cells that normally express mir-27b at the onset of differentiation, when pax3 protein levels undergo rapid down-regulation. interference with mir-27b function results in continuing pax3 expression leading to more proliferation and a delay in the onset of differentiation. pax7 levels are not affected. introduction of mir-27b antagomirs at a site of muscle injury in vivo also affects pax3 expression and regeneration in vivo. we therefore conclude that mir-27b regulates pax3 protein levels and this down-regulation ensures rapid and robust entry into the myogenic differentiation program.",1
"microrna cluster mir-17-92 has been implicated in cardiovascular development and function, yet its precise mechanisms of action in these contexts are uncertain. this study aimed to investigate the role of mir-17-92 in morphogenesis and function of cardiac and smooth muscle tissues. to do so, a mouse model of conditional overexpression of mir-17-92 in cardiac and smooth muscle tissues was generated. extensive cardiac functional studies identified a dose-dependent induction of dilated, hypertrophic cardiomyopathy, and arrhythmia inducibility in transgenic animals, which correlated with premature mortality (98.3 ± 42.5 d, p<0.0001). expression analyses revealed the abundance of pten transcript, a known mir-17-92 target, to be inversely correlated with mir-17-92 expression levels and heart size. in addition, we demonstrated through 3'-utr luciferase assays and expression analyses that connexin43 (cx43) is a novel direct target of mir-19a/b and its expression is suppressed in transgenic hearts. taken together, these data demonstrate that dysregulated expression of mir-17-92 during cardiovascular morphogenesis results in a lethal cardiomyopathy, possibly in part through direct repression of pten and cx43. this study highlights the importance of mir-17-92 in both normal and pathological functions of the heart, and provides a model that may serve as a useful platform to test novel antiarrhythmic therapeutics.",1
"objectives this study evaluated the regulation and function of micro-rnas (mirs) in bone marrow-mononuclear cells (bmcs). background although cell therapy with bmcs may represent a therapeutic option to treat patients with heart disease, the impaired functionality of patient-derived cells remains a major challenge. small noncoding mirs post-transcriptionally control gene expression patterns and play crucial roles in modulating cell survival and function. methods micro-rnas were detected by mir profiling in bmcs isolated from healthy volunteers (n = 6) or from patients with myocardial infarction (n = 6), and the results were confirmed by polymerase chain reaction (pcr) in a larger cohort (n = 37). the function of selected mirs was determined by gain-of-function studies in vitro and by locked nuclear acid (lna) modified inhibitors in vitro and in vivo. results we identified several mirs that are up-regulated in bmcs from patients with myocardial infarction compared with bmcs from healthy controls, including the pro-apoptotic and antiproliferative mir-34a and the hypoxia-controlled mir-210. inhibition of mir-34 by lna-34a significantly reduced mir-34a expression and blocked hydrogen peroxide-induced cell death of bmc in vitro, whereas overexpression of mir-34a reduced the survival of bmcs in vitro. pre-treatment of bmcs with lna-34a ex vivo significantly increased the therapeutic benefit of transplanted bmcs in mice after acute myocardial infarction (ami). conclusions these results demonstrate that cardiovascular disease modulates the mir expression of bmcs in humans. reducing the expression of the pro-apoptotic mir-34a improves the survival of bmcs in vitro and enhances the therapeutic benefit of cell therapy in mice after ami.",1
"recent evidence shows that altered microrna-9 (mir-9) expression is implicated in the progression of gastric cancer. however, the exact roles and underlying mechanisms of mir-9 in the proliferation, invasion and metastasis of gastric cancer still remain unknown. in this study, mir-9 was found to be down-regulated and inversely correlated with the expression of cyclin d1 and v-ets erythroblastosis virus e26 oncogene homolog 1 (ets1) in gastric cancer tissues and cell lines. bioinformatics analysis revealed the putative mir-9 binding sites in the 3'-untranslated regions (3'-utr) of cyclin d1 and ets1 mrna. ectopic expression or knockdown of mir-9 resulted in responsively altered expression of cyclin d1, ets1 and their downstream targets phosphorylated retinoblastoma and matrix metalloproteinase 9 in cultured gastric cancer cell lines sgc-7901 and ags. in the luciferase reporter system, mir-9 directly targeted the 3'-utr of cyclin d1 and ets1, and these effects were abolished by mutating the mir-9 binding sites. over-expression of mir-9 suppressed the proliferation, invasion, and metastasis of sgc-7901 and ags cells in vitro and in vivo. restoration of mir-9-mediated down-regulation of cyclin d1 and ets1 by transient transfection, rescued the cancer cells from decrease in proliferation, migration and invasion. furthermore, anti-mir-9 inhibitor promoted the proliferation, migration and invasion of gastric cancer cells, while knocking down of cyclin d1 or ets1 partially phenocopied the effects of mir-9 over-expression. these data indicate that mir-9 suppresses the expression of cyclin d1 and ets1 via the binding sites in their 3'-utr, thus inhibiting the proliferation, invasion and metastasis of gastric cancer.",1
"background the wnt signaling pathway is involved in the control of cell proliferation and differentiation during skeletal muscle development. secreted frizzled-related proteins (sfrps), such as sfrp1, function as inhibitors of wnt signaling. microrna-1/206(mirna-1/206) is specifically expressed in skeletal muscle and play a critical role in myogenesis. the mirna-mrna profiles and bioinformatics study suggested that the sfrp1 gene was potentially regulated by mirna-1/206 during porcine skeletal muscle development. methods to understand the function of sfrp1 and mirna-1/206 in swine myogenesis, we first predicted the targets of mirna-1/206 with the targetscan and pictar programs, and analyzed the molecular characterization of the porcine sfrp1 gene. we performed a temporal-spatial expression analysis of sfrp1 mrna and mirna-206 in tongcheng pigs (a chinese indigenous breed) by quantitative real-time polymerase chain reaction, and conducted the co-expression analyses of sfrp1 and mirna-1/206. subsequently, the interaction between sfrp1 and mirna-1/206 was validated via dual luciferase and western blot assays. results the bioinformatics analysis predicted sfrp1 to be a target of mirna-1/206. the expression level of the sfrp1 was highly varied across numerous pig tissues and it was down-regulated during porcine skeletal muscle development. the expression level of the sfrp1 was significantly higher in the embryonic skeletal compared with postnatal skeletal muscle, whereas mir-206 showed the inverse pattern of expression. a significant negative correlation was observed between the expression of mir-1/206 and sfrp1 during porcine skeletal muscle development (p conclusions our results indicate that the sfrp1 gene is regulated by mir-1/206 and potentially affects skeletal muscle development. these findings increase understanding of the biological functions and the regulation of the sfrp1 gene in mammals.",1
"background app expression misregulation can cause genetic alzheimer's disease (ad). recent evidences support the hypothesis that polymorphisms located in microrna (mirna) target sites could influence the risk of developing neurodegenerative disorders such as parkinson's disease (pd) and frontotemporal dementia. recently, a number of single nucleotide polymorphisms (snps) located in the 3'utr of app have been found in ad patients with family history of dementia. because mirnas have previously been implicated in app expression regulation, we set out to determine whether these polymorphisms could affect mirna function and therefore app levels. results bioinformatics analysis identified twelve putative mirna bindings sites located in or near the app 3'utr variants t117c, a454g and a833c. among those candidates, seven mirnas, including mir-20a, mir-17, mir-147, mir-655, mir-323-3p, mir-644, and mir-153 could regulate app expression in vitro and under physiological conditions in cells. using luciferase-based assays, we could show that the t117c variant inhibited mir-147 binding, whereas the a454g variant increased mir-20a binding, consequently having opposite effects on app expression. conclusions taken together, our results provide proof-of-principle that app 3'utr polymorphisms could affect ad risk through modulation of app expression regulation, and set the stage for further association studies in genetic and sporadic ad.",1
"the molecular mechanisms for regulation of the genes involved in the biosynthesis of methionine and cysteine are poorly characterized in bacillus subtilis. analyses of the recently completed b. subtilis genome revealed 11 copies of a highly conserved motif. in all cases, this motif was located in the leader region of putative transcriptional units, upstream of coding sequences that included genes involved in methionine or cysteine biosynthesis. additional copies were identified in clostridium acetobutylicum and staphylococcus aureus, indicating conservation in other gram-positive genera. the motif includes an element resembling an intrinsic transcriptional terminator, suggesting that regulation might be controlled at the level of premature termination of transcription. the 5' portion of all of the leaders could fold into a conserved complex structure. analysis of the yitj gene, which is homologous to escherichia coli meth and metf, revealed that expression was induced by starvation for methionine and that induction was independent of the promoter and dependent on the leader region terminator. mutation of conserved primary sequence and structural elements supported a model in which the 5' portion of the leader forms an anti-antiterminator structure, which sequesters sequences required for the formation of an antiterminator, which, in turn, sequesters sequences required for the formation of the terminator; the anti-antiterminator is postulated to be stabilized by the binding of some unknown factor when methionine is available. this set of genes is proposed to form a new regulon controlled by a global termination control system, which we designate the s box system, as most of the genes are involved in sulphur metabolism and biosynthesis of methionine and cysteine.",1
"microrna-137 (mir-137) expression has been reported to be decreased in astrocytic tumors in two expression profiling studies but its role in the pathogenesis of oligodendroglial tumors is still limited. in this study, we demonstrate that mir-137 expression is significantly downregulated in a cohort of 35 oligodendroglial tumors and nine glioma cell lines compared with normal brains. lower mir-137 expression is associated with shorter progressive-free survival and overall survival. restoration of mir-137 expression in an oligodendroglial cells tc620, and also glioblastoma cells of u87 and u373 significantly suppressed cell growth, anchorage-independent growth, as well as invasion. demethylation and deacetylation treatments resulted in upregulation of mir-137 expression in tc620 cells. in silico analysis showed that cse1 chromosome segregation 1-like (yeast) (cse1l) is a potential target gene of mir-137. luciferase reporter assay demonstrated that mir-137 negatively regulates cse1l by interaction between mir-137 and complementary sequences in the 3' utr of cse1l. immunohistochemistry revealed that cse1l is upregulated in oligodendroglial tumors. knockdown of cse1l resulted in similar outcomes as overexpressing mir-137 in oligodendroglioma cells and glioblastoma cells. overall, our data suggest that mir-137 regulates growth of glioma cells and targets cse1l, providing further understanding in the tumorigenesis of gliomas.",1
"rationale retention of abnormal α1-antitrypsin (aat) activates the unfolded protein response in aat-deficient monocytes. the regulatory role of micrornas (mirnas) in unfolded protein responses and chronic obstructive pulmonary disease pathogenesis has not been investigated. objectives to investigate mirna expression and function in mm and zz monocytes and identify mirna(s) regulating the unfolded protein response. methods peripheral blood monocytes were isolated from asymptomatic and symptomatic mm and zz individuals for mirna expression profiling and pyrosequencing analysis. mirna/gene and protein expression was measured with quantitative polymerase chain reaction and western blotting. overexpression and inhibition studies were performed with pre-mir or anti-mir, respectively. luciferase reporter genes were used to elucidate direct mirna-target interactions. inflammatory cytokines were detected using the meso scale discovery plex assays. measurements and main results forty-three mirnas were differentially expressed, with mir-199a-5p most highly up-regulated in asymptomatic zz versus mm monocytes. mir-199a-2 promoter hypermethylation inhibits mir-199a-5p expression and was increased in symptomatic mm and zz monocytes compared with asymptomatic counterparts. grp78, activating transcription factor 6, p50, and p65 were increased in symptomatic versus asymptomatic zz monocytes. reciprocal down- or up-regulation of these markers was observed after mirna modulation. direct mir-199a-5p targeting of activating transcription factor 6, p50, and p65 by mir-199a-5p was demonstrated using luciferase reporter systems. overexpression of mir-199a-5p also decreased other arms of the upr and expression of cytokines that are not putative targets. conclusions mir-199a-5p is a key regulator of the unfolded protein response in aat-deficient monocytes, and epigenetic silencing of its expression regulates this process in chronic obstructive pulmonary disease.",1
"the activation of ras signaling is a major early event of oncogenesis in many contexts, yet paradoxically, ras signaling induces cellular senescence, which prevents tumorigenesis. thus, ras-activated cells must overcome senescence to develop into cancer. through a genetic screen in drosophila melanogaster , we found that the ets family transcriptional activator pointed (pnt) was necessary and sufficient to trigger cellular senescence upon ras activation and blocked ras-induced tumor growth in eye-antennal discs. through analyses of mosaic discs using various genetic tools, we identified a mechanism of tumor progression in which loss of cell polarity, a common driver of epithelial oncogenesis, abrogated ras-induced cellular senescence through microrna-mediated inhibition of pnt. mechanistically, polarity defects in ras-activated cells caused activation of the hippo effector yorkie (yki), which induced the expression of the microrna bantam bantam -mediated repression of the e3 ligase-associated protein tribbles (trbl) relieved ras- and akt-dependent inhibition of the transcription factor foxo. the restoration of foxo activity in ras-activated cells induced the expression of the micrornas mir-9c and mir-79 , which led to reduced pnt expression, thereby abrogating cellular senescence and promoting tumor progression. our findings provide a mechanistic explanation for how ras-activated tumors progress toward malignancy by overcoming cellular senescence.",1
"microrna-21 (mir-21) is a key regulator of oncogenic processes. it is significantly elevated in the majority of human tumors and functionally linked to cellular proliferation, survival and migration. in this study, we used two experimental-based strategies to search for novel mir-21 targets. on the one hand, we performed a proteomic approach using two-dimensional differential gel electrophoresis (2d-dige) to identify proteins suppressed upon enhanced mir-21 expression in lncap human prostate carcinoma cells. the tumor suppressor acidic nuclear phosphoprotein 32 family, member a (anp32a) (alias pp32 or lanp) emerged as the most strongly downregulated protein. on the other hand, we applied a mathematical approach to select correlated gene sets that are negatively correlated with primary-mir-21 (pri-mir-21) expression in published transcriptome data from 114 b-cell lymphoma cases. among these candidates, we found tumor suppressor smarca4 (alias brg1) together with the already validated mir-21 target, pdcd4. anp32a and smarca4, which are both involved in chromatin remodeling processes, were confirmed as direct mir-21 targets by immunoblot analysis and reporter gene assays. furthermore, knock down of anp32a mimicked the effect of enforced mir-21 expression by enhancing lncap cell viability, whereas overexpression of anp32a in the presence of high mir-21 levels abrogated the mir-21-mediated effect. in a172 glioblastoma cells, enhanced anp32a expression compensated for the effects of anti-mir-21 treatment on cell viability and apoptosis. in addition, mir-21 expression clearly increased the invasiveness of lncap cells, an effect also seen in part upon downregulation of anp32a. in conclusion, these results suggest that downregulation of anp32a contributes to the oncogenic function of mir-21.",1
"the developmental cycle of the obligate intracellular pathogen chlamydia trachomatis serovar l2 is controlled in part by the small non-coding rna (srna), ihta. all chlamydia alternate in a regulated fashion between the infectious elementary body (eb) and the replicative reticulate body (rb) which asynchronously re-differentiates back to the terminal eb form at the end of the cycle. the histone like protein hcta is central to rb:eb differentiation late in the cycle as it binds to and occludes the genome, thereby repressing transcription and translation. the srna ihta is a critical component of this regulatory loop as it represses translation of hcta until late in infection at which point ihta transcription decreases, allowing hcta expression to occur and rb to eb differentiation to proceed. it has been reported that ihta is expressed during infection by the human pathogens c. trachomatis serovars l2, d and l2b and c. pneumoniae. we show in this work that ihta is also expressed by the animal pathogens c. caviae and c. muridarum. expression of hcta in e. coli is lethal and co-expression of ihta relieves this phenotype. to determine if regulation of hcta by ihta is a conserved mechanism across pathogenic chlamydial species, we cloned hcta and ihta from c. trachomatis serovar d, c. muridarum, c. caviae and c. pneumoniae and assayed for rescue of growth repression in e. coli co-expression studies. in each case, co-expression of ihta with the cognate hcta resulted in relief of growth repression. in addition, expression of each chlamydial species ihta rescued the lethal phenotype of c. trachomatis serovar l2 hcta expression. as biolayer interferometry studies indicate that ihta interacts directly with hcta message for all species tested, we predict that conserved sequences of ihta are necessary for function and/or binding.",1
"neural patterning relies on transcriptional cross-repressive interactions that ensure unequivocal assignment of neural progenitor identity to proliferating cells. progenitors of spinal motor neurons (pmn) and v2 interneurons (p2) are specified by a pair of cross-repressive transcription factors, olig2 and irx3. lineage tracing revealed that many p2 progenitors transiently express the pmn marker olig2 during spinal cord development. here we demonstrate that the repression of olig2 in p2 domain is controlled by mir-17-3p microrna-mediated silencing of olig2 mrna. mice lacking all micrornas or just the mir-17∼92 cluster manifest a dorsal shift in pmn/p2 boundary and impairment in the production of v2 interneurons. our findings suggest that microrna-mediated repression of olig2 mrna plays a critical role during the patterning of ventral spinal progenitor domains by shifting the balance of cross-repressive interactions between olig2 and irx3 transcription factors.",1
"mirnas have emerged as master regulators of cancer-related events. mirna dysregulation also occurs in kaposi sarcoma (ks). exploring the roles of ks-associated mirnas should help to identify novel angiogenesis and lymphangiogenesis pathways. in the present study, we show that kaposi sarcoma-associated herpesvirus (kshv), the etiological agent of ks, induces global mirna changes in lymphatic endothelial cells (lecs). specifically, the mir-221/mir-222 cluster is down-regulated, whereas mir-31 is up-regulated. both latent nuclear antigen (lana) and kaposin b repress the expression of the mir-221/mir-222 cluster, which results in an increase of endothelial cell (ec) migration. in contrast, mir-31 stimulates ec migration, so depletion of mir-31 in kshv-transformed ecs reduces cell motility. analysis of the putative mirna targets among kshv-affected genes showed that ets2 and ets1 are the downstream targets of mir-221 and mir-222, respectively. fat4 is one of the direct targets of mir-31. overexpression of ets1 or ets2 alone is sufficient to induce ec migration, whereas a reduction in fat4 enhances ec motility. our results show that kshv regulates multiple mirna-mrna networks to enhance ec motility, which eventually contributes to ks progression by promoting the spread of malignant ks progenitor cells. targeting kshv-regulated mirnas or genes might allow the development of novel therapeutic strategies that induce angiogenesis or allow the treatment of pathogenic (lymph)angiogenesis.",1
"aim keloid is a benign dermal tumor with excessive hyperplasia and deposition of collagen. as a common tumor suppressor gene, mir-133a-3p has not been studied in keloid. this study will delve into the specific mechanism of mir-133a-3p in keloid. methods normal skin fibroblasts and keloid fibroblasts (kfs) were first isolated from patients' normal skin and keloid, and cells were identified by morphological observation and immunofluorescence. the expressions of mir-133a-3p and extracellular matrix (ecm)-associated markers (collagen i, iii and α smooth muscle activin) were detected by quantitative real time-polymerase chain reaction (qrt-pcr). cell viability and apoptosis of kfs were examined by cell counting kit-8 assay, flow cytometry, and caspase-3 colorimetry. targetscan predicted target gene for mir-133a-3p was verified by luciferase assay, qrt-pcr and western blot (wb). wb was used to study protein expression of tgfbr1, phosphorylated -smad2 (p-smad2) and smad2. finally, a series of rescue experiments were performed to verify the intervention of target genes on mir-133a-3p. results mir-133a-3p was lowly expressed in keloid tissue and kfs. overexpression of mir-133a-3p inhibited the expression of ecm-associated markers, reduced kfs viability, and promoted apoptosis. it was verified that interference regulator 5 (irf5) is mir-133a-3p target gene. the rescue experiments showed that irf5 reversed the effect of mir-133a-3p mimic on inhibiting fibrosis, and reversed the effects on promoting apoptosis and reducing cell proliferation. conclusion overexpressed mir-133a-3p inhibits fibrosis by down-regulating irf5 and thus inhibiting the tgf-β/smad2 pathway. and it also promotes kfs apoptosis and reduces proliferation.",1
"the full length, positive-strand genome of the moloney murine leukemia virus contains a ""core encapsidation signal"" that is essential for efficient genome packaging during virus assembly. we have determined the structure of a 101-nucleotide rna that contains this signal (called mpsi) using a novel isotope-edited nmr approach. the method is robust and should be generally applicable to larger rnas. mpsi folds into three stem loops, two of which (sl-c and sl-d) co-stack to form an extended helix. the third stem loop (sl-b) is connected to sl-c by a flexible, four-nucleotide linker. the structure contains five mismatched base-pairs, an unusual c.cg base-triple platform, and a novel ""a-minor k-turn,"" in which unpaired adenosine bases a340 and a341 of a ggaa bulge pack in the minor groove of a proximal stem, and a bulged distal uridine (u319) forms a hydrogen bond with the phosphodiester of a341. phylogenetic analyses indicate that these essential structural elements are conserved among the murine c-type retroviruses.",1
"pre-eclampsia is thought to be a systemic disease of maternal endothelial cell dysfunctions. mirnas regulate various basic biological functions in cells, including stem cells. mesenchymal stem cells exist in almost all tissues and are the key cellular source for tissue repair and regeneration. our aims are to investigate whether mirnas regulate mscs in fetal-maternal interfaces to influence the pathogenesis of pre-eclampsia. the differential expression of mirnas in decidua-derived mesenchymal stem cells of all patients with severe pre-eclampsia (n = 20) and normal groups (n = 20) was first screened by microarray analysis and validated by quantitative real-time pcr analysis. the integrated bioinformatics analysis showed that mir-16 showed the highest number of connections in the mirna go network and the mirna gene network. moreover, over-expressed mir-16 inhibited the proliferation and migration of decidua-derived mesenchymal stem cells and induced cell-cycle arrest by targeting cyclin e1. interestingly, over-expression of mir-16 by decidua-derived mesenchymal stem cells reduced the ability of human umbilical vein endothelial cells to form blood vessels and reduced the migration of trophoblast cells. furthermore, decidua-derived mesenchymal stem cell-expressed endothelial growth factor vegf-a was involved in migration of trophoblast cells and human umbilical vein endothelial cells as well as tube and network formation. importantly, the levels of cyclin e1 and vegf-a were negatively correlated with the level of mir-16 expression in decidua-derived mesenchymal stem cells from the patients with severe pre-eclampsia. together, these data suggest that the alteration of mir-16 expression in decidua-derived mesenchymal stem cells may be involved in the development of pre-eclampsia.",1
"idiopathic pulmonary fibrosis (ipf) is a fatal disorder resulting from the progressive remodeling of lungs, with no known effective treatment. although transforming growth factor (tgf)-β has a well-established role in lung fibrosis, clinical experience with neutralizing antibodies to tgf-β has been disappointing, and strategies to directly suppress tgf-β1 secretion are needed. in this study we used a combination of in silico, in vitro, and in vivo approaches to identify micrornas involved in tgf-β1 regulation and to validate the role of mir-326 in pulmonary fibrosis.we show that hsa-mir-326 regulates tgf-β1 expression and that hsa-mir-326 levels are inversely correlated to tgf-β1 protein levels in multiple human cell lines. the increase in tgf-β1 expression during the progression of bleomycin-induced lung fibrosis in mice was associated with loss of mmu-mir-326. restoration of mmu-mir-326 levels by intranasal delivery of mir-326 mimics was sufficient to inhibit tgf-β1 expression and attenuate the fibrotic response. moreover, human ipf lung specimens had markedly diminished mir-326 expression as compared with nonfibrotic lungs. additional targets of mir-326 controlling tgf-β signaling and fibrosis-related pathways were identified, and mir-326 was found to down-regulate profibrotic genes, such as ets1, smad3, and matrix metalloproteinase 9, whereas it up-regulates antifibrotic genes, such as smad7. our results suggest for the first time that mir-326 plays a key role in regulating tgf-β1 expression and other profibrotic genes and could be useful in developing better therapeutic strategies for alleviating lung fibrosis.",1
"inflammatory cytokines such as interleukin-17 (il-17) promote inflammatory autoimmune diseases. although several micrornas (mirnas) have been shown to regulate autoimmune pathogenesis by affecting lymphocyte development and function, the role of mirnas in resident cells present in inflammatory lesions remains unclear. here we show that mir-23b is downregulated in inflammatory lesions of humans with lupus or rheumatoid arthritis, as well as in the mouse models of lupus, rheumatoid arthritis or multiple sclerosis. il-17 downregulates mir-23b expression in human fibroblast-like synoviocytes, mouse primary kidney cells and astrocytes and is essential for the downregulation of mir-23b during autoimmune pathogenesis. in turn, mir-23b suppresses il-17-, tumor necrosis factor α (tnf-α)- or il-1β-induced nf-κb activation and inflammatory cytokine expression by targeting tgf-β-activated kinase 1/map3k7 binding protein 2 (tab2), tab3 and inhibitor of nuclear factor κ-b kinase subunit α (ikk-α) and, consequently, represses autoimmune inflammation. thus, il-17 contributes to autoimmune pathogenesis by suppressing mir-23b expression in radio-resident cells and promoting proinflammatory cytokine expression.",1
"background exosomes from cancer cells or immune cells, carrying bio-macromolecules or micrornas (mirnas), participate in tumor pathogenesis and progression by modulating microenvironment. our study aims to investigate the role of these microrna-501-3p (mir-501-3p) containing exosomes derived from tumor-associated macrophage (tam) in the progression of pancreatic ductal adenocarcinoma (pdac). methods firstly, the function of tam recruitment in pdac tissues was assessed, followed by identification of the effects of m2 macrophage-derived exosomes on pdac cell activities and tumor formation and metastasis in mice. in silico analysis was conducted to predict differentially expressed genes and regulatory mirnas related to pdac treated with macrophages, which determined mir-501-3p and tgfbr3 for subsequent experiments. next, gain- and loss-of-function experiments were performed to examine their role in pdac progression with the involvement of the tgf-β signaling pathway. results tam recruitment in pdac tissues was associated with metastasis. highly expressed mir-501-3p was observed in pdac tissues and tam-derived exosomes. both m2 macrophage-derived exosomes and mir-501-3p promoted pdac cell migration and invasion, as well as tumor formation and metastasis in nude mice. mir-501-3p was verified to target tgfbr3. pdac cells presented with down-regulated tgfbr3, which was further decreased in response to m2 macrophage treatment. tgf-β signaling pathway activation was implicated in the promotion of mir-501-3p in pdac development. the suppression of macrophage-derived exosomal mir-501-3p resulted in the inhibition of tumor formation and metastasis in vivo. conclusion m2 macrophage-derived exosomal mir-501-3p inhibits tumor suppressor tgfbr3 gene and facilitates the development of pdac by activating the tgf-β signaling pathway, which provides novel targets for the molecular treatment of pdac.",1
"microrna-663 (mir-663) has been detected in a large variety of tumor types; however, it still holds both tumor suppressive and oncogenic roles in different tumor types. the mirna-chip microarray assay revealed downregulation of mir-663 in papillary thyroid carcinoma (ptc); however, the effect of mir-663 on ptc cell invasion and migration remains unknown. accordingly, this study aimed to investigate the potential involvement of mir-663 in ptc. in this study, mir-663 expression level was measured via quantitative real-time pcr in 91 pairs of human ptc and adjacent normal tissues and in two human ptc cell lines. the effect of mir-663 on ptc cell invasion and migration were studied by transwell and wound healing assays. in addition, the mir-663 target was searched and the underlying mechanism was clarified by reporter assay and rescue experiment. the current study confirmed that mir-663 expression was inhibited in ptc tissue samples and ptc cell lines. there were statistically significant differences in expression of mir-663 with regard to age and tumor size. upregulation of mir-663 suppressed ptc cell invasion and migration. further study showed that transforming growth factor beta 1 (tgfβ1) was the direct target of mir-663 and mediated the effect of mir-663 on ptc development. by targeting tgfβ1, mir-663 efficiently regulates the expression of epithelial-mesenchymal transition (emt) markers and matrix metalloproteinases (mmps). the data indicated that mir-663 may suppress tumor invasion and migration by targeting tgfβ1 and regulate emt progress of ptc cells.",1
"subnuclear fractionation and coprecipitation by antibodies against the nucleolar protein nop1 demonstrate that the essential saccharomyces cerevisiae rna snr30 is localized to the nucleolus. by using aminomethyl trimethyl-psoralen, snr30 can be cross-linked in vivo to 35s pre-rrna. to determine whether snr30 has a role in rrna processing, a conditional allele was constructed by replacing the authentic snr30 promoter with the gal10 promoter. repression of snr30 synthesis results in a rapid depletion of snr30 and a progressive increase in cell doubling time. rrna processing is disrupted during the depletion of snr30; mature 18s rrna and its 20s precursor underaccumulate, and an aberrant 23s pre-rrna intermediate can be detected. initial results indicate that this 23s pre-rrna is the same as the species detected on depletion of the small nucleolar rna-associated proteins nop1 and gar1 and in an snr10 mutant strain. it was found that the 3' end of 23s pre-rrna is located in the 3' region of its1 between cleavage sites a2 and b1 and not, as previously suggested, at the b1 site, snr30 is the fourth small nucleolar rna shown to play a role in rrna processing.",1
"dysregulation of micrornas is a common feature in human cancers, including breast cancer (bc). here we describe the epigenetic regulation of mir-148a and mir-152 and their impact on bc cells. due to the hypermethylation of cpg island, the expression levels of both mir-148a and mir-152 (mir-148a/152) are decreased in bc tissues and cells. dnmt1, the dna methyltransferase 1 for the maintenance methylation, is aberrantly up-regulated in bc and its overexpression is responsible for hypermethylation of mir-148a and mir-152 promoters. intriguingly, we found that dnmt1 expression, which is one of the targets of mir-148a/152, is inversely correlated with the expression levels of mir-148a/152 in bc tissues. those results lead us to propose a negative feedback regulatory loop between mir-148a/152 and dnmt1 in bc. more importantly, we demonstrate that igf-ir and irs1, often overexpressed in bc, are two novel targets of mir-148a/152. overexpression of mir-148a or mir-152 significantly inhibits bc cell proliferation, colony formation, and tumor angiogenesis via targeting igf-ir and irs1 and suppressing their downstream akt and mapk/erk signaling pathways. our results suggest a novel mir-148a/152-dnmt1 regulatory circuit and reveal that mir-148a and mir-152 act as tumor suppressors by targeting igf-ir and irs1, and that restoration of mir-148a/152 expression may provide a strategy for therapeutic application to treat bc patients.",1
"micrornas (mirnas) play important roles in regulating a plethora of physiological and pathophysiogical processes including neurodegeneration. in both hiv associated dementia in humans and its monkey model siv encephalitis we find mir-21, a mirna largely known for its link to oncogenesis, to be significantly upregulated in the brain. in situ hybridization of the diseased brain sections revealed induction of mir-21 in neurons. mir-21 can be induced in neurons by prolonged n-methyl-d-aspartic acid receptor stimulation, an excitotoxic process active in hiv and other neurodegenerative diseases. introduction of mir-21 into human neurons leads to pathological functional defects. furthermore, we show that mir-21 specifically targets the mrna of myocyte enhancer factor 2c (mef2c), a transcription factor crucial for neuronal function, and reduces its expression. mef2c is dramatically downregulated in neurons of hiv-associated dementia patients as well as monkeys with sive. together, this study elucidates a novel role for mir-21 in the brain, not only as a potential signature of neurological disease but also as a crucial effector of hiv induced neuronal dysfunction and neurodegeneration.",1
"the cellular prion protein (prp c ) is best known for its misfolded disease-causing conformer, prp sc . because the availability of prp c is often limiting for prion propagation, understanding its regulation may point to possible therapeutic targets. we sought to determine to what extent the human micrornaome is involved in modulating prp c levels through direct or indirect pathways. we probed prp c protein levels in cells subjected to a genome-wide library encompassing 2019 mirna mimics using a robust time-resolved fluorescence-resonance screening assay. screening was performed in three human neuroectodermal cell lines: u-251 mg, chp-212 and sh-sy5y. the three screens yielded 17 overlapping high-confidence mirna mimic hits, 13 of which were found to regulate prp c biosynthesis directly via binding to the prnp 3'utr, thereby inducing transcript degradation. the four remaining hits (mir-124-3p, 192-3p, 299-5p and 376b-3p) did not bind either the 3'utr or cds of prnp, and were therefore deemed indirect regulators of prp c . our results show that multiple mirnas regulate prp c levels both directly and indirectly. these findings may have profound implications for prion disease pathogenesis and potentially also for their therapy. furthermore, the possible role of prp c as a mediator of aβ toxicity suggests that its regulation by mirnas may also impinge on alzheimer's disease.",1
"micrornas have recently emerged as key regulators of gastric cancers. here we found that mir-145, mir-133a and mir-133b were down-regulated in gastric cancer tissues and cell lines. overexpression of mir-145, mir-133a and mir-133b induced g1 cell cycle arrest and inhibited cell proliferation, migration and invasion in vitro. mir-145, mir-133a and mir-133b targeted the transcription factor sp1, knockdown of which reduced the expression of mmp-9 and cyclin d1 that were involved in cell growth and invasion. thus, our findings demonstrated for the first time that mir-145, mir-133a and mir-133b suppressed the proliferation, migration, invasion and cell cycle progression of gastric cancer cells through decreasing expression of sp1 and its downstream proteins.",1
"retrovirus insertion-mediated random mutagenesis was applied in 3t3-l1 preadipocyte cells to better understand the molecular basis of obesity (the expansion of individual adipocytes). we found that tryptophan hydroxylase-1, a rate-limiting enzyme for the synthesis of serotonin (5-ht), is expressed in adipocytes and is required for their differentiation. a 5-ht type 2a receptor (5-ht(2a)r) antagonist, ketanserin, and a 5-ht(2c)r antagonist, sb-242084, inhibited adipocyte differentiation. because 5-ht(2c)r mrna levels are up-regulated during adipocyte differentiation and micro-rna (mir)-448 is located in the fourth intron of htr2c, we also studied the role of mir-448 in 3t3-l1 cells. through a bioinformatics approach, krüppel-like factor 5 (klf5) was identified as a potential target of mir-448. using a luciferase reporter assay, we confirmed that mir-448 targets the klf5 3'-intranslated region. overexpression of mir-448 reduced the expression of klf5 and adipocyte differentiation, which was confirmed by the reduced expression of adipogenic genes and triglyceride accumulation. to examine the loss of mir-448 function, we constructed a decoy gene that had tandem complementary sequences for mir-448 in the 3'-untranslated region of a luciferase gene under the control of a cytomegalovirus promoter. when the mir-448 decoy gene was introduced into 3t3-l1 preadipocytes, klf5 was up-regulated and triglyceride concentration was increased. in this study, we identified the regulation of adipocyte differentiation by 5-ht, 5-ht(2a)r, and 5-ht(2c)r. mir-448-mediated repression of klf5 was identified as a negative regulator for adipocyte differentiation.",1
"vertebrate tissues exhibit mechanical homeostasis, showing stable stiffness and tension over time and recovery after changes in mechanical stress. however, the regulatory pathways that mediate these effects are unknown. a comprehensive identification of argonaute 2-associated micrornas and mrnas in endothelial cells identified a network of 122 microrna families that target 73 mrnas encoding cytoskeletal, contractile, adhesive and extracellular matrix (cam) proteins. the level of these micrornas increased in cells plated on stiff versus soft substrates, consistent with homeostasis, and suppressed targets via microrna recognition elements within the 3' untranslated regions of cam mrnas. inhibition of drosha or argonaute 2, or disruption of microrna recognition elements within individual target mrnas, such as connective tissue growth factor, induced hyper-adhesive, hyper-contractile phenotypes in endothelial and fibroblast cells in vitro, and increased tissue stiffness, contractility and extracellular matrix deposition in the zebrafish fin fold in vivo. thus, a network of micrornas buffers cam expression to mediate tissue mechanical homeostasis.",1
"microrna-1 (mir-1) is an evolutionarily conserved, striated muscle-enriched mirna. most mammalian genomes contain two copies of mir-1, and in mice, deletion of a single locus, mir-1-2, causes incompletely penetrant lethality and subtle cardiac defects. here, we report that deletion of mir-1-1 resulted in a phenotype similar to that of the mir-1-2 mutant. compound mir-1 knockout mice died uniformly before weaning due to severe cardiac dysfunction. mir-1-null cardiomyocytes had abnormal sarcomere organization and decreased phosphorylation of the regulatory myosin light chain-2 (mlc2), a critical cytoskeletal regulator. the smooth muscle-restricted inhibitor of mlc2 phosphorylation, telokin, was ectopically expressed in the myocardium, along with other smooth muscle genes. mir-1 repressed telokin expression through direct targeting and by repressing its transcriptional regulator, myocardin. our results reveal that mir-1 is required for postnatal cardiac function and reinforces the striated muscle phenotype by regulating both transcriptional and effector nodes of the smooth muscle gene expression network. doi:",1
"micrornas (mirnas) are small non-protein coding rnas and post-transcriptionally regulate cellular gene expression. in animal development, mirnas play essential roles such as stem cell maintenance, organogenesis, and apoptosis. using gain-of-function (gof) screening with 160 mirna lines in drosophila melanogaster, we identified a set of mirnas which regulates body fat contents and named them microcats (micrornas controlling adipose tissue). further examination of egg-to-adult developmental kinetics of selected mirna lines showed a negative correlation between fat content and developmental time. comparison of microcats with loss-of-function mirna screening data uncovered mir-969 as an essential regulator of adiposity. subsequently, we demonstrated adipose tissue-specific knock-down of gustatory receptor 47b (gr47b), a mir-969 target, greatly reduced the amount of body fat, recapitulating the mir-969 gof phenotype.",1
"female sterile (1) yb (yb) is a primary component of yb bodies, perinuclear foci considered to be the site of piwi-interacting rna (pirna) biogenesis in drosophila ovarian somatic cells (oscs). yb consists of three domains: helicase c-terminal (hel-c), rna helicase, and extended tudor (etud) domains. we previously showed that the rna helicase domain is necessary for yb-rna interaction, yb body formation, and pirna biogenesis. here, we investigate the functions of hel-c and etud and reveal that hel-c is dedicated to yb-yb homotypic interaction, while etud is necessary for yb-rna association, as is the rna helicase domain. all of these domains are indispensable for yb body formation and transposon-repressing pirna production. strikingly, however, genic pirnas unrelated to transposon silencing are produced in oscs where yb bodies are disassembled. we also reveal that yb bodies are liquid-like multivalent condensates whose assembly depends on yb-yb homotypic interaction and yb binding particularly with flamenco rna transcripts, the source of transposon-repressing pirnas. new insights into yb body assembly and biological relevance of yb bodies in transposon silencing have emerged.",1
"the translation of many heat shock and virulence genes is controlled by rna thermometers. usually, they are located in the 5'-untranslated region (5'-utr) and block the shine-dalgarno (sd) sequence by base pairing. destabilization of the structure at elevated temperature permits ribosome binding and translation initiation. we have identified a new type of rna thermometer in the 5'-utr of the salmonella agsa gene, which codes for a small heat shock protein. transcription of the agsa gene is controlled by the alternative sigma factor sigma(32). additional translational control depends on a stretch of four uridines that pair with the sd sequence. mutations in this region affect translation in vivo. structure probing experiments demonstrate a temperature-controlled opening of the sd region in vitro. toeprinting (primer extension inhibition) shows that ribosome binding is dependent on high temperatures. together with a postulated rna thermometer upstream of the yersinia pestis virulence gene lcrf (virf), the 5'-utr of salmonella agsa might be the founding member of a new class of rna thermometers that we propose to name 'fouru' thermometers.",1
"epithelial-mesenchymal transition (emt) is an important parameter related to breast cancer survival. among several micrornas predicted to target emt-related genes, mir-506 is a novel mirna found to be significantly related to breast cancer patient survival in a meta-analysis. mir-506 suppressed the expression of mesenchymal genes such as vimentin, snai2, and cd151 in mda-mb-231 human breast cancer cell line. moreover, nf-κb bound to the upstream promoter region of mir-506 to suppress transcription. overexpression of mir-506 inhibited tgfβ-induced emt and suppressed adhesion, invasion, and migration of mda-mb-231 cells. from these results, we concluded that mir-506 plays a key role in the process of emt through posttranslational control of emt-related genes.",1
"although micrornas (mirnas) are postulated to fine-tune many developmental processes, their relationships with specific targets and tissues remain largely undefined. the mesenchymal transcription factor barx1 controls spleen and stomach morphogenesis and is required to specify stomach-specific epithelium in adjacent endoderm. barx1 expression is precisely regulated in space and time, with a sharp drop in stomach levels after epithelial specification. we tested the hypothesis that specific mirnas mediate this marked decline in barx1 levels. depletion of the mirna-processing enzyme dicer in cultured stomach mesenchyme and conditional dicer gene deletion in mice significantly increased barx1 levels, disrupted stomach and intestine development and caused spleen agenesis. computational and experimental studies identified mir-7a and mir-203 as candidate mirnas that regulate barx1 and are expressed in inverse proportion to it in the fetal mouse stomach. through specific interactions with cognate sequences in the barx1 3' untranslated region, mir-7a and mir-203 repress barx1 expression in stomach mesenchymal cells and its function in inducing gastric epithelium. these results indicate that mirnas are required for proper digestive tract organogenesis and that mir-7a and mir-203 control expression of the stomach homeotic regulator barx1.",1
"background previous studies have demonstrated pivotal roles of disintegrin and metalloproteinase 10 (adam10) in the pathogenesis of sepsis. microrna- (mir-) 23b has emerged as an anti-inflammatory factor that prevents multiple autoimmune diseases. however, the underlying mechanisms of mir-23b in the regulation of adam10 and sepsis remain uncharacterized. methods the expression levels of adam10 and mir-23b were detected by quantitative rt-pcr and western blot analysis. cytokine production and thp-1 cell apoptosis were measured by enzyme-linked immunosorbent and annexin v apoptosis assays. bioinformatics analyses and qrt-pcr, western blot, and luciferase reporter assays were performed to identify adam10 as the target gene of mir-23b. results mir-23b expression was downregulated in the peripheral blood mononuclear cells of sepsis patients and lps-induced thp-1 cells and was negatively correlated with the expression of adam10 and inflammatory cytokines. mir-23b regulated adam10 expression by directly binding to the 3'-utr of adam10 mrna. the overexpression of mir-23b alleviated the lps-stimulated production of inflammatory cytokines (tnf- α , il-1 β , and il-6) and apoptosis by targeting adam10 in thp-1 cells. the inhibitor or knockdown of adam10 elicited effects similar to those of mir-23b on thp-1 cells upon lps stimulation. conclusions the present study demonstrated that mir-23b negatively regulated lps-induced inflammatory responses by targeting adam10. the molecular regulatory mechanism of mir-23b in adam10 expression and sepsis-induced inflammatory consequences may provide potential therapeutic targets for sepsis.",1
"background hepatocellular carcinoma (hcc) ranks fourth among the malignancies leading to cancer-related deaths all around the world. it is increasingly evident that long non-coding rnas (lncrnas) are a key mode of hepatocarcinogenesis. as the most prevalent mrna modification form, n 6 -methyladenosine (m 6 a) regulates gene expression by impacting multiple aspects of mrna metabolism. however, there are still no reports on genome-wide screening and functional annotation of m 6 a-methylated lncrnas in hcc. methods the m 6 a modification and biologic functions of arhgap5-as1 in hcc were investigated through a series of biochemical assays. clinical implications of arhgap5-as1 were examined in tissues from hcc patients. results after systematically analysing the m 6 a-seq data of hcc cells, we identified 22 candidate lncrnas with evidently dysregulated m 6 a levels. among these lncrnas, we found that arhgap5-as1 is the lncrna with the highest levels of m 6 a modification and significantly increased expression in hcc specimens. mettl14 acts as the m 6 a writer of arhgap5-as1 and igf2bp2 stabilises the lncrna as its m 6 a reader. arhgap5-as1 remarkably promotes malignant behaviours of hcc cells ex vivo and in vivo. we identified oncoprotein csde1 working as the interacting protein of the lncrna and trim28 as the e3 ligase of csde1 in hcc. interestingly, arhgap5-as1 could attenuate interactions between csde1 and trim28, which prevents the degradation of csde1 via the ubiquitin-proteasome pathway. elevated levels of csde1 coordinate oncogenic rna regulons, promote translation of vim and rac1 and activate the erk pathway, which contributes to hcc prognosis. conclusions our study reveals a new paradigm in m 6 a-modified lncrnas controlling csde1-mediated oncogenic rna regulons and highlights lncrnas as potential targets for future therapeutics against hcc.",1
"mir-519d belongs to the chromosome 19 mirna cluster (c19mc), the largest human mirna cluster. one of its members, mir-519d, is over-expressed in hepatocellular carcinoma (hcc) and we characterized its contribution to hepatocarcinogenesis. in hcc cells, the over-expression of mir-519d promotes cell proliferation, invasion and impairs apoptosis following anticancer treatments. these functions are, at least in part, exerted through the direct targeting of cdkn1a/p21, pten, akt3 and timp2. the mechanisms underlying mir-519d aberrant expression in hcc were assayed by genomic dna amplification, methylation analysis and chip assay. the aberrant hypomethylation of c19mc and tp53 were respectively identified as an epigenetic change allowing the aberrant expression of mir-519d and one of the factors able to activate its transcription. in conclusion, we assessed the oncogenic role of mir-519d in hcc by characterizing its biological functions, including the modulation of response to anticancer treatments and by identifying cdkn1a/p21, pten, akt3 and timp2 among its targets.",1
"gastric cancer (gc) is one of the most common malignant tumors and recent data demonstrates the tumor suppressor role of vgll4 in gc, but the mechanisms for vgll4 downregulation in gc remain to be elucidated. here, we confirmed the suppressor role of vgll4 on proliferation and invasion in gc cells with over-activated yap-tead signal, and indicated the reverse correlation between expression patters of vgll4 and mir-222. bioinformatics analysis combined with experimental confirmation revealed vgll4 is a direct target of mir-222 in gc cells. functionally, mir-222 inhibitor significantly inhibited gc cells proliferation and invasion and vgll4 knockdown abolished the effects of mir-222 inhibitor. moreover, tead1 knockdown resulted in decrease of mir-222 expression and increase of vgll4 expression, and also resulted in reduction of luciferase activity driven by mir-222 promoter in gc cells, suggesting over-activated tead1 positively feedback transcriptionally regulates mir-222 expression via physically binding to the mir-222 promoter indicated by chip assay. collectively, our findings implied the important role of mir-222/vgll4/yap-tead1 regulatory loop maintaining over-activated yap-tead1 signal in gc cells, and enriched the rationale of vgll4 in gc based on which a promising therapeutic strategy will be developed.",1
"micrornas are a group of endogenously expressed, single-stranded, 18-24 nt rnas that regulate diverse cellular pathways. although documented evidence indicates that some micrornas can function as oncogenes or tumor-suppressors, the role of mir-214 in regulating human cervical cancer cells remains unexplored. we determined the expression level of mir-214 and found it is downregulated in cervical cancer compared with normal tissue. overexpression of mir-214 in hela cells, a human cervical cancer cell line, significantly inhibited cell proliferation according to the mtt and colony forming assays. hela cells that stably overexpress mir-214 downregulate the expression of mek3 and jnk1 at both mrna and protein levels. further investigation revealed that mir-214 regulates the expression of mek3 and jnk1 by targeting the 3'utrs of these genes. collectively, these results suggest that mir-214 negatively regulates hela cell proliferation by targeting the noncoding regions of mek3 and jnk1 mrnas.",1
"quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers. this process allows community-wide synchronization of gene expression. a screen for additional components of the vibrio harveyi and vibrio cholerae quorum-sensing circuits revealed the protein hfq. hfq mediates interactions between small, regulatory rnas (srnas) and specific messenger rna (mrna) targets. these interactions typically alter the stability of the target transcripts. we show that hfq mediates the destabilization of the mrna encoding the quorum-sensing master regulators luxr (v. harveyi) and hapr (v. cholerae), implicating an srna in the circuit. using a bioinformatics approach to identify putative srnas, we identified four candidate srnas in v. cholerae. the simultaneous deletion of all four srnas is required to stabilize hapr mrna. we propose that hfq, together with these srnas, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode.",1
"microrna (mirna) functions in the pathogenesis of major neurodegenerative diseases such as alzheimer's disease (ad) are only beginning to emerge. we have observed significantly elevated levels of a specific mirna, mir-26b, in the defined pathological areas of human postmortem brains, starting from early stages of ad (braak iii). ectopic overexpression of mir-26b in rat primary postmitotic neurons led to the dna replication and aberrant cell cycle entry (cce) and, in parallel, increased tau-phosphorylation, which culminated in the apoptotic cell death of neurons. similar tau hyperphosphorylation and cce are typical features of neurons in pre-ad brains. sequence-specific inhibition of mir-26b in culture is neuroprotective against oxidative stress. retinoblastoma protein (rb1), a major tumor suppressor, appears as the key direct mir-26b target, which mediates the observed neuronal phenotypes. the downstream signaling involves upregulation of rb1/e2f cell cycle and pro-apoptotic transcriptional targets, including cyclin e1, and corresponding downregulation of cell cycle inhibitor p27/kip1. it further leads to nuclear export and activation of cdk5, a major kinase implicated in tau phosphorylation, regulation of cell cycle, and death in postmitotic neurons. therefore, upregulation of mir-26b in neurons causes pleiotropic phenotypes that are also observed in ad. elevated levels of mir-26b may thus contribute to the ad neuronal pathology.",1
"ephb2 is an important member of the receptor tyrosine kinases. recently, ephb2 was shown to facilitate t-cell migration and monocyte activation. however, the effects of ephb2 on b cells remain unknown. in this study, the expression of ephb2 on b cells was tested by western blot, and the roles of ephb2 in b-cell proliferation, cytokine secretion, and immunoglobulin (ig) production were evaluated using ephb2 sirna interference in human b cells from healthy volunteers. our study revealed that ephb2 was distributed on naive b cells and was up-regulated on activated b cells. moreover, b-cell proliferation (decreased by 22%, p<0.05), tnf-α secretion (decreased by 40%, p<0.01) and igg production (decreased by 26%, p < 0.05) were depressed concordantly with the down-regulated ephb2 expression. subsequently, we screened micrornas that could regulate ephb2 expression in b cells, and discovered that mir-185 directly targeted to ephb2 mrna and suppressed its expression. furthermore, mir-185 overexpression inhibited b-cell activation, and the inhibitor of mir-185 enhanced b-cell activation. moreover, abatement of ephb2 through mir-185 mimics or ephb2 sirna attenuated the activation of src-p65 and notch1 signaling pathways in human b cells. our study first suggested that ephb2 was involved in human naive b cell activation through src-p65 and notch1 signaling pathways and could be regulated by mir-185.",1
"micrornas are important in cancer development and progression. in the present study, the clinical significance and function of microrna-711 (mir-711) expression in breast cancer were investigated. the expression level of mir-711 was analyzed in breast cancer tissue samples using reverse transcription-quantitative polymerase chain reaction. cell proliferation, colony formation, apoptosis and transwell assays were performed in breast cancer cell lines transfected with mir-711 mimics or inhibitors, or control sequence. mir-711 was found to be upregulated in 30 formalin-fixed paraffin-embedded breast cancer tissue samples compared with paired non-cancerous breast tissues (p in vitro , overexpression of mir-711 resulted in a significant increase in proliferation, colony formation, migration and invasion of breast cancer cells. by contrast, downregulating mir-711 inhibited cell proliferation, colony formation, migration and invasion and enhanced the rate of apoptosis of breast cancer cells. to the best of our knowledge, the present study is the first to demonstrate that mir-711 is an independent prognostic factor and serves an important oncogenic function in breast cancer, suggesting that mir-711 is a potential biomarker of prognosis and a molecular therapeutic target in breast cancer.",1
"micrornas (mirnas) represent an abundant group of small non-coding rnas that regulate gene expression, and have been demonstrated to play roles as tumor suppressor genes (oncogenes), and affect homeostatic processes such as development, cell proliferation, and cell death. subsequently, epidermal growth factor-like domain 7 (egfl7), which is confirmed to be involved in cellular responses such as cell migration and blood vessel formation, is identified as a potential mir-126 target by bioinformatics. however, there is still no evidence showing egfl7's relationship with mir-126 and the proliferation of lung cancer cells. the aim of this work is to investigate whether mir-126, together with egfl7, have an effect on non-small cell lung cancer (nsclc) cells' proliferation. therefore, we constructed overexpressed mir-126 plasmid to target egfl7 and transfected them into nsclc cell line a549 cells. then, we used methods like quantitative rt-pcr, western blot, flow cytometry assay, and immunohistochemistry staining to confirm our findings. the result was that overexpression of mir-126 in a549 cells could increase egfl7 expression. furthermore, the most notable finding by cell proliferation related assays is that mir-126 can inhibit a549 cells proliferation in vitro and inhibit tumor growth in vivo by targeting egfl7. as a result, our study demonstrates that mir-126 can inhibit proliferation of non-small cell lung cancer cells through one of its targets, egfl7.",1
"the bacterial small heat shock protein ibpa protects client proteins from aggregation. due to redundancy in the cellular chaperone network, deletion of the ibpa gene often leads to only a mild or no phenotypic defect. in this study, we show that a pseudomonas putida ibpa deletion mutant has a severe growth defect under heat stress conditions and reduced survival during recovery revealing a critical role of ibpa in heat tolerance. transcription of the ibpa gene depends on the alternative heat shock sigma factor σ(32). production of ibpa protein only at heat shock temperatures suggested additional translational control. we conducted a comprehensive structural and functional analysis of the 5' untranslated regions of the ibpa genes from p. putida and pseudomonas aeruginosa. both contain a rose-type rna thermometer that is substantially shorter and simpler than previously reported rose elements. comprised of two hairpin structures only, they inhibit translation at low temperature and permit translation initiation after a temperature upshift. both elements regulate reporter gene expression in escherichia coli and ribosome binding in vitro in a temperature-dependent manner. structure probing revealed local melting of the second hairpin whereas the first hairpin remained unaffected. high sequence and structure conservation of pseudomonal ibpa untranslated regions and their ability to confer thermoregulation in vivo suggest that short rose-like thermometers are commonly used to control ibpa synthesis in pseudomonas species.",1
"micrornas (mirna) have tumor suppressive and oncogenic potential in human cancer, but whether and how mirnas control cell cycle progression is not understood. to address this question, we carried out a comprehensive analysis of mirna expression during serum stimulation of quiescent human cells. time course analyses revealed that four mirnas are up-regulated and >100 mirnas are down-regulated, as cells progress beyond the g(1)-s phase transition. we analyzed the function of two up-regulated mirnas (mir-221 and mir-222) that are both predicted to target the cell growth suppressive cyclin-dependent kinase inhibitors p27 and p57. our results show that mir-221 and mir-222 both directly target the 3' untranslated regions of p27 and p57 mrnas to reduce reporter gene expression, as well as diminish p27 and p57 protein levels. functional studies show that mir-221 and mir-222 prevent quiescence when elevated during growth factor deprivation and induce precocious s-phase entry, thereby triggering cell death. thus, the physiologic up-regulation of mir-221 and mir-222 is tightly linked to a cell cycle checkpoint that ensures cell survival by coordinating competency for initiation of s phase with growth factor signaling pathways that stimulate cell proliferation.",1
"objective to investigate the expression and effect of the microrna-34 (mir-34) family on apoptosis in rheumatoid arthritis synovial fibroblasts (rasfs). methods expression of the mir-34 family in synovial fibroblasts with or without stimulation with toll-like receptor (tlr) ligands, tumor necrosis factor α (tnfα), interleukin-1β (il-1β), hypoxia, or 5-azacytidine was analyzed by real-time polymerase chain reaction (pcr). promoter methylation was studied by combined bisulfite restriction analysis. the effects of overexpression and silencing of mir-34a and mir-34a* on apoptosis were analyzed by annexin v/propidium iodide staining. production of x-linked inhibitor of apoptosis protein (xiap) was assessed by real-time pcr and immunohistochemistry analysis. reporter gene assay was used to study the signaling pathways of mir-34a*. results basal expression levels of mir-34a* were found to be reduced in synovial fibroblasts from ra patients compared to osteoarthritis patients, whereas levels of mir-34a, mir-34b/b*, and mir-34c/c* did not differ. neither tnfα, il-1β, tlr ligands, nor hypoxia altered mir-34a* expression. however, we demonstrated that the promoter of mir-34a/34a* was methylated and showed that transcription of the mir-34a duplex was induced upon treatment with demethylating agents. enforced expression of mir-34a* led to an increased rate of fasl- and trail-mediated apoptosis in rasfs. moreover, levels of mir-34a* were highly correlated with expression of xiap, which was found to be up-regulated in ra synovial cells. finally, we identified xiap as a direct target of mir-34a*. conclusion our data provide evidence of a methylation-specific down-regulation of proapoptotic mir-34a* in rasfs. decreased expression of mir- 34a* results in up-regulation of its direct target xiap, thereby contributing to resistance of rasfs to apoptosis.",1
"srna-xcc1 is a trans-acting srna recently identified from the plant pathogenic bacterium xanthomonas campestris pathovar campestris (xcc). here, the phylogenetic distribution, predicted secondary structure and regulation of expression of srna-xcc1 were analyzed. the analysis showed (1) a total 81 srna-xcc1 homologs that are found in some bacterial strains that are taxonomically unrelated, belonging to the α-, β-, γ- and δ-proteobacteria (2) that some srna-xcc1 homologs are located in a plasmid-borne transposon or near a transposase coding gene, (3) that srna-xcc1 is encoded by a integron gene cassette in xcc and srna-xcc1 homologs occur in integron gene cassettes of some uncultured bacteria and (4) that srna-xcc1 homologs have a highly conserved sequence motif and a stable consensus secondary structure. these findings strongly support the idea that srna-xcc1 represents a novel family of srnas which may be originally captured by integrons from natural environments and then spread among different bacterial species via horizontal gene transfer, possibly by means of transposons and plasmids. the expression analysis results demonstrated that the transcription of srna-xcc1 is under the positive control of the key virulence regulators hrpg and hrpx, indicating that srna-xcc1 may be involved in the virulence regulation of xcc.",1
"genes in caenorhabditis elegans operons are transcribed as polycistronic pre-mrnas in which downstream gene products are trans spliced to a specialized spliced leader, sl2. sl2 is donated by a 110-nucleotide rna, sl2 rna, present in the cell as an sm-bound snrnp. sl2 rna can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. here we report an in vivo mutational analysis of the sl2 rna. some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss in trans-splicing efficiency. however, the primary sequence of stem ii is crucial for sl2 trans splicing. similarly, the conserved primary sequence of the third stem-loop plays a key role in trans splicing. while mutations in stem-loop iii allow snrnp formation, a single nucleotide substitution in the loop prevents trans splicing. in contrast, the analogous region of sl1 rna is not highly conserved, and its mutation does not abrogate function. thus, stem-loop iii appears to confer a specific function to sl2 rna. finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for sl2 rna expression.",1
"micrornas (mirnas) are short, non-coding rnas with post-transcriptional regulatory function, playing crucial roles in cancer development and progression of human melanoma. previous studies have indicated that mir-769 was implicated in diverse biological processes. however, the underlying mechanism of mir-769 in human melanoma has not been intensively investigated. in this present study, we aimed to investigate the role of mir-769 and its target genes in human melanoma. we found that mir-769 expression was strongly increased in human melanoma cells and clinical tissues compared with their corresponding controls. overexpression of mir-769 promoted cell proliferation in human melanoma cell line a375, whereas mir-769-in reverses the function. glycogen synthase kinase-3 beta (gsk3b), a potential target gene of mir-769, and was validated by luciferase assay. further studies revealed that mir-769 regulated cell proliferation of human melanoma by directly suppressing gsk3b expression and the knockdown of gsk3b expression reversed the effect of mir-769-in on human melanoma cell proliferation. in summary, our data demonstrated that mir-769 might act as a tumor promoter by targeting gsk3b during development of human melanoma.",1
"expression of genes involved in absorption, distribution, metabolism, and excretion (adme) of drugs is impaired in pathophysiologic conditions such as cholestasis and inflammation. the mechanisms of adme gene down-regulation remain unclear. in our previous study, strongly elevated levels of micrornas (mirna) mir-21, mir-34a, and mir-130b in cholestatic liver and of mir-21 and mir-130b during inflammation were observed. using heparg cells, which retain many functional characteristics of human hepatocytes, we investigated the potential of these mirnas to down-regulate adme genes. cells were transfected with the corresponding mirna mimics, chemically modified double-stranded rnas that mimic endogenous mirnas, followed by mrna profiling by quantitative reverse-transcription polymerase chain reaction. activities of six cytochrome p450 enzymes (cyp1a2, cyp2b6, cyp2c8, cyp2c9, cyp2c19, and cyp3a4) were determined with a liquid chromatography with tandem mass spectrometric cocktail assay. although mir-21 and mir-34a showed few effects, transfection of mir-130b led to significantly lower expression of nuclear receptors constitutive androstane receptor (car) and farnesoid x receptor (fxrα), the cyps 1a1, 1a2, 2a6, 2c8, 2c9, and 2c19, as well as gsta2. furthermore, mir-130b negatively affected activity levels of all measured p450s by at least 30%. reporter gene assays employing the cyp2c9 3'-untranslated region (3'-utr) confirmed direct regulation by mir-130b. these data support mir-130b as a potential negative regulator of drug metabolism by directly and/or indirectly affecting the expression of several adme genes. this may be of relevance in pathophysiologic conditions such as cholestasis and inflammation, which are associated with increased mir-130b expression.",1
"background the main cause of death in medulloblastoma is recurrence associated with leptomeningeal dissemination. during this process, the role of micrornas (mirs) in the acquisition of metastatic phenotype remains poorly understood. this study aimed to identify the mir involved in leptomeningeal dissemination and to elucidate its biological functional mechanisms. materials and methods we analyzed the mir expression profiles of 29 medulloblastomas according to the presence of cerebrospinal fluid (csf) seeding. differentially expressed mirs (demirs) were validated in 29 medulloblastoma tissues and three medulloblastoma cell lines. the biological functions of the selected mirs were evaluated using in vitro and in vivo studies. results a total of 12 demirs were identified in medulloblastoma with seeding, including mir-192. the reduced expression of mir-192 was confirmed in the tumor seeding group and in the medulloblastoma cells. overexpression of mir-192 inhibited cellular proliferation by binding dhfr. mir-192 decreased cellular anchoring via the repression of itgav, itgb1, itgb3, and cd47. animals in the mir-192-treated group demonstrated a reduction of spinal seeding (p conclusions medulloblastoma with seeding showed specific demirs compared with those without. mir-192 suppresses leptomeningeal dissemination of medulloblastoma by modulating cell proliferation and anchoring ability.",1
"maintenance of motor neuron structure and function is crucial in development and motor behaviour. however, the genetic regulatory mechanism of motor neuron function remains less well understood. in the present study, we identify a novel neuroprotective role of the microrna mir-969 in drosophila motor neurons. mir-969 is highly expressed in motor neurons. loss of mir-969 results in early-onset and age-progressive locomotion impairment. flies lacking mir-969 also exhibit shortened lifespan. moreover, mir-969 is required in motor neurons. we further identify kay as a functionally important target of mir-969. together, our results indicate that mir-969 can protect motor neuron function by limiting kay activity in drosophila .",1
"long non-coding rnas contribute to dosage compensation in both mammals and drosophila by inducing changes in the chromatin structure of the x-chromosome. in drosophila melanogaster, rox1 and rox2 are long non-coding rnas that together with proteins form the male-specific lethal (msl) complex, which coats the entire male x-chromosome and mediates dosage compensation by increasing its transcriptional output. studies on polytene chromosomes have demonstrated that when both rox1 and rox2 are absent, the msl-complex becomes less abundant on the male x-chromosome and is relocated to the chromocenter and the 4th chromosome. here we address the role of rox rnas in msl-complex targeting and the evolution of dosage compensation in drosophila. we performed chip-seq experiments which showed that msl-complex recruitment to high affinity sites (has) on the x-chromosome is independent of rox and that the has sequence motif is conserved in d. simulans. additionally, a complete and enzymatically active msl-complex is recruited to six specific genes on the 4th chromosome. interestingly, our sequence analysis showed that in the absence of rox rnas, the msl-complex has an affinity for regions enriched in hoppel transposable elements and repeats in general. we hypothesize that rox mutants reveal the ancient targeting of the msl-complex and propose that the role of rox rnas is to prevent the binding of the msl-complex to heterochromatin.",1
"background micrornas (mirnas) are frequently dysregulated in human cancers and can act as either potent oncogenes or tumor suppressor genes. in the present study, we intend to prove that the gene pten (phosphatase and tensin homolog deleted on chromosome ten) is a target gene of mir-205 and to investigate the suppressive effects on pten transcriptional activity by enhancing mir-205 expression in endometrial cancer ishikawa cells. methods using ishikawa cells as model systems, we up-regulated mir-205 expression by transient transfection with mir-205 mimics. a luciferase reporter assay, qrt-pcr and western blotting assays were used to verify whether pten is a direct target of mir-205. meanwhile, the modulatory role of mir-205 in the akt (protein kinase b) pathway was evaluated by determining the akt phosphorylation. as a biological counterpart, we investigated cell apoptosis using flow cytometry. results our data indicate that mir-205 down-regulates the expression of pten through direct interaction with the putative binding site in the 3'-untranslated region (3'-utr) of pten. moreover, we documented the functional interactions of mir-205 and pten, which have a downstream effect on the regulation of the akt pathway, explaining, at least in part, the inhibitory effects on ishikawa cell apoptosis of enhancing mir-205 expression. conclusions for the first time, we demonstrate that the expression of pten is directly regulated by mir-205 in endometrial cancer cells and leads the inhibition of cellular apoptosis. this relationship could be targeted for new therapeutic strategies for endometrial cancer.",1
"ammonia detoxification, which takes place via the hepatic urea cycle, is essential for nitrogen homeostasis and physiological well-being. it has been reported that a reduction in dietary protein reduces urea nitrogen. micrornas (mirnas) are major regulatory non-coding rnas that have significant effects on several metabolic pathways; however, little is known on whether mirnas regulate hepatic urea synthesis. the objective of this study was to assess the mirna expression profile in a low protein diet and identify mirnas involved in the regulation of the hepatic urea cycle using a porcine model. weaned 28-days old piglets were fed a corn-soybean normal protein diet (np) or a corn-soybean low protein diet (lp) for 30 d. hepatic and blood samples were collected, and the mirna expression profile was assessed by sequencing and qrt-pcr. furthermore, we evaluated the possible role of mir-19b in urea synthesis regulation. there were 25 differentially expressed mirnas between the np and lp groups. six of these mirnas were predicted to be involved in urea cycle metabolism. mir-19b negatively regulated urea synthesis by targeting sirt5, which is a positive regulator of cps1, the rate limiting enzyme in the urea cycle. our study presented a novel explanation of ureagenesis regulation by mirnas.",1
"systemic lupus erythematosus (sle) is a chronic autoimmune disease, and its pathogenesis remains mostly unknown. micrornas (mirs) has drawn much attention as a crucial regulator of autoimmune diseases. in this study, we demonstrated that mir-873 expression was significantly up-regulated in patients with sle, and its expression was positively associated with the disease severity. cd4 + t cells, especially the th17 subset, were found to be the major source of mir-873 expression. using gain- and loss-of-function approaches, we further showed that mir-873 could facilitate the differentiation of cd4 + t cells into th17 lineage. moreover, forkhead box o1 (foxo1), one member of the foxo family, was identified as a novel target gene of mir-873, and foxo1 has been known as an inhibitor of th17 cell differentiation. foxo1 was observed to be markedly decreased in pbmc of patients with sle. notably, in vivo lentivirus-mediated inhibition of mir-873 significantly alleviated the disease severity of spontaneous sle in mrl/lpr mice, with down-regulated levels of autoantibodies, proteinuria, and il-17a. our data reveal a novel mechanism in which the elevated mir-873 in pbmc of sle promotes th17 cell differentiation through down-regulation of foxo1. in vivo blockade of mir-873 may serve as a novel therapeutic approach in the treatment of sle.",1
"objective lineage-negative bone marrow cells (lin- bmcs) are enriched in endothelial progenitor cells and mediate vascular repair. aging-associated senescence and apoptosis result in reduced number and functionality of lin- bmcs, impairing their prorepair capacity. the molecular mechanisms underlying lin- bmc senescence and apoptosis are poorly understood. micrornas (mirnas) regulate many important biological processes. the identification of mirna-mrna networks that modulate the health and functionality of lin- bmcs is a critical step in understanding the process of vascular repair. the aim of this study was to characterize the role of the mir-146a-polo-like kinase 2 (plk2) network in regulating lin- bmc senescence, apoptosis, and their angiogenic capability. approach and results transcriptome analysis in lin- bmcs isolated from young and aged wild-type and apoe -/- (apolipoprotein e) mice showed a significant age-associated increase in mir-146a expression. in silico analysis, expression study and luciferase reporter assay established plk2 as a direct target of mir-146a. mir-146a overexpression in young lin- bmcs inhibited plk2 expression, resulting in increased senescence and apoptosis, via p16ink4a/p19arf and p53, respectively, as well as impaired angiogenic capacity in vitro and in vivo. conversely, suppression of mir-146a in aged lin- bmcs increased plk2 expression and rejuvenated lin- bmcs, resulting in decreased senescence and apoptosis, leading to improved angiogenesis. conclusions (1) mir-146a regulates lin- bmc senescence and apoptosis by suppressing plk2 expression that, in turn, activates p16ink4a/p19arf and p53 and (2) modulation of mir-146a or its target plk2 may represent a potential therapeutic intervention to improve lin- bmc-mediated angiogenesis and vascular repair.",1
"objective the goal of this study was to determine the expression signature and the potential role of micrornas in human arteries with arteriosclerosis obliterans (aso). methods and results the expression profiles of micrornas in human arteries with aso and in normal control arteries were determined by quantitative reverse transcription-polymerase chain reaction array. among the 617 detected micrornas, multiple micrornas were aberrantly expressed in arteries with aso. some of these dysregulated micrornas were further verified by quantitative reverse transcription-polymerase chain reaction. among them, microrna-21 (mir-21) was mainly located in arterial smooth muscle cells (asmcs) and was increased by more than 7-fold in aso that was related to hypoxia inducible factor 1-α. in cultured human asmcs, cell proliferation and migration were significantly decreased by inhibition of mir-21. 3'-untranslated region luciferase assay confirmed that tropomyosin 1 was a target of mir-21 that was involved in mir-21-mediated cellular effects, such as cell shape modulation. conclusion the results suggest that mir-21 is able to regulate asmc function by targeting tropomyosin 1. the hypoxia inducible factor-1 α/mir-21/tropomyosin 1 pathway may play a critical role in the pathogenesis of aso. these findings might provide a new therapeutic target for human aso.",1
"micrornas are naturally existing, small, noncoding rna molecules that downregulate posttranscriptional gene expression. their expression pattern and function in the heart remain unknown. here we report an array of micrornas that are differentially and temporally regulated during cardiac hypertrophy. significantly, the muscle-specific microrna-1 (mir-1) was singularly downregulated as early as day 1 (0.56+/-0.036), persisting through day 7 (0.29+/-0.14), after aortic constriction-induced hypertrophy in a mouse model. overexpression experiments showed that mir-1 inhibited its in silico-predicted, growth-related targets, including ras gtpase-activating protein (rasgap), cyclin-dependent kinase 9 (cdk9), fibronectin, and ras homolog enriched in brain (rheb), in addition to protein synthesis and cell size. thus, we propose that micrornas play an essential regulatory role in the development of cardiac hypertrophy, wherein downregulation of mir-1 is necessary for the relief of growth-related target genes from its repressive influence and induction of hypertrophy.",1
"cholesterol efflux from macrophages is a critical mechanism to prevent the development of atherosclerosis. although pparγ is known to be a potent sterol sensor that play a fundamental role in cholesterol metabolism, the potential effects of pparγ responsive mirna still need to be revealed. in this study, we found that mir-613 is inversely correlated with lxrα and abca1 in pparγ activated thp-1 cells. pparγ negatively regulates the expression of mir-613 at transcriptional level, and mir-613 suppressed lxrα and abca1 by targeting the 3'-utr of their mrnas. furthermore, downregulation of lxrα and abca1 by mir-613 inhibited cholesterol efflux from pparγ activated thp-1 macrophages. these results revealed an alternative mechanism for pparγ regulation and provided a potential target for the treatment of cholesterol metabolic diseases.",1
"mantle cell lymphoma (mcl) is one of the most aggressive b-cell lymphomas. although several protein-coding genes are altered, expression signature and importance of microrna (mirna) have not been well documented in this malignancy. here, we performed mirna expression profile in 30 patients with mcl using a platform containing 515 human mirnas. eighteen mirnas were down-regulated and 21 were up-regulated in mcl compared with normal b lymphocytes. the most frequently altered mirnas are decrease of mir-29a/b/c, mir-142-3p/5p, and mir-150 and increase of mir-124a and mir-155. notably, expression levels of mir-29 family are associated with prognosis. the patients with significant down-regulated mir-29 had short survival compared with those who express relatively high levels of mir-29. the prognostic value of mir-29 is comparable with the mantle cell lymphoma international prognostic index. furthermore, we demonstrate mir-29 inhibition of cdk6 protein and mrna levels by direct binding to 3'-untranslated region. inverse correlation between mir-29 and cdk6 was observed in mcl. because cyclin d1 overexpression is a primary event and exerts its function through activation of cdk4/cdk6, our results in primary mcl cells indicate that down-regulation of mir-29 could cooperate with cyclin d1 in mcl pathogenesis. thus, our findings provide not only mirna expression signature but also a novel prognostic marker and pathogenetic factor for this malignancy.",1
"phorbol 12-myristate 13-acetate (pma) induces megakaryocytic differentiation of the human chronic myelocytic leukemia cell line k562. we examined the potential regulatory role of micrornas (mirnas) in this process. genome-wide expression profiling identified 21 mirnas (mirs) that were induced by the treatment of k562 cells with pma. among them, the expression of mir-34a, mir-221, and mir-222 was induced in the early stages and maintained throughout the late stages of differentiation. cell signaling analysis showed that the activation of extracellular signal-regulated protein kinase (erk) in response to pma strongly induced mir-34a expression by transactivation via the activator protein-1 binding site in the upstream region of the mir-34a gene. reporter gene assays identified mitogen-activated protein kinase kinase 1 (mek1) as a direct target of mir-34a and c-fos as a direct target of mir-221/222. although overexpression of the three mirnas had little effect on cell differentiation, overexpression of mir-34a significantly repressed the proliferation of k562 cells with a concomitant reduction in mek1 protein expression. conversely, a locked nucleic acid probe against mir-34a significantly enhanced the proliferation of pma-treated k562 cells. taken together, the results show that pma activates the mek-erk pathway and strongly induces mirna-34a expression, which in turn inhibits cell proliferation by repressing the expression of mek1. thus, the results highlight an important regulatory role for mir-34a in the process of megakaryocytic differentiation, especially in the arrest of cell growth, which is a prerequisite for cells to enter differentiation.",1
"the signal recognition particle (srp) is a ribonucleoprotein complex which participates in the targeting of protein to cellular membranes. the rna component of the srp has been found in all domains of life, but the size of the molecule and the number of rna secondary structure elements vary considerably between the different phylogenetic groups. we continued our efforts to identify new srp rnas, compare their sequences, discover new secondary structure elements, conserved motifs, and other properties. we found additional proof for the variability in the apical loop of helix 8, and we identified several bacteria which lack all of their srp components. based on the distribution of srp rna features within the taxonomy, we suggest seven alignment groups: bacteria with a small (4.5s) srp rna, bacteria with a large (6s) srp rna, archaea, fungi (ascomycota), metazoa group, protozoa group, and plants. the proposed divisions improve the prediction of more distantly related srp rnas and provide a more inclusive representation of the srp rna family. updates of the rfam srp rna sequence collection are expected to benefit from the suggested groupings.",1
"micrornas (mirnas) regulate cell physiology by altering protein expression, but the biology of platelet mirnas is largely unexplored. we tested whether platelet mirna levels were associated with platelet reactivity by genome-wide profiling using platelet rna from 19 healthy subjects. we found that human platelets express 284 mirnas. unsupervised hierarchical clustering of mirna profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. seventy-four mirnas were differentially expressed (de) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. using whole genome mrna expression data on these same subjects, we computationally generated a high-priority list of mirna-mrna pairs in which the de platelet mirnas had binding sites in 3'-untranslated regions of de mrnas, and the levels were negatively correlated. three mirna-mrna pairs (mir-200b:prkar2b, mir-495:klhl5, and mir-107:clock) were selected from this list, and all 3 mirnas knocked down protein expression from the target mrna. reduced activation from platelets lacking prkar2b supported these findings. in summary, (1) platelet mirnas are able to repress expression of platelet proteins, (2) mirna profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional mirnas in platelets.",1
"ablation of a single mirna gene rarely leads to a discernable developmental phenotype in mice, in some cases because of compensatory effects by other functionally related mirnas. here, we report that simultaneous inactivation of two functionally related mirna clusters (mir-34b/c and mir-449) encoding five mirnas (mir-34b, mir-34c, mir-449a, mir-449b, and mir-449c) led to sexually dimorphic, partial perinatal lethality, growth retardation, and infertility. these developmental defects correlated with the dysregulation of ∼ 240 target genes, which are mainly involved in three major cellular functions, including cell-fate control, brain development and microtubule dynamics. our data demonstrate an essential role of a mirna family in brain development, motile ciliogenesis, and spermatogenesis.",1
"numerous studies have recently suggested that mirnas contribute to the development of various types of human cancer as well as to their invasive and metastatic capacities. the aim of this study was to investigate the functional significance of mir-424 and to identify its possible target genes in osteosarcoma (os) cells. previously, inhibition of fatty acid synthase (fasn) has been shown to suppress os cell proliferation, invasion and migration. the prediction was made using the microrna.org and targetscan.human6.0.database. the results showed that fasn is a promising target gene of mir-424. fasn may be a direct target of mir-424 as shown by the luciferase reporter assays. furthermore, mir-424 expression was increased in osteosarcoma cells by transfection with has-mir-424. fasn mrna and protein expression levels were measured by rt-pcr and western blot analysis. cell migration and invasion was measured using transwell migration and transwell invasion assays. expression levels of fasn mrna and protein were greatly decreased in u2os cells transfected with has-mir-424. the migration and invasion of cells was significantly decreased by the upregulation of mir-424. these findings suggested that mir-424 plays a key role in inhibiting os cell migration and invasion through targeting fasn.",1
"the translation initiation gtpase eukaryotic translation initiation factor 5b (eif5b) binds to the factor eif1a and catalyzes ribosomal subunit joining in vitro. we show that rapid depletion of eif5b in saccharomyces cerevisiae results in the accumulation of eif1a and mrna on 40s subunits in vivo, consistent with a defect in subunit joining. substituting ala for the last five residues in eif1a (eif1a-5a) impairs eif5b binding to eif1a in cell extracts and to 40s complexes in vivo. consistently, overexpression of eif5b suppresses the growth and translation initiation defects in yeast expressing eif1a-5a, indicating that eif1a helps recruit eif5b to the 40s subunit prior to subunit joining. the gtpase-deficient eif5b-t439a mutant accumulated on 80s complexes in vivo and was retained along with eif1a on 80s complexes formed in vitro. likewise, eif5b and eif1a remained associated with 80s complexes formed in the presence of nonhydrolyzable gdpnp, whereas these factors were released from the 80s complexes in assays containing gtp. we propose that eif1a facilitates the binding of eif5b to the 40s subunit to promote subunit joining. following 80s complex formation, gtp hydrolysis by eif5b enables the release of both eif5b and eif1a, and the ribosome enters the elongation phase of protein synthesis.",1
"long noncoding rnas (lncrnas) are emerging as regulators of many basic cellular pathways. several lncrnas are selectively expressed in the developing retina, although little is known about their functional role in this tissue. vax2os1 is a retina-specific lncrna whose expression is restricted to the mouse ventral retina. here we demonstrate that spatiotemporal misexpression of vax2os1 determines cell cycle alterations in photoreceptor progenitor cells. in particular, the overexpression of vax2os1 in the developing early postnatal mouse retina causes an impaired cell cycle progression of photoreceptor progenitors toward their final committed fate and a consequent delay of their differentiation processes. at later developmental stages, this perturbation is accompanied by an increase of apoptotic events in the photoreceptor cell layer, in comparison with control retinas, without affecting the proper cell layering in the adult retina. similar results are observed in mouse photoreceptor-derived 661w cells in which vax2os1 overexpression results in an impairment of the cell cycle progression rate and cell differentiation. based on these results, we conclude that vax2os1 is involved in the control of cell cycle progression of photoreceptor progenitor cells in the ventral retina. therefore, we propose vax2os1 as the first example of lncrna that acts as a cell cycle regulator in the mammalian retina during development.",1
"abnormal mitochondrial fission participates in the pathogenesis of many diseases. long non-coding rnas (lncrnas) are emerging as new players in gene regulation, but how lncrnas operate in the regulation of mitochondrial network is unclear. here we report that a lncrna, named cardiac apoptosis-related lncrna (carl), can suppress mitochondrial fission and apoptosis by targeting mir-539 and phb2. the results show that phb2 is able to inhibit mitochondrial fission and apoptosis. mir-539 is responsible for the dysfunction of phb2 and regulates mitochondrial fission and apoptosis by targeting phb2. further, we show that carl can act as an endogenous mir-539 sponge that regulates phb2 expression, mitochondrial fission and apoptosis. our present study reveals a model of mitochondrial fission regulation that is composed of carl, mir-539 and phb2. modulation of their levels may provide a new approach for tackling apoptosis and myocardial infarction.",1
"micrornas (mirnas) have been reported to be of great importance in a wide range of physiological and pathological processes, including acute coronary syndrome (acs). however, the exact role of mirnas in the pathogenesis of acs has not been fully elucidated. in this study, we found that mir-101 was significantly upregulated in the serum samples of patients with acute coronary syndrome compared with healthy controls. in human umbilical vein endothelial cells (huvecs), the overexpression of mir-101 drastically promoted cell apoptosis and inhibited cell migration. mechanistically, mir-101 repressed the expression of chd5 by targeting its 3'-untranslated region (3'utr). the silencing of chd5 also induced cell apoptosis and suppressed cell migration in huvecs. taken together, our findings suggest that the mir-101-chd5 axis may play an important role in the biological behaviors of endothelial cells during the pathogenesis of acs and may afford an effective diagnostic marker and a powerful therapy for this disease.",1
"we previously found hydrogen sulfide (h2s) to be a new proangiogenic factor. however, the mechanisms underlying the cardiovascular effect of this small gas molecule remain largely unknown. the aim of the present study was to identify the essential micrornas (mirnas) involved in the transduction of h2s signals in vascular endothelial cells (ecs). the expression of mir-640 and its signaling elements, vascular endothelial growth factor receptor 2 (vegfr2), hypoxia inducible factor 1-α (hif1a), and mammalian target of rapamycin (mtor), was measured using quantitative pcr and western blotting. overexpression and inhibition of mir-640 were performed to clarify their roles in mediating the effect of h2s. in addition, knockdown of vegfr2, hif1a, and mtor was performed using sirnas, dominant negative mutants, or inhibitors to examine their roles in the transduction of the h2s signals. mir-640 levels decreased in vascular ecs that were treated with h2s, whereas overexpression of mir-640 blunted the proangiogenic effect of h2s. knockdown of either vegfr2 or mtor blunted the downregulation of mir-640 and the proangiogenic effect induced by h2s. in addition, mir-640 bound to the 3'-utr of hif1a mrna and then inhibited the expression of hif1a. the inhibition could be recovered by treating cells with h2s. thus we concluded that mir-640 plays a pivotal role in mediating the proangiogenic effect of h2s; h2s acts through downregulation of the expression of mir-640 and increasing the levels of hif1a through the vegfr2-mtor pathway.",1
"genetic and biochemical studies have established a central role for alpha-synuclein accumulation in the pathogenesis of parkinson disease. here, two micrornas, namely mir-7 and mir-153, have been identified to regulate alpha-synuclein levels post-transcriptionally. these micrornas bind specifically to the 3'-untranslated region of alpha-synuclein and down-regulate its mrna and protein levels, with their effect being additive. they are expressed predominantly in the brain with a pattern that mirrors synuclein expression in different tissues as well as during neuronal development, indicating that they play a tuning role in the amount of alpha-synuclein produced. overexpression of mir-7 and mir-153 significantly reduces endogenous alpha-synuclein levels, whereas inhibition of mir-7 and mir-153 enhances translation of a luciferase construct bearing the alpha-synuclein 3'-untranslated region in primary neurons. these findings reveal a significant additional mechanism by which alpha-synuclein is regulated and point toward new therapeutic regimes for lowering endogenous alpha-synuclein levels in patients with familial or sporadic parkinson disease.",1
"microrna-146a is upregulated in the brains of patients with alzheimer's disease (ad). here, we show that the rho-associated, coiled-coil containing protein kinase 1 (rock1) is a target of microrna-146a in neural cells. knockdown of rock1 mimicked the effects of microrna-146a overexpression and induced abnormal tau phosphorylation, which was associated with inhibition of phosphorylation of the phosphatase and tensin homolog (pten). the rock1/pten pathway has been implicated in the neuronal hyperphosphorylation of tau that occurs in ad. to determine the function of rock1 in ad, brain tissue from 17 donors with low, intermediate or high probability of ad pathology were obtained and analyzed. data showed that rock1 protein levels were reduced and rock1 colocalised with hyperphosphorylated tau in early neurofibrillary tangles. intra-hippocampal delivery of a microrna-146a specific inhibitor (antagomir) into 5xfad mice showed enhanced hippocampal levels of rock1 protein and repressed tau hyperphosphorylation, partly restoring memory function in the 5xfad mice. our in vitro and in vivo results confirm that dysregulation of microrna-146a biogenesis contributes to tau hyperphosphorylation and ad pathogenesis, and inhibition of this microrna could be a viable novel in vivo therapy for ad.",1
"recent reports in alzheimer's disease (ad) research suggest that alterations in microrna (mirna) expression are associated with disease pathology. our previous studies suggest that a disintegrin and metalloproteinase 10 (adam10) expression is important in ad and could be modulated by an extended regulatory region that includes the 3' untranslated region. in this study, we have investigated the role of trans-acting factors in adam10 gene regulation. our study shows that mirna-140-5p has enhanced expression in the ad postmortem brain hippocampus using high-throughput mirna arrays and quantitative real-time polymerase chain reaction. interestingly, we have also seen that mirna-140-5p seed sequence is present on 3' untranslated region of both adam10 and its transcription factor sox2. the specific interaction of mirna-140-5p with both adam10 and sox2 signifies high regulatory importance of this mirna in controlling adam10 expression. thus, this investigation unravels mechanisms underlying adam10 downregulation by mir-140-5p and suggests that dysfunctional regulation of adam10 expression is exacerbated by ad-related neurotoxic effects. these findings underscore the importance of understanding the impact of trans-acting factors in the modulation of ad pathophysiology.",1
"new evidence indicates that termination of transcription is an important regulatory step, closely related to transcriptional interference and even transcriptional initiation. however, how this occurs is poorly understood. recently, in vivo analysis of transcriptional termination for the human beta-globin gene revealed a new phenomenon--co-transcriptional cleavage (cotc). this primary cleavage event within beta-globin pre-messenger rna, downstream of the poly(a) site, is critical for efficient transcriptional termination by rna polymerase ii. here we show that the cotc process in the human beta-globin gene involves an rna self-cleaving activity. we characterize the autocatalytic core of the cotc ribozyme and show its functional role in efficient termination in vivo. the identified core cotc is highly conserved in the 3' flanking regions of other primate beta-globin genes. functionally, it resembles the 3' processive, self-cleaving ribozymes described for the protein-encoding genes from the myxomycetes didymium iridis and physarum polycephalum, indicating evolutionary conservation of this molecular process. we predict that regulated autocatalytic cleavage elements within pre-mrnas may be a general phenomenon and that functionally it may provide the entry point for exonucleases involved in mrna maturation, turnover and, in particular, transcriptional termination.",1
"micrornas (mirnas) associate with argonaute (ago) proteins to direct widespread posttranscriptional gene repression. although association with ago typically protects mirnas from nucleases, extensive pairing to some unusual target rnas can trigger mirna degradation. we found that this target-directed mirna degradation (tdmd) required the zswim8 cullin-ring e3 ubiquitin ligase. this and other findings support a mechanistic model of tdmd in which target-directed proteolysis of ago by the ubiquitin-proteasome pathway exposes the mirna for degradation. moreover, loss-of-function studies indicated that the zswim8 cullin-ring ligase accelerates degradation of numerous mirnas in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived mirnas. these results elucidate the mechanism of tdmd and expand its inferred role in shaping mirna levels in bilaterian animals.",1
"rnaiii, the effector of the agr quorum-sensing system, plays a key role in virulence gene regulation in staphylococcus aureus, but how rnaiii transcriptionally regulates its downstream genes is not completely understood. here, we show that rnaiii stabilizes mgra mrna, thereby increasing the production of mgra, a global transcriptional regulator that affects the expression of many genes. the mgra gene is transcribed from two promoters, p1 and p2, to produce two mrna transcripts with long 5' utr. two adjacent regions of the mgra mrna utr transcribed from the upstream p2 promoter, but not the p1 promoter, form a stable complex with two regions of rnaiii near the 5' and 3' ends. we further demonstrate that the interaction has several biological effects. we propose that mgra can serve as an intermediary regulator through which agr exerts its regulatory function.",1
"micrornas (mirnas) are short, single-stranded non-coding rnas that repress their target genes by binding their 3' utrs. these rnas play critical roles in myogenesis. to gain knowledge about mirnas involved in the regulation of myogenesis, porcine longissimus muscles were collected from 18 developmental stages (33-, 40-, 45-, 50-, 55-, 60-, 65-, 70-, 75-, 80-, 85-, 90-, 95-, 100- and 105-day post-gestation fetuses, 0 and 10-day postnatal piglets and adult pigs) to identify mirnas using solexa sequencing technology. we detected 197 known mirnas and 78 novel mirnas according to comparison with known mirnas in the mirbase (release 17.0) database. moreover, variations in sequence length and single nucleotide polymorphisms were also observed in 110 known mirnas. expression analysis of the 11 most abundant mirnas were conducted using quantitative pcr (qpcr) in eleven tissues (longissimus muscles, leg muscles, heart, liver, spleen, lung, kidney, stomach, small intestine and colon), and the results revealed that ssc-mir-378, ssc-mir-1 and ssc-mir-206 were abundantly expressed in skeletal muscles. during skeletal muscle development, the expression level of ssc-mir-378 was low at 33 days post-coitus (dpc), increased at 65 and 90 dpc, peaked at postnatal day 0, and finally declined and maintained a comparatively stable level. this expression profile suggested that ssc-mir-378 was a new candidate mirna for myogenesis and participated in skeletal muscle development in pigs. target prediction and kegg pathway analysis suggested that bone morphogenetic protein 2 (bmp2) and mitogen-activated protein kinase 1 (mapk1), both of which were relevant to proliferation and differentiation, might be the potential targets of mir-378. luciferase activities of report vectors containing the 3'utr of porcine bmp2 or mapk1 were downregulated by mir-378, which suggested that mir-378 probably regulated myogenesis though the regulation of these two genes.",1
"micrornas are negative gene regulators and play important roles in cardiac development and disease. as evident by cardiomyopathy following cardiac-specific dicer knockdown they also are required for maintaining normal cardiac contractile function but the specific role of mir-1 in the process is poorly understood. to characterize the role of mir-1 in particular and to identify its specific targets we created a tamoxifen-inducible, cardiac-specific dicer knockdown mouse and demonstrated that dicer downregulation results in a dramatic and rapid decline in cardiac function concurrent with significantly reduced levels of mir-1. the importance of mir-1 was established by mir-1 antagomir treatment of wild-type mice, which replicated the cardiac-specific dicer knockdown phenotype. down-regulation of mir-1 was associated with up-regulation of its predicted target sorcin, an established modulator of calcium signaling and excitation-contraction coupling, subsequently verified as a mir-1 target with luciferase constructs. sirna-mediated knockdown of sorcin effectively rescued the cardiac phenotypes after dicer or mir-1 knockdown affirming sorcin as a critical mediator of the acute cardiomyopathy observed. the regulatory relationship between mir-1 and sorcin was further confirmed in cultured mouse cardiomyocytes where modulation of mir-1 was associated with discordant sorcin levels and dysregulation of calcium signaling. pathological relevance of our findings included decreased mir-1 and increased sorcin expression in end-stage cardiomyopathy. these findings demonstrate the importance of mir-1 in cardiac function and in the pathogenesis of heart failure via sorcin-dependent calcium homeostasis.",1
"the down-regulation of peroxisome proliferator-activated receptor γ (pparγ) expression has been found to correlate with the proliferation of pulmonary artery smooth muscle cells (pasmc), pulmonary vascular remodeling and pulmonary hypertension, while the molecular mechanisms underlying pparγ reduction in pasmc remain largely unclear. the aim of the current study is to address this issue. endothelin-1 (et-1) dose- and time-dependently resulted in pparγ reduction and proliferation of primary cultured rat pasmc, which was accompanied by the activation of nuclear factor-kappab (nf-κb) and subsequent induction of microrna-27a/b (mir-27a/b) expression. chromatin immunoprecipitation assay revealed that nf-κb directly bound to the promoter regions of mir-27a/b. luciferase reporter assay identified that mir-27a/b directly regulates the expression of pparγ in pasmc. further study indicated that the presence of either nf-κb inhibitor pyrrolidinedithiocarbamate or prior silencing mir-27a/b with anti-mirna oligonucleotides suppressed et-1-induced pparγ reduction and proliferation of pasmc, while overexpression of mir-27a/b reduced pparγ expression and enhanced pasmc proliferation. taken together, our study demonstrates that et-1 stimulates mir-27a/b expression by activation of the nf-κb pathway, which in turn results in pparγ reduction and contributes to et-1-induced pasmc proliferation.",1
"human neurodegenerative diseases have the temporal hallmark of afflicting the elderly population. ageing is one of the most prominent factors to influence disease onset and progression, yet little is known about the molecular pathways that connect these processes. to understand this connection it is necessary to identify the pathways that functionally integrate ageing, chronic maintenance of the brain and modulation of neurodegenerative disease. micrornas (mirna) are emerging as critical factors in gene regulation during development; however, their role in adult-onset, age-associated processes is only beginning to be revealed. here we report that the conserved mirna mir-34 regulates age-associated events and long-term brain integrity in drosophila, providing a molecular link between ageing and neurodegeneration. fly mir-34 expression exhibits adult-onset, brain-enriched and age-modulated characteristics. whereas mir-34 loss triggers a gene profile of accelerated brain ageing, late-onset brain degeneration and a catastrophic decline in survival, mir-34 upregulation extends median lifespan and mitigates neurodegeneration induced by human pathogenic polyglutamine disease protein. some of the age-associated effects of mir-34 require adult-onset translational repression of eip74ef, an essential ets domain transcription factor involved in steroid hormone pathways. our studies indicate that mirna-dependent pathways may have an impact on adult-onset, age-associated events by silencing developmental genes that later have a deleterious influence on adult life cycle and disease, and highlight fly mir-34 as a key mirna with a role in this process.",1
"mobilization of plasma membrane (pm) cholesterol to the endoplasmic reticulum is essential for cellular cholesterol homeostasis. the mechanisms regulating this retrograde, intermembrane cholesterol transfer are not well understood. because mutant cells with defects in pm to endoplasmic reticulum cholesterol trafficking can be isolated on the basis of resistance to amphotericin b, we conducted an amphotericin b loss-of-function screen in chinese hamster ovary (cho) cells using insertional mutagenesis to identify genes that regulate this trafficking mechanism. mutant line a1 displayed reduced cholesteryl ester formation from pm-derived cholesterol and increased de novo cholesterol synthesis, indicating a deficiency in retrograde cholesterol transport. genotypic analysis revealed that the a1 cell line contained one disrupted allele of the u60 small nucleolar rna (snorna) host gene, resulting in haploinsufficiency of the box c/d snorna u60. complementation and mutational studies revealed the u60 snorna to be the essential feature from this locus that affects cholesterol trafficking. lack of alteration in predicted u60-mediated site-directed methylation of 28 s rrna in the a1 mutant suggests that the u60 snorna modulates cholesterol trafficking by a mechanism that is independent of this canonical function. our study adds to a growing body of evidence for participation of small noncoding rnas in cholesterol homeostasis and is the first to implicate a snorna in this cellular function.",1
"drosophila elav is the founding member of the conserved family of hu rna-binding proteins (rbps), which play crucial and diverse roles in post-transcriptional regulation. elav has long served as the canonical neuronal marker. surprisingly, although elav has a well-characterized neural cis-regulatory module, we find endogenous elav is also ubiquitously transcribed and post-transcriptionally repressed in non-neural settings. mutant clones of multiple mirna pathway components derepress ubiquitous elav protein. our re-annotation of the elav transcription unit shows not only that it generates extended 3' utr isoforms, but also that its universal 3' utr isoform is much longer than previously believed. this longer common 3' utr includes multiple conserved, high-affinity sites for the mir-279/996 family. of several mirna mutants tested, endogenous elav and a transgenic elav 3' utr sensor are derepressed in mutant clones of mir-279/996 we also observe cross-repression of elav by mei-p26, another rbp derepressed in non-neural mirna pathway clones. ubiquitous elav has regulatory capacity, since derepressed elav can stabilize an elav-responsive sensor. repression of elav in non-neural territories is crucial as misexpression here has profoundly adverse consequences. altogether, we define unexpected post-transcriptional mechanisms that direct appropriate cell type-specific expression of a conserved neural rbp.",1
"micrornas (mirnas) can play important gene regulatory roles in nematodes, insects, and plants by basepairing to mrnas to specify posttranscriptional repression of these messages. however, the mrnas regulated by vertebrate mirnas are all unknown. here we predict more than 400 regulatory target genes for the conserved vertebrate mirnas by identifying mrnas with conserved pairing to the 5' region of the mirna and evaluating the number and quality of these complementary sites. rigorous tests using shuffled mirna controls supported a majority of these predictions, with the fraction of false positives estimated at 31% for targets identified in human, mouse, and rat and 22% for targets identified in pufferfish as well as mammals. eleven predicted targets (out of 15 tested) were supported experimentally using a hela cell reporter system. the predicted regulatory targets of mammalian mirnas were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.",1
"micrornas are endogenously expressed, small non-coding rnas that regulate gene expression by targeting mrnas for translational repression or degradation. our previous studies indicated that mir-874 played a suppressive role in gastric cancer (gc) development and progression. however, the role of mir-874 in tumor angiogenesis and the mechanisms underlying its function in gc remained to be clarified. here, gain- and loss-of-function assays demonstrated that mir-874 inhibited the tumor angiogenesis of gc cells in vitro and in vivo. through reporter gene and western blot assays, stat3 was shown to be a direct target of mir-874. overexpression of stat3 rescued the loss of tumor angiogenesis caused by mir-874. conversely, the stat3-shrna attenuated the increased tumor angiogenesis caused by the mir-874-inhibitor. furthermore, the levels of mir-874 were inversely correlated with those of stat3 protein in gc tissues. taken together, these findings indicate that down-regulation of mir-874 contributes to tumor angiogenesis through stat3 in gc, highlighting the potential of mir-874 as a target for human gc therapy.",1
"long noncoding rnas (lncrnas) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. here, we identified braveheart (bvht), a heart-associated lncrna in mouse. using multiple embryonic stem cell (esc) differentiation strategies, we show that bvht is required for progression of nascent mesoderm toward a cardiac fate. we find that bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (mesp1), a master regulator of a common multipotent cardiovascular progenitor. we also show that bvht interacts with suz12, a component of polycomb-repressive complex 2 (prc2), during cardiomyocyte differentiation, suggesting that bvht mediates epigenetic regulation of cardiac commitment. finally, we demonstrate a role for bvht in maintaining cardiac fate in neonatal cardiomyocytes. together, our work provides evidence for a long noncoding rna with critical roles in the establishment of the cardiovascular lineage during mammalian development.",1
"cold induction of cspa, the paradigm escherichia coli cold-shock gene, is mainly subject to posttranscriptional control, partly promoted by cis-acting elements of its transcript, whose secondary structure at 37 degrees c and at cold-shock temperature has been elucidated here by enzymatic and chemical probing. the structures, which were also validated by mutagenesis, demonstrate that cspa mrna undergoes a temperature-dependent structural rearrangement, likely resulting from stabilization in the cold of an otherwise thermodynamically unstable folding intermediate. at low temperature, the ""cold-shock"" structure is more efficiently translated and somewhat less susceptible to degradation than the 37 degrees c structure. overall, our data shed light on a molecular mechanism at the basis of the cold-shock response, indicating that cspa mrna is able to sense temperature downshifts, adopting functionally distinct structures at different temperatures, even without the aid of trans-acting factors. unlike with other previously studied rna thermometers, these structural rearrangements do not result from melting of hairpin structures.",1
"increasing evidence has indicated that aberrant expression of mirnas has been shown to be strongly implicated in the initiation and progression of glioblastoma. here, we identified a novel tumor suppressive mirna, mir-564, and investigated its role and therapeutic effect for glioblastoma. we showed that mir-564 was down-regulated in human glioblastoma tissues and cell lines. introduction of mir-564 dramatically inhibited cell growth and invasion in glioblastoma cells. subsequent experiments revealed that transforming growth factor-β1 (tgf-β1) was a direct and functional target of mir-564 in glioblastoma cells. furthermore, overexpression of mir-564 decreased p-smad and smad4 expression, which are the downstream signaling molecules of tgf-β. meanwhile, ectopic of mir-564 reduced the messenger rna (mrna) and protein expression of epidermal growth factor receptor (egfr) and mmp9. furthermore, the upregulation of mir-564 suppressed tgf-β-mediated u87 proliferation and migration. the expression of egfr and mmp9 was upregulated in glioblastoma tissues compared to their normal tissues. the egfr and mmp9 expression levels were inverse correlated with the expression of mir-564. mir-564 suppressed the growth of u87-engrafted tumors. these findings reveal that mir-564/tgf-β1 signaling that may be required for glioblastoma development and may consequently serve as a new therapeutic target for the treatment of glioblastoma.",1
"background the mechanism underlying the ability of virulent salmonella organisms to escape clearance by macrophages is incompletely understood. here, we report a novel mechanism by which salmonella escapes macrophages. methods microarray and quantitative real-time polymerase chain reaction analyses were used to screen key micrornas regulating salmonella-host cell interactions. target gene was tested using luciferase reporter and western blot assays. the role of microrna 128 (mir-128) was assayed using intestinal epithelial cells and a mouse infection model. results the mir-128 level in human intestinal epithelial ht29 cells was strongly increased by infection with strain se2472, and the elevation in mir-128 levels in mouse intestine and colon tissues correlated with the level of salmonella infection in mice. macrophage colony-stimulating factor (m-csf) was identified as a target of mir-128, and increased mir-128 levels in epithelial cells due to infection with strain se2472 significantly decreased the level of cell-secreted m-csf, leading to impaired m-csf-mediated macrophage recruitment. the secreted proteins from salmonella were identified as possible effectors to induce mir-128 expression via the p53 signaling pathway. moreover, intragastric delivery of anti-mir-128 antagomir into mice significantly increased m-csf-mediated macrophage recruitment and suppressed salmonella infection. conclusions salmonella can upregulate intestinal epithelial mir-128 expression, which, in turn, decreases levels of epithelial cell-secreted m-csf and m-csf-induced macrophage recruitment.",1
"il-10 is a key regulator of the immune system that critically determines health and disease. its expression is finely tuned both at the transcriptional and posttranscriptional levels. although the importance of posttranscriptional regulation of il-10 has been previously shown, understanding the underlying mechanisms is still in its infancy. in this study, using a combination of bioinformatics and molecular approaches, we report that microrna (hsa-mir-106a) regulates il-10 expression. the hsa-mir-106a binding site in the 3' utr of il10 has been identified by site-directed mutagenesis studies. also, the involvement of transcription factors, sp1 and egr1, in the regulation of hsa-mir-106a expression and concomitant decrease in the il-10 expression, has also been demonstrated. in summary, our results showed that il-10 expression may be regulated by mir-106a, which is in turn transcriptionally regulated by egr1 and sp1.",1
"purpose glycogen synthase kinase-3β (gsk-3β) is a serine/threonine kinase involved in cancer development. herein, we demonstrated the role of gsk-3β in endometrial cancer (ec) and identified new therapeutic targets. results gsk-3β was overexpressed in ec tissues, and was positively correlated with international federation of gynecology and obstetrics (figo) staging, dedifferentiation, and myometrial infiltration depth. besides, gsk-3β overexpression predicted lower cumulative and relapse-free survival rate. si-gsk-3β transfection suppressed cell proliferation, migration, invasion, and promoted cell apoptosis through downregulating nf-kb, cyclin d1 and mmp9 expression whereas upregulating p21 expression. bioinformatic predictions and dual-luciferase reporter assays showed that gsk-3β was a possible target of mir-129. mir-129 transfection reduced gsk-3β expression, and exhibited the same trend as si-gsk-3β transfection in cell function experiments. the nude mouse xenograft assay showed that mir-129 overexpression may suppress tumor growth through downregulating gsk-3β expression. further studies showed that azd1080, a gsk-3β inhibitor, could also inhibit ec cell proliferation, migration and invasion, while induced cell apoptosis through modulating relevant genes downstream of gsk-3β signaling. experimental design gsk-3β expression was determined in ec tissue and normal endometrial tissues by immunohistochemistry. after gsk-3β down-regulation by si-gsk-3β, microrna-129 mimic transfection or gsk-3β inhibitor exposure, ec cell phenotypes and related molecules were examined. conclusions our results demonstrate for the first time that gsk-3β may be a novel and important therapeutic target for the treatment of endometrial carcinoma. gsk-3β inhibitor azd1080 may be an effective drug for treating endometrial carcinoma.",1
"background chronic fatigue syndrome (cfs/me) is a complex multisystem disease of unknown aetiology which causes debilitating symptoms in up to 1% of the global population. although a large cohort of genes have been shown to exhibit altered expression in cfs/me patients, it is currently unknown whether microrna (mirna) molecules which regulate gene translation contribute to disease pathogenesis. we hypothesized that changes in microrna expression in patient leukocytes contribute to cfs/me pathology, and may therefore represent useful diagnostic biomarkers that can be detected in the peripheral blood of cfs/me patients. methods mirna expression in peripheral blood mononuclear cells (pbmc) from cfs/me patients and healthy controls was analysed using the ambion bioarray v1. mirna demonstrating differential expression were validated by qrt-pcr and then replicated in fractionated blood leukocyte subsets from an independent patient cohort. the cfs/me associated mirna identified by these experiments were then transfected into primary nk cells and gene expression analyses conducted to identify their gene targets. results microarray analysis identified differential expression of 34 mirna, all of which were up-regulated. four of the 34 mirna had confirmed expression changes by qrt-pcr. fractionating pbmc samples by cell type from an independent patient cohort identified changes in mirna expression in nk-cells, b-cells and monocytes with the most significant abnormalities occurring in nk cells. transfecting primary nk cells with hsa-mir-99b or hsa-mir-330-3p, resulted in gene expression changes consistent with nk cell activation but diminished cytotoxicity, suggesting that defective nk cell function contributes to cfs/me pathology. conclusion this study demonstrates altered microrna expression in the peripheral blood mononuclear cells of cfs/me patients, which are potential diagnostic biomarkers. the greatest degree of mirna deregulation was identified in nk cells with targets consistent with cellular activation and altered effector function.",1
"the current study mainly evaluated the plasma level of microrna (mir)-136 in knee osteoarthritis (koa) patients and determined if mir-136 could be used as a potential biomarker to screen koa patients from healthy controls. it was demonstrated that plasma mir-136 was significantly decreased in the plasma of koa patients. moreover, the reduction in plasma mir-136 negatively correlated with the severity of koa. additionally, the increase in the serum interleukin (il)-17 level positively correlated with the severity of koa. more importantly, dual luciferase assays and western blot assays indicated that il-17 was a target gene of mir-136. further analysis showed that plasma mir-136 could be used as a biomarker to screen koa patients from healthy controls. in summary, for the first time, the present study revealed that through targeting il-17, decreased plasma mir-136 levels could be used as a potential biomarker to screen koa patients from healthy controls.",1
"the epstein barr virus (ebv) contributes to the tumor phenotype through a limited set of primarily non-coding viral rnas, including 31 mature mirnas. here we investigated the impact of ebv mirnas on remodeling the tumor cell transcriptome. strikingly, ebv mirnas displayed exceptionally abundant expression in primary ebv-associated burkitt's lymphomas (bls) and gastric carcinomas (gcs). to investigate viral mirna targeting, we used the high-resolution approach, clash in gc and bl cell models. affinity constant calculations of targeting efficacies for clash hits showed that viral mirnas bind their targets more effectively than their host counterparts, as did kaposi's sarcoma-associated herpesvirus (kshv) and murine gammaherpesvirus 68 (mhv68) mirnas. using public bl and gc rna-seq datasets, we found that high ebv mirna targeting efficacies translates to enhanced reduction of target expression. pathway analysis of high efficacy ebv mirna targets showed enrichment for innate and adaptive immune responses. inhibition of the immune response by ebv mirnas was functionally validated in vivo through the finding of inverse correlations between ebv mirnas and immune cell infiltration and t-cell diversity in bl and gc datasets. together, this study demonstrates that ebv mirnas are potent effectors of the tumor transcriptome that play a role in suppressing host immune response.",1
"micrornas play key roles in many biological processes, and are frequently dysregulated in tumor cells. however, there are few studies on how micrornas are dysregulated. mir-139-5p, an important tumor suppressor, is often underexpressed in gastrointestinal cancer cells. here, we describe post-transcriptional regulation of this intronic microrna in human colorectal cancer. mir-139-5p is expressed independently of its overexpressed host gene pde2a in colorectal cancer tissues and cell lines. the mir-139-5p target genes igf1r, rock2 and rap1b exert regulatory effects on the mir-139-5p expression level, relying on their ability to compete for mir-139-5p binding. these overexpressed target genes also regulate each others' protein levels through 3'-utrs, thus regulating tumor cell growth and motility properties. our study provides a mechanistic, experimentally validated rationale for intronic microrna dysregulation in colorectal cancer, revealing novel oncogenic roles of igf1r, rock2 and rap1b 3'-utrs.",1
"the pro-apoptotic p53 target noxa is a bh3-only protein that antagonizes the function of selected anti-apoptotic bcl-2 family members. while much is known regarding the transcriptional regulation of noxa, its posttranscriptional regulation remains relatively unstudied. in this study, we therefore investigated whether noxa is regulated by micrornas. using a screen combining luciferase reporters, bioinformatic target prediction analysis and microrna expression profiling, we identified mir-200c as a negative regulator of noxa expression. mir-200c was shown to repress basal expression of noxa, as well as noxa expression induced by various stimuli, including proteasomal inhibition. luciferase reporter experiments furthermore defined one mir-200c target site in the noxa 3'utr that is essential for this direct regulation. in spite of the mir-200c:noxa interaction, mir-200c overexpression led to increased sensitivity to the clinically used proteasomal inhibitor bortezomib in several cell lines. this apparently contradictory finding was reconciled by the fact that in cells devoid of noxa expression, mir-200c overexpression had an even more pronounced positive effect on apoptosis induced by proteasomal inhibition. together, our data define mir-200c as a potentiator of bortezomib-induced cell death. at the same time, we show that mir-200c is a novel negative regulator of the pro-apoptotic bcl-2 family member noxa.",1
"the importance of micrornas in the regulation of various aspects of biology and disease is well recognized. however, what remains largely unappreciated is that a significant number of mirnas are embedded within and are often co-expressed with protein-coding host genes. such a configuration raises the possibility of a functional interaction between a mirna and the gene it resides in. this is exemplified by the drosophila melanogaster de2f1 gene that harbors two mirnas, mir-11 and mir-998, within its last intron. mir-11 was demonstrated to limit the proapoptotic function of de2f1 by repressing cell death genes that are directly regulated by de2f1, however the biological role of mir-998 was unknown. here we show that one of the functions of mir-998 is to suppress de2f1-dependent cell death specifically in rbf mutants by elevating egfr signaling. mechanistically, mir-998 operates by repressing dcbl, a negative regulator of egfr signaling. significantly, dcbl is a critical target of mir-998 since dcbl phenocopies the effects of mir-998 on de2f1-dependent apoptosis in rbf mutants. importantly, this regulation is conserved, as the mir-998 seed family member mir-29 repressed c-cbl, and enhanced mapk activity and wound healing in mammalian cells. therefore, the two intronic mirnas embedded in the de2f1 gene limit the apoptotic function of de2f1, but operate in different contexts and act through distinct mechanisms. these results also illustrate that examining an intronic mirna in the context of its host's function can be valuable in elucidating the biological function of the mirna, and provide new information about the regulation of the host gene itself.",1
"vascular endothelial growth factor (vegf) signaling plays an important role in angiogenesis. in the vegf signaling pathway, the key components are vegf and its receptors, flt-1 and kdr. in this study, we show that transfection of synthetic mir-200b reduced protein levels of vegf, flt-1, and kdr. in a549 cells, mir-200b targeted the predicted binding sites in the 3'-untranslated region (3'-utr) of vegf, flt-1, and kdr as revealed by a luciferase reporter assay. when transfected with mir-200b, the ability of huvecs to form a capillary tube on matrigel and vegf-induced phosphorylation of erk1/2 were significantly reduced. taken together, these results suggest that mir-200b negatively regulates vegf signaling by targeting vegf and its receptors and that mir-200b may have therapeutic potential as an angiogenesis inhibitor.",1
"background mirnas have been implicated in numerous tumorigenic pathways, and previous studies have associated mir-202 dysregulation with various cancer types, including follicular lymphoma. methods the mir-202 targetome was identified by ribonucleoprotein immunoprecipitation-microarray (rip-chip), and functional interactions among identified targets were investigated using the ingenuity pathway analysis tool. we also conducted a population-based genetic association study of a polymorphism within the mir-202 stem-loop sequence and risk of non-hodgkin lymphoma. in vitro gain-of-function experiments were further conducted to elucidate the functional significance of the variant. results a total of 141 potential members of the mir-202 targetome were identified by a transcriptome-wide rip-chip assay. functional interactions among identified targets suggested that mir-202-regulated genes are involved in biologic pathways relevant for hematologic function and cancer. consistent with this, a genetic association analysis using human blood samples revealed a significant association between a germline mutation (rs12355840) in the mir-202 precursor sequence and follicular lymphoma risk. an in vitro functional assay further showed that the variant allele resulted in diminished mir-202 levels, possibly by altering precursor-processing efficiency. conclusions taken together, our findings suggest that mir-202 is involved in follicular lymphomagenesis. impact these findings implicate mir-202 as a potential tumor suppressor in follicular lymphoma and warrant the investigation of mir-202 as a novel biomarker of follicular lymphoma risk.",1
"alzheimer's disease (ad) is considered as one of the most common neural degenerative diseases in human. although the continuous investigations about ad have been made in recent decades, the pathogenesis of this disease is still not definitely confirmed. microrna-125b (mir-125b) is extensive expressed in many types of human tissues and played pivotal regulatory roles in diverse biological process. in the present study, we aimed to explore the roles of mir-125b in regulating neurons cell apoptosis under ad condition. the possible molecular mechanisms were also investigated. we found that mir-125b was up-regulated in patients with ad. transfection with mir-125b significantly enhanced the apoptosis of neurons cells and phosphorylation of tau by activation of cyclin-dependent kinase 5 (cdk5) and p35/25. forkhead box q1 (foxq1) was the direct target gene of mir-125b, which involved in the effects of mir-125b on neurons cell apoptosis and phosphorylation of tau. our research interpreted the mechanism of up-regulation of mir-125b in pathological tau phosphorylation and ad occurrence. mir-125b may be a novel regulator of ad progress and could be as a therapeutic target for ad therapy.",1
"the gene for a previously unidentified small nuclear rna has been cloned from saccharomyces cerevisiae and its nucleotide sequence has been determined. the rna, snr30, was mapped to a unique coding sequence 605 nucleotides long. snr30 appears to be one of the most abundant snrnas of s, cerevisiae in that it can be resolved by ethidium bromide staining on one-dimensional denaturing gels of total yeast rna. like other snrnas, snr30 is enriched in nuclei preparations and possesses a trimethyl guanosine cap structure at its 5' end. after substituting one allele of the wild type gene in a diploid strain for a deleted gene, after sporulation, haploid strains carrying the deletion were unable to grow, indicating that snr30 is required for an essential, but as yet, unknown function. the nucleotide sequence close to the initiation site of the snr30 gene is similar to that of other yeast snr genes whose transcripts are associated with pre-rrna, suggesting that snr30 is related to this group of snrnas.",1
"domain v of the 23s/25s/28s rrna of the large ribosomal subunit constitutes the active center for the protein folding activity of the ribosome (pfar). using in vitro transcribed domain v rrnas from escherichia coli and saccharomyces cerevisiae as the folding modulators and human carbonic anhydrase as a model protein, we demonstrate that pfar is conserved from prokaryotes to eukaryotes. it was shown previously that 6-aminophenanthridine (6ap), an antiprion compound, inhibits pfar. here, using uv cross-linking followed by primer extension, we show that the protein substrates and 6ap interact with a common set of nucleotides on domain v of 23s rrna. mutations at the interaction sites decreased pfar and resulted in loss or change of the binding pattern for both the protein substrates and 6ap. moreover, kinetic analysis of human carbonic anhydrase refolding showed that 6ap decreased the yield of the refolded protein but did not affect the rate of refolding. thus, we conclude that 6ap competitively occludes the protein substrates from binding to rrna and thereby inhibits pfar. finally, we propose a scheme clarifying the mechanism by which 6ap inhibits pfar.",1
"background micrornas (mirnas) are shown to be involved in the regulation of circadian clock. however, it remains largely unknown whether mirnas can regulate the core clock genes (clock and bmal1). results in this study, we found that mir-142-3p directly targeted the 3'utr of human bmal1 and mouse bmal1. the over-expression (in 293et and nih3t3 cells) and knockdown (in u87mg cells) of mir-142-3p reduced and up-regulated the bmal1/bmal1 mrna and protein levels, respectively. moreover, the expression level of mir-142-3p oscillated in serum-shocked nih3t3 cells and the results of chip and luciferase reporter assays suggested that the expression of mir-142-3p was directly controlled by clock/bmal1 heterodimers in nih3t3 cells. conclusions our study demonstrates that mir-142-3p can directly target the 3'utr of bmal1. in addition, the expression of mir-142-3p is controlled by clock/bmal1 heterodimers, suggesting a potential negative feedback loop consisting of the mirnas and the core clock genes. these findings open new perspective for studying the molecular mechanism of circadian clock.",1
"base pairing between the 5' end of u7 small nuclear rna (snrna) and the histone downstream element (hde) in replication-dependent histone pre-mrnas is the key event in 3'-end processing that leads to generation of mature histone mrnas. we have cloned the drosophila u7 snrna and demonstrated that it is required for histone pre-mrna 3'-end processing in a drosophila nuclear extract. the 71-nt drosophila u7 snrna is encoded by a single gene that is embedded in the direct orientation in an intron of the eip63e gene. the u7 snrna gene contains conserved promoter elements typical of other drosophila snrna genes, and the coding sequence is followed by a 3' box indicating that the drosophila u7 snrna gene is an independent transcription unit. drosophila u7 snrna contains a trimethyl-guanosine cap at the 5' end and a putative sm-binding site similar to the unique sm-binding site found in other u7 snrnas. drosophila u7 snrna is approximately 10 nt longer than mammalian u7 snrnas because of an extended 5' sequence and has only a limited potential to form a stem-loop structure near the 3' end. the extended 5' end of drosophila u7 snrna can base pair with the hde in all five drosophila histone pre-mrnas. blocking the 5' end of the u7 snrna with a complementary oligonucleotide specifically blocks processing of a drosophila histone pre-mrna. changes in the hde that abolish or decrease processing efficiency result in a reduced ability to recruit u7 snrna to the pre-mrna.",1
"telomerase is composed of protein and rna. the rna serves as a template for telomere dna synthesis and may also be important for enzyme structure or catalysis. we have used the presence of conserved sequence elements in the promoter and template regions to amplify by pcr the telomerase rna genes from six different hypotrichous ciliates: oxytricha nova, oxytricha trifallax, stylonychia mytilis, stylonychia lemnae, euplotes aediculatus, and euplotes eurystomus. rnaseh cleavage of the o. nova rna in extracts by use of a complementary oligonucleotide leads to loss of telomerase activity, supporting the identification. primary sequence and biochemical experiments suggest that the templates of oxytricha and stylonychia are circularly permuted relative to that of e. aediculatus. on the basis of the pause sites, the former two add g4t4 during a single primer elongation cycle, whereas e. aediculatus adds g3t4g. the only primary sequence element outside the template that is conserved between these phylogenetically distant telomerase rnas is the sequence 5'-(c)uguca-3', which precedes the template regions by exactly two bases. we propose a common secondary structure model that is based on nucleotide covariations, a model which resembles that proposed previously for tetrahymenine telomerase rnas.",1
"radiation therapy is a common treatment for prostate cancer, however recurrence remains a problem. microrna expression is altered in prostate cancer and may promote therapy resistance. through bioinformatic analyses of tcga and cpc-gene patient cohorts, we identified higher mir-191 expression in tumor versus normal tissue, and increased expression in higher gleason scores. in vitro and in vivo experiments demonstrated that mir-191 overexpression promotes radiation survival, and contributes to a more aggressive phenotype. retinoid x receptor alpha, rxra, was discovered to be a novel target of mir-191, and knockdown recapitulated radioresistance. furthermore, treatment of prostate cancer cells with the rxra agonist 9-cis-retinoic acid restored radiosensitivity. supporting this relationship, patients with high mir-191 and low rxra abundance experienced quicker biochemical recurrence. reduced rxra translated to a higher risk of distant failure after radiotherapy. notably, this mir-191/rxra interaction was conserved in a novel primary cell line derived from radiorecurrent prostate cancer. together, our findings demonstrate that mir-191 promotes prostate cancer survival after radiotherapy, and highlights retinoids as a potential option to improve radiotherapy response.",1
"objectives in mammals, the heart grows by hypertrophy but not proliferation of cardiomyocytes after birth. the paucity of cardiomyocyte proliferation limits cardiac regeneration in a variety of heart diseases. to explore the efficient strategies that drive cardiomyocyte proliferation, we employed in vitro and in vivo models to investigate the function of mirna-204, which was demonstrated to regulate the proliferation and differentiation of human cardiac progenitor cells in our previous study. methods and results mirna-204 overexpression markedly promoted cardiomyocyte proliferation in both neonatal and adult rat cardiomyocytes in vitro. transgenic mice with the cardiac-specific overexpression of mirna-204 exhibited excessive cardiomyocyte proliferation throughout the embryonic and adult stages, leading to a pronounced increase in ventricular mass. accordingly, the cell cycle regulators, including cyclin a, cyclin b, cyclin d2, cyclin e, cdc2 and pcna, were upregulated in mirna-204 transgenic embryonic hearts. furthermore, we demonstrated that mirna-204 directly targeted jarid2. knockdown of jarid2 mimicked the pro-proliferative effect of mirna-204 overexpression on cultured rat cardiomyocytes, whereas enhanced expression of jarid2 conferred the myocytes with substantial resistance to proliferation by mirna-204 overexpression. conclusion our findings identify a conserved role for mirna-204 in regulating cardiomyocyte proliferation by targeting the jarid2 signaling pathway.",1
"we have recently reported that micrornas (mir)-221 and mir-222 were up-regulated in human thyroid papillary carcinomas in comparison with the normal thyroid tissue. bioinformatic analysis proposed the p27(kip1) protein, a key regulator of cell cycle, as a candidate target for the mir-221/222 cluster. here, we report that the enforced expression of mir-221 and mir-222 was able to reduce p27(kip1) protein levels in thyroid carcinoma and hela cells in the absence of significant changes in specific p27(kip1) mrna levels. this effect is direct as mir-221 and mir-222 negatively regulate the expression of the 3'-untranslated region-based reporter construct from the p27(kip1) gene, and is dependent on two target sites in this region. consistent with these results, an enforced expression of the mir-221 and mir-222 induced the thyroid papillary carcinoma cell line (tpc-1) to progress to the s phase of the cell cycle. it is likely that the negative regulation of p27(kip1) by mir-221 and mir-222 might also have a role in vivo since we report an inverse correlation between mir-221 and mir-222 up-regulation and down-regulation of the p27(kip1) protein levels in human thyroid papillary carcinomas. therefore, the data reported here demonstrate that mir-221 and mir-222 are endogenous regulators of p27(kip1) protein expression, and thereby, the cell cycle.",1
"non-alcoholic fatty liver disease (nafld) is characterized by hepatic fat accumulation and is presently the most common chronic liver disease. however, the mechanisms underlying the development of steatosis remain unclear. micrornas (mirnas) are small non-coding rnas that modulate a variety of biological functions. we have investigated the role of mirna in the development of steatosis. we found that mir-467b expression is significantly downregulated in liver tissues of high-fat diet fed mice and in steatosis-induced hepatocytes. the downregulation of mir-467b resulted in the upregulation of hepatic lipoprotein lipase (lpl), the direct target of mir-467b. moreover, the interaction between mir-467b and lpl was associated with insulin resistance, a major cause of nafld. these results suggest that downregulation of mir-467b is involved in the development of hepatic steatosis by modulating the expression of its target, lpl.",1
"est1, est2, est3 and tlc1 function in a single pathway for telomere replication in the yeast saccharomyces cerevisiae , as would be expected if these genes all encode components of the same complex. est2p, the reverse transcriptase protein subunit, and tlc1, the templating rna, are subunits of the catalytic core of yeast telomerase . in contrast, mutations in est1, est3 or cdc13 eliminate telomere replication in vivo but are dispensable for in vitro telomerase catalytic activity . est1p and cdc13p, as components of telomerase and telomeric chromatin, respectively, cooperate to recruit telomerase to the end of the chromosome . however, est3p has not yet been biochemically characterized and thus its specific role in telomere replication is unclear. we show here that est3p is a stable component of the telomerase holoenzyme and furthermore, association of est3p with the enzyme requires an intact catalytic core. as predicted for a telomerase subunit, fusion of est3p to the high affinity cdc13p telomeric dna binding domain greatly increases access of telomerase to the telomere. est1p is also tightly associated with telomerase; however, est1p is capable of forming a stable tlc1-containing complex even in the absence of est2p or est3p. yeast telomerase therefore contains a minimum of three est proteins for which there is both in vivo and in vitro evidence for their role in telomere replication as subunits of the telomerase complex.",1
"background androgen receptor (ar) signalling is critical to the initiation and progression of prostate cancer (pca). transcriptional activity of ar involves chromatin recruitment of co-activators, including the p300/cbp-associated factor (pcaf). distinct mirna expression profiles have been identified in pca cells during the development and progression of the disease. whether mirnas regulate pcaf expression in pca cells to regulate ar transcriptional activity is still unclear. methods expression of pcaf was investigated in several pca cell lines by qrt-pcr, western blot, and immunocytochemistry. the effects of pcaf expression on ar-regulated transcriptional activity and cell growth in pca cells were determined by chromatin immunoprecipitation, reporter gene construct analysis, and mts assay. targeting of pcaf by mir-17-5p was evaluated using the luciferase reporter assay. results pcaf was upregulated in several pca cell lines. upregulation of pcaf promoted ar transcriptional activation and cell growth in cultured pca cells. expression of pcaf in pca cells was associated with the downregulation of mir-17-5p. targeting of the 3'-untranslated region of pcaf mrna by mir-17-5p caused translational suppression and rna degradation, and, consequently, modulation of ar transcriptional activity in pca cells. conclusions pcaf is upregulated in cultured pca cells, and upregulation of pcaf is associated with the downregulation of mir-17-5p. targeting of pcaf by mir-17-5p modulates ar transcriptional activity and cell growth in cultured pca cells.",1
"long noncoding rnas (lncrnas) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. using a conservative pipeline to identify lncrnas that have important biological functions, we identified 363 lncrnas in the lung and foregut endoderm. importantly, we show that these lncrnas are spatially correlated with transcription factors across the genome. in-depth expression analyses of lncrnas with genomic loci adjacent to the critical transcription factors nkx2.1, gata6, foxa2 (forkhead box a2), and foxf1 mimic the expression patterns of their protein-coding neighbor. loss-of-function analysis demonstrates that two lncrnas, ll18/nanci (nkx2.1-associated noncoding intergenic rna) and ll34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. in particular, we show that ll18/nanci acts upstream of nkx2.1 and downstream from wnt signaling to regulate lung endoderm gene expression. these studies reveal that lncrnas play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.",1
"cholesterol metabolism is tightly regulated at the cellular level. here we show that mir-33, an intronic microrna (mirna) located within the gene encoding sterol-regulatory element-binding factor-2 (srebf-2), a transcriptional regulator of cholesterol synthesis, modulates the expression of genes involved in cellular cholesterol transport. in mouse and human cells, mir-33 inhibits the expression of the adenosine triphosphate-binding cassette (abc) transporter, abca1, thereby attenuating cholesterol efflux to apolipoprotein a1. in mouse macrophages, mir-33 also targets abcg1, reducing cholesterol efflux to nascent high-density lipoprotein (hdl). lentiviral delivery of mir-33 to mice represses abca1 expression in the liver, reducing circulating hdl levels. conversely, silencing of mir-33 in vivo increases hepatic expression of abca1 and plasma hdl levels. thus, mir-33 appears to regulate both hdl biogenesis in the liver and cellular cholesterol efflux.",1
"the u3 snorna is an exceptional box c/d snorna, which is involved in pre-rrna processing without directing chemical modifications. we report here on a comprehensive computational survey resulting in u3 sequences for more than 90 additional eukaryotes. this extended data basis is used to improve the secondary structure models. the detailed investigation of the structural variation of u3 snornas turns out to be much more extensive than previously thought. many fungal u3 genes, in addition, contain introns. u3 promoters are snrna-like but show substantial variations even between related species.",1
"metabolic organs such as the liver and adipose tissue produce several peptide hormones that influence metabolic homeostasis. fat bodies, the drosophila counterpart of liver and adipose tissues, have been thought to analogously secrete several hormones that affect organismal physiology, but their identity and regulation remain poorly understood. previous studies have indicated that microrna mir-8, functions in the fat body to non-autonomously regulate organismal growth, suggesting that fat body-derived humoral factors are regulated by mir-8. here, we found that several putative peptide hormones known to have mitogenic effects are regulated by mir-8 in the fat body. most members of the imaginal disc growth factors and two members of the adenosine deaminase-related growth factors are up-regulated in the absence of mir-8. drosophila insulin-like peptide 6 (dilp6) and imaginal morphogenesis protein-late 2 (imp-l2), a binding partner of dilp, are also up-regulated in the fat body of mir-8 null mutant larvae. the fat body-specific reintroduction of mir-8 into the mir-8 null mutants revealed six peptides that showed fat-body organ-autonomous regulation by mir-8. amongst them, only imp-l2 was found to be regulated by u-shaped, the mir-8 target for body growth. however, a rescue experiment by knockdown of imp-l2 indicated that imp-l2 alone does not account for mir-8's control over the insect's growth. our findings suggest that multiple peptide hormones regulated by mir-8 in the fat body may collectively contribute to drosophila growth.",1
"increasing evidence indicates that microrna (mir)-506 plays a vital role in tumorigenesis; however, the role of mir-506 in gastric cancer (gc) is unclear and needs further investigation. in the present study, we showed that the decrease in the expression of mir-506 is associated with tumor size, pathological tumor node metastasis (tnm) stage, and lymph node metastasis in 63 gc patient tumors. we found that patients with lower expression of mir-506 had a poor prognosis than that with the patients with high expression of mir-506. notably, the ectopic expression of mir-506 was sufficient to inhibit cell proliferation, invasion, and epithelial-mesenchymal transition in the gc cells. moreover, results from luciferase reporter assays identified mir-506 as a direct regulator of yes-associated protein 1 (yap1). reintroduction of yap1 rescues mir-506-induced effects on sgc-7901 cell proliferation and invasion. this function of mir-506/yap1 axis is clinically significant, as the level of mir-506 is inversely correlated with yap1 mrna expression in matched tissues. thus, our study demonstrates that mir-506 may act as a tumor suppressor in gc and that the mir-506/yap1 axis may help us better understand the molecular mechanisms of gc progression.",1
"micrornas (mirnas) as modulators of gene expression have been described to display both tumor-promoting and tumor-suppressive functions. although their role has been studied in different tumor types, little is known about how they regulate nuclear factor κb (nf-κb) signaling in breast cancer. here, we performed an unbiased whole genome mirna (mirome) screen to identify novel modulators of nf-κb pathway in breast cancer. the screen identified 13 mirna families whose members induced consistent effects on nf-κb activity. among those, the mir-520/373 family inhibited nf-κb signaling through direct targeting of rela and thus strongly reduced expression and secretion of the pro-inflammatory cytokines interleukin (il)-6 and il-8. with a combination of in vitro and in vivo approaches, we propose a metastasis-suppressive role of mir-520/373 family. mir-520c and mir-373 abrogated both in vitro cell invasion and in vivo intravasation of highly invasive mda-mb-231 cells. however, knockdown of rela did not affect their metastatic ability. mrna profiling of mda-mb-231 cells on overexpression of mir-520/373 members revealed a strong downregulation of transforming growth factor-β (tgf-β) signaling. mechanistically, the metastasis-suppressive role of mir-520/373 can be attributed to direct suppression of tgfbr2, as the silencing of tgfbr2 phenocopied the effects of mir-520/373 overexpression on suppression of smad-dependent expression of the metastasis-promoting genes parathyroid hormone-related protein, plasminogen activator inhibitor-1 and angiopoietin-like 4 as well as tumor cell invasion, in vitro and in vivo. a negative correlation between mir-520c and tgfbr2 expression was observed in estrogen receptor negative (er(-)) breast cancer patients but not in the er positive (er(+)) subtype. remarkably, decreased expression of mir-520c correlated with lymph node metastasis specifically in er(-) tumors. taken together, our findings reveal that mir-520/373 family has a tumor-suppressive role in er(-) breast cancer by acting as a link between the nf-κb and tgf-β pathways and may thus contribute to the interplay of tumor progression, metastasis and inflammation.",1
"the microrna mir-125b is multi-faceted, with the ability to function as a tumor suppressor or an oncogene, depending on the cellular context. to date, the pro-apoptotic role of mir-125b and its underlying mechanisms are unexplored. in this study, both gain- and loss-of-function experiments revealed that mir-125b expression not only induced spontaneous apoptosis in various cell lines derived from the liver, lung and colorectal cancers, but also sensitized cancer cells to diverse apoptotic stimuli, including nutrient starvation and chemotherapeutic treatment. furthermore, downregulation of mir-125b was a frequent event in hepatocellular carcinoma (hcc) tissues, and the mir-125b level was positively associated with the rate of apoptosis in hcc tissues. subsequent investigations identified mcl-1, bcl-w and interleukin (il)-6r as direct targets of mir-125b. restoration of mir-125b expression not only diminished the expression of mcl-1 and bcl-w directly but also indirectly reduced the mcl-1 and bcl-xl levels by attenuating il-6/signal transducer and activator of transcription 3 signaling. consistent with these findings, introduction of mir-125b reduced the mitochondrial membrane potential and promoted the cleavage of pro-caspase-3. these data indicate that mir-125b may promote apoptosis by suppressing the anti-apoptotic molecules of the bcl-2 family and mir-125b downregulation may facilitate tumor development by conferring upon cells the capability to survive under conditions of nutrient deprivation and chemotherapeutic treatment. our findings highlight the importance of mir-125b in the regulation of apoptosis and suggest mir-125b as an attractive target for anti-cancer therapy.",1
"objectives pulmonary arterial hypertension (pah) is a fast progressing vascular disease characterized by uncontrolled cell proliferation of pulmonary artery smooth muscle cells (pasmcs). some studies have suggested that pah and cancers share an apoptosis-resistant state, featuring excessive cell proliferation. the mir-34 family consists of tumour-suppressive mirnas, and its reduced expression has been reported in numerous cancers; however, its role in hypoxia-induced pah has not been previously studied. materials and methods mir-34 family expression was evaluated in a rat model with hypoxia and in cultured hypoxic pasmcs, using real-time quantitative pcr (rt-qpcr). function of mir-34 family was assessed by transfecting mir-34 mimics and inhibitors. dual luciferase reporter gene assays, rt-qpcr and western blotting were performed to validate target genes of mir-34. results significant down-regulation of mir-34a in hypoxic lung tissue, pulmonary artery and pasmcs was identified and then effects of mir-34a in modulating cell proliferation in human pulmonary artery smooth muscle cells (hpasmcs) was investigated in vitro. reduction of mir-34a levels in hpasmcs caused increased proliferation and these effects were reversed by overexpression of mir-34a. mir-34a overexpression down-regulated platelet-derived growth factor receptor alpha (pdgfra) expression, which is a key factor in pah development. these results suggest that mir-34a is a potential regulator of proliferation in pasmcs, and that it could be used as a novel treatment strategy in pah.",1
"given the emerging role of micrornas (mirs) in cancer progression, the present study investigated the role and underlying mechanism of mir‑103 in colorectal cancer (crc). reverse transcription‑quantitative polymerase chain reaction was conducted to quantify the expression levels of mir‑103 in clinical specimens and cell lines. the role of mir‑103 in crc was examined using mtt, colony formation and transwell assays. in addition, a luciferase reporter assay was used to confirm an associated between the 3' untranslated region of zonula occuldens‑1 (zo‑1) and mir‑103. the results demonstrated that mir‑103 was upregulated in crc. overexpression of mir‑103 promoted crc cell proliferation and migration in vitro, whereas downregulation of mir‑103 inhibited cell proliferation and migration. zo‑1 was identified as a direct target of mir‑103, revealing its expression to be inversely correlated with mir‑103 expression in crc samples. in conclusion, the present study revealed that mir‑103 has strong tumor‑promoting effects via of targeting zo‑1 in crc and has potential development of mirna‑based targeted approaches for the treatment of crc.",1
"increasing evidence suggests that mirnas play important regulatory roles in the nervous system. however, the molecular mechanisms of how specific mirnas affect neuronal development and functions remain less well understood. in the present study, we provide evidence that the conserved microrna mir-210 regulates lipid metabolism and prevents neurodegeneration in the drosophila retina. mir-210 is specifically expressed in the photoreceptor neurons and other sensory organs. genetic deletion of mir-210 leads to lipid droplet accumulation and photoreceptor degeneration in the retina. these effects are associated with abnormal activation of the drosophila sterol regulatory element-binding protein signaling. we further identify the acetyl-coenzyme a synthetase (acs) as one functionally important target of mir-210 in this context. reduction of acs in the mir-210 mutant background suppresses the neurodegeneration defects, suggesting that mir-210 acts through regulation of the acs transcript. together, these results reveal an unexpected role of mir-210 in controlling lipid metabolism and neuronal functions.",1
"messenger rnas (mrnas) often contain binding sites for multiple, different micrornas (mirnas). however, the biological significance of this feature is unclear, since such co-targeting mirnas could function coordinately, independently, or redundantly with one another. here, we show that two co-transcribed drosophila mirnas, let-7 and mir-125, non-redundantly regulate a common target, the transcription factor chronologically inappropriate morphogenesis (chinmo). we first characterize novel adult phenotypes associated with loss of both let-7 and mir-125, which are derived from a common, polycistronic transcript that also encodes a third mirna, mir-100. consistent with the coordinate upregulation of all three mirnas in aging flies, these phenotypes include brain degeneration and shortened lifespan. however, transgenic rescue analysis reveal separable roles for these mirnas: adult mir-125 but not let-7 mutant phenotypes are associated with ectopic chinmo expression in adult brains and are suppressed by chinmo reduction. in contrast, let-7 is predominantly responsible for regulating chinmo during nervous system formation. these results indicate that let-7 and mir-125 function during two distinct stages, development and adulthood, rather than acting at the same time. these different activities are facilitated by an increased rate of processing of let-7 during development and a lower rate of decay of the accumulated mir-125 in the adult nervous system. thus, this work not only establishes a key role for the highly conserved mir-125 in aging. it also demonstrates that two co-transcribed mirnas function independently during distinct stages to regulate a common target, raising the possibility that such biphasic control may be a general feature of clustered mirnas.",1
"tetraspanin 1 (tspan1) has been reported to be upregulated in gastric cancer (gc). however, whilst tspan1 is positively correlated with clinical stage and negatively correlated with survival rates, its function in gc remains elusive. here we show that expression of tspan1 is significantly higher in gc tissues compared to non-cancerous tissues. furthermore, we demonstrate that rnai-mediated down-regulation of tspan1 expression markedly blocks gc cell proliferation, cell cycle progression and invasive activity. we identified tspan1 as a novel target gene of mir-573. overexpression of mir-573 suppressed proliferation and invasion of gc cells by down-regulation of tspan1 expression. restoration of tspan1 rescued the effects of mir-573 overexpression. therefore, our findings suggest that the mir-573/tspan1 axis is important in the control of gastric carcinogenesis.",1
"objective our recent studies have highlighted membrane type-1 matrix metalloproteinase (mmp)-14 as a selective marker for an invasive subset of macrophages potentially related to atherosclerotic plaque progression. moreover, colony stimulating factors (csf) may exert divergent effects on macrophage mmp expression, possibly through micrornas. we, therefore, aim to identify and test the pathophysiological role of micrornas, which modulate macrophage mmp-14 expression in atherosclerotic plaque progression. approach and results compared with macrophage csf-differentiated macrophages, granulocyte/macrophage csf-matured macrophages exhibited reduced mmp-14 mrna levels but increased protein expression and activity, which resulted in heightened macrophage invasion. microrna-24, identified to target mmp-14, was accordingly increased in macrophage csf compared with granulocyte/macrophage csf macrophages. silencing microrna-24 in macrophage csf macrophages significantly increased mmp-14 expression and enhanced their invasive capacity, mimicking granulocyte/macrophage csf macrophages, and suggesting that granulocyte/macrophage csf modulates mmp-14 protein expression and subsequent macrophage invasion in a microrna-24-dependent manner. in human coronary atherosclerotic plaques, increased mmp-14 protein expression in foam cell macrophages was associated with lesions exhibiting histological characteristics associated with an unstable phenotype. furthermore, microrna-24 expression in these atherosclerotic plaques was inversely related to mmp-14 protein expression. moreover, stable plaques contained higher microrna-24 levels than unstable plaques, and microrna-24 colocalized with foam cell macrophages that exhibited low mmp-14 protein expression. finally, in atherosclerotic mice (apolipoprotein e-deficient), microrna-24 inhibition increased plaque size and macrophage mmp-14 expression. conclusions taken together, our data demonstrates that downregulation of microrna-24 promotes an invasive macrophage subset and plays a novel regulatory role in mmp-14 proteolytic activity and, therefore, plaque stability, highlighting its therapeutic potential.",1
"atherosclerosis (as), known as the chronic inflammatory disease, results from the dysfunction of vascular endothelial cells (vecs). transforming growth factor-β1 (tgf-β1) has been reported to be induced by oxidized low-density lipoprotein (ox-ldl) and contribute to as-related vascular endothelial cell damage. this work planned to study the mechanism of tgf-β1 in vascular endothelial cell damage. we found that tgf-β1 was activated by ox-ldl in human umbilical vascular endothelial cells (huvecs). silence of tgf-β1 reversed the inductive effect of ox-ldl on apoptosis and inflammatory response of huvecs. mechanistically, microrna-4286 (mir-4286) targeted and inhibited tgf-β1 to inhibit smad3, and smad3 bound to the promoter of mir-4286 to repress its transcription. rescue assays indicated that mir-4286 ameliorated the ox-ldl-induced apoptosis and inflammatory response through inhibiting tgf-β1. in conclusion, our study first demonstrated that mir-4286/tgf-β1/smad3-negative feedback loop ameliorated vascular endothelial cell damage by attenuating apoptosis and inflammatory response, providing new thoughts for promoting the treatment of as.",1
"micrornas (mirnas) are short non-coding rna regulators that control gene expression mainly through post-transcriptional silencing. we previously identified mir-205 in a signature for human cervical cancer using a deep sequencing approach. in this study, we confirmed that mir-205 expression was frequently higher in human cervical cancer than their matched normal tissue samples. functionally, we demonstrate that mir-205 promotes cell proliferation and migration in human cervical cancer cells. to further understand the biological roles of mir-205, we performed in vivo crosslinking and argonaute 2 immunoprecipitation of mirna ribonucleoprotein complexes followed by microarray analysis (clip-chip) to identify its potential mrna targets. applying clip-chip on gain- and loss-of-function experiments, we identified a set of transcripts as potential targets of mir-205. several targets are functionally involved in cellular proliferation and migration. two of them, cyr61 and ctgf, were further validated by western blot analysis and quantification of mrna enrichment in the ago2 immunoprecipitates using qrt-pcr. furthermore, both cyr61 and ctgf were downregulated in cervical cancer tissues. in summary, our findings reveal novel functional roles and targets of mir-205 in human cervical cancer, which may provide new insights about its role in cervical carcinogenesis and its potential value for clinical diagnosis.",1
"the escherichia coli host factor i, hfq, binds to many small regulatory rnas and is required for oxys rna repression of fhla and rpos mrna translation. here we report that hfq is a bacterial homolog of the sm and sm-like proteins integral to rna processing and mrna degradation complexes in eukaryotic cells. hfq exhibits the hallmark features of sm and sm-like proteins: the sm1 sequence motif, a multisubunit ring structure (in this case a homomeric hexamer), and preferential binding to polyu. we also show that hfq increases the oxys rna interaction with its target messages and propose that the enhancement of rna-rna pairing may be a general function of hfq, sm, and sm-like proteins.",1
"hepatitis delta virus (hdv) and cytoplasmic polyadenylation element-binding protein 3 (cpeb3) ribozymes form a family of self-cleaving rnas characterized by a conserved nested double-pseudoknot and minimal sequence conservation. secondary structure-based searches were used to identify sequences capable of forming this fold, and their self-cleavage activity was confirmed in vitro. active sequences were uncovered in several marine organisms, two nematodes, an arthropod, a bacterium, and an insect virus, often in multiple sequence families and copies. sequence searches based on identified ribozymes showed that plants, fungi, and a unicellular eukaryote also harbor the ribozymes. in anopheles gambiae, the ribozymes were found differentially expressed and self-cleaved at basic developmental stages. our results indicate that hdv-like ribozymes are abundant in nature and suggest that self-cleaving rnas may play a variety of biological roles.",1
"u8 snorna is the rna component of a small nucleolar ribonucleoprotein (u8 snornp) required for accumulation of mature 5.8s and 28s rrnas, components of the large ribosomal subunit. we have identified two putative u8 genes in xenopus laevis. sequence analysis of the coding regions of these two genes indicate that both differ at several positions from the previously characterized u8 rna and that the two differ from each other. functional analysis of these genes indicates that both are transcribed in vivo, produce stable u8 transcripts, and are capable of facilitating pre-rrna processing in vivo. these data demonstrate that natural sequence variation exists among the u8 snorna genes in xenopus. alignment of these three xenopus u8 sequences with the previously described mammalian u8 homologues in mouse, rat and human has provided information about evolutionarily conserved sequence and structural elements in u8 rna. identification and functional characterization of these naturally occurring variants in xenopus has helped identify regions in u8 rna that may be critical for function.",1
"ethanolamine, a product of the breakdown of phosphatidylethanolamine from cell membranes, is abundant in the human intestinal tract and in processed foods. effective utilization of ethanolamine as a carbon and nitrogen source may provide a survival advantage to bacteria that inhabit the gastrointestinal tract and may influence the virulence of pathogens. in this work, we describe a unique series of posttranscriptional regulatory strategies that influence expression of ethanolamine utilization genes (eut) in enterococcus, clostridium, and listeria species. one of these mechanisms requires an unusual 2-component regulatory system. regulation involves specific sensing of ethanolamine by a sensor histidine kinase (eutw), resulting in autophosphorylation and subsequent phosphoryl transfer to a response regulator (eutv) containing a rna-binding domain. our data suggests that eutv is likely to affect downstream gene expression by interacting with conserved transcription termination signals located within the eut locus. breakdown of ethanolamine requires adenosylcobalamin (adocbl) as a cofactor, and, intriguingly, we also identify an intercistronic adocbl riboswitch that has a predicted structure different from previously established adocbl riboswitches. we demonstrate that association of adocbl to this riboswitch prevents formation of an intrinsic transcription terminator element located within the intercistronic region. together, these results suggest an intricate and carefully coordinated interplay of multiple regulatory strategies for control of ethanolamine utilization genes. gene expression appears to be directed by overlapping posttranscriptional regulatory mechanisms, each responding to a particular metabolic signal, conceptually akin to regulation by multiple dna-binding transcription factors.",1
"previous reports suggested that u11, in contrast to u12 or other small nuclear (sn)rnas of the u12-type spliceosome, might be either highly divergent or absent in drosophila melanogaster. affinity purification of drosophila u12-containing complexes has led to the identification of the fly u11 snrna, which contains a potential u12-type 5' splice-site-interacting sequence, but whose sequence and length differs significantly from vertebrate and plant u11. analysis of u12-type introns revealed an a-rich region directly downstream of drosophila, but not human, u12-type 5' splice sites. this finding, coupled with the presence of a highly divergent u11 snrna, and the apparent absence of drosophila homologs of human u11 proteins, suggest that u12-type 5' splice site recognition might be different in flies. a comparison of u11 snrnas that we have identified from vertebrates, plants, and insects, suggests that an evolutionarily divergent u11 snrna may be unique to drosophila and not characteristic of insects in general.",1
"introduction experimental and clinical evidence points to a critical role of progesterone and the nuclear progesterone receptor (pr) in controlling mammary gland tumorigenesis. however, the molecular mechanisms of progesterone action in breast cancer still remain elusive. on the other hand, micro rnas (mirnas) are short ribonucleic acids which have also been found to play a pivotal role in cancer pathogenesis. the role of mirna in progestin-induced breast cancer is poorly explored. in this study we explored progestin modulation of mirna expression in mammary tumorigenesis. methods we performed a genome-wide study to explore progestin-mediated regulation of mirna expression in breast cancer. mir-16 expression was studied by rt-qpcr in cancer cell lines with silenced pr, signal transducer and activator of transcription 3 (stat3) or c-myc, treated or not with progestins. breast cancer cells were transfected with the precursor of mir-16 and proliferation assays, western blots or in vivo experiments were performed. target genes of mir-16 were searched through a bioinformatical approach, and the study was focused on cyclin e. reporter gene assays were performed to confirm that cyclin e 3'utr is a direct target of mir-16. results we found that nine mirnas were upregulated and seven were downregulated by progestin in mammary tumor cells. mir-16, whose function as a tumor suppressor in leukemia has already been shown, was identified as one of the downregulated mirnas in murine and human breast cancer cells. progestin induced a decrease in mir-16 levels via the classical pr and through a hierarchical interplay between stat3 and the oncogenic transcription factor c-myc. a search for mir-16 targets showed that the ccne1 gene, encoding the cell cycle regulator cyclin e, contains conserved putative mir-16 target sites in its mrna 3' utr region. we found that, similar to the molecular mechanism underlying progestin-modulated mir-16 expression, stat3 and c-myc participated in the induction of cyclin e expression by progestin. moreover, overexpression of mir-16 abrogated the ability of progestin to induce cyclin e upregulation, revealing that cyclin e is a novel target of mir-16 in breast cancer. overexpression of mir-16 also inhibited progestin-induced breast tumor growth in vitro and in vivo, demonstrating for the first time, a role for mir-16 as a tumor suppressor in mammary tumorigenesis. we also found that the erbb ligand heregulin (hrg) downregulated the expression of mir-16, which then participates in the proliferative activity of hrg in breast tumor cells. conclusions in this study, we reveal the first progestin-regulated mirna expression profile and identify a novel role for mir-16 as a tumor suppressor in progestin- and growth factor-induced growth in breast cancer.",1
"myocardial tissue injury caused by ischemia and hypoxia is a major cause of fatal diseases, including coronary atherosclerosis resulting from myocardial infarction and stroke. a number of micrornas have been demonstrated to function as protectors against ischemia-reperfusion (i/r) and/or hypoxia-reperfusion (h/r)-induced myocardial injury, including microrna-21 (mir-21). however, the protective mechanism of mir-21 has not been fully elucidated. the present study demonstrated that mir-21 had an anti-apoptotic role in i/r-induced myocardial damage in vivo and in h/r-induced h9c2 cell death in vitro. of note, the present study indicates that a common molecular mechanism is likely to exist in i/r- and h/r-induced cardiocyte apoptosis. during i/r and h/r, forced expression of mir-21 upregulated the akt signaling activity via suppressing the expression of phosphatase and tensin homolog (pten) and the increased activity of akt signaling further inhibited apoptosis partially by increasing the ratio of b-cell lymphoma 2(bcl-2)/bcl-2-associated x protein, which further suppressed the expression of caspase-3. in conclusion, to the best of our knowledge, it was shown for the first time that mir-21 had a protective role in i/r- and h/r-induced cardiocyte apoptosis via the pten/akt-dependent mechanism. the present study indicates that mir-21 may be a promising agent for the treatment of i/r and h/r-induced myocardial injury.",1
"it is increasingly clear that the biological functions of a transcription factor cannot be fully understood solely on the basis of protein-coding genes that fall under its control. many transcription factors regulate expression of mirnas, which affect the cell by modulating translation and stability of mrnas. the identities and the roles of nf-κb-regulated mirnas have been attracting research interest for a long time. we revisited this issue in a system with controlled expression of one of the key regulators of nf-κb, ripk1. several regulated mirnas were identified, including mir-146a, mir-215 and mir-497. the mirnas were also inducible by il-1β, but not when nf-κb activity was repressed by mutant iκbα. the presence of a mir-497 site was predicted in the 3'-utr of ikbkb gene, which encodes ikkβ. using appropriately engineered reporters, we confirmed that this site can be a target of suppressive action of mir-497. our findings suggest that nf-κb controls expression of a mirna, which may reduce production of ikkβ. considering the role of ikkβ in the canonical pathway of nf-κb activation, our observations may indicate a new mechanism that modulates the magnitude of such activation, as well as the propensity of a cell to engage canonical vs. non-canonical pathways.",1
"aminoacyl-trna (aa-trna) formation, an essential process in protein biosynthesis, is generally achieved by direct attachment of an amino acid to trna by the aa-trna synthetases. an exception is gln-trna synthesis, which in eukaryotes is catalyzed by glutaminyl-trna synthetase (glnrs), while most bacteria, archaea, and chloroplasts employ the transamidation pathway, in which a trna-dependent glutamate modification generates gln-trna. mitochondrial protein synthesis is carried out normally by mitochondrial enzymes and organelle-encoded trnas that are different from their cytoplasmic counterparts. early work suggested that mitochondria use the transamidation pathway for gln-trna formation. we found no biochemical support for this in saccharomyces cerevisiae mitochondria, but demonstrated the presence of the cytoplasmic glnrs in the organelle and its involvement in mitochondrial gln-trna synthesis. in addition, we showed in vivo localization of cytoplasmic trnagln in mitochondria and demonstrated its role in mitochondrial translation. we furthermore reconstituted in vitro cytoplasmic trnagln import into mitochondria by a novel mechanism. this trna import mechanism expands our knowledge of rna trafficking in the eukaryotic cell. these findings change our view of the evolution of organellar protein synthesis.",1
"trefoil factor 1 (tff1), a member of the trefoil peptide family, is not only associated with mucosal protection and restoration but is also correlated with tumorigenesis of the gastrointestinal tract. in an early study, we performed sequence analysis and identified one potential mir423-5p binding site within the 3'-untranslated region of tff1 using microrna target prediction tools. in the current study, we demonstrated that the coding dna region within tff1 is also a candidate for mir218-5p targeting. we used real-time pcr and in situ hybridization to analyze the correlation between mir218-5p and tff1 expression in tumor lesions and paracancerous tissue in gastric cancer (gc) samples. additionally, endogenous and exogenous tff1 were suppressed by mir218-5p in gastric cancer cells and influenced the progression of gc in an erk1/2-dependent manner. targeting mir218-5p may provide a novel strategy for the treatment of gc.",1
"cervical cancer (cc) remains a highly prevalent cancer and mortality globally among women globally. the aim of the present study was to assess the ability of mir-374b to regulate cc cells through jam-2, whilst exploring whether the underlying mechanism and its relation to the p38/erk signaling pathway. during the study, microrna-374b (mir-374b) was observed to have been expressed at a low level among cc tissues. hence, a series of mir-374b mimics, mir-374b inhibitors, sirna against jam-2, sb202190 (an inhibitor for p38), and pd98059 (an inhibitor for erk) were introduced to treat cc siha cells and normal cervical ect1/e6e7 cells. mtt, flow cytometry, scratch test, and transwell assays were applied to determine cell viability, apoptosis, migration, and invasion. the inhibitory role of the p38/erk signaling pathway was observed in the cc cells treated with mir-374b mimics or sirna against jam-2. mir-374b mimic exposure was found to reduce cell viability, migration, and invasion, but induce apoptosis. mir-374b inhibitor exposure was observed to have induced effects on the cc cells in a contrary manner to those induced by that of the mir-374b mimics. the key findings of the study demonstrated that mir-374b significantly inhibits cell proliferation, migration, and invasion through the blockade of the p38/erk signaling pathway activation, as well as negatively binding to jam-2, highlighting its potential as a therapeutic target for cc.",1
"background micrornas have roles in the regulation of the epithelial-mesenchymal transition (emt). findings have shown that mir-506 inhibits the expression of snai2 and that low expression of mir-506 is associated with poor prognoses in ovarian and breast cancers. this study investigated the role of mir-506 in survival and the emt in patients with gastric cancer. methods in this study, mir-506 and snai2 mrna levels were measured in 141 cases of gastric cancer by quantitative reverse transcription polymerase chain reaction, and the protein expressions of snai2 and e-cadherin in 39 cases were validated by immunohistochemical analysis. next, the associations between their expression levels and clinicopathologic factors were evaluated. in addition, cell proliferation, migration, and luciferase activity of the 3' untranslated region (utr) of snai2 were analyzed using pre-mir-506 precursor in two human gastric cancer cell lines. results low expression of mir-506 was significantly correlated with poor overall survival in both the univariate analysis (p = 0.016) and the multivariate analysis (p conclusions the emt was directly suppressed by mir-506, and its low expression was an independent prognostic factor in gastric cancer patients. the data indicated that mir-506 may act as a tumor suppressor and could be a novel therapeutic agent.",1
"computational comparative techniques were applied to analysis of the aromatic amino acid regulon in gram-positive bacteria. a new candidate transcription regulation signal of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase and shikimate kinase genes was identified in streptococcus and lactococcus species. new t-boxes were found upstream of aromatic amino acid biosynthesis and transport genes in the bacillus/clostridium group. the substrate specificity of proteins from the paba/trpg family was assigned based on metabolic reconstruction and analysis of regulatory signals and phylogenetic patterns. new candidate tryptophan transporters were identified; their specificity was predicted by analysis of t-box regulatory sites. comparison of all available genomes shows that regulation of genes of the aromatic amino acid biosynthesis pathway is quite labile and involves at least four regulatory systems, two at the dna level and two more involving competition of alternative rna secondary structures for transcription and/or translation regulation at the rna level.",1
"background recent reports indicate that micrornas (mirnas) play a critical role in malignancies. however, the role that mirnas play in pancreatic cancer remains to be determined. the purpose of this study was to investigate aberrantly expressed mirnas in pancreatic cancer tissues and demonstrate their roles in disease progression. results we detected the expression patterns of mirnas in 10 pancreatic cancer tissues and their adjacent benign tissues by quantitative real time-pcr (qrt-pcr) and found that mir-15a and mir-214 were dysregulated in the tumor samples. this is the first time that mir-214 has been identified as aberrantly expressed in pancreatic cancer. in vitro experiments showed that overexpression of mir-15a inhibited the viability of pancreatic cancer cells, whereas overexpression of mir-214 decreased the sensitivity of the cells to gemcitabine (gem). furthermore, we identified wnt3a and fgf7 as potential targets of mir-15a and ing4 as a target of mir-214. conclusions aberrant expression of mirnas such as mir-15a and mir-214 results in different cellular effects in pancreatic cancer. downregulation of mir-15a might contribute to proliferation of pancreatic cancer cells, whereas upregulation of mir-214 in pancreatic cancer specimens might be related to the poor response of pancreatic cancer cells to chemotherapy. mir-15a directly targets multiple genes relevant in pancreatic cancer, suggesting that it may serve as a novel therapeutic target for treatment of the disease.",1
"background microrna-7 (mir-7) has been reported to be a tumour suppressor gene. however, whether it has a role in the growth of non-small-cell lung cancer (nsclc) and what is its target involved in the tumour growth is still under investigation. methods nsclc tissue sample, nsclc cell lines and tissue microarray were investigated in this study. total rna, mirna and protein were used for rt-pcr and western blot analysis. immunohistochemistry was performed in tissues microarray. cell culture and intervention experiments were performed in vitro and in vivo. bioinformatics prediction, western blot and luciferase assay were identified the target of mir-7. results in this study, we found that the expression of mir-7 was significantly downregulated not only in nsclc cell lines, but also in human nsclc tissues compared with the matched adjacent tissues. restoration of its expression through mir-7 mimics in a549 and h1299 nsclc cells inhibited cell proliferation, colony formation, and cell-cycle progression in vitro. more importantly, the tumorigenicity in nude mice was reduced after administration of mir-7 in vivo. in advance, through bioinformatic analysis, luciferase assay and western blot, we identified a novel target of mir-7, pa28gamma (a proteasome activator) to be enrolled in the regulation with tumour. pa28gamma mrna and protein levels are markedly upregulated in nsclc cell lines and tumour samples, exhibiting a strong inverse relation with that of mir-7. in addition, knockdown of pa28gamma induced similar effects as overexpression of mir-7 in nsclc cells. furthermore, mir-7 overexpression or silencing of pa28gamma reduced the cyclind1 expression at mrna and protein level in nsclc cell lines. conclusion all these findings strongly imply that the overexpression of pa28gamma resulted from mir-7 downexpression in nsclc has an important role in promoting cancer cell progress and consequently results in nsclc growth. thus, strategies targeting pa28gamma and/or mir-7 may become promising molecular therapies in nsclc treatment.",1
"transforming growth factor-beta (tgf-β) is a pleiotropic cytokine with important effects on processes such as fibrosis, angiogenesis, and immunosupression. using bioinformatics, we identified smad2, one of the mediators of tgf-β signaling, as a predicted target for a microrna, microrna-155 (mir-155). micrornas are a class of small non-coding rnas that have emerged as an important class of gene expression regulators. mir-155 has been found to be involved in the regulation of the immune response in myeloid cells. here, we provide direct evidence of binding of mir-155 to a predicted binding site and the ability of mir-155 to repress smad2 protein expression. we employed a lentivirally transduced monocyte cell line (thp1-155) containing an inducible mir-155 transgene to show that endogenous levels of smad2 protein were decreased after sustained overexpression of mir-155. this decrease in smad2 led to a reduction in both tgf-β-induced smad-2 phosphorylation and smad-2-dependent activation of the expression of the caga(12)luc reporter plasmid. overexpression of mir-155 altered the cellular responses to tgf-β by changing the expression of a set of genes that is involved in inflammation, fibrosis, and angiogenesis. our study provides firm evidence of a role for mir-155 in directly repressing smad2 expression, and our results demonstrate the relevance of one of the two predicted target sites in smad2 3'-utr. altogether, our data uncover an important role for mir-155 in modulating the cellular response to tgf-β with possible implications in several human diseases where homeostasis of tgf-β might be altered.",1
"the silkworm bombyx mori uses a wz sex determination system that is analogous to the one found in birds and some reptiles. in this system, males have two z sex chromosomes, whereas females have z and w sex chromosomes. the silkworm w chromosome has a dominant role in female determination, suggesting the existence of a dominant feminizing gene in this chromosome. however, the w chromosome is almost fully occupied by transposable element sequences, and no functional protein-coding gene has been identified so far. female-enriched piwi-interacting rnas (pirnas) are the only known transcripts that are produced from the sex-determining region of the w chromosome, but the function(s) of these pirnas are unknown. here we show that a w-chromosome-derived, female-specific pirna is the feminizing factor of b. mori. this pirna is produced from a pirna precursor which we named fem. fem sequences were arranged in tandem in the sex-determining region of the w chromosome. inhibition of fem-derived pirna-mediated signalling in female embryos led to the production of the male-specific splice variants of b. mori doublesex (bmdsx), a gene which acts at the downstream end of the sex differentiation cascade. a target gene of fem-derived pirna was identified on the z chromosome of b. mori. this gene, which we named masc, encoded a ccch-type zinc finger protein. we show that the silencing of masc messenger rna by fem pirna is required for the production of female-specific isoforms of bmdsx in female embryos, and that masc protein controls both dosage compensation and masculinization in male embryos. our study characterizes a single small rna that is responsible for primary sex determination in the wz sex determination system.",1
"for toxin/antitoxin (ta) systems, no toxin has been identified that functions by cleaving dna. here, we demonstrate that ralr and rala of the cryptic prophage rac form a type i ta pair in which the antitoxin rna is a trans-encoded small rna with 16 nucleotides of complementarity to the toxin mrna. we suggest the newly discovered antitoxin gene be named rala for ralr antitoxin. toxin ralr functions as a non-specific endonuclease that cleaves methylated and unmethylated dna. the rna chaperone hfq is required for rala antitoxin activity and appears to stabilize rala. also, ralr/rala is beneficial to the escherichia coli host for responding to the antibiotic fosfomycin. hence, our results indicate that cryptic prophage genes can be functionally divergent from their active phage counterparts after integration into the host genome.",1
"microrna mir-155 is expressed at elevated levels in human cancers including cancers of the lung, breast, colon, and a subset of lymphoid malignancies. in b cells, mir-155 is induced by the oncogenic latency gene expression program of the human herpesvirus epstein-barr virus (ebv). two other oncogenic herpesviruses, kaposi's sarcoma-associated herpesvirus and marek's disease virus, encode functional homologues of mir-155, suggesting a role for this microrna in the biology and pathogenesis of these viruses. bone morphogenetic protein (bmp) signaling is involved in an array of cellular processes, including differentiation, growth inhibition, and senescence, through context-dependent interactions with multiple signaling pathways. alteration of this pathway contributes to a number of disease states including cancer. here, we show that mir-155 targets the 3' untranslated region of multiple components of the bmp signaling cascade, including smad1, smad5, hivep2, cebpb, runx2, and myo10. targeting of these mediators results in the inhibition of bmp2-, bmp6-, and bmp7-induced id3 expression as well as bmp-mediated ebv reactivation in the ebv-positive b-cell line, mutu i. further, mir-155 inhibits smad1 and smad5 expression in the lung epithelial cell line a549, it inhibits bmp-mediated induction of the cyclin-dependent kinase inhibitor p21, and it reverses bmp-mediated cell growth inhibition. these results suggest a role for mir-155 in controlling bmp-mediated cellular processes, in regulating bmp-induced ebv reactivation, and in the inhibition of antitumor effects of bmp signaling in normal and virus-infected cells.",1
"micrornas (mirnas) have been implicated in cell-cycle regulation and in some cases shown to have a role in tissue growth control. depletion of mirnas was found to have an effect on tissue growth rates in the wing primordium of drosophila, a highly proliferative epithelium. dicer-1 (dcr-1) is a double-stranded rnaseiii essential for mirna biogenesis. adult cells lacking dcr-1, or with reduced dcr-1 activity, were smaller than normal cells and gave rise to smaller wings. dcr-1 mutant cells showed evidence of being susceptible to competition by faster growing cells in vivo and the mirna machinery was shown to promote g(1)-s transition. we present evidence that dcr-1 acts by regulating the trim-nhl protein mei-p26, which in turn regulates dmyc protein levels. mei-p26 is a direct target of mirnas, including the growth-promoting bantam mirna. thus, regulation of tissue growth by the mirna pathway involves a double repression mechanism to control dmyc protein levels in a highly proliferative and growing epithelium.",1
"mirnas regulate gene expression by inhibiting translation or by targeting messenger rna (mrna) for degradation in a post-transcriptional fashion. in the present study, we show that ectopic expression of mir-34a reduces both mrna and protein levels of cyclin d1 (ccnd1) and cyclin-dependent kinase 6 (cdk6). we also demonstrate that mir-34a targets the 3'-untranslated mrna region of ccnd1 as well as cdk6, which in turn interferes with phosphorylation of retinoblastoma. in addition, we show that overexpression of mir-34a induces a significant g1 cell-cycle arrest in the a549 cell line. taken together, our data suggest that the effects of mir-34a on g1 cell cycle arrest are through the down-regulation of ccnd1 and cdk6, which is associated with other targets of mir-34a either additively or synergistically.",1
"mir-17 approximately 92, mir-106b approximately 25, and mir-106a approximately 363 belong to a family of highly conserved mirna clusters. amplification and overexpression of mir-1792 is observed in human cancers, and its oncogenic properties have been confirmed in a mouse model of b cell lymphoma. here we show that mice deficient for mir-17 approximately 92 die shortly after birth with lung hypoplasia and a ventricular septal defect. the mir-17 approximately 92 cluster is also essential for b cell development. absence of mir-17 approximately 92 leads to increased levels of the proapoptotic protein bim and inhibits b cell development at the pro-b to pre-b transition. furthermore, while ablation of mir-106b approximately 25 or mir-106a approximately 363 has no obvious phenotypic consequences, compound mutant embryos lacking both mir-106b approximately 25 and mir-17 approximately 92 die at midgestation. these results provide key insights into the physiologic functions of this family of micrornas and suggest a link between the oncogenic properties of mir-17 approximately 92 and its functions during b lymphopoiesis and lung development.",1
"the small nuclear rna (snrna) components of the spliceosome undergo many conformational rearrangements during its assembly, catalytic activation and disassembly. the u4 and u6 snrnas are incorporated into the spliceosome as a base-paired complex within the u4/u6.u5 small nuclear ribonucleoprotein (tri-snrnp). u4 and u6 are then unwound in order for u6 to pair with u2 to form the spliceosome's active site. after splicing, u2/u6 is unwound and u6 annealed to u4 to reassemble the tri-snrnp. u6 rearrangements are crucial for spliceosome formation but are poorly understood. we have used single-molecule förster resonance energy transfer and unwinding assays to identify interactions that promote u4/u6 unwinding and have studied their impact in yeast. we find that u4/u6 is efficiently unwound using dna oligonucleotides by coupling unwinding of u4/u6 stem ii with strand invasion of stem i. unwinding is stimulated by the u6 telestem, which transiently forms in the intact u4/u6 rna complex. stabilization of the telestem in vivo results in accumulation of u4/u6 di-snrnp and impairs yeast growth. our data reveal conserved mechanisms for u4/u6 unwinding and indicate telestem dynamics are critical for tri-snrnp assembly and stability.",1
"the purpose of this study was to identify new tumor suppressor micrornas (mirna; mir) in bladder cancer, conduct functional analysis of their suppressive role, and identify their specific target genes. to explore tumor suppressor mirs in bladder cancer, mir microarray was conducted using sv-huc-1, t24, j82, and tccsup cells. expression of mir-493 in bladder cancer (t24, j82, and tccsup) cells was downregulated compared with normal sv-huc-1 cells. also, the expression of mir-493 was significantly lower in bladder cancer tissues than in their corresponding noncancerous tissues. transfection of mir-493 into t24 or j82 cells decreased their cell growth and migration abilities. on the basis of this result, to identify potential mir-493 target genes, we used target scan algorithms to identify target oncogenes related to invasion and migration. mir-493 decreased 3'-untranslated region luciferase activity and protein expression of fzd4 and rhoc. mir-493 also decreased binding of rhoc and rock-1. mir-493 is a new tumor suppressor mirna in bladder cancer and inhibits cell motility through downregulation of rhoc and fzd4.",1
"inflammaging refers to low-grade, chronically activated innate immunity that has deleterious effects on healthy lifespan. however, little is known about the intrinsic signaling pathway that elicits innate immune genes during aging. here, using drosophila melanogaster, we profile the microrna targetomes in young and aged animals, and reveal dawdle, an activin-like ligand of the tgf-β pathway, as a physiological target of microrna-252. we show that microrna-252 cooperates with forkhead box o, a conserved transcriptional factor implicated in aging, to repress dawdle. unopposed dawdle triggers hyperactivation of innate immune genes coupled with a decline in organismal survival. using adult muscle tissues, single-cell sequencing analysis describes that dawdle and its downstream innate immune genes are expressed in distinct cell types, suggesting a cell nonautonomous mode of regulation. we further determine the genetic cascade by which dawdle signaling leads to increased kenny/ikkγ protein, which in turn activates relish/nf-κb protein and consequentially innate immune genes. finally, transgenic increase of microrna-252 and forkhead box o pathway factors in wild-type drosophila extends lifespan and mitigates the induction of innate immune genes in aging. together, we propose that microrna-252 and forkhead box o promote healthy longevity by cooperative inhibition on dawdle-mediated inflammaging.",1
"an increasing body of evidence highlights an intriguing interaction between micrornas and transcriptional factors involved in determining cell fate, including the well known ""genome guardian"" p53. here we show that mir-205, oncosuppressive microrna lost in breast cancer, is directly transactivated by oncosuppressor p53. moreover, evaluating mir-205 expression in a panel of cell lines belonging to the highly aggressive triple negative breast cancer (tnbc) subtype, which still lacks an effective targeted therapy and characterized by an extremely undifferentiated and mesenchymal phenotype, we demonstrated that this microrna is critically down-expressed compared to a normal-like cell line. re-expression of mir-205 where absent strongly reduces cell proliferation, cell cycle progression and clonogenic potential in vitro, and inhibits tumor growth in vivo, and this tumor suppressor activity is at least partially exerted through targeting of e2f1, master regulator of cell cycle progression, and lamc1, component of extracellular matrix involved in cell adhesion, proliferation and migration.",1
"three yeast snrnas (snr20, snr7, and snr14) have been implicated in pre-mrna splicing. snr20 and snr7 contain domains of homology to u2 and u5, respectively, and each is required for viability. these rnas are found associated with the spliceosome, as is snr14. we show here that snr14 is also an essential gene product. sequence analysis reveals that, like snr7 and snr20, snr14 contains a consensus binding site for the sm antigen, a feature common to all mammalian snrnas involved in splicing. moreover, snr14 exhibits several blocks of sequence and structural homology to u4, which in metazoans is found in association with u6. native gel electrophoresis demonstrates that snr14 is in fact base-paired with another yeast snrna, designated snr6, which has primary sequence homology to u6. we conclude that snr14 is the yeast analog of u4.",1
"recent studies have shown that myocardial ischemia/reperfusion (i/r)-induced necrosis can be controlled by multiple genes. in this study, we observed that both strands (5p and 3p) of mir-223 were remarkably dysregulated in mouse hearts upon i/r. precursor mir-223 (pre-mir-223) transgenic mouse hearts exhibited better recovery of contractile performance over reperfusion period and lesser degree of myocardial necrosis than wild type hearts upon ex vivo and in vivo myocardial ischemia. conversely, pre-mir-223 knock-out (ko) mouse hearts displayed opposite effects. furthermore, we found that the rip1/rip3/mlkl necroptotic pathway and inflammatory response were suppressed in transgenic hearts, whereas they were activated in pre-mir-223 ko hearts upon i/r compared with wild type controls. accordingly, treatment of pre-mir-223 ko mice with necrostatin-1s, a potent necroptosis inhibitor, significantly decreased i/r-triggered cardiac necroptosis, infarction size, and dysfunction. mechanistically, we identified two critical cell death receptors, tnfr1 and dr6, as direct targets of mir-223-5p, whereas mir-223-3p directly suppressed the expression of nlrp3 and iκb kinase α, two important mediators known to be involved in i/r-induced inflammation and cell necroptosis. our findings indicate that mir-223-5p/-3p duplex works together and cooperatively inhibits i/r-induced cardiac necroptosis at multiple layers. thus, pre-mir-223 may constitute a new therapeutic agent for the treatment of ischemic heart disease.",1
"a microrna expression screen was performed analyzing 157 different micrornas in laser-microdissected tissues from benign melanocytic nevi (n = 10) and primary malignant melanomas (n = 10), using quantitative real-time pcr. differential expression was found for 72 micrornas. members of the let-7 family of micrornas were significantly downregulated in primary melanomas as compared with benign nevi, suggestive for a possible role of these molecules as tumor suppressors in malignant melanoma. interestingly, similar findings had been described for lung and colon cancer. overexpression of let-7b in melanoma cells in vitro downregulated the expression of cyclins d1, d3, and a, and cyclin-dependent kinase (cdk) 4, all of which had been described to play a role in melanoma development. the effect of let-7b on protein expression was due to targeting of 3'-untranslated regions (3'utrs) of individual mrnas, as exemplified by reporter gene analyses for cyclin d1. in line with its downmodulating effects on cell cycle regulators, let-7b inhibited cell cycle progression and anchorage-independent growth of melanoma cells. taken together, these findings not only point to new regulatory mechanisms of early melanoma development, but also may open avenues for future targeted therapies of this tumor.",1
"alzheimer's disease (ad) is a serious neurodegenerative disease, and micrornas (mirnas) have been linked to its pathogenesis. mir-603, a novel primate-specific mirna and an intronic mirna of a human brain highly expressed gene kiaa1217, is implicated in the risk and pathogenesis of ad. the rs11014002 single nucleotide polymorphism (snp) (c/u), which locates in mir-603 precursor (pre-mir-603), exhibits a protective effect towards ad risk. additionally, the rs11014002 snp promotes the biogenesis of mature mir-603. mir-603 downregulates lrpap1 mrna and protein levels through directly binding the 3' untranslated region (3'utr) of lrpap1. moreover, mir-603 increases lrp1 protein expression. lrpap1 and lrp1, playing opposite roles, are involved in aβ clearance and pathogenesis of ad. strikingly, mir-603 exhibits a relatively higher expression and there is a loss of a negative correlation between mir-603 and lrpap1/rnd1 mrna levels in the hippocampi of patients with ad. in addition, mir-603 directly downregulates a key neuronal apoptotic component-e2f1, and prevents hela cells from undergoing h2o2-induced apoptosis. this work suggests that mir-603 may be a novel ad-relevant mirna and that its rs11014002 snp may serve as a protective factor against ad.",1
"a small noncoding bacterial ribonucleic acid of 62-64 nucleotides, rydc, was identified in the genomes of escherichia coli, salmonella, and shigella. in vivo, rydc binds to the rna-binding protein hfq, and it is unstable when hfq is absent. mobility assays reveal that complex formation between rydc and hfq is specific, with an apparent binding constant of approximately 300 nm. sequence alignments combined with structural probing demonstrate that rydc folds as a pseudoknot. hfq binds the loops crossing the deep and shallow grooves of the pseudoknotted rna and reorganizes its overall conformation. an interaction with a polycistronic mrna, yejabef, which encodes a putative abc transporter, was detected by affinity purification of immobilized rna-hfq complexes. in vivo, the yejabef operon is expressed on minimal medium. remarkably, its expression is reduced when rydc is absent, and the operon is degraded when rydc expression is stimulated. this observation correlates with the growth defects associated with a stimulation of its expression in vivo, generating a thermosensitive phenotype that affects growth on minimal media supplemented with glycerol, maltose, or ribose. we conclude that rydc regulates the yejabef-encoded abc permease at the mrna level. this small rna may contribute to optimal adaptation of some enterobacteria to environmental conditions.",1
"hepatocyte nuclear factor (hnf)-4α is a key member of the transcription factor network regulating hepatocyte differentiation and function. genetic and molecular evidence suggests that expression of hnf-4α is mainly regulated at the transcriptional level. activation of hnf-4a gene involves the interaction of distinct sets of transcription factors and co-transcription factors within enhancer and promoter regions. here we study the inhibitory effect of micrornas (mirnas) on the 3'-untranslated region (3'-utr) of hnf-4a mrna. the potential recognition elements of a set of mirnas were identified utilizing bioinformatics analysis. the family members of mir-34 and mir-449, including mir-34a, mir-34c-5p and mir-449a, share the same target elements located at two distinct locations within the 3'-utr of hnf-4a. the over-expression of mir-34a, mir-34c-5p or mir-449a in hepg2 cells led to a significant decrease in the activity of luciferase reporter carrying 3'-utr of hnf-4a. the repressive effect on reporter activity was partially or fully eliminated when one or two of the binding site(s) for mir-34a/mir-34c-5p/mir-449a were deleted within the 3'-utr. the protein level of hnf-4α was dramatically reduced by over-expression of mir-34a, mir-34c-5p and mir-449a, which correlates with a decrease in the binding activity of hnf-4α and transactivation of hnf-4α target genes. these results suggest that the recognition sites of mir-34a, mir-34c-5p and mir-449a within 3'-utr of hnf-4a are functional. the mechanism of down-regulation of the binding activity and transactivation of hnf-4α by the mirnas involves the decrease in hnf-4α protein level via mirnas selectively targeting hnf-4a 3'-utr, leading to the translational repression of hnf-4α expression.",1
"expression of mir-143 and mir-145 is reduced in hematopoietic stem/progenitor cells (hspcs) of myelodysplastic syndrome patients with a deletion in the long arm of chromosome 5. here we show that mice lacking mir-143/145 have impaired hspc activity with depletion of functional hematopoietic stem cells (hscs), but activation of progenitor cells (hpcs). we identify components of the transforming growth factor β (tgfβ) pathway as key targets of mir-143/145. enforced expression of the tgfβ adaptor protein and mir-145 target, disabled-2 (dab2), recapitulates the hsc defect seen in mir-143/145 -/- mice. despite reduced hsc activity, older mir-143/145 -/- and dab2-expressing mice show elevated leukocyte counts associated with increased hpc activity. a subset of mice develop a serially transplantable myeloid malignancy, associated with expansion of hpc. thus, mir-143/145 play a cell context-dependent role in hspc function through regulation of tgfβ/dab2 activation, and loss of these mirnas creates a preleukemic state.",1
"deep vein thrombosis (dvt) is a common complication of surgery. endothelial progenitor cells (epcs) are recruited into resolving venous thrombi. in this report, we investigated the effects of mir-126 on epcs function and venous thrombus resolution. we demonstrated that overexpression of mir-126 enhanced epcs' migration and tubulogenic activity in vitro, and promoted epcs' homing and thrombus resolving in vivo. moreover, we identified that mir-126 directly targeted pik3r2 and affected pi3k/akt signaling axis. overall, our findings demonstrated that mir-126 promoted epcs function through suppressing pik3r2 expression and modulation of mir-126 may represent a potential therapeutic intervention for treating dvt.",1
"background a proliferation-inducing ligand (april) is a tumor-necrosis factor (tnf) family member and is a novel cytokine crucial in sustaining lymphocytic leukemia b cell survival and proliferation. however, its role in gastric cancer (gc) remains unclear. in this study, we investigated the expression pattern and prognostic role of april in gc. methods expression of april was assessed by immunohistochemistry and real-time pcr. prognostic role of april expression was evaluated. we also discovered the effect of april on chemo-resistance in gc cells and the underlying mechanisms. results april mrna levels were significantly increased in gc tissues compared with adjacent tissues and high expression levels of april in tumor cells significantly correlated with poor overall survival in patients receiving cisplatin adjuvant treatment. overexpression of april in ags cells significantly attenuated the therapeutic efficacy of cisplatin in vitro and in vivo. in contrast, silence of april in sgc7901 cells enhanced cisplatin-induced tumor suppression. our data further revealed that the canonical nf-κb pathway was involved in april-mediated chemo-resistance. in addition, expression of april was regulated by mir-145 in gc cells. conclusion april is a novel clinical chemo-resistance biomarker for gastric cancer and might be a promising therapeutic target for gc patients.",1
"small rnas (srnas) play a pivotal role in bacterial gene regulation. however, the srnas of the vast majority of bacteria with sequenced genomes still remain unknown since srna genes are usually difficult to recognize and thus not annotated. here, expression of seven srnas (bjrc2a, bjrc2b, bjrc2c, bjrc68, bjrc80, bjrc174 and bjrc1505) predicted by genome comparison of bradyrhizobium and rhodopseudomonas members, was verified by rna gel blot hybridization, microarray and deep sequencing analyses of rna from the soybean symbiont bradyrhizobium japonicum usda 110. bjrc2a, bjrc2b and bjrc2c belong to the rna family rf00519, while the other srnas are novel. for some of the srnas we observed expression differences between free-living bacteria and bacteroids in root nodules. the amount of bjrc1505 was decreased in nodules. by contrast, the amount of bjrc2a, bjrc68, bjrc80, bjrc174 and the previously described 6s rna was increased in nodules, and accumulation of truncated forms of these srnas was observed. comparative genomics and deep sequencing suggest that bjrc2a is an antisense rna regulating the expression of inositol-monophosphatase. the analyzed srnas show a different degree of conservation in rhizobiales, and expression of homologs of bjrc2, bjrc68, bjrc1505, and 6s rna was confirmed in the free-living purple bacterium rhodopseudomonas palustris 5d.",1
"background long non-coding rnas (lncrnas) constitute a novel class of non-coding rnas. lncrnas regulate gene expression, thus having the possibility to modulate disease progression. in this study, we investigated the changes of lncrnas expression in the heart after myocardial infarction (mi). results adult male c57/bl6 mice were subjected to coronary ligation or sham operation. in a derivation group of 4 mi and 4 sham-operated mice sacrificed 24 hours after surgery, microarray analysis showed that mi was associated with up-regulation of 20 lncrnas and down-regulation of 10 lncrnas (fold-change >2). among these, 2 lncrnas, called myocardial infarction-associated transcript 1 (mirt1) and 2 (mirt2), showed robust up-regulation in the mi group: 5-fold and 13-fold, respectively. up-regulation of these 2 lncrnas after mi was confirmed by quantitative pcr in an independent validation group of 8 mi and 8 sham-operated mice (9-fold and 16-fold for mirt1 and mirt2, p conclusion myocardial infarction induces important changes in the expression of lncrnas in the heart. this study motivates further investigation of the role of lncrnas in left ventricular remodeling.",1
"background atrial fibrillation is characterized by progressive atrial structural and electrical changes (atrial remodeling) that favor arrhythmia recurrence and maintenance. reduction of l-type ca(2+) current (i(ca,l)) density is a hallmark of the electrical remodeling. alterations in atrial micrornas could contribute to the protein changes underlying atrial fibrillation-induced atrial electrical remodeling. this study was undertaken to compare mir-21 levels in isolated myocytes from atrial appendages obtained from patients in sinus rhythm and with chronic atrial fibrillation (caf) and to determine whether l-type ca(2+) channel subunits are targets for mir-21. methods and results quantitative polymerase chain reaction analysis showed that mir-21 was expressed in human atrial myocytes from patients in sinus rhythm and that its expression was significantly greater in caf myocytes. there was an inverse correlation between mir-21 and the mrna of the α1c subunit of the calcium channel (cacna1c) expression and i(ca,l) density. computational analyses predicted that cacna1c and the mrna of the β2 subunit of the calcium channel (cacnb2) could be potential targets for mir-21. luciferase reporter assays demonstrated that mir-21 produced a concentration-dependent decrease in the luciferase activity in chinese hamster ovary cells transfected with cacna1c and cacnb2 3' untranslated region regions. mir-21 transfection in hl-1 cells produced changes in i(ca,l) properties qualitatively similar to those produced by caf (ie, a marked reduction of i(ca,l) density and shift of the inactivation curves to more depolarized potentials). conclusions our results demonstrated that caf increases mir-21 expression in enzymatically isolated human atrial myocytes. moreover, it decreases i(ca,l) density by downregulating ca(2+) channel subunits expression. these results suggested that this microrna could participate in the caf-induced i(ca,l) downregulation and in the action potential duration shortening that maintains the arrhythmia.",1
"the lncrna h19 has been recently shown to be upregulated and play important roles in gastric cancer tumorigenesis. however, the precise molecular mechanism of h19 and its mature product mir-675 in the carcinogenesis of gastric cancer remains unclear. in this study, we found that mir-675 was positively expressed with h19 and was a pivotal mediator in h19-induced gastric cancer cell growth promotion. subsequently, the tumor suppressor runt domain transcription factor1 (runx1) was confirmed to be a direct target of mir-675 using a luciferase reporter assay and western blotting analyses. a series of rescue assays indicated that runx1 mediated h19/mir-67-induced gastric cancer cell phenotypic changes. moreover, the inverse relationship between the expression of runx1 and h19/mir-675 was also revealed in gastric cancer tissues and gastric cancer cell lines. taken together, our study demonstrated that the novel pathway h19/mir-675/runx1 regulates gastric cancer development and may serve as a potential target for gastric cancer therapy.",1
"non-alcoholic fatty liver disease (nafld) is one of the most common liver diseases, but its underlying mechanism is poorly understood. here we show that hepatocyte nuclear factor 4α (hnf4α), a liver-enriched nuclear hormone receptor, is markedly inhibited, whereas mir-34a is highly induced in patients with non-alcoholic steatohepatitis, diabetic mice and mice fed a high-fat diet. mir-34a is essential for hnf4α expression and regulates triglyceride accumulation in human and murine hepatocytes. mir-34a inhibits very low-density lipoprotein secretion and promotes liver steatosis and hypolipidemia in an hnf4α-dependent manner. as a result, increased mir-34a or reduced hnf4α expression in the liver attenuates the development of atherosclerosis in apoe(-/-) or ldlr(-/-) mice. these data indicate that the mir-34a-hnf4α pathway is activated under common conditions of metabolic stress and may have a role in the pathogenesis of nafld and in regulating plasma lipoprotein metabolism. targeting this pathway may represent a novel approach for the treatment of nafld.",1
"unlabelled repeated extragenic palindromes (reps) in the enterobacterial genomes are usually composed of individual palindromic units separated by linker sequences. a total of 355 annotated reps are distributed along the escherichia coli genome. rna sequence (rnaseq) analysis showed that almost 80% of the reps in e. coli are transcribed. the dna sequence of rep325 showed that it is a cluster of six repeats, each with two palindromic units capable of forming cruciform structures in supercoiled dna. here, we report that components of the rep325 element and at least one of its rna products play a role in bacterial nucleoid dna condensation. these rna not only are present in the purified nucleoid but bind to the bacterial nucleoid-associated hu protein as revealed by rna ip followed by microarray analysis (rip-chip) assays. deletion of rep325 resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (tem), and expression of one of the rep325 rnas, nucleoid-associated noncoding rna 4 (narna4), from a plasmid restored the wild-type condensed structure. independently, chromosome conformation capture (3c) analysis demonstrated physical connections among various rep elements around the chromosome. these connections are dependent in some way upon the presence of hu and the rep325 element; deletion of hu genes and/or the rep325 element removed the connections. finally, narna4 together with hu condensed dna in vitro by connecting rep325 or other dna sequences that contain cruciform structures in a pairwise manner as observed by atomic force microscopy (afm). on the basis of our results, we propose molecular models to explain connections of remote cruciform structures mediated by hu and narna4. importance nucleoid organization in bacteria is being studied extensively, and several models have been proposed. however, the molecular nature of the structural organization is not well understood. here we characterized the role of a novel nucleoid-associated noncoding rna, narna4, in nucleoid structures both in vivo and in vitro. we propose models to explain how narna4 together with nucleoid-associated protein hu connects remote dna elements for nucleoid condensation. we present the first evidence of a noncoding rna together with a nucleoid-associated protein directly condensing nucleoid dna.",1
"human bone marrow-derived mesenchymal stem cells (hmscs) are an attractive candidate for cell therapy in heart disease. low survival and incomplete electromechanical integration between resident cardiomyocytes and transplanted hmscs remain unsolved. in order for an infarcted heart to tolerate transplantation, differentiation capacity in stem cells must be reinforced. in this study, we found that compound 56, an epidermal growth factor receptor (egfr) inhibitor, promotes cardiogenic differentiation of hmscs and the transplantation of hmscs treated with compound 56 resulted in enhancement of heart functions. furthermore, hmscs transfected with microrna-133a (mir-133a), which targets egfr, were observed to express cardiac-specific markers. we also discovered that luciferase activity is exclusively decreased by targeting egfr in hmscs transfected with mir-133a mimic. these results suggest that egfr plays a key role in the regulation of cardiogenic differentiation in hmscs.",1
"the embryonic stem cell (esc) transcriptional and epigenetic networks are controlled by a multilayer regulatory circuitry, including core transcription factors (tfs), posttranscriptional modifier micrornas (mirnas), and some other regulators. however, the role of large intergenic noncoding rnas (lincrnas) in this regulatory circuitry and their underlying mechanism remains undefined. here, we demonstrate that a lincrna, linc-ror, may function as a key competing endogenous rna to link the network of mirnas and core tfs, e.g., oct4, sox2, and nanog. we show that linc-ror shares mirna-response elements with these core tfs and that linc-ror prevents these core tfs from mirna-mediated suppression in self-renewing human esc. we suggest that linc-ror forms a feedback loop with core tfs and mirnas to regulate esc maintenance and differentiation. these results may provide insights into the functional interactions of the components of genetic networks during development and may lead to new therapies for many diseases.",1
"we aim to investigate the role of mir-98-mediated macrophage polarization in hepatocellular carcinoma (hcc) progression and to explore the underlying mechanism. a total of 25 paired hcc and matched adjacent normal tissues (ants) were collected. we incubated human blood monocytes isolated from healthy male donors with culture medium collected from hepg2 cells for 7 days. the mrna and protein expression was detected by qrt-pcr and western blot, respectively. levels of cytokines secreted in culture medium were measured using the specific elisa kits. the mir-98 mimic/inhibitor was transfected to explore the role of mir-98 in hcc-conditioned tumor-associated macrophages (tams). hepg2 cells were then cultured with condition medium from hcc-conditioned tams pretreated with mir-98 mimic/inhibitor, and cell migration and invasion assays were performed. luciferase reporter assay was performed to analyze the interaction between mir-98 and interleukin (il)-10. our results showed that mir-98 was downregulated and il-10 was upregulated in hcc tissues and hcc-conditioned tams. further studies identified that il-10 was a direct target gene of mir-98 in hcc-conditioned tams. moreover, mir-98 regulated the levels of inflammatory cytokines in hcc-conditioned tams. hcc-conditioned tams pretreated with mir-98 regulated migration and invasion of hepg2 cells in vitro, and the effects were significantly reversed by il-10. in conclusion, mir-98 not only regulated expression of inflammatory cytokines in hcc-conditioned tams, but also modulated the capacity of hcc-conditioned tams to regulate hepg2 cell migration and invasion, at least in part, by targeting il-10. as a result, mir-98 may suppress the progress of hcc.",1
"certain plus-strand rna plant viruses that are uncapped and nonpolyadenylated rely on rna elements in their 3' untranslated region, termed 3'-cap-independent translational enhancers (3'cites), for efficient translation of their proteins. here, we have investigated the properties of the y-shaped class of 3'cite present in the tombusvirus carnation italian ringspot virus (cirv). while some types of 3'cite have been found to function through recruitment of translation initiation factors to the viral genome, no trans-acting translation-related factors have yet been identified for the y-shaped 3'cite. our results indicate that the cirv 3'cite complexes with eif4f and eifiso4f, with the former mediating translation more efficiently than the latter. in nature, some classes of 3'cite are present in several different viral genera, suggesting that these elements hold a high degree of modularity. here, we test this concept by engineering chimeric viruses containing heterologous 3'cites and show that the y-shaped class of 3'cite in cirv can be replaced by two alternative types of 3'cite, i.e., a panicum mosaic virus-like 3'cite or an i-shaped 3'cite, without any major loss in in vitro translation or replication efficiency in protoplasts. the heterologous 3'cites also mediated whole-plant infections of nicotiana benthamiana, where distinct symptoms were observed for each of the alternative 3'cites and 3'cite evolution occurred during serial passaging. our results supply new information on y-shaped 3'cite function and provide insights into 3'cite virus-host compatibilities.",1
"background micrornas (mirna) have been documented playing a critical role in cancer progression. although mir-338-3p has been implicated in several cancers, its role in gastric cancer is still unknown. the aim of our study was to investigate the role of mir-338-3p in gastric cancer progression. methods expression levels of mir-338-3p in gastric cancer cell lines and tissues were determined by quantitative real-time pcr (qrt-pcr). the effect of mir-338-3p on proliferation was evaluated by mtt assay, cell migration and invasion were evaluated by transwell migration and invasion assays. furthermore, luciferase reporter assay was conducted to confirm the target gene of mir-338-3p, and the results were validated in gastric cancer cells. results in the present study, we found that mir-338-3p was down-regulated in both gastric cancer cell lines and tissues. enforced expression of mir-338-3p inhibited proliferation, migration and invasion of gastric cancer cells in vitro. moreover, we identified a disintegrin and metalloproteinase 17 (adam17) gene as potential target of mir-338-3p. importantly, adam17 rescued the mir-338-3p mediated inhibition of cell proliferation, migration and invasion. conclusions our study suggested that mir-338-3p is significantly decreased in gastric cancer, and inhibits cell proliferation, migration and invasion partially via the downregulation of adam17. thus, mir-338-3p may represent a potential therapeutic target for gastric cancer intervention.",1
"hepatocellular carcinoma (hcc) is the third leading cause of cancer-related mortality worldwide. current standard practices for treatment of hcc are less than satisfactory because of metastasis and recurrence, which are primarily attributed to the angiogenesis. so, the anti-angiogenesis treatment has become the new approach for hcc therapy. in addition to treating leukemia, arsenic trioxide (as2o3) also suppresses other solid tumors, including hcc. however, the roles of as2o3 in the angiogenesis potential of hcc cells remain unclear. in our present study, as2o3 attenuated the angiogenic ability by the microrna-491 (mir-491)-mediated inhibition of tgf-β/smad3/nf-κb signal pathway in mhcc97h and mhcc97l cells. briefly, in these cells, as2o3 improved the expression of mir-491 via dna-demethylation; mir-491, which targeted the smad3-3'-utr, decreased the expression/function of smad3, leading to the inactivation of nf-κb/il-6/stat-3 signaling; knockdown of mir-491 abolished the as2o3-induced inhibitions of the tgf-β/smad3/nf-κb pathway, the vegf secretion, and the angiogenesis. by understanding a novel mechanism whereby as2o3 inhibits the angiogenic potential in hcc cells, our study would help in the design of future strategies of developing as2o3 as a potential chemopreventive agent when used alone or in combination with other current anticancer drugs.",1
"recent bioinformatics-aided searches have identified many new small rnas (srnas) in the intergenic regions of the bacterium escherichia coli. here, a shot-gun cloning approach (rnomics) was used to generate cdna libraries of small sized rnas. besides many of the known srnas, we found new species that were not predicted previously. the present work brings the number of srnas in e.coli to 62. experimental transcription start site mapping showed that some srnas were encoded from independent genes, while others were processed from mrna leaders or trailers, indicative of a parallel transcriptional output generating srnas co-expressed with mrnas. two of these rnas (sroa and srog) consist of known (thi and rfn) riboswitch elements. we also show that two recently identified srnas (ryeb and srac/ryea) interact, resulting in rnase iii-dependent cleavage. to the best of our knowledge, this represents the first case of two non-coding rnas interacting by a putative antisense mechanism. in addition, intracellular metabolic stabilities of srnas were determined, including ones from previous screens. the wide range of half-lives ( 32 min) indicates that srnas cannot generally be assumed to be metabolically stable. the experimental characterization of srnas analyzed here suggests that the definition of an srna is more complex than previously assumed.",1
"down-regulation of mir-138 (microrna-138) has been frequently observed in various cancers, including hnscc (head and neck squamous cell carcinoma). our previous studies suggest that down-regulation of mir-138 is associated with mesenchymal-like cell morphology and enhanced cell migration and invasion. in the present study, we demonstrated that these mir-138-induced changes were accompanied by marked reduction in e-cad (e-cadherin) expression and enhanced vim (vimentin) expression, characteristics of emt (epithelial-mesenchymal transition). on the basis of a combined experimental and bioinformatics analysis, we identified a number of mir-138 target genes that are associated with emt, including vim, zeb2 (zinc finger e-box-binding homeobox 2) and ezh2 (enhancer of zeste homologue 2). direct targeting of mir-138 to specific sequences located in the mrnas of the vim, zeb2 and ezh2 genes was confirmed using luciferase reporter gene assays. our functional analyses (knock-in and knock-down) demonstrated that mir-138 regulates the emt via three distinct pathways: (i) direct targeting of vim mrna and controlling the expression of vim at a post-transcriptional level, (ii) targeting the transcriptional repressors (zeb2) which in turn regulating the transcription activity of the e-cad gene, and (iii) targeting the epigenetic regulator ezh2 which in turn modulates its gene silencing effects on the downstream genes including e-cad. these results, together with our previously observed mir-138 effects on cell migration and invasion through targeting rhoc (rho-related gtp-binding protein c) and rock2 (rho-associated, coiled-coil-containing protein kinase 2) concurrently, suggest that mir-138 is a multi-functional molecular regulator and plays major roles in emt and in hnscc progression.",1
"small non-coding micrornas (mirnas) can modulate the outcome of virus infection. here we explore the role of mirnas in insect-virus interactions, in vivo, using the natural drosophila melanogaster-drosophila c virus (dcv) model system. comparison of the mirna expression profiles in dcv-infected and uninfected flies showed altered mirna levels due to dcv infection, with the largest change in abundance observed for mir-956-3p. knockout of mir-956 resulted to delayed dcv-induced mortality and decreased viral accumulation compared to wild-type flies. a screen of 84 putative mir-956-3p target genes identified regulation of ectoderm-expressed 4 (ect4) in mir-956 knockout flies and, separately, dcv infection. in ect4 knockdown flies dcv-induced mortality occurred more quickly and virus accumulation was increased. taken together, results suggest that the host-protective and antiviral consequences of mir-956 suppression during in vivo infection of d. melanogaster with its natural pathogen dcv is conferred through mir-956-3p induction of its target ect4.",1
"unlabelled c-myc is a well-known oncogene frequently up-regulated in different malignancies, whereas liver-specific microrna (mir)-122, a bona fide tumor suppressor, is down-regulated in hepatocellular cancer (hcc). here we explored the underlying mechanism of reciprocal regulation of these two genes. real-time reverse-transcription polymerase chain reaction (rt-pcr) and northern blot analysis demonstrated reduced expression of the primary, precursor, and mature mir-122 in c-myc-induced hccs compared to the benign livers, indicating transcriptional suppression of mir-122 upon myc overexpression. indeed, chromatin immunoprecipitation (chip) assay showed significantly reduced association of rna polymerase ii and histone h3k9ac, markers of active chromatin, with the mir-122 promoter in tumors relative to the c-myc-uninduced livers, indicating transcriptional repression of mir-122 in c-myc-overexpressing tumors. the chip assay also demonstrated a significant increase in c-myc association with the mir-122 promoter region that harbors a conserved noncanonical c-myc binding site in tumors compared to the livers. ectopic expression and knockdown studies showed that c-myc indeed suppresses expression of primary and mature mir-122 in hepatic cells. additionally, hnf-3β, a liver enriched transcription factor that activates mir-122 gene, was suppressed in c-myc-induced tumors. notably, mir-122 also repressed c-myc transcription by targeting transcriptional activator e2f1 and coactivator tfdp2, as evident from ectopic expression and knockdown studies and luciferase reporter assays in mouse and human hepatic cells. conclusion c-myc represses mir-122 gene expression by associating with its promoter and by down-regulating hnf-3β expression, whereas mir-122 indirectly inhibits c-myc transcription by targeting tfdp2 and e2f1. in essence, these results suggest a double-negative feedback loop between a tumor suppressor (mir-122) and an oncogene (c-myc).",1
"while transcriptional regulation of the primary and secondary metabolism of the model organism streptomyces coelicolor is well studied, little is still known about the role small noncoding rnas (srnas) play in regulating gene expression in this organism. here, we report the identification of a second target of the srna scr5239, an srna highly conserved in streptomycetes. the 159 nt long srna binds its target, the mrna of the cobalamin independent methionine synthase mete (sco0985), at the 5' end of its open reading frame thereby repressing translation. we show that a high methionine level induces expression of scr5239 itself. this leads, in a negative feedback loop, to the repression of methionine biosynthesis. in contrast to the first reported target of this srna, the agarase daga, this interaction seems to be conserved in a wide number of streptomycetes.",1
"rationale the mir-143/145 cluster is highly expressed in smooth muscle cells (smcs), where it regulates phenotypic switch and vascular homeostasis. whether it plays a role in neighboring endothelial cells (ecs) is still unknown. objective to determine whether smcs control ec functions through passage of mir-143 and mir-145. methods and results we used cocultures of smcs and ecs under different conditions, as well as intact vessels to assess the transfer of mir-143 and mir-145 from one cell type to another. imaging of cocultured cells transduced with fluorescent mirnas suggested that mirna transfer involves membrane protrusions known as tunneling nanotubes. furthermore, we show that mirna passage is modulated by the transforming growth factor (tgf) β pathway because both a specific transforming growth factor-β (tgfβ) inhibitor (sb431542) and an shrna against tgfβrii suppressed the passage of mir-143/145 from smcs to ecs. moreover, mir-143 and mir-145 modulated angiogenesis by reducing the proliferation index of ecs and their capacity to form vessel-like structures when cultured on matrigel. we also identified hexokinase ii (hkii) and integrin β 8 (itgβ8)-2 genes essential for the angiogenic potential of ecs-as targets of mir-143 and mir-145, respectively. the inhibition of these genes modulated ec phenotype, similarly to mir-143 and mir-145 overexpression in ecs. these findings were confirmed by ex vivo and in vivo approaches, in which it was shown that tgfβ and vessel stress, respectively, triggered mir-143/145 transfer from smcs to ecs. conclusions our results demonstrate that mir-143 and mir-145 act as communication molecules between smcs and ecs to modulate the angiogenic and vessel stabilization properties of ecs.",1
"rationale recently, there has been significant interest in the therapeutic administration of mirna mimics and inhibitors to treat cardiovascular disease. in particular, mir-27b has emerged as a regulatory hub in cholesterol and lipid metabolism and potential therapeutic target for treating atherosclerosis. despite this, the impact of mir-27b on lipid levels in vivo remains to be determined. as such, here we set out to further characterize the role of mir-27b in regulating cholesterol metabolism in vitro and to determine the effect of mir-27b overexpression and inhibition on circulating and hepatic lipids in mice. methods and results our results identify mir-27b as an important regulator of ldlr activity in human and mouse hepatic cells through direct targeting of ldlr and ldlrap1. in addition, we report that modulation of mir-27b expression affects abca1 protein levels and cellular cholesterol efflux to apoa1 in human hepatic huh7 cells. overexpression of pre-mir-27b in the livers of wild-type mice using aav8 vectors increased pre-mir-27b levels 50-fold and reduced hepatic abca1 and ldlr expression by 50% and 20%, respectively, without changing circulating and hepatic cholesterol and triglycerides. to determine the effect of endogenous mir-27b on circulating lipids, wild-type mice were fed a western diet for one month and injected with 5 mg/kg of lna control or lna anti-mir-27b oligonucleotides. following two weeks of treatment, the expression of abca1 and ldlr were increased by 10-20% in the liver, demonstrating effective inhibition of mir-27b function. intriguingly, no differences in circulating and hepatic lipids were observed between treatment groups. conclusions the results presented here provide evidence that short-term modulation of mir-27b expression in wild-type mice regulates hepatic ldlr and abca1 expression but does not influence plasma and hepatic lipid levels.",1
"micrornas (mirnas) are a class of small noncoding rnas, which regulate gene expression in the posttranscriptional level. they are involved in cancer occurrence and development. different members of the same mirna family may have different roles. since the fact that metastasis is the main cause of cancer-related death and mir-129 has three members, in this study, we focused on the migration inhibitory role of mir-129-1-3p in gastric cancer and explored the possible mechanisms. we first compared the expression of three mir-129 family members, mir-129-5p, mir-129-1-3p, and mir-129-2-3p, between gastric carcinoma tissues and surgical margin non-cancer samples by quantitative real-time reverse transcription-polymerase chain reaction (qrt-pcr). then, we selected mir-129-1-3p for further analysis and transfected its mimic and inhibitor into gastric cancer bgc-823 cells, respectively. then, we compared the bgc-823 cells' migration capacity by transwell assay. finally, we predicted the possible targets of mir-129-1-3p and selected one target for further analysis by qrt-pcr and luciferase reporter assay. the results showed that the expression of mir-129-1-3p in gastric carcinoma was significantly lower than that in surgical margin samples. and mir-129-1-3p could inhibit the migration of bgc-823 cells. from the candidates, we selected bradykinin receptor b2 (bdkrb2), which was reported relating to metastasis, as a target for further analysis. qrt-pcr showed that the expression of bdkrb2 was negatively related to mir-129-1-3p. luciferase reporter assay showed that bdkrb2 was the target of the mir-129-1-3p. in summary, mir-129-1-3p inhibits the bgc-823 cell migration by targeting bdkrb2.",1
"production of renin is critically dependent on modulation of ren mrna stability. here we sought to elucidate the molecular mechanisms involved. transfections of renin-expressing calu-6 cells with reporter constructs showed that a cis-acting 34-nucleotide au-rich ""renin stability regulatory element"" in the ren 3'-untranslated region (3'-utr) contributes to basal ren mrna instability. yeast three-hybrid screening with the ren 3'-utr as bait isolated hadhb (hydroxyacyl-coa dehydrogenase/3-ketoacyl-coa thiolase/enoyl-coa hydratase (trifunctional protein) beta-subunit) as a novel ren mrna-binding protein. recombinant hadhb bound specifically to the 3'-utr of ren mrna, as did the known mrna stabilizers hur and cp1 (poly(c)-binding protein-1). this required the renin stability regulatory element. forskolin, which augments ren mrna stability in calu-6 cells, increased binding of several proteins, including hur and cp1, to the ren 3'-utr, whereas 4-bromocrotonic acid, a specific thiolase inhibitor, decreased binding and elevated renin protein levels. upon decreasing hadhb mrna with rna interference, renin protein and mrna stability increased, whereas rna interference against hur caused these to decrease. immunoprecipitation and reverse transcription-pcr of calu-6 extracts confirmed that hadhb, hur, and cp1 each associate with ren mrna in vivo. intracellular imaging revealed distinct localization of hadhb to mitochondria, hur to nuclei, and cp1 throughout the cell. immunohistochemistry demonstrated enrichment of hadhb in renin-producing renal juxtaglomerular cells. in conclusion, hadhb, hur, and cp1 are novel ren mrna-binding proteins that target a cis-element in the 3'-utr of ren mrna and regulate renin production. camp-mediated increased ren mrna stability may involve stimulation of hur and cp1, whereas ren mrna decay may involve thiolase-dependent pathways.",1
"objective our previous study demonstrated that fascin homolog 1 (fscn1) might have an oncogenic function in bladder cancer (bc) and that its expression was regulated by specific micrornas (mirnas). recently, lim and sh3 protein 1 (lasp1) as well as fscn1 have been reported as actin filament bundling proteins in the same complexes attached to the inner surfaces of cell membranes. we hypothesize that lasp1 as well as fscn1 have an oncogenic function and that is regulated by mirnas targeting lasp1 mrna. methods the expression levels of lasp1 mrna in 86 clinical samples were evaluated by real-time rt-pcr. lasp1-knockdown bc cell lines were transfected by sirna in order to examine cellular viability by xtt assay, wound healing assay, and matrigel invasion assay. we employed web-based software in order to search for candidate mirnas targeting lasp1 mrna, and we focused on mir-1, mir-133a, mir-145, and mir-218. the luciferase reporter assay was used to confirm the actual binding sites between the mirnas and lasp1 mrna. results real-time rt-pcr showed that lasp1 mrna expression was higher in 76 clinical bc specimens than in 10 normal bladder epitheliums (p conclusion our data indicate that lasp1 may have an oncogenic function and that it might be regulated by mir-1, mir-133a, and mir-218, which may function as tumor suppressive mirnas in bc.",1
"background diastolic dysfunction in response to hypertrophy is a major clinical syndrome with few therapeutic options. micrornas act as negative regulators of gene expression by inhibiting translation or promoting degradation of target mrnas. previously, we reported that genetic deletion of the cardiac-specific mir-208a prevents pathological cardiac remodeling and upregulation of myh7 in response to pressure overload. whether this mirna might contribute to diastolic dysfunction or other forms of heart disease is currently unknown. methods and results here, we show that systemic delivery of an antisense oligonucleotide induces potent and sustained silencing of mir-208a in the heart. therapeutic inhibition of mir-208a by subcutaneous delivery of antimir-208a during hypertension-induced heart failure in dahl hypertensive rats dose-dependently prevents pathological myosin switching and cardiac remodeling while improving cardiac function, overall health, and survival. transcriptional profiling indicates that antimir-208a evokes prominent effects on cardiac gene expression; plasma analysis indicates significant changes in circulating levels of mirnas on antimir-208a treatment. conclusions these studies indicate the potential of oligonucleotide-based therapies for modulating cardiac mirnas and validate mir-208 as a potent therapeutic target for the modulation of cardiac function and remodeling during heart disease progression.",1
"long non-coding rnas (lncrnas) play an important role in various physiological and pathological processes. however, the biological role of lncrna meg8 in liver fibrosis is largely unknown. in this study, we found that meg8 was over-expressed in activated hepatic stellate cells (hscs), injured hepatocytes (hcs) and fibrotic livers. furthermore, we revealed that meg8 suppressed the expression of the pro-fibrogenic and proliferation genes in activated hscs. in addition, silencing meg8 significantly inhibited the expression of the epithelial markers, while noticeably promoted the expression of the mesenchymal markers in primary hcs and aml12 cells. mechanistically, we demonstrated that meg8 suppressed hscs activation and epithelial-mesenchymal transition (emt) of hcs through inhibiting the notch pathway. in conclusion, our findings indicate that meg8 may serve as a novel protective molecule and a potential therapeutic target of liver fibrosis.",1
"wss25 is a sulfated polysaccharide that inhibits angiogenesis. however, the mechanism underlying the regulation of angiogenesis by wss25 is not well understood. using microrna (mirna) microarray analysis, a total of 25 mirnas were found to be upregulated and 12 (including mir-210) downregulated by wss25 in human microvascular endothelial cells (hmec-1). interestingly, dicer, a key enzyme for mirna biosynthesis, was downregulated by wss25 in hmec-1 cells. further studies indicated that hmec-1 cell tube formation and mir-210 expression were suppressed while ephrin-a3 expression was enhanced by the silencing of dicer. in contrast, hmec-1 cell tube formation and mir-210 expression were induced while ephrin-a3 expression was suppressed by dicer overexpression. moreover, mir-210 was downregulated while ephrin-a3 was upregulated by wss25 in hmec-1 cells. hmec-1 cell migration and tube formation were arrested, while ephrin-a3 expression was augmented by anti-mir-210. in addition, hmec-1 cell tube formation was significantly attenuated or augmented when ephrin-a3 was overexpressed or silenced, respectively. nevertheless, the tube formation blocked by wss25 could be partially rescued by manipulation of dicer, mir-210 and ephrin-a3. these results suggest a new pathway whereby wss25 inhibits angiogenesis via suppression of dicer, leading to downregulation of mir-210 and upregulation of ephrin-a3.",1
"background human mir-34c has been reported to be associated with various human malignancies; however, it remains unknown whether mir-34c is involved in chemoresistance in gastric cancer. the aim of this study was to investigate the role of mir-34c in gastric cancer. materials and methods the adenosine triphosphate-based tumor chemosensitivity assay was used to measure drug sensitivity in gastric cancer samples. the expression levels of mirna were determined by reverse transcriptase polymerase chain reaction (pcr) and those of protein were by western blot analysis. luciferase activity assay was used to verify the target genes of mirnas. mtt assay was used to test the drug-resistant phenotype changes in cancer cells via overregulation of mirnas. the methylation status of neighboring cpg islands of mir-34c-5p was analyzed by bisulfite sequencing pcr and methylation-specific pcr. results quantitative real-time polymerase chain reaction demonstrated that expression of mir-34c-5p was downregulated in paclitaxel-resistant gastric cancer samples (p conclusions dna methylation, dysregulation of mir-34c-5p, and mapt expression are critical factors in the chemoresistance of gastric cancer to paclitaxel.",1
"although it is well established that embryonic stem (es) cells have the potential to differentiate into dopamine neurons, the molecular basis of this process, particularly the role of micrornas (mirnas), remains largely unknown. here we report that mir-132 plays a key role in the differentiation of dopamine neurons by directly regulating the expression of nurr1 (also known as nuclear receptor subfamily 4 group a member 2; nr4a2). we constructed a mouse es cell line cgr8, which stably expresses gfp under the tyrosine hydroxylase (th) promoter, so the th-positive neurons could be easily sorted using fluorescence-activated cell sorting (facs). then, we performed a mirna array analysis on the purified th-positive neurons and found that 45 of 585 mirnas had more than a fivefold change in expression level during dopamine neuron differentiation. among the 45 mirnas, we were particularly interested in mir-132 because this mirna has been reported to be highly expressed in neurons and to have a potential role in neurodegenerative diseases. we found that the direct downregulation of endogenous mir-132 induced by mir-132 antisense oligonucleotide (mir-132-aso) promoted the differentiation of th-positive neurons, whereas ectopic expression of mir-132 in es cells reduced the number of differentiated th-positive neurons but did not change the total number of differentiated neurons. furthermore, we identified that mir-132-aso could substantially reverse the mir-132-mediated suppression of th-positive neuron differentiation. moreover, through a bioinformatics assay we identified the nurr1 gene as a potential molecular target of mir-132. using a luciferase-reporter assay and western blot analysis, we demonstrated that mir-132 could directly regulate the expression of nurr1. collectively, our data provide the first evidence that mir-132 is an important molecule regulating es cell differentiation into dopamine neurons by directly targeting nurr1 gene expression.",1
"most long non-coding rnas (lncrnas) encoded by eukaryotic genomes remain uncharacterized. here we focus on a set of intergenic lncrnas in fission yeast. deleting one of these lncrnas exhibited a clear phenotype: drug sensitivity. detailed analyses of the affected locus revealed that transcription of the nc-tgp1 lncrna regulates drug tolerance by repressing the adjacent phosphate-responsive permease gene transporter for glycerophosphodiester 1 (tgp1(+)). we demonstrate that the act of transcribing nc-tgp1 over the tgp1(+) promoter increases nucleosome density, prevents transcription factor access and thus represses tgp1(+) without the need for rna interference or heterochromatin components. we therefore conclude that tgp1(+) is regulated by transcriptional interference. accordingly, decreased nc-tgp1 transcription permits tgp1(+) expression upon phosphate starvation. furthermore, nc-tgp1 loss induces tgp1(+) even in repressive conditions. notably, drug sensitivity results directly from tgp1(+) expression in the absence of the nc-tgp1 rna. thus, transcription of an lncrna governs drug tolerance in fission yeast.",1
"background micrornas (mirnas) are endogenously expressed small non-coding rnas that regulate gene expression at post-transcriptional level. the recent discovery of the involvement of these rnas in the control of angiogenesis renders them very attractive in the development of new approaches for restoring the angiogenic balance. whereas mirna-21 has been demonstrated to be highly expressed in endothelial cells, the potential function of this mirna in angiogenesis has never been investigated. methodology/principal findings we first observed in endothelial cells a negative regulation of mir-21 expression by serum and bfgf, two pro-angiogenic factors. then using in vitro angiogenic assays, we observed that mir-21 acts as a negative modulator of angiogenesis. mir-21 overexpression reduced endothelial cell proliferation, migration and the ability of these cells to form tubes whereas mir-21 inhibition using a lna-anti-mir led to opposite effects. expression of mir-21 in endothelial cells also led to a reduction in the organization of actin into stress fibers, which may explain the decrease in cell migration. further mechanistic studies showed that mir-21 targets rhob, as revealed by a decrease in rhob expression and activity in mir-21 overexpressing cells. rhob silencing impairs endothelial cell migration and tubulogenesis, thus providing a possible mechanism for mir-21 to inhibit angiogenesis. finally, the therapeutic potential of mir-21 as an angiogenesis inhibitor was demonstrated in vivo in a mouse model of choroidal neovascularization. conclusions/significance our results identify mir-21 as a new angiogenesis inhibitor and suggest that inhibition of cell migration and tubulogenesis is mediated through repression of rhob.",1
"to examine the role of telomerase in normal and neoplastic growth, the telomerase rna component (mtr) was deleted from the mouse germline. mtr-/- mice lacked detectable telomerase activity yet were viable for the six generations analyzed. telomerase-deficient cells could be immortalized in culture, transformed by viral oncogenes, and generated tumors in nude mice following transformation. telomeres were shown to shorten at a rate of 4.8+/-2.4 kb per mtr-/- generation. cells from the fourth mtr-/- generation onward possessed chromosome ends lacking detectable telomere repeats, aneuploidy, and chromosomal abnormalities, including end-to-end fusions. these results indicate that telomerase is essential for telomere length maintenance but is not required for establishment of cell lines, oncogenic transformation, or tumor formation in mice.",1
"downregulation of mir-145 in a variety of cancers suggests a possible tumor suppressor function for this microrna. here, we show that mir-145 expression is reduced in bladder cancer and urothelial carcinoma in situ, compared with normal urothelium, using transcription profiling and in situ hybridization. ectopic expression of mir-145 induced extensive apoptosis in urothelial carcinoma cell lines (t24 and sw780) as characterized by caspase activation, nuclear condensation and fragmentation, cellular shrinkage, and detachment. however, cell death also proceeded upon caspase inhibition by the pharmacological inhibitor zvad-fmk and ectopic expression of anti-apoptotic bcl-2, indicating the activation of an alternative caspase-independent death pathway. microarray analysis of transcript levels in t24 cells, before the onset of cell death, showed destabilization of mrnas enriched for mir-145 7mer target sites. among these, direct targeting of cbfb, ppp3ca, and clint1 was confirmed by a luciferase reporter assay. notably, a 22-gene signature targeted on enforced mir-145 expression in t24 cells was significantly (p<0.00003) upregulated in 55 ta bladder tumors with concomitant reduction of mir-145. our data indicate that reduction in mir-145 expression may provide bladder cancer cells with a selective advantage by inhibition of cell death otherwise triggered in malignant cells.",1
"hepatitis b virus (hbv) replication is initiated by binding of its reverse transcriptase (p) to the apical stem-loop (al) and primer loop (pl) of epsilon, a highly conserved rna element at the 5'-end of the rna pregenome. mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their p-epsilon interaction. here, nmr and uv thermodynamic data on al (and pl) from these three species are presented. the stabilities of the duck and heron als were found to be similar, and much lower than that of human. nmr data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron al. in duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35 degrees c well below the overall al melting temperature. surprisingly, the duck- and heron als were both found to be capped by a stable well-structured uguu tetraloop. all avian als are expected to adhere to this because of their conserved sequence. duck pl is stable and structured and, in view of sequence similarities, the same is expected for heron - and human pl.",1
"a fibrotic or pathological scar is an undesired consequence of skin wound healing and may trigger a series of problems. an attenuated inflammatory response is a significant characteristic of fetal skin wound healing, which can contribute to the scarless healing of fetal skin. according to deep sequencing data, microrna‑149 (mir‑149) expression was increased in mid-gestational compared with that in late‑gestational fetal skin keratinocytes. it was demonstrated that overexpression of mir‑149 in hacat cells can downregulate the expression of pro‑inflammatory cytokines interleukin (il)‑1α, il‑1β, and il‑6 at basal levels and in inflammatory conditions. furthermore, mir‑149 was revealed to indirectly accelerate transforming growth factor‑β3 and collagen type iii expression in fibroblasts, which are essential cells in extracellular matrix remodeling. in a rat skin wound model, mir‑149 improved the quality of the arrangement of collagen bundles and reduced inflammatory cell infiltration during skin wound healing. these results indicate that mir‑149 may be a potential regulator in improving the quality of skin wound healing.",1
"unlabelled cl(-) /hco3- anion exchanger 2 (ae2) participates in intracellular ph homeostasis and secretin-stimulated biliary bicarbonate secretion. ae2/slc4a2 gene expression is reduced in liver and blood mononuclear cells from patients with primary biliary cirrhosis (pbc). our previous findings of hepatic and immunological features mimicking pbc in ae2-deficient mice strongly suggest that decreased ae2 expression might be involved in the pathogenesis of pbc. here, we tested the potential role of microrna 506 (mir-506) - predicted as candidate to target ae2 mrna - for the decreased expression of ae2 in pbc. real-time quantitative polymerase chain reaction showed that mir-506 expression is increased in pbc livers versus normal liver specimens. in situ hybridization in liver sections confirmed that mir-506 is up-regulated in the intrahepatic bile ducts of pbc livers, compared with normal and primary sclerosing cholangitis livers. precursor-mediated overexpression of mir-506 in sv40-immortalized normal human cholangiocytes (h69 cells) led to decreased ae2 protein expression and activity, as indicated by immunoblotting and microfluorimetry, respectively. moreover, mir-506 overexpression in three-dimensional (3d)-cultured h69 cholangiocytes blocked the secretin-stimulated expansion of cystic structures developed under the 3d conditions. luciferase assays and site-directed mutagenesis demonstrated that mir-506 specifically may bind the 3'untranslated region (3'utr) of ae2 messenger rna (mrna) and prevent protein translation. finally, cultured pbc cholangiocytes showed decreased ae2 activity, together with mir-506 overexpression, compared to normal human cholangiocytes, and transfection of pbc cholangiocytes with anti-mir-506 was able to improve their ae2 activity. conclusion mir-506 is up-regulated in cholangiocytes from pbc patients, binds the 3'utr region of ae2 mrna, and prevents protein translation, leading to diminished ae2 activity and impaired biliary secretory functions. in view of the putative pathogenic role of decreased ae2 in pbc, mir-506 may constitute a potential therapeutic target for this disease.",1
"aims high-density lipoproteins (hdls) are circulating micelles that transport proteins, lipids, and mirnas. hdl-transported mirnas (hdl-mirnas) have lately received attention but their effects on vascular cells are not fully understood. additionally, whether cardiovascular risk factors affect hdl-mirnas levels and mirna transfer to recipient cells remains equally poorly known. here, we have investigated the changes induced by hypercholesterolaemia on hdl-mirna levels and its effect on recipient endothelial cells (ecs). methods and results pigs were kept on a high-fat diet (hc; n = 10) or a normocholesterolaemic chow (nc; n = 10) for 10 days reaching cholesterol levels of 321.0 (229.7-378.5) mg/dl and 74.0 (62.5-80.2) mg/dl, respectively. hdl particles were isolated, purified, and quantified. hdl-mirna profiling (n = 149 mirnas) of hc- and nc-hdls was performed by multipanel qpcr. cell cultures of porcine aortic ecs were used to determine whether hdl-mirnas were delivered to ecs. potential target genes modulated by mirnas were identified by bioinformatics and candidate mirnas were validated by molecular analysis. in vivo effects in the coronary arteries of normocholesterolaemic swine administered hc- or nc-hdls were analysed. among the hdl-mirnas, four were found in different amounts in hc- and nc-hdl (p conclusion hypercholesterolaemia induces changes in the mirna content of hdl enhancing mir126 and its delivery to ecs with the consequent down-regulation of its target gene hif1α.",1
"dysregulated expression of micrornas (mirnas) in various tissues has been associated with a variety of diseases, including cancers. here we demonstrate that mirnas are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. the levels of mirnas in serum are stable, reproducible, and consistent among individuals of the same species. employing solexa, we sequenced all serum mirnas of healthy chinese subjects and found over 100 and 91 serum mirnas in male and female subjects, respectively. we also identified specific expression patterns of serum mirnas for lung cancer, colorectal cancer, and diabetes, providing evidence that serum mirnas contain fingerprints for various diseases. two non-small cell lung cancer-specific serum mirnas obtained by solexa were further validated in an independent trial of 75 healthy donors and 152 cancer patients, using quantitative reverse transcription polymerase chain reaction assays. through these analyses, we conclude that serum mirnas can serve as potential biomarkers for the detection of various cancers and other diseases.",1
"b-cell acute lymphoblastic leukemia (b-all) is often associated with chromosomal translocations leading to the deregulation of proto-oncogenes. micrornas can also be affected by chromosomal alterations and thus contribute to carcinogenesis. the microrna, mir-125b-1, is overexpressed in b-all cases with the t(11;14)(q24;q32) translocation; therefore, we sought to determine the role of this microrna in b-cell fate. we used murine pre-bi cells alongside murine and human leukemic b-cell lines to show that mir-125b expression enhances proliferation by targeting b-cell regulator of immunoglobulin heavy-chain transcription (bright)/arid3a, an activator of immunoglobulin heavy-chain transcription. accordingly, this target gene was downregulated in b-all patients with the t(11;14)(q24;q32) translocation. repression of bright/arid3a blocked differentiation and conferred a survival advantage to ba/f3 cells under interleukin-3 starvation. in addition, overexpression of mir-125b protected pre-bi and leukemic b-cell lines from apoptosis by blockade of caspase activation by a mechanism that was independent of p53 and bak1. in summary, mir-125b can act as an oncogene in b-all by targeting arid3a and mediating its repression, thus leading to a blockage in differentiation, increased proliferation and inhibition of apoptosis.",1
"mammalian neuronal stem cells produce multiple neuron types in the course of an individual's development. similarly, neuronal progenitors in the drosophila brain generate different types of closely related neurons that are born at specific time points during development. we found that in the post-embryonic drosophila brain, steroid hormones act as temporal cues that specify the cell fate of mushroom body (mb) neuroblast progeny. chronological regulation of neurogenesis is subsequently mediated by the microrna (mirna) let-7, absence of which causes learning impairment due to morphological mb defects. the mirna let-7 is required to regulate the timing of α'/β' to α/β neuronal identity transition by targeting the transcription factor abrupt. at a cellular level, the ecdysone-let-7-ab signalling pathway controls the expression levels of the cell adhesion molecule fasciclin ii in developing neurons that ultimately influences their differentiation. our data propose a novel role for mirnas as transducers between chronologically regulated developmental signalling and physical cell adhesion.",1
"the mir-99 family is one of the evolutionarily most ancient microrna families, and it plays a critical role in developmental timing and the maintenance of tissue identity. recent studies, including reports from our group, suggested that the mir-99 family regulates various physiological processes in adult tissues, such as dermal wound healing, and a number of disease processes, including cancer. by combining 5 independent genome-wide expression profiling experiments, we identified a panel of 266 unique transcripts that were down-regulated in epithelial cells transfected with mir-99 family members. a comprehensive bioinformatics analysis using 12 different sequence-based microrna target prediction algorithms revealed that 81 out of these 266 down-regulated transcripts are potential direct targets for the mir-99 family. confirmation experiments and functional analyses were performed to further assess 6 selected mir-99 target genes, including mammalian target of rapamycin (mtor), homeobox a1 (hoxa1), ctd small phosphatase-like (ctdspl), n-myristoyltransferase 1 (nmt1), transmembrane protein 30a (tmem30a), and swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (smarca5). hoxa1 is a known proto-oncogene, and it also plays an important role in embryonic development. the direct targeting of the mir-99 family to two candidate binding sequences located in the hoxa1 mrna was confirmed using a luciferase reporter gene assay and a ribonucleoprotein-immunoprecipitation (rip-ip) assay. ectopic transfection of mir-99 family reduced the expression of hoxa1, which, in consequence, down-regulated the expression of its downstream gene (i.e., bcl-2) and led to reduced proliferation and cell migration, as well as enhanced apoptosis. in summary, we identified a number of high-confidence mir-99 family target genes, including proto-oncogene hoxa1, which may play an important role in regulating epithelial cell proliferation and migration during physiological disease processes, such as dermal wound healing and tumorigenesis.",1
"micrornas (mirnas) are small non-protein-coding rnas that function as negative gene expression regulators. in the present study, we investigated mirnas role in endothelial cell response to hypoxia. we found that the expression of mir-210 progressively increased upon exposure to hypoxia. mir-210 overexpression in normoxic endothelial cells stimulated the formation of capillary-like structures on matrigel and vascular endothelial growth factor-driven cell migration. conversely, mir-210 blockade via anti-mirna transfection inhibited the formation of capillary-like structures stimulated by hypoxia and decreased cell migration in response to vascular endothelial growth factor. mir-210 overexpression did not affect endothelial cell growth in both normoxia and hypoxia. however, anti-mir-210 transfection inhibited cell growth and induced apoptosis, in both normoxia and hypoxia. we determined that one relevant target of mir-210 in hypoxia was ephrin-a3 since mir-210 was necessary and sufficient to down-modulate its expression. moreover, luciferase reporter assays showed that ephrin-a3 was a direct target of mir-210. ephrin-a3 modulation by mir-210 had significant functional consequences; indeed, the expression of an ephrin-a3 allele that is not targeted by mir-210 prevented mir-210-mediated stimulation of both tubulogenesis and chemotaxis. we conclude that mir-210 up-regulation is a crucial element of endothelial cell response to hypoxia, affecting cell survival, migration, and differentiation.",1
"purpose radioresistance severely restricts the clinical treatment of nasopharyngeal carcinoma (npc). accumulating evidence demonstrates that aberrant expression of micrornas (mirnas) contributes to cancer progression and sensitivity to radiation. therefore, we aimed to identify mirnas associated with radioresistance in npc. methods aberrant mirna-324-3p expression in npc cne-2 cells with radioresistance (cne-2-rs), compared to its parental cells, was screened by high-throughput sequencing technology and determined by quantitative reverse transcription-polymerase chain reaction analysis (qrt-pcr) analysis. bioinformatic analysis was used to predict the downstream target genes of mirna-324-3p. then, functional and mechanical analyses of mirna-324-3p in npc radioresistance were performed by overexpression and down-regulation of mirna-324-3p in cne-2-rs cells and its parental cells. finally, the clinical significance of mirna-324-3p and wnt2b was investigated in npc tissues. results our data reveal that the expression of mirna-324-3p is significantly decreased in cne-2-rs cells compared to its parental cells, and wnt2b is predicted to be the downstream target of mirna-324-3p. both overexpression and down-regulation of mirna-324-3p following irradiation result in radiosensitivity alterations and protein changes of wnt2b signalling pathway in cne-2-rs cells and its parental cells. importantly, down-regulation of mirna-324-3p and up-regulation of wnt2b are significantly correlated with advanced clinical stages of npc and this inverse expression pattern is also observed in npc tissues before and after irradiation. conclusions the present study reveals that mirna-324-3p contributes to the radioresistance of npc by regulating the wnt2b signalling pathway. both mirna-324-3p and wnt2b are potential biomarkers for radioresistance in npc, which may serve as valuable targets for reversing radioresistance in the management of npc.",1
"small rna (srna) molecules regulate a vast array of processes in biology, but evidence for adaptive evolution of srna sequences has been indirect. here, we identify an srna, pxr, that negatively regulates fruiting body development in myxococcus xanthus. we further show that a spontaneous evolutionary mutation in pxr abolished its regulatory function and thereby adaptively restored developmental proficiency to a socially defective m. xanthus cheater. in wild-type m. xanthus, development is initiated only upon starvation, but deletion of pxr allows development to proceed even while nutrients remain abundant. thus, pxr serves as a major checkpoint controlling the transition from growth to development in the myxobacteria. these findings show that an srna molecule governs a complex form of multicellular development in prokaryotes and directly demonstrate the ability of srna regulators to facilitate evolutionary adaptations of major phenotypic effect.",1
"the stepwise assembly of the highly dynamic spliceosome is guided by rna-dependent atpases of the dead-box family, whose regulation is poorly understood. in the canonical assembly model, the u4/u6.u5 triple snrnp binds only after joining of the u1 and, subsequently, u2 snrnps to the intron-containing pre-mrna. catalytic activation requires the exchange of u6 for u1 snrna at the 5' splice site, which is promoted by the dead-box protein prp28. because prp8, an integral u5 snrnp protein, is thought to be a central regulator of dead-box proteins, we conducted a targeted search in prp8 for cold-insensitive suppressors of a cold-sensitive prp28 mutant, prp28-1. we identified a cluster of suppressor mutations in an n-terminal bromodomain-like sequence of prp8. to identify the precise defect in prp28-1 strains that is suppressed by the prp8 alleles, we analyzed spliceosome assembly in vivo and in vitro. surprisingly, in the prp28-1 strain, we observed a block not only to spliceosome activation but also to one of the earliest steps of assembly, formation of the atp-independent commitment complex 2 (cc2). the prp8 suppressor partially corrected both the early assembly and later activation defects of prp28-1, supporting a role for this u5 snrnp protein in both the atp-independent and atp-dependent functions of prp28. we conclude that the u5 snrnp has a role in the earliest events of assembly, prior to its stable incorporation into the spliceosome.",1
"mammalian genomes are pervasively transcribed to produce thousands of long non-coding rnas (lncrnas). a few of these lncrnas have been shown to recruit regulatory complexes through rna-protein interactions to influence the expression of nearby genes, and it has been suggested that many other lncrnas can also act as local regulators. such local functions could explain the observation that lncrna expression is often correlated with the expression of nearby genes. however, these correlations have been challenging to dissect and could alternatively result from processes that are not mediated by the lncrna transcripts themselves. for example, some gene promoters have been proposed to have dual functions as enhancers, and the process of transcription itself may contribute to gene regulation by recruiting activating factors or remodelling nucleosomes. here we use genetic manipulation in mouse cell lines to dissect 12 genomic loci that produce lncrnas and find that 5 of these loci influence the expression of a neighbouring gene in cis. notably, none of these effects requires the specific lncrna transcripts themselves and instead involves general processes associated with their production, including enhancer-like activity of gene promoters, the process of transcription, and the splicing of the transcript. furthermore, such effects are not limited to lncrna loci: we find that four out of six protein-coding loci also influence the expression of a neighbour. these results demonstrate that cross-talk among neighbouring genes is a prevalent phenomenon that can involve multiple mechanisms and cis-regulatory signals, including a role for rna splice sites. these mechanisms may explain the function and evolution of some genomic loci that produce lncrnas and broadly contribute to the regulation of both coding and non-coding genes.",1
"microrna (mirna)-induced silencing complexes (miriscs) repress translation and promote degradation of mirna targets. target degradation occurs through the 5'-to-3' messenger rna (mrna) decay pathway, wherein, after shortening of the mrna poly(a) tail, the removal of the 5' cap structure by decapping triggers irreversible decay of the mrna body. here, we demonstrate that mirisc enhances the association of the decapping activators dcp1, me31b and hpat with deadenylated mirna targets that accumulate when decapping is blocked. dcp1 and me31b recruitment by mirisc occurs before the completion of deadenylation. remarkably, mirisc recruits dcp1, me31b and hpat to engineered mirna targets transcribed by rna polymerase iii, which lack a cap structure, a protein-coding region and a poly(a) tail. furthermore, mirisc can trigger decapping and the subsequent degradation of mrna targets independently of ongoing deadenylation. thus, mirisc increases the local concentration of the decapping machinery on mirna targets to facilitate decapping and irreversibly shut down their translation.",1
"micrornas (mirnas) are key post-transcriptional regulators of gene expression and commonly deregulated in carcinogenesis. to explore functionally crucial tumor-suppressive (ts)-mirnas in hepatocellular carcinoma (hcc), we performed integrative function- and expression-based screenings of ts-mirnas in six hcc cell lines. the screenings identified seven mirnas, which showed growth-suppressive activities through the overexpression of each mirna and were endogenously downregulated in hcc cell lines. further expression analyses using a large panel of hcc cell lines and primary tumors demonstrated four mirnas, mir-101, -195, -378 and -497, as candidate ts-mirnas frequently silenced in hccs. among them, two clustered mirnas mir-195 and mir-497 showed significant growth-suppressive activity with induction of g1 arrest. comprehensive exploration of their targets using argonute2-immunoprecipitation-deep-sequencing (ago2-ip-seq) and genome-wide expression profiling after their overexpression followed by pathway analysis, revealed a significant enrichment of cell cycle regulators. among the candidates, we successfully identified ccne1, cdc25a, ccnd3, cdk4, and btrc as direct targets for mir-497 and mir-195. moreover, target genes frequently upregulated in hcc in a tumor-specific manner, such as cdk6, ccne1, cdc25a and cdk4, showed an inverse correlation in the expression of mir-195 and mir-497, and their targets. these results suggest the molecular pathway regulating cell cycle progression to be integrally altered by downregulation of mir-195 and mir-497 expression, leading to the aberrant cell proliferation in hepatocarcinogenesis.",1
"increasing data shows mir-29a is a key regulator of oncogenic processes. it is significantly down-regulated in some kind of human tumors and possibly functionally linked to cellular proliferation, survival and migration. however, the mechanism remains unclear. in this study, we report mir-29a is significantly under-expressed in gastric cancer compared to the healthy donor. the microvessel density is negatively related to mir-29a expression in gastric cancer tissues. the ectopic expression of mir-29a significantly inhibits proliferation and invasion of gastric cancer cells. furthermore, western blot combined with the luciferase reporter assays demonstrate that vascular endothelial growth factor a (vegf-a) is direct target of mir-29a. this is the first time mir-29a was found to suppress the tumor microvessel density in gastric cancer by targeting vegf-a. taken together, these results suggest that mir-29a is a tumor suppressor in gastric cancer. restoration of mir-29a in gastric cancer may be a promising therapeutic approach.",1
"ocular neovascularization is a vision-threatening complication of ischemic retinopathy that develops in various ocular disorders, such as retinopathy of prematurity (rop) and diabetic retinopathy. both ang-2 and vegf are implicated in this pathogenesis. however, their inter-regulation still remains elusive. competitive endogenous rnas (cernas) are messenger rna (mrna) molecules that affect each other expression through the competition for the shared mirna. herein, we assessed whether the expression of ang-2 and vegf is interdependent through the sequestration of common mirnas. bioinformatics prediction and 3'-utr luciferase assay revealed that ang-2 and vegf is commonly targeted by mir-351. silencing either ang-2 or vegf increases the availabilities of shared mir-351, therefore reduces the activity of luc-ang-2 3'-utr. the interdependence of vegf and ang-2 is mirna- and 3'-utr dependent, as silencing dicer abolishes the interdependence. we also found that mir-351 dependency of vegf-ang-2 crosstalk occurs in retinal endothelial cells and rat retinas. mir-351 over-expression significantly reduces the level of vegf and ang-2 expression in vivo and in vitro. overall, mirna-dependent crosstalk between ang-2 and vegf plays a role in hypoxia-induced microvascular response. mirna-based therapy can affect the expression of ang-2 and vegf, which represents a therapeutic potential for the treatment of vascular disease.",1
"background patients of coronary artery disease (cad) with type 2 diabetes mellitus (dm2) show increased mortality risk than cad patients without dm2, while few biomarkers can be used to discriminate them. methods fifty-nine patients of cad with dm2 (dm2-cad group), 79 patients of cad without dm2 (cad group), and 63 healthy control subjects were recruited. circulating mir-130 (mir-130a and mir-130b) and ppar-γ (peroxisome proliferator-activated receptor gamma) were measured and their pearson correlation was analyzed. 3' utr binding prediction and luciferase assay were used to determine the target relationship between mir-130 and ppar-γ. receiver operating characteristics (roc) analysis was performed to test the discrimination ability of mir-130 between dm2-cad and cad groups. results mir-130a and mir-130b showed decreased expression in dm2-cad group when compared with the cad group and health control. both bioinformatics and luciferase assays showed that mir-130 could bind the 3' utr of ppar-γ. furthermore, mir-130 negatively correlated with ppar-γ in both cad and dm2-cad group in pearson's coefficient analysis. both mir-130a and mir-130b were able to discriminate dm2-cad group from cad group and control subjects. conclusion circulating mir-130 may regulate the expression of ppar-γ and can be used as a biomarker to discriminate dm2-cad from cad.",1
"previous studies have demonstrated the utility of microarray expression analysis to identify potential microrna targets. nevertheless, technical limitations intrinsic to this platform constrain its ability to fully exploit the potential of assessing transcript level changes to explore microrna targetomes. high-throughput multiplexed illumina-based next-generation sequencing (ngs) provides a digital readout of absolute transcript levels and imparts a higher level of accuracy and dynamic range than microarray platforms. we used illumina ngs to analyze transcriptome changes induced by the human microrna mir155. this analysis resulted in a larger inferred targetome than similar studies carried out using microarray platforms. a comparison with 3' utr reporter data demonstrated general concordance between ngs and corresponding 3' utr reporter results. nonharmonious results were investigated more deeply using transcript structure information assembled from the ngs data. this analysis revealed that transcript structure plays a substantial role in mitigated targeting and in frank targeting failures. with its high level of accuracy, its broad dynamic range, its utility in assessing transcript structure, and its capacity to accurately interrogate global direct and indirect transcriptome changes, ngs is a useful tool for investigating the biology and mechanisms of action of micrornas.",1
"the aim of this study was to investigate the role of micrornas (mirnas or mirs) in vascular smooth muscle cell (vsmc) proliferation and to elucidate the underlying molecular mechanisms. in a previous study, using microarray analysis, differentially expressed mirnas were identified in primary vsmcs isolated from the medial layer of the thoracic aorta obtained from spontaneously hypertensive rats (shrs) and wistar kyoto (wky) rats. among others, mir-1 was identified to be downregulated in vsmcs from shrs. thus, in the present study, we focused on mir-1, the downregulation of which was confirmed by rt-qpcr and western blot analysis in vsmcs isolated from shrs. we identified insulin-like growth factor 1 (igf1) as a potential target gene of mir-1, and we subsequently validated igf1 as a target gene of mir-1 by luciferase assay. the results revealed that the exogenous overexpression of mir-1 significantly suppressed the expression of igf1. additionally, we demonstrated that the downregulation of igf1 by the introduction of mir-1 attenuated the proliferation of the vsmcs, suggesting that igf1 is a target gene of mir-1 and that the effects of mir-1 are mediated through igf1. in conclusion, the findings of our study demonstrate that mir-1 is significantly downregulated in vsmcs and that it is an important regulator of cell proliferation. therefore, igf1 may be involved in the regulation of vsmc proliferation by targeting mir-1.",1
"the bacteriophage lambda ciii gene product has a regulatory function in the lysis-lysogeny decision following infection. the availability of a set of ciii expression mutants allowed us to establish the structure-function relationship of the ciii mrna. we demonstrate, using defined in vitro systems, that the ciii mrna is present in two conformations at equilibrium. mutations that have been shown to lead to ciii overexpression were found to freeze the rna in one conformation (structure b), and permit efficient binding to the 30 s ribosomal subunit. mutations that have been shown to prevent ciii translation cause the mrna to assume the alternative conformation (structure a). in this structure, the translation initiation region is occluded, thereby preventing 30 s ribosomal subunit binding. by varying the temperature or mg2+ concentration it was possible to alter the relative proportion of the alternative structures in wild-type mrna. we suggest that the regulation of the equilibrium between the two mrna conformations provides a mechanism for the control of ciii gene expression.",1
"recently mir-182 has been reported to be over-expressed in prostate cancer (pc) tissues, however detailed functional analysis of mir-182-5p has not been carried out. the purpose of this study was to: 1. analyze the function of mir-182-5p in prostate cancer, 2. assess its usefulness as a tumor marker, 3. identify mir-182-5p target genes in pc, 4. investigate the potential for mir-182-5p inhibitor to be used in pc treatment. initially we found that mir-182-5p expression was significantly higher in prostate cancer tissues and cell lines compared to normal prostate tissues and cells. moreover high mir-182-5p expression was associated with shorter overall survival in pc patients. to study the functional significance of mir-182-5p, we knocked down mir-182-5p with mir-182-5p inhibitor. after mir-182-5p knock-down, prostate cancer cell proliferation, migration and invasion were decreased. we identified foxf2, reck and mtss1 as potential target genes of mir-182-5p using several algorithms which was confirmed by 3'utr luciferase assay and western analysis. knock-down of mir-182-5p also significantly decreased in vivo prostate tumor growth. in conclusion this is the first report documenting that over-expression of mir-182-5p is associated with prostate cancer progression and potentially useful as a prognostic biomarker. also knock down of mir-182-5p in order to increase expression of tumor suppressor genes foxf2, reck and mtss1 may be of therapeutic benefit in prostate cancer treatment.",1
"using microrna array analyses of in vitro hiv-1-infected cd4(+) cells, we find that several host micrornas are significantly up- or downregulated around the time hiv-1 infection peaks in vitro. while microrna-223 levels were significantly enriched in hiv-1-infected cd4(+)cd8(-) pbmcs, microrna-29a/b, microrna-155 and microrna-21 levels were significantly reduced. based on the potential for microrna binding sites in a conserved sequence of the nef-3'-ltr, several host micrornas potentially could affect hiv-1 gene expression. among those micrornas, the microrna-29 family has seed complementarity in the hiv-1 3'-utr, but the potential suppressive effect of microrna-29 on hiv-1 is severely blocked by the secondary structure of the target region. our data support a possible regulatory circuit at the peak of hiv-1 replication which involves downregulation of microrna-29, expression of nef, the apoptosis of host cd4 cells and upregulation of microrna-223.",1
"interleukin-8 (il-8), which is secreted by cancer cells undergoing epithelial-mesenchymal transition (emt), can promote emt in adjacent epithelial-like cells. micrornas (mirnas/mirs) can affect the expression of target genes via binding to their 3'-untranslated regions (3'-utrs), which may subsequently affect the biological behaviors of cancer cells. in our previous study, mir-520c-3p was predicted to directly target the 3'-utr of il-8. therefore, the present study was carried out to investigate whether mir-520c-3p can interact with the il-8 gene and regulate the emt of breast cancer cells. web-based prediction algorithms were used to identify mirnas that potentially target the il-8 transcript. luciferase reporter assays were used to confirm the targeting of il-8 by mir-520c-3p. reverse transcription-quantitative pcr and western blot analyses were used to examine the levels of il-8 and emt-related genes in breast cancer cells. the functional impact of mir-520c-3p on emt phenotype was evaluated using transwell and wound-healing assays, and rescue experiments were conducted by overexpressing il-8 to determine its effect on cell properties. mir-520c-3p was predicted by all three databases, which strongly suggested its interaction with the 3'-utr of il-8. the relative renilla luciferase activity of luciferase reporter construct containing the wild-type 3'-utr of il-8 was markedly decreased by mir-520c-3p transfection when compared with scrambled mirna control transfection (p<0.001). in addition, compared with the scrambled mirna control transfection, the overexpression of mir-520c-3p significantly reduced the expression of il-8, and resulted in increased e-cadherin and decreased vimentin and fibronectin levels in mcf-7 and t47d cells (all p<0.001). introduction of mir-520c-3p inhibited the invasion and migration of mcf-7 and t47d cells (all p<0.001). by contrast, the rescue of il-8 expression led to the recovery of emt-related protein expression patterns and cell motility and invasion capabilities. in conclusion, aberrant mir-520c-3p expression may lead to reduced il-8 expression and promote the mesenchymal phenotype in breast cancer cells, thereby increasing invasive growth.",1
"excessive proliferation of human pulmonary artery smooth muscle cells (hpasmc) is one of the major factors that trigger vascular remodeling in hypoxia-induced pulmonary hypertension. several studies have implicated that hypoxia inhibits the tumor suppressor p21 (cdkn1a). however, the precise mechanism is unknown. the mouse model of hypoxia-induced ph and in vitro experiments were used to assess the impact of micrornas (mirnas) on the expression of cdkn1a. in these experiments, the mirna family mir-130 was identified to regulate the expression of cdkn1a. transfection of hpasmc with mir-130 decreased the expression of cdkn1a and, in turn, significantly increased smooth muscle proliferation. conversely, inhibition of mir-130 by anti-mirs and seed blockers increased the expression of cdkn1a. reporter gene analysis proved a direct mir-130-cdkn1a target interaction. exposure of hpasmc to hypoxia was found to induce the expression of mir-130 with concomitant decrease of cdkn1a. these findings were confirmed in the mouse model of hypoxia-induced pulmonary hypertension showing that the use of seed blockers against mir-130 restored the expression of cdkn1a. these data suggest that mirna family mir-130 plays an important role in the repression of cdkn1a by hypoxia. mir-130 enhances hypoxia-induced smooth muscle proliferation and might be involved in the development of right ventricular hypertrophy and vascular remodeling in pulmonary hypertension.",1
"chronic exposure to copper and its dyshomeostasis have been linked to accelerated cognitive decline and potentially increasing risk for alzheimer's disease (ad). we and others have previously demonstrated that exposure to copper through drinking water significantly increased parenchymal amyloid-beta (aβ) plaques and decreased endothelial low-density lipoprotein receptor-related protein 1 (lrp1) in mouse models of ad. in this study, we determined the underlying mechanisms that microrna critically mediated the copper-induced loss of endothelial lrp1. in human primary microvascular endothelial cells (mvecs), microrna-200b-3p, -200c-3p, and -205-5p were significantly elevated within the 24-h exposure to copper and returned to baseline after 48-h postexposure, which corresponded with the temporal change of lrp1 expression in these cells. transient expression of synthetic microrna-200b-3p, -200c-3p, or -205-5p on mvecs significantly decreased endothelial lrp1, and cotreatment of synthetic antagomirs effectively prevented the loss of lrp1 during copper exposure, collectively supporting the key regulatory role of these micrornas in copper-induced loss of lrp1. in mice, a significant reduction of lrp1 in cortical vasculature was evident following 9 months exposure to 1.3 ppm copper in drinking water, although the levels of cortical microrna-205-5p, -200b-3p, and -200c-3p were only marginally elevated. this, however, correlated with increased vascular accumulation of aβ and impairment of spatial memory, indicating that copper exposure has the pivotal role in the vascular damage and development of cognitive decline.",1
"background recent discoveries of the atherosclerosis-related mirnas shed new light on the treatment of cardiovascular diseases. of note, mir-106b ~ 25 cluster and mir-17 ~ 92 cluster are paralogs. up till now, plenty of researches have shown the role of mir-17 ~ 92 cluster in tumor and atherosclerosis, but mir-106b ~ 25 cluster has stayed mysterious in atherosclerosis field. this study was designed to investigate how mir-106b functions in the atherosclerosis-related angiogenesis and to explore the functioning processes of mir-106b, so as to seek out a new target for the treatment of atherosclerosis. methods up and down regulation of mir-106b expression was achieved through transfection in huvecs so as to investigate the function of mir-106b. next we predicted the target genes of mir-106b and detected them using qrt-pcr and western blot technique. at last, luciferase assay was conducted to verify the direct target gene of mir-106b. data are expressed as mean ± sem. two treatment groups were compared by mann-whitney u test or student's t-test. results were considered statistically significant when p results the results showed mir-106b up-regulation groups formed less tubes than control groups while the down-regulation groups showed the opposite. meanwhile, no obvious effect on apoptosis was observed in endothelial cells. next we predicted the target genes of mir-106b and finally settled down to mapk14 (mitogen-activated protein kinase), stat3 (signal transducers and activators of transcription 3), jak1(janus kinase 1) and vegfa(vascular endothelial growth factor a) as candidate target genes. our results revealed over-expressed mir-106b represses stat3 expression, while mir-106b inhibition resulted in stat3 up-regulation. ultimately, luciferase assay confirmed stat3 mrna is the direct target of mir-106b. conclusions our research demonstrated that mir-106b modulate angiogenesis in endothelial cells through affecting expression of stat3, which occurs by direct target action. therefore, we affirmed that mir-106b exerts an anti-angiogenic effect in endothelial cells via stat3-involved signaling pathway, via directly targeting stat3.",1
"we have shown that micrornas (mirnas) are necessary for renin cell specification and kidney vascular development. here, we used a screening strategy involving microarray and in silico analyses, along with in situ hybridization and in vitro functional assays to identify mirnas important for renin cell identity. microarray studies using vascular smooth muscle cells (smcs) of the renin lineage and kidney cortex under normal conditions and after reacquisition of the renin phenotype revealed that of 599 mirnas, 192 were expressed in smcs and 234 in kidney cortex. in silico analysis showed that the highly conserved mir-330 and mir-125b-5p have potential binding sites in smoothelin (smtn), calbindin 1, smooth muscle myosin heavy chain, α-smooth muscle actin, and renin genes important for the myoepithelioid phenotype of the renin cell. rt-pcr studies confirmed mir-330 and mir-125b-5p expression in kidney and smcs. in situ hybridization revealed that under normal conditions, mir-125b-5p was expressed in arteriolar smcs and in juxtaglomerular (jg) cells. under conditions that induce reacquisition of the renin phenotype, mir-125b-5p was downregulated in arteriolar smcs but remained expressed in jg cells. mir-330, normally absent, was expressed exclusively in jg cells of treated mice. in vitro functional studies showed that overexpression of mir-330 inhibited smtn expression in smcs. on the other hand, mir-125b-5p increased smtn expression, whereas its inhibition reduced smtn expression. our results demonstrate that mir-330 and mir-125b-5p are markers of jg cells and have opposite effects on renin lineage cells: one inhibiting and the other favoring their smooth muscle phenotype.",1
"microrna-10b (mir-10b) is commonly elevated in glioblastoma (gbm), while not expressed in normal brain tissues. targeted inhibition of mir-10b has pleiotropic effects on gbm derived cell lines, it reduces gbm growth in animal models, but does not affect normal neurons and astrocytes. this data raises the possibility of developing mir-10b-targeting gbm therapy. however, the mechanisms contributing to mir-10b-mediated glioma cell survival and proliferation are unexplored. we found that inhibition of mir-10b has distinct effects on specific glioma cell lines. in cells expressing high levels of tumor suppressor p21waf1/cip1, it represses e2f1-mediated transcription, leading to down-regulation of multiple e2f1 target genes encoding for s-phase specific proteins, epigenetic modulators, and mirnas (e.g. mir-15/16), and thereby stalling progression through the s-phase of cell cycle. subsequently, mir-15/16 activities are reduced and many of their direct targets are de-repressed, including ubiquitin ligase fbxw7 that destabilizes cyclin e. conversely, gbm cells expressing low p21 level, or after p21 knock-down, exhibit weaker or no e2f1 response to mir-10b inhibition. comparative analysis of the cancer genome atlas revealed a strong correlation between mir-10b and multiple e2f target genes in gbm and low-grade glioma. taken together, these findings indicate that mir-10b regulates e2f1-mediated transcription in gbm, in a p21-dependent fashion.",1
"long noncoding rnas (lncrnas) are involved in a diversity of biological processes. it is known that differential expression of thousands of lncrnas occurs in host during influenza a virus (iav) infection. however, only few of them have been well characterized. here, we identified a lncrna, named as interferon (ifn)-stimulated lncrna (isr), which can be significantly upregulated in response to iav infection in a mouse model. a sequence alignment revealed that lncrna isr is present in mice and human beings, and indeed, we found that it was expressed in several human and mouse cell lines and tissues. silencing lncrna isr in a549 cells resulted in a significant increase in iav replication, whereas ectopic expression of lncrna isr reduced the viral replication. interestingly, interferon-β (ifn-β) treatment was able to induce lncrna isr expression, and induction of lncrna isr by viral infection was nearly abolished in host deficient of ifnar1, a type i ifn receptor. furthermore, the level of iav-induced lncrna isr expression was decreased either in retinoic acid-inducible gene i ( rig-i ) knockout a549 cells and mice or by nuclear factor κ-light-chain-enhancer of activated b cells (nf-κb) inhibitor treatment. together, these data elucidate that lncrna isr is regulated by rig-i -dependent signaling that governs ifn-β production during iav infection, and has an inhibitory capacity in viral replication.",1
"microrna (mirna or mir) inhibition of oncogenic related pathways has been shown to be a promising therapeutic approach for cancer. aberrant lipid and cholesterol metabolism is involved in prostate cancer development and progression to end-stage disease. we recently demonstrated that a key transcription factor for lipogenesis, sterol regulatory element-binding protein-1 (srebp-1), induced fatty acid and lipid accumulation and androgen receptor (ar) transcriptional activity, and also promoted prostate cancer cell growth and castration resistance. srebp-1 was overexpressed in human prostate cancer and castration-resistant patient specimens. these experimental and clinical results indicate that srebp-1 is a potential oncogenic transcription factor in prostate cancer. in this study, we identified two mirnas, mir-185 and 342, that control lipogenesis and cholesterogenesis in prostate cancer cells by inhibiting srebp-1 and 2 expression and down-regulating their targeted genes, including fatty acid synthase (fasn) and 3-hydroxy-3-methylglutaryl coa reductase (hmgcr). both mir-185 and 342 inhibited tumorigenicity, cell growth, migration and invasion in prostate cancer cell culture and xenograft models coincident with their blockade of lipogenesis and cholesterogenesis. intrinsic mir-185 and 342 expression was significantly decreased in prostate cancer cells compared to non-cancerous epithelial cells. restoration of mir-185 and 342 led to caspase-dependent apoptotic death in prostate cancer cells. the newly identified mirnas, mir-185 and 342, represent a novel targeting mechanism for prostate cancer therapy.",1
"the epigenetic regulation of micrornas is one of several mechanisms underlying carcinogenesis. we found that microrna-195 (mir-195) and microrna-378 (mir-378) were significantly down-regulated in gastric cancer tissues and gastric cancer cell lines. the expression of mir-195 and mir-378 in gastric cancer cells was significantly restored by 5-aza-dc, a demethylation reagent. the low expression of mir-195 and mir-378 was closely related to the presence of promoter cpg island methylation. treatment with mir-195/mir-378 mimics strikingly suppressed the growth of gastric cancer cells whereas promoted the growth of normal gastric epithelial cells. in contrast, administration of mir-195/mir-378 inhibitors significantly prevented the growth of normal gastric epithelial cells. expression of cyclin-dependent kinase 6 and vascular endothelial growth factor was down-regulated by exogenous mir-195 and mir-378, respectively. in conclusion, mir-195 and mir-378 are abnormally expressed and epigenetically regulated in gastric cancer cell lines and tissues via the suppression of cdk6 and vegf signaling, suggesting that mir-195 and mir-378 have tumor suppressor properties in gastric cancer.",1
"proper regulation of osmotic balance and response to tissue damage is crucial in maintaining intestinal stem cell (isc) homeostasis. we found that drosophila mir-263a downregulates the expression of epithelial sodium channel (enac) subunits in enterocytes (ecs) to maintain osmotic and isc homeostasis. in the absence of mir-263a, the intraluminal surface of the intestine displays dehydration-like phenotypes, na + levels are increased in ecs, stress pathways are activated in ecs, and iscs overproliferate. furthermore, mir-263a mutants have increased bacterial load and expression of antimicrobial peptides. strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (cf) in which loss-of-function mutations in the chloride channel cf transmembrane conductance regulator can elevate the activity of enac, suggesting that drosophila could be used as a model for cf. finally, we provide evidence that overexpression of mir-183, the human ortholog of mir-263a, can also directly target the expressions of all three subunits of human enac.",1
"unlabelled micrornas (mirnas) play a critical role in regulation of tumor metastasis. however, the role of these molecules in hepatocellular carcinoma (hcc) has not been fully elucidated. in this study, we employed mirna-sequencing and identified 22 mirnas involved in hcc metastasis. one of these, mir-28-5p, was down-regulated in hccs. this down-regulation correlated with tumor metastasis, recurrence, and poor survival. biofunctional investigations revealed that mir-28-5p deficiency promoted tumor growth and metastasis in nude mice without altering the in vitro biological characteristics of hcc cells. through gene expression profiles and bioinformatics analysis, we identified interleukin-34 (il-34) as a direct target of mir-28-5p, and the effects of mir-28-5p deficiency on hcc growth and metastasis was dependent on il-34-mediated tumor-associated macrophage (tam) infiltration. moreover, we found that tams induced by mir-28-5p-il-34 signaling inhibit mir-28-5p expression on hcc cells by transforming growth factor beta 1, resulting in an mir-28-5p-il-34-macrophage-positive feedback loop. in clinical hcc samples, mir-28-5p levels were inversely correlated with il-34 expression and the number of tams. patients with low mir-28-5p expression, high il-34 levels, and high numbers of tams had a poor prognosis with shorter overall survival and time to recurrence. conclusion a mir-28-5p-il-34-macrophage feedback loop modulates hcc metastasis and serves as a novel prognostic factor as well as a therapeutic target for hcc.",1
"background mir-17-92 cluster and its paralogues have emerged as crucial regulators of many oncogenes and tumor suppressors. transforming growth factor-β receptor ii (tgfβr2), as an important tumor suppressor, is involved in various cancer types. however, it is in cancer that only two mirnas of this cluster and its paralogues have been reported so far to regulate tgfβr2. mir-93 is oncogenic, but its targetome in cancer has not been fully defined. the role of mir-93 in nasopharyngeal carcinoma (npc) still remains largely unknown. methods we firstly evaluated the clinical signature of tgfβr2 down-regulation in clinical samples, and next used a mirna expression profiling analysis followed by multi-validations, including luciferase reporter assay, to identify mirnas targeting tgfβr2 in npc. in vitro and in vivo studies were performed to further investigate the effects of mirna-mediated tgfβr2 down-regulation on npc aggressiveness. finally, mechanism studies were conducted to explore the associated pathway and genes influenced by this mirna-mediated tgfβr2 down-regulation. results tgfβr2 was down-regulated in more than 50% of npc patients. it is an unfavorable prognosis factor contributing to clinical npc aggressiveness. a cluster set of 4 tgfβr2-associated mirnas was identified; they are all from mir-17-92 cluster and its paralogues, of which mir-93 was one of the most significant mirnas, directly targeting tgfβr2, promoting cell proliferation, invasion and metastasis in vitro and in vivo. moreover, mir-93 resulted in the attenuation of smad-dependent tgf-β signaling and the activation of pi3k/akt pathway by suppressing tgfβr2, further promoting npc cell uncontrolled growth, invasion, metastasis and emt-like process. impressively, the knockdown of tgfβr2 by sirna displayed a consentaneous phenocopy with the effect of mir-93 in npc cells, supporting tgfβr2 is a major target of mir-93. our findings were also substantiated by investigation of the clinical signatures of mir-93 and tgfβr2 in npc. conclusion the present study reports an involvement of mir-93-mediated tgfβr2 down-regulation in npc aggressiveness, thus giving extended insights into molecular mechanisms underlying cancer aggressiveness. approaches aimed at blocking mir-93 may serve as a promising therapeutic strategy for treating npc patients.",1
"purpose micrornas (mirnas) are short non-coding rna molecules, which post-transcriptionally regulate genes expression and play crucial roles in diverse biological processes. recent studies have shown that dysregulation of mirnas might modulate the resistance of cancer cells to anti-cancer drugs, yet the modulation mechanism is not fully understood. we aimed to investigate the possible role of mirnas in the development of multidrug resistance (mdr) in human gastric and lung cancer cell lines. methods mirna quantitative real-time pcr was used to detect the different mirna expression levels between drug resistant and parental cancer cells. mtt (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was used to test the drug-resistant phenotype changes in cancer cells via over or downregulation of mirnas. dual-luciferase activity assay was used to verify the target genes of mirnas. western blot analysis and apoptosis assay were used to elucidate the mechanism of mirnas on modulating drug resistance in cancer cells. results mir-200bc/429 cluster was downregulated, while bcl2 and xiap were upregulated in both mdr sgc7901/vcr (vincristine) and a549/cddp (cisplatin) cells, compared with the parental sgc7901 and a549 cells, respectively. overexpression of mir-200bc/429 cluster sensitized sgc7901/vcr and a549/cddp cells to anti-cancer drugs, respectively. both bcl2 and xiap 3'-utr reporters constructed in mdr cells suggested that bcl2 and xiap were the common target genes of the mir-200bc/429 cluster. enforced mir-200bc/429 cluster expression reduced bcl2 and xiap protein level and sensitized both mdr cells to vcr-induced and cddp-induced apoptosis, respectively. conclusions our findings first suggest that mir-200bc/429 cluster could play a role in the development of mdr in both gastric and lung cancer cell lines, at least in part by modulation of apoptosis via targeting bcl2 and xiap.",1
"phenotypic modulation of vascular smooth muscle cells (vsmcs) plays a critical role in the pathogenesis of a variety of proliferative vascular diseases. recently, we have found that microrna (mirna) mir-145 is the most abundant mirna in normal vascular walls and in freshly isolated vsmcs; however, the role of mir-145 in vsmc phenotypic modulation and vascular diseases is currently unknown. here we find that mir-145 is selectively expressed in vsmcs of the vascular wall and its expression is significantly downregulated in the vascular walls with neointimal lesion formation and in cultured dedifferentiated vsmcs. more importantly, both in cultured rat vsmcs in vitro and in balloon-injured rat carotid arteries in vivo, we demonstrate that the noncoding rna mir-145 is a novel phenotypic marker and a novel phenotypic modulator of vsmcs. vsmc differentiation marker genes such as sm alpha-actin, calponin, and sm-mhc are upregulated by premir-145 or adenovirus expressing mir-145 (ad-mir-145) but are downregulated by the mir-145 inhibitor 2'ome-mir-145. we have further identified that mir-145-mediated phenotypic modulation of vsmcs is through its target gene klf5 and its downstream signaling molecule, myocardin. finally, restoration of mir-145 in balloon-injured arteries via ad-mir-145 inhibits neointimal growth. we conclude that mir-145 is a novel vsmc phenotypic marker and modulator that is able of controlling vascular neointimal lesion formation. these novel findings may have extensive implications for the diagnosis and therapy of a variety of proliferative vascular diseases.",1
"liver cancer is the sixth most common malignant tumour and ranks in the top three cancers with regard to mortality due to metastasis and postsurgical recurrence. it is significant to understand the mechanisms underlying liver cancer for diagnosis and treatment. cumulative evidence suggests that the abnormal regulation of micrornas (mirnas/mirs) may contribute to the development and metastasis of cancer. mir‑124a acts as a tumour suppressor in osteosarcoma, endometrial carcinoma, prostate cancer, and glioblastoma. however, the effects of mir‑124a in liver cancer and its biological mechanism are not fully understood. it has been demonstrated that mir‑124a is downregulated and interleukin (il)‑11 is upregulated in the liver cancer tissues. in the present study, mir‑124a upregulation inhibited cell proliferation, migration and promoted cell apoptosis. through a dual‑luciferase reporter assay, it was verified that il‑11 is a direct target of mir‑124a. furthermore, the overexpression of mir‑124a repressed the secretion of il‑11 from hepatoma cells. finally, it was identified that mimics of mir‑124a increased the expression of tissue inhibitor of matrix metalloproteinase‑2 (timp‑2) and caspase‑3 and decreased the expression levels of matrix metalloproteinase 2 (mmp2), mmp9, b‑cell lymphoma 2, signal transducer and activator of transcription 3 (stat3), and phosphorylated‑stat3. in conclusion, the results indicated that mir‑124a has an important role as a tumour suppressor gene by targeting il‑11. these findings may provide novel insights for clinical treatments to prevent the development of liver cancer.",1
"rationale for study micrornas (mirnas) are small noncoding rnas that regulate protein expression at post-transcriptional level. we hypothesized that a specific pool of endothelial mirnas could be selectively regulated by flow conditions and inflammatory signals, and as such be involved in the development of atherosclerosis. objective to identify mirnas, called atheromirs, which are selectively regulated by shear stress and oxidized low-density lipoproteins (oxldl), and to determine their role in atherogenesis. methods and results large-scale mirna profiling in huvecs identified mir-92a as an atheromir candidate, whose expression is preferentially upregulated by the combination of low shear stress (ss) and atherogenic oxldl. ex vivo analysis of atheroprone and atheroprotected areas of mouse arteries and human atherosclerotic plaques demonstrated the preferential expression of mir-92a in atheroprone low ss regions. in ldlr(-/-) mice, mir-92a expression was markedly enhanced by hypercholesterolemia, in particular in atheroprone areas of the aorta. assessment of endothelial inflammation in gain- and loss-of-function experiments targeting mir-92a expression revealed that mir-92a regulated endothelial cell activation by oxldl, more specifically under low ss conditions, which was associated with modulation of kruppel-like factor 2 (klf2), kruppel-like factor 4 (klf4), and suppressor of cytokine signaling 5. mir-92a expression was regulated by signal transducer and activator of transcription 3 in ss- and oxldl-dependent manner. furthermore, specific in vivo blockade of mir-92a expression in ldlr(-/-) mice reduced endothelial inflammation and altered the development of atherosclerosis, decreasing plaque size and promoting a more stable lesion phenotype. conclusions upregulation of mir-92a by oxldl in atheroprone areas promotes endothelial activation and the development of atherosclerotic lesions. therefore, mir-92a antagomir seems as a new atheroprotective therapeutic strategy.",1
"a combined effect of functional constraints and random mutational events is responsible for the sequence evolution of the human mitochondrial dna (mtdna) control region. most studies targeting this noncoding segment usually focus on its primary sequence information disregarding other informative levels such as secondary or tertiary dna conformations. in this work, we combined the most recent developments in dna folding calculations with a phylogenetic comparative approach in order to investigate the formation of intrastrand secondary structures in the human mtdna control region. our most striking results are those regarding a new cloverleaf-like secondary structure predicted for a 93-bp stretch of the control region 5'-peripheral domain. randomized sequences indicated that this structure has a more negative folding energy than the average of random sequences with the same nucleotide composition. in addition, a sliding window scan across the complete mitochondrial genome revealed that it stands out as having one of the highest folding potential. moreover, we detected several lines of evidence of both negative and positive selection on this structure with high levels of conservation at the structure-relevant stem regions and the occurrence of compensatory base changes in the primate lineage. in the light of previous data, we discuss the possible involvement of this structure in mtdna replication and/or transcription. we conclude that maintenance of this structure is responsible for the observed heterogeneity in the rate of substitution among sites in part of the human hypervariable region i and that it is a hot spot for the 3' end of human mtdna deletions.",1
"dorsal closure is an epithelial remodeling process taking place during drosophila embryogenesis. jnk signaling coordinates dorsal closure. we identify and characterize acal as a novel negative dorsal closure regulator. acal represents a new level of jnk regulation. the acal locus codes for a conserved, long, non-coding, nuclear rna. long non-coding rnas are an abundant and diverse class of gene regulators. mutations in acal are lethal. acal mrna expression is dynamic and is processed into a collection of 50 to 120 bp fragments. we show that acal lies downstream of raw, a pioneer protein, helping explain part of raw functions, and interacts genetically with polycomb. acal functions in trans regulating mrna expression of two genes involved in jnk signaling and dorsal closure: connector of kinase to ap1 (cka) and anterior open (aop). cka is a conserved scaffold protein that brings together jnk and jun, and aop is a transcription factor. misregulation of cka and aop can account for dorsal closure phenotypes in acal mutants.",1
"purpose the epithelial-to-mesenchymal transition (emt) is a cell development-regulated process in which noncoding rnas act as crucial modulators. recent studies have implied that emt may contribute to resistance to epidermal growth factor receptor (egfr)-directed therapy. the aims of this study were to determine the potential role of micrornas (mirna) in controlling emt and the role of emt in inducing the sensitivity of human bladder cancer cells to the inhibitory effects of the anti-egfr therapy. experimental design mirna array screening and real-time reverse transcription-pcr were used to identify and validate the differential expression of mirnas involved in emt in nine bladder cancer cell lines. a list of potential mir-200 direct targets was identified through the targetscan database. the precursor of mir-200b and mir-200c was expressed in umuc3 and t24 cells using a retrovirus or a lentivirus construct, respectively. protein expression and signaling pathway modulation, as well as intracellular distribution of egfr and errfi-1, were validated through western blot analysis and confocal microscopy, whereas errfi-1 direct target of mir-200 members was validated by using the wild-type and mutant 3'-untranslated region/errfi-1/luciferse reporters. results we identified a tight association between the expression of mirnas of the mir-200 family, epithelial phenotype, and sensitivity to egfr inhibitors-induced growth inhibition in bladder carcinoma cell lines. stable expression of mir-200 in mesenchymal umuc3 cells increased e-cadherin levels, decreased expression of zeb1, zeb2, errfi-1, and cell migration, and increased sensitivity to egfr-blocking agents. the changes in egfr sensitivity by silencing or forced expression of errfi-1 or by mir-200 expression have also been validated in additional cell lines, umuc5 and t24. finally, luciferase assays using 3'-untranslated region/errfi-1/luciferase and mir-200 cotransfections showed that the direct down-regulation of errfi-1 was mir-200-dependent because mutations in the two putative mir-200-binding sites have rescued the inhibitory effect. conclusions members of the mir-200 family appear to control the emt process and sensitivity to egfr therapy in bladder cancer cells and the expression of mir-200 is sufficient to restore egfr dependency at least in some of the mesenchymal bladder cancer cells. the targets of mir-200 include errfi-1, which is a novel regulator of egfr-independent growth.",1
"objective to explore the role and regulation of guanine nucleotide-binding protein g(i), α-1 subunit (gnai1) in hepatocellular carcinoma (hcc). methods expression of gnai1 in hcc samples was determined by qrt-pcr and immunohistochemical (ihc) staining. huh-7 and snu-387 cells stably expressing gnai1 were established by the infection of lentivirus transducing unit containing gnai1. sirna against gnai1 was transfected into smmc-7721 cells to knock down the gnai1 expression in hcc cells. mir-320a/c/d mimics were transfected into smmc-7721 and sk-hep-1 cells and the expression of gnai1 was determined by western blot. the migration and invasion of huh-7, snu-387, sk-hep-1 and smmc-7721 cells were investigated by transwell assays. results the gnai1 protein was significantly downregulated in hcc samples without changes in its mrna levels. gnai1 could inhibit the migration and invasion of hcc cells in vitro. further investigations indicated that gnai1 was a target of mir-320a/c/d in hcc cells. transwell assays demonstrated that these micrornas could promote the migratory ability and invasivesess of hcc cells in vitro. conclusions gnai1 is downregulated in hcc and inhibits the migration and invasion of hcc cells. this study is the first to investigate the role of gnai1 in cancer. regulation of gnai1 by mir-320a/c/d indicates new therapeutic avenues for targeting hcc metastasis.",1
"we report that elevated microrna-133b (mir-133b) acts as an oncogene in human cervical carcinoma to promote tumorigenesis and metastasis. in situ hybridization confirmed that mir-133b is localized in proliferating human cervical carcinoma cells with levels progressively elevating throughout advancing stages. cellular studies showed that mir-133b enhances cell proliferation and colony formation by targeting mammalian sterile 20-like kinase 2 (mst2), cell division control protein 42 homolog (cdc42) and ras homolog gene family member a (rhoa), which subsequently results in activation of the tumorigenic protein kinase b alpha (akt1) and mitogen-activated protein kinase (erk1 and erk2, here abbreviated as erk) signaling pathways. mouse experiments revealed that upregulation of mir-133b in cervical carcinoma cells strongly promotes both in vivo tumorigenesis and independent metastasis to the mouse lung. the data indicates that upregulation of mir-133b shortens the latency of cervical carcinoma. together, these findings suggest that mir-133b could be a potent marker for the early onset of cervical carcinoma.",1
"the study of adult neural cell production has concentrated on neurogenesis. the mechanisms controlling adult gliogenesis are still poorly understood. here, we provide evidence for a homeostatic process that maintains the population of glial cells in the drosophila adult brain. flies lacking microrna mir-31a start adult life with a normal complement of glia, but transiently lose glia due to apoptosis. mir-31a expression identifies a subset of predominantly gliogenic adult neural progenitor cells. failure to limit expression of the predicted e3 ubiquitin ligase, rchy1, in these cells results in glial loss. after an initial decline in young adults, glial numbers recovered due to compensatory overproduction of new glia by adult progenitor cells, indicating an unexpected plasticity of the drosophila nervous system. experimentally induced ablation of glia was also followed by recovery of glia over time. these studies provide evidence for a homeostatic mechanism that maintains the number of glia in the adult fly brain.",1
"little is known about the potential role of micrornas (mirnas) in the carcinogenesis of gastric cancer induced by helicobacter pylori (h. pylori). here, we showed that microrna-222 (mir-222) was up-regulated in h. pylori-infected gastric mucosa and gastric cancer. ectopic expression of mir-222 promoted cell proliferation and colony formation in vitro. mechanistically, we identified reck as a novel target of mir-222, and also confirmed their relationship by the inverse correlation of mrna expression ex vivo. furthermore, we found that rna interference silencing of reck can mimic the oncogenic effects of mir-222. collectively, h. pylori may function as an initiator in the process of carcinogenesis by up-regulating mir-222, which further participates in the progression of cancer by promoting proliferation and inhibiting reck.",1
"although large numbers of micrornas (mirnas) expressed in alzheimer disease (ad) have been detected, their functions and mechanisms of regulation remain to be fully clarified. beta-site amyloid precursor protein cleaving enzyme 1 (bace1) has been one of the prime therapeutic targets for ad. here, we identified that mir-124 levels are gradually decreased in ad. in addition, we demonstrated that mir-124 suppresses bace1 expression by directly targeting the 3'utr of bace1 mrna in vitro . inhibition of mir-124 significantly increased bace1 levels in neuronal cells. in contrast, mir-124 overexpression significantly suppressed bace1 expression in cells. and finally we determined that downregulation of mir-124 alleviated aβ-induced viability inhibition and decreased apoptosis in sh-sy5y cells. our results demonstrated that mir-124 is a potent negative regulator of bace1 in the cellular ad phenotype and might be involved in the pathogenesis of ad.",1
"cldn1 (claudin1) is essential for intercellular junctions and has been reported to be involving in cell migration and metastasis, making it as an oncogene in various cancer types. however, the biological function roles and regulatory mechanisms of cldn1 in hepatocellular carcinoma (hcc) are still not clarified. in this study, we found down-regulation of mir-29a and up-regulation of cldn1 in hcc tissues and cell lines. further found an inverse relation between the expressions of mir-29a and cldn1 in hcc. dual-luciferase reporter assay indicated that mir-29a regulated the expression of cldn1 by binding to its 3' untranslated region (3'utr). knockdown of cldn1 led to decrease in tumor cell growth and migration capacities in vitro and in vivo. while overexpression of mir-29a suppressed tumor growth and migration, these effects could be reversed by re-expressing cldn1. taken together, out data suggested that mir-29a may regulate tumor growth and migration by targeting cldn1, providing promising therapeutic targets for hcc.",1
"micrornas (mirnas) are short rna molecules that regulate gene expression by binding to target messenger rnas and by controlling protein production or causing rna cleavage. to date, functions have been assigned to only a few of the hundreds of identified mirnas, in part because of the difficulty in identifying their targets. the short length of mirnas and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods. here we screen conserved 3' utr sequences from the drosophila melanogaster genome for potential mirna targets. the screening procedure combines a sequence search with an evaluation of the predicted mirna-target heteroduplex structures and energies. we show that this approach successfully identifies the five previously validated let-7, lin-4, and bantam targets from a large database and predict new targets for drosophila mirnas. our target predictions reveal striking clusters of functionally related targets among the top predictions for specific mirnas. these include notch target genes for mir-7, proapoptotic genes for the mir-2 family, and enzymes from a metabolic pathway for mir-277. we experimentally verified three predicted targets each for mir-7 and the mir-2 family, doubling the number of validated targets for animal mirnas. statistical analysis indicates that the best single predicted target sites are at the border of significance; thus, target predictions should be considered as tentative until experimentally validated. we identify features shared by all validated targets that can be used to evaluate target predictions for animal mirnas. our initial evaluation and experimental validation of target predictions suggest functions for two mirnas. for others, the screen suggests plausible functions, such as a role for mir-277 as a metabolic switch controlling amino acid catabolism. cross-genome comparison proved essential, as it allows reduction of the sequence search space. improvements in genome annotation and increased availability of cdna sequences from other genomes will allow more sensitive screens. an increase in the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection. while the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone.",1
"micrornas control a wide array of biological processes including cell differentiation, proliferation, and apoptosis whose dysregulation is a hallmark of cancer. microrna-21 (mir-21) is overexpressed in many cancers including glioblastoma and contributes to tumor resistance to chemotherapy. we investigated whether mir-21 mediated chemoresistance to the chemotherapeutic agent vm-26 in glioblastoma cells and sought to identify the candidate target genes for mir-21 by gene expression profiling. here we report that mir-21 was involved in mediating chemoresistance to vm-26 in glioblastoma cells. suppression of mir-21 by specific antisense oligonucleotides in glioblastoma cell u373 mg led to enhanced cytotoxicities of vm-26 against u373 mg cells. we further identified and validated lrrfip1, whose product is an inhibitor of nf-kappab signaling, as a direct target gene of mir-21. our findings suggest that mir-21 represents a promising target for therapeutic manipulation to increase the efficacy of chemotherapeutic agents in treating glioblastoma, a highly lethal type of cancer.",1
"the role of mir-26a in cancer cells seemed controversial in previous studies. until now, the role of mir-26a in gastric cancer remains undefined. in this study, we found that mir-26a was strongly downregulated in gastric cancer (gc) tissues and cell lines, and its expression levels were associated with lymph node metastasis and clinical stage, as well as overall survival and replase-free survival of gc. we also found that ectopic expression of mir-26a inhibited gc cell proliferation and gc metastasis in vitro and in vivo. we further identified a novel mechanism of mir-26a to suppress gc growth and metastasis. fgf9 was proved to be a direct target of mir-26a, using luciferase assay and western blot. fgf9 overexpression in mir-26a-expressing cells could rescue invasion and growth defects of mir-26a. in addition, mir-26a expression inversely correlated with fgf9 protein levels in gc. taken together, our data suggest that mir-26a functions as a tumor suppressor in gc development and progression, and holds promise as a prognostic biomarker and potential therapeutic target for gc.",1
"recent years, the role of long non-coding rnas (lncrnas) in atrial fibrillation (af) has been gradually elucidated. in the current study, we measured the expression of ten af-related lncrnas to do qrt-pcr analysis. lncrna kcnq1 overlapping transcript 1 (kcnq1ot1) was found to be significantly upregulated in af model and ang-ii-induced mice heart. cacna1c has been reported as a biomarker in atrial fibrillation. here, we found that the expression pattern of cacna1c was consistent with that of kcnq1ot1. electrophysiological study was conducted to demonstrate the effect of kcnq1ot1 and cacna1c on the effective refractory period (erp), interatrial conduction time (iact), incidence of af and af duration of ang-ii-induced mice heart. mechanically, kcnq1ot1 contributed to the upregulation of cacna1c by binding with mir-384. furthermore, yy1 could activate the transcription of kcnq1ot1 and cacna1c. in conclusion, the present study revealed that yy1-induced upregulation of lncrna kcnq1ot1 regulates angiotensin ii-induced atrial fibrillation by regulating mir-384/cacna1c axis.",1
"we sequenced drosophila head rna to identify a small set of mirnas that undergo robust circadian cycling. we concentrated on a cluster of six mirnas, mir-959-964, all of which peak at about zt12 or lights off. the cluster pri-mirna is transcribed under bona fide circadian transcriptional control, and all six mature mirnas have short half-lives, a requirement for cycling. a viable gal4 knockin strain localizes prominent cluster mirna expression to the adult head fat body. analysis of cluster knockout and overexpression strains indicates that innate immunity, metabolism, and feeding behavior are under cluster mirna regulation. manipulation of food intake also affects the levels and timing of cluster mirna transcription with no more than minor effects on the core circadian oscillator. these observations indicate a feedback circuit between feeding time and cluster mirna expression function as well as a surprising role of posttranscriptional regulation in the circadian control of these phenotypes.",1
"unlabelled the pathological relevance and significance of micrornas (mirnas) in hepatocarcinogenesis have attracted much attention in recent years; however, little is known about the underlying molecular mechanisms through which mirnas are involved in the development and progression of hepatocellular carcinoma (hcc). in this study, we demonstrate that mir-30d is frequently up-regulated in hcc and that its expression is highly associated with the intrahepatic metastasis of hcc. furthermore, the enhanced expression of mir-30d could promote hcc cell migration and invasion in vitro and intrahepatic and distal pulmonary metastasis in vivo, while silencing its expression resulted in a reduced migration and invasion. galphai2 (gnai2) was identified as the direct and functional target of mir-30d with integrated bioinformatics analysis and messenger rna array assay. this regulation was further confirmed by luciferase reporter assays. in addition, our results, for the first time, showed that gnai2 was frequently suppressed in hcc by way of quantitative reverse-transcription polymerase chain reaction and immunohistochemical staining assays. the increase of the gnai2 expression significantly inhibits, whereas knockdown of the gnai2 expression remarkably enhances hcc cell migration and invasion, indicating that gnai2 functions as a metastasis suppressor in hcc. the restoration of gnai2 can inhibit mir-30d-induced hcc cell invasion and metastasis. conclusion the newly identified mir-30d/gnai2 axis elucidates the molecular mechanism of hcc cell invasion and metastasis and represents a new potential therapeutic target for hcc treatment.",1
"increasing evidence suggests that there is a unique cell subpopulation in melanoma that can form nonadherent melanospheres in serum-free stem cell medium, mimicking aggressive malignancy. using melanospheres as a model to investigate progression mechanisms, we found that mir-519d overexpression was sufficient to promote cell proliferation, migration, invasion, and adhesion in vitro and lung metastatic capability in vivo the cell adhesion receptor epha4 was determined to be a direct target of mir-519d. forced expression of epha4 reversed the effects of mir-519d overexpression, whereas silencing of epha4 phenocopied the effect of mir-519d. malignant progression phenotypes were also affected at the level of epithelial-to-mesenchymal transition and the erk1/2 signaling pathway inversely affected by mir-519d or epha4 expression. in clinical specimens of metastatic melanoma, we observed significant upregulation of mir-519d and downregulation of epha4, in the latter case correlated inversely with overall survival. taken together, our results suggest a significant functional role for mir-519d in determining epha4 expression and melanoma progression. significance: these results suggest a significant role for mir-519d in determining expression of a pivotal cell adhesion molecule that may impact risks of malignant progression in many cancers. cancer res; 78(1); 216-29. ©2017 aacr .",1
"background mir-221 and mir-222 (mir-221/222) are frequently up-regulated in various types of human malignancy including glioblastoma. recent studies have reported that mir-221/222 regulate cell growth and cell cycle progression by targeting p27 and p57. however the underlying mechanism involved in cell survival modulation of mir-221/222 remains elusive. results here we showed that mir-221/222 inhibited cell apoptosis by targeting pro-apoptotic gene puma in human glioma cells. enforced expression of mir-22/222 induced cell survival whereas knockdown of mir-221/222 rendered cells to apoptosis. further, mir-221/222 reduced puma protein levels by targeting puma-3'utr. introducing puma cdna without 3'utr abrogated mir-221/222-induced cell survival. notably, knockdown of mir-221/222 induces puma expression and cell apoptosis and considerably decreases tumor growth in xenograft model. finally, there was an inverse relationship between puma and mir-221/222 expression in glioma tissues. conclusion to our knowledge, these data indicate for the first time that mir-221/222 directly regulate apoptosis by targeting puma in glioblastoma and that mir-221/222 could be potential therapeutic targets for glioblastoma intervention.",1
"human telomerase reverse transcriptase (htert) plays a key role in tumor invasion and metastasis, but the mechanism of its involvement in these processes is not clear. the purpose of this study is to investigate the possible molecular mechanism of htert in the promotion of gastric cancer (gc) metastasis. we found that the up-regulation of htert in gastric cancer cells could inhibit the expression of mir-29a and enhance the expression of integrin β1 (itgb1). in addition, the invasive capacity of gastric cancer cells was also highly increased after htert overexpression. our study also found that the restoration of mir-29a suppressed the expression of itgb1 and inhibited gc cell metastasis both in vitro and in vivo. taken together, our results suggested that htert may promote gc metastasis through the htert-mir-29a-itgb1 regulatory pathway.",1
"purpose microrna-124a (mir-124a), an abundant microrna in the central neuron system, has been linked to tumor progression. here, we investigated the role of mir-124a in uveal melanoma development. methods expression of mir-124a in uveal melanoma cells was examined using real time rt-pcr. the effect of mir-124a on cell proliferation, migration, and invasion was analyzed using mts assay, flow cytometry, and transwell experiments. the ability of mir-124a to repress tumor growth was tested in vivo. target genes of mir-124a were first predicted by bioinformatics, confirmed using a luciferase assay, and their expression determined by western blotting. dna methylation and histone modification of mir-124a was analyzed by methylation-specific pcr and chip assay. finally, epigenetic drugs were used to alter the expression of mir-124a. results mir-124a expression was downregulated in both uveal melanoma cells and clinical specimens. transient transfection of mir-124a into uveal melanoma cells inhibited cell growth, migration, and invasion. moreover, introduction of mir-124a suppressed in vivo growth of tumor. potential targets of mir-124a were found to include cdk4, cdk6, cyclin d2, and ezh2. knockdown of ezh2 by sirna resulted in inhibition of uveal melanoma cell migration and invasion. in addition, mir-124a expression was found to be regulated via epigenetic mechanisms, with its expression restored when cells were treated with a dna hypomethylating agent, 5-aza-2'-deoxycytidine, and a histone deacetylase inhibitor, trichostatin a. conclusions our results demonstrated that mir-124a could function as a potent tumor suppressor by regulation of multiple targets, and was epigenetically silenced in the development of uveal melanoma.",1
"gene regulation by small rnas (srnas) has been extensively studied in various bacteria. however, the presence and roles of srnas in mycobacteria remain largely unclear. immunoprecipitation of rna chaperone hfq to enrich for srnas is one of the effective methods to isolate srnas. however, the lack of an identified mycobacterial hfq restricts the feasibility of this approach. we developed a novel method that takes advantage of the conserved inherent srnas-binding capability of heterologous hfq from escherichia coli to enrich srnas from mycobacterium smegmatis, a model organism for studying mycobacterium tuberculosis. we validated 12 trans-encoded and 12 cis-encoded novel srnas in m. smegmatis. many of these srnas are differentially expressed at exponential phase compared with stationary phase, suggesting that srnas are involved in the growth of mycobacteria. intriguingly, five of the cis-encoded novel srnas target known transposases. phylogenetic conservation analysis shows that these srnas are pathogenicity dependent. we believe that our findings will serve as an important reference for future analysis of srnas regulation in mycobacteria and will contribute significantly to the development of srnas prediction programs. moreover, this novel method of using heterologous hfq for srnas enrichment can be of general use for the discovery of bacterial srnas in which no endogenous hfq is identified.",1
"micrornas (mirnas) are approximately 22-nucleotide rnas that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression. here, we report that the mirna iab-4 locus in the drosophila hox cluster is transcribed convergently from both dna strands, giving rise to two distinct functional mirnas. both sense and antisense mirna products target neighboring hox genes via highly conserved sites, leading to homeotic transformations when ectopically expressed. we also report sense/antisense mirnas in mouse and find antisense transcripts close to many mirnas in both flies and mammals, suggesting that additional sense/antisense pairs exist.",1
"temperature is an important parameter that free-living cells monitor constantly. the expression of heat-shock, cold-shock and some virulence genes is coordinated in response to temperature changes. apart from protein-mediated transcriptional control mechanisms, translational control by rna thermometers is a widely used regulatory strategy. rna thermometers are complex rna structures that change their conformation in response to temperature. most, but not all, rna thermometers are located in the 5'-untranslated region and mask ribosome-binding sites by base pairing at low temperatures. melting of the structure at increasing temperature permits ribosome access and translation initiation. different cis-acting rna thermometers and a trans-acting thermometer will be presented.",1
"glioblastoma multiforme (gbm) is a heterogeneous disease despite its seemingly uniform pathology. deconvolution of the cancer genome atlas's gbm gene expression data has unveiled the existence of distinct gene expression signature underlying discrete gbm subtypes. recent conflicting findings proposed that microrna (mirna)-10b exclusively regulates glioma growth or invasion but not both. we showed that silencing of mirna-10b by baculoviral decoy vectors in a glioma cell line resembling the mesenchymal subtype of gbm reduces its growth, invasion and angiogenesis while promoting apoptosis in vitro. in an orthotopic human glioma mouse model, inhibition of mirna-10b diminishes the invasiveness, angiogenicity and growth of the mesenchymal subtype-like glioma cells in the brain and significantly prolonged survival of glioma-bearing mice. we demonstrated that the pleiotropic nature of mirna-10b was due to its suppression of multiple tumor suppressors, including tp53, foxo3, cyld, pax6, ptch1, hoxd10 and notch1. in particular, sirna-mediated knockdown experiments identified tp53, pax6, notch1 and hoxd10 as invasion regulatory genes in our mesenchymal subtype-like glioma cells. by interrogating the rembrandt, we noted that dysregulation of many direct targets of mirna-10b was associated with significantly poorer patient survival. thus, our study uncovers a novel role for mirna-10b in regulating angiogenesis and suggests that mirna-10b may be a pleiotropic regulator of gliomagenesis.",1
"micrornas (mirnas) are a class of noncoding rnas that post-transcriptionally regulate gene expression in plants and animals. to investigate the influence of mirnas on transcript levels, we transfected mirnas into human cells and used microarrays to examine changes in the messenger rna profile. here we show that delivering mir-124 causes the expression profile to shift towards that of brain, the organ in which mir-124 is preferentially expressed, whereas delivering mir-1 shifts the profile towards that of muscle, where mir-1 is preferentially expressed. in each case, about 100 messages were downregulated after 12 h. the 3' untranslated regions of these messages had a significant propensity to pair to the 5' region of the mirna, as expected if many of these messages are the direct targets of the mirnas. our results suggest that metazoan mirnas can reduce the levels of many of their target transcripts, not just the amount of protein deriving from these transcripts. moreover, mir-1 and mir-124, and presumably other tissue-specific mirnas, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans.",1
"background & aims micro-rna (mirna) are endogenous regulatory rna molecules that modulate gene expression. alterations in mirna expression can contribute to tumor growth by modulating the functional expression of critical genes involved in tumor cell proliferation or survival. our aims were to identify specific mirna involved in the regulation of cholangiocarcinoma growth and response to chemotherapy. methods mirna expression in malignant and nonmalignant human cholangiocytes was assessed using a microarray. expression of selected mirna and their precursors was evaluated by northern blots and real-time polymerase chain reaction, respectively. the effect of selected mirna on cell growth and response to chemotherapy was assessed using mirna-specific antisense oligonucleotides to decrease mirna expression or with precursor mirna to increase cellular expression. results mirna expression was markedly different in malignant cholangiocytes, with decreased expression of many mirna compared with nonmalignant cells. a cluster of mirna, including mir-320, mir-200b, mir-21, mir-23a, mir-141, mir-27a, and mir-34a, were expressed in all cell lines. mir-21, mir-141, and mir-200b were highly over-expressed in malignant cholangiocytes. inhibition of mir-21 and mir-200b increased sensitivity to gemcitabine, whereas inhibition of mir-141 decreased cell growth. treatment of tumor cell xenografts with systemic gemcitabine altered the expression of a significant number of mirna. mir-21 modulates gemcitabine-induced apoptosis by phosphatase and tensin homolog deleted on chromosome 10 (pten)-dependent activation of pi 3-kinase signaling. potential target genes that were modulated by selected mirna were identified. conclusions alterations in mirna expression contribute to tumor growth and response to chemotherapy. aberrantly expressed mirna or their targets will provide mechanistic insight and therapeutic targets for cholangiocarcinoma.",1
"aberrant expression of microrna (mirna) has been previously demonstrated to play an important role in a wide range of cancer types and further elucidation of its role in the mechanisms underlying tumorigenesis, anticarcinogenesis and potential chemotherapeutics is warranted. we chose the anti-benzopyrene-7,8-diol-9,10-epoxide-transformed human bronchial epithelial cell line 16hbe-t to study mirnas involved in anticarcinogenesis. in resveratrol-treated cells, we found that mir-622 was upregulated, whereas it was downregulated in 16hbe-t cells, suggesting that mir-622 potentially acts as a tumor suppressor. increasing the level of mir-622 by transient transfection-induced inhibition of proliferation and g(0) arrest in 16hbe-t cells and the lung cancer cell line h460 as demonstrated by cell viability and cell cycle analysis. mir-622 dramatically suppressed the ability of 16hbe-t cells to form colonies in vitro and to develop tumors in nude mice. according to bioinformatics analysis, k-ras messenger rna was predicted as a putative mir-622 target; this was confirmed by western blot and luciferase reporter assays. cell growth retardation was inhibited upon knockdown of k-ras and an increase in the level of mir-622 in 16hbe-t cells. furthermore, mir-622 inhibitor partially impaired the growth of 16hbe-t cells as demonstrated by luciferase reporter activity and k-ras protein expression in 16hbe-t cells. in summary, mir-622 functions as a tumor suppressor by targeting k-ras and impacting the anticancer effect of resveratrol. therefore, mir-622 is potentially useful as a clinical therapy. mir-622 impacts the k-ras signal pathway and the potentially anticarcinogenic or chemotherapeutic properties warrant further investigation.",1
"epstein-barr virus (ebv) is a γ-herpesvirus that is linked to the development of posttransplant lymphoproliferative disorder (ptld) in solid organ recipients. we previously demonstrated that ebv(+) b cell lymphoma cell lines isolated from patients with ptld produce human il-10 as an autocrine growth factor. however, little is known regarding il-10 regulation in b cells. here we show that ebv infection markedly alters the expression of host b cell microrna, a class of small noncoding rna that is an important regulator of transcriptional and posttranscriptional gene expression. gene arrays reveal unique microrna profiles in ebv(+) b cell lymphoma lines from patients with ptld, compared to normal b cells or in vitro generated ebv(+) lymphoblastoid cell lines. we show that microrna-194 expression is uniquely suppressed in ebv(+) b cell lines from ptld patients and that the 3'untranslated region of il-10 is targeted by microrna-194. overexpression of microrna-194 attenuates il-10 production and increases apoptosis of ebv(+) b cell lymphoma lines. together, these data indicate that ebv co-opts the host b cell microrna network and specifically suppresses microrna-194 to override control of il-10 expression. thus, modulation of microrna-194 may constitute a novel approach to inhibiting proliferation of ebv(+) b cell lymphomas in ptld.",1
"upon stress, profound post-transcriptional adjustments of gene expression occur in spatially restricted, subcellular, membraneless compartments, or ribonucleoprotein (rnp) granules, which are formed by liquid phase separation of rna-binding proteins with low complexity sequence domains (lcds). here, we show that rbfox1 is an lcd-containing protein that aggregates into liquid droplets and amyloid-like fibers and promiscuously joins different nuclear and cytoplasmic rnp granules. using drosophila oogenesis as an in vivo system for stress response, we demonstrate a mechanism by which rbfox1 promotes cell survival. the stress-dependent mirna mir-980 acts to buffer rbfox1 levels, since it targets only those rbfox1 transcripts that contain extended 3'utrs. reduced mir-980 expression during stress leads to increased rbfox1 levels, widespread formation of various rnp granules, and increased cell viability. we show that human rbfox proteins also contain multiple lcds and form membraneless compartments, suggesting that the rnp granule-linked control of cellular adaptive responses may contribute to a wide range of rbfox-associated pathologies in humans.",1
"aims dysregulation of the bone morphogenetic protein receptor type 2 (bmpr2) is a hallmark feature that has been described in several forms of pulmonary hypertension. we recently identified the microrna mir-20a within a highly conserved pathway as a regulator of the expression of bmpr2. to address the pathophysiological relevance of this pathway in vivo, we employed antagomir-20a and investigated whether specific inhibition of mir-20a could restore functional levels of bmpr2 and, in turn, might prevent pulmonary arterial vascular remodelling. methods and results for specific inhibition of mir-20a, cholesterol-modified rna oligonucleotides (antagomir-20a) were synthesized. the experiments in mice were performed by using the hypoxia-induced mouse model for pulmonary hypertension and animal tissues were analysed for right ventricular hypertrophy and pulmonary arterial vascular remodelling. treatment with antagomir-20a enhanced the expression levels of bmpr2 in lung tissues; moreover, antagomir-20a significantly reduced wall thickness and luminal occlusion of small pulmonary arteries and reduced right ventricular hypertrophy. to assess bmpr2 signalling and proliferation, we performed in vitro experiments with human pulmonary arterial smooth muscle cells (hpasmcs). transfection of hpasmcs with antagomir-20a resulted in activation of downstream targets of bmpr2 showing increased activation of id-1 and id-2. proliferation of hpasmcs was found to be reduced upon transfection with antagomir-20a. conclusion this is the first report showing that mir-20a can be specifically targeted in an in vivo model for pulmonary hypertension. our data emphasize that treatment with antagomir-20a restores functional levels of bmpr2 in pulmonary arteries and prevents the development of vascular remodelling.",1
"renal tubulointerstitial fibrosis is the common end point of progressive renal disease. microrna (mir)-214 and mir-21 are upregulated in models of renal injury, but the function of mir-214 in this setting and the effect of its manipulation remain unknown. we assessed the effect of inhibiting mir-214 in an animal model of renal fibrosis. in mice, genetic deletion of mir-214 significantly attenuated interstitial fibrosis induced by unilateral ureteral obstruction (uuo). treatment of wild-type mice with an anti-mir directed against mir-214 (anti-mir-214) before uuo resulted in similar antifibrotic effects, and in vivo biodistribution studies demonstrated that anti-mir-214 accumulated at the highest levels in the kidney. notably, in vivo inhibition of canonical tgf-β signaling did not alter the regulation of endogenous mir-214 or mir-21. whereas mir-21 antagonism blocked smad 2/3 activation, mir-214 antagonism did not, suggesting that mir-214 induces antifibrotic effects independent of smad 2/3. furthermore, tgf-β blockade combined with mir-214 deletion afforded additional renal protection. these phenotypic effects of mir-214 depletion were mediated through broad regulation of the transcriptional response to injury, as evidenced by microarray analysis. in human kidney tissue, mir-214 was detected in cells of the glomerulus and tubules as well as in infiltrating immune cells in diseased tissue. these studies demonstrate that mir-214 functions to promote fibrosis in renal injury independent of tgf-β signaling in vivo and that antagonism of mir-214 may represent a novel antifibrotic treatment in the kidney.",1
"dysregulation of specific micrornas (mirnas) is found to play a vital role in carcinogenesis and progression of gastric cancer (gc). in the present study, we investigated the expression profiles of mirnas in gastric cancer. let-7b was found downregulated remarkably in gastric cancer tissues and was correlated with helicobacter pylori infection, tumor stage, and lymphatic metastasis. ectopic expression of let-7b suppressed the growth, migration, invasion, and tumorigenicity of gc cells, whereas let-7b knockdown promoted these phenotypes. bioinformatic analysis predicted collagen triple helix repeat containing 1 (cthrc1) as a direct target of let-7b. luciferase assay showed that let-7b repressed the activity of cthrc1 through binding its 3'utr. western blotting also confirmed that the protein levels of cthrc1 were decreased by let-7b. cthrc1 was significantly upregulated and reversely correlated with let-7b levels in gc. co-expression of let-7b and cthrc1 without its 3'utr could rescue cell growth, migration, and invasion inhibited by let-7b. these results suggest that let-7b may directly target cthrc1 and function as a tumor suppressor gene in gc.",1
"following a myocardial infarction (mi), fibroblasts differentiate to myofibroblasts, which possess some of the characteristics of smooth muscle cells (smcs) and contribute to wound healing. previous studies suggested that the mir-143/-145 cluster plays a critical role in smc differentiation. therefore, we determined whether mir-145 promoted differentiation of cardiac fibroblasts to myofibroblasts. following coronary occlusion in mice, myocardial mir-145 expression was downregulated at 3 days but was restored at 7 days. in vitro studies showed that hypoxia also downregulated mir-145 in cardiac fibroblasts. the number of α-smooth muscle actin (α-sma) positive cells in fibroblast cultures was employed to determine their transdifferentiation to cardiac myofibroblasts and was increased by 73.5% after transient transfection with mir-145. ultrastructural analysis of α-sma stress fibers revealed that ~95% of the α-sma(+) cells treated with mir-145 organized their actin-filament bundles with a specific orientation compared to only 15% in the scrambled control group. this orientation of the sma bundles and their integration with the filamentous actin fibers of the cytoskeleton permit infarct wound contraction. structural and functional studies showed that mir-145 induced a myofibroblast phenotype, and mir-145 also potentiated the production of mature collagen by myofibroblasts. repression of klf5, a target of mir-145, was validated by a chimeric luciferase construct tagged with the full-length 3'-utr of klf5. a dramatic decrease in klf5 and a corresponding increase in myocardin expression were observed after transfecting cultured fibroblasts with mir-145. similar results were found in vivo: the transient decrease in mir-145 expression 3 days post-mi was associated with an increase in klf5 and a decrease in myocardin. in addition, in vivo delivery of a mir-145 antagomir 1 day prior to and 2 and 6 days after mi decreased myofibroblast formation and increased scar size. the antagomir also reversed the suppressed expression of klf5 protein in the scar region at day 7 after mi. in summary, we describe a novel association between mir-145 and fibroblast differentiation toward myofibroblasts. these observations provide a new approach to promote endogenous scar healing and contracture by stimulating the transdifferentiation of cardiac fibroblasts to myofibroblasts.",1
"micrornas have emerged in recent years as important regulators of cell function in both normal and diseased cells. mirnas coordinately regulate large suites of target genes by mrna degradation and/or translational inhibition. the mrna target specificities of mirnas in animals are primarily encoded within a 7 nt ""seed region"" mapping to positions 2-8 at the molecule's 5' end. we here combine computational analyses with experimental studies to explore the functional significance of sequence variation within the seed region of human mirnas. the results indicate that a substitution of even a single nucleotide within the seed region changes the spectrum of mrna targets by >50%. the high functional cost of even single nucleotide changes within seed regions is consistent with their high sequence conservation among mirna families both within and between species and suggests processes that may underlie the evolution of mirna regulatory control.",1
"saccharomyces cerevisiae snr30 is an essential box h/aca small nucleolar rna (snorna) required for the processing of 18s rrna. here, we show that the previously characterized human, reptilian, amphibian, and fish u17 snornas represent the vertebrate homologues of yeast snr30. we also demonstrate that u17/snr30 is present in the fission yeast schizosaccharomyces pombe and the unicellular ciliated protozoan tetrahymena thermophila. evolutionary comparison revealed that the 3'-terminal hairpins of u17/snr30 snornas contain two highly conserved sequence motifs, the m1 (auauuccua) and m2 (aaaccau) elements. mutation analysis of yeast snr30 demonstrated that the m1 and m2 elements are essential for early cleavages of the 35s pre-rrna and, consequently, for the production of mature 18s rrna. the m1 and m2 motifs occupy the opposite strands of an internal loop structure, and they are located invariantly 7 nucleotides upstream from the aca box of u17/snr30 snornas. u17/snr30 is the first identified box h/aca snorna that possesses an evolutionarily conserved role in the nucleolytic processing of eukaryotic pre-rrna.",1
"sterol regulatory element-binding proteins (srebps) have evolved as a focal point for linking lipid synthesis with other pathways that regulate cell growth and survival. here, we have uncovered a polycistrionic microrna (mirna) locus that is activated directly by srebp-2. two of the encoded mirnas, mir-182 and mir-96, negatively regulate the expression of fbxw7 and insig-2, respectively, and both are known to negatively affect nuclear srebp accumulation. direct manipulation of this mirna pathway alters nuclear srebp levels and endogenous lipid synthesis. thus, we have uncovered a mechanism for the regulation of intracellular lipid metabolism mediated by the concerted action of a pair of mirnas that are expressed from the same srebp-2-regulated mirna locus, and each targets a different protein of the multistep pathway that regulates srebp function. these studies reveal an mirna ""operon"" analogous to the classic model for genetic control in bacterial regulatory systems.",1
"when adapting to environmental stress, cells attenuate and reprogram their translational output. in part, these altered translation profiles are established through changes in the interactions between rna-binding proteins and mrnas. the argonaute 2 (ago2)/microrna (mirna) machinery has been shown to participate in stress-induced translational up-regulation of a particular mrna, cat-1; however, a detailed, transcriptome-wide understanding of the involvement of ago2 in the process has been lacking. here, we profiled the overall changes in ago2-mrna interactions upon arsenite stress by cross-linking immunoprecipitation (clip) followed by high-throughput sequencing (clip-seq). ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (utr) and coding sequence (cds) sites exhibiting stronger interaction. interestingly, target sites that were destined for release from ago2 upon stress were depleted in mirna complementarity signatures, suggesting an alternative mode of interaction. to compare the changes in ago2-binding patterns across transcripts with changes in their translational states, we measured mrna profiles on ribosome/polysome gradients by rna sequencing (rna-seq). increased ago2 occupancy correlated with stronger repression of translation for those mrnas, as evidenced by a shift toward lighter gradient fractions upon stress, while release of ago2 was associated with the limited number of transcripts that remained translated. taken together, these data point to a role for ago2 and the mammalian mirnas in mediating the translational component of the stress response.",1
"elevated levels of fibrinogen are associated with increased risk of cardiovascular disease, whereas low fibrinogen can lead to a bleeding disorder. we investigated whether micrornas (mirnas), known to act as post-transcriptional regulators of gene expression, regulate fibrinogen production. using transfection of a library of 470 annotated human mirna precursor molecules in huh7 hepatoma cells and quantitative measurements of fibrinogen production, we identified 23 mirnas with down-regulating (up to 64% decrease) and 4 with up-regulating effects (up to 129% increase) on fibrinogen production. among the down-regulating mirnas, we investigated the mechanism of action of 3 hsa-mir-29 family members and hsa-mir-409-3p. overexpression of hsa-mir-29 members led to decreased steady-state levels of all fibrinogen gene (fga, fgb, and fgg) transcripts in huh7 cells. luciferase reporter gene assays demonstrated that this was independent of mirna-fibrinogen 3'-untranslated region interactions. in contrast, overexpression of hsa-mir-409-3p specifically lowered fibrinogen bβ mrna levels, and this effect was dependent on a target site in the fibrinogen bβ mrna 3'-untranslated region. this study adds to the known mechanisms that control fibrinogen production, points toward a potential cause of variable circulating fibrinogen levels, and demonstrates that a screening approach can identify mirnas that regulate clinically important proteins.",1
"background epstein-barr virus (ebv) is a human herpesvirus implicated in cancer and autoimmune disorders. little is known concerning the roles of rna structure in this important human pathogen. this study provides the first comprehensive genome-wide survey of rna and rna structure in ebv. results novel ebv rnas and rna structures were identified by computational modeling and rna-seq analyses of ebv. scans of the genomic sequences of four ebv strains (ebv-1, ebv-2, gd1, and gd2) and of the closely related macacine herpesvirus 4 using the rnaz program discovered 265 regions with high probability of forming conserved rna structures. secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. the analysis of rna-seq data uncovered the first observation of a stable intronic sequence rna (sisrna) in ebv. the abundance of this sisrna rivals that of the well-known and highly expressed ebv-encoded non-coding rnas (ebers). conclusion this work identifies regions of the ebv genome likely to generate functional rnas and rna structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. enhanced understanding of the ebv transcriptome will guide future experimental analyses of the discovered rnas and rna structures.",1
"micrornas (mirnas) have been recognized as significantly involved in prostate cancer (pca). since androgen receptor (ar) plays a central role in pca carcinogenesis and progression, it is imperative to systematically elucidate the causal association between ar and mirnas, focusing on the molecular mechanisms by which mirnas mediate ar signalling. in this study, we performed a series of time-course microarrays to observe the dynamic genome-wide expressions of mrnas and mirnas in parallel in hormone-sensitive prostate cancer lncap cells stimulated by androgen. accordingly, we introduced response score to identify ar target mirnas, as well as modulation score to identify mirna target mrnas. based on theoretical identification and experimental validation, novel mechanisms addressing cell viability in pca were unravelled for 3 mirnas newly recognized as ar targets. (1) mir-19a is directly up-regulated by ar, and represses suz12, rab13, sc4mol, psap and abca1, respectively. (2) mir-27a is directly up-regulated by ar, and represses abca1 and pds5b. (3) mir-133b is directly up-regulated by ar, and represses cdc2l5, ptprk, rb1cc1, and cpne3, respectively. moreover, we found mir-133b is essential to pca cell survival. our study gives certain clues on mirnas mediated ar signalling to cell viability by influencing critical pathways, especially by breaking through androgen's growth restriction effect on normal prostate tissue.",1
"the minor spliceosome is evolutionarily conserved in higher eukaryotes, but its biological significance remains poorly understood. here, by precise crispr/cas9-mediated disruption of the u12 and u6atac snrnas, we report that a defective minor spliceosome is responsible for spinal muscular atrophy (sma) associated phenotypes in drosophila. using a newly developed bioinformatic approach, we identified a large set of minor spliceosome-sensitive splicing events and demonstrate that three sensitive intron-containing neural genes, pcyt2, zmynd10, and fas3, directly contribute to disease development as evidenced by the ability of their cdnas to rescue the sma-associated phenotypes in muscle development, neuromuscular junctions, and locomotion. interestingly, many splice sites in sensitive introns are recognizable by both minor and major spliceosomes, suggesting a new mechanism of splicing regulation through competition between minor and major spliceosomes. these findings reveal a vital contribution of the minor spliceosome to sma and to regulated splicing in animals.",1
"functional impairment of endothelial colony-forming cells (ecfcs), a specific cell lineage of endothelial progenitor cells (epcs) is highly associated with the severity of coronary artery disease (cad), the most common type of cardiovascular disease (cvd). emerging evidence show that circulating micrornas (mirnas) in cad patients' body fluid hold a great potential as biomarkers. however, our knowledge of the role of circulating mirna in regulating the function of ecfcs and the progression of cad is still in its infancy. we showed that when ecfcs from healthy volunteers were incubated with conditioned medium or purified exosomes of cultured cad ecfcs, the secretory factors from cad ecfcs dysregulated migration and tube formation ability of healthy ecfcs. it is known that exosomes influence the physiology of recipient cells by introducing rnas including mirnas. by using small rna sequencing (smrna-seq), we deciphered the circulating mirnome in the plasma of healthy individual and cad patients, and found that the plasma mirna spectrum from cad patients was significantly different from that of healthy control. interestingly, smrna-seq of both healthy and cad ecfcs showed that twelve mirnas that had a higher expression in the plasma of cad patients also showed higher expression in cad ecfcs when compared with healthy control. this result suggests that these mirnas may be involved in the regulation of ecfc functions. for identification of potential mrna targets of the differentially expressed mirna in cad patients, cdna microarray analysis was performed to identify the angiogenesis-related genes that were down-regulated in cad ecfcs and pearson's correlation were used to identify mirnas that were negatively correlated with the identified angiogenesis-related genes. rt-qpcr analysis of the five mirnas that negatively correlated with the down-regulated angiogenesis-related genes in plasma and ecfc of cad patients showed mir-146a-5p and mir-146b-5p up-regulation compared to healthy control. knockdown of mir-146a-5p or mir-146b-5p in cad ecfcs enhanced migration and tube formation activity in diseased ecfcs. contrarily, overexpression of mir-146a-5p or mir-146b-5p in healthy ecfc repressed migration and tube formation in ecfcs. targetscan analysis showed that mir-146a-5p and mir-146b-5p target many of the angiogenesis-related genes that were down-regulated in cad ecfcs. knockdown of mir-146a-5p or mir-146b-5p restores cav1 and rhoj levels in cad ecfcs. reporter assays confirmed the direct binding and repression of mir-146a-5p and mir-146b-5p to the 3'-utr of mrna of rhoj, a positive regulator of angiogenic potential in endothelial cells. consistently, rhoj knockdown inhibited the migration and tube formation ability in ecfcs. collectively, we discovered the dysregulation of mir-146a-5p/rhoj and mir-146b-5p/rhoj axis in the plasma and ecfcs of cad patients that could be used as biomarkers or therapeutic targets for cad and other angiogenesis-related diseases.",1
"the first step in the replication of the plus-stranded poliovirus rna is the synthesis of a complementary minus strand. this process is initiated by the covalent attachment of ump to the terminal protein vpg, yielding vpgpu and vpgpupu. we have previously shown that these products can be made in vitro in a reaction that requires only synthetic vpg, utp, poly(a), purified poliovirus rna polymerase 3d(pol), and mg(2+) (a. v. paul, j. h. van boom, d. filippov, and e. wimmer, nature 393:280-284, 1998). since such a poly(a)-dependent process cannot confer sufficient specificity to poliovirus rna replication, we have developed a new assay to search for a viral rna template in conjunction with viral or cellular factors that could provide this function. we have now discovered a small rna hairpin in the coding region of protein 2c as the site in pv1(m) rna that is used as the primary template for the in vitro uridylylation of vpg. this hairpin has recently been described in poliovirus rna as being an essential structure for the initiation of minus strand rna synthesis (i. goodfellow, y. chaudhry, a. richardson, j. meredith, j. w. almond, w. barclay, and d. j. evans, j. virol. 74:4590-4600, 2000). the uridylylation reaction either with transcripts of cre(2c) rna or with full-length pv1(m) rna as the template is strongly stimulated by the addition of purified viral protein 3cd(pro). deletion of the cre(2c) rna sequences from minigenomes eliminates their ability to serve as template in the reaction. a similar signal in the coding region of vp1 in hrv14 rna (k. l. mcknight and s. m. lemon, rna 4:1569-1584, 1998) and the poliovirus cre(2c) can be functionally exchanged in the assay. the mechanism by which the vpgpupu precursor, made specifically on the cre(2c) template, might be transferred to the site where it serves as primer for poliovirus rna synthesis, remains to be determined.",1
"the replication and infectivity of the lipotropic hepatitis c virus (hcv) are regulated by cellular lipid status. among differentially expressed micrornas (mirnas), we found that mir-27a was preferentially expressed in hcv-infected liver over hepatitis b virus (hbv)-infected liver. gene expression profiling of huh-7.5 cells showed that mir-27a regulates lipid metabolism by targeting the lipid synthetic transcription factor rxrα and the lipid transporter atp-binding cassette subfamily a member 1. in addition, mir-27a repressed the expression of many lipid metabolism-related genes, including fasn, srebp1, srebp2, pparα, and pparγ, as well as apoa1, apob100, and apoe3, which are essential for the production of infectious viral particles. mir-27a repression increased the cellular lipid content, decreased the buoyant density of hcv particles from 1.13 to 1.08 g/cm(3), and increased viral replication and infectivity. mir-27a overexpression substantially decreased viral infectivity. furthermore, mir-27a enhanced in vitro interferon (ifn) signaling, and patients who expressed high levels of mir-27a in the liver showed a more favorable response to pegylated ifn and ribavirin combination therapy. interestingly, the expression of mir-27a was upregulated by hcv infection and lipid overload through the adipocyte differentiation transcription factor c/ebpα. in turn, upregulated mir-27a repressed hcv infection and lipid storage in cells. thus, this negative feedback mechanism might contribute to the maintenance of a low viral load and would be beneficial to the virus by allowing it to escape host immune surveillance and establish a persistent chronic hcv infection.",1
"small regulatory rnas (srnas) are conserved among a wide range of bacteria. they modulate the translational efficiency of target mrnas through base-pairing with the help of rna chaperone hfq. the present study identified a novel srna, esr41 (enterohemorrhagic escherichia coli o157 small rna #41), from an intergenic region of an enterohemorrhagic e. coli (ehec) o157:h7 sakai-specific sequence that is not present in the nonpathogenic e. coli k-12. esr41 was detected as an rna molecule approximately 70 nucleotides long with a 3' gc-rich palindrome sequence followed by a long poly(u), which is a characteristic of rho-independent terminators and is also a structural feature required for the action of hfq. ehec o157 harboring a multicopy plasmid carrying the esr41 gene increased cell motility and the expression of flic, a gene encoding a major flagellar component. these results indicate that esr41 stimulates flic expression in ehec o157. furthermore, the increase in cell motility induced by esr41 was also observed in the e. coli k-12, suggesting that target genes controlled by esr41 are present in both ehec o157 and k-12.",1
"micrornas (mirnas) regulate the synthesis of cytokines in response to toll-like receptor (tlr) activation. our recent microarray study comparing normal and inflamed human dental pulps showed that mirna-181 (mir-181) family is differentially expressed in the presence of inflammation. prior studies have reported that the dental pulp, which is composed primarily of tlr4/2+ fibroblasts, expresses elevated levels of cytokines including interleukin-8 (il-8) when inflamed. in this study, we employed an in-vitro model to determine the role of the mirna-181 family in the tlr agonist-induced response in human fibroblasts. tlr4/2+ primary human dental pulp fibroblasts were stimulated with lipopolysaccharide from porphyromonas gingivalis (pg lps), a known oral pathogen, and il-8 and mir-181 expression measured. an inversely proportional relationship between il-8 and mir-181a was observed. in-silico analysis identified a mir-181a-binding site on the 3' untranslated region (utr) of il-8, which was confirmed by dual-luciferase assays. mir-181a directly binds to the 3'utr of il-8, an important inflammatory component of the immune response, and modulates its levels. this is the very first report demonstrating mir-181a regulation of il-8.",1
"the type iv secretion system encoded by the virb operon is required for full virulence of brucella sp., and the present study links the rna chaperone hfq to wild-type expression of virb in brucella abortus 2308. studies employing virb-lacz fusions, quantitative reverse transcription-pcr, and immunoblot analysis showed that both transcription and translation of virb are decreased in an isogenic hfq mutant compared to those in the parental strain. these results led to the hypothesis that hfq regulation of virb is mediated through an intermediate transcriptional regulator. subsequent experiments determined that expression of the gene encoding the putative brucella quorum-sensing regulator babr (also known as blxr), a known virb regulator, is also controlled by hfq at the posttranscriptional level, and a cis-acting element in the 5' untranslated region of the babr transcript responsible for this regulation was identified. consistent with its role as a virb regulator, recombinant brucella babr binds to the virb promoter region in electrophoretic mobility shift assays. however, experiments employing a babr mutant strain determined that babr is a repressor, not an activator, of virb transcription. these findings suggest that hfq regulates virb expression through both babr-dependent and babr-independent pathways.",1
"during the nucleolar maturation of eukaryotic ribosomal rnas, many selected uridines are converted into pseudouridine by a thus far undefined mechanism. the nucleolus contains a large number of small rnas (snornas) that share two conserved sequence elements, box h and aca. in this study, we demonstrate that site-specific pseudouridylation of rrnas relies on short ribosomal signal sequences that are complementary to sequences in box h/aca snornas. genetic depletion and reconstitution studies on yeast snr5 and snr36 snornas demonstrate that box h/aca snornas function as guide rnas in rrna pseudouridylation. these results define a novel function for snornas and further reinforce the idea that base pairing is the most common way to obtain specific substrate-""enzyme"" interactions during rrna maturation.",1
"micrornas (mirna) are small noncoding rnas that participate in diverse biological processes by suppressing target gene expression. altered expression of mir-21 has been reported in cancer. to gain insights into its potential role in tumorigenesis, we generated mir-21 knockout colon cancer cells through gene targeting. unbiased microarray analysis combined with bioinformatics identified cell cycle regulator cdc25a as a mir-21 target. mir-21 suppressed cdc25a expression through a defined sequence in its 3'-untranslated region. we found that mir-21 is induced by serum starvation and dna damage, negatively regulates g(1)-s transition, and participates in dna damage-induced g(2)-m checkpoint through down-regulation of cdc25a. in contrast, mir-21 deficiency did not affect apoptosis induced by a variety of commonly used anticancer agents or cell proliferation under normal cell culture conditions. furthermore, mir-21 was found to be underexpressed in a subset of cdc25a-overexpressing colon cancers. our data show a role of mir-21 in modulating cell cycle progression following stress, providing a novel mechanism of cdc25a regulation and a potential explanation of mir-21 in tumorigenesis.",1
"mir-27a regulates cell differentiation in a variety of diseases. however, whether and how mir-27a participates in laryngeal cancer cell differentiation remains unknown. therefore, we explored role and molecular mechanism of mir-27a in laryngeal cancer differentiation in the study. we found that mir-27a expression was inversely correlated with laryngeal cancer differentiation degree based on the clinical pathological diagnosis of each patient. mir-27 asignificantly rescued differentiation and inhibited β-catenin, lef1, oct4 and sox2 in wnt/β-catenin pathway in all-trans-retinoic acid (atra)-induced laryngeal cancer cells. bindings of rarα to mir-27a and mir-27a to gsk-3β were confirmed by chip and luciferase reporter assays, respectively. in conclusion, mir-27a is a negative regulator in laryngeal cancer differentiation. rarα-mediated mir-27a transcriptional inactivation releases the inhibition of mir-27a on gsk-3β leading to laryngeal cancer differentiation through gsk-3β-involved wnt/β-catenin pathway, suggesting that mir-27a is a usefully therapeutic target at least in atra-induced laryngeal cancer differentiation.",1
"micrornas (mirnas) are small noncoding rnas that control gene expression by inducing rna cleavage or translational inhibition. most human mirnas are intragenic and are transcribed as part of their hosting transcription units. we hypothesized that the expression profiles of mirna host genes and of their targets are inversely correlated and devised a novel procedure, hoctar (host gene oppositely correlated targets), which ranks predicted mirna target genes based on their anti-correlated expression behavior relative to their respective mirna host genes. hoctar is the first tool for systematic mirna target prediction that utilizes the same set of microarray experiments to monitor the expression of both mirnas (through their host genes) and candidate targets. we applied the procedure to 178 human intragenic mirnas and found that it performs better than currently available prediction softwares in pinpointing previously validated mirna targets. the high-scoring hoctar predicted targets were enriched in gene ontology categories, which were consistent with previously published data, as in the case of mir-106b and mir-93. by means of overexpression and loss-of-function assays, we also demonstrated that hoctar is efficient in predicting novel mirna targets and we identified, by microarray and qrt-pcr procedures, 34 and 28 novel targets for mir-26b and mir-98, respectively. overall, we believe that the use of hoctar significantly reduces the number of candidate mirna targets to be tested compared to the procedures based solely on target sequence recognition. finally, our data further confirm that mirnas have a significant impact on the mrna levels of most of their targets.",1
"the gtpase k-ras is involved in a variety of cellular processes such as differentiation, proliferation and survival. however, activating mutations, which frequently occur in many types of cancer, turn kras into one of the most prominent oncogenes. likewise, mir-200c is a key player in tumorigenesis functioning as a molecular switch between an epithelial, non-migratory, chemosensitive and a mesenchymal, migratory, chemoresistant state. while it has been reported that kras is modulated by several tumor suppressor mirnas, this is the first report on the regulation of kras by mir-200c, both playing a pivotal role in oncogenesis. we show that kras is a predicted target of mir-200c and that the protein expression of kras inversely correlates with the mir-200c expression in a panel of human breast cancer cell lines. kras was experimentally validated as a target of mir-200c by western blot analyses and luciferase reporter assays. furthermore, the inhibitory effect of mir-200c-dependent kras silencing on proliferation and cell cycle was demonstrated in different breast and lung cancer cell lines. thereby, the particular role of kras was dissected from the role of all the other mir-200c targets by specific knockdown experiments using sirna against kras. cell lines harboring an activating kras mutation were similarly affected by mir-200c as well as by the sirna against kras. however, in a cell line with wild-type kras only mir-200c was able to change proliferation and cell cycle. our findings suggest that mir-200c is a potent inhibitor of tumor progression and therapy resistance, by regulating a multitude of oncogenic pathways including the ras pathway. thus, mir-200c may cause stronger anti-tumor effects than a specific sirna against kras, emphasizing the potential role of mir-200c as tumor suppressive mirna.",1
"micrornas (mirs) play important roles in modulating gene expression during the processes of tumorigenesis and tumor development. previous studies have found that mir-145 is down-regulated in the stomach neoplasm and is related to tumor migration and invasion. however, both the molecular mechanism and function of mir-145 in gastric cancer remain unclear. the present study is the first demonstration of the significant down-regulation of mir-145 expression in infiltrative gastric cancer compared to expanding gastric cancer. additionally, correlation analyses revealed strong inverse correlations between mir-145 and fscn1 expression levels in infiltrative gastric cancer. furthermore, we demonstrated that mir-145 directly targets fscn1 and suppresses cell migration and invasion in gastric cancer. knocking down the expression of fscn1 led to the suppression of migration and invasion in gastric cancer cells, and re-expressing fscn1 in mir-145-overexpressing cells reversed their migration and invasion defects. thus, we concluded that mir-145 regulates cell migration and invasion in gastric cancer primarily by directly targeting fscn1.",1
"more and more mirnas have been shown to regulate gene expression in the heart and dysregulation of their expression has been linked to cardiovascular diseases including the mir-199a/214 cluster. however, the signature of circulating mir-214 expression and its possible roles during the development of heart failure has been less well studied. in this study, we elucidated the biological and clinical significance of mir-214 dysregulation in heart failure. firstly, circulating mir-214 was measured by quantitative pcr, and we found that mir-214 was upregulated in the serum of chronic heart failure patients, as well as in hypertrophic and failing hearts of humans and mice. adeno-associated virus serotype 9 (aav9)-mediated mir-214 silencing attenuates isoproterenol (iso) infusion-induced cardiac dysfunction and impairment of cardiac angiogenesis in mice. mechanistically, mir-214 overexpression reduces angiogenesis of huvecs by targeting xbp1, an important transcription factor of unfolded protein response, and xbp1 silencing decreases huvecs proliferation and angiogenesis similar to mir-214 overexpression. furthermore, ectopic expression of xbp1 enhances endothelial cells proliferation and tube formation, and reverses anti-angiogenic effect of mir-214 over expression. all these findings suggest that mir-214 is an important regulator of angiogenesis in heart in vitro and in vivo, likely via regulating the expression of xbp1, and demonstrate that mir-214 plays an essential role in the control/inhibition of cardiac angiogenesis.",1
"myocardial infarction (mi) is the leading cause of death worldwide. micrornas regulate the expression of their target genes, thus mediating a plethora of pathophysiological functions. recently, mirna-24 emerged as an important but controversial mirna involved in post-mi responses. here, we aimed at clarifying the effect of adenovirus-mediate intra-myocardial delivery of a decoy for mirna-24 in a mouse mi model and to investigate the impact of mirna-24 inhibition on angiogenesis and cardiovascular apoptosis. after mi induction, mirna-24 expression was lower in the peri-infarct tissue and its resident cardiomyocytes and fibroblasts; while it increased in endothelial cells (ecs). local adenovirus-mediated mirna-24 decoy delivery increased angiogenesis and blood perfusion in the peri-infarct myocardium, reduced infarct size, induced fibroblast apopotosis and overall improved cardiac function. notwithstanding these beneficial effects, mirna-24 decoy increased cardiomyocytes apoptosis. in vitro, mirna-24 inhibition enhanced ecs survival, proliferation and networking in capillary-like tubes and induced cardiomyocyte and fibroblast apoptosis. finally, we identified enos as a novel direct target of mir-24 in human cultured ecs and in vivo. our findings suggest that mirna-24 inhibition exerts distinct biological effects on ecs, cardiomyocytes and fibroblasts. the overall result of post-infarction local mirna-24 inhibition appears to be therapeutic.",1
"tissue fibrosis is a significant health issue associated with organ dysfunction and failure. increased deposition of collagen and other extracellular matrix (ecm) proteins in the interstitial area is a major process in tissue fibrosis. the microrna-29 (mir-29) family has been demonstrated as anti-fibrotic micrornas. our recent work showed that dysregulation of mir-29 contributes to the formation of cardiac fibrosis in animal models of uremic cardiomyopathy, whereas replenishing mir-29 attenuated cardiac fibrosis in these animals. however, excessive overexpression of mir-29 is a concern because micrornas usually have multiple targets, which could result in unknown and unexpected side effect. in the current study, we constructed a novel col1a1-mir-29b vector using collagen 1a1 (col1a1) promoter, which can strategically express mir-29b-3p (mir-29b) in response to increased collagen synthesis and reach a dynamic balance between collagen and mir-29b. our experimental results showed that in mouse embryonic fibroblasts (mef cells) transfected with col1a1-mir-29b vector, the mir-29b expression is about 1000 times less than that in cells transfected with cmv-mir-29b vector, which uses cytomegalovirus (cmv) as a promoter for mir-29b expression. moreover, tgf-β treatment increased the mir-29b expression by about 20 times in cells transfected with col1a1-mir-29b, suggesting a dynamic response to fibrotic stimulation. western blot using cell lysates and culture media demonstrated that transfection of col1a1-mir-29b vector significantly reduced tgf-β induced collagen synthesis and secretion, and the effect was as effective as the cmv-mir-29b vector. using rna-sequencing analysis, we found that 249 genes were significantly altered (180 upregulated and 69 downregulated, at least 2-fold change and adjusted p-value <0.05) after tgf-β treatment in mef cells transfected with empty vector. the kyoto encyclopedia of genes and genomes (kegg) pathway analysis using gage r-package showed that the top 5 upregulated pathways after tgf-β treatment were mostly fibrosis-related, including focal adhesion, ecm reaction, and tgf-β signaling pathways. as expected, transfection of col1a1-mir-29b or cmv-mir-29b vector partially reversed the activation of these pathways. we also analyzed the expression pattern of the top 100 mir-29b targeting genes in these cells using the rna-sequencing data. we identified that mir-29b targeted a broad spectrum of ecm genes, but the inhibition effect is mostly moderate. in summary, our work demonstrated that the col1a1-mir-29b vector can be used as a dynamic regulator of collagen and other ecm protein expression in response to fibrotic stimulation, which could potentially reduce unnecessary side effect due to excessive mir-29b levels while remaining an effective potential therapeutic approach for fibrosis.",1
"ubiquitin deconjugation of key signalling molecules by deubiquitinases (dubs) such as cylindromatosis (cyld), a20, and otu deubiquitinase 7b (otud7b) has emerged as an important regulatory mechanism in the downregulation of nf-κb signalling and homeostasis. however, how these serial negative regulations are simultaneously disrupted to result in constitutive activation of nf-κb signalling in cancers remains puzzling. here, we report that the mir-500 directly repressed the expression of cyld, otud7b, and the a20 complex component tax1-binding protein 1 (tax1bp1), leading to ubiquitin conjugation of receptor-interacting protein 1 (rip1) and sustained nf-ä¸b activation. furthermore, we found that mir-500 promoted gastric cancer cell proliferation, survival, and tumorigenicity. importantly, mir-500 was upregulated in gastric cancer and was highly correlated with malignant progression and poor survival. hence, we report the uncovering of a novel mechanism for constitutive nf-κb activation, indicating the potentially pivotal role of mir-500 in the progression of gastric cancer.",1
"the escherichia coli clpyq (hsluv) complex is an atp-dependent protease, and the clpq⁺y⁺ (hslv⁺u⁺) operon encodes two heat shock proteins, clpq and clpy, respectively. the transcriptional (op) or translational (pr) clpq⁺::lacz fusion gene was constructed, with the clpq⁺y⁺ promoter fused to a lacz reporter gene. the clpq⁺::lacz (op or pr) fusion gene was each crossed into lambda phage. the λlpq⁺::lacz⁺ (op), a transcriptional fusion gene, was used to form lysogens in the wild-type, rpoh or/and rpos mutants. upon shifting the temperature up from 30 ° c to 42 ° c, the wild-type λclpq⁺::lacz⁺ (op) demonstrates an increased β-galactosidase (βgal) activity. however, the βgal activity of clpq⁺::lacz⁺ (op) was decreased in the rpoh and rpoh rpos mutants but not in the rpos mutant. the levels of clpq⁺::lacz⁺ mrna transcripts correlated well to their βgal activity. similarly, the expression of the clpq⁺::lacz⁺ gene fusion was nearly identical to the clpq⁺y⁺ transcript under the in vivo condition. the clpq(m1)::lacz⁺, containing a point mutation in the -10 promoter region for rpoh binding, showed decreased βgal activity, independent of activation by rpoh. we conclude that rpoh itself regulates clpq⁺y⁺ gene expression. in addition, the clpq⁺y⁺ message carries a conserved 71 bp at the 5' untranslated region (5'utr) that is predicted to form the stem-loop structure by analysis of its rna secondary structure. the clpq(m2)δ40::lacz⁺, with a 40 bp deletion in the 5'utr, showed a decreased βgal activity. in addition, from our results, it is suggested that this stem-loop structure is necessary for the stability of the clpq⁺y⁺ message.",1
"rationale macrophage cholesterol homeostasis maintenance is the result of a balance between influx, endogenous synthesis, esterification/hydrolysis and efflux. excessive accumulation of cholesterol leads to foam cell formation, which is the major pathology of atherosclerosis. previous studies have shown that mir-27 (mir-27a and mir-27b) may play a key role in the progression of atherosclerosis. objective we set out to investigate the molecular mechanisms of mir-27a/b in intracellular cholesterol homeostasis. methods and results in the present study, our results have shown that the mir-27 family is highly conserved during evolution, present in mammals and directly targets the 3' utr of abca1, lpl, and acat1. apoa1, abcg1 and sr-b1 lacking mir-27 bind sites should not be influenced by mir-27 directly. mir-27a and mir-27b directly regulated the expression of endogenous abca1 in different cells. treatment with mir-27a and mir-27b mimics reduced apoa1-mediated cholesterol efflux by 33.08% and 44.61% in thp-1 cells, respectively. mir-27a/b also regulated hdl-mediated cholesterol efflux in thp-1 macrophages and affected the expression of apoa1 in hepg2 cells. however, mir-27a/b had no effect on total cellular cholesterol accumulation, but regulated the levels of cellular free cholesterol and cholesterol ester. we further found that mir-27a/b regulated the expression of lpl and cd36, and then affected the ability of thp-1 macrophages to uptake dil-oxldl. finally, we identified that mir-27a/b regulated cholesterol ester formation by targeting acat1 in thp-1 macrophages. conclusion these findings indicate that mir-27a/b affects the efflux, influx, esterification and hydrolysis of cellular cholesterol by regulating the expression of abca1, apoa1, lpl, cd36 and acat1.",1
"the majority of plants are able to form the arbuscular mycorrhizal (am) symbiosis in association with am fungi. during symbiosis development, plant cells undergo a complex reprogramming resulting in profound morphological and physiological changes. micrornas (mirnas) are important components of the regulatory network of plant cells. to unravel the impact of mirnas and mirna-mediated mrna cleavage on root cell reprogramming during am symbiosis, we carried out high-throughput (illumina) sequencing of small rnas and degradome tags of medicago truncatula roots. this led to the annotation of 243 novel mirnas. an increased accumulation of several novel and conserved mirnas in mycorrhizal roots suggest a role of these mirnas during am symbiosis. the degradome analysis led to the identification of 185 root transcripts as mature mirna and also mirna*-mediated mrna cleavage targets. several of the identified mirna targets are known to be involved in root symbioses. in summary, the increased accumulation of specific mirnas and the mirna-mediated cleavage of symbiosis-relevant genes indicate that mirnas are an important part of the regulatory network leading to symbiosis development.",1
"background glioblastoma is an extraordinarily aggressive disease that requires more effective therapeutic options. snail family zinc finger 1, dysregulated in many neoplasms, has been reported to be involved in gliomas. however, the biological mechanisms underlying snai1 function in gliomas need further investigation. methods quantitative real-time pcr was used to measure microrna-128 (mir-128) expression level and western blot was performed to detect protein expression in u87 and u251 cells and human brain tissues. cell cycle, cck-8, transwell and wound-healing assays were performed. dual-luciferase reporter assay was used for identifying the mechanism of snai1 and mir-128b regulation. the mechanism of mir-128 targeting sp1 was also tested by luciferase reporter assay. immunohistochemistry and in situ hybridisation staining were used for quantifying snai1, sp1 and mir-128 expression levels in human glioma samples. results the chinese glioma genome atlas (cgga) data revealed that snai1 was up-regulated in glioma and we confirmed the findings in normal and glioma tissues. snai1 depletion by shrna retarded the cell cycle and suppressed proliferation and invasion in glioma cell lines. the cgga data showed that the pearson correlation index between snai1 and mir-128 was negatively correlated. snai1 suppressed mir-128b expression by binding to the mir-128b specific promoter motif, and mir-128 targeted sp1 via binding to the 3'-untranslated region of sp1. moreover, introduction of mir-128 anti-sense oligonucleotide alleviated the cell cycle retardation, proliferation and invasion inhibition induced by snai1 shrna. immunohistochemistry and in situ hybridisation analysis of snai1, sp1 and mir-128 unraveled their expression levels and correlations in glioma samples. conclusions we propose that the snai1/mir-128/sp1 axis, which plays a vital role in glioma progression, may come to be a clinically relevant therapeutic target.",1
"background pvt1 was up-regulated in patients with gastric cancer (gc) and might be as a novel biomarker for predicting gc. however, the exact mechanism of pvt1 exerting functions in gc was still poorly understood. emerging evidence suggests that long noncoding rnas may act as endogenous microrna (mirna) sponges to bind to mirnas and regulate their function. aim this study aimed to determine the function of pvt1 on mir-152 expression in gc cells. methods the levels of pvt1 and mir-152 were determined in gc tissues by quantitative real-time pcr. the expression of mir-152 was detected in gc cells transfected with pvt1 plasmid or sipvt1. luciferase assay was performed to verify the regulation of mir-152 to cd151 or fgf2 expression and pvt1 to mir-152 expression. the effects of pvt1 on the expression of cd151 and fgf2 were evaluated by western blot. results pvt1 was up-regulated in gc tissues than that in the matched normal tissues, and mrna level of mir-152 was decreased. mir-152 was negatively associated with pvt1 expression in gc tissues. based on the in silico analysis, we found that pvt1 have three binding sequences for mir-152. moreover, pvt1 might inhibit the expression of mir-152 and increased the expression of cd151 and fgf2 through regulating mir-152. pvt1 was positively associated with cd151 and fgf2 expression in gc tissues. conclusions pvt1 might act as a ""sponge"" to inhibit mir-152 in gastric cancer cells. pvt1 is a promising molecular target to improve the diagnosis and therapy of gc.",1
"microrna (mirna) can function as tumor suppressors or oncogenes, and also as potential specific cancer biomarkers; however, there are few published studies on mirna in synovial sarcomas, and their function remains unclear. we transfected the oncomir mirna precursor virus library into synovial sarcoma fuji cells followed by a colony formation assay to identify mirnas to confer an aggressive tumorigenicity, and identified mir-17-5p from the large colonies. mir-17 was found to be induced by a chimeric oncoprotein ss18-ssx specific for synovial sarcoma, and all examined cases of human synovial sarcoma expressed mir-17, even at high levels in several cases. overexpression of mir-17 in synovial sarcoma cells, fuji and hs-syii, increased colony forming ability in addition to cell growth, but not cell motility and invasion. tumor volume formed in mice in vivo was significantly increased by mir-17 overexpression with a marked increase of mib-1 index. according to pictar and miranda algorithms, which predicted cdkn1a (p21) as a putative target of mir-17, a luciferase assay was performed and revealed that mir-17 directly targets the 3'-utr of p21 mrna. indeed, p21 protein level was remarkably decreased by mir-17 overexpression in a p53-independent manner. it is noteworthy that mir-17 succeeded in suppressing doxorubicin-evoked higher expression of p21 and conferred the drug resistance. meanwhile, introduction of anti-mir-17 in fuji and hs-syii cells significantly decreased cell growth, consistent with rescued expression of p21. taken together, mir-17 promotes the tumor growth of synovial sarcomas by post-transcriptional suppression of p21, which may be amenable to innovative therapeutic targeting in synovial sarcoma.",1
"background the mir-513 subfamily belongs to an x-linked primate-specific mir506-514 cluster. across primate species, there have been several duplication events and different species each possess a variety of mir-513 copies, indicating it underwent rapid evolution. evidence suggests that this subfamily is preferentially expressed in the testis, but otherwise, to date, the evolutionary history and functional significance of this mirna subfamily has remained largely unexplored. results we analyzed the evolutionary pattern of gene duplications and their functional consequence for the mir-513 subfamily in primates. sequence comparisons showed that the duplicated copies of mir-513 were derived from transposable element (mer91c). moreover, duplication events of the mir-513 subfamily seem to have occurred independently in platyrrhini (new world monkeys) and catarrhini (old world monkeys, apes and humans) after they diverged. different copies of the mir-513 subfamily (mir-513a/b/c) have different seed sequences, due to after-duplication sequence divergences, which eventually led to functional divergences. the results of functional assays indicated that mir-513b could inhibit the expression of its target gene, the down-regulator of transcription 1 (dr1) at both the mrna and protein levels. in the developing testis of rhesus macaques, we observed a temporal coupling of expression levels between mir-513b and dr1, suggesting that mir-513b could affect male sexual maturation by negatively regulating the development-stage related functioning of dr1. conclusions the mir-513 subfamily underwent multiple independent gene duplications among five different lineages of primates. the after-duplication sequence divergences among the different copies of mir-513 led to functional divergence of these copies in primates.",1
"stem cell differentiation is modulated by several key molecules, including cytokines, hormones, and engineered peptides. emerging evidence suggests that microrna has potential applications in stem cell engineering, such as in osteoblastic differentiation. micrornas (mirnas) bind to the 3'-untranslated region (utr) sequence of target mrna, thereby attenuating protein synthesis. our goal was to evaluate the delivery of mirna, i.e., mirna-29b, to stem cells to promote osteoblastic differentiation because this mirna is known to target anti-osteogenic factors gene expression. despite the important role of mirnas, their application has been limited due to poor cell/tissue penetration. the authors attempted to overcome this limitation by using a cell-penetrating peptide (cpp) carrier. herein, the arginine-rich cpp, called the lowmolecular weight protamine (lmwp), is the sequence from natural protamine. we worked out the difficult problem to transfect into hmscs by the complex with lmwp, and then we investigated synthetic double-stranded mir-29b could be induced osteoblast differentiation.",1
"background various micrornas (mirnas) are up- or downregulated in tumors. however, the repression of cognate mirna targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. to define mirna targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired mirna-mrna expression data with a set of validated mirna targets and pathway inference. results to generate a biochemically-validated set of mirna-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (ago2-par-clip) in mcf7 cells. we then defined putative mirna-target interactions using a computational model, which ranked and selected additional targetscan-predicted interactions based on features of our ago2-par-clip binding-site data. we subselected modeled interactions according to the abundance of their constituent mirna and mrna transcripts in tumors, and we took advantage of the variability of mirna expression within molecular subtypes to detect mirna repression. interestingly, our data suggest that mirna families control subtype-specific pathways; for example, mir-17, mir-19a, mir-25, and mir-200b show high mirna regulatory activity in the triple-negative, basal-like subtype, whereas mir-22 and mir-24 do so in the her2 subtype. an independent dataset validated our findings for mir-17 and mir-25, and showed a correlation between the expression levels of mir-182 targets and overall patient survival. pathway analysis associated mir-17, mir-19a, and mir-200b with leukocyte transendothelial migration. conclusions we combined par-clip data with patient expression data to predict regulatory mirnas, revealing potential therapeutic targets and prognostic markers in breast cancer.",1
"the developmental and evolutionary mechanisms behind the emergence of human-specific brain features remain largely unknown. however, the recent ability to compare our genome to that of our closest relative, the chimpanzee, provides new avenues to link genetic and phenotypic changes in the evolution of the human brain. we devised a ranking of regions in the human genome that show significant evolutionary acceleration. here we report that the most dramatic of these 'human accelerated regions', har1, is part of a novel rna gene (har1f) that is expressed specifically in cajal-retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. har1f is co-expressed with reelin, a product of cajal-retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. har1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.",1
"the androgen receptor (ar) stimulates and represses gene expression to promote the initiation and progression of prostate cancer. here, we report that androgen represses the mir-99a/let7c/125b-2 cluster through ar and anti-androgen drugs block the androgen-repression of the mirna cluster. ar directly binds to the host gene of the mir-99a/let7c/125b-2 cluster, linc00478. expression of the cluster is repressed or activated by chromatin remodelers ezh2 or jmjd3 in the presence or absence of androgen, respectively. bioinformatics analysis reveals a significant enrichment of targets of mir-99a, let-7c and mir-125b in androgen-induced gene sets, suggesting that downregulation of the mir-99a/let7c/125b-2 cluster by androgen protects many of their target mrnas from degradation and indirectly assists in the gene induction. we validated the hypothesis with 12 potential targets of the mir-99a/let7c/125b-2 cluster induced by androgen: 9 out of the 12 mrnas are downregulated by the microrna cluster. to ascertain the biological significance of this hypothesis, we focused on igf1r, a known prostate cancer growth factor that is induced by androgen and directly targeted by the mir-99a/let7c/125b-2 cluster. the androgen-induced cell proliferation is ameliorated to a similar extent as anti-androgen drugs by preventing the repression of the micrornas or induction of igf1r in androgen-dependent prostate cancer cells. expression of a microrna-resistant form of igf1r protects these cells from inhibition by the mir-99a/let7c/125b-2 cluster. these results indicate that a thorough understanding of how androgen stimulates prostate cancer growth requires not only an understanding of genes directly induced/repressed by ar, but also of genes indirectly induced by ar through the repression of key micrornas.",1
"micrornas (mirnas) are a class of short ( approximately 22-nt) noncoding rna molecules that downregulate expression of their mrna targets. since their discovery as regulators of developmental timing in caenorhabditis elegans, hundreds of mirnas have been identified in both animals and plants. here, we report a technique for visualizing detailed mirna expression patterns in mouse embryos. we elucidate the tissue-specific expression of several mirnas during embryogenesis, including two encoded by genes embedded in homeobox (hox) clusters, mir-10a and mir-196a. these two mirnas are expressed in patterns that are markedly reminiscent of those of hox genes. furthermore, mir-196a negatively regulates hoxb8, indicating that its restricted expression pattern probably reflects a role in the patterning function of the hox complex.",1
"the expression of the phosphate transporter pho84 in fission yeast schizosaccharomyces pombe is repressed in phosphate-rich medium and induced during phosphate starvation. two other phosphate-responsive genes in s. pombe ( pho1 and tgp1 ) had been shown to be repressed in cis by transcription of a long noncoding (lnc) rna from the upstream flanking gene, but whether pho84 expression is regulated in this manner is unclear. here, we show that repression of pho84 is enforced by transcription of the spbc8e4.02c locus upstream of pho84 to produce a lncrna that we name prt2 ( p ho - r epressive t ranscript 2). we identify two essential elements of the prt2 promoter, a homold box and a tata box, mutations of which inactivate the prt2 promoter and de-repress the downstream pho84 promoter under phosphate-replete conditions. we find that prt2 promoter inactivation also elicits a cascade effect on the adjacent downstream prt (lncrna) and pho1 (acid phosphatase) genes, whereby increased pho84 transcription down-regulates prt lncrna transcription and thereby de-represses pho1 our results establish a unified model for the repressive arm of fission yeast phosphate homeostasis, in which transcription of prt2 , prt , and nc-tgp1 lncrnas interferes with the promoters of the flanking pho84 , pho1 , and tgp1 genes, respectively.",1
"coordinate control of t cell proliferation, survival, and differentiation are essential for host protection from pathogens and cancer. long-lived memory cells, whose precursors are formed during the initial immunological insult, provide protection from future encounters, and their generation is the goal of many vaccination strategies. micrornas (mirnas) are key nodes in regulatory networks that shape effective t cell responses through the fine-tuning of thousands of genes. here, using compound conditional mutant mice to eliminate mir-15/16 family mirnas in t cells, we show that mir-15/16 restrict t cell cycle, survival, and memory t cell differentiation. high throughput sequencing of rna isolated by cross-linking immunoprecipitation of ago2 combined with gene expression analysis in mir-15/16-deficient t cells indicates that these effects are mediated through the direct inhibition of an extensive network of target genes within pathways critical to cell cycle, survival, and memory.",1
"micrornas (mirs) regulate inflammation and bmp antagonists, thus they have potential uses as therapeutic reagents. however, the molecular function of mir-200c in modulating proinflammatory and bone metabolic mediators and osteogenic differentiation is not known. after mir-200c was transduced into a human embryonic palatal mesenchyme (hepm) (a cell line of preosteoblasts), using lentiviral vectors, the resulting mir-200c overexpression increased osteogenic differentiation biomarkers, including osteocalcin (ocn) transcripts and calcium content. mir-200c expression also down-regulated interleukin (il)-6, il-8, and chemokine (c-c motif) ligand (ccl)-5 under lipopolysaccharide (lps) stimulation and increased osteoprotegerin (opg) in these cells. mir-200c directly regulates the expression of il-6, il-8 and ccl-5 transcripts by binding to their 3'utrs. a plasmid-based mir-200c inhibitor effectively reduces their binding activities. additionally, mir-200c delivered using polyethylenimine (pei) nanoparticles effectively inhibits il-6, il-8 and ccl-5 in primary human periodontal ligament fibroblasts and increases the biomarkers of osteogenic differentiation in human bone marrow mesenchymal stem cells (mscs), including calcium content, alp, and runx2. these data demonstrate that mir-200c represses il-6, il-8 and ccl-5 and improves osteogenic differentiation. mir-200c may potentially be used as an effective means to prevent periodontitis-associated bone loss by arresting inflammation and osteoclastogenesis and enhancing bone regeneration.",1
"angiogenesis is essential for recovery from various neurovascular diseases, such as ischemic stroke. previous studies have revealed the regulatory role of micrornas in angiogenesis in various types of cancer cells. however, the role of mir-487b in angiogenesis and how it regulates the angiogenic process of endothelial cells remain unclear. in this study, we found mir-487b was up-regulated in the plasma of ischemic stroke patients. further, over-expression of mir-487b enhanced cell proliferation, migration, invasion and tube formation in human umbilical vein endothelial cells. using bioinformatic analysis, we found a putative binding site of mir-487b in the 3' untranslated regions of thrombospondin 1 mrna, an endogenous inhibitor of angiogenesis. this direct binding was confirmed by luciferase assay. these results demonstrate that mir-487b regulates angiogenesis by directly targeting thbs1 in huvecs, indicating that mir-487b may contribute to angiogenesis and the functional recovery from ischemic stroke. mir-487b could represent a potential therapeutic option for neurovascular disease.",1
"background micrornas have emerged as important gene regulators and are recognized as important molecules in carcinogenesis. however, the effects of microrna-1303 (mir-1303) on gastric cancer (gc) cells and the upstream regulation of gc-associated claudin-18 gene (cldn18) remain unclear. mir-1303 may be involved in the tumorigenesis of gc by targeting cldn18. aims the purpose of this study was to explore the effect of mir-1303 targeting of cldn18 on the proliferation, migration and invasion of human gc cells. methods the expression of mir-1303 and claudin-18 in gc tissues and gastric cancer cell lines were detected by qrt-pcr and western blotting, respectively. cck8 and colony formation assays were performed to study the influence of mir-1303 on the proliferation of the gc cell lines. transwell and wound-healing assays were carried out to investigate the effect of mir-1303 on the invasion and migration of gc cell lines. luciferase reporter assays, restore assays and western blotting were used to demonstrate whether cldn18 is a direct target of mir-1303. results mir-1303 was significantly overexpressed whereas claudin-18 was downregulated in gc tissues and cell lines, which was significantly associated with tumor size, location invasion, histologic type and tumor-node-metastasis stage. cell proliferation rates were reduced, and cell invasion and migratory ability was significantly restricted in mir-1303 inhibitor-transfected groups. mir-1303 could bind to the putative binding sites in cldn18 mrna 3'-utr and visibly lower the expression of claudin-18. the introduction of claudin-18 without 3'-utr restored the mir-1303 promoting migration function. conclusions downregulation of mir-1303 can inhibit proliferation, migration and invasion of gc cells by targeting cldn18.",1
"preeclampsia is a pregnancy-specific syndrome mainly characterized by hypertensive disorder and proteinuria after gestational weeks 20. so far the etiology of preeclampsia remains unclear. we previously reported that preeclamptic placentas exhibited decreased mrna expression and hypermethylation in promoter region of the paternally imprinted h19 gene compared with normal placentas. h19 has recently been identified to encode the precursor of mir-675, indicating a possible novel functional pathway of the imprinting gene. the aim of the present study was to identify the roles of h19 gene via mir-675 pathway in human trophoblast cells, and to figure out the involvement of this pathway in pathogenesis of preeclampsia. knockdown of h19 gene or inhibition of mir-675 exhibited similar proliferation-promoting effect in human trophoblastic jeg-3 cells. target gene prediction in combination with luciferase assay revealed that mir-675 could directly downregulate nodal modulator 1 (nomo1) protein expression by binding to 3'-utr sequence of nomo1. overexpression of nomo1 in jeg-3 cells could rescue mir-675-surppressed cell proliferation and phosphorylation of smad2, while nodal had additive effect with mir-675 in suppression cell proliferation and activation of smad2. in early-onset preeclamptic placentas, expression levels of h19 gene and mir-675 were appreciably lower, while nomo1 protein level was higher than those in normal placentas. taken together, our data suggested that h19 gene could inhibit human trophoblast cell proliferation via encoding mir-675 that targeted nomo1, and aberrantly lowered expression of h19 in placenta may participate in the excessive proliferation of trophoblast cells observed in early-onset severe preeclampsia by downregulating mir-675 which targets nomo1 and interferes with nodal signaling.",1
"micrornas play key roles during ovary development, with emerging evidence suggesting that mir-202-5p is specifically expressed in female animal gonads. granulosa cells (gcs) are somatic cells that are closely related to the development of female gametes in mammalian ovaries. however, the biological roles of mir-202-5p in gcs remain unknown. here, we show that mir-202-5p is specifically expressed in gcs and accumulates in extracellular vesicles (evs) from large growth follicles in goat ovaries. in vitro assays showed that mir-202-5p induced apoptosis and suppressed the proliferation of goat gcs. we further revealed that mir-202-5p is a functional mirna that targets the transforming growth factor-beta type ii receptor ( tgfβr2 ). mir-202-5p attenuated tgf-β/smad signaling through the degradation of tgfβr2 at both the mrna and protein level, decreasing p-smad3 levels in gcs. moreover, we verified that steroidogenic factor 1 (sf1) is a transcriptional factor that binds to the promoters of mir-202 and cytochrome p450 family 19 subfamily a member 1 ( cyp19a1 ) through luciferase reporter and chromatin immunoprecipitation (chip) assays. that contributed to positive correlation between mir-202-5p and cyp19a1 expression and estradiol (e2) release. furthermore, sf1 repressed tgfβr2 and p-smad3 levels in gcs through the transactivation of mir-202-5p. taken together, these results suggest a mechanism by which mir-202-5p regulates canonical tgf-β/smad signaling through targeting tgfβr2 in gcs. this provides insight into the transcriptional regulation of mir-202 and cyp19a1 during goat ovarian follicular development.",1
"increasing evidence supports the association of catenin-δ1 (ctnnd1, p120ctn) with tumour development and progression. however, the mechanism and clinical significance of ctnnd1 deregulation in gastric cancer remain unknown. the expression level and cellular localization of ctnnd1 were determined by immunohistochemistry in 126 human gastric cancer and 50 non-tumourous tissues. the cellular localization of ctnnd1 and epithelial cadherin (e-cadherin) were detected by immunofluorescence. cell proliferation, apoptosis, migration and invasion assays were performed to assess the effect of ctnnd1 cdna or ctnnd1 sirna transfection on gastric cancer cells. luciferase assay, western blot analysis and in vivo assays were used to determine whether ctnnd1 could be regulated by mir-145. the results demonstrate that the cytoplasmic localization of ctnnd1 protein, rather than expression level, was indicative of higher clinical stage, positive lymph node metastasis and poorer prognosis in gastric cancers. ctnnd1 could promote gastric cancer cell migration and invasion with little effect on cellular proliferation and apoptosis. ctnnd1 was proved to be a direct target gene for mir-145. besides suppressing cytoplasmic ctnnd1 expression, mir-145 could recover the membranous localization of ctnnd1 and e-cadherin. we conclude that cytoplasmic ctnnd1 can serve as an independent prognostic factor for patients with gastric cancers. mir-145 inhibits invasion of gastric cancer cells not only by down-regulating cytoplasmic ctnnd1 expression but also by inducing the translocation of ctnnd1 and e-cadherin from the cytoplasm to the cell membrane through down-regulating n-cadherin.",1
"background the 14-3-3 family of proteins have been reported to play an important role in development in various mouse models, but the context specific developmental functions of 14-3-3ζ remain to be determined. in this study, we identified a context specific developmental function of 14-3-3ζ. results targeted deletion of 14-3-3ζ in the c57bl/6j murine genetic background led to neonatal lethality due to respiratory distress and could be rescued by out-breeding to the cd-1 or backcrossing to the fvb/nj congenic background. histological analysis of lung sections from 18.5 days post coitum embryos (dpc) showed that 14-3-3ζ-/- lung development is arrested at the pseudoglandular stage and exhibits vascular defects. the expression of mir-126, an endothelial-specific mirna known to regulate lung vascular integrity was down-regulated in the lungs of the 14-3-3ζ-/- embryos in the c57bl/6j background as compared to their wild-type counterparts. loss of 14-3-3ζ in endothelial cells inhibited the angiogenic capability of the endothelial cells as determined by both trans-well migration assays and tube formation assays and these defects could be rescued by re-expressing mir-126. mechanistically, loss of 14-3-3ζ led to reduced erk1/2 phosphorylation resulting in attenuated binding of the transcription factor ets2 on the mir-126 promoter which ultimately reduced expression of mir-126. conclusion our data demonstrates that mir-126 is an important angiogenesis regulator that functions downstream of 14-3-3ζ and downregulation of mir-126 plays a critical role in 14-3-3ζ-loss induced defects in lung vasculature in the c57bl/6j genetic background.",1
"nrf2 plays pivotal roles in coordinating the antioxidant response and maintaining redox homeostasis. nrf2 expression is exquisitely regulated; nrf2 expression is suppressed under unstressed conditions but strikingly induced under oxidative stress. previous studies showed that stress-induced nrf2 up-regulation results from both the inhibition of nrf2 degradation and enhanced nrf2 translation. in the present study, we elucidate the mechanism underlying translational control of nrf2. an internal ribosomal entry site (ires) was identified within the 5' untranslated region of human nrf2 mrna. the ires(nrf2) contains a highly conserved 18s rrna binding site (rbs) that is required for internal initiation. this ires(nrf2) also contains a hairpin structured inhibitory element (ie) located upstream of the rbs. deletion of this ie remarkably enhanced translation. significantly, treatment of cells with hydrogen peroxide (h(2)o(2)) and phyto-oxidant sulforaphane further stimulated ires(nrf2)-mediated translation initiation despite the attenuation of global protein synthesis. polyribosomal profile assay confirmed that endogenous nrf2 mrnas were recruited into polysomal fractions under oxidative stress conditions. collectively, these data demonstrate that nrf2 translation is suppressed under normal conditions and specifically enhanced upon oxidant exposure by internal initiation, and provide a mechanistic explanation for translational control of nrf2 by oxidative stress.",1
"micrornas regulate networks of genes to orchestrate cellular functions. mir-125b, the vertebrate homologue of the caenorhabditis elegans microrna lin-4, has been implicated in the regulation of neural and hematopoietic stem cell homeostasis, analogous to how lin-4 regulates stem cells in c. elegans. depending on the cell context, mir-125b has been proposed to regulate both apoptosis and proliferation. because the p53 network is a central regulator of both apoptosis and proliferation, the dual roles of mir-125b raise the question of what genes in the p53 network might be regulated by mir-125b. by using a gain- and loss-of-function screen for mir-125b targets in humans, mice, and zebrafish and by validating these targets with the luciferase assay and a novel mirna pull-down assay, we demonstrate that mir-125b directly represses 20 novel targets in the p53 network. these targets include both apoptosis regulators like bak1, igfbp3, itch, puma, prkra, tp53inp1, tp53, zac1, and also cell-cycle regulators like cyclin c, cdc25c, cdkn2c, edn1, ppp1ca, sel1l, in the p53 network. we found that, although each mirna-target pair was seldom conserved, mir-125b regulation of the p53 pathway is conserved at the network level. our results lead us to propose that mir-125b buffers and fine-tunes p53 network activity by regulating the dose of both proliferative and apoptotic regulators, with implications for tissue stem cell homeostasis and oncogenesis.",1
"the transcription factor activator protein 1 (ap-1) is formed through the dimerization of immediate-early genes fos and jun family members. activator protein 1 is known as a pivotal regulator of major biological events such as cell proliferation, differentiation, organogenesis, memory formation, and apoptosis. during a search for micrornas (mirnas; small, endogenous, noncoding rnas that repress gene expression of target mrnas in animals posttranscriptionally) that are differentially expressed in the mouse paraventricular and supraoptic nuclei after 10 days of drinking 2% saline, one candidate microrna that is relatively highly expressed, mmu-mir-7b (mir-7b), was studied further because sequence analysis suggested a likely interaction with the 3' untranslated region of fos mrna. we show that mir-7b expression inhibits fos translation in vitro and that it and its host gene are prominently expressed in the pvn and other brain areas, including the suprachiasmatic nucleus. no effect on fos mrna levels was observed. normally, fos is expressed at low to undetectable levels in cells, but it shows rapid induction and decay after acute stimuli. various pathways have been identified through which fos family proteins are degraded; our results indicate a significant additional mechanism by which fos protein and activity may be regulated.",1
"eber2 is an abundant nuclear noncoding rna expressed by the epstein-barr virus (ebv). probing its possible chromatin localization by chart revealed eber2's presence at the terminal repeats (trs) of the latent ebv genome, overlapping previously identified binding sites for the b cell transcription factor pax5. eber2 interacts with pax5 and is required for the localization of pax5 to the trs. eber2 knockdown phenocopies pax5 depletion in upregulating the expression of lmp2a/b and lmp1, genes nearest the trs. knockdown of eber2 also decreases ebv lytic replication, underscoring the essential role of the trs in viral replication. recruitment of the eber2-pax5 complex is mediated by base-pairing between eber2 and nascent transcripts from the tr locus. the interaction is evolutionarily conserved in the related primate herpesvirus cehv15 despite great sequence divergence. using base-pairing with nascent rna to guide an interacting transcription factor to its dna target site is a previously undescribed function for a trans-acting noncoding rna.",1
"the hepatic low-density lipoprotein receptor (ldlr) pathway is essential for clearing circulating ldl cholesterol (ldl-c). whereas the transcriptional regulation of ldlr is well characterized, the post-transcriptional mechanisms that govern ldlr expression are just beginning to emerge. here we develop a high-throughput genome-wide screening assay to systematically identify micrornas (mirnas) that regulate ldlr activity in human hepatic cells. from this screen we identified and characterized mir-148a as a negative regulator of ldlr expression and activity and defined a sterol regulatory element-binding protein 1 (srebp1)-mediated pathway through which mir-148a regulates ldl-c uptake. in mice, inhibition of mir-148a increased hepatic ldlr expression and decreased plasma ldl-c. moreover, we found that mir-148a regulates hepatic expression of atp-binding cassette, subfamily a, member 1 (abca1) and circulating high-density lipoprotein cholesterol (hdl-c) levels in vivo. these studies uncover a role for mir-148a as a key regulator of hepatic ldl-c clearance through direct modulation of ldlr expression and demonstrate the therapeutic potential of inhibiting mir-148a to ameliorate an elevated ldl-c/hdl-c ratio, a prominent risk factor for cardiovascular disease.",1
"drosophila have served as a model for research on innate immunity for decades. however, knowledge of the post-transcriptional regulation of immune gene expression by micrornas (mirnas) remains rudimentary. in the present study, using small rna-seq and bioinformatics analysis, we identified 67 differentially expressed mirnas in drosophila infected with escherichia coli compared to injured flies at three time-points. furthermore, we found that 21 of these mirnas were potentially involved in the regulation of imd pathway-related genes. strikingly, based on uas-mirnas line screening and dual-luciferase assay, we identified that mir-9a and mir-981 could both negatively regulate drosophila antibacterial defenses and decrease the level of the antibacterial peptide, diptericin. taken together, these data support the involvement of mirnas in the regulation of the drosophila imd pathway.",1
"objective micrornas play key roles in modulating a variety of cellular processes by posttranscriptional regulation of their target genes. vascular endothelial growth factor (vegf), vegf receptor-2 (vegfr2), and fibroblast growth factor receptor-1 (fgfr1) were identified by bioinformatic approaches and subsequently validated as targets of microrna (mir)-16 and mir-424 in endothelial cells (ecs). methods and results mimetics of these micrornas reduced vegf, vegfr2, and fgfr1 expression, whereas specific antagonists enhanced their expression. expression of mature mir-16 and mir-424 was upregulated on vegf or basic fibroblast growth factor (bfgf) treatment. this upregulation was accompanied by a parallel increase in primary transcript (pri-mir)-16-1 and pri-mir-16-2 but not in pri-mir-424 levels, indicating a vegf/bfgf-dependent transcriptional and posttranscriptional regulation of mir-16 and mir-424, respectively. reduced expression of vegfr2 and fgfr1 by mir-16 or mir-424 overexpression regulated vegf and bfgf signaling through these receptors, thereby affecting the activity of downstream components of the pathways. functionally, mir-16 or mir-424 overexpression reduced proliferation, migration, and cord formation of ecs in vitro, and lentiviral overexpression of mir-16 reduced the ability of ecs to form blood vessels in vivo. conclusion we conclude that these mirnas fine-tune the expression of selected endothelial angiogenic mediators in response to these growth factors. altogether, these findings suggest that mir-16 and mir-424 play important roles in regulating cell-intrinsic angiogenic activity of ecs.",1
"accumulating evidence has implicated the deregluation of mirnas in tumorigenesis. previous studies have reported that microrna-195 (mir-195) is markedly down-regulated in human glioblastoma cells, compared with normal brain tissue, but the biological role of mir-195 in glioblastoma development is currently unknown. in this study, we define a tumor-suppressor role for mir-195 in human glioblastoma cells. over-expression of mir-195 in glioblastoma cell lines robustly arrested cell cycle progression and significantly repressed cellular invasion. we identified e2f3 and ccnd3 as functional downstream targets of mir-195 in glioblastoma cells. through knockdown studies, we demonstrated that e2f3 was the dominant effector of mir-195-mediated cell cycle arrest and that ccnd3 was a key mediator of mir-195-induced inhibition of glioblastoma cell invasion. furthermore, we showed that p27(kip1) was an important regulator downstream of ccnd3 and that the accumulation of p27(kip1) in the cytoplasm might be responsible for the mir-195-mediated cell invasion inhibition in glioblastoma cells. this work provides evidence for the initial mechanism by which mir-195 negatively regulates both the proliferation and invasion of glioblastoma cells, suggesting that the down-regulation of mir-195 might contribute to the malignant transformation of glioblastoma cells and could be a molecular signature associated with glioblastoma progression.",1
"micrornas comprise a novel group of gene regulators implicated in the development of different types of cancer; however, their role in primary pigmented nodular adrenocortical disease (ppnad) has not been investigated. ppnad is a bilateral adrenal hyperplasia often associated with carney complex, a multiple neoplasia syndrome; both disorders are caused by protein kinase a (pka) regulatory subunit type 1a (prkaria)-inactivating mutations. we identified a 44-microrna gene signature of ppnad after comparing ppnad with normal adrenal samples. specifically, 33 micrornas were up-regulated and 11 down-regulated in ppnad relative to normal tissues. these results were validated by stem loop real-time pcr analysis. comparison of microrna microarray data with clinicopathologic variables revealed a negative correlation (r = -0.9499) between let-7b expression and cortisol levels in patients with ppnad. integration of microrna microarray with serial analysis of gene expression data together with bioinformatic algorithm predictions revealed nine microrna-gene target pairs with a potential role in adrenal pathogenesis. using a ppnad cell line, we showed that mir-449 was up-regulated and identified its direct target, wnt1-inducible signaling pathway protein 2 (wisp2); in addition, pharmacologic inhibition of pka resulted in the up-regulation of mir-449 leading to the suppression of wisp2. overall, we investigated, for the first time, the microrna profile and its clinical significance in ppnad; these data also suggest that pka, via microrna regulation, affects the wnt signaling pathway, which through expression and clinical studies is suspected to be a primary mediator of prkar1a-related tumorigenesis.",1
"loss of the growth-suppressive effects of bone morphogenetic protein (bmp) signaling has been demonstrated to promote pulmonary arterial endothelial cell dysfunction and induce pulmonary arterial smooth muscle cell (pasmc) proliferation, leading to the development of pulmonary arterial hypertension (pah). micrornas (mirs) mediate higher order regulation of cellular function through coordinated modulation of mrna targets; however, mir expression is altered by disease development and drug therapy. here, we examined treatment-naive patients and experimental models of pah and identified a reduction in the levels of mir-140-5p. inhibition of mir-140-5p promoted pasmc proliferation and migration in vitro. in rat models of pah, nebulized delivery of mir-140-5p mimic prevented the development of pah and attenuated the progression of established pah. network and pathway analysis identified smad-specific e3 ubiquitin protein ligase 1 (smurf1) as a key mir-140-5p target and regulator of bmp signaling. evaluation of human tissue revealed that smurf1 is increased in patients with pah. mir-140-5p mimic or smurf1 knockdown in pasmcs altered bmp signaling, further supporting these factors as regulators of bmp signaling. finally, smurf1 deletion protected mice from pah, demonstrating a critical role in disease development. together, these studies identify both mir-140-5p and smurf1 as key regulators of disease pathology and as potential therapeutic targets for the treatment of pah.",1
"micrornas (mirnas) regulate the expression of target mrnas in plants and animals . plant mirna targets have been predicted on the basis of their extensive and often conserved complementarity to the mirnas , as well as on mirna overexpression experiments ; many of these target predictions have been confirmed by isolation of the products of mirna-directed cleavage. here, we present a transcriptome-wide experimental method, called ""degradome sequencing,"" to directly detect cleaved mirna targets without relying on predictions or overexpression. the 5' ends of polyadenylated, uncapped mrnas from arabidopsis were directly sampled, resulting in an empirical snapshot of the degradome. mirna-mediated-cleavage products were easily discerned from an extensive background of degraded mrnas, which collectively covered the majority of the annotated transcriptome. many previously known arabidopsis mirna targets were confirmed, and several novel targets were also discovered. quantification of cleavage fragments revealed that those derived from tas transcripts, which are unusual in their production of abundant secondary small interfering rnas (sirnas), accumulated to very high levels. a subset of secondary sirnas are also known to direct cleavage of targets in trans; degradome sequencing revealed many cleaved targets of these trans-acting sirnas (ta-sirnas). this empirical method is broadly applicable to the discovery and quantification of cleaved targets of small rnas without a priori predictions.",1
"hsa-mir-33a and hsa-mir-33b, intronic micrornas (mirnas) located within the sterol regulatory element-binding protein 2 and 1 genes (srebp-2 and -1), respectively, have recently been shown to regulate lipid homeostasis in concert with their host genes. although the functional role of mir-33a and -b has been highly investigated, the role of their passenger strands, mir-33a* and -b*, remains unclear. here, we demonstrate that mir-33a* and -b* accumulate to steady-state levels in human, mouse, and nonhuman primate tissues and share a similar lipid metabolism target gene network as their sister strands. analogous to mir-33, mir-33* represses key enzymes involved in cholesterol efflux (abca1 and npc1), fatty acid metabolism (crot and cpt1a), and insulin signaling (irs2). moreover, mir-33* also targets key transcriptional regulators of lipid metabolism, including src1, src3, nfyc, and rip140. importantly, inhibition of either mir-33 or mir-33* rescues target gene expression in cells overexpressing pre-mir-33. consistent with this, overexpression of mir-33* reduces fatty acid oxidation in human hepatic cells. altogether, these data support a regulatory role for the mirna* species and suggest that mir-33 regulates lipid metabolism through both arms of the mir-33/mir-33* duplex.",1
"anti-mirna antisense inhibitors (amos) have demonstrated their utility in mirna research and potential in mirna therapy. here we report a modified amo approach in which multiple antisense units are engineered into a single unit that is able to simultaneously silence multiple-target mirnas, the multiple-target amo or mtg-amo. we validated the technique with two separate mtg-amos: anti-mir-21/anti-mir-155/anti-mir-17-5p and anti-mir-1/anti-mir-133. we first verified the ability of the mtg-amos to antagonize the repressive actions of their target mirnas using luciferase reporter activity assays and to specifically knock down the levels of their target mirnas using real-time rt-pcr methods. we then used the mtg-amo approach to identify several tumor suppressors-tgfbi, apc and bcl2l11 as the target genes for oncogenic mir-21, mir-155 and mir-17-5p, respectively, and two cardiac ion channel genes hcn2 (encoding a subunit of cardiac pacemaker channel) and cacna1c (encoding the alpha-subunit of cardiac l-type ca(2+) channel) for the muscle-specific mir-1 and mir-133. we further demonstrated that the mtg-amo targeting mir-21, mir-155 and mir-17-5p produced a greater inhibitory effect on cancer cell growth, compared with the regular single-target amos. moreover, while using the regular single-target amos excluded hcn2 as a target gene for either mir-1 or mir-133, the mtg-amo approach is able to reveal hcn2 as the target for both mir-1 and mir-133. our findings suggest the mtg-amo as an improved approach for mirna target finding and for studying function of mirnas. this approach may find its broad application for exploring biological processes involving multiple mirnas and multiple genes.",1
"micrornas (mirnas) have been reported to be involved in many neurodegenerative diseases. the present study focused on the role of hsa-mir-144-3p in one of the neurodegenerative diseases, parkinson's disease (pd). our study showed a remarkable down-regulation of mir-144-3p expression in 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (mptp)-treated sh-sy5y cells. mir-144-3p was then overexpressed and silenced in human sh-sy5y cells by mirna-mimics and mirna-inhibitor transfections, respectively. furthermore, β-amyloid precursor protein (app) was identified as a target gene of mir-144-3p via a luciferase reporter assay. we found that mir-144-3p overexpression significantly inhibited the protein expression of app. since mitochondrial dysfunction has been shown to be one of the major pathological events in pd, we also focused on the role of mir-144-3p and app in regulating mitochondrial functions. our study demonstrated that up-regulation of mir-144-3p increased expression of the key genes involved in maintaining mitochondrial function, including peroxisome proliferator-activated receptor γ coactivator-1α (pgc-1α), nuclear respiratory factor 1 (nrf-1) and mitochondrial transcription factor a (tfam). moreover, there was also a significant increase in cellular atp, cell viability and the relative copy number of mtdna in the presence of mir-144-3p overexpression. in contrast, mir-144-3p silencing showed opposite effects. we also found that app overexpression significantly decreased atp level, cell viability, the relative copy number of mtdna and the expression of these three genes, which reversed the effects of mir-144-3p overexpression. taken together, these results show that mir-144-3p plays an important role in maintaining mitochondrial function, and its target gene app is also involved in this process.",1
"the pseudouridine at position 43 in vertebrate u2 snrna is one of the most conserved post-transcriptional modifications of spliceosomal snrnas; the equivalent position is pseudouridylated in u2 snrnas in different phyla including fungi, insects, and worms. pseudouridine synthase pus1p acts alone on u2 snrna to form this pseudouridine in yeast saccharomyces cerevisiae and mouse. furthermore, in s. cerevisiae , pus1p is the only pseudouridine synthase for this position. using an in vivo yeast cell system, we tested enzymatic activity of pus1p from the fission yeast schizosaccharomyces pombe , the worm caenorhabditis elegans , the fruit fly drosophila melanogaster , and the frog xenopus tropicalis we demonstrated that pus1p from c. elegans has no enzymatic activity on u2 snrna when expressed in yeast cells, whereas in similar experiments, position 44 in yeast u2 snrna (equivalent to position 43 in vertebrates) is a genuine substrate for pus1p from s. cerevisiae , s. pombe , drosophila , xenopus , and mouse. however, when we analyzed u2 snrnas from pus1 knockout mice and the pus1δ s. pombe strain, we could not detect any changes in their modification patterns when compared to wild-type u2 snrnas. in s. pombe , we found a novel box h/aca rna encoded downstream from the rpc10 gene and experimentally verified its guide rna activity for positioning ψ43 and ψ44 in u2 snrna. in vertebrates, we showed that scarna8 (also known as u92 scarna) is a guide for u2-ψ43 in addition to its previously established targets u2-ψ34/ψ44.",1
"mirna let-7e is involved in stem cell differentiation, and metalloproteinases are among its potential target genes. we hypothesized that the inhibitory action of let-7e on regulation of mmp9 expression could represent a crucial mechanism during differentiation of adipose-derived stem cells (ascs). ascs were differentiated with all-trans retinoic acid (atra) to promote differentiation, and the effect of let-7 silencing during differentiation was tested. results indicate that ascs cultured with atra differentiated into cells of the epithelial lineage. we found that ascs cultured with atra or transfected with mirna let-7e expressed epithelial markers such as cytokeratin-18 and early renal organogenesis markers such as pax2, wt1, wnt4 and megalin. conversely, the specific knockdown of mirna let-7e in ascs significantly decreased the expression of these genes, indicating its vital role during the differentiation process. using luciferase reporter assays, we also showed that mmp9 is a direct target of mirna let-7e. thus, our results suggest that mirna let-7e acts as a matrix metalloproteinase-9 (mmp9) inhibitor and differentiation inducer in ascs.",1
"micrornas (mirnas) act as important gene regulators in human genomes and their aberrant expression links to many malignancies. we previously identified a different characteristic mirna expression profile in cervical cancer from that in cervical normal tissues, including the downregulated mir-424. however, the role and mechanism of mir-424 in cervical cancer still remain unknown. here, we focused on identifying the tumor-suppressive function and clinical significance of mir-424 and exploring the mechanistic relevance by characterizing its target. we showed a significantly decreased expression of mir-424 in 147 cervical cancer tissues versus 74 cervical normal tissues by performing quantitative rt-pcr. in 147 cervical cancer tissue samples, low-level expression of mir-424 was positively correlated with poor tumor differentiation, advanced clinical stage, lymph node metastasis and other poor prognostic clinicopathological parameters. further in vitro observations showed that enforced expression of mir-424 inhibited cell growth by both enhancing apoptosis and blocking g1/s transition, and suppressed cell migration and invasion in two human cervical cancer cell lines, siha and caski, implying that mir-424 functions as a tumor suppressor in the progression of cervical cancer. interestingly, overexpression of mir-424 inhibited the expression of protein checkpoint kinase 1 (chk1) and phosphorylated chk1 (p-chk1) at residues ser345 and decreased the activity of luciferase-reporter containing the 3'-untranslated region (utr) of chk1 with predicted mir-424-binding site. moreover, mir-424 expression levels were inversely correlated with chk1 and p-chk1 protein levels in both cervical cancer and normal tissues. furthermore, rnai-mediated knockdown of chk1 decreased matrix metalloproteinase 9 expression and phenocopied the tumor suppressive effects of mir-424 in cell models. taken together, our results identify a crucial tumor suppressive role of mir-424 in the progression of cervical cancer at least partly via upreglating the expression of chk1 and p-chk1, and suggest that mir-424 might be a candidate of prognostic predictor or an anticancer therapeutic target for cervical cancer patients.",1
"the terminal half of the 5' untranslated region (utr) in the (+)-strand rna genome of tomato bushy stunt virus was analyzed for possible roles in viral rna replication. computer-aided thermodynamic analysis of secondary structure, phylogenetic comparisons for base-pair covariation, and chemical and enzymatic solution structure probing were used to analyze the 78 nucleotide long 5'-terminal sequence. the results indicate that this sequence adopts a branched secondary structure containing a three-helix junction core. the t-shaped domain (tsd) formed by this terminal sequence is closed by a prominent ten base-pair long helix, termed stem 1 (s1). deletion of either the 5' or 3' segment forming s1 (coordinates 1-10 or 69-78, respectively) in a model subviral rna replicon, i.e. a prototypical defective interfering (di) rna, reduced in vivo accumulation levels of this molecule approximately 20-fold. compensatory-type mutational analysis of s1 within this replicon revealed a strong correlation between formation of the predicted s1 structure and efficient di rna accumulation. rna decay studies in vivo did not reveal any notable changes in the physical stabilities of di rnas containing disrupted s1s, thus implicating rna replication as the affected process. further investigation revealed that destabilization of s1 in the (+)-strand was significantly more detrimental to di rna accumulation than (-)-strand destabilization, therefore s1-mediated activity likely functions primarily via the (+)-strand. the essential role of s1 in di rna accumulation prompted us to examine the 5'-proximal secondary structure of a previously identified mutant di rna, rna b, that lacks the 5' utr but is still capable of low levels of replication. mutational analysis of a predicted s1-like element present within a cryptic 5'-terminal tsd confirmed the importance of the former in rna b accumulation. collectively, these data support a fundamental role for the tsd, and in particular its s1 subelement, in tombusvirus rna replication.",1
"micrornas (mirnas) are small noncoding rnas that exert their functions by targeting specific mrna sequences. many studies have demonstrated that mirnas are crucial for cancer progression, during which they can act as either oncogenes or tumor suppressors. previous research has shown that mir-335 is downregulated in breast cancer, and it has been shown to be a breast cancer suppressor. in addition, emerging evidence indicates that erythropoietin-producing hepatocellular a4 (epha4) is implicated in cancer cell proliferation, migration, and invasion. however, little is known about the relationship between mir-335 and epha4 in breast cancer. in the present study, we used bioinformatic and biochemical analyses to demonstrate that epha4 is a direct downstream target of mir-335 in human breast cancer mcf-7 and mda-mb-23 cells and revealed that mir-335 negatively regulates the expression of epha4 in these cells. further investigation revealed that mir-335 overexpression inhibits mcf-7 and mda-mb-231 cell proliferation and that this inhibition is attenuated by epha4 coexpression. similarly, mir-335 overexpression also inhibited growth and downregulated epha4 expression in tumors in nude mice. moreover, our results demonstrated that mir-335 overexpression suppresses migration and invasion in mcf-7 and mda-mb-231 cells, an effect that was reversed by epha4 overexpression. these findings confirmed that epha4 is a direct target gene of mir-335 and that mir-335 suppresses breast cancer cell proliferation and motility in part by directly inhibiting epha4 expression.",1
"emerging evidence highlights the role of the long noncoding rna (lncrna) kcnq1ot1 in fracture healing. osteoblast proliferation, migration, and survival are pivotal during this process. in this study, we aimed to improve our understanding of the regulatory role of lncrna kcnq1ot1 during osteoblast proliferation, migration, and survival. we searched the gene expression omnibus databases and lncbase experimental v.2 to identify key micrornas (mirnas) targets of kcnq1ot1. mir-701-3p was selected as a differentially expressed mirna and rna immunoprecipitation assays were performed to verify its interaction with kcnq1ot1. fibroblast growth factor receptor 3 (fgfr3) was also identified as a target of mir-701-3p. we further identified kcnq1ot1 as a competing endogenous rna of mir-701-3p that could influence osteoblast proliferation, migration, and apoptosis in vitro and in vivo. taken together, our results indicate that the kcnq1ot1/mir-701-3p/fgfr3 axis is an important regulator of osteoblast proliferation, migration, and apoptosis, and provide a new therapeutic avenue for fracture healing.",1
"background this study investigated how mir-21 expression is reflected in acute myocardial infarction and explored the role of mir-21 and the pten/vegf signaling pathway in cardiac microvascular endothelial cells. material and methods we used an in vivo lad rat model to simulate acute myocardial infarction. mir-21 mimics and mir-21 inhibitors were injected and transfected into model rats in order to alter mir-21 expression. cardiac functions were evaluated using echocardiographic measurement, elisa, and masson staining. in addition, lenti-pten and vegf sirna were transfected into cmec cells using standard procedures for assessing the effect of pten and vege on cell proliferation, apoptosis, and angiogenesis. mir-21, pten, and vegf expressions were examined by rt-pcr and western blot. the relationship between mir-21 and pten was determined by the luciferase activity assay. results we demonstrated that mir-21 bonded with the 3'-utr of pten and suppressed pten expressions. established models significantly induced cardiac infarct volume and endothelial injury marker expressions as well as mir-21 and pten expressions (p<0.05). mir-21 mimics exhibited significantly protective effects since they down-regulated both infarction size and injury marker expressions by increasing vegf expression and inhibiting pten expression (p<0.05). in addition, results from in vitro research show that lenti-pten and vegf sirna can notably antagonize the effect of mir-21 on cell proliferation, apoptosis, and angiogenesis (p<0.05). conclusions mir-21 exerts protective effects on endothelial injury through the pten/vegf pathway after acute myocardial infarction.",1
"fibroblast growth factor 1 (fgf-1) is a powerful angiogenic factor whose gene structure contains four promoters, giving rise to a process of alternative splicing resulting in four mrnas with alternative 5' untranslated regions (5' utrs). here we have identified, by using double luciferase bicistronic vectors, the presence of internal ribosome entry sites (iress) in the human fgf-1 5' utrs, particularly in leaders a and c, with distinct activities in mammalian cells. dna electrotransfer in mouse muscle revealed that the ires present in the fgf-1 leader a has a high activity in vivo. we have developed a new regulatable tet off bicistronic system, which allowed us to rule out the possibility of any cryptic promoter in the fgf-1 leaders. fgf-1 iress a and c, which were mapped in fragments of 118 and 103 nucleotides, respectively, are flexible in regard to the position of the initiation codon, making them interesting from a biotechnological point of view. furthermore, we show that fgf-1 iress a of murine and human origins show similar ires activity profiles. enzymatic and chemical probing of the fgf-1 ires a rna revealed a structural domain conserved among mammals at both the nucleotide sequence and rna structure levels. the functional role of this structural motif has been demonstrated by point mutagenesis, including compensatory mutations. these data favor an important role of iress in the control of fgf-1 expression and provide a new ires structural motif that could help ires prediction in 5' utr databases.",1
"microrna-224 (mir-224) is frequently over-expressed in liver and colorectal cancers. we and others have previously described the role of mir-224 over-expression in cell proliferation in vitro but we have yet to identify the relevant mir-224 direct target. in this study, we further demonstrated that mir-224 up-regulation promotes cell proliferation using both in vitro assays and in vivo tumor growth models. we systematically screened for high confidence mir-224 targets by overlapping in silico predicted targets from multiple algorithms and significantly down-regulated genes in mir-224-expressing cells from whole genome expression microarrays. a total of 72 high confidence mir-224 targets were identified and found to be enriched in various cancer-related processes. smad family member 4 (smad4) is experimentally validated as the direct cellular target through which mir-224 promotes cell proliferation. the clinical relevance of our experimental observations was supported by a statistically significant inverse correlation between mir-224 and smad4 transcript expression in tumor versus paired adjacent non-tumorous tissues from hcc patients (p<0.001, r= -0.45, r(2) =0.122). furthermore, mir-224 up-regulation and smad4 down-regulation is significantly associated with poorer patient survival (p<0.05). in summary, mir-224/smad4 pathway is a clinically relevant pathway to provide new insights in understanding hcc. (191 words).",1
"background the let-7 and lin-4 micrornas belong to a class of temporally expressed, noncoding regulatory rnas that function as heterochronic switch genes in the nematode c. elegans. heterochronic genes control the relative timing of events during development and are considered a major force in the rapid evolution of new morphologies. let-7 is highly conserved and in drosophila is temporally coregulated with the lin-4 homolog, mir-125. little is known, however, about their requirement outside the nematode or whether they universally control the timing of developmental processes. results we report the generation of a drosophila mutant that lacks let-7 and mir-125 activities and that leads to a pleiotropic phenotype arising during metamorphosis. we focus on two defects and demonstrate that loss of let-7 and mir-125 results in temporal delays in two distinct metamorphic processes: the terminal cell-cycle exit in the wing and maturation of neuromuscular junctions (nmjs) at adult abdominal muscles. we identify the abrupt (ab) gene, encoding a nuclear protein, as a bona fide let-7 target and provide evidence that let-7 governs the maturation rate of abdominal nmjs during metamorphosis by regulating ab expression. conclusions drosophila iet-7 and mir-125 mutants exhibit temporal misregulation of specific metamorphic processes. as in c. elegans, drosophila let-7 is both necessary and sufficient for the appropriate timing of a specific cell-cycle exit, indicating that its function as a heterochronic microrna is conserved. the ab gene is a target of let-7, and its repression in muscle is essential for the timing of nmj maturation during metamorphosis. our results suggest that let-7 and mir-125 serve as conserved regulators of events necessary for the transition from juvenile to adult life stages.",1
"fibroblasts can be directly reprogrammed into cardiomyocyte-like cells (icms) by overexpression of cardiac transcription factors or micrornas. however, induction of functional cardiomyocytes is inefficient, and molecular mechanisms of direct reprogramming remain undefined. here, we demonstrate that addition of mir-133a (mir-133) to gata4, mef2c, and tbx5 (gmt) or gmt plus mesp1 and myocd improved cardiac reprogramming from mouse or human fibroblasts by directly repressing snai1, a master regulator of epithelial-to-mesenchymal transition. mir-133 overexpression with gmt generated sevenfold more beating icms from mouse embryonic fibroblasts and shortened the duration to induce beating cells from 30 to 10 days, compared to gmt alone. snai1 knockdown suppressed fibroblast genes, upregulated cardiac gene expression, and induced more contracting icms with gmt transduction, recapitulating the effects of mir-133 overexpression. in contrast, overexpression of snai1 in gmt/mir-133-transduced cells maintained fibroblast signatures and inhibited generation of beating icms. mir-133-mediated snai1 repression was also critical for cardiac reprogramming in adult mouse and human cardiac fibroblasts. thus, silencing fibroblast signatures, mediated by mir-133/snai1, is a key molecular roadblock during cardiac reprogramming.",1
"like other cancers, aberrant gene regulation features significantly in hepatocellular carcinoma (hcc). micrornas (mirnas) were recently found to regulate gene expression at the post-transcriptional/translational levels. the expression profiles of 157 mirnas were examined in 19 hcc patients, and 19 up-regulated and 3 down-regulated mirnas were found to be associated with hcc. putative gene targets of these 22 mirnas were predicted in silico and were significantly enriched in 34 biological pathways, most of which are frequently dysregulated during carcinogenesis. further characterization of microrna-224 (mir-224), the most significantly up-regulated mirna in hcc patients, revealed that mir-224 increases apoptotic cell death as well as proliferation and targets apoptosis inhibitor-5 (api-5) to inhibit api-5 transcript expression. significantly, mir-224 expression was found to be inversely correlated with api-5 expression in hcc patients (p < 0.05). hence, our findings define a true in vivo target of mir-224 and reaffirm the important role of mirnas in the dysregulation of cellular processes that may ultimately lead to tumorigenesis.",1
"recent studies have shown that cancer stem cells (cscs) play an important role in the development of pancreatic cancer. multiple oncogenes and signaling pathways have been confirmed to participate in the stemness maintenance and tumorigenicity of cscs, including sex-determining region y-box 2 (sox2) and signal transduction and activation of transcription 3 (stat3), which may provide novel therapeutic targets on pancreatic cancer. here, we reported in pancreatic cancer tissues and cells that mir-1181 expression was markedly downregulated, and the low mir-1181 expression was associated with poorer overall survival and disease-free survival in pancreatic cancer patients. furthermore, overexpression of mir-1181 inhibited, whereas downregulation of mir-1181 promoted, cscs-like phenotypes in vitro and tumorigenicity in vivo in pancreatic cancer cells. moreover, we demonstrated that mir-1181 directly suppressed sox2 and stat3 expression, resulting in downregulation of sox2 and inhibition of the stat3 pathway. hence, our results suggest that mir-1181 plays a vital role in inhibiting the cscs-like phenotypes in pancreatic cancer and might represent a potential target for anti-pancreatic cancer.",1
"micrornas (mirnas) are the most abundant rna species found in serum, and recently, several mirnas have been found to be associated with osteoporosis. however, the development of such associated mirnas into diagnostic and therapeutic targets remains unaddressed, mostly because of a lack of functional validation. here, we identified circulating mir-338 associated with postmenopausal osteoporosis, and performed functional validation in vivo and in vitro . methods : we collected the serum from postmenopausal osteoporosis patients (n=15) and female volunteers of the same age but with normal bone density (n=15) and examined the enrichment of mir-338 cluster. we also confirmed such enrichment using mice subjected to ovariectomy at different stages. we employed primary bone marrow stromal cells from mice and the mc-3t3 cell line along with crispr, rna-seq and chip-qpcr to validate the biological function of secreted mir-338 cluster on osteoblastic differentiation and their upstream regulators. moreover, we generated mir-338 knockout mice and ovx mice injected with an inhibitor against mir-338 cluster to confirm its biological function in vivo . results : we observed a significant enrichment of mir-338 cluster in postmenopausal osteoporosis patients. such enrichment was also prominent in serum from mice subjected to ovariectomy and was detected much earlier than bone density decreases revealed by micro-ct. we also confirmed the presence of an estrogen-dependent runx2 / sox4 /mir-338 positive feedback loop that modulated osteoblast differentiation, providing a possible explanation for our clinical findings. moreover, deletion of the mir-338 cluster or direct intravenous injection of an mir-338 cluster inhibitor significantly prevented osteoporosis after ovariectomy. conclusion : circulating mir-338 cluster in the serum could serve as a promising diagnostic and therapeutic target for postmenopausal osteoporosis patients.",1
"proper gene expression relies on a class of ubiquitously expressed, uridine-rich small nuclear rnas (snrnas) transcribed by rna polymerase ii (rnapii). vertebrate snrnas are transcribed from a unique promoter, which is required for proper 3'-end formation, and cleavage of the nascent transcript involves the activity of a poorly understood set of proteins called the integrator complex. to examine 3'-end formation in drosophila melanogaster, we developed a cell-based reporter that monitors aberrant 3'-end formation of snrna through the gain in expression of green fluorescent protein (gfp). we used this reporter in drosophila s2 cells to determine requirements for u7 snrna 3'-end formation and found that processing was strongly dependent upon nucleotides located within the 3' stem-loop as well as sequences likely to comprise the drosophila equivalent of the vertebrate 3' box. substitution of the actin promoter for the snrna promoter abolished proper 3'-end formation, demonstrating the conserved requirement for an snrna promoter in drosophila. we tested the requirement for all drosophila integrator subunits and found that integrators 1, 4, 9, and 11 were essential for 3'-end formation and that integrators 3 and 10 may be dispensable for processing. depletion of cleavage and polyadenylation factors or of histone pre-mrna processing factors did not affect u7 snrna processing efficiency, demonstrating that the integrator complex does not share components with the mrna 3'-end processing machinery. finally, flies harboring mutations in either integrator 4 or 7 fail to complete development and accumulate significant levels of misprocessed snrna in the larval stages.",1
"cyclin-dependent kinase 5 regulatory subunit 1 (cdk5r1) encodes p35, the main activatory subunit of cyclin-dependent kinase 5 (cdk5). the p35/cdk5 active complex plays a fundamental role in brain development and functioning, but its deregulated activity has also been implicated in various neurodegenerative disorders, including alzheimer's disease (ad). cdk5r1 displays a large and highly evolutionarily conserved 3'-untranslated region (3'-utr), a fact that has suggested a role for this region in the post-transcriptional control of cdk5r1 expression. our group has recently demonstrated that two mirnas, mir-103 and mir-107, regulate cdk5r1 expression and affect the levels of p35. mir-103 and mir-107 belong to the mir-15/107 family, a group of evolutionarily conserved mirnas highly expressed in human cerebral cortex. in this work, we tested the hypothesis that other members of this group of mirnas, in addition to mir-103 and mir-107, were able to modulate cdk5r1 expression. we provide evidence that several mirnas belonging to the mir-15/107 family regulate p35 levels. bace1 expression levels were also found to be modulated by different members of this family. furthermore, overexpression of these mirnas led to reduced app phosphorylation levels at the cdk5-specific thr668 residue. we also show that mir-15/107 mirnas display reduced expression levels in hippocampus and temporal cortex, but not in cerebellum, of ad brains. moreover, increased cdk5r1 mrna levels were observed in ad hippocampus tissues. our results suggest that the downregulation of the mir-15/107 family might have a role in the pathogenesis of ad by increasing the levels of cdk5r1/p35 and consequently enhancing cdk5 activity.",1
"micrornas (mirna) are a class of small rna molecules that regulate numerous critical cellular processes and bind to partially complementary sequences resulting in down-regulation of their target genes. due to the incomplete homology of the mirna to its target site identification of mirna target genes is difficult and currently based on computational algorithms predicting large numbers of potential targets for a given mirna. to enable the identification of biologically relevant mirna targets, we describe a novel functional assay based on a 3'-utr-enriched library and a positive/negative selection strategy. as proof of principle we have used mir-130a and its validated target mafb to test this strategy. identification of mafb and five additional targets and their subsequent confirmation as mir-130a targets by western blot analysis and knockdown experiments validates this strategy for the functional identification of mirna targets.",1
"background micrornas (mirs) are small noncoding rnas that posttranscriptionally control gene expression. small-animal studies suggest that mirs might offer novel therapeutic targets in cardiovascular diseases such as cardioprotection of murine hearts after myocardial infarction via mir-92a inhibitors. because the functional benefits of mir-92a inhibitors in larger preclinical models are not known, we assessed the therapeutic efficacy of mir-92a inhibition in a porcine model of ischemia and reperfusion. methods and results pigs (n=5 per group) underwent percutaneous ischemia/reperfusion (60 min/72 h or 7 days, respectively). locked nucleic acid-modified antisense mir-92a (lna-92a) was applied either regionally (antegrade or retrograde) with a catheter or systemically (intravenously). lna-92a significantly (p conclusions regional lna-92a delivery reduces mir-92a levels and infarct size and postischemic loss of function. lna-92a exerts cell-protective, proangiogenic, and anti-inflammatory effects. mir-92a inhibition might be a novel therapeutic tool to preserve cardiac function after ischemia.",1
"micrornas (mirs) are small rnas that regulate gene expression at the posttranscriptional level. mir-27 is expressed in endothelial cells, but the specific functions of mir-27b and its family member mir-27a are largely unknown. here we demonstrate that overexpression of mir-27a and mir-27b significantly increased endothelial cell sprouting. inhibition of both mir-27a and mir-27b impaired endothelial cell sprout formation and induced endothelial cell repulsion in vitro. in vivo, inhibition of mir-27a/b decreased the number of perfused vessels in matrigel plugs and impaired embryonic vessel formation in zebrafish. mechanistically, mir-27 regulated the expression of the angiogenesis inhibitor semaphorin 6a (sema6a) in vitro and in vivo and targeted the 3'-untranslated region of sema6a. silencing of sema6a partially reversed the inhibition of endothelial cell sprouting and abrogated the repulsion of endothelial cells mediated by mir-27a/b inhibition, indicating that sema6a is a functionally relevant mir-27 downstream target regulating endothelial cell repulsion. in summary, we show that mir-27a/b promotes angiogenesis by targeting the angiogenesis inhibitor sema6a, which controls repulsion of neighboring endothelial cells.",1
"we applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate rna motifs. we predicted six to be riboswitches, which are mrna elements that regulate gene expression on binding a specific metabolite. in separate studies, we confirmed that two of these are novel riboswitches. three other riboswitch candidates are upstream of either a putative transporter gene in the order lactobacillales, citric acid cycle genes in burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. the remaining riboswitch candidate, the widespread genes for the environment, for membranes and for motility (gemm) motif, is associated with genes important for natural competence in vibrio cholerae and the use of metal ions as electron acceptors in geobacter sulfurreducens. among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkc/yxkd, but has a different structure. we identified possible non-coding rnas in five phyla, and several additional cis-regulatory rnas, including one in epsilon-proteobacteria (upstream of purd, involved in purine biosynthesis), and one in cyanobacteria (within an atp synthase operon). these candidate rnas add to the growing list of rna motifs involved in multiple cellular processes, and suggest that many additional rnas remain to be discovered.",1
"the mir-17-92 microrna cluster is often activated in cancer cells, but the identity of its targets remains elusive. using silac and quantitative mass spectrometry, we examined the effects of activation of the mir-17-92 cluster on global protein expression in neuroblastoma (nb) cells. our results reveal cooperation between individual mir-17-92 mirnas and implicate mir-17-92 in multiple hallmarks of cancer, including proliferation and cell adhesion. most importantly, we show that mir-17-92 is a potent inhibitor of tgf-β signaling. by functioning both upstream and downstream of psmad2, mir-17-92 activation triggers downregulation of multiple key effectors along the tgf-β signaling cascade as well as direct inhibition of tgf-β-responsive genes.",1
"background diabetes mellitus impairs endothelial cell (ec) function and postischemic reparative neovascularization by molecular mechanisms that are not fully understood. micrornas negatively regulate the expression of target genes mainly by interaction in their 3' untranslated region. methods and results we found that microrna-503 (mir-503) expression in ecs is upregulated in culture conditions mimicking diabetes mellitus (high d-glucose) and ischemia-associated starvation (low growth factors). under normal culture conditions, lentivirus-mediated mir-503-forced expression inhibited ec proliferation, migration, and network formation on matrigel (comparisons versus lentivirus.gfp control). conversely, blocking mir-503 activity by either adenovirus-mediated transfer of a mir-503 decoy (ad.decoymir-503) or by antimir-503 (antisense oligonucleotide) improved the functional capacities of ecs cultured under high d-glucose/low growth factors. we identified ccne1 and cdc25a as direct mir-503 targets which are downregulated by high glucose/low growth factors in ecs. next, we obtained evidence that mir-503 expression is increased in ischemic limb muscles of streptozotocin-diabetic mice and in ecs enriched from these muscles. moreover, ad.decoymir-503 delivery to the ischemic adductor of diabetic mice corrected diabetes mellitus-induced impairment of postischemic angiogenesis and blood flow recovery. we finally investigated mir-503 and target gene expression in muscular specimens from the amputated ischemic legs of diabetic patients. as controls, calf biopsies of nondiabetic and nonischemic patients undergoing saphenous vein stripping were used. in diabetic muscles, mir-503 expression was remarkably higher, and it inversely correlated with cdc25 protein expression. plasma mir-503 levels were also elevated in the diabetic individuals. conclusions our data suggest mir-503 as a possible therapeutic target in diabetic patients with critical limb ischemia.",1
"the two first cell fate decisions taken in the mammalian embryo generate three distinct cell lineages: one embryonic, the epiblast, and two extraembryonic, the trophoblast and primitive endoderm. mirnas are essential for early development, but it is not known if they are utilized in the same way in these three lineages. we find that in the pluripotent epiblast they inhibit apoptosis by blocking the expression of the proapoptotic protein bcl2l11 (bim) but play little role in the initiation of gastrulation. in contrast, in the trophectoderm, mirnas maintain the trophoblast stem cell compartment by directly inhibiting expression of cdkn1a (p21) and cdkn1c (p57), and in the primitive endoderm, they prevent differentiation by maintaining erk1/2 phosphorylation through blocking the expression of mapk inhibitors. therefore, we show that there are fundamental differences in how stem cells maintain their developmental potential in embryonic and extraembryonic tissues through mirnas.",1
"development of metastatic disease accounts for the vast majority of cancer-related deaths. nevertheless, few treatments exist that are designed to specifically inhibit processes that drive tumor metastasis. the imprinted dlk1-dio3 region contains tumor-suppressing mirnas, but their identity and function remain indeterminate. in this study we identify seven mirnas in the imprinted dlk1-dio3 region that function cooperatively to repress the epithelial-to-mesenchymal transition, a critical step that drives tumor metastasis, as well as proliferation of carcinoma cells. these seven mirnas (mirs 300, 382, 494, 495, 539, 543, and 544) repress a signaling network comprising twist1, bmi1, zeb1/2, and mir-200 family mirnas and silencing of the cluster, which occurs via hypermethylation of upstream cpg islands in human ductal carcinomas, confers morphological, molecular, and function changes consistent with an epithelial-to-mesenchymal transition. moreover, ectopic expression of mir-544 independently inhibited proliferation of numerous tumor cell lines by inducing the atm cell cycle checkpoint pathway. these results establish the dlki-dio3 mirna cluster as a critical checkpoint regulating tumor growth and metastasis and implicate epigenetic modification of the cluster in driving tumor progression. these results also suggest that promoter methylation status and mirna expression levels represent new diagnostic tools and therapeutic targets to predict and inhibit, respectively, tumor metastasis in carcinoma patients.",1
"micrornas (mirnas) are small (18-22 nucleotide) non-coding, endogenous regulatory rna molecules, and they regulate gene expression at the post-transcriptional level through binding to their target mrnas by base-pairing and subsequently inducing either translational repression or mrna destabilization by plants, animals, and some viruses. in this study, combining microarray techniques with qrt-pcr, we found that mir-126-3p expression showed significant difference in the mouse mammary cycle during pregnancy, particularly on transition from pregnancy to lactation. bioinformatics were used to predict target gene of mir-126-3p, and luciferase activity assay to test it, it showed that the progesterone receptor (pgr) 3'utr is directly targeted by mir-126-3p. in this study, mouse mammary epithelial cells as cell model in vitro were used to study the function of mir-126-3p. using gene silencing and over-expression for mir-126-3p, the expression of pgr protein and the secretion of casein were detected by western blotting and hplc, respectively. to determine whether mir-126-3p can affect mouse mammary epithelial cells viability, cells were analyzed by casy-yy. in conclusion, pgr gene confirmed mir-126-3p target genes through luciferase activity and western blotting. and mir-126-3p could also inhibit proliferation of mouse mammary epithelial cells (p < 0.01) and expression of β-casein (p < 0.01), and down-regulate pgr protein (p < 0.05). our results suggested that mir-126-3p inhibited expression of pgr protein level as well as the proliferation of mammary epithelial cells, therefore mir-126-3p could play an important role in the process of mammary gland development.",1
"inflammation involves a coordinated, sequential, and self limiting sequence of events controlled by positive and negative regulatory mechanisms. recent studies have shown that micrornas (mirnas), an evolutionarily conserved class of endogenous 22-nucleotide noncoding rnas, contribute to the regulation of inflammation by repressing gene expression at the posttranscriptional level. in this study, we characterize the profile of mirnas induced by lps in human polymorphonuclear neutrophils (pmn) and monocytes. in particular, we identify mir-9 as the only mirna (among 365 analyzed) up-regulated in both cell types after tlr4 activation. mir-9 is also induced by tlr2 and tlr7/8 agonists and by the proinflammatory cytokines tnf-alpha and il-1beta, but not by ifngamma. among the 3 different genes encoding mir-9 precursors in humans, we show that lps selectively induces the transcription of mir-9-1 located in the croc4 locus, in a myd88- and nf-kappab-dependent manner. in pmn and monocytes, lps regulates nfkb1 at both the transcriptional and posttranscriptional levels, and a conserved mir-9 seed sustained a mir-9-dependent inhibition of the nfkb1 transcript. overall, these data suggest that tlr4-activated nf-kappab rapidly increases the expression of mir-9 that operates a feedback control of the nf-kappab-dependent responses by fine tuning the expression of a key member of the nf-kappab family.",1
"multidrug resistance (mdr) is commonly correlated with the poor prognosis of chronic myelogenous leukemia. aberrant expression of micrornas (mirnas) plays an important role in the mdr of various types of cancers. microrna-9 (mir-9) has been confirmed to be dysregulated in many types of cancers. however, the relationship between mir-9 and mdr in chronic myelogenous leukemia (cml) remains largely unknown. in the present study, we showed that mir‑9-3p (mir-9) was downregulated in adriamycin (adr)‑resistant k562/adr cells and cml/mdr patients. overexpression of mir-9 was sufficient to reverse cancer cell resistance to multiple chemotherapeutics in vitro and sensitized tumors to chemotherapy in vivo. furthermore, we found that abcb1 is a direct target of mir-9. these findings suggest that mir-9 plays a critical role in mdr in cml by targeting abcb1. these results provide new evidence of mir-9 as a biomarker for clinical diagnosis and as a potential therapeutic target for cml.",1
"animal micrornas (mirna) are implicated in the control of nearly all cellular functions. due to high sequence redundancy within the mirna gene pool, loss of most of these 21- to 24-bp long rnas individually does not cause a phenotype. thus, only very few mirnas have been associated with clear functional roles. we constructed a transgenic uas-mirna library in drosophila melanogaster that contains 180 fly mirnas. this library circumvents the redundancy issues by facilitating the controlled misexpression of individual mirnas and is a useful tool to complement loss-of-function approaches. demonstrating the effectiveness of our library, 78 mirnas induced clear phenotypes. most of these mirnas were previously unstudied. furthermore, we present a simple system to create gfp sensors to monitor mirna expression and test direct functional interactions in vivo. finally, we focus on the mir-92 family and identify a direct target gene that is responsible for the specific wing phenotype induced by the misexpression of mir-92 family members.",1
"lineage-negative bone marrow cells (lin-bmcs) have reparative potential for overcoming endothelial dysfunction and reducing cardiovascular risk. here, we found that mir-188 is upregulated and mitogen-activated protein kinase kinase kinase 3 (map3k3) is downregulated in aged lin-bmcs, whereas their expression is reversed in young lin-bmcs. we identified and confirmed map3k3 as a direct target of mir-188. mir-188 overexpression or map3k3 silencing in young lin-bmcs increases p16 and p21 expression, enhances cell senescence, and decreases the ability for cell proliferation, migration, and tube formation. conversely, mir-188 suppression in aged lin-bmcs yields the opposite results. we further found that map3k3 is involved in mir-188-induced promotion of lin-bmc senescence. all data reveal that mir-188 induces lin-bmc senescence by targeting map3k3 expression, thus, providing new theoretical basis for the prevention and treatment of cardiovascular diseases.",1
"aims/hypothesis we aimed to identify micrornas (mirnas) associated with type 2 diabetes and risk of developing the disease in skeletal muscle biopsies from phenotypically well-characterised twins. methods we measured muscle mirna levels in monozygotic (mz) twins discordant for type 2 diabetes using arrays. further investigations of selected mirnas included target prediction, pathway analysis, silencing in cells and association analyses in a separate cohort of 164 non-diabetic mz and dizygotic twins. the effects of elevated glucose and insulin levels on mirna expression were examined, and the effect of low birthweight (lbw) was studied in rats. results we identified 20 mirnas that were downregulated in mz twins with diabetes compared with their non-diabetic co-twins. differences for members of the mir-15 family (mir-15b and mir-16) were the most statistically significant, and these mirnas were predicted to influence insulin signalling. indeed, mir-15b and mir-16 levels were associated with levels of key insulin signalling proteins, mir-15b was associated with the insulin receptor in non-diabetic twins and knockdown of mir-15b/mir-16 in myocytes changed the levels of insulin signalling proteins. lbw in twins and undernutrition during pregnancy in rats were, in contrast to overt type 2 diabetes, associated with increased expression of mir-15b and/or mir-16. elevated glucose and insulin suppressed mir-16 expression in vitro. conclusions type 2 diabetes is associated with non-genetic downregulation of several mirnas in skeletal muscle including mir-15b and mir-16, potentially targeting insulin signalling. the paradoxical findings in twins with overt diabetes and twins at increased risk of the disease underscore the complexity of the regulation of muscle insulin signalling in glucose homeostasis.",1
"in several drosophila cell types, mrna transport depends on microtubules, the molecular motor dynein and trans-acting factors including egalitarian and bicaudal-d. however, the molecular basis of transcript recognition by the localization machinery is poorly understood. here, we characterize the features of hairy pair-rule rna transcripts that mediate their apical localization, using in vivo injection of fluorescently labelled mrnas into syncytial blastoderm embryos. we show that a 121-nucleotide element within the 3'-untranslated region is necessary and sufficient to mediate apical transport. the signal comprises two essential stem-loop structures, in which double-stranded stems are crucial for localization. base-pair identities within the stems are not essential, but can contribute to the efficiency of localization, suggesting that specificity is mediated by higher-order structure. using time-lapse microscopy, we measure the kinetics of localization and show that impaired localization of mutant signals is due to delayed formation of active motor complexes and, unexpectedly, to slower movement. these findings, and those from co-injecting wild-type and mutant rnas, suggest that the efficiency of molecular motors is modulated by the character of their cargoes.",1
"in yeast saccharomyces cerevisiae, 25s rrna makes up the major mass and shape of the 60s ribosomal subunit. during translation initiation, the 60s subunit joins the 40s initiation complex, producing the 80s initiation complex. during elongation, the 60s subunit binds the cca-ends of aminoacyl- and peptidyl-trnas at the a-loop and p-loop, respectively, transferring the peptide onto the α-amino group of the aminoacyl-trna. to study the role of 25s rrna in translation in vivo, we randomly mutated 25s rrna and isolated and characterized seven point mutations that affected yeast cell growth and polysome profiles. four of these mutations, g651a, a1435u, a1446g and a1587g, change a base involved in base triples crucial for structural integrity. three other mutations change bases near the ribosomal surface: c2879u and u2408c alter the a-loop and p-loop, respectively, and g1735a maps near a eukarya-specific bridge to the 40s subunit. by polysome profiling in mmslδ mutants defective in nonfunctional 25s rrna decay, we show that some of these mutations are defective in both the initiation and elongation phases of translation. of the mutants characterized, c2879u displays the strongest defect in translation initiation. the ribosome transit-time assay directly shows that this mutation is also defective in peptide elongation/termination. thus, our genetic analysis not only identifies bases critical for structural integrity of the 60s subunit, but also suggests a role for bases near the peptidyl transferase center in translation initiation.",1
"micrornas (mirnas) play vital roles in several biological processes, including apoptosis, by negatively regulating the expression of target genes. the molecular mechanisms of the key survival signal, akt family, have been widely explored. however, it remains to be ascertained whether akt1, the predominant isoform in most tissue, is a direct target of mirna. in this study, we identified akt1 and e2f1 to be two direct targets of mir-149* and b-myb to be an indirect target by reporter assays and western blot analyses. ectopic expression of mir-149*-induced apoptosis in be2c, a neuroblastoma cell line, and in hela cells. silencing of akt1 or e2f1 expression also led to similar apoptotic changes in these two cell lines, suggesting that the pro-apoptotic effects of mir-149* were exerted by repressing akt1 and e2f1 expressions. importantly, analysis of primary neuroblastoma samples revealed a significant inverse correlation of mir-149* with e2f1 expressions (p=0.026). interestingly, using the reporter assays, excess mir-149 introduced by transfection to simulated its preponderance in the in vivo condition, could not overcome the repressive function of mir-149* on the target genes. this implies that the pro-apoptotic function of mir-149* may not be dampened by its predominant cognate, mir-149, in vivo. our findings not only provided the first evidence that akt1 is a direct target of mirna but also demonstrated that mir-149* is a pro-apoptotic mirna by repressing the expression of akt1 and e2f1.",1
"colorectal cancer (crc) is one of the leading causes of cancer deaths in western countries. a significant number of crc patients undergoing curatively intended surgery subsequently develop recurrence and die from the disease. micrornas (mirnas) are aberrantly expressed in cancers and appear to have both diagnostic and prognostic significance. in this study, we identified novel mirnas associated with recurrence of crc, and their possible mechanism of action. taqman(®) human microrna array set v2.0 was used to profile the expression of 667 mirnas in 14 normal colon mucosas and 46 microsatellite stable crc tumors. four mirnas (mir-362-3p, mir-570, mir-148 a* and mir-944) were expressed at a higher level in tumors from patients with no recurrence (p<0.015), compared with tumors from patients with recurrence. a significant association with increased disease free survival was confirmed for mir-362-3p in a second independent cohort of 43 crc patients, using single taqman(®) microrna assays. in vitro functional analysis showed that over-expression of mir-362-3p in colon cancer cell lines reduced cell viability, and proliferation mainly due to cell cycle arrest. e2f1, usf2 and ptpn1 were identified as potential mir-362-3p targets by mrna profiling of hct116 cells over-expressing mir-362-3p. subsequently, these genes were confirmed as direct targets by luciferase reporter assays and their knockdown in vitro phenocopied the effects of mir-362-3p over-expression. we conclude that mir-362-3p may be a novel prognostic marker in crc, and hypothesize that the positive effects of augmented mir-362-3p expression may in part be mediated through the targets e2f1, usf2 and ptpn1.",1
"background leukemia is the most common malignant proliferative disease in children. our previous study found that mir-99a was up-regulated in pediatric primary aml using microrna expression profiles. up to date, although there is a certain number of reports on microrna expression features and functions in pediatric acute myeloid leukemia (aml) and chronic myeloid leukemia (cml), the expression and function of mir-99a in these diseases remain to be investigated. methods qrt-pcr was performed to measure the expression level of mir-99a in 88 samples including 68 pediatric acute myeloid leukemia patients, 8 chronic myeloid leukemia patients and 12 pediatric controls. mtt assay, apoptosis assay, dual-luciferase reporter transfection assay and western blot analysis were used to investigate the function of mir-99a. results mir-99a was highly expressed in pediatric-onset aml (m1-m5) and cml, while significantly lowly expressed during complete remission of these diseases. mtt assay indicated that the proliferations of k562 and hl60 cells were significantly promoted by mir-99a, and apoptosis assessment by annexin v/propidium iodide staining demonstrated that the apoptosis of these cells was inhibited by mir-99a. additionally, dual-luciferase reporter transfection assay and western blot analysis indicated that mir-99a may target ctdspl and trib2, which are two tumor suppressor genes. conclusions this study revealed that mir-99a may play a potential oncogenic role in pediatric myeloid leukemia including aml and cml via regulating tumor suppressors ctdspl and trib2, suggesting that these two leukemias might share some common biological pathways involved in the generation and development of disease and mir-99a could be a common therapeutic target for myeloid leukemias treatment.",1
"gastric cancer (gc) remains one of the most common types of malignant cancer, and the molecular mechanism underlying its metastasis is still largely unclear. micrornas have emerged as important regulators of metastasis because of their ability to act on multiple signaling pathways. in our study, we found that mir-144 is significantly downregulated in both highly metastatic gc cell lines and tissues. results from both gain-of-function and loss-of-function experiments demonstrate that increased mir-144 expression significantly reduced gc cell migration, whereas decreased mir-144 expression dramatically enhanced gc cell migration. the met proto-oncogene (met), which is often amplified in human cancers and functions as an important regulator of cell growth and tumor invasion, was identified as a direct target of mir-144. moreover, silencing of met using small interfering rna (sirna) recapitulated the anti-metastatic function of mir-144, whereas restoring met expression attenuated the function of mir-144 in gc cells. furthermore, we found that mir-144, by targeting met, suppresses phosphorylation of akt. finally, we observed an inverse correlation between the expression of mir-144 and met mrna in gc metastatic tissues. in summary, mir-144 suppresses gc progression by directly downregulating met expression, which subsequently prevents activation of the pro-oncogenic akt pathway. reintroduction of mir-144 expression in gc cells presents an attractive therapeutic approach to block the metastasis of gastric cancer.",1
"micrornas (mirnas) from the gene cluster mir-143-145 are diminished in cells of colorectal tumor origin when compared with normal colon epithelia. until now, no report has addressed the coordinate action of these mirnas in colorectal cancer (crc). in this study, we performed a comprehensive molecular and functional analysis of the mirna cluster regulatory network. first, we evaluated proliferation, migration, anchorage-independent growth and chemoresistance in the colon tumor cell lines after mir-143 and mir-145 restoration. then, we assessed the contribution of single genes targeted by mir-143 and mir-145 by reinforcing their expression and checking functional recovery. restoring mir-143 and mir-145 in colon cancer cells decreases proliferation, migration and chemoresistance. we identified cluster of differentiation 44 (cd44), kruppel-like factor 5 (klf5), kirsten rat sarcoma 2 viral oncogene homolog (kras) and v-raf murine sarcoma viral oncogene homolog b1 (braf) as proteins targeted by mir-143 and mir-145. their re-expression can partially revert a decrease in transformation properties caused by the overexpression of mir-143 and mir-145. in addition, we determined a set of mrnas that are diminished after reinforcing mir-143 and mir-145 expression. the whole transcriptome analysis ascertained that downregulated transcripts are enriched in predicted target genes in a statistically significant manner. a number of additional genes, whose expression decreases as a direct or indirect consequence of mir-143 and mir-145, reveals a complex regulatory network that affects cell signaling pathways involved in transformation. in conclusion, we identified a coordinated program of gene repression by mir-143 and mir-145, in crc, where either of the two mirnas share a target transcript, or where the target transcripts share a common signaling pathway. major mediators of the oncosuppression by mir-143 and mir-145 are genes belonging to the growth factor receptor-mitogen-activated protein kinase network and to the p53 signaling pathway.",1
"in colorectal cancer, the mechanisms underlying tumor aggressiveness require further elucidation. taking advantage of a large panel of human metastatic colorectal cancer xenografts and matched stem-like cell cultures (m-colospheres), here we show that the overexpression of microrna 483-3p (mirna-483-3p; also known as mir-483-3p), encoded by a frequently amplified gene locus, confers an aggressive phenotype. in m-colospheres, endogenous or ectopic mirna-483-3p overexpression increased proliferative response, invasiveness, stem cell frequency, and resistance to differentiation. transcriptomic analyses and functional validation found that mirna-483-3p directly targets ndrg1, known as a metastasis suppressor involved in egfr family downregulation. mechanistically, mirna-483-3p overexpression induced the signaling pathway triggered by erbb3, including akt and gsk3β, and led to the activation of transcription factors regulating epithelial-mesenchymal transition (emt). consistently, treatment with selective anti-erbb3 antibodies counteracted the invasive growth of mirna-483-3p-overexpressing m-colospheres. in human colorectal tumors, mirna-483-3p expression inversely correlated with ndrg1 and directly correlated with emt transcription factor expression and poor prognosis. these results unveil a previously unrecognized link between mirna-483-3p, ndrg1, and erbb3-akt signaling that can directly support colorectal cancer invasion and is amenable to therapeutic targeting.",1
"microrna (mirna) deregulation in prostate cancer (pca) contributes to pca initiation and metastatic progression. to comprehensively define the cancer-associated changes in mirna targeting and function in commonly studied models of pca, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the argonaute protein in a panel of pca cell lines modeling different stages of pca progression. using this comprehensive catalogue of mirna targets, we analyzed mirna targeting on known drivers of pca and examined tissue-specific and stage-specific pathway targeting by mirnas. we found that androgen receptor is the most frequently targeted pca oncogene and that mir-148a targets the largest number of known pca drivers. globally, tissue-specific and stage-specific changes in mirna targeting are driven by homeostatic response to active oncogenic pathways. our findings indicate that, even in advanced pca, the mirna pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. these findings are important because they are the first to globally characterize mirna changes in pca and demonstrate how the mirna target spectrum responds to staged tumorigenesis.",1
"ezh2 functions as a histone h3 lys 27 (h3k27) methyltransferase when comprising the polycomb-repressive complex 2 (prc2). trimethylation of h3k27 (h3k27me3) correlates with transcriptionally repressed chromatin. the means by which prc2 targets specific chromatin regions is currently unclear, but noncoding rnas (ncrnas) have been shown to interact with prc2 and may facilitate its recruitment to some target genes. here we show that ezh2 interacts with hotair and xist. ezh2 is phosphorylated by cyclin-dependent kinase 1 (cdk1) at threonine residues 345 and 487 in a cell cycle-dependent manner. a phospho-mimic at residue 345 increased hotair ncrna binding to ezh2, while the phospho-mimic at residue 487 was ineffectual. an ezh2 domain comprising t345 was found to be important for binding to hotair and the 5' end of xist.",1
"micrornas (mirnas) have been suggested to play critical roles in tumorigenesis as well as in the development of therapies for the treatment of cancers. however, the tumor-associated mirnas in gastric cancers remain poorly understood. here, we report on mir-542-3p in gastric cancers, which has been widely studied in other cancers as a tumor suppressor. real-time quantitative pcr analysis demonstrated that mir-542-3p was significantly down-regulated in gastric cancer tissues (p < 0.0001) and cell lines (p < 0.001). overexpression of mir-542-3p significantly inhibited cell growth of gastric cancer cells both in vitro (p < 0.01) and in vivo (p < 0.01). notably, overexpression of mir-542-3p apparently reduced the protein expression of astrocyte-elevated gene-1 (aeg-1) (p < 0.01). the dual-luciferase reporter assay validated that mir-542-3p directly bound the 3'-untranslated region (utr) of aeg-1, which could be abolished by mutation of the predicted mir-542-3p binding site. furthermore, overexpression of mir-542-3p markedly inhibited the activation of oncogenic signaling pathways including the akt, β-catenin and nuclear factor-κb pathways. additionally, overexpression of aeg-1 without the 3'-utr partially reversed the cell growth arrest induced by mir-542-3p overexpression in gastric cancer cells (p < 0.05). taken together, these data suggest that mir-542-3p might function as a tumor suppressor in gastric cancer, potentially by targeting the oncogene aeg-1, implying a potential role for mir-542-3p in the development of therapeutic methods for gastric cancer.",1
"an innovative approach for cardiac regeneration following injury is to induce endogenous cardiomyocyte (cm) cell cycle re-entry. in the present study, cms from adult rat hearts were isolated and transfected with cel-mir-67 (control) and rno-mir-210. a significant increase in cm proliferation and mono-nucleation were observed in mir-210 group, in addition to a reduction in cm size, multi-nucleation, and cell death. when compared to control, β-catenin and bcl-2 were upregulated while apc (adenomatous polyposis coli), p16, and caspase-3 were downregulated in mir-210 group. in silico analysis predicted cell cycle inhibitor, apc, as a direct target of mir-210 in rodents. moreover, compared to control, a significant increase in cm survival and proliferation were observed with sirna-mediated inhibition of apc. furthermore, mir-210 overexpressing c57bl/6 mice (210-tg) were used for short-term ischemia/reperfusion study, revealing smaller cell size, increased mono-nucleation, decreased multi-nucleation, and increased cm proliferation in 210-tg hearts in contrast to wild-type (ntg). likewise, myocardial infarction (mi) was created in adult mice, echocardiography was performed, and the hearts were harvested for immunohistochemistry and molecular studies. compared to ntg, 210-tg hearts showed a significant increase in cm proliferation, reduced apoptosis, upregulated angiogenesis, reduced infarct size, and overall improvement in cardiac function following mi. β-catenin, bcl-2, and vegf (vascular endothelial growth factor) were upregulated while apc, p16, and caspase-3 were downregulated in 210-tg hearts. overall, constitutive overexpression of mir-210 rescues heart function following cardiac injury in adult mice via promoting cm proliferation, cell survival, and angiogenesis. key messages mirna-210 transfected adult rat cms show proliferation and reduced cell death in vitro. cell cycle inhibitor apc is a target of mir-210. mir-210 overexpressing (210-tg) mouse hearts show cms cell cycle re-entry and survival post myocardial injury. 210-tg mice show significant neovascularization and angiogenic potential post myocardial infarction. 210-tg hearts show reduced infarct size following ischemic injury.",1
"the subventricular zone (svz) is the largest neurogenic niche in the adult mammalian brain. we found that the brain-enriched microrna mir-124 is an important regulator of the temporal progression of adult neurogenesis in mice. knockdown of endogenous mir-124 maintained purified svz stem cells as dividing precursors, whereas ectopic expression led to precocious and increased neuron formation. furthermore, blocking mir-124 function during regeneration led to hyperplasias, followed by a delayed burst of neurogenesis. we identified the sry-box transcription factor sox9 as being a physiological target of mir-124 at the transition from the transit amplifying cell to the neuroblast stage. sox9 overexpression abolished neuronal differentiation, whereas sox9 knockdown led to increased neuron formation. thus mir-124-mediated repression of sox9 is important for progression along the svz stem cell lineage to neurons.",1
"background in the male drosophila, the x chromosome is transcriptionally upregulated to achieve dosage compensation, in a process that depends on association of the msl proteins with the x chromosome. a role for non-coding rnas has been suggested in recent studies. the rox1 and rox2 rnas are male-specific, non-coding rnas that are produced by, and also found associated with, the dosage-compensated male x chromosome. whether rox rnas are physically part of the msl complex has not been resolved. results we found that rox rnas colocalize with the msl proteins and are highly unstable unless the msl complex is coexpressed, suggesting a physical interaction. we were able to immunoprecipitate rox2 rna from male tissue-culture cells with antibodies to the proteins msl1 and mle, consistent with an integral association with msl complexes. localization of rox1 and rox2 rnas in mutants indicated an order of msl-complex assembly in which rox2 rna is incorporated early in a process requiring the mle helicase. we also found that the rox2 gene, like rox1, is a nucleation site for msl complex spreading into flanking chromatin in cis. conclusions our results support a model in which msl proteins assemble at specific chromatin entry sites (including the rox1 and rox2 genes); the rox rnas join the complex at their sites of synthesis; and complete complexes spread in cis to dosage compensate most genes on the x chromosome.",1
"the cluster of imprinted genes located in the dlk1-dio3 domain spanning 1 mb plays an essential role in controlling pre- and postnatal growth and differentiation in mice and humans. the failure of parent-of-origin-dependent gene expression in this domain results in grave disorders, leading to death in some cases. however, little is known about the role of maternally expressed non-coding rnas (ncrnas) including many mirnas and snornas in this domain. in order to further understand the role of these ncrnas, we created gtl2-mutant mice harboring a 10 kb deletion in exons 1-5. the mutant mice exhibited a very unique inheritance mode: when the deletion was inherited from the mother (mat-ko), the pups were born with normal phenotypes; however, all of them died within 4 weeks after birth, probably due to severely hypoplastic pulmonary alveoli and hepatocellular necrosis. mice carrying the paternal deletion (pat-ko) showed severe growth retardation and perinatal lethality. interestingly, the homozygous mutants (homo-ko) survived and developed into fertile adults. our results show that these phenotypes occur due to altered expression of the dlk1-dio3 cluster genes including mirnas and snornas via the cis and trans effects.",1
"adipogenesis is tightly regulated by altering gene expression, and tnf-α is a multifunctional cytokine that plays an important role in regulating lipogenesis. micrornas are strong post-transcriptional regulators of cell differentiation. in our previous work, we found high expression of mir-181a in a fat-rich pig breed. using bioinformatic analysis, mir-181a was identified as a potential regulator of tnf-α. here, we validated tnf-α as the target of mir-181a by a dual luciferase assay. in response to adipogenesis, a mimic or inhibitor was used to overexpress or reduce mir-181a expression in porcine pre-adipocytes, which were then induced into mature adipocytes. overexpression of mir-181a accelerated accumulation of lipid droplets, increased the amount of triglycerides, and repressed tnf-α protein expression, while the inhibitor had the opposite effect. at the same time, tnf-alpha rescued the increased lipogenesis by mir181a mimics. additionally, mir-181a suppression decreased the expression of fatty synthesis associated genes pde3b (phosphodiesterase 3b), lpl (lipoprotein lipase), pparγ (proliferator-activated receptor-γ), glut1 (glucose transporter), glut4, adiponectin and fasn (fatty acid synthase), as well as key lipolytic genes hsl (hormone-sensitive lipase) and atgl (adipose triglyceride lipase) as revealed by quantitative real-time pcr. our study provides the first evidence of the role of mir-181a in adipocyte differentiation by regulation of tnf-α, which may became a new therapeutic target for anti-obesity drugs.",1
"recent advances in micrornaome have made micrornas (mirnas) a compelling novel class of biomarker in cancer biology. in the present study, the role of mir-23a in the carcinogenesis of colorectal cancer (crc) was investigated. cell viability, apoptosis, and caspase 3/7 activation analyses were conducted to determine the potentiality of apoptosis resistance function of mir-23a in crc. luciferase assay was performed to verify a putative target site of mir-23a in the 3'-utr of apoptosis protease activating factor 1 (apaf1) mrna. the expression levels of mir-23a and apaf1 in crc cell lines (sw480 and sw620) and clinical samples were assessed using reverse transcription-quantitative real-time pcr (rt-qpcr) and western blot. we found that the inhibition of mir-23a in sw480 and sw620 cell lines resulted in significant reduction of cell viability and promotion of cell apoptosis. moreover, mir-23a up-regulation was coupled with apaf1 down-regulation in crc tissue samples. taken together, mir-23a was identified to regulate apoptosis in crc. our study highlights the potential application of mir-23a/apaf1 regulation axis in mirna-based therapy and prognostication.",1
"pathogenic escherichia coli strains carrying the afa-8 gene cluster are frequently associated with extra-intestinal infections in humans and animals. the afa-8 a to e genes determine the formation of an afimbrial adhesive sheath consisting of the afad-viii invasin and the afae-viii adhesin at the bacterial cell surface. this structure is thought to be required for host colonization. we characterized a new gene encoding the small rna afar, which is transcribed in cis from the complementary strand of the 3' untranslated region of the afad messenger rna, within the afad-afae intercistronic region. afar is a trans-acting hfq-dependent antisense small rna that binds the 5' untranslated region of the afad messenger rna, initiating several ribonuclease e-dependent cleavages, thereby downregulating production of the afad-viii invasin. afar transcription is dependent on σ(e), a member of the stress response family of extracytoplasmic alternative sigma factors. we found that the afar-dependent regulatory pathway was controlled by temperature, allowing the production of the afad-viii invasin at temperatures above 37 °c. our findings suggest that the entry of afa-8-positive pathogenic e. coli strains into epithelial cells is tightly regulated by the afar small rna.",1
"the abundance of myc protein must be exquisitely controlled to avoid growth abnormalities caused by too much or too little myc. an intriguing mode of regulation exists in which myc protein itself leads to reduction in its abundance. we show here that dmyc binds to the mir-308 locus and increases its expression. using our gain-of-function approach, we show that an increase in mir-308 causes a destabilization of dmyc mrna and reduced dmyc protein levels. in vivo knockdown of mir-308 confirmed the regulation of dmyc levels in embryos. this regulatory loop is crucial for maintaining appropriate dmyc levels and normal development. perturbation of the loop, either by elevated mir-308 or elevated dmyc, caused lethality. combining elevated levels of both, therefore restoring balance between mir-308 and dmyc levels, resulted in lower apoptotic activity and suppression of lethality. these results reveal a sensitive feedback mechanism that is crucial to prevent the pathologies caused by abnormal levels of dmyc.",1
"objective inflammatory stimuli released into atherosclerotic plaque microenvironment regulate vessel formation by modulating gene expression and translation. micrornas are a class of short noncoding rnas, acting as posttranscriptional regulators of protein-coding genes involved in various biological processes, including vascular cell biology. among them, microrna-221/222 (mir-221/222) seem to negatively modulate vascular remodeling by targeting different target genes. here, we investigated their potential contribution to inflammation-mediated neovessel formation. methods and results we used quantitative real-time rt-pcr amplification to analyze expression of 7 micrornas previously linked to vascular biology, such as mir-17-5p, mir-21, mir-126, mir-210, mir-221, mir-222, and mir-296 and found high levels of expression for all of them in quiescent endothelial cells. however, mir-126, mir-221, mir-222, and mir-296 turned out to be down-modulated in endothelial cells exposed to inflammatory stimuli. applying a gain-of-function approach, we demonstrated that, among them, only mir-222 was involved in inflammation-mediated vascular remodeling. in addition, we identified signal transducer and activator of transcription 5a (stat5a) as a bona fide target of mir-222 and observed that mir-222 negatively correlated with stat5a expression in human endothelial cells from advanced neovascularized atherosclerotic lesions. conclusions we identified stat5a as a novel mir-222 target, and this finding opens up new perspectives for treatment of vascular diseases.",1
"alphavirus genome replication is a multistep asymmetric process. several lines of evidence suggest that the template preference of the rna replicase is regulated by proteolytic cleavage of the viral nonstructural polyprotein. cis-acting rna elements in the viral genome also play crucial roles in regulating genome replication and subgenomic rna transcription. in this report, a series of rna templates were analyzed in vitro and in vivo to define functional elements in the 5' end of the genome. the 5' utr was shown to contain distinct core promoter elements for both minus- and plus-strand synthesis. in addition, two conserved stem-loop structures within the nsp1 coding sequence enhanced rna replication but were not required. studies with chimeric templates and trans-competition experiments suggest that the 5' determinant for minus-strand initiation can differ among alphaviruses and binds to one or more limiting replicase components. the results provide compelling evidence that the 5' and 3' ends of alphavirus genome rnas must interact to initiate replication and we propose one model for how this interaction might occur. in addition to providing new insight into the initiation of alphavirus genome replication, these results have implications for the development of improved alphavirus vector systems with reduced recombination potential.",1
"cancer cells show characteristic gene expression profiles. recent studies support the potential importance of microrna (mirna) expression signatures as biomarkers and therapeutic targets. the membrane-anchored protease regulator reck is downregulated in many cancers, and forced expression of reck in tumor cells results in decreased malignancy in animal models. reck is also essential for mammalian development. in this study, we found that reck is a target of at least three groups of mirnas (mir-15b/16, mir-21 and mir-372/373); that reck mutants lacking the target sites for these mirna show augmented tumor/metastasis-suppressor activities; and that mir-372/373 are upregulated in response to hypoxia through hif1alpha and twist1, whereas mir-21 is upregulated by ras/erk signaling. these data indicate that the hypoxia- and ras-signaling pathways converge on reck through mirnas, cooperatively downregulating this tumor suppressor and thereby promoting malignant cell behavior.",1
"the purpose of our study is to understand the protective role of mir-455-3p against abnormal amyloid precursor protein (app) processing, amyloid beta (aβ) formation, defective mitochondrial biogenesis/dynamics and synaptic damage in ad progression. in-silico analysis of mir-455-3p has identified the app gene as a putative target. using mutant app cells, mir-455-3p construct, biochemical and molecular assays, immunofluorescence and transmission electron microscopy (tem) analyses, we studied the protective effects of mir-455-3p on - 1) app regulation, amyloid beta (aβ)(1-40) & (1-42) levels, mitochondrial biogenesis & dynamics; 3) synaptic activities and 4) cell viability & apoptosis. our luciferase reporter assay confirmed the binding of mir-455-3p at the 3'utr of app gene. immunoblot, sandwich elisa and immunostaining analyses revealed that the reduced levels of the mutant app, aβ(1-40) & aβ(1-42), and c99 by mir-455-3p. we also found the reduced levels of mrna and proteins of mitochondrial biogenesis (pgc1α, nrf1, nrf2, and tfam) and synaptic genes (synaptophysin and psd95) in mutant app cells; on the other hand, mutant app cells that express mir-455-3p showed increased mrna and protein levels of biogenesis and synaptic genes. additionally, expression of mitochondrial fission proteins (drp1 and fis1) were decreased while the fusion proteins (opa1, mfn1 and mfn2) were increased by mir-455-3p. our tem analysis showed a decrease in mitochondria number and an increase in the size of mitochondrial length in mutant app cells transfected with mir-455-3p. based on these observations, we cautiously conclude that mir-455-3p regulate app processing and protective against mutant app-induced mitochondrial and synaptic abnormalities in ad.",1
"background accumulating evidence suggests that microrna-590 (mir-590) has protective effects on cardiovascular diseases, but the mechanism is unknown. interestingly, previous studies from our laboratory and others have shown that macrophage-derived lipoprotein lipase (lpl) might accelerate atherosclerosis by promoting lipid accumulation and inflammatory response. however, the regulation of lpl at the post-transcriptional level by micrornas has not been fully understood. in this study, we explored whether mir-590 affects the expression of lpl and its potential subsequent effects on lipid accumulation and pro-inflammatory cytokine secretion in human thp-1 macrophages. methods and results using bioinformatics analyses and dual-luciferase reporter assays, we found that mir-590 directly inhibited lpl protein and mrna expression by targeting lpl 3'utr. lpl activity assays showed that mir-590 reduced lpl activity in the culture media. oil red o staining and high-performance liquid chromatography assays showed that mir-590 had inhibitory effects on the lipid accumulation in human thp-1 macrophages. we also illustrated that mir-590 alleviated pro-inflammatory cytokine secretion in human thp-1 macrophages as measured by elisa. with the method of small interfering rna, we found that lpl sirna can inhibit the mir-590 inhibitor-induced increase in lipid accumulation and secretion of pro-inflammatory cytokines in oxldl-treated human thp-1 macrophages. conclusions mir-590 attenuates lipid accumulation and pro-inflammatory cytokine secretion by targeting lpl gene in human thp-1 macrophages. therefore, targeting mir-590 may offer a promising strategy to treat atherosclerotic cardiovascular diseases.",1
"aims growing evidence links microrna to the process of peripheral vascular disease. recently, we have found that microrna-1298(mir-1298) is one of the most significantly down-regulated micrornas in human arteries with arteriosclerosis obliterans (aso) of the lower extremities. however, little is known regarding its role in the process of aso. the present study aimed to investigate the expression, regulatory mechanisms, and functions of mir-1298 in the process of aso. methods and results using quantitative reverse-transcription pcr and in situ hybridization assays, mir-1298 was observed predominantly expressed in the vascular smooth muscle cells (vsmcs) and was significantly down-regulated in aso compared with normal arteries. pyrosequencing analysis revealed that the mir-1298 dna upstream of cpg sites were hypermethylated in aso compared with normal arteries. next, the luciferase reporter assay revealed that mir-1298 down-regulation is related with upstream dna cpg site hypermethylation. introducing a mir-1298 mimic into cultured vsmcs significantly attenuated cell proliferation and migration. connexin 43 (cx43) was validated to be a functional target of mir-1298 that was involved in the mir-1298-mediated cellular effects. finally, lentivirus-mediated delivery of mir-1298 and its target cx43 into a rat carotid balloon injury model indicated that re-overexpression of mir-1298 significantly decreased neointimal formation by targeting connexin 43. conclusion our data demonstrate a specific role of the upstream dna methylation/mir-1298/cx43 pathway in regulating vsmc function and suggest that modulation of mir-1298 levels may offer a novel therapeutic approach for aso.",1
"nkx2.2as is an endogenous antisense transcript to nkx2.2 gene, subcellularly located in the cytoplasm. we tested if nkx2.2as transcripts have any biological function by regulating transcription level of nkx2.2 coding gene in the differentiation of neural stem cells. forced expression of nkx2.2as in neural stem cells enhanced induction of differentiation along lineage of oligodendrocytes. further analyses showed that overexpression of nkx2.2as induced modest increase in nkx2.2 mrna level, suggesting that the upregulation of nkx2.2 mrna level can be a minor cause of enhanced induction of oligodendrocytic differentiation by nkx2.2as overexpression. these results together imply that nkx2.2as has a certain biological function which is likely to be not only based on the affect on transcription level of nkx2.2 coding gene in cis, but also on the other mechanisms.",1
"unlabelled hepatitis c virus (hcv)-induced chronic liver disease is a leading cause of hepatocellular carcinoma (hcc). however, the molecular mechanisms underlying hcc development following chronic hcv infection remain poorly understood. micrornas (mirnas) play an important role in homeostasis within the liver, and deregulation of mirnas has been associated with liver disease, including hcc. while host mirnas are essential for hcv replication, viral infection in turn appears to induce alterations of intrahepatic mirna networks. although the cross talk between hcv and liver cell mirnas most likely contributes to liver disease pathogenesis, the functional involvement of mirnas in hcv-driven hepatocyte injury and hcc remains elusive. here we combined a hepatocyte-like cell-based model system, high-throughput small rna sequencing, computational analysis, and functional studies to investigate hcv-mirna interactions that may contribute to liver disease and hcc. profiling analyses indicated that hcv infection differentially regulated the expression of 72 mirnas by at least 2-fold, including mirnas that were previously described to target genes associated with inflammation, fibrosis, and cancer development. further investigation demonstrated that the mir-146a-5p level was consistently increased in hcv-infected hepatocyte-like cells and primary human hepatocytes, as well as in liver tissue from hcv-infected patients. genome-wide microarray and computational analyses indicated that mir-146a-5p overexpression modulates pathways that are related to liver disease and hcc development. furthermore, we showed that mir-146a-5p has a positive impact on late steps of the viral replication cycle, thereby increasing hcv infection. collectively, our data indicate that the hcv-induced increase in mir-146a-5p expression both promotes viral infection and is relevant for pathogenesis of liver disease. importance hcv is a leading cause of chronic liver disease and cancer. however, how hcv induces liver cancer remains poorly understood. there is accumulating evidence that a viral cure does not eliminate the risk for hcc development. thus, there is an unmet medical need to develop novel approaches to predict and prevent virus-induced hcc. mirna expression is known to be deregulated in liver disease and cancer. furthermore, mirnas are essential for hcv replication, and hcv infection alters mirna expression. however, how mirnas contribute to hcv-driven pathogenesis remains elusive. here we show that hcv induces mirnas that may contribute to liver injury and carcinogenesis. the mir-146a-5p level was consistently increased in different cell-based models of hcv infection and in hcv patient-derived liver tissue. furthermore, mir-146a-5p increased hcv infection. collectively, our data are relevant to understanding viral pathogenesis and may open perspectives for novel biomarkers and prevention of virus-induced liver disease and hcc.",1
"background micrornas (mirnas) have been reported to play an important role in tumorigenesis. in this study, the role of mir-15a and mir-16-1 in gastric adenocarcinoma (gac) was investigated. methods the expression of mir-15a and mir-16-1 in cell lines and primary tumors was examined by mirna qrt-pcr. proliferative assays, colony formation, cell invasion and migration, flow cytometry analysis and in vivo study were performed by ectopic expression of mir-15a and mir-16-1. the putative target genes of mir-15a and mir-16-1 were explored by targetscan and further validated. results we found that mir-15a and mir-16-1 were down-regulated in gac cell lines and primary tumor samples compared with normal gastric epithelium. functional study demonstrated that ectopic expression of mir-15a and mir-16-1 suppressed cell proliferation, monolayer colony formation, invasion and migration, and xenograft formation in vivo. in addition, mir-15a and mir-16-1 induced g0/g1 cell cycle arrest which was further confirmed by western blot and qrt-pcr of related cell cycle regulators. yap1 was confirmed to be a functional target of mir-15a and mir-16-1 in gac. yap1 re-expression partly abrogated the inhibitory effect of mir-15a and mir-16-1 in gac cells. in clinical samples, yap1 protein expression shows negative correlation with mir-15a and mir-16-1 expression. conclusion in conclusion, targeting yap1 by tumor suppressor mirna mir-15a and mir-16-1 plays inhibitory effect and this might have a therapeutic potential in gac.",1
"autophagy has become one of the most important mechanisms of chemotherapy resistance by supporting the survival of tumor cells under metabolic and therapeutic stress. here, we showed that mir-22 inhibited autophagy and promoted apoptosis to increase the sensitivity of colorectal cancer (crc) cells to 5-fluorouracil (5-fu) treatment both in vitro and in vivo. b-cell translocation gene 1 (btg1) was identified as a new target of mir-22, which could reverse the inhibition of autophagy induced by mir-22. thus, mir-22 may function as an important switch between autophagy and apoptosis to regulate 5-fu sensitivity through post-transcriptional silencing of btg1. promisingly, mir-22 could be considered as both a predictor of 5-fu sensitivity for personalized treatment and a therapeutic target for colorectal cancer.",1
"micrornas (mirnas) play integral roles in diverse processes including tumorigenesis. mirna gene loci are often found in close conjunction, and such clustered mirna genes are transcribed from a common promoter to generate polycistronic primary transcript. the primary transcript (pri-mirna) is then processed by two rnase iii proteins to release the mature mirnas. although it has been speculated that the mirnas in the same cluster may play related biological functions, this has not been experimentally addressed. here we report that the mirnas in two clusters (mir-106b approximately 93 approximately 25 and mir-222 approximately 221) suppress the cip/kip family members of cdk inhibitors (p57(kip2), p21(cip1) and p27(kip1)). we show that mir-25 targets p57 through the 3'-utr. furthermore, mir-106b and mir-93 control p21 while mir-222 and mir-221 regulate both p27 and p57. ectopic expression of these mirnas results in activation of cdk2 and facilitation of g1/s phase transition. consistent with these results, both clusters are abnormally upregulated in gastric cancer tissues compared to the corresponding normal tissues. ectopic expression of mir-222 cluster enhanced tumor growth in the mouse xenograft model. our study demonstrates the functional associations between clustered mirnas and further implicates that effective cancer treatment may require a combinatorial approach to target multiple oncogenic mirna clusters.",1
"in addition to being a hallmark of neurodegenerative disease, axon degeneration is used during development of the nervous system to prune unwanted connections. in development, axon degeneration is tightly regulated both temporally and spatially. here, we provide evidence that degeneration cues are transduced through various kinase pathways functioning in spatially distinct compartments to regulate axon degeneration. intriguingly, glycogen synthase kinase-3 (gsk3) acts centrally, likely modulating gene expression in the cell body to regulate distally restricted axon degeneration. through a combination of genetic and pharmacological manipulations, including the generation of an analog-sensitive kinase allele mutant mouse for gsk3β, we show that the β isoform of gsk3, not the α isoform, is essential for developmental axon pruning in vitro and in vivo. additionally, we identify the dleu2/mir15a/16-1 cluster, previously characterized as a regulator of b-cell proliferation, and the transcription factor tbx6, as likely downstream effectors of gsk3β in axon degeneration.",1
"motivation post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. the central players are the rna-binding proteins, and experimental technologies for probing their activities have advanced rapidly over the course of the past decade. statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however. results we introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of clip and rip-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions. availability and implementation we have implemented our method in a software tool called piranha. source code and binaries, licensed under the gnu general public license (version 3) are freely available for download from contact andrewds@usc.edu supplementary information supplementary data available at bioinformatics online.",1
"three distinct classes of s-adenosyl-l-methionine (sam)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. the s(mk) box (sam-iii) translational riboswitch has been identified in the sam synthetase gene in members of the lactobacillales. here we report the 2.2-a crystal structure of the enterococcus faecalis s(mk) box riboswitch. the y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for sam recognition. the shine-dalgarno sequence, which is sequestered by base-pairing with the anti-shine-dalgarno sequence in response to sam binding, also directly participates in sam recognition. the riboswitch makes extensive interactions with the adenosine and sulfonium moieties of sam but does not appear to recognize the tail of the methionine moiety. we captured a structural snapshot of the s(mk) box riboswitch sampling the near-cognate ligand s-adenosyl-l-homocysteine (sah) in which sah was found to adopt an alternative conformation and fails to make several key interactions.",1
"the aim of this study was to investigate the function of mir-183 in renal cancer cells and the mechanisms mir-183 regulates this process. in this study, level of mir-183 in clinical renal cancer specimens was detected by quantitative real-time pcr. mir-183 was up- and down-regulated in two renal cancer cell lines achn and a498, respectively, and cell proliferation, caspase 3/7 activity, colony formation, in vitro migration and invasion were measured; and then the mechanisms of mir-183 regulating was analyzed. we found that mir-183 was up-regulated in renal cancer tissues; inhibition of endogenous mir-183 suppressed in vitro cell proliferation, colony formation, migration, and invasion and stimulated caspase 3/7 activity; up-regulated mir-183 increased cell growth and metastasis and suppressed caspase 3/7 activity. we also found that mir-183 directly targeted tumor suppressor, specifically the 3'utr of three subunits of protein phosphatase 2a (pp2a-cα, pp2a-cβ, and pp2a-b56-γ) transcripts, inhibiting their expression and regulated the downstream regulators p21, p27, mmp2/3/7 and timp1/2/3/4. these results revealed the oncogenes role of mir-183 in renal cancer cells via direct targeting protein phosphatase 2a.",1
"micrornas (mirnas) are a class of 19- to 23-nt, small, noncoding rnas, which bind the 3' utr of target mrnas to mediate translational repression in animals. mirnas have been shown to regulate developmental processes, such as self-renewal of stem cells, neuronal differentiation, myogenesis, and cancer. a functional role of mirnas in the regulation of neurotransmitter synthesis has yet to be ascribed. we used mesenchymal stem cells (mscs) as a model to study mirna-mediated neurotransmitter regulation in developing neuronal cells. mscs are mesoderm-derived cells, primarily resident in adult bone marrow, which can generate functional neuronal cells. we have previously shown that human msc-derived neuronal cells express the neurotransmitter gene, tac1, but do not synthesize the gene's encoded peptide, the neurotransmitter substance p (sp), unless stimulated with the inflammatory mediator il-1alpha. these findings suggested a potential role for mirnas in the regulation of sp synthesis. here, we report on the mirna profile of undifferentiated human mscs and msc-derived neuronal cells by using mirna-specific bioarrays. mirnas that were increased in the neuronal cells and decreased after il-1alpha stimulation were analyzed by the miranda algorithm to predict tac1 mrna targets. putative mir-130a, mir-206, and mir-302a binding sites were predicted within the 3' utr of tac1. target validation using a luciferase reporter system confirmed the mir-130a and mir-206 sites. specific inhibition of mir-130a and mir-206 in the neuronal cells resulted in sp synthesis and release. the studies provide a different approach in ascribing a new regulatory role for mirnas in regulating neurotransmitter synthesis.",1
"cardiac fibrosis is characterized by aberrant proliferation of cardiac fibroblasts and exaggerated deposition of extracellular matrix (ecm) in the myocardial interstitial, and ultimately impairs cardiac function. it is still controversial whether microrna-21 (mir-21) participates in the process of cardiac fibrosis. our previous study confirmed that transforming growth factor beta receptor iii (tgfβriii) is a negative regulator of tgf-β pathway. here, we aimed to decipher the relationship between mir-21 and tgfβriii in the pathogenic process of myocardial fibrosis. we found that tgf-β1 and mir-21 were up-regulated, whereas tgfβriii was down-regulated in the border zone of mouse hearts in response to myocardial infarction. after transfection of mir-21 into cardiac fibroblasts, tgfβriii expression was markedly reduced and collagen content was increased. and, luciferase results confirmed that tgfβriii was a target of mir-21. it suggests that up-regulation of mir-21 could increase the collagen content and at least in part through inhibiting tgfβriii. conversely, we also confirmed that overexpression of tgfβriii could inhibit the expression of mir-21 and reduce collagen production in fibroblasts. further studies showed that overexpression of tgfβriii could also deactivate tgf-β1 pathway by decreasing the expression of tgf-β1 and phosphorylated-smad3 (p-smad3). tgf-β1 has been proven as a positive regulator of mir-21. taken together, we found a novel reciprocal loop between mir-21 and tgfβriii in cardiac fibrosis caused by myocardial infarction in mice, and targeting this pathway could be a new strategy for the prevention and treatment of myocardial remodeling.",1
"purpose micrornas (mirnas) may act as oncogenes or tumor suppressor genes and, as such, they may play a role in cancer development. we investigated mir-429 expression levels in a cohort of esophageal carcinomas (ec) to assess its impact on ec cell growth, apoptosis and invasion. methods qrt-pcr assays were used to quantify mir-429 expression levels in 32 paired ec samples and adjacent non-neoplastic tissues. assays for cell growth, apoptosis, caspase activity and trans-well invasion were used to evaluate the effects of mir-429 expression on ec cells. luciferase reporter and western blotting assays were used to test whether the bcl-2 and specificity protein 1 (sp1) mrnas serve as major targets of mir-429. results the expression levels of mir-429 in ec tissues were found to be lower than those in adjacent non-neoplastic tissues (p conclusions in primary ec tissues mir-429 is expressed at low levels. up-regulation of mir-429 inhibits invasion and promotes apoptosis in ec cells by targeting bcl-2 and sp1. our findings suggest that bcl-2 and sp1 may serve as major targets of mir-429. this study paves the way for a better understanding of the mechanism underlying ec pathogenesis and the development of novel, targeted therapies.",1
"gastric cancer causes nearly one million deaths worldwide per year. although helicobacter pylori infection is the main risk factor, in about 80% or more of gastric cancers, the molecular pathway underlying h. pylori infection leading to the development of gastric cancers remains unclear. recently accumulating evidence suggests that micrornas (mirnas) may regulate diverse biological processes and may be important in tumorigenesis. mir-21 has been frequently observed to be aberrantly overexpressed in various tumors. using taqman quantitative real-time pcr, we confirmed that mir-21 was significantly overexpressed in human gastric cancer tissues and cell lines. remarkably, mir-21 was also significantly overexpressed in h. pylori-infected gastric mucosa, implying that overexpression of mir-21 in gastric cancer may be due in part to h. pylori infection. more importantly, we showed that forced expression of mir-21 significantly enhanced cell proliferation and invasion in ags cells, a human gastric cancer cell line, whereas knockdown of mir-21 by inhibitor caused a significant reduction in cell proliferation and a significant increase in apoptosis. furthermore, we demonstrated that knockdown of mir-21 significantly decreased cell invasion and migration of ags cells. finally, we showed that reck, a known tumor suppressor in gastric cancer, is a bona fide target of mir-21. taken together, mir-21 may be important in the initiation and progression of gastric cancers as an oncomir, likely through regulating reck. our findings suggest a potential regulatory pathway in which h. pylori infection upregulates expression of mir-21, which in turn downregulates reck, and then leads to the development of gastric cancer.",1
"rationale establishment of a functional vasculature requires the interconnection and remodeling of nascent blood vessels. precise regulation of factors that influence endothelial cell migration and function is essential for these stereotypical vascular patterning events. the secreted slit ligands and their robo receptors constitute a critical signaling pathway controlling the directed migration of both neurons and vascular endothelial cells during embryonic development, but the mechanisms of their regulation are incompletely understood. objective to identify micrornas regulating aspects of the slit-robo pathway and vascular patterning. methods and results here, we provide evidence that microrna (mir)-218, which is encoded by an intron of the slit genes, inhibits the expression of robo1 and robo2 and multiple components of the heparan sulfate biosynthetic pathway. using in vitro and in vivo approaches, we demonstrate that mir-218 directly represses the expression of robo1, robo2, and glucuronyl c5-epimerase (glce), and that an intact mir-218-slit-robo regulatory network is essential for normal vascularization of the retina. knockdown of mir-218 results in aberrant regulation of this signaling axis, abnormal endothelial cell migration, and reduced complexity of the retinal vasculature. conclusions our findings link slit gene expression to the posttranscriptional regulation of robo receptors and heparan sulfate biosynthetic enzymes, allowing for precise control over vascular guidance cues influencing the organization of blood vessels during development.",1
"dicer is essential for plant, caenorhabditis elegans, and drosophila antiviral responses because of its role in generating small interfering rna (sirna) from viral genomes. we show that because of impaired mirna production, mice with a variant dicer1 allele (dicer1(d/d)) were more susceptible to vesicular stomatitis virus (vsv) infection. we did not detect vsv genome-derived sirna in wild-type cells or any alteration of interferon-mediated antiviral responses by dicer1 deficiency. rather, we found that host mir24 and mir93 could target viral large protein (l protein) and phosphoprotein (p protein) genes, and a lack of mir24 and mir93 was responsible for increased vsv replication in dicer1(d/d) cells. our data suggest that host mirna can play a role in host interactions with viruses.",1
"hand2 is an ancestral regulator of heart development and one of four transcription factors that control the reprogramming of fibroblasts into cardiomyocytes. deletion of hand2 in mice results in right ventricle hypoplasia and embryonic lethality. hand2 expression is tightly regulated by upstream enhancers that reside within a super-enhancer delineated by histone h3 acetyl lys27 (h3k27ac) modifications. here we show that transcription of a hand2-associated long non-coding rna, which we named upperhand (uph), is required to maintain the super-enhancer signature and elongation of rna polymerase ii through the hand2 enhancer locus. blockade of uph transcription, but not knockdown of the mature transcript, abolished hand2 expression, causing right ventricular hypoplasia and embryonic lethality in mice. given the substantial number of uncharacterized promoter-associated long non-coding rnas encoded by the mammalian genome, the uph-hand2 regulatory partnership offers a mechanism by which divergent non-coding transcription can establish a permissive chromatin environment.",1
"purpose we investigated the potential functions of mir-34a in cd44 transcriptional complexes in renal cell carcinoma. materials and methods we detected mir-34a expression by quantitative real-time polymerase chain reaction. oligonucleotides were used to over express mir-34a. cell proliferation and xenograft assays, colony formation and flow cytometry were done to examine effects on cancer cell proliferation in vitro and in vivo. luciferase assay was performed to verify the precise target of mir-34a. results promoter methylation contributed to mir-34a loss in the achn, 786-o and sn12pm6 renal carcinoma cell lines. ectopic over expression of mir-34a restrained cell growth, tube formation and migration/invasion, and significantly suppressed the growth of renal carcinoma xenografts and metastasis in nude mice. dual luciferase assay revealed that cd44 was a direct target of mir-34a in renal cancer cells and cd44 knockdown by rnai in renal cancer cells suppressed tumor progression. in contrast, cd44 ectopic expression partially reversed the antitumor effects of mir-34a in renal cancer cells. conclusions our findings indicate that mir-34a targets cd44 in renal cancer cells and suppresses renal cancer cell growth, tube formation and metastasis in vitro and in vivo. thus, mir-34a may be a potential molecular target for novel therapeutic strategies for clear cell renal carcinoma.",1
"many neural lineages display a temporal pattern, but the mechanisms controlling the ordered production of neuronal subtypes remain unclear. here, we show that drosophila let-7 and mir-125, cotranscribed from the let-7-complex (let-7-c) locus, regulate the transcription factor chinmo to control temporal cell fate in the mushroom body (mb) lineage. we find that let-7-c is activated in postmitotic neurons born during the larval-to-pupal transition, when transitions among three mb subtypes occur. loss or increase of let-7-c delays or accelerates these transitions, respectively, and leads to cell fate transformations. consistent with our identification of let-7 and mir-125 sites in a recently identified ∼6 kb extension of the chinmo 3' utr, chinmo is elevated in let-7-c mutant mbs. in addition, we show that let-7-c acts upstream of chinmo and that let-7-c phenotypes are caused by elevated chinmo. thus, these heterochronic mirnas, originally identified in c. elegans, underlie progenitor cell multipotency during the development of diverse bilateria.",1
"the three genomic rnas of alfalfa mosaic virus each contain a unique 5' untranslated region (5' utr). replacement of the 5' utr of rna 1 by that of rna 2 or 3 yielded infectious replicons. the sequence of a putative 5' stem-loop structure in rna 1 was found to be required for negative-strand rna synthesis. a similar putative 5' stem-loop structure is present in rna 2 but not in rna 3.",1
"microrna (mirna) expression profiling studies revealed a number of mirnas dysregulated in the malignant brain tumor glioblastoma. molecular functions of these mirnas in gliomagenesis are mainly unknown. we show that inhibition of mir-10b, a mirna not expressed in human brain and strongly upregulated in both low-grade and high-grade gliomas, reduces glioma cell growth by cell-cycle arrest and apoptosis. these cellular responses are mediated by augmented expression of the direct targets of mir-10b, including bcl2l11/bim, tfap2c/ap-2γ, cdkn1a/p21, and cdkn2a/p16, which normally protect cells from uncontrolled growth. analysis of the cancer genome atlas expression data set reveals a strong positive correlation between numerous genes sustaining cellular growth and mir-10b levels in human glioblastomas, while proapoptotic genes anticorrelate with the expression of mir-10b. furthermore, survival of glioblastoma patients expressing high levels of mir-10 family members is significantly reduced in comparison to patients with low mir-10 levels, indicating that mir-10 may contribute to glioma growth in vivo. finally, inhibition of mir-10b in a mouse model of human glioma results in significant reduction of tumor growth. altogether, our experiments validate an important role of mir-10b in gliomagenesis, reveal a novel mechanism of mir-10b-mediated regulation, and suggest the possibility of its future use as a therapeutic target in gliomas.",1
"cancer-secreted micrornas (mirnas) are emerging mediators of cancer-host crosstalk. here we show that mir-105, which is characteristically expressed and secreted by metastatic breast cancer cells, is a potent regulator of migration through targeting the tight junction protein zo-1. in endothelial monolayers, exosome-mediated transfer of cancer-secreted mir-105 efficiently destroys tight junctions and the integrity of these natural barriers against metastasis. overexpression of mir-105 in nonmetastatic cancer cells induces metastasis and vascular permeability in distant organs, whereas inhibition of mir-105 in highly metastatic tumors alleviates these effects. mir-105 can be detected in the circulation at the premetastatic stage, and its levels in the blood and tumor are associated with zo-1 expression and metastatic progression in early-stage breast cancer.",1
"micrornas (mirnas/mirs) are a cluster of short non-protein coding rnas that negatively regulate gene expression, which is involved in fundamental cellular processes, including the response of tumor cells to chemotherapeutic agents. the present study investigated the role of mir-106a in the development of drug resistance in ovarian cancer cells. the expression of mir-106a in the ovarian cancer ovcar3 cell line and the cisplatin (cddp)-resistant ovarian cancer ovcar3/cis cell line was detected using stem-loop quantitative (q)pcr. the ovcar3 and ovcar3/cis cells were transfected with mimics or inhibitors of mir-106a or with negative control (nc) rna using lipofectamine 2000. luciferase reporter assays were used to determine whether pdcd4 was a direct target of mir-106a in the ovcar3 cells. the expression levels of the pdcd4 proteins were assessed using qrt-pcr and western blotting, respectively. drug sensitivity was analyzed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, while apoptosis was determined by fluorescence-activating cell sorting analysis. the expression levels of mir-106a were upregulated in the cddp-resistant ovarian cancer ovcar3/cis cell line compared with the parental ovcar3 cell line. however, the pdcd4 protein levels were decreased in the ovcar3/cis cells compared with the ovcar3 cells. the luciferase reporter assays revealed that pdcd4 was a direct mir-106a target in the ovcar3 cells. transfection of the ovcar3/cis cells with inhibitors of mir-106a enhanced the sensitivity of the ovcar3/cis cells to cddp and increased cddp-induced apoptosis. the expression of the pdcd4 protein and the sensitivity to cddp was decreased in the ovcar3 cells that were transfected with the mimics of mir-106a. the knockdown of pdcd4 expression using pdcd4-specific sirnas in the ovcar3 cells demonstrated that pdcd4 is a key signaling molecule in ovcar3 cell cddp-induced resistance. mir-106a may be involved in the development of drug resistance and the regulation of pdcd4 expression, at least in part, by modulating cddp-induced apoptosis in ovarian cancer cells.",1
"malignant pleural mesothelioma (mpm) is a rapidly fatal malignancy that is increasing in incidence in japan. in this study, we performed gene and microrna (mirna) expression profiling to identify novel therapeutic targets in mpm cells. based on relative sensitivities to pemetrexed (pem) and the histone deacetylase (hdac) inhibitor, vorinostat (saha), 211h cells were determined to be the only sensitive mpm cell line out of the 6 tested. on the same series of cell lines, we performed whole genome transcriptomic profiling via dna microarrays and pathway analysis of the derived data. of particular note, il-18 gene expression levels were significantly higher in the cell lines that were either drug resistant or displayed intermediate sensitivity, compared to the sensitive 211h cell line. pathway analysis revealed il-18 as an important gene associated with drug sensitivity of mpm cells. a relationship between il-18 overexpression and drug resistance was also observed following targeted assessment of 10 cytokine genes using quantitative rt-pcr. mirna expression profiles were evaluated in the mpm cell line panel in order to discern the mechanism of il-18 induction in the drug-resistant lines. we found that mir-379 and mir-411 belonged to the same cluster of mirnas located on chromosome 14q32 that commonly target the il-18 gene. luciferase reporter assays revealed that mir-379 and mir-411 directly target the il-18 gene. introduction of mir-379 plus mir-411, as well as il-18 silencing, significantly suppressed the invasive capacity of meso1 cells in vitro. furthermore, the use of either pem or saha together with mir-379 plus mir-411 mimics mediated increased sensitivity to these drugs in meso1 cells. these results suggest that the mir-379/411 cluster may provide new therapeutic opportunities for advanced mpm patients, depending on the nature of il-18 gene expression.",1
"the smallest catalytic rna identified to date is a manganese-dependent ribozyme that requires only a complex between gaaa and uuu to effect site-specific cleavage. we show here that this ribozyme occurs naturally in the 3'-utr of vg1 and beta-actin mrnas. in accord with earlier studies with model rnas, cleavage occurs only in the presence of manganese or cadmium ions and proceeds optimally near 30 degrees c and physiological ph. the time course of cleavage in vg1 mrna best fits a two-step process in which both steps are first-order. in vg1 mrna, the ribozyme is positioned adjacent to a polyadenylation signal, but has no influence on translation of the mrna in xenopus oocytes. putative gaaa ribozyme structures are also near polyadenylation sites in yeast and rat actin mrnas. analysis of sequences in the polya cleavage site and 3'-utr database (pacdb) revealed no particular bias in the frequency or distribution of the gaaa motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts. nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mrnas.",1
"background idiopathic pulmonary fibrosis (ipf) is progressive and rapidly fatal. improved understanding of pathogenesis is required to prosper novel therapeutics. epigenetic changes contribute to ipf; therefore, micrornas may reveal novel pathogenic pathways. objectives we sought to determine the regulatory role of microrna (mir)-155 in the profibrotic function of murine lung macrophages and fibroblasts, ipf lung fibroblasts, and its contribution to experimental pulmonary fibrosis. methods bleomycin-induced lung fibrosis in wild-type and mir-155 -/- mice was analyzed by histology, collagen, and profibrotic gene expression. mechanisms were identified by in silico and molecular approaches and validated in mouse lung fibroblasts and macrophages, and in ipf lung fibroblasts, using loss-and-gain of function assays, and in vivo using specific inhibitors. results mir-155 -/- mice developed exacerbated lung fibrosis, increased collagen deposition, collagen 1 and 3 mrna expression, tgf-β production, and activation of alternatively activated macrophages, contributed by deregulation of the mir-155 target gene the liver x receptor (lxr)α in lung fibroblasts and macrophages. inhibition of lxrα in experimental lung fibrosis and in ipf lung fibroblasts reduced the exacerbated fibrotic response. similarly, enforced expression of mir-155 reduced the profibrotic phenotype of ipf and mir-155 -/- fibroblasts. conclusions we describe herein a molecular pathway comprising mir-155 and its epigenetic lxrα target that when deregulated enables pathogenic pulmonary fibrosis. manipulation of the mir-155/lxr pathway may have therapeutic potential for ipf.",1
"glioblastoma (gbm) is one of the most common and aggressive primary brain tumors in adults. deregulated expression of micrornas (mirnas) has been associated with gbm progression through alterations in either oncogenic or tumor suppressor targets. here, we elucidated the function and the possible molecular mechanisms of mir-449a in human gbm cell lines and tumor specimens-derived glioblastoma stem cells (gscs). quantitative real-time pcr demonstrated that mir-449a was down-regulated in human gbm cell lines and gscs. functionally, mir-449a acted as a tumor suppressor by reducing cell proliferation, migration and invasion as well as inducing apoptosis in human gbm cell lines and gscs. myc-associated zinc-finger protein (maz) was identified as a direct target of mir-449a, mediating these tumor-suppressive effects, demonstrated by western blot assay and luciferase assays. moreover, over-expression of mir-449a inhibited the expression of podoplanin (pdpn) by down-regulating maz which could positively control the promoter activities via binding to the promoter of pdpn, demonstrated by luciferase assays and chromatin immunoprecipitation assays. further, the pi3k/akt pathway was blocked when maz was down-regulated by mir-449a. this process was coincided with the up-regulation of apoptotic proteins and the down-regulation of anti-apoptotic proteins, mmp2 and mmp9. furthermore, nude mice carrying over-expressed mir-449a combined with knockdown maz tumors produced the smallest tumors and the highest survival. these results elucidated a novel molecular mechanism of gbm progression, and may thus suggest a promising application for gbm treatment.",1
"ribose methylation of eukaryotic rrna is directed by box c/d small nucleolar rnas (snornas), which pinpoint the nucleotide to be methylated in specific position within the rrna sequence. here, we report the identification of a novel double-guide c/d box snorna termed snr88 that directs methylation of two previously undetermined sites in 25s rrna from the fission yeast. knockout of the predicted tata box of the snr88 gene resulted in the complete blocking of its expression, showing that snr88 is an independently transcribed gene and dispensable for yeast viability. the depletion of snr88 abolished 25s rrna methylation at u2304 and u2497 simultaneously. interestingly, an unusual pause of reverse transcription at u2495 was observed, which implies an unknown structure of 25s rrna related to ribose methylation at u2497 in the fission yeast.",1
"aim atorvastatin, a hmg-coa reductase inhibitor, used in the treatment of hypercholesterolemia, has been previously shown to regulate abcb1 expression in vivo and in vitro. we hypothesized that the statin could regulate gene expression of abcb1 transporter via micrornas. methods expression of micrornas and abcb1 mrna was examined in atorvastatin-treated and control cells using real-time pcr. mir-491-3p mimic and inhibitor were transfected in caco-2 and abcb1 expression was monitored by western blot and real-time pcr. results in hepg2 cells, none of the micrornas predicted to target abcb1 3'utr was regulated by atorvastatin treatment. in agreement with this, abcb1 3'utr activity was not modulated in hepg-2 cells after 48h-treatment as measured by luciferase assay. in caco-2 cells, atorvastatin treatment provoked a decrease in luciferase activity and, accordingly, mir-491-3p was upregulated about 2.7 times after 48h-statin treatment. luciferase analysis of mir-491-3p with a mimetic or inhibitor of mir-491-3p revealed that this microrna could target abcb1 3'utr, as after mir-491-3p inhibition, abcb1 levels were increased by two-fold, and mir-491-3p superexpression decreased abcb1 3'utr activity. finally, functional analysis revealed that treatment with mir-491-3p inhibitor could reverses atorvastatin attenuation of abcb1 (pg-p) protein levels. conclusion our results suggest atorvastatin control abcb1 expression via mir-491-3p in caco-2 cells. this finding may be an important mechanism of statin drug-drug interaction, since common concomitant drugs used in the prevention of cardiovascular diseases are abcb1 substrates.",1
"tgf-β/smad signaling induces epithelial-mesenchymal transition (emt) and tumor metastasis. as essential mediators in this pathway, smad2 and smad3 have been extensively studied and found to promote emt and the subsequent mobility as well as invasiveness of lung cancer cells. in the present study, we determined that mir-136 directly targeted smad2 and smad3, leading to reduced migration and invasiveness of lung adenocarcinoma (adc) cell lines, accompanied by increased epithelial markers as well as decreased mesenchymal markers. moreover, ectopic expression of either smad2 or smad3 partially restored the malignant phenotype of adc cells overexpressing mir-136. taken together, our data demonstrate that mir-136 may play a tumor-suppressive role by repressing emt and prometastatic traits via targeting smad2 and smad3. the potent antimetastasis property of mir-136 and its multitarget mechanism provide new insights in developing novel therapeutic approaches.",1
"background acquired protein s (ps) deficiency is highly associated with elevated circulating estrogen levels resulting from pregnancy, oral contraceptives, and estrogen replacement therapy; however, the mechanism of estrogen-mediated acquired ps deficiency remains poorly understood. increasing evidence indicates that estrogen receptor signaling can indirectly modulate the expression of target genes at the post-transcriptional level by modulating the expression of micrornas (mirnas), and mirnas have also been demonstrated to be involved in the regulation of hemostasis. objectives to investigate the mechanism of estrogen-mediated downregulation of pros1 expression by the microrna mir-494. methods computational analyses of the pros1 3'-untranslated region (utr) were performed to identify putative mirna-binding sites, and direct targeting of the pros1 3'-utr by mir-494 was determined with dual luciferase reporter assays in huh-7 cells. reporter vectors containing the pros1 3'-utr sequence with deleted mir-494-binding sites were also analyzed with luciferase reporter assays. the effects of estrogen on mir-494 and pros1 mrna levels in huh-7 cells were determined by quantitative real-time pcr, and estrogen-mediated changes to secreted ps levels in culture supernatant of huh-7 cells were measured with an elisa. results the pros1 3'-utr sequence contains three putative mir-494-binding sites. mir-494 directly targets pros1, and mir-494 levels are upregulated following estrogen treatment in huh-7 liver cells in association with downregulated pros1 mrna and ps levels. conclusions the results from this study provide the first evidence for mirna downregulation of pros1 by mir-494, and suggest that mir-494 is involved in the mechanism of estrogen-mediated downregulation of ps expression.",1
"introduction mir-200c and other members of the mir-200 family promote epithelial identity by directly targeting zeb1 and zeb2, which repress e-cadherin and other genes involved in polarity. loss of mir-200c is often observed in carcinoma cells that have undergone epithelial to mesenchymal transition (emt). restoration of mir-200c to such cells leads to a reduction in stem cell-like characteristics, reduced migration and invasion, and increased sensitivity to taxanes. here we investigate the functional role of novel targets of mir-200c in the aggressive behavior of breast and endometrial cancer cells. methods putative target genes of mir-200c identified by microarray profiling were validated as direct targets using dual luciferase reporter assays. following restoration of mir-200c to triple negative breast cancer and type 2 endometrial cancer cell lines that had undergone emt, levels of endogenous target mrna and respective protein products were measured. migration and sensitivity to anoikis were determined using wound healing assays or cell-death elisas and viability assays respectively. results we found that restoration of mir-200c suppresses anoikis resistance, a novel function for this influential mirna. we identified novel targets of mir-200c, including genes encoding fibronectin 1 (fn1), moesin (msn), neurotrophic tyrosine receptor kinase type 2 (ntrk2 or trkb), leptin receptor (lepr), and rho gtpase activating protein 19 (arhgap19). these targets all encode proteins normally expressed in cells of mesenchymal or neuronal origin; however, in carcinoma cells that lack mir-200c they become aberrantly expressed and contribute to the emt phenotype and aggressive behavior. we showed that these targets are inhibited upon restoration of mir-200c to aggressive breast and endometrial cancer cells. we demonstrated that inhibition of msn and/or fn1 is sufficient to mediate the ability of mir-200c to suppress cell migration. lastly, we showed that targeting of trkb mediates the ability of mir-200c to restore anoikis sensitivity. conclusions mir-200c maintains the epithelial phenotype not only by targeting zeb1/2, which usually facilitates restoration of e-cadherin expression, but also by actively repressing a program of mesenchymal and neuronal genes involved in cell motility and anoikis resistance.",1
"background mirnas, endogenous oligonucleotide rnas, play an important role in mammary gland carcinogenesis and tumor progression. detection of their expression and investigation of their functions could lead to discovery of novel biomarkers for breast cancer. methods in situ hybridization was used to detect mir-133a expression in formalin-fixed paraffin-embedded breast surgical specimens from 26 benign, 34 pericancerously normal and 90 cancerous tissues. qrt-pcr was performed to assess mir-133a levels in 6 breast cell lines and 10 benign and 18 cancerous fresh breast tissue specimens. cell viability, migration, and invasion assays were used to determine the role of mir-133a in regulation of breast cancer cell growth, migration, and invasion, respectively. luciferase assay was performed to assess mir-133a binding to fscn1 gene. results expression of mir-133a was reduced from normal through benign to cancerous breast tissues. expression of mir-133a was also low in breast cancer cell lines. the reduced mir-133a expression was associated with lymph nodes metastasis, high clinical stages, and shorter relapse-free survivals of patients with breast cancer. furthermore, transfection of mir-133a oligonucleotides slightly inhibited growth but significantly decreased migration and invasion capacity of breast cancer cells, compared with negative controls, whereas knockdown of mir-133a expression induced breast cancer cell migration and invasion. in addition, we identified a putative mir-133a binding site in the 3'-untranslated region (utr) of fascin1 (fscn1) gene using an online bioinformatical tool. we found that mir-133a transfection significantly reduced expression of fscn1 mrna and protein. the luciferase reporter assay confirmed that fscn1 was the direct target gene of mir-133a. conclusions mir-133a expression was lost in breast cancer tissues, loss of which was associated with lymph nodes metastasis, high clinical stages and shorter relapse-free survivals of patients with breast cancer. functionally, mir-133a can suppress tumor cell invasion and migration and targeted the expression of fscn1. future study will verify whether detection of mir-133a expression can served as a novel biomarker for breast cancer progression and patient prognosis.",1
"the transforming growth factor-β (tgf-β) signaling pathway is one of the major pathways essential for normal embryonic development and tissue homeostasis, with anti-tumor but also pro-metastatic properties in cancer. this pathway directly regulates several target genes that mediate its downstream functions, however very few micrornas (mirnas) have been identified as targets. mirnas are modulators of gene expression with essential roles in development and a clear association with diseases including cancer. little is known about the transcriptional regulation of the primary transcripts (pri-mirna, pri-mir) from which several mature mirnas are often derived. here we present the identification of mirnas regulated by tgf-β signaling in mouse embryonic stem (es) cells and early embryos. we used an inducible es cell system to maintain high levels of the tgf-β activated/phosphorylated smad2/3 effectors, which are the transcription factors of the pathway, and a specific inhibitor that blocks their activation. by performing short rna deep-sequencing after 12 hours smad2/3 activation and after 16 hours inhibition, we generated a database of responsive mirnas. promoter/enhancer analysis of a subset of these mirnas revealed that the transcription of pri-mir-181c/d and the pri-mir-341∼3072 cluster were found to depend on activated smad2/3. several of these mirnas are expressed in early mouse embryos, when the pathway is known to play an essential role. treatment of embryos with tgf-β inhibitor caused a reduction of their levels confirming that they are targets of this pathway in vivo. furthermore, we showed that pri-mir-341∼3072 transcription also depends on foxh1, a known smad2/3 transcription partner during early development. together, our data show that mirnas are regulated directly by the tgf-β/smad2/3 pathway in es cells and early embryos. as somatic abnormalities in functions known to be regulated by the tgf-β/smad2/3 pathway underlie tumor suppression and metastasis, this research also provides a resource for mirnas involved in cancer.",1
"specific micrornas (mirnas), small non-coding rnas that support homeostatic gene expression, are significantly altered in abundance in human neurological disorders. in monocytes, increased expression of an nf-κb-regulated mirna-146a down-regulates expression of the interleukin-1 receptor-associated kinase-1 (irak-1), an essential component of toll-like/il-1 receptor signaling. here we extend those observations to the hippocampus and neocortex of alzheimer disease (ad) brain and to stressed human astroglial (hag) cells in primary culture. in 66 control and ad samples we note a significant up-regulation of mirna-146a coupled to down-regulation of irak-1 and a compensatory up-regulation of irak-2. using mirna-146a-, irak-1-, or irak-2 promoter-luciferase reporter constructs, we observe decreases in irak-1 and increases in mirna-146a and irak-2 expression in interleukin-1β (il-1β) and amyloid-β-42 (aβ42) peptide-stressed hag cells. nf-κb-mediated transcriptional control of human irak-2 was localized to between -119 and +12 bp of the immediate irak-2 promoter. the nf-κb inhibitors curcumin, pyrrolidine dithiocarbamate or cay10512 abrogated both irak-2 and mirna-146a expression, whereas irak-1 was up-regulated. incubation of a protected antisense mirna-146a was found to inhibit mirna-146a and restore irak-1, whereas irak-2 remained unaffected. these data suggest a significantly independent regulation of irak-1 and irak-2 in ad and in il-1β+aβ42 peptide-stressed hag cells and that an inducible, nf-κb-sensitive, mirna-146a-mediated down-regulation of irak-1 coupled to an nf-κb-induced up-regulation of irak-2 expression drives an extensively sustained inflammatory response. the interactive signaling of nf-κb and mirna-146a further illustrate interplay between inducible transcription factors and pro-inflammatory mirnas that regulate brain irak expression. the combinatorial use of nf-κb inhibitors with mirna-146a or antisense mirna-146a may have potential as a bi-pronged therapeutic strategy directed against irak-2-driven pathogenic signaling.",1
"human c-myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. however, the regulatory mechanisms of its expression and biological functions remain largely unclear. recently, c-myb has been shown to be targeted by microrna-150 (mir-150) which thereby controls b cell differentiation in mice. in this study, we demonstrated that c-myb is an evolutionary conserved target of mir-150 in human and zebrafish, using reporter assays. ectopic expression of mir-150 in breast cancer and leukemic cells repressed endogenous c-myb at both messenger rna (mrna) and protein levels. among several leukemia cell lines, primary leukemia cells, and normal lymphocytes, expression levels of mir-150 inversely correlated with c-myb. the mir-150 overexpression or c-myb silencing in zebrafish zygotes led to similar and serious phenotypic defects in zebrafish, and the phenotypic aberrations induced by mir-150 could be reversed by coinjection of c-myb mrna. our findings suggest that c-myb is an evolutionally conserved target of mir-150 and mir-150/c-myb interaction is important for embryonic development and possibly oncogenesis.",1
"recently, it has been found that inappropriate expression of micrornas (mirnas) is strongly associated with carcinogenesis. in this study, we demonstrated that the expression of mirnas (mirs) -143 and -145, the levels of which were previously shown to be reduced in colon cancers and various kinds of established cancer cell lines, was also decreased in most of the b-cell malignancies examined, including chronic lymphocytic leukemias (cll), b-cell lymphomas, epstein-barr virus (ebv)-transformed b-cell lines, and burkitt lymphoma cell lines. all samples from 13 cll patients and eight of nine b-cell lymphoma ones tested exhibited an extremely low expression of mirs-143 and -145. the expression levels of mirs-143 and -145 were consistently low in human burkitt lymphoma cell lines and were inversely associated with the cell proliferation observed in the ebv-transformed b-cell lines. moreover, the introduction of either precursor or mature mir-143 and -145 into raji cells resulted in a significant growth inhibition that occurred in a dose-dependent manner and the target gene of mirna-143 was determined to be erk5, as previously reported in human colon cancer dld-1 cells. taken together, these findings suggest that mirs-143 and -145 may be useful as biomarkers that differentiate b-cell malignant cells from normal cells and contribute to carcinogenesis in b-cell malignancies by a newly defined mechanism.",1
"background mir-338-3p is a recently discovered mirna and is involved in cell differentiation. however, few data are yet available on the aberrant expression of mir-338-3p in human colorectal carcinoma (crc). this work aimed to investigate the relationship between mir-338-3p expression pattern and clinicopathological features of human crc and the possible regulative mechanisms. methods the 40 crc, adjacent nontumorous tissues and 2 human crc-derived cell lines (sw-480 and sw-620) were collected, respectively, and the total rna and protein were isolated routinely. the mir-338-3p expression pattern was detected by real-time reverse transcription-polymerase chain reaction (rt-pcr) and northern blotting. smoothened (smo, possible target of mir-338-3p) mrna and corresponding protein expression pattern were detected by semiquantitative rt-pcr and western blotting. mir-338-3p expression patterns were compared between nontumor mucosa and crc samples, graded by progression-related factors. disease outcome was calculated by kaplan-meier survival analysis to determine whether mir-338-3p was related to disease-free survival (dfs) and overall survival (os) of patients. moreover, smo 3'-utr fragment was pcr amplified from genome dna of human colon and inserted into a luciferase reporter plasmid. the luciferase reporter plasmid construct was then transfected into crc cells together with pre-mir-338-3p or anti-mir-338-3p and the luciferase activity in the transfected cells was detected. results the expression of mir-338-3p was significantly downregulated in crcs than those in the adjacent nontumorous tissues, and the value was negatively related to advanced tnm stage and local invasion (p conclusions mir-338-3p is expressed differentially in crc and associated with progression and prognosis of crc. smo might be a possible target of mir-338-3p, which made it a potential antitumor candidate for treatment and prevention of crc.",1
"aim the fragile x mental retardation protein (fmrp), the product of the fmr1 gene, is responsible for the fragile x syndrome (fxs). fmrp regulates mirna expression and is involved in mirna-mediated gene silencing. however, the question of whether fmrp is, in turn, regulated by mirnas remains unanswered. main methods we detected the fmrp expression pattern by in situ hybridization. mir-315 overexpression and knockout models were generated by germ-line transformation and ends-out homologous recombination, respectively. western blotting and immunohistochemistry were used to detect drosophila fmrp (dfmrp) and a luciferase reporter assay was used to confirm the regulation of dfmr1 mrna by mir-315. synaptic structural quantification and electrophysiological methods were used to compare synaptic functions among groups. key findings here, we determined that the transcription product of dfmr1, the drosophila homologue of fmr1, is a direct target of mir-315. mir-315 is mainly expressed in the nervous system of drosophila. flies overexpressing mir-315 showed pupation defects and reduced hatching rates. a homozygous mir-315 knockout status is embryonic lethal in flies. these observations indicate that mir-315 is a key regulator of the drosophila nervous system. furthermore, computational prediction and cell-based luciferase and in vivo assays demonstrated that dfmr1 is directly targeted by mir-315. lastly, using the neuromuscular junction as a model, we found that mir-315 regulates synaptic structure and transmission by targeting dfmr1. significance these findings provide compelling evidence that mir-315 targets dfmr1 in the drosophila nervous system, acting as a regulatory factor for the fine-tuned modulation of fmrp expression.",1
"we perform a large-scale rna sequencing study to experimentally identify genes that are downregulated by 25 mirnas. this rna-seq dataset is combined with public mirna target binding data to systematically identify mirna targeting features that are characteristic of both mirna binding and target downregulation. by integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide mirna target prediction. all prediction data can be accessed at mirdb ( ).",1
"endometriosis is a common disease seen by gynecologists. clinical features involve pelvic pain and unexplained infertility. although endometriosis is pathologically characterized by endometrial tissue outside the normal uterine location, endometriosis is otherwise not easily explained. endometriomas, endometriotic cysts of the ovary, typically cause pain and distortion of pelvic anatomy. to begin to understand the pathogenesis of endometriomas, we describe the first transcriptome-micrornaome analysis of endometriomas and eutopic endometrium using next-generation sequencing technology. using this approach, we generated a total of more than 54 million independent small rna reads from our 19 clinical samples. at the microrna level, we found 10 microrna that were up-regulated (mir-202, 193a-3p, 29c, 708, 509-3-5p, 574-3p, 193a-5p, 485-3p, 100, and 720) and 12 microrna that were down-regulated (mir-504, 141, 429, 203, 10a, 200b, 873, 200c, 200a, 449b, 375, and 34c-5p) in endometriomas compared with endometrium. using in silico prediction algorithms, we correlated these microrna with their corresponding differentially expressed mrna targets. to validate the functional roles of microrna, we manipulated levels of mir-29c in an in vitro system of primary cultures of human endometrial stromal fibroblasts. extracellular matrix genes that were potential targets of mir-29c in silico were significantly down-regulated using this biological in vitro system. in vitro functional studies using luciferase reporter constructs further confirmed that mir-29c directly affects specific extracellular matrix genes that are dysregulated in endometriomas. thus, mir-29c and other abnormally regulated microrna appear to play important roles in the pathophysiology of uterine function and dysfunction.",1
"micrornas (mirnas) have been reported to be involved in tumor metastasis. in this study, we investigated the function of mir-506 in the metastasis of human hepatocellular carcinoma (hcc). we found that mir-506 is significantly downregulated in the primary tissue of metastatic hcc and in highly metastatic hcc cell lines. overexpression of mir-506 suppressed hcc cell migration, invasion, and metastasis both in vitro and in vivo . furthermore, mir-506 was found to specifically target the 3' untranslated region (3'-utr) of interleukin 8 ( il8 ) mrna. spearman's correlation analysis revealed that mir-506 expression inversely correlated with il8 mrna and protein expression in hcc tissue samples. il8 treatment reversed mir-506-induced suppression of hcc cell migration and invasiveness. thus, mir-506 acts as a tumor suppressor that may inhibit the migration, invasiveness, and metastasis of hcc cells by targeting il8 .",1
"pulmonary hypertension (ph) is a progressive and often fatal disorder whose pathogenesis involves pulmonary artery smooth muscle cell (pasmc) proliferation. although modern ph therapies have significantly improved survival, continued progress rests on the discovery of novel therapies and molecular targets. microrna (mir)-21 has emerged as an important non-coding rna that contributes to ph pathogenesis by enhancing vascular cell proliferation, however little is known about available therapies that modulate its expression. we previously demonstrated that peroxisome proliferator-activated receptor gamma (pparγ) agonists attenuated hypoxia-induced hpasmc proliferation, vascular remodeling and ph through pleiotropic actions on multiple targets, including transforming growth factor (tgf)-β1 and phosphatase and tensin homolog deleted on chromosome 10 (pten). pten is a validated target of mir-21. we therefore hypothesized that antiproliferative effects conferred by pparγ activation are mediated through inhibition of hypoxia-induced mir-21 expression. human pasmc monolayers were exposed to hypoxia then treated with the pparγ agonist, rosiglitazone (rsg,10 μm), or in parallel, c57bl/6j mice were exposed to hypoxia then treated with rsg. rsg attenuated hypoxic increases in mir-21 expression in vitro and in vivo and abrogated reductions in pten and pasmc proliferation. antiproliferative effects of rsg were lost following sirna-mediated pten depletion. furthermore, mir-21 mimic decreased pten and stimulated pasmc proliferation, whereas mir-21 inhibition increased pten and attenuated hypoxia-induced hpasmc proliferation. collectively, these results demonstrate that pparγ ligands regulate proliferative responses to hypoxia by preventing hypoxic increases in mir-21 and reductions in pten. these findings further clarify molecular mechanisms that support targeting pparγ to attenuate pathogenic derangements in ph.",1
"background mirnas are now recognized as key regulator elements in gene expression. although they have been associated with a number of human diseases, their implication in acute and chronic asthma and their association with lung remodelling have never been thoroughly investigated. methodology/principal findings in order to establish a mirnas expression profile in lung tissue, mice were sensitized and challenged with ovalbumin mimicking acute, intermediate and chronic human asthma. levels of lung mirnas were profiled by microarray and in silico analyses were performed to identify potential mrna targets and to point out signalling pathways and biological processes regulated by mirna-dependent mechanisms. fifty-eight, 66 and 75 mirnas were found to be significantly modulated at short-, intermediate- and long-term challenge, respectively. inverse correlation with the expression of potential mrna targets identified mmu-mir-146b, -223, -29b, -29c, -483, -574-5p, -672 and -690 as the best candidates for an active implication in asthma pathogenesis. a functional validation assay was performed by cotransfecting in human lung fibroblasts (wi26) synthetic mirnas and engineered expression constructs containing the coding sequence of luciferase upstream of the 3'utr of various potential mrna targets. the bioinformatics analysis identified mirna-linked regulation of several signalling pathways, as matrix metalloproteinases, inflammatory response and tgf-β signalling, and biological processes, including apoptosis and inflammation. conclusions/significance this study highlights that specific mirnas are likely to be involved in asthma disease and could represent a valuable resource both for biological makers identification and for unveiling mechanisms underlying the pathogenesis of asthma.",1
"background several micrornas (mirs) have been shown to regulate gene expression in the heart, and dysregulation of their expression has been linked to cardiac disease. mir-378 is strongly expressed in the mammalian heart but so far has been studied predominantly in cancer, in which it regulates cell survival and tumor growth. methods and results here, we report tight control of cardiomyocyte hypertrophy through mir-378. in isolated primary cardiomyocytes, mir-378 was found to be both necessary and sufficient to repress cardiomyocyte hypertrophy. bioinformatic prediction suggested that factors of the mitogen-activated protein kinase (mapk) pathway are enriched among mir-378 targets. using mrna and protein expression analysis along with luciferase assays, we validated 4 key components of the mapk pathway as targets of mir-378: mapk1 itself, insulin-like growth factor receptor 1, growth factor receptor-bound protein 2, and kinase suppressor of ras 1. rna interference with these targets prevented the prohypertrophic effect of antimir-378, suggesting their functional relation with mir-378. because mir-378 significantly decreases in cardiac disease, we sought to compensate for its loss through adeno-associated virus-mediated, cardiomyocyte-targeted expression of mir-378 in an in vivo model of cardiac hypertrophy (pressure overload by thoracic aortic constriction). restoration of mir-378 levels significantly attenuated thoracic aortic constriction-induced cardiac hypertrophy and improved cardiac function. conclusions our data identify mir-378 as a regulator of cardiomyocyte hypertrophy, which exerts its activity by suppressing the mapk signaling pathway on several distinct levels. restoration of disease-associated loss of mir-378 through cardiomyocyte-targeted adeno-associated virus-mir-378 may prove to be an effective therapeutic strategy in myocardial disease.",1
"mir-608 has been indicated to play an important role in the pathogenesis of various inflammation-related diseases, including sepsis and several types of cancers. however, there is little information about the underlying mechanism, especially in inflammatory cells. in this study, an hsa-mir-608-inhibition cell model was constructed in u937 cells using a lentivirus, and gene expression profiles were determined by a cdna microarray. altogether, 682 genes showed a difference greater than 1.2-fold, including 184 genes downregulated and 498 genes upregulated. among these genes, one potential mir-608-target gene, elane, was further investigated. a positive relationship between the expression of mir-608 and that of elane was found both in vivo and in vitro. in addition, decreased expression of mir-608 resulted in overexpression of elane at both the mrna and protein levels. cotransfection of hek293t cells with a mir-608 mimic inhibited reporter activity, and mutation of the mirna seed sequences abolished the repression of reporter activity. these results suggest that mir-608 is an important posttranscriptional regulator of elane expression in human monocytes and may play an important role in the process of inflammation. mir-608 and neutrophil elastase may be novel targets for the diagnosis or treatment of sepsis.",1
"small noncoding micrornas (mirnas) can contribute to cancer development and progression and are differentially expressed in normal tissues and cancers. from a large-scale mirnome analysis on 540 samples including lung, breast, stomach, prostate, colon, and pancreatic tumors, we identified a solid cancer mirna signature composed by a large portion of overexpressed mirnas. among these mirnas are some with well characterized cancer association, such as mir-17-5p, mir-20a, mir-21, mir-92, mir-106a, and mir-155. the predicted targets for the differentially expressed mirnas are significantly enriched for protein-coding tumor suppressors and oncogenes (p < 0.0001). a number of the predicted targets, including the tumor suppressors rb1 (retinoblastoma 1) and tgfbr2 (transforming growth factor, beta receptor ii) genes were confirmed experimentally. our results indicate that mirnas are extensively involved in cancer pathogenesis of solid tumors and support their function as either dominant or recessive cancer genes.",1
"the role of micrornas (mirnas) as coordinators of stem cell fate has emerged over the last decade. we have used human embryonic stem cells to identify mirnas involved in neural lineage commitment induced by the inhibition of tgfβ-like molecule-mediated pathways. among several candidate mirnas expressed in the fetal brain, the two isoforms of mir-125 alone were detected in a time window compatible with a role in neural commitment in vitro. functional analysis indicated that mir-125 isoforms were actively involved in the promotion of pluripotent cell conversion into sox1-positive neural precursors. mir-125 promotes neural conversion by avoiding the persistence of non-differentiated stem cells and repressing alternative fate choices. this was associated with the regulation by mir-125 of smad4, a key regulator of pluripotent stem cell lineage commitment. activation of mir-125 was directly responsive to the levels of tgfβ-like molecules, placing mir-125 at the core of mechanisms that lead to the irreversible neural lineage commitment of pluripotent stem cells in response to external stimuli.",1
"inflammation is a common component of acute injuries of the central nervous system (cns) such as ischemia, and degenerative disorders such as alzheimer's disease. glial cells play important roles in local cns inflammation, and an understanding of the roles for micrornas in glial reactivity in injury and disease settings may therefore lead to the development of novel therapeutic interventions. here, we show that the mir-181 family is developmentally regulated and present in high amounts in astrocytes compared to neurons. overexpression of mir-181c in cultured astrocytes results in increased cell death when exposed to lipopolysaccharide (lps). we show that mir-181 expression is altered by exposure to lps, a model of inflammation, in both wild-type and transgenic mice lacking both receptors for the inflammatory cytokine tnf-α. knockdown of mir-181 enhanced lps-induced production of pro-inflammatory cytokines (tnf-α, il-6, il-1β, il-8) and hmgb1, while overexpression of mir-181 resulted in a significant increase in the expression of the anti-inflammatory cytokine il-10. to assess the effects of mir-181 on the astrocyte transcriptome, we performed gene array and pathway analysis on astrocytes with reduced levels of mir-181b/c. to examine the pool of potential mir-181 targets, we employed a biotin pull-down of mir-181c and gene array analysis. we validated the mrnas encoding mecp2 and x-linked inhibitor of apoptosis as targets of mir-181. these findings suggest that mir-181 plays important roles in the molecular responses of astrocytes in inflammatory settings. further understanding of the role of mir-181 in inflammatory events and cns injury could lead to novel approaches for the treatment of cns disorders with an inflammatory component.",1
"we report here that mir-155 and mir-125b play a role in innate immune response. lps stimulation of mouse raw 264.7 macrophages resulted in the up-regulation of mir-155 and down-regulation of mir-125b levels. the same changes also occurred when c57bl/6 mice were i.p. injected with lps. furthermore, the levels of mir-155 and mir-125b in raw 264.7 cells displayed oscillatory changes in response to tnf-alpha. these changes were impaired by pretreating the cells with the proteasome inhibitor mg-132, suggesting that these two micrornas (mirnas) may be at least transiently under the direct control of nf-kappab transcriptional activity. we show that mir-155 most probably directly targets transcript coding for several proteins involved in lps signaling such as the fas-associated death domain protein (fadd), ikappab kinase epsilon (ikkepsilon), and the receptor (tnfr superfamily)-interacting serine-threonine kinase 1 (ripk1) while enhancing tnf-alpha translation. in contrast, mir-125b targets the 3'-untranslated region of tnf-alpha transcripts; therefore, its down-regulation in response to lps may be required for proper tnf-alpha production. finally, emu-mir-155 transgenic mice produced higher levels of tnf-alpha when exposed to lps and were hypersensitive to lps/d-galactosamine-induced septic shock. altogether, our data suggest that the lps/tnf-alpha-dependent regulation of mir-155 and mir-125b may be implicated in the response to endotoxin shock, thus offering new targets for drug design.",1
"comparison of htlv-iii, the putative aids virus, with other related viruses, may help to reveal more about the origin of aids in humans. in this study, the nucleotide sequence of the gag and pol genes of an equine infectious anemia virus (eiav) proviral dna clone was determined. the sequence was compared with that of htlv-iii and of visna, a pathogenic lentivirus of sheep. the results show that these viruses constitute a family clearly distinct from that of the type c viruses or the blv-htlv-i and -ii group. within the family, eiav, htlv-iii, and visna appear to be equally divergent from a common evolutionary ancestor.",1
"mir-93/106b and their host gene minichromosome maintenance complex component 7 (mcm7) reside at chr7q22, a region frequently rearranged in leiomyomas. we explored the expression of mir-93/106b in leiomyoma and paired myometrium (n = 63) from untreated and patients exposed to hormonal therapies (gnrh agonist, depo-provera, and oral contraceptives) from african-americans and caucasians and their regulatory functions in isolated paired (n = 15) leiomyoma and myometrial smooth muscle cells and the leiomyosarcoma cell line. at tissue level leiomyomas expressed significantly lower levels of mir-93 and elevated mcm7 as compared with myometrium with limited racial influence or hormonal exposure on their expression. assessing the regulatory function of mir-93/106b through doxycycline-inducible lentiviral transduction in a microarray analysis, tissue factor (f3) and il8 were identified as their possible targets. at the tissue level, leiomyomas expressed a significantly lower level of f3 and an elevated il-8 level, which exhibited an inverse relationship with mir-93 but with limited racial or hormonal influences. the gain of function of mir-93/106b in leiomyoma smooth muscle cells, myometrial smooth muscle cells, and the leiomyosarcoma cell line dose dependently repressed f3 and il8 through direct interactions with their respective 3'-untranslated region and indirectly through f3 repression inhibited il8, ctgf, and pai-1 expression, confirmed by using small interfering rna silencing or factor vlla (fviia) activation of f3, as well as reducing the rate of proliferation, while increasing caspase-3/7 activity. we concluded that differential expression of mir-93/106b and their direct and/or indirect regulatory functions on f3, il8, ctgf, and pai-1 expression, with key roles in inflammation and tissue turnover may be of significance in the outcome of leiomyoma growth and associated symptoms.",1
"micrornas (mirnas) are short non-coding rnas that interfere with translation of specific target mrnas and thereby regulate diverse biological processes. recent studies have suggested that mirnas might have a role in osteoblast differentiation and bone formation. here, we show that mir-542-3p, a well-characterized tumor suppressor whose downregulation is tightly associated with tumor progression via c-src-related oncogenic pathways, inhibits osteoblast proliferation and differentiation. mirna array profiling in medicarpin (a pterocarpan with proven bone-forming effects) induced mice calvarial osteoblast cells and further validation by quantitative real-time pcr revealed that mir-542-3p was downregulated during osteoblast differentiation. over-expression of mir-542-3p inhibited osteoblast differentiation, whereas inhibition of mir-542-3p function by anti-mir-542-3p promoted expression of osteoblast-specific genes, alkaline phosphatase activity and matrix mineralization. target prediction analysis tools and experimental validation by luciferase 3' utr reporter assay identified bmp-7 (bone morphogenetic protein 7) as a direct target of mir-542-3p. it was seen that over-expression of mir-542-3p leads to repression of bmp-7 and inhibition of bmp-7/pi3k- survivin signaling. this strongly suggests that mir-542-3p suppresses osteogenic differentiation and promotes osteoblast apoptosis by repressing bmp-7 and its downstream signaling. furthermore, silencing of mir-542-3p led to increased bone formation, bone strength and improved trabecular microarchitecture in sham and ovariectomized (ovx) mice. although mir-542-3p is known to be a tumor repressor, we have identified second complementary function of mir-542-3p where it inhibits bmp-7-mediated osteogenesis. our findings suggest that pharmacological inhibition of mir-542-3p by anti-mir-542-3p could represent a therapeutic strategy for enhancing bone formation in vivo.",1
"when embryonic stem cells (escs) differentiate, they must both silence the esc self-renewal program and activate new tissue-specific programs. in the absence of dgcr8 (dgcr8(-/-)), a protein required for microrna (mirna) biogenesis, mouse escs are unable to silence self-renewal. here we show that the introduction of let-7 mirnas-a family of mirnas highly expressed in somatic cells-can suppress self-renewal in dgcr8(-/-) but not wild-type escs. introduction of esc cell cycle regulating (escc) mirnas into the dgcr8(-/-) escs blocks the capacity of let-7 to suppress self-renewal. profiling and bioinformatic analyses show that let-7 inhibits whereas escc mirnas indirectly activate numerous self-renewal genes. furthermore, inhibition of the let-7 family promotes de-differentiation of somatic cells to induced pluripotent stem cells. together, these findings show how the escc and let-7 mirnas act through common pathways to alternatively stabilize the self-renewing versus differentiated cell fates.",1
"in the absence of a 5' cap, plant positive-strand rna viruses have evolved a number of different elements in their 3' untranslated region (utr) to attract initiation factors and/or ribosomes to their templates. these 3' cap-independent translational enhancers (3' cites) take different forms, such as i-shaped, y-shaped, t-shaped, or pseudoknotted structures, or radiate multiple helices from a central hub. common features of most 3' cites include the ability to bind a component of the translation initiation factor eif4f complex and to engage in an rna-rna kissing-loop interaction with a hairpin loop located at the 5' end of the rna. the two t-shaped structures can bind to ribosomes and ribosomal subunits, with one structure also able to engage in a simultaneous long-distance rna-rna interaction. several of these 3' cites are interchangeable and there is evidence that natural recombination allows exchange of modular cite units, which may overcome genetic resistance or extend the virus's host range.",1
"the poor prognosis of glioblastoma multiforme (gbm) is largely attributed to their highly invasive nature and mmp-9 plays a pivotal role in regulating invasiveness of malignant glioma cells. micrornas (mirnas) are small non-coding rnas that have been shown to regulate a wide range of biological processes via targeting messenger rna. previous reports have shown many oncogenes regulate survival and invasion via targeting mmp-9 in gbm. but no literature indicates that mirnas regulate glioma cell invasion through targeting mmp-9. here, we show mmp-9 overexpression conferred a poor prognosis in 163 gbm patients. furthermore, mmp-9 specific mirna expression profile (14 positively and 31 negatively correlated mirnas with mmp-9) was established via mirna microarrays in 60 gbm samples. among them, two mirnas: mir-885-5p and mir-491-5p, were chosen for functional validation for their high positive correlation with mmp-9 expression. and upregulation of mir-885-5p and mir-491-5p were demonstrated to reduce the levels of mmp-9 expression and inhibit cellular invasion in u251 and u87 glioma cells. furthermore, we found that mir-491-5p suppressed glioma cell invasion via targeting mmp-9 directly. to our knowledge, this is the first study to identify the mmp-9 specific microrna signature which may provide potential targets for anti-invasion therapy in gbm.",1
"the median survival of patients with mantle cell lymphoma (mcl) ranges from 3 to 5 years with current chemotherapeutic regimens. a common secondary genomic alteration detected in mcl is chromosome 13q31-q32 gain/amplification, which targets a microrna (mirna) cluster, mir-17∼92. on the basis of gene expression profiling, we found that high level expression of c13orf25, the primary transcript from which these mirnas are processed, was associated with poorer survival in patients with mcl (p=0.021). we demonstrated that the protein phosphatase phlpp2, an important negative regulator of the pi3k/akt pathway, was a direct target of mir-17∼92 mirnas, in addition to pten and bim. these proteins were down-modulated in mcl cells with overexpression of the mir-17∼92 cluster. overexpression of mir-17∼92 activated the pi3k/akt pathway and inhibited chemotherapy-induced apoptosis in mcl cell lines. conversely, inhibition of mir-17∼92 expression suppressed the pi3k/akt pathway and inhibited tumor growth in a xenograft mcl mouse model. targeting the mir-17∼92 cluster may therefore provide a novel therapeutic approach for patients with mcl.",1
"background micrornas (mirnas) bind to mrnas and target them for translational inhibition or transcriptional degradation. it is thought that most mirna-mrna interactions involve the seed region at the 5' end of the mirna. the importance of seed sites is supported by experimental evidence, although there is growing interest in interactions mediated by the central region of the mirna, termed centered sites. to investigate the prevalence of these interactions, we apply a biotin pull-down method to determine the direct targets of ten human mirnas, including four isomirs that share centered sites, but not seeds, with their canonical partner mirnas. results we confirm that mirnas and their isomirs can interact with hundreds of mrnas, and that imperfect centered sites are common mediators of mirna-mrna interactions. we experimentally demonstrate that these sites can repress mrna activity, typically through translational repression, and are enriched in regions of the transcriptome bound by ago. finally, we show that the identification of imperfect centered sites is unlikely to be an artifact of our protocol caused by the biotinylation of the mirna. however, the fact that there was a slight bias against seed sites in our protocol may have inflated the apparent prevalence of centered site-mediated interactions. conclusions our results suggest that centered site-mediated interactions are much more frequent than previously thought. this may explain the evolutionary conservation of the central region of mirnas, and has significant implications for decoding mirna-regulated genetic networks, and for predicting the functional effect of variants that do not alter protein sequence.",1
"the notch signaling pathway plays a central role in the development of various organisms. however, dysregulation of micrornas (mirnas), which are crucial regulators of gene expression, can disrupt signaling pathways at all stages of development. although notch signaling is involved in wing development in drosophila, the mechanism underlying mirna-based regulation of the notch signaling pathway is unclear. here, we report that loss of drosophila mir-252 increases the size of adult wings, whereas the overexpression of mir-252 in specific compartments of larval wing discs leads to patterning defects in the adult wings. the mir-252 overexpression-induced wing phenotypes were caused by aberrant notch signaling with intracellular accumulation of the full-length notch receptor during development, which could be due to defects in intracellular notch trafficking associated with its recycling to the plasma membrane and autophagy-mediated degradation. moreover, we identified rab6 as a direct target of mir-252-5p; rab6 encodes a small ras-like gtpase that regulates endosomal trafficking pathways. consistent with this finding, rnai-mediated downregulation of rab6 led to similar defects in both wing patterning and notch signaling. notably, co-overexpression of rab6 completely rescued the wing phenotype associated with mir-252 overexpression, further supporting that rab6 is a biologically relevant target of mir-252-5p in the context of wing development. thus, our data indicate that the mir-252-5p-rab6 regulatory axis is involved in drosophila wing development by controlling the notch signaling pathway.",1
"atherosclerosis (as) is a common disease, which is serious hazard to human health. as the main pathological basis of ischemic cardiac and cerebral vascular disease, including coronary heart disease, cerebrovascular disease, and thromboembolic disease, it is a chronic inflammatory lesion of the arterial vessel wall. so far the pathogenesis of as has not been fully understood. therefore, it is still lack of effective clinical prevention and treatment of drugs. more and more evidence indicate that mirna plays an important role in the pathophysiology of many diseases, especially the occurrence and development of cardiovascular diseases. mirnas are widely detected in human coronary artery endothelial cells, which might participate in diverse biological functions through targeting different as associated genes. the aim of this study was to investigate the molecular mechanisms underlying mir-30s roles in as. our study found the high expression of mir-30b and mir-30e in as clinical samples, identified the regulatory relationship of mir-30b and mir-30e to itga4 and plcg1, respectively, and initially explored the effects of mir-30b and mir-30e on cell cycle and apoptosis through targeting itga4 and plcg1. these data may provide a theoretical basis for clarifying the mechanism of mir-30s in as.",1
"the integral telomerase rna subunit templates the synthesis of telomeric repeats. the biological accumulation of human telomerase rna (htr) requires htr h/aca domain assembly with the same proteins that assemble on other human h/aca rnas. despite this shared rnp composition, htr accumulation is particularly sensitized to disruption by disease-linked h/aca protein variants. we show that contrary to expectation, htr-specific sequence requirements for biological accumulation do not act at an htr-specific step of h/aca rnp biogenesis; instead, they enhance htr binding to the shared, chaperone-bound scaffold of h/aca core proteins that mediates initial rnp assembly. we recapitulate physiological h/aca rnp assembly with a preassembled naf1/dyskerin/nop10/nhp2 scaffold purified from cell extract and demonstrate that distributed sequence features of the htr 3' hairpin synergize to improve scaffold binding. our findings reveal that the htr h/aca domain is distinguished from other human h/aca rnas not by a distinct set of rna-protein interactions but by an increased efficiency of rnp assembly. our findings suggest a unifying mechanism for human telomerase deficiencies associated with h/aca protein variants.",1
"rna interference mediated through antisense transcripts is a fundamentally important mechanism regulating gene expression that remains incompletely understood. here, we have used next-generation sequencing to determine from mouse cd4+ t cells the functional implications of antisense transcripts binding to argonaute (ago) proteins that mediate rna interference and post-transcriptional gene silencing. this effort identified 90 new micrornas (mirnas) and six endogenous hairpin rna-derived small interfering rnas (sirnas) mapping to distinct introns. unexpectedly, 69 mirnas were expressed as non-canonical isomirs as the dominant ago-binding transcript, with extensive 3' terminal nucleotide modifications. furthermore, differential expression analysis between ago1- and ago2-bound mirnas suggested preferential binding of isomirs ending with 3' adenine residues to ago1 and 3' uridine residues to ago2. analysis of the putative targets of all mirnas suggested a striking preference for regulating transcription and transcription factors with additional evidence of a functional division of labor between ago proteins in this regard. we further provide evidence that multiple mitochondrial genomic loci serve as the source of endogenous cis-natural antisense transcripts. these findings imply diversity in ago protein function based on differential mirna binding and indicate that rna interference-based gene regulation is more complex than previously recognized.",1
"purpose adipogenic differentiation of adipose tissue-derived mesenchymal stem cells (amscs) is critical to many disease-related disorders, such as obesity and diabetes. studies have demonstrated that mirna-138 (mir-138) is closely involved in adipogenesis. however, the mechanisms affected by mir-138 remain unclear. this work aimed to investigate interactions between mir-138 and lipoprotein lipase (lpl), a key lipogenic enzyme, in amscs. materials and methods human amscs (hamscs) isolated from human abdomen tissue were subjected to adipogenic differentiation medium. quantitative real-time polymerase chain reaction and western blot assay were applied to measure the expressions of mir-138, lpl, and the two adipogenic transcription factors cytidine-cytidine-adenosine-adenosine-thymidine enhancer binding protein alpha (c/ebpα) and peroxisome proliferator-activated receptor gamma (pparγ). the relationship between mir-138 and lpl was predicted utilizing the mirtarbase database and validated by dual luciferase reporter assay. results showing increases in c/ebpα and pparγ expression levels, hamscs were induced into adipogenic differentiation. during adipogenesis of hamscs, mir-138 expression was significantly downregulated. overexpression of mir-138 by transfection inhibited hamscs adipogenic differentiation in vitro. mechanically, lpl was a target of mir-138. lpl expression was upregulated during adipogenesis of hamscs, and this upregulation was reversed by mir-138 overexpression. functionally, silencing of lpl by transfection exerted similar inhibition of the expressions of c/ebpα and pparγ. meanwhile, lpl ectopic expression was able to partly abolish the suppressive effect of mir-138 overexpression on adipogenic differentiation of hamscs. conclusion upregulation of mir-138 inhibits adipogenic differentiation of hamscs by directly downregulating lpl.",1
"two core small nucleolar rnp (snornp) proteins, nop1p (fibrillarin in vertebrates) and nop58p (also known as nop5p) have previously been reported to be specifically associated with the box c+d class of small nucleolar rnas (snornas). here we report that nop56p, a protein related in sequence to nop58p, is a bona fide box c+d snornp component; all tested box c+d snornas were coprecipitated with protein a-tagged nop56p. analysis of in vivo snornp assembly indicated that nop56p was stably associated with the snornas only in the presence of nop1p. in contrast, nop58p and nop1p associate independently with the snornas. genetic depletion of nop56p resulted in inhibition of early pre-rrna processing events at sites a(0), a(1), and a(2) and mild depletion of 18s rrna. however, nop56p depletion did not lead to codepletion of the box c+d snornas. this is in contrast to nop58p, which was required for the accumulation of all tested box c+d snornas. unexpectedly, we found that nop1p was specifically required for the synthesis and accumulation of box c+d snornas processed from pre-mrna introns and polycistronic transcripts.",1
"our recent study showed that mir-2861 promotes osteoblast differentiation by targeting histone deacetylase 5, resulting in increased runt-related transcription factor 2 (runx2) protein production. here we identified another new microrna (mirna) (mir-3960) that played a regulatory role in osteoblast differentiation through a regulatory feedback loop with mir-2861. mir-3960 and mir-2861 were found clustered at the same loci. mir-3960 was transcribed during bone morphogenic protein 2 (bmp2)-induced osteogenesis of st2 stromal cells. overexpression of mir-3960 promoted bmp2-induced osteoblastogenesis. however, the inhibition of mir-3960 expression attenuated the osteoblastogenesis. homeobox a2 (hoxa2), a repressor of runx2 expression, was confirmed to be a target of mir-3960. electrophoretic mobility shift assay and chromatin immunoprecipitation experiments confirmed that runx2 bound to the promoter of the mir-3960/mir-2861 cluster. furthermore, overexpression of runx2 induced mir-3960/mir-2861 transcription, and block of runx2 expression attenuated bmp2-induced mir-3960/mir-2861 transcription. here we report that mir-3960 and mir-2861, transcribed together from the same mirna polycistron, both function in osteoblast differentiation through a novel runx2/mir-3960/mir-2861 regulatory feedback loop. our findings provide new insights into the roles of mirnas in osteoblast differentiation.",1
"the functional study of lncrnas in skeletal muscle satellite cells (scs) remains at the infancy stage. here we identify sam (sugt1 asssociated muscle) lncrna that is enriched in the proliferating myoblasts. global deletion of sam has no overt effect on mice but impairs adult muscle regeneration following acute damage; it also exacerbates the chronic injury-induced dystrophic phenotype in mdx mice. consistently, inducible deletion of sam in scs leads to deficiency in muscle regeneration. further examination reveals that sam loss results in a cell-autonomous defect in the proliferative expansion of myoblasts. mechanistically, we find sam interacts and stabilizes sugt1, a co-chaperon protein key to kinetochore assembly during cell division. loss of sam or sugt1 both disrupts kinetochore assembly in mitotic cells due to the mislocalization of two components: dsn1 and hec1. altogether, our findings identify sam as a regulator of sc proliferation through facilitating sugt1 mediated kinetochore assembly during cell division.",1
"genome-wide association studies (gwass) have linked genes to various pathological traits. however, the potential contribution of regulatory noncoding rnas, such as micrornas (mirnas), to a genetic predisposition to pathological conditions has remained unclear. we leveraged gwas meta-analysis data from >188,000 individuals to identify 69 mirnas in physical proximity to single-nucleotide polymorphisms (snps) associated with abnormal levels of circulating lipids. several of these mirnas (mir-128-1, mir-148a, mir-130b, and mir-301b) control the expression of key proteins involved in cholesterol-lipoprotein trafficking, such as the low-density lipoprotein (ldl) receptor (ldlr) and the atp-binding cassette a1 (abca1) cholesterol transporter. consistent with human liver expression data and genetic links to abnormal blood lipid levels, overexpression and antisense targeting of mir-128-1 or mir-148a in high-fat diet-fed c57bl/6j and apoe-null mice resulted in altered hepatic expression of proteins involved in lipid trafficking and metabolism, and in modulated levels of circulating lipoprotein-cholesterol and triglycerides. taken together, these findings support the notion that altered expression of mirnas may contribute to abnormal blood lipid levels, predisposing individuals to human cardiometabolic disorders.",1
"micrornas (mirnas) have critical roles in the regulation of gene expression; however, as mirna activity requires base pairing with only 6-8 nucleotides of messenger rna, predicting target mrnas is a major challenge. recently, high-throughput sequencing of rnas isolated by crosslinking immunoprecipitation (hits-clip) has identified functional protein-rna interaction sites. here we use hits-clip to covalently crosslink native argonaute (ago, also called eif2c) protein-rna complexes in mouse brain. this produced two simultaneous data sets-ago-mirna and ago-mrna binding sites-that were combined with bioinformatic analysis to identify interaction sites between mirna and target mrna. we validated genome-wide interaction maps for mir-124, and generated additional maps for the 20 most abundant mirnas present in p13 mouse brain. ago hits-clip provides a general platform for exploring the specificity and range of mirna action in vivo, and identifies precise sequences for targeting clinically relevant mirna-mrna interactions.",1
"hiv-1 infection leads to the development of hiv-associated neurological disorders. the hiv-1 tat protein has been reported to exert an adverse effect on blood-brain barrier integrity and permeability. perturbation in permeability is mainly caused by disruptions in adherens junctions and tight junction proteins. we have identified hiv-1 tat c-induced disruption of ve-cadherin mediated by mirna-101 in human brain microvascular endothelial cells (bmvecs). hiv-1 tat c increased the expression of mir-101, which led to downregulation of ve-cadherin. overexpression of mir-101 resulted into the suppression of ve-cadherin. inhibition of mir-101 by the mirna inhibitor enhanced the expression of ve-cadherin. we have demonstrated that ve-cadherin is a direct target of mir-101 using a luciferase reporter assay, which showed that mutated ve-cadherin 3'utr and mir-101 cotransfection did not change luciferase activity. by overexpression and knockdown of mir-101, we have demonstrated that the expression level of claudin-5 is governed by the expression of ve-cadherin. these findings demonstrate a novel mechanism for the regulation of barrier permeability by mir-101 via posttranscriptional regulation of ve-cadherin in human bmvecs exposed to the hiv-1 tat c protein.",1
"micrornas (mirnas) are post-transcriptional regulators that target specific mrnas for repression and thus play key roles in many biological processes, including insect wing morphogenesis. mir-2 is an invertebrate-specific mirna family that has been predicted in the fruit fly, drosophila melanogaster, to be involved in regulating the notch signaling pathway. we show here that mir-2 plays a critical role in wing morphogenesis in the silkworm, bombyx mori, a lepidopteran model insect. transgenic over-expression of a mir-2 cluster using a gal4/uas system results in deformed adult wings, supporting the conclusion that mir-2 regulates functions essential for normal wing morphogenesis. two genes, abnormal wing disc (awd) and fringe (fng), which are positive regulators in notch signaling, are identified as mir-2 targets and validated by a dual-luciferase reporter assay. the relative abundance of both awd and fng expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. furthermore, somatic mutagenesis analysis of awd and fng using the crispr/cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the mir-2 overexpression transgenic animals. the critical role of mir-2 in bombyx wing morphogenesis may provide a potential target in future lepidopteran pest control.",1
"background and aims alcohol-induced gut leakiness is a key factor in alcoholic liver disease (ald); it allows endotoxin to enter the circulation and initiate liver damage. zonula occludens 1 (zo-1) protein is a major component of tight junctions that regulates intestinal permeability. micrornas (mirnas) are recently discovered regulatory molecules that inhibit expression of their target genes. the aims of our study were (i) to investigate the effect of alcohol on mirna-212 (mir-212) and on expression of its predicted target gene, zo-1, (ii) to study the potential role of mir-212 in the pathophysiology of ald in man. methods using a taqman mirna assay system, we measured mir-212 expression levels in colon biopsy samples from patients with ald and in caco-2 cells (a human intestinal epithelial cell line) treated with or without etoh. we measured zo-1 protein levels using western blots. zo-1 mrna was assayed using real-time pcr. intestinal barrier integrity was measured using fluorescein sulfonic acid clearance and immunofluorescent staining for zo-1. results ethanol increased mir-212 expression, decreased zo-1 protein levels, disrupted tight junctions, and increased the permeability of monolayers of caco-2 cells. an mir-212 over-expression is correlated with hyperpermeability of the monolayer barrier. mir-212 levels were higher in colon biopsy samples in patients with ald than in healthy controls; zo-1 protein levels were lower. conclusion these data suggest a novel mechanism for alcohol-induced gut leakiness, one in which etoh induces mir-212 over-expression which causes gut leakiness by down-regulating zo-1 translation. this mechanism is a potential therapeutic target for leaky gut in patients with or at risk for ald.",1
"cellular and systemic responses to low oxygen levels are principally mediated by hypoxia inducible factors (hifs), a family of evolutionary conserved heterodimeric transcription factors, whose alpha- and beta-subunits belong to the bhlh-pas family. in normoxia, hifα is hydroxylated by specific prolyl-4-hydroxylases, targeting it for proteasomal degradation, while in hypoxia the activity of these hydroxylases decreases due to low oxygen availability, leading to hifα accumulation and expression of hif target genes. to identify micrornas required for maximal hif activity, we conducted an overexpression screen in drosophila melanogaster, evaluating the induction of a hif transcriptional reporter. mir-190 overexpression enhanced hif-dependent biological responses, including terminal sprouting of the tracheal system, while in mir-190 loss of function embryos the hypoxic response was impaired. in hypoxic conditions, mir-190 expression was upregulated and required for induction of hif target genes by directly inhibiting the hif prolyl-4-hydroxylase fatiga. thus, mir-190 is a novel regulator of the hypoxia response that represses the oxygen sensor fatiga, leading to hifα stabilization and enhancement of hypoxic responses.",1
"iga nephropathy (igan) is the most common type of primary glomerulonephritis, characterized by mesangial deposition of pathogenic iga and the injury to mesangial cells. our previous studies indicate that secretory iga (siga) plays an important role in the pathogenesis of igan, and mir-16 is involved in destructive process in mesangial cells mediated by the siga from igan patients. our current study aimed to study the role of mirnas in the effect of siga from igan patients on mesangial cells. microrna microarray and cytokines assay were performed to obtain the differential micrornas expression profile in human renal mesangial cells stimulated by siga from igan patients (p-siga) with the cells treated by siga from healthy subjects (n-sga) as control. the micrornas with the most significant differences in microarray analysis were validated by quantitative rt-pcr. among them, mir-100-3p and mir-877-3p were selected to predict target gene related to cytokines detecting in this study. fifty-six differentially expressed micrornas were chosen and 17 micrornas with the most prominent changes were validated. compared with n-siga, p-siga increased the production of interleukin (il)-1β, il-8, monocyte chemotactic protein-1 and transforming growth factor-β1. in addition, we for the first time demonstrated that over-production of il-8 induced by the siga was regulated by down-expression of mir-100-3p in mesangial cells. similarly, il-1β over-production was regulated by down-expression of mir-877-3p. our findings represent a pathogenic micrornas expression profiling in human mesangial cells activated by p-siga. furthermore, we provide a new explanation characterizing the molecular mechanism responsible for the regulation of il-1β and il-8 production in p-siga-triggered mesangial cells.",1
"we have derived a secondary structure model for the c-myc internal ribosome entry segment (ires) by using information from chemical probing of the c-myc ires rna to constrain structure prediction programs. our data suggest that the ires is modular in nature, and can be divided into two structural domains linked by a long unstructured region. both domains are required for full ires function. domain 1 is a complex element that contains a gnnra apical loop and an overlapping double pseudoknot motif that is topologically unique amongst published rna structures. domain 2, the smaller of the two, contains an apical auuu loop. we have located the ribosome landing site and have shown that ribosomes enter in a 16 nt region downstream of the pseudoknots in a situation similar to that observed in several viral iress. to test the structure, several key regions of the ires were mutated and, interestingly, it appears that some of the structural elements that we have identified function to repress c-myc ires function. this has profound implications for de-regulation of c-myc expression by mutations occurring in the ires.",1
"unlabelled micrornas have been shown to function in cartilage development and homeostasis, as well as in progression of osteoarthritis. the objective of the current study was to identify micrornas involved in the onset or early progression of osteoarthritis and characterise their function in chondrocytes. microrna expression in mouse knee joints post-dmm surgery was measured over 7 days. expression of mir-29b-3p was increased at day 1 and regulated in the opposite direction to its potential targets. in a mouse model of cartilage injury and in end-stage human oa cartilage, the mir-29 family was also regulated. sox9 repressed expression of mir-29a-3p and mir-29b-3p via the 29a/b1 promoter. tgfβ1 decreased expression of mir-29a, b, and c (3p) in primary chondrocytes, whilst il-1β increased (but lps decreased) their expression. the mir-29 family negatively regulated smad, nfκb, and canonical wnt signalling pathways. expression profiles revealed regulation of new wnt-related genes. amongst these, fzd3, fzd5, dvl3, frat2, and ck2a2 were validated as direct targets of the mir-29 family. these data identify the mir-29 family as micrornas acting across development and progression of oa. they are regulated by factors which are important in oa and impact on relevant signalling pathways. key messages expression of the mir-29 family is regulated in cartilage during osteoarthritis. sox9 represses expression of the mir-29 family in chondrocytes. the mir-29 family is regulated by tgf-β1 and il-1 in chondrocytes. the mir-29 family negatively regulates smad, nfκb, and canonical wnt signalling. several wnt-related genes are direct targets of the mir-29 family.",1
"repression of an essential nucleolar small nuclear rna (snrna) gene of saccharomyces cerevisiae was shown to result in impaired production of 18s rrna. the effect, observed for an snrna species of 128 nucleotides (snr128), was evident within one generation after the onset of snr128 gene repression and correlated well with depletion of the snrna. the steady-state mass ratio of 18s rna to 25s rna decreased eightfold over the course of the analysis. results from pulse-chase assays revealed the basis of the imbalance to be underaccumulation of 18s rna and its 20s precursor. this effect appears to result from impairment of processing of the 35s rrna transcript at sites that define the 20s species coupled with rapid turnover of unstable intermediates. possible bases for the effects observed are discussed. a common u14 designation is proposed for the structurally related yeast snrna and 4.5s hybrnas from amphibians and mammals.",1
"il-6/stat3 is associated with the regulation of transcription of key cellular regulatory genes (micrornas) during different types of liver injury. this study evaluated the role of il-6/stat3 in regulating mirna and mir-21 in alcoholic liver disease. by microarray, we identified that ethanol feeding significantly up-regulated 0.8% of known micrornas in mouse liver compared with controls, including mir-21. similarly, the treatment of normal human hepatocytes (n-heps) and hepatic stellate cells (hscs) with ethanol and il-6 significantly increased mir-21 expression. overexpression of mir-21 decreased ethanol-induced apoptosis in both n-heps and hscs. the expression level of mir-21 was significantly increased after stat3 activation in n-heps and hscs, in support of the concept that the 5'-promoter region of mir-21 is regulated by stat3. using real time pcr, we confirmed that mir-21 activation is associated with ethanol-linked stat3 binding of the mir-21 promoter. a combination of bioinformatics, pcr array, dual-luciferase reporter assay, and western blot analysis revealed that fas ligand (tnf superfamily, member 6) (faslg) and death receptor 5 (dr5) are the direct targets of mir-21. furthermore, inhibition of mir-21 by specific vivo-morpholino and knock-out of il-6 in ethanol-treated mice also increased the expression of dr5 and faslg in vivo during alcoholic liver injury. the identification of mir-21 as an important regulator of hepatic cell survival, transformation, and remodeling in vitro, as well as its upstream modulators and downstream targets, will provide insight into the involvement of altered mirna expression in contributing to alcoholic liver disease progression and testing novel therapeutic approaches for human alcoholic liver diseases.",1
"aims we have recently reported that microrna-34a (mir-34a) regulates vascular smooth muscle cell (vsmc) differentiation from stem cells in vitro and in vivo. however, little is known about the functional involvements of mir-34a in vsmc functions and vessel injury-induced neointima formation. in the current study, we aimed to establish the causal role of mir-34a and its target genes in vsmc proliferation, migration and neointima lesion formation. methods and results various pathological stimuli regulate mir-34a expression in vsmcs through a transcriptional mechanism, and the p53 binding site is required for mir-34a gene regulation by these stimuli. mir-34a over-expression in serum-starved vsmcs significantly inhibited vsmc proliferation and migration, while knockdown of mir-34a dramatically promoted vsmc proliferation and migration, respectively. notch homolog 1 (notch1), a well-reported regulator in vsmc functions and arterial remodeling, was predicted as one of the top targets of mir-34a by using several computational mirna target prediction tools, and was negatively regulated by mir-34a in vsmcs. luciferase assay showed mir-34a substantially repressed wild type notch1-3'-utr-luciferase activity in vsmcs, but not mutant notch1-3'-utr-luciferease reporter, confirming the notch1 is the functional target of mir-34a in vsmcs. data from co-transfection experiments also revealed that mir-34a inhibited vsmc proliferation and migration through modulating notch gene expression levels. importantly, the expression level of mir-34a was significantly down-regulated in injured arteries, and mir-34a perivascular over-expression significantly reduced notch1 expression levels, decreased vsmc proliferation, and inhibited neointima formation in wire-injured femoral arteries. conclusion our data have demonstrated that mir-34a is an important regulator in vsmc functions and neointima hyperplasia, suggesting its potential therapeutic application for vascular diseases.",1
"in mammals, birth entails complex metabolic adjustments essential for neonatal survival. using a mouse knockout model, we identify crucial biological roles for the mir-379/mir-410 cluster within the imprinted dlk1-dio3 region during this metabolic transition. the mir-379/mir-410 locus, also named c14mc in humans, is the largest known placental mammal-specific mirna cluster, whose 39 mirna genes are expressed only from the maternal allele. we found that heterozygote pups with a maternal--but not paternal--deletion of the mirna cluster display partially penetrant neonatal lethality with defects in the maintenance of energy homeostasis. this maladaptive metabolic response is caused, at least in part, by profound changes in the activation of the neonatal hepatic gene expression program, pointing to as yet unidentified regulatory pathways that govern this crucial metabolic transition in the newborn's liver. not only does our study highlight the physiological importance of mirna genes that recently evolved in placental mammal lineages but it also unveils additional layers of rna-mediated gene regulation at the dlk1-dio3 domain that impose parent-of-origin effects on metabolic control at birth and have likely contributed to mammal evolution.",1
"the epithelial-mesenchymal transition (emt) is a crucial step in epithelial cancer invasion and metastasis. the aims of this study were to investigate and validate unidentified micro rnas (mirnas) that regulate emt and to reveal their clinical relevance in epithelial cancer patients. by applying mirna array screening in a natural epithelial-mesenchymal phenotype cell line pair and in a transforming growth factor β-induced emt cell model, we found mir-153 was markedly downregulated in the cells that underwent an emt. a close association was confirmed between inhibition of mir-153 and the emt phenotype, as well as the invasive ability of epithelial cancer cells. ectopic expression of mir-153 in mesenchymal-like cells resulted in an epithelial morphology change with decreased cellular invasive ability. on the contrary, transfection of a mir-153 inhibitor in epithelial-like cells led to a mesenchymal phenotype change. in vivo ectopic expression of mir-153 significantly inhibited tumor cell metastasis formation. data from the dual-luciferase reporter gene assay showed, for the first time, that snai1 and zeb2 were direct targets of mir-153. inverse correlations were also observed between mir-153 and sna1 and zeb2 levels in oral cancer patients' samples. furthermore, low expression level of mir-153 was found to be significantly related to metastasis and poor prognosis in oral cancer patients. these data demonstrate that mir-153 is a novel regulator of emt by targeting snai1 and zeb2 and indicate its potential therapeutic value for reducing cancer metastasis.",1
"background most patients with breast cancer in advanced stages of the disease suffer from bone metastases which lead to fractures and nerve compression syndromes. microrna dysregulation is an important event in the metastases of breast cancer to bone. microrna-124 (mir-124) has been proved to inhibit cancer progression, whereas its effect on bone metastases of breast cancer has not been reported. therefore, this study aimed to investigate the role and underlying mechanism of mir-124 in bone metastases of breast cancer. methods in situ hybridization (ish) was used to detect the expression of mir-124 in breast cancer tissues and bone metastatic tissues. ventricle injection model was constructed to explore the effect of mir-124 on bone metastasis in vivo. the function of cancer cell derived mir-124 in the differentiation of osteoclast progenitor cells was verified in vitro. dual-luciferase reporter assay was conducted to confirm interleukin-11 (il-11) as a mir-124 target. the involvement of mir-124/il-11 in the prognosis of breast cancer patients with bone metastasis was determined by kaplan-meier analysis. results herein, we found that mir-124 was significantly reduced in metastatic bone tissues from breast cancers. down-regulation of mir-124 was associated with aggressive clinical characteristics and shorter bone metastasis-free survival and overall survival. restoration of mir-124 suppressed, while inhibition of mir-124 promoted the bone metastasis of breast cancer cells in vivo. at the cellular level, gain of function and loss-of function assays indicated that cancer cell-derived mir-124 inhibited the survival and differentiation of osteoclast progenitor cells. at the molecular level, we demonstrated that il-11 partially mediated osteoclastogenesis suppression by mir-124 using in vitro and in vivo assays. furthermore, il-11 levels were inversely correlated with mir-124, and up-regulation il-11 in bone metastases was associated with a poor prognosis. conclusions thus, the identification of a dysregulated mir-124/il-11 axis helps elucidate mechanisms of breast cancer metastases to bone, uncovers new prognostic markers, and facilitates the development of novel therapeutic targets to treat and even prevent bone metastases of breast cancer.",1
"the hippo signaling pathway is highly conserved from drosophila to mammals and plays a central role in maintaining organ size and tissue homeostasis. the blood-brain barrier (bbb) physiologically isolates the brain from circulating blood or the hemolymph system, and its integrity is strictly maintained to perform sophisticated neuronal functions. until now, the underlying mechanisms of subperineurial glia (spg) growth and bbb maintenance during development are not clear. here, we report an mir-285 -yorkie (yki)/multiple ankyrin repeats single kh domain (mask) double-negative feedback loop that regulates spg growth and bbb integrity. flies with a loss of mir-285 have a defective bbb with increased spg ploidy and disruptive septate junctions. mechanistically, mir-285 directly targets the yki cofactor mask to suppress yki activity and down-regulates the expression of its downstream target cyclin e , a key regulator of cell cycle. disturbance of cyclin e expression in spg causes abnormal endoreplication, which leads to aberrant dna ploidy and defective septate junctions. moreover, the expression of mir-285 is increased by knockdown of yki or mask and is decreased with yki overexpression, thus forming a double-negative feedback loop. this regulatory loop is crucial for sustaining an appropriate yki/mask activity and cyclin e level to maintain spg ploidy and bbb integrity. perturbation of this signaling loop, either by dysregulated mir-285 expression or yki activity, causes irregular spg ploidy and bbb disruption. furthermore, ectopic expression of mir-285 promotes canonical hippo pathway-mediated apoptosis independent of the p53 or jnk pathway. collectively, these results reveal an exquisite regulatory mechanism for bbb maintenance through an mir-285 -yki/mask regulatory circuit.",1
"gaucher disease is an autosomal recessive disorder caused by deficiency of the enzyme glucocerebrosidase. although it is a monogenic disease, there is vast phenotypic heterogeneity, even among patients with the same genotype. micrornas (mirnas) are small non-coding rnas involved in many biological processes and diseases. to determine whether mirnas can affect glucocerebrosidase activity, we performed a screen of 875 different mirna mimics. the screen was performed using gaucher fibroblasts, and glucocerebrosidase activity was used as the initial outcome parameter. we found several mirnas that either up- or down-regulated glucocerebrosidase activity. in follow-up assays, we confirmed that one specific mirna (mir-127-5p) down-regulated both glucocerebrosidase activity and protein levels by down-regulation of limp-2, the receptor involved in proper trafficking of glucocerebrosidase from the endoplasmic reticulum to the lysosome. a conditioned media assay demonstrated that cells treated with this mirna secreted glucocerebrosidase into the extracellular environment, supporting impaired limp-2 function. two other mirnas, mir-16-5p and mir-195-5p, were found to up-regulate glucocerebrosidase activity by greater than 40% and to enhance expression and protein levels of the enzyme. in conclusion, we show that mirnas can alter glucocerebrosidase activity in patient cells, indicating that mirnas can potentially act as modifiers in gaucher disease.",1
"the regulation of gene expression in cells, including by micrornas (mirnas), is a dynamic process. current methods for identifying mirna targets by combining sequence and mirna and mrna expression data do not adequately use the temporal information and thus miss important mirnas and their targets. we developed the mirna dynamic regulatory events miner (mirdrem), a probabilistic modeling method that uses input-output hidden markov models to reconstruct dynamic regulatory networks that explain how temporal gene expression is jointly regulated by mirnas and transcription factors. we measured mirna and mrna expression for postnatal lung development in mice and used mirdrem to study the regulation of this process. the reconstructed dynamic network correctly identified known mirnas and transcription factors. the method has also provided predictions about additional mirnas regulating this process and the specific developmental phases they regulate, several of which were experimentally validated. our analysis uncovered links between mirnas involved in lung development and differentially expressed mirnas in idiopathic pulmonary fibrosis patients, some of which we have experimentally validated using proliferation assays. these results indicate that some disease progression pathways in idiopathic pulmonary fibrosis may represent partial reversal of lung differentiation.",1
"abcc9 genetic polymorphisms are associated with increased risk for various human diseases including hippocampal sclerosis of aging. the main goals of this study were 1 > to detect the abcc9 variants and define the specific 3' untranslated region (3'utr) for each variant in human brain, and 2 > to determine whether a polymorphism (rs704180) associated with risk for hippocampal sclerosis of aging pathology is also associated with variation in abcc9 transcript expression and/or splicing. rapid amplification of abcc9 cdna ends (3'race) provided evidence of novel 3' utr portions of abcc9 in human brain. in silico and experimental studies were performed focusing on the single nucleotide polymorphism, rs704180. analyses from multiple databases, focusing on rs704180 only, indicated that this risk allele is a local expression quantitative trait locus (eqtl). analyses of rna from human brains showed increased abcc9 transcript levels in individuals with the risk genotype, corresponding with enrichment for a shorter 3' utr which may be more stable than variants with the longer 3' utr. microrna transfection experiments yielded results compatible with the hypothesis that mir-30c causes down-regulation of sur2 transcripts with the longer 3' utr. thus we report evidence of complex abcc9 genetic regulation in brain, which may be of direct relevance to human disease. abcc9 gene variants are associated with increased risk for hippocampal sclerosis of aging (hs-aging--a prevalent brain disease with symptoms that mimic alzheimer's disease). we describe novel abcc9 variants in human brain, corresponding to altered 3'utr length, which could lead to targeting by mir-30c. we also determined that the hs-aging risk mutation is associated with variation in abcc9 transcript expression.",1
"vertebrate genomes each encode hundreds of micro-rnas (mirnas), yet for few of these mirnas is there empirical evidence as to which mrna(s) they regulate. here we report the identification of human lin-28 mrna as a regulatory target of human mir-125b and its homolog mir-125a. studies of mir-125b function in mouse p19 embryonal carcinoma cells induced to develop into neurons suggest a role for this regulatory mirna in mammalian neuronal differentiation, since its increased concentration in these cells contributes to lin-28 downregulation. within the lin-28 3' untranslated region (utr) are two conserved mirna responsive elements (mires) that mediate repression by mir-125b and mir-125a. simultaneous deletion of both mires renders the lin-28 3' utr almost completely insensitive to these mirnas, indicating that these two mires are the principal elements in the lin-28 3' utr that respond to mir-125. at the 3' end of each element is an adenosine residue that makes a significant contribution to function irrespective of its complementarity to the 5'-terminal nucleotide of mir-125. by contrast to most earlier reports of gene repression by other mirnas that are imperfectly complementary to their targets, lin-28 downregulation by mir-125 involves reductions in both translational efficiency and mrna abundance. the decrease in the mrna concentration is achieved by a posttranscriptional mechanism that is independent of the inhibitory effect on translation.",1
"the branch site of group ii introns is typically a bulged adenosine near the 3'-end of intron domain 6. the branch site is chosen with extraordinarily high fidelity, even when the adenosine is mutated to other bases or if the typically bulged adenosine is paired. given these facts, it has been difficult to discern the mechanism by which the proper branch site is chosen. in order to dissect the determinants for branch-point recognition, new mutations were introduced in the vicinity of the branch site and surrounding domains. single mutations did not alter the high fidelity for proper branch-site selection. however, several combinations of mutations moved the branch site systematically to new positions along the domain 6 stem. analysis of those mutants, together with a new alignment of domain 5 and domain 6 sequences, reveals a set of structural determinants that appear to govern branch-site selection by group ii introns.",1
"background the hippo tumor-suppressor pathway has emerged as a key signaling pathway that controls tissue size in drosophila. hippo signaling restricts tissue size by promoting apoptosis and cell-cycle arrest, and animals carrying clones of cells mutant for hippo develop severely overgrown adult structures. the hippo pathway is thought to exert its effects by modulating gene expression through the phosphorylation of the transcriptional coactivator yorkie. however, how yorkie regulates growth, and thus the identities of downstream target genes that mediate the effects of hippo signaling, are largely unknown. results here, we report that the bantam microrna is a downstream target of the hippo signaling pathway. in common with hippo signaling, the bantam microrna controls tissue size by regulating cell proliferation and apoptosis. we found that hippo mutant cells had elevated levels of bantam activity and that bantam was required for yorkie-driven overgrowth. additionally, overexpression of bantam was sufficient to rescue growth defects of yorkie mutant cells and to suppress the cell death induced by hippo hyperactivation. hippo regulates bantam independently of cyclin e and diap1, two other hippo targets, and overexpression of bantam mimics overgrowth phenotypes of hippo mutant cells. conclusions our data indicate that bantam is an essential target of the hippo signaling pathway to regulate cell proliferation, cell death, and thus tissue size.",1
"only few small, regulatory rnas encoded opposite another gene have been identified in bacteria. here, we report the characterization of a locus where a small rna (symr) is encoded in cis to an sos-induced gene whose product shows homology to the antitoxin maze (syme). synthesis of the syme protein is tightly repressed at multiple levels by the lexa repressor, the symr rna and the lon protease. syme co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased rna degradation. these properties are shared with several rna endonuclease toxins of the toxin-antitoxin modules, and we show that the syme protein represents evolution of a toxin from the abrb fold, whose representatives are typically antitoxins. we suggest that syme promotion of rna cleavage may be important for the recycling of rnas damaged under sos-inducing conditions.",1
"increasing significance of tumor-stromal interaction in development and progression of cancer implies that signaling molecules in the tumor microenvironment (tme) might be the effective therapeutic targets for hepatocellular carcinoma (hcc). here, the role of microrna mir-199a-3p in the regulation of tme and development of hcc has been investigated by several in vitro and in vivo assays. expression of mir-199a-3p was observed significantly low in hcc tissues and its overexpression remarkably inhibited in vivo tumor growth and metastasis to lung in nod-scid mice. in vitro restoration of mir-199a-3p expression either in endothelial cells (ecs) or in cancer cells (cacs) significantly diminished migration of ecs in co-culture assay. again incubation of mir-199a-3p transfected ecs with either conditioned media (cm) of cacs or recombinant vegf has reduced tube formation, in ecs and it was also dropped upon growth in cm of either anti-vegf antibody-treated or mir-199a-3p-transfected cacs. in addition, bioinformatics and luciferase-reporter assays revealed that mir-199a-3p inhibited vegf secretion from cacs and vegfr1 and vegfr2 expression on ecs and thus restricted cross talk between cacs and ecs. again, restoration of mir-199a-3p in hepatic stellate cells (hscs) reduced migration and invasion of cacs in co-culture assay, while it was enhanced by the overexpression of hgf suggesting mir-199a-3p has hindered hsc-cacs cross talk probably by inhibiting hgf and regulating matrix metalloproteinase mmp2, which were found as targets of mir-199a-3p subsequently by luciferase-reporter assay and gelatin zymography, respectively. thus, these findings collectively highlight that mir-199a-3p restricts metastasis, invasion and angiogenesis in hcc and hence it may be considered as one of the powerful effective therapeutics for management of hcc patients.",1
"quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. during the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont sinorhizobium meliloti, we predicted and verified a direct interaction between the 5'-utr of sini mrna encoding the autoinducer synthase and a small rna (srna), which we named rcsr1. in vitro, rcsr1 prevented cleavage in the 5'-utr of sini by rnase e and impaired sini translation. in line with low ribosomal occupancy and transcript destabilization upon binding of rcsr1 to sini, overproduction of rcsr1 in s. meliloti resulted in lower level and shorter half-life of sini mrna, and in decreased autoinducer amount. although rcsr1 can influence quorum sensing via sini, its level did not vary at different cell densities, but decreased under salt stress and increased at low temperature. we found that rcsr1 and its stress-related expression pattern, but not the interaction with sini homologs, are conserved in sinorhizobium, rhizobium and agrobacterium. consistently, overproduction of rcsr1 in s. meliloti and agrobacterium tumefaciens inhibited growth at high salinity. we identified conserved targets of rcsr1 and showed that most conserved interactions and the effect on growth under salt stress are mediated by the first stem-loop of rcsr1, while its central part is responsible for the species-specific interaction with sini. we conclude that rcsr1 is an ancient, stress-related riboregulator in rhizobia and propose that it links stress responses to quorum sensing in s. meliloti.",1
"telomerase is a ribonucleoprotein reverse transcriptase that replicates the ends of chromosomes, thus maintaining genome stability. telomerase ribonucleoprotein assembly is primarily mediated by the rna binding domain (trbd) of the enzyme. here we present the high-resolution trbd structure of the vertebrate, takifugu rubripes (trtrbd). the structure shows that with the exception of the n-terminal linker, the trtrbd is conserved with the tribolium castaneum and tetrahymena thermophila trbds, suggesting evolutionary conservation across species. the structure provides a view of the structural organization of the vertebrate-specific vsr motif that binds the activation domain (cr4/5) of the rna component of telomerase. it also reveals a motif (tfly) that forms part of the t-cp pocket implicated in template boundary element (tbe) binding. mutant proteins of conserved residues that consist of part of the t and tfly motifs disrupt trtrbd-tbe binding and telomerase activity and processivity, supporting an essential role of these motifs in telomerase rnp assembly and function.",1
"micrornas aberrant behavior in heptocellular carcinoma (hcc) plays a major role in hcc pathogenesis. mir-615-5p expression has never been evaluated in hcc. we showed that mir-615-5p was preferentially expressed in hcc, cirrhotic liver tissues and hcc cell lines, but undetected in normal livers. forced mir-615-5p expression in hcc cell lines led to significant decrease in cell growth and migration. in-silico predication revealed insulin-like growth factor-ii (igf-ii) as a potential downstream target for mir-615-5p. forcing the expression of mir-615-5p showed downregulation of igf-ii mrna, as well as inhibition of the luciferase activity in a luciferase reporter vector harboring the igf-ii-3'utr target sequence. mir-615-5p acts as tumor-suppressor in hcc through targeting igf-ii.",1
"pulmonary arterial hypertension (pah) is characterized by vascular remodeling associated with obliteration of pulmonary arterioles and formation of plexiform lesions composed of hyperproliferative endothelial and vascular smooth-muscle cells. here we describe a microrna (mirna)-dependent association between apelin (apln) and fibroblast growth factor 2 (fgf2) signaling in pulmonary artery endothelial cells (paecs). apln deficiency in these cells led to increased expression of fgf2 and its receptor fgfr1 as a consequence of decreased expression of mir-424 and mir-503, which directly target fgf2 and fgfr1. mir-424 and mir-503 were downregulated in pah, exerted antiproliferative effects in paecs and inhibited the capacity of paec-conditioned medium to induce the proliferation of pulmonary artery smooth-muscle cells. reconstitution of mir-424 and mir-503 in vivo ameliorated pulmonary hypertension in experimental models. these studies identify an apln-dependent mirna-fgf signaling axis needed for the maintenance of pulmonary vascular homeostasis.",1
"reduced microrna (mirna) let-7a expression and the activation of insulin-like growth factor-1 receptor (igf1r) signalling are both involved in prostate cancer and progression. in the present study, we demonstrated that the growth inhibitory effect of let-7a1 is directly related to targeting igf1r gene expression in pc-3 cells. targetscan predicted three potential target sites (t1, t2 and t3) of let-7a in the 3' untranslational region (3' utr) of igf1r mrna. real-time pcr, western blot and luciferase reporter assays were used to detect the effects of let-7a1 overexpression or let-7a1 inhibitor on the igf1r gene expression in pc-3 cells. the results indicated that let-7a1 could inhibit igf1r expression by directly targeting the t1 and t2 sites in the 3' utr of the igf1r mrna. we then used rt-pcr, luciferase reporter assays, 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyl-2h-tetrazolium bromide (mtt) assay, flow cytometry and hoechst 33342 staining to examine whether let-7a1-mediated inhibition of igf1r expression also affects the igf1r-mediated signalling events, including elk1 activity and c-fos gene expression, proliferation, apoptosis and cell cycle. we demonstrated that let-7a1-mediated igf1r downregulation was accompanied by attenuation of elk1 activity and c-fos expression, inhibition of cell proliferation, enhanced apoptosis and cell cycle arrest, and that loss function of let-7a1 via inhibition can upregulate igf1r accompanied by an increase of elk1 activity and c-fos expression, thereby enhancing cell proliferation. altogether, these findings suggest that let-7a may be novel therapeutic candidate for prostate cancer.",1
"expression of the cytokine-inducible src homology 2 (cis) protein and suppressors of cytokine signaling (socs) proteins represents an important element of host cell reactions in response to infection. we have demonstrated previously that cryptosporidium parvum infection down-regulates microrna-98 (mir-98) and let-7 to induce cis expression in biliary epithelial cells. we report here that down-regulation of mir-98 and let-7 also coordinates epithelial expression of socs4 after c. parvum infection. targeting of the socs4 3' untranslated region by mir-98 or let-7 resulted in translational repression. functional manipulation of mir-98 caused reciprocal alterations in socs4 protein expression. transfection of mir-98 precursor abolished c. parvum-stimulated socs4 up-regulation. moreover, expression of socs4 in epithelial cells showed an inhibitory effect on phosphorylation of signal transducers and activators of transcription proteins induced by c. parvum. these data suggest that mirnas play an important role in the coordinated regulation of cis and socs expression in epithelial cells in response to c. parvum infection.",1
"micrornas (mirnas) are noncoding rnas of approximately 22 nucleotides in length that negatively regulate the post-transcriptional expression by translational repression and/or destabilization of protein-coding mrnas. the impact of mirnas on protein output was recently shown that although some targets were repressed without detectable changes in mrna levels, those translationally repressed by more than a third also displayed detectable mrna destabilization, and, for the more highly repressed targets, mrna destabilization usually comprised the major component of repression. thus, comparative profilings of mirnas and mrnas from the same samples of different cell types may identify the putative targets of mirnas. in this investigation, both mirna and mrna profiles from the undifferentiated human embryonic stem cell line hes-t3 (t3es), hes-t3 derived embryoid bodies (t3eb), and hes-t3 differentiated fibroblast-like cells (t3df) were compared, and 58 genes were found to be targets of four hes cell-specific mirnas mir-302d, mir-372, mir-200c and/or mir-367 by inverse expression levels (highly negative correlation) of mirnas to their target mrnas. approximately half of these 58 targets are involved in gene transcription. three common target genes trps1, klf13 and mbnl2 of three highly expressed mirnas mir-302d, mir-372, and mir-200c were identified, and the target sites of both mir-302d and mir-372 in the 3'utr of trps1, klf13, and mbnl2 genes were confirmed by the luciferase assay. the highly expressed mrnas and mirna target mrnas involved in kegg pathways among t3es, t3eb, and t3df cells were also compared, and the expression levels of target mrnas predicted by abundantly expressed mirnas were found to be three- to sixfold lower than those of non-target mrnas involved in the same signaling pathways.",1
"firre encodes a lncrna involved in nuclear organization. here, we show that firre rna expressed from the active x chromosome maintains histone h3k27me3 enrichment on the inactive x chromosome (xi) in somatic cells. this trans-acting effect involves suz12, reflecting interactions between firre rna and components of the polycomb repressive complexes. without firre rna, h3k27me3 decreases on the xi and the xi-perinucleolar location is disrupted, possibly due to decreased ctcf binding on the xi. we also observe widespread gene dysregulation, but not on the xi. these effects are measurably rescued by ectopic expression of mouse or human firre/firre transgenes, supporting conserved trans-acting roles. we also find that the compact 3d structure of the xi partly depends on the firre locus and its rna. in common lymphoid progenitors and t-cells firre exerts a cis-acting effect on maintenance of h3k27me3 in a 26 mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncrna.",1
"thousands of atypical micrornas (mirnas) have been described in the genomes of animals; however, it is unclear if many of these non-canonical mirnas can measurably influence phenotypes. mirtrons are the largest class of non-canonical mirnas that are produced from hairpins excised by splicing, which after debranching become substrates for dicer and load into risc. most mirtrons require additional processing after splicing to remove 'tail' residues interposed between one of the host intron splice sites and base of the hairpin precursor structure. despite most mirtrons requiring tail removal no function has been elucidated for a tailed species, indeed for all mirtrons identified function has only been assigned to a single species. here we study mir-1017, a mirtron with a 3' tail, which is well expressed and conserved in drosophila species. we found that mir-1017 can extend lifespan when ectopically expressed in the neurons, which seems partly due to this mirna targeting its host transcript, acetylcholine receptor dα2. unexpectedly we found that not only did mir-1017 function in trans but also in cis by affecting splicing of dα2. this suggests a mechanism for mirtron evolution where initial roles of structural elements in splicing lead to secondary acquisition of trans-regulatory function.",1
"the aim of the present study was to investigate the expression of microrna (mir)-146a in the pulmonary macrophages, peripheral blood mononuclear cells and serum of patients with lung injury caused by paraquat poisoning, as well as the underlying mechanism of its regulation in the disease. a total of 26 patients with lung injury caused by paraquat poisoning were included in the present study. in addition, 33 healthy subjects were included as the control group. the expression levels of interleukin (il)-6 mrna and mir-146a was determined by reverse transcription-quantitative polymerase chain reaction (rt-qpcr). western blotting was used to measure il-6 protein expression, while enzyme-linked immunosorbent assay was also performed to determine the secretion of il-6 protein. a dual-luciferase reporter assay was conducted to examine whether il-6 mrna is a direct target of mir-146a. patients with lung injury caused by paraquat poisoning exhibited higher il-6 mrna and protein levels as compared with those in healthy subjects. in addition, mir-146a expression in patients with paraquat poisoning-induced lung injury was significantly reduced in comparison with that in healthy subjects. notably, the overexpression of mir-146a by mimic transfection downregulated the expression of il-6 in pulmonary macrophages. the results of dual-luciferase reporter assay demonstrated that il-6 mrna was a direct target of mir-146a. therefore, the present study demonstrated that increased expression of il-6 in patients with lung injury caused by paraquat poisoning is associated with decreased expression of mir-146a. furthermore, mir-146a may regulate the occurrence and immune response of lung injury caused by paraquat poisoning and this process is possibly achieved via il-6, an important cytokine that mediates inflammation.",1
"whereas methods to comprehensively study cellular roles of protein-coding genes are available, techniques to systematically investigate long noncoding rnas (lncrnas), which have been implicated in diverse biological pathways, are limited. here we report combined knockdown and localization analysis of noncoding rnas (c-klan) that merges functional characterization and localization approaches to study lncrnas. using this technique we identified transcripts that regulate mouse embryonic stem cell identity.",1
"we present a linkage map of intracisternal a-particle (iap) proviral loci. the iap family consists of 2000 endogenous proviral elements that are widely dispersed in the mouse genome. the map was constructed by using an interspecific backcross and markers defined by oligonucleotide probes specific for subclasses of expressed iap elements. in genomic dna from c57bl/6j mouse, these probes each detected from 12 to 44 hindiii restriction fragments that represent junctions between proviral and 5'-flanking dna. the fragments have characteristic strain distribution patterns (sdps) that are particularly polymorphic in the dnas of c57bl/6j and mus spretus mice used for the backcross. iap loci were placed on the map by comparison of their distribution patterns with those of known genetic markers in the backcross. the map includes 51 iap loci that have not been previously mapped and 23 iap proviruses that had been previously mapped in recombinant inbred (ri) strains. comparable map positions were obtained with the iap markers in the interspecific backcross and the ri strains. the mapped iap loci were widely dispersed on the x chromosome (chr) and all of the autosomes except chrs 9 and 19, providing useful genetic markers for linkage studies.",1
"macroautophagy (autophagy) is a lysosome-dependent degradation process that has been implicated in age-associated diseases. autophagy is involved in both cell survival and cell death, but little is known about the mechanisms that distinguish its use during these distinct cell fates. here, we identify the microrna mir-14 as being both necessary and sufficient for autophagy during developmentally regulated cell death in drosophila. loss of mir-14 prevented induction of autophagy during salivary gland cell death, but had no effect on starvation-induced autophagy in the fat body. moreover, misexpression of mir-14 was sufficient to prematurely induce autophagy in salivary glands, but not in the fat body. importantly, mir-14 regulates this context-specific autophagy through its target, inositol 1,4,5-trisphosphate kinase 2 (ip3k2), thereby affecting inositol 1,4,5-trisphosphate (ip3) signaling and calcium levels during salivary gland cell death. this study provides in vivo evidence of microrna regulation of autophagy through modulation of ip3 signaling.",1
"metabolic diseases are characterized by the failure of regulatory genes or proteins to effectively orchestrate specific pathways involved in the control of many biological processes. in addition to the classical regulators, recent discoveries have shown the remarkable role of small noncoding rnas (micrornas ) in the posttranscriptional regulation of gene expression. in this regard, we have recently demonstrated that mir-33a and mir33b, intronic mirnas located within the sterol regulatory element-binding protein (srebp) genes, regulate lipid metabolism in concert with their host genes. here, we show that mir-33b also cooperates with srebp1 in regulating glucose metabolism by targeting phosphoenolpyruvate carboxykinase (pck1) and glucose-6-phosphatase (g6pc), key regulatory enzymes of hepatic gluconeogenesis. overexpression of mir-33b in human hepatic cells inhibits pck1 and g6pc expression, leading to a significant reduction of glucose production. importantly, hepatic srebp1c/mir-33b levels correlate inversely with the expression of pck1 and g6pc upon glucose infusion in rhesus monkeys. taken together, these results suggest that mir-33b works in concert with its host gene to ensure a fine-tuned regulation of lipid and glucose homeostasis, highlighting the clinical potential of mir-33a/b as novel therapeutic targets for a range of metabolic diseases.",1
"micrornas (mirnas) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. to provide an unbiased view of human mirna targets, we developed a technique for ligation and sequencing of mirna-target rna duplexes associated with human ago1. here, we report data sets of more than 18,000 high-confidence mirna-mrna interactions. the binding of most mirnas includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of mirna-mrna interactions involve the mirna 3' end, with little evidence for 5' contacts, and some of these were functionally validated. analyses of mirna:mrna base pairing showed that mirna species systematically differ in their target rna interactions, and strongly overrepresented motifs were found in the interaction sites of several mirnas. we speculate that these affect the response of risc to mirna-target binding.",1
"nuclear factor-erythroid 2-related factor 2 (nrf2/nfe2l2), a redox-sensitive transcription factor plays a critical role in adaptation to cellular stress and affords cellular defense by initiating transcription of antioxidative and detoxification genes. while a protein can be regulated at multiple levels, control of nrf2 has been largely studied at post-translational regulation points by keap1. importantly, post-transcriptional/translational based regulation of nrf2 is less understood and to date there are no reports on such mechanisms in neuronal systems. in this context, studies involving the role of micrornas (mirs) which are normally considered as fine tuning regulators of protein production through translation repression and/or post-transcriptional alterations, are in place. in the current study, based on in-silico analysis followed by immunoblotting and real time analysis, we have identified and validated for the first time that human nfe2l2 could be targeted by mir153/mir27a/mir142-5p/mir144 in neuronal, sh-sy5y cells. co-transfection studies with individual mir mimics along with either wt 3' utr of human nrf2 or mutated mirna targeting seed sequence within nrf2 3' utr, demonstrated that nrf2 is a direct regulatory target of these mirs. in addition, ectopic expression of mir153/mir27a/mir142-5p/mir144 affected nrf2 mrna abundance and nucleo-cytoplasmic concentration of nrf2 in a keap1 independent manner resulting in inefficient transactivating ability of nrf2. furthermore, forced expression of mirs diminished gclc and gsr expression resulting in alteration of nrf2 dependent redox homeostasis. finally, bioinformatics based mirna-disease network analysis (mdn) along with extended computational network analysis of nrf2 associated pathologic processes suggests that if in a particular cellular scenario where any of these mir153/mir27a/mir142-5p/mir144 either individually or as a group is altered, it could affect nrf2 thus triggering and/or determining the fate of wide range of disease outcomes.",1
"aims our aim was to identify new micrornas (mirnas) implicated in pathological vascular smooth muscle cells (vsmcs) proliferation and characterize their mechanism of action. methods and results micrornas microarray and qrt-pcr results lead us to focus on mir-424 or its rat ortholog mir-322 (mir-424/322). in vitro mir-424/322 level was decreased shortly after the induction of proliferation and increased in a time-dependent manner later on. in vivo its expression increased in the rat carotid artery from day 4 up to day 30 after injury. mir-424/322 overexpression in vitro inhibited proliferation and migration without affecting apoptosis and prevented vsmc dedifferentiation. furthermore, mir-424/322 overexpression resulted in decreased expression of its predicted targets: cyclin d1 and ca(2+)-regulating proteins calumenin and stromal-interacting molecule 1 (stim1). using reporter luciferase assays, we confirmed that cyclin d1 and calumenin mrnas were direct targets of mir-322, whereas mir-322 effect on stim1 was indirect. nevertheless, consistent with the decreased stim1 level, the store-operated ca(2+) entry was reduced. we hypothesized that mir-424/322 could be a negative regulator of proliferation overridden in pathological situations. thus, we overexpressed mir-424/322 in injured rat carotid arteries using an adenovirus, and demonstrated a protective effect against restenosis. conclusion our results demonstrate that mir-424/322 is up-regulated after vascular injury. this is likely an adaptive response to counteract proliferation, although this mechanism is overwhelmed in pathological situations such as injury-induced restenosis.",1
"a cryo-em reconstruction of the translating yeast 80s ribosome was analyzed. computationally separated rrna and protein densities were used for docking of appropriately modified rrna models and homology models of yeast ribosomal proteins. the core of the ribosome shows a remarkable degree of conservation. however, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. as in the bacterial ribosome, bridges between the subunits are mainly formed by rna contacts. four new bridges are present at the periphery. the position of the p site trna coincides precisely with its prokaryotic counterpart, with mainly rrna contributing to its molecular environment. this analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.",1
"micrornas (mirs) are small non-protein-coding rnas that bind to specific mrnas and inhibit translation or promote mrna degradation. recent reports have indicated that mir-33, which is located within the intron of sterol regulatory element-binding protein (srebp) 2, controls cholesterol homoeostasis and may be a potential therapeutic target for the treatment of atherosclerosis. here we show that deletion of mir-33 results in marked worsening of high-fat diet-induced obesity and liver steatosis. using mir-33(-/-)srebf1(+/-) mice, we demonstrate that srebp-1 is a target of mir-33 and that the mechanisms leading to obesity and liver steatosis in mir-33(-/-) mice involve enhanced expression of srebp-1. these results elucidate a novel interaction between srebp-1 and srebp-2 mediated by mir-33 in vivo.",1
"background micrornas (mirnas/mirs) are small conserved rna molecules of 22 nucleotides that negatively modulate gene expression primarily through base paring to the 3' untranslated region of target messenger rnas. the muscle-specific mir-1 has been implicated in cardiac hypertrophy, heart development, cardiac stem cell differentiation, and arrhythmias through targeting of regulatory proteins. in this study, we investigated the molecular mechanisms through which mir-1 intervenes in regulation of muscle cell growth and differentiation. methods and results on the basis of bioinformatics tools, biochemical assays, and in vivo models, we demonstrate that (1) insulin-like growth factor-1 (igf-1) and igf-1 receptor are targets of mir-1; (2) mir-1 and igf-1 protein levels are correlated inversely in models of cardiac hypertrophy and failure as well as in the c2c12 skeletal muscle cell model of differentiation; (3) the activation state of the igf-1 signal transduction cascade reciprocally regulates mir-1 expression through the foxo3a transcription factor; and (4) mir-1 expression correlates inversely with cardiac mass and thickness in myocardial biopsies of acromegalic patients, in which igf-1 is overproduced after aberrant synthesis of growth hormone. conclusions our results reveal a critical role of mir-1 in mediating the effects of the igf-1 pathway and demonstrate a feedback loop between mir-1 expression and the igf-1 signal transduction cascade.",1
"background the microrna 125b is a double-faced gene expression regulator described both as a tumor suppressor gene (in solid tumors) and an oncogene (in hematologic malignancies). in human breast cancer, it is one of the most down-regulated mirnas and is able to modulate erbb2/3 expression. here, we investigated its targets in breast cancer cell lines after mirna-mimic transfection. we examined the interactions of the validated targets with erbb2 oncogene and the correlation of mir-125b expression with clinical variables. methods mir-125b possible targets were identified after transfecting a mirna-mimic in mcf7 cell line and analyzing gene expression modifications with agilent microarrays and sylamer bioinformatic tool. erythropoietin (epo) and its receptor (epor) were validated as targets of mir-125b by luciferase assay and their expression was assessed by rt-qpcr in 42 breast cancers and 13 normal samples. the molecular talk between epor and erbb2 transcripts, through mir-125b, was explored transfecting mda-md-453 and mda-mb-157 with erbb2 rna and using rt-qpcr. results we identified a panel of genes down-regulated after mir-125b transfection and putative targets of mir-125b. among them, we validated erythropoietin (epo) and its receptor (epor) - frequently overexpressed in breast cancer--as true targets of mir-125b. moreover, we explored possible correlations with clinical variables and we found a down-regulation of mir-125b in metastatic breast cancers and a significant positive correlation between epor and erbb2/her2 levels, that are both targets of mir-125b and function as competing endogenous rnas (cernas). conclusions taken together our results show a mechanism for epo/epor and erbb2 co-regulation in breast cancer and confirm the importance of mir-125b in controlling clinically-relevant cancer features.",1
"the 3' ends of late mrnas of the ati gene, encoding the major component of the a-type inclusions, are generated by endoribonucleolytic cleavage at a specific site in the primary transcript . in this study, sequence analysis of cdnas of the 3' ends of ati mrnas showed these mrnas are 3' polyadenylated at the rna cleavage site. this suggests that ati mrna 3' end formation involves cleavage of a late transcript, with subsequent 3' polyadenylation of the 5' cleavage product. the rna cis-acting element, the ax element, directing orientation-dependent formation of these mrna 3' ends, was mapped to a 345-bp alui-xbai fragment. deletion analyses of this fragment showed that the boundaries of the ax element are within -5 and +38 of the rna cleavage site. scanning mutagenesis showed that the ax element contains at least two subelements: subelement i, 5'-uuuau downward arrowccgauaauuc-3', containing the cleavage site ( downward arrow), separated from the downstream subelement ii, 5'-aauuucggauuugaaugc-3', by a 10-nucleotide region, whose composition may be altered without effect on rna 3' end formation. these features, which differ from those of other elements controlling rna processing, suggest that the ax element is a component of a novel mechanism of rna 3' end formation.",1
"high-altitude acclimatization is a representative example of vertebrates' acclimatization to harsh and extreme environments. previous studies reported sufficient evidence for a molecular genetic basis of high-altitude acclimatization, and genomic patterns of genetic variation among populations and species have been widely elucidated in recent years. however, understanding of the mirna role in high-altitude acclimatization have lagged behind, especially in non-model species. to investigate mirna expression alterations of goats that were induced by high-altitude stress, we performed comparative mirna transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle, and spleen) in two goat populations from distinct altitudes (600 and 3000 m). we obtained the expression value of 1391 mature mirnas and identified 138 differentially expressed (de) mirnas between high and low altitudes. combined with tissue specificity analysis, we illustrated alterations of expression levels among altitudes and tissues, and found that there were coexisting tissue-specific and -conserved mechanisms for hypoxia acclimatization. notably, the interplay between de mirna and de target genes strongly indicated post-transcriptional regulation in the hypoxia inducible factor 1, insulin, and p53 signaling pathways, which might play significant roles in high-altitude acclimatization in domestic goats. it's also worth noting that we experimentally confirmed mir-106a-5p to have a negative regulation effect on angiogenesis by directly targeting flt-1 . these results provide insight into the complicated mirna expression patterns and regulatory mechanisms of high-altitude acclimatization in domestic goats.",1
"transitions between pluripotent and differentiated states are marked by dramatic epigenetic changes. cellular differentiation is tightly linked to x chromosome inactivation (xci), whereas reprogramming to induced pluripotent stem cells (ipscs) is associated with x chromosome reactivation (xcr). xcr reverses the silent state of the inactive x, occurring in mouse blastocysts and germ cells. in spite of its importance, little is known about underlying mechanisms. here, we examine the role of the long noncoding tsix rna and the germline factor, prdm14. in blastocysts, xcr is perturbed by mutation of either tsix or prdm14. in ipscs, xcr is disrupted only by prdm14 deficiency, which also affects ipsc derivation and maintenance. we show that tsix and prdm14 directly link xcr to pluripotency: first, prdm14 represses rnf12 by recruiting polycomb repressive complex 2; second, tsix enables prdm14 to bind xist. thus, our study provides functional and mechanistic links between cellular and x chromosome reprogramming.",1
"micrornas (mirnas) are regulators of global gene expression and function in a broad range of biological processes. recent studies have suggested that mirnas can function as tumor suppressors or oncogenes by modulating the activities of evolutionarily conserved signaling pathways that are commonly dysregulated in cancer. we report the identification of the mir-310 to mir-313 (mir-310/13) cluster as a novel antagonist of wingless (drosophila wnt) pathway activity in a functional screen for drosophila mirnas. we demonstrate that mir-310/13 can modulate armadillo (arm; drosophila β-catenin) expression and activity by directly targeting the 3'-utrs of arm and pangolin (drosophila tcf) in vivo. notably, the mir-310/13-deficient flies exhibit abnormal germ and somatic cell differentiation in the male gonad, which can be rescued by reducing arm protein levels or activity. our results implicate a previously unrecognized function for mir-310/13 in dampening the activity of arm in early somatic and germline progenitor cells, whereby inappropriate/sustained activation of arm-mediated signaling or cell adhesion may impact normal differentiation in the drosophila male gonad.",1
"micrornas have been suggested to play a vital role in regulate tumor progression and invasion. however, the expression of mir-335 in colorectal cancer (crc) and its clinical significance are not known. here, we report that mir-335 is a tumor suppressor by regulating expression of zeb2. in this study, we showed that downregulated mir-335 levels in highly invasive crc cell lines and tissues. kaplan-meier survival analysis indicated that patients with reduced mir-335 had a poor overall survival. furthermore, enhancing the expression of mir-335 inhibited crc cell migration and invasion in vitro and lung and liver metastasis in vivo, while silencing its expression resulted in increased migration and invasion. additionally, we identified a novel mir-335 target, zeb2, and the direct interaction between them was verified by 3'-untranslated region dual-luciferase reporter assay. in conclusion, our results demonstrate that mir-335 functions as a tumor suppressor and play a role in inhibiting metastasis of crc cells through targeting zeb2. these findings suggest that mir-335 may be useful as a new potential therapeutic target for crc.",1
"aberrant smooth muscle cell (smc) plasticity has been implicated in a variety of vascular disorders including atherosclerosis, restenosis, and abdominal aortic aneurysm (aaa) formation. while the pathways governing this process remain unclear, epigenetic regulation by specific micrornas (mirnas) has been demonstrated in smcs. we hypothesized that additional mirnas might play an important role in determining vascular smc phenotype. microarray analysis of mirnas was performed on human aortic smcs undergoing phenotypic switching in response to serum withdrawal, and identified 31 significantly regulated entities. we chose the highly conserved candidate mirna-26a for additional studies. inhibition of mirna-26a accelerated smc differentiation, and also promoted apoptosis, while inhibiting proliferation and migration. overexpression of mirna-26a blunted differentiation. as a potential mechanism, we investigated whether mirna-26a influences tgf-β-pathway signaling. dual-luciferase reporter assays demonstrated enhanced smad signaling with mirna-26a inhibition, and the opposite effect with mirna-26a overexpression in transfected human cells. furthermore, inhibition of mirna-26a increased gene expression of smad-1 and smad-4, while overexpression inhibited smad-1. microrna-26a was also found to be downregulated in two mouse models of aaa formation (2.5- to 3.8-fold decrease, p < 0.02) in which enhanced switching from contractile to synthetic phenotype occurs. in summary, mirna-26a promotes vascular smc proliferation while inhibiting cellular differentiation and apoptosis, and alters tgf-β pathway signaling. microrna-26a represents an important new regulator of smc biology and a potential therapeutic target in aaa disease.",1
"aberrant regulation of cholesterol homeostasis is associated with obesity as well as multiple types of cancer. however, the mechanism behind these is largely missing. here, we show that microrna (mirna)-128-2 is not only a pro-apoptotic microrna but it also alters the expression of genes involved in cellular cholesterol homeostasis. cholesterol efflux via atp-binding cassette transporters (abca1 and abcg1) is a mechanism for cells to eliminate excess cholesterol and prevent cellular cholesterol accumulation. the regulation of these pathways is complex with transcriptional regulation by sterol-regulatory element-binding protein (srebp) and liver x receptor/retinoid x receptor (rxr) transcription factors but poorly understood at the post-transcriptional levels. mir-128-2 increases the expression of srebp2 and decreases the expression of srebp1 in hepg2, mcf7 and hek293t cells independent of sirtuin 1 (sirt1) status. mir-128-2 inhibits the expression of abca1, abcg1 and rxrα directly through a mir-128-2-binding site within their respective 3'untranslated regions. the administration of mir-128-2 leads to decline in the protein and mrna levels of abca1, abcg1 and rxrα. conversely, anti-mirna treatment leads to increased abca1, abcg1 and rxrα expression. the inverse correlation between mir-128-2 and its targets viz. abca1 and abcg1 was also established during high-fat diet in different mice tissues. our data show that cholesterol efflux is attenuated by mir-128-2 overexpression and, conversely, stimulated by mir-128-2 silencing. further, we also observed the induction of er stress response by mir-128-2. in this study, we provide the first evidence of mir-128-2 to be a new regulator of cholesterol homeostasis. our study shows dual role of mir-128-2, as a pro-apoptotic molecule as well as a regulator of cholesterol homeostasis.",1
"objective to investigate the modulation of micrornas (mirnas) upon the neuronal differentiation of mesenchymal stem cells (mscs) through targeting re-1 silencing factor (rest), a mature neuronal gene suppressor in neuronal and un-neuronal cells. methods rat bone marrow derived-mscs were induced into neuron-like cells (msc-ncs) by dmso and bha in vitro. the expression of neuron specific enolase (nse), microtubule-associated protein tau (tau), rest and its target genes, including synaptosomal-associated protein 25 (snap25) and l1 cell adhesion molecular (l1cam), were detected in mscs and msc-ncs. mirna array analysis was conducted to screen for the upregulated mirnas after neuronal differentiation. targetscan was used to predict the relationship between these mirnas and rest gene, and dual luciferase reporter assay was applied to validate it. gain and loss of function experiments were used to study the role of mir-29a upon neuronal differentiation of mscs. the knockdown of rest was conducted to show that mir-29a affected this process through targeting rest. results mscs were induced into neuron-like cells which presented neuronal cell shape and expressed nse and tau. the expression of rest declined and the expression of snap25 and l1cam increased upon the neuronal differentiation of mscs. among 14 upregulated mirnas, mir-29a was validated to target rest gene. during the neuronal differentiation of mscs, mir-29a inhibition blocked the downregulation of rest, as well as the upregulation of snap25, l1cam, nse and tau. rest knockdown rescued the effect of mir-29a inhibition on the expression of nse and tau. meanwhile, mir-29a knockin significantly decreased the expression of rest and increased the expression of snap25 and l1cma in mscs, but did not significantly affect the expression of nse and tau. conclusion mir-29a regulates neurogenic markers through targeting rest in mesenchymal stem cells, which provides advances in neuronal differentiation research and stem cell therapy for neurodegenerative diseases.",1
"bile secretion is essential for whole body sterol homeostasis. loss-of-function mutations in specific canalicular transporters in the hepatocyte disrupt bile flow and result in cholestasis. we show that two of these transporters, abcb11 and atp8b1, are functional targets of mir-33, a micro-rna that is expressed from within an intron of srebp-2. consequently, manipulation of mir-33 levels in vivo with adenovirus or with antisense oligonucleotides results in changes in bile secretion and bile recovery from the gallbladder. using radiolabelled cholesterol, we show that systemic silencing of mir-33 leads to increased sterols in bile and enhanced reverse cholesterol transport in vivo. finally, we report that simvastatin causes, in a dose-dependent manner, profound hepatotoxicity and lethality in mice fed a lithogenic diet. these latter results are reminiscent of the recurrent cholestasis found in some patients prescribed statins. importantly, pretreatment of mice with anti-mir-33 oligonucleotides rescues the hepatotoxic phenotype. therefore, we conclude that mir-33 mediates some of the undesired, hepatotoxic effects of statins.",1
"background micrornas (mirnas) regulate various biological processes through inhibiting the translation of rna transcripts. although mirna-1 (mir-1) and mirna-133 (mir-133) are abundantly expressed in the adult heart and involved in cardiac hypertrophy, the roles of these mirnas in spontaneous myocardial differentiation are unknown. methods and results the levels of mir-1 and mir-133 in mouse embryonic stem (es) cells were increased during spontaneous differentiation by 2-dimensional culture, but reduced during forced myocardial differentiation by a histone deacetylase inhibitor, trichostatin a. the overexpression of mir-1 or mir-133 by lentiviral infection reduced the expression of a cardiac-specific gene, nkx2.5, during differentiation of es cells. in addition, mir-1 also inhibited alpha-myosin heavy chain expression. the results of luciferase assays revealed that mir-1 recognizes and targets the 3' untranslated region of cyclin-dependent kinase-9 (cdk9) in es cells. overexpression of mir-1 decreased the protein amounts of cdk9 without affecting the mrna levels, indicating that mir-1 post-transcriptionally inhibits cdk9 translation. conclusions mir-1 and mir-133 may play significant roles in the myocardial differentiation of mouse es cells, and cdk9 may be involved in this process as a target of mir-1.",1
"long noncoding rnas (lncrnas) are emerging as important regulators of cellular functions, but their roles in oligodendrocyte myelination remain undefined. through de novo transcriptome reconstruction, we establish dynamic expression profiles of lncrnas at different stages of oligodendrocyte development and uncover a cohort of stage-specific oligodendrocyte-restricted lncrnas, including a conserved chromatin-associated lncol1. co-expression network analyses further define the association of distinct oligodendrocyte-expressing lncrna clusters with protein-coding genes and predict lncrna functions in oligodendrocyte myelination. overexpression of lncol1 promotes precocious oligodendrocyte differentiation in the developing brain, whereas genetic inactivation of lncol1 causes defects in cns myelination and remyelination following injury. functional analyses illustrate that lncol1 interacts with suz12, a component of polycomb repressive complex 2, to promote oligodendrocyte maturation, in part, through suz12-mediated repression of a differentiation inhibitory network that maintains the precursor state. together, our findings reveal a key lncrna epigenetic circuitry through interaction with chromatin-modifying complexes in control of cns myelination and myelin repair.",1
"unlabelled mirnas are a group of small, noncoding rnas that modulate the translation of genes by binding to specific target sites in the target mrna. this study investigated the biologic function and molecular mechanism of mir-21 in human cholangiocarcinoma. in situ hybridization analysis of human cholangiocarcinoma specimens showed increased mir-21 in cholangiocarcinoma tissue compared with the noncancerous biliary epithelium. lentiviral transduction of mir-21 enhanced human cholangiocarcinoma cell growth and clonogenic efficiency in vitro, whereas inhibition of mir-21 decreased these parameters. overexpression of mir-21 also promoted cholangiocarcinoma growth using an in vivo xenograft model system. the nad(+)-linked 15-hydroxyprostaglandin dehydrogenase (15-pgdh/hpgd), a key enzyme that converts the protumorigenic prostaglandin e2 (pge2) to its biologically inactive metabolite, was identified as a direct target of mir-21 in cholangiocarcinoma cells. in parallel, cyclooxygenase-2 (cox2) overexpression and pge2 treatment increased mir-21 levels and enhanced mir-21 promoter activity in human cholangiocarcinoma cells. implications cholangiocarcinogenesis and tumor progression are regulated by a novel interplay between cox-2/pge2 and mir-21 signaling, which converges at 15-pgdh.",1
"micrornas (mirnas) regulate many physiological processes including body growth. insulin/igf signalling is the primary regulator of animal body growth, but the extent to which mirnas act in insulin-producing cells (ipcs) is unclear. here we generate a uas-mirna library of drosophila stocks and perform a genetic screen to identify mirnas whose overexpression in the ipcs inhibits body growth in drosophila. through this screen, we identify mir-9a as an evolutionarily conserved regulator of insulin signalling and body growth. ipc-specific mir-9a overexpression reduces insulin signalling and body size. of the predicted targets of mir-9a, we find that loss of mir-9a enhances the level of snpfr1. we show via an in vitro binding assay that mir-9a binds to snpfr1 mrna in insect cells and to the mammalian orthologue npy2r in rat insulinoma cells. these findings indicate that the conserved mir-9a regulates body growth by controlling snpfr1/npyr-mediated modulation of insulin signalling.",1
"interleukin (il)-32 has been recognized as a proinflammatory cytokine that participates in responses to viral infection. however, little is known about how il-32 is induced in response to viral infection and the mechanisms of il-32-mediated antiviral activities. we discovered that il-32 is elevated by hepatitis b virus (hbv) infection both in vitro and in vivo and that hbv induced il-32 expression at the level of both transcription and post-transcription. furthermore, microrna-29b was found to be a key factor in hbv-regulated il-32 expression by directly targeting the mrna 3'-untranslated region of il-32. antiviral analysis showed that il-32 was not sufficient to alter hbv replication in hepg2.2.15 cells. to mimic the viremic phase of viral infection, freshly isolated peripheral blood mononuclear cells were treated with il-32γ, the secretory isoform, and the supernatants were used for antiviral assays. surprisingly, these supernatants exhibited extensive antiviral activity against multiplex viruses besides hbv. thus, we speculated that the il-32γ-treated peripheral blood mononuclear cells produced and secreted an unknown antiviral factor. using antibody neutralization assays, we identified the factor as interferon (ifn)-λ1 and not ifn-α. further studies indicated that il-32γ effectively inhibited hbv replication in a hydrodynamic injection mouse model. clinical data showed that elevated levels of ifn-λ1 both in serum and liver tissue of hbv patients were positively correlated to the increased levels of il-32. our results demonstrate that elevated il-32 levels during viral infection mediate antiviral effects by stimulating the expression of ifn-λ1.",1
"in a survey of 20 knockout mouse lines designed to examine the biological functions of large intergenic non-coding rnas (lincrnas), we have found a variety of phenotypes, ranging from perinatal lethality to defects associated with premature aging and morphological and functional abnormalities in the lungs, skeleton, and muscle. each mutant allele carried a lacz reporter whose expression profile highlighted a wide spectrum of spatiotemporal and tissue-specific transcription patterns in embryos and adults that informed our phenotypic analyses and will serve as a guide for future investigations of these genes. our study shows that lincrnas are a new class of encoded molecules that, like proteins, serve essential and important functional roles in embryonic development, physiology, and homeostasis of a broad array of tissues and organs in mammals.",1
"we experimentally identified and characterized 97 novel, non-protein-coding rna candidates (npcrnas) from the human pathogen salmonella enterica serovar typhi (hereafter referred to as s. typhi). three were specific to s. typhi, 22 were restricted to salmonella species and 33 were differentially expressed during s. typhi growth. we also identified salmonella pathogenicity island-derived npcrnas that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of s. typhi. an in-depth characterization of s. typhi styr-3 npcrna showed that it specifically interacts with ramr, the transcriptional repressor of the rama gene, which is involved in the multidrug resistance (mdr) of salmonella. styr-3 interfered with ramr-dna binding activity and thus potentially plays a role in regulating rama gene expression, resulting in the mdr phenotype. our study also revealed a large number of cis-encoded antisense npcrna candidates, supporting previous observations of global sense-antisense regulatory networks in bacteria. finally, at least six of the npcrna candidates interacted with the s. typhi hfq protein, supporting an important role of hfq in npcrna networks. this study points to novel functional npcrna candidates potentially involved in various regulatory roles including the pathogenicity of s. typhi.",1
"despite advances in clinical therapies and technologies, the prognosis for patients with malignant glioma is poor. our previous research demonstrated that glioma stem cells (gscs) were crucial for glioma malignancy and accelerated tumor migration and invasion. the migration and invasion of malignant glioma cells into the surrounding normal brain tissues cause the poor outcome. mir-145, a mirna found to be expressed in neurons, was recently found to have reduced expression in glioblastoma multiforme tumors. and mir-145 loss in glioma cells led to increased cell proliferation and invasion. however, its function on the migration and invasion of gscs was still unknown. in this study, we aimed to identify the effects and mechanisms of mir-145 on the migration and invasion of gscs. our investigations revealed that mir-145 was low expressed in malignant glioma tissues and their corresponding gscs. knockdown of mir-145 in vitro could enhance the migration and invasion of gscs, while up-regulation of mir-145 had the opposite effects. further investigation of the potential mechanism demonstrated that the function of mir-145 in regulating the migration and invasion of gscs is mediated by its targeting of abcg2 mrna. abcg2 is an atp-binding cassette transporter protein, which was identified to be overexpressed in gscs and higher-grade glioma tissues. we found that mir-145 was negative correlated with abcg2 levels in gscs, and reduction in abcg2 expression decreased the cell migration and invasion of gscs. further, a luciferase reporter proved that abcg2 was a direct target of mir-145 in gscs. thus, these findings underscore the potential of mir-145 to regulate the migration and invasion of gscs through targeting abcg2.",1
"aims the aims of the present study are to determine the mirna expression signature in rat hearts after ischaemic preconditioning (ip) and to identify an ip-regulated mirna, mir-21, in ip-mediated cardiac protection, and the potential cellular and molecular mechanisms involved. methods and results the mirna expression signature was investigated in rat hearts. among the 341 arrayed mirnas, 40 mirnas were differentially expressed (21 up and 19 down) in rat hearts with ip, compared with their controls. some of these differentially expressed mirnas were further verified by quantitative reverse transcriptase-polymerase chain reaction. remarkably, mir-21 was one of most upregulated mirnas in hearts after ip. in vivo, ip-mediated cardiac protection against ischaemia/reperfusion injury was inhibited by knockdown of cardiac mir-21. in cultured cardiac myocytes, we identified that mir-21 also had a protective effect on hypoxia/reoxygenation-induced cell apoptosis that was associated with its target gene, programmed cell death 4. the protective effect of mir-21 on cardiac cell apoptosis was further confirmed in rat hearts after ischaemia/reperfusion injury in vivo. conclusion the results suggest that mirnas are involved in ip-mediated cardiac protection. identifying the roles of ip-regulated mirnas in cardiac protection may provide novel therapeutic and preventive targets for ischaemic heart disease.",1
"we describe a program, trnascan-se, which identifies 99-100% of transfer rna genes in dna sequence while giving less than one false positive per 15 gigabases. two previously described trna detection programs are used as fast, first-pass prefilters to identify candidate trnas, which are then analyzed by a highly selective trna covariance model. this work represents a practical application of rna covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. trnascan-se searches at approximately 30 000 bp/s. additional extensions to trnascan-se detect unusual trna homologues such as selenocysteine trnas, trna-derived repetitive elements and trna pseudogenes.",1
"most biological catalysts are made of protein; however, eight classes of natural ribozymes have been discovered that catalyse fundamental biochemical reactions. the central functions of ribozymes in modern organisms support the hypothesis that life passed through an 'rna world' before the emergence of proteins and dna. we have identified a new class of ribozymes that cleaves the messenger rna of the glms gene in gram-positive bacteria. the ribozyme is activated by glucosamine-6-phosphate (glcn6p), which is the metabolic product of the glms enzyme. additional data indicate that the ribozyme serves as a metabolite-responsive genetic switch that represses the glms gene in response to rising glcn6p concentrations. these findings demonstrate that ribozyme switches may have functioned as metabolite sensors in primitive organisms, and further suggest that modern cells retain some of these ancient genetic control systems.",1
"the pol genes of retroviruses are translated as gag-pol fusion proteins by ribosomal frameshifting within the gag-pol overlap region. during the ribosomal frameshift event, the gag open reading frame is shifted -1 nt to allow in-phase reading of the pol open reading frame. a consensus frameshift signal sequence of gggaaac within the gag-pol overlap region of feline immunodeficiency virus (fiv) has been identified followed by a sequence that has the potential for a pseudoknot tertiary structure. using recombinant baculoviruses in which the frameshift occurs efficiently, the consensus sequence has been shown to be the site of the frameshift event. a mutation creating a termination codon just downstream of the putative frameshift signal sequence but upstream of the potential pseudoknot structure made a shorter gag product, but did not affect the efficiency of frameshifting. a mutation creating a termination codon just upstream of the putative frameshift signal made a shorter product and essentially abrogated frameshifting. mutations in the first stem or the second stem in the potential pseudoknot structure severely reduced the frameshifting efficiency. mutations which altered the length between the frameshift signal and the pseudoknot structure (the so-called spacer region) also reduced the frameshift efficiency. the insertion of a palindromic sequence, which could form a hairpin structure just upstream of the frameshift signal sequence, also affected the frameshifting. these results support the view that the ribosomal frameshift event in the fiv gag-pol region involves the identified signal sequence and appears to require the precisely positioned downstream sequence and indicated pseudoknot structure for efficient frameshifting.",1
"transcription by rna polymerase ii in saccharomyces cerevisiae and in humans is widespread, even in genomic regions that do not encode proteins. the purpose of such intergenic transcription is largely unknown, although it can be regulatory. we have discovered a role for one case of intergenic transcription by studying the s. cerevisiae ser3 gene. our previous results demonstrated that transcription of ser3 is tightly repressed during growth in rich medium. we now show that the regulatory region of this gene is highly transcribed under these conditions and produces a non-protein-coding rna (srg1). expression of the srg1 rna is required for repression of ser3. additional experiments have demonstrated that repression occurs by a transcription-interference mechanism in which srg1 transcription across the ser3 promoter interferes with the binding of activators. this work identifies a previously unknown class of transcriptional regulatory genes.",1
"the calponin 3 (cnn3) gene has important functions involved in skeletal muscle development. micrornas (mirnas) play critical role in myogenesis by influencing the mrna stability or protein translation of target gene. based on paired microrna and mrna profiling in the prenatal skeletal muscle of pigs, our previous study suggested that cnn3 was differentially expressed and a potential target for mir-1. to further understand the biological function and regulation mechanism of cnn3, we performed co-expression analysis of cnn3 and mir-1 in developmental skeletal muscle tissues (16 stages) from tongcheng (a chinese domestic breed, obese-type) and landrace (a western, lean-type) pigs, respectively. subsequently, dual luciferase and western blot assays were carried out. during skeletal muscle development, we observe a significantly negative expression correlation between the mir-1 and cnn3 at mrna level. our dual luciferase and western blot results suggested that the cnn3 gene was regulated by mir-1. we identified four single nucleotide polymorphisms (snps) contained within the cnn3 gene. association analysis indicated that these cnn3 snps are significantly associated with birth weight (bw) and the 21-day weaning weight of the piglets examined. these facts indicate that cnn3 is a candidate gene associated with growth traits and regulated by mir-1 during skeletal muscle development in pigs.",1
"background structured noncoding rnas perform many functions that are essential for protein synthesis, rna processing, and gene regulation. structured rnas can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve rna secondary structure. results by applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured rnas and inferred putative functions for many of these. twelve candidate metabolite-binding rnas were identified, three of which were validated, including one reported herein that binds the coenzyme s-adenosylmethionine. newly identified cis-regulatory rnas are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by helicobacter, and many other physiological processes. a candidate riboswitch termed crcb is represented in both bacteria and archaea. another rna motif may control gene expression from 3'-untranslated regions of mrnas, which is unusual for bacteria. many noncoding rnas that likely act in trans are also revealed, and several of the noncoding rna candidates are found mostly or exclusively in metagenome dna sequences. conclusions this work greatly expands the variety of highly structured noncoding rnas known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. given the sustained rate of rna discovery over several similar projects, we expect that far more structured rnas remain to be discovered from bacterial and archaeal organisms.",1
"iron is both essential for bacterial growth and toxic at higher concentrations; thus, iron homeostasis is tightly regulated. in neisseria meningitidis the majority of iron-responsive gene regulation is mediated by the ferric uptake regulator protein (fur), a protein classically defined as a transcriptional repressor. recently, however, microarray studies have identified a number of genes in n. meningitidis that are iron and fur activated, demonstrating a new role for fur as a transcriptional activator. since fur has been shown to indirectly activate gene transcription through the repression of small regulatory rna molecules in other organisms, we hypothesized that a similar mechanism could account for fur-dependent, iron-activated gene transcription in n. meningitidis. in this study, we used a bioinformatics approach to screen for the presence of fur-regulated small rna molecules in n. meningitidis mc58. this screen identified one small rna, herein named nrrf (for neisserial regulatory rna responsive to iron ), which was demonstrated to be both iron responsive and fur regulated and which has a well-conserved orthologue in n. gonorrhoeae. in addition, this screen identified a number of other likely, novel small rna transcripts. lastly, we utilized a new bioinformatics approach to predict regulatory targets of the nrrf small rna. this analysis led to the identification of the sdha and sdhc genes, which were subsequently demonstrated to be under nrrf regulation in an nrrf mutant. this study is the first report of small rnas in n. meningitidis and the first to use a bioinformatics approach to identify, a priori, regulatory targets of a small rna.",1
"the p53 transcription factor is a key tumor suppressor and a central regulator of the stress response. to ensure a robust and precise response to cellular signals, p53 gene expression must be tightly regulated from the transcriptional to the post-translational levels. computational predictions suggest that several micrornas are involved in the post-transcriptional regulation of p53. here we demonstrate that mir-125b, a brain-enriched microrna, is a bona fide negative regulator of p53 in both zebrafish and humans. mir-125b-mediated down-regulation of p53 is strictly dependent on the binding of mir-125b to a microrna response element in the 3' untranslated region of p53 mrna. overexpression of mir-125b represses the endogenous level of p53 protein and suppresses apoptosis in human neuroblastoma cells and human lung fibroblast cells. in contrast, knockdown of mir-125b elevates the level of p53 protein and induces apoptosis in human lung fibroblasts and in the zebrafish brain. this phenotype can be rescued significantly by either an ablation of endogenous p53 function or ectopic expression of mir-125b in zebrafish. interestingly, mir-125b is down-regulated when zebrafish embryos are treated with gamma-irradiation or camptothecin, corresponding to the rapid increase in p53 protein in response to dna damage. ectopic expression of mir-125b suppresses the increase of p53 and stress-induced apoptosis. together, our study demonstrates that mir-125b is an important negative regulator of p53 and p53-induced apoptosis during development and during the stress response.",1
"objective this study aimed to explore the role of mirnas in pathogenesis of endometriosis. methodology endometrial samples from 57 females with endometriosis and 44 non-endometriotic controls were compared for the expression of a selected group of mirnas. the regulatory function on downstream target was also explored. results the expression of mir-93 and mir106a was significantly reduced in endometriotic samples compared to that in non-endometriotic samples. high levels of mmp3 and vegfa were detected in more than 50% ectopic endometrium tissues. a negative association was found between the expression of mir-93 and the protein levels of mmp3 (pearson correlation, r=-0.39, p=0.0025) or vegfa (pearson correlation, r=-0.37, p=0.0047) in samples from endometriosis patients. mechanistically, mir-93 targeted mmp3 and vegfa by directly binding to the 3'utr of mmp3 and vegfa mrnas, and thereby inhibited the proliferation, migration and invasive capability of endometrial stromal cells (escs). conclusion the finding of this study suggests that deregulation of mir-93 contribute to endometriosis by up-regulation of mmp3 and vegfa and thus provide potential therapeutic targets for the treatment of endometriosis.",1
"rnase mitochondrial rna processing (mrp) is an essential, evolutionarily conserved endoribonuclease composed of 10 different protein subunits and a single rna. rnase mrp has established roles in multiple pathways including ribosome biogenesis, cell cycle regulation, and mitochondrial dna replication. although each of these functions is important to cell growth, additional functions may exist given the essential nature of the complex. to identify novel rnase mrp substrates, we utilized rna immunoprecipitation and microarray chip analysis to identify rna that physically associates with rnase mrp. we identified several new potential substrates for rnase mrp including a cell cycle-regulated transcript, cts1; the yeast homolog of the mammalian p27(kip1), sic1; and the u2 rna component of the spliceosome. in addition, we found rnase mrp to be involved in the regulation of the ty1 transposon rna. these results reinforce and broaden the role of rnase mrp in cell cycle regulation and help to identify new roles of this endoribonuclease.",1
"micrornas (mirnas or mirs) are small, non-coding rnas that modulate mrna stability and post-transcriptional translation. a growing body of evidence indicates that specific mirnas can affect the cellular function of cardiomyocytes. in the present study, mirnas that are highly expressed in the heart were overexpressed in neonatal rat ventricular myocytes, and cellular atp levels were assessed. as a result, mir-15b, -16, -195, and -424, which have the same seed sequence, the most critical determinant of mirna targeting, decreased cellular atp levels. these results suggest that these mirnas could specifically down-regulate the same target genes and consequently decrease cellular atp levels. through a bioinformatics approach, adp-ribosylation factor-like 2 (arl2) was identified as a potential target of mir-15b. it has already been shown that arl2 localizes to adenine nucleotide transporter 1, the exchanger of adp/atp in mitochondria. overexpression of mir-15b, -16, -195, and -424 suppressed the activity of a luciferase reporter construct fused with the 3'-untranslated region of arl2. in addition, mir-15b overexpression decreased arl2 mrna and protein expression levels. the effects of arl2 sirna on cellular atp levels were the same as those of mir-15b, and the expression of arl2 could restore atp levels reduced by mir-15b. a loss-of-function study of mir-15b resulted in increased arl2 protein and cellular atp levels. electron microscopic analysis revealed that mitochondria became degenerated in cardiomyocytes that had been transduced with mir-15b and arl2 sirna. the present results suggest that mir-15b may decrease mitochondrial integrity by targeting arl2 in the heart.",1
"citrus tristeza virus (ctv), a member of the closteroviridae, has a 19.3-kb messenger-sense rna genome consisting of 12 open reading frames with nontranslated regions (ntr) at the 5' and 3' termini. the 273 nucleotide (nt) 3'-ntr is highly conserved ( approximately 95%) among the sequenced ctv isolates in contrast to the highly diverse 5'-ntr sequences. the 3' replication signals were mapped to the 3' 234 nts within the ntr. this region of ctv does not contain a poly-a tract nor does it appear to fold as a trna-mimic. instead, a computer-predicted thermodynamically stable secondary structure comprised of 10 stem-and-loop (sl) structures, referred to as sl1 to sl10 (5' to 3'), was common to all ctv isolates. this putative structure was used as a guide to examine the 3' requirements for replication in vivo. the resulting data suggest that a complex 3' structure is required for those functions that provide for efficient replication of ctv in vivo such as minus-strand initiation, regulation of strand asymmetry, effective translation of the myriad of viral mrnas, or stability of rnas. deletions into the 3'-ntr, up to 66 nts from the 5' direction and 11 nts from the 3' direction, deleting or disrupting putative sl1, sl2 and sl3, or sl10, resulted in continued replication, suggesting that these sequences are not essential for basal-level replication, but are required for efficient replication. predicted stem loops 3 through 10 were examined by mutations designed to alter the primary structures while preserving the secondary structures. mutations designed to disrupt the predicted stems of sl3, sl5, sl7, sl9, or sl10 resulted in substantially reduced levels of replication, while compensatory mutations resulted in partial restorations of replication, suggesting that these predicted secondary structures are involved in replication. also, the putative loop sequences of sl5, sl6, sl7, and sl9 tolerated mutagenesis with continued but reduced levels of replication. in contrast, all mutations introduced into putative sl4, sl8, and the stem of sl6 prevented replication, suggesting that the primary structure of these regions make up the core of the 3' replication signal. the 3' triplet, cca, was shown to be necessary for efficient replication, but deletion of eleven nts to expose an internal cca resulted in continued replication.",1
"internally located, cis-acting rna replication elements (cre) have been identified within the genomes of viruses representing each of the major picornavirus genera (enterovirus, rhinovirus, aphthovirus, and cardiovirus) except hepatovirus. previous efforts to identify a stem-loop structure with cre function in hepatitis a virus (hav), the type species of this genus, by phylogenetic analyses or thermodynamic predictions have not succeeded. however, a region of markedly suppressed synonymous codon variability was identified in alignments of hav sequences near the 5' end of the 3d(pol)-coding sequence of hav, consistent with noncoding constraints imposed by an underlying rna secondary structure. subsequent mfold predictions identified a 110-nucleotide (nt) complex stem-loop in this region with a typical aaaca/g cre motif in its top loop. a potentially homologous rna structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and hav. mutations that disrupted secondary rna structure or the aaaca/g motif, without altering the amino acid sequence of 3d(pol), ablated replication of a subgenomic hav replicon in transfected human hepatoma cells. replication competence could be rescued by reinsertion of the native 110-nt stem-loop structure (but not an abbreviated 45-nt stem-loop) upstream of the hav coding sequence in the replicon. these results suggest that this stem-loop is functionally similar to cre elements of other picornaviruses and likely involved in templating vpg uridylylation as in other picornaviruses, despite its significantly larger size and lower free folding energy.",1
"long noncoding rnas are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. xist controls the inactivation of an entire x chromosome in female placental mammals. here we develop and integrate several orthogonal structure-interaction methods to demonstrate that xist rna-protein complex folds into an evolutionarily conserved modular architecture. chimeric rnas and clustered protein binding in frip and eclip experiments align with long-range rna secondary structure, revealing discrete xist domains that interact with distinct sets of effector proteins. crispr-cas9-mediated permutation of the xist a-repeat location shows that a-repeat serves as a nucleation center for multiple xist-associated proteins and m 6 a modification. thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of rbp binding and m 6 a modification. together, this work builds a comprehensive structure-function model for the xist rna-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.",1
"mounting evidence suggests involvement of deregulated microrna (mirna) expression during the complex events of tumorigenesis. among such deregulated mirnas in cancer, mir-125b expression is reported to be consistently low in breast cancers. in this study, we screened a panel of breast cancer cell lines (bccls) for mir-125b expression and detected decreased expression in 14 of 19 bccls. due to the heterogeneity of breast cancers, mcf7 cells were chosen as a model system for erbb2 independent breast cancers to restore mir-125b expression (mcf7-125b) to investigate the phenotypical and related functional changes. earlier, mir-125b was shown to regulate cell motility by targeting erbb2 in erbb2 overexpressing breast cancer cells. here we showed decreased motility and migration in mir-125b expressing mcf7 cells, independent of erbb2. mcf7-125b cells demonstrated profoundly decreased cytoplasmic protrusions detected by phalloidin staining of filamentous actin along with decreased motility and migration behaviors detected by in vitro wound closure and transwell migration assays compared to empty vector transfected cells (mcf7-ev). among possible numerous targets of mir-125b, we showed arid3b (at-rich interactive domain 3b) to be a novel target with roles in cell motility in breast cancer cells. when arid3b was transiently silenced, the decreased cell migration was also observed. in light of these findings, mir-125b continues to emerge as an interesting regulator of cancer related phenotypes.",1
"micrornas (mirnas) function as genetic modulators that regulate gene expression, and are, thus, involved in a wide range of biological roles, including tumor cell migration and invasion. mir-125a-3p is a mature form of mir-125a, derived from the 3'-end of pre-mir-125a. our group has previously reported that mir-125a-3p functions as a tumor suppressor gene that inhibits the migration and invasion of lung cancer cells. here, we report the discovery of a new regulatory layer of the rhoa-actomyosin pathway through which mir-125a-3p controls tumor cell migration. overexpression of mir-125a-3p by transfection of sense‑mir‑125a-3p resulted in decreased rhoa protein levels, while the levels of rhoa mrna remained constant. the concentrations of both rhoa-gtp protein and actin filaments decreased after mir-125a-3p overexpression in the a549 lung cancer cell line. conversely, knockdown of mir-125a-3p by transfection of antisense-mir-125a-3p resulted in increased rhoa protein levels while the levels of rhoa mrna remained unchanged. however, the concentration of both rhoa-gtp protein and actin filaments increased. to further demonstrate that rhoa is a potential target of mir‑125a-3p, luciferase reporter constructs containing the rhoa 3'utr demonstrated reduced reporter activity after ectopic expression of mir-125a-3p. moreover, luciferase reporter constructs containing the rhoa 3'utr mutant did not show significantly changed reporter activity. furthermore, a549 cells demonstrated reduced migratory capacity after treatment with the rho inhibitor ct04. our results indicate that the loss of mir-125a‑3p-controlled regulation of the rhoa-actomyosin pathway can lead to increased migration of tumor cells because of the upregulation of rhoa expression. in particular, an increased intracellular concentration of rhoa-gtp protein in a549 cells leads to the accumulation of actin filaments. these results provide new insights into the role of the mir-125a family in lung cancer.",1
"micrornas are small non-coding rnas that are able to regulate gene expression and play important roles in some biological and pathological processes, including the myocardial ischemia/reperfusion (i/r) injury. recent findings demonstrated that mir-1 exacerbated i/r-induced injury. this study was to investigate theanti-apoptotic property of mir-1 inhibition and the potential regulatory mechanism. results showed mir-1 expression reduced in the heart of rats undergoing myocardial i/r and the cardiomyocytes receiving hypoxia/reoxygenation (h/r) injury, but the serum mir-1 expression increased. the targets of mir-1 were predicted by cdna microarray, and bcl-2 and gadd45β were selected as candidate targets. western blot assay and qpcr showed bcl-2 and gadd45β protein and mrna expressions increased after i/r injury and h/r injury. bcl-2 was a direct target of mir-1 as shown in previous studies. luciferase assay and western blot assay revealed gadd45β was a direct target of mir-1, and mir-1 suppressed gadd45β expression via binding to its 3'utr. furthermore, mir-1 inhibition increased bcl-2 expression and reduced ia/aar (infarct area/area at risk) ratio and cell apoptosis in rats undergoing myocardial i/r as well as in cardiomyocytes receiving h/r injury. importantly, bcl-2 knockdown restored these consequences following mir-1 inhibition. however, gadd45β knockdown reduced ia/aar ratio and cell apoptosis in vivo and in vitro, but failed torestore above consequences after mir-1 inhibition. in conclusion mir-1 inhibition protects against h/r-induced apoptosis of myocytes by directly targeting bcl-2 but not gadd45β.",1
"micrornas (mirnas) are small, non-coding rnas which regulate gene expression at the post-transcriptional level. abnormal expression of mirnas occurs frequently in human tumors. despite the fact that reduced expression of mir-128 has been observed in glioma tissues and cells, the role of mir-128 in tumors has not been fully characterized. in the present study, cell adhesion assays indicated that overexpression of mir-128 can promote cell-cell adhesion. target site prediction algorithms indicated that mir-128 binds the 3'-untranslated regions of erythropoietin-producing hepatocellular receptor (eph)b1 and ephb2 mrnas. luciferase reporter assays confirmed that mir-128 binds and regulates ephb1 and ephb2 mrnas. overexpression of ephb2 reduced the ability of mir-128 to promote cell-cell adhesion. the wound-healing assay indicated that mir-128 significantly inhibited cell migration via ephb2. this study revealed the novel functions of mir-128 in cell-cell adhesion and cell migration in glioma cells through the regulation of ephb2, and identified ephb1 and ephb2 as novel mir-128 targets.",1
"we have characterized a putative precursor rna (15.5s) for the 15s ribosomal rna in mitochondria of saccharomyces cerevisiae. hybrids were formed with mitochondrial rna and mtdna fragments terminally labelled at restriction sites located within the gene coding for 15s ribosomal rna and treated with s1 nuclease (berk, a.j. and sharp, j.a. (1977) 12, 721-732). sites of resistant hybrids were measured by agarose gel electrophoresis and end points of rnas determined. the 15.5s rna is approximately 80 nucleotides longer than the 15s ribosomal rna, with the extra sequences being located at the 5'-end. both 15s ribosomal rna and 15.5s rna are fully localised within a 2000 base pair hapii fragment. this putative precursor and the mature 15s ribosomal rna are also found in petite mutants which retain the 15s ribosomal rna gene. the petite mutant with the smallest genetic complexity has its end point of deletion (junction) just outside the hapii site located in the 5' flank of the 15s ribosomal rna genes as determined by s1 nuclease analysis. this leaves a dna stretch approximately 300 base pairs long where an initiation signal for mitochondrial transcription may be present.",1
"background spliceosomal snrnas and ribosomal rnas in metazoans contain numerous modified residues that are functionally important. the most common modifications are site-specific 2'-o-methylation and pseudouridylation, both directed by small ribonucleoprotein particles. each particle is composed of a short guide rna and a set of several proteins. all previously characterized modification guide rnas in metazoa are encoded in and processed from introns. results we have identified and characterized three novel guide rnas for conserved 2'-o-methylation of u2, u4, and u12 snrnas. two guides, termed mgu2-25/61 and mgu12-22/u4-8, appear to be independently transcribed as judged by the presence of methylated guanosine caps at their 5' ends and upstream promoters similar to those of telomerase rna. these guide rnas are each composed of a canonical box c/d snorna and a novel box c/d snorna-like domain, where the c'/d' motif, rather than c/d, can be folded into a conserved kink-turn structure. the snorna-like domains are predicted to direct 2'-o-methylation of invariant g residues that occupy analogous positions in the u2 and u12 snrna secondary structures. a third guide, mgu2-19/30 rna, is composed of two canonical box c/d snorna domains encoded within a single intron. conclusions this is the first description in metazoan cells of 5'-capped modification guide rnas that appear to be independently transcribed. since plant, yeast, and protozoan guide rnas are mostly independently transcribed, the identification of such rnas argues that ancestral metazoans possessed independently transcribed guide rnas and only later, during the evolution of metazoan organisms, did the guide rna genes shift to introns.",1
"the critical role of noncoding small rnas (srnas) in the bacterial response to changing conditions is increasingly recognized. however, a specific role for srnas during antibiotic exposure has not been investigated in staphylococcus aureus. here, we used illumina rna-seq to examine the srna response of multiresistant sequence type 239 (st239) s. aureus after exposure to four antibiotics (vancomycin, linezolid, ceftobiprole, and tigecycline) representing the major classes of antimicrobials used to treat methicillin-resistant s. aureus (mrsa) infections. we identified 409 potential srnas and then compared global srna and mrna expression profiles at 2 and 6 h, without antibiotic exposure and after exposure to each antibiotic, for a vancomycin-susceptible strain (jkd6009) and a vancomycin-intermediate strain (jkd6008). exploration of this data set by multivariate analysis using a novel implementation of nonnegative matrix factorization (nmf) revealed very different responses for mrna and srna. where mrna responses clustered with strain or growth phase conditions, the srna responses were predominantly linked to antibiotic exposure, including srna responses that were specific for particular antibiotics. a remarkable feature of the antimicrobial response was the prominence of antisense srnas to genes encoding proteins involved in protein synthesis and ribosomal function. this study has defined a large srna repertoire in epidemic st239 mrsa and shown for the first time that a subset of srnas are part of a coordinated transcriptional response to specific antimicrobial exposures in s. aureus. these data provide a framework for interrogating the role of staphylococcal srnas in antimicrobial resistance and exploring new avenues for srna-based antimicrobial therapies.",1
"micrornas (mirnas) are endogenously expressed 20-24 nucleotide rnas thought to repress protein translation through binding to a target mrna (1-3). only a few of the more than 250 predicted human mirnas have been assigned any biological function. in an effort to uncover mirnas important during adipocyte differentiation, antisense oligonucleotides (asos) targeting 86 human mirnas were transfected into cultured human pre-adipocytes, and their ability to modulate adipocyte differentiation was evaluated. expression of 254 mirnas in differentiating adipocytes was also examined on a mirna microarray. here we report that the combination of expression data and functional assay results identified a role for mir-143 in adipocyte differentiation. mir-143 levels increased in differentiating adipocytes, and inhibition of mir-143 effectively inhibited adipocyte differentiation. in addition, protein levels of the proposed mir-143 target erk5 (4) were higher in aso-treated adipocytes. these results demonstrate that mir-143 is involved in adipocyte differentiation and may act through target gene erk5.",1
"post-transcriptional regulatory mechanisms are widespread in bacteria. interestingly, current published data hint that some of these mechanisms may be non-random with respect to their phylogenetic distribution. although small, trans-acting regulatory rnas commonly occur in bacterial genomes, they have been better characterized in gram-negative bacteria, leaving the impression that they may be less important for firmicutes. it has been presumed that gram-positive bacteria, in particular the firmicutes, are likely to utilize cis-acting regulatory rnas located within the 5' mrna leader region more often than trans-acting regulatory rnas. in this analysis we catalog, by a deep sequencing-based approach, both classes of regulatory rna candidates for bacillus subtilis, the model microorganism for firmicutes. we successfully recover most of the known small rna regulators while also identifying a greater number of new candidate rnas. we anticipate these data to be a broadly useful resource for analysis of post-transcriptional regulatory strategies in b. subtilis and other firmicutes.",1
"genistein has been shown to suppress the growth of several cancers through modulation of various pathways. however, the effects of genistein on the regulation of oncogenic microrna-151 (mir-151) have not been reported. in this study, we investigated whether genistein could alter the expression of oncogenic mir-151 and its target genes that are involved in the progression and metastasis of prostate cancer (pca). real-time rt-pcr showed that the expression of mir-151 was higher in pc3 and du145 cells compared with rwpe-1 cells. treatment of pc3 and du145 cells with 25 µm genistein down-regulated the expression of mir-151 compared with vehicle control. inhibition of mir-151 in pca cells by genistein significantly inhibited cell migration and invasion. in-silico analysis showed that several genes (casz1, il1rapl1, sox17, n4bp1 and arhgdia) suggested to have tumor suppressive functions were target genes of mir-151. luciferase reporter assays indicated that mir-151 directly binds to specific sites on the 3'utr of target genes. quantitative real-time pcr analysis showed that the mrna expression levels of the five target genes in pc3 and du145 were markedly changed with mir-151 mimics and inhibitor. kaplan-meier curves and log-rank tests revealed that high expression levels of mir-151 had an adverse effect on survival rate. this study suggests that genistein mediated suppression of oncogenic mirnas can be an important dietary therapeutic strategy for the treatment of pca.",1
"pulmonary artery hypertension (pah) is a fatal disorder. recent studies suggest that microrna (mirna) plays an important role in regulating proliferation of pulmonary artery smooth muscle cells (pasmc), which underlies the pathology of pah however, the exact mechanism of action of mirnas remains elusive. in this study, we found that mir-339 was highly expressed in the cardiovascular system and was downregulated by a group of cytokines and growth factors, especially pdgf-bb and fgf2. functional analyses revealed that mir-339 can inhibit proliferation of pasmc also, mir-339 inhibited fgf2-induced proliferation, but had no effect on proliferation induced by pdgf-bb the fibroblast growth factor receptor substrate 2 (frs2) was identified as a potential direct target of mir-339. consistent with the actions of mir-339, knockdown of frs2 only inhibited fgf2- but not pdgf-bb-induced proliferation of pasmc in addition, our results showed that inhibition of erk and pi3k abrogated the downregulation of mir-339 induced by pdgf-bb finally, mir-339 expression was found to be decreased in the pulmonary arteries of rats with mct-induced pah our study is the first report on the biological role of mir-339 in regulating proliferation of pasmc by targeting fgf signaling, providing new mechanistic insights into pasmc proliferation and pathogenesis of pah.",1
"aim the regulation of human dental pulp inflammation is not fully understood. this study aims to investigate the effect of mir-4691-3p on the cgas-sting signalling cascade and its downstream cytokines production in human dental pulp cells (hdpcs). methodology normal dental pulp tissue and pulp tissue with irreversible pulpitis from third molars were collected. hdpcs were isolated from pulp tissue. the expression of sting mrna and mir-4691-3p was measured by quantitative real-time pcr. bioinformatic computation via targetscanhuman 8.0 and a luciferase reporter assay was used to identify the targets of mir-4691-3p. a mir-4691-3p mimic and inhibitor were used to upregulate or downregulate mir-4691-3p expression in hdpcs. hdpcs were transfected with c-di-amp, c-di-gmp, cgamp, interferon stimulatory dna (isd) and bacterial genomic dna. immunoblot was performed to detect the phosphorylation of tbk1, p65 and irf3. enzyme-linked immunoassay was performed to detect the cytokines including ifn-β, tnf or il-6 downstream of cgas-sting. results mir-4691-3p expression was increased in human dental pulp tissue with irreversible pulpitis. treatment of hdpcs using recombinant human ifn-β, tnf or il-6 also upregulated mir-4691-3p. the bioinformatic prediction and luciferase reporter assay confirmed that sting was a direct target of mir-4691-3p. the mir-4691-3p mimic suppressed sting expression, the phosphorylation of tbk1, p65 and irf3, and the ifn-β, tnf or il-6 production. in contrast, the mir-4691-3p inhibitor enhanced the sting expression, the phosphorylation of tbk1, p65 and irf3 and the ifn-β, tnf or il-6 production. conclusions mir-4691-3p negatively regulates the cgas-sting pathway by directly targeting sting. this provides insight to utilize mirna-dependent regulatory effect to treat endodontic disease as well as sting-dependent systemic inflammatory disease.",1
"poor survival and function of transplanted cells in ischemic and inflamed myocardium likely compromises the functional benefit of stem cell-based therapies. we have earlier reported that co-administration of interleukin (il)-10 and bmpac enhances cell survival and improves left ventricular (lv) functions after acute myocardial infarction (mi) in mice. we hypothesized that il-10 regulates microrna-375 (mir-375) signaling in bmpacs to enhance their survival and function in ischemic myocardium after mi and attenuates left ventricular dysfunction after mi. mir-375 expression is significantly upregulated in bmpacs upon exposure to inflammatory/hypoxic stimulus and also after mi. il-10 knockout mice display significantly elevated mir-375 levels. we report that ex vivo mir-375 knockdown in bmpac before transplantation in the ischemic myocardium after mi significantly improve the survival and retention of transplanted bmpacs and also bmpac-mediated post-infarct repair, neovascularization, and lv functions. our in vitro studies revealed that knockdown of mir-375-enhanced bmpac proliferation and tube formation and inhibited apoptosis; over expression of mir-375 in bmpac had opposite effects. mechanistically, mir-375 negatively regulated 3-phosphoinositide-dependent protein kinase-1 (pdk-1) expression and pdk-1-mediated activation of pi3kinase/akt signaling. interestingly, bmpac isolated from il-10-deficient mice showed elevated basal levels of mir-375 and exhibited functional deficiencies, which were partly rescued by mir-375 knockdown, enhancing bmpac function in vitro and in vivo. taken together, our studies suggest that mir-375 is negatively associated with bmpac function and survival and il-10-mediated repression of mir-375 enhances bmpac survival and function.",1
"background gastrointestinal stromal tumours (gist) are characterised by high expression of kit and etv1, which cooperate in gist oncogenesis. our aim was to identify micrornas that are deregulated in gist, have a role in gist pathogenesis, and could potentially be used as therapeutic tool. methods differentially expressed micrornas between primary gist (n=50) and gastrointestinal leiomyosarcomas (gi-lms, n=10) were determined using microarrays. selected microrna mimics were transfected into gist-882 and gist-t1 cell lines to study the effects of microrna overexpression on gist cells. luciferase reporter assays were used to establish regulation of target genes by selected micrornas. results mir-17-92 and mir-221/222 cluster members were significantly (p conclusion micrornas that may have an essential role in gist pathogenesis were identified, in particular mir-17/20a/222 that target kit and etv1. delivering these micrornas therapeutically could hold great potential for gist management, especially in imatinib-resistant disease.",1
"unraveling the gene regulatory networks that govern development and function of the mammalian heart is critical for the rational design of therapeutic interventions in human heart disease. using the drosophila heart as a platform for identifying novel gene interactions leading to heart disease, we found that the rho-gtpase cdc42 cooperates with the cardiac transcription factor tinman/nkx2-5. compound cdc42, tinman heterozygous mutant flies exhibited impaired cardiac output and altered myofibrillar architecture, and adult heart-specific interference with cdc42 function is sufficient to cause these same defects. we also identified k(+) channels, encoded by dsur and slowpoke, as potential effectors of the cdc42-tinman interaction. to determine whether a cdc42-nkx2-5 interaction is conserved in the mammalian heart, we examined compound heterozygous mutant mice and found conduction system and cardiac output defects. in exploring the mechanism of nkx2-5 interaction with cdc42, we demonstrated that mouse cdc42 was a target of, and negatively regulated by mir-1, which itself was negatively regulated by nkx2-5 in the mouse heart and by tinman in the fly heart. we conclude that cdc42 plays a conserved role in regulating heart function and is an indirect target of tinman/nkx2-5 via mir-1.",1
"micrornas (mirnas) are post-transcriptional regulators of gene expression. heterozygous loss-of-function point mutations of mirna genes are associated with several human congenital disorders 1-5 , but neomorphic (gain-of-new-function) mutations in mirnas due to nucleotide substitutions have not been reported. here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated mir140 gene encoding microrna-140 (mir-140) in a novel autosomal dominant human skeletal dysplasia. mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of mir-140-null mice 6 . this mutant mirna gene yields abundant mutant mir-140-5p expression without mirna-processing defects. in chondrocytes, the mutation causes widespread derepression of wild-type mir-140-5p targets and repression of mutant mir-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. furthermore, the mutant mir-140-5p seed competes with the conserved rna-binding protein ybx1 for overlapping binding sites. this finding may explain the potent target repression and robust in vivo effect by this mutant mirna even in the absence of evolutionary selection of mirna-target rna interactions, which contributes to the strong regulatory effects of conserved mirnas 7,8 . our study presents the first case of a pathogenic gain-of-function mirna mutation and provides molecular insight into neomorphic actions of emerging and/or mutant mirnas.",1
"background upregulated by atheroprotective flow, the transcription factor krüppel-like factor 2 (klf2) is crucial for maintaining endothelial function. micrornas (mirnas) are noncoding small rnas that regulate gene expression at the posttranscriptional level. we examined the role of mirnas, particularly mir-92a, in the atheroprotective flow-regulated klf2. methods and results dicer knockdown increased the level of klf2 mrna in human umbilical vein endothelial cells, suggesting that klf2 is regulated by mirna. in silico analysis predicted that mir-92a could bind to the 3' untranslated region of klf2 mrna. overexpression of mir-92a decreased the expression of klf2 and the klf2-regulated endothelial nitric oxide synthase and thrombomodulin at mrna and protein levels. a complementary finding is that mir-92a inhibitor increased the mrna and protein expression of klf2, endothelial nitric oxide synthase, and thrombomodulin. subsequent studies revealed that atheroprotective laminar flow downregulated the level of mir-92a precursor to induce klf2, and the level of this flow-induced klf2 was reduced by mir-92a precursor. furthermore, mir-92a level was lower in human umbilical vein endothelial cells exposed to the atheroprotective pulsatile shear flow than under atheroprone oscillatory shear flow. anti-ago1/2 immunoprecipitation coupled with real-time polymerase chain reaction revealed that pulsatile shear flow decreased the functional targeting of mir-92a precursor/klf2 mrna in human umbilical vein endothelial cells. consistent with these findings, mouse carotid arteries receiving mir-92a precursor exhibited impaired vasodilatory response to flow. conclusions atheroprotective flow patterns decrease the level of mir-92a, which in turn increases klf2 expression to maintain endothelial homeostasis.",1
"mirnas regulate the expression of genes in both normal physiology and disease. while mirnas have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. such single-gene approaches have significant limitations, relying on mirna expression levels and heuristic predictions of mrna-binding sites. this results in only circumstantial evidence of mirna-target interaction and typically leads to large numbers of false positive predictions. here, we used a genome-wide approach (high-throughput sequencing of rna isolated by crosslinking immunoprecipitation, hits-clip) to define direct mirna-mrna interactions in three breast cancer subtypes (estrogen receptor positive, her2 amplified, and triple negative). focusing on steroid receptor signaling, we identified two novel regulators of the er pathway (mir-9-5p and mir-193a/b-3p), which together target multiple genes involved in er signaling. moreover, this approach enabled the definition of mir-9-5p as a global regulator of steroid receptor signaling in breast cancer. we show that mirna targets and networks defined by hits-clip under physiologic conditions are predictive of patient outcomes and provide global insight into mirna regulation in breast cancer.",1
"micrornas (mirnas) are a family of endogenous small non-coding rnas which regulate mrnas at the post-transcriptional level. mirnas have been identified in both normal physiological and pathological conditions. to date, a limited number of mirnas have been shown to be involved in the regulation of insulin secretion. we have identified a panel of 10 mirnas down-regulated in glucose non-responsive min6 cells compared to glucose responsive cells using taqman low density mirna arrays. of these 10 mirna targets, subsequent functional investigations involving knockdown of mir-200a, mir-130a and mir-410 levels suggested that they may decrease the capability of min6 cells to secrete insulin in response to stimulatory levels of glucose. conversely, experiment with over-expression of mir-410 suggest that it may enhance levels of glucose stimulated insulin secretion. in this study, we have also identified 21 mirnas not previously known to have a potential murine homologue.",1
"unlabelled micrornas (mirnas) have been reported to be associated with the development of cancers. however, the function of mirnas in human hepatocellular carcinoma (hcc) remains largely undefined. here we found that overexpression of mir-10a promoted the migration and invasion of qgy-7703 and hepg2 cells in vitro but suppressed metastasis in vivo. cell adhesion assays showed that mir-10a suppressed hcc cell-matrix adhesion, which could explain the results of the in vivo animal experiments. the eph tyrosine kinase receptor, epha4, was identified as the direct and functional target gene of mir-10a. knockdown of epha4 phenocopied the effect of mir-10a and ectopic expression of epha4 restored the effect of mir-10a on migration, invasion, and adhesion in hcc cells. we further demonstrated that mir-10a and epha4 regulated the epithelial-mesenchymal transition process and the β1-integrin pathway to affect cell invasion and adhesion. conclusion our findings highlight the importance of mir-10a in regulating the metastatic properties of hcc by directly targeting epha4 and may provide new insights into the pathogenesis of hcc.",1
"the role of mir-361-3p in the pathology of alzheimer's disease is unknown. the target scan was used to screen potential target genes of mir-361-3p, and β-site amyloid precursor protein (app) cleaving enzyme 1 (bace1) was emphasized. results from western blotting and reverse transcription-quantitative polymerase chain reaction (rt-pcr) showed that down-regulated mir-361-3p was correlated with up-regulated bace1 in alzheimer's disease patients' brains. luciferase assay confirmed that mir-361-3p directly targets bace1. mir-361-3p overexpression and knockdown experiments were performed and found that mir-361-3p could regulate the expression of bace1, and the accumulation of app-β in appswe transfected sh-sy5y cell. a morris water maze test was performed and showed that overexpression of mir-361-3p improved cognitive deficits in app/ps1 mice. we found mir-361-3p inhibited β-amyloid accumulation by targeting bace1, which thus weakened cognitive deficits in alzheimer's disease.",1
"rationale endothelial cells in situ are largely quiescent, and their isolation and culture are associated with the switch to a proliferative phenotype. objective to identify antiangiogenic micrornas expressed by native endothelial cells that are altered after isolation and culture, as well as the protein targets that regulate responses to growth factors. methods and results profiling studies revealed that mir-223 was highly expressed in freshly isolated human, murine, and porcine endothelial cells, but those levels decreased in culture. in primary cultures of endothelial cells, vascular endothelial cell growth factor and basic fibroblast growth factor further decreased mir-223 expression. the overexpression of precursor-mir-223 did not affect basal endothelial cell proliferation but abrogated vascular endothelial cell growth factor-induced and basic fibroblast growth factor-induced proliferation, as well as migration and sprouting. inhibition of mir-223 in vivo using specific antagomirs potentiated postnatal retinal angiogenesis in wild-type mice, whereas recovery of perfusion after femoral artery ligation and endothelial sprouting from aortic rings from adult mir-223(-/y) animals were enhanced. mir-223 overexpression had no effect on the growth factor-induced activation of erk1/2 but inhibited the vascular endothelial cell growth factor-induced and basic fibroblast growth factor-induced phosphorylation of their receptors and activation of akt. β1 integrin was identified as a target of mir-223 and its downregulation reproduced the defects in growth factor receptor phosphorylation and akt signaling seen after mir-223 overexpression. reintroduction of β1 integrin into mir-223-ovexpressing cells was sufficient to rescue growth factor signaling and angiogenesis. conclusions these results indicate that mir-223 is an antiangiogenic microrna that prevents endothelial cell proliferation at least partly by targeting β1 integrin.",1
"in drosophila, the as yet uncloned heterochromatic locus flamenco (flam) controls mobilization of the endogenous retrovirus gypsy through the repeat-associated small interfering (rasi) rna silencing pathway. restrictive alleles (flamr) downregulate accumulation of gypsy transcripts in the somatic follicular epithelium of the ovary. in contrast, permissive alleles (flamp) are unable to repress gypsy. dip1, the closest transcription unit to a flam-insertional mutation, was considered as a good candidate to be a gypsy regulator, since it encodes a dsrna-binding protein. to further characterize the locus we analyzed p-induced flam mutants and generated new mutations by transposon mobilization. we show that flam is required somatically for morphogenesis of the follicular epithelium, the tissue where gypsy is repressed. this developmental activity is necessary to control gypsy and another retroelement, zam. we also show that flam is not dip1, as none of the new permissive mutants affect the dip1 coding sequence. in addition, two deletions removing dip1 coding sequences do not affect any of the flamenco functions. our results suggest that flamenco extends proximally to dip1, spanning >130 kb of transposon-rich heterochromatin. we propose a model explaining the multiple functions of this large heterochromatic locus.",1
"micrornas play extensive roles in cellular development. analysis of the microrna expression pattern during intestinal cell proliferation in early life is likely to unravel molecular mechanisms behind intestinal development and have implications for therapeutic intervention. in this study, we isolated mouse intestinal crypt cells, examined the differences in microrna expression upon igf-1 stimulated proliferation and identified mir-103 as a one of the key regulators. mouse intestinal crypt cells were cultured and treated with igf-1 for 24 h. microrna microarray showed that multiple micrornas are regulated by igf-1, and mir-103 was the most sharply down-regulated. expression of mir-103 in mouse intestinal crypt cells was confirmed by real-time q-pcr. sequence analyses showed that, among the 1040 predicted mir-103 target genes, ccne1, cdk2, and creb1 contain complementary sequences to the mir-103 seed region that are conserved between human and mouse. we further demonstrated that mir-103 controls the expression level of these three genes in mouse crypt cells by luciferase assay and immunoblotting assay. taken together, our data suggest that in mouse intestinal crypt cells, mir-103 is part of the g1/s transition regulatory network, which targets ccne1, cdk2, and creb1 during igf-1 stimulated proliferation.",1
"objectives mir-21 induces neoplastic transformation, cell proliferation, and metastasis and downregulates programmed cell death4 (pdcd4) in some cancers. the aim of this study was to investigate the roles and interactions of pdcd4 and mir-21 in human renal cell carcinoma (rcc). materials and methods a total of 32 paired tumor and normal tissue specimens from rcc patients as well as three renal cancer cell lines (786-o, a498, caki-1) and one normal epithelial kidney cell line (hk-2) were studied. the expression levels of pdcd4 (protein and mrna) and mir-21 were examined by western blot analysis and by qrt-pcr and luciferase reporter assays. furthermore, we transfected 786-o cells with pre-mir-21 (mimics) and anti-mir-21 (inhibitor) and then again analyzed the expression of pdcd4 protein and mrna, and determined cell proliferation and transformation capabilities by edu and soft agar colony formation assay. results mir-21 expression was significantly upregulated in rcc, metastatic rcc specimens and renal cancer cell lines (a498, 786-o, caki-1) compared to normal non-metastatic rcc specimens and hk-2 cells (p 0.05). moreover, we observed a significant reduction in pdcd4 protein levels in mir-21mimic-transfected cells, but a significant increase in mir-21inhibitor-transfected cells (p 0.05). furthermore, mir-21mimic-transfected cells exhibited increased cell proliferation and transformation capacity according to edu analysis and soft agar formation assay, whereas mir-21inhibitor-transfected cells exhibited the opposite phenomenon(p conclusions mir-21 not only promoted cancer cell hyperplasia and contributed to tumor cell transformation and metastasis, but also post-transcriptionally downregulated pdcd4 protein expression. pdcd4 and mir-21 expression levels potentially play an important role in renal cell cancer.",1
"a growing amount of evidence supports that microrna (mirna) dysregulation is involved in cancer progression by directly downregulating multiple targets. elucidating the underlying mechanism of mirna in carcinogenesis may improve diagnostic and therapeutic strategies for malignancy. in the current study, we found that mir-105 expression was markedly downregulated in both hepatocellular carcinoma (hcc) cell lines and clinical hcc tissues, compared with normal human hepatocyte and adjacent non-cancerous tissues, respectively. ectopic mir-105 expression suppressed, whereas inhibiting mir-105 promoted the proliferation and tumorigenicity of hcc cells both in vitro and in vivo. furthermore, we demonstrated that mir-105 could deactivated the phosphoinositide 3-kinase (pi3k)/akt signaling pathway by downregulating insulin receptor substrate-1, 3-phosphoinositide-dependent protein kinase-1 and akt1 directly, resulting in increasing cyclin-dependent kinase inhibitors 1a and 1b (p21(cip1) and p27(kip1)) and decreasing cyclin d1 expression in hcc. therefore, our results suggest that mir-105 functions as a potential tumor suppressor by inhibiting the pi3k/akt signaling pathway and might represent a potential therapeutic target for hcc patients.",1
"micrornas (mirnas) are small non-coding rnas of 19-25 nucleotides that are involved in the regulation of critical cell processes such as apoptosis, cell proliferation and differentiation. however, little is known about the role of mirnas in granulopoiesis. here, we report the expression of mirnas in acute promyelocytic leukemia patients and cell lines during all-trans-retinoic acid (atra) treatment by using a mirna microarrays platform and quantitative real time-polymerase chain reaction (qrt-pcr). we found upregulation of mir-15a, mir-15b, mir-16-1, let-7a-3, let-7c, let-7d, mir-223, mir-342 and mir-107, whereas mir-181b was downregulated. among the upregulated mirnas, mir-107 is predicted to target nfi-a, a gene that has been involved in a regulatory loop involving mir-223 and c/ebpa during granulocytic differentiation. indeed, we have confirmed that mir-107 targets nf1-a. to get insights about atra regulation of mirnas, we searched for atra-modulated transcription factors binding sites in the upstream genomic region of the let-7a-3/let-7b cluster and identified several putative nuclear factor-kappa b (nf-kappab) consensus elements. the use of reporter gene assays, chromatin immunoprecipitation and site-directed mutagenesis revealed that one proximal nf-kappab binding site is essential for the transactivation of the let-7a-3/let-7b cluster. finally, we show that atra downregulation of ras and bcl2 correlate with the activation of known mirna regulators of those proteins, let-7a and mir-15a/mir-16-1, respectively.",1
"the cytoplasmic polyadenylation element binding-protein (cpeb) is an rna-binding protein that participates in translational control. cpeb2, cpeb3 and cpeb4 are paralog proteins very similar among themselves referred as the cpeb2 subfamily. to gain insight into common mechanisms of regulation of the cpeb2 subfamily transcripts, we looked for putative cis-acting elements present in the 3'-utrs of the three paralogs. we found different families of mirnas predicted to target all subfamily members. most predicted target sites for these families are located in paralog positions suggesting that these putative regulatory motifs were already present in the ancestral gene. we validated target sites for mir-92 and mir-26 in the three paralogs using mutagenesis of mirna-binding sites in reporter constructs combined with over-expression and depletion of mirnas. both mir-92 and mir-26 induced a decrease in luciferase activity associated to a reduction in mrna levels of the reporter constructs. we also showed that the endogenous mirnas co-regulate cpeb2, cpeb3 and cpeb4 transcripts, supporting our hypothesis that these genes have a common regulatory mechanism mediated by mirnas. we also suggest that the ancestral pattern of mirna-binding motifs was maintained throughout the generation of highly conserved elements in each of the 3'-utrs.",1
"accumulating evidence has shown that micrornas are involved in multiple processes in cancer development and progression. recently, mir-335 has been identified as a tumor-suppressing microrna in many human cancers. however, the specific function of mir-335 in osteosarcoma is unclear at this point. in this study, we found that the expression of mir-335 in osteosarcoma tissues and cell lines was much lower than that in normal control, respectively, and the downregulated mir-335 was significantly associated with lymph-node metastasis. transfection of mir-335 mimics could significantly inhibit the cell migration and invasion in mg-63 and u2os osteosarcoma cell lines. moreover, we also showed that rock1 was negatively regulated by mir-335 at the posttranscriptional level, via a specific target site within the 3'utr by luciferase reporter assay. the expression of rock1 was inversely correlated with mir-335 expression in osteosarcoma tissues, and knockdown of rock1 by sirna-inhibited osteosarcoma cells migration and invasion resembling that of mir-335 overexpression. thus, our findings suggest that mir-335 acts as tumor suppressor by targeting the rock1 gene and inhibiting osteosarcoma cells migration and invasion. the findings of this study contribute to current understanding of the functions of mir-335 in osteosarcoma.",1
"adam10, overexpressed in tongue squamous cell carcinoma (tscc), has been well documented for its role in tumor progression and metastasis. in the present study, we evaluated the inhibition effect of micrornas (mirnas) on the tscc and identified that mir-140-5p could directly targets adam10 and inhibits the invasion and migration of tscc cells. lamc1, hdac7 and pax6, clustered into migration-related genes, were validated to be direct targets of mir-140-5p, while igf1r and psen1 were not responsible to the regulation. most intriguingly, erbb4 was upregulated by mir-140-5p even though the interaction between erbb4 3'utr and mir-140-5p existed simultaneously. meanwhile, adam10 is involved in the ""positive"" regulation of erbb4 and negative regulation of pax6 by mir-140-5p. taken together, our results suggest that mir-140-5p play a role in tscc cell migration and invasion, and two brand new relationships between mirna and its targets emerged: (1) adam10 is not just a direct target of mir-140-5p, the repressed adam10 also helps to enhance the effect of mir-140-5p to other target genes: erbb4 and pax6; (2) erbb4 is ""positively"" regulated by mir-140-5p.",1
"aims viral myocarditis (vm) is an important cause of heart failure and sudden cardiac death in young healthy adults; it is also an aetiological precursor of dilated cardiomyopathy. we explored the role of the mir-221/-222 family that is up-regulated in vm. methods and results here, we show that microrna-221 (mir-221) and mir-222 levels are significantly elevated during acute vm caused by coxsackievirus b3 (cvb3). both mirs are expressed by different cardiac cells and by infiltrating inflammatory cells, but their up-regulation upon myocarditis is mostly exclusive for the cardiomyocyte. systemic inhibition of mir-221/-222 in mice increased cardiac viral load, prolonged the viraemic state, and strongly aggravated cardiac injury and inflammation. similarly, in vitro, overexpression of mir-221 and mir-222 inhibited enteroviral replication, whereas knockdown of this mir-cluster augmented viral replication. we identified and confirmed a number of mir-221/-222 targets that co-orchestrate the increased viral replication and inflammation, including ets1/2, irf2, bcl2l11, tox, bmf, and cxcl12. in vitro inhibition of irf2, tox, or cxcl12 in cardiomyocytes significantly dampened their inflammatory response to cvb3 infection, confirming the functionality of these targets in vm and highlighting the importance of mir-221/-222 as regulators of the cardiac response to vm. conclusions the mir-221/-222 cluster orchestrates the antiviral and inflammatory immune response to viral infection of the heart. its inhibition increases viral load, inflammation, and overall cardiac injury upon vm.",1
"excessive stress, e.g. due to biomechanical overload or ischemia/reperfusion is a potent inductor of cardiomyocyte apoptosis, which contributes to maladaptive remodeling. despite substantial progress in the understanding of the molecular pathophysiology, many components of the signaling pathways underlying remodeling in general and apoptosis in particular still remain unknown. recent evidence suggests that micrornas (mirs) play an important role in the heart's response to increased cardiac stress. to identify novel modulators of stress-dependent remodeling, we conducted a genome-wide mir-screen of mechanically stretched neonatal rat cardiomyocytes (nrcm). out of 351 mirs, eight were significantly regulated by biomechanical stress, including microrna-20a, which is part of the mir17-92 cluster. interestingly, further expression analyses also revealed upregulation of microrna-20a in an in vitro hypoxia/""reperfusion"" model. given the potential apoptosis-modulating properties of the mir17-92 cluster, we subjected nrcm to hypoxia and subsequent reoxygenation. admir-20a significantly inhibited hypoxia-mediated apoptosis in a dose-dependent fashion, while targeted knockdown of mir-20a in nrcm induced cardiomyocyte apoptosis. mechanistically, the antiapoptotic effect of mir-20a appears to be mediated through direct targeting and subsequent downregulation of the proapoptotic factor egln3. thus, mir-20a is upregulated in acute biomechanical stress as well as hypoxia and inhibits apoptosis in cardiomyocytes. these properties reveal mir-20a as a cardioprotective micro-rna and a potential target for novel therapeutic strategies to prevent cardiac remodeling.",1
"the emergence of staphylococcus aureus strains that are resistant to glycopeptides has led to alarming scenarios where serious staphylococcal infections cannot be treated. the bacterium expresses many small regulatory rnas (srnas) that have unknown biological functions for the most part. here we show that an s. aureus srna, sprx (alias rsaor), shapes bacterial resistance to glycopeptides, the invaluable treatments for methicillin-resistant staphylococcal infections. modifying sprx expression levels influences vancomycin and teicoplanin glycopeptide resistance. comparative proteomic studies have identified that sprx specifically downregulates stage v sporulation protein g, spovg. spovg is produced from the yabj-spovg operon and contributes to s. aureus glycopeptide resistance. sprx negatively regulates spovg expression by direct antisense pairings at the internal translation initiation signals of the second operon gene, without modifying bicistronic mrna expression levels or affecting yabj translation. the sprx and yabj-spovg mrna domains involved in the interaction have been identified, highlighting the importance of a cu-rich loop of sprx in the control of spovg expression. we have shown that spovg might not be the unique sprx target involved in the glycopeptide resistance and demonstrated that the regulation of glycopeptide sensitivity involves the cu-rich domain of sprx. here we report the case of a srna influencing antibiotic resistance of a major human pathogen.",1
"hepatocellular carcinoma is one of the most common and lethal cancers worldwide, especially in developing countries. in the present study, we found that the expression of a microrna, mir-590-5p, was down-regulated and s100a10 was up-regulated in six hepatocellular carcinoma cell lines. the reporter gene assay showed that overexpression of mir-590-5p effectively reduced the activity of luciferase expressed by a vector bearing the 3' untranslated region of s100a10 mrna. ectopic mir-590-5p overexpression mediated by lentiviral infection decreased expression of s100a10. infection of lv-mir-590-5p inhibited cell growth and induced cell cycle g1 arrest in hepg2 cells. in addition, mir-590-5p expression suppressed the expression of wnt5a, cmyc and cyclin d1, and increased the phosphorylation of β-catenin and expression of caspase 3, which may contribute to the inhibitory effect of mir-590-5p on cell growth. taken together, our data suggest that down-regulation of mir-590-5p is involved in hepatocellular carcinoma and the restoration of mir-590-5p can impair the growth of cancer cells, suggesting that mir-590-5p may be a potential target molecule for the therapy of hepatocellular carcinoma.",1
"micrornas have been associated with many different biological functions, but little is known about their roles in conditioned behavior. we demonstrate that drosophila mir-980 is a memory suppressor gene functioning in multiple regions of the adult brain. memory acquisition and stability were both increased by mir-980 inhibition. whole cell recordings and functional imaging experiments indicated that mir-980 regulates neuronal excitability. we identified the autism susceptibility gene, a2bp1, as an mrna target for mir-980. a2bp1 levels varied inversely with mir-980 expression; memory performance was directly related to a2bp1 levels. in addition, a2bp1 knockdown reversed the memory gains produced by mir-980 inhibition, consistent with a2bp1 being a downstream target of mir-980 responsible for the memory phenotypes. our results indicate that mir-980 represses a2bp1 expression to tune the excitable state of neurons, and the overall state of excitability translates to memory impairment or improvement.",1
"micro-rnas are small noncoding rnas, which diminish the stability and/or translation of mrnas. this study examined whether mir-206, previously shown to be elevated in estrogen receptor (er)alpha-negative breast cancer, regulates the expression of eralpha. two putative mir-206 sites, (heralpha1 and heralpha2), were found in silico within the 3'-untranslated region of human eralpha mrna. transfection of mcf-7 cells with pre-mir-206 or 2'-o-methyl antagomir-206 specifically decreased or increased, respectively, eralpha mrna levels. overexpression of pre-mir-206 reduced eralpha and beta-actin protein levels, with no effect on erbeta, e-cadherin, or glyceraldehyde-3-phosphate dehydrogenase. reporter constructs containing the heralpha1 or heralpha2 binding sites inserted into the 3'-untranslated region of the luciferase mrna conferred a 1.6- and 2.2-fold repression of luciferase activity, respectively, in hela cells. both mir-206 sites responded accordingly to exogenous hsa-pre-mir-206 and 2'-o-methyl antagomir-206, and both sites were rendered inactive by mutations that disrupted hybridization to the 5'-seed of mir-206. a c-->t single nucleotide polymorphism in the heralpha1 site increased repression of luciferase activity to approximately 3.3-fold in hela cells. mir-206 levels were higher in eralpha-negative mb-mda-231 cells than eralpha-positive mcf-7 cells, but only the eralpha1 site mediated significantly more repression in reporter constructs. mir-206 expression was strongly inhibited by eralpha agonists, but not by an erbeta agonist or progesterone, indicating a mutually inhibitory feedback loop. these findings provide the first evidence for the posttranscriptional regulation of eralpha by a micro-rna in the context of breast cancer.",1
"rna splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with dna- and other rna-processing machineries in the nucleus. however, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. here, through affinity purification using drosophila lysates, an interaction is identified between the minor spliceosomal 65k/rnpc3 and ankrd11, a cofactor of histone deacetylase 3 (hdac3). using a crispr/cas9 system, deletion strains are constructed and found that both dm65k δ/δ and dmankrd11 δ/δ mutants have reduced histone deacetylation at lys9 of histone h3 (h3k9) and lys5 of histone h4 (h4k5) in their heads, exhibiting various neural-related defects. the 65k-ankrd11 interaction is also conserved in human cells, and the hsankrd11 middle-uncharacterized domain mediates hs65k association with hdac3. cleavage under targets and tagmentation (cut&tag) assays revealed that hsankrd11 is a bridging factor, which facilitates the synergistic common chromatin-binding of hdac3 and hs65k. knockdown (kd) of hsankrd11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby h3k9. ultimately, this study demonstrates that expression changes of many genes caused by hsankrd11-kd are due to the decreased common chromatin-binding of hdac3 and hs65k and subsequently reduced deacetylation of h3k9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.",1
"aims diabetic nephropathy (dn) is a major diabetic complication characterized by mesangial proliferation and glomerular hypertrophy. micrornas might play an important role in these pathological processes. the aim of this study is to examine the possible association of mir-34a as one of the micrornas with dn and underlying mechanisms in vitro and in vivo. methods according to previous results of microarray which compared the different micrornas between diabetic and normal control mice, mir-34a was chosen and its expression was detected by qrt-pcr. cell viability was then assessed using cell counting kit-8 (cck8) and 5-ethynyl-20-deoxyuridine (edu) incorporation. antagomir was injected in db/db mice to down regulate mir-34a. average diameter of glomeruli was analyzed by periodic acid-schiff (pas) stain of kidney. luciferase gene report assay was then performed to identify the target gene of mir-34a. additional immunoblotting and immunohistochemical analyses were implemented to verify the expression level of growth arrest-specific 1 (gas1). results mir-34a expression level was increased under high glucose condition in vitro and in vivo. down-regulation of mir-34a inhibits mice mesangial cells (mmcs) proliferation in vitro and alleviates glomerular hypertrophy in vivo. gas1 was proved to be the target of mir-34a through luciferase report. moreover, up-regulation of gas1 expression was observed in the presence of mir-34a antagomir as compared with mir-34a antagomir-nc in high-glucose-treated mmcs and db/db mice, respectively. conclusions mir-34a regulated mesangial proliferation and glomerular hypertrophy by directly inhibiting gas1 in early dn.",1
"background in an important model for neuroscience, songbirds learn to discriminate songs they hear during tape-recorded playbacks, as demonstrated by song-specific habituation of both behavioral and neurogenomic responses in the auditory forebrain. we hypothesized that micrornas (mirnas or mirs) may participate in the changing pattern of gene expression induced by song exposure. to test this, we used massively parallel illumina sequencing to analyse small rnas from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence. results in the auditory forebrain, we identified 121 known mirnas conserved in other vertebrates. we also identified 34 novel mirnas that do not align to human or chicken genomes. five conserved mirnas showed significant and consistent changes in copy number after song exposure across three biological replications of the song-silence comparison, with two increasing (tgu-mir-25, tgu-mir-192) and three decreasing (tgu-mir-92, tgu-mir-124, tgu-mir-129-5p). we also detected a locus on the z sex chromosome that produces three different novel mirnas, with supporting evidence from northern blot and taqman qpcr assays for differential expression in males and females and in response to song playbacks. one of these, tgu-mir-2954-3p, is predicted (by targetscan) to regulate eight song-responsive mrnas that all have functions in cellular proliferation and neuronal differentiation. conclusions the experience of hearing another bird singing alters the profile of mirnas in the auditory forebrain of zebra finches. the response involves both known conserved mirnas and novel mirnas described so far only in the zebra finch, including a novel sex-linked, song-responsive mirna. these results indicate that mirnas are likely to contribute to the unique behavioural biology of learned song communication in songbirds.",1
"background the molecular mechanisms underlying the early development of atrial fibrillation (af) remain poorly understood. emerging evidence suggests that abnormal epigenetic modulation via micrornas (mirnas) might be involved in the pathogenesis of paroxysmal af (paf). objective to identify key molecular changes associated with paf, we conducted state-of-the-art transcriptomic studies to identify the abnormal mirna-mrna interactions potentially driving af development. methods high-quality total rna including mirna was isolated from atrial biopsies of age-matched and sex-matched paf patients and control patients in sinus rhythm (sr; n=4 per group) and used for rna-sequencing and mirna microarray. results were analyzed bioinformatically and validated using quantitative real-time (qrt)-pcr and 3'utr luciferase reporter assays. results 113 genes and 49 mirnas were differentially expressed (de) in paf versus sr patients. gene ontology analysis revealed that most of the de genes were involved in the ""gonadotropin releasing hormone receptor pathway"" and ""p53 pathway"". of these de genes, bioinformatic analyses identified 23 pairs of putative mirna-mrna interactions that were altered in paf (involving 15 mirnas and 17 mrnas). using qrt-pcr and 3'utr luciferase reporter assays, the interaction between upregulation of mir-199a-5p and downregulation of fkbp5 was confirmed in samples from paf patients. conclusion our combined transcriptomic analysis and mirna microarray study of atrial samples from paf patients revealed novel pathways and mirna-mrna regulations that may be relevant in the development of paf. future studies are required to investigate the potential involvement of the gonadotropin releasing hormone receptor and p53 pathways in af pathogenesis.",1
"a novel family of riboswitches, called sam-iv, is the fourth distinct set of mrna elements to be reported that regulate gene expression via direct sensing of s-adenosylmethionine (sam or adomet). sam-iv riboswitches share conserved nucleotide positions with the previously described sam-i riboswitches, despite rearranged structures and nucleotide positions with family-specific nucleotide identities. sequence analysis and molecular recognition experiments suggest that sam-i and sam-iv riboswitches share similar ligand binding sites, but have different scaffolds. our findings support the view that rna has considerable structural versatility and reveal that riboswitches exploit this potential to expand the scope of rna in genetic regulation.",1
"toll-like receptors (tlrs) are major receptors that enable inflammatory cells to recognize invading microbial pathogens. micrornas are small non-coding rnas that play important regulatory roles in a variety of biological processes. in this study, we found that a microrna, mir-147, was induced upon stimulation of multiple tlrs and functioned as a negative regulator of tlr-associated signaling events in murine macrophages. we first demonstrated that the nmes1 transcript was a functional primary mir-147. mir-147 was induced in lps-stimulated mouse macrophages and under in vivo conditions in the lungs of lps-treated mice. expression of mir-147 was greater after cellular activation by tlr4 than after engagement of either tlr2 or tlr3, suggesting that maximal induction of mir-147 required activation of both nf-kappab and irf3. tlr4-induced mir-147 expression was both myd88- and trif-dependent. the mir-147 promoter was responsive to tlr4 stimulation and both nf-kappab and stat1alpha bound to the mir-147 promoter. mir-147 mimics or induced expression of mir-147 decreased, whereas mir-147 knockdown increased inflammatory cytokine expression in macrophages stimulated with ligands to tlr2, tlr3, and tlr4. these data demonstrate a negative-feedback loop in which tlr stimulation induces mir-147 to prevent excessive inflammatory responses.",1
"an argonaute homolog and a functional dicer have been identified in the ancient eukaryote giardia lamblia, which apparently lacks the ability to perform rna interference (rnai). the giardia argonaute plays an essential role in growth and is capable of binding specifically to the m(7)g-cap, suggesting a potential involvement in microrna (mirna)-mediated translational repression. to test such a possibility, small rnas were isolated from giardia trophozoites, cloned, and sequenced. a 26-nucleotide (nt) small rna (mir2) was identified as a product of dicer-processed snorna glsr17 and localized to the cytoplasm by fluorescence in situ hybridization, whereas glsr17 was found primarily in the nucleolus of only one of the two nuclei in giardia. three other small rnas were also identified as products of snornas, suggesting that the latter could be novel precursors of mirnas in giardia. putative mir2 target sites were identified at the 3'-untranslated regions (utr) of 22 variant surface protein mrnas using the miranda program. in vivo expression of renilla luciferase mrna containing six identical mir2 target sites in the 3'-utr was reduced by 40% when co-transfected with synthetic mir2, while the level of luciferase mrna remained unaffected. thus, mir2 likely affects translation but not mrna stability. this repression, however, was not observed when argonaute was knocked down in giardia using a ribozyme-antisense rna. instead, an enhancement of luciferase expression was observed, suggesting a loss of endogenous mir2-mediated repression when this protein is depleted. additionally, the level of mir2 was significantly reduced when dicer was knocked down. in all, the evidence indicates the presence of a snorna-derived mirna-mediated translational repression in giardia.",1
"rnase mrp is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer rna sequences from a variety of sources. the bulk of rnase mrp activity is found in the nucleus where its function remains unknown. two different approaches have resulted in predictions of distinct secondary structures for rnase mrp rna. in order to analyze more definitively the higher-order structure of rnase mrp rna, we have conducted a phylogenetic comparison of the available rnase mrp rna sequences from human, mouse, rat, cow, toad, and yeast. the resulting secondary structure shares features in common with previously described structures for prokaryotic and eukaryotic rnase p rnas (1) and rnase mrp rnas (2, 3). in addition, the phylogenetic structure is consistent with available chemical modification data on rnase mrp rna and with the detailed analysis of the to antigen binding domain located near the 5' end of the rnase mrp rna. the structure is not limited to rnase mrp rnas, but can be expanded to cover both eukaryotic rnase p rnas and rnase p/mrp rnas from plants.",1
"to improve regeneration of the injured myocardium, cardiomyocyte progenitor cells (cmpcs) have been put forward as a potential cell source for transplantation therapy. although cell transplantation therapy displayed promising results, many issues need to be addressed before fully appreciating their impact. one of the hurdles is poor graft-cell survival upon injection, thereby limiting potential beneficial effects. here, we attempt to improve cmpcs survival by increasing microrna-155 (mir-155) levels, potentially to improve engraftment upon transplantation. using quantitative pcr, we observed a 4-fold increase of mir-155 when cmpcs were exposed to hydrogen-peroxide stimulation. flow cytometric analysis of cell viability, apoptosis and necrosis showed that necrosis is the main cause of cell death. overexpressing mir-155 in cmpcs revealed that mir-155 attenuated necrotic cell death by 40 ± 2.3%via targeting receptor interacting protein 1 (rip1). in addition, inhibiting rip1, either by pre-incubating the cells with a rip1 specific inhibitor, necrostatin-1 or sirna mediated knockdown, reduced necrosis by 38 ± 2.5% and 33 ± 1.9%, respectively. interestingly, analysing gene expression using a pcr-array showed that increased mir-155 levels did not change cell survival and apoptotic related gene expression. by targeting rip1, mir-155 repressed necrotic cell death of cmpcs, independent of activation of akt pro-survival pathway. mir-155 provides the opportunity to block necrosis, a conventionally thought non-regulated process, and might be a potential novel approach to improve cell engraftment for cell therapy.",1
"the aberrantly expressed micrornas (mirnas) including mir-200a-3p have been reported in the brains of alzheimer's disease (ad) patients in recent researches. nevertheless, the role of mir-200a-3p in ad has not been characterized. the purpose of this study was to examine whether mir-200a-3p regulated β-ameyloid (a β)-induced neuronal apoptosis by targeting sirt1, a known anti-apoptotic protein. an increased level of mir-200a-3p and a decreased level of sirt1 in the hippocampus of appswe/ps delta e9 mice (a model for ad) were observed. to construct an in vitro cell model of ad, pc12 cells were cultured in presence of a β 25-35 . the results of flow cytometry analysis showed that the apoptosis rate and cleaved-caspase-3 expression in pc12 cells exposed to a β 25-35 were remarkably increased, but the apoptosis rate and cleaved-caspase-3 activity were decreased when cells were transfected with anti-mir-200a-3p. on the other hand, mtt assay showed that the cell survival rate was increased in the a β 25-35 + anti-mir-200a-3p group compared with the a β 25-35 + anti-mir-nc group. dual-luciferase reporter gene assay validated the predicted mir-200a-3p binding sites in the 3'- utr of sirt1 mrna. in addition, downregulation of sirt1 promoted a β 25-35 -induced neuronal apoptosis and cleavedcaspase- 3 level in pc12 cells, whereas anti-mir-200a-3p reversed these effects. knockdown of sirt1 decreased the inhibitory effect of a β 25-35 on cell viability, while anti-mir-200a-3p attenuated this effect. overall, the results suggest that suppression of mir-200a-3p attenuates a β 25-35 -induced apoptosis in pc12 cells by targeting sirt1. thus, mir-200a-3p may be a potential therapeutic target for treatment of ad.",1
"objective there is evidence that interleukin-6 (il-6) upregulation plays a critical role in immunopathology of systemic lupus erythematosus (sle). microrna- (mirna-) 98 was predicted to bind with the 3'-untranslated region (3'-utr) of il-6 gene. we hypothesized mir-98 through its regulation of il-6 gene expression to influence cytokine production from peripheral blood mononuclear cells (pbmcs) in sle. methods the expression of mir-98 and il-6 mrna in the pbmcs of 41 sle patients and 20 healthy controls (hc) was detected by quantitative reverse transcription pcr (qrt-pcr). the correlations between mir-98 expression and clinical features were evaluated. luciferase reporter assay was performed to identify mir-98 targets. mir-98 mimics, mir-98 inhibitor, and il-6 overexpression vector were generated. cell viability of pbmcs was assessed using mtt assay. gene expression and protein level were determined by qrt-pcr and western blotting. tnf- α , il-8, il-1 β , and il-10 levels in cultured supernatants were quantified using elisa. results the expression of mir-98 was downregulated in pbmcs of sle patients, and its expression is negatively associated with il-6 levels. mir-98 expression was correlated with disease activity, lupus nephritis, and anti-dsdna antibody. il-6 mrna was a target gene of mir-98. il-6 overexpression promoted the proliferation of pbmcs and increased the levels of tnf- α , il-8, il-1 β , and il-10. those effects were further enhanced by mir-98 inhibitor, while were suppressed by mir-98 mimics. mir-98 regulated the levels of stat3 phosphorylation via its target gene il-6. conclusion the current study revealed that mir-98 could ameliorate stat3-mediated cell proliferation and inflammatory cytokine production via its target gene il-6 in patients with sle. these results suggest that mir-98 might serve as a potential target for sle treatment and other il-6-mediated diseases.",1
"background microrna-101 (mir-101) expression is negatively associated with tumor growth and blood vessel formation in several solid epithelial cancers. however, the role of mir-101 in human breast cancer remains elusive. results mir-101 was significantly decreased in different subtypes of human breast cancer tissues compared with that in adjacent normal breast tissues (p conclusions this study demonstrates that down-regulation of mir-101 in different subtypes of human breast cancer tissues is linked to the increase of cellular proliferation and invasiveness via targeting stmn1, which highlights novel regulatory mechanism in breast cancer and may provide valuable clues for the future clinical diagnosis of breast cancer.",1
"microrna-126 (mir-126) is a pivotal post-transcriptional regulator, which has been validated as a suppressor in gastric cancer (gc). however, the downstream of its tumor inhibiting function has not been totally clear. l-type amino-acid transporter 1 (lat-1) is a novel member of system l-type transporters involving in cell proliferation, and we have previously validated that lat-1 played a role of promotor in gc. in this study, we further detected and confirmed that lat-1 was exactly targeted by mir-126 in gc. we found lat-1 was significantly downregulated in gc mkn-45 cell lines by using mir-126 mimics, along with an impairment on cell proliferation and cell cycle. additionally, by overexpressing lat-1 in mkn-45 cells which was firstly treated with mir-126 mimics, the ability of cell proliferation in mkn-45 cells was definitely rescued. thus, our results suggests and consolidates the standpoint that mir-126 plays a pivotal role in gc suppressing the process of gc cell, and this function is at least partly taken to implement by mir-126s's post-transcriptional effect on lat-1. this might provide us likely potential biomarkers and targets for gc prevention, diagnosis and therapeutic treatment.",1
"micrornas (mirnas) are a recently discovered set of regulatory genes that constitute up to an estimated 1% of the total number of genes in animal genomes, including caenorhabditis elegans, drosophila, mouse, and humans . in animals, mirnas regulate genes by attenuating protein translation through imperfect base pair binding to 3' utr sequences of target genes. a major challenge in understanding the regulatory role of mirnas is to accurately predict regulated targets. we have developed an algorithm for predicting targets that does not rely on evolutionary conservation. as one of the features of this algorithm, we incorporate the folded structure of mrna. by using drosophila mirnas as a test case, we have validated our predictions in 10 of 15 genes tested. one of these validated genes is mad as a target for bantam. furthermore, our computational and experimental data suggest that mirnas have fewer targets than previously reported.",1
"the 25s tri-snrnp (small nuclear ribonucleoprotein) is a central unit of the nuclear pre-mrna splicing machinery. the u4, u5 and u6 snrnas undergo numerous rearrangements in the spliceosome, and knowledge of all of the tri-snrnp proteins is crucial to the detailed investigation of the rna dynamics during the spliceosomal cycle. here we characterize by mass spectrometric methods the proteins of the purified tri-snrnp from the yeast saccharomyces cerevisiae. in addition to the known tri-snrnp proteins (only one, lsm3p, eluded detection), we identified eight previously uncharacterized proteins. these include four sm-like proteins (lsm2p, lsm5p, lsm6p and lsm7p) and four specific proteins named snu13p, dib1p, snu23p and snu66p. snu13p comprises a putative rna-binding domain. interestingly, the schizosaccharomyces pombe orthologue of dib1p, dim1p, was previously assigned a role in cell cycle progression. the role of snu23p, snu66p and, additionally, spp381p in pre-mrna splicing was investigated in vitro and/or in vivo. finally, we show that both tri-snrnps and the u2 snrnp are co-precipitated with protein a-tagged versions of snu23p, snu66p and spp381p from extracts fractionated by glycerol gradient centrifugation. this suggests that these proteins, at least in part, are also present in a tetra-snrnp complex.",1
"micrornas (mirnas) are endogenous small non-coding rnas that post-transcriptionally regulate gene expression in eukaryotes. in drosophila melanogaster, up to 240 mirnas have been identified by computational methods or experimental approaches. however, most of their biological functions are still unknown. here, we identified mir-960 as a suppressor of hedgehog (hh) signaling pathway. ectopic mir-960 obviously represses the expression levels of target genes. this activity is mediated by direct inhibition of smoothened (smo), costal-2 (cos2) and fused (fu), which are essential signaling transduction components of hh pathway. through in vivo sensor assay and in vitro luciferase assay, we found that mir-960 directly binds to the 3'utrs of smo, cos2 and fu mrnas to block their translation. additionally, we demonstrated that mir-960 cannot suppress wg and dpp signaling pathways. together, our results indicate that mir-960 can specifically suppress hh pathway by directly targeting three important signaling transducers smo, cos2 and fu.",1
"in this study, we uncover a role for micrornas in drosophila germline stem cell (gsc) maintenance. disruption of dicer-1 function in gscs during adult life results in gsc loss. surprisingly, however, loss of dicer-1 during development does not result in a gsc maintenance defect, although a defect is seen if both dicer-1 and dicer-2 function are disrupted. loss of the bantam microrna mimics the dicer-1 maintenance defect when induced in adult gscs, suggesting that bantam plays a key role in gsc self-renewal. mad, a component of the tgf-beta pathway, behaves similarly to dicer-1: adult gsc maintenance requires mad if it is lost during adult life, but not if it is lost during pupal development. overall, these results show stage-specific differential sensitivity of gsc maintenance to certain perturbations, and suggest that there may be dcr-2 dependent redundancy of gsc maintenance mechanisms during development that is lost in later life.",1
"japanese encephalitis virus (jev), a single-stranded rna (ssrna) virus, is the leading cause of encephalitis in asia. microglial activation is one of the key events in jev-induced neuroinflammation. although the various micrornas (mirnas) has been shown to regulate microglia activation during pathological conditions including neuroviral infections, till date, the involvement of mirnas in jev infection has not been evaluated. hence, we sought to evaluate the possible role of mirnas in mediating jev-induced microglia activation. initial screening revealed significant up-regulation of mir-29b in jev-infected mouse microglial cell line (bv-2) and primary microglial cells. furthermore, using bioinformatics tools, we identified tumor necrosis factor alpha-induced protein 3, a negative regulator of nuclear factor-kappa b signaling as a potential target of mir-29b. interestingly, in vitro knockdown of mir-29b resulted in significant over-expression of tumor necrosis factor alpha-induced protein 3, and subsequent decrease in nuclear translocation of pnf-κb. jev infection in bv-2 cell line elevated inducible nitric oxide synthase, cyclooxygenase-2, and pro-inflammatory cytokine expression levels, which diminished after mir-29b knockdown. collectively, our study demonstrates involvement of mir-29b in regulating jev- induced microglial activation.",1
"ifn-γ is a cytokine with important roles in the innate and adaptive immune responses. this cytokine is secreted by activated t cells, nk cells and macrophages. studies on the regulation of human ifn-γ expression had been previously focused on the promoter region. consequently, the role of micrornas (mirs) in this regulation has not been investigated yet. as mir-24 and mir-181 were found to have potential target sites in ifn-γ mrna 3'utr, we assessed their impact on ifn-γ expression by co-stimulating pb cd4+ t cells with anti-cd3, anti-cd28, il-12, and il-18. this co-stimulation cocktail induced an abundant secretion of ifn-γ together with a down-regulation of mir-24, and mir-181. existence of a link between these two phenomena was further substantiated by transfection and transduction assays that showed that these two mirs negatively regulate ifn-γ expression by directly binding to their target sites in the mrna. thus, identifying target sites for mir-24 and mir-181 in ifn-γ-3'utr points to a novel regulatory mechanism of this crucial gene.",1
"viral interfering rna (virna) has been identified from several viral genomes via directly deep rna sequencing of the virus-infected cells, including zika virus (zikv). once produced by endoribonuclease dicer, virnas are loaded onto the argonaute (ago) family proteins of the rna-induced silencing complexes (riscs) to pair with their rna targets and initiate the cleavage of target genes. however, the identities of functional zikv virnas and their viral rna targets remain largely unknown. our recent study has shown that zikv capsid protein interacted with dicer and antagonized its endoribonuclease activity, which requires its histidine residue at the 41 st amino acid. accordingly, the engineered zikv-h41r loss-of-function (lof) mutant virus no longer suppresses dicer enzymatic activity nor inhibits mirna biogenesis in nscs. by combining ago-associated rna sequencing, deep sequencing analysis in zikv-infected human neural stem cells (nscs), and miranda target scanning, we defined 29 zikv derived virna profiles in nscs, and established a complex interaction network between the virnas and their viral targets. more importantly, we found that virna production from the zikv mrna is dependent on dicer function and is a limiting factor for zikv virulence in nscs. as a result, much higher levels of virnas generated from the zikv-h41r virus-infected nscs. therefore, our mapping of virnas to their rna targets paves a way to further investigate how virnas play the role in anti-viral mechanisms, and perhaps other unknown biological functions.",1
"long non-coding rnas (lncrnas) have gained widespread attention in recent years as a key regulator of diverse biological processes, but the knowledge of the mechanisms by which they act is still very limited. differentially expressed lncrna smad5 antisense rna 1 (smad5-as1) in nasopharyngeal carcinoma (npc) and normal samples shown by in silico analyses were selected as the main subject, and then microrna-195 (mir-195) was suggested to bind to smad5-as1 and smad5. therefore, the purpose of the present study was to investigate the effects of smad5-as1/mir-195/smad5 on epithelial-mesenchymal transition (emt) in npc cells. high expression of smad5-as1 and smad5 but low mir-195 expression was determined in npc tissues and npc cell lines by rt-qpcr and western blot analysis. smad5-as1 could upregulate smad5 expression by competitively binding to mir-195 in npc cells. loss- and gain-of-function investigations were subsequently conducted in npc cells (cne-2 and cne-1) to explore the role of smad5-as, mir-195 and smad5 in npc progression by assessing cellular biological functions and tumorigenic ability in vivo as well as determining the expression of emt markers. downregulation of smad5-as1 or smad5 or overexpression of mir-195 led to inhibited npc cell proliferation, invasion and migration and reversed emt, enhanced apoptosis in vitro as well as restrained tumor growth in vivo . in conclusion, our findings indicate that silencing of lncrna smad5-as1 induces the downregulation of smad5 by mir-195, eventually repressing emt in npc. hence, smad5-as1 may represent a potential therapeutic target for npc intervention.",1
"microrna-3662 (mir-3662) is minimally expressed in normal human tissues but is highly expressed in all types of cancers, including breast cancer. as determined with the cancer genome atlas dataset, mir-3662 expression is higher in triple-negative breast cancers (tnbcs) and african american breast cancers than in other breast cancer types. however, the functional role of mir-3662 remains a topic of debate. here, we found that inhibition or knockout of endogenous, mature mir-3662 in tnbc cells suppresses proliferation and migration in vitro and tumor growth and metastasis in vivo. functional analysis revealed that, for tnbc cells, knockout of mir-3662 reduces the activation of wnt/β-catenin signaling. furthermore, using crispr-mediated mir-3662 activation and repression, dual-luciferase assays, and mirna/mrna immunoprecipitation assays, we established that hmg-box transcription factor 1 (hbp-1), a wnt/β-catenin signaling inhibitor, is a target of mir-3662 and is most likely responsible for mir-3662-mediated tnbc cell proliferation. our results suggest that mir-3662 has an oncogenic function in tumor progression and metastasis via an mir-3662-hbp1 axis, regulating the wnt /β-catenin signaling pathway in tnbc cells. since mir-3662 expression occurs a tumor-specific manner, it is a promising biomarker and therapeutic target for patients who have tnbcs with dysregulation of mir-3662, especially african americans.",1
"microrna (mirna) coordinate complex gene expression networks in cells that are vital to support highly specialised morphology and cytoarchitecture. neurons express a rich array of mirna, including many that are specific or enriched, which have important functions in this context and implications for neurological conditions. while the neurological function of a number of brain-derived mirnas have been examined thoroughly, the mechanistic basis of many remain obscure. in this case, we investigated the transcriptome-wide impact of schizophrenia-associated mir-1271-5p in response to bidirectional modulation. alteration of mir-1271-5p induced considerable changes to mrna abundance and translation, which spanned a diverse range of cellular functions, including directly targeted genes strongly associated with cytoskeletal dynamics and cellular junctions. mechanistic analyses additionally revealed that upregulation of mir-1271-5p predominantly repressed mrnas through destabilisation, wherein 3'utr and coding sequence binding sites exhibited similar efficacy. knockdown, however, produced no discernible trend in target gene expression and strikingly resulted in increased expression of the highly conserved mir-96-5p, which shares an identical seed region with mir-1271-5p, suggesting the presence of feedback mechanisms that sense disruptions to mirna levels. these findings indicate that, while bidirectional regulation of mir-1271-5p results in substantial remodeling of the neuronal transcriptome, these effects are not inverse in nature. in addition, we provide further support for the idea that destabilisation of mrna is the predominant mechanism by which mirnas regulate complementary mrnas.",1
"cuedc2, a cue-domain-containing protein, modulates inflammation, but its involvement in tumorigenesis is still poorly understood. here, we report that cuedc2 is a key regulator of macrophage function and critical for protection against colitis-associated tumorigenesis. cuedc2 expression is dramatically upregulated during macrophage differentiation, and cuedc2 deficiency results in excessive production of proinflammatory cytokines. the level of cuedc2 in macrophages is modulated by mir- 324-5p. we find that cuedc2 ko mice are more susceptible to dextran-sodium-sulfate-induced colitis, and macrophage transplantation results suggest that the increased susceptibility results from the dysfunction of macrophages lacking cuedc2. furthermore, we find that cuedc2 ko mice are more prone to colitis-associated cancer. importantly, cuedc2 expression is almost undetectable in macrophages in human colon cancer, and this decreased cuedc2 expression is associated with high levels of interleukin-4 and mir-324-5p. thus, cuedc2 plays a crucial role in modulating macrophage function and is associated with both colitis and colon tumorigenesis.",1
"individuals with diabetes mellitus suffer from impaired angiogenesis and this contributes to poorer peripheral arterial disease outcomes. in experimental peripheral arterial disease, angiogenesis and perfusion recovery are impaired in mice with diabetes. we recently showed that a disintegrin and metalloproteinase domain-containing protein 12 (adam12) is upregulated in ischemic endothelial cells and plays a key role in post-ischemic angiogenesis and perfusion recovery following experimental peripheral arterial disease. here we investigated the role of mir29a in the regulation of endothelial cell adam12 expression in ischemia and how hyperglycemia negatively affects this regulation. we also explored whether modulating mir29a can improve impaired post-ischemic angiogenesis associated with hyperglycemia. additionally, we tested whether mir29a modulation could improve post ischemic angiogenesis in the setting of impaired vascular endothelial growth factor signaling. we forced mir29a expression in ischemic endothelial cells and assessed adam12 expression. we also evaluated whether hyperglycemia in vivo and in vitro impair ischemia-induced adam12 upregulation and mir29a downregulation. lastly, we determined whether modulating endothelial cell mir29a expression in ischemia and hyperglycemia could improve impaired endothelial cell functions. we found under ischemic conditions where adam12 is upregulated in endothelial cells, mir29a is downregulated. forced expression of mir29a in ischemic endothelial cell prevented adam12 upregulation . in ischemic hind limbs of mice with type 1 diabetes and in endothelial cells exposed to simulated ischemia plus hyperglycemia, adam12 upregulation and mir29a downregulation were blunted while angiogenesis was impaired. knocking down mir29a with an mir29a inhibitor was sufficient to improve adam12 upregulation and angiogenesis in simulated ischemia plus hyperglycemia. it was also sufficient to improve perfusion recovery in type 1 diabetes mellitus mice in vivo and angiogenesis in vitro even when vascular endothelial growth factor signaling was impaired with blocking antibodies. in conclusion, mir29a regulates endothelial cell adam12 upregulation in ischemia and this is impaired in hyperglycemia. modulating mir29a improves impaired post-ischemic angiogenesis associated with hyperglycemia. impact statement individuals with diabetes are more likely to develop peripheral arterial disease (pad), and when pad is present, in those with diabetes, it is more severe and there is currently no effective medical treatment for impaired blood flow which occurs in diabetics with pad. the current work advances the field by providing an understanding of a molecular mechanism involved in impaired post ischemic angiogenesis in diabetes. it shows for the first time that failure to downregulate mir29a in ischemic diabetic tissues is a major contributing factor to poor perfusion recovery in experimental pad, and mir29a is elevated in skeletal muscle samples from human diabetics compared with levels in those without diabetes. knocking down the elevated mir29a in ischemic diabetic mouse hind limbs improved perfusion recovery following experimental pad. this shows mir29a modulation as a novel therapeutic target for improving blood flow in diabetics with pad.",1
"gomafu/miat/rncr2 is a long noncoding rna that has been proposed to control retinal cell specification, stem cell differentiation and alternative splicing of schizophrenia-related genes. however, how gomafu controls these biological processes at the molecular level has remained largely unknown. in this study, we identified the rna-binding protein celf3 as a novel gomafu-associating protein. knockdown of celf3 led to the down-regulation of gomafu, and cross-link rna precipitation analysis confirmed specific binding between celf3 and gomafu. in the neuroblastoma cell line neuro2a, celf3 formed novel nuclear bodies (named cs bodies) that colocalized with sf1, another gomafu-binding protein. gomafu, however, was not enriched in the cs bodies; instead, it formed distinct nuclear bodies in separate regions in the nucleus. these observations suggest that gomafu indirectly modulates the function of the splicing factors sf1 and celf3 by sequestering these proteins into separate nuclear bodies.",1
"microrna deregulation is involved in tumor initiation and progression. the aim of this study was to identify and validate the microrna candidates that contribute to the metastasis of oral tongue squamous cell carcinoma (otscc). using microarrays, a panel of differentially expressed micrornas was identified in paired otscc cell lines with different metastatic potential. selected microrna candidates (including hsa-mir-222) were further validated using quantitative pcr approach. functional analysis indicated that hsa-mir-222 inhibits otscc cell invasion. ectopic transfection of hsa-mir-222 reduced the expression of mmp1 and sod2 in otscc cell lines. direct targeting of hsa-mir-222 to specific sequences located in the 3'-untranslated regions of both mmp1 and sod2 mrnas were confirmed using luciferase reporter gene assays. furthermore, sod2 knockdown by sirna led to the downregulation of mmp1 expression. taken together, these results suggested that hsa-mir-222 regulates the mmp1 expression through both direct cis-regulatory mechanism (targeting mmp1 mrna) and indirect trans-regulatory mechanism (indirect controlling of mmp1 gene expression by targeting sod2). our results indicate that hsa-mir-222 plays an important role in otscc invasion, and may serve as a novel therapeutic target for otscc patients at risk of metastatic disease.",1
"in humans, telomerase reverse transcriptase (htert) determines the activity of telomerase. htert is an ideal anticancer target because it is universally expressed in cancer cells and plays a crucial role in carcinogenesis. in this study, we report the mir-1182-mediated post-transcriptional regulation of htert. over-expression of mir-1182 in different gastric cancer cells decreased htert protein levels. bioinformation and dual-luciferase assays revealed that mir-1182 modulated htert by binding to its open reading frame (orf), and this mirna recognizes elements in the nucleotide region between 2695 and 2719 of htert mrna. over-expression of htert by transfecting pires2-htert into u2os cells was abolished by mir-1182, while pires2-htert-mt, in which mir-1182 target site was synonymously mutated, failed to respond to mir-1182. further investigation revealed that mir-1182 inhibited gastric cancer proliferation and migration by targeting the orf1 of htert. we also found that mir-1182 could attenuate the proliferative and metastatic potential of sgc-7901 cell in vivo. moreover, we found a statistically significant inverse correlation between mir-1182 and htert protein levels in tissues from 42 gastric cancer patients. these data indicate that mir-1182 suppresses tert, and thus it could be an effective target for the treatment of gastric cancer.",1
"wnt/β-catenin signaling is required for embryonic dermal fibroblast cell fate, and dysregulation of this pathway is sufficient to promote fibrosis in adult tissue. the downstream modulators of wnt/β-catenin signaling required for controlling cell fate and dermal fibrosis remain poorly understood. the discovery of regulatory long non-coding rnas (lncrnas) and their pivotal roles as key modulators of gene expression downstream of signaling cascades in various contexts prompted us to investigate their roles in wnt/β-catenin signaling. here, we have identified lncrnas and protein-coding rnas that are induced by β-catenin activity in mouse dermal fibroblasts using next generation rna-sequencing. the differentially expressed protein-coding mrnas are enriched for extracellular matrix proteins, glycoproteins, and cell adhesion, and many are also dysregulated in human fibrotic tissues. we identified 111 lncrnas that are differentially expressed in response to activation of wnt/β-catenin signaling. to further characterize the role of mouse lncrnas in this pathway, we validated two novel wnt signaling- induced non-coding rna (wincr) transcripts referred to as wincr1 and wincr2 . these two lncrnas are highly expressed in mouse embryonic skin and perinatal dermal fibroblasts. furthermore, we found that wincr1 expression levels in perinatal dermal fibroblasts affects the expression of key markers of fibrosis (e.g., col1a1 and mmp10 ), enhances collagen contraction, and attenuates collective cell migration. our results show that β-catenin signaling-responsive lncrnas may modulate dermal fibroblast behavior and collagen accumulation in dermal fibrosis, providing new mechanistic insights and nodes for therapeutic intervention.",1
"srsf1, srsf2 and hnrnp a1 are splicing factors that regulate the expression of oncogenes and tumor suppressors. srsf1 and srsf2 contribute to the carcinogenesis in the kidney. despite their importance, the mechanisms regulating their expression in cancer are not entirely understood. here, we investigated the microrna-mediated regulation of srsf1, srsf2 and hnrnp a1 in renal cancer. the expression of micrornas predicted to target srsf1, srsf2 and hnrnp a1 was disturbed in renal tumors compared with controls. using qpcr, western blot/icc and luciferase reporter system assays we identified micrornas that contribute to the regulation of expression of srsf1 (mir-10b-5p, mir-203a-3p), srsf2 (mir-183-5p, mir-200c-3p), and hnrnp a1 (mir-135a-5p, mir-149-5p). silencing of srsf1 and srsf2 enhanced the expression of their targeting micrornas. mir-183-5p and mir-200c-3p affected the expression of srsf2-target genes, tnfrsf1b, tnfrsf9, cradd and tp53. 3'utr variants of srsf1 and srsf2 differed by the presence of mirna-binding sites. in conclusion, we identified a group of micrornas that contribute to the regulation of expression of srsf1, srsf2 and hnrnp a1. the micrornas targeting srsf1 and srsf2 are involved in a regulatory feedback loop. micrornas mir-183-5p and mir-200c-3p that target srsf2, affect the expression of genes involved in apoptotic regulation.",1
"micrornas (mirnas) are small non-coding rna molecules of 21-24 nt that regulate the expression of other genes by transcriptional inhibition or translational repression. multiple lines of evidence suggest that mirnas play important roles in tumor development and progression. we identified 24 mirnas markedly and aberrantly expressed in human cervical cancer. the most significantly deregulated was mir-143 as determined by mirna microarray analysis. mir-143 was introduced into hela cells and it was found that the overexpression of mir-143 significantly inhibited hela cell proliferation and promoted apoptosis; anti-mir-143 rescued the effects. hela cells transfected with pre-mir-143, pre‑anti-mir-143 or control mirna precursor were injected subcutaneously into the flanks of female athymic nude mice, and the overexpression of mir-143 suppressed the formation of tumors. compared with normal cervical tissues, the levels of bcl-2 were increased in mir-143-downregulated tissues. sustained overexpression of mir-143 in hela cells resulted in suppression of bcl-2 expression, and knockdown of mir-143 by anti-mir-143 increased bcl-2 expression. in addition, overexpression of bcl-2 partially reversed the inhibition of proliferation and promotion of apoptosis in the hela cells caused by mir-143. furthermore, mir-143 suppressed the activity of a luciferase reporter carrying the 3'-utr of bcl-2, which was abolished by mutation of the predicted mir-143-binding site, indicating that bcl-2 is a mir-143 target gene. our study revealed a molecular link between mir-143 and bcl‑2. direct involvement in the regulation of bcl-2 may be one of the mechanisms through which mir-143 may play a role in the pathogenesis of cervical cancer.",1
"in human epithelial cancers, the microrna (mirna) mir-30d is amplified with high frequency and serves as a critical oncomir by regulating metastasis, apoptosis, proliferation, and differentiation. autophagy, a degradation pathway for long-lived protein and organelles, regulates the survival and death of many cell types. increasing evidence suggests that autophagy plays an important function in epithelial tumor initiation and progression. using a combined bioinformatics approach, gene set enrichment analysis, and mirna target prediction, we found that mir-30d might regulate multiple genes in the autophagy pathway including becn1, bnip3l, atg12, atg5, and atg2. our further functional experiments demonstrated that the expression of these core proteins in the autophagy pathway was directly suppressed by mir-30d in cancer cells. finally, we showed that mir-30d regulated the autophagy process by inhibiting autophagosome formation and lc3b-i conversion to lc3b-ii. taken together, our results provide evidence that the oncomir mir-30d impairs the autophagy process by targeting multiple genes in the autophagy pathway. this result will contribute to understanding the molecular mechanism of mir-30d in tumorigenesis and developing novel cancer therapy strategy.",1
"autosomal dominant polycystic kidney disease (adpkd) is a debilitating disease that is characterized by the accumulation of numerous fluid-filled cysts in the kidney. adpkd is primarily caused by mutations in two genes, pkd1 and pkd2 long noncoding rnas (lncrna), defined by a length >200 nucleotides and absence of a long orf, have recently emerged as epigenetic regulators of development and disease; however, their involvement in pkd has not been explored previously. here, we performed deep rna-seq to identify lncrnas that are dysregulated in two orthologous mouse models of adpkd (kidney-specific pkd1 and pkd2 mutant mice). we identified a kidney-specific, evolutionarily conserved lncrna called hoxb3os that was down-regulated in cystic kidneys from pkd1 and pkd2 mutant mice. the human ortholog hoxb3-as1 was down-regulated in cystic kidneys from adpkd patients. hoxb3os was highly expressed in renal tubules in adult wt mice, whereas its expression was lost in the cyst epithelium of mutant mice. to investigate the function of hoxb3os , we utilized crispr/cas9 to knock out its expression in mimcd3 cells. deletion of hoxb3os resulted in increased phosphorylation of mtor and its downstream targets, including p70 s6 kinase, ribosomal protein s6, and the translation repressor 4e-bp1. consistent with activation of mtorc1 signaling, hoxb3os mutant cells displayed increased mitochondrial respiration. the hoxb3os mutant phenotype was partially rescued upon re-expression of hoxb3os in knockout cells. these findings identify hoxb3os as a novel lncrna that is down-regulated in adpkd and regulates mtor signaling and mitochondrial respiration.",1
"type 2 diabetes mellitus (t2dm) is a complex disease characterized by the inability of the insulin-producing β cells in the endocrine pancreas to overcome insulin resistance in peripheral tissues. to determine if micrornas are involved in the pathogenesis of human t2dm, we sequenced the small rnas of human islets from diabetic and nondiabetic organ donors. we identified a cluster of micrornas in an imprinted locus on human chromosome 14q32 that is highly and specifically expressed in human β cells and dramatically downregulated in islets from t2dm organ donors. the downregulation of this locus strongly correlates with hypermethylation of its promoter. using hits-clip for the essential risc-component argonaute, we identified disease-relevant targets of the chromosome 14q32 micrornas, such as iapp and tp53inp1, that cause increased β cell apoptosis upon overexpression in human islets. our results support a role for micrornas and their epigenetic control by dna methylation in the pathogenesis of t2dm.",1
"alzheimer disease (ad) results, in part, from the excess accumulation of the amyloid-β (aβ) peptide as neuritic plaques in the brain. the short aβ peptide is derived from the large transmembrane aβ precursor protein (app). the rate-limiting step in the production of aβ from app is mediated by the β-site app-cleaving enzyme 1 (bace1). dysregulation of bace1 levels leading to excess aβ deposition is implicated in sporadic ad. thus, elucidating the full complement of regulatory pathways that control bace1 expression is key to identifying novel drug targets central to the aβ-generating process. micrornas (mirnas) are expected to participate in this molecular network. here, we identified a known mirna, mir-339-5p, as a key contributor to this regulatory network. two distinct mir-339-5p target sites were predicted in the bace1 3'-utr by in silico analyses. co-transfection of mir-339-5p with a bace1 3'-utr reporter construct resulted in significant reduction in reporter expression. mutation of both target sites eliminated this effect. delivery of the mir-339-5p mimic also significantly inhibited expression of bace1 protein in human glioblastoma cells and human primary brain cultures. delivery of target protectors designed against the mir-339-5p bace1 3'-utr target sites in primary human brain cultures significantly elevated bace1 expression. finally, mir-339-5p levels were found to be significantly reduced in brain specimens isolated from ad patients as compared with age-matched controls. therefore, mir-339-5p regulates bace1 expression in human brain cells and is most likely dysregulated in at least a subset of ad patients making this mirna a novel drug target.",1
"background micrornas (mirnas) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. mirnas and related target genes have been widely studied in model plants such as arabidopsis and rice; however, the number of identified mirnas in soybean (glycine max) is limited, and global identification of the related mirna targets has not been reported in previous research. results in our study, a small rna library and a degradome library were constructed from developing soybean seeds for deep sequencing. we identified 26 new mirnas in soybean by bioinformatic analysis and further confirmed their expression by stem-loop rt-pcr. the mirna star sequences of 38 known mirnas and 8 new mirnas were also discovered, providing additional evidence for the existence of mirnas. through degradome sequencing, 145 and 25 genes were identified as targets of annotated mirnas and new mirnas, respectively. go analysis indicated that many of the identified mirna targets may function in soybean seed development. additionally, a soybean homolog of arabidopsis suppressor of gene silencing 3 (atsgs3) was detected as a target of the newly identified mirna soy_25, suggesting the presence of feedback control of mirna biogenesis. conclusions we have identified large numbers of mirnas and their related target genes through deep sequencing of a small rna library and a degradome library. our study provides more information about the regulatory network of mirnas in soybean and advances our understanding of mirna functions during seed development.",1
"it has been previously demonstrated that mir-1934 was specially regulated by adiponectin, an anti-inflammatory adipokine, in adipose tissue (at) in vivo. herein we investigated the role of mir1934 in the regulation of inflammatory response. compared with chow-diet fed mice, mir1934 expression was down-regulated in epididymal at of high-fat diet-induced obese mice. mir1934 expression was down-regulated as well in omental at of obese subjects in comparison with lean subjects. the circulating mir-1934 was also lower in obese subjects and its levels were correlated negatively with body mass index (bmi), waist circumference (wc), low-density lipoprotein cholesterol (ldl-c), insulin resistance and high-sensitivity c-reactive protein (hs-crp). the down-regulation of mir1934 in obesity was mimicked by tnf-α treatment of 3t3-l1 adipocytes. moreover, overexpression of mir1934 suppressed the tnf-α-induced gene expression of interleukin-6 (il-6) and monocyte chemotactic protein-1 (mcp-1) in 3t3-l1 adipocytes. de novo formed at in nude mice transplanted with 3t3-l1 preadipocytes overexpressing mir1934 displayed a reduction in il-6, tnf-α, il-1β and an enhancement in il-10 gene expression when compared with transplant with 3t3-l1 preadipocytes overexpressing mir1934 scrambled control sequence. these results suggest that mir1934 is an important anti-inflammatory factor and may represent a novel mechanism for controlling at inflammation.",1
"mammalian genomes encode multiple layers of regulation, including a class of rna molecules known as long non-coding rnas (lncrnas). these are >200 nucleotides in length and similar to mrnas, they are capped, polyadenylated, and spliced. in contrast to mrnas, lncrnas are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. however, little is known about lncrna function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. to help address this need, we performed a whole-genome identification of lncrnas using rna-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. we identified 3,239 lncrna genes, most of which were intergenic (lincrnas) and 721 are novel. we examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. the spatial and temporal patterns of three lncrnas, two of which are in proximity to genes associated with hearing and deafness, were explored further. our findings indicate that lncrnas are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.",1
"histone modification is known to be associated with multidrug resistance phenotypes. cancer cell lines that are resistant or have been made resistant to anti-cancer drugs showed lower expression levels of histone deacetylase-3 (hdac3), among the histone deacetylase(s), than cancer cell lines that were sensitive to anti-cancer drugs. celastrol and taxol decreased the expression of hdac3 in cancer cell lines sensitive to anti-cancer drugs. hdac3 negatively regulated the invasion, migration, and anchorage-independent growth of cancer cells. hdac3 conferred sensitivity to anti-cancer drugs in vitro and in vivo. targetscan analysis predicted mir-326 as a negative regulator of hdac3. chip assays and luciferase assays showed a negative feedback loop between hdac3 and mir-326. mir-326 decreased the apoptotic effect of anti-cancer drugs, and the mir-326 inhibitor increased the apoptotic effect of anti-cancer drugs. mir-326 enhanced the invasion and migration potential of cancer cells. the mir-326 inhibitor negatively regulated the tumorigenic, metastatic, and angiogenic potential of anti-cancer drug-resistant cancer cells. hdac3 showed a positive feedback loop with mirnas such as mir-200b, mir-217, and mir-335. mir-200b, mir-217, and mir-335 negatively regulated the expression of mir-326 and the invasion and migration potential of cancer cells while enhancing the apoptotic effect of anti-cancer drugs. targetscan analysis predicted mir-200b and mir-217 as negative regulators of cancer-associated gene, a cancer/testis antigen, which is known to regulate the response to anti-cancer drugs. hdac3 and mir-326 acted upstream of the cancer-associated gene. thus, we show that the mir-326-hdac3 feedback loop can be employed as a target for the development of anti-cancer therapeutics.",1
"u4 small nuclear rna (snrna) is essential for pre-mrna splicing, although its role is not yet clear. on the basis of a model structure (c. guthrie and b. patterson, annu. rev. genet. 22:387-419, 1988), the molecule can be thought of as having six domains: stem ii, 5' stem-loop, stem i, central region, 3' stem-loop, and 3'-terminal region. we have carried out extensive mutagenesis of the yeast u4 snrna gene (snr14) and have obtained information on the effect of mutations at 105 of its 160 nucleotides. fifteen critical residues in the u4 snrna have been identified in four domains: stem ii, the 5' stem-loop, stem i, and the 3'-terminal region. these domains have been shown previously to be insensitive to oligonucleotide-directed rnase h cleavage (y. xu, s. petersen-bjørn, and j. d. friesen, mol. cell. biol. 10:1217-1225, 1990), suggesting that they are involved in intra- or intermolecular interactions. stem ii, a region that base pairs with u6 snrna, is the most sensitive to mutation of all u4 snrna domains. in contrast, stem i is surprisingly insensitive to mutational change, which brings into question its role in base pairing with u6 snrna. all mutations in the putative sm site of u4 snrna yield a lethal or conditional-lethal phenotype, indicating that this region is important functionally. only two nucleotides in the 5' stem-loop are sensitive to mutation; most of this domain can tolerate point mutations or small deletions. the 3' stem-loop, while essential, is very tolerant of change. a large portion of the central domain can be removed or expanded with only minor effects on phenotype, suggesting that it has little function of its own. analysis of conditional mutations in stem ii and stem i indicates that although these single-base changes do not have a dramatic effect on u4 snrna stability, they are defective in rna splicing in vivo and in vitro, as well as in spliceosome assembly. these results are discussed in the context of current knowledge of the interactions involving u4 snrna.",1
"objective genistein is a soy isoflavone that has antitumor activity both in vitro and in vivo. it has been shown that genistein inhibits many type of cancers including prostate cancer (pca) by regulating several cell signaling pathways and micrornas (mirnas). recent studies suggest that the long non-coding rnas (lncrnas) are also involved in many cellular processes. at present there are no reports about the relationship between gensitein, mirnas and lncrnas. in this study, we focused on mirnas, lncrna that are regulated by genistein and investigated their functional role in pca. method microarray (sureprint g3 human ge 8×60k) was used for expression profiling of genistein treated and control pca cells (pc3 and du145). functional assay (cell proliferation, migration, invasion, apoptosis and cell cycle assays) were performed with the pca cell lines, pc3 and du145. both in vitro and in vivo (nude mouse) models were used for growth assays. luciferase reporter assays were used for binding of mir-34a to hotair. results lncrna profiling showed that hotair was highly regulated by genistein and its expression was higher in castration-resistant pca cell lines than in normal prostate cells. knockdown (sirna) of hotair decreased pca cell proliferation, migration and invasion and induced apoptosis and cell cycle arrest. mir-34a was also up-regulated by genistein and may directly target hotair in both pc3 and du145 pca cells. conclusions our results indicated that genistein inhibited pca cell growth through down-regulation of oncogenic hotair that is also targeted by tumor suppressor mir-34a. these findings enhance understanding of how genistein regulates lncrna hotair and mir-34a in pca.",1
"tumor metastasis involves a series of biological steps during which the tumor cells acquire the ability to invade surrounding tissues and survive outside the original tumor site. during the early stages, the cancer cells undergo an epithelial-mesenchymal transition (emt). wnt/β-catenin signaling is known to drive emt and metastasis. here we report that wnt/β-catenin signaling is hyperactivated in metastatic breast cancer cells that express microrna 374a (mir-374a). in breast cancer cell lines, ectopic overexpression of mir-374a promoted emt and metastasis both in vitro and in vivo. furthermore, mir-374a directly targeted and suppressed multiple negative regulators of the wnt/β-catenin signaling cascade, including wif1, pten, and wnt5a. notably, mir-374a was markedly upregulated in primary tumor samples from patients with distant metastases and was associated with poor metastasis-free survival. these results demonstrate that mir-374a maintains constitutively activated wnt/β-catenin signaling and may represent a therapeutic target for early metastatic breast cancer.",1
"dengue virus is a positive-strand rna virus and a member of the genus flavivirus, which includes west nile, yellow fever, and tick-borne encephalitis viruses. flavivirus genomes are translated as a single polyprotein that is subsequently cleaved into 10 proteins, the first of which is the viral capsid (c) protein. dengue virus type 2 (denv2) and other mosquito-borne flaviviruses initiate translation of c from a start codon in a suboptimal context and have multiple in-frame augs downstream. here, we show that an rna hairpin structure in the capsid coding region (chp) directs translation start site selection in human and mosquito cells. the ability of the chp to direct initiation from the first start codon is proportional to its thermodynamic stability, is position dependent, and is sequence independent, consistent with a mechanism in which the scanning initiation complex stalls momentarily over the first aug as it begins to unwind the chp. the chp of tick-borne flaviviruses is not maintained in a position to influence start codon selection, which suggests that this coding region cis element may serve another function in the flavivirus life cycle. here, we demonstrate that the denv2 chp and both the first and second augs of c are necessary for efficient viral replication in human and mosquito cells. while numerous regulatory elements have been identified in the untranslated regions of rna viral genomes, we show that the chp is a coding-region rna element that directs start codon selection and is required for viral replication.",1
"micrornas (mirnas) post-transcriptionally regulate the expression of thousands of distinct mrnas. while some regulatory interactions help to maintain basal cellular functions, others are likely relevant in more specific settings, such as response to stress. here we describe such a role for the mir-290-295 cluster, the dominant mirna cluster in mouse embryonic stem cells (mescs). examination of a target list generated from bioinformatic prediction, as well as expression data following mirna loss, revealed strong enrichment for apoptotic regulators, two of which we validated directly: caspase 2, the most highly conserved mammalian caspase, and ei24, a p53 transcriptional target. consistent with these predictions, mescs lacking mirnas were more likely to initiate apoptosis following genotoxic exposure to gamma irradiation or doxorubicin. knockdown of either candidate partially rescued this pro-apoptotic phenotype, as did transfection of members of the mir-290-295 cluster. these findings were recapitulated in a specific mir-290-295 deletion line, confirming that they reflect mirna functions at physiological levels. in contrast to the basal regulatory roles previously identified, the pro-survival phenotype shown here may be most relevant to stressful gestations, where pro-oxidant metabolic states induce dna damage. similarly, this cluster may mediate chemotherapeutic resistance in a neoplastic context, making it a useful clinical target.",1
"box c/d snornas are known to guide site-specific ribose methylation of ribosomal rna. here, we demonstrate a novel and unexpected role for box c/d snornas in guiding 18s rrna acetylation in yeast. our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18s rrna catalyzed by kre33 is guided by two orphan box c/d snornas-snr4 and snr45 -not known to be involved in methylation in yeast. we identified kre33 binding sites on these snornas as well as on the 18s rrna, and demonstrate that both snr4 and snr45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the h/aca snornps. we show that base pairing between these snornas and 18s rrna requires the putative helicase activity of kre33, which is also needed to aid early pre-rrna processing. compared to yeast, the number of orphan box c/d snornas in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.",1
"eighty-eight ischemic stroke patients with massive cerebral infarction (mci) who met our selection criteria were included in this study. mci was assessed using the glasgow coma scale (gcs) at hospital admission and at 2 weeks. the sera of all patients and controls were sampled at 48 h after the patients' attacks, and the sera of patients with mci who had no severe cardiopulmonary complications, including those with hemorrhagic transformation (ht), were sampled again at 2 weeks. the relative expression of let-7 mirna in the serum was determined by real-time qrt-pcr, and the blood levels of lipids, glucose, high-sensitivity c-reactive protein (hs-crp), homocysteine and blood pressure were measured at admission. interleukin-6 (il-6) levels were detected by elisa, and a luciferase assay was performed to confirm that il-6 was a gene target of let-7. the relative expression of let-7f was significantly down-regulated in mci without ht patients compared with controls (p<0.001), and it was positively correlated with gcs (p<0.01) and negatively correlated with hs-crp (p<0.01). the relative expression of let-7f was significantly up-regulated in mci patients with ht (p<0.01). il-6 is a direct target gene for let-7f, and il-6 expression was increased in mci without ht patients compared to controls (p<0.01). the expression of let-7f in serum is associated with mci without ht, which specifically inhibits il-6. this suggests that let-7f may control inflammation in patients with mci without ht.",1
"micrornas are small noncoding rna molecules that control expression of target genes. our previous studies show that mir-21 is overexpressed in tumor tissues compared with the matched normal tissues. moreover, suppression of mir-21 by antisense oligonucleotides inhibits tumor cell growth both in vitro and in vivo. however, it remains largely unclear as to how mir-21 affects tumor growth, because our understanding of mir-21 targets is limited. in this study, we performed two-dimensional differentiation in-gel electrophoresis of tumors treated with anti-mir-21 and identified the tumor suppressor tropomyosin 1 (tpm1) as a potential mir-21 target. in agreement with this, there is a putative mir-21 binding site at the 3'-untranslated region (3'-utr) of tpm1 variants v1 and v5. thus, we cloned the 3'-utr of tpm1 into a luciferase reporter and found that although mir-21 down-regulated the luciferase activity, anti-mir-21 up-regulated it. moreover, deletion of the mir-21 binding site abolished the effect of mir-21 on the luciferase activity, suggesting that this mir-21 binding site is critical. western blot with the cloned tpm1-v1 plus the 3'-utr indicated that tpm1 protein level was also regulated by mir-21, whereas real-time quantitative reverse transcription-pcr revealed no difference at the mrna level, suggesting translational regulation. finally, overexpression of tpm1 in breast cancer mcf-7 cells suppressed anchorage-independent growth. thus, down-regulation of tpm1 by mir-21 may explain, at least in part, why suppression of mir-21 can inhibit tumor growth, further supporting the notion that mir-21 functions as an oncogene.",1
"long non-coding rnas (lncrnas) function in a wide range of processes by diverse mechanisms, though their roles in regulation of oncogenes and/or tumor suppressors remain rather elusive. we performed a global search for lncrnas affecting myc activity using a systems biology-based approach with a k supercomputer and the gimlet algorism based on local distance correlations. consequently, mymlr was identified and experimentally shown to maintain myc transcriptional activity and cell cycle progression despite the low levels of expression. a proteomic search for mymlr-binding proteins identified pcbp2, while it was also found that mymlr places a 557-kb upstream enhancer region in the proximity of the myc promoter in cooperation with pcbp2. these findings implicate a crucial role for mymlr in regulation of the archetypical oncogene myc and warrant future studies regarding the involvement of low copy number lncrnas in regulation of other crucial oncogenes and tumor suppressor genes.",1
"micrornas are short rna molecules that are often expressed in specific tissues and regulate a variety of developmental processes. we used locked nucleic acid probes in in situ hybridisation reactions to study the distribution of microrna-449 (mir449) during mouse embryonic development in order to obtain clues about its function/s. between e9.75 and e11.5, mir449 was found to be expressed specifically in the developing roof plate of the fourth ventricle within the domain of roof plate marker, lmx1a. from e12.5 onwards, this expression became restricted to the epithelial cell layer of the fourth ventricle choroid plexus. mir449 also became detectable specifically in the choroid plexuses of the lateral and 3rd ventricles at e13.5 and e15.5, respectively. northern blot analysis of adult brain also showed a selective and enriched expression in the choroid plexus tissue. potential target genes regulated by mir449 were selected for experimental validation in luciferase-reporter assays and the transcription factor e2f5, which regulates csf production, was verified as a mir449 target gene. taken together, these findings suggest that mir449 has a specific role in the development and functioning of choroid plexuses.",1
"vertebrate brain hosts a diverse collection of micrornas, but little is known about their functions in vivo. here we propose that mouse microrna-9 (mir-9) targets foxg1 mrnas for proper generation of cajal-retzius cells in the medial pallium. mir-9 expression is mediolaterally graded, being most intense in the cortical hem; it contrasts with the foxg1 expression in a reciprocal gradient. the 3' untranslated regions of tetrapod, but not of teleost, foxg1 mrnas conserve mir-9 target sequences and are regulated by mir-9. gain- and loss-of-function analyses of mir-9 showed that mir-9 negatively regulates endogenous foxg1 protein level. moreover, mir-9 overexpression in developing telencephalon at e11.5 by electroporation resulted in ectopic reelin-positive cells over the cortex beyond the marginal zone. in addition, inhibition of endogenous mir-9 function by antisense oligonucleotides caused the regression of wnt3a-positive cortical hem and reduction of reelin-, p73-, and neurod1-positive cells.",1
"micrornas play diverse roles in various physiological processes during drosophila development. in the present study, we reported that mir-11 regulates pupal size during drosophila metamorphosis via targeting ras85d with the following evidences: pupal size was increased in the mir-11 deletion mutant; restoration of mir-11 in the mir-11 deletion mutant rescued the increased pupal size phenotype observed in the mir-11 deletion mutant; ectopic expression of mir-11 in brain insulin-producing cells (ipcs) and whole body shows consistent alteration of pupal size; dilps and ras85d expressions were negatively regulated by mir-11 in vivo; mir-11 targets ras85d through directly binding to ras85d 3'-untranslated region in vitro; removal of one copy of ras85d in the mir-11 deletion mutant rescued the increased pupal size phenotype observed in the mir-11 deletion mutant. thus, our current work provides a novel mechanism of pupal size determination by micrornas during drosophila melanogaster metamorphosis.",1
"cd38, a membrane protein expressed in airway smooth muscle (asm) cells, plays a role in cellular ca(2+) dynamics and asm contractility. in human asm (hasm) cells, tnf-α induces cd38 expression through activation of mapks, nf-κb, and ap-1, and its expression is differentially elevated in cells from asthmatic patients compared with cells from nonasthmatic subjects. the cd38 3'-untranslated region (utr) has targets for mir-140-3p. we hypothesized that mir-140-3p regulates cd38 expression in hasm cells by altering cd38 mrna stability. basal and tnf-α-induced expression of mir-140-3p was determined in nonasthmatic asm (naasm) and asthmatic asm (aasm) cells. naasm and aasm cells were transfected with control, mir-140-3p mimic, or mir-140-3p antagomirs, and cd38 expression and cd38 mrna stability were determined. luciferase reporter assays were used to determine mir-140-3p binding to the cd38 3'-utr. activation of p38, erk, and jnk mapks, nf-κb, and ap-1 was determined in mir-140-3p mimic-transfected naasm. tnf-α attenuated mir-140-3p expression in naasm and aasm cells, but at a greater magnitude in aasm cells. cd38 mrna expression was attenuated by mir-140-3p mimic at comparable magnitude in naasm and aasm cells. mutated mir-140-3p target on the cd38 3'-utr reversed the inhibition of luciferase activity by mir-140-3p mimic. cd38 mrna stability was unaltered by mir-140-3p mimic in naasm or aasm cells following arrest of transcription. tnf-α-induced activation of p38 mapk and nf-κb was attenuated by mir-140-3p mimic. the findings indicate that mir-140-3p modulates cd38 expression in hasm cells through direct binding to the cd38 3'-utr and indirect mechanisms involving activation of p38 mapk and nf-κb. furthermore, indirect mechanisms appear to play a major role in the regulation of cd38 expression.",1
"micrornas (mirnas) are endogenous, small noncoding rnas that play important roles in various cellular functions and tumor development. recent studies have indicated that mir-21 is one of the important mirnas associated with tumor growth and metastasis, but the role and molecular mechanism of mir-21 in regulating tumor angiogenesis remain to be elucidated. in this study, mir-21 was overexpressed by transfecting pre-mir-21 into human prostate cancer cells and tumor angiogenesis was assayed using chicken chorioallantoic membrane (cam). we found that overexpression of mir-21 in du145 cells increased the expression of hif-1α and vegf, and induced tumor angiogenesis. akt and extracellular regulated kinases (erk) 1/2 are activated by mir-21. inhibition of mir-21 by the antigomir blocked this process. overexpression of the mir-21 target, pten, also inhibited tumor angiogenesis by partially inactivating akt and erk and decreasing the expression of hif-1 and vegf. the akt and erk inhibitors, ly294002 and u0126, suppressed hif-1α and vegf expression and angiogenesis. moreover, inhibition of hif-1α expression alone abolished mir-21-inducing tumor angiogenesis, indicating that hif-1α is required for mir-21-upregulated angiogenesis. therefore, we demonstrate that mir-21 induces tumor angiogenesis through targeting pten, leading to activate akt and erk1/2 signaling pathways, and thereby enhancing hif-1α and vegf expression; hif-1α is a key downstream target of mir-21 in regulating tumor angiogenesis.",1
"accumulating evidence has indicated that micrornas (mirnas) act as critical epigenetic regulators in tumor carcinogenesis. here, we report that mir-199a-3p was significantly upregulated in gastric cancer (gc) cell lines and tissues. functional studies demonstrated that mir-199a-3p dramatically increased cell proliferation and suppressed cell apoptosis both in vitro and in vivo. furthermore, the transcriptional regulator zinc fingers and homeoboxes 1 (zhx1) was identified as one of the direct downstream targets of mir-199a-3p, mir-199a-3p bound to the zhx1 3′ untranslated region (3′utr) to regulate zhx1 protein expression. in addition, the expression of mir-199a-3p was inversely associated with that of zhx1 in gc cell lines. overexpression of mir-199a-3p in sgc-7901 cells inhibited zhx1 expression, while reduction in mir-199a-3p by inhibitors in nci-n87 cells enhanced zhx1 expression. moreover, restoring zhx1 expression in sgc-7901/mir-199a-3p cells inhibited the cell proliferation induced by mir-199a-3p. taken together, these findings suggest that mir-199a-3p may function as a novel tumor promoter in gc and its oncogenic activity may involve the direct targeting and inhibition of zhx1.",1
"the sxy (tfox) gene product is the central regulator of dna uptake by naturally competent gamma-proteobacteria such as haemophilus influenzae, vibrio cholerae and probably escherichia coli. however, the mechanisms regulating sxy gene expression are not understood despite being key to understanding the physiological role of dna uptake. we have isolated mutations in h. influenzae sxy that greatly elevate translation and thus cause competence to develop in otherwise non-inducing conditions (hypercompetence). in vitro nuclease analysis confirmed the existence of an extensive secondary structure at the 5' end of sxy mrna that sequesters the ribosome-binding site and start codon in a stem-loop. all of the hypercompetence mutations reduced mrna base pairing, and one was shown to cause a global destabilization that increased translational efficiency. conversely, mutations engineered to add mrna base pairs strengthened the secondary structure, resulting in reduced translational efficiency and greatly reduced competence for genetic transformation. transfer of wild-type cells to starvation medium improved translational efficiency of sxy while independently triggering the sugar starvation regulator (crp) to stimulate transcription at the sxy promoter. thus, mrna secondary structure is responsive to conditions where dna uptake will be favorable, and transcription of sxy is simultaneously enhanced if crp activation signals that energy supplies are limited.",1
"tgf-β promotes cell migration and invasion, an attribute that is linked to the pro-metastasis function of this cytokine in late stage cancers. the lim 1863 colon carcinoma organoid undergoes epithelial-mesenchymal transition (emt) in response to tgf-β. this process is markedly accelerated by tnf-α, and we found that the levels of mir-21 and mir-31 were prominently elevated under the synergistic actions of tgf-β/tnf-α. consistent with this, overexpression of either mir-21 or mir-31 significantly enhanced the effect of tgf-β alone on lim 1863 morphological changes. more importantly, transwell assays demonstrated the positive effects of both mir-21 and mir-31 in tgf-β regulation of lim 1863 motility and invasiveness. elevated levels of mir-21 and mir-31 also enhanced motility and invasiveness of other colon carcinoma cell lines. we present compelling evidence that tiam1, a guanidine exchange factor of the rac gtpase, is a direct target of both mir-21 and mir-31. indeed in lim 1863 cells, suppression of tiam1 is required for mir-21/mir-31 to enhance cell migration and invasion. therefore, we have uncovered mir-21 and mir-31 as downstream effectors of tgf-β in facilitating invasion and metastasis of colon carcinoma cells.",1
"microglia are innate immune cells in the central nervous system (cns), that supplies neurons with key factors for executing autophagosomal/lysosomal functions. macroautophagy/autophagy is a cellular catabolic process that maintains cell balance in response to stress-related stimulation. abnormal autophagy occurs with many pathologies, such as cancer, and autoimmune and neurodegenerative diseases. hence, clarification of the mechanisms of autophagy regulation is of utmost importance. recently, researchers presented micrornas (mirnas) as novel and potent modulators of autophagic activity. here, we found that mir223 deficiency significantly ameliorated cns inflammation, demyelination and the clinical symptoms of experimental autoimmune encephalomyelitis (eae) and increased resting microglia and autophagy in brain microglial cells. in contrast, the autophagy inhibitor 3-methylademine (3-ma) aggravated the clinical symptoms of eae in wild-type (wt) and mir223-deficienct mice. furthermore, it was confirmed that mir223 deficiency in mice increased the protein expression of atg16l1 (autophagy related 16-like 1 ) and lc3-ii in bone marrow-derived macrophage cells compared with cells from wt mice. indeed, the cellular level of atg16l1 was decreased in bv2 cells upon mir223 overexpression and increased following the introduction of antagomirs. we also showed that the 3' utr of atg16l1 contained functional mir223-responsive sequences and that overexpression of atg16l1 returned autophagy to normal levels even in the presence of mir223 mimics. collectively, these data indicate that mir223 is a novel and important regulator of autophagy and that atg16l1 is a mir223 target in this process, which may have implications for improving our understanding of the neuroinflammatory process of eae. abbreviations: 3-ma: 3-methylademine; actb/β-actin: actin, beta; atg: autophagy related; atg16l1: autophagy related 16-like 1 (s. cerevisiae); becn1: beclin 1, autophagy related; cnr2: cannabinoid receptor 2 (macrophage); cns: central nervous system; cq: chloroquine; eae: experimental autoimmune encephalomyelitis; foxo3: forkhead box o3; gapdh: glyceraldehyde-3-phosphate dehydrogenase; h&e: hematoxylin and eosin; itgam: integrin alpha m; lps: lipoplysaccharide; map1lc3/lc3: microtubule-associated protein 1 light chain 3; mirnas: micrornas; ms: multiple sclerosis; pparg: peroxisome proliferator activated receptor gamma; ptprc: protein tyrosine phosphatase, receptor type, c; ra: rheumatoid arthritis; sqstm1: sequestosome 1; tb: tuberculosis; timm23: translocase of inner mitochondrial membrane 23; tlr: toll-like receptor.",1
"the first micrornas were discovered some 20 years ago, but only a small fraction of the microrna-encoding genes have been described in detail yet. here we report the molecular analysis of a computationally predicted drosophila melanogaster microrna gene, mir-282. we show that the mir-282 gene is the source of a 4.9-kb-long primary transcript with a 5' cap and a 3'-poly(a) sequence and a mature microrna of ∼25 bp. our data strongly suggest the existence of an independent mir-282 gene conserved in holometabolic insects. we give evidence that the mir-282 locus encodes a functional transcript that influences viability, longevity, and egg production in drosophila. we identify the nervous system-specific adenylate cyclase (rutabaga) as a target of mir-282 and assume that one of the main functions of mir-282 is the regulation of adenylate cyclase activity in the nervous system during metamorphosis.",1
"background cardiac fibrosis occurs because of disruption of the extracellular matrix network leading to myocardial dysfunction. angiotensin ii (angii) has been implicated in the development of cardiac fibrosis. recently, micrornas have been identified as an attractive target for therapeutic intervention in cardiac pathologies; however, the underlying mechanism of micrornas in cardiac fibrosis remains unclear. next-generation sequencing analysis identified a novel characterized microrna, mir-1954, that was significantly reduced in angii-infused mice. the finding led us to hypothesize that deficiency of mir-1954 triggers cardiac fibrosis. methods and results a transgenic mouse was created using α-mhc (α-myosin heavy chain) promoter and was challenged with angii infusion. angii induced cardiac hypertrophy and remodeling. the in vivo overexpression of mir-1954 showed significant reduction in cardiac mass and blood pressure in angii-infused mice. further analysis showed significant reduction in cardiac fibrotic genes, hypertrophy marker genes, and an inflammatory gene and restoration of a calcium-regulated gene (atp2a2 ; also known as serca2), but no changes were observed in apoptotic genes. thbs1 (thrombospondin 1) is indicated as a target gene for mir-1954. conclusions our findings provide evidence, for the first time, that mir-1954 plays a critical role in cardiac fibrosis by targeting thbs1. we conclude that promoting the level of mir-1954 would be a promising strategy for the treatment of cardiac fibrosis.",1
"peripartum cardiomyopathy (ppcm) is a life-threatening pregnancy-associated cardiomyopathy in previously healthy women. although ppcm is driven in part by the 16-kda n-terminal prolactin fragment (16k prl), the underlying molecular mechanisms are poorly understood. we found that 16k prl induced microrna-146a (mir-146a) expression in ecs, which attenuated angiogenesis through downregulation of nras. 16k prl stimulated the release of mir-146a-loaded exosomes from ecs. the exosomes were absorbed by cardiomyocytes, increasing mir-146a levels, which resulted in a subsequent decrease in metabolic activity and decreased expression of erbb4, notch1, and irak1. mice with cardiomyocyte-restricted stat3 knockout (cko mice) exhibited a ppcm-like phenotype and displayed increased cardiac mir-146a expression with coincident downregulation of erbb4, nras, notch1, and irak1. blocking mir-146a with locked nucleic acids or antago-mirs attenuated ppcm in cko mice without interrupting full-length prolactin signaling, as indicated by normal nursing activities. finally, mir-146a was elevated in the plasma and hearts of ppcm patients, but not in patients with dilated cardiomyopathy. these results demonstrate that mir-146a is a downstream-mediator of 16k prl that could potentially serve as a biomarker and therapeutic target for ppcm.",1
"osteoarthritis (oa) is characterized by progressive destruction of articular cartilage, resulting in significant disability. inflammatory cytokines commonly initiate the extreme changes in the synovium and cartilage microenvironment of the oa patients, subsequently resulting in cell dysfunctions, especially synoviocyte dysfunction. we revealed that the expression of osteopontin (opn), which has been reported to regulate expression of various inflammatory factors associating with the pathogenesis of oa including matrix metalloprotease 13 (mmp13), interlukine-6 and 8 (il-6 and il-8), is significantly upregulated in oa tissues. in the present study, online tools were used to screen out the candidate mirnas of opn. among the candidate mirnas, mir-181c inhibited opn mrna expression the most strongly. ectopic expression of mir-181c significantly repressed synoviocyte proliferation, as well as the levels of opn, mmp13, il-6, and il-8. further, the candidate lncrnas of mir-181c were screened out by using dianatools; among which neat1 showed to inversely regulate mir-181c. by performing luciferase assays, we revealed that neat1 competed with opn for mir-181c binding. after neat1 knockdown, mmp13, il-6, and il-8 expression was reduced; the synoviocyte proliferation was repressed, as well as opn protein levels; the suppressive effect of neta1 knockdown on synoviocyte proliferation and the indicated factors were partially reversed by mir-181c inhibition. in oa tissues, opn mrna, and neat1 expression was upregulated, whereas mir-181c expression was downregulated, indicating that targeting neat1 to rescue mir-181c expression so as to inhibit opn expression and synoviocyte proliferation might be an efficient strategy for oa treatment. j. cell. biochem. 118: 3775-3784, 2017. © 2017 wiley periodicals, inc.",1
"regulation of the positive transcription elongation factor, p-tefb, plays a major role in controlling mammalian transcription and this is accomplished in part by controlled release of p-tefb from the 7sk snrnp that sequesters the kinase in an inactive state. we demonstrate here that a similar p-tefb control system exists in drosophila. we show that an rna previously suggested to be a 7sk homolog is, in fact, associated with p-tefb, through the action of a homolog of the human hexim1/2 proteins (dhexim). in addition, a drosophila la related protein (now called dlarp7) is shown to be the functional homolog of human larp7. the drosophila 7sk snrnp (d7sk snrnp) responded to treatment of cells with p-tefb inhibitors and to nuclease treatment of cell lysates by releasing p-tefb. supporting a critical role for the d7sk snrnp in drosophila development, dlarp7 and dhexim were found to be ubiquitously expressed throughout embryos and tissues at all stages. importantly, knockdown of dhexim was embryonic lethal, and reduction of dhexim in specific tissues led to serious developmental defects. our results suggest that regulation of p-tefb by the d7sk snrnp is essential for the growth and differentiation of tissues required during drosophila development.",1
"micrornas are noncoding rnas inhibiting expression of numerous target genes, and a few have been shown to act as oncogenes or tumor suppressors. we show that microrna-7 (mir-7) is a potential tumor suppressor in glioblastoma targeting critical cancer pathways. mir-7 potently suppressed epidermal growth factor receptor expression, and furthermore it independently inhibited the akt pathway via targeting upstream regulators. mir-7 expression was down-regulated in glioblastoma versus surrounding brain, with a mechanism involving impaired processing. importantly, transfection with mir-7 decreased viability and invasiveness of primary glioblastoma lines. this study establishes mir-7 as a regulator of major cancer pathways and suggests that it has therapeutic potential for glioblastoma.",1
"dna damage activates tp53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. tp53 orchestrates these responses directly by transcriptionally modulating genes, including micrornas (mirnas), and by regulating mirna biogenesis through interacting with the drosha complex. however, whether the association between mirnas and ago2 is regulated following dna damage is not yet known. here, we show that, following dna damage, tp53 interacts with ago2 to induce or reduce ago2's association of a subset of mirnas, including multiple let-7 family members. furthermore, we show that specific mutations in tp53 decrease rather than increase the association of let-7 family mirnas, reducing their activity without preventing tp53 from interacting with ago2. this is consistent with the oncogenic properties of these mutants. using ago2 rip-seq and par-clip-seq, we show that the dna damage-induced increase in binding of let-7 family members to the risc complex is functional. we unambiguously determine the global mirna-mrna interaction networks involved in the dna damage response, validating them through the identification of mirna-target chimeras formed by endogenous ligation reactions. we find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. additionally, we observe that mirnas, whose cellular abundance or differential association with ago2 is regulated by tp53, are involved in an intricate network of regulatory feedback and feedforward circuits. tp53-mediated regulation of ago2-mirna interaction represents a new mechanism of mirna regulation in carcinogenesis.",1
"eukaryotic nucleoli contain a large family of box c+d small nucleolar rna (snorna) species, all of which are associated with a common protein nop1p/fibrillarin. nop58p was identified in a screen for synthetic lethality with nop1p and shown to be an essential nucleolar protein. here we report that a protein a-tagged version of nop58p coprecipitates all tested box c+d snornas and that genetic depletion of nop58p leads to the loss of all tested box c+d snornas. the box h+aca class of snornas are not coprecipitated with nop58p, and are not codepleted. the yeast box c+d snornas include two species, u3 and u14, that are required for the early cleavages in pre-rrna processing. consistent with this, nop58p depletion leads to a strong inhibition of pre-rrna processing and 18s rrna synthesis. unexpectedly, depletion of nop58p leads to the accumulation of 3' extended forms of u3 and u24, showing that the protein is also involved in snorna synthesis. nop58p is the second common component of the box c+d snornps to be identified and the first to be shown to be required for the stability and for the synthesis of these snornas.",1
"cd146, an endothelial biomarker, has been shown to be aberrantly upregulated during pathological angiogenesis and functions as a coreceptor for vascular endothelial growth factor receptor 2 (vegfr-2) to promote disease progression. however, the regulatory mechanisms of cd146 expression during angiogenesis remain unclear. using a microrna screening approach, we identified a novel negative regulator of angiogenesis, microrna 329 (mir-329), that directly targeted cd146 and inhibited cd146-mediated angiogenesis in vitro and in vivo. endogenous mir-329 expression was downregulated by vegf and tumor necrosis factor alpha (tnf-α), resulting in the elevation of cd146 in endothelial cells. upregulation of cd146 facilitated an endothelial response to vegf-induced src kinase family (skf)/p38 mitogen-activated protein kinase (mapk)/nf-κb activation and consequently promoted endothelial cell migration and tube formation. our animal experiments showed that treatment with mir-329 repressed excessive cd146 expression on blood vessels and significantly attenuated neovascularization in a mouse model of pathological angiogenesis. our findings provide the first evidence that cd146 expression in angiogenesis is regulated by mir-329 and suggest that mir-329 could present a potential therapeutic tool for the treatment of angiogenic diseases.",1
"micrornas (mirnas) are small non-coding rnas that regulate gene expression, primarily at the post-transcriptional level. growing evidence suggests that mirnas function as oncogenes or tumor suppressors in human cancers. the down-regulation of mir-145 has been reported in many types of human cancer, including prostate cancer (pc), suggesting that mir-145 functions as a tumor suppressor. using the pc cell lines, pc3 and du145, gain-of-function assays revealed that mir-145 transfection inhibited cell proliferation, migration and invasion. fascin homolog 1 (fscn1), an actin-bundling protein, is a candidate target gene of mir-145 based on genome-wide gene expression analysis. a luciferase reporter assay showed a significantly decreased signal at two mir-145 target sites at the 3'utr of fscn1, suggesting that mir-145 directly regulates fscn1. in fscn1 loss-of-function assays, cell growth, migration and invasion were all inhibited, implying that fscn1 is associated with the progression of pc. the identification of tumor suppressive mirnas and their target genes could provide new insights into the potential mechanisms of prostate carcinogenesis.",1
"micrornas (mirnas) regulate gene expression directly through base pairing to their targets or indirectly through participating in multi-scale regulatory networks. often mirnas take part in feed-forward motifs where a mirna and a transcription factor act on shared targets to achieve accurate regulation of processes such as cell differentiation. here we show that the expression levels of mir-27a and mir-29a inversely correlate with the mrna levels of lipoprotein lipase (lpl), their predicted combinatorial target, and its key transcriptional regulator peroxisome proliferator-activated receptor gamma (pparg) during 3t3-l1 adipocyte differentiation. more importantly, we show that lpl, a key lipogenic enzyme, can be negatively regulated by the two mirna families in a combinatorial fashion on the mrna and functional level in maturing adipocytes. this regulation is mediated through the lpl 3'utr as confirmed by reporter gene assays. in addition, a small mathematical model captures the dynamics of this feed-forward motif and predicts the changes in lpl mrna levels upon network perturbations. the obtained results might offer an explanation to the dysregulation of lpl in diabetic conditions and could be extended to quantitative modeling of regulation of other metabolic genes under similar regulatory network motifs.",1
"upon recognition of viral components by pattern recognition receptors, such as the toll-like receptors (tlrs) and retinoic acid-inducible gene i (rig-i)-like helicases, cells are activated to produce type i interferon (ifn) and proinflammatory cytokines. these pathways are tightly regulated by the host to prevent an inappropriate cellular response, but viruses can modulate these pathways to proliferate and spread. in this study, we revealed a novel mechanism in which hepatitis c virus (hcv) evades the immune surveillance system to proliferate by activating microrna-21 (mir-21). we demonstrated that hcv infection upregulates mir-21, which in turn suppresses hcv-triggered type i ifn production, thus promoting hcv replication. furthermore, we demonstrated that mir-21 targets two important factors in the tlr signaling pathway, myeloid differentiation factor 88 (myd88) and interleukin-1 receptor-associated kinase 1 (irak1), which are involved in hcv-induced type i ifn production. hcv-mediated activation of mir-21 expression requires viral proteins and several signaling components. moreover, we identified a transcription factor, activating protein-1 (ap-1), which is partly responsible for mir-21 induction in response to hcv infection through pkcε/jnk/c-jun and pkcα/erk/c-fos cascades. taken together, our results indicate that mir-21 is upregulated during hcv infection and negatively regulates ifn-α signaling through myd88 and irak1 and may be a potential therapeutic target for antiviral intervention.",1
"breast cancer is the most common cancer in women worldwide. local invasion, metastasis, and chemotherapy resistance are the obstacles for treatment of breast cancer. in this study, we aim to investigate the role of mir-144 in breast cancer. we demonstrate that the expression of mir-144 is downregulated in breast cancer and cell lines, and lower mir-144 expression is associated with poor differentiation, higher clinical stage, and lymph node metastasis in patients with breast cancer. the rescue of mir-144 expression is able to inhibit the cell proliferation and the ability of cell migration and invasion. in addition, we show that mir-144 can directly target at 3'-untranslation region of zinc finger e-box-binding homeobox 1 and 2, that is, zeb1 and zeb2, and regulate their expression at transcriptional and translational levels. moreover, we also demonstrate that ectopic expression of mir-144 can inhibit the process of epithelial mesenchymal transition in mcf-7 and mda-mb-231 cells. thus, we here demonstrate that mir-144 functions as a tumor suppressor in breast cancer at least partly through inhibiting zeb1/2-mediated epithelial mesenchymal transition process. our findings indicate that the mir-144-zeb1/2 signaling could represent a promising therapeutic target for breast cancer treatment.",1
"substantial evidence indicates that microrna-21 (mir-21) is a key oncomir in carcinogenesis and is significantly elevated in multiple myeloma (mm). in this study, we explored the role of mir-21 in human mm cells and searched for mir-21 targets. by knocking down the expression of endogenous mir-21 in u266 myeloma cells, we observed reduced growth, an arrested cell cycle, and increased apoptosis. to further understand its molecular mechanism in the pathogenesis of mm, we employed a silac (stable isotope labeling by amino acids in cell culture)-based quantitative proteomic strategy to systematically identify potential targets of mir-21. in total, we found that the expression of 178 proteins was up-regulated significantly by mir-21 inhibition, implying that they could be potential targets of mir-21. among these, the protein inhibitor of activated stat3 (pias3) was confirmed as a direct mir-21 target by western blotting and reporter gene assays. we further demonstrated that mir-21 enhances the stat3-dependent signal pathway by inhibiting the function of pias3 and that down-regulation of pias3 contributes to the oncogenic function of mir-21. this elucidation of the role of pias3 in the mir-21-stat3 positive regulatory loop not only may shed light on the molecular basis of the biological effects of mir-21 observed in mm cells but also has direct implications for the development of novel anti-mm therapeutic strategies.",1
"background & aims oncogene polycomb group protein enhancer of zeste homolog 2 (ezh2) has been proposed to be a target gene of putative tumor suppressor microrna-101 (mir-101). the aim of our study was to investigate the functional role of both mir-101 and ezh2 in human hepatocellular carcinoma (hcc). methods mir-101 and ezh2 expressions were evaluated in tumor tissues of 99 hcc patients and 7 liver cancer cell lines by real-time pcr. luciferase reporter assay was employed to validate whether ezh2 represents a target gene of mir-101. the effect of mir-101 on hcc growth as well as programmed cell death was studied in vitro and in vivo. results mir-101 expression was significantly downregulated in most of hcc tissues and all cell lines, whereas ezh2 was significantly overexpressed in most of hcc tissues and all cell lines. there was a negative correlation between expression levels of mir-101 and ezh2. luciferase assay results confirmed ezh2 as a direct target gene of mir-101, which negatively regulates ezh2 expression in hcc. ectopic overexpression of mir-101 dramatically repressed proliferation, invasion, colony formation as well as cell cycle progression in vitro and suppressed tumorigenicity in vivo. furthermore, mir-101 inhibited autophagy and synergized with either doxorubicin or fluorouracil to induce apoptosis in tumor cells. conclusion tumor suppressor mir-101 represses hcc progression through directly targeting ezh2 oncogene and sensitizes liver cancer cells to chemotherapeutic treatment. our findings provide significant insights into molecular mechanisms of hepatocarcinogenesis and may have clinical relevance for the development of novel targeted therapies for hcc.",1
"this study aims to explore the effect of mir-330 targeting vav1 on amyloid β-protein (aβ) production, oxidative stress (os), and mitochondrial dysfunction in alzheimer's disease (ad) mice through the mapk signaling pathway. putative targeted gene of mir-330 was performed by a mirna target prediction website and dual-luciferase reporter gene assay. ad mouse model was successfully established. fourteen c57 mice were randomized into ad and control groups. the positive protein expression rate of vav1 was measured by immunohistochemistry. neuron cells were assigned into control, blank, negative control (nc), mir-330 mimics, mir-330 inhibitors, sirna-vav1, and mir-330 inhibitors + sirna-vav1 groups. expression of mir-330, vav1, erk1, jnk1, p38mapk, aβ, cox, and lipoprotein receptor-related protein-1 (lrp-1) were determined using rt-qpcr and western blotting. colorimetry was applied to measure the levels of os parameters of superoxide dismutase (sod) and malondialdehyde (mda). aβ production in brain tissue was detected using elisa, while that in neuron cell was measured by radioimmunoassay. mir-330 was down-regulated in neuron cells of ad mice and vav1 was negatively regulated by mir-330. compared with the control group, the positive protein expression rate of vav1 was significantly elevated in the ad group. overexpression of mir-330 decreased the expression of vav1, erk1, jnk1, p38mapk, and aβ, but increased the expression of cox and lrp-1. ad mice revealed elevated aβ production and mda with decreased sod level. the result indicates that overexpressed mir-330 targeting vav1 through the mapk signaling pathway reduces aβ production and alleviates os and mitochondrial dysfunction in ad.",1
"liver x receptor α (lxrα) plays a critical role in the transcriptional control of lipid metabolism. lxr activation induces the expression of lipogenic genes, which promote hepatic steatosis and steatohepatitis. however, the regulation of lxr is not fully understood. micrornas (mirs) are regarded as important negative regulators of gene expression. in this study, we found that mir-1/mir-206 repressed lxrα-induced accumulation of lipid droplets in hepatocytes. in addition, bioinformatic analysis predicted a same putative target-site for mir-1/mir-206 located within the 3'-untranslated region (3'-utr) of lxrα mrna. the reporter assay revealed that mir-1/mir-206 directly targeted the 3'-utr of lxrα mrna. furthermore, mir-1/mir-206 repressed lxrα expression at both mrna and protein levels, accompanied with the inhibition of expression of lxrα target genes, such as sterol-regulatory element binding protein 1c, fatty acid synthase, carbohydrate responsive element-binding protein and acetyl-coa carboxylase 1, which are important effectors of lxrα implicated in lipogenesis. moreover, ectopic expression of lxrα without the 3'-utr dramatically attenuated the mir-1/mir-206-induced decrease of lipogenic genes and lipid droplet accumulation. taken together, we for the first time demonstrated that mir-1/mir-206 attenuated lxrα-induced lipogenesis by targeting the 3'-utr of lxrα mrna, suggesting that mir-1/mir-206-lxrα pathway may be a novel target for the treatment of lipogenesis-associated diseases.",1
"neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells. recurrent genomic alterations include mycn and alk amplification as well as recurrent patterns of gains and losses of whole or large partial chromosome segments. a recent whole genome sequencing effort yielded no frequently recurring mutations in genes other than those affecting alk. however, the study further stresses the importance of dna copy number alterations in this disease, in particular for genes implicated in neuritogenesis. here we provide additional evidence for the importance of focal dna copy number gains and losses, which are predominantly observed in mycn amplified tumors. a focal 5 kb gain encompassing the mycn regulated mir-17~92 cluster as sole gene was detected in a neuroblastoma cell line and further analyses of the array cgh data set demonstrated enrichment for other mycn target genes in focal gains and amplifications. next we applied an integrated genomics analysis to prioritize mycn down regulated genes mediated by mycn driven mirnas within regions of focal heterozygous or homozygous deletion. we identified rgs5, a negative regulator of g-protein signaling implicated in vascular normalization, invasion and metastasis, targeted by a focal homozygous deletion, as a new mycn target gene, down regulated through mycn activated mirnas. in addition, we expand the mir-17~92 regulatory network controlling tgfß signaling in neuroblastoma with the ring finger protein 11 encoding gene rnf11, which was previously shown to be targeted by the mir-17~92 member mir-19b. taken together, our data indicate that focal dna copy number imbalances in neuroblastoma (1) target genes that are implicated in mycn signaling, possibly selected to reinforce mycn oncogene addiction and (2) serve as a resource for identifying new molecular targets for treatment.",1
"to define structural elements critical for rna replication in human parechovirus 1 (hpev1), a replicon with chloramphenicol acetyltransferase as a reporter gene and an infectious virus cdna clone have been used. it was observed that there are cis-acting signals required for hpev1 replication located within the 5'-terminal 112 nucleotides of the genome and that these include two terminal stem-loops, sl-a and sl-b, together with a pseudoknot element. significant disruption of any of these structures impaired both rna replication and virus growth. in view of the similarity in terminal structures to several picornaviruses, such as cardioviruses and hepatoviruses, the insights generated in this work are of wider significance for understanding picornavirus replication.",1
"onco-mir-182-5p has been reported to be over-expressed in bladder cancer (bc) tissues however a detailed functional analysis of mir-182-5p has not been carried out in bc. therefore the purpose of this study was to: 1. conduct a functional analysis of mir-182-5p in bladder cancer, 2. assess its usefulness as a tumor marker, 3. identify mir-182-5p target genes in bc. initially we found that mir-182-5p expression was significantly higher in bladder cancer compared to normal tissues and high mir-182-5p expression was associated with shorter overall survival in bc patients. to study the functional significance of mir-182-5p, we over-expressed mir-182-5p with mir-182-5p precursor and observed that cell proliferation, migration and invasion abilities were increased in bc cells. however cell apoptosis was inhibited by mir-182-5p. we also identified smad4 and reck as potential target genes of mir-182-5p using several algorithms. 3'utr luciferase activity of these target genes was significantly decreased and protein expression of these target genes was significantly up-regulated in mir-182-5p inhibitor transfected bladder cancer cells. mir-182-5p also increased nuclear beta-catenin expression and while smad4 repressed nuclear beta-catenin expression. in conclusion, our data suggests that mir-182-5p plays an important role as an oncogene by knocking down reck and smad4, resulting in activation of the wnt-beta-catenin signaling pathway in bladder cancer.",1
"one- and two-dimensional gel electrophoresis of proteins from bovine aortic endothelial cells (baec) incubated with atp revealed the preferential labelling of a cell-associated 21 kda substrate. the labelling of this band was detectable within 30 s, increased up to 30 min and was stable for at least 3 h following the wash-out of the atp. this protein was also labelled after incubation of the cells with atp. incorporation of radioactivity into the 21 kda band did not occur if the endothelial cells were treated with low concentrations of trypsin (0.01%) before or after the labelling period. the pattern of baec protein phosphorylation by atp was completely different from that of the fetal calf serum used for the cell culture. the presence of serum during the incubation of baec with atp did not modify qualitatively the labelling pattern and, in particular, did not enhance the phosphorylation of the 21 kda substrate; this suggests that neither the kinase nor the 21 kda substrate are adsorbed serum proteins. staurosporine, a protein kinase inhibitor with low specificity, decreased the labelling of the 21 kda protein with an ic50 of 2 nm. in contrast, at 100 nm, staurosporine did not decrease the accumulation of inositol phosphates induced by atp via the activation of p2y receptors. these data indicate the presence of aortic endothelial cells of an ecto-kinase which uses extracellular atp to produce the selective and long-lived phosphorylation of a 21 kda endothelial substrate. ecto-phosphorylation of this protein might play a role in the modulation of endothelial cell functions by atp, in addition to the p2y receptors . the exquisite sensitivity of ecto-phosphorylation to inhibition by staurosporine and its specific inhibition by some isoquinolinesulphonamide compounds provide potential pharmacological tools to investigate this hypothesis.",1
"background the vestibular apparatus of the vertebrate inner ear uses three fluid-filled semicircular canals to sense angular acceleration of the head. malformation of these canals disrupts the sense of balance and frequently causes circling behavior in mice. the epistatic circler (ecl) is a complex mutant derived from wildtype swr/j and c57l/j mice. ecl circling has been shown to result from the epistatic interaction of an swr-derived locus on chromosome 14 and a c57l-derived locus on chromosome 4, but the causative genes have not been previously identified. methodology/principal findings we developed a mouse chromosome substitution strain (css-14) that carries an swr/j chromosome 14 on a c57bl/10j genetic background and, like ecl, exhibits circling behavior due to lateral semicircular canal malformation. we utilized css-14 to identify the chromosome 14 ecl gene by positional cloning. our candidate interval is located upstream of bone morphogenetic protein 4 (bmp4) and contains an inner ear-specific, long non-coding rna that we have designated rubie (rna upstream of bmp4 expressed in inner ear). rubie is spliced and polyadenylated, and is expressed in developing semicircular canals. however, we discovered that the swr/j allele of rubie is disrupted by an intronic endogenous retrovirus that causes aberrant splicing and premature polyadenylation of the transcript. rubie lies in the conserved gene desert upstream of bmp4, within a region previously shown to be important for inner ear expression of bmp4. we found that the expression patterns of bmp4 and rubie are nearly identical in developing inner ears. conclusions/significance based on these results and previous studies showing that bmp4 is essential for proper vestibular development, we propose that rubie is the gene mutated in ecl mice, that it is involved in regulating inner ear expression of bmp4, and that aberrant bmp4 expression contributes to the ecl phenotype.",1
"micrornas (mirnas), non-coding rnas that function as post-transcriptional gene regulators, play a pivotal role in cancer development. in the present study, we elucidated the roles of mir-520b and mir-520e in breast cancer cells. we examined the expression levels of mir-520b and mir-520e in the immortalized breast cell line, hbl-100, and in three breast cancer cell lines: mcf-7, lm-mcf-7 and mda-mb-231. we show the expression levels of mir-520b and mir-520e in the breast cancer cell lines were lower than that in the hbl-100 cells. furthermore, the breast cancer cell lines showed less sensitivity to complement-dependent cytotoxicity (cdc). we found that overexpression of mir-520b and mir-520e increases the sensitivity of the breast cancer cells to cdc, whereas further suppression of mir-520b and mir-520e decreases the sensitivity of the breast cancer cells to cdc. we then demonstrate that mir-520b and mir-520e are able to directly target the 3'untranslated regions (3'utr) of the membrane-bound complement regulatory protein cd46; suggesting that mir-520b and mir-520e down-regulate cd46 at post-transcriptional level. enzyme-linked immunosorbent assay (elisa) showed that overexpression of mir-520b and mir-520e results in the increased expression of c3b, which is mediated by downregulated cd46. these results suggest that mirna-520b and mir-520e mediated down-regulation of cd46 induces opsonization of cancer cells via an alternative pathway resulting in complement activation. thus, we conclude that mir-520b and mir-520e contribute to cdc in breast cancer cells via directly targeting the 3'utr of cd46.",1
"the imbalance between adipogenic and osteogenic differentiation in bone marrow mesenchymal stem cells (bmscs) plays a significant role in the pathogenesis of steroid-induced osteonecrosis of the femoral head (onfh). several micrornas (mirnas) are involved in regulating adipogenesis and osteogenesis. in this study, we established a steroid-induced onfh rat model to identify the potential relevant mirnas. we identified 9 up-regulated and 28 down-regulated mirnas in the onfh rat model. of these, mir-27a was down-regulated and negatively correlated with peroxisome proliferator-activated receptor gamma (pparγ) and gremlin 1 (grem1) expression. further studies confirmed that pparγ and grem1 were direct targets of mirna-27a. additionally, adipogenic differentiation was enhanced by mir-27a down-regulation, whereas mirna-27a up-regulation attenuated adipogenesis and promoted osteogenesis in steroid-induced rat bmscs. moreover, mirna-27a up-regulation had a stronger effect on adipogenic and osteogenic differentiation in steroid-induced rat bmscs than si-pparγ and si-grem1. in conclusion, we identified 37 differentially expressed mirnas in the steroid-induced onfh model, of which mir-27a was down-regulated. our results showed that mir-27a up-regulation could inhibit adipogenesis and promote osteogenesis by directly targeting pparγ and grem1. thus, mir-27a is likely a key regulator of adipogenesis in steroid-induced bmscs and a potential therapeutic target for onfh treatment.",1
"the neural selector gene cut, a homeobox transcription factor, is required for the specification of the correct identity of external (bristle-type) sensory organs in drosophila. targets of cut function, however, have not been described. here, we study bereft (bft) mutants, which exhibit loss or malformation of a majority of the interommatidial bristles of the eye and cause defects in other external sensory organs. these mutants were generated by excising a p element located at chromosomal location 33ab, the enhancer trap line e8-2-46, indicating that a gene near the insertion site is responsible for this phenotype. similar to the transcripts of the gene nearest to the insertion, reporter gene expression of e8-2-46 coincides with cut in the support cells of external sensory organs, which secrete the bristle shaft and socket. although bft transcripts do not obviously code for a protein product, its expression is abolished in bft deletion mutants, and the integrity of the bft locus is required for (interommatidial) bristle morphogenesis. this suggests that disruption of the bft gene is the cause of the observed bristle phenotype. we also sought to determine what factors regulate the expression of bft and the enhancer trap line. the correct specification of individual external sensory organ cells involves not only cut, but also the lineage genes numb and tramtrack. we demonstrate that mutations of these three genes affect the expression levels at the bft locus. furthermore, cut overexpression is sufficient to induce ectopic bft expression in the pns and in nonneuronal epidermis. on the basis of these results, we propose that bft acts downstream of cut and tramtrack to implement correct bristle morphogenesis.",1
"aims free fatty acids induce apoptosis in cardiomyocytes, which is implicated in lipotoxic cardiomyopathy. however, the underlying mechanisms remain not fully understood. micrornas (mirnas) are non-coding small rnas that control gene expression at the post-transcriptional level. dysregulated mirnas have been shown to be involved in heart diseases. this study was to examine whether mir-195 regulates palmitate-induced cardiomyocyte apoptosis by targeting sirt1, a known anti-apoptotic protein. methods and results in cultured neonatal mouse cardiomyocytes, palmitate up-regulated mir-195 expression, increased reactive oxygen species (ros) production, and induced apoptosis as determined by up-regulation of caspase-3 activity and dna fragmentation. inhibition of mir-195 decreased ros production and apoptosis in palmitate-stimulated cardiomyocytes. in contrast, a mir-195 mimic enhanced palmitate-induced ros production and apoptosis. the induction of mir-195 correlated with a reduction in sirt1 and bcl-2. we further showed that mir-195 targeted and inhibited sirt1 expression through two target sites located in the 3' un-translational region of sirt1 mrna. in concordance, inhibition of mir-195 increased sirt1 protein in cardiomyocytes whereas the mir-195 mimic reduced it. activation of sirt1 or overexpression of bcl-2 inhibited palmitate-induced apoptosis. on the other hand, inhibition of sirt1 enhanced apoptosis. the inhibitory effect of sirt1 on apoptosis was associated with a reduction in ros. conclusions this study demonstrates a pro-apoptotic role of mir-195 in cardiomyocytes and identifies sirt1 as a direct target of mir-195. the effect of mir-195 on apoptosis is mediated through down-regulation of sirt1 and bcl-2 and ros production. thus, mir-195 may be a new therapeutic target for lipotoxic cardiomyopathy.",1
"the posttranscriptional regulator, microrna-21 (mir-21), is up-regulated in many forms of cancer, as well as during cardiac hypertrophic growth. to understand its role, we overexpressed it in cardiocytes where it revealed a unique type of cell-to-cell ""linker"" in the form of long slender outgrowths and branches. we subsequently confirmed that mir-21 directly targets and down-regulates the expression of sprouty2 (spry2), an inhibitor of branching morphogenesis and neurite outgrowths. we found that beta-adrenergic receptor (betaar) stimulation induces up-regulation of mir-21 and down-regulation of spry2 and is, likewise, associated with connecting cell branches. knockdown of spry2 reproduced the branching morphology in cardiocytes, and vice versa, knockdown of mir-21 using a specific 'mirna eraser' or overexpression of spry2 inhibited betaar-induced cellular outgrowths. these structures enclose sarcomeres and connect adjacent cardiocytes through functional gap junctions. to determine how this aspect of mir-21 function translates in cancer cells, we knocked it down in colon cancer sw480 cells. this resulted in disappearance of their microvillus-like protrusions accompanied by spry2-dependent inhibition of cell migration. thus, we propose that an increase in mir-21 enhances the formation of various types of cellular protrusions through directly targeting and down-regulating spry2.",1
"micrornas (mirna) are short rna molecules regulating the expression of specific mrnas. we investigated the expression pattern and potential targets of mouse mir-140 and found that mir-140 is specifically expressed in cartilage tissues of mouse embryos during both long and flat bone development. mir-140 expression was detected in the limbs of e11.5 embryos in the primorida of future bones both in the fore and hindlimb and across autopod, zeugopod and stylopod. all digits of e14.5 fore- and hindlimbs showed accumulation of mir-140, except the first digit of the hindlimb. mir-140 expression was also detected in the cartilagenous base of e17.5 skulls and in the sternum, the proximal rib heads and the developing vertebral column of e15.5 embryos. a potential target of mir-140, histone deacetylase 4, was validated experimentally and the possible role of mir-140 in long bone development is discussed.",1
"micrornas are abundant in animal genomes and have been predicted to have important roles in a broad range of gene expression programmes. despite this prominence, there is a dearth of functional knowledge regarding individual mammalian micrornas. using a loss-of-function allele in mice, we report here that the myeloid-specific microrna-223 (mir-223) negatively regulates progenitor proliferation and granulocyte differentiation and activation. mir-223 (also called mirn223) mutant mice have an expanded granulocytic compartment resulting from a cell-autonomous increase in the number of granulocyte progenitors. we show that mef2c, a transcription factor that promotes myeloid progenitor proliferation, is a target of mir-223, and that genetic ablation of mef2c suppresses progenitor expansion and corrects the neutrophilic phenotype in mir-223 null mice. in addition, granulocytes lacking mir-223 are hypermature, hypersensitive to activating stimuli and display increased fungicidal activity. as a consequence of this neutrophil hyperactivity, mir-223 mutant mice spontaneously develop inflammatory lung pathology and exhibit exaggerated tissue destruction after endotoxin challenge. our data support a model in which mir-223 acts as a fine-tuner of granulocyte production and the inflammatory response.",1
"micrornas have been suggested to modulate a variety of cellular events. here we report that mir-24 regulates erythroid differentiation by influencing the expression of human activin type i receptor alk4 (halk4). ectopic expression of mir-24 reduces the mrna and protein levels of halk4 by targeting the 3'-untranslated region of halk4 mrna and interferes with activin-induced smad2 phosphorylation and reporter expression. furthermore, mir-24 represses the activin-mediated accumulation of hemoglobin, an erythroid differentiation marker, in erythroleukemic k562 cells and decreases erythroid colony-forming and burst-forming units of cd34+ hematopoietic progenitor cells. alk4 expression is inversely correlated with mir-24 expression during the early stages of erythroid differentiation, and the forced expression of mir-24 leads to a delay of activin-induced maturation of hematopoietic progenitor cells in liquid culture. thus, our findings define a regulation mode of mir-24 on erythropoiesis by impeding alk4 expression.",1
"the rox1 and rox2 rnas have been suggested to be components of the dosage compensation machinery in drosophila. we show that both rox rnas colocalize with the male-specific lethal proteins at hundreds of specific bands along the male x chromosome. the rox rnas and msl proteins also colocalize with the x chromosome in all somatic cells and are expressed in the same temporal pattern throughout development. genetic analysis shows that the functions of the rox genes are redundant and required for the association of the msl proteins with the male x chromosome. these data provide compelling evidence for a direct function of the rox rnas in dosage compensation.",1
"ribosomal rnas contain a number of modified nucleotides. the most abundant nucleotide modifications found within rrnas fall into two types: 2'-o-ribose methylations and pseudouridylations. in eukaryotes, small nucleolar guide rnas, the snornas that are the rna components of the snornps, specify the position of these modifications. the 2'-o-ribose methylations and pseudouridylations are guided by the box c/d and box h/aca snornas, respectively. the role of these modifications in rrna remains poorly understood as no clear phenotype has yet been assigned to the absence of specific 2'-o-ribose methylations or pseudouridylations. only very recently, a slight translation defect and perturbation of polysome profiles was reported in yeast for the absence of the psi at position 2919 within the lsu rrna. here we report the identification and characterization in yeast of a novel intronic h/aca snorna that we called snr191 and that guides pseudouridylation at positions 2258 and 2260 in the lsu rrna. most interestingly, these two modified bases are the most conserved pseudouridines from bacteria to human in rrna. the corresponding human snorna is hu19. we show here that, in yeast, the presence of this snorna, and hence, most likely, of the conserved pseudouridines it specifies, is not essential for viability but provides a growth advantage to the cell.",1
"cardiac remodeling caused by acute myocardial infarction (ami) represents a major challenge for heart failure research. mir-155 has been identified as a key mediator of cardiac inflammation and hypertrophy. in this study, we investigate the role of mir-155 in cardiac remodeling induced by ami. we demonstrate that mir-155 expressed in cardiac fibroblasts is a potent contributor to cardiac remodeling. we reveal that in vivo, mir-155 knockout improves left ventricular function, reduces infarct size, and attenuates collagen deposition, whereas overexpression of mir-155 produces the opposite effects. mir-155 knockout also inhibits cardiac fibroblast proliferation and differentiation into myofibroblasts. in addition, downregulation of tumor protein p53-inducible nuclear protein 1 (tp53inp1) by small interfering rna reverses the effects of mir-155 knockout on cardiac fibroblasts. our data reveal that knockout of mir-155 in cardiac fibroblasts improves cardiac remodeling by targeting tp53inp1, which may be a novel treatment strategy for cardiac remodeling.",1
"vertebrate genomes contain major (>99.5%) and minor (<0.5%) introns that are spliced by the major and minor spliceosomes, respectively. major intron splicing follows the exon-definition model, whereby major spliceosome components first assemble across exons. however, since most genes with minor introns predominately consist of major introns, formation of exon-definition complexes in these genes would require interaction between the major and minor spliceosomes. here, we report that minor spliceosome protein u11-59k binds to the major spliceosome u2af complex, thereby supporting a model in which the minor spliceosome interacts with the major spliceosome across an exon to regulate the splicing of minor introns. inhibition of minor spliceosome snrnas and u11-59k disrupted exon-bridging interactions, leading to exon skipping by the major spliceosome. the resulting aberrant isoforms contained a premature stop codon, yet were not subjected to nonsense-mediated decay, but rather bound to polysomes. importantly, we detected elevated levels of these alternatively spliced transcripts in individuals with minor spliceosome-related diseases such as roifman syndrome, lowry-wood syndrome and early-onset cerebellar ataxia. in all, we report that the minor spliceosome informs splicing by the major spliceosome through exon-definition interactions and show that minor spliceosome inhibition results in aberrant alternative splicing in disease.",1
"a diverse catalog of long noncoding rnas (lncrnas), which lack protein-coding potential, are transcribed from the mammalian genome. they are emerging as important regulators in gene expression networks by controlling nuclear architecture and transcription in the nucleus and by modulating mrna stability, translation and post-translational modifications in the cytoplasm. in this review, we highlight recent progress in cellular functions of lncrnas at the molecular level in mammalian cells.",1
"rna components have been identified in preparations of rnase p from a number of eucaryotic sources, but final proof that these rnas are true rnase p subunits has been elusive because the eucaryotic rnas, unlike the procaryotic rnase p ribozymes, have not been shown to have catalytic activity in the absence of protein. we previously identified such an rna component in saccharomyces cerevisiae nuclear rnase p preparations and have now characterized the corresponding, chromosomal gene, called rpr1 (rnase p ribonucleoprotein 1). gene disruption experiments showed rpr1 to be single copy and essential. characterization of the gene region located rpr1 600 bp downstream of the ura3 coding region on chromosome v. we have sequenced 400 bp upstream and 550 bp downstream of the region encoding the major 369-nucleotide rpr1 rna. the presence of less abundant, potential precursor rnas with an extra 84 nucleotides of 5' leader and up to 30 nucleotides of 3' trailing sequences suggests that the primary rpr1 transcript is subjected to multiple processing steps to obtain the 369-nucleotide form. complementation of rpr1-disrupted haploids with one variant of rpr1 gave a slow-growth and temperature-sensitive phenotype. this strain accumulates trna precursors that lack the 5' end maturation performed by rnase p, providing direct evidence that rpr1 rna is an essential component of this enzyme.",1
"neuroendocrine neoplasms (nens) represent relatively rare tumors. the lack of diagnostic, therapeutic method and prognostic factors makes them a challenge to us. we retrospectively reviewed the data of 205 nens patients among which 157 cases were followed-up. proprotein convertase subtilisin/kexin 9 (pcsk9), a regulator of low density lipoprotein cholesterol (ldl-c), was confirmed as a target gene of microrna-224. we found an increased incidence of nens from 2012 to 2015. women were usually diagnosed at earlier stages than men (p < 0.05). tumor grading was associated with primary tumor site, especially esophagus and cardia nens all at g3 (p <0.001). age, tumor grading and ldl-c levels were independent risk factors of digestive nens. low ldl-c level was significantly correlated with survival rate and median overall survival (os, p < 0.05). microrna-224 agomir and pcsk9 sirna could promote apoptosis and suppress proliferation, invasion of bon-1 cells (p < 0.05), but increase the level of glucocorticoid (gc, p < 0.05). taken together, age, tumor grading and ldl-c level are independent risk factors of nens. the mir-224/pcsk9/gc axis binds to tumorigenesis and prognosis of pancreatic nens (p-nens).",1
"estrogen receptor beta1 (erbeta1) downregulation occurs in many breast cancers, but the responsible molecular mechanisms remain unclear. here, we report that levels of erbeta1 expression are negatively regulated by the microrna mir-92. expression analysis in a cohort of primary breast tumors confirmed a significant negative correlation between mir-92 and both erbeta1 mrna and protein. inhibition of mir-92 in mcf-7 cells increased erbeta1 expression in a dose-dependent manner, whereas mir-92 overexpression led to erbeta1 downregulation. reporter constructs containing candidate mir-92 binding sites in the 3'-untranslated region (utr) of erbeta1 suggested by bioinformatics analysis confirmed that mir-92 downregulated erbeta1 via direct targeting of its 3'-utr. our results define a potentially important mechanism for downregulation of erbeta1 expression in breast cancer.",1
"previously, we reported that a novel subpopulation of young mesenchymal stem cells (ymscs) existed in old bone marrow, which possessed high antiaging properties as well as excellent efficacy for cardiac repair. micrornas (mirnas) have emerged as key regulators in post-transcriptional gene expression programs, and however, it is unknown whether mirnas directly control stem cell senescence. here we present the first evidence that mir-195 overexpressed in old mscs (omscs) induces stem cell senescence deteriorating their regenerative ability by directly deactivating telomerase reverse transcriptase (tert), and abrogation of mir-195 can reverse stem cell aging. mirnas profiling analysis in ymscs and omscs by microarray showed that mir-140, mir-146a/b, and mir-195 were significantly upregulated in omscs, which led us to hypothesize that these are age-induced mirnas involved in stem cell senescence. of these mirnas, we found mir-195 directly targeted 3'-untranslated region of tert gene by computational target prediction analysis and luciferase assay, and knockdown of mir-195 significantly increased tert expression in omscs. strikingly, mir-195 inhibition significantly induced telomere relengthening in omscs along with reduced expression of senescence-associated β-galactosidase. moreover, silencing mir-195 in omscs by transfection of mir-195 inhibitor significantly restored antiaging factors expression including tert and sirt1 as well as phosphorylation of akt and foxo1. notably, abrogation of mir-195 markedly restored proliferative abilities in omscs. transplantation of omscs with knocked out mir-195 reduced infarction size and improved lv function. in conclusion, rejuvenation of aged stem cells by mir-195 inhibition would be a promising autologous therapeutic strategy for cardiac repair in the elderly patients.",1
"interleukin 17 (il-17)-producing t helper cells (t(h)-17 cells) are increasingly recognized as key participants in various autoimmune diseases, including multiple sclerosis. although sets of transcription factors and cytokines are known to regulate t(h)-17 differentiation, the role of noncoding rna is poorly understood. here we identify a t(h)-17 cell-associated microrna, mir-326, whose expression was highly correlated with disease severity in patients with multiple sclerosis and mice with experimental autoimmune encephalomyelitis (eae). in vivo silencing of mir-326 resulted in fewer t(h)-17 cells and mild eae, and its overexpression led to more t(h)-17 cells and severe eae. we also found that mir-326 promoted t(h)-17 differentiation by targeting ets-1, a negative regulator of t(h)-17 differentiation. our data show a critical role for microrna in t(h)-17 differentiation and the pathogenesis of multiple sclerosis.",1
"micrornas (mirnas) play an important role in the development, differentiation, proliferation, survival, and oncogenesis of cells and organisms including nervous system. however, the role of mirnas in primary neurons of dorsal root ganglion (drg) after injury was not clear. in this study, a mirna microarray analysis was performed, and a total of 21 mirnas were found to be down-regulated following unilateral sciatic nerve transection. the mir-144, mir-145, and mir-214 were further validated using quantitative reverse transcriptase pcr (qrt-pcr). moreover, in situ hybridization (ish) experiments using locked nucleic acid (lna)-modified dna oligonucleotide probes verified that mir-144, mir-145, and mir-214 were expressed in primary neurons of drg and down-regulated following sciatic nerve transection. predictions of potential mirna targets involved were identified by performing a bioinformatics analysis. these predictions were tested using mirna luciferase reporter vectors, with robo2 and srgap2 evaluated as the potential targets of mir-145 and mir-214, respectively. the role of mir-145 in cultured primary neurons was also investigated, and the result found that mir-145 mir-145 inhibited neurite growth and down-regulated robo2 expression. finding from this study suggested that mirnas of drg can mediated the course of regeneration including through slit-robo-srgap signaling pathway after injury.",1
"aims impaired myocardial sarcoplasmic reticulum calcium atpase 2a (serca2a) activity is a hallmark of failing hearts, and serca2a gene therapy improves cardiac function in animals and patients with heart failure (hf). deregulation of micrornas has been demonstrated in hf pathophysiology. we studied the effects of therapeutic aav9.serca2a gene therapy on cardiac mirnome expression and focused on regulation, expression, and function of mir-1 in reverse remodelled failing hearts. methods and results we studied a chronic post-myocardial infarction hf model treated with aav9.serca2a gene therapy. heart failure resulted in a strong deregulation of the cardiac mirnome. mir-1 expression was decreased in failing hearts, but normalized in reverse remodelled hearts after aav9.serca2a gene delivery. increased akt activation in cultured cardiomyocytes led to phosphorylation of foxo3a and subsequent exclusion from the nucleus, resulting in mir-1 gene silencing. in vitro serca2a expression also rescued mir-1 in failing cardiomyocytes, whereas serca2a inhibition reduced mir-1 levels. in vivo, akt and foxo3a were highly phosphorylated in failing hearts, but reversed to normal by aav9.serca2a, leading to cardiac mir-1 restoration. likewise, enhanced sodium-calcium exchanger 1 (ncx1) expression during hf was normalized by serca2a gene therapy. validation experiments identified ncx1 as a novel functional mir-1 target. conclusion serca2a gene therapy of failing hearts restores mir-1 expression by an akt/foxo3a-dependent pathway, which is associated with normalized ncx1 expression and improved cardiac function.",1
"purpose the aim of the study was to test the hypotheses that injury stimulates the expression of mir-205, which in turn inhibits kcnj10 channels by targeting its 3' utr, thereby facilitating the wound-healing process in human corneal epithelial cells (hcecs). methods a stem-loop qrt-pcr was used to examine the mir-205 expression. brdu cell proliferation assay and wound scratch assay were applied to measure the effect of mir-205 mimic or antagomer in hcecs. the patch-clamp technique, dual luciferase reporter assay, and western blot analysis were employed to test whether mir-205 regulates kcnj10, one of the target genes of mir-205. both of the primary human and mouse corneal epithelial cells (ph/mcecs) were employed to further confirm the observations obtained in hcecs. results the scratch injury in ph/mcecs increased the expression of mir-205 and decreased the expression of kcnj10 within 24 hours. the notion that mir-205 may target kcnj10 was supported by dual luciferase reporter assay showing an inhibition effect of mir-205 on 3' utr of kcnj10. application of mir-205 antagomer significantly delayed the regrowth in wounded hcecs. however, inhibition of kcnj10 partially abolished the effect from mir-205 antagomer and restored the healing process. moreover, overexpression mir-205 antagomer enhanced the protein expression of kcnj10 but not kcnj16. in addition, patch-clamp demonstrated that inhibition of endogenous mir-205 expression increased ba²⁺-sensitive inwardly rectifying k⁺ channels. in addition, an electrophysiological study of phcecs showed the presence of kcnj10-like 20 ps k⁺ channels and scratch injury significantly decreased the ba²⁺-sensitive inwardly rectifying k⁺ currents. conclusions mir-205 stimulates wound healing by inhibiting its target gene kcnj10.",1
"the evolutionarily conserved hedgehog (hh) signaling plays a critical role in embryogenesis and adult tissue homeostasis. aberrant hh signaling often leads to various forms of developmental anomalies and cancer. since altered microrna (mirna) expression is associated with developmental defects and tumorigenesis, it is not surprising that several mirnas have been found to regulate hh signaling. however, these mirnas are mainly identified through small-scale in vivo screening or in vitro assays. as mirnas preferentially reduce target gene expression via the 3' untranslated region, we analyzed the effect of reduced expression of core components of the hh signaling cascade on downstream signaling activity, and generated a transgenic drosophila toolbox of in vivo mirna sensors for core components of hh signaling, including hh , patched ( ptc ), smoothened ( smo ), costal 2 ( cos2 ), fused ( fu ), suppressor of fused ( su(fu) ), and cubitus interruptus ( ci ). with these tools in hand, we performed a genome-wide in vivo mirna overexpression screen in the developing drosophila wing imaginal disc. of the twelve mirnas identified, seven were not previously reported in the in vivo hh regulatory network. moreover, these mirnas may act as general regulators of hh signaling, as their overexpression disrupts hh signaling-mediated cyst stem cell maintenance during spermatogenesis. to identify direct targets of these newly discovered mirnas, we used the mirna sensor toolbox to show that mir-10 and mir-958 directly target fu and smo , respectively, while the other five mirnas act through yet-to-be-identified targets other than the seven core components of hh signaling described above. importantly, through loss-of-function analysis, we found that endogenous mir-10 and mir-958 target fu and smo , respectively, whereas deletion of the other five mirnas leads to altered expression of hh signaling components, suggesting that these seven newly discovered mirnas regulate hh signaling in vivo . given the powerful effects of these mirnas on hh signaling, we believe that identifying their bona fide targets of the other five mirnas will help reveal important new players in the hh regulatory network.",1
"expression of all yersinia pathogenicity factors encoded on the virulence plasmid, including the yop effector and the ysc type iii secretion genes, is controlled by the transcriptional activator lcrf in response to temperature. here, we show that a protein- and rna-dependent hierarchy of thermosensors induce lcrf synthesis at body temperature. thermally regulated transcription of lcrf is modest and mediated by the thermo-sensitive modulator ymoa, which represses transcription from a single promoter located far upstream of the yscw-lcrf operon at moderate temperatures. the transcriptional response is complemented by a second layer of temperature-control induced by a unique cis-acting rna element located within the intergenic region of the yscw-lcrf transcript. structure probing demonstrated that this region forms a secondary structure composed of two stemloops at 25°c. the second hairpin sequesters the lcrf ribosomal binding site by a stretch of four uracils. opening of this structure was favored at 37°c and permitted ribosome binding at host body temperature. our study further provides experimental evidence for the biological relevance of an rna thermometer in an animal model. following oral infections in mice, we found that two different y. pseudotuberculosis patient isolates expressing a stabilized thermometer variant were strongly reduced in their ability to disseminate into the peyer's patches, liver and spleen and have fully lost their lethality. intriguingly, yersinia strains with a destabilized version of the thermosensor were attenuated or exhibited a similar, but not a higher mortality. this illustrates that the rna thermometer is the decisive control element providing just the appropriate amounts of lcrf protein for optimal infection efficiency.",1
"our recent studies of microrna (mirna) expression signatures demonstrated that microrna-1291 (mir-1291) was significantly downregulated in renal cell carcinoma (rcc) clinical specimens and was a putative tumor-suppressive mirna in rcc. the aim of the present study was to investigate the functional significance of mir-1291 in cancer cells and to identify novel mir-1291-mediated cancer pathways and target genes in rcc. expression of mir-1291 was significantly downregulated in rcc tissues compared with adjacent non-cancerous tissues. restoration of mature mir-1291 in rcc cell lines (a498 and 786-o) revealed significant inhibition of cell proliferation, migration and invasion, suggesting that mir-1291 functioned as a tumor suppressor. to identify mir-1291-mediated molecular pathways and targets, we used gene expression analysis (expression of rcc clinical specimens and mir-1291-transfected a498 cells) and in silico database analysis. our data demonstrated that 79 signaling pathways were significantly regulated by tumor-suppressive mir-1291 in rcc cells. moreover, solute career family 2 member 1 (slc2a1) was a candidate target of mir-1291 regulation. the slc2a1 gene provides instructions for producing glucose transporter protein type 1 (glut1). luciferase reporter assays showed that mir-1291 directly regulated slc2a1/glut1. in rcc clinical specimens, the expression of slc2a1/glut1 mrna was significantly higher in cancer tissues than in non-cancerous tissues. a significant inverse correlation was recognized between slc2a1/glut1 and mir-1291 expression (r = -0.55, p < 0.0001). loss of tumor-suppressive mir-1291 enhanced rcc cell proliferation, migration and invasion through targeting slc2a1/glut1. the identification of novel tumor-suppressive mir-1291-mediated molecular pathways and targets has provided new insights into rcc oncogenesis and metastasis.",1
"long noncoding rnas (lncrnas) have been implicated in numerous cellular processes including brain development. however, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. here, we leveraged a cohort of 13 lncrnanull mutant mouse models to investigate the spatiotemporal expression of lncrnas in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncrna loci. we show that several lncrnas are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. we further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncrna loci. finally, we found that 4 of the 13 lncrnas significantly affect the expression of several neighboring proteincoding genes in a cis-like manner. by providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncrna locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease.",1
"the microrna-371-373 (mir-371-373) cluster is specifically expressed in human embryonic stem cells (escs) and is thought to be involved in stem cell maintenance. recently, micrornas (mirnas) of this cluster were shown to be frequently upregulated in several human tumors. however, the regulatory mechanism for the involvement of the mir-371-373 cluster in human escs or cancer cells remains unclear. in this study, we explored the relationship between this mirna cluster and the wnt/β-catenin-signaling pathway, which has been shown to be involved in both stem cell maintenance and tumorigenesis. we show that mir-371-373 expression is induced by lithium chloride and is positively correlated with wnt/β-catenin-signaling activity in several human cancer cell lines. mechanistically, three tcf/lef1-binding elements (tbes) were identified in the promoter region and shown to be required for wnt-dependent activation of mir-371-373. interestingly, we also found that mir-372&373, in turn, activate wnt/β-catenin signaling. in addition, four protein genes related to the wnt/β-catenin-signaling pathway were identified as direct targets of mir-372&373, including dickkopf-1 (dkk1), a well-known inhibitor of wnt/β-catenin signaling. using a lentiviral system, we showed that overexpression of mir-372 or mir-373 promotes cell growth and the invasive activity of tumor cells as knockdown of dkk1. taken together, our study demonstrates a novel β-catenin/lef1-mir-372&373-dkk1 regulatory feedback loop, which may have a critical role in regulating the activity of wnt/β-catenin signaling in human cancer cells.",1
"metastatic disease remains the primary cause of death for individuals with t cell acute lymphoblastic leukemia (t-all). micrornas (mirnas) play important roles in the pathogenesis of t-all by inhibiting gene expression at posttranscriptional levels. the goal of the current project is to identify any significant mirnas in t-all metastasis. we observed mir-146b-5p to be downregulated in t-all patients and cell lines, and bioinformatics analysis implicated mir-146b-5p in the hematopoietic system. mir-146b-5p inhibited the migration and invasion in t-all cells. interleukin-17a (il-17a) was predicted to be a target of mir-146b-5p; this was confirmed by luciferase assays. interestingly, t-all patients and cell lines secreted il-17a and expressed the il-17a receptor (il-17ra). il-17a/il-17ra interactions promoted strong t-all cell migration and invasion responses. gene set enrichment analysis (gsea) and quantitative polymerase chain reaction (qpcr) analysis indicated that matrix metallopeptidase-9 (mmp9), was a potential downstream effector of il-17a activation, and nuclear factor kappa-light-chain-enhancer of activated b cells (nf-κb) signaling was also implicated in this process. moreover, il-17a activation promoted t-all cell metastasis to the liver in il17a -/- mouse models. these results indicate that reduced mir-146b-5p expression in t-all may lead to the upregulation of il-17a, which then promotes t-all cell migration and invasion by upregulating mmp9 via nf-κb signaling.",1
"background micrornas (mirnas) are well recognized as gene regulators and have been implicated in the regulation of development as well as human diseases. mir-143 is located at a fragile site on chromosome 5 frequently deleted in cancer, and has been reported to be down-regulated in several cancers including colon cancer. methods to gain insight into the role of mir-143 in colon cancer, we used a microarray-based approach in combination with seed site enrichment analysis to identify mir-143 targets. results as expected, transcripts down-regulated upon mir-143 overexpression had a significant enrichment of mir-143 seed sites in their 3'utrs. here we report the identification of hexokinase 2 (hk2) as a direct target of mir-143. we show that re-introduction of mir-143 in the colon cancer cell line dld-1 results in a decreased lactate secretion. conclusion we have identified and validated hk2 as a mir-143 target. furthermore, our results indicate that mir-143 mediated down-regulation of hk2 affects glucose metabolism in colon cancer cells. we hypothesize that loss of mir-143-mediated repression of hk2 can promote glucose metabolism in cancer cells, contributing to the shift towards aerobic glycolysis observed in many tumors.",1
"accumulation of il-17-producing th17 cells is associated with the development of multiple autoimmune diseases; however, the contribution of microrna (mirna) pathways to the intrinsic control of th17 development remains unclear. here, we demonstrated that mir-21 expression is elevated in th17 cells and that mice lacking mir-21 have a defect in th17 differentiation and are resistant to experimental autoimmune encephalomyelitis (eae). furthermore, we determined that mir-21 promotes th17 differentiation by targeting and depleting smad-7, a negative regulator of tgf-β signaling. moreover, the decreases in th17 differentiation in mir-21-deficient t cells were associated with defects in smad-2/3 activation and il-2 suppression. finally, we found that treatment of wt mice with an anti-mir-21 oligonucleotide reduced the clinical severity of eae, which was associated with a decrease in th17 cells. thus, we have characterized a t cell-intrinsic mirna pathway that enhances tgf-β signaling, limits the autocrine inhibitory effects of il-2, and thereby promotes th17 differentiation and autoimmunity.",1
"most eukaryotic mrnas are translated by a ""scanning ribosome"" mechanism. we have found that unlike the type member of the genus tobamovirus, translation of the 3'-proximal coat protein (cp) gene of a crucifer infecting tobamovirus (crtmv) (dorokhov et al., 1993; 1994) occurred in vitro by an internal ribosome entry mechanism. three types of synthetic dicistronic rna transcripts were constructed and translated in vitro: (i) ""mp-cp-3'ntr"" transcripts contained movement protein (mp) gene, cp gene and the 3'-nontranslated region of crtmv rna. these constructs were structurally equivalent to dicistronic subgenomic rnas produced by tobamoviruses in vivo. (ii) ""deltanpt-cp"" transcripts contained partially truncated neomycin phosphotransferase i gene and cp gene. (iii) ""cp-gus"" transcripts contained the first cp gene and the gene of escherichia coli beta-glucuronidase (gus) at the 3'-proximal position. the results indicated that the 148-nt region upstream of the cp gene of crtmv rna contained an internal ribosome entry site (ires(cp)) promoting internal initiation of translation in vitro. dicistronic ires(cp), containing chimeric mrnas with the 5'-terminal stem-loop structure preventing translation of the first gene (mp, deltanpt, or cp), expressed the cp or gus genes despite their 3'-proximal localization. the capacity of crtmv ires(cp) for mediating internal translation distinguishes this cp tobamovirus from the well-known-type member of the genus, tmv ui. the equivalent 148-nt sequence from tmv rna was incapable of mediating internal translation. two mutants were used to study structural elements of ires(cp). it was concluded that integrity of ires(cp) was essential for internal initiation. the crtmv provides a new example of internal initiation of translation, which is markedly distinct from iress shown for picornaviruses and other viral and eukaryotic mrnas.",1
"genes for three novel snrnas of saccharomyces cerevisiae have been isolated, sequenced and tested for essentiality. the rnas encoded by these genes are designated snr34, snr35 and snr36 respectively and contain 203, 204 and 182 nucleotides. each rna is derived from a single copy gene and all three rnas are believed to be nucleolar, i.e. snornas, based on extraction properties and association with fibrillarin. snr34 and snr35 contain a trimethylguanosine cap, but this feature is absent from snr36. the novel rnas lack elements conserved among several other snornas, including box c, box d and long sequence complementarities with rrna. genetic disruption analyses showed each of the rnas to be dispensable and a haploid strain lacking all three rnas and a previously characterized fourth snorna (snr33) is also viable. no differences in the levels of precursors or mature rrnas were apparent in the four gene knock-out strain. possible roles for the new rnas in ribosome biogenesis are discussed.",1
"micrornas (mirnas) play a key role in the regulation of almost all the physiological and pathological processes, including bone metabolism. recent studies have suggested that mir-27 might play a key role in osteoblast differentiation and bone formation. increasing evidence indicates that the canonical wnt signaling pathway contributes to different stages of bone formation. in this study, we identify mir-27a can promote osteoblast differentiation by repressing a new target, secreted frizzled-related proteins 1 (sfrp1) expression at the transcriptional level. here, 21 candidate targets of mir-27a involved in canonical wnt/β-catenin signaling were predicted, and a significant decrease in sfrp1 luciferase activity was observed both in 293t and mg63 cells co-transfected with the matched luciferase reporter constructs and mir-27a mimic. furthermore, the presence of exogenous mir-27a significantly decreased sfrp1 mrna and protein expression in hfob1.19 cells during both proliferation and osteogenic differentiation. the over-expression of mir-27a or knockdown sfrp1 significantly increased the percentage of apoptotic hfobs, the percentage of cells in the g2-m phase of the cell cycle and the expression of key osteoblastic markers, including alp, spp1, runx2 and alp activity. over-expression of mir-27a or knockdown of endogenous sfrp1 led to an accumulation of β-catenin in hfobs. in the present study, we demonstrate that mir-27a induced gene silencing effect is a vital mechanism contributing to bone metabolism in hfob cells in vitro, which is partly affected by the post-transcriptional regulation of sfrp1, during osteoblast proliferation, apoptosis and differentiation.",1
"recent studies have identified a class of small non-coding rna molecules, named microrna (mirna), that is dysregulated in malignant brain glioblastoma. substantial data have indicated that mirna-16 (mir-16) plays a significant role in tumors of various origins. this mirna has been linked to various aspects of carcinogenesis, including cell apoptosis and migration. however, the molecular functions of mir-16 in gliomagenesis are largely unknown. we have shown that the expression of mir-16 in human brain glioma tissues was lower than in non-cancerous brain tissues, and that the expression of mir-16 decreased with increasing degrees of malignancy. our data suggest that the expression of mir-16 and nuclear factor (nf)-κb1 was negatively correlated with glioma levels. microrna-16 decreased glioma malignancy by downregulating nf-κb1 and mmp9, and led to suppressed invasiveness of human glioma cell lines shg44, u87, and u373. our results also indicated that upregulation of mir-16 promoted apoptosis by suppressing bcl2 expression. finally, the upregulation of mir-16 in a nude mice model of human glioma resulted in significant suppression of glioma growth and invasiveness. taken together, our experiments have validated the important role of mir-16 as a tumor suppressor gene in glioma growth and invasiveness, and revealed a novel mechanism of mir-16-mediated regulation in glioma growth and invasiveness through inhibition of bcl2 and the nf-κb1/mmp-9 signaling pathway. therefore, our experiments suggest the possible future use of mir-16 as a therapeutic target in gliomas.",1
"pancreatic ductal adenocarcinoma (pdac), which accounts for 96% of all pancreatic cancer cases, is characterized by rapid progression, invasion and metastasis. transforming growth factor-beta (tgf-β) signaling is an essential pathway in metastatic progression and micrornas (mirna) play central roles in the regulation of various biological and pathologic processes including cancer metastasis. however, the molecular mechanisms involved in regulation of mirnas and activation of tgf-β signaling in pdac remain to be established. the results of this study suggested that mir-323-3p expression in pdac tissues and cell lines was significantly decreased compared to levels in normal pancreatic tissues and primary cultured pancreatic duct epithelial cells. further investigation revealed that mir-323-3p directly targeted and suppressed smad2 and smad3, both key components in tgf-β signaling. lower levels of mir-323-3p predicted poorer prognosis in patients with pdac. ectopic overexpression of mir-323-3p significantly inhibited, while silencing of mir-323-3p increased the migration and invasion abilities of pdac cells in vitro. moreover, using an in vivo mouse model, we demonstrated that overexpressing of mir-323-3p significantly reduced, while knockdown of mir-323-3p enhanced lung metastatic colonization of panc-1 cells. furthermore, mir-323-3p-induced tgf-b signaling inhibition and cell motility suppression were partially rescued by overexpressing of smad2 and smad3 in pdac cells. our findings suggest that re-expression of mir-323-3p might offer a novel therapeutic target against metastasis in patients with pdac.",1
"micrornas (mirnas) have been shown to play critical roles in regulating the progress of leukemia. we performed mirna expression profile in six chinese patients with chronic lymphocytic leukemia (cll), and in peripheral b cells from pooled 30 healthy donors, using a platform containing 866 human mirnas. the most frequent changes in mirnas in cll cells included downregulation of mir-126, mir-572, mir-494, mir-923, mir-638, mir-130a, mir-181a and mir-181b and up-regulation of mir-29a, mir-660, mir-20a, mir-106b, mir-142-5p, mir-101, mir-30b, mir-34a, mir-let-7f, mir-21 and mir-155. among the mirnas down-regulated in cll cells, we showed that mir-181a/b expression levels were significantly lower in poor prognostic subgroups defined by unmutated immunoglobulin heavy chain variable status and p53 aberrations. furthermore, under-expression of mir-181a and mir-181b was associated with shorter overall survival and treatment-free survival in cll patients. we further evaluated fludarabine-induced apoptosis after transfection of primary cll cells from 40 patients with mir-15a, mir-16-1, mir-34a, mir-181a and mir-181b mimics. transfection of mir-34a, mir-181a and mir-181b mimics into cll cells from p53 wild-type patients led to significant increase in apoptosis compared with mirna control. however, enforced expression of these mirnas had no effect on b-cll cells from p53-attenuated patients. we further demonstrated that mir-181a and mir-181b inhibiting bcl-2, mcl-1 and x-linked inhibitor of apoptosis protein by direct binding to 3'utr. thus, these results suggest that mir-181a/b may play important roles in the pathogenesis of cll and may provide a possible therapeutic avenue and a sensitive indicator of the activity of the p53 axis in cll.",1
"aberrant expression of micrornas has been implicated in many cancers. we recently demonstrated differential expression of several micrornas in medulloblastoma. in this study, the regulation and function of microrna 218 (mir-218), which is significantly underexpressed in medulloblastoma, was evaluated. re-expression of mir-218 resulted in a significant decrease in medulloblastoma cell growth, cell colony formation, cell migration, invasion, and tumor sphere size. we used c17.2 neural stem cells as a model to show that increased mir-218 expression results in increased cell differentiation and also decreased malignant transformation when transfected with the oncogene rest. these results suggest that mir-218 acts as a tumor suppressor in medulloblastoma. micrornas function by down-regulating translation of target mrnas. targets are determined by imperfect base pairing of the microrna to the 3'-utr of the mrna. to comprehensively identify actual mir-218 targets, medulloblastoma cells overexpressing mir-218 and control cells were subjected to high throughput sequencing of rna isolated by cross-linking immunoprecipitation, a technique that identifies the mrnas bound to the rna-induced silencing complex component protein argonaute 2. high throughput sequencing of mrnas identified 618 genes as targets of mir-218 and included both previously validated targets and many targets not predicted computationally. additional work further confirmed cdk6, rictor, and ctsb (cathepsin b) as targets of mir-218 and examined the functional role of one of these targets, cdk6, in medulloblastoma.",1
"introduction non-small-cell lung cancer (nsclc) accounts for more than half of all lung cancer cases. cytokines play an important role in nsclc, including il-27. il-27 inhibits nsclc progression; however, the mechanism is not clear. the purpose of this study is to investigate the effects of il-27 on nsclc cell proliferation and metastasis. materials and methods nsclc cells were treated with il-27 or transfected with mir-935, and the cell proliferation was assayed by cell counting kit-8 (cck-8) and colony formation. cell metastasis was analyzed by transwell chamber system and wound healing assay. il-27 protein in the medium was analyzed by elisa. il-27 mrna expression was measured by quantitative reverse transcriptase-pcr. results we found that il-27 played an inhibiting role in nsclc cell proliferation and metastasis. the molecular mechanism of the suppressing role of il-27 in nsclc was regulated by mir-935. il-27 expression was negatively associated with mir-935 in the clinical nsclc samples. conclusion the study revealed that il-27 decreased lung cancer cell proliferation and metastasis via mir-935.",1
"identification of protein targets for micrornas (mirnas) is a significant challenge due to the complexity of mirna-mediated regulation. we have previously demonstrated that mir-193b targets estrogen receptor-α (erα) and inhibits estrogen-induced growth of breast cancer cells. here, we applied a high-throughput strategy using quantitative itraq (isobaric tag for relative and absolute quantitation) reagents to identify other target proteins regulated by mir-193b in breast cancer cells. itraq analysis of pre-mir-193b transfected mcf-7 cells resulted in identification of 743 unique proteins, of which 39 were down-regulated and 44 up-regulated as compared with negative control transfected cells. computationally predicted targets of mir-193b were highly enriched (sevenfold) among the proteins whose level of expression decreased after mir-193b transfection. only a minority of these (13%) showed similar effect at the mrna level illustrating the importance of post-transcriptional regulation. the most significantly repressed proteins were selected for validation experiments. these data confirmed 14-3-3ζ (ywhaz), serine hydroxyl transferase (shmt2), and aldo-keto reductase family 1, member c2 (akr1c2) as direct, previously uncharacterized, targets of mir-193b. functional rnai assays demonstrated that specific combinations of knockdowns of these target genes by sirnas inhibited growth of mcf-7 cells, mimicking the effects of the mir-193b overexpression. interestingly, the data imply that besides targeting erα, the mir-193b effects include suppression of the local production of estrogens and other steroid hormones mediated by the akr1c2 gene, thus provoking two separate molecular mechanisms inhibiting steroid-dependent growth of breast cancer cells. in conclusion, we present here a proteomic screen to identify targets of mir-193b, and a systems biological approach to mimic its effects at the level of cellular phenotypes. this led to the identification of multiple genes whose combinatorial knock-down likely mediates the strong anti-cancer effects observed for mir-193b in breast cancer cells.",1
"rationale endothelial microrna-126 (mir-126) modulates vascular development and angiogenesis. however, its role in the regulation of smooth muscle cell (smc) function is unknown. objective to elucidate the role of mir-126 secreted by endothelial cells (ecs) in regulating smc turnover in vitro and in vivo, as well as the effects of shear stress on the regulation. methods and results coculture of smcs with ecs or treatment of smcs with conditioned media from static ec monoculture (ec-cm) increased smc mir-126 level and smc turnover; these effects were abolished by inhibition of endothelial mir-126 and by the application of laminar shear stress to ecs. smc mir-126 did not increase when treated with ec-cm from ecs subjected to inhibition of mir biogenesis, or with cm from sheared ecs. depletion of extracellular/secreted vesicles in ec-cm did not affect the increase of smc mir-126 by ec-cm. biotinylated mir-126 or flag (dykddddk epitope)-tagged argonaute2 transfected into ecs was detected in the cocultured or ec-cm-treated smcs, indicating a direct ec-to-smc transmission of mir-126 and argonaute2. endothelial mir-126 represses forkhead box o3, b-cell lymphoma 2, and insulin receptor substrate 1 mrnas in the cocultured smcs, suggesting the functional roles of the transmitted mir-126. systemic depletion of mir-126 in mice inhibited neointimal lesion formation of carotid arteries induced by cessation of blood flow. administration of ec-cm or mir-126 mitigated the inhibitory effect. conclusions endothelial mir-126 acts as a key intercellular mediator to increase smc turnover, and its release is reduced by atheroprotective laminar shear stress.",1
"background junctional adhesion molecule (jam)-a expressed in endothelial, epithelial, and blood cells can regulate permeability and leukocyte extravasation. atherosclerosis develops at sites of disturbed flow in large arteries, but the mechanisms guiding inflammatory cells into these predilection sites remain unknown. methods and results to characterize cell-specific functions of jam-a in atherosclerosis, we used apolipoprotein e-deficient mice with a somatic or endothelium-specific deficiency in jam-a and bone marrow chimeras with jam-a-deficient leukocytes. we show that impaired jam-a expression in endothelial cells reduced mononuclear cell recruitment into the arterial wall and limited atherosclerotic lesion formation in hyperlipidemic mice. in contrast, jam-a deficiency in bone marrow cells impeded monocyte de-adhesion, thereby increasing vascular permeability and lesion formation, whereas somatic jam-a deletion revealed no significant effects. regions with disturbed flow displayed a focal enrichment and luminal redistribution of endothelial jam-a and were preferentially protected by its deficiency. the functional expression and redistribution of endothelial jam-a was increased by oxidized low-density lipoprotein, but confined by atheroprotective laminar flow through an upregulation of microrna (mir)-145, which repressed jam-a. conclusions our data identify endothelial jam-a as an important effector molecule integrating atherogenic conditions to direct inflammatory cell entry at predilection sites of atherosclerosis.",1
"human adenocarcinomas commonly harbor mutations in the kras and myc proto-oncogenes and the tp53 tumor suppressor gene. all three genetic lesions are potentially pro-angiogenic, as they sustain production of vascular endothelial growth factor (vegf). yet kras-transformed mouse colonocytes lacking p53 formed indolent, poorly vascularized tumors, whereas additional transduction with a myc-encoding retrovirus promoted vigorous vascularization and growth. in addition, vegf levels were unaffected by myc, but enhanced neovascularization correlated with downregulation of anti-angiogenic thrombospondin-1 (tsp1) and related proteins, such as connective tissue growth factor (ctgf). both tsp1 and ctgf are predicted targets for repression by the mir-17-92 microrna cluster, which was upregulated in colonocytes coexpressing k-ras and c-myc. indeed, mir-17-92 knockdown with antisense 2'-o-methyl oligoribonucleotides partly restored tsp1 and ctgf expression; in addition, transduction of ras-only cells with a mir-17-92-encoding retrovirus reduced tsp1 and ctgf levels. notably, mir-17-92-transduced cells formed larger, better-perfused tumors. these findings establish a role for micrornas in non-cell-autonomous myc-induced tumor phenotypes.",1
"we previously reported the identification of the kis2 common retrovirus integration site, located on mouse chromosome x, in radiation leukemia virus-induced t-cell leukemias. tumors with a provirus at the kis2 locus overexpressed a novel noncoding rna (ncrna) with a complex splicing pattern and no polya tail. database upgrade revealed the presence of a microrna (mirna) cluster, mir-106-363, just downstream of the kis2 ncrnas. we found that kis2 ncrnas are the pri-mirna of mir-106-363, and we present evidence that kis2 ncrna overexpression in mouse tumors results in mir-106a, mir-19b-2, mir-92-2, and mir-20b accumulation. we show the oncogenic potential of those mirnas in anchorage independence assay and confirm pri-mir-106-363 overexpression in 46% of human t-cell leukemias tested. this overexpression contributes in rising mir-92 and mir-19 levels, as this is the case for mir-17-92 cluster overexpression. furthermore, we identified myosin regulatory light chain-interacting protein, retinoblastoma-binding protein 1-like, and possibly homeodomain-interacting protein kinase 3 as target genes of this mirna cluster, which establishes a link between these genes and t-cell leukemia for the first time.",1
"mir-137 is a highly conserved brain-enriched microrna (mirna) that has been associated with neuronal function and proliferation. here, we show that drosophila mir-137 null mutants display increased body weight with enhanced triglyceride content and decreased locomotor activity. in addition, when challenged by nutrient deprivation, mir-137 mutants exhibit reduced motivation to feed and prolonged survival. we show through genetic epistasis and rescue experiments that this starvation resistance is due to a disruption in insulin signaling. our studies further show that mir-137 null mutants exhibit a drastic reduction in levels of the phosphorylated/activated insulin receptor, inr (inr-p). we investigated if this is due to the predicted mir-137 target, protein tyrosine phosphatase 61f (ptp61f), ortholog of mammalian tc-ptp/ptp1b, which are known to dephosphorylate inr-p. indeed, levels of an endogenously tagged gfp-ptp61f are significantly elevated in mir-137 null mutants, and we show that overexpression of ptp61f alone is sufficient to mimic many of the metabolic phenotypes of mir-137 mutants. finally, we knocked-down elevated levels of ptp61f in the mir-137 null mutant background and show that this rescues levels of inr-p, restores normal body weight and triglyceride content, starvation sensitivity, as well as attenuates locomotor and starvation-induced feeding defects. our study supports a model in which mir-137 is critical for dampening levels of ptp61f, thereby maintaining normal insulin signaling and energy homeostasis.",1
"in response to nitrogen deficiency, some cyanobacteria develop heterocysts, a terminally differentiated cell type, specialized for the fixation of atmospheric nitrogen. in nostocales, this differentiation process is controlled by two major regulators, ntca and hetr, but additional unknown factors are likely to be involved as well. in the context of a genome-wide search for potential non-coding rnas, we identified an array of 12 tandem repeats that is transcribed in large amounts when cells enter conditions that trigger cell differentiation and switch to nitrogen fixation. the main accumulating transcript, which we suggest designating nitrogen stress-induced rna 1 (nsir1), has properties similar to regulatory non-coding rnas. in anabaena sp. pcc 7120, it is about 60 nt in length, has a very distinct predicted secondary structure, and is expressed very early and transiently after nitrogen step-down. moreover, its expression requires hetr and ntca and is restricted to cells that are differentiating into heterocysts, clearly placing nsir1 within the regulon that controls the switch to nitrogen fixation and heterocyst formation. the genomic arrangement of nsir1, located upstream of hetf, a gene whose product is involved in heterocyst formation, is conserved in all five nostocales whose genomes are completely sequenced. additionally, we detected nsir1 expression in 19 different heterocyst-forming cyanobacteria. our data suggest that every repeat is a complete transcriptional unit furnished with a cell-type-specific promoter and a rho-independent terminator, which gives rise to a very high nsir1 transcript level. nsir1 is the first known bacterial non-coding rna that is specifically upregulated in response to nitrogen step-down.",1
"background previously, using mirna microarray, we have found that mir-29c is significantly downregulated in advanced gastric carcinoma. in the present study, we investigated whether mir-29c functions as a tumor-suppressor mirna in gastric carcinoma cells. for this purpose, we verified the downregulation of mir-29c in gastric carcinoma tissues, and assessed the biological effect of mir-29c on gastric carcinoma cells. results in mir-29c-transfected cells, both proliferation and colony formation ability on soft agar were significantly decreased. although apoptosis was not induced, brdu incorporation and the proportion of cells positive for phospho-histone h3 (s10) were significantly decreased in mir-29c-transfected cells, indicating that mir-29c may be involved in the regulation of cell proliferation. to explain the mechanism of growth suppression by mir-29c, we explored differentially expressed genes (>2-fold) in mir-29c-transfected cells in comparison with negative control transfected cells using microarray. rcc2, ppic and cdk6 were commonly downregulated in mir-29c-transfected mkn45, mkn7 and mkn74 cells, and all of the genes harbored mir-29c target sequences in the 3'-utr of their mrna. rcc2 and ppic were actually upregulated in gastric carcinoma tissues, and therefore both were identified as possible targets of mir-29c in gastric carcinoma. to ascertain whether downregulation of rcc2 and/or ppic is involved in the growth suppression by mir-29c, we transfected sirnas against rcc2 and ppic into mkn45 and determined cell viability, the rate of brdu incorporation, and caspase activity. we found that rcc2-knockdown decreased both cell viability and brdu incorporation without any increase of caspase activity, while ppic-knockdown did not, indicating that downregulation of rcc2 may be at least partly responsible for the growth suppression by mir-29c. conclusions our findings indicate that mir-29c may have tumor-suppressive functions in gastric carcinoma cells, and that its decreased expression may confer a growth advantage on tumor cells via aberrant expression of rcc2.",1
"chemotherapy resistance frequently drives tumour progression. however, the underlying molecular mechanisms are poorly characterized. in this study, we explored mir-137's role in the chemosensitivity of lung cancer. we found that the expression level of mir-137 is down-regulated in the human lung cancer tissues and the resistant cells strains: a549/paclitaxel(a549/ptx) and a549/cisplatin (a549/cddp) when compared with lung cancer a549 cells. moreover, we found that overe-expression of mir-137 inhibited cell proliferation, migration, cell survival and arrest the cell cycle in g1 phase in a549/ptx and a549/cddp. furthermore, repression of mir-137 significantly promoted cell growth, migration, cell survival and cell cycle g1/s transition in a549 cells. we further demonstrated that the tumor suppressive role of mir-137 was mediated by negatively regulating nuclear casein kinase and cyclin-dependent kinase substrate1(nucks1) protein expression. importantly, mir-137 inhibits a549/ptx, a549/cddp growth and angiogenesis in vivo. our study is the first to identify the tumor suppressive role of over-expressed mir-137 in chemosensitivity. identification of a novel mirna-mediated pathway that regulates chemosensitivity in lung cancer will facilitate the development of novel therapeutic strategies in the future.",1
"micrornas (mirnas) are short non-coding rnas that have been implicated in fine-tuning gene regulation, although the precise roles of many are still unknown. pancreatic development is characterized by the complex sequential expression of a gamut of transcription factors. we have performed mirna expression profiling at two key stages of mouse embryonic pancreas development, e14.5 and e18.5. mir-124a2 expression was strikingly increased at e18.5 compared with e14.5, suggesting a possible role in differentiated beta-cells. among the potential mir-124a gene targets identified by biocomputation, foxa2 is known to play a role in beta-cell differentiation. to evaluate the impact of mir-124a2 on gene expression, we overexpressed or down-regulated mir-124a2 in min6 beta-cells. as predicted, mir-124a2 regulated foxa2 gene expression, and that of its downstream target, pancreatic duodenum homeobox-1 (pdx-1). foxa2 has been described as a master regulator of pancreatic development and also of genes involved in glucose metabolism and insulin secretion, including the atp-sensitive k(+) (k(atp)) channel subunits, kir6.2 and sur-1. correspondingly, mir-124a2 overexpression decreased, and anti-mir-124a2 increased kir6.2 and sur-1 mrna levels. moreover, mir-124a2 modified basal and glucose- or kcl-stimulated intracellular free ca(2+) concentrations in single min6 and ins-1 (832/13) beta-cells, without affecting the secretion of insulin or co-transfected human growth hormone, consistent with an altered sensitivity of the beta-cell exocytotic machinery to ca(2+). in conclusion, whereas the precise role of microrna-124a2 in pancreatic development remains to be deciphered, we identify it as a regulator of a key transcriptional protein network in beta-cells responsible for modulating intracellular signaling.",1
"strand-selection is the final step of microrna biogenesis in which functional mature mirnas are generated from one or both arms of precursor. the preference of strand-selection is diverse during development and tissue formation, however, its pathological effect is still unknown. here we find that two mirna arms from the same precursor, mir-574-5p and mir-574-3p, are inversely expressed and play exactly opposite roles in gastric cancer progression. higher-5p with lower-3p expression pattern is significantly correlated with higher tnm stages and poor prognosis of gastric cancer patients. the increase of mir-574-5p/-3p ratio, named mir-574 arm-imbalance is partially due to the dynamic expression of their highly complementary targets in gastric carcinogenesis, moreover, the arm-imbalance of mir-574 is in turn involved and further promotes gastric cancer progression. our results indicate that mir-574 arm-imbalance contribute to gastric cancer progression and re-modification of the mir-574-targets homeostasis may represent a promising strategy for gastric cancer therapy.",1
"consumption of the long-chain ω-3 (n-3) polyunsaturated fatty acid docosahexaenoic acid (dha) is associated with a reduced risk of cardiovascular disease and greater chemoprevention. however, the mechanisms underlying the biologic effects of dha remain unknown. it is well known that micrornas (mirnas) are versatile regulators of gene expression. therefore, we aimed to determine if the beneficial effects of dha may be modulated in part through mirnas. loss of dicer 1 ribonuclease type iii (dicer) in enterocyte caco-2 cells supplemented with dha suggested that several lipid metabolism genes are modulated by mirnas. analysis of mirnas predicted to target these genes revealed several mirna candidates that are differentially modulated by fatty acids. among the mirnas modulated by dha were mir-192 and mir-30c. overexpression of either mir-192 or mir-30c in enterocyte and hepatocyte cells suggested an effect on the expression of genes related to lipid metabolism, some of which were confirmed by endogenous inhibition of these mirnas. our results show in enterocytes that dha exerts its biologic effect in part by regulating genes involved in lipid metabolism and cancer. moreover, this response is mediated through mirna activity. we validate novel targets of mir-30c and mir-192 related to lipid metabolism and cancer including nuclear receptor corepressor 2, isocitrate dehydrogenase 1, dicer, caveolin 1, atp-binding cassette subfamily g (white) member 4, retinoic acid receptor β, and others. we also present evidence that in enterocytes dha modulates the expression of regulatory factor x6 through these mirnas. alteration of mirna levels by dietary components in support of their pharmacologic modulation might be valuable in adjunct therapy for dyslipidemia and other related diseases.",1
"microrna (mir)-150 has been reported to be dramatically downregulated in human epithelial ovarian cancer (eoc) tissues and patients' serum compared to normal controls. this study aimed to investigate clinical significance and molecular mechanisms of mir-150 in eoc. in the current study, quantitative real-time pcr analysis showed that mir-150 was significantly downregulated in human eoc tissues compared to normal tissue samples. then, we demonstrated the significant associations of mir-150 downregulation with aggressive clinicopathological features of eoc patients, including high clinical stage and pathological grade, and shorter overall and progression-free survivals. more importantly, the multivariate analysis identified mir-150 expression as an independent prognostic biomarker in eoc. after that, luciferase reporter assays demonstrated that zinc finger e-box binding homeobox 1 (zeb1), a crucial regulator of epithelial-to-mesenchymal transition (emt), was a direct target of mir-150 in eoc cells. moreover, we found that the ectopic expression of mir-150 could efficiently inhibit cell proliferation, invasion and metastasis by suppressing the expression of zeb1. furthermore, we also observed a significantly negative correlation between mir-150 and zeb1 mrna expression in eoc tissues (rs = -0.45, p<0.001). in conclusion, these findings offer the convincing evidence that aberrant expression of mir-150 may play a role in tumor progression and prognosis in patients with eoc. moreover, our data reveal that mir-150 may function as a tumor suppressor and modulate eoc cell proliferation, and invasion by directly and negatively regulating zeb1, implying the re-expression of mir-150 might be a potential therapeutic strategy for eoc.",1
"a search for general regulators of cancer metastasis has yielded a set of micrornas for which expression is specifically lost as human breast cancer cells develop metastatic potential. here we show that restoring the expression of these micrornas in malignant cells suppresses lung and bone metastasis by human cancer cells in vivo. of these micrornas, mir-126 restoration reduces overall tumour growth and proliferation, whereas mir-335 inhibits metastatic cell invasion. mir-335 regulates a set of genes whose collective expression in a large cohort of human tumours is associated with risk of distal metastasis. mir-335 suppresses metastasis and migration through targeting of the progenitor cell transcription factor sox4 and extracellular matrix component tenascin c. expression of mir-126 and mir-335 is lost in the majority of primary breast tumours from patients who relapse, and the loss of expression of either microrna is associated with poor distal metastasis-free survival. mir-335 and mir-126 are thus identified as metastasis suppressor micrornas in human breast cancer.",1
"in salmonella typhimurium, different conformations of the pyrc and pyrd leader transcripts are produced as a result of nucleotide sensitive selection of the transcriptional start site. the ctp-initiated transcripts, synthesized at high intracellular ctp/gtp pool ratios (repressing conditions), have the potential of forming a stable secondary structure at the 5' end, thereby sequestering the site for translational initiation. at low ctp/gtp pool ratios (derepressing conditions), transcription starts 2-3 bp further downstream, resulting in transcripts with limited potential for stem-loop formation and therefore open for translational initiation. the conformation of the leader regions of wild type pyrc and pyrd mrna has been investigated by chemical and enzymatic probing of rna isolated from cultures grown in repressing and derepressing conditions. as controls and to obtain further information on the relation between the leader rna conformation and the regulatory mechanism, the probing experiments also included pyrc and pyrd mrna from mutants that contain a base substitution at a position that destabilizes the putative hairpin. in accordance with predictions based on the nucleotide sequence, the results showed that the 5' end of pyrc and pyrd leader mrna isolated from repressed cultures is folded into a secondary structure, whereas it is largely unstructured in mrna isolated from derepressed cultures.",1
"tumor initiation and growth depend on its microenvironment in which cancer-associated fibroblasts (cafs) in tumor stroma play an important role. prostaglandin e2 (pge2) and interleukin (il)-6 signal pathways are involved in the crosstalk between tumor and stromal cells. however, how pge2-mediated signaling modulates this crosstalk remains unclear. here, we show that microrna (mir)-149 links pge2 and il-6 signaling in mediating the crosstalk between tumor cells and cafs in gastric cancer (gc). mir-149 inhibited fibroblast activation by targeting il-6 and mir-149 expression was substantially suppressed in the cafs of gc. mir-149 negatively regulated cafs and their effect on gc development both in vitro and in vivo. cafs enhanced epithelial-to-mesenchymal transition (emt) and the stem-like properties of gc cells in a mir-149-il-6-dependent manner. in addition to il-6, pge2 receptor 2 (ptger2/ep2) was revealed as another potential target of mir-149 in fibroblasts. furthermore, h. pylori infection, a leading cause of human gc, was able to induce cyclooxygenase-2 (cox-2)/pge2 signaling and to enhance pge2 production, resulting in the hypermethylation of mir-149 in cafs and increased il-6 secretion. our findings indicate that mir-149 mediates the crosstalk between tumor cells and cafs in gc and highlight the potential of interfering mirnas in stromal cells to improve cancer therapy.",1
"micrornas (mirnas) are short (∼22 nucleotides) regulatory rnas that can modulate gene expression and are aberrantly expressed in many diseases including cancer. previous studies have shown that mirnas inhibit the translation and facilitate the degradation of their targeted messenger rnas (mrnas) making them attractive candidates for use in cancer therapy. however, the potential clinical utility of mirnas in cancer therapy rests heavily upon our ability to understand and accurately predict the consequences of fluctuations in levels of mirnas within the context of complex tumor cells. to evaluate the predictive power of current models, levels of mirnas and their targeted mrnas were measured in laser captured micro-dissected (lcm) ovarian cancer epithelial cells (cepi) and compared with levels present in ovarian surface epithelial cells (ose). we found that the predicted inverse correlation between changes in levels of mirnas and levels of their mrna targets held for only ∼11% of predicted target mrnas. we demonstrate that this low inverse correlation between changes in levels of mirnas and their target mrnas in vivo is not merely an artifact of inaccurate mirna target predictions but the likely consequence of indirect cellular processes that modulate the regulatory effects of mirnas in vivo. our findings underscore the complexities of mirna-mediated regulation in vivo and the necessity of understanding the basis of these complexities in cancer cells before the therapeutic potential of mirnas can be fully realized.",1
"the untranslated leader of the dimeric hiv-1 rna genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the hiv-1 genome using a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and uv-crosslinking experiments. we used a recently developed rna folding algorithm (pfold) to predict the common secondary structure of an alignment of 20 divergent hiv-1 sequences. combining this analysis with biochemical data, we present a secondary structure model for the entire 744 nucleotide fragment, which incorporates previously recognized and novel structural elements. in particular, our data provided strong evidence for a long-distance interaction between the region encompassing the aug gag initiation codon and an upstream region and we demonstrate that this feature is highly conserved in distantly related human and animal retroviruses. to obtain information about tertiary interactions we applied an intramolecular uv-crosslinking strategy and identified a novel tertiary interaction within the pbs hairpin structure.",1
"gastric cancer (gc) is one of the most common malignant tumors worldwide. emerging evidence has shown that abnormal micrornas (mirnas) expression is involved in tumorigenesis. mir-329 was previously reported to act as a tumor suppressor or oncogene in some types of cancer. however, its function in gastric cancer (gc) is unclear. here, we found that mir-329 was down-regulated in gc compared with adjacent controls. enforced expression of mir-329 inhibited proliferation, migration and invasion of gastric cancer cells in vitro. we identified t lymphoma invasion and metastasis 1 (tiam1) gene as potential target of mir-329. mir-329 levels inversely correlated with tiam1 expression in gc. importantly, tiam1 rescued the mir-329-mediated inhibition of cell invasion and proliferation. finally, reintroduction of mir-329 significantly inhibited tumor formation of gc in the xenograft mice. our findings suggest that mir-329 is a tumor suppressor and potential therapeutic target of gc.",1
"large-scale cancer genomics projects are profiling hundreds of tumors at multiple molecular layers, including copy number, mrna and mirna expression, but the mechanistic relationships between these layers are often excluded from computational models. we developed a supervised learning framework for integrating molecular profiles with regulatory sequence information to reveal regulatory programs in cancer, including mirna-mediated regulation. we applied our approach to 320 glioblastoma profiles and identified key mirnas and transcription factors as common or subtype-specific drivers of expression changes. we confirmed that predicted gene expression signatures for proneural subtype regulators were consistent with in vivo expression changes in a pdgf-driven mouse model. we tested two predicted proneural drivers, mir-124 and mir-132, both underexpressed in proneural tumors, by overexpression in neurospheres and observed a partial reversal of corresponding tumor expression changes. computationally dissecting the role of mirnas in cancer may ultimately lead to small rna therapeutics tailored to subtype or individual.",1
"recently, a new regulatory circuitry has been identified in which rnas can crosstalk with each other by competing for shared micrornas. such competing endogenous rnas (cernas) regulate the distribution of mirna molecules on their targets and thereby impose an additional level of post-transcriptional regulation. here we identify a muscle-specific long noncoding rna, linc-md1, which governs the time of muscle differentiation by acting as a cerna in mouse and human myoblasts. downregulation or overexpression of linc-md1 correlate with retardation or anticipation of the muscle differentiation program, respectively. we show that linc-md1 ""sponges"" mir-133 and mir-133 to regulate the expression of maml1 and mef2c, transcription factors that activate muscle-specific gene expression. finally, we demonstrate that linc-md1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in duchenne muscle cells. we conclude that the cerna network plays an important role in muscle differentiation.",1
"long non-coding rnas (lncrnas) have been recently recognized as a major class of regulators in mammalian systems. lncrnas function by diverse and heterogeneous mechanisms in gene regulation, and are key contributors to development, neurological disorders, and cancer. this emerging importance of lncrnas, along with recent reports of a functional lncrna encoded by the mouse dlx5-dlx6 locus, led us to interrogate the biological significance of another distal-less antisense lncrna, the previously uncharacterized dlx1 antisense (dlx1as) transcript. we have functionally ablated this antisense rna via a highly customized gene targeting approach in vivo. mice devoid of dlx1as rna are viable and fertile, and display a mild skeletal and neurological phenotype reminiscent of a dlx1 gain-of function phenotype, suggesting a role for this non-coding antisense rna in modulating dlx1 transcript levels and stability. the reciprocal relationship between dlx1as and dlx1 places this sense-antisense pair into a growing class of mammalian lncrna-mrna pairs characterized by inverse regulation.",1
"background phenotypic switching of vascular smooth muscle cells from a contractile to a synthetic state is implicated in diverse vascular pathologies, including atherogenesis, plaque stabilization, and neointimal hyperplasia. however, very little is known about the role of long noncoding rna (lncrna) during this process. here, we investigated a role for lncrnas in vascular smooth muscle cell biology and pathology. methods and results using rna sequencing, we identified >300 lncrnas whose expression was altered in human saphenous vein vascular smooth muscle cells following stimulation with interleukin-1α and platelet-derived growth factor. we focused on a novel lncrna (ensembl: rp11-94a24.1), which we termed smooth muscle-induced lncrna enhances replication (smilr). following stimulation, smilr expression was increased in both the nucleus and cytoplasm, and was detected in conditioned media. furthermore, knockdown of smilr markedly reduced cell proliferation. mechanistically, we noted that expression of genes proximal to smilr was also altered by interleukin-1α/platelet-derived growth factor treatment, and has2 expression was reduced by smilr knockdown. in human samples, we observed increased expression of smilr in unstable atherosclerotic plaques and detected increased levels in plasma from patients with high plasma c-reactive protein. conclusions these results identify smilr as a driver of vascular smooth muscle cell proliferation and suggest that modulation of smilr may be a novel therapeutic strategy to reduce vascular pathologies.",1
"background increasing evidence has shown that micrornas function as oncogenes or tumor suppressors in human malignancies, but the roles of microrna (mir)-497 in human cervical cancer still remain unclear. our aim was to analyze the clinicopathologic and prognostic significance of mir-497 in human cervical cancer and to investigate the effects of mir-497 on the malignant phenotype of cervical cancer cells. methods first, we detected mir-497 expression in the hpv-16-immortalized cervical epithelial cell lines and 4 other cervical cancer cell lines (hela, caski, siha, and hela-s3). then the expression of mir-497 was analyzed in cervical cancer tissues and paired nontumor tissues, and its correlation with clinicopathologic features and survival was analyzed. finally, the roles of mir-497 in regulation of tumor proliferation, apoptosis, migration, invasion, and target gene expression were further investigated. results mir-497 was downregulated in cervical cancer cells or tissues compared with hpv-16-immortalized cervical epithelial cell lines or the paired nontumor tissues. also, the decrease in mir-497 correlated closely with the criteria of the international federation of gynaecology and obstetrics stage and lymph node metastases in patients with cervical cancer. multivariate cox analysis showed that low mir-497 expression appeared to be an unfavorable prognostic factor. transient forced expression of mir-497 decreased the growth and colony-formation capacity of hela and siha cells by inducing caspase-3-dependent apoptosis. forced expression of mir-497 suppressed the migration and invasiveness of cervical cancer cells. by computational mirna target prediction and functional analysis, mir-497 was demonstrated to bind to the 3' untranslated regions of igf-1r mrna, and upregulation of mir-497 downregulated igf-1r protein expression. further investigation showed that small interfering rna-mediated igf-1r knockdown could mimic the effect of enforced mir-497 expression on the malignant phenotypes of cervical cancer cells. conclusion mir-497 may be a potential prognostic marker and functions as a tumor suppressor in human cervical cancer by post-transcriptionally targeting igf-1r.",1
"stem-cell-based therapy for cardiovascular disease, especially ischemic heart disease (ihd), is a promising approach to facilitating neovascularization through the migration of stem cells to the ischemic site and their subsequent differentiation into endothelial cells (ecs). hypoxia is a chief feature of ihd and the stem cell niche. however, whether hypoxia promotes stem cell differentiation into ecs or causes them to retain their stemness is controversial. here, the differentiation of pluripotent stem cells (ipscs) into endothelial cells (ecs) was induced under hypoxia. though the angiogenic capability and angiogenesis-related autocrine/paracrine factors of the ecs were improved under hypoxia, the level of hypoxia inducible factor 1α (hif-1α) was nonetheless found to be restricted along with the ec differentiation. the down-regulation of hif-1α was found to have been caused by vegf-induced microrna-155 (mir-155). moreover, mir-155 was also found to enhance the angiogenic capability of induced ecs by targeting e2f2 transcription factor. hence, mir-155 not only contributes to controlling hif-1α expression under hypoxia but also promotes angiogenesis, which is a key feature of mature ecs. revealing the real role of hypoxia and clarifying the function of mir-155 in ec differentiation may facilitate improvement of angiogenic gene- and stem-cell-based therapies for ischemic heart disease.",1
"mdv1-mir-m4 is one of 25 micrornas (mirnas) expressed by marek's disease virus (mdv-1), an oncogenic alphaherpesvirus that induces fatal t-cell lymphoma in chickens. mdv1-mir-m4 was shown to be the second functional viral ortholog of mir-155, a cellular mirna that plays a crucial role in several physiological and pathological processes in lymphocyte biology. in this study, we investigated a panel of putative mdv1-mir-m4 targets involved in gene networks affecting both cellular and viral life cycles. using luciferase reporter assays, we showed that mdv1-mir-m4-5p and mir-155 efficiently targeted a common set of 3' untranslated regions (3'utr) of six cellular genes (gpm6b, rreb1, c-myb, map3k7ip2, pu.1 and c/ebp). in addition, we also investigated the interactions between mdv1-mir-m4-5p and mdv1-mir-m43p and viral mrnas encoding ul28 and ul32 in both reporter and western blot assays. mdv1-mir-m4 specifically inhibited the translation of these two viral proteins, which are involved in the cleavage/packaging of herpesvirus dna.",1
"thermodynamically predicted secondary structure analysis of the 3'-terminal 305 nucleotides (nt) of the rubella virus (rub) genome, a region conserved in all rub defective interfering rnas, revealed four stem-loop (sl) structures; sl1 and sl2 are both located in the e1 coding region, while sl3 and sl4 are within the 59-nt 3' untranslated region (utr) preceding the poly(a) tract. sl2 is a structure shown to interact with human calreticulin (cal), an autoantigen potentially involved in rub rna replication and pathogenesis. rnase mapping indicated that sl2 and sl3 are in equilibrium between two conformations, in the second of which the previously proposed cal binding site in sl2, a u-u bulge, is not formed. site-directed mutagenesis of the 3' utr with a rub infectious clone, robo302, revealed that most of the 3' utr is required for viral viability except for the 3'-terminal 5 nt and the poly(a) tract, although poly(a) was rapidly regenerated during subsequent replication. maintenance of the overall sl3 structure, the 11-nt single-stranded sequence between sl3 and sl4, and the sequences forming sl4 were all important for viral viability. studies on the interaction between host factors and the 3' utr showed the formation of three rna-protein complexes by gel mobility shift assay, and uv-induced cross-linking detected six host protein species, with molecular masses of 120, 80, 66, 55, 48, and 36 kda, interacting with the 3' utr. site-directed mutagenesis of sl2 by nucleotide substitutions showed that maintenance of sl2 stem rather than the u-u bulge was critical in cal binding since mutants having the u-u bulge base paired had a similar binding activity for cal as the native structure whereas mutants having the sl2 stem destabilized had much lower binding activity. however, all of these mutations gave rise to viable viruses when introduced into robo302, indicating that binding of cal to sl2 is independent of viral viability.",1
"background recent studies have identified critical roles for micrornas (mirnas) in a variety of cellular processes, including regulation of cardiomyocyte death. however, the signature of mirna expression and possible roles of mirna in the ischemic heart have been less well studied. methods and results we performed mirna arrays to detect the expression pattern of mirnas in murine hearts subjected to ischemia/reperfusion (i/r) in vivo and ex vivo. surprisingly, we found that only mir-320 expression was significantly decreased in the hearts on i/r in vivo and ex vivo. this was further confirmed by taqman real-time polymerase chain reaction. gain-of-function and loss-of-function approaches were employed in cultured adult rat cardiomyocytes to investigate the functional roles of mir-320. overexpression of mir-320 enhanced cardiomyocyte death and apoptosis, whereas knockdown was cytoprotective, on simulated i/r. furthermore, transgenic mice with cardiac-specific overexpression of mir-320 revealed an increased extent of apoptosis and infarction size in the hearts on i/r in vivo and ex vivo relative to the wild-type controls. conversely, in vivo treatment with antagomir-320 reduced infarction size relative to the administration of mutant antagomir-320 and saline controls. using targetscan software and proteomic analysis, we identified heat-shock protein 20 (hsp20), a known cardioprotective protein, as an important candidate target for mir-320. this was validated experimentally by utilizing a luciferase/gfp reporter activity assay and examining the expression of hsp20 on mir-320 overexpression and knockdown in cardiomyocytes. conclusions our data demonstrate that mir-320 is involved in the regulation of i/r-induced cardiac injury and dysfunction via antithetical regulation of hsp20. thus, mir-320 may constitute a new therapeutic target for ischemic heart diseases.",1
"skin stem cells (scs) are specified and rapidly expanded to fuel body growth during early development. however, the molecular mechanisms that govern the amplification of skin scs remain unclear. here we report an essential role for mir-205, one of the most highly expressed micrornas in skin scs, in promoting neonatal expansion of these cells. unlike most mammalian mirnas, genetic deletion of mir-205 causes neonatal lethality with severely compromised epidermal and hair follicle growth. in the mir-205 knockout skin scs, phospho-akt is significantly downregulated, and the scs prematurely exit the cell cycle. in the hair follicle, this accelerates the transition of the neonatal scs towards quiescence. we identify multiple mir-205-targeted negative regulators of pi(3)k signalling that mediate the repression of phospho-akt and restrict the proliferation of scs. our findings reveal an essential role for mir-205 in maintaining the expansion of skin scs by antagonizing negative regulators of pi(3)k signalling.",1
"purpose bladder cancer is one of the world's top ten malignant tumors. the crucial role of microrna in carcinogenesis has been well emphasized. considering mirna expression was tumor stage-, tissue-, or even development-specific, more experimental evidences about the functions of mirnas in bladder cancer should be discovered to advance applying of mirna in the diagnosis or therapy of cancer. methods mir-708 level in bladder carcinoma and adjacent noncancerous tissues was tested by real-time qpcr. cell apoptosis was analyzed by using flow cytometry. the tumorigenicity of bladder carcinoma cells was evaluated in nude mice model. luciferase reporter gene assays were performed to identify the interaction between mir-708 and 3'utr of caspase-2 mrna. the protein level of caspase-2 was determined by western blotting. results in this study, we reported that mir-708 was frequently dysregulated in human bladder carcinoma tissues compared to normal tissues. in addition, we found that silencing of mir-708 could promote the t24 and 5637 cells to apoptosis and inhibit the bladder tumor growth in vivo. also, caspase-2 was proved to be one of direct targets of mir-708 in t24 and 5637 cells. further results showed that caspase-2 was involved in the mir-708 regulated cell apoptosis. conclusions all together, these results suggest mir-708 may act as an oncogene and induce the carcinogenicity of bladder cancer by down-regulating caspase-2 level.",1
"wnt signaling pathways are a highly conserved pathway, which plays an important role from the embryonic development to bone formation. the effect of wnt pathway on osteogenesis relies on their cellular environment and the expression of target genes. however, the molecular mechanism of that remains unclear. on the basis of the preliminary results, we observed the contrary effect of canonical wnt signaling on osteogenic differentiation of periodontal ligament stem cells (pdlscs) in the different culture environment. furthermore, we found that the expression level of mir-17 was also varied with the change in the culture environment. therefore, we hypothesized that mir-17 and canonical wnt signaling may have potential interactions, particularly the inner regulation relationship in different microenvironments. in this paper, we observed that canonical wnt signaling promoted osteogenesis of pdlscs in the fully culture medium, while inhibited it in the osteogenic differentiation medium. interestingly, alteration in the expression level of endogenous mir-17 could partially reverse the different effect of canonical wnt signaling. furthermore, the role of mir-17 was because of its target gene tcf3 (transcription factor 3), a key transcription factor of canonical wnt pathway. overexpression of tcf3 attenuated the effect of mir-17 on modulating canonical wnt signaling. finally, we elucidated that tcf3 enhanced osteogenesis both in vitro and in vivo. in brief, the different level of mir-17 was the main cause of the different effect of canonical wnt signaling, and tcf3 was the crucial node of mir-17-canonial wnt signaling regulation loop. this understanding of micrornas regulating signaling pathways in different microenvironments may pave the way for fine-tuning the process of osteogenesis in bone-related disorders.",1
"background reprogramming energy metabolism has been an emerging hallmark of cancer cells. micrornas play important roles in glucose metabolism. methods the targets of microrna-26a (mir-26a) were predicted by bioinformatics tools. the efficacy of mir-26a binding the 3'-untranslated region (utr) of pyruvate dehydrogenase protein x component (pdhx) mrna was evaluated using a dual-luciferase reporter assay. the pdhx expression at the mrna and protein level in several colon cancer cell lines was quantified with real-time pcr and western blot analysis respectively. the effects of mir-26a on glucose metabolism were determined by detecting the content of glucose consumption, production of lactate, pyruvate, and acetyl-coenzyme a. results the expression of mir-26a is inversely associated with the level of its targeting protein pdhx in several colon cancer cell lines with different malignancy potentials. mir-26a inhibits pdhx expression by direct targeting the 3'-utr of pdhx mrna. the glucose consumption and lactate concentration were both greatly increased in colon cancer cells than the normal colon mucosal epithelia under physiological conditions. the overexpression of mir-26a in hct116 cells efficiently improved the accumulation of pyruvate and decreased the production of acetyl coenzyme a. meanwhile the inhibition of mir-26a expression induced inverse biological effects. conclusions mir-26a regulates glucose metabolism of colorectal cancer cells by direct targeting the pdhx, which inhibits the conversion of pyruvate to acetyl coenzyme a in the citric acid cycle.",1
"objective the atp-binding cassette transporter a1 (abca1) is a major regulator of macrophage cholesterol efflux and protects cells from excess intracellular cholesterol accumulation; however, the mechanism involved in posttranscriptional regulation of abca1 is poorly understood. we previously showed that microrna-33 (mir-33) is 1 regulator. here, we investigated the potential contribution of other micrornas (mirnas) to posttranscriptional regulation of abca1 and macrophage cholesterol efflux. methods and results we performed a bioinformatic analysis for identifying mirna target prediction sites in abca1 gene and an unbiased genome-wide screen to identify mirnas modulated by cholesterol excess in mouse peritoneal macrophages. quantitative real-time reverse transcription-polymerase chain reaction confirmed that mir-758 is repressed in cholesterol-loaded macrophages. under physiological conditions, high dietary fat excess in mice repressed mir-758 both in peritoneal macrophages and, to a lesser extent, in the liver. in mouse and human cells in vitro, mir-758 repressed the expression of abca1, and conversely, the inhibition of this mirna by using anti-mir-758 increased abca1 expression. in mouse cells, mir-758 reduced cellular cholesterol efflux to apolipoprotein a1 (apoa1), and anti-mir-758 increased it. mir-758 directly targets the 3'-untranslated region of abca1 as assessed by 3'-untranslated region luciferase reporter assays. interestingly, mir-758 is highly expressed in the brain, where it also targets several genes involved in neurological functions, including slc38a1, ntm, epha7, and mytl1. conclusion we identified mir-758 as a novel mirna that posttranscriptionally controls abca1 levels in different cells and regulates macrophage cellular cholesterol efflux to apoa1, opening new avenues to increase apoa1 and raise high-density lipoprotein levels.",1
"endothelial progenitor cells (epcs) participate in angiogenesis by differentiating into endothelial cells (ecs) and may be developed to treat ischemia/reperfusion injury. micrornas (mirs) are a type of non-coding rna that are 18-25 nucleotides in length and serve a role in angiogenesis. it has been demonstrated that mir-138 regulates hypoxia-induced ec dysfunction. however, to the best of our knowledge, the exact role of mir-138 in the regulation of hypoxia-induced epcs has not previously been reported. in the present study, data collected from an mtt assay indicated that hypoxia treatment enhanced epc proliferation, which was accompanied by an upregulation of hypoxia-inducible factor 1α (hif-1α) expression. mir-138 overexpression inhibited hypoxia-induced epc proliferation and induced cell cycle arrest at the g1 stage. a mechanistic investigation revealed that mir-138 negatively regulated hif-1α protein levels but did not affect hif-1α mrna levels in epcs. moreover, results from a dual luciferase reporter assay demonstrated that hif-1α was a direct target of mir-138 in epcs. furthermore, upregulation of mir-138 suppressed the hypoxia-induced upregulation of hif-1α. downstream factors of hif-1α were also investigated and it was observed that the upregulation of mir-138 inhibited the hypoxia-induced upregulation of vascular endothelial growth factor, as well as the activity of mitogen-activated protein kinase and akt signaling in epcs. in summary, the present study suggested that mir-138 inhibits hypoxia-induced epc proliferation, possibly by inhibiting hif-1α-mediated signaling.",1
"resident cells, such as fibroblast-like synoviocytes (fls), play a crucial role in rheumatoid arthritis (ra). they are implicated in the inflammatory response and play a key role in osteoarticular destruction. moreover, ra fls spread ra to unaffected joints. pathogen-associated molecular patterns and damage-associated molecular patterns have been found to activate ra fls by interacting with pattern recognition receptors, such as tlr. ra fls express a large number of tlr, and tlr2 was demonstrated to be involved in ra inflammation. because microrna have emerged as important controllers of tlr expression and signaling, the aim of this study was to evaluate their potential involvement in the control of tlr2 expression by ra fls. we first showed that tlr2 expression is strongly upregulated in ra fls in response to tlr2 ligands. using a microrna microarray analysis, we identified one mirna in activated ra fls, mir-19b, which was downregulated and predicted to target tlr2 mrna. downregulation of mir-19b and mir-19a, which belongs to the same cluster, was confirmed by real-time quantitative pcr. transfection of ra fls with mir-19a/b mimics decreased tlr2 protein expression. in parallel, we found that both il-6 and matrix metalloproteinase 3 secretion was significantly downregulated in activated fls transfected with either mimic. moreover, using a luciferase assay, we showed that mir-19a/b directly target tlr2 mrna. taken together, our data point toward an important role for mir-19a/b in the regulation of il-6 and matrix metalloproteinase 3 release by controlling tlr2 expression, as well as provide evidence that mir-19a/b can act as negative regulators of inflammation in humans.",1
"microrna (mirna) are important regulators of many biological processes, but the targets for most mirna are still poorly defined. in this study, we profiled the expression of mirna during myogenesis, from proliferating myoblasts through to terminally differentiated myotubes. microarray results identified six significantly differentially expressed mirna that were more than 2-fold different in myotubes. from this list, mirna-26a (mir-26a), an up-regulated mirna, was further examined. overexpression of mir-26a in murine myogenic c2c12 cells induced creatine kinase activity, an enzyme that markedly increases during myogenesis. further, myod and myogenin mrna expression levels were also up-regulated. these results suggest that increased expression of mir-26a promotes myogenesis. through a bioinformatics approach, we identified the histone methyltransferase, enhancer of zeste homolog 2 (ezh2), as a potential target of mir-26a. overexpression of mir-26a suppressed the activity of a luciferase reporter construct fused with the 3'-untranslated region of ezh2. in addition, mir-26a overexpression decreased ezh2 mrna expression. these results reveal a model of regulation during myogenesis whereby the up-regulation of mir-26a acts to post-transcriptionally repress ezh2, a known suppressor of skeletal muscle cell differentiation.",1
"the expression of micrornas is altered in various cancer types, leading to their definition as onco- and tumor-suppressor micrornas. in our study, we investigated the role of mir-335 in the formation of sporadic human breast cancer and its involvement in the regulatory network of the breast cancer susceptibility gene brca1. to validate single components of the brca1 cascade, microrna overexpression was performed in a cell culture model with subsequent protein analysis and luciferase reporter assays. here, we were able to identify mir-335 as simultaneously regulating the known brca1 activators erα, igf1r, sp1 and the repressor id4, including a feedback regulation of mir-335 expression by estrogens. overexpression of mir-335 resulted in an upregulation of brca1 mrna expression, suggesting a functional dominance of id4 signaling. the relevance of the mir-335 regulation for human breast cancer was confirmed in primary sporadic breast cancer specimens with significantly decreased mir-335 levels (p < 0.05) in comparison to normal controls. interestingly, the microrna expression level correlated positively to the brca1 transcript level, supporting the hypothesis of a mir-335-mediated regulation of the tumor suppressor gene. functionally, overexpression of mir-335 led to decreased cell viability and an increase in apoptosis, supporting its tumor-suppressive function. in summary, our data indicate that mir-335 affects different targets in the upstream brca1-regulatory cascade with impact on key cellular functions such as proliferation and apoptosis. deregulation of the microrna during breast cancer development and progression may thereby lead to an increased tumorigenic potential by inactivating crucial tumor-suppressive signals.",1
"breast cancer resistance protein (bcrp/abcg2) is a molecular determinant of pharmacokinetic properties of many drugs in humans. to understand post-transcriptional regulation of abcg2 and the role of micrornas (mirnas) in drug disposition, we found that microrna-328 (mir-328) might readily target the 3'-untranslated region (3'-utr) of abcg2 when considering target-site accessibility. we then noted 1) an inverse relation between the levels of mir-328 and abcg2 in mcf-7 and mcf-7/mx100 breast cancer cells and 2) that mir-328 levels could be rescued in mcf-7/mx100 cells by transfection with mir-328 plasmid. luciferase reporter assays showed that abcg2 3'-utr-luciferase activity was decreased more than 50% in mcf-7/mx100 cells after transfection with mir-328 plasmid, the activity was increased over 100% in mcf-7 cells transfected with a mir-328 antagomir, and disruption of mir-328 response element within abcg2 3'-utr led to a 3-fold increase in luciferase activity. furthermore, the level of abcg2 protein was down-regulated when mir-328 was over-expressed, and the level was up-regulated when mir-328 was inhibited by selective antagomir. altered abcg2 protein expression was associated with significantly declined or elevated levels of abcg2 3'-utr and coding sequence mrnas, suggesting possible involvement of the mechanism of mrna cleavage. finally, mir-328-directed down-regulation of abcg2 expression in mcf-7/mx100 cells resulted in an increased mitoxantrone sensitivity, as manifested by a significantly lower ic(50) value (2.46 +/- 1.64 microm) compared with the control (151 +/- 32 microm). together, these findings suggest that mir-328 targets abcg2 3'-utr and, consequently, controls abcg2 protein expression and influences drug disposition in human breast cancer cells.",1
"objectives mir-181a is involved in immunity, metabolism, tumor suppression or carcinogenesis reported by many other studies. however, its role in the development of chemosensitivity to adriamycin in low-invasive breast cancer cells remains unclear. the aim of this study is to define the function role of mir-181a in promoting the efficacy of adriamycin-based neoadjuvant chemotherapy. methods cell survival analysis was detected by cell counting kit-8 assay. apoptotic cells were quantitatively detected using fitc annexin v apoptosis detection kit i. bcl-2 protein expression was measured by western blot. luciferase reporter vector with the putative bcl-2 3' untranslated region (3'utr) was constructed to explore whether bcl-2 was a direct target gene of mir-181a. real-time pcr was performed to test the expression of mir-181a and bcl-2 in the selected breast cancer tissue samples. results the down-regulation of mir-181a decreased adriamycin-induced apoptosis in mcf-7 cells. transfected with mir-181a mimic in cells resulted in the decreased expression of bcl-2. the alteration of mir-181a expression did not significantly affect the chemosensitivity to adriamycin in mcf-7 and mcf-7/adr cells with genetic knockout of bcl-2. mir-181a may suppress bcl-2 expression by forming imperfect base pairing with the 3'utr of bcl-2 gene such that a negative relationship between mir-181a and bcl-2 in mcf-7 and mcf-7/adr cells is observed. conclusions at least in part, the detection of mir-181a may direct the clinical medication in patients with neoadjuvant chemotherapy because of mir-181a enhanced adriamycin-induced apoptosis via targeting bcl-2.",1
"bufalin is used to treat many patients with solid malignant tumors clinically. bufalin could induce gastric cancer cell apoptosis via bax. microrna (mirna) plays important roles in gene regulation. however, mirna involving in bufalin inducing apoptosis of gastric cancer cells remains to futher research. to study the regulatory role of mirna in bufalin induced cancer cell apoptosis. firstly, we verifed that bufalin could induce gastric cancer cell apoptosis by inducing bax expression. mir-298 was predicted as a regulator of bax and further study verified bax was a target gene of mir-298 by luciferase reporter assay. mir-298 could down-regulate bax on mrna and protein level in gastric cancer cells. mir-298 promoted cell proliferation and inhibited apoptosis of gastric cancer cells. it was also found that bufalin inhibited cell proliferation and promoted cell apoptosis by down-regualtion of mir-298. in summary, bufalin-associated mir-298 may indirectly be involved in cell proliferation and apoptosis by targeting bax, pointing to use as a potential molecular target in gastric cancer therapy.",1
"ribosomal 5s rna (5s rrna) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. it is thought to enhance protein synthesis by stabilization of a ribosome structure. this paper presents the updated database of 5s rrna and their genes (5s rdna). its short characteristics are presented in the introduction. the database contains 2280 primary structures of 5s rrna and 5s rrna genes. these include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. the database is available on line through the world wide web at",1
"the yeast u4/u6.u5 pre-mrna splicing small nuclear ribonucleoprotein (snrnp) is a 25s small nuclear ribonucleoprotein particle similar in size, composition, and morphology to its counterpart in human cells. the yeast u4/u6.u5 snrnp complex has been purified to near homogeneity by affinity chromatography and preparative glycerol gradient sedimentation. we show that there are at least 24 proteins stably associated with this particle and performed mass spectrometry microsequencing to determine their identities. in addition to the seven canonical core sm proteins, there are a set of u6 snrnp specific sm proteins, eight previously described u4/u6.u5 snrnp proteins, and four novel proteins. two of the novel proteins have likely rna binding properties, one has been implicated in the cell cycle, and one has no identifiable sequence homologues or functional motifs. the purification of the low abundance u4/u6.u5 snrnp from yeast and the powerful sequencing methodologies using small amounts of protein make possible the rapid identification of novel and previously unidentified components of large, low-abundance macromolecular machines from any genetically manipulable organism.",1
"rationale pulmonary hypertensive remodeling is characterized by excessive proliferation, migration, and proinflammatory activation of adventitial fibroblasts. in culture, fibroblasts maintain a similar activated phenotype. the mechanisms responsible for generation/maintenance of this phenotype remain unknown. objective we hypothesized that aberrant expression of microrna-124 (mir-124) regulates this activated fibroblast phenotype and sought to determine the signaling pathways through which mir-124 exerts effects. methods and results we detected significant decreases in mir-124 expression in fibroblasts isolated from calves and humans with severe pulmonary hypertension. overexpression of mir-124 by mimic transfection significantly attenuated proliferation, migration, and monocyte chemotactic protein-1 expression of hypertensive fibroblasts, whereas anti-mir-124 treatment of control fibroblasts resulted in their increased proliferation, migration, and monocyte chemotactic protein-1 expression. furthermore, the alternative splicing factor, polypyrimidine tract-binding protein 1, was shown to be a direct target of mir-124 and to be upregulated both in vivo and in vitro in bovine and human pulmonary hypertensive fibroblasts. the effects of mir-124 on fibroblast proliferation were mediated via direct binding to the 3' untranslated region of polypyrimidine tract-binding protein 1 and subsequent regulation of notch1/phosphatase and tensin homolog/foxo3/p21cip1 and p27kip1 signaling. we showed that mir-124 directly regulates monocyte chemotactic protein-1 expression in pulmonary hypertension/idiopathic pulmonary arterial hypertension fibroblasts. furthermore, we demonstrated that mir-124 expression is suppressed by histone deacetylases and that treatment of hypertensive fibroblasts with histone deacetylase inhibitors increased mir-124 expression and decreased proliferation and monocyte chemotactic protein-1 production. conclusions stable decreases in mir-124 expression contribute to an epigenetically reprogrammed, highly proliferative, migratory, and inflammatory phenotype of hypertensive pulmonary adventitial fibroblasts. thus, therapies directed at restoring mir-124 function, including histone deacetylase inhibitors, should be investigated.",1
"recently, bace1 expression was shown to be regulated by micrornas, small endogenous rna molecules that regulate protein expression through sequence-specific interaction with messenger rna. here, we showed that microrna-29c (mir-29c), a mirna that is enriched in the brain and highly expressed in the appswe/psδe9 mouse lowers bace1 protein in vitro and in transgenic mir-29c mice. in silico analysis identified two putative target sites in the bace1 mrna for the mir-29c family. we chose sh-sy5y, hek-293t cell lines and mir-29c transgenic mice for these studies to validate our hypothesis. significantly, over-expression of mir-29c in sh-sy5y, hek-293t cell lines and mir-29c transgenic mice downregulated bace1 protein levels. our findings suggest that mir-29c may be an endogenous regulator of bace1 protein expression.",1
"purpose inflammation participates centrally in all stages of atherosclerosis (as), which begins with pro-inflammatory processes and inflammatory changes in the endothelium, related to lipid metabolism. microrna (mirna) inhibition of inflammation related to sirt1 has been shown to be a promising therapeutic approach for as. however, the mechanism of action is unknown. methods we investigated whether mirnas regulate the sirt1 and its downstream srebp-lipogenesis-cholesterogenesis metabolic pathway in human umbilical vein endothelial cells (huvecs). huvecs were transfected with mir-132 mimics and inhibitors, and then treated with or without tumor necrosis factor α (tnfα). the effects of mir-132 on pro-inflammatory processes, proliferation and apoptosis were assessed. results we identified that the relative 3' utr luciferase activities of sirt1 were significantly decreased in mir-132 transfected huvecs (0.338 ± 0.036) compared to control (p = 0.000). mir-132 inhibited sirt1 expression of mrna level in huvecs (0.53 ± 0.06) (p conclusions sirt1 mrnas are direct targets of mir-132. mir-132 controls lipogenesis and cholesterogenesis in huvecs by inhibiting sirt1 and srebp-1c expression and their downstream regulated genes, including fasn and hmgcr. inhibition of sirt1 by mir-132 was associated with lipid metabolism-dependent pro-inflammatory processes in huvecs. the newly identified mirna, mir-132 represents a novel targeting mechanism for as therapy.",1
"the various roles of micrornas (mirnas) in controlling the phenotype of cancer cells are the focus of contemporary research efforts. we have recently shown that mir-17 directly targets the adar1 gene and thereby enhances melanoma cell aggressiveness. mir-17 and mir-20a belong to the mir-17/92 complex, and their mature forms are identical except for two non-seed nucleotides. nevertheless, here we show that these two mirnas carry markedly different effects on melanoma cells. a strong positive correlation was observed between the expression of mir-17 and mir-20a among various melanoma cultures. luciferase assays showed that mir-17 but not mir-20a directly targets the 3' untranslated region of the adar1 gene. ectopic expression of these mirnas in melanoma cells differentially alters the expression of five exemplar targetscan-predicted target genes: adar1, itgb8, tgfbr2, mmp2 and vegf-a. whole-genome expression microarrays confirm a markedly differential effect on the transcriptome. functionally, over-expression of mir-20a but not of mir-17 in melanoma cells inhibits net proliferation in vitro. the differential functional effect was observed following ectopic expression of the mature mirna or of the pre-mirna sequences. this suggests that the two non-seed nucleotides dictate target sequence recognition and overall functional relevance. these mirnas are clearly not redundant in melanoma cell biology.",1
"chemoresistance prevents the curative cancer therapy, our understanding of which remains inadequate. among the differentially expressed genes between the chemosensitive (5637) and chemoresistant (h-bc) bladder cancer cell lines, the expression level of the psen1 gene (presenilin 1), a key component of the γ-secretase, is negatively correlated with chemoresistance. a small interfering rna mediated repression of the psen1 gene suppresses cell apoptosis and de-sensitizes 5637 cells, while overexpression of the presenilin 1 sensitizes h-bc cells to the drug-triggered cell death. as a direct target of microrna-193a-3p that promotes the multi-chemoresistance of the bladder cancer cell, psen1 acts as an important executor for the microrna-193a-3p's positive impact on the multi-chemoresistance of bladder cancer, probably via its activating effect on dna damage response pathway. in addition to the mechanistic insights, the key players in this microrna-193a-3p/psen1 axis are likely the diagnostic and/or therapeutic targets for an effective chemotherapy of bladder cancer.",1
"defects in insulin signalling are among the most common and earliest defects that predispose an individual to the development of type 2 diabetes. micrornas have been identified as a new class of regulatory molecules that influence many biological functions, including metabolism. however, the direct regulation of insulin sensitivity by micrornas in vivo has not been demonstrated. here we show that the expression of micrornas 103 and 107 (mir-103/107) is upregulated in obese mice. silencing of mir-103/107 leads to improved glucose homeostasis and insulin sensitivity. in contrast, gain of mir-103/107 function in either liver or fat is sufficient to induce impaired glucose homeostasis. we identify caveolin-1, a critical regulator of the insulin receptor, as a direct target gene of mir-103/107. we demonstrate that caveolin-1 is upregulated upon mir-103/107 inactivation in adipocytes and that this is concomitant with stabilization of the insulin receptor, enhanced insulin signalling, decreased adipocyte size and enhanced insulin-stimulated glucose uptake. these findings demonstrate the central importance of mir-103/107 to insulin sensitivity and identify a new target for the treatment of type 2 diabetes and obesity.",1
"mir-302 is the major microrna found in human embryonic stem cells and induced pluripotent stem cells, but its function has been unclear. in mice, there is evidence that mir-302 may silence p21cip1 (cdkn1a) to promote cell proliferation, whereas studies in human reprogrammed pluripotent stem cells suggested that elevated mir-302 expression inhibited cell cycle transit. here, we clarify this difference, reporting that in human cells, mir-302 simultaneously suppressed both the cyclin e-cdk2 and cyclin d-cdk4/6 pathways to block>70% of the g1-s cell cycle transition. concurrent silencing of bmi-1, a cancer stem cell marker targeted by mir-302, further promoted tumor suppressor functions of p16ink4a and p14/p19arf directed against cdk4/6-mediated cell proliferation. among all g1 phase checkpoint regulators, human p21cip1 was found not to be a valid target of mir-302. overall, our findings indicate that mir-302 inhibits human pluripotent stem cell tumorigenicity by enhancing multiple g1 phase arrest pathways rather than by silencing p21cip1.",1
"the genome of the radiation-resistant eubacterium deinococcus radiodurans contains an ortholog of an rna-binding protein known as the ro 60-kd autoantigen. this protein, which was previously identified only in higher eukaryotes, is normally bound to small rnas known as y rnas. we show that the ro protein ortholog rsr contributes to the resistance of d. radiodurans to uv irradiation. rsr binds several small rnas, encoded upstream of rsr, that accumulate following uv irradiation. one of these rnas resembles a y rna. these results suggest that ro rnps could similarly contribute to the recovery of higher cells following uv irradiation.",1
"microrna‑133a (mir‑133a) is downregulated in various types of human malignancy, including hepatocellular carcinoma (hcc), renal cell carcinoma, esophageal squamous cell carcinoma, bladder cancer, ileal carcinoid and rhabdomyosarcoma. the aim of the present study was to examine the effects of mir‑133a on hcc cell proliferation, colony formation, migration and invasion. mir‑133a was transfected into the hcc hepg2 and smmc‑7721 cell lines and the expression levels of mir‑133a were determined; in addition, cell viability assays, colony formation assays, cell migration assays, cell invasion assays, western blot analyses and luciferase assays were performed in the hcc cell lines. the results demonstrated that mir‑133a significantly inhibited cell proliferation, colony formation, migration and invasion in hepg2 and smmc‑7721 cells. to the best of our knowledge, the present study also provided the first evidence that mir‑133a directly downregulated the expression of matrix metallopeptidase 9 (mmp‑9) in the hcc cells. in conclusion, the results of the present study indicated that mir‑133a may have suppressed cell proliferation, colony formation, migration and invasion via the downregulation of mmp‑9 in hcc cell lines. therefore, mmp‑9 may be used for the development of novel molecular markers and therapeutic approaches to inhibit hepatocellular carcinoma metastasis.",1
"development of bone metastases is dependent on the cancer cell-bone cell interactions in the bone microenvironment. transforming growth factor β (tgf-β) is released from bone during osteoclastic bone resorption and induces production of osteolytic factors, such as interleukin 11 (il-11), in breast cancer cells. il-11 in turn increases osteolysis by stimulating osteoclast function, launching a vicious cycle of cancer growth and bone destruction. we aimed to identify and functionally characterize micrornas (mirnas) that mediate the bone metastatic process, focusing on mirnas that regulate the tgf-β induction of il-11. first, we profiled the expression of 455 mirnas in a highly bone metastatic mda-mb-231(sa) variant as compared to the parental mda-mb-231 breast cancer cell line and found 16 mirnas (3.5%) having a >3-fold expression difference between the two cell types. we then applied a cell-based overexpression screen with pre-mirna constructs to functionally identify mirnas regulating tgf-β-induced il-11 production. this analysis pinpointed mir-204, mir-211, and mir-379 as such key regulators. these mirnas were shown to directly target il11 by binding to its 3' utr. mir-379 also inhibited smad2/3/4-mediated transcriptional activity. gene expression analysis of mir-204 and mir-379-transfected cells indicated that these mirnas downregulated the expression of several genes involved in tgf-β signaling, including prostaglandin-endoperoxide synthase 2 (ptgs2). in addition, there was a significant correlation between the genes downregulated by mir-379 and a set of genes upregulated in basal subtype of breast cancer. taken together, the functional evidence and clinical correlations imply novel mechanistic links between mirnas and the key steps in the bone metastatic process in breast cancer, with potential clinical relevance.",1
"we report here the consequences of mutations of a novel locus, named bantam, whose product is involved in the regulation of growth in drosophila. bantam mutant animals are smaller than wild type, due to a reduction in cell number but not cell size, and do not have significant disruptions in patterning. conversely, overexpression of the bantam product using the ep element ep(3)3622 causes overgrowth of wing and eye tissue. overexpression in clones of cells results in an increased rate of cell proliferation and a matched increase in cellular growth rate, such that the resulting tissue is composed of more cells of a size comparable to wild type. these effects are strikingly similar to those associated with alterations in the activity of the cyclind-cdk4 complex. however, epistasis and genetic interaction analyses indicate that bantam and cyclind-cdk4 operate independently. thus, the bantam locus represents a novel regulator of tissue growth.",1
"micrornas (mirs) are small non-protein-coding rnas that bind to specific mrnas and inhibit translation or promote mrna degradation. recent reports, including ours, indicated that mir-33a located within the intron of sterol regulatory element-binding protein (srebp) 2 controls cholesterol homeostasis and can be a possible therapeutic target for treating atherosclerosis. primates, but not rodents, express mir-33b from an intron of srebf1. therefore, humanized mice, in which a mir-33b transgene is inserted within a srebf1 intron, are required to address its function in vivo. we successfully established mir-33b knock-in (ki) mice and found that protein levels of known mir-33a target genes, such as abca1, abcg1, and srebp-1, were reduced compared with those in wild-type mice. as a consequence, macrophages from the mir-33b ki mice had a reduced cholesterol efflux capacity via apoa-i and hdl-c. moreover, hdl-c levels were reduced by almost 35% even in mir-33b ki hetero mice compared with the control mice. these results indicate that mir-33b may account for lower hdl-c levels in humans than those in mice and that mir-33b is possibly utilized for a feedback mechanism to regulate its host gene srebf1. our mice will also aid in elucidating the roles of mir-33a/b in different genetic disease models.",1
"angiogenesis is critical to tumor progression. the homeobox gene gax inhibits angiogenesis in vascular endothelial cells (ecs). we have identified a microrna (mir-130a) that regulates gax expression and hypothesized that it plays a major role in modulating gax activity in ecs. a 280-bp fragment from the gax 3'-untranslated region (3'-utr) containing 2 mir-130a targeting sites was observed to be required for the rapid down-regulation of gax expression by serum and proangiogenic factors, whereas the activity of the gax promoter did not vary with exposure to serum or proangiogenic factors. this same 280-bp sequence in the gax 3'-utr cloned into the psicheck2-luciferase vector mediated serum-induced down-regulation of the reporter gene when placed 3' of it. finally, forced expression of mir-130a inhibits gax expression through this specific gax 3'-utr sequence. a genome-wide search for other possible mir-130a binding sites revealed an mir-130a targeting site in the 3'-utr of the antiangiogenic homeobox gene hoxa5, the expression and antiangiogenic activity of which are also inhibited by mir-130a. from these data, we conclude that mir-130a is a regulator of the angiogenic phenotype of vascular ecs largely through its ability to modulate the expression of gax and hoxa5.",1
"trna fragments (trfs) are small rnas comparable to the size and function of mirnas. trfs are generally dicer independent, are found associated with ago, and can repress expression of genes post-transcriptionally. given that this expands the repertoire of small rnas capable of post-transcriptional gene expression, it is important to predict trf targets with confidence. some attempts have been made to predict trf targets, but are limited in the scope of trf classes used in prediction or limited in feature selection. we hypothesized that established mirna target prediction features applied to trfs through a random forest machine learning algorithm will immensely improve trf target prediction. using this approach, we show significant improvements in trf target prediction for all classes of trfs and validate our predictions in two independent cell lines. finally, gene ontology analysis suggests that among the trfs conserved between mice and humans, the predicted targets are enriched significantly in neuronal function, and we show this specifically for trf-3009a. these improvements to trf target prediction further our understanding of trf function broadly across species and provide avenues for testing novel roles for trfs in biology. we have created a publicly available website for the targets of trfs predicted by trforest.",1
"target predictions and validations are major obstacles facing microrna (mirna) researchers. animal mirna target prediction is challenging because of limited mirna sequence complementarity to the targets. in addition, only a small number of predicted targets have been experimentally validated and the mirna mechanism is poorly understood. here we present a novel algorithm for animal mirna target prediction. the algorithm combines relevant parameters for mirna target recognition and heuristically assigns different weights to these parameters according to their relative importance. a score calculation scheme is introduced to reflect the strength of each parameter. we also performed microarray time course experiments to identify downregulated genes due to mirna overexpression. the computational target prediction is combined with the mirna transfection experiment to systematically identify the gene targets of human mir-124. mir-124 overexpression led to a significant downregulation of many cell cycle related genes. this may be the result of direct suppression of a few cell growth inhibitors at the early stage of mirna overexpression, and these targeted genes were continuously suppressed over a long period of time. our high-throughput approach can be generalized to globally identify the targets and functions of other mirnas.",1
"breast cancer is a recurrent type of cancer among women worldwide. despite remarkable progress in the prevention, detection, and treatment of breast cancer, it still remains a major chronic problem worldwide and poses significant challenges, like metastasis to distant organs, demanding the need for novel biomarkers and therapeutic targets. focal adhesion kinase (fak), a member of the protein tyrosine kinases, has been shown to be expressed in high levels in breast tumors. of late, fak has emerged as an impending curative target in breast carcinoma, with few of the small molecular inhibitors reaching the clinical trial stage. in the current study, we established that microrna 551a (mir-551a) precisely regulates fak by binding to the complementary sequences in the 3' untranslated region (utr) of mrnas of fak and inhibits its expression in breast carcinoma cell lines. further, results from human breast carcinoma samples illustrated that mir-551a levels were substantially downregulated in tumor samples, with a concurrent rise in the expression of fak. functional experimental studies using mir-551a-overexpressing breast cancer cells and nude mouse xenograft models revealed the tumor suppressor role of mir-551a. we also found that mir-551a expression decreased the invasion and migratory ability of breast carcinoma cells by inhibiting mmp-9 activity. regulation studies performed utilizing promoter luciferase assays, chromatin immunoprecipitation (chip), and electrophoretic mobility shift assay (emsa) revealed that c-fos binds to the mir-551a promoter and activates it. further, we observed a considerable increase in the amount of mir-551a levels upon c-fos overexpression. all of these results showed that mir-551a can be of clinical relevance in understanding the regulation of fak in breast tumorigenesis.",1
"rationale atherosclerosis and aneurysms are leading causes of mortality worldwide. micrornas (mirs) are key determinants of gene and protein expression, and atypical mir expression has been associated with many cardiovascular diseases; although their contributory role to atherosclerotic plaque and abdominal aortic aneurysm stability are poorly understood. objective to investigate whether mir-181b regulates tissue inhibitor of metalloproteinase-3 expression and affects atherosclerosis and aneurysms. methods and results here, we demonstrate that mir-181b was overexpressed in symptomatic human atherosclerotic plaques and abdominal aortic aneurysms and correlated with decreased expression of predicted mir-181b targets, tissue inhibitor of metalloproteinase-3, and elastin. using the well-characterized mouse atherosclerosis models of apoe - /- and ldlr -/- , we observed that in vivo administration of locked nucleic acid anti-mir-181b retarded both the development and the progression of atherosclerotic plaques. systemic delivery of anti-mir-181b in angiotensin ii-infused apoe -/- and ldlr -/- mice attenuated aneurysm formation and progression within the ascending, thoracic, and abdominal aorta. moreover, mir-181b inhibition greatly increased elastin and collagen expression, promoting a fibrotic response and subsequent stabilization of existing plaques and aneurysms. we determined that mir-181b negatively regulates macrophage tissue inhibitor of metalloproteinase-3 expression and vascular smooth muscle cell elastin production, both important factors in maintaining atherosclerotic plaque and aneurysm stability. validation studies in timp3 -/- mice confirmed that the beneficial effects afforded by mir-181b inhibition are largely tissue inhibitor of metalloproteinase-3 dependent, while also revealing an additional protective effect through elevating elastin synthesis. conclusions our findings suggest that the management of mir-181b and its target genes provides therapeutic potential for limiting the progression of atherosclerosis and aneurysms and protecting them from rupture.",1
"objective vascular smooth muscle cells (vsmc) from type 2 diabetic db/db mice exhibit enhanced proinflammatory responses implicated in accelerated vascular complications. we examined the role of microrna(mir)-200 family members and their target zeb1, an e-box binding transcriptional repressor, in these events. methods and results the expression levels of mir-200b, mir-200c, and mir-429 were increased, although protein levels of zeb1 were decreased in vsmc and aortas from db/db mice relative to control db/+ mice. transfection of mir-200 mimics into vsmc downregulated zeb1 by targeting its 3'-utr, upregulated the inflammatory genes cyclooxygenase-2 and monocyte chemoattractant protein-1, and promoted monocyte binding in db/+vsmc. in contrast, mir-200 inhibitors reversed the enhanced monocyte binding of db/dbvsmc. zeb1 gene silencing with sirnas also increased these proinflammatory responses in db/+vsmc confirming negative regulatory role of zeb1. both mir-200 mimics and zeb1 sirnas increased cyclooxygenase-2 promoter transcriptional activity. chromatin immunoprecipitation showed that zeb1 occupancy at inflammatory gene promoters was reduced in vsmc from type 2 diabetic db/db mice. furthermore, zeb1 knockdown increased mir-200 levels demonstrating a feedback regulatory loop. conclusion disruption of the reciprocal negative regulatory loop between mir-200 and zeb1 under diabetic conditions enhances proinflammatory responses of vsmc implicated in vascular complications.",1
"although numerous long noncoding rnas (lncrnas) have been identified, our understanding of their roles in mammalian physiology remains limited. here, we investigated the physiologic function of the conserved lncrna norad in vivo. deletion of norad in mice results in genomic instability and mitochondrial dysfunction, leading to a dramatic multi-system degenerative phenotype resembling premature aging. loss of tissue homeostasis in norad -deficient animals is attributable to augmented activity of pumilio proteins, which act as post-transcriptional repressors of target mrnas to which they bind. norad is the preferred rna target of pumilio2 (pum2) in mouse tissues and, upon loss of norad , pum2 hyperactively represses key genes required for mitosis and mitochondrial function. accordingly, enforced pum2 expression fully phenocopies norad deletion, resulting in rapid-onset aging-associated phenotypes. these findings provide new insights and open new lines of investigation into the roles of noncoding rnas and rna binding proteins in normal physiology and aging.",1
"micrornas play critical roles in the development and progression of colorectal cancer (crc). mir-154 acts as a tumor suppressor in several tumors; however, its role in crc is poorly understood. herein, we found that mir-154 was decreased in crc tissues and cell lines. ectopic expression of mir-154 remarkably suppressed cell proliferation and colony formation, migration and invasion in crc cells. the toll-like receptor 2 (tlr2) was found to be a direct target of mir-154 in crc cells. inhibition of tlr2 performed similar effects with mir-154 overexpression on crc cells, and overexpression of tlr2 could significantly reverse the tumor suppressive effects of mir-154 on crc cells. this study suggests an essential role for mir-154 in crc.",1
"emerging evidence suggests that micrornas (mirs) play critical roles in the development and progression of non-small cell lung cancer (nsclc). in a previous study, the present authors demonstrated that mir-154 acts as a tumor suppressor in nsclc; however, its underlying molecular mechanism and target in nsclc remain poorly understood. in the present study, ectopic expression of mir-154 remarkably suppressed cell migration and invasion in nsclc cells. zinc finger e-box binding homeobox 2 (zeb2) was identified as a direct target of mir-154 in nsclc cells. furthermore, overexpression of mir-154 could decrease the expression of zeb2 at the messenger rna and protein levels. ectopic expression of mir-154 also increased the levels of e-cadherin, an epithelial marker, and decreased the levels of vimentin, a mesenchymal marker, which contributed to suppress epithelial-mesenchymal transition (emt) and to inhibit cell migration and invasion. in addition, downregulation of zeb2 exerted similar effects to those caused by mir-154 overexpression on nsclc cell migration and invasion, while upregulation of zeb2 could significantly reverse the inhibitory effects on migration and invasion caused by mir-154 on nsclc cells. these findings demonstrated that mir-154 inhibited migration and invasion of nsclc cells by regulating emt through targeting zeb2, suggesting that mir-154 may be a potential anticancer therapeutic target for nsclc.",1
"background & aims hepatocellular carcinoma (hcc) is an aggressive cancer with a poor prognosis mainly due to metastasis. micrornas are endogenous small noncoding rnas that regulate cellular gene expression and are functionally linked to tumourigenesis. using microarray analysis, we recently identified 20 mirnas associated with hcc metastasis. here, we carried out further analyses on one of these micrornas, let-7g, to determine whether it is functionally linked to hcc metastasis. methods quantitative real-time polymerase chain reaction was used to determine the level of mature let-7g transcript in hcc clinical specimens and its correlation with patient survival. ectopic expression of let-7g was carried out in hcc cell lines to assess its influence on cell growth, migration, and invasion. results we confirmed that the level of let-7g was significantly lower in metastatic hccs compared to metastasis-free hccs. moreover, low let-7g expression in a tumour was predictive of poor survival in hcc patients. functional studies indicated that ectopic expression of let-7g significantly inhibits hcc cell migration and cell growth. in-silico analysis revealed members of soluble collagens as potential targets of let-7g. consistently, the levels of type i collagen alpha2 (col1a2) and let-7g were inversely correlated in hcc clinical specimens. col1a2 was experimentally validated as a direct target of let-7g. moreover, addition of col1a2 counteracted the inhibitory effect of let-7g on cell migration. conclusions these results suggest that let-7g may suppress hcc metastasis partially through targeting col1a2.",1
"background increasing evidence has suggested that dysregulation of certain micrornas (mirnas) may contribute to human disease including carcinogenesis and tumor metastasis in human. mir-124-3p is down-regulated in various cancers, and modulates proliferation and aggressiveness of cancer cells. however, the roles of mir-124-3p in human bladder cancer are elusive. thus, this study was conducted to investigate the biological functions and its molecular mechanisms of mir-124-3p in human bladder cancer cell lines, discussing whether it has a potential to be a therapeutic biomarker of bladder cancer. methods three human bladder cancer cell lines and samples from ten patients with bladder cancer were analyzed for the expression of mir-124-3p by quantitative rt--pcr. exogenetic overexpression of mir-124-3p was established by transfecting mimics into t24, um-uc-3 and j82 cells, after that cell proliferation and cell cycle were assessed by mtt assay, flow cytometry and colony-forming assay. cell motility and invasion ability were evaluated by wound healing assay and transwell assay. tissue microarray, and immunohistochemistry with antibodies against rock1, mmp2 and mmp9 was performed using the peroxidase and dab methods. the target gene of mir-124-3p was determined by luciferase assays, quantitative rt--pcr and western blot. the regulation of epithelial-to-mesenchymal transition by mir-124-3p was analyzed by western blot. results mir-124-3p is frequently down-regulated in bladder cancer both in three bladder cancer cell lines, t24, um-uc-3, j82 and clinical samples. overexpression of mir-124-3p induced g1-phase arrest in t24, um-uc-3 and j82 cell lines and suppressed cell growth in colony-forming assay. mir-124-3p significantly repressed the capability of migration and invasion of bladder cancer cells. in addition, rock1 was identified as a new target of mir-124-3p. rock1, mmp2, mmp9 were up-regulated in bladder cancer tissues. furthermore, we demonstrated mir-124-3p could inhibit bladder cancer cell epithelial mesenchymal transfer, and regulated the expression of c-met, mmp2, mmp9. conclusions mir-124-3p can repress the migration and invasion of bladder cancer cells via regulating rock1. our data indicate that mir-124-3p could be a tumor suppressor and may have a potential to be a diagnostics or predictive biomarker in bladder cancer.",1
"chronic inflammation is increasingly recognized as an important component of tumorigenesis and metabolic diseases. the roles of microrna149* (mirna149*) in inflammation remain poorly understood. here, we demonstrate that mir-149* is a suppressor of stat3-mediated inflammation. mir-149* -/- mice were generated with crispr/cas9 technique. in a lipopolysaccharide (lps)-induced inflammation model, mir-149* -/- mice show more severe liver injury and inflammation, compared with wild-type (wt) mice. mir-149* -/- mice also displayed elevated messenger rna (mrna) levels of interleukin (il)-6, inducible nitric oxide synthase (inos), complement c3 (c3) and il-4 in response to lps. then mir-149* agomir administration is largely able to alleviate the lps-induced some inflammatory gene expression in wt mouse liver. in vitro, mir-149* mimics inhibited expression of stat3-meidated inflammatory mediators induced by lps and suppresses the phosphorylation of stat3 and its transcription activity in hepg2 cells. these findings identify mir-149* as a negative mediator of inflammation that may serve as an attractive therapeutic tool for immune and inflammatory liver diseases.",1
"ribonuclease p (rnase p) is a ribonucleoprotein that catalyzes the 5' maturation of precursor transfer rna in the presence of magnesium ions. the bacterial rnase p holoenzyme consists of one catalytically active rna component and a single essential but catalytically inactive protein. in contrast, yeast nuclear rnase p is more complex with one rna subunit and nine protein subunits. we have devised an affinity purification protocol to gently and rapidly purify intact yeast nuclear rnase p holoenzyme for transient kinetic studies. in pre-steady-state kinetic studies under saturating substrate concentrations, we observed an initial burst of trna formation followed by a slower, linear, steady-state turnover, with the burst amplitude equal to the concentration of the holoenzyme used in the reaction. these data indicate that the rate-limiting step in turnover occurs after pre-trna cleavage, such as mature trna release. additionally, the steady-state rate constants demonstrate a large dependence on temperature that results in nonlinear arrhenius plots, suggesting that a kinetically important conformational change occurs during catalysis. finally, deletion of the 3' trailer in pre-trna has little or no effect on the steady-state kinetic rate constants. these data suggest that, despite marked differences in subunit composition, the minimal kinetic mechanism for cleavage of pre-trna catalyzed by yeast nuclear rnase p holoenzyme is similar to that of the bacterial rnase p holoenzyme.",1
"the embryonic stem cell-specific cell cycle-regulating (escc) family of micrornas (mirnas) enhances reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells. here we show that the human escc mirna orthologs hsa-mir-302b and hsa-mir-372 promote human somatic cell reprogramming. furthermore, these mirnas repress multiple target genes, with downregulation of individual targets only partially recapitulating the total mirna effects. these targets regulate various cellular processes, including cell cycle, epithelial-mesenchymal transition (emt), epigenetic regulation and vesicular transport. escc mirnas have a known role in regulating the unique embryonic stem cell cycle. we show that they also increase the kinetics of mesenchymal-epithelial transition during reprogramming and block tgfβ-induced emt of human epithelial cells. these results demonstrate that the escc mirnas promote dedifferentiation by acting on multiple downstream pathways. we propose that individual mirnas generally act through numerous pathways that synergize to regulate and enforce cell fate decisions.",1
"microrna (mir)-146a is known to be overexpressed in osteoarthritis (oa). however, the role of mir-146a in oa has not yet been fully elucidated. in the present study, we applied mechanical pressure of 10 mpa to human chondrocytes for 60 min in order to investigate the expression of mir-146a and apoptosis following the mechanical pressure injury. normal human chondrocytes were transfected with an mir-146a mimic or an inhibitor to regulate mir-146a expression. potential target genes of mir-146a were predicted using bioinformatics. moreover, luciferase reporter assay confirmed that smad4 was a direct target of mir-146a. the expression levels of mir-146a, smad4 and vascular endothelial growth factor (vegf) were quantified by quantitative reverse transcription pcr and/or western blot analysis. the effects of mir-146a on apoptosis were detected by annexin v-fluorescein isothiocyanate (fitc)/propidium iodide (pi) flow cytometry. the results indicated that mechanical pressure affected chondrocyte viability and induced the early apoptosis of chondrocytes. mechanical pressure injury increased the expression levels of mir-146a and vegf and decreased the levels of smad4 in the chondrocytes. in the human chondrocytes, the upregulation of mir-146a induced apoptosis, upregulated vegf expression and downregulated smad4 expression. in addition, the knockdown of mir-146a reduced cell apoptosis, upregulated smad4 expression and downregulated vegf expression. smad4 was identified as a direct target of mir-146a by harboring a mir‑146a binding sequence in the 3'-untranslated region (3'-utr) of its mrna. furthermore, the upregulation of vegf induced by mir‑146a was mediated by smad4 in the chondrocytes subjected to mechanical pressure injury. these results demonstrated that mir-146a was overexpressed in our chondrocyte model of experimentally induced human mechanical injury, accompanied by the upregulation of vegf and the downregulation of smad4 in vitro. moreover, our data suggest that mir-146a is involved in human chondrocyte apoptosis in response to mechanical injury, and may contribute to the mechanical injury of chondrocytes, as well as to the pathogenesis of oa by increasing the levels of vegf and damaging the transforming growth factor (tgf)-β signaling pathway through the targeted inhibition of smad4 in cartilage.",1
"micrornas (mirnas) are regulators of myriad cellular events, but evidence for a single mirna that can efficiently differentiate multipotent stem cells into a specific lineage or regulate direct reprogramming of cells into an alternative cell fate has been elusive. here we show that mir-145 and mir-143 are co-transcribed in multipotent murine cardiac progenitors before becoming localized to smooth muscle cells, including neural crest stem-cell-derived vascular smooth muscle cells. mir-145 and mir-143 were direct transcriptional targets of serum response factor, myocardin and nkx2-5 (nk2 transcription factor related, locus 5) and were downregulated in injured or atherosclerotic vessels containing proliferating, less differentiated smooth muscle cells. mir-145 was necessary for myocardin-induced reprogramming of adult fibroblasts into smooth muscle cells and sufficient to induce differentiation of multipotent neural crest stem cells into vascular smooth muscle. furthermore, mir-145 and mir-143 cooperatively targeted a network of transcription factors, including klf4 (kruppel-like factor 4), myocardin and elk-1 (elk1, member of ets oncogene family), to promote differentiation and repress proliferation of smooth muscle cells. these findings demonstrate that mir-145 can direct the smooth muscle fate and that mir-145 and mir-143 function to regulate the quiescent versus proliferative phenotype of smooth muscle cells.",1
"rna activation has been reported to be induced by small interfering rnas (sirnas) that act on the promoters of several genes containing e-cadherin. in this study, we present an alternative mechanism of e-cadherin activation in human pc-3 cells by sirnas previously reported to possess perfect-complementary sequences to e-cadherin promoter. we found that activation of e-cadherin can be also induced via suppression of zeb1, which is a transcriptional repressor of e-cadherin, by seed-dependent silencing mechanism of these sirnas. the functional seed-complementary sites of the sirnas were found in the coding region in addition to the 3' untranslated region of zeb1 mrna. promoter analyses indicated that e-boxes, which are zeb1-binding sites, in the upstream promoter region are indispensable for e-cadherin transcription by the sirnas. thus, the results caution against ignoring sirna seed-dependent silencing effects in genome-wide transcriptional regulation. in addition, members of mir-302/372/373/520 family, which have the same seed sequences with one of the sirnas containing perfect-complementarity to e-cadherin promoter, are also found to activate e-cadherin transcription. thus, e-cadherin could be upregulated by the suppression of zeb1 transcriptional repressor by mirnas in vivo.",1
"background micrornas are a group of small rnas that regulate gene expression at the posttranscriptional level. they regulate almost every aspect of cellular processes. in this study, we investigated whether mir-27b regulates pulmonary fibroblast activation. results we found that mir-27b was down-regulated in fibrotic lungs and fibroblasts from an experimental mouse model of pulmonary fibrosis. the overexpression of mir-27b with a lentiviral vector inhibited tgfβ1-stimulated mrna expression of collagens (col1a1, col3a1, and col4a1) and alpha-smooth muscle actin, and protein expression of col3a1 and alpha-smooth muscle actin in ll29 human pulmonary fibroblasts. mir-27b also reduced contractile activity of ll29. tgfβ receptor 1 and smad2 were identified as the targets of mir-27b by 3'-untranslated region luciferase reporter and western blotting assays. conclusions our results suggest that mir-27b is an anti-fibrotic microrna that inhibits fibroblast activation by targeting tgfβ receptor 1 and smad2. this discovery may provide new targets for therapeutic interventions of idiopathic pulmonary fibrosis.",1
"aim to investigate the metastatic effects and mechanisms of mir-197 in hepatocellular carcinoma (hcc). methods and results the levels of mir-197 increased in hcc cells and tissues compared with a normal hepatic cell line (lo2) and adjacent nontumorous liver tissues, respectively. mir-197 expression negatively correlated with cd82 mrna expression in these cell lines and tissues. dual luciferase reporter assay and western blot confirmed a direct interaction between mir-197 and cd82 3'utr sequences. after mir-197 was silenced in hcc cells, cd82 expression increased. in the presence of human hepatocyte growth factor (hgf), cells silenced for anti-mir-197 exhibited elongated cellular tails and diminished lamellipodia due to reductions in both rock activity and the levels of rac 1 protein. downregulation of mir-197 along with the upregulation of cd82 in hcc cells resulted in the inhibition of hcc migration and invasion in vitro and in vivo. conclusion taken together, these data suggest that anti-mir-197 suppresses hcc migration and invasion by targeting cd82. the regulation of the mir-197/cd82 axis could be a novel therapeutic target in future hcc effective therapy.",1
"background human bone marrow mesenchymal stem cells (hbmscs) are multipotent cells that can differentiate into a variety of cell types. elevated expression of peroxisome proliferator-activated receptor-γ (pparγ) promotes the adipogenic differentiation of hbmscs, and reduces their osteogenic differentiation. micrornas (mirnas) have been shown to play important roles in the regulation of hbmscs differentiation. because bioinformatic analysis has indicated that pparγ is a candidate target of mir-548d-5p, the aim of this study was to assess the impact of mir-548d-5p on the dexamethasone-induced adipogenic differentiation of hbmscs. methods a quantitative rt-pcr (qrt-pcr) assay was used to compare mir-548d-5p expression levels in dexamethasone-induced hbmscs and uninduced control cells. oil red o staining, cellular triglyceride (tg) content, and the mrna and protein levels of pparγ and ccaat/enhancer binding protein α (c/ebpα) were used to evaluate the adipogenic differentiation of hbmscs. alkaline phosphatase (alp) activity and levels of osteocalcin (ocn) and runx2 were used to evaluate the osteogenic potential of hbmscs. results compared with untreated cells, mir-548d-5p expression levels were downregulated during dexamethasone-induced adipogenic differentiation of hbmscs. in contrast to the profuse oil red o staining in the cytoplasm of dexamethasone + scrambled mirna-treated cells, there was limited staining in the cytoplasm of dexamethasone + mir-548d-5p-treated cells, indicating the absence of adipocytes. moreover, compared with scrambled mirna-treated cells, treatment with mir-548d-5p suppressed cellular levels of pparγ and c/ebpα mrna and protein, and cell tg content (p conclusions mir-548d-5p is downregulated during dexamethasone-induced adipogenic differentiation of hbmscs. by directly targeting and downregulating pparγ, mir-548d-5p suppresses the dexamethasone-induced adipogenic differentiation of hbmscs and enhances their osteogenic potential. our findings suggest that mir-548d-5p has potential in the treatment of corticosteroid-induced osteonecrosis of the femoral head.",1
"micrornas (mirnas) comprise a novel class of endogenous, small, noncoding rnas that negatively regulate gene expression. functionally, an individual mirna is as important as a transcription factor because it is able to regulate the expression of its multiple target genes. recently, mir-221 and mir-222 have been found to play a critical role in cancer cell proliferation. however, their roles in vascular smooth muscle cell (vsmc) biology are currently unknown. in the present study, the time course changes and cellular distribution of mir-221 and mir-222 expression were identified in rat carotid arteries after angioplasty, in which their expression was upregulated and localized in vsmcs in the injured vascular walls. in cultured vsmcs, mir-221 and mir-222 expression was increased by growth stimulators. knockdown of mir-221 and mir-222 resulted in decreased vsmc proliferation in vitro. using both gain-of-function and loss-of-function approaches, we found that p27(kip1) and p57(kip2) were 2 target genes that were involved in mir-221- and mir-222-mediated effect on vsmc growth. finally, knockdown of mir-221 and mir-222 in rat carotid arteries suppressed vsmc proliferation in vivo and neointimal lesion formation after angioplasty. the results indicate that mir-221 and mir-222 are novel regulators for vsmc proliferation and neointimal hyperplasia. these findings may also represent promising therapeutic targets in proliferative vascular diseases.",1
"epstein-barr virus (ebv) controls gene expression to transform human b cells and maintain viral latency. high-throughput sequencing and crosslinking immunoprecipitation (hits-clip) identified mrna targets of 44 ebv and 310 human micrornas (mirnas) in jijoye (latency iii) ebv-transformed b cells. while 25% of total cellular mirnas are viral, only three viral mrnas, all latent transcripts, are targeted. thus, mirnas do not control the latent/lytic switch by targeting ebv lytic genes. unexpectedly, 90% of the 1664 human 3'-untranslated regions targeted by the 12 most abundant ebv mirnas are also targeted by human mirnas via distinct binding sites. half of these are targets of the oncogenic mir-17∼92 mirna cluster and associated families, including mrnas that regulate transcription, apoptosis, wnt signalling, and the cell cycle. reporter assays confirmed the functionality of several ebv and mir-17 family mirna-binding sites in ebv latent membrane protein 1 (lmp1), ebv bhrf1, and host caprin2 mrnas. our extensive list of ebv and human mirna targets implicates mirnas in the control of ebv latency and illuminates viral mirna function in general.",1
"background colorectal cancer (crc) is the most common digestive system malignancy. the molecular events involved in the development and progression of crc remain unclear. recently, more and more evidences have showed that deregulated mirnas participate in colorectal carcinogenesis. methods the expression levels of mir-138 were first examined in crc cell lines and tumor tissues by real-time pcr. the in vitro and in vivo functional effects of mir-138 were examined further. luciferase reporter assays were conducted to confirm the targeting associations. kaplan-meier analysis and log-rank tests were performed to estimate the overall survival and disease free survival rate. results mir-138 was found to be down-regulated in human colorectal cancer tissues and cell lines. ectopic expression of mir-138 resulted in a dramatic inhibition of crc migration and invasion in vitro and in vivo. twist basic helix-loop-helix transcription factor 2 gene (twist2) was identified as one of the functional target. restoration of mir-138 resulted in a dramatic reduction of the expression of twist2 at both mrna and protein levels by directly targeting its 3'-untranslated region (3'utr). up-regulation of twist2 was detected in crc tumors compared with adjacent normal tissues (p conclusion these data highlight a pivotal role for mir-138 in the regulation of crc metastasis by targeting twist2, and suggest a potential application of mir-138 in prognosis prediction and crc treatment.",1
"u21 is an intron-encoded snorna in vertebrates which contains a 13-nt tract of complementarity to an invariant sequence in eukaryotic 28s rrna. here, we report the characterization of its drosophila melanogaster homolog which is the first case of an intron-encoded snorna in an invertebrate metazoan. in d. melanogaster, u21 is encoded within the arf-1 (adp ribosylation factor 1) gene, whereas in chicken and mammals it is found in the ribosomal protein l5 gene. in d. melanogaster, like in vertebrates, u21 is devoid of a 5' trimethylguanosine cap, thus, likely resulting from processing of intronic rna. the only portion of u21 sequence preserved between d. melanogaster and vertebrates, in addition to the hallmark box c and box d motifs, corresponds precisely to the 13-nt complementary to rrna, pointing to an important role of the pairing of u21 to pre-rrna.",1
"the replication-dependent histone mrnas in metazoa are not polyadenylated, in contrast to the bulk of mrna. instead, they contain an rna stem-loop (sl) structure close to the 3' end of the mature rna, and this 3' end is generated by cleavage using a machinery involving the u7 snrnp and protein factors such as the stem-loop binding protein (slbp). this machinery of 3' end processing is related to that of polyadenylation as protein components are shared between the systems. it is commonly believed that histone 3' end processing is restricted to metazoa and green algae. in contrast, polyadenylation is ubiquitous in eukarya. however, using computational approaches, we have now identified components of histone 3' end processing in a number of protozoa. thus, the histone mrna stem-loop structure as well as the slbp protein are present in many different protozoa, including dictyostelium, alveolates, trypanosoma, and trichomonas. these results show that the histone 3' end processing machinery is more ancient than previously anticipated and can be traced to the root of the eukaryotic phylogenetic tree. we also identified histone mrnas from both metazoa and protozoa that are polyadenylated but also contain the signals characteristic of histone 3' end processing. these results provide further evidence that some histone genes are regulated at the level of 3' end processing to produce either polyadenylated rnas or rnas with the 3' end characteristic of replication-dependent histone mrnas.",1
"we have discovered a large and highly conserved rna motif that typically resides in a noncoding section of a multigene messenger rna in extremophilic gram-positive eubacteria. rnas of this class adopt an ornate secondary structure, are large compared with most other noncoding rnas, and have been identified only in certain extremophilic bacteria. these ornate, large, extremophilic (ole) rnas have a length of approximately 610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. structural probing of the ole rna from bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. the patterns of structural conservation, and its unique phylogenetic distribution, suggest that ole rna carries out a complex and critical function only in certain extremophilic bacteria.",1
"while thousands of long noncoding rnas (lncrnas) have been identified, few lncrnas that control neural stem cell (nsc) behavior are known. here, we identify pinky (pnky) as a neural-specific lncrna that regulates neurogenesis from nscs in the embryonic and postnatal brain. in postnatal nscs, pnky knockdown potentiates neuronal lineage commitment and expands the transit-amplifying cell population, increasing neuron production several-fold. pnky is evolutionarily conserved and expressed in nscs of the developing human brain. in the embryonic mouse cortex, pnky knockdown increases neuronal differentiation and depletes the nsc population. pnky interacts with the splicing regulator ptbp1, and ptbp1 knockdown also enhances neurogenesis. in nscs, pnky and ptbp1 regulate the expression and alternative splicing of a core set of transcripts that relates to the cellular phenotype. these data thus unveil pnky as a conserved lncrna that interacts with a key rna processing factor and regulates neurogenesis from embryonic and postnatal nsc populations.",1
"embryo loss is a major factor affecting profitability in the pig industry. embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. previous investigations have shown that the embryo loss rate in meishan pigs is significantly lower than in commercial breeds. most studies have focused on embryonic mortality during early gestation, but little is known about losses during mid-late gestation. in this study, we performed a transcriptome analysis of endometrial tissue in mid-late gestation sows (gestation days 49 and 72) sampled from two breeds (meishan (ms) and duroc (du)) that have different embryo loss rates. we identified 411, 1113, 697, and 327 differentially expressed genes, and 14, 36, 57, and 43 differentially expressed mirnas in four comparisons (du49 vs. du72, du49 vs. ms49, du72 vs. ms72, and ms49 vs. ms72), respectively. subsequently; seven differentially expressed mrnas and mirnas were validated using qpcr. functional analysis suggested the differentially expressed genes and mirnas target genes mainly involved in regulation of hormone levels, blood vessel development, developmental process involved in reproduction, embryonic placenta development, and the immune system. a network analysis of potential mirna-gene interactions revealed that differentially expressed mirnas in meishan pigs are involved in the response to estradiol and oxygen levels, and affect angiogenesis and blood vessel development. the binding site on ssc-mir-503 for epidermal growth factor ( egf ) and the binding site on ssc-mir-671-5p for estrogen receptor α (esr1) were identified using a dual luciferase assay. the results of this study will enable further exploration of mirna-mrna interactions important in pig pregnancy and will help to uncover molecular mechanisms affecting embryonic mortality in pigs during mid-late gestation.",1
"severe lung inflammation and alveolar hemorrhage can be life-threatening in systemic lupus erythematosus (sle) patients if not treated early and aggressively. neutrophil influx is the driver key of this pathology, but little is known regarding the molecular events regulating this recruitment. here, we uncover a role for il-16/mir-125a in this pathology and show not only that il-16 is a target for mir-125a but that reduced mir-125a expression in sle patients associates with lung involvement. furthermore, in the pristane model of acute ""sle-like"" lung inflammation and alveolar hemorrhage, we observed reduced pulmonary mir-125a and enhanced il-16 expression. neutrophil infiltration was markedly reduced in the peritoneal lavage of pristane-treated il-16-deficient mice and elevated following i.n. delivery of il-16. moreover, a mir-125a mimic reduced pristane-induced il-16 expression and neutrophil recruitment and rescued lung pathology. mechanistically, il-16 acts directly on the pulmonary epithelium and markedly enhances neutrophil chemoattractant expression both in vitro and in vivo, while the mir-125a mimic can prevent this. our results reveal a role for mir-125a/il-16 in regulating lung inflammation and suggest this axis may be a therapeutic target for management of acute lung injury in sle.",1
"postnatal heart stem and progenitor cells are a potential therapeutic tool for cardiomyopathies, but little is known about the mechanisms that control cardiac differentiation. recent work has highlighted an important role for microribonucleic acids (mirnas) as regulators of cardiac and skeletal myogenesis. in this paper, we isolated cardiac progenitors from neonatal β-sarcoglycan (sgcb)-null mouse hearts affected by dilated cardiomyopathy. unexpectedly, sgcb-null cardiac progenitors spontaneously differentiated into skeletal muscle fibers both in vitro and when transplanted into regenerating muscles or infarcted hearts. differentiation potential correlated with the absence of expression of a novel mirna, mir669q, and with down-regulation of mir669a. other mirnas are known to promote myogenesis, but only mir669a and mir669q act upstream of myogenic regulatory factors to prevent myogenesis by directly targeting the myod 3' untranslated region. this finding reveals an added level of complexity in the mechanism of the fate choice of mesoderm progenitors and suggests that using endogenous cardiac stem cells therapeutically will require specially tailored procedures for certain genetic diseases.",1
"we have cloned and sequenced one of the two genes encoding a 255 nucleotide small nuclear rna from the fission yeast schizosaccharomyces pombe. based on the presence of four regions of primary sequence conservation and a predicted secondary structure similar to that previously proposed for human u3, we conclude that this molecule is the fission yeast homologue of this mammalian snrna. the 5' one-third of fission yeast u3 is, however, unable to form a single stable hairpin as proposed for this region of the human rna, but rather folds into two stem-loop structures. by analogy to fission yeast u3, we propose revised secondary structures containing two hairpins for this portion of the u3-like snrnas from saccharomyces cerevisiae and dictyostelium discoideum. thus, our data suggest that the structure of u3 snrna has diverged in lower and higher eukaryotes.",1
"background micrornas are broadly accepted as crucial regulators of cardiovascular development, and dysregulation of their expression has been linked to cardiac disease. microrna cluster mir-17-92 has been implicated in cardiac development and function, yet its defined mechanisms of action in this context are uncertain. here, we focused on mir-19b, a key component of the mir-17-92 cluster proven to induce cardiomyocyte proliferation in vitro. we aimed to identify the biological significance of mir-19b in cardiac development and its underlying molecular mechanism of action in vivo. methods we micro-injected zebrafish embryos with different concentrations (0, 2, 4 and 8 μm) of mir-19b mimics or a negative control, and assessed the embryo malformation rate, mortality rate, hatching rate and heart abnormalities at 72 hours post-fertilization (72 hpf). results we found that overexpression of mir-19b impacted left-right symmetry and cardiac development of zebrafish embryos, characterized by pericardial edema, slower heart rate and cardiac looping defects in a dose-dependent manner. moreover, several important signaling molecules in the wnt signaling pathway were abnormally expressed, suggesting that overexpression of mir-19b induces the inhibition of the wnt signaling pathway by directly targeting ctnnb1. interestingly, the deformed cardiac phenotype was partially rescued by treatment with the gsk3β inhibitor lithium chloride. conclusion our findings suggest that mir-19b regulates laterality development and heart looping in zebrafish embryos by targeting ctnnb1.",1
"rnase mrp is a site-specific ribonucleoprotein endoribonuclease that cleaves rna sequence complementary to mammalian mitochondrial origins of replication in a manner consistent with a role in primer rna metabolism. the same activity in the yeast saccharomyces cerevisiae has recently been identified; it cleaves an rna substrate complementary to a yeast mitochondrial origin of replication at an exact site of linkage of rna to dna. we have purified this yeast enzyme further and detect a single, novel rna of 340 nucleotides associated with the enzymatic activity. the single-copy nuclear gene for this rna was sequenced and mapped to the right arm of chromosome xiv. the identity of the clone, as encoding the rna copurifying with enzymatic activity, was confirmed by a match to the directly determined sequence of the rna. the gene sequence also identified a 340-nucleotide rna in total yeast rna and in purified rnase mrp enzyme preparations. inspection of the sequence of the yeast rna revealed homologies to the rna component of mouse rnase mrp, 49% overall with specific regions of much greater similarity. the flanking regions of the gene showed characteristics of an rna polymerase ii transcription unit, including a tataaa box and a 7/8 match to the yeast cell cycle box uas. the rnase mrp rna gene was deleted by insertional replacement and found to be essential for cellular viability, indicating a critical nuclear role for rnase mrp.",1
"aim to investigate the biological role and underlying mechanism of mir-132 in colorectal cancer (crc) progression and invasion. methods quantitative rt-pcr analysis was used to examine the expression levels of mir-132 in five crc cell lines (sw480, sw620, hct116, ht29 and lovo) and a normal colonic cell line ncm460, as well as in tumor tissues with or without metastases. the kaplan-meier method was used to analyze the prognostic significance of mir-132 in crc patients. the biological effects of mir-132 were assessed in crc cell lines using the transwell assay. quantitative rt-pcr and western blot analyses were employed to evaluate the expression of mir-132 targets. the regulation of zeb2 by mir-132 was confirmed using the luciferase activity assay. results mir-132 was significantly down-regulated in the crc cell lines compared with the normal colonic cell line (p conclusion our study indicated that mir-132 plays an important role in the invasion and metastasis of crc.",1
"background the human ether-a-go-go-related gene (herg) is the major molecular component of the rapidly activating delayed rectifier k + current (i kr ). impairment of herg function is believed to be a mechanism causing long-qt syndromes (lqts). growing evidences have shown that micrornas (mirnas) are involved in functional modulation of the herg pathway. the purpose of this study was to screen and validate mirnas that regulate the herg pathway. the mirnas identified in this study will provide new tools to assess the mechanism of lqts. methods six mirnas were selected by algorithm predictions based on potential interaction with herg. the effects of each mirna on herg were assessed by use of the dual-luciferase reporter assay system, qrt-pcr, western blotting, and confocal fluorescence microscopy. furthermore, whole-cell patch clamp technique was used to validate the effect of mir-103a-1 on the electrophysiological characteristic of the i kr of the herg protein channel. results mir-134, mir-103a-1, mir-143, and mir-3619 significantly downregulated luciferase activity (p conclusions expression and functions of herg are regulated by specific mirnas.",1
"although micrornas (mirnas) are involved in many biological processes, the mechanisms whereby mirnas regulate osteoblastic differentiation are poorly understood. here, we found that bmp-4-induced osteoblastic differentiation of bone marrow-derived st2 stromal cells was promoted and repressed after transfection of sense and antisense mir-210, respectively. a reporter assay demonstrated that the activin a receptor type 1b (acvr1b) gene was a target for mir-210. furthermore, inhibition of transforming growth factor-beta (tgf-beta)/activin signaling in st2 cells with sb431542 promoted osteoblastic differentiation. we conclude that mir-210 acts as a positive regulator of osteoblastic differentiation by inhibiting the tgf-beta/activin signaling pathway through inhibition of acvr1b.",1
"genetic deficits and loss of function for the triggering receptor expressed in myeloid cells 2 (trem2; encoded at chr6p21.1), a transmembrane spanning stimulatory receptor of the immunoglobulin/lectin-like gene superfamily, have been associated with deficiencies in phagocytosis and the innate immune system in alzheimer's disease. in this study, we provide evidence that trem2 is downregulated in samples of sporadic alzheimer hippocampal ca1 compared with age-matched controls. a nuclear factor-кb (nf-кb)-sensitive mirna-34a (encoded at chr1p36.22), upregulated in alzheimer's disease, was found to target the 299 nucleotide human trem2 mrna 3'-untranslated region (3'-utr) and downregulate the expression of a trem2-3'-utr reporter vector. a stabilized anti-mirna-34a (am-34a) quenched this pathogenic response. the results suggest that an epigenetic mechanism involving an nf-кb-mediated, mirna-34a-regulated downregulation of trem2 expression may shape innate immune and phagocytic responses that contribute to inflammatory neurodegeneration.",1
"the trna-like structure at the 3' end of turnip yellow mosaic virus (tymv) rna was studied in order to determine the role of this structure in the initiation of minus-strand synthesis in vitro. deletions in the 5'-to-3' direction up to the pseudoknot structure did not result in a decrease of transcription efficiency. however, transcription efficiency was reduced twofold when a fragment of 21 nucleotides, comprising the 3'-terminal hairpin, was used as a template. trna(phe) from yeast, escherichia coli 5s rrna, and the 3'-terminal 208 nucleotides of alfalfa mosaic virus rna 3 could not be transcribed by the rna-dependent rna polymerase (rdrp) of tymv. various mutations in the sequences of loop regions l1 and l2 or of stem region s1 of the pseudoknot were tested to further investigate the importance of the pseudoknot structure. the results were compared with those obtained in an earlier study on aminoacylation with the same mutants (r. m. w. mans, m. h. van steeg, p. w. g. verlaan, c. w. a. pleij, and l. bosch, j. mol. biol. 223:221-232; 1992). mutants which still harbor a stable pseudoknot, as proven by probing its structure, have a transcription efficiency very close to that of the wild-type virus. disruption of the pseudoknot structure, however, gives rise to a drop in transcription efficiency to about 50%. no indications of base-specific interactions between l1, l2, or s1 of the pseudoknot and the rdrp were found.",1
"stem-cell antigen 1-positive (sca-1+) cardiac stem cells (cscs), a vital kind of cscs in humans, promote cardiac repair in vivo and can differentiate to cardiomyocytes with 5'-azacytizine treatment in vitro. however, the underlying molecular mechanisms are unknown. β-arrestin2 is an important scaffold protein and highly expressed in the heart. to explore the function of β-arrestin2 in sca-1+ csc differentiation, we used β-arrestin2-knockout mice and overexpression strategies. real-time pcr revealed that β-arrestin2 promoted 5'-azacytizine-induced sca-1+ csc differentiation in vitro. because the microrna 155 (mir-155) may regulate β-arrestin2 expression, we detected its role and relationship with β-arrestin2 and glycogen synthase kinase 3 (gsk3β), another probable target of mir-155. real-time pcr revealed that mir-155, inhibited by β-arrestin2, impaired 5'-azacytizine-induced sca-1+ csc differentiation. on luciferase report assay, mir-155 could inhibit the activity of β-arrestin2 and gsk3β, which suggests a loop pathway between mir-155 and β-arrestin2. furthermore, β-arrestin2-knockout inhibited the activity of gsk3β. akt, the upstream inhibitor of gsk3β, was inhibited in β-arrestin2-knockout mice, so the activity of gsk3β was regulated by β-arrestin2 not akt. we transplanted sca-1+ cscs from β-arrestin2-knockout mice to mice with myocardial infarction and found similar protective functions as in wild-type mice but impaired arterial elastance. furthermore, low level of β-arrestin2 agreed with decreased phosphorylation of akt and increased phophorylation of gsk3β, similar to in vitro findings. the β-arrestin2/mir-155/gsk3β pathway may be a new mechanism with implications for treatment of heart disease.",1
"background aging is a major risk factor for the development of atherosclerosis and coronary artery disease. through a microarray approach, we have identified a microrna (mir-217) that is progressively expressed in endothelial cells with aging. mir-217 regulates the expression of silent information regulator 1 (sirt1), a major regulator of longevity and metabolic disorders that is progressively reduced in multiple tissues during aging. methods and results mir-217 inhibits sirt1 expression through a mir-217-binding site within the 3'-utr of sirt1. in young human umbilical vein endothelial cells, human aortic endothelial cells, and human coronary artery endothelial cells, mir-217 induces a premature senescence-like phenotype and leads to an impairment in angiogenesis via inhibition of sirt1 and modulation of foxo1 (forkhead box o1) and endothelial nitric oxide synthase acetylation. conversely, inhibition of mir-217 in old endothelial cells ultimately reduces senescence and increases angiogenic activity via an increase in sirt1. mir-217 is expressed in human atherosclerotic lesions and is negatively correlated with sirt1 expression and with foxo1 acetylation status. conclusions our data pinpoint mir-217 as an endogenous inhibitor of sirt1, which promotes endothelial senescence and is potentially amenable to therapeutic manipulation for prevention of endothelial dysfunction in metabolic disorders.",1
"micrornas have been appreciated in various cellular functions, including the regulation of angiogenesis. mesenchymal-stem-cells (mscs) transplanted to the mi heart improve cardiac function through paracrine-mediated angiogenesis. however, whether micrornas regulate msc induced angiogenesis remains to be clarified. using microrna microarray analysis, we identified a microrna expression profile in hypoxia-treated mscs and observed that among all dysregulated micrornas, microrna-377 was decreased the most significantly. we also validated that vascular endothelial growth factor (vegf) is a target of microrna-377 using dual-luciferase reporter assay and western-blotting. knockdown of endogenous microrna-377 promoted tube formation in human umbilical vein endothelial cells. we then engineered rat mscs with lentiviral vectors to either overexpress microrna-377 (msc mir-377) or knockdown microrna-377 (msc anti-377) to investigate whether microrna-377 regulated msc-induced myocardial angiogenesis, using mscs infected with lentiviral empty vector to serve as controls (msc null). four weeks after implantation of the microrna-engineered mscs into the infarcted rat hearts, the vessel density was significantly increased in msc anti-377-hearts, and this was accompanied by reduced fibrosis and improved myocardial function as compared to controls. adverse effects were observed in msc mir-377-treated hearts, including reduced vessel density, impaired myocardial function, and increased fibrosis in comparison with msc null-group. these findings indicate that hypoxia-responsive microrna-377 directly targets vegf in mscs, and knockdown of endogenous microrna-377 promotes msc-induced angiogenesis in the infarcted myocardium. thus, microrna-377 may serve as a novel therapeutic target for stem cell-based treatment of ischemic heart disease.",1
"although microrna-21 (mir-21) is emerging as an oncogene and has been shown to target several tumor suppressor genes, including programmed cell death 4 (pdcd4), its precise mechanism of action on cancer stem cells (cscs) is unclear. herein, we report that folfox-resistant hct-116 and ht-29 cells that are enriched in cscs show a 3- to 7-fold upregulation of pre- and mature mir-21 and downregulation of pdcd4. likewise, overexpression of mir-21 in hct-116 cells, achieved through stable transfection, led to the downregulation of pdcd4 and transforming growth factor beta receptor 2 (tgfβr2). in contrast, the levels of β-catenin, tcf/lef activity and the expression of c-myc, cyclin-d, which are increased in cscs, are also augmented in mir-21 overexpressing colon cancer cells, accompanied by an increased sphere forming ability in vitro and tumor formation in scid mice. downregulation of tgfβr2 could be attributed to decreased expression of the receptor as evidenced by reduction in the activity of the luciferase gene construct comprising tgfβr2-3' untranslated region (utr) sequence that binds to mir-21. moreover, we observed that downregulation of mir-21 enhances luciferase-tgfβr2-3' utr activity suggesting tgfβr2 as being one of the direct targets of mir-21. further support is provided by the observation that transfection of tgfβr2 in hct-116 cells attenuates tcf/lef luciferase activity, accompanied by decreased expression of β-catenin, c-myc and cyclin-d1. our current data suggest that mir-21 plays an important role in regulating stemness by modulating tgfβr2 signaling in colon cancer cells.",1
"mscs possess potent immunosuppressive capacity. we have reported that mouse mscs inhibit t cell proliferation and function via nitric oxide. this immune regulatory capacity of mscs is induced by the inflammatory cytokines ifnγ together with either tnfα or il-1β. this effect of inflammatory cytokines on mscs is extraordinary; logarithmic increases in the expression of inos and chemokines are often observed. to investigate the molecular mechanisms underlying this robust effect of cytokines, we examined the expression of micrornas in mscs before and after cytokine treatment. we found that mir-155 is most significantly up-regulated. furthermore, our results showed that mir-155 inhibits the immunosuppressive capacity of mscs by reducing inos expression. we further demonstrated that mir-155 targets tak1-binding protein 2 (tab2) to regulate inos expression. additionally, knockdown of tab2 reduced inos expression. in summary, our study demonstrated that mir-155 inhibits the immunosuppressive capacity of mscs by reducing inos expression by targeting tab2. our data revealed a novel role of mir-155 in regulating the immune modulatory activities of mscs.",1
"micrornas are increasingly recognized as playing important roles in hepatocellular carcinoma (hcc) tumorigenesis. here we identified an essential role for mir-362-5p in the regulation of hcc development. we found that mir-362-5p was significantly up-regulated in hccs and associated with hcc progression. inhibition of mir-362-5p in hcc cells dramatically decreased cell proliferation, clonogenicity, migration and invasion in vitro as well as tumor growth and metastasis in vivo. we subsequently identified that cyld was a target gene of mir-362-5p. furthermore, knockdown of cyld expression partially counteracted the tumor suppressive effects of mir-362-5p inhibitors. finally, we have shown that mir-362-5p acts through cyld to activate the nf-κb signaling pathway, which contributes to hcc progression. taken together, our findings indicate that mir-362-5p belongs to a new class of oncomir that regulates hcc cell aggressiveness, thus providing new insight into the molecular mechanisms underlying hcc development. this study also suggests that mir-362-5p may serve as a novel therapeutic target for mirna based hcc therapy.",1
"mirnas are an important class of regulators that play roles in cellular homeostasis and disease. muscle-specific mirnas, mir-1-1 and mir-1-2, have been found to play important roles in regulating cell proliferation and cardiac function. redundancy between mir-1-1 and mir-1-2 has previously impeded a full understanding of their roles in vivo. to determine how mir-1s regulate cardiac function in vivo, we generated mice lacking mir-1-1 and mir-1-2 without affecting nearby genes. mir-1 double knockout (mir-1 dko) mice were viable and not significantly different from wild-type controls at postnatal day 2.5. thereafter, all mir-1 dko mice developed dilated cardiomyopathy (dcm) and died before p17. massively parallel sequencing showed that a large portion of upregulated genes after deletion of mir-1s is associated with the cardiac fetal gene program including cell proliferation, glycolysis, glycogenesis, and fetal sarcomere-associated genes. consistent with gene profiling, glycogen content and glycolytic rates were significantly increased in mir-1 dko mice. estrogen-related receptor β (errβ) was identified as a direct target of mir-1, which can regulate glycolysis, glycogenesis, and the expression of sarcomeric proteins. cardiac-specific overexpression of errβ led to glycogen storage, cardiac dilation, and sudden cardiac death around 3-4 weeks of age. we conclude that mir-1 and its primary target errβ act together to regulate the transition from prenatal to neonatal stages by repressing the cardiac fetal gene program. loss of this regulation leads to a neonatal dcm.",1
"background smoking is the leading cause of copd. exploring molecular markers and understanding the pathogenic mechanisms of smoking-related copd are helpful for early clinical diagnosis and treatment of the disease. this study aims to identify specific circulating micrornas (mirnas) from the blood of copd patients with a long history of smoking. methods blood samples from four different groups were collected, and mirna microarray was performed. differential expression of mirnas was verified by quantitative polymerase chain reaction. in vitro, thp-1 cells were cultured and stimulated with cigarette smoke extract (cse) or transfected with mir-149-3p inhibitor/mimics. protein levels of toll-like receptor 4 (tlr-4) and nuclear factor κb (nf-κb) were detected using western blot and immunofluorescence. interleukin (il)-1β and tumor necrosis factor (tnf)-α levels were determined by an enzyme-linked immunosorbent assay. results mirna profiling revealed that the expression of 56 mirnas was changed between the four groups. expression of mir-149-3p in group c (non-smoker non-copd) was higher than in group s (smoker non-copd), s-copd (smoker with stable copd) and ae-copd (smoker with acute exacerbation copd). cse stimulation down-regulated the expression of mir-149-3p and up-regulated the tlr-4 and nf-κb levels in thp-1 cells. transfecting mir-149-3p inhibitors in thp-1 cells also increased the expression of its target genes. furthermore, overexpression of mir-149-3p inhibited the tlr-4/nf-κb signaling pathways and reduced the secretion of il-1β and tnf-α. conclusion this study found that smoking can induce differential expression of circulating mir-nas, such as down-regulation of mir-149-3p. reducing mir-149-3p may increase the inflammatory response in copd patients through the regulation of the tlr-4/nf-κb signaling pathway.",1
"by using a sensitive search program based on hidden markov models (hmm), we identified 74 viruses carrying frameshift sites among 1500 fully sequenced virus genomes. these viruses are clustered in specific families or genera. sequence analysis of the frameshift sites identified here, along with previously characterized sites, identified a strong bias toward the two nucleotides 5' of the shifty heptamer signal. functional analysis in the yeast saccharomyces cerevisiae demonstrated that high frameshifting efficiency is correlated with the presence of a psi39 modification in the trna present in the e site of the ribosome at the time of frameshifting. these results demonstrate that an extended signal is involved in eukaryotic frameshifting and suggest additional interactions between trnas and the ribosome during decoding.",1
"micrornas (mirna) are short non-coding rnas widely implicated in gene regulation. most metazoan mirnas utilize the rnase iii enzymes drosha and dicer for biogenesis. one notable exception is the rna polymerase ii transcription start sites (tss) mirnas whose biogenesis does not require drosha. the functional importance of the tss-mirna biogenesis is uncertain. to better understand the function of tss-mirnas, we applied a modified crosslinking, ligation, and sequencing of hybrids on argonaute (ago-qclash) to identify the targets for tss-mirnas in hct116 colorectal cancer cells with or without drosha knockout. we observed that mir-320a hybrids dominate in tss-mirna hybrids identified by ago-qclash. targets for mir-320a are enriched for the eif2 signaling pathway, a downstream component of the unfolded protein response. consistently, in mir-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eif2 signaling. within the ago-qclash data, we identified the endoplasmic reticulum (er) chaperone calnexin as a direct mir-320a down-regulated target, thus connecting mir-320a to the unfolded protein response. during er stress, but not amino acid deprivation, mir-320a up-regulates atf4, a critical transcription factor for resolving er stress. in summary, our study investigates the targetome of the tss-mirnas in colorectal cancer cells and establishes mir-320a as a regulator of unfolded protein response.",1
"neural crest cells (nccs) are a subset of multipotent, migratory stem cells that populate a large number of tissues during development and are important for craniofacial and cardiac morphogenesis. although micrornas (mirnas) have emerged as important regulators of development and disease, little is known about their role in ncc development. here, we show that loss of mirna biogenesis by ncc-specific disruption of murine dicer results in embryos lacking craniofacial cartilaginous structures, cardiac outflow tract septation and thymic and dorsal root ganglia development. dicer mutant embryos had reduced expression of dlx2, a transcriptional regulator of pharyngeal arch development, in the first pharyngeal arch (pa1). mir-452 was enriched in nccs, was sufficient to rescue dlx2 expression in dicer mutant pharyngeal arches, and regulated non-cell-autonomous signaling involving wnt5a, shh and fgf8 that converged on dlx2 regulation in pa1. correspondingly, knockdown of mir-452 in vivo decreased dlx2 expression in the mandibular component of pa1, leading to craniofacial defects. these results suggest that post-transcriptional regulation by mirnas is required for differentiation of ncc-derived tissues and that mir-452 is involved in epithelial-mesenchymal signaling in the pharyngeal arch.",1
"cystic fibrosis (cf) is one of the most common lethal genetic diseases in which the role of micrornas has yet to be explored. predicted to be regulated by mir-126, tom1 (target of myb1) has been shown to interact with toll-interacting protein, forming a complex to regulate endosomal trafficking of ubiquitinated proteins. tom1 has also been proposed as a negative regulator of il-1beta and tnf-alpha-induced signaling pathways. mir-126 is highly expressed in the lung, and we now show for the first time differential expression of mir-126 in cf versus non-cf airway epithelial cells both in vitro and in vivo. mir-126 downregulation in cf bronchial epithelial cells correlated with a significant upregulation of tom1 mrna, both in vitro and in vivo when compared with their non-cf counterparts. introduction of synthetic pre-mir-126 inhibited luciferase activity in a reporter system containing the full length 3'-untranslated region of tom1 and resulted in decreased tom1 protein production in cf bronchial epithelial cells. following stimulation with lps or il-1beta, overexpression of tom1 was found to downregulate nf-kappab luciferase activity. conversely, tom1 knockdown resulted in a significant increase in nf-kappab regulated il-8 secretion. these data show that mir-126 is differentially regulated in cf versus non-cf airway epithelial cells and that tom1 is a mir-126 target that may have an important role in regulating innate immune responses in the cf lung. to our knowledge, this study is the first to report of a role for tom1 in the tlr2/4 signaling pathways and the first to describe microrna involvement in cf.",1
"the aberrant expression of micrornas (mirnas) is always associated with tumor development and progression. microvascular proliferation is one of the unique pathologic features of glioblastoma (gbm) . in this study, the microvasculature from gbm or normal brain tissue derived from neurosurgeries was purified and total rna was isolated from purified microvasculature. the difference of mirna expression profiles between glioblastoma microvasculature and normal brain capillaries was investigated. it was found that mir-7-5p in gbm microvessels was significantly reduced compared with that in normal brain capillaries. in the in vitro experiments, overexpression of mir-7-5p significantly inhibited human umbilical vein endothelial cell proliferation. forced expression of mir-7-5p in human umbilical vein endothelial cells in vitro significantly reduced the protein level of raf1 and repressed the activity of the luciferase, a reporter vector carrying the 3'-untranslated region of raf1. these findings indicate that raf1 is one of the mir-7-5p target genes. furthermore, a significant inverse correlation between mir-7-5p expression and raf1 protein level in gbm microvasculature was found. these data suggest that mir-7-5p functions as a tumor suppressor gene to regulate gbm microvascular endothelial cell proliferation potentially by targeting the raf1 oncogene, implicating an important role for mir-7-5p in the pathogenesis of gbm. it may serve as a guide for the antitumor angiogenesis drug development.",1
"micrornas are predicted to regulate approximately 30% of all human genes by targeting sequences in their 3' utr. polymorphisms in 3' utr of several genes have been reported to affect gene expression, but the mechanism is not fully understood. here, we demonstrate that 829c-->t, a naturally occurring snp, near the mir-24 binding site in the 3' utr of human dihydrofolate reductase (dhfr) affects dhfr expression by interfering with mir-24 function, resulting in dhfr overexpression and methotrexate resistance. mir-24 has a conserved binding site in dhfr 3' utr. dhfr with wt and 3' utr containing the 829c-->t mutation were expressed in dg44 cells that lack dhfr. overexpression of mir-24 in cells with wt dhfr resulted in down-regulation of dhfr protein, whereas no effect on dhfr protein expression was observed in the mutant 3' utr-expressing cells. inhibition of endogenous mir-24 with a specific inhibitor led to up-regulation of dhfr in wt and not in mutant cells. cells with the mutant 3' utr had a 2-fold increase in dhfr mrna half-life, expressed higher dhfr mrna and dhfr protein, and were 4-fold more resistant to methotrexate as compared with wt cells. snp-829c-->t, therefore, leads to a decrease in microrna binding leading to overexpression of its target and results in resistance to methotrexate. we demonstrate that a naturally occurring mirsnp (a snp located at or near a microrna binding site in 3' utr of the target gene or in a microrna) is associated with enzyme overproduction and drug resistance.",1
"a family of small non-coding rnas, ~22 nt in length, known as micrornas (mirnas), regulating ~30% of all human gene expression, have been reported to be involved in the pathogenesis of a number of types of cancers, including laryngeal squamous cell carcinoma (lscc). in the current study, mir-34a and mir-34c were observed to be downregulated in human lscc tissues. ectopic expression of mir-34a and mir-34c in hep-2 cells significantly induced the cell proliferation and migration ability in vitro. udp-n-acetyl-α-d-galactosamine:polypeptide-n-acetylgalactosaminyltransferase 7 (galnt7), whose expression is negatively regulated by mir-34a and mir-34c in hep-2 cells, is confirmed to be a novel direct target gene of mir-34a and mir-34c. in conclusion, the current results suggest that mir-34a and mir-34c may function as tumor suppressors in lscc through downregulation of galnt7. the study of mir-34a, mir-34c and its novel target, galnt7, may serve as novel potential makers for lscc therapy.",1
"background several lines of evidence have suggested that estrogen receptor alpha (eralpha)-negative breast tumors, which are highly aggressive and nonresponsive to hormonal therapy, arise from eralpha-positive precursors through different molecular pathways. because micrornas (mirnas) modulate gene expression, we hypothesized that they may have a role in er-negative tumor formation. methods gene expression profiles were used to highlight the global changes induced by mirna modulation of eralpha protein. mirna transfection and luciferase assays enabled us to identify new targets of mirna 206 (mir-206) and mirna cluster 221-222 (mir-221-222). northern blot, luciferase assays, estradiol treatment, and chromatin immunoprecipitation were performed to identify the mir-221-222 transcription unit and the mechanism implicated in its regulation. results different global changes in gene expression were induced by overexpression of mir-221-222 and mir-206 in er-positive cells. mir-221 and -222 increased proliferation of eralpha-positive cells, whereas mir-206 had an inhibitory effect (mean absorbance units : mir-206: 500 au, 95% confidence interval ) = 480 to 520; mir-221: 850 au, 95% ci = 810 to 873; mir-222: 879 au, 95% ci = 850 to 893; p conclusions these findings suggest that the negative regulatory loop involving mir-221-222 and eralpha may confer proliferative advantage and migratory activity to breast cancer cells and promote the transition from er-positive to er-negative tumors.",1
"gw182 family proteins interact with argonaute proteins and are required for the translational repression, deadenylation and decay of mirna targets. to elicit these effects, gw182 proteins interact with poly(a)-binding protein (pabp) and the ccr4-not deadenylase complex. although the mechanism of mirna target deadenylation is relatively well understood, how gw182 proteins repress translation is not known. here, we demonstrate that gw182 proteins decrease the association of eif4e, eif4g and pabp with mirna targets. eif4e association is restored in cells in which mirna targets are deadenylated, but decapping is inhibited. in these cells, eif4g binding is not restored, indicating that eif4g dissociates as a consequence of deadenylation. in contrast, pabp dissociates from silenced targets in the absence of deadenylation. pabp dissociation requires the interaction of gw182 proteins with the ccr4-not complex. accordingly, not1 and pop2 cause dissociation of pabp from bound mrnas in the absence of deadenylation. our findings indicate that the recruitment of the ccr4-not complex by gw182 proteins releases pabp from the mrna poly(a) tail, thereby disrupting mrna circularization and facilitating translational repression and deadenylation.",1
"purpose nuclear factor-κb (nf-κb), a key regulator of immune and inflammatory responses, plays important roles in diabetes-induced microvascular complications including diabetic retinopathy (dr). thrombin activates nf-κb through protease-activated receptor (par)-1, a member of the g-protein-coupled receptor (gpcr) superfamily, and contributes to dr. the current study is to uncover the roles of microrna (mirna) in thrombin-induced nf-κb activation and retinal endothelial functions. methods target prediction was performed using the targetscan algorithm. predicted target was experimentally validated by luciferase reporter assays. human retinal endothelial cells (hrecs) were transfected with mirna mimics or antimirs and treated with thrombin. expression levels of mir-146 and related protein-coding genes were analyzed by quantitative (q)rt-pcr. functional changes of hrecs were analyzed by leukocyte adhesion assays. results we identified that caspase-recruitment domain (card)-containing protein 10 (card10), an essential scaffold/adaptor protein of gpcr-mediated nf-κb activation pathway, is a direct target of mir-146. thrombin treatment resulted in nf-κb-dependent upregulation of mir-146 in hrecs; while transfection of mir-146 mimics resulted in significant downregulation of card10 and prevented thrombin-induced nf-κb activation, suggest that a negative feedback regulation of mir-146 on thrombin-induced nf-κb through targeting card10. furthermore, overexpression of mir-146 prevented thrombin-induced increased leukocyte adhesion to hrecs. conclusions we uncovered a novel negative feedback regulatory mechanism on thrombin-induced gpcr-mediated nf-κb activation by mir-146. in combination with the negative feedback regulation of mir-146 on the il-1r/toll-like receptor (tlr)-mediated nf-κb activation in recs that we reported previously, our results underscore a pivotal, negative regulatory role of mir-146 on multiple nf-κb activation pathways and related inflammatory processes in dr.",1
"atherosclerosis is a progressive condition of the large arteries that can cause coronary artery disease (cad). growing amounts of evidence have indicated that micrornas (mirnas, mirs) can be used as diagnostic biomarkers in many cellular processes associated with cad. mir-362-3p has been implicated in many biological cellular functions. however, little is known about the role of mir-362-3p during atherosclerosis. in the present study, significant downregulation of mir-362-3p was observed in 110 atherosclerotic cad patients and not in the 84 controls. the upregulation of mir-362-3p was demonstrated to inhibit vascular smooth muscle cell (vsmc) proliferation and migration, and impede the g1/s cell cycle transition. bioinformatics analysis indicated that a disintegrin and metalloproteinase with thrombospondin motifs 1 (adamts1) was a direct target of mir-362-3p. subsequent experiments demonstrated that mir-362-3p binds to the 3'-untranslated region (utr) of adamts1 and decreases its levels of mrna and protein expression. overexpression of adamts1 partially restored the mir-362-3p-mediated inhibition of vsmc proliferation, cell cycle, and migration. upregulation of adamts1 in plasma samples was detected in atherosclerotic cad patients. taken together, our findings suggested that mir-362-3p inhibits the proliferation and migration of vsmcs by directly targeting adamts1, which might provide novel insight into the molecular mechanisms underlying the action of mir-362-3p in atherosclerosis.",1
"delta like 1 homolog (dlk1) exists in both transmembrane and soluble molecular forms, and is implicated in cellular growth and plays multiple roles in development, tissue regeneration, and cancer. thus, dlk1 levels are critical for cell function, and abnormal dlk1 expression can be lethal; however, little is known about the underlying mechanisms. we here report that mir-15a modulates dlk1 levels in preadipocytes thus providing a mechanism for dlk1 regulation that further links it to cell cycle arrest and cancer since mir-15a is deregulated in these processes. in preadipocytes, mir-15a increases with cell density, and peaks at the same stage where membrane dlk1(m) and soluble dlk1(s) are found at maximum levels. remarkably, mir-15a represses the amount of all dlk1 variants at the mrna level but also the level of dlk1(m) protein while it increases the amount of dlk1(s) supporting a direct repression of dlk1 and a parallel effect on the protease that cleaves off the dlk1 from the membrane. in agreement with previous studies, we found that mir-15a represses cell numbers, but additionally, we report that mir-15a also increases cell size. conversely, anti-mir-15a treatment decreases cell size while increasing cell numbers, scenarios that were completely rescued by addition of purified dlk1(s). our data thus imply that mir-15a regulates cell size and proliferation by fine-tuning dlk1 among others, and further emphasize mir-15a and dlk1 levels to play important roles in growth signaling networks.",1
"twin-ribozyme introns are formed by two ribozymes belonging to the group i family and occur in some ribosomal rna transcripts. the group i-like ribozyme, gir1, liberates the 5' end of a homing endonuclease messenger rna in the slime mold didymium iridis. we demonstrate that this cleavage occurs by a transesterification reaction with the joining of the first and the third nucleotide of the messenger by a 2',5'-phosphodiester linkage. thus, a group i-like ribozyme catalyzes an rna branching reaction similar to the first step of splicing in group ii introns and spliceosomal introns. the resulting short lariat, by forming a protective 5' cap, might have been useful in a primitive rna world.",1
"recent studies have revealed that micrornas (mirs) play important roles in the regulation of angiogenesis. in this study, we have characterized mir-382 upregulation by hypoxia and the functional relevance of mir-382 in tumor angiogenesis. mirs induced by hypoxia in mkn1 human gastric cancer cells were investigated using mirna microarrays. we selected mir-382 and found that the expression of mir-382 was regulated by hif-1α. conditioned media (cm) from mkn1 cells transfected with a mir-382 inhibitor (antagomir-382) under hypoxic conditions significantly decreased vascular endothelial cell (ec) proliferation, migration and tube formation. algorithmic programs (target scan, miranda and cbio) predicted that phosphatase and tensin homolog (pten) is a target gene of mir-382. deletion of mir382-binding sequences in the pten mrna 3'-untranslated region (utr) diminished the luciferase reporter activity. subsequent study showed that the overexpression of mir-382 or antagomir-382 down- or upregulated pten and its downstream target akt/mtor signaling pathway, indicating that pten is a functional target gene of mir-382. in addition, pten inhibited mir-382-induced in vitro and in vivo angiogenesis as well as vegf secretion, and the inhibition of mir-382 expression reduced xenograft tumor growth and microvessel density in tumors. taken together, these results suggest that mir-382 induced by hypoxia promotes angiogenesis and acts as an angiogenic oncogene by repressing pten.",1
"this article has been retracted: please see elsevier policy on article withdrawal ( this article has been retracted at the request of the editors. this article was published on december 8, 2009. in november 2021, the ohio state university notified the cancer cell editors that this article contains ten instances of plagiarized text; that figures 1g, 5b, 5e, 7d, and 7f were falsified; and that part of figure 1g in the article is the same as part of figure 1b in another article that was later retracted (garofalo et al., 2008, plos one 3, e4070, the university recommended the editors correct or retract the article. given the extent and severity of these issues, the editors are retracting the article. s.-s. s. agrees with the retraction, and m.g., g.d.l., g.n., f.p., p.s., p.g., g.c., and c.m.c. disagree with the retraction; all other authors couldn't be reached or didn't respond.",1
"accumulating lines of evidence have revealed the involvement of long non-coding rnas (lncrnas) in the control and elimination of invading mycobacterium tuberculosis (mtb) by macrophage. in this study, we sought to elucidate the role of miat on autophagy and apoptosis of mtb-infected macrophage and to reveal the molecular mechanism. we observed that the expression of miat was heightened while mir-665 level was declined in thp-1 cells with bacillus calmette-guerin (bcg) infection in a time-dependent manner. functionally, disruption of miat effectively facilitated cell viability and restricted apoptosis ability concomitant with the downregulation of bax and cleaved caspase-3 along with an accumulation of bcl-2 in bcg-infected thp-1 cells. concurrently, the interference of miat dramatically disinhibited macrophage autophagy as characterized by diminution of autophagy related markers lc3-ii and beclin-1 as well as increment of p62 in thp-1 cells following bcg infection. concordantly, depletion of miat was found to noticeably aggrandize mtb survival. importantly, miat served as a cerna for sponging mir-665 and negatively regulated its expression. ulk1 was identified as an authentic target of mir-665 and modulated by miat. mechanistically, the functional role of miat depletion in macrophage apoptosis and autophagy were tremendously abrogated by the depression of mir-665 and enrichment of ulk1. overall, the preceding observations clearly illuminated that miat was elevated in human macrophage response to bcg infection, and functioned as a negative regulator in autophagy and antimicrobial effects by manipulating mir-665/ulk1 axis during mtb infection, which may provide a promising target for developing an anti-bacterial against tb.",1
"background the dystrophin glycoprotein complex (dgc) is at the center of significant inheritable diseases, such as muscular dystrophies that can be fatal and impair neuronal function in addition to muscle degeneration. recent evidence has shown that it can control cellular homeostasis and work via dystrophin signaling to regulate microrna gene expression which implies that disease phenotypes hide an entourage of regulatory and homeostatic anomalies. uncovering these hidden processes could shed new light on the importance of proper dgc function for an organism's overall welfare and bring forth new ideas for treatments. results to better understand a role for the dgc in these processes, we used the genetically advantageous drosophila muscular dystrophy model to conduct a whole animal microarray screen. since we have recently found that dystrophic symptoms can be caused by stress even in wild type animals and are enhanced in mutants, we screened stressed animals for microrna misregulation as well. we were able to define micrornas misregulated due to stress and/or dystrophy. our results support the hypothesis that there is a dystrophin and dystroglycan dependent circuitry of processes linking stress response, dystrophic conditions and cellular signaling and that micrornas play an important role in this network. verification of a subset of our results was conducted via q-pcr and revealed that mir-956, mir-980 and mir-252 are regulated via a dystroglycan-dystrophin-syntrophin dependent pathway. conclusions the results presented in this study support the hypothesis that there is a dystrophin and dystroglycan dependent circuitry of processes that includes regulation of micrornas. dystrophin signaling has already been found to occur in mammalian musculature; however, our data reveals that this regulation is evolutionarily conserved and also present in at least neuronal tissues. our data imply that dystroglycan-dystrophin-syntrophin signaling through control of multiple micrornas is involved in highly managed regulation of gene expression required to adapt cellular homeostasis that is compromised under stress and dystrophic conditions.",1
"the fushi tarazu gene is essential for the establishment of the drosophila embryonic body plan. when first expressed in early embryogenesis, fushi tarazu mrna is uniformly distributed over most of the embryo. subsequently, fushi tarazu mrna expression rapidly evolves into a pattern of seven stripes that encircle the embryo. the instability of fushi tarazu mrna is probably crucial for attaining this localized pattern of expression. mrna stability in transgenic embryos was measured by a new method that does not use drugs or external interference. experiments using hybrid genes that fuse fushi tarazu sequences to those of the stable ribosomal protein a1 mrna provide evidence for at least two destabilizing elements in the fushi tarazu mrna, one located within the 5' one-third of the mrna and the other near the 3' end (termed fie3 for ftz instability element 3'). the fie3 lies within a 201-nucleotide sequence just upstream of the polyadenylation signal and can act autonomously to destabilize a heterologous mrna. further deletion constructs identified an essential 68-nucleotide element within the fie3. lack of homology between this element and other previously identified destabilization sequences suggests that fie3 contains a novel rna destabilization element.",1
"dysregulated expression of bone morphogenetic protein receptor type ii (bmpr2) is a pathogenetic hallmark of pulmonary hypertension. downregulation of bmpr2 protein but not mrna has been observed in multiple animal models mimicking the disease, indicating a posttranscriptional mechanism of regulation. because micrornas (mirnas) regulate gene expression mainly through inhibition of target gene translation, we hypothesized that mirnas may play a role in the modulation of bmpr2. performing a computational algorithm on the bmpr2 gene, several mirnas encoded by the mirna cluster 17/92 (mir-17/92) were retrieved as potential regulators. ectopic overexpression of mir-17/92 resulted in a strong reduction of the bmpr2 protein, and a reporter gene system showed that bmpr2 is directly targeted by mir-17-5p and mir-20a. by stimulation experiments, we found that the mir-17/92 cluster is modulated by interleukin (il)-6, a cytokine involved in the pathogenesis of pulmonary hypertension. because il-6 signaling is mainly mediated by stat3 (signal transducer and activator of transcription 3), the expression of stat3 was knocked down by small interfering rna, which abolished the il-6-mediated expression of mir-17/92. consistent with these data, we found a highly conserved stat3-binding site in the promoter region of the mir-17/92 gene (c13orf25). promoter studies confirmed that il-6 enhances transcription of c13orf25 through this distinct region. finally, we showed that persistent activation of stat3 leads to repressed protein expression of bmpr2. taken together, we describe here a novel stat3-mir-17/92-bmpr2 pathway, thus providing a mechanistic explanation for the loss of bmpr2 in the development of pulmonary hypertension.",1
"accumulating evidence has shown that micrornas are involved in multiple processes in gastric cancer (gc) development and progression. aberrant expression of mir-497 has been frequently reported in cancer studies; however, the role and mechanism of its function in gc remains unknown. here, we reported that mir-497 was frequently downregulated in gc tissues and associated with aggressive clinicopathological features of gc patients. further in vitro observations showed that the enforced expression of mir-497 inhibited cell proliferation by blocking the g1/s transition and decreased the invasion of gc cells, implying that mir-497 functions as a tumor suppressor in the progression of gc. in vivo study indicated that restoration of mir-497 inhibited tumor growth and metastasis. luciferase assays revealed that mir-497 inhibited eif4e expression by targeting the binding sites in the 3'-untranslated region of eif4e mrna. qrt-pcr and western blot assays verified that mir-497 reduced eif4e expression at both the mrna and protein levels. a reverse correlation between mir-497 and eif4e expression was noted in gc tissues. taken together, our results identify a crucial tumor suppressive role of mir-497 in the progression of gc and suggest that mir-497 might be an anticancer therapeutic target for gc patients.",1
"micrornas (mirnas) negatively regulate partially complementary target messenger rnas. target selection in animals is dictated primarily by sequences at the mirna 5' end. we demonstrated that despite their small size, specific mirnas contain additional sequence elements that control their posttranscriptional behavior, including their subcellular localization. we showed that human mir-29b, in contrast to other studied animal mirnas, is predominantly localized to the nucleus. the distinctive hexanucleotide terminal motif of mir-29b acts as a transferable nuclear localization element that directs nuclear enrichment of mirnas or small interfering rnas to which it is attached. our results indicate that mirnas sharing common 5' sequences, considered to be largely redundant, might have distinct functions because of the influence of cis-acting regulatory motifs.",1
"fragile x-associated tremor/ataxia syndrome (fxtas), a late-onset neurodegenerative disorder, has been recognized in older male fragile x premutation carriers and is uncoupled from fragile x syndrome. using a drosophila model of fxtas, we previously showed that transcribed premutation repeats alone are sufficient to cause neurodegeneration. mirnas are sequence-specific regulators of post-transcriptional gene expression. to determine the role of mirnas in rcgg repeat-mediated neurodegeneration, we profiled mirna expression and identified selective mirnas, including mir-277, that are altered specifically in drosophila brains expressing rcgg repeats. we tested their genetic interactions with rcgg repeats and found that mir-277 can modulate rcgg repeat-mediated neurodegeneration. furthermore, we identified drep-2 and vimar as functional targets of mir-277 that could modulate rcgg repeat-mediated neurodegeneration. finally, we found that hnrnp a2/b1, an rcgg repeat-binding protein, can directly regulate the expression of mir-277. these results suggest that sequestration of specific rcgg repeat-binding proteins could lead to aberrant expression of selective mirnas, which may modulate the pathogenesis of fxtas by post-transcriptionally regulating the expression of specific mrnas involved in fxtas.",1
"micrornas are small non-coding rnas that repress the expression of their target proteins. the roles of micrornas in the development of alzheimer's disease (ad) are not clear. in this study we show that mir-200c represses the expression of pten protein. pten downregulation by mir-200c supports the survival and differentiation of cultured neurons. ad is a progressive neurodegenerative disease signified by beta amyloid (aβ) peptide aggregation and deposition. in a mouse model of ad that is induced by appswe and ps1 δ e9 double transgenes, we found aβ deposition results in neuronal er stress that induces mir200c. pharmacological blockade of er stress inhibited aβ-induced mir-200c overexpression in ad brains. mir-200c was detected in the serum of both ad mice and human ad patients. these findings suggest that mir-200c functions as part of the neuronal cell-intrinsic adaptive machinery, and supports neuronal survival and differentiation in response to aβ induced er-stress by downregulating pten.",1
"micrornas (mirnas) are an emerging group of short, noncoding rnas that play an important role in regulating expression of classical genes. thus far little is known about their role in autoimmune demyelination. in this study, we analyzed changes in the mirna profile in cd4(+) t cells that occurred during the recognition of the myelin autoantigen, mog(35-55). we found that, both in vivo and in vitro, myelin antigen stimulation resulted in significant up-regulation of mir-301a, mir-21, and mir-155. furthermore, these three mirnas were overexpressed in t cells infiltrating the cns in animals with experimental autoimmune encephalomyelitis. use of specific mirna antagonists, antagomirs, revealed that mir-301a contributed to the development of the t-helper type 17 subset via targeting the il-6/23-stat3 pathway. this contribution appeared to be mediated by the mir-301a effect on the expression of the pias3, a potent inhibitor of the stat3 pathway. manipulation of mir-301a levels or pias3 expression in myelin-specific cd4(+) t cells led to significant changes in the severity of experimental autoimmune encephalomyelitis. thus, we have identified a role of mir-301a in regulating the function of myelin-reactive t-helper type 17 cells, supporting a role for mir-301a and pias3 as candidates for therapeutic targets for controlling of autoimmune demyelination.",1
"small rnas (srnas) that act by base pairing with trans-encoded mrnas modulate metabolism in response to a variety of environmental stimuli. here, we describe an hfq-binding srna (fnrs) whose expression is induced upon a shift from aerobic to anaerobic conditions and which acts to downregulate the levels of a variety of mrnas encoding metabolic enzymes. anaerobic induction in minimal medium depends strongly on fnr but is also affected by the arca and crp transcription regulators. whole genome expression analysis showed that the levels of at least 32 mrnas are downregulated upon fnrs overexpression, 15 of which are predicted to base pair with fnrs by targetrna. the srna is highly conserved across its entire length in numerous enterobacteria, and mutational analysis revealed that two separate regions of fnrs base pair with different sets of target mrnas. the majority of the target genes were previously reported to be downregulated in an fnr-dependent manner but lack recognizable fnr binding sites. we thus suggest that fnrs extends the fnr regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions.",1
"rna transcripts are subject to posttranscriptional gene regulation involving hundreds of rna-binding proteins (rbps) and microrna-containing ribonucleoprotein complexes (mirnps) expressed in a cell-type dependent fashion. we developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular rbps and mirnps. the crosslinked sites are revealed by thymidine to cytidine transitions in the cdnas prepared from immunopurified rnps of 4-thiouridine-treated cells. we determined the binding sites and regulatory consequences for several intensely studied rbps and mirnps, including pum2, qki, igf2bp1-3, ago/eif2c1-4 and tnrc6a-c. our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. the precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.",1
"background long non-coding rnas (lncrnas) are known to play important roles in different cell contexts, including cancers. however, little is known about lncrnas in cholangiocarcinoma (cca), a cholangiocyte malignancy with poor prognosis, associated with chronic inflammation and damage to the biliary epithelium. the aim of the study is to identify if any lncrna might associate with inflammation or oxidative stress in cca and regulate the disease progression. methods in this study, rna-seqs datasets were used to identify aberrantly expressed lncrnas. small interfering rna and overexpressed plasmids were used to modulate the expression of lncrnas, and luciferase target assay rna immunoprecipitation (rip) was performed to explore the mechanism of mirna-lncrna sponging. results we firstly analyzed five available rna-seqs datasets to investigate aberrantly expressed lncrnas which might associate with inflammation or oxidative stress. we identified that two lncrnas, h19 and hulc, were differentially expressed among all the samples under the treatment of hypoxic or inflammatory factors, and they were shown to be stimulated by short-term oxidative stress responses to h 2 o 2 and glucose oxidase in cca cell lines. further studies revealed that these two lncrnas promoted cholangiocyte migration and invasion via the inflammation pathway. h19 and hulc functioned as competing endogenous rnas (cernas) by sponging let-7a/let-7b and mir-372/mir-373, respectively, which activate pivotal inflammation cytokine il-6 and chemokine receptor cxcr4. conclusions our study revealed that h19 and hulc, up-regulated by oxidative stress, regulate cca cell migration and invasion by targeting il-6 and cxcr4 via cerna patterns of sponging let-7a/let-7b and mir-372/mir-373, respectively. the results suggest that these lncrnas might be the chief culprits of cca pathogenesis and progression. the study provides new insight into the mechanism linking lncrna function with cca and may serve as novel targets for the development of new countermeasures of cca.",1
"the nuclear matrix protein cip1-interacting zinc finger protein 1 (ciz1) promotes dna replication in association with cyclins and has been linked to adult and pediatric cancers. here we show that ciz1 is highly enriched on the inactive x chromosome (xi) in mouse and human female cells and is retained by interaction with the rna-dependent nuclear matrix. ciz1 is recruited to xi in response to expression of x inactive-specific transcript (xist) rna during the earliest stages of x inactivation in embryonic stem cells and is dependent on the c-terminal nuclear matrix anchor domain of ciz1 and the e repeats of xist ciz1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder. interestingly, in mouse embryonic fibroblast cells derived from ciz1-null embryos, xist rna localization is disrupted, being highly dispersed through the nucleoplasm rather than focal. focal localization is reinstated following re-expression of ciz1. focal localization of xist rna is also disrupted in activated b and t cells isolated from ciz1-null animals, suggesting a possible explanation for female-specific lymphoproliferative disorder. together, these findings suggest that ciz1 has an essential role in anchoring xist to the nuclear matrix in specific somatic lineages.",1
"dysregulation of aldosterone or cortisol production can predispose to hypertension, as seen in aldosterone-producing adenoma, a form of primary aldosteronism. we investigated the role of microrna (mirna) in their production, with particular emphasis on the cyp11b1 (11β-hydroxylase) and cyp11b2 (aldosterone synthase) genes, which produce the enzymes responsible for the final stages of cortisol and aldosterone biosynthesis, respectively. knockdown of dicer1, a key enzyme in mirna maturation, significantly altered cyp11b1 and cyp11b2 expression in a human adrenocortical cell line. screening of nondiseased human adrenal and aldosterone-producing adenoma samples yielded reproducible but distinctive mirna expression signatures for each tissue type, with levels of certain mirna, including microrna-24 (mir-24), differing significantly between the 2. bioinformatic analysis identified putative binding sites for several mirna, including mir-24, in the 3' untranslated region of cyp11b1 and cyp11b2 mrnas. in vitro manipulation of mir-24 confirmed its ability to modulate cyp11b1 and cyp11b2 expression, as well as cortisol and aldosterone production. this study demonstrates that dicer-dependent mirna, including mir-24, can post-transcriptionally regulate expression of the cyp11b1 and cyp11b2 genes. normal adrenal tissue and aldosterone-producing adenoma differ significantly and reproducibly in their mirna expression profiles, with mir-24 significantly downregulated in the latter. adrenal mirna may, therefore, be a novel and valid target for the therapeutic manipulation of corticosteroid biosynthesis.",1
"we determined the effects of maternal diet-induced obesity on offspring adipose tissue insulin signalling and mirna expression in the aetiology of insulin resistance in later life. although body composition and glucose tolerance of 8-week-old male offspring of obese dams were not dysregulated, serum insulin was significantly (p<0.05) elevated. key insulin signalling proteins in adipose tissue were down-regulated, including the insulin receptor, catalytic (p110β) and regulatory (p85α) subunits of pi3k as well as akt1 and 2 (all p<0.05). the largest reduction observed was in irs-1 protein (p<0.001), which was regulated post-transcriptionally. concurrently, mir-126, which targets irs-1, was up-regulated (p<0.05). these two features were maintained in isolated primary pre-adipocytes and differentiated adipocytes in-vitro. we have therefore established that maternal diet-induced obesity programs adipose tissue insulin resistance. we hypothesise that maintenance of the phenotype in-vitro strongly suggests that this mechanism is cell autonomous and may drive insulin resistance in later life.",1
"the role of mirnas in regulating megakaryocyte differentiation was examined using bipotent k562 human leukemia cells. mir-34a is strongly up-regulated during phorbol ester-induced megakaryocyte differentiation, but not during hemin-induced erythrocyte differentiation. enforced expression of mir-34a in k562 cells inhibits cell proliferation, induces cell-cycle arrest in g(1) phase, and promotes megakaryocyte differentiation as measured by cd41 induction. mir-34a expression is also up-regulated during thrombopoietin-induced differentiation of cd34(+) hematopoietic precursors, and its enforced expression in these cells significantly increases the number of megakaryocyte colonies. mir-34a directly regulates expression of myb, facilitating megakaryocyte differentiation, and of cdk4 and cdk6, to inhibit the g(1)/s transition. however, these mir-34a target genes are down-regulated rapidly after inducing megakaryocyte differentiation before mir-34a is induced. this suggests that mir-34a is not responsible for the initial down-regulation but may contribute to maintaining their suppression later on. previous studies have implicated mir-34a as a tumor suppressor gene whose transcription is activated by p53. however, in p53-null k562 cells, phorbol esters induce mir-34a expression independently of p53 by activating an alternative phorbol ester-responsive promoter to produce a longer pri-mir-34a transcript.",1
"breast cancer is the most common cancer in women around the world. however, the molecular mechanisms underlying breast cancer pathogenesis are only partially understood. here, in this study, we found that p2x7r was up-regulated and mir-216b was down-regulated in breast cancer cell lines and tissues. using bioinformatic analysis and 3'utr luciferase reporter assay, we determined p2x7r can be directly targeted by mir-216b, which can down-regulate endogenous p2x7r mrna and protein levels. ectopic expression of mir-216b mimics leads to inhibited cell growth and apoptosis, while blocking expression of the mir-216b results in increased cell proliferation. furthermore, our findings demonstrate that knockdown of p2x7r promotes apoptosis in breast cancer cells through down-regulating bcl-2 and increasing the cleavage caspase-3 protein level. finally, we confirmed that down-regulation of mir-216b in breast cancer is inversely associated with p2x7r expression level. together, these findings establish mir-216b as a novel regulator of p2x7r and a potential therapeutic target for breast cancer.",1
"gene expression is regulated in a context-dependent, cell-type-specific manner. condition-specific transcription is dependent on the presence of transcription factors (tfs) that can activate or inhibit its target genes (global context). additional factors, such as chromatin structure, histone, or dna modifications, also influence the activity of individual target genes (individual context). the role of the global and individual context for post-transcriptional regulation has not systematically been investigated on a large scale and is poorly understood. here we show that global and individual context dependency is a pervasive feature of microrna-mediated regulation. our comprehensive and highly consistent data set from several high-throughput technologies (par-clip, rip-chip, 4su-tagging, and silac) provides strong evidence that context-dependent microrna target sites (cdts) are as frequent and functionally relevant as constitutive target sites (cts). furthermore, we found the global context to be insufficient to explain the cdts, and that flanking sequence motifs provide individual context that is an equally important factor. our results demonstrate that, similar to tf-mediated regulation, global and individual context dependency are prevalent in microrna-mediated gene regulation, implying a much more complex post-transcriptional regulatory network than is currently known. the necessary tools to unravel post-transcriptional regulations and mechanisms need to be much more involved, and much more data will be needed for particular cell types and cellular conditions in order to understand microrna-mediated regulation and the context-dependent post-transcriptional regulatory network.",1
"a requisite step in the biosynthesis of trna is the removal of 5' leader sequences from trna precursors. we have detected an rnase p activity in yeast mitochondrial extracts that can carry out this reaction on a homologous precursor trna. this mitochondrial rnase p was sensitive to both micrococcal nuclease and protease, demonstrating that it requires both a nucleic acid and protein for activity. the presence of rnase p activity in vitro directly correlated with the presence of a locus on yeast mitochondrial dna previously shown by genetic and biochemical studies to be required for trna maturation. the product of the locus, the 9s rna, and this newly described mitochondrial rnase p activity cofractionated, providing further evidence that the 9s rna is the rna component of yeast mitochondrial rnase p.",1
"activation of pre-messenger rna (pre-mrna) splicing requires 5' splice site recognition by u1 small nuclear rna (snrna), which is replaced by u5 and u6 snrna. here we use crosslinking to investigate snrna interactions with the 5' exon adjacent to the 5' splice site, prior to the first step of splicing. u1 snrna was found to interact with four different 5' exon positions using one specific sequence adjacent to u1 snrna helix 1. this novel interaction of u1 we propose occurs before u1-5' splice site base pairing. in contrast, u5 snrna interactions with the 5' exon of the pre-mrna progressively shift towards the 5' end of u5 loop 1 as the crosslinking group is placed further from the 5' splice site, with only interactions closest to the 5' splice site persisting to the 5' exon intermediate and the second step of splicing. a novel yeast u2 snrna interaction with the 5' exon was also identified, which is atp dependent and requires u2-branchpoint interaction. this study provides insight into the nature and timing of snrna interactions required for 5' splice site recognition prior to the first step of pre-mrna splicing.",1
"lung cancer is the most common cancer as well as the leading cause of cancer-related mortalities worldwide. macrophages are the most abundant immune cells in primary and metastatic tumors, and contribute to tumor initiation, progression and metastasis. macrophages have been shown to demonstrate a high level of plasticity, with the ability to undergo dynamic transition between m1 and m2 polarized phenotypes. in the present study, we investigated a pivotal role of mir-130a in macrophage polarization and whether it was associated with poor prognosis in non-small cell lung cancer (nsclc), using rt-qpcr and western blot analyses. the in vitro experiments showed that mirna-130a was expressed at a higher level in m1 compared to m2 macrophages. the enforced expression of mir-130a in macrophages resulted in a significantly increased production of proinflammatory cytokines, whereas deletion of mir-130a impaired the m2‑associated gene expression and led to an m1-biased response. mechanistically, the bioinformatics analysis revealed that proliferator-activated receptor γ (pparγ) is a potential target of mir-130a. additionally, the luciferase assay confirmed that pparγ translation was suppressed by mir-130a through the interaction with the 3'utr of pparγ mrna. a subsequent analysis revaled that the induction of mir-130a suppressed pparγ protein expression. in nsclc patients, the results showed that mir-130a downregulation exhibited clinical relevance as it was correlated with poor prognosis and increased tumor stage and metastasis. in addition, mir‑130a was inversely correlated with the macrophage marker, cd163, and target gene, pparγ. taken together, the results established mir-130a as a molecular switch during macrophage development and as a potential target for the treatment of nsclc.",1
"while studies of the evolutionary histories of protein families are commonplace, little is known on noncoding rnas beyond micrornas and some snornas. here we investigate in detail the evolutionary history of the nine spliceosomal snrna families (u1, u2, u4, u5, u6, u11, u12, u4atac, and u6atac) across the completely or partially sequenced genomes of metazoan animals. representatives of the five major spliceosomal snrnas were found in all genomes. none of the minor splicesomal snrnas were detected in nematodes or in the shotgun traces of oikopleura dioica, while in all other animal genomes at most one of them is missing. although snrnas are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. in general, animal snrna secondary structures are highly conserved, albeit, in particular, u11 and u12 in insects exhibit dramatic variations. an analysis of genomic context of snrnas reveals that they behave like mobile elements, exhibiting very little syntenic conservation.",1
"we have identified the saccharomyces cerevisiae homolog of the signal recognition particle (srp) and characterized its function in vivo. s. cerevisiae srp is a 16s particle that includes a homolog of the signal sequence-binding protein subunit of srp (srp54p) and a small cytoplasmic rna (scr1). surprisingly, the genes encoding scr1 and srp54p are not essential for growth, though srp-deficient cells grow poorly, suggesting that srp function can be partially by-passed in vivo. protein translocation across the er membrane is impaired in srp-deficient cells, indicating that yeast srp, like its mammalian counterpart, functions in this process. unexpectedly, the degree of the translocation defect varies for different proteins. the ability of some proteins to be efficiently targeted in srp-deficient cells may explain why previous genetic and biochemical analyses in yeast and bacteria did not reveal components of the srp-dependent protein targeting pathway.",1
"unlabelled backgroundobjective: micrornas (mirnas) are small noncoding rnas (ribonucleic acids), approximately 22 nucleotides in length, that function as regulators of gene expression. dysregulation of mirnas has been associated with the initiation and progression of oncogenesis in humans. the cell division cycle (cdc)25 phosphatases are important regulators of the cell cycle. their abnormal expression detected in a number of tumors implies that their dysregulation is involved in malignant transformation. methods using mirna target prediction software, we found that mir-141 could target the 3' untranslated region (3'utr) sequence of cdc25b. to shed light on the role of mir-141 in renal cell carcinogenesis, the expression of mir-141 was examined by real-time polymerase chain reaction (rt-pcr) in renal cell carcinoma and normal tissues. the impact of mir-141 re-expression on 769-p cells was analyzed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (mtt) and colony-forming assay. a luciferase reporter assay was applied to prove the functionality of the mir-141 binding site. results mir-141 is significantly downregulated in renal cell carcinoma. mir-141 re-expression suppressed cell growth in 769-p cells. luciferase expression from a reporter vector containing the cdc25b-3'utr was decreased when this construct was transfected with mir-141 in 769-p cells. the overexpression of mir-141 suppressed the endogenous cdc25b protein level in 769-p cells. conclusion for the first time, we demonstrated that cdc25b is a direct target of mir-141 in renal cell carcinoma. the transcriptional loss of mir-141 and the resultant increase in cdc25b expression facilitates increased genomic instability at an early stage of renal cell carcinoma development.",1
"human embryonic stem (hes) cells have the capacities to propagate for extended periods and to differentiate into cell types from all three germ layers both in vitro and in vivo. these characteristics of self-renewal and pluripotency enable hes cells having the potential to provide an unlimited supply of different cell types for tissue replacement, drug screening, and functional genomics studies. the hes-t3 cells with normal female karyotype cultured on either mouse embryonic fibroblasts (mef) in hes medium (containing 4 ng/ml bfgf) (t3mf) or feeder-free matrigel in mef-conditioned medium (supplemented with additional 4 ng/ml bfgf) (t3cm) were found to express very similar profiles of mrnas and micrornas, indicating that the unlimited self-renewal and pluripotency of hes cells can be maintained by continuing culture on these two conditions. however, the expression profiles, especially micrornas, of the hes-t3 cells cultured on matrigel in hes medium supplemented with 4 ng/ml bfgf and 5 ng/ml activin a (t3ba) were found to be different from those of t3mf and t3cm cells. in t3ba cells, four hes cell-specific micrornas mir-372, mir-302d, mir-367, and mir-200c, as well as three other micrornas mir-199a, mir-19a, and mir-217, were found to be up-regulated, whereas five mirnas mir-19b, mir-221, mir-222, let-7b, and let-7c were down-regulated by activin a. thirteen abundantly differentially expressed mrnas, including nr4a2, erbb4, cxcr4, pcdh9, tmeff2, cd24, and cox6a1 genes, targeted by seven over-expressed mirnas were identified by inverse expression levels of these seven micrornas to their target mrnas in t3ba and t3cm cells. the nr4a2, erbb4, and cxcr4 target genes were further found to be regulated by egf and/or tnf. the 50 abundantly differentially expressed genes targeted by five under-expressed mirnas were also identified. the abundantly expressed mrnas in t3ba and t3cm cells were also analyzed for the network and signaling pathways, and roles of activin a in cell proliferation and differentiation were found. these findings will help elucidate the complex signaling network which maintains the self-renewal and pluripotency of hes cells.",1
"heading aims abdominal aortic aneurysm (aaa) is featured by the growth impediment and apoptosis surge of vsmcs (vascular smooth muscle cells). micrornas (mirnas) are suggested to affect cellular behaviors including cell growth and apoptosis. this study concentrated on unraveling the emerging role of mir-28-5p in abdominal aortic aneurysm. materials and methods previously, mir-28-5p was reported to be highly expressed in aaa. functional assays were utilized to determine the role of mir-28-5p in vsmc apoptosis. to narrow down the downstream mrnas, bioinformatics methods were utilized. the interaction between mir-28-5p and gria4 (glutamate ionotropic receptor ampa type subunit 4) or lypd3 (ly6/plaur domain containing 3) was explored. candidate circrnas (circular rnas) of mir-28-5p were identified. rescue analyses validated function of circcbfb (core-binding factor subunit beta)/mir-28-5p/gria4/lypd3 axis in vsmc apoptosis and growth. key findings mir-28-5p acted as an apoptosis driver while circcbfb, gria4 and lypd3 exerted anti-apoptosis effects in vsmcs. mechanically, gria4 and lypd3 were suppressed by mir-28-5p. moreover, circcbfb served as a sponge of mir-28-5p, releasing gria4 and lypd3 from mir-28-5p suppression. functionally, gria4, lypd3 and mir-28-5p were required in circcbfb-mediated vsmc apoptosis. significance this work unveiled an innovative axis of circcbfb/mir-28-5p/gria4/lypd3 in vsmc apoptosis, exerting its potential in providing new thoughts in aaa management.",1
"micrornas (mirnas) are posttranscriptional modulators of gene expression and play an important role in many developmental processes. recent studies suggest roles of mirnas in carcinogenesis. fragile histidine triad (fhit) gene deletion, methylation, and reduced fhit protein expression occur in about 70% of human epithelial tumors and are clearly associated with tumor progression. although it has been previously reported that fhit(-/-)cells exhibit more resistance to multi-dna damage inducers, including ionizing radiation, it remains unclear how mirnas targeting fhit in dna damage response play the role. this study reports that mir-143 directly targets fhit and that overexpression of mir-143 results in significant g2-phase arrest and protects cells from dna damage-induced killing. these results indicate an association of fhit gene inactivation with increased survival after dna damage and also provide useful information for mirna-based drug development in two directions: protect cells from dna damage-induced killing and sensitize cells to radiation therapy.",1
"we describe the crystal structure of the complete thermus thermophilus 70s ribosome containing bound messenger rna and transfer rnas (trnas) at 5.5 angstrom resolution. all of the 16s, 23s, and 5s ribosomal rna (rrna) chains, the a-, p-, and e-site trnas, and most of the ribosomal proteins can be fitted to the electron density map. the core of the interface between the 30s small subunit and the 50s large subunit, where the trna substrates are bound, is dominated by rna, with proteins located mainly at the periphery, consistent with ribosomal function being based on rrna. in each of the three trna binding sites, the ribosome contacts all of the major elements of trna, providing an explanation for the conservation of trna structure. the trnas are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with trna translocation with intersubunit movement.",1
"transfer rnas (trnas) are ubiquitous adapter molecules that link specific codons in messenger rna (mrna) with their corresponding amino acids during protein synthesis. the trna genes of drosophila have been investigated for over half a century but have lacked systematic identification and nomenclature. here, we review and integrate data within flybase and the genomic trna database (gtrnadb) to identify the full complement of trna genes in the d. melanogaster nuclear and mitochondrial genomes. we apply a logical and informative nomenclature to all trna genes, and provide an overview of their characteristics and genomic features.",1
"the protective effect of hydrogen sulfide (h2s) against myocardial ischemia/reperfusion (ir) injury via anti-apoptotic signaling is well established, but the underlying mechanism remains unclear. recently, mirnas have been identified as important mediators of myocardial injury by regulating apoptosis-related genes. it was found in our previous preliminary study that microrna-1 (mir-1) expression underwent a significant change in ir group compared to h2s preconditioned group, indicating that mir-1 possessed myocyte-specific properties. in the present study, we intended to see whether mir-1 participated in h2s protection of cardiomyocytes against ir-induced apoptosis by regulating apoptosis-related genes. cardiomyocytes of neonatal rats were subjected to hypoxia/reoxygenation (hr) injury with or without h2s preconditioning, while the myocardium of adult sd rats was subjected to ir with or without h2s preconditioning. it was found that hr injury increased apoptosis of cardiac myocytes, up-regulated the expression of mir-1, and down-regulated the expression of bcl-2. h2s preconditioning attenuated cardiomyocyte apoptosis and ldh release, as well as enhanced cell viability following hr injury. mir-1 was up-regulated by hr and down-regulated by h2s preconditioning. in contrast, bcl-2 was down-regulated by hr and up-regulated by h2s preconditioning. in addition, bcl-2 protein was down-regulated by the mir-1 mimic in a dose-dependent manner. h2s also attenuated ir-induced cardiomyocyte apoptosis in vivo. mir-1 regulated h2s protection of cardiomyocytes against ir-induced apoptosis by stimulating bcl-2. these results implicate mir-1 as an important regulator of h2s on the ir myocardium.",1
"micrornas (mirnas) are a class of small noncoding rnas that have gained status as important regulators of gene expression. here, we investigated the function and molecular mechanisms of the mir-208 family of mirnas in adult mouse heart physiology. we found that mir-208a, which is encoded within an intron of alpha-cardiac muscle myosin heavy chain gene (myh6), was actually a member of a mirna family that also included mir-208b, which was determined to be encoded within an intron of beta-cardiac muscle myosin heavy chain gene (myh7). these mirnas were differentially expressed in the mouse heart, paralleling the expression of their host genes. transgenic overexpression of mir-208a in the heart was sufficient to induce hypertrophic growth in mice, which resulted in pronounced repression of the mir-208 regulatory targets thyroid hormone-associated protein 1 and myostatin, 2 negative regulators of muscle growth and hypertrophy. studies of the mir-208a tg mice indicated that mir-208a expression was sufficient to induce arrhythmias. furthermore, analysis of mice lacking mir-208a indicated that mir-208a was required for proper cardiac conduction and expression of the cardiac transcription factors homeodomain-only protein and gata4 and the gap junction protein connexin 40. together, our studies uncover what we believe are novel mirna-dependent mechanisms that modulate cardiac hypertrophy and electrical conduction.",1
"previous studies have suggested that the hif transcription factors can both activate and inhibit gene expression. here we show that hif1 regulates the expression of mir-210 in a variety of tumor types through a hypoxia-responsive element. expression analysis in primary head and neck tumor samples indicates that mir-210 may serve as an in vivo marker for tumor hypoxia. by argonaute protein immunoprecipitation, we identified 50 potential mir-210 targets and validated randomly selected ones. the majority of these 50 genes are not classical hypoxia-inducible genes, suggesting mir-210 represses genes expressed under normoxia that are no longer necessary to adapt and survive in a hypoxic environment. when human head and neck or pancreatic tumor cells ectopically expressing mir-210 were implanted into immunodeficient mice, mir-210 repressed initiation of tumor growth. taken together, these data implicate an important role for mir-210 in regulating the hypoxic response of tumor cells and tumor growth.",1
"bone marrow-derived mesenchymal stem cells (mscs) are able to migrate to tumors, where they promote tumorigenesis and cancer metastasis. however, the molecular phenotype of the recruited mscs at the tumor microenvironment and the genetic programs underlying their role in cancer progression remains largely unknown. by using a three-dimensional rotary wall vessel coculture system in which human mscs were grown alone or in close contact with lncap, c4-2 or pc3 prostate cancer cell lines, we established in vitro matched pairs of normal and cancer-associated msc derivatives to study the stromal response of mscs to prostate cancer. we observed that prostate cancer-associated mscs acquired a higher potential for adipogenic differentiation and exhibited a stronger ability to promote prostate cancer cell migration and invasion compared with normal mscs both in vitro and in experimental animal models. the enhanced adipogenesis and the pro-metastatic properties were conferred by the high levels of il-6 secretion by cancer-associated mscs and were reversible by functionally inhibiting of il-6. we also found that il-6 is a direct target gene for the let-7 microrna, which was downregulated in cancer-associated mscs. the overexpression of let-7 via the transfection of let-7 precursors decreased il-6 expression and repressed the adipogenic potential and metastasis-promoting activity of cancer-associated mscs, which was consistent with the inhibition of il-6 3'utr luciferase activity. conversely, the treatment of normal mscs with let-7 inhibitors resulted in effects similar to those seen with il-6. taken together, our data demonstrated that mscs co-evolve with prostate cancer cells in the tumor microenvironment, and the downregulation of let-7 by cancer-associated mscs upregulates il-6 expression. this upregulation triggers adipogenesis and facilitates prostate cancer progression. these findings not only provide key insights into the molecular basis of tumor-stroma interactions but also pave the way for new treatments for metastatic prostate cancer.",1
"pancreatic cancer is a disease with an extremely poor prognosis. tumor protein 53-induced nuclear protein 1 (tp53inp1) is a proapoptotic stress-induced p53 target gene. in this article, we show by immunohistochemical analysis that tp53inp1 expression is dramatically reduced in pancreatic ductal adenocarcinoma (pdac) and this decrease occurs early during pancreatic cancer development. tp53inp1 reexpression in the pancreatic cancer-derived cell line miapaca2 strongly reduced its capacity to form s.c., i.p., and intrapancreatic tumors in nude mice. this anti-tumoral capacity is, at least in part, due to the induction of caspase 3-mediated apoptosis. in addition, tp53inp1(-/-) mouse embryonic fibroblasts (mefs) transformed with a retrovirus expressing e1a/ras(v12) oncoproteins developed bigger tumors than tp53inp1(+/+) transformed mefs or tp53inp1(-/-) transformed mefs with restored tp53inp1 expression. finally, tp53inp1 expression is repressed by the oncogenic micro rna mir-155, which is overexpressed in pdac cells. tp53inp1 is a previously unknown mir-155 target presenting anti-tumoral activity.",1
"telomerase rna is an integral part of telomerase, the ribonucleoprotein enzyme that catalyzes the synthesis of telomeric dna. the rna moiety contains a templating domain that directs the synthesis of a species-specific telomeric repeat and may also be important for enzyme structure and/or catalysis. phylogenetic comparisons of telomerase rna sequences from various tetrahymena spp. and hypotrich ciliates have revealed two conserved secondary structure models that share many features. we have cloned and sequenced the telomerase rna genes from an additional six tetrahymena spp. (t. vorax, t. borealis, t. australis, t. silvana, t. capricornis and t. paravorax). inclusion of these sequences, most notably that from t. paravorax, in a phylogenetic comparative analysis allowed us to more narrowly define structural elements that may be necessary for a minimal telomerase rna. a primary sequence element, positioned 5' of the template and conserved between all previously known ciliate telomerase rnas, has been reduced from 5'-(c)uguca-3' to the 4 nt sequence 5'-guca-3'. conserved secondary structural features and the impact they have on the general organization of ciliate telomerase rnas is discussed.",1
"objective the function of micrornas is highly context and cell type dependent because of their highly dynamic expression pattern and the regulation of multiple mrna targets. microrna-155 (mir-155) plays an important role in the innate immune response by regulating macrophage function; however, the effects of mir-155 in macrophages on atherosclerosis are controversial. we hypothesized that the stage-dependent target selection of mir-155 in macrophages determines its effects on atherosclerosis. approach and results the expression of mir-155 increased in lesional macrophages of apolipoprotein e-deficient mice between 12 and 24 weeks of a high-cholesterol diet. mir155 knockout in apolipoprotein e-deficient mice enhanced lesion formation, increased the lesional macrophage content, and promoted macrophage proliferation after 12 weeks of the high-cholesterol diet. in vitro, mir-155 inhibited macrophage proliferation by suppressing colony-stimulating factor-1 receptor, which was upregulated in lesional macrophages of mir155(-/-) apolipoprotein e-deficient mice. by contrast, mir155 deficiency reduced necrotic core formation and the deposition of apoptotic cell debris, thereby preventing the progression of atherosclerosis between 12 and 24 weeks of the high-cholesterol diet. mir-155 inhibited efferocytosis in vitro by targeting b-cell leukemia/lymphoma 6 and thus activating rhoa (ras homolog gene family, member a). accordingly, b-cell leukemia/lymphoma 6 was upregulated in lesional macrophages of mir155(-/-) apolipoprotein e-deficient mice after 24 weeks, but not after 12 weeks of the high-cholesterol diet. conclusions our findings demonstrate a stage-specific role of mir-155 in lesion formation. mir-155 suppressed macrophage proliferation by targeting colony-stimulating factor-1 receptor in early and impaired efferocytosis by downregulating b-cell leukemia/lymphoma 6 in advanced atherosclerosis. therefore, targeting the interaction between mir-155 and b-cell leukemia/lymphoma 6 may be a promising approach to inhibit the progression of atherosclerosis.",1
"microrna (mirna) sponges are vital components of posttranscriptional gene regulation. yet, only a limited number of mirna sponges have been identified. here, we show that the recently evolved noncoding tumor suppressor transcript, antisense rna to tp73 gene (tp73-as1), functions as a natural sponge of human-specific mirna mir-941. we find unusually nine high-affinity mir-941 binding sites clustering within 1 kb region on tp73-as1, which forms mir-941 sponge region. this sponge region displays increased sequence constraint only in humans, and its formation can be traced to the tandem expansion of a 71-nt-long sequence containing a single mir-941 binding site in old world monkeys. we further confirm tp73-as1 functions as an efficient mir-941 sponge based on massive transcriptome data analyses, wound-healing assay, and argonaute protein immunoprecipitation experiments conducted in cell lines. the expression of mir-941 and its sponge correlate inversely across multiple healthy and cancerous tissues, with mir-941 being highly expressed in tumors and preferentially repressing tumor suppressors. thus, the tp73-as1 and mir-941 duo represents an unusual case of the extremely rapid evolution of noncoding regulators controlling cell migration, proliferation, and tumorigenesis.",1
"the five small nuclear rnas (snrnas) involved in mammalian pre-mrna splicing (u1, u2, u4, u5, and u6) are well conserved in length, sequence, and especially secondary structure. these five snrnas from saccharomyces cerevisiae show notable size and sequence differences from their metazoan counterparts. this is most striking for the large s. cerevisiae u1 and u2 snrnas, for which no secondary structure models currently exist. because of the importance of u1 snrna in the early steps of ""spliceosome"" assembly, we wanted to compare the highly conserved secondary structure of metazoan u1 snrna (approximately 165 nucleotides) with that of s. cerevisiae u1 snrna (568 nucleotides). to this end, we have cloned and sequenced the u1 gene from two other yeast species possessing large u1 rnas. using computer-derived structure predictions, phylogenetic comparisons, and structure probing, we have arrived at a secondary structure model for s. cerevisiae u1 snrna. the results show that most elements of higher eukaryotic u1 snrna secondary structure are conserved in s. cerevisiae. the hundreds of ""extra"" nucleotides of yeast u1 rna, also highly structured, suggest that large insertions and/or deletions have occurred during the evolution of the u1 gene.",1
"how body size is determined is a long-standing question in biology, yet its regulatory mechanisms remain largely unknown. here, we find that a conserved microrna mir-8 and its target, ush, regulate body size in drosophila. mir-8 null flies are smaller in size and defective in insulin signaling in fat body that is the fly counterpart of liver and adipose tissue. fat body-specific expression and clonal analyses reveal that mir-8 activates pi3k, thereby promoting fat cell growth cell-autonomously and enhancing organismal growth non-cell-autonomously. comparative analyses identify ush and its human homolog, fog2, as the targets of fly mir-8 and human mir-200, respectively. ush/fog2 inhibits pi3k activity, suppressing cell growth in both flies and humans. fog2 directly binds to p85alpha, the regulatory subunit of pi3k, and interferes with the formation of a pi3k complex. our study identifies two novel regulators of insulin signaling, mir-8/mir-200 and ush/fog2, and suggests their roles in adolescent growth, aging, and cancer.",1
"aims micrornas (mirnas) are small non-coding rnas that regulate translational repression of target mrnas. accumulating evidence indicates that various mirnas, expressed in a spatially and temporally controlled that manner in the brain plays a key role in neuronal development. however, at present, the pathological implication of aberrant mirna expression in neurodegenerative events remains largely unknown. to identify mirnas closely associated with neurodegeneration, we performed mirna expression profiling of brain tissues of various neurodegenerative diseases. methods we initially studied the frontal cortex derived from three amyotrophic lateral sclerosis patients by using a microarray of 723 human mirnas. this was followed by enlargement of study population with quantitative rt-pcr analysis (n = 21). results by microarray analysis, we identified up-regulation of mir-29a, mir-29b and mir-338-3p in amyotrophic lateral sclerosis brains, but due to a great interindividual variation, we could not validate these results by quantitative rt-pcr. however, we found significant down-regulation of mir-29a in alzheimer disease (ad) brains. the database search on targetscan, pictar and mirbase target identified neurone navigator 3 (nav3), a regulator of axon guidance, as a principal target of mir-29a, and actually nav3 mrna levels were elevated in ad brains. mir-29a-mediated down-regulation of nav3 was verified by the luciferase reporter assay. by immunohistochemistry, nav3 expression was most evidently enhanced in degenerating pyramidal neurones in the cerebral cortex of ad. conclusions these observations suggest the hypothesis that underexpression of mir-29a affects neurodegenerative processes by enhancing neuronal nav3 expression in ad brains.",1
"micrornas (mirnas) are small, noncoding rnas that regulate expression of many genes. recent studies suggest roles of mirnas in carcinogenesis. we and others have shown that expression profiles of mirnas are different in lung cancer vs. normal lung, although the significance of this aberrant expression is poorly understood. among the reported down-regulated mirnas in lung cancer, the mirna (mir)-29 family (29a, 29b, and 29c) has intriguing complementarities to the 3'-utrs of dna methyltransferase (dnmt)3a and -3b (de novo methyltransferases), two key enzymes involved in dna methylation, that are frequently up-regulated in lung cancer and associated with poor prognosis. we investigated whether mir-29s could target dnmt3a and -b and whether restoration of mir-29s could normalize aberrant patterns of methylation in non-small-cell lung cancer. here we show that expression of mir-29s is inversely correlated to dnmt3a and -3b in lung cancer tissues, and that mir-29s directly target both dnmt3a and -3b. the enforced expression of mir-29s in lung cancer cell lines restores normal patterns of dna methylation, induces reexpression of methylation-silenced tumor suppressor genes, such as fhit and wwox, and inhibits tumorigenicity in vitro and in vivo. these findings support a role of mir-29s in epigenetic normalization of nsclc, providing a rationale for the development of mirna-based strategies for the treatment of lung cancer.",1
"microrna-34a (mir-34a) is thought to be involved in nonalcoholic fatty liver disease (nafld). however, the association between altered expression of mir-34a and the pathophysiological features of nafld remains unclear. here, we investigated the mechanisms by which mir-34a influences nafld through the pparα-related pathway. real-time quantitative pcr, western blotting and other assays kit were used to investigate the expression and function of mir-34a in an nafld model. cultured cells transfected with mir-34a inhibitor and c57bl/6 mice injected with the mir-34a inhibitor through vein tail were conducted for the effects of mir-34a on its target. mir-34a levels were significantly upregulated in steatosis-induced hepatocytes and in liver tissues of high-fat diet-fed mice. the upregulation of mir-34a resulted in the downregulation of hepatic pparα and sirt1 that are the direct targets of mir-34a. silencing mir-34a led to an initially increased expression of pparα, sirt1 and pparα's downstream genes. activation of the central metabolic sensor ampk was also increased. the mir-34a inhibitor suppressed lipid accumulation and improved the degree of steatosis. taken together, our data indicated that decreased expression of mir-34a potentially contributes to altered lipid metabolism in nafld. downregulation of mir-34a may be a therapeutic strategy against nafld by regulating its target pparα and sirt1.",1
"cricket paralysis-like viruses have a dicistronic positive-strand rna genome. these viruses produce capsid proteins through internal ribosome entry site (ires)-mediated translation. the ires element of one of these viruses, plautia stall intestine virus (psiv), forms a pseudoknot immediately upstream from the capsid coding sequence, and initiates translation from other than methionine. previously, we estimated that the ires element of psiv consists of seven stem-loops using the program mfold; however, experimental evidence of the predicted structures was not shown, except for stem-loop vi, which was responsible for formation of the pseudoknot. to determine the whole structure of the psiv-ires element, we introduced compensatory mutations into the upstream mfold-predicted helical segments. mutation analysis showed that stem-loop v exists as predicted, but stem-loop iv is shorter than predicted. the structure of stem-loop iii is different from predicted, and stem-loops i and ii are not necessary for ires activity. in addition, we identified two new pseudoknots in the ires element of psiv. the complementary sequence segments that are responsible for formation of the two pseudoknots are also observed in cricket paralysis virus (crpv) and crpv-like viruses such as drosophila c virus (dcv), rhopalosiphum padi virus (rhpv), himetobi p virus (hipv), triatoma virus (trv), and black queen-cell virus (bqcv), although each sequence is distinct in each virus. considering the three pseudoknots, we constructed a tertiary structure model of the psiv-ires element. this structural model is applicable to other crpv-like viruses, indicating that other crpv-like viruses can also initiate translation from other than methionine.",1
"micrornas (mirnas) are small, noncoding rnas that regulate gene expression posttranscriptionally. we investigated the hypothesis that bone morphogenetic protein (bmp) signaling regulates mirnas in cardiac progenitor cells. bmp2 and bmp4 regulate oft myocardial differentiation via regulation of the mirna-17-92 cluster. in bmp mutant embryos, myocardial differentiation was delayed, and multiple mirnas encoded by mirna-17-92 were reduced. we uncovered functional mirna-17-92 seed sequences within the 3' utr of cardiac progenitor genes such as isl1 and tbx1. in both bmp and mirna-17-92 mutant embryos, isl1 and tbx1 expression failed to be correctly downregulated. transfection experiments indicated that mirna-17 and mirna-20a directly repressed isl1 and tbx1. genetic interaction studies uncovered a synergistic interaction between mirna-17-92 cluster and bmp4, providing direct in vivo evidence for the bmp-mirna-17-92 regulatory pathway. our findings indicate that bmp signaling directly regulates a mirna-mediated effector mechanism that downregulates cardiac progenitor genes and enhances myocardial differentiation.",1
"grp78, a major endoplasmic reticulum chaperone and signaling regulator, is commonly overexpressed in cancer. moreover, induction of grp78 by a variety of anti-cancer drugs, including histone deacetylase inhibitors, confers chemoresistance to cancer, thereby contributing to tumorigenesis. thus, therapies aimed at decreasing grp78 levels, which results in the inhibition of tumor cell proliferation and resensitization of tumor cells to chemotherapeutic drugs may hold promise for cancer treatment. despite advances in our understanding of grp78 actions, little is known about endogenous inhibitors controlling its expression. as endogenous regulators, micrornas (mirnas) play important roles in modulating gene expression; therefore, we sought to identify mirna(s) that target grp78, under the hypothesis that these mirnas may serve as therapeutic agents. here, we report that three mirnas (mir-30d, mir-181a, mir-199a-5p) predicted to target grp78 are down-regulated in prostate, colon and bladder tumors, and human cancer cell lines. we show that in c42b prostate cancer cells, these mirnas down-regulate grp78 and induce apoptosis by directly targeting its 3' untranslated region. importantly, we demonstrate that the three mirnas act cooperatively to decrease grp78 levels, suggesting that multiple mirnas may be required to efficiently control the expression of some genes. in addition, delivery of multiple mirnas by either transient transfection or lentivirus transduction increased the sensitivity of cancer cells to the histone deacetylase inhibitor, trichostatin a, in c42b, hct116 and hl-60 cells. together, our results indicate that the delivery of co-transcribed mirnas can efficiently suppress grp78 levels and grp78-mediated chemoresistance, and suggest that this strategy holds therapeutic potential.",1
"alzheimer's disease (ad) is the multifactorial neurodegenerative disorder causing progressive memory loss and cognitive impairment. the aberrant accumulation of amyloid-β (aβ) and neuroinflammation are two major events in ad. bace1 is required for the cleavage of amyloid precursor protein (app) to generate aβ, which stimulates the nuclear transcription factor κb (nf-κb) signaling, leading to the secretion of inflammatory cytokines. and nf-κb can up-regulate the expression of bace1. mirnas are small non-coding rnas that regulate gene transcription. mir-15b down-regulates bace1 expression while it is unclear whether mir-15b can regulate aβ in human neuronal cells, and if so, whether it is by targetting nf-κb. sh-sy5y cell line was transfected with swedish app mutant (appswe) as an in vitro ad model. quantitative pcr (qpcr), wb, and elisa were used to detected related gene expression intracellularly or in supernatant. dual luciferase assay was used to validate mirna and targets binding. mir-15b inhibits expression of bace1and app. moreover, the reduced level of aβ was observed in response to mir-15b mimics in sh-sh5y/appswe cells. mir-15b directly targetted the conserved bace1 3'utr to regulate its expression. in addition, the inhibition of appswe-induced secretion of inflammatory cytokines and the suppression of nf-κb activation by mir-15b were validated. and mir-15b directly targetted the 3'utrs of nf-κb1 and inhibitor of nf-κb (iκb) kinase α (ikk-α), encoding nf-κb1 and ikk-α, respectively. our study suggests that mir-15b inhibits aβ accumulation through targetting nf-κb signaling and bace1 and serves as a potential molecular target for ad therapy.",1
"mek1/2 inhibitors such as azd6244 are in clinical trials for the treatment of multiple cancers, including breast cancer. targeted kinase inhibition can induce compensatory kinome changes, rendering single therapeutic agents ineffective. to identify target proteins to be used in a combinatorial approach to inhibit tumor cell growth, we used a novel strategy that identified micrornas (mirnas) that synergized with azd6244 to inhibit the viability of the claudin-low breast cancer cell line mda-mb-231. screening of a mirna mimic library revealed the ability of mir-9-3p to significantly enhance azd6244-induced extracellular signal-regulated kinase inhibition and growth arrest, while mir-9-3p had little effect on growth alone. promoter methylation of mir-9 genes correlated with low expression of mir-9-3p in different breast cancer cell lines. consistent with mir-9-3p having synthetic enhancer tumor suppressor characteristics, mir-9-3p expression in combination with mek inhibitor caused a sustained loss of c-myc expression and growth inhibition. the β1 integrin gene (itgb1) was identified as a new mir-9-3p target, and the growth inhibition seen with small interfering rna knockdown or antibody blocking of itgb1 in combination with mek inhibitor phenocopied the growth inhibition seen with mir-9-3p plus azd6244. the mirna screen led to identification of a druggable protein, itgb1, whose functional inhibition synergizes with mek inhibitor.",1
"polymorphisms in 3' untranslated region (utr) of cancer-related genes might affect their regulation by micrornas (mirnas) and thereby contribute to carcinogenesis. in this study, we screened single nucleotide polymorphisms (snps) in 3' utr of cancer-related genes and investigated their effects on risk of lung cancer. first, we genotyped seven snps in a chinese han population with 600 lung cancer patients and 600 matched healthy controls and found that compared with the tt genotype of rs2239680 in 3' utr of baculoviral iap repeat containing 5 (birc5), c allele was associated with a significantly increased risk of lung cancer and advanced pathologic stage, with the odds ratio for participants carrying the ct or cc genotype being 1.50 [95% confidence interval (ci) 1.20-1.89, p c change resulted in altered regulation of birc5 expression. moreover, birc5 was over expressed in lung cancer tissues compared with the normal lung tissues, and the protein levels of birc5 correlated with snp genotypes in normal lung tissues. our findings defined a 3' utr snp in human birc5 oncogene that may increase individual susceptibility to lung cancer probably by attenuating the interaction between mir-335 and birc5.",1
"signal recognition particle (srp) targets proteins for co-translational insertion through or into the endoplasmic reticulum membrane. mammalian srp slows nascent chain elongation by the ribosome during targeting in vitro. this 'elongation arrest' activity requires the srp9/14 subunit of the particle and interactions of the c-terminus of srp14. we have purified srp from saccharomyces cerevisiae and demonstrated that it too has elongation arrest activity. a yeast srp containing srp14p truncated at its c-terminus (delta c29) did not maintain elongation arrest, was substantially deficient in promoting translocation and interfered with targeting by wild-type srp. in vivo, this mutation conferred a constitutive defect in the coupling of protein translation and translocation and temperature-sensitive growth, but only a slight defect in protein translocation. in combination, these data indicate that the primary defect in srp delta c29 is in elongation arrest, and that this is a physiologically important and conserved function of eukaryotic srp.",1
"biliary atresia (ba) is a pediatric liver disease of unknown underlying etiology, in which fibroinflammatory destruction of the extrahepatic biliary system leads to obstructive cholestasis. micrornas are a class of short (18-23 nucleotide), noncoding rna molecules, which act as negative regulators of target mrna stability and translation. the importance of these molecules in normal and diseased liver has been demonstrated, but their potential role in the pathogenesis of ba has not been addressed. we have profiled changes in liver microrna levels in an established mouse model of the disease, identified significantly altered transcripts, and defined the spatial expression patterns of selected micrornas. two of these, mir-29a/29b1, are upregulated in experimental ba. using antisense oligonucleotide-mediated inhibition in mice, we have delineated the full set of hepatic genes regulated by mir-29 and identified 2 mrna targets of potential pathological relevance in experimental ba, igf1 and il1rap. we have used reporter assays to confirm that igf1 and il1rap are direct targets of mir-29.",1
"multicellular organisms grow through both proliferation and growth of their individual cells. we have conducted a p-element-based misexpression screen for genes whose upregulation alters wing disc growth during development. one particular group of four p elements, all inserted at cytological location 61c7-8, exhibited specific overgrowth upon misexpression in proliferating imaginal tissues. clonal analysis revealed that upon misexpression, cell number was increased but cell size was not affected, indicating that cell growth and proliferation were induced in a coordinate manner. loss of function at the locus produced small flies with reduced cell number, consistent with the presence of a gene encoding a positive growth regulator. we characterized a new transcription unit initiating in a region adjacent to the p insertions, which generated a complex series of polyadenylated transcripts. although these rnas were induced in response to misexpression, none was sufficient by itself to recapitulate overgrowth when overexpressed. this suggested either that a particular combination of these transcripts was necessary or that other sequences are involved.",1
"long noncoding rnas (lncrnas) are an emerging class of regulators that play crucial roles in regulating the strength and duration of innate immunity. however, little is known about the regulation of drosophila innate immunity-related lncrnas. in this study, we first revealed that overexpression of lncrna-cr33942 could strengthen the expression of the imd pathway antimicrobial peptide (amp) genes diptericin ( dpt ) and attacin-a ( atta ) after infection, and vice versa. secondly, rna-seq analysis of lncrna-cr33942 -overexpressing flies post gram-negative bacteria infection confirmed that lncrna-cr33942 positively regulated the drosophila immune deficiency (imd) pathway. mechanistically, we found that lncrna-cr33942 interacts and enhances the binding of nf-κb transcription factor relish to dpt and atta promoters, thereby facilitating dpt and atta expression. relish could also directly promote lncrna-cr33942 transcription by binding to its promoter. finally, rescue experiments and dynamic expression profiling post-infection demonstrated the vital role of the relish/ lncrna-cr33942 /amp regulatory axis in enhancing imd pathway and maintaining immune homeostasis. our study elucidates novel mechanistic insights into the role of lncrna-cr33942 in activating drosophila imd pathway and the complex regulatory interaction during the innate immune response of animals.",1
"mir-126 is a microrna expressed predominately by endothelial cells and controls angiogenesis. we found mir-126 was required for the innate response to pathogen-associated nucleic acids and that mir-126-deficient mice had greater susceptibility to infection with pseudotyped hiv. profiling of mirna indicated that mir-126 had high and specific expression by plasmacytoid dendritic cells (pdcs). moreover, mir-126 controlled the survival and function of pdcs and regulated the expression of genes encoding molecules involved in the innate response, including tlr7, tlr9 and nfkb1, as well as kdr, which encodes the growth factor receptor vegfr2. deletion of kdr in dcs resulted in reduced production of type i interferon, which supports the proposal of a role for vegfr2 in mir-126 regulation of pdcs. our studies identify the mir-126-vegfr2 axis as an important regulator of the innate response that operates through multiscale control of pdcs.",1
"non-coding rnas regulate many biological processes including neurogenesis. the brain-enriched mir-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. to systematically chart its regulatory functions, we used crispr/cas9 gene editing to disrupt all six mir-124 alleles in human induced pluripotent stem cells. upon neuronal induction, mir-124-deleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. using rna-induced-silencing-complex precipitation, we identified 98 high-confidence mir-124 targets, of which some directly led to decreased viability. by performing advanced transcription-factor-network analysis, we identified indirect mir-124 effects on apoptosis, neuronal subtype differentiation, and the regulation of previously uncharacterized zinc finger transcription factors. our data emphasize the need for combined experimental- and system-level analyses to comprehensively disentangle and reveal mirna functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain.",1
"aims to establish a functional link between microrna-107 (mir-107) and stem cell survival during ischemic preconditioning (ipc) of stem cells with multiple cycles of brief anoxia/re-oxygenation (10 or 30 min, one to three cycles) and show that the cytoprotective effects were independent of hypoxamir-210. results we demonstrated the induction of mir-107 in response to the ipc-induced activation of akt/hypoxia inducible factor-1α (hif-1α) in preconditioned mesenchymal stem cells ((pc)msc), which showed improved survival during subsequent exposure to 6 h of lethal anoxia (p innovation cytoprotection afforded by ipc is regulated by mir-107 induction via pdcd10 independent of mir-210/casp8ap2 signaling, and the simultaneous abrogation mir-107/mir-210 has a stronger effect on the loss of (pc)msc survival. conclusion ipc enhances stem cell survival via the combined participation of hypoxia responsive mirs mir-107 and mir-210 via their respective putative target genes pdcd10 and casp8ap2.",1
"microrna (mirna) regulates expression of protein coding genes and has been implicated in diverse cellular processes including neuronal differentiation, cell growth and death. to identify the role of mirna in neuronal differentiation, sh-sy5y and imr-32 cells were treated with dopamine cocktail and retinoic acid to induce differentiation. detection of mirnas in differentiated cells revealed that expression of many mirnas was altered significantly. among the altered mirnas, human brain expressed mir-432 induced neurite projections, arrested cells in g0-g1, reduced cell proliferation and could significantly repress nestin/nes, rcor1/corest and mecp2. our results reveal that mir-432 regulate neuronal differentiation of human neuroblastoma cells.",1
"the l-type calcium channel (ltcc) is one of the major ion channels that are known to be associated with the electrical remodeling of atrial fibrillation (af). in af, there is significant downregulation of the ltcc, but the underlying mechanism for such downregulation is not clear. we have previously reported that microrna-499 (mir-499) is significantly upregulated in patients with permanent af and that kcnn3, the gene that encodes the small-conductance calcium-activated potassium channel 3 (sk3), is a target of mir-499. we found that cacnb2, an important subunit of the ltcc, is also a target of mir-499. we hypothesize that mir-499 plays an important role in af electrical remodeling by regulating the expression of cacnb2 and the ltcc. in atrial tissue from patients with permanent af, cacnb2 was significantly downregulated by 67% ( n = 4, p cacnb2 was confirmed by luciferase reporter assay and by the increased presence of cacnb2 mrna in argonaute pulled-down microrna-induced silencing complexes after transfection with the mir-499 mimic. in addition, downregulation of cacnb2 resulted in the downregulation of protein levels of the pore-forming α-subunit (cacna1c). in conclusion, upregulation of atrial mir-499 induces the downregulation of cacnb2 expression and may contribute to the electrical remodeling in af.",1
"vitamin b(1) in its active form thiamin pyrophosphate is an essential coenzyme that is synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; hmp) and thiazole (hydroxyethylthiazole) moieties in bacteria. using comparative analysis of genes, operons, and regulatory elements, we describe the thiamin biosynthetic pathway in available bacterial genomes. the previously detected thiamin-regulatory element, thi box (miranda-rios, j., navarro, m., and soberon, m. (2001) proc. natl. acad. sci. u. s. a. 98, 9736-9741), was extended, resulting in a new, highly conserved rna secondary structure, the thi element, which is widely distributed in eubacteria and also occurs in some archaea. search for thi elements and analysis of operon structures identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms. in particular, we assign the thiamin transporter function to yuaj in the bacillus/clostridium group and the hmp transporter function to an abc transporter thixyz in some proteobacteria and firmicutes. by analogy to the model of regulation of the riboflavin biosynthesis, we suggest thiamin-mediated regulation based on formation of alternative rna structures involving the thi element. either transcriptional or translational attenuation mechanism may operate in different taxonomic groups, dependent on the existence of putative hairpins that either act as transcriptional terminators or sequester translation initiation sites. based on analysis of co-occurrence of the thiamin biosynthetic genes in complete genomes, we predict that eubacteria, archaea, and eukaryota have different pathways for the hmp and hydroxyethylthiazole biosynthesis.",1
"using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar rna (snorna) genes in the recently released draft sequence of the rice genome was carried out. this analysis identified 120 different box c/d snorna genes with a total of 346 gene variants, which were predicted to guide 135 2'-o-ribose methylation sites in rice rrnas. though not exhaustive, this analysis has revealed that rice has the highest number of known box c/d snornas among eukaryotes. interestingly, although many snorna genes are conserved between rice and arabidopsis, almost half of the identified snorna genes are rice specific, which may highlight further the differences in rrna methylation patterns between monocotyledons and dicotyledons. in addition to 76 singletons, 70 clusters involving 270 snorna genes were also found in rice. the large number of the novel snorna polycistrons found in the introns of rice protein-coding genes is in contrast to the one-snorna-per-intron organization of vertebrates and yeast, and of arabidopsis in which only a few intronic snorna gene clusters were identified. furthermore, due to a high degree of gene duplication, rice snorna genes are clearly redundant and exhibit great sequence variation among isoforms, allowing generation of new snornas for selection. thus, the large snorna gene family in plants can serve as an excellent model for a rapid and functional evolution.",1
"to investigate the role of mirna in controlling human embryonic stem (hes) cell differentiation toward the endothelial lineage and chick embryonic blood vessel formation, undifferentiated hes cells were first cultured on matrigel-coated flasks and in endothelial cell growth medium-2 (egm-2) to initiate endothelial cell (ec) differentiation. cd146(+) cells were isolated from differentiating hes cells and expanded in vitro. the in vitro expanded cd146(+) cells were positive for ec markers, capable of ac-ldl uptake, lectin binding, and the formation of vascular structures in vitro and in vivo. mirna gain/loss-of-function analyses revealed that mir-150 and mir-200c were crucial in ec differentiation. transcriptional repressor zinc finger e-box-binding homeobox 1 (zeb1) was identified as the communal target gene of mirna-200c and -150, and inhibition of zeb1 was required for mirna-200c or -150 mediated ec gene expressions. moreover, we demonstrated that zeb1 could transcriptionally repress ec gene expression through direct binding to promoters of ec genes. finally, we also demonstrated that mirna-200c and -150 played an important role in chick embryonic blood vessel formation by in vivo inhibition of mirna-200c or -150 in developing chick embryos, and blocking zeb1 signaling in cd146-positive cells could rescue the inhibitory effects of mir-200c inhibiton in in vivo vasculogenesis. our findings revealed that mir-150 and mir-200c play an important role in human endothelial lineage specification and chick embryonic vasculogenesis by targeting zeb1.",1
"th17 cells are central to the pathogenesis of autoimmune disease, and recently specific noncoding micrornas have been shown to regulate their development. however, it remains unclear whether micrornas are also involved in modulating th17 cell effector functions. consequently, we examined the role of mir-155 in differentiated th17 cells during their induction of experimental autoimmune encephalomyelitis. using adoptive transfer experiments, we found that highly purified, myelin oligodendrocyte glycoprotein ag-specific th17 cells lacking mir-155 were defective in their capacity to cause experimental autoimmune encephalomyelitis. gene expression profiling of purified mir-155(-/-)il-17f(+) th17 cells identified a subset of effector genes that are dependent on mir-155 for their proper expression through a mechanism involving repression of the transcription factor ets1. among the genes reduced in the absence of mir-155 was il-23r, resulting in mir-155(-/-) th17 cells being hyporesponsive to il-23. taken together, our study demonstrates a critical role for mir-155 in th17 cells as they unleash autoimmune inflammation and finds that this occurs through a signaling network involving mir-155, ets1, and the clinically relevant il-23-il-23r pathway.",1
"rnase mrp is a site-specific ribonucleoprotein endoribonuclease that cleaves rna from the mitochondrial origin of replication in a manner consistent with a role in priming leading-strand dna synthesis. despite the fact that the only known rna substrate for this enzyme is complementary to mitochondrial dna, the majority of the rnase mrp activity in a cell is found in the nucleus. the recent characterization of this activity in saccharomyces cerevisiae and subsequent cloning of the gene coding for the rna subunit of the yeast enzyme have enabled a genetic approach to the identification of a nuclear role for this ribonuclease. since the gene for the rna component of rnase mrp, nme1, is essential in yeast cells and rnase mrp in mammalian cells appears to be localized to nucleoli within the nucleus, we utilized both regulated expression and temperature-conditional mutations of nme1 to assay for a possible effect on rrna processing. depletion of the rna component of the enzyme was accomplished by using the glucose-repressed gal1 promoter. shortly after the shift to glucose, the rna component of the enzyme was found to be depleted severely, and rrna processing was found to be normal at all sites except the b1 processing site. the b1 site, at the 5' end of the mature 5.8s rrna, is actually composed of two cleavage sites 7 nucleotides apart. this cleavage normally generates two species of 5.8s rrna at a ratio of 10:1 (small to large) in most eukaryotes. after rnase mrp depletion, yeast cells were found to have almost exclusively the larger species of 5.8s rrna. in addition, an aberrant 309-nucleotide precursor that stretched from the a2 to e processing sites of rrna accumulated in these cells. temperature-conditional mutations in the rnase mrp rna gene gave an identical phenotype. translation in yeast cells depleted of the smaller 5.8s rrna was found to remain robust, suggesting a possible function for two 5.8s rrnas in the regulated translation of select messages. these results are consistent with rnase mrp playing a role in a late step of rrna processing. the data also indicate a requirement for having the smaller form of 5.8s rrna, and they argue for processing at the b1 position being composed of two separate cleavage events catalyzed by two different activities.",1
"micrornas (mirnas) have been implicated in neoplasm growth, metastasis, vasculogenesis, and drug resistance. it has been validated that abnormal mir-195 expression was related with poor survival of prostate cancer (pc); however, its role in the resistance to chemotherapeutic drugs docetaxel (doc) in pc is still acquainted scarcely. in our study, the lower expression of mir-195 was appeared in doc-resistant pc cells (du145/doc) rather than doc-sensitive du145 cells. the up-regulation of mir-195 lowered the ic50 of doc, facilitated the apoptosis and inhibited the colony formation ability in du145/doc cells. moreover, we also found that mir-195 had the binding site with clusterin (clu) by the online targetscan database mining. luciferase tests revealed that mir-195 binds to the 3'-utr of clu. mir-195 overexpression decreased the amassment of clu in du145/doc cells. knockdown of clu diminished the ic50 of doc and enhanced the apoptosis of du145/doc cells, which was consistent with the influence of mir-195 on doc-induced cell apoptosis. taken together, our results illuminated that mir-195 improved the sensitivity of resistant pc cells to doc by suppressing clu. hence, mir-195 may be a potentially promising molecular target for drug resistance of pc.",1
"the computational detection of novel selenoproteins in genomic sequences is usually achieved through identification of secis, a conserved secondary structure element found in the 3' utr of animal selenoprotein mrnas. previous studies have used ""descriptors"" specifying the number of base pairs and the conserved nucleotides in secis to identify this element. a major drawback of the ""descriptor"" approach is that the number of detections in current genomic or transcript databases largely exceeds the number of true selenoproteins. in this study, we use instead the erpin program to detect secis elements. erpin is based on a lod-score profile algorithm that uses a training-set of aligned rna sequences as input. from an initial alignment of 44 animal secis sequences, we performed a series of iterative searches in which the training set was progressively enriched up to 117 confirmed secis elements, from a large collection of metazoan species. about 200 high-scoring candidates were also detected. we show that erpin scores for these candidates can be converted into expect values, thus enabling their statistical evaluation. the most interesting secis candidates are presented.",1
"mir-1 is a small noncoding rna molecule that modulates gene expression in heart and skeletal muscle. loss of drosophila mir-1 produces defects in somatic muscle and embryonic heart development, which have been partly attributed to mir-1 directly targeting delta to decrease notch signaling. here, we show that overexpression of mir-1 in the fly wing can paradoxically increase notch activity independently of its effects on delta. analyses of potential mir-1 targets revealed that mir-1 directly regulates the 3'utr of the e3 ubiquitin ligase nedd4 analysis of embryonic and adult fly heart revealed that the nedd4 protein regulates heart development in drosophila larval fly hearts overexpressing mir-1 have profound defects in actin filament organization that are partially rescued by concurrent overexpression of nedd4. these results indicate that mir-1 and nedd4 act together in the formation and actin-dependent patterning of the fly heart. importantly, we have found that the biochemical and genetic relationship between mir-1 and the mammalian ortholog nedd4-like ( nedd4l ) is evolutionarily conserved in the mammalian heart, potentially indicating a role for nedd4l in mammalian postnatal maturation. thus, mir-1 -mediated regulation of nedd4/nedd4l expression may serve to broadly modulate the trafficking or degradation of nedd4/nedd4l substrates in the heart.",1
"previous studies have demonstrated that high mobility group a proteins have a critical role on the onset of human pituitary adenomas. indeed, both high mobility group a (hmga) genes are overexpressed in pituitary adenomas, and consistently transgenic mice overexpressing either the hmga1 or the hmga2 gene develop mixed growth hormone/prolactin (gh-prl)-secreting pituitary adenomas. trisomy of chromosome 12, where hmga2 is located, and/or amplification of the hmga2 gene locus account for the hmga2 overexpression in most human prolactinomas. conversely, hmga1 overexpression is not associated to any rearrangement or amplification of the hmga1 locus. we have first identified micro rnas (mirnas) able to target both hmga1 and hmga2 messenger rnas. then, all of these mirnas have been found downregulated in pituitary adenomas of different histotypes, compared with normal pituitary. interestingly, their downregulation was also observed in nonfunctioning pituitary adenomas where hmga2 overexpression is not associated to any alteration of the hmga2 locus. functional studies show that all these hmga-targeting mirnas inhibit the proliferation of the rat pituitary adenoma cell line gh3. therefore, these results indicate that the downregulation of the mirnas able to target the hmga genes could contribute to increase hmga protein levels in human pituitary adenomas, and then to pituitary tumorigenesis.",1
"secondary and tertiary structures in the 3' untranslated region (utr) of plus-strand rna viruses have been postulated to function as control elements in rna replication, transcription, and translation. here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3' utr of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted structure is required for the replication of a defective interfering rna genome. the pseudoknot is phylogenetically conserved among coronaviruses both in location and in shape but only partially in nucleotide sequence, and evolutionary covariation of bases to maintain g. u pairings indicates that it functions in the plus strand. rnase probing of synthetic transcripts provided additional evidence of its tertiary structure and also identified the possible existence of two conformational states. these results indicate that the 3' utr pseudoknot is involved in coronavirus rna replication and lead us to postulate that it functions as a regulatory control element.",1
"heavy metal pollution has been a worldwide prevalent problem, and particularly a threat to ecosystem integrity and animals' health. previous studies on the mechanisms of heavy metal toxicity have focused on protein-coding genes, whereas most genomic transcripts are long non-coding rnas (lncrnas). although lncrnas are known to play important regulatory roles in biological processes, their role in heavy metal stress regulation is still not fully understood. we here developed an insect embryo cell model for studying metal toxicity and the underlying regulatory mechanisms. we performed genome-wide screening and functional characterization of lncrnas induced by two essential and two non-essential heavy metals in drosophila embryo-derived s2 cells. we identified 4894 lncrnas, of which 1410 were novel. forty-one lncrnas, together with 328 mrnas, were induced by all the four heavy metals. lncrna-mrna co-expression network and pathway enrichment analysis showed that detoxification metabolism, circadian rhythm, and apoptosis regulation pathways were activated in response to heavy metal stress. lncrna cr44138 was remarkably upregulated in cells exposed to the four heavy metals and was associated with the apoptosis pathway. expression interference confirmed that cr44138 aggravated cytotoxicity-induced apoptosis in cells under heavy metals stress. this study highlights the important role of lncrnas in regulating the cellular response to heavy metals. this study also lays the foundation for discovering the novel regulatory mechanisms and developing diagnostic biomarkers of the toxic effects of heavy metal pollutants on organisms.",1
"purpose advanced metastatic prostate cancer (pca) is a fatal disease, with only palliative therapeutic options. though almost 80% of cases of metastatic pca present bone metastasis, our current understanding of the molecular mechanisms that govern this metastatic dissemination remains fragmentary. the main objective of the present study was to identify microrna (mirna) genes that regulate metastatic pca. experimental design mirna expression profiling was done in human prostate cell lines to identify dysregulated mirna components of advanced pca. mir-203 expression was assessed in prostate carcinoma cell lines and clinical specimens by real-time pcr and in situ hybridization. to assess the biological significance of mir-203, mir-203 was reexpressed in bone metastatic pca cell lines followed by in vitro and in vivo functional assays. results mir-203 expression is specifically attenuated in bone metastatic pca suggesting a fundamental antimetastatic role for this mirna. reintroduction of mir-203 in bone metastatic pca cell lines suppresses metastasis via inhibition of several critical steps of the metastatic cascade including epithelial-mesenchymal transition, invasion, and motility. ectopic mir-203 significantly attenuated the development of metastasis in a bone metastatic model of pca. importantly, mir-203 regulates a cohort of pro-metastatic genes including zeb2, bmi, survivin, and bone-specific effectors including runx2, a master regulator of bone metastasis. conclusions mir-203 is an ""antimetastatic"" mirna in pca that acts at multiple steps of the pca metastatic cascade via repression of a cohort of prometastatic targets. mir-203 may be an attractive target for therapeutic intervention in advanced pca.",1
"mitochondrial import of trna is now considered as a quasi-universal phenomenon. in the yeast saccharomyces cerevisiae, one of the three lysine isoacceptors, the trna(lys)1 with the anticodon cuu (trna-k1), is encoded by the nuclear genome and distributed between the cytoplasmic (> 95%) and mitochondrial (< 5%) compartments. in vivo and in vitro import assays were developed to study the mechanisms of trna-k1 mitochondrial import. transmembrane translocation of the trna requires the intactness of at least two of the components of the mitochondrial import machinery of pre-proteins, mom19 and mim44, as well as energy of atp hydrolysis and an electrochemical potential across the inner membrane. the import of trna-k1 involves formation of an rnp complex on the mitochondrial outer membrane. trna-k1 import is also dependent upon cytosolic protein factors, one of which was identified as the precursor of the mitochondrial lysyl-trna synthetase (msk). although essential for trna-k1 import in vitro and in vivo, pre-msk is however not sufficient to direct the import in vitro, which suggests the need of additional cytosolic factor(s). the trna can be imported in its mature form and nucleoside modification is not essential. aminoacylation of the imported trna by the cytoplasmic lysyl-trna synthetase is a prerequisite for import. possible mechanisms of intracellular partitioning and mitochondrial membrane translocation of trna-k1 are discussed.",1
"micro(mi)rna-based post-transcriptional regulatory mechanisms have been broadly implicated in the assembly and modulation of synaptic connections required to shape neural circuits, however, relatively few specific mirnas have been identified that control synapse formation. using a conditional transgenic toolkit for competitive inhibition of mirna function in drosophila, we performed an unbiased screen for novel regulators of synapse morphogenesis at the larval neuromuscular junction (nmj). from a set of ten new validated regulators of nmj growth, we discovered that mir-34 mutants display synaptic phenotypes and cell type-specific functions suggesting distinct downstream mechanisms in the presynaptic and postsynaptic compartments. a search for conserved downstream targets for mir-34 identified the junctional receptor cntnap4/neurexin-iv (nrx-iv) and the membrane cytoskeletal effector adducin/hu-li tai shao (hts) as proteins whose synaptic expression is restricted by mir-34. manipulation of mir-34, nrx-iv or hts-m function in motor neurons or muscle supports a model where presynaptic mir-34 inhibits nrx-iv to influence active zone formation, whereas, postsynaptic mir-34 inhibits hts to regulate the initiation of bouton formation from presynaptic terminals.",1
"purpose microrna 125a-5p (mir-125a-5p) has been reported to be a tumor suppressor in malignancies of the breast, ovary, lung, and central nervous system. however, the clinical significance of mir-125a-5p in human gastrointestinal cancer has not been explored. we investigated a tumor inhibitory effect of mir-125a-5p in gastric cancer, focusing in particular on the mir-125a-erbb2 (her2, her-2/neu) pathway. experimental design quantitative rt-pcr was used to evaluate mir-125a-5p expression in 87 gastric cancer cases to determine the clinicopathologic significance of mir-125a-5p expression. the regulation of erbb2 by mir-125a-5p was examined with precursor mir-125a-transfected cells. furthermore, we investigated whether mir-125a-5p suppresses proliferation of gastric cancer cells in combination with trastuzumab, a monoclonal antibody against erbb2. results low expression levels of mir-125a-5p were associated with enhanced malignant potential such as tumor size (p = 0.0068), tumor invasion (p = 0.031), liver metastasis (p = 0.029), and poor prognosis (p = 0.0069). multivariate analysis indicated that low mir-125a-5p expression was an independent prognostic factor for survival. in vitro assays showed that erbb2 is a direct target of mir-125a-5p, which potently suppressed the proliferation of gastric cancer cells, and, interestingly, the growth inhibitory effect was enhanced in combination with trastuzumab. conclusions mir-125a-5p is a meaningful prognostic marker. furthermore, mir-125a-5p mimic alone or in combination with trastuzumab could be a novel therapeutic approach against gastric cancer.",1
"cardiac hypertrophy, which is characterized by the enlargement of cell size, reactivation of fetal genes, remains one of the most important triggers to heart failure. increasing evidence shows that microrna (mirna) is extensively involved in the pathogenesis of cardiac hypertrophy. but the effects of mirnas on cardiomyocyte hypertrophy have not been completely solved yet. here, we showed that a collection of mirnas was aberrantly expressed in hypertrophic cardiomyocytes induced by phenylephrine (pe) or angiotensin ii (ang ii). among them, mir-22 was the most strikingly up-regulated mirna. to investigate the role of mir-22 in hypertrophy, both over-expression and knock-down assays were performed on cardiomyocytes. the results showed that up-regulation of mir-22 significantly increased the cell size and markedly influenced the expression of hypertrophic markers, including induction of nppa and reduction of myh6. in contrast, reduction of mir-22 level attenuated either pe- or ang ii-induced hypertrophic reaction. furthermore, several genes, including pten, were identified as potential targets of mir-22 by bioinformatic algorithms. using luciferase analysis, mir-22 could significantly suppress the luciferase activity of reporter fused with 3' untranslated region of pten mrna. furthermore, up-regulation of mir-22 could suppress the protein level of pten and reduction of mir-22 level markedly increased the protein level of pten in cardiomyocytes by western blot analysis, suggesting that the contribution of mir-22 to cardiomyocyte hypertrophy may be partially through targeting pten. taken together, mirnas were dynamically regulated in cardiomyocyte hypertrophy and attenuation of mir-22 in rat cardiomyocytes efficiently protected from hypertrophic effects through derepressing pten.",1
"background beta-site amyloid precursor protein cleaving enzyme 1 (bace1) is conceived as a potential target for therapies against alzheimer disease (ad) which is characterized by the accumulation of plaques formed of short β-amyloid (appβ) peptides. recently, such micrornas, as mir-29a, mir-29b-1 have been shown to correlate with abnormally high levels of bace1 and appβ in sporadic ad. methods in order to confirm whether mir-29c correlates with the bace1 upregulation in sporadic ad, we firstly evaluated the expression of mir-29c and bace1, the appβ accumulation in sporadic ad brain tissues and analyzed the correlation of mir-29c with bace1. then we determined the regulation of mir-29c in human heuroblastoma sh-sy5y cells on the bace1 expression and appβ accumulation. and finally we determined the targeting to 3' utr of bace1 by mir-29c by a luciferase reporter. results it was demonstrated that mir-29c was downregulated in sporadic ad brains, in an association with an upregulation of bace1 in both mrna and protein level of bace1, and also an elevated appβ accumulation. and the manipulated high level of mir-29c with mir-29c mimics transfection significantly reduced the protein level of bace1 and appβ accumulation in human neuroblastoma sh-sy5y cells. further luciferase reporter assay demonstrated that mir-29c targets the 3' utr of bace1 and downregulated the bace1 in hek293 cells. conclusion present study indicated that mir-29c was downregulated in sporadic ad brains, and it targeted the 3' utr of bace1, reduced the bace1 expression, and downregulated the appβ accumulation in vitro.",1
"micrornas (mirnas) have been found to be involved in cancer initiation, progression and metastasis and, as such, have been suggested as tools for cancer detection and therapy. in this work, a large-scale screening of the complete mirna mimics library demonstrated that hsa-mir-15a-3p had a pro-apoptotic role in the following human cancer cells: hela, aspc-1, mda-mb-231, kb3, me180, hct-116 and a549. mir-15a-3p is a novel member of the pro-apoptotic mirna cluster, mir-15a/16, which was found to activate caspase-3/7 and to cause viability loss in b/cmba.ov cells during preliminary screening. subsequent microarrays and bioinformatics analyses identified the following four anti-apoptotic genes: bcl2l1, naip5, fgfr2 and mybl2 as possible targets for the mmu-mir-15a-3p in b/cmba.ov cells. follow-up studies confirmed the pro-apoptotic role of hsa-mir-15a-3p in human cells by its ability to activate caspase-3/7, to reduce cell viability and to inhibit the expression of bcl2l1 (bcl-xl) in hela and aspc-1 cells. mir-15-3p was also found to reduce viability in hek293, mda-mb-231, kb3, me180, hct-116 and a549 cell lines and, therefore, may be considered for apoptosis modulating therapies in cancers associated with high bcl-xl expression (cervical, pancreatic, breast, lung and colorectal carcinomas). the capability of hsa-mir-15a-3p to induce apoptosis in these carcinomas may be dependent on the levels of bcl-xl expression. the use of endogenous inhibitors of bcl-xl and other anti-apoptotic genes such as hsa-mir-15a-3p may provide improved options for apoptosis-modulating therapies in cancer treatment compared with the use of artificial antisense oligonucleotides.",1
"histone deacetylase (hdac) inhibitors are emerging as a novel class of anti-tumor agents and have manifested the ability to decrease proliferation and increase apoptosis in different cancer cells. a significant number of genes have been identified as potential effectors responsible for the anti-tumor function of hdac inhibitor. however, the molecular mechanisms of these hdac inhibitors in this process remain largely undefined. in the current study, we searched for micrornas (mirs) that were affected by hdac inhibitor trichostatin (tsa) and investigated their effects in endometrial cancer (emc) cells. our data showed that tsa significantly inhibited the growth of emc cells and induced their apoptosis. among the mirnas that altered in the presence of tsa, the mir-106b-93-25 cluster, together with its host gene mcm7, were obviously down-regulated in emc cells. p21 and bim, which were identified as target genes of mir-106b-93-25 cluster, increased in tsa treated tumor cells and were responsible for cell cycle arrest and apoptosis. we further identified myc as a regulator of mir-106b-93-25 cluster and demonstrated its down-regulation in the presence of tsa resulted in the reduction of mir-106b-93-25 cluster and up-regulation of p21 and bim. more important, we found mir-106b-93-25 cluster was up-regulated in clinical emc samples in association with the overexpression of mcm7 and myc and the down-regulation of p21 and bim. thus our studies strongly indicated tsa inhibited emc cell growth and induced cell apoptosis and cell cycle arrest at least partially through the down-regulation of the mir-106b-93-25 cluster and up-regulation of it's target genes p21 and bim via myc.",1
"mirnas have attracted more attention in recent years as regulators of sleep and circadian rhythms after their roles in circadian rhythm and sleep were discovered. in this study, we explored the roles of the mir-276a on daily sleep in drosophila melanogaster, and found a regulatory cycle for the mir-276a pathway, in which mir-276a, regulated by the core clock/cycle (clk/cyc) transcription factor upstream, regulates sleep via suppressing targets tim and npfr1. (a) loss of mir-276a function makes the flies sleep more during both daytime and nighttime, while flies with gain of mir-276a function sleep less; (b) mir-276a is widely expressed in the mushroom body (mb), the pars intercerebralis (pi) and some clock neurons lateral dorsal neurons (lnds), in which tim neurons is important for sleep regulation; (c) mir-276a promoter is identified to locate in the 8th fragment (afrag8) of the pre-mir-276a, and this fragment is directly activated and regulated by clk/cyc; (4) mir-276a is rhythmically oscillating in heads of the wild-type w 1118 , but this oscillation disappears in the loss of function mutant clk jrk ; (5) the neuropeptide f receptor 1 (npfr1) was found to be a downstream target of mir-276a. these results clarify that the mir-276a is a very important factor for sleep regulation.",1
"ulcerative colitis (uc) is an inflammatory bowel disease (ibd) characterized by mucosa damage associated with an uncontrolled inflammatory response. this immunological impairment leads to altered inflammatory mediators such as il-33, which is shown to increase in the mucosa of active uc (auc) patients. micrornas present a distorted feature in inflamed colonic mucosa and are potential il-33 regulating candidates in uc. therefore, we studied the microrna and mrna profiles in inflamed colonic samples of uc patients, evaluating the effect of a microrna (selected by in silico analysis and its expression in uc patients), on il-33 under inflammatory conditions. we found that inflamed mucosa ( n = 8) showed increased expression of 40 micrornas and 2,120 mrnas, while 49 micrornas and 1,734 mrnas were decreased, as determined by microarrays. in particular, il-33 mrna showed a 3.8-fold increase and eight members of a microrna family (mir-378), which targets il-33 mrna in the 3'utr, were decreased (-3.9 to -3.0 times). we selected three members of the mir-378 family (mir-378a-3p, mir-422a, and mir-378c) according to background information and interaction energy analysis, for further correlation analyses with il-33 expression through qpcr and elisa, respectively. we determined that auc ( n = 24) showed high il-33 levels, and decreased expression of mir-378a-3p and mir-422a compared to inactive uc ( n = 10) and controls ( n = 6). moreover, both micrornas were inversely correlated with il-33 expression, while mir-378c does not show a significant difference. to evaluate the effect of tnfα on the studied micrornas, auc patients with anti-tnf therapy were compared to auc receiving other treatments. the levels of mir-378a-3p and mir-378c were higher in auc patients with anti-tnf. based on these findings, we selected mir-378a-3p to exploring the molecular mechanism involved by in vitro assays, showing that over-expression of mir-378a-3p decreased the levels of an il-33 target sequence β-gal-reporter gene in hek293 cells. stable mir-378a-3p over-expression/inhibition inversely modulated il-33 content and altered viability of ht-29 cells. additionally, in an inflammatory context, tnfα decreased mir-378a-3p levels in ht-29 cells enhancing il-33 expression. together, our results propose a regulatory mechanism of il-33 expression exerted by mir-378a-3p in an inflammatory environment, contributing to the understanding of uc pathogenesis.",1
"colorectal cancer (crc) is one of the leading causes of cancer-related mortality worldwide. micrornas (mirs) are single-stranded, noncoding rnas that are important in many biological processes. although the oncogenic and tumor-suppressive functions of several mirs have been characterized, their precise biological roles remain largely unexplored. in the present study, the role of mir-133b was identified in the regulation of crc cell proliferation and apoptosis. mir-133b expression was shown to be greatly downregulated in human crc cells compared to normal colon cells. downregulation of mir-133b expression was also significant in six of eight human crc tissues compared with adjacent normal tissues. in the crc cell lines sw-620 and ht-29, ectopic expression of mir-133b potently affected tumor cell proliferation and apoptosis in vitro and in vivo by direct targeting of the receptor tyrosine kinase met. transfection of sw-620 and ht-29 cells with mir-133b significantly suppressed a luciferase-reporter containing the met-3'-untranslated region. taken together, these results provide evidence that mir-133b regulated tumor cell proliferation and apoptosis through modulation of the met signaling pathway.",1
"endothelial cells play essential roles in maintenance of vascular integrity, angiogenesis, and wound repair. we show that an endothelial cell-restricted microrna (mir-126) mediates developmental angiogenesis in vivo. targeted deletion of mir-126 in mice causes leaky vessels, hemorrhaging, and partial embryonic lethality, due to a loss of vascular integrity and defects in endothelial cell proliferation, migration, and angiogenesis. the subset of mutant animals that survives displays defective cardiac neovascularization following myocardial infarction. the vascular abnormalities of mir-126 mutant mice resemble the consequences of diminished signaling by angiogenic growth factors, such as vegf and fgf. accordingly, mir-126 enhances the proangiogenic actions of vegf and fgf and promotes blood vessel formation by repressing the expression of spred-1, an intracellular inhibitor of angiogenic signaling. these findings have important therapeutic implications for a variety of disorders involving abnormal angiogenesis and vascular leakage.",1
"purpose to investigate the interactions between microrna-29 (mir-29), a negative regulator of extracellular matrix (ecm), and transforming growth factors (tgf)β-1 and tgfβ-2. methods changes in expression of the mir-29 family were analyzed by quantitative-pcr (q-pcr) after treatment with tgfβ1 and tgfβ2 (1 ng/ml). tgfβ1 and tgfβ2 were evaluated at gene expression and protein levels by q-pcr and elisa, respectively, in human trabecular meshwork (htm) cells transfected with mir-29b or scramble control. tgfβ1 promoter activity was analyzed using an adenovirus with the reporter seap. the effects of mir-29b and tgfβ2 on ecm gene expression were evaluated in cells transfected with mir-29b or scramble control and treated with tgfβ2, and the expression of ecm genes was analyzed by q-pcr. results tgfβ2 but not tgfβ1, downregulated the three members of the mir-29 family. overexpression of mir-29b antagonized the effects of tgfβ2 on the expression of several ecm components. mir-29b decreased the expression of tgfβ1 at the promoter, transcript, and protein levels but had only a minor effect on the expression of active tgfβ2. the inhibition of tgfβ1 by mir-29b was partially recovered after co-transfection with a plasmid-expressing bone morphogenetic protein 1. conclusions results showed some level of crosstalk between tgfβs and mir-29. specifically, the downregulation of mir-29 by tgfβ2 contributed to the induction of several ecm components by this cytokine in tm cells. this observation, together with the inhibitory effects of mir-29b on the expression of tgfβ1, suggests that the mir-29 family could play an important role in modulating tgfβs on the outflow pathway.",1
"background micrornas (mirnas) play an important role in development and are associated with birth defects. data are scant on the role of mirnas in birth defects arising from exposure to environmental factors such as alcohol. methods in this study, we determined the expression levels of 509 mature mirnas in fetal mouse brains with or without prenatal ethanol exposure using a mirna microarray technique, verified by northern blot and pcr. mouse embryos in culture were used to examine the effect of ethanol treatment on expression of the putative target genes of mir-10a (hoxa1 and other hox members) at mrna and protein level. open field and morris water maze tests were also performed at post-natal day 35. results ethanol treatment induced major fetal teratogenesis in mice and caused mental retardation in their offspring, namely lower locomotor activity (p 1.5) in fetal brains with prenatal ethanol exposure, whereas mir-200a, mir-496, mir-296, mir-30e-5p, mir-362, mir-339, mir-29c and mir-154 were down-regulated (fold change conclusions the study provided new insights into the role of mirnas and their target genes in the pathogenesis of fetal alcohol syndrome.",1
"the x inactive-specific transcript ( xist ) gene is the master regulator of x chromosome inactivation in mammals. xist produces a long noncoding (lnc)rna that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence x-linked genes in cis recent years have seen significant progress in identifying important functional elements in xist rna, their associated rna-binding proteins (rbps), and the downstream pathways for chromatin modification and gene silencing. in this review, we summarize progress in understanding both how these pathways function in xist-mediated silencing and the complex interplay between them.",1
"background microrna mir-214 has been implicated in many biological cellular functions, but the impact of mir-214 and its target genes on vascular smooth muscle cell (vsmc) proliferation, migration, and neointima smooth muscle cell hyperplasia is unknown. methods and results expression of mir-214 was closely regulated by different pathogenic stimuli in vsmcs through a transcriptional mechanism and decreased in response to vascular injury. overexpression of mir-214 in serum-starved vsmcs significantly decreased vsmc proliferation and migration, whereas knockdown of mir-214 dramatically increased vsmc proliferation and migration. gene and protein biochemical assays, including proteomic analyses, showed that nck associated protein 1 (nckap1)-a major component of the wave complex that regulates lamellipodia formation and cell motility-was negatively regulated by mir-214 in vsmcs. luciferase assays showed that mir-214 substantially repressed wild-type but not the mir-214 binding site mutated version of nckap1 3' untranslated region luciferase activity in vsmcs. this result confirmed that nckap1 is the functional target of mir-214 in vsmcs. nckap1 knockdown in vsmcs recapitulates the inhibitory effects of mir-214 overexpression on actin polymerization, cell migration, and proliferation. data from cotransfection experiments also revealed that inhibition of nckap1 is required for mir-214-mediated lamellipodia formation, cell motility, and growth. importantly, locally enforced expression of mir-214 in the injured vessels significantly reduced nckap1 expression levels, inhibited vsmc proliferation, and prevented neointima smooth muscle cell hyperplasia after injury. conclusions we uncovered an important role of mir-214 and its target gene nckap1 in modulating vsmc functions and neointima hyperplasia. our findings suggest that mir-214 represents a potential therapeutic target for vascular diseases.",1
"activation of mammalian innate and acquired immune responses must be tightly regulated by elaborate mechanisms to control their onset and termination. micrornas have been implicated as negative regulators controlling diverse biological processes at the level of posttranscriptional repression. expression profiling of 200 micrornas in human monocytes revealed that several of them (mir-146a/b, mir-132, and mir-155) are endotoxin-responsive genes. analysis of mir-146a and mir-146b gene expression unveiled a pattern of induction in response to a variety of microbial components and proinflammatory cytokines. by means of promoter analysis, mir-146a was found to be a nf-kappab-dependent gene. importantly, mir-146a/b were predicted to base-pair with sequences in the 3' utrs of the tnf receptor-associated factor 6 and il-1 receptor-associated kinase 1 genes, and we found that these utrs inhibit expression of a linked reporter gene. these genes encode two key adapter molecules downstream of toll-like and cytokine receptors. thus, we propose a role for mir-146 in control of toll-like receptor and cytokine signaling through a negative feedback regulation loop involving down-regulation of il-1 receptor-associated kinase 1 and tnf receptor-associated factor 6 protein levels.",1
"micrornas (mirnas), recently identified noncoding small rnas, are emerging as key regulators in homeostasis of the immune system. therefore, aberrant expression of mirnas may be linked to immune dysfunction, such as in chronic inflammation and autoimmunity. in this study, we investigated the potential role of mirnas in estrogen-mediated regulation of innate immune responses, as indicated by up-regulation of lipopolysaccharide (lps)-induced interferon-gamma (ifngamma), inducible nitric oxide synthase (inos), and nitric oxide in splenic lymphocytes from estrogen-treated mice. we found that mir-146a, a negative regulator of toll-like receptor (tlr) signaling, was decreased in freshly isolated splenic lymphocytes from estrogen-treated mice compared with placebo controls. increasing the activity of mir-146a significantly inhibited lps-induced ifngamma and inos expression in mouse splenic lymphocytes. further, mirna microarray and real-time reverse transcriptase-polymerase chain reaction (rt-pcr) analysis revealed that estrogen selectively up-regulates/down-regulates the expression of mirnas in mouse splenic lymphocytes. mir-223, which is markedly enhanced by estrogen, regulates lps-induced ifngamma, but not inos or nitric oxide in splenic lymphocytes. inhibition of mir-223 activity decreased lps-induced ifngamma in splenic lymphocytes from estrogen-treated mice. our data are the first to demonstrate the selective regulation of mirna expression in immune cells by estrogen and are indicative of an important role of mirnas in estrogen-mediated immune regulation.",1
"repair of bone defects presents a serious clinical challenge as it is difficult to restore bone function and regenerate bone loss. in the present study, the effects of lentivirus‑mediated transfection of bone marrow mesenchymal stem cells (bmscs) with microrna (mir)‑26a on bone regeneration were investigated in a mouse bone defect repair model. marker of proliferation ki67 (ki67) staining was employed to detect the cell proliferation capacity and alkaline phosphatase (alp) staining was used to investigate osteogenic differentiation. a mouse model of cranial bone defects was established. β‑tricalcium phosphate biomaterials co‑cultured with the transfected bmscs were implanted into the defect areas of mouse models. micro‑computed tomography, and hematoxylin and eosin and toluidine blue staining, were used to detect bone regeneration in the defect areas and the degradation of scaffolds. mir‑26a expression, and the mrna and protein expression of osteogenesis‑associated cytokines, were detected using reverse transcription‑quantitative polymerase chain reaction and western blot analysis. separated and cultured bmscs highly expressed cd29 and cd105, but not cd34 and cd45, as determined by flow cytometry. mir‑26a expression and the positive cell rate of ki67 and alp staining in bmscs transfected with plvthm‑mir‑26a were increased. the bmsc and negative control‑transfected bmsc groups exhibited increased bone regeneration in the defect areas, increased bone volume of newly formed bones, and elevated mrna and protein expression of runt‑related transcription factor 2 (runx2) and osteocalcin (oc), compared with the blank group. however, the mir‑26a‑transfected bmsc group exhibited further increases in bone regeneration and the volume of newly formed bones, and further elevations of the mrna and protein expression levels of runx2 and oc. the present findings demonstrated that lentivirus‑mediated modification of bmscs enhanced bone regeneration during the repair of cranial bone defects in mice.",1
"mir-263a/b are members of a conserved family of micrornas that are expressed in peripheral sense organs across the animal kingdom. here we present evidence that mir-263a and mir-263b play a role in protecting drosophila mechanosensory bristles from apoptosis by down-regulating the pro-apoptotic gene head involution defective. both micrornas are expressed in the bristle progenitors, and despite a difference in their seed sequence, they share this key common target. in mir-263a and mir-263b deletion mutants, loss of bristles appears to be sporadic, suggesting that the role of the micrornas may be to ensure robustness of the patterning process by promoting survival of these functionally specified cells. in the context of the retina, this mechanism ensures that the interommatidial bristles are protected during the developmentally programmed wave of cell death that prunes excess cells in order to refine the pattern of the pupal retina.",1
"the epstein-barr virus (ebv)-encoded latent membrane protein 1 (lmp1) is a functional homologue of the tumor necrosis factor receptor family and contributes substantially to the oncogenic potential of ebv through activation of nuclear factor kappab (nf-kappab). micrornas (mirnas) are a class of small rna molecules that are involved in the regulation of cellular processes such as growth, development, and apoptosis and have recently been linked to cancer phenotypes. through mirna microarray analysis, we demonstrate that lmp1 dysregulates the expression of several cellular mirnas, including the most highly regulated of these, mir-146a. quantitative reverse transcription-pcr analysis confirmed induced expression of mir-146a by lmp1. analysis of mir-146a expression in ebv latency type iii and type i cell lines revealed substantial expression of mir-146a in type iii (which express lmp1) but not in type i cell lines. reporter studies demonstrated that lmp1 induces mir-146a predominantly through two nf-kappab binding sites in the mir-146a promoter and identified a role for an oct-1 site in conferring basal and induced expression. array analysis of cellular mrnas expressed in akata cells transduced with an mir-146a-expressing retrovirus identified genes that are directly or indirectly regulated by mir-146a, including a group of interferon-responsive genes that are inhibited by mir-146a. since mir-146a is known to be induced by agents that activate the interferon response pathway (including lmp1), these results suggest that mir-146a functions in a negative feedback loop to modulate the intensity and/or duration of the interferon response.",1
"the nucleolytic activity of animal argonaute proteins is deeply conserved, despite its having no obvious role in microrna-directed gene regulation. in mice, ago2 (also known as eif2c2) is uniquely required for viability, and only this family member retains catalytic competence. to investigate the evolutionary pressure to conserve argonaute enzymatic activity, we engineered a mouse with catalytically inactive ago2 alleles. homozygous mutants died shortly after birth with an obvious anaemia. examination of micrornas and their potential targets revealed a loss of mir-451, a small rna important for erythropoiesis. though this microrna is processed by drosha (also known as rnasen), its maturation does not require dicer. instead, the pre-mirna becomes loaded into ago and is cleaved by the ago catalytic centre to generate an intermediate 3' end, which is then further trimmed. our findings link the conservation of argonaute catalysis to a conserved mechanism of microrna biogenesis that is important for vertebrate development.",1
"micrornas (mirnas) are incorporated into mirnp complexes and regulate protein expression post-transcriptionally through binding to 3'-untranslated regions of target mrnas. here we describe a recapitulation of let-7 mirna-mediated translational repression in a cell-free system, which was established with extracts prepared from hek293f cells overexpressing mirna pathway components. in this system, both the cap and poly(a) tail are required for the translational repression, and let-7 directs the deadenylation of target mrnas. our work suggests that let-7 mirnps containing argonaute and gw182 impair the synergistic enhancement of translation by the 5'-cap and 3'-poly(a) tail, resulting in translational repression.",1
"micrornas are a large and essential class of gene regulators that play key roles in development, homeostasis, and disease. they are necessary for normal skeletal development, and their expression is altered in arthritis. however, the specific role of individual micrornas is only beginning to be unraveled. using microrna expression profiling in healthy human articular cartilage cells (chondrocytes), we identified mir-1247 expression as highly correlated with that of the differentiated cell phenotype. transcribed from the dlk1-dio3 locus, the function of mir-1247 is completely unknown. in mice its expression level was relatively high in cartilage tissue, and correlated with cartilage-associated microrna mir-675 across a range of 15 different mouse tissues. to further probe mir-1247 function, overexpression and inhibition studies were performed in isolated human chondrocytes. modulation of mir-1247 was found to exert profound phenotypic effects altering expression levels of cartilage master regulator transcription factor sox9. sox9 is essential for cartilage development and subsequent function throughout life, and mutations in this gene result in severe dwarfism. putative mir-1247 binding sites were further investigated using luciferase reporter assays, which indicated binding of mir-1247 to a highly conserved region in the coding sequence of sox9 but not in its 3'-utr. interestingly, depletion of sox9 in human chondrocytes resulted in increased levels of the mature, processed microrna, suggesting a negative feedback loop between mir-1247 and its target sox9.",1
"objective to give a new insight into the mechanism of apoe dysregulation and microrna-1908 in alzheimer's disease (ad). methods plasma apoe levels were measured in 20 ad patients and 20 healthy controls. thp-1 was maintained in rpmi1640 with 10% fetal bovine serum. quantitative real-time polymerase chain reaction was performed to detect 13-microrna and apoe mrna in cultured cell lines. enzyme-linked immunosorbent assay was used to measure human apoe in the plasma or culture medium of cell lines and also used to quantify the human aβ42 in the culture medium of cell lines. results we found plasma apoe level reduced in ad patients (2.28 vs 3.78 μg/ml, p conclusions our study provides new insight into the mechanism of apoe dysregulation in ad patients, and microrna-1908 might be a therapeutic target for ad treatment.",1
"aim to investigate the potential roles and mechanisms of mir-17-5p/20a in human gastric cancer development and progression. methods quantitative real-time polymerase chain reaction (qrt-pcr) was employed to determine mir-17-5p/20a expression profiles in 110 gastric cancer tissues. micrornas' (mirnas) mimics and inhibitors were used to reveal their function in gastric cancer. antagomirs were applied to treating gastric cancer cell derived xenograft in vivo. western blot and luciferase assays were performed to uncover the targets and mechanisms of mir-17-5p/20a. results mir-17-5p/20a levels were upregulated in human gastric cancer tissues. overexpression of mir-17-5p/20a promoted gastric cancer cell cycle progression and inhibited cell apoptosis, whereas knockdown of mir-17-5p/20a resulted in cell cycle arrest and increased apoptosis. p21 and tumour protein p53-induced nuclear protein 1 (tp53inp1) were validated as the targets of mir-17-5p/20a. antagomirs against mir-17-5p/20a significantly inhibited gastric cancer growth via upregulation of p21 and tp53inp1 in a mouse xenograft model. the negative relationship between mir-17-5p/20a and tp53inp1 was observed in patient gastric cancer tissues. murine double minute 2 (mdm2) was found to be involved in mirna regulation and function. targeted inhibition of mdm2 in a mirna mimic-transfected gastric cancer cell line abolished mir-17-5p/20a function and inhibition of p21 expression. mdm2 restoration by pcmv-mdm2 rescued the functionality. conclusions our findings indicate that mir-17-5p/20a promote gastric cancer cell proliferation and inhibit cell apoptosis via post-transcriptional modulation of p21 and tp53inp1. they may be promising therapeutic markers for gastric cancer. mdm2 contributes to mir-17-5p/20a function and inhibition of p21 in gastric cancer, and may be a novel mechanism underlying the oncogenic roles of mir-17-5p/20a.",1
"bacterial small noncoding rnas (srnas) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. in this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium nitrosomonas europaea for the presence and expression of srnas. fifteen genes encoding putative srnas (psrnas) were identified. most of these genes showed altered expression in a variety of experimental conditions. the transcripts of two psrnas were further characterized by mapping their 5'- and 3'-ends and by real-time pcr. the results of these analyses suggested that one of them, psrna11, is involved in iron homeostasis in n. europaea.",1
"proper resolution of inflammation is vital for repair and restoration of homeostasis after tissue damage, and its dysregulation underlies various noncommunicable diseases, such as cardiovascular and metabolic diseases. macrophages play diverse roles throughout initial inflammation, its resolution, and tissue repair. differential metabolic reprogramming is reportedly required for induction and support of the various macrophage activation states. here we show that a long noncoding rna (lncrna), lncfao , contributes to inflammation resolution and tissue repair in mice by promoting fatty acid oxidation (fao) in macrophages. lncfao is induced late after lipopolysaccharide (lps) stimulation of cultured macrophages and in ly6c hi monocyte-derived macrophages in damaged tissue during the resolution and reparative phases. we found that lncfao directly interacts with the hadhb subunit of mitochondrial trifunctional protein and activates fao. lncfao deletion impairs resolution of inflammation related to endotoxic shock and delays resolution of inflammation and tissue repair in a skin wound. these results demonstrate that by tuning mitochondrial metabolism, lncfao acts as a node of immunometabolic control in macrophages during the resolution and repair phases of inflammation.",1
"recent evidence suggests that lncrnas play an integral regulatory role in numerous functions, including determination of cellular identity. we determined global expression (rna-seq) and genome-wide profiles (chip-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hescs) undergoing differentiation to define a high-confidence set of 40 lncrnas, which are p53 transcriptional targets. we focused on lncrnas highly expressed in pluripotent hescs and repressed by p53 during differentiation to identify lncpress1 as a p53-regulated transcript that maintains hesc pluripotency in concert with core pluripotency factors. rna-seq of hescs depleted of lncpress1 revealed that lncpress1 controls a gene network that promotes pluripotency. further, we found that lncpress1 physically interacts with sirt6 and prevents sirt6 chromatin localization, which maintains high levels of histone h3k56 and h3k9 acetylation at promoters of pluripotency genes. in summary, we describe a p53-regulated, pluripotency-specific lncrna that safeguards the hesc state by disrupting sirt6 activity.",1
"micrornas (mirnas) are small, non-coding rnas that function as key post-transcriptional regulators in neural development, brain function, and neurological diseases. growing evidence indicates that mirnas are also important mediators of nerve regeneration, however, the affected signaling mechanisms are not clearly understood. in the present study, we show that nerve injury-induced mir-431 stimulates regenerative axon growth by silencing kremen1, an antagonist of wnt/beta-catenin signaling. both the gain-of-function of mir-431 and knockdown of kremen1 significantly enhance axon outgrowth in murine dorsal root ganglion neuronal cultures. using cross-linking with ago-2 immunoprecipitation, and 3'-untranslated region (utr) luciferase reporter assay we demonstrate mir-431 direct interaction on the 3'-utr of kremen1 mrna. together, our results identify mir-431 as an important regulator of axonal regeneration and a promising therapeutic target.",1
"variations in microrna (mirna) gene and/or target repertoire are likely to be key drivers of phenotypic differences between species. to better understand these changes, we developed a computational method that identifies signatures of species-specific target site gain and loss associated with mirna acquisition. interestingly, several of the mirnas implicated in mouse 3' utr evolution derive from a single rapidly expanded rodent-specific mirna cluster. located in the intron of sfmbt2, a maternally imprinted polycomb gene, these mirnas (referred to as the sfmbt2 cluster) are expressed in both embryonic stem cells and the placenta. one abundant mirna from the cluster, mir-467a, functionally overlaps with the mir-290-295 cluster in promoting growth and survival of mouse embryonic stem cells. predicted novel targets of the remaining cluster members are enriched in pathways regulating cell survival. two relevant species-specific target candidates, lats2 and dedd2, were validated in cultured cells. we suggest that the rapid evolution of the sfmbt2 cluster may be a result of intersex conflict for growth regulation in early mammalian development and could provide a general model for the genomic response to acquisition of mirnas and similar regulatory factors.",1
"introduction c-c chemokine receptor type 7 (ccr7) plays an important role in chemotactic and metastatic responses in various cancers, including breast cancer. in the present study, the authors demonstrated that microrna (mirna) let-7a downregulates ccr7 expression and directly influences the migration and invasion of breast cancer cells. methods the expression of ccr7, its ligand ccl21, and let-7a was detected in breast cancer cell lines and in breast cancer patient tissues. synthetic let-7a and an inhibitor of let-7a were transfected into mda-mb-231 and mcf-7 breast cancer cells, respectively, and cell proliferation, cell migration, and invasion assays were performed. to confirm the fact that 3'utr of ccr7 is a direct target of let-7a, a luciferase assay for the reporter gene expressing the let-7a binding sites of ccr7 3'utr was used. an in vivo invasion animal model system using transparent zebrafish embryos was also established to determine the let-7a effect on breast cancer cell invasion. results first, a higher expression of both ccr7 and ccl21 in malignant tissues than in their normal counterparts from breast cancer patients was observed. in addition, a reverse correlation in the expression of ccr7 and let-7a in breast cancer cell lines and breast cancer patient tissues was detected. synthetic let-7a decreased breast cancer cell proliferation, migration, and invasion, as well as ccr7 protein expression in mda-mb-231 cells. the let-7a inhibitor reversed the let-7a effects on the mcf-7 cells. the 3'utr of ccr7 was confirmed as a direct target of let-7a by using the luciferase assay for the reporter gene expressing let-7a ccr7 3'utr binding sites. notably, when analyzing in vivo invasion, mda-mb 231 cells after synthetic let-7a transfection were unable to invade the vessels in zebrafish embryos. conclusions the results from the present study suggest that targeting of ccl21-ccr7 signaling is a valid approach for breast cancer therapy and that let-7a directly binds to the 3'utr of ccr7 and blocks its protein expression, thereby suppressing migration and invasion of human breast cancer cells. furthermore, the present study underscores the therapeutic potential of let-7a as an antitumor and antimetastatic manager in breast cancer patients.",1
"the drosophila midgut has emerged as an attractive model system to study stem cell biology. extensive studies have been carried out to investigate the mechanisms of how the signaling pathways integrate to regulate intestinal stem cells (iscs), yet, whether the micrornas are involved in isc self-renewal and maintenance is unknown. here we demonstrate that the bantam microrna is expressed specifically at high levels in drosophila midgut precursor cells (including iscs and enteroblasts) and secretory enteroendocrine cells while at extremely low levels in enterocytes. furthermore, overexpression of bantam microrna results in increase of the division of the midgut precursor cells, whereas loss of bantam microrna decreases their proliferation. the mechanical studies show that bantam microrna is essential for the hpo pathway induced cell-autonomous isc self-renewal, while it is disposable for egfr and notch pathways mediated isc proliferation. more interestingly, we find that bantam microrna is not required for the hpo pathway mediated non-cell-autonomous isc proliferation, revealing a novel mechanism by which the hpo signaling pathway specifies its transcriptional targets in specific tissue to exhibit its biological functions.",1
"some truncating mutations of the apc tumor suppressor gene are associated with an attenuated phenotype of familial adenomatous polyposis coli (aapc). this work demonstrates that apc alleles with 5' mutations produce apc protein that down-regulates beta-catenin, inhibits beta-catenin/t cell factor-mediated transactivation, and induces cell-cycle arrest. transfection studies demonstrate that cap-independent translation is initiated internally at an aug at codon 184 of apc. furthermore, apc coding sequence between aapc mutations and aug 184 permits internal ribosome entry in a bicistronic vector. these data suggest that aapc alleles in vivo may produce functional apc by internal initiation and establish a functional correlation between 5' apc mutations and their associated clinical phenotype.",1
"bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. specific response genes that are regulated by a subset of alternative σ(70)-like transcription factors have evolved in order to respond to this changing environment. recently, we have described the existence of a σ(e) regulon including the anti-σ-factor mser in the obligate human bacterial pathogen neisseria meningitidis. to unravel the complete σ(e) regulon in n. meningitidis, we sequenced total rna transcriptional content of wild type meningococci and compared it with that of mser mutant cells (δmser) in which σ(e) is highly expressed. eleven coding genes and one non-coding gene were found to be differentially expressed between h44/76 wildtype and h44/76δmser cells. five of the 6 genes of the σ(e) operon, msra/msrb, and the gene encoding a pepsy-associated tm helix family protein showed enhanced transcription, whilst ania encoding a nitrite reductase and nspa encoding the vaccine candidate neisserial surface protein a showed decreased transcription. analysis of differential expression in igrs showed enhanced transcription of a non-coding rna molecule, identifying a σ(e) dependent small non-coding rna. together this constitutes the first complete exploration of an alternative σ-factor regulon in n. meningitidis. the results direct to a relatively small regulon indicative for a strictly defined response consistent with a relatively stable niche, the human throat, where n. meningitidis resides.",1
"due to invasion and intrahepatic metastasis, the prognosis for patients with hepatocellular carcinoma (hcc) is poor. however, the mechanisms underlying these processes of hcc remain unclear. cancer stem cells may be involved in early systemic dissemination and metastasis formation and side population (sp) cells isolated from diverse cancer cells possess stem cell-like properties. however, the mechanisms involved in migration and invasion of cancer stem cells are not well understood. in this study, we identified and isolated populations of sp cells from hcc cell lines using flow cyto-metry. sp cells showed higher levels of migration and invasion capability. higher expression of mir-21 was observed in sp cells. silencing of mir-21 led to a reduction in the migration and invasion of these cells and overexpression of mir-21 can increase in cell migration and invasion. overexpression of mir-21 did not cause degradation of pten or reck or pdcd4 mrna but drastically inhibited its protein expression. consistent with these results, silencing mir-21 increased the levels of pten, reck and pdcd4 protein, respectively. the role of silencing mir-21 was partially attenuated by silencing of pten or reck or pdcd4 mrna. the results of this study revealed the aberrant expression of mir-21 in sp cells and showed that mir-21 regulates the expression of multiple target proteins that are associated with tumor dissemination. mir-21 is a pro-metastatic mirna in sp cells and raises the possibility that therapy of hcc may be improved by pharmaceutical strategies directed towards mir-21.",1
"background hmga2 expression has been shown to be associated with enhanced selective chemosensitivity towards the topoisomerase (topo) ii inhibitor, doxorubicin, in cancer cells. although the roles of signaling cascades and proteins as regulatory factors in development, neoplasia and adaptation to the environment are becoming well established, evidence for the involvement of regulatory small rna molecules, such as micrornas (mirnas) as important regulators of both transcriptional and posttranscriptional gene silencing is presently mounting. results here we report that hmga2 expression in head and neck squamous cell carcinoma (hnscc) cells is regulated in part by mirna-98 (mir-98). albeit hmga2 is associated with enhanced selective chemosensitivity towards topoisomerase (topo) ii inhibitor, doxorubicin in hnscc, the expression of hmga2 is thwarted by hypoxia. this is accompanied by enhanced expression of mirna-98 and other mirnas, which predictably target hmga2. moreover, we show that transfection of pre-mir-98trade mark during normoxia diminishes hmga2 and potentiates resistance to doxorubicin and cisplatin. these findings implicate the role of a mirna as a key element in modulating tumors in variable microenvironments. conclusion these studies validate the observation that hmga2 plays a prominent role in governing genotoxic responses. however, this may only represent cells growing under normal oxygen tensions. the demonstration that mirna profiles are altered during hypoxia and repress a genotoxic response indicates that changes in microenvironment in eukaryotes mimic those of lower species and plants, where, for example, abiotic stresses regulate the expression of thousands of genes in plants at both transcriptional and posttranscriptional levels through a number of mirnas and other small regulatory rnas.",1
"enhancer-derived rnas are thought to act locally by contributing to their parent enhancer function. whether large domains of clustered enhancers (super-enhancers) also produce cis-acting rnas, however, remains unclear. unlike typical enhancers, super-enhancers form large spans of robustly transcribed chromatin, amassing capped and polyadenylated rnas that are sufficiently abundant to sustain trans functions. here, we show that one such rna, alncrna-ec7/bloodlinc, is transcribed from a super-enhancer of the erythroid membrane transporter slc4a1/band3 but diffuses beyond this site. bloodlinc localizes to trans-chromosomal loci encoding critical regulators and effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor hnrnpu. inhibiting bloodlinc or hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. thus, bloodlinc is a trans-acting super-enhancer rna that potentiates red blood cell development.",1
"micrornas (mirnas) are regulatory rnas found in multicellular eukaryotes, including humans, where they are implicated in cancer. the let-7 mirna times seam cell terminal differentiation in c. elegans. here we show that the let-7 family negatively regulates let-60/ras. loss of let-60/ras suppresses let-7, and the let-60/ras 3'utr contains multiple let-7 complementary sites (lcss), restricting reporter gene expression in a let-7-dependent manner. mir-84, a let-7 family member, is largely absent in vulval precursor cell p6.p at the time that let-60/ras specifies the 1 degrees vulval fate in that cell, and mir-84 overexpression suppresses the multivulva phenotype of activating let-60/ras mutations. the 3'utrs of the human ras genes contain multiple lcss, allowing let-7 to regulate ras expression. let-7 expression is lower in lung tumors than in normal lung tissue, while ras protein is significantly higher in lung tumors, providing a possible mechanism for let-7 in cancer.",1
"members of the mir-200 family of micro rnas (mirnas) have been shown to inhibit epithelial-mesenchymal transition (emt). emt of tubular epithelial cells is the mechanism by which renal fibroblasts are generated. here we show that mir-200 family members inhibit transforming growth factor-beta (tgf-beta)-induced emt of tubular cells. unilateral ureter obstruction (uuo) is a common model of emt of tubular cells and subsequent tubulointerstitial fibrosis. in order to examine the role of mir-200 family members in tubulointerstitial fibrosis, their expression was investigated in the kidneys of uuo mice. the expression of mir-200 family mirnas was increased in a time-dependent manner, with induction of mir-200b most pronounced. to clarify the effect of mir-200b on tubulointerstitial fibrosis, we injected mir-200b precursor intravenously. a single injection of 0.5 nm mir-200b precursor was sufficient to inhibit the increase of collagen types i, iii and fibronectin in obstructed kidneys, and amelioration of fibrosis was confirmed by observation of the kidneys with azan staining. mir-200 family members have been previously shown to inhibit emt by reducing the expression of zeb-1 and zeb-2 which are known repressors of e-cadherin. we demonstrated that expression of zeb-1 and zeb-2 was increased after ureter obstruction and that administration of the mir-200b precursor reversed this effect. in summary, these results indicate that mir-200 family is up-regulated after ureter obstruction, mir-200b being strongly induced, and that mir-200b ameliorates tubulointerstitial fibrosis in obstructed kidneys. we suggest that members of the mir-200 family, and mir-200b specifically, might constitute novel therapeutic targets in kidney disease.",1
"escherichia coli trnalyssuu, as well as human trnalys3suu, has 2-thiouridine derivatives at wobble position 34 (s2u*34). unlike the native trnalyssuu, the full-length, unmodified transcript of human trnalys3uuu and the unmodified trnalys3uuu anticodon stem/loop (asllys3uuu) did not bind aaa- or aag-programmed ribosomes. in contrast, the completely unmodified yeast trnaphe anticodon stem/loop (aslphegaa) had an affinity (kd = 136+/-49 nm) similar to that of native yeast trnaphegmaa (kd = 103+/-19 nm). we have found that the single, site-specific substitution of s2u34 for u34 to produce the modified asllyssuu was sufficient to restore ribosomal binding. the modified asllyssuu bound the ribosome with an affinity (kd = 176+/-62 nm) comparable to that of native trnalyssuu (kd = 70+/-7 nm). furthermore, in binding to the ribosome, the modified asllys3suu produced the same 16s p-site trna footprint as did native e. coli trnalyssuu, yeast trnaphegmaa, and the unmodified aslphegaa. the unmodified asllys3uuu had no footprint at all. investigations of thermal stability and structure monitored by uv spectroscopy and nmr showed that the dynamic conformation of the loop of modified asllys3suu was different from that of the unmodified asllysuuu, whereas the stems were isomorphous. based on these and other data, we conclude that s2u34 in trnalyssuu and in other s2u34-containing trnas is critical for generating an anticodon conformation that leads to effective codon interaction in all organisms. this is the first example of a single atom substitution (u34-->s2u34) that confers the property of ribosomal binding on an otherwise inactive trna.",1
"fragile x syndrome, a common form of inherited mental retardation, is caused by the loss of fragile x mental retardation protein (fmrp). we have previously demonstrated that dfmr1, the drosophila ortholog of the fragile x mental retardation 1 gene, plays a role in the proper maintenance of germline stem cells in drosophila ovary; however, the molecular mechanism behind this remains elusive. in this study, we used an immunoprecipitation assay to reveal that specific micrornas (mirnas), particularly the bantam mirna (bantam), are physically associated with dfmrp in ovary. we show that, like dfmr1, bantam is not only required for repressing primordial germ cell differentiation, it also functions as an extrinsic factor for germline stem cell maintenance. furthermore, we find that bantam genetically interacts with dfmr1 to regulate the fate of germline stem cells. collectively, our results support the notion that the fmrp-mediated translation pathway functions through specific mirnas to control stem cell regulation.",1
"the replication of positive-strand rna viral genomes involves various cis-acting rna sequences. generally, regulatory rna sequences are present at or near genomic termini; however, internal replication elements (ires) also exist. here we report the structural and functional characterization of an ire present in the readthrough portion of the p92 polymerase gene of tomato bushy stunt virus. analysis of this element in the context of a noncoding defective interfering rna revealed a functional core structure composed of two noncontiguous segments of sequence that interact with each other to form an extended helical conformation. ire activity required maintenance of several base-paired sections as well as two distinct structural features: (i) a short, highly conserved segment that can potentially form two different and mutually exclusive structures and (ii) an internal loop that contains a critical cc mismatch. the ire was also shown to play an essential role within the context of the viral genome. in vivo analysis with novel rna-based temperature-sensitive genomic mutants and translationally active subgenomic viral replicons revealed the following about the ire: (i) it is active in the positive strand, (ii) it is dispensable late in the viral rna replication process, and (iii) it is functionally inhibited by active translation over its sequence. together, these results suggest that ire activity is required in the cytosol at an early step in the viral replication process, such as template recruitment and/or replicase complex assembly.",1
"long non-coding rna growth arrest-specific 5 (gas5) has been demonstrated to be involved in the pathogenesis of atherosclerosis (as). the purpose of the present study was to investigate the underlying mechanisms of gas5 on the inflammation and lipid metabolic disorders of as. apoe -/- mice were fed on a high fat diet (hfd) and thp-1 macrophages were treated with ox-ldl to construct as model in vivo and in vitro, respectively. the detections of blood lipids and inflammatory cytokines were performed using corresponding assay kits. qrt-pcr was used to assess the expression of gas5 and mir-135a. western blot was performed to detect pparα and cpt1 levels. the targeted interaction between gas5 and mir-135a was determined by dual-luciferase reporter assay and rna immunoprecipitation assay. our data revealed that gas5 was upregulated in as mice model and ox-ldl-treated macrophages. gas5 silencing alleviated lipid metabolic disorders and inflammation in as mice and ox-ldl-treated macrophages. moreover, gas5 directly targeted mir-135a and repressed mir-135a expression. mir-135a expression restoration abrogated the alleviative effects of gas5 silencing on inflammation and lipid metabolic disorders in ox-ldl-treated macrophages. in conclusion, our study suggested that gas5 silencing repressed the malignant progression of as at least partly through upregulation of mir-135a. targeting gas5 might be a promising treatment strategy for as management.",1
"the extracellular matrix (ecm) is a determining factor in the tumor microenvironment that restrains or promotes malignant growth. in this report, we show how the molecular chaperone protein hsp47 functions as a nodal hub in regulating an ecm gene transcription network. a transcription network analysis showed that hsp47 expression was activated during breast cancer development and progression. hsp47 silencing reprogrammed human breast cancer cells to form growth-arrested and/or noninvasive structures in 3d cultures, and to limit tumor growth in xenograft assays by reducing deposition of collagen and fibronectin. coexpression network analysis also showed that levels of microrna(mir)-29b and -29c were inversely correlated with expression of hsp47 and ecm network genes in human breast cancer tissues. we found that mir-29 repressed expression of hsp47 along with multiple ecm network genes. ectopic expression of mir-29b suppressed malignant phenotypes of breast cancer cells in 3d culture. clinically, increased expression of hsp47 and reduced levels of mir-29b and -29c were associated with poor survival outcomes in breast cancer patients. our results show that hsp47 is regulated by mir-29 during breast cancer development and progression, and that increased hsp47 expression promotes cancer progression in part by enhancing deposition of ecm proteins.",1
"although hundreds of distinct animal micrornas (mirnas) are known, the specific biological functions of only a handful are understood at present. here, we demonstrate that three different families of drosophila mirnas directly regulate two large families of notch target genes, including basic helix-loop-helix (bhlh) repressor and bearded family genes. these mirnas regulate notch target gene activity via gy-box (gucuucc), brd-box (agcuuua), and k-box (cugugaua) motifs. these are conserved sites in target 3'-untranslated regions (3'-utrs) that are complementary to the 5'-ends of mirnas, or ""seed"" regions. collectively, these motifs represent >40 mirna-binding sites in notch target genes, and we show all three classes of motif to be necessary and sufficient for mirna-mediated regulation in vivo. importantly, many of the validated mirna-binding sites have limited pairing to mirnas outside of the ""box:seed"" region. consistent with this, we find that seed-related mirnas that are otherwise quite divergent can regulate the same target sequences. finally, we demonstrate that ectopic expression of several notch-regulating mirnas induces mutant phenotypes that are characteristic of notch pathway loss of function, including loss of wing margin, thickened wing veins, increased bristle density, and tufted bristles. collectively, these data establish insights into mirna target recognition and demonstrate that the notch signaling pathway is a major target of mirna-mediated regulation in drosophila.",1
"heparin, which has been used as an anticoagulant drug for decades, inhibits angiogenesis, whereas thrombin promotes tumor-associated angiogenesis. however, the mechanisms underlying the regulation of angiogenesis by heparin and thrombin are not well understood. here, we show that microrna-10b (mir-10b) is down-regulated by heparin and up-regulated by thrombin in human microvascular endothelial cells (hmec-1). overexpression of mir-10b induces hmec-1 cell migration, tube formation, and angiogenesis, and down-regulates homeobox d10 (hoxd10) expression via direct binding of mir-10b to the putative 3' utr of hoxd10. in addition, hmec-1 cell migration and tube formation are induced by hoxd10 knockdown, whereas angiogenesis is arrested when hoxd10 expression is increased after anti-mir-10b or heparin treatments. furthermore, expression of mir-10b and its transcription factor twist are up-regulated by thrombin, whereas hoxd10 expression is impaired by thrombin. using quartz crystal microbalance analysis, we show that heparin binds to thrombin, thereby inhibiting thrombin-induced expression of twist and mir-10b. however, the expression of mir-10b is not attenuated by heparin any more after thrombin expression is silenced by its sirna. interestingly, we find that heparin attenuates mir-10b expression and induces hoxd10 expression in vivo to inhibit angiogenesis and impair the growth of mda-mb-231 tumor xenografts. these results provide insight into the molecular mechanism by which heparin and thrombin regulate angiogenesis.",1
"cajal bodies (cbs) are nuclear organelles that are usually identified by the marker protein p80-coilin. because no orthologue of coilin is known in drosophila melanogaster, we identified d. melanogaster cbs using probes for other components that are relatively diagnostic for cbs in vertebrate cells. u85 small cb-specific rna, u2 small nuclear rna, the survival of motor neurons protein, and fibrillarin occur together in a nuclear body that is closely associated with the nucleolus. based on its similarity to cbs in other organisms, we refer to this structure as the d. melanogaster cb. surprisingly, the d. melanogaster u7 small nuclear rnp resides in a separate nuclear body, which we call the histone locus body (hlb). the hlb is invariably colocalized with the histone gene locus. thus, canonical cb components are distributed into at least two nuclear bodies in d. melanogaster. the identification of these nuclear bodies now permits a broad range of questions to be asked about cb structure and function in a genetically tractable organism.",1
"the putative tumor suppressor mir145 is transcriptionally regulated by tp53 and is downregulated in many tumors; however, its role in prostate cancer is unknown. on the other hand, bcl2/adenovirus e1b 19-kda interacting protein 3 (bnip3) is overexpressed in various tumors, including prostate cancer, and may transcriptionally repress the apoptosis-inducing factor (aif) gene. although bnip3 transcription is controlled by hypoxia-inducible factor 1alpha (also elevated in prostate cancer), we postulated the posttranscriptional regulation of bnip3 by mir145 through bioinformatics analysis, and herein we experimentally showed that mir145 negatively regulated bnip3 by targeting its 3'-untranslated region. artificial overexpression of mir145 by using adenoviral vectors in prostate cancer pc-3 and du145 cells significantly downregulated bnip3, together with the upregulation of aif, reduced cell growth, and increased cell death. artificial overexpression of wild-type tp53 in pc-3 cells (which lack tp53 protein) and du145 cells (in which mutated nonfunctioning tp53 is expressed) significantly upregulated mir145 expression with consequent effects on bnip3 and cell behavior as with mir145 overexpression. analysis of prostate cancer (n = 134) and benign prostate (n = 83) tissue sample showed significantly decreased mir145 and increased bnip3 expression in prostate cancer (p < 0.001), particularly in those with tumor progression, and both molecular changes were associated with unfavorable outcome. abnormalities of the mir145-bnip3 pair as part of tp53-mir145-bnip3-aif network may play a major role in prostate cancer pathogenesis and progression.",1
"cytokines are central components of the mucosal inflammatory responses that take place during the development of crohn's disease. cell-specific combination therapies against cytokines may lead to increased efficacy and even reduced side effects. therefore, a colonic macrophage-specific therapy using mir-16 precursors that can target both tnf-α and il-12p40 was tested for its efficacy in experimental colitic mice. galactosylated low molecular weight chitosan (g-lmwc) associated with mir-16 precursors were intracolonically injected into mice. the cellular localization of mir-16 precursors was determined. the therapeutic effects and possible mechanism were further studied in 2,4,6-trinitrobenzene sulfonic acid (tnbs)-induced colitic mice. the results show that specific upregulation of mir-16 level in colonic macrophages significantly reduces tnf-α and il-12p40 expression, which could suppress the associated mucosal inflammation and ultimately result in the relief of colitic symptoms. this strategy, based on the dual silencing of colonic macrophage-specific cytokines, represents a potential therapeutic approach that may be valuable for colitis therapy.",1
"6s rna is an abundant noncoding rna in escherichia coli that binds to sigma70 rna polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. we have computationally identified >100 new 6s rna homologs in diverse eubacterial lineages. two abundant bacillus subtilis rnas of unknown function (bsra and bsrb) and cyanobacterial 6sa rnas are now recognized as 6s homologs. structural probing of e. coli 6s rna and a b. subtilis homolog supports a common secondary structure derived from comparative sequence analysis. the conserved features of 6s rna suggest that it binds rna polymerase by mimicking the structure of dna template in an open promoter complex. interestingly, the two b. subtilis 6s rnas are discoordinately expressed during growth, and many proteobacterial 6s rnas could be cotranscribed with downstream homologs of the e. coli ygfa gene encoding a putative methenyltetrahydrofolate synthetase. the prevalence and robust expression of 6s rnas emphasize their critical role in bacterial adaptation.",1
"excessive βar stimulation is an independent factor in inducing pathological cardiac hypertrophy. here, we report mir-145 regulates both expression and localization of gata6, thereby protecting the heart against cardiomyocyte hypertrophy induced by isoproterenol (iso). the protective activity of mir-145 was associated with down-regulation of anf, bnp and β-mhc expression, a decreased rate of protein synthesis, inhibited cardiomyocyte growth and the modulation of several signaling pathways including erk1/2, jnk and akt-gsk3β. the anti-hypertrophic effect was abrogated by exogenous over-expression of transcription factor gata6 which was further identified as a direct target of mir-145. in addition, gsk3β antagonists, licl and tdzd8, restored the nuclear accumulation of gata6, which was attenuated by mir-145 finally, we observed a dynamic pattern of mir-145 expression in iso-treated nrcms and in the hearts of tac mice. together, our results identify mir-145 as an important regulator in cardiac hypertrophy.",1
"chronic inflammation is fundamental for the induction of insulin resistance in the muscle tissue of vertebrates. although several mirnas are thought to be involved in the development of insulin resistance, the role of mirnas in the association between inflammation and insulin resistance in muscle tissue is poorly understood. herein, we investigated the aberrant expression of mirnas by conducting mirna microarray analysis of tnf-α-treated mouse c2c12 myotubes. we identified two mirnas that were upregulated and six that were downregulated by a >1.5-fold change compared to normal cells. among the findings, qrt-pcr analysis confirmed that mir-494 is consistently upregulated by tnf-α-induced inflammation. overexpression of mir-494 in cho(ir/irs1) and c2c12 myoblasts suppressed insulin action by down-regulating phosphorylations of gsk-3α/β, as160 and p70s6k, downstream of akt. moreover, overexpression of mir-494 did not regulate tnf-α-mediated inflammation . among genes bearing the seed site for mir-494, rt-pcr analysis showed that the expression of stxbp5, an inhibitor of glucose transport, was downregulated following mir-494 inhibition. in contrast, the expression of pten decreased in the cells analyzed, thus showing that both positive and negative regulators of insulin action may be simultaneously controlled by mir-494. to investigate the overall effect of mir-494 on insulin signaling, we performed a pcr array analysis containing 84 genes related to the insulin signaling pathway, and we observed that 25% of genes were downregulated (p<0.05) and 11% were upregulated (p<0.05). these results confirm that mir-494 might contribute to insulin sensitivity by positive and negative regulation of the expression of diverse genes. of note, pcr array data showed downregulation of slc2a4, a coding gene for glut4. altogether, the present study concludes that the upregulation of mir-494 expression by tnf-α-mediated inflammation exacerbates insulin resistance. therefore, we suggest that mir-494 could prove an important target for the diagnosis and therapy of inflammation-mediated insulin resistance in muscle.",1
"acute myeloid leukemia (aml) with t(8;16)(p11;p13) (t(8;16) aml) has unique clinico-biological characteristics, but its microrna pattern is unknown. we analyzed 670 micrornas in seven patients with t(8;16) aml and 113 with other aml subtypes. hierarchical cluster analysis showed that all t(8;16) aml patients grouped in an independent cluster. supervised analysis revealed a distinctive signature of 94-micrornas, most of which were downregulated, including mir-21 and cluster mir-17-92. the mrna expression analysis of two known transcription factors of these micrornas (stat3 and c-myc, respectively) showed significant downregulation of stat3 (p=0.04). a bioinformatic analysis showed that 29 of the downregulated micrornas might be regulated by methylation; we treated a t(8;16) aml sample with 5-aza-2'-deoxycytidine (5-aza-dc) and trichostatin a and found that 27 micrornas were re-expressed after treatment. however, there was no difference in methylation status between t(8;16) and other aml subtypes, either overall or in the microrna promoter. cross-correlation of mrna and microrna expression identified ret as a potential target of several micrornas. a renilla-luciferase assay and flow cytometry after transfection with pre-micrornas confirmed that ret is regulated by mir-218, mir-128, mir-27b, mir-15a and mir-195. in conclusion, t(8;16) aml harbors a specific microrna signature that is partially epigenetically regulated and targets ret proto-oncogene.",1
"the role of tgf-β signaling in tumorigenesis is paradoxical: it can be tumor suppressive or tumor promotional, depending on context. the metastatic regulator, six1, was recently shown to mediate this switch, providing a novel means to explain this elusive 'tgf-β paradox'. herein, we identify a mechanism by which six1 activates the tumor promotional arm of tgf-β signaling, via its ability to upregulate the mir-106b-25 microrna cluster, and further identify a novel function for this cluster of micrornas. although expression of the mir-106b-25 cluster is known to overcome tgf-β-mediated growth suppression via targeting p21 and bim, we demonstrate for the first time that this same cluster can additionally target the inhibitory smad7 protein, resulting in increased levels of the tgf-β type i receptor and downstream activation of tgf-β signaling. we further show that the mir-106b-25 cluster is sufficient to induce an epithelial-to-mesenchymal transition and a tumor initiating cell phenotype, and that it is required downstream of six1 to induce these phenotypes. finally, we demonstrate a significant correlation between mir-106b, six1, and activated tgf-β signaling in human breast cancers, and further show that high levels of mir-106b and mir-93 in breast tumors significantly predicts shortened time to relapse. these findings expand the spectrum of oncogenic functions of mir-106b-25, and may provide a novel molecular explanation, through the six1 regulated mir-106b-25 cluster, by which tgf-β signaling shifts from tumor suppressive to tumor promoting.",1
"micrornas (mirnas) are small rnas with diverse regulatory roles. the mir-124 mirna is expressed in neurons in the developing and adult nervous system. here we show that overexpression of mir-124 in differentiating mouse p19 cells promotes neurite outgrowth, while blocking mir-124 function delays neurite outgrowth and decreases acetylated alpha-tubulin. altered neurite outgrowth also was observed in mouse primary cortical neurons when mir-124 expression was increased, or when mir-124 function was blocked. in uncommitted p19 cells, mir-124 expression led to disruption of actin filaments and stabilization of microtubules. expression of mir-124 also decreased cdc42 protein and affected the subcellular localization of rac1, suggesting that mir-124 may act in part via alterations to members of the rho gtpase family. furthermore, constitutively active cdc42 or rac1 attenuated neurite outgrowth promoted by mir-124. to obtain a broader perspective, we identified mrnas downregulated by mir-124 in p19 cells using microarrays. mrnas for proteins involved in cytoskeletal regulation were enriched among mrnas downregulated by mir-124. a mir-124 variant with an additional 5' base failed to promote neurite outgrowth and downregulated substantially different mrnas. these results indicate that mir-124 contributes to the control of neurite outgrowth during neuronal differentiation, possibly by regulation of the cytoskeleton.",1
"bc1 rna is a small non-messenger rna common in dendritic microdomains of neurons in rodents. in order to investigate its possible role in learning and behaviour, we compared controls and knockout mice from three independent founder lines established from separate embryonic stem cells. mutant mice were healthy with normal brain morphology and appeared to have no neurological deficits. a series of tests for exploration and spatial memory was carried out in three different laboratories. the tests were chosen as to ensure that different aspects of spatial memory and exploration could be separated and that possible effects of confounding variables could be minimised. exploration was studied in a barrier test, in an open-field test, and in an elevated plus-maze test. spatial memory was investigated in a barnes maze and in a morris water maze (memory for a single location), in a multiple t-maze and in a complex alley maze (route learning), and in a radial maze (working memory). in addition to these laboratory tasks, exploratory behaviour and spatial memory were assessed under semi-naturalistic conditions in a large outdoor pen. the combined results indicate that bc1 rna-deficient animals show behavioural changes best interpreted in terms of reduced exploration and increased anxiety. in contrast, spatial memory was not affected. in the outdoor pen, the survival rates of bc1-depleted mice were lower than in controls. thus, we conclude that the neuron-specific non-messenger bc1 rna contributes to the aptive modulation of behaviour.",1
"aims the aim of this study was (a) to determine the role of micro-223 (mir-223) in gastric cancer and (b) to elucidate its regulatory mechanism on the fbxw7/hcdc4 gene. materials and methods artificial mir-223 and control oligonucleotide was transfected into gastric cancer cell line sgc7901 by using lipofectamine2000. apoptosis of mir-223 group and control group cells was analyzed by flow cytometry, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide and colony formation assays were performed to detect the cell viability, to survey migration of mir-223 group and control group cells; scratch wound-healing motility assays, transwell assay, and western blot test were performed to measure the variance of hfbxw7. luciferase reporter assay, which was done by pluc-hfbxw7 wt-3'-utr co-transfected with plmp-hsa-mir-223 or plmp plasmid (as control) into hek293t cells, used to detect whether hfbxw7 is a direct target gene of mir-223. gastric cancer cell line sgc7901 transfected with mir-223 or control oligonucleotide was resuspended in ecm gel and then was injected into the flank of nude mice, 4 weeks later, the nude mice were euthanized. the tumors were excised then were measured and weighted. sybr-green i-based real-time rt-pcr study was used to detect the level of mir-223 in 22 gastric cancer tissue and corresponding gastric mucosa tissues. immunohistochemical method was applied to detect the protein of hfbxw7. results gastric cancer cell line sgc7901, transfected with mir-223, showed significant reduction in cellular apoptosis and increased proliferation and invasion in vitro. similar results were found in tumorigenesis assays performed in nude mice. moreover, 19 of 22 cancer tissue samples highly expressed mir-223, when compared with patient-matched normal gastric mucosa. specifically, patients with lymph node metastasis or metastatic disease (m1) at an advanced pathological stage showed significantly higher expression of mir-223. fbxw7/hcdc4 protein (fbw7) levels in gastric cancer cases were inversely correlated with mir-223 expression. overexpression of mir-223 in gastric cancer cell lines decreased fbw7 expression at the translational level and decreased fbxw7/hcdc4-driven luciferase-reporter activity. conclusion in summary, the data indicated that mir-223 targets fbxw7/hcdc4 expression at the post-transcriptional level and appears to regulate cellular apoptosis, proliferation, and invasion in gastric cancer. mir-223 may serve as a novel therapeutic target in gastric cancer.",1
"objective to improve regeneration of the injured myocardium, it is necessary to enhance the intrinsic capacity of the heart to regenerate itself and/or replace the damaged tissue by cell transplantation. cardiomyocyte progenitor cells (cmpcs) are a promising cell population, easily expanded and efficiently differentiated into beating cardiomyocytes. recently, several studies have demonstrated that micrornas (mirnas) are important for stem cell maintenance and differentiation via translational repression. we hypothesize that mirnas are also involved in proliferation/differentiation of the human cmpcs in vitro. methods and results human fetal cmpcs were isolated, cultured, and efficiently differentiated into beating cardiomyocytes. mirna expression profiling demonstrated that muscle-specific mir-1 and mir-499 were highly upregulated in differentiated cells. transient transfection of mir-1 and -499 in cmpc reduced proliferation rate by 25% and 15%, respectively, and enhanced differentiation into cardiomyocytes in human cmpcs and embryonic stem cells, likely via the repression of histone deacetylase 4 or sox6. histone deacetylase 4 and sox6 protein levels were reduced, and small interference rna (sirna)-mediated knockdown of sox6 strongly induced myogenic differentiation. conclusions mirnas regulate the proliferation of human cmpc and their differentiation into cardiomyocytes. by modulating mir-1 and -499 expression levels, human cmpc function can be altered and differentiation directed, thereby enhancing cardiomyogenic differentiation.",1
"growing evidence indicates that micrornas (mirnas or mirs) are involved in basic cell functions and oncogenesis. here we report that mir-133 has a critical role in determining cardiomyocyte hypertrophy. we observed decreased expression of both mir-133 and mir-1, which belong to the same transcriptional unit, in mouse and human models of cardiac hypertrophy. in vitro overexpression of mir-133 or mir-1 inhibited cardiac hypertrophy. in contrast, suppression of mir-133 by 'decoy' sequences induced hypertrophy, which was more pronounced than that after stimulation with conventional inducers of hypertrophy. in vivo inhibition of mir-133 by a single infusion of an antagomir caused marked and sustained cardiac hypertrophy. we identified specific targets of mir-133: rhoa, a gdp-gtp exchange protein regulating cardiac hypertrophy; cdc42, a signal transduction kinase implicated in hypertrophy; and nelf-a/whsc2, a nuclear factor involved in cardiogenesis. our data show that mir-133, and possibly mir-1, are key regulators of cardiac hypertrophy, suggesting their therapeutic application in heart disease.",1
"unlabelled cell secretion is an important mechanism for stem cell-based therapeutic angiogenesis, along with cell differentiation to vascular endothelial cells or smooth muscle cells. cell-released microvesicles (mvs) have been recently implicated to play an essential role in intercellular communication. the purpose of this study was to explore the potential effects of stem cell-released mvs in proangiogenic therapy. we observed for the first time that mvs were released from adipose-derived stem cells (ascs) and were able to increase the migration and tube formation of human umbilical vein endothelial cells (huvecs). endothelial differentiation medium (edm) preconditioning of ascs upregulated the release of mvs and enhanced the angiogenic effect of the released mvs in vitro. rna analysis revealed that microrna was enriched in asc-released mvs and that the level of microrna-31 (mir-31) in mvs was notably elevated upon edm-preconditioning of mv-donor ascs. further studies exhibited that mir-31 in mvs contributed to the migration and tube formation of huvecs, microvessel outgrowth of mouse aortic rings, and vascular formation of mouse matrigel plugs. moreover, factor-inhibiting hif-1, an antiangiogenic gene, was identified as the target of mir-31 in huvecs. our findings provide the first evidence that mvs from ascs, particularly from edm-preconditioned ascs, promote angiogenesis and the delivery of mir-31 may contribute the proangiogenic effect. significance this study provides the evidence that microvesicles (mvs) from adipose-derived stem cells (ascs), particularly from endothelial differentiation medium (edm)-preconditioned ascs, promote angiogenesis. an underlying mechanism of the proangiogenesis may be the delivery of microrna-31 via mvs from ascs to vascular endothelial cells in which factor-inhibiting hif-1 is targeted and suppressed. the study findings reveal the role of mvs in mediating asc-induced angiogenesis and suggest a potential mv-based angiogenic therapy for ischemic diseases.",1
"background angiogenesis is a critical component of many pathological conditions, and micrornas (mirnas) are indispensable in angiogenesis. it is unclear whether mirnas regulate angiogenesis in the presence of high concentrations of uric acid (hua), and the underlying mechanisms remain unknown. methods and results it was found that hua inhibited the angiogenic ability of endothelial cells. mirna expression profiling was conducted using microarray assays in hua-stimulated endothelial cells. eighteen differentially expressed mirnas were subjected to bioinformatic analyses. the results indicated that mir-92a was negatively regulated and was closely related to angiogenesis. furthermore, the effects of mir-92a on hua-stimulated endothelial cell angiogenesis and the underlying mechanisms were investigated in dual-luciferase reporter assays, electrophoretic mobility shift assays, immunoblot assays, and tube formation assays. it was determined that krüppel-like factor 2 (klf2) is a target gene of mir-92a, and klf2 binds the vascular endothelial growth factor-a (vegfa) promoter to inhibit its expression. mir-92a and vegfa overexpression or klf2 downregulation alleviates the hua-mediated inhibition of angiogenesis in endothelial cells in vitro. conclusions this study reported that there is a novel pathway regulating angiogenesis under hua conditions. in the presence of hua, mir-92a downregulation increased klf2 expression, subsequently inhibiting vegfa, which resulted in decreased angiogenesis. thus, this study reports a possible mechanism for cardiovascular injury caused by hyperuricemia and suggests that the mir-92a-klf2-vegfa axis may be a target for hyperuricemia treatment.",1
"dysregulation of long non-coding rnas (lncrnas) has been implicated in many cancer developments. previous studies showed that lncrna linc00941 was aberrantly expressed in oral squamous cell carcinoma (oscc). however, its role in oscc development remains elusive. in this study, we demonstrated that in oscc cells, ep300 activates linc00941 transcription through up-regulating its promoter h3k27ac modification. up-regulated linc00941 in turn activates caprin2 expression by looping to caprin2 promoter. functional assays suggest that both linc00941 and caprin2 play pivotal roles in promoting oscc cell proliferation and colony formation. in vivo assay further confirmed the role of linc00941 in promoting oscc cell tumour formation. lastly, we showed that the role of linc00941 and caprin2 in oscc progression was mediated through activating the canonical wnt/β-catenin signaling pathway. thus, linc00941/caprin2/ wnt/β-catenin signaling pathway provides new therapeutic targets for oscc treatment.",1
"aims fragile x mental retardation protein (fmrp) plays a vital role in mrna trafficking and translation inhibition to regulate the synthesis of local proteins in neuronal axons and dendritic terminals. however, there are no reports on microrna (mirna)-mediated regulation of fmrp levels in drosophila. here, we aimed to identify mirnas regulating fmrp levels in drosophila. main methods using online software, we predicted and selected 11 mirnas potentially acting on the drosophila fragile x mental retardation 1 (dfmr1) transcript. these candidates were screened for modulation of dfmr1 transcript levels at the cellular level using a dual luciferase reporter system. in addition, we constructed a transgenic drosophila model overexpressing mir-219 in the nervous system and quantified dfmrp by western blotting. the neuromuscular junction phenotype in the model was studied by immunofluorescence staining. key findings among the 11 mirnas screened, mir-219 and mir-960 reduced luciferase gene activity by binding to the 3'-utr of the dfmr1 transcript. mutation of the mir-219 or mir-960 binding sites on the transcript resulted in complete or partial elimination of the mirna-induced repression. western blots revealed that dfmrp expression was decreased in the mir-219 overexpression model (elav>mir-219). drosophila larvae overexpressing mir-219 showed morphological abnormalities at the neuromuscular junction (increased synaptic boutons and synaptic branches). this finding is consistent with some phenotypes observed in dfmr1 mutants. significance our results suggest that mir-219 regulates dfmr1 expression in drosophila and is involved in fragile x syndrome pathogenesis. collectively, these findings expand the current understanding of mirna-mediated regulation of target molecule-related functions.",1
"micrornas, a class of 22-nucleotide non-coding rnas, modulate gene expression by associating with the 3'-untranslated regions (3'- utrs) of messenger rnas (mrnas). although multiple mirnas are known to be regulated during angiogenesis, their individual roles in blood vessel development are still not fully understood. herein, we investigate the role of mir-29c in regulating cell cycle and angiogenic phenotype of endothelial cells. the results showed that igf-1 is highly expressed and down-regulated by mir-29c in human umbilical vein endothelial cells (huvec). consistent with this preliminary finding, introduction of exogenous mir-29c or mir-29c inhibitor alters cell cycle progression, proliferation and tube formation of huvec, respectively. furthermore, by using luciferase reporter assay, we find that the expression of igf-1, a suppressor transcription factor, is directly regulated by mir-29c through 3'-utr. in addition, we show that the selective inhibition of pi3k/akt pathway prior to mir-29c stimulation prevents the expression of angiogenesis suppressor mirnas that are family and cluster specific. as a conclusion, we find that mir-29c plays a significant role in regulating cell cycle, proliferation and angiogenic properties of huvecs. this function is likely mediated through igf-1 proteins at the post-transcriptional level. as a novel molecular target, mir-29c may have a potential value in the treatment of angiogenesis-associated diseases, such as cardiovascular diseases and cancers.",1
"c-myc stimulates angiogenesis in tumors through mechanisms that remain incompletely understood. recent work indicates that c-myc upregulates the mir-17∼92 microrna cluster and downregulates the angiogenesis inhibitor thrombospondin-1, along with other members of the thrombospondin type 1 repeat superfamily. here, we show that downregulation of the thrombospondin type 1 repeat protein clusterin in cells overexpressing c-myc and mir-17∼92 promotes angiogenesis and tumor growth. however, clusterin downregulation by mir-17∼92 is indirect. it occurs as a result of reduced transforming growth factor-β (tgfβ) signaling caused by targeting of several regulatory components in this signaling pathway. specifically, mir-17-5p and mir-20 reduce the expression of the type ii tgfβ receptor and mir-18 limits the expression of smad4. supporting these results, in human cancer cell lines, levels of the mir-17∼92 primary transcript mir17hg negatively correlate with those of many tgfβ-induced genes that are not direct targets of mir-17∼92 (e.g., clusterin and angiopoietin-like 4). furthermore, enforced expression of mir-17∼92 in mir17hg(low) cell lines (e.g., glioblastoma) results in impaired gene activation by tgfβ. together, our results define a pathway in which c-myc activation of mir-17∼92 attenuates the tgfβ signaling pathway to shut down clusterin expression, thereby stimulating angiogenesis and tumor cell growth.",1
"micrornas (mirnas) are small noncoding rnas that posttranscriptionally regulate gene expression by binding to 3'-untranslated regions (3'utrs) of target mrnas. kaposi's sarcoma-associated herpesvirus (kshv), a virus linked to malignancies including primary effusion lymphoma (pel), encodes 12 mirna genes, but only a few regulatory targets are known. we found that kshv-mir-k12-11 shares 100% seed sequence homology with hsa-mir-155, an mirna frequently found to be up-regulated in lymphomas and critically important for b-cell development. based on this seed sequence homology, we hypothesized that both mirnas regulate a common set of target genes and, as a result, could have similar biological activities. examination of five pel lines showed that pels do not express mir-155 but do express high levels of mir-k12-11. bioinformatic tools predicted the transcriptional repressor bach-1 to be targeted by both mirnas, and ectopic expression of either mir-155 or mir-k12-11 inhibited a bach-1 3'utr-containing reporter. furthermore, bach-1 protein levels are low in cells expressing either mirna. gene expression profiling of mirna-expressing stable cell lines revealed 66 genes that were commonly down-regulated. for select genes, mirna targeting was confirmed by reporter assays. thus, based on our in silico predictions, reporter assays, and expression profiling data, mir-k12-11 and mir-155 regulate a common set of cellular targets. given the role of mir-155 during b-cell maturation, we speculate that mir-k12-11 may contribute to the distinct developmental phenotype of pel cells, which are blocked in a late stage of b-cell development. together, these findings indicate that kshv mir-k12-11 is an ortholog of mir-155.",1
"comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding rnas (ncrnas) from bacterial genomic dna sequence datasets. previously, we developed a computational pipeline to more comprehensively identify structured ncrna representatives from individual bacterial genomes. this search process exploits the fact that genomic regions serving as templates for the transcription of structured rnas tend to be present in longer than average noncoding 'intergenic regions' (igrs) that are enriched in g and c nucleotides compared to the remainder of the genome. in the present study, we apply this computational pipeline to identify structured ncrna candidates from 26 diverse bacterial species. numerous novel structured ncrna motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. our findings support recent predictions that hundreds of novel ribo-switch classes and other ncrnas remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.",1
"hypoxia stimulates pulmonary artery smooth muscle cell (pasmc) proliferation. recent studies have implicated an important role for micrornas (mirnas) in hypoxia-mediated responses in various cellular processes, including cell proliferation. in this study, we investigated the role of microrna-21 (mir-21) in hypoxia-induced pasmc proliferation and migration. we first demonstrated that mir-21 expression increased by ∼3-fold in human pasmc after 6 h of hypoxia (3% o₂) and remained high (∼2-fold) after 24 h of hypoxia. knockdown of mir-21 with anti-mir-21 inhibitors significantly reduced hypoxia-induced cell proliferation, whereas mir-21 overexpression in normoxia enhanced cell proliferation. we also found that mir-21 is essential for hypoxia-induced cell migration. protein expression of mir-21 target genes, specifically programmed cell death protein 4 (pdcd4), sprouty 2 (spry2), and peroxisome proliferator-activated receptor-α (pparα), was decreased in hypoxia and in pasmc overexpressing mir-21 in normoxia and increased in hypoxic cells in which mir-21 was knocked down. in addition, pparα 3'-untranslated region (utr) luciferase-based reporter gene assays demonstrated that pparα is a direct target of mir-21. taken together, our findings indicate that mir-21 plays a significant role in hypoxia-induced pulmonary vascular smooth muscle cell proliferation and migration by regulating multiple gene targets.",1
"photoreceptors in the crystalline drosophila eye are recruited by receptor tyrosine kinase (rtk)/ras signaling mediated by epidermal growth factor receptor (egfr) and the sevenless (sev) receptor. analyses of an allelic deletion series of the mir-279/996 locus, along with a panel of modified genomic rescue transgenes, show that drosophila eye patterning depends on both mirnas. transcriptional reporter and activity sensor transgenes reveal expression and function of mir-279/996 in non-neural cells of the developing eye. moreover, mir-279/996 mutants exhibit substantial numbers of ectopic photoreceptors, particularly of r7, and cone cell loss. these mirnas restrict rtk signaling in the eye, since mir-279/996 nulls are dominantly suppressed by positive components of the egfr pathway and enhanced by heterozygosity for an egfr repressor. mir-279/996 limit photoreceptor recruitment by targeting multiple positive rtk/ras signaling components that promote photoreceptor/r7 specification. strikingly, deletion of mir-279/996 sufficiently derepresses rtk/ras signaling so as to rescue a population of r7 cells in r7-specific rtk null mutants boss and sev , which otherwise completely lack this cell fate. altogether, we reveal a rare setting of developmental cell specification that involves substantial mirna control.",1
"non-coding rnas (ncrnas) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncrnas are the small nucleolar (sno) and small nuclear (sn) rnas. in this study, we have identified and characterized a collection of sno and snrnas in giardia lamblia, by exploiting our discovery of a conserved 12 nt rna processing sequence motif found in the 3' end regions of a large number of g. lamblia ncrna genes. rna end mapping and other experiments indicate the motif serves to mediate ncrna 3' end formation from mono- and di-cistronic rna precursor transcripts. remarkably, we find the motif is also utilized in the processing pathway of all four previously identified trans-spliced g. lamblia introns, revealing a common rna processing pathway for ncrnas and trans-spliced introns in this organism. motif sequence conservation then allowed for the bioinformatic and experimental identification of additional g. lamblia ncrnas, including new u1 and u6 spliceosomal snrna candidates. the u6 snrna candidate was then used as a tool to identity novel u2 and u4 snrnas, based on predicted phylogenetically conserved snrna-snrna base-pairing interactions, from a set of previously identified g. lamblia ncrnas without assigned function. the giardia snrnas retain the core features of spliceosomal snrnas but are sufficiently evolutionarily divergent to explain the difficulties in their identification. most intriguingly, all of these snrnas show structural features diagnostic of u2-dependent/major and u12-dependent/minor spliceosomal snrnas.",1
"proliferation and migration of endothelial cells (ecs) and vascular smooth muscle cells (vsmcs) are critical processes involved in atherosclerosis. recent studies have revealed that micrornas (mirnas) can be detected in circulating blood with a stable form and the expression profiles differ in many cellular processes associated with coronary artery disease (cad). however, little is known about their role, especially serum-derived mirnas, in ecs and vsmcs phenotype modulation during atherosclerosis. we compared the mirna expressions in serum samples from 13 atherosclerotic cad patients and 5 healthy control subjects and identified 36 differentially expressed mirnas. the expression of selected mirnas (mir-135b-5p and mir-499a-3p) was further validated in 137 serum samples. interestingly, mir-135b-5p and mir-499a-3p directly regulated a common target gene: myocyte enhancer factor 2c (mef2c) which plays an important role in modulating cell phenotype of cardiovascular systems. furthermore, our results indicated that the 2 elevated mirnas could jointly promote ecs and vsmcs proliferation and migration by repressing mef2c expression. together, our findings demonstrated a serum-based mirna expression profile for atherosclerotic cad patients, potentially revealing a previously undocumented mechanism for cell proliferation and migration mediated by mir-135b-5p and mir-499a-3p, and might provide novel insights into the role of circulating mirnas in atherosclerosis pathogenesis.",1
"one of the fundamental issues in biology is understanding how organ size is controlled. tissue growth has to be carefully regulated to generate well-functioning organs, and defects in growth control can result in tumor formation. the hippo signaling pathway is a universal growth regulator and has been implicated in cancer. in drosophila , the hippo pathway acts through the mirna bantam to regulate cell proliferation and apoptosis. even though the bantam targets regulating apoptosis have been determined, the target genes controlling proliferation have not been identified thus far. in this study, we identify the gene tribbles as a direct bantam target gene. tribbles limits cell proliferation by suppressing g2/m transition. we show that tribbles regulation by bantam is central in controlling tissue growth and tumorigenesis. we expand our study to other cell cycle regulators and show that deregulated g2/m transition can collaborate with oncogene activation driving tumor formation.",1
"recent evidence suggests that ribosomal rnas have functional roles in translation. we describe here a new ribosomal rna mutation that causes translational suppression and antibiotic resistance in eukaryotic cells. using random mutagenesis of the cloned ribosomal rna gene and in vivo selection, we isolated a c --> u mutation in the universally conserved sarcin/ricin domain in saccharomyces cerevisiae 25s ribosomal rna. this mutation changes the putative cg pair, which closes the gaga tetraloop in the sarcin/ricin domain, into a weaker ug pair without eliminating ribosomal sensitivity to ricin. we show that suppression of several uga, uag, and frameshift mutations is evident when a portion of the cellular ribosomal rna contains the c --> u mutation. cells that contain essentially all mutant ribosomal rna grow only 10% slower than the wild-type, but show increased suppression as well as resistance to paramomycin, g418, and hygromycin, and sensitivity to cycloheximide. our results provide genetic evidence for the participation of the sarcin/ricin loop in maintaining translational accuracy and are discussed in terms of a hypothesis that this ribosomal rna region normally undergoes a conformational change during translation.",1
"staphylococcus aureus, a pathogen responsible for hospital and community-acquired infections, expresses many virulence factors under the control of numerous regulatory systems. here we show that one of the small pathogenicity island rnas, named sprd, contributes significantly to causing disease in an animal model of infection. we have identified one of the targets of sprd and our in vivo data demonstrate that sprd negatively regulates the expression of the sbi immune-evasion molecule, impairing both the adaptive and innate host immune responses. sprd interacts with the 5' part of the sbi mrna and structural mapping of sprd, its mrna target, and the 'sprd-mrna' duplex, in combination with mutational analysis, reveals the molecular details of the regulation. it demonstrates that the accessible sprd central region interacts with the sbi mrna translational start site. we show by toeprint experiments that sprd prevents translation initiation of sbi mrna by an antisense mechanism. sprd is a small regulatory rna required for s. aureus pathogenicity with an identified function, although the mechanism of virulence control by the rna is yet to be elucidated.",1
"micrornas (mirnas) modulate gene expression by inhibiting mrna translation and promoting mrna degradation, but little is known of their potential roles in organ formation or function. mir-133a-1 and mir-133a-2 are identical, muscle-specific mirnas that are regulated during muscle development by the srf transcription factor. we show that mice lacking either mir-133a-1 or mir-133a-2 are normal, whereas deletion of both mirnas causes lethal ventricular-septal defects in approximately half of double-mutant embryos or neonates; mir-133a double-mutant mice that survive to adulthood succumb to dilated cardiomyopathy and heart failure. the absence of mir-133a expression results in ectopic expression of smooth muscle genes in the heart and aberrant cardiomyocyte proliferation. these abnormalities can be attributed, at least in part, to elevated expression of srf and cyclin d2, which are targets for repression by mir-133a. these findings reveal essential and redundant roles for mir-133a-1 and mir-133a-2 in orchestrating cardiac development, gene expression, and function and point to these mirnas as critical components of an srf-dependent myogenic transcriptional circuit.",1
"background the epidermal growth factor receptor (egfr) and hippo signaling pathways control cell proliferation and apoptosis to promote tissue growth during development. misregulation of these pathways is implicated in cancer. our understanding of the mechanisms that integrate the activity of these pathways remains fragmentary. this study identifies bantam microrna as a common target of these pathways and suggests a mechanistic link between them. results the egfr pathway acts through bantam to control tissue growth. bantam expression is regulated by the egfr pathway, acting via repression of the transcriptional repressor capicua. thus egfr signaling induces bantam expression by alleviating the effects of a repressor. bantam in turn acts in a negative feedback loop to limit capicua expression. conclusions bantam appears to be a transcriptional target of both the egfr and hippo growth control pathways. feedback regulation by bantam on capicua provides a means to link signal propagation by the egfr pathway to activity of the hippo pathway and may play an important role in integration of these two pathways in growth control.",1
"micrornas are endogenous small noncoding rnas that regulate gene expression negatively at posttranscriptional level. this latest addition to the complex gene regulatory circuitry revolutionizes our way to understanding physiological and pathological processes in the human body. here we investigated the possible role of micrornas in the development of multidrug resistance (mdr) in gastric cancer cells. microrna expression profiling revealed a limited set of micrornas with altered expression in multidrug- resistant gastric cancer cell line sgc7901/vcr compared to its parental sgc7901 cell line. among the downregulated micrornas are mir-15b and mir-16, members of mir-15/16 family, whose expression was further validated by qrt-pcr. in vitro drug sensitivity assay demonstrated that overexpression of mir-15b or mir-16 sensitized sgc7901/vcr cells to anticancer drugs whereas inhibition of them using antisense oligonucleotides conferred sgc7901 cells mdr. the downregulation of mir-15b and mir-16 in sgc7901/vcr cells was concurrent with the upregulation of bcl-2 protein. enforced mir-15b or mir-16 expression reduced bcl-2 protein level and the luciferase activity of a bcl2 3' untranslated region-based reporter construct in sgc7901/vcr cells, suggesting that bcl2 is a direct target of mir-15b and mir-16. moreover, overexpression of mir-15b or mir-16 could sensitize sgc7901/vcr cells to vcr-induced apoptosis. taken together, our findings suggest that mir-15b and mir-16 could play a role in the development of mdr in gastric cancer cells at least in part by modulation of apoptosis via targeting bcl2.",1
"the small (160 nt) adenovirus rna, va rnai, antagonizes the activation of the cellular protein kinase pkr (also known as dai), a key regulator of gene expression. va rna consists of two stems separated by a complex region, the central domain, that is essential for its function. a notable feature of the central domain is a pair of tetranucleotides, gggu and accc, which are mutually complementary and phylogenetically conserved. to investigate their role in the structure and function of va rna, we generated three sets of mutations designed to disrupt the putative stem and to restore it with different nucleotides. substitutions in either of the tetranucleotides abrogated va rna function in two independent pkr-based assays, demonstrating the importance of these sequences in vivo. compensating mutants restored function, indicating that the two tetranucleotides pair in the cell, but all of the compensating mutants were less active than wild-type va rna. the effects of the mutations on rna structure were probed by nuclease sensitivity analysis. pronounced changes in two loops in the central domain correlated closely with the formation and disruption of the stem, suggesting that the tetranucleotide stem defines a critical element in the structure of the central domain through tertiary interactions with the two loops. a model for the central domain is presented that accommodates these findings and also accounts for the known sites of pkr interaction.",1
"we have investigated the mechanism underlying the immunoregulatory function of membrane ig-like transcript 3 (ilt3) and soluble ilt3fc. microrna (mirna) expression profile identified genes that were downregulated in ilt3-induced human cd8(+) t suppressor cells (ts) while upregulated in t cells primed in the absence of ilt3. we found that mir-21, mir-30b, and mir-155 target the 3'-untranslated region of genes whose expression was strongly increased in ilt3fc-induced ts, such as dual specificity phosphatase 10, b cell cll/lymphoma 6, and suppressor of cytokine signaling 1, respectively. transfection of mirna mimics or inhibitors and site-specific mutagenesis of their 3'-untranslated region binding sites indicated that b cell cll/lymphoma 6, dual specificity phosphatase 10, and suppressor of cytokine signaling 1 are direct targets of mir-30b, mir-21, and mir-155. primed cd8(+) t cells transfected with mir-21&30b, mir-21&155, or mir-21&30b&155 inhibitors displayed suppressor activity when added to autologous cd3-triggered cd4 t cells. luciferase reporter assays of mir-21 and mir-155 indicated that their transcription is highly dependent on ap-1. analysis of activated t cells showed that ilt3fc inhibited the translocation to the nucleus of the ap-1 subunits, fosb and c-fos, and the phosphorylation of zap70 and phospholipase c-γ 1. in conclusion, ilt3fc inhibits t cell activation and induces the generation of ts targeting multiple inflammatory mirna pathways.",1
"micrornas (mirna) play an important role in post-transcriptional gene regulation of several physiological and pathological processes. in multiple sclerosis (ms), a chronic inflammatory and degenerative disease of the cns, and in its mouse model, the experimental autoimmune encephalomyelitis (eae), mirna dysregulation has been mainly related to immune system dysfunction and white matter (wm) pathology. however, little is known about their role in gray matter pathology. here, we explored mirna involvement in the inflammation-driven alterations of synaptic structure and function, collectively known as synaptopathy, a neuropathological process contributing to excitotoxic neurodegeneration in ms/eae. particularly, we observed that mir-142-3p is increased in the csf of patients with active ms and in eae brains. we propose mir-142-3p as a molecular mediator of the il-1β-dependent downregulation of the glial glutamate-aspartate transporter (glast), which causes an enhancement of the glutamatergic transmission in the eae cerebellum. the synaptic abnormalities mediated by il-1β and the clinical and neuropathological manifestations of eae disappeared in mir-142 knock-out mice. furthermore, we observed that in vivo mir-142-3p inhibition, either by a preventive and local treatment or by a therapeutic and systemic strategy, abolished il-1β- and glast-dependent synaptopathy in eae wild-type mice. consistently, mir-142-3p was responsible for the glutamatergic synaptic alterations caused by csf of patients with ms, and csf levels of mir-142-3p correlated with prospective ms disease progression. our findings highlight mir-142-3p as key molecular player in il-1β-mediated synaptic dysfunction, possibly leading to excitotoxic damage in both eae and ms diseases. inhibition of mir-142-3p could be neuroprotective in ms. significance statement current studies suggest the role of glutamate excitotoxicity in the development and progression of multiple sclerosis (ms) and of its mouse model experimental autoimmune encephalomyelitis (eae). the molecular mechanisms linking inflammation and synaptic alterations in ms/eae are still unknown. here, we identified mir-142-3p as a determinant molecular actor in inflammation-dependent synaptopathy typical of both ms and eae. mir-142-3p was upregulated in the csf of ms patients and in eae cerebellum. inhibition of mir-142-3p, locally in eae brain and in a ms chimeric ex vivo model, recovered glutamatergic synaptic enhancement typical of eae/ms. we proved that mir-142-3p promoted the il-1β-dependent glutamate dysfunction by targeting glutamate-aspartate transporter (glast), a crucial glial transporter involved in glutamate homeostasis. finally, we suggest mir-142-3p as a negative prognostic factor in patients with relapsing-remitting multiple sclerosis.",1
"many microrna (mirna) loci exhibit compelling hairpin structures on both sense and antisense strands; however, the possibility that a mirna gene might produce functional species from its antisense strand has not been examined. we report here that antisense transcription of the hox mirna locus mir-iab-4 generates the novel pre-mirna hairpin mir-iab-8, which is then processed into endogenous mature mirnas. sense and antisense iab-4/iab-8 mirnas are functionally distinguished by their distinct domains of expression and targeting capabilities. we find that mir-iab-8-5p, like mir-iab-4-5p, is also relevant to hox gene regulation. ectopic mir-iab-8 can strongly repress the hox genes ultrabithorax and abdominal-a via extensive arrays of conserved target sites, and can induce a dramatic homeotic transformation of halteres into wings. we generalize the antisense mirna principle by showing that several other loci in both invertebrates and vertebrates are endogenously processed on their antisense strands into mature mirnas with distinct seeds. these findings demonstrate that antisense transcription and processing contributes to the functional diversification of mirna genes.",1
"key features of diabetic nephropathy (dn) include the accumulation of extracellular matrix proteins such as collagen 1-alpha 1 and -2 (col1a1 and -2). transforming growth factor beta1 (tgf-beta), a key regulator of these extracellular matrix genes, is increased in mesangial cells (mc) in dn. by microarray profiling, we noted that tgf-beta increased col1a2 mrna in mouse mc (mmc) but also decreased mrna levels of an e-box repressor, deltaef1. tgf-beta treatment or short hairpin rnas targeting deltaef1 increased enhancer activity of upstream e-box elements in the col1a2 gene. tgf-beta also decreased the expression of smad-interacting protein 1 (sip1), another e-box repressor similar to deltaef1. interestingly, we noted that sip1 is a target of microrna-192 (mir-192), a key mir highly expressed in the kidney. mir-192 levels also were increased by tgf-beta in mmc. tgf-beta treatment or transfection with mir-192 decreased endogenous sip1 expression as well as reporter activity of a sip1 3' utr-containing luciferase construct in mmc. conversely, a mir-192 inhibitor enhanced the luciferase activity, confirming sip1 to be a mir-192 target. furthermore, mir-192 synergized with deltaef1 short hairpin rnas to increase col1a2 e-box-luc activity. importantly, the in vivo relevance was noted by the observation that mir-192 levels were enhanced significantly in glomeruli isolated from streptozotocin-injected diabetic mice as well as diabetic db/db mice relative to corresponding nondiabetic controls, in parallel with increased tgf-beta and col1a2 levels. these results uncover a role for mirs in the kidney and dn in controlling tgf-beta-induced col1a2 expression by down-regulating e-box repressors.",1
"inflammation can act as a crucial mediator of epithelial-to-mesenchymal transition (emt). in this study, we show that oncostatin m (osm) is expressed in an autocrine/paracrine fashion in invasive breast carcinoma. osm stimulation promotes spontaneous lung metastasis of mcf-7 xenografts in nude mice. a conspicuous epigenetic transition was induced by osm stimulation not only in breast cancer cell lines but also in mcf-7 xenografts in nude mice. the expression of mir-200 and let-7 family members in response to osm stimulation was downregulated in a signal transducer and activator of transcription factor 3 (stat3)-dependent manner, resulting in comprehensive alterations of the transcription factors and oncoproteins targeted by these micrornas. inhibition of stat3 activation or the ectopic expression of let-7 and mir-200 effectively reversed the mesenchymal phenotype of breast cancer cells. stat3 promotes the transcription of lin-28 by directly binding to the lin-28 promoter, resulting in the repression of let-7 expression and concomitant upregulation of the let-7 target, high-mobility group a protein 2 (hmga2). knock down of hmga2 significantly impairs osm-driven emt. our data indicate that downregulation of let-7 and mir-200 levels initiates and maintains osm-induced emt phenotypes, and hmga2 acts as a master switch of osm-induced emt. these findings highlight the importance of stat3-coordinated lin-28b-let-7-hmga2 and mir-200-zeb1 circuits in the cytokine-mediated phenotypic reprogramming of breast cancer cells.",1
"studies have shown that the expression of cd133, leucine-rich-repeat-containing g-protein-coupled receptor 5 (lgr5), and atp binding cassette (abc)g2 proteins is associated with malignancy and poor prognosis in colon cancer. however, molecular regulation mechanism of the three proteins has not been elucidated. here, we report that microrna-142-3p (mir-142-3p) inhibits the expression of cd133, lgr5, and abcg2 in colon cancer cells by binding to both the 3'-untranslated region and the coding sequences of the three genes. the mir-142-3p was markedly decreased in colon cancer specimens, in which it was negatively correlated with the expression of cd133, lgr5, and abcg2. reduction of mir-142-3p corresponds to poor differentiation and bigger tumor size in colon cancers. moreover, mir-142-3p levels were reduced in cells that formed spheres compared to cells that were cultured in regular media. transfection of mir-142-3p mimics in colon cancer cells downregulated cyclin d1 expression, induced g1 phase cell cycle arrest, and elevated the sensitivity of the cells to 5-fluorouracil. furthermore, oct4 suppressed mir-142-3p, and hypomethylation of the oct4 promoter was associated with a reduction in mir-142-3p. finally, the mir-142-3p inhibited the growth of colon cancer cells in vivo, which was accompanied by the downregulation of cd133, lgr5, and abcg2 in tumor tissues. our results elucidate a novel regulation pathway in colon cancer cells and suggest a potential therapeutic approach for colon cancer therapy.",1
"circadian rhythms in metazoan eukaryotes are controlled by an endogenous molecular clock. it functions in many locations, including subsets of brain neurons (clock neurons) within the central nervous system. although the molecular clock relies on transcription/translation feedback loops, posttranscriptional regulation also plays an important role. here, we show that the abundant drosophila melanogaster microrna mir-276a regulates molecular and behavioral rhythms by inhibiting expression of the important clock gene timeless (tim). misregulation of mir-276a in clock neurons alters tim expression and increases arrhythmicity under standard constant darkness (dd) conditions. mir-276a expression itself appears to be light-regulated because its levels oscillate under 24-h light-dark (ld) cycles but not in dd. mir-276a is regulated by the transcription activator chorion factor 2 in flies and in tissue-culture cells. evidence from flies mutated using the clustered, regularly interspaced, short palindromic repeats (crispr) tool shows that mir-276a inhibits tim expression: deleting the mir-276a-binding site in the tim 3' utr causes elevated levels of tim and ∼50% arrhythmicity. we suggest that this pathway contributes to the more robust rhythms observed under light/dark ld conditions than under dd conditions.",1
"t cell receptor (tcr) signals can elicit full activation with acquisition of effector functions or a state of anergy. here, we ask whether micrornas affect the interpretation of tcr signaling. we find that dicer-deficient cd4 t cells fail to correctly discriminate between activating and anergy-inducing stimuli and produce il-2 in the absence of co-stimulation. excess il-2 production by dicer-deficient cd4 t cells was sufficient to override anergy induction in wt t cells and to restore inducible foxp3 expression in il2-deficient cd4 t cells. phosphorylation of akt on s473 and of s6 ribosomal protein was increased and sustained in dicer-deficient cd4 t cells, indicating elevated mtor activity. the mtor components mtor and rictor were posttranscriptionally deregulated, and the micrornas let-7 and mir-16 targeted the mtor and rictor mrnas. remarkably, returning mtor and rictor to normal levels by deleting one allele of mtor and one allele of rictor was sufficient to reduce akt s473 phosphorylation and to reduce co-stimulation-independent il-2 production in dicer-deficient cd4 t cells. these results show that micrornas regulate the expression of mtor components in t cells, and that this regulation is critical for the modulation of mtor activity. hence, micrornas contribute to the discrimination between t cell activation and anergy.",1
"tumor-associated factors are related to increased accumulation of cd11b(+) gr1(+) myeloid-derived suppressor cells (mdscs). however, the exact mechanism of how genetic factors control the expansion of mdscs in tumor-bearing hosts remains elusive. herein, we found that tumor-associated mdscs and their subsets, mononuclear mdscs and polymorphonuclear mdscs, have decreased expression of mir-223 when compared to cd11b(+) gr1(+) cells from the spleen of disease-free mice. with the differentiation of cd11b(+) gr1(+) mdscs from bone marrow cells (bmcs) upon exposure to tumor-associated factors, the expression of both pri-mir-223 and mature mir-223 was downregulated, indicating that the expression of mir-223 could be regulated by tumor-associated factors. interestingly, mir-223 remarkably inhibits differentiation of bmcs into cd11b(+) gr1(+) mdscs in the presence of tumor-associated factors by targeting myocyte enhancer factor 2c (mef2c). using reconstituted s.c. tumor models, mir-223 also suppresses accumulation of cd11b(+) gr1(+) mdscs, whereas its targeting molecule mef2c increases the number of mdscs. tumor growth is slower in mice infused by mir223-engineered bmcs than in mice infused with control transfected bmcs. as mir-223 and its target molecule mef2c are highly conserved between mice and humans, the modulation of mir-223 in tumor-induced cd11b(+) gr1(+) mdscs may exert an important role in controlling the increased accumulation of cd11b(+) gr1(+) mdscs in patients with tumor.",1
"glioblastomas (gbm) are very difficult to treat and their aggressiveness is one of the main reasons for this as well as for the frequent recurrences. micrornas post-transcriptionally regulate their target genes through interaction between their seed sequence and 3'utr of the target mrnas. we previously reported that mir-296-3p is regulated by neurofibromatosis 2 (nf2) and enhances the invasiveness of gbm cells via socs2/stat3. in this study, we investigated whether mir-296-5p, which originates from the same precursor mirna as mir-296-3p, can increase the invasiveness of gbm cells. it was observed that mir-296-5p potentiated the invasion of various gbm cells including ln229, t98g, and u87mg. through bioinformatics approaches, two genes were identified as mir-296-5p targets: caspase-8 (casp8) and nerve growth factor receptor (ngfr). from results obtained from ago2 immunoprecipitation and luciferase assays, we found that mir-296-5p downregulates casp8 and ngfr through direct interaction between seed sequence of the mirna and 3'utr of the target mrna. knockdown of casp8 or ngfr also increased the invasive ability of gbm cells, indicating that casp8 and ngfr are involved in potentiation of invasiveness by mir-296-5p. consistent with our findings, casp8 was downregulated in brain metastatic lung cancer cells, which have a high level of mir-296-5p, compared to parental cells, suggesting that mir-296-5p may be generally associated with the acquisition of invasiveness. collectively, our results implicate mir-296-5p as a potential cause of invasiveness in cancer and suggest it as a promising therapeutic target for gbm.",1
"background & aims after myofibroblastic transdifferentiation, hepatic stellate cells (hsc), mainly involved in liver fibrosis by extracellular matrix production, exhibit an altered growth factor profile including increased expression of neuronal mediators. here, we analyzed putative targets of neuronal micrornas mir-9, mir-125b, and mir-128 by deep sequencing of the transcript population, interacting with the mirna/argonaute 2 (ago2) complex in myofibroblastic hsc. methods microrna expression was quantified by real-time pcr in primary hsc, isolated from the rat or human liver. myofibroblastic hsc were transfected either with mimics or inhibitors of mir-9, mir-125b, and mir-128. rna from immunoprecipitated ago2-mirna/transcript complexes was purified and used for next generation sequencing. additionally, gene expression was investigated in quiescent and activated primary hsc, treated with the mir-128 mimic or inhibitor, by microarray analysis. results during myofibroblastic transdifferentiation of hsc, mir-9, mir-125b, and mir-128 expression was markedly increased. transcriptome analysis of ago2 bound mrna by deep sequencing identified a broad spectrum of transcripts that interact with neuronal mirnas in myofibroblastic hsc. in particular, in hsc overexpressing mir-128, many members of the chemokine family were bound to the ago2 repression complex. furthermore, a comprehensive profiling of gene expression demonstrates the high impact of neuronal mirnas on the chemokine network. conclusions ago2 immunoprecipitation followed by deep sequencing is a useful tool to identify novel mirna targets. upregulation of neuronal mir-9, mir-125b, and mir-128 during myofibroblastic transition and the identified interaction with a wide range of chemokines and chemokine receptors suggest a prominent role of neuronal mirnas in the inflammatory response of hsc during fibrosis.",1
"micrornas (mirnas) regulate target mrnas through a combination of translational repression and mrna destabilization, with mrna destabilization dominating at steady state in the few contexts examined globally. here, we extend the global steady-state measurements to additional mammalian contexts and find that regardless of the mirna, cell type, growth condition, or translational state, mrna destabilization explains most (66%->90%) mirna-mediated repression. we also determine the relative dynamics of translational repression and mrna destabilization for endogenous mrnas as a mirna is induced. although translational repression occurs rapidly, its effect is relatively weak, such that by the time consequential repression ensues, the effect of mrna destabilization dominates. these results imply that consequential mirna-mediated repression is largely irreversible and provide other insights into the nature of mirna-mediated regulation. they also simplify future studies, dramatically extending the known contexts and time points for which monitoring mrna changes captures most of the direct mirna effects.",1
"micrornas (mirnas) are a class of ~22 nt non-coding rna molecules in metazoans capable of down-regulating target gene expression by binding to the complementary sites in the mrna transcripts. many individual mirnas are implicated in a broad range of biological pathways, but functional characterization of mirna clusters in concert is limited. here, we report that mir-959-962 cluster (mir-959/960/961/962) can weaken drosophila immune response to bacterial infection evidenced by the reduced expression of antimicrobial peptide drosomycin ( drs ) and short survival within 24 h upon infection. each of the four mirna members is confirmed to contribute to the reduced drs expression and survival rate of drosophila . mechanically, rt-qpcr and dual-luciferase reporter assay verify that tube and dorsal ( dl ) mrnas, key components of toll pathway, can simultaneously be targeted by mir-959 and mir-960, mir-961, and mir-962, respectively. furthermore, mir-962 can even directly target to the 3' untranslated region (utr) of toll . in addition, the dynamic expression pattern analysis in wild-type flies reveals that four mirna members play important functions in drosophila immune homeostasis restoration at the late stage of micrococcus luteus ( m. luteus ) infection. taken together, our results identify four mirna members from mir-959-962 cluster as novel suppressors of toll signaling and enrich the repertoire of immune-modulating mirna in drosophila .",1
"transforming growth factor β1 (tgf-β), enriched in the tumor microenvironment and broadly immunosuppressive, inhibits natural killer (nk) cell function by yet-unknown mechanisms. here we show that tgf-β-treated human nk cells exhibit reduced tumor cytolysis and abrogated perforin polarization to the immune synapse. this result was accompanied by loss of surface expression of activating killer ig-like receptor 2ds4 and nkp44, despite intact cytoplasmic stores of these receptors. instead, tgf-β depleted dnax activating protein 12 kda (dap12), which is critical for surface nk receptor stabilization and downstream signal transduction. mechanistic analysis revealed that tgf-β induced microrna (mir)-183 to repress dap12 transcription/translation. this pathway was confirmed with luciferase reporter constructs bearing the dap12 3' untranslated region as well as in human nk cells by use of sense and antisense mir-183. moreover, we documented reduced dap12 expression in tumor-associated nk cells in lung cancer patients, illustrating this pathway to be consistently perturbed in the human tumor microenvironment.",1
"lung cancer is the major cause of cancer death globally. micrornas are evolutionally conserved small noncoding rnas that are critical for the regulation of gene expression. aberrant expression of microrna (mirna) has been implicated in cancer initiation and progression. in this study, we demonstrated that the expression of mir-429 are often upregulated in non-small cell lung cancer (nsclc) compared with normal lung tissues, and its expression level is also increased in nsclc cell lines compared with normal lung cells. overexpression of mir-429 in a549 nsclc cells significantly promoted cell proliferation, migration and invasion, whereas inhibition of mir-429 inhibits these effects. furthermore, we demonstrated that mir-429 down-regulates pten, rassf8 and timp2 expression by directly targeting the 3'-untranslated region of these target genes. taken together, our results suggest that mir-429 plays an important role in promoting the proliferation and metastasis of nsclc cells and is a potential target for nsclc therapy.",1
"micrornas (mirnas) have been demonstrated to participate in many important cellular processes including radiosensitization. vegf family, an important regulator of angiogenesis, also plays a crucial role in the regulation of cancer cell radiosensitivity. vegfr2 mediates the major growth and permeability actions of vegf in a paracrine/autocrine manner. mir-200c, at the nexus of epithelial-mesenchymal transition (emt), is predicted to target vegfr2. the purpose of this study is to test the hypothesis that regulation of vegfr2 pathway by mir-200c could modulate the radiosensitivity of cancer cells. bioinformatic analysis, luciferase reporter assays and biochemical assays were carried out to validate vegfr2 as a direct target of mir-200c. the radiosensitizing effects of mir-200c on a549 cells were determined by clonogenic assays. the downstream regulating mechanism of mir-200c was explored with western blotting assays, fcm, tube formation assays and migration assays. we identified vegfr2 as a novel target of mir-200c. the ectopic mir-200c increased the radiosensitivity of a549 while mir-200c down-regulation decreased it. besides, we proved that mir-200c radiosensitized a549 cells by targeting vegf-vegfr2 pathway specifically, thus leading to inhibition of its downstream pro-survival signaling transduction and angiogenesis, and serves as a potential target for radiosensitizition research.",1
"two core microrna (mirna) pathway proteins, dicer and argonaute, are found in giardia lamblia, a deeply branching parasitic protozoan. there are, however, no apparent homologues of drosha or exportin5 in the genome. here, we report a 26 nucleotide (nt) rna derived from a 106 nt box c/d snorna, glsr2. this small rna, designated mir5, localizes to the 3' end of glsr2 and has a 75 nt hairpin precursor. glsr2 is processed by the dicer from giardia (gldcr) and generated mir5. immunoprecipitation of the argonaute from giardia (glago) brought down mir5. when a renilla luciferase transcript with a 26 nt mir5 antisense sequence at the 3'-untranslated region (3' utr) was introduced into giardia trophozoites, luciferase expression was reduced ∼25% when synthetic mir5 was also introduced. the luciferase mrna level remained, however, unchanged, suggesting translation repression by mir5. this inhibition was fully reversed by introducing also a 2'-o-methylated antisense inhibitor of mir5, suggesting that mir5 acts by interacting specifically with the antisense sequence in the mrna. a partial antisense knock down of gldcr or glago in giardia indicated that the former is needed for mir5 biogenesis whereas the latter is required for mir5-mediated translational repression. potential targets for mir5 with canonical seed sequences were predicted bioinformatically near the stop codon of giardia mrnas. four out of the 21 most likely targets were tested in the luciferase reporter assay. mir5 was found to inhibit luciferase expression (∼20%) of transcripts carrying these potential target sites, indicating that snorna-derived mirna can regulate the expression of multiple genes in giardia.",1
"mir-195, which exhibits a proliferation-inhibiting role in different tumors, has been reported to be down-regulated in the ectopic endometrium. the aim of this study was to determine the impact of mir-195 on the biological characteristic of the endometrial stromal cells (escs). mir-195 has been presumed to target the 3'-untranslated regions (3'-utr) of fractalkine (fkn), which also plays important roles in endometriosis. fluorescence reporter assays showed that mir-195 effectively binds to the 3'-utr of fkn. the normal escs showed a significant higher mir-195 expression than that of eutopic and ectopic escs associated with endometriosis, while the fkn expression showed opposite results. mir-195 mimics inhibited proliferation and growth and induced apoptosis of eutopic escs, and these effects were abolished by fkn-sirna. mir-195 could decrease the expression of survivin, matrix metalloproteinase-9 (mmp9) and up-regulate the expression of cd82, tissue inhibitor of metalloproteinase 1 (timp1) and timp2 of eutopic escs by targeting fkn. our study has demonstrated for the first time that mir-195 plays important roles in regulating the functions of escs through targeting fkn. the information may be useful for developing a new therapeutic strategy for endometriosis.",1
"background micrornas (mirnas) are small, non-coding rnas (20-24 nucleotides) that post-transcriptionally modulate gene expression by negatively regulating the stability or translational efficiency of their target mrnas. the aim of this study was to investigate the expression pattern of microrna-26b (mir-26b) in human breast cancer, and its potential role in disease pathogenesis. methods quantitative reverse transcription-polymerase chain reaction (qrt-pcr) was performed to determine the expression level of mir-26b in 38 breast cancer specimens and adjacent normal breast tissues. mtt assays were conducted to explore the impact of mir-26b overexpression on the proliferation of human mda-mb-231 breast cancer cells. luciferase reporter assays were employed to validate regulation of a putative target of mir-26b. the effect of modulating mir-26b on endogenous levels of this target were subsequently confirmed via qrt-pcr and western blot. results mir-26b expression was relatively decreased in breast cancer specimens compared with adjacent normal tissues (p conclusions mir-26b may act as a tumor suppressor in breast cancer. the overexpression of mir-26b inhibits cellular growth by targeting ptgs2, suggesting its use as a potential therapeutic target for breast cancer.",1
"hedgehog (hh) signaling is critical for many developmental processes and for the genesis of diverse cancers. hh signaling comprises a series of negative regulatory steps, from hh reception to gene transcription output. we previously showed that stability of antagonistic regulatory proteins, including the coreceptor smoothened (smo), the kinesin-like costal-2 (cos2), and the kinase fused (fu), is affected by hh signaling activation. here, we show that the level of these three proteins is also regulated by a microrna cluster. indeed, the overexpression of this cluster and resulting microrna regulation of the 3'-utrs of smo, cos2, and fu mrna decreases the levels of the three proteins and activates the pathway. further, the loss of the microrna cluster or of dicer function modifies the 3'-utr regulation of smo and cos2 mrna, confirming that the mrnas encoding the different hh components are physiological targets of micrornas. nevertheless, an absence of neither the microrna cluster nor of dicer activity creates an hh-like phenotype, possibly due to dose compensation between the different antagonistic targets. this study reveals that a single signaling pathway can be targeted at multiple levels by the same micrornas.",1
"the mechanisms that control energy homeostasis and tissue growth during development are closely linked through the insulin signal transduction pathway. changes in the level of insulin and other hormones reflect the nutritional status of the animal to control circulating sugar levels and fat metabolism. systemic defects in insulin responsiveness can lead to elevated circulating glucose levels and fat accumulation. here we present evidence that the microrna mir-278 plays a role in the control of energy homeostasis in drosophila. mir-278 mutants have elevated insulin production and are correspondingly lean. despite the elevated insulin levels, mir-278 mutants have elevated circulating sugar, mobilized from adipose-tissue glycogen stores. we provide evidence that mir-278 mutants are insulin resistant and that mir-278 acts through regulation of the expanded transcript.",1
"expression of the escherichia coli rnc-era-reco operon is regulated posttranscriptionally by ribonuclease iii (rnase iii), encoded in the rnc gene. rnase iii initiates rapid decay of the rnc operon mrna by cleaving a double-stranded region of the rnc leader. this region, termed rnco, is portable, conferring stability and rnase iii regulation to heterologous rnas. here, we report the detailed analysis of rnco structure and function. the first 215 nt of the rnc leader are sufficient for its function. dimethylsulfate (dms) modification in vivo revealed distinct structural elements in this region: a 13-nt single-stranded 5' leader, followed by a 6-bp stem-loop structure (i), a larger stem-loop structure (ii) containing the rnase iii site, a single-stranded region containing the rnc translation initiation site, and a small stem-loop structure (iii) at the 3' terminus of rnco, wholly within the rnc coding region. genetic analysis revealed the function of these structural elements. the single-stranded leader is not required for stability or rnase iii control, stem-loop ii is required only for rnase iii control, and both stem-loops i and iii are required for stability. stem-loop ii effectively serves only as the site at which rnase iii cleaves to remove stem-loop i and thereby initiates decay, after which rnase iii plays no role. mutations at the cleavage site underscore the importance of base pairing for efficient rnase iii attack. when stem-loops i and ii were replaced with an artificial hairpin structure, stability was restored only partially, but was restored almost fully when a single-stranded leader was also added.",1
"the complete sequence of the 16,295 bp mouse l cell mitochondrial dna genome has been determined. genes for the 12s and 16s ribosomal rnas; 22 trnas; cytochrome c oxidase subunits i, ii and iii; atpase subunit 6; cytochrome b; and eight unidentified proteins have been located. the genome displays exceptional economy of organization, with trna genes interspersed between rrna and protein-coding genes with zero or few noncoding nucleotides between coding sequences. only two significant portions of the genome, the 879 nucleotide displacement-loop region containing the origin of heavy-strand replication and the 32 nucleotide origin of light-strand replication, do not encode a functional rna species. all of the remaining nucleotide sequence serves as a defined coding function, with the exception of 32 nucleotides, of which 18 occur at the 5' ends of open reading frames. mouse mitochondrial dna is unique in that the translational start codon is aun, with any of the four nucleotides in the third position, whereas the only translational stop codon is the orthodox uaa. the mouse mitochondrial dna genome is highly homologous in overall sequence and in gene organization to human mitochondrial dna, with the descending order of conserved regions being trna genes; origin of light-strand replication; rrna genes; known protein-coding genes; unidentified protein-coding genes; displacement-loop region.",1
"stable intronic sequence rnas (sisrnas) have been found in xenopus tropicalis, human cell lines, and epstein-barr virus; however, the biological significance of sisrnas remains poorly understood. we identify sisrnas in drosophila melanogaster by deep sequencing, reverse transcription polymerase chain reaction, and northern blotting. we characterize a sisrna (sisr-1) from the regena (rga) locus and show that it can be processed from the precursor messenger rna (pre-mrna). we also document a cis-natural antisense transcript (astr) from the rga locus, which is highly expressed in early embryos. during embryogenesis, astr promotes robust rga pre-mrna expression. interestingly, sisr-1 represses astr, with consequential effects on rga pre-mrna expression. our results suggest a model in which sisr-1 modulates its host gene expression by repressing astr during embryogenesis. we propose that sisr-1 belongs to a class of sisrnas with probable regulatory activities in drosophila.",1
"a significant portion of eukaryotic small ncrna transcriptome is composed by small nucleolar rnas. from archaeal to mammalian cells, these molecules act as guides in the site-specific pseudouridylation or methylation of target rnas. we used a bioinformatics search program to detect drosophila putative orthologues of u79, one out of ten snornas produced by gas5, a human ncrna involved in apoptosis, susceptibility to cancer and autoimmune diseases. this search led to the definition of a list of u79-related fly snornas whose genomic organization, evolution and expression strategy are discussed here. we report that an intriguing novel specimen, named dm46e3, is transcribed as a longer, unspliced precursor from the reverse strand of eiger, a fly regulatory gene that plays a key role in cell differentiation, apoptosis and immune response. expression of dm46e3 was found significantly up-regulated in a mutant strain in which eiger transcription is greatly reduced, suggesting that these two sense-antisense genes may be mutually regulated. relevant to its function, dm46e3 concentrated specifically in the cajal bodies, followed a dynamic spatial expression profile during embryogenesis and displayed a degenerate antisense element that enables it to target u1b, a developmentally regulated isoform of the u1 spliceosomal snrna that is particularly abundant in embryos.",1
"micrornas (mirnas) play an important role in insulin signaling and insulin secretion, but the role of mirnas in the association between obesity and hepatic insulin resistance is largely unknown. this study reports that saturated fatty acid (sfa) and high fat diet (hfd) significantly induce mir-195 expression in hepatocytes, and that the insulin receptor (insr), not insulin receptor substrate-1 (irs-1), is a direct target of mir-195. furthermore, the ectopic expression of mir-195 suppresses the expression of insr, thereby impairing the insulin signaling cascade and glycogen synthesis in hepg2 cells. these findings suggest that the dysregulation of mir-195 by sfa is a detrimental factor for hepatic insulin sensitivity.",1
"among other factors, changes in gene expression on the human evolutionary lineage have been suggested to play an important role in the establishment of human-specific phenotypes. however, the molecular mechanisms underlying these expression changes are largely unknown. here, we have explored the role of microrna (mirna) in the regulation of gene expression divergence among adult humans, chimpanzees, and rhesus macaques, in two brain regions: prefrontal cortex and cerebellum. using a combination of high-throughput sequencing, mirna microarrays, and q-pcr, we have shown that up to 11% of the 325 expressed mirna diverged significantly between humans and chimpanzees and up to 31% between humans and macaques. measuring mrna and protein expression in human and chimpanzee brains, we found a significant inverse relationship between the mirna and the target genes expression divergence, explaining 2%-4% of mrna and 4%-6% of protein expression differences. notably, mirna showing human-specific expression localize in neurons and target genes that are involved in neural functions. enrichment in neural functions, as well as mirna-driven regulation on the human evolutionary lineage, was further confirmed by experimental validation of predicted mirna targets in two neuroblastoma cell lines. finally, we identified a signature of positive selection in the upstream region of one of the five mirna with human-specific expression, mir-34c-5p. this suggests that mir-34c-5p expression change took place after the split of the human and the neanderthal lineages and had adaptive significance. taken together these results indicate that changes in mirna expression might have contributed to evolution of human cognitive functions.",1
"the discovery of small non-coding micrornas has revealed novel mechanisms of post-translational regulation of gene expression, the implications of which are still incompletely understood. we focused on microrna 21 (mir-21), which is expressed in cardiac valve endothelium during development, in order to better understand its mechanistic role in cardiac valve development. using a combination of in vivo gene knockdown in zebrafish and in vitro assays in human cells, we show that mir-21 is necessary for proper development of the atrioventricular valve (av). we identify pdcd4b as a relevant in vivo target of mir-21 and show that protection of pdcd4b from mir-21 binding results in failure of av development. in vitro experiments using human pulmonic valve endothelial cells demonstrate that mir-21 overexpression augments endothelial cell migration. pdcd4 knockdown alone was sufficient to enhance endothelial cell migration. these results demonstrate that mir-21 plays a necessary role in cardiac valvulogenesis, in large part due to an obligatory downregulation of pdcd4.",1
"micrornas (mirs) are a novel class of cellular bioactive molecules with critical functions in the regulation of gene expression in normal biology and disease. mirs are frequently misexpressed in cancer, with potent biological consequences. however, relatively little is known about mirs in pediatric cancers, including sarcomas. moreover, the mechanisms behind aberrant mir expression in cancer are poorly understood. ewing sarcoma is an aggressive pediatric malignancy driven by ews/ets fusion oncoproteins, which are gain-of-function transcriptional regulators. we employed stable silencing of ews/fli1, the most common of the oncogenic fusions, and global mir profiling to identify ews/fli1-regulated mirs with oncogenesis-modifying roles in ewing sarcoma. in this report, we characterize a group of mirs (100, 125b, 22, 221/222, 27a and 29a) strongly repressed by ews/fli1. strikingly, all of these mirs have predicted targets in the insulin-like growth factor (igf) signaling pathway, a pivotal driver of ewing sarcoma oncogenesis. we demonstrate that mirs in this group negatively regulate the expression of multiple pro-oncogenic components of the igf pathway, namely igf-1, igf-1 receptor, mammalian/mechanistic target of rapamycin and ribosomal protein s6 kinase a1. consistent with tumor-suppressive functions, these mirs manifest growth inhibitory properties in ewing sarcoma cells. our studies thus uncover a novel oncogenic mechanism in ewing sarcoma, involving post-transcriptional derepression of igf signaling by the ews/fli1 fusion oncoprotein via mirs. this novel pathway may be amenable to innovative therapeutic targeting in ewing sarcoma and other malignancies with activated igf signaling.",1
"understanding how the genome empowers the nervous system to express behaviors remains a critical challenge in behavioral genetics. the startle response is an attractive behavioral model for studies on the relationship between genes, brain, and behavior, as the ability to respond rapidly to harmful changes in the environment is a universal survival trait. drosophila melanogaster provides a powerful system in which genetic studies on individuals with controlled genetic backgrounds and reared under controlled environmental conditions can be combined with neuroanatomical studies to analyze behaviors. in a screen of 720 lines of d. melanogaster, carrying single p transposon insertions, we found 267 lines that showed significant changes in startle-induced locomotor behavior. excision of the transposon reversed this effect in five lines out of six tested. we infer that most of the 267 lines show mutant effects on startle-induced locomotion that are caused by the transposon insertions. we selected a subset of 15 insertions in the same genetic background in autosomal genes with strong mutant effects and crossed them to generate all 105 possible nonreciprocal double heterozygotes. these hybrids revealed an extensive network of epistatic interactions on the behavioral trait. in addition, we observed changes in neuroanatomy that were caused by these 15 mutations, individually and in their double heterozygotes. we find that behavioral and neuroanatomical phenotypes are determined by a common set of genes that are organized as partially overlapping genetic networks.",1
"lowering intraocular pressure (iop) delays or prevents the loss of vision in primary open-angle glaucoma (poag) patients with high iop and in those with normal tension glaucoma showing progression. abundant evidence demonstrates that inhibition of contractile machinery of the trabecular meshwork cells is an effective method to lower iop. however, the mechanisms involved in the regulation of trabecular contraction are not well understood. although micrornas have been shown to play important roles in the regulation of multiple cellular functions, little is known about their potential involvement in the regulation of iop. here, we showed that mir-200c is a direct postranscriptional inhibitor of genes relevant to the physiologic regulation of tm cell contraction including the validated targets zinc finger e-box binding homeobox 1 and 2 (zeb1 and zeb2), and formin homology 2 domain containing 1 (fhod1), as well as three novel targets: lysophosphatidic acid receptor 1 (lpar1/edg2), endothelin a receptor (etar), and rhoa kinase (rhoa). consistently, transfection of tm cells with mir-200c resulted in strong inhibition of contraction in collagen populated gels as well as decreased cell traction forces exerted by individual tm cells. finally, delivery of mir-200c to the anterior chamber of living rat eyes resulted in a significant decrease in iop, while inhibition of mir-200c using an adenoviral vector expressing a molecular sponge led to a significant increase in iop. these results demonstrate for the first time the ability of a mirna to regulate trabecular contraction and modulate iop in vivo, making mir-200c a worthy candidate for exploring ways to alter trabecular contractility with therapeutic purposes in glaucoma.",1
"the signal recognition particle (srp) is an evolutionarily conserved ribonucleoprotein (rnp) complex that functions in protein targeting to the endoplasmic reticulum (er) membrane. only two protein subunits of the srp, srp54p and sec65p, and the rna subunit, scr1, were previously known in the yeast saccharomyces cerevisiae. purification of yeast srp by immunoaffinity chromatography revealed five additional proteins. amino acid sequencing and cloning of the genes encoding four of these proteins demonstrated that the yeast srp contains homologs (termed srp14p, srp68p and srp72p) of the srp14, srp68 and srp72 subunits found in mammalian srp. the yeast srp also contains a 21 kda protein (termed srp21p) that is not homologous to any protein in mammalian srp. an additional 7 kda protein may correspond to the mammalian srp9. disruption of any one of the four genes encoding the newly identified srp proteins results in slow cell growth and inefficient protein translocation across the er membrane. these phenotypes are indistinguishable from those resulting from the disruption of genes encoding srp components identified previously. these data indicate that a lack of any of the analyzed srp components results in loss of srp function. scr1 rna and srp proteins are at reduced levels in cells lacking any one of the newly identified proteins. in contrast, srp components are present at near wild type levels and srp subparticles are present in cells lacking either srp54p or sec65p. thus srp14p, srp21p, srp68p and srp72p, but not sec65p or srp54p, are required for stable expression of the yeast srp.",1
"micrornas (mirnas) are short non-coding single-stranded rnas with approximately 22 nucleotides in length that negatively regulate the mrna translation of a target gene. mir-2b-1 belongs to the largest mir-2 family in drosophila melanogaster with 8 members and this mirna family is conserved in invertebrates. mirnas play key roles in gene regulation, cell proliferation, cell death, cell differentiation and cell developmental homeostasis in multicellular organisms. its role in various human diseases is continuously being studied. mirnas also found out to be crucial in maintaining stem cell niche in d. melanogaster gonads. we have identified that ectopic overexpression of mir-2b-1 of d. melanogaster causes testicular bulging (a tumour like phenotype) in 3-5 days old adult flies. hence, we have performed a transcriptomic (rna-seq) analysis to understand the role of mir-2b-1 in the development, maintenance, and differentiation of d. melanogaster adult testis stem cells. data are available from geo (accession number gse211399).",1
"uridine-rich small nuclear ribonucleoproteins (u snrnps) are involved in key steps of pre-mrna processing in the nucleus of eukaryotic cells. u snrnps are enriched in the nucleus in discrete organelles that include speckles, cajal bodies, and histone locus bodies. however, most u snrnps are assembled in the cytoplasm, not in the nucleus. despite extensive biochemical information, little is known about the spatial organization of u snrnps in the cytoplasm. here we show that u snrnps in drosophila are concentrated in discrete cytoplasmic structures, which we call u bodies, because they contain the major u snrnps. in addition to snrnps, u bodies contain essential snrnp assembly factors, suggesting that u bodies are sites for assembly or storage of snrnps before their import into the nucleus. u bodies invariably associate with p bodies, which are involved in rna surveillance and decay. genetic disruption of p body components affects the organization of u bodies, suggesting that the two cytoplasmic bodies may cooperate in regulating aspects of snrnp metabolism. the identification of u bodies provides an opportunity to correlate specific biochemical steps of snrnp biogenesis with structural features of the cytoplasm.",1
"several recent studies have found a conserved microrna (mirna) family, the mir-34s, to be direct transcriptional targets of p53. mir-34 activation can recapitulate elements of p53 activity, including induction of cell-cycle arrest and promotion of apoptosis, and loss of mir-34 can impair p53-mediated cell death. these data reinforce the growing awareness that non-coding rnas are key players in tumour development by placing mirnas in a central role in a well-known tumour-suppressor network.",1
"the hallmarks of pancreatic cancer are limitless replicative potential as well as tissue invasion and metastasis, leading to an extremely aggressive disease with shockingly high lethality. however, the molecular mechanisms underlying these characteristics remain largely unclear. herein, we report the results of a differential mirna expression screen that compared pancreatic cancer tissues and normal pancreatic tissues, where the pancreatic cancer tissues had highly downregulated mir-29c with relative wnt cascade hyperactivation. mir-29c directly suppressed the following wnt upstream regulators: frequently rearranged in advanced t-cell lymphomas 2 (frat2), low-density lipoprotein receptor-related protein 6 (lrp6), frizzled-4 (fzd4) and frizzled-5 (fzd5). furthermore, transforming growth factor-β (tgf-β) inhibited mir-29c expression, leading to wnt activation. significantly, our results were consistent with an important correlation between mir-29c levels and tgf-β hyperactivation and the activated wnt cascade in human pancreatic cancer specimens. these findings reveal a novel mechanism for wnt hyperactivation in pancreatic cancer and may suggest a new target for clinical intervention in pancreatic cancer.",1
"micrornas (mirnas) are small, non-coding rnas that function as post-transcriptional regulators of gene expression. the deregulated expression of mirnas is associated with a variety of diseases, including breast cancer. in the present study, we found that mir-495 was markedly up-regulated in clinical breast cancer samples by quantitative real time-pcr (qrt-pcr). junctional adhesion molecule a (jam-a) was predicted to be a potential target of mir-495 by bioinformatics analysis and was subsequently verified by luciferase assay and western blotting. jam-a was found to be negatively correlated with the migration of breast cancer cells through loss-of-function and gain-of-function assays, and the inhibition of jam-a by mir-495 promoted the migration of mcf-7 and mda-mb-231 cells. furthermore, overexpression of jam-a could restore mir-495-induced breast cancer cell migration. taken together, our findings suggest that mir-495 could facilitate breast cancer progression through the repression of jam-a, making this mirna a potential therapeutic target.",1
"papillary thyroid carcinoma (ptc) is the most common endocrine malignancy and ret/ptc rearrangements represent key genetic events frequently associated to this cancer, enhancing proliferation and dedifferentiation by activation of the ret/ptc-ras-braf-mitogen-activated protein kinase (mapk) pathway. recently, let-7 microrna was found to reduce ras levels in lung cancer, acting as a tumor suppressor gene. here, we report that ret/ptc3 oncogenic activation in pccl3 rat thyroid cells markedly reduces let-7f expression. moreover, stable transfection of let-7 microrna in tpc-1 cells, which harbor ret/ptc1 rearrangement, inhibits mapk activation. as a result, let-7f was capable of reducing tpc-1 cell growth, and this might be explained, at least in part, by decreased messenger rna (mrna) expression of cell cycle stimulators such as myc and ccnd1 (cyclin d1) and increased p21 cell cycle inhibitor mrna. in addition, let-7 enhanced transcriptional expression of molecular markers of thyroid differentiation such as titf1 and tg. thus, reduced expression of let-7f might be an essential molecular event in ret/ptc malignant transformation. moreover, let-7f effects on thyroid growth and differentiation might attenuate neoplastic process of ret/ptc papillary thyroid oncogenesis through impairment of mapk signaling pathway activation. this is the first functional demonstration of an association of let-7 with thyroid cancer cell growth and differentiation.",1
"the blood-tumor barrier (btb) hinders delivery of chemotherapeutic drugs to tumors in the brain; previous studies have shown that the btb can be selectively opened by endothelial monocyte activating polypeptide-ii (emap-ii), but the specific mechanism involved remains elusive. in this study, we found that microrna-429 (mir-429) expression in glioma vascular endothelial cells (gecs) was far lower than in human brain microvascular endothelial cells (ecs). mir-429 had lower expression in gecs and glioma tissues compared to ecs or normal tissues of the brain. furthermore, mir-429 had lower expression in high grade glioma (hgg) than in low grade glioma (lgg). in in vitro btb models, we also found that emap-ii significantly increased btb permeability, decreased expression of zo-1, occludin and claudin-5 in gecs, in a time- and dose-dependent manner. emap-ii greatly increased mir-429 expression in gecs of the btb models in vitro . overexpression of mir-429 in gecs significantly decreased the transepithelial electric resistance (teer) values in btb models, and led to enhanced horseradish peroxidase (hrp) flux. overexpression of mir-429 in gecs significantly decreased the expression of tight junction (tj)-associated proteins (zo-1, occludin and claudin-5), and decreased the distribution continuity. silencing of mir-429 in gecs increased the expression of tj-associated proteins and the distribution continuity. the dual-luciferase reporter assay revealed that zo-1 and occludin were target genes of mir-429, and we demonstrated that mir-429 overexpression markedly down-regulated protein expression of p70s6k, as well as its phosphorylation levels. the dual-luciferase reporter assay also showed that p70s6k was a target gene of mir-429; mir-429 overexpression down-regulated expression and phosphorylation levels of p70s6k, and also decreased phosphorylation levels of s6 and increased btb permeability. conversely, silencing of mir-429 increased the expression and phosphorylation levels of p70s6k, and increased phosphorylation levels of s6, while decreasing btb permeability. in conclusion, the results indicated that emap-ii caused an increase in mir-429 expression that directly targeted tj-associated proteins, which were negatively regulated; on the other hand, mir-429 down-regulated the expression of tj-associated proteins by targeting p70s6k, also negatively regulated. as a result, the btb permeability increased.",1
"while hundreds of genes have recently been implicated in an organism's response to thermal stress, our insight into the cellular and physiological mechanisms affected by these genes has advanced to a lesser extent. we focus on an enigmatic drosophila heat stress rna gene, hsr-omega, which encodes two rna transcripts that are constitutively expressed in almost all developing and adult tissues, omega-n in the nucleus and omega-c in the cytoplasm; both being readily induced to high levels by mild heat stress. we derived three hsr-omega mutant lines via imprecise p-element excision and characterised them for changes in expression, in both the presence and absence of heat stress. viability estimates indicate that a low level of omega-n is required for normal development. consistent with the model of omega-n as a negative regulator of intron-processed mrna levels the mutants displayed a 1.5-fold increase in rates of protein synthesis measured in ovarian tissue in the absence of heat stress, a result suggesting that an important function of hsr-omega is the modulation of general protein synthesis. the mutants had little effect on two measures commonly used to assess heat tolerance, heat-knockdown time and heat hardening ability, suggesting that more subtle heat-related fitness components need to be examined for effects of these mutations.",1
"we focus on unique roles of mir-200c in breast, ovarian, and endometrial cancers. members of the mir-200 family target zeb1, a transcription factor which represses e-cadherin and other genes involved in polarity. we demonstrate that the double negative feedback loop between mir-200c and zeb1 is functional in some, but not all cell lines. restoration of mir-200c to aggressive cancer cells causes a decrease in migration and invasion. these effects are independent of e-cadherin status. additionally, we observe that restoration of mir-200c to ovarian cancer cells causes a decrease in adhesion to laminin. we have previously reported that reintroduction of mir-200c to aggressive cells that lack mir-200c expression restores sensitivity to paclitaxel. we now prove that this ability is a result of direct targeting of class iii beta-tubulin (tubb3). introduction of a tubb3 expression construct lacking the mir-200c target site into cells transfected with mir-200c mimic results in no change in sensitivity to paclitaxel. lastly, we observe a decrease in proliferation in cells transfected with mir-200c mimic, and cells where zeb1 is knocked down stably, demonstrating that the ability of mir-200c to enhance sensitivity to paclitaxel is not due to an increased proliferation rate.",1
"dysregulation of micrornas (mirnas) has been associated with carcinogenesis in oral squamous cell carcinoma (oscc). in the present study, we investigated the expression and function of mir-99b-3p in human oscc. we found that the expression levels of mir-99b-3p decreased in 21 clinical oscc samples (84%). furthermore, ectopic expression of mir-99b-3p inhibited oscc cell proliferation by downregulating glycogen synthase kinase-3β (gsk3β), an mir-99b-3p' target gene, at the mrna and protein levels, both in vitro and in vivo. moreover, the silencing of gsk3β recapitulated the cellular and molecular effects in a similar manner to the overexpression of mir-99b-3p, which included inhibition of oscc cell proliferation and suppression of p65 (rela) and g1 regulators (cyclin d1, cdk4 and cdk6) in vitro. our data suggest that mir-99b-3p functions as a tumor suppressor in oscc via gsk3β downregulation.",1
"very few of the enzymes required for eukaryotic precursor ribosomal rna (pre-rrna) processing have been identified. ribonuclease (rnase) mrp was characterized as a nuclease that cleaves mitochondrial replication primers, but it is predominantly nucleolar. previous genetic evidence revealed that this ribonucleoprotein is required, directly or indirectly, for cleavage of the yeast pre-rrna in vivo at site a3. here, an in vitro processing system that accurately reproduces this cleavage is described. biochemical purification and the use of extracts depleted of the mrp rna demonstrate that endonucleolytic cleavage of the pre-rrna is directly mediated by rnase mrp. this establishes a role for rnase mrp in the nucleolus.",1
"the mrna of vascular endothelial growth factor (vegf), the major angiogenic growth factor, contains an unusually long (1,038 nucleotides) and structured 5' untranslated region (utr). according to the classical translation initiation model of ribosome scanning, such a 5' utr is expected to be a strong translation inhibitor. in vitro and bicistronic strategies were used to show that the vegf mrna translation was cap independent and occurred by an internal ribosome entry process. for the first time, we demonstrate that two independent internal ribosome entry sites (iress) are present in this 5' utr. ires a is located within the 300 nucleotides upstream from the aug start codon. rna secondary structure prediction and site-directed mutagenesis allowed the identification of a 49-nucleotide structural domain (d4) essential to ires a activity. uv cross-linking experiments revealed that ires a activity was correlated with binding of a 100-kda protein to the d4 domain. ires b is located in the first half of the 5' utr. an element between nucleotides 379 and 483 is required for its activity. immunoprecipitation experiments demonstrated that a main ires b-bound protein was the polypyrimidine tract binding protein (ptb), a well-known regulator of picornavirus iress. however, we showed that binding of the ptb on ires b does not seem to be correlated with its activity. evidence is provided of an original cumulative effect of two iress, probably controlled by different factors, to promote an efficient initiation of translation at the same aug codon.",1
"micrornas modulate tumorigenesis through suppression of specific genes. as many tumour types rely on overlapping oncogenic pathways, a core set of micrornas may exist, which consistently drives or suppresses tumorigenesis in many cancer types. here we integrate the cancer genome atlas (tcga) pan-cancer data set with a microrna target atlas composed of publicly available argonaute crosslinking immunoprecipitation (ago-clip) data to identify pan-tumour microrna drivers of cancer. through this analysis, we show a pan-cancer, coregulated oncogenic microrna 'superfamily' consisting of the mir-17, mir-19, mir-130, mir-93, mir-18, mir-455 and mir-210 seed families, which cotargets critical tumour suppressors via a central gugc core motif. we subsequently define mutations in microrna target sites using the ago-clip microrna target atlas and tcga exome-sequencing data. these combined analyses identify pan-cancer oncogenic cotargeting of the phosphoinositide 3-kinase, tgfβ and p53 pathways by the mir-17-19-130 superfamily members.",1
"accumulating evidence suggests that micrornas (mirnas) contribute to a myriad of kidney diseases. however, the regulatory role of mirnas on the key molecules implicated in kidney fibrosis remains poorly understood. bone morphogenetic protein-7 (bmp-7) and its related bmp-6 have recently emerged as key regulators of kidney fibrosis. using the established unilateral ureteral obstruction (uuo) model of kidney fibrosis as our experimental model, we examined the regulatory role of mirnas on bmp-7/6 signaling. by analyzing the potential mirnas that target bmp-7/6 in silica, we identified mir-22 as a potent mirna targeting bmp-7/6. we found that expression levels of bmp-7/6 were significantly elevated in the kidneys of the mir-22 null mouse. importantly, mice with targeted deletion of mir-22 exhibited attenuated renal fibrosis in the uuo model. consistent with these in vivo observations, primary renal fibroblast isolated from mir-22-deficient uuo mice demonstrated a significant increase in bmp-7/6 expression and their downstream targets. this phenotype could be rescued when cells were transfected with mir-22 mimics. interestingly, we found that mir-22 and bmp-7/6 are in a regulatory feedback circuit, whereby not only mir-22 inhibits bmp-7/6, but mir-22 by itself is induced by bmp-7/6. finally, we identified two bmp-responsive elements in the proximal region of mir-22 promoter. these findings identify mir-22 as a critical mirna that contributes to renal fibrosis on the basis of its pivotal role on bmp signaling cascade.",1
"pai-1 (plasminogen activator inhibitor-1) is a key physiological inhibitor of fibrinolysis. previously, we have reported plgf (placental growth factor)-mediated transcriptional up-regulation of pai-1 (serpine1) mrna expression via activation of hif-1α (hypoxia-inducible factor-1α) and ap-1 (activator protein-1) in hpmvecs (human pulmonary microvascular endothelial cells), which resulted in elevated pai-1 in humans with sca (sickle cell anaemia). in the present study, we have identified the role of post-transcriptional mechanism(s) of plgf-mediated accumulation of pai-1 mrna in hpmvecs by examining the role of micrornas (mirnas/mirs) in plgf-induced pai-1 mrna stability. our results show reduced expression of mir-30c and mir-301a, but not of mir-99a, in response to plgf, which have evolutionarily conserved binding sites in the 3'-utr (3'-untranslated region) of pai-1 mrna. transfection of anti-mir-30c or anti-mir-301a oligonucleotides resulted in increased pai-1 mrna levels, which were increased further with plgf stimulation. conversely, overexpression of pre-mir-30c or pre-mir-301a resulted in an attenuation of plgf-induced pai-1 mrna and protein levels. luciferase reporter assays using wild-type and mutant 3'-utr constructs confirmed that the pai-1 3'-utr is indeed a direct target of mir-30c and mir-301a. finally, plasma levels of mir-30c and mir-301a were significantly down-regulated in patients with sca compared with normal controls. these results provide a post-transcriptional regulatory mechanism of plgf-induced pai-1 elevation.",1
"rationale endothelial progenitor cells (epcs) contribute to the regeneration of endothelium. aging-associated senescence results in reduced number and function of epcs, potentially contributing to increased cardiac risk, reduced angiogenic capacity, and impaired cardiac repair effectiveness. the mechanisms underlying epc senescence are unknown. increasing evidence supports the role of micrornas in regulating cellular senescence. objective we aimed to determine whether micrornas regulated epc senescence and, if so, what the underlying mechanisms are. methods and results to map the microrna/gene expression signatures of epc senescence, we performed microrna profiling and microarray analysis in lineage-negative bone marrow cells from young and aged wild-type and apolipoprotein e-deficient mice. we identified 2 micrornas, microrna-10a* (mir-10a*), and mir-21, and their common target gene hmga2 as critical regulators for epc senescence. overexpression of mir-10a* and mir-21 in young epcs suppressed hmga2 expression, caused epc senescence, as evidenced by senescence-associated β-galactosidase upregulation, decreased self-renewal potential, increased p16(ink4a)/p19(arf) expression, and resulted in impaired epc angiogenesis in vitro and in vivo, resembling epcs derived from aged mice. in contrast, suppression of mir-10a* and mir-21 in aged epcs increased hmga2 expression, rejuvenated epcs, resulting in decreased senescence-associated β-galactosidase expression, increased self-renewal potential, decreased p16(ink4a)/p19(arf) expression, and improved epc angiogenesis in vitro and in vivo. importantly, these phenotypic changes were rescued by mirna-resistant hmga2 cdna overexpression. conclusions mir-10a* and mir-21 regulate epc senescence via suppressing hmga2 expression and modulation of micrornas may represent a potential therapeutic intervention in improving epc-mediated angiogenesis and vascular repair.",1
"the exact expression profile and potential involvement of mir-625-5p in the tumor biology of cervical carcinoma are still elusive. in this study, we aimed to analyze the expression status and possible involvements of mir-625-5p in both clinical tissue samples and cell culture of cervical carcinoma. the relative expression levels of mir-625-5p and nf-κb transcript were determined by real-time polymerase chain reaction. cell proliferation was measured using cell counting kit-8. the protein levels of cyclin d1, cdk4, nf-κb, and gapdh were examined by western blotting. the regulatory effects of mir-625-5p on nf-κb and malat1 were interrogated by luciferase reporter assay. we demonstrated that mir-625-5p was downregulated and predicted better survival in cervical carcinoma. ectopic over-expression of mir-625-5p inhibited cell growth via targeting nf-κb. we further identified malat1 as the competitive endogenous long non-coding rna for mir-625-5p, and over-expression of malat1 attenuated the inhibitory effect of mir-625-5p on nf-κb signaling in cervical carcinoma. our study characterized the suppressive expression of mir-625-5p in cervical carcinoma and unraveled the importance of malat1/mir-625-5p/nf-κb signaling in this disease.",1
"background congestive heart failure (chf) causes atrial fibrotic remodeling, a substrate for atrial fibrillation (af) maintenance. microrna29 (mir29) targets extracellular matrix proteins. in the present study, we examined mir29b changes in patients with af and/or chf and in a chf-related af animal model and assessed its potential role in controlling atrial fibrous tissue production. methods and results control dogs were compared with dogs subjected to ventricular tachypacing for 24 hours, 1 week, or 2 weeks to induce chf. atrial mir29b expression decreased within 24 hours in both whole atrial tissue and atrial fibroblasts (-87% and -92% versus control, respectively; p conclusions mir29 likely plays a role in atrial fibrotic remodeling and may have value as a biomarker and/or therapeutic target.",1
"rrna molecules undergo extensive posttranscriptional modification, predominantly 2'-o-ribose methylation and pseudouridine formation, both of which are guided by the numerous small nucleolar rnas in eukaryotes. here, we describe an exception to this rule. the essential yeast nucleolar protein spb1p is a site-specific rrna methyltransferase modifying the universally conserved g2922 that is located within the a loop of the catalytic center of the ribosome. the equivalent position in bacteria is the docking site for aminoacyl-trna, and it is critical for translation. in sharp contrast to other 2'-o-methylriboses that are formed on the primary transcript, gm2922 appears at a late processing stage, during the maturation of the 27s pre-rrna. thus, eukaryotes have maintained a site-specific enzyme to catalyze the methylation of a nucleotide that plays a crucial role in ribosome biogenesis and translation.",1
"kshv is the etiological agent of kaposi's sarcoma (ks), primary effusion lymphoma (pel), and a subset of multicentriccastleman's disease (mcd). the fact that kshv-encoded mirnas are readily detectable in all kshv-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. mirna-mediated regulation of gene expression is a complex network with each mirna having many potential targets, and to date only few kshv mirna targets have been experimentally determined. a detailed understanding of kshv mirna functions requires high-through putribonomics to globally analyze putative mirna targets in a cell type-specific manner. we performed ago hits-clip to identify viral and cellular mirnas and their cognate targets in two latently kshv-infected pel cell lines. ago hits-clip recovered 1170 and 950 cellular kshv mirna targets from bcbl-1 and bc-3, respectively. importantly, enriched clusters contained kshv mirna seed matches in the 3'utrs of numerous well characterized targets, among them thbs1, bach1, and c/ebpβ. kshv mirna targets were strongly enriched for genes involved in multiple pathways central for kshv biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in kshv pathogenesis and potentially tumorigenesis. a limited number of viral transcripts were also enriched by hits-clip including vil-6 expressed only in a subset of pel cells during latency. interestingly, ago hits-clip revealed extremely high levels of ago-associated kshv mirnas especially in bc-3 cells where more than 70% of all mirnas are of viral origin. this suggests that in addition to seed match-specific targeting of cellular genes, kshv mirnas may also function by hijacking riscs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human mirnas. in summary, we provide an extensive list of cellular and viral mirna targets representing an important resource to decipher kshv mirna function.",1
"in patients with duchenne muscular dystrophy (dmd), the absence of a functional dystrophin protein results in sarcolemmal instability, abnormal calcium signaling, cardiomyopathy, and skeletal muscle degeneration. using the dystrophin-deficient sapje zebrafish model, we have identified micrornas (mirnas) that, in comparison to our previous findings in human dmd muscle biopsies, are uniquely dysregulated in dystrophic muscle across vertebrate species. mir-199a-5p is dysregulated in dystrophin-deficient zebrafish, mdx(5cv) mice, and human muscle biopsies. mir-199a-5p mature mirna sequences are transcribed from stem loop precursor mirnas that are found within the introns of the dynamin-2 and dynamin-3 loci. the mir-199a-2 stem loop precursor transcript that gives rise to the mir-199a-5p mature transcript was found to be elevated in human dystrophic muscle. the levels of expression of mir-199a-5p are regulated in a serum response factor (srf)-dependent manner along with myocardin-related transcription factors. inhibition of srf-signaling reduces mir-199a-5p transcript levels during myogenic differentiation. manipulation of mir-199a-5p expression in human primary myoblasts and myotubes resulted in dramatic changes in cellular size, proliferation, and differentiation. mir-199a-5p targets several myogenic cell proliferation and differentiation regulatory factors within the wnt signaling pathway, including fzd4, jag1, and wnt2. overexpression of mir-199a-5p in the muscles of transgenic zebrafish resulted in abnormal myofiber disruption and sarcolemmal membrane detachment, pericardial edema, and lethality. together, these studies identify mir-199a-5p as a potential regulator of myogenesis through suppression of wnt-signaling factors that act to balance myogenic cell proliferation and differentiation.",1
"micrornas (mirnas) are endogenous non-coding rna molecules that inhibit protein translation in a sequence specific manner. we carried out microarray analyses of 180 human pre-mirnas in neuroblastoma cell, sh-sy5y, following stimulation by tpa. twelve of the pre-mirnas were up-regulated by the tpa stimulation. we also explored mirna target genes associated with neuronal differentiation. some mirnas have complementarity with 3'utr of the notch1 gene, a regulator of neuronal differentiation, and luciferase assay showed that overexpression of these mirnas reduced the luciferase activity of reporter genes containing the notch1-3'utr sequence. our results suggest that mirnas can be associated with tpa induced signalling pathways and expression of notch1 gene.",1
"we have used chemical modification analysis to probe the solution structure of the hairpin ribozyme. the modifying reagents dimethylsulfate, 1-cyclohexyl-n'-heptadeca-1(17),2,11,13,15-pentaenato) nickel(ii) perchlorate were used to probe functional groups that participate in watson-crick and non-canonical base-pairs. our results confirm the existence of four short helices (3 to 6 bp) within the ribozyme-substrate complex, and demonstrate that one intramolecular helix (helix 4) is comprised of three base-pairs rather than the previously suggested five. in the absence of magnesium, the ribozyme is observed to fold into its secondary structure. upon addition of magnesium, a striking difference in chemical modification is observed, particularly at sites within the ribozyme's large internal loop (loop b) that are essential for catalytic function (bases 21 to 26). moreover, magnesium-dependent folding clearly destabilizes an a-u base-pair in a region where a proposed bend is required to juxtapose the catalytically essential loops a and b. upon addition of substrate, no changes are observed in the structure of helix 3, loop b or helix 4. however, strong protection of bases in the substrate-binding domain is observed, including those located across internal loop a. the modification data are consistent with the formation of a previously proposed tertiary structure motif within loop b that includes non-canonical g-a, a-u and a-a base-pairs, and that is identical with those identified by nmr analysis of loop e of 5 s rrna and the sarcin/ricin loop of 28 s rrna. our results indicate that the hairpin ribozyme adopts a stable magnesium-dependent tertiary structure to which the substrate binds without inducing major conformational changes, and that substrate recognition is likely to involve non-canonical base-pairs between the ribozyme and substrate sequences adjacent to the cleavage site.",1
"the opportunistic pathogen pseudomonas aeruginosa pao1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. here, we report the discovery and characterization of a novel small non-coding rna: nrsz (nitrogen-regulated srna). we show that under nitrogen limitation, nrsz is induced by the ntrb/c two component system, an important regulator of nitrogen assimilation and p. aeruginosa's swarming motility, in concert with the alternative sigma factor rpon. furthermore, we demonstrate that nrsz modulates p. aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. this regulation takes place through the post-transcriptional control of rhla, a gene essential for rhamnolipids synthesis. interestingly, we also observed that nrsz is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for nrsz regulatory functions.",1
"background choriocarcinoma is a gestational trophoblastic tumor which causes high mortality if left untreated. micrornas (mirnas) are small non protein-coding rnas which inhibit target gene expression. the role of mirnas in choriocarcinoma, however, is not well understood. in this study, we examined the effect of mir-34a in choriocarcinoma. methods mir-34a was either inhibited or ectopically expressed transiently in two choriocarcinoma cell lines (bewo and jeg-3) respectively. its actions on cell invasion, proliferation and colony formation at low cell density were examined. the mir-34a putative target notch ligand delta-like 1 (dll1) was identified by adoption of different approaches including: in-silico analysis, functional luciferase assay and western blotting. real-time quantitative polymerase chain reaction was used to quantify changes in the expression of matrix proteinase in the treated cells. to nullify the effect of mir-34a ectopic expression, we activated notch signaling through force-expression of the notch intracellular domain in the mir-34a force-expressed cells. in addition, we studied the importance of dll1 in bewo cell invasion through ligand stimulation and antibody inhibition. furthermore, the induction in tumor formation of mir-34a-inhibited bewo cells in scid mice was investigated. results transient mir-34a force-expression significantly suppressed cell proliferation and invasion in bewo and jeg-3 cells. in silicon mirna target prediction, luciferase functional assays and western blotting analysis demonstrated that mir-34a regulated dll1 expression in both cell lines. although force-expression of mir-34a suppressed the expression of dll1 and notch1, the extent of suppression was higher in dll1 than notch1 in both cell lines. mir-34a-mediated dll1 suppression led to reduced matrix metallopeptidase 9 and urokinase-type plasminogen activator expression. the effect of mir-34a on cell invasion was partially nullified by notch signaling activation. dll1 ligand stimulated while anti-dll1 antibody treatment suppressed cell invasion. mice inoculated with bewo cells transfected with mir-34a inhibitor had significantly larger xenografts and stronger dll1 expression than those with cells transfected with the control inhibitor. conclusions mir-34a reduced cell proliferation and invasiveness, at least, partially through its inhibitory effect on dll1.",1
"the mechanism contributing to blood-brain barrier (bbb) disruption, involved in poststroke edema and hemorrhagic transformation, is important but elusive. we investigated microrna-21 (mir-21)-mediated mechanism in the disruption of bbb following cerebral ischemia-reperfusion (i/r) injury. rats with cerebral i/r injury were prepared after middle cerebral artery occlusion and subsequent reperfusion. the underlying regulatory mechanisms of mir-382 were investigated with treatment of mir-382 mimics, mir-382 inhibitors, or sb203580 (an inhibitor of the mapk signaling pathway) prior to i/r modeling. compared with sham-operated rats, rats following i/r showed increased longa's scores, ischemic hemisphere volume, cerebral infarct volume, eb content in brain tissues, enhanced levels of p38, inos, and mmp-9. the ectopic expression of mir-21 by mimics and mapk signaling inhibition by sb203580 reduced longa's scores, ischemic hemisphere volume, cerebral infarct volume, eb content in brain tissues, decreased levels of p38, map2k3, inos, and mmp-9. the luciferase activity determination showed mir-21 bound to map2k3 in its 3'utr. mir-21 downregulation mediated by inhibitors appeared to yield an opposed trend. we also found that mapk signaling inhibition by sb203580 could rescue rats with treatment of mir-382 inhibitors. the study highlights the neuroprotective role of mir-21 during cerebral i/r injury and its preventive effect against bbb disruption by blocking the mapk signaling pathway via targeted inhibition of map2k3, potentially opening a novel therapeutic avenue for the treatment of cerebral ischemia.",1
"aggressive cancer cells gain robust tumor vascular mimicry (vm) capability that promotes tumor growth and metastasis. ve-cadherin is aberrantly overexpressed in vasculogenic cancer cells and regarded as a master gene of tumor vm. although micrornas (mirnas) play an important role in modulating tumor angiogenesis and cancer metastasis, the mirna that targets ve-cadherin expression in cancer cells to inhibit tumor cell-mediated vm is enigmatic. in this study, we found that mir-27b levels are negatively co-related to ve-cadherin expression in ovarian cancer cells and tumor cell-mediated vm, and demonstrated that mir-27b could bind to the 3'-untranslated region (3'utr) of ve-cadherin mrna. overexpression of mir-27b in aggressive ovarian cancer cell lines hey1b and es2 significantly diminished intracellular ve-cadherin expression; convincingly, the inhibitory effect of mir-27b could be reversed by mir-27b specific inhibitor. intriguingly, mir-27b not only effectively suppressed ovarian cancer cell migration and invasion, but also markedly inhibited formation of ovarian cancer cell-mediated capillary-like structures in vitro and suppressed generation of functional tumor blood vessels in mice. together, our study suggests that mir-27b functions as a new inhibitor of ovarian cancer cell-mediated vm through suppression of ve-cadherin expression, providing a new potential drug candidate for antitumor vm and anti-ovarian cancer therapy.",1
"micrornas (mirnas) are endogenous approximately 22-nucleotide rnas that mediate important gene-regulatory events by pairing to the mrnas of protein-coding genes to direct their repression. repression of these regulatory targets leads to decreased translational efficiency and/or decreased mrna levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mrna levels. for both ectopic and endogenous mirna regulatory interactions, lowered mrna levels account for most (>/=84%) of the decreased protein production. these results show that changes in mrna levels closely reflect the impact of mirnas on gene expression and indicate that destabilization of target mrnas is the predominant reason for reduced protein output.",1
"expression of microrna-129-5p (mir-129-5p) has been reported to decrease in gastric cancer (gc). however, little information is available about how mir-129-5p affects cell migration and invasion of gc. cancer samples and matched non-tumor adjacent tissues were obtained from patients with gc. besides, peripheral blood samples were collected from both the patients and healthy volunteers. expression of mir-129-5p was analyzed by real-time pcr (rt-pcr). after transfection with mir-129-5p mimics, mir-129-5p inhibitor, or negative controls in human gc cell line sgc-7901, cell viability, colony-formation ability, migration, and invasion assay were evaluated. luciferase reporter assay, rt-pcr, and enzyme-linked immunosorbent assay (elisa) were performed to explore whether interleukin-8 was a target of mir-129-5p. further, small interfering rna (sirna) against il-8 was transfected into cells, and then the effects of mir-129-5p inhibitor on migration and invasion were assessed. mir-129-5p was down-regulated in both gc samples and blood samples compared to their matched non-tumor adjacent tissues and healthy volunteers (both p < 0.05). compared to the control group, transfection with mir-129-5p inhibitor markedly increased the cell viability, colony-forming ability, and numbers of migrated and invaded cells. luciferase reporter assay confirmed that il-8 was a direct target of mir-129-5p, and il-8 was negatively regulated by mir-129-5p. co-transfection of mir-129-5p inhibitor with si-il-8 reversed the effect of mir-129-5p inhibitor on the migration and invasion of the cells. mir-129-5p and regulates migration and invasion of gc cells by targeting il-8.",1
"increasing evidence suggests that micrornas (mirnas) play important roles in impaired endothelial cell (ec) angiogenesis during aging. however, their exact roles in the aging process remain unclear. we aimed to determine whether mirnas cause angiogenesis defects in ecs during aging and to uncover the underlying mechanisms. to study the mirna-induced changes in ecs during aging, we performed microarray analyses on arterial ecs collected from young and aging mice. using qrt-pcr, we showed that microrna-125a-5p (mir-125a-5p) expression was approximately 2.9 times higher in old endothelial cells (oecs) compared with samples collected from young animals. western blot assays showed a lower expression level of an mir-125a-5p target known as related transcriptional enhancer factor-1 (rtef-1) in oecs compared with its expression levels in young cells. overexpression of mir-125a-5p in young endothelial cells (yecs) using pre-mir-125a-5p caused the downregulation of rtef-1, endothelial nitric oxide synthase (enos) and vascular endothelial growth factor (vegf) and resulted in impaired angiogenesis, as evidenced by spheroid sprouting and tube formation assays in vitro. conversely, repression of mir-125a-5p in oecs using anti-mir-125a-5p increased rtef-1, enos and vegf expression and improved ec angiogenesis. importantly, impaired angiogenesis caused by knock-down of rtef-1 was not efficiently rescued by anti-mir-125a-5p. dual-luciferase reporter gene analysis showed that rtef-1 is a direct target of mir-125a-5p, which regulates angiogenesis by repressing rtef-1 expression and modulating enos and vegf expression. these findings indicate that mir-125a-5p and rtef-1 are potential therapeutic targets for improving ec-mediated angiogenesis in elderly individuals.",1
"precise temporal control is needed for rna viral genomes to translate sufficient replication-required products before clearing ribosomes and initiating replication. a 3' translational enhancer in turnip crinkle virus (tcv) overlaps an internal t-shaped structure (tss) that binds to 60s ribosomal subunits. the higher-order structure in the region was examined through alteration of critical sequences revealing novel interactions between an h-type pseudoknot and upstream residues, and between the tss and internal and terminal loops of an upstream hairpin. our results suggest that the tss forms a stable scaffold that allows for simultaneous interactions with external sequences through base pairings on both sides of its large internal symmetrical loop. binding of tcv rna-dependent rna polymerase (rdrp) to the region potentiates a widespread conformational shift with substantial rearrangement of the tss region, including the element required for efficient ribosome binding. degrading the rdrp caused the rna to resume its original conformation, suggesting that the initial conformation is thermodynamically favored. these results suggest that the 3' end of tcv folds into a compact, highly interactive structure allowing rdrp access to multiple elements including the 3' end, which causes structural changes that potentiate the shift between translation and replication.",1
"micrornas (mirnas) can regulate the proliferative status of pulmonary artery smooth muscle cells (pasmcs), which is a core factor modulating pulmonary vascular remodeling diseases, such as atherosclerosis and pulmonary arterial hypertension (pah). our previous work has shown that mir-4632, a rarely reported mirna, is significantly downregulated in platelet-derived growth factor (pdgf)-bb-stimulated human pulmonary artery smooth muscle cells (hpasmcs), yet its cell function and the underlying molecular mechanisms remain to be elucidated. here, we find that mir-4632 is highly expressed in hpasmcs and its expression significantly decreased in response to different stimuli. functional studies revealed that mir-4632 inhibited proliferation and promoted apoptosis of hpasmcs but had no effects on cell contraction and migration. furthermore, the cjun was identified as a direct target gene of mir-4632, while knockdown of cjun was necessary for mir-4632-mediated hpasmc proliferation and apoptosis. in addition, the downregulation of mir-4632 by pdgf-bb was found to associate with histone deacetylation through the activation of pdgf receptor/phosphatidylinositol 3'-kinase/histone deacetylase 4 signaling. finally, the expression of mir-4632 was reduced in the serum of patients with pah. overall, our results suggest that mir-4632 plays an important role in regulating hpasmc proliferation and apoptosis by suppression of cjun, providing a novel therapeutic mirna candidate for the treatment of pulmonary vascular remodeling diseases. it also implies that serum mir-4632 has the potential to serve as a circulating biomarker for pah diagnosis.",1
"evasion of apoptosis is a known feature of cancer cells. one mechanism of deregulating the apoptotic pathway is through overexpression of antiapoptotic bcl2 family members. abt-263 (navitoclax) is a first-in-class bcl2 family inhibitor that restores the ability of cancer cells to undergo apoptosis. however, many cancer cells are resistant to abt-263 due to high levels of a bcl2 family member, mcl1, which is not targeted by the drug. mcl1 expression is regulated transcriptionally, translationally, and through proteasome-mediated degradation. recently, mcl1 expression was shown to be affected by micrornas (mirna). to identify mirnas that modulate the sensitivity of cancer cells to abt-263, we screened a library of 810 human mirna mimics in hct-116 cells in the presence of abt-263. the screen revealed 19 mirnas that sensitize hct-116 cells to abt-263. fifteen of these mirnas were also shown to sensitize chl1 melanoma cells to the same agent. we further evaluated 12 of the strongest sensitizers in these cell lines. we found that these sensitizers induced apoptosis only in the presence of abt-263. in addition, whereas all 12 of these mirnas reduced mcl1 protein expression, only 10 of them targeted mcl1 through direct binding to the 3'-untranslated region of the gene, raising the possibility that other resistance regulators of mcl1 expression may be identified using our method. finally, because sensitizing mirna expression is lower in tumors compared with normal tissues, our data can facilitate the design of mirna replacement therapies to increase sensitivity to bcl2 antagonists.",1
"hypercholesterolemia is an important risk factor for coronary heart disease. although a lot of research has been conducted, the regulation of cholesterol metabolism is still largely unknown. some mirnas have been found to play critical role in the cholesterol metabolism. mir-98 is a mirna whose function has been reported mainly in tumorigenesis. in this study, we elucidate a novel role of mir-98 in cholesterol metabolism. we found that the expression of mir-98 was decreased significantly in hypercholesterolemic patients compared with healthy control subjects. furthermore, we identified that srebp-2, an important transcriptional factor in cholesterol metabolism, was a direct target of mir-98. overexpression of mir-98 significantly repressed the 3'-utr reporter activities of srebp-2 in a dose-dependent manner in hepg2 cells, while the effect of mir-98 was blocked when the binding site of mir-98 within the srebp-2 3'-utr was mutated. and overexpression of mir-98 reduced both the mrna and protein levels of hmgcr and ldlr significantly in vitro, which are two target genes of srebp-2. furthermore, mir-98 overexpression reduced the intracellular total cholesterol levels dramatically. moreover, we overexpressed the mir-98 by lentiviral tail vein injection in vivo. compared with the control mice, the mir-98 overexpression mice showed lower serum cholesterol level and decreased srebp-2, hmgcr as well as ldlr expression. our data confirmed that reduced expression of mir-98 potentially contributes to disturbance of cholesterol metabolism. mir-98 might be a novel therapeutic target to hypercholesterolemia.",1
"rationale abdominal aortic aneurysms constitute a degenerative process in the aortic wall. both the mir-29 and mir-15 families have been implicated in regulating the vascular extracellular matrix. objective our aim was to assess the effect of the mir-15 family on aortic aneurysm development. methods and results among the mir-15 family members, mir-195 was differentially expressed in aortas of apolipoprotein e-deficient mice on angiotensin ii infusion. proteomics analysis of the secretome of murine aortic smooth muscle cells, after mir-195 manipulation, revealed that mir-195 targets a cadre of extracellular matrix proteins, including collagens, proteoglycans, elastin, and proteins associated with elastic microfibrils, albeit mir-29b showed a stronger effect, particularly in regulating collagens. systemic and local administration of cholesterol-conjugated antagomirs revealed better inhibition of mir-195 compared with mir-29b in the uninjured aorta. however, in apolipoprotein e-deficient mice receiving angiotensin ii, silencing of mir-29b, but not mir-195, led to an attenuation of aortic dilation. higher aortic elastin expression was accompanied by an increase of matrix metalloproteinases 2 and 9 in mice treated with antagomir-195. in human plasma, an inverse correlation of mir-195 was observed with the presence of abdominal aortic aneurysms and aortic diameter. conclusions we provide the first evidence that mir-195 may contribute to the pathogenesis of aortic aneurysmal disease. although inhibition of mir-29b proved more effective in preventing aneurysm formation in a preclinical model, mir-195 represents a potent regulator of the aortic extracellular matrix. notably, plasma levels of mir-195 were reduced in patients with abdominal aortic aneurysms suggesting that micrornas might serve as a noninvasive biomarker of abdominal aortic aneurysms.",1
"predicting the impact of micrornas (mirnas) on target proteins is challenging because of their different regulatory effects at the transcriptional and translational levels. in this study, we applied a novel protein lysate microarray (lma) technology to systematically monitor for target protein levels after high-throughput transfections of 319 pre-mirs into breast cancer cells. we identified 21 mirnas that downregulated the estrogen receptor-alpha (eralpha), as validated by western blotting and quantitative real time-pcr, and by demonstrating the inhibition of estrogen-stimulated cell growth. five potent eralpha-regulating mirnas, mir-18a, mir-18b, mir-193b, mir-206 and mir-302c, were confirmed to directly target eralpha in 3'-untranslated region reporter assays. the gene expression signature that they repressed highly overlapped with that of a small interfering rna against eralpha, and across all the signatures tested, was most closely associated with the repression of known estrogen-induced genes. furthermore, mir-18a and mir-18b showed higher levels of expression in eralpha-negative as compared with eralpha-positive clinical tumors. in summary, we present systematic and direct functional evidence of mirnas inhibiting eralpha signaling in breast cancer, and demonstrate the high-throughput lma technology as a novel, powerful technique in determining the relative impact of various mirnas on key target proteins and associated cellular processes and pathways.",1
"tumor-suppressor pdcd4 inhibits transformation and invasion and is downregulated in cancers. so far, it has not been studied as to whether mirnas, suppressing target expression by binding to the 3'-utr, regulate pdcd4 or invasion. the present study was conducted to investigate the regulation of pdcd4, and invasion/intra-vasation, by mirnas. a bioinformatics search revealed a conserved target-site for mir-21 within the pdcd4-3'-utr at 228-249 nt. in 10 colorectal cell lines, an inverse correlation of mir-21 and pdcd4-protein was observed. transfection of colo206f-cells with mir-21 significantly suppressed a luciferase-reporter containing the pdcd4-3'-utr, whereas transfection of rko with anti-mir-21 increased activity of this construct. this was abolished when a construct mutated at the mir-21/nt228-249 target site was used instead. anti-mir-21-transfected rko cells showed an increase of pdcd4-protein and reduced invasion. moreover, these cells showed reduced intra-vasation and lung metastasis in a chicken-embryo-metastasis assay. in contrast, overexpression of mir-21 in colo206f significantly reduced pdcd4-protein amounts and increased invasion, while pdcd4-mrna was unaltered. resected normal/tumor tissues of 22 colorectal cancer patients demonstrated an inverse correlation between mir-21 and pdcd4-protein. this is the first study to show that pdcd4 is negatively regulated by mir-21. furthermore, it is the first report to demonstrate that mir-21 induces invasion/intravasation/metastasis.",1
"objective micrornas (mirs) play important regulatory roles in lipid metabolism. apolipoprotein b (apob), as the only essential scaffolding protein in the assembly of very-low-density lipoproteins, is a target to treat hyperlipidemia and atherosclerosis. we aimed to find out mirs that reduce apob expression. approach and results bioinformatic analyses predicted that hsa-mir-548p can interact with apob mrna. mir-548p or control mir was transfected in human and mouse liver cells to test its role in regulating apob secretion and mrna expression levels. site-directed mutagenesis was used to identify the interacting site of mir-548p in human apob 3'-untranslated region. fatty acid oxidation and lipid syntheses were examined in mir-548p overexpressing cells to investigate its function in lipid metabolism. we observed that mir-548p significantly reduces apob secretion from human hepatoma cells and primary hepatocytes. mechanistic studies showed that mir-548p interacts with the 3'-untranslated region of human apob mrna to enhance post-transcriptional degradation. bioinformatic algorithms suggested 2 potential binding sites of mir-548p on human apob mrna. site-directed mutagenesis studies revealed that mir-548p targets site i involving both seed and supplementary sequences. mir-548p had no effect on fatty acid oxidation but significantly decreased lipid synthesis in human hepatoma cells by reducing hmgcr (3-hydroxy-3-methylglutaryl-coenzyme a reductase) and acsl4 (acyl-coa synthetase long-chain family member 4) enzymes involved in cholesterol and fatty acid synthesis. in summary, mir-548p reduces lipoprotein production and lipid synthesis by reducing expression of different genes in human liver cells. conclusions these studies suggest that mir-548p regulates apob secretion by targeting mrna. it is likely that it could be useful in treating atherosclerosis, hyperlipidemia, and hepatosteatosis.",1
"unbalanced apoptosis is a major cause of structural remodelling of vasculatures associated with pah (pulmonary arterial hypertension), whereas the underlying mechanisms are still elusive. mirnas (micrornas) regulate the expression of several proteins that are important for cell fate, including differentiation, proliferation and apoptosis. it is possible that these regulatory rna molecules play a role in the development of pah. to test this hypothesis, we studied the effect of several mirnas on the apoptosis of cultured pasmcs (pulmonary artery smooth muscle cells) and identified mir-138 to be an important player. mir-138 was expressed in pasmcs, and its expression was subjected to regulation by hypoxia. expression of exogenous mir-138 suppressed pasmc apoptosis, prevented caspase activation and disrupted bcl-2 signalling. the serine/threonine kinase mst1, an amplifier of cell apoptosis, seemed to be a target of mir-138, and the activation of the akt pathway was necessary for the anti-apoptotic effect of mir-138. therefore the results of the present study suggest that mir-138 appears to be a negative regulator of pasmc apoptosis, and plays an important role in hpvr (hypoxic pulmonary vascular remodelling).",1
"genes regulated by the same mirna can be discovered by virtue of their coexpression at the transcriptional level and the presence of a conserved mirna-binding site in their 3' utrs. using this principle we have integrated the three best performing and complementary algorithms into a framework for inference of regulation by mirnas (firm) from sets of coexpressed genes. we demonstrate the utility of firm by inferring a cancer-mirna regulatory network through the analysis of 2240 gene coexpression signatures from 46 cancers. by analyzing this network for functional enrichment of known hallmarks of cancer we have discovered a subset of 13 mirnas that regulate oncogenic processes across diverse cancers. we have performed experiments to test predictions from this mirna-regulatory network to demonstrate that mirnas of the mir-29 family (mir-29a, mir-29b, and mir-29c) regulate specific genes associated with tissue invasion and metastasis in lung adenocarcinoma. further, we highlight the specificity of using firm inferences to identify mirna-regulated genes by experimentally validating that mir-767-5p, which partially shares the mir-29 seed sequence, regulates only a subset of mir-29 targets. by providing mechanistic linkage between mirna dysregulation in cancer, their binding sites in the 3'utrs of specific sets of coexpressed genes, and their associations with known hallmarks of cancer, firm, and the inferred cancer mirna-regulatory network will serve as a powerful public resource for discovery of potential cancer biomarkers.",1
"two rna stem-loop structures in the gag gene have been implicated as representing the primary encapsidation (packaging) signal for bovine leukemia virus (blv), a member of the delta retrovirus of the retroviridae. in this study, we conducted an analysis of these rna structures, stem loop 1 (sl1) and stem loop 2 (sl2), to determine if both the loop and the stem nucleotide bases are important for rna encapsidation. we have found that the primary sequence of the unpaired bases located in the loop regions of both sl1 and sl2 are important for efficient rna encapsidation and virus replication. the primary sequence of the bases that form the stems for both sl1 and sl2 was observed to aid in efficient encapsidation and replication. we also observed that the order of sl1 and sl2 is important for rna encapsidation and virus replication efficiency. a viral rna with two copies of either sl1 or sl2 was found to replicate and package rna as efficiently as a viral rna with only one copy of sl1 or sl2. this provides evidence that sl1 and sl2 are not functionally equivalent. sequences from human t cell leukemia virus type 1 (htlv-1) that are located in the same region of htlv-1 as the sl1 and sl2 of blv were used to replace the blv sl1, sl2, or both in a blv rna. these blv rnas were still encapsidated and replicated, suggesting that these sequences may function as an encapsidation signal in htlv-1. the chimeric rnas did not replicate as well as the parental, indicating that the primary nucleotide sequence along with the secondary and tertiary structure of the rna plays a role in efficient rna encapsidation and replication.",1
"mir-133 was found to be specifically expressed in cardiac and skeletal muscle in previous studies. there are two members in the mir-133 family: mir-133a and mir-133b. although previous studies indicated that mir-133a was related to myogenesis, the signaling pathways regulated by mir-133 were still not very clear. in this study, we showed that both mir-133a and mir-133b were upregulated during myogenesis through solexa sequencing. we confirmed that mir-133 could promote myoblast differentiation and inhibit cell proliferation through the regulation of the extracellular signal-regulated kinase (erk) signaling pathway in c2c12 cells. fgfr1 and pp2ac, which both participate in signal transduction of the erk1/2 pathway, were found to be negatively regulated by mir-133a and mir-133b at the post-transcriptional level. also, downregulation of erk1/2 phosphorylation by mir-133 was detected. fgfr1 and pp2ac were also found to repress c2c12 differentiation by specific sirnas. in addition, we found that inhibition of erk1/2 pathway activity can inhibit c2c12 cell proliferation and promote the initiation of differentiation but form short and small myotubes. furthermore, we found that the expression of mir-133 was negatively regulated by erk1/2 signaling pathway. in summary, we demonstrated the role of mir-133 in myoblast and further revealed a new feedback loop between mir-133 and the erk1/2 signaling pathway involving an exquisite mechanism for regulating myogenesis.",1
"activation of peroxisome proliferator-activated receptor alpha (pparalpha) leads to hepatocellular proliferation and liver carcinomas. the early events mediating these effects are unknown. a novel mechanism by which pparalpha regulates gene expression and hepatocellular proliferation was uncovered. microrna (mirna) expression profiling demonstrated that activated pparalpha was a major regulator of hepatic mirna expression. of particular interest, let-7c, an mirna important in cell growth, was inhibited following 4-h treatment and 2-week and 11-month sustained treatment with the potent pparalpha agonist wy-14,643 in wild-type mice. let-7c was shown to target c-myc via direct interaction with the 3' untranslated region of c-myc. the pparalpha-mediated induction of c-myc via let-7c subsequently increased expression of the oncogenic mir-17-92 cluster; these events did not occur in pparalpha-null mice. overexpression of let-7c decreased c-myc and mir-17 and suppressed the growth of hepa-1 cells. furthermore, using the human pparalpha-expressing mouse model, which is responsive to wy-14,643 effects on beta-oxidation and serum triglycerides but resistant to hepatocellular proliferation and tumorigenesis, we demonstrated a critical role for let-7c in liver oncogenesis. wy-14,643 treatment did not inhibit let-7c or induce c-myc and mir-17 expression. these observations reveal a let-7c signaling cascade critical for pparalpha agonist-induced liver proliferation and tumorigenesis.",1
"background micrornas are short (∼22 nt) non-coding regulatory rnas that control gene expression at the post-transcriptional level. here the functional impact of micrornas on cell cycle arrest during neuronal lineage differentiation of unrestricted somatic stem cells from human cord blood (ussc) was analyzed. methodology/principal findings expression profiling revealed downregulation of micrornas mir-17, -20a, and -106b in ussc differentiated into neuronal lineage but not in ussc differentiated into osteogenic lineage. transfection experiments followed by ki67 immunostainings demonstrated that each of these micrornas was able to promote proliferation of native ussc and to prevent in part cell cycle arrest during neuronal lineage differentiation of ussc. bioinformatic target gene predictions followed by experimental target gene validations revealed that mir-17, -20a, and -106b act in a common manner by downregulating an overlapping set of target genes mostly involved in regulation and execution of g(1)/s transition. pro-proliferative target genes cyclind1 (ccnd1) and e2f1 as well as anti-proliferative targets cdkn1a (p21), pten, rb1, rbl1 (p107), rbl2 (p130) were shown as common targets for mir-17, -20a, and -106b. furthermore, these micrornas also downregulate wee1 which is involved in g(2)/m transition. most strikingly, mir-17, -20a, and -106b were found to promote cell proliferation by increasing the intracellular activity of e2f transcription factors, despite the fact that mir-17, -20a, and -106b directly target the transcripts that encode for this protein family. conclusions/significance mir-17, -20a, and -106b downregulate a common set of pro- and anti-proliferative target genes to impact cell cycle progression of ussc and increase intracellular activity of e2f transcription factors to govern g(1)/s transition.",1
"background it is widely accepted that cognitive and memory deficits in alzheimer's disease (ad) primarily result from synaptic failure. however, the mechanisms that underlie synaptic and cognitive dysfunction remain unclear. methods we utilized molecular biology techniques, electrophysiological recordings, fluorescence in situ hybridization (fish), immuno- and golgi-staining, chromatin immunoprecipitation (chip); lentivirus (lv)-based microrna overexpression and 'sponging', and behavioral tests to assess upregulated mir-30b causing synaptic and cognitive declines in app transgenic (tg) mice. findings we provide evidence that expression of mir-30b, which targets molecules important for maintaining synaptic integrity, including ephrin type-b receptor 2 (ephb2), sirtuin1 (sirt1), and glutamate ionotropic receptor ampa type subunit 2 (glua2), is robustly upregulated in the brains of both ad patients and app transgenic (tg) mice, an animal model of ad, while expression of its targets is significantly downregulated. overexpression of mir-30b in the hippocampus of normal wild-type (wt) mice impairs synaptic and cognitive functions, mimicking those seen in tg mice. conversely, knockdown of endogenous mir-30b in tg mice prevents synaptic and cognitive decline. we further observed that expression of mir-30b is upregulated by proinflammatory cytokines and aβ42 through nf-κb signaling. interpretation our results provide a previously undefined mechanism by which unregulated mir-30b causes synaptic and cognitive dysfunction in ad, suggesting that reversal of dysregulated mir-30b in the brain may prevent or slow cognitive declines in ad. fund: this work was supported by national institutes of health grants r01ns076815, r01mh113535, r01ag058621, p30gm103340 pilot project, and by the lsuhsc school of medicine research enhancement program grant (to c.c.).",1
"viral noncoding rnas have been shown to play an important role in virus-host interplay to facilitate virus replication. we report that members of the genus flavivirus, a large group of medically important encephalitic rna viruses, produce a unique and highly structured noncoding rna of 0.3-0.5 kb derived from the 3' untranslated region of the viral genome. using west nile virus as a model, we show that this subgenomic rna is a product of incomplete degradation of viral genomic rna by cellular ribonucleases. highly conserved rna structures located at the beginning of the 3' untranslated region render this rna resistant to nucleases, and the resulting subgenomic rna product is essential for virus-induced cytopathicity and pathogenicity. thus, flaviviruses evolved a unique strategy to generate a noncoding rna product that allows them to kill the host more efficiently.",1
"the pericardial fluid (pf) is contained in the pericardial sac surrounding the heart. microrna (mirna) exchange via exosomes (endogenous nanoparticles) contributes to cell-to-cell communication. we investigated the hypotheses that the pf is enriched with mirnas secreted by the heart and that it mediates vascular responses through exosome exchange of mirnas. the study was developed using leftover material from aortic valve surgery. we found that in comparison with peripheral plasma, the pf contains exosomes enriched with mirnas co-expressed in patients' myocardium and vasculature. at a functional level, pf exosomes improved survival, proliferation, and networking of cultured endothelial cells (ecs) and restored the angiogenic capacity of ecs depleted (via dicer silencing) of their endogenous mirna content. moreover, pf exosomes improved post-ischemic blood flow recovery and angiogenesis in mice. mechanistically, (1) let-7b-5p is proangiogenic and inhibits its target gene, tgfbr1, in ecs; (2) pf exosomes transfer a functional let-7b-5p to ecs, thus reducing their tgfbr1 expression; and (3) let-7b-5p depletion in pf exosomes impairs the angiogenic response to these nanoparticles. collectively, our data support the concept that pf exosomes orchestrate vascular repair via mirna transfer.",1
"in phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. here, we introduce the phylogenetic terrace aware (pta) data structure for the efficient analysis under partition models. in the presence of missing data pta exploits (partial) terraces and induced partition trees to save computation time. we show that an implementation of pta in iq-tree leads to a substantial speedup of up to 4.5 and 8 times compared with the standard iq-tree and raxml implementations, respectively. pta is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.",0
"a number of databases on the plant metabolome describe the chemistry and biosynthesis of plant chemicals. however, no such database is specifically focused on foods and more precisely on polyphenols, one of the major classes of phytochemicals. as antioxidants, polyphenols influence human health and may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, some cancers or type 2 diabetes. to determine polyphenol intake in populations and study their association with health, it is essential to have detailed information on their content in foods. however this information is not easily collected due to the variety of their chemical structures and the variability of their content in a given food. phenol-explorer is the first comprehensive web-based database on polyphenol content in foods. it contains more than 37,000 original data points collected from 638 scientific articles published in peer-reviewed journals. the quality of these data has been evaluated before they were aggregated to produce final representative mean content values for 502 polyphenols in 452 foods. the web interface allows making various queries on the aggregated data to identify foods containing a given polyphenol or polyphenols present in a given food. for each mean content value, it is possible to trace all original content values and their literature sources. phenol-explorer is a major step forward in the development of databases on food constituents and the food metabolome. it should help researchers to better understand the role of phytochemicals in the technical and nutritional quality of food, and food manufacturers to develop tailor-made healthy foods. database url:",0
"false positives in a genome-wide association study (gwas) can be effectively controlled by a fixed effect and random effect mixed linear model (mlm) that incorporates population structure and kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. the modified mlm method, multiple loci linear mixed model (mlmm), incorporates multiple markers simultaneously as covariates in a stepwise mlm to partially remove the confounding between testing markers and kinship. to completely eliminate the confounding, we divided mlmm into two parts: fixed effect model (fem) and a random effect model (rem) and use them iteratively. fem contains testing markers, one at a time, and multiple associated markers as covariates to control false positives. to avoid model over-fitting problem in fem, the associated markers are estimated in rem by using them to define kinship. the p values of testing markers and the associated markers are unified at each iteration. we named the new method as fixed and random model circulating probability unification (farmcpu). both real and simulated data analyses demonstrated that farmcpu improves statistical power compared to current methods. additional benefits include an efficient computing time that is linear to both number of individuals and number of markers. now, a dataset with half million individuals and half million markers can be analyzed within three days.",0
"the present paper deals with the karyotype analysis of three species in the abies (pinaceae) from east asia including a. georgei orr var. smithii (viguie et ganssen)cheng et l.k.fu.a.nephrolepis(trautv.)maxim.and a.holophylla maxim. the karyotype fmulas of the species are k(2n)=24=18m(2sc)+6sm, 18m(6sc)+6sm and 14m(6sc)+10sm respectively. their chromosome complements are 2n=24=4l+8m2+10m1+2s. 4l+8m2+8m1+4s and 2l+12m2+8m1+2s according to the standard defined by kuo et al (1972) based on relative length. they belong to 2a type of stebbins^ karyotypic asymmetry. the karyotypes of the species are reported for the first time. the karyotype of a. nephrolepis is more symmetry and more primitive than that of a.georgei var. smithii and a.holophylla.",0
"lateral assemblies of glycolipids and cholesterol, ""rafts,"" have been implicated to play a role in cellular processes like membrane sorting, signal transduction, and cell adhesion. we studied the structure of raft domains in the plasma membrane of non-polarized cells. overexpressed plasma membrane markers were evenly distributed in the plasma membrane. we compared the patching behavior of pairs of raft markers (defined by insolubility in triton x-100) with pairs of raft/non-raft markers. for this purpose we cross-linked glycosyl-phosphatidylinositol (gpi)-anchored proteins placental alkaline phosphatase (plap), thy-1, influenza virus hemagglutinin (ha), and the raft lipid ganglioside gm1 using antibodies and/or cholera toxin. the patches of these raft markers overlapped extensively in bhk cells as well as in jurkat t-lymphoma cells. importantly, patches of gpi-anchored plap accumulated src-like protein tyrosine kinase fyn, which is thought to be anchored in the cytoplasmic leaflet of raft domains. in contrast patched raft components and patches of transferrin receptor as a non-raft marker were sharply separated. taken together, our data strongly suggest that coalescence of cross-linked raft elements is mediated by their common lipid environments, whereas separation of raft and non-raft patches is caused by the immiscibility of different lipid phases. this view is supported by the finding that cholesterol depletion abrogated segregation. our results are consistent with the view that raft domains in the plasma membrane of non-polarized cells are normally small and highly dispersed but that raft size can be modulated by oligomerization of raft components.",0
"in response to the coronavirus disease 2019 (covid-19) pandemic, 107 countries had implemented national school closures by march 18, 2020. it is unknown whether school measures are effective in coronavirus outbreaks (eg, due to severe acute respiratory syndrome , middle east respiratory syndrome, or covid-19). we undertook a systematic review by searching three electronic databases to identify what is known about the effectiveness of school closures and other school social distancing practices during coronavirus outbreaks. we included 16 of 616 identified articles. school closures were deployed rapidly across mainland china and hong kong for covid-19. however, there are no data on the relative contribution of school closures to transmission control. data from the sars outbreak in mainland china, hong kong, and singapore suggest that school closures did not contribute to the control of the epidemic. modelling studies of sars produced conflicting results. recent modelling studies of covid-19 predict that school closures alone would prevent only 2-4% of deaths, much less than other social distancing interventions. policy makers need to be aware of the equivocal evidence when considering school closures for covid-19, and that combinations of social distancing measures should be considered. other less disruptive social distancing interventions in schools require further consideration if restrictive social distancing policies are implemented for long periods.",0
"tumor metastasis is a major contributor to the death of cancer patients. it is driven not only by the intrinsic alterations in tumor cells, but also by the implicated cross-talk between cancer cells and their altered microenvironment components. tumor-associated macrophages (tams) are the key cells that create an immunosuppressive tumor microenvironment (tme) by producing cytokines, chemokines, growth factors, and triggering the inhibitory immune checkpoint proteins release in t cells. in doing so, tams exhibit important functions in facilitating a metastatic cascade of cancer cells and, meanwhile, provide multiple targets of certain checkpoint blockade immunotherapies for opposing tumor progression. in this article, we summarize the regulating networks of tam polarization and the mechanisms underlying tam-facilitated metastasis. based on the overview of current experimental evidence dissecting the critical roles of tams in tumor metastasis, we discuss and prospect the potential applications of tam-focused therapeutic strategies in clinical cancer treatment at present and in the future.",0
"zo-1, zo-2, and zo-3, which contain three pdz domains (pdz1 to -3), are concentrated at tight junctions (tjs) in epithelial cells. tj strands are mainly composed of two distinct types of four-transmembrane proteins, occludin, and claudins, between which occludin was reported to directly bind to zo-1/zo-2/zo-3. however, in occludin-deficient intestinal epithelial cells, zo-1/zo-2/zo-3 were still recruited to tjs. we then examined the possible interactions between zo-1/zo-2/zo-3 and claudins. zo-1, zo-2, and zo-3 bound to the cooh-terminal yv sequence of claudin-1 to -8 through their pdz1 domains in vitro. then, claudin-1 or -2 was transfected into l fibroblasts, which express zo-1 but not zo-2 or zo-3. claudin-1 and -2 were concentrated at cell-cell borders in an elaborate network pattern, to which endogenous zo-1 was recruited. when zo-2 or zo-3 were further transfected, both were recruited to the claudin-based networks together with endogenous zo-1. detailed analyses showed that zo-2 and zo-3 are recruited to the claudin-based networks through pdz2 (zo-2 or zo-3)/pdz2 (endogenous zo-1) and pdz1 (zo-2 or zo-3)/cooh-terminal yv (claudins) interactions. in good agreement, pdz1 and pdz2 domains of zo-1/zo-2/zo-3 were also recruited to claudin-based tjs, when introduced into cultured epithelial cells. the possible molecular architecture of tj plaque structures is discussed.",0
"to document the marketing and distribution of nano-enabled products into the commercial marketplace, the woodrow wilson international center for scholars and the project on emerging nanotechnologies created the nanotechnology consumer products inventory (cpi) in 2005. the objective of this present work is to redevelop the cpi by leading a research effort to increase the usefulness and reliability of this inventory. we created eight new descriptors for consumer products, including information pertaining to the nanomaterials contained in each product. the project was motivated by the recognition that a diverse group of stakeholders from academia, industry, and state/federal government had become highly dependent on the inventory as an important resource and bellweather of the pervasiveness of nanotechnology in society. we interviewed 68 nanotechnology experts to assess key information needs. their answers guided inventory modifications by providing a clear conceptual framework best suited for user expectations. the revised inventory was released in october 2013. it currently lists 1814 consumer products from 622 companies in 32 countries. the health and fitness category contains the most products (762, or 42% of the total). silver is the most frequently used nanomaterial (435 products, or 24%); however, 49% of the products (889) included in the cpi do not provide the composition of the nanomaterial used in them. about 29% of the cpi (528 products) contain nanomaterials suspended in a variety of liquid media and dermal contact is the most likely exposure scenario from their use. the majority (1288 products, or 71%) of the products do not present enough supporting information to corroborate the claim that nanomaterials are used. the modified cpi has enabled crowdsourcing capabilities, which allow users to suggest edits to any entry and permits researchers to upload new findings ranging from human and environmental exposure data to complete life cycle assessments. there are inherent limitations to this type of database, but these modifications to the inventory addressed the majority of criticisms raised in published literature and in surveys of nanotechnology stakeholders and experts. the development of standardized methods and metrics for nanomaterial characterization and labelling in consumer products can lead to greater understanding between the key stakeholders in nanotechnology, especially consumers, researchers, regulators, and industry.",0
"the ability of fungal-derived beta-glucan particles to induce leukocyte activation and the production of inflammatory mediators, such as tumor necrosis factor (tnf)-alpha, is a well characterized phenomenon. although efforts have been made to understand how these carbohydrate polymers exert their immunomodulatory effects, the receptors involved in generating these responses are unknown. here we show that dectin-1 mediates the production of tnf-alpha in response to zymosan and live fungal pathogens, an activity that occurs at the cell surface and requires the cytoplasmic tail and immunoreceptor tyrosine activation motif of dectin-1 as well as toll-like receptor (tlr)-2 and myd88. this is the first demonstration that the inflammatory response to pathogens requires recognition by a specific receptor in addition to the tlrs. furthermore, these studies implicate dectin-1 in the production of tnf-alpha in response to fungi, a critical step required for the successful control of these pathogens.",0
"advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. this potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. we introduce pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two illumina libraries with small e.g., 180 bp and large e.g., 3-5 kb inserts. pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. for both haploid and diploid genomes, pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. furthermore, pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. pilon is freely available as open source software.",0
"cellular senescence is an important mechanism for preventing the proliferation of potential cancer cells. recently, however, it has become apparent that this process entails more than a simple cessation of cell growth. in addition to suppressing tumorigenesis, cellular senescence might also promote tissue repair and fuel inflammation associated with aging and cancer progression. thus, cellular senescence might participate in four complex biological processes (tumor suppression, tumor promotion, aging, and tissue repair), some of which have apparently opposing effects. the challenge now is to understand the senescence response well enough to harness its benefits while suppressing its drawbacks.",0
"understanding the concept of extrapolation of dose between species is important for pharmaceutical researchers when initiating new animal or human experiments. interspecies allometric scaling for dose conversion from animal to human studies is one of the most controversial areas in clinical pharmacology. allometric approach considers the differences in body surface area, which is associated with animal weight while extrapolating the doses of therapeutic agents among the species. this review provides basic information about translation of doses between species and estimation of starting dose for clinical trials using allometric scaling. the method of calculation of injection volume for parenteral formulation based on human equivalent dose is also briefed.",0
"we report a single-cell bisulfite sequencing (scbs-seq) method that can be used to accurately measure dna methylation at up to 48.4% of cpg sites. embryonic stem cells grown in serum or in 2i medium displayed epigenetic heterogeneity, with '2i-like' cells present in serum culture. integration of 12 individual mouse oocyte datasets largely recapitulated the whole dna methylome, which makes scbs-seq a versatile tool to explore dna methylation in rare cells and heterogeneous populations.",0
"in 2008 the national center for health statistics released a dual energy x-ray absorptiometry (dxa) whole body dataset from the nhanes population-based sample acquired with modern fan beam scanners in 15 counties across the united states from 1999 through 2004. the nhanes dataset was partitioned by gender and ethnicity and dxa whole body measures of %fat, fat mass/height(2), lean mass/height(2), appendicular lean mass/height(2), %fat trunk/%fat legs ratio, trunk/limb fat mass ratio of fat, bone mineral content (bmc) and bone mineral density (bmd) were analyzed to provide reference values for subjects 8 to 85 years old. dxa reference values for adults were normalized to age; reference values for children included total and sub-total whole body results and were normalized to age, height, or lean mass. we developed an obesity classification scheme by using estabbody mass index (bmi) classification thresholds and prevalences in young adults to generate matching classification thresholds for fat mass index (fmi; fat mass/height(2)). these reference values should be helpful in the evaluation of a variety of adult and childhood abnormalities involving fat, lean, and bone, for establishing entry criteria into clinical trials, and for other medical, research, and epidemiological uses.",0
"the quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. the experiments were performed on two 30 w air-cooled incoatec iµs microfocus sources with multilayer optics mounted on a bruker d8 goniometer with a smart apex ii ccd detector. all data were analysed, processed and refined using standard bruker software. the results show that ag k α radiation can be beneficial when heavy elements are involved. a numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. fortunately the empirical corrections implemented in sadabs , although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. in three of the cases studied (two ag and one mo) the final shelxl r 1 against all data after application of empirical corrections implemented in sadabs was below 1%. since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. for this, sadabs uses the transmission factor of a spherical crystal with a user-defined value of μ r (where μ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. the results presented here suggest that the iucr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.",0
"colabfold offers accelerated prediction of protein structures and complexes by combining the fast homology search of mmseqs2 with alphafold2 or rosettafold. colabfold's 40-60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. coupled with google colaboratory, colabfold becomes a free and accessible platform for protein folding. colabfold is open-source software available at and its novel environmental databases are available at .",0
"a number of state-of-the-art protein structure prediction servers have been developed by researchers working in the bioinformatics unit at university college london. the popular psipred server allows users to perform secondary structure prediction, transmembrane topology prediction and protein fold recognition. more recent servers include disopred for the prediction of protein dynamic disorder and dompred for domain boundary prediction. these servers are available from our software home page at",0
"background the purpose was to: 1) perform a systematic review of studies examining the relation between physical activity, fitness, and health in school-aged children and youth, and 2) make recommendations based on the findings. methods the systematic review was limited to 7 health indicators: high blood cholesterol, high blood pressure, the metabolic syndrome, obesity, low bone density, depression, and injuries. literature searches were conducted using predefined keywords in 6 key databases. a total of 11,088 potential papers were identified. the abstracts and full-text articles of potentially relevant papers were screened to determine eligibility. data was abstracted for 113 outcomes from the 86 eligible papers. the evidence was graded for each health outcome using established criteria based on the quantity and quality of studies and strength of effect. the volume, intensity, and type of physical activity were considered. results physical activity was associated with numerous health benefits. the dose-response relations observed in observational studies indicate that the more physical activity, the greater the health benefit. results from experimental studies indicate that even modest amounts of physical activity can have health benefits in high-risk youngsters (e.g., obese). to achieve substantive health benefits, the physical activity should be of at least a moderate intensity. vigorous intensity activities may provide even greater benefit. aerobic-based activities had the greatest health benefit, other than for bone health, in which case high-impact weight bearing activities were required. conclusion the following recommendations were made: 1) children and youth 5-17 years of age should accumulate an average of at least 60 minutes per day and up to several hours of at least moderate intensity physical activity. some of the health benefits can be achieved through an average of 30 minutes per day. . 2) more vigorous intensity activities should be incorporated or added when possible, including activities that strengthen muscle and bone . 3) aerobic activities should make up the majority of the physical activity. muscle and bone strengthening activities should be incorporated on at least 3 days of the week .",0
"microglia make up the innate immune system of the central nervous system and are key cellular mediators of neuroinflammatory processes. their role in central nervous system diseases, including infections, is discussed in terms of a participation in both acute and chronic neuroinflammatory responses. specific reference is made also to their involvement in alzheimer's disease where microglial cell activation is thought to be critically important in the neurodegenerative process.",0
"measurements have been made of cytoplasmic ph, (phi) and free mg2+ concentration, ( i), in pig and mouse lymphocytes. phi was measured in four ways: by a digitonin null-point technique; by direct measurement of the ph of freeze-thawed cell pellets; from the 31p nuclear magnetic resonance (nmr) spectrum of intracellular inorganic phosphate; and by the use of a newly synthesized, intracellularly-trappable fluorescent ph indicator. in hepes buffered physiological saline with ph 7.4 at 37 degrees c, phi was close to 7.0. addition of physiological levels of hco3- and co2 transiently acidified the cells by approximately 0.1 u. mitogenic concentrations of concanavalin a (con a) had no measurable effect on ph in the first hour. i was assessed in three ways: (a) from the external mg2+ null-point at which the ionophore a23187 produced no net movement of mg2+ or h+; (b) by mg-sensitive electrode measurements in freeze-thawed pellets; and (c) from the 31p nuclear magnetic resonance spectrum of the gamma-phosphate of intracellular atp. total cell mg2+ was approximately 12 mmol per liter cell water. the nmr data indicated i greater than 0.5 mm. the null-point method gave i approximately 0.9 nm. the electrode measurements gave 1.35 mm, which was thought to be an overestimate. exposure to mitogenic doses of con a for 1 h gave no detectable change in total or free mg2+.",0
"we evaluated the performance of a large language model called chatgpt on the united states medical licensing exam (usmle), which consists of three exams: step 1, step 2ck, and step 3. chatgpt performed at or near the passing threshold for all three exams without any specialized training or reinforcement. additionally, chatgpt demonstrated a high level of concordance and insight in its explanations. these results suggest that large language models may have the potential to assist with medical education, and potentially, clinical decision-making.",0
"tolerance is the usual outcome of inhalation of harmless antigen, yet t helper (th) type 2 cell sensitization to inhaled allergens induced by dendritic cells (dcs) is common in atopic asthma. here, we show that both myeloid (m) and plasmacytoid (p) dcs take up inhaled antigen in the lung and present it in an immunogenic or tolerogenic form to draining node t cells. strikingly, depletion of pdcs during inhalation of normally inert antigen led to immunoglobulin e sensitization, airway eosinophilia, goblet cell hyperplasia, and th2 cell cytokine production, cardinal features of asthma. furthermore, adoptive transfer of pdcs before sensitization prevented disease in a mouse asthma model. on a functional level, pdcs did not induce t cell division but suppressed the generation of effector t cells induced by mdcs. these studies show that pdcs provide intrinsic protection against inflammatory responses to harmless antigen. therapies exploiting pdc function might be clinically effective in preventing the development of asthma.",0
"amazon mechanical turk (amt) is an online crowdsourcing service where anonymous online workers complete web-based tasks for small sums of money. the service has attracted attention from experimental psychologists interested in gathering human subject data more efficiently. however, relative to traditional laboratory studies, many aspects of the testing environment are not under the experimenter's control. in this paper, we attempt to empirically evaluate the fidelity of the amt system for use in cognitive behavioral experiments. these types of experiment differ from simple surveys in that they require multiple trials, sustained attention from participants, comprehension of complex instructions, and millisecond accuracy for response recording and stimulus presentation. we replicate a diverse body of tasks from experimental psychology including the stroop, switching, flanker, simon, posner cuing, attentional blink, subliminal priming, and category learning tasks using participants recruited using amt. while most of replications were qualitatively successful and validated the approach of collecting data anonymously online using a web-browser, others revealed disparity between laboratory results and online results. a number of important lessons were encountered in the process of conducting these replications that should be of value to other researchers.",0
"we describe a framework for defining pilot and feasibility studies focusing on studies conducted in preparation for a randomised controlled trial. to develop the framework, we undertook a delphi survey; ran an open meeting at a trial methodology conference; conducted a review of definitions outside the health research context; consulted experts at an international consensus meeting; and reviewed 27 empirical pilot or feasibility studies. we initially adopted mutually exclusive definitions of pilot and feasibility studies. however, some delphi survey respondents and the majority of open meeting attendees disagreed with the idea of mutually exclusive definitions. their viewpoint was supported by definitions outside the health research context, the use of the terms 'pilot' and 'feasibility' in the literature, and participants at the international consensus meeting. in our framework, pilot studies are a subset of feasibility studies, rather than the two being mutually exclusive. a feasibility study asks whether something can be done, should we proceed with it, and if so, how. a pilot study asks the same questions but also has a specific design feature: in a pilot study a future study, or part of a future study, is conducted on a smaller scale. we suggest that to facilitate their identification, these studies should be clearly identified using the terms 'feasibility' or 'pilot' as appropriate. this should include feasibility studies that are largely qualitative; we found these difficult to identify in electronic searches because researchers rarely used the term 'feasibility' in the title or abstract of such studies. investigators should also report appropriate objectives and methods related to feasibility; and give clear confirmation that their study is in preparation for a future randomised controlled trial designed to assess the effect of an intervention.",0
"there is growing recognition of the role of diet and other environmental factors in modulating the composition and metabolic activity of the human gut microbiota, which in turn can impact health. this narrative review explores the relevant contemporary scientific literature to provide a general perspective of this broad area. molecular technologies have greatly advanced our understanding of the complexity and diversity of the gut microbial communities within and between individuals. diet, particularly macronutrients, has a major role in shaping the composition and activity of these complex populations. despite the body of knowledge that exists on the effects of carbohydrates there are still many unanswered questions. the impacts of dietary fats and protein on the gut microbiota are less well defined. both short- and long-term dietary change can influence the microbial profiles, and infant nutrition may have life-long consequences through microbial modulation of the immune system. the impact of environmental factors, including aspects of lifestyle, on the microbiota is particularly poorly understood but some of these factors are described. we also discuss the use and potential benefits of prebiotics and probiotics to modify microbial populations. a description of some areas that should be addressed in future research is also presented.",0
"our decisions are guided by information learnt from our environment. this information may come via personal experiences of reward, but also from the behaviour of social partners. social learning is widely held to be distinct from other forms of learning in its mechanism and neural implementation; it is often assumed to compete with simpler mechanisms, such as reward-based associative learning, to drive behaviour. recently, neural signals have been observed during social exchange reminiscent of signals seen in studies of associative learning. here we demonstrate that social information may be acquired using the same associative processes assumed to underlie reward-based learning. we find that key computational variables for learning in the social and reward domains are processed in a similar fashion, but in parallel neural processing streams. two neighbouring divisions of the anterior cingulate cortex were central to learning about social and reward-based information, and for determining the extent to which each source of information guides behaviour. when making a decision, however, the information learnt using these parallel streams was combined within ventromedial prefrontal cortex. these findings suggest that human social valuation can be realized by means of the same associative processes previously established for learning other, simpler, features of the environment.",0
"two new sars-cov-2 lineages with the n501y mutation in the receptor-binding domain of the spike protein spread rapidly in the united kingdom. we estimated that the earlier 501y lineage without amino acid deletion δ69/δ70, circulating mainly between early september and mid-november, was 10% (6-13%) more transmissible than the 501n lineage, and the 501y lineage with amino acid deletion δ69/δ70, circulating since late september, was 75% (70-80%) more transmissible than the 501n lineage.",0
"background convalescent plasma is frequently administered to patients with covid-19 and has been reported, largely on the basis of observational data, to improve clinical outcomes. minimal data are available from adequately powered randomized, controlled trials. methods we randomly assigned hospitalized adult patients with severe covid-19 pneumonia in a 2:1 ratio to receive convalescent plasma or placebo. the primary outcome was the patient's clinical status 30 days after the intervention, as measured on a six-point ordinal scale ranging from total recovery to death. results a total of 228 patients were assigned to receive convalescent plasma and 105 to receive placebo. the median time from the onset of symptoms to enrollment in the trial was 8 days (interquartile range, 5 to 10), and hypoxemia was the most frequent severity criterion for enrollment. the infused convalescent plasma had a median titer of 1:3200 of total sars-cov-2 antibodies (interquartile range, 1:800 to 1:3200). no patients were lost to follow-up. at day 30 day, no significant difference was noted between the convalescent plasma group and the placebo group in the distribution of clinical outcomes according to the ordinal scale (odds ratio, 0.83; 95% confidence interval , 0.52 to 1.35; p = 0.46). overall mortality was 10.96% in the convalescent plasma group and 11.43% in the placebo group, for a risk difference of -0.46 percentage points (95% ci, -7.8 to 6.8). total sars-cov-2 antibody titers tended to be higher in the convalescent plasma group at day 2 after the intervention. adverse events and serious adverse events were similar in the two groups. conclusions no significant differences were observed in clinical status or overall mortality between patients treated with convalescent plasma and those who received placebo. (plasmar clinicaltrials.gov number, nct04383535.).",0
"most life science processes involve, at the atomic scale, recognition between two molecules. the prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. docking programs have a wide range of applications ranging from protein engineering to drug design. this article presents swissdock, a web server dedicated to the docking of small molecules on target proteins. it is based on the eadock dss engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. an efficient ajax/html interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. for automated docking tasks, a programmatic soap interface has been set up and template programs can be downloaded in perl, python and php. the web site also provides an access to a database of manually curated complexes, based on the ligand protein database. a wiki and a forum are available to the community to promote interactions between users. the swissdock web site is available online at we believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.",0
"background the covid-19 pandemic is having negative effects on societies' mental health. both the pandemic and the measures taken to combat it can affect individuals' mental health. aims the purpose of this study was to evaluate the levels of depression, anxiety and health anxiety in turkish society during the covid-19 pandemic, and to examine the factors affecting these. method the study was performed using an online questionnaire. participants were asked to complete a sociodemographic data form, the hospital anxiety and depression scale (hads) and the health anxiety inventory (hai). the effects on depression, anxiety and health anxiety levels of factors such as age, sex, marital status, living with an individual aged above 60, the presence of a new coronavirus+ patient among friends or relatives, previous and current psychiatric illness and presence of accompanying chronic disease were then investigated. results in terms of hads cut-off points, 23.6% ( n = 81) of the population scored above the depression cut-off point, and 45.1% ( n = 155) scored above the cut-off point for anxiety. in regression analysis, female gender, living in urban areas and previous psychiatric illness history were found as risk factors for anxiety; living in urban areas was found as risk factor for depression; and female gender, accompanying chronic disease and previous psychiatric history were found as risk factors for health anxiety. conclusion the results of this cross-sectional study suggest that the groups most psychologically affected by the covid-19 pandemic are women, individuals with previous psychiatric illness, individuals living in urban areas and those with an accompanying chronic disease. priority might therefore be attached to these in future psychiatric planning.",0
"several coronavirus disease 2019 (covid-19) vaccines are currently in human trials. in june 2020, we surveyed 13,426 people in 19 countries to determine potential acceptance rates and factors influencing acceptance of a covid-19 vaccine. of these, 71.5% of participants reported that they would be very or somewhat likely to take a covid-19 vaccine, and 48.1% reported that they would accept their employer's recommendation to do so. differences in acceptance rates ranged from almost 90% (in china) to less than 55% (in russia). respondents reporting higher levels of trust in information from government sources were more likely to accept a vaccine and take their employer's advice to do so.",0
"exacerbations of chronic obstructive pulmonary disease (copd) are episodes of worsening of symptoms, leading to substantial morbidity and mortality. copd exacerbations are associated with increased airway and systemic inflammation and physiological changes, especially the development of hyperinflation. they are triggered mainly by respiratory viruses and bacteria, which infect the lower airway and increase airway inflammation. some patients are particularly susceptible to exacerbations, and show worse health status and faster disease progression than those who have infrequent exacerbations. several pharmacological interventions are effective for the reduction of exacerbation frequency and severity in copd such as inhaled steroids, long-acting bronchodilators, and their combinations. non-pharmacological therapies such as pulmonary rehabilitation, self-management, and home ventilatory support are becoming increasingly important, but still need to be studied in controlled trials. the future of exacerbation prevention is in assessment of optimum combinations of pharmacological and non-pharmacological therapies that will result in improvement of health status, and reduction of hospital admission and mortality associated with copd.",0
"background reliable prediction of antibody, or b-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. a correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. subsequently, thornton and colleagues proposed a method for identifying continuous epitopes in the protein regions protruding from the protein's globular surface. the aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes. results here we present ellipro, a web-tool that implements thornton's method and, together with a residue clustering algorithm, the modeller program and the jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. ellipro has been tested on a benchmark dataset of discontinuous epitopes inferred from 3d structures of antibody-protein complexes. in comparison with six other structure-based methods that can be used for epitope prediction, ellipro performed the best and gave an auc value of 0.732, when the most significant prediction was considered for each protein. since the rank of the best prediction was at most in the top three for more than 70% of proteins and never exceeded five, ellipro is considered a useful research tool for identifying antibody epitopes in protein antigens. ellipro is available at conclusion the results from ellipro suggest that further research on antibody epitopes considering more features that discriminate epitopes from non-epitopes may further improve predictions. as ellipro is based on the geometrical properties of protein structure and does not require training, it might be more generally applied for predicting different types of protein-protein interactions.",0
"background the rapid growth in the use of mobile phone applications (apps) provides the opportunity to increase access to evidence-based mental health care. objective our goal was to systematically review the research evidence supporting the efficacy of mental health apps for mobile devices (such as smartphones and tablets) for all ages. methods a comprehensive literature search (2008-2013) in medline, embase, the cochrane central register of controlled trials, psycinfo, psyctests, compendex, and inspec was conducted. we included trials that examined the effects of mental health apps (for depression, anxiety, substance use, sleep disturbances, suicidal behavior, self-harm, psychotic disorders, eating disorders, stress, and gambling) delivered on mobile devices with a pre- to posttest design or compared with a control group. the control group could consist of wait list, treatment-as-usual, or another recognized treatment. results in total, 5464 abstracts were identified. of those, 8 papers describing 5 apps targeting depression, anxiety, and substance abuse met the inclusion criteria. four apps provided support from a mental health professional. results showed significant reductions in depression, stress, and substance use. within-group and between-group intention-to-treat effect sizes ranged from 0.29-2.28 and 0.01-0.48 at posttest and follow-up, respectively. conclusions mental health apps have the potential to be effective and may significantly improve treatment accessibility. however, the majority of apps that are currently available lack scientific evidence about their efficacy. the public needs to be educated on how to identify the few evidence-based mental health apps available in the public domain to date. further rigorous research is required to develop and test evidence-based programs. given the small number of studies and participants included in this review, the high risk of bias, and unknown efficacy of long-term follow-up, current findings should be interpreted with caution, pending replication. two of the 5 evidence-based mental health apps are currently commercially available in app stores.",0
"background alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. with our comprehensive approach to health accounting within the global burden of diseases, injuries, and risk factors study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (dalys) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older. methods using 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and dalys. we made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health. findings globally, alcohol use was the seventh leading risk factor for both deaths and dalys in 2016, accounting for 2·2% (95% uncertainty interval 1·5-3·0) of age-standardised female deaths and 6·8% (5·8-8·0) of age-standardised male deaths. among the population aged 15-49 years, alcohol use was the leading risk factor globally in 2016, with 3·8% (95% ui 3·2-4·3) of female deaths and 12·2% (10·8-13·6) of male deaths attributable to alcohol use. for the population aged 15-49 years, female attributable dalys were 2·3% (95% ui 2·0-2·6) and male attributable dalys were 8·9% (7·8-9·9). the three leading causes of attributable deaths in this age group were tuberculosis (1·4% of total deaths), road injuries (1·2% ), and self-harm (1·1% ). for populations aged 50 years and older, cancers accounted for a large proportion of total alcohol-attributable deaths in 2016, constituting 27·1% (95% ui 21·2-33·3) of total alcohol-attributable female deaths and 18·9% (15·3-22·6) of male deaths. the level of alcohol consumption that minimised harm across health outcomes was zero (95% ui 0·0-0·8) standard drinks per week. interpretation alcohol use is a leading risk factor for global disease burden and causes substantial health loss. we found that the risk of all-cause mortality, and of cancers specifically, rises with increasing levels of consumption, and the level of consumption that minimises health loss is zero. these results suggest that alcohol control policies might need to be revised worldwide, refocusing on efforts to lower overall population-level consumption. funding bill & melinda gates foundation.",0
"a new technique employing continuous recirculating perfusion of the rat liver in situ, shaking of the liver in buffer in vitro, and filtration of the tissue through nylon mesh, results in the conversion of about 50% of the liver into intact, isolated parenchymal cells. the perfusion media consist of: (a) calcium-free hanks' solution containing 0.05% collagenase and 0.10% hyaluronidase, and (b) magnesium and calcium-free hanks' solution containing 2 mm ethylenediaminetetraacetate. biochemical and morphologic studies indicate that the isolated cells are viable. they respire in a medium containing calcium ions, synthesize glucose from lactate, are impermeable to inulin, do not stain with trypan blue, and retain their structural integrity. electron microscopy of biopsies taken during and after perfusion reveals that desmosomes are quickly cleaved. hemidesmosome-containing areas of the cell membrane invaginate and appear to pinch off and migrate centrally. tight and gap junctions, however, persist on the intact, isolated cells, retaining small segments of cytoplasm from formerly apposing parenchymal cells. cells which do not retain tight and gap junctions display swelling of golgi vacuoles and vacuoles in the peripheral cytoplasm. cytoplasmic vacuolization in a small percentage of cells and potassium loss are the only indications of cell injury detected. by other parameters measured, the isolated cells are comparable to normal hepatic parenchymal cells in situ in appearance and function.",0
"tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. to date, the approach has not been systematically validated in ground truth studies. based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent). however, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups. taken together, our results demonstrate and confirm fundamental ambiguities inherent in tract reconstruction based on orientation information alone, which need to be considered when interpreting tractography and connectivity results. our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.",0
"background neonatal interventions are largely focused on reduction of mortality and progression towards millennium development goal 4 (child survival). however, little is known about the global burden of long-term consequences of intrauterine and neonatal insults. we did a systematic review to estimate risks of long-term neurocognitive and other sequelae after intrauterine and neonatal insults, especially in low-income and middle-income countries. methods we searched medline, cumulative index to nursing and allied health literature, the cochrane library, and embase for studies published between jan 1, 1966, and june 30, 2011, that reported neurodevelopmental sequelae after preterm or neonatal insult. for unpublished studies and grey literature, we searched dissertation abstracts international and the who library. we reviewed publications that had data for long-term outcome after defined neonatal insults. we summarised the results with medians and iqrs, and calculated the risk of at least one sequela after insult. findings of 28,212 studies identified by our search, 153 studies were suitable for inclusion, documenting 22,161 survivors of intrauterine or neonatal insults. the overall median risk of at least one sequela in any domain was 39·4% (iqr 20·0-54·8), with a risk of at least one severe impairment in any insult domain of 18·5% (7·7-33·3), of at least one moderate impairment of 5·0% (0·0-13·3%), and of at least one mild impairment of 10·0% (1·4-17·9%). the pooled risk estimate of at least one sequela (weighted mean) associated with one or more of the insults studied (excluding hiv) was 37·0% (95% ci 27·0-48·0%) and this risk was not significantly affected by region, duration of the follow-up, study design, or period of data collection. the most common sequelae were learning difficulties, cognition, or developmental delay (n=4032; 59%); cerebral palsy (n=1472; 21%); hearing impairment (n=1340; 20%); and visual impairment (n=1228; 18%). only 40 (26%) studies included data for multidomain impairments. these studies included 2815 individuals, of whom 1048 (37%) had impairments, with 334 (32%) having multiple impairments. interpretation intrauterine and neonatal insults have a high risk of causing substantial long-term neurological morbidity. comparable cohort studies in resource-poor regions should be done to properly assess the burden of these conditions, and long-term outcomes, such as chronic disease, and to inform policy and programme investments. funding the bill & melinda gates foundation, saving newborn lives, and the wellcome trust.",0
"unlabelled a motif is a short dna or protein sequence that contributes to the biological function of the sequence in which it resides. over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix. results we describe find individual motif occurrences (fimo), a software tool for scanning dna or protein sequences with motifs described as position-specific scoring matrices. the program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a p-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. fimo provides output in a variety of formats, including html, xml and several santa cruz genome browser formats. the program is efficient, allowing for the scanning of dna sequences at a rate of 3.5 mb/s on a single cpu. availability and implementation fimo is part of the meme suite software toolkit. a web server and source code are available at",0
"the predictive value of kras mutation in metastatic colorectal cancer (mcrc) patients treated with cetuximab plus chemotherapy has recently been suggested. in our study, 59 patients with a chemotherapy-refractory mcrc treated with cetuximab plus chemotherapy were included and clinical response was evaluated according to response evaluation criteria in solid tumours (recist). tumours were screened for kras mutations using first direct sequencing, then two sensitive methods based on snapshot and pcr-ligase chain reaction (lcr) assays. clinical response was evaluated according to gene mutations using the fisher exact test. times to progression (ttp) were calculated using the kaplan-meier method and compared with log-rank test. a kras mutation was detected in 22 out of 59 tumours and, in six cases, was missed by sequencing analysis but detected using the snapshot and pcr-lcr assays. remarkably, no kras mutation was found in the 12 patients with clinical response. kras mutation was associated with disease progression (p=0.0005) and ttp was significantly decreased in mutated kras patients (3 vs 5.5 months, p=0.015). our study confirms that kras mutation is highly predictive of a non-response to cetuximab plus chemotherapy in mcrc and highlights the need to use sensitive molecular methods, such as snapshot or pcr-lcr assays, to ensure an efficient mutation detection.",0
"single nucleotide polymorphism (snp) discovery and genotyping are essential to genetic mapping. there remains a need for a simple, inexpensive platform that allows high-density snp discovery and genotyping in large populations. here we describe the sequencing of restriction-site associated dna (rad) tags, which identified more than 13,000 snps, and mapped three traits in two model organisms, using less than half the capacity of one illumina sequencing run. we demonstrated that different marker densities can be attained by choice of restriction enzyme. furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in f(2) individuals. barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. to further demonstrate the ease of the rad sequencing approach we identified polymorphic markers and mapped an induced mutation in neurospora crassa. sequencing of rad markers is an integrated platform for snp discovery and genotyping. this approach should be widely applicable to genetic mapping in a variety of organisms.",0
"implementation strategies have unparalleled importance in implementation science, as they constitute the 'how to' component of changing healthcare practice. yet, implementation researchers and other stakeholders are not able to fully utilize the findings of studies focusing on implementation strategies because they are often inconsistently labelled and poorly described, are rarely justified theoretically, lack operational definitions or manuals to guide their use, and are part of 'packaged' approaches whose specific elements are poorly understood. we address the challenges of specifying and reporting implementation strategies encountered by researchers who design, conduct, and report research on implementation strategies. specifically, we propose guidelines for naming, defining, and operationalizing implementation strategies in terms of seven dimensions: actor, the action, action targets, temporality, dose, implementation outcomes addressed, and theoretical justification. ultimately, implementation strategies cannot be used in practice or tested in research without a full description of their components and how they should be used. as with all intervention research, their descriptions must be precise enough to enable measurement and 'reproducibility.' we propose these recommendations to improve the reporting of implementation strategies in research studies and to stimulate further identification of elements pertinent to implementation strategies that should be included in reporting guidelines for implementation strategies.",0
"plasmodb ( is a functional genomic database for plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. plasmodb belongs to a family of genomic resources that are housed under the eupathdb ( bioinformatics resource center (brc) umbrella. the latest release, plasmodb 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. data in plasmodb can be queried by selecting the data of interest from a query grid or drop down menus. various results can then be combined with each other on the query history page. search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.",0
"motivation the emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. the next revolution came with the era of long-read sequencing. these technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. results in this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. to evaluate the results, we developed quast-lg-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. using quast-lg, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference. availability and implementation supplementary information supplementary data are available at bioinformatics online.",0
"this paper provides guidelines for performing mendelian randomization investigations. it is aimed at practitioners seeking to undertake analyses and write up their findings, and at journal editors and reviewers seeking to assess mendelian randomization manuscripts. the guidelines are divided into ten sections: motivation and scope, data sources, choice of genetic variants, variant harmonization, primary analysis, supplementary and sensitivity analyses (one section on robust statistical methods and one on other approaches), extensions and additional analyses, data presentation, and interpretation. these guidelines will be updated based on feedback from the community and advances in the field. updates will be made periodically as needed, and at least every 24 months.",0
"beta-thalassemias are a group of hereditary blood disorders characterized by anomalies in the synthesis of the beta chains of hemoglobin resulting in variable phenotypes ranging from severe anemia to clinically asymptomatic individuals. the total annual incidence of symptomatic individuals is estimated at 1 in 100,000 throughout the world and 1 in 10,000 people in the european union. three main forms have been described: thalassemia major, thalassemia intermedia and thalassemia minor. individuals with thalassemia major usually present within the first two years of life with severe anemia, requiring regular red blood cell (rbc) transfusions. findings in untreated or poorly transfused individuals with thalassemia major, as seen in some developing countries, are growth retardation, pallor, jaundice, poor musculature, hepatosplenomegaly, leg ulcers, development of masses from extramedullary hematopoiesis, and skeletal changes that result from expansion of the bone marrow. regular transfusion therapy leads to iron overload-related complications including endocrine complication (growth retardation, failure of sexual maturation, diabetes mellitus, and insufficiency of the parathyroid, thyroid, pituitary, and less commonly, adrenal glands), dilated myocardiopathy, liver fibrosis and cirrhosis). patients with thalassemia intermedia present later in life with moderate anemia and do not require regular transfusions. main clinical features in these patients are hypertrophy of erythroid marrow with medullary and extramedullary hematopoiesis and its complications (osteoporosis, masses of erythropoietic tissue that primarily affect the spleen, liver, lymph nodes, chest and spine, and bone deformities and typical facial changes), gallstones, painful leg ulcers and increased predisposition to thrombosis. thalassemia minor is clinically asymptomatic but some subjects may have moderate anemia. beta-thalassemias are caused by point mutations or, more rarely, deletions in the beta globin gene on chromosome 11, leading to reduced (beta+) or absent (beta0) synthesis of the beta chains of hemoglobin (hb). transmission is autosomal recessive; however, dominant mutations have also been reported. diagnosis of thalassemia is based on hematologic and molecular genetic testing. differential diagnosis is usually straightforward but may include genetic sideroblastic anemias, congenital dyserythropoietic anemias, and other conditions with high levels of hbf (such as juvenile myelomonocytic leukemia and aplastic anemia). genetic counseling is recommended and prenatal diagnosis may be offered. treatment of thalassemia major includes regular rbc transfusions, iron chelation and management of secondary complications of iron overload. in some circumstances, spleen removal may be required. bone marrow transplantation remains the only definitive cure currently available. individuals with thalassemia intermedia may require splenectomy, folic acid supplementation, treatment of extramedullary erythropoietic masses and leg ulcers, prevention and therapy of thromboembolic events. prognosis for individuals with beta-thalassemia has improved substantially in the last 20 years following recent medical advances in transfusion, iron chelation and bone marrow transplantation therapy. however, cardiac disease remains the main cause of death in patients with iron overload.",0
"the uncontrolled spread of the coronavirus disease 2019 (covid-19) has called for unprecedented measures, to the extent that the italian government has imposed a quarantine on the entire country. quarantine has a huge impact and can cause considerable psychological strain. the present study aims to establish the prevalence of psychiatric symptoms and identify risk and protective factors for psychological distress in the general population. an online survey was administered from 18-22 march 2020 to 2766 participants. multivariate ordinal logistic regression models were constructed to examine the associations between sociodemographic variables; personality traits; depression, anxiety, and stress. female gender, negative affect, and detachment were associated with higher levels of depression, anxiety, and stress. having an acquaintance infected was associated with increased levels of both depression and stress, whereas a history of stressful situations and medical problems was associated with higher levels of depression and anxiety. finally, those with a family member infected and young person who had to work outside their domicile presented higher levels of anxiety and stress, respectively. this epidemiological picture is an important benchmark for identifying persons at greater risk of suffering from psychological distress and the results are useful for tailoring psychological interventions targeting the post-traumatic nature of the distress.",0
"multiple, segregated fronto-cerebellar circuits have been characterized in nonhuman primates using transneuronal tracing techniques including those that target prefrontal areas. here, we used functional connectivity mri (fcmri) in humans (n = 40) to identify 4 topographically distinct fronto-cerebellar circuits that target 1) motor cortex, 2) dorsolateral prefrontal cortex, 3) medial prefrontal cortex, and 4) anterior prefrontal cortex. all 4 circuits were replicated and dissociated in an independent data set (n = 40). direct comparison of right- and left-seeded frontal regions revealed contralateral lateralization in the cerebellum for each of the segregated circuits. the presence of circuits that involve prefrontal regions confirms that the cerebellum participates in networks important to cognition including a specific fronto-cerebellar circuit that interacts with the default network. overall, the extent of the cerebellum associated with prefrontal cortex included a large portion of the posterior hemispheres consistent with a prominent role of the cerebellum in nonmotor functions. we conclude by providing a provisional map of the topography of the cerebellum based on functional correlations with the frontal cortex.",0
"background this study aims to examine the worldwide prevalence of post-coronavirus disease 2019 (covid-19) condition, through a systematic review and meta-analysis. methods pubmed, embase, and isearch were searched on july 5, 2021 with verification extending to march 13, 2022. using a random-effects framework with dersimonian-laird estimator, we meta-analyzed post-covid-19 condition prevalence at 28+ days from infection. results fifty studies were included, and 41 were meta-analyzed. global estimated pooled prevalence of post-covid-19 condition was 0.43 (95% confidence interval , .39-.46). hospitalized and nonhospitalized patients had estimates of 0.54 (95% ci, .44-.63) and 0.34 (95% ci, .25-.46), respectively. regional prevalence estimates were asia (0.51; 95% ci, .37-.65), europe (0.44; 95% ci, .32-.56), and united states of america (0.31; 95% ci, .21-.43). global prevalence for 30, 60, 90, and 120 days after infection were estimated to be 0.37 (95% ci, .26-.49), 0.25 (95% ci, .15-.38), 0.32 (95% ci, .14-.57), and 0.49 (95% ci, .40-.59), respectively. fatigue was the most common symptom reported with a prevalence of 0.23 (95% ci, .17-.30), followed by memory problems (0.14; 95% ci, .10-.19). conclusions this study finds post-covid-19 condition prevalence is substantial; the health effects of covid-19 seem to be prolonged and can exert stress on the healthcare system.",0
"background reading skills are important for accessing health information, using health care services, managing one's health and achieving desirable health outcomes. our objective was to assess the diagnostic accuracy of the single item literacy screener (sils) to identify limited reading ability, one component of health literacy, as measured by the s-tofhla. methods cross-sectional interview with 999 adults with diabetes residing in vermont and bordering states. participants were randomly recruited from primary care practices in the vermont diabetes information system june 2003-december 2004. the main outcome was limited reading ability. the primary predictor was the sils. results of the 999 persons screened, 169 (17%) had limited reading ability. the sensitivity of the sils in detecting limited reading ability was 54% and the specificity was 83% with an area under the receiver operating characteristics curve (roc) of 0.73 . seven hundred seventy (77%) screened negative on the sils and 692 of these subjects had adequate reading skills (negative predictive value = 0.90 ). of the 229 who scored positive on the sils, 92 had limited reading ability (positive predictive value = 0.4 ). conclusion the sils is a simple instrument designed to identify patients with limited reading ability who need help reading health-related materials. the sils performs moderately well at ruling out limited reading ability in adults and allows providers to target additional assessment of health literacy skills to those most in need. further study of the use of the sils in clinical settings and with more diverse populations is warranted.",0
"background low-dose aspirin is of definite and substantial net benefit for many people who already have occlusive vascular disease. we have assessed the benefits and risks in primary prevention. methods we undertook meta-analyses of serious vascular events (myocardial infarction, stroke, or vascular death) and major bleeds in six primary prevention trials (95,000 individuals at low average risk, 660,000 person-years, 3554 serious vascular events) and 16 secondary prevention trials (17,000 individuals at high average risk, 43,000 person-years, 3306 serious vascular events) that compared long-term aspirin versus control. we report intention-to-treat analyses of first events during the scheduled treatment period. findings in the primary prevention trials, aspirin allocation yielded a 12% proportional reduction in serious vascular events (0.51% aspirin vs 0.57% control per year, p=0.0001), due mainly to a reduction of about a fifth in non-fatal myocardial infarction (0.18%vs 0.23% per year, p interpretation in primary prevention without previous disease, aspirin is of uncertain net value as the reduction in occlusive events needs to be weighed against any increase in major bleeds. further trials are in progress. funding uk medical research council, british heart foundation, cancer research uk, and the european community biomed programme.",0
"much biomedical research is observational. the reporting of such research is often inadequate, which hampers the assessment of its strengths and weaknesses and of a study's generalisability. the strengthening the reporting of observational studies in epidemiology (strobe) initiative developed recommendations on what should be included in an accurate and complete report of an observational study. we defined the scope of the recommendations to cover three main study designs: cohort, case-control, and cross-sectional studies. we convened a 2-day workshop in september 2004, with methodologists, researchers, and journal editors to draft a checklist of items. this list was subsequently revised during several meetings of the coordinating group and in e-mail discussions with the larger group of strobe contributors, taking into account empirical evidence and methodological considerations. the workshop and the subsequent iterative process of consultation and revision resulted in a checklist of 22 items (the strobe statement) that relate to the title, abstract, introduction, methods, results, and discussion sections of articles. 18 items are common to all three study designs and four are specific for cohort, case-control, or cross-sectional studies. a detailed explanation and elaboration document is published separately and is freely available on the web sites of plos medicine, annals of internal medicine, and epidemiology. we hope that the strobe statement will contribute to improving the quality of reporting of observational studies.",0
"here, we describe two freely available web servers for molecular docking. the patchdock method performs structure prediction of protein-protein and protein-small molecule complexes. the symmdock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. the inputs to the servers are either protein pdb codes or uploaded protein structures. the services are available at the methods behind the servers are very efficient, allowing large-scale docking experiments.",0
"motivation sequence-based methods to delimit species are central to dna taxonomy, microbial community surveys and dna metabarcoding studies. current approaches either rely on simple sequence similarity thresholds (otu-picking) or on complex and compute-intensive evolutionary models. the otu-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. coalescent-based species delimitation approaches often rely on bayesian statistics and markov chain monte carlo sampling, and can therefore only be applied to small datasets. results we introduce the poisson tree processes (ptp) model to infer putative species boundaries on a given phylogenetic input tree. we also integrate ptp with our evolutionary placement algorithm (epa-ptp) to count the number of species in phylogenetic placements. we compare our approaches with popular otu-picking methods and the general mixed yule coalescent (gmyc) model. for de novo species delimitation, the stand-alone ptp model generally outperforms gymc as well as otu-picking methods when evolutionary distances between species are small. ptp neither requires an ultrametric input tree nor a sequence similarity threshold as input. in the open reference species delimitation approach, epa-ptp yields more accurate results than de novo species delimitation methods. finally, epa-ptp scales on large datasets because it relies on the parallel implementations of the epa and raxml, thereby allowing to delimit species in high-throughput sequencing data. availability and implementation the code is freely available at .",0
"the interpro database ( classifies protein sequences into families and predicts the presence of functionally important domains and sites. here, we report recent developments with interpro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new interpro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. these developments extend and enrich the information provided by interpro, and provide greater flexibility in terms of data access. we also show that interpro's sequence coverage has kept pace with the growth of uniprotkb, and discuss how our evaluation of residue coverage may help guide future curation activities.",0
"we present a new update to metaboanalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. since the last major update in 2015, metaboanalyst has continued to evolve based on user feedback and technological advancements in the field. for this year's update, four new key features have been added to metaboanalyst 4.0, including: (1) real-time r command tracking and display coupled with the release of a companion metaboanalystr package; (2) a ms peaks to pathways module for prediction of pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a biomarker meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a network explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. the user interface of metaboanalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. the underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the human metabolome database (hmdb). a docker image of metaboanalyst is also available to facilitate download and local installation of metaboanalyst. metaboanalyst 4.0 is freely available at",0
"background global development goals increasingly rely on country-specific estimates for benchmarking a nation's progress. to meet this need, the global burden of diseases, injuries, and risk factors study (gbd) 2016 estimated global, regional, national, and, for selected locations, subnational cause-specific mortality beginning in the year 1980. here we report an update to that study, making use of newly available data and improved methods. gbd 2017 provides a comprehensive assessment of cause-specific mortality for 282 causes in 195 countries and territories from 1980 to 2017. methods the causes of death database is composed of vital registration (vr), verbal autopsy (va), registry, survey, police, and surveillance data. gbd 2017 added ten va studies, 127 country-years of vr data, 502 cancer-registry country-years, and an additional surveillance country-year. expansions of the gbd cause of death hierarchy resulted in 18 additional causes estimated for gbd 2017. newly available data led to subnational estimates for five additional countries-ethiopia, iran, new zealand, norway, and russia. deaths assigned international classification of diseases (icd) codes for non-specific, implausible, or intermediate causes of death were reassigned to underlying causes by redistribution algorithms that were incorporated into uncertainty estimation. we used statistical modelling tools developed for gbd, including the cause of death ensemble model (codem), to generate cause fractions and cause-specific death rates for each location, year, age, and sex. instead of using un estimates as in previous versions, gbd 2017 independently estimated population size and fertility rate for all locations. years of life lost (ylls) were then calculated as the sum of each death multiplied by the standard life expectancy at each age. all rates reported here are age-standardised. findings at the broadest grouping of causes of death (level 1), non-communicable diseases (ncds) comprised the greatest fraction of deaths, contributing to 73·4% (95% uncertainty interval 72·5-74·1) of total deaths in 2017, while communicable, maternal, neonatal, and nutritional (cmnn) causes accounted for 18·6% (17·9-19·6), and injuries 8·0% (7·7-8·2). total numbers of deaths from ncd causes increased from 2007 to 2017 by 22·7% (21·5-23·9), representing an additional 7·61 million (7·20-8·01) deaths estimated in 2017 versus 2007. the death rate from ncds decreased globally by 7·9% (7·0-8·8). the number of deaths for cmnn causes decreased by 22·2% (20·0-24·0) and the death rate by 31·8% (30·1-33·3). total deaths from injuries increased by 2·3% (0·5-4·0) between 2007 and 2017, and the death rate from injuries decreased by 13·7% (12·2-15·1) to 57·9 deaths (55·9-59·2) per 100 000 in 2017. deaths from substance use disorders also increased, rising from 284 000 deaths (268 000-289 000) globally in 2007 to 352 000 (334 000-363 000) in 2017. between 2007 and 2017, total deaths from conflict and terrorism increased by 118·0% (88·8-148·6). a greater reduction in total deaths and death rates was observed for some cmnn causes among children younger than 5 years than for older adults, such as a 36·4% (32·2-40·6) reduction in deaths from lower respiratory infections for children younger than 5 years compared with a 33·6% (31·2-36·1) increase in adults older than 70 years. globally, the number of deaths was greater for men than for women at most ages in 2017, except at ages older than 85 years. trends in global ylls reflect an epidemiological transition, with decreases in total ylls from enteric infections, respiratory infections and tuberculosis, and maternal and neonatal disorders between 1990 and 2017; these were generally greater in magnitude at the lowest levels of the socio-demographic index (sdi). at the same time, there were large increases in ylls from neoplasms and cardiovascular diseases. yll rates decreased across the five leading level 2 causes in all sdi quintiles. the leading causes of ylls in 1990-neonatal disorders, lower respiratory infections, and diarrhoeal diseases-were ranked second, fourth, and fifth, in 2017. meanwhile, estimated ylls increased for ischaemic heart disease (ranked first in 2017) and stroke (ranked third), even though yll rates decreased. population growth contributed to increased total deaths across the 20 leading level 2 causes of mortality between 2007 and 2017. decreases in the cause-specific mortality rate reduced the effect of population growth for all but three causes: substance use disorders, neurological disorders, and skin and subcutaneous diseases. interpretation improvements in global health have been unevenly distributed among populations. deaths due to injuries, substance use disorders, armed conflict and terrorism, neoplasms, and cardiovascular disease are expanding threats to global health. for causes of death such as lower respiratory and enteric infections, more rapid progress occurred for children than for the oldest adults, and there is continuing disparity in mortality rates by sex across age groups. reductions in the death rate of some common diseases are themselves slowing or have ceased, primarily for ncds, and the death rate for selected causes has increased in the past decade. funding bill & melinda gates foundation.",0
"background envenoming resulting from snakebites is an important public health problem in many tropical and subtropical countries. few attempts have been made to quantify the burden, and recent estimates all suffer from the lack of an objective and reproducible methodology. in an attempt to provide an accurate, up-to-date estimate of the scale of the global problem, we developed a new method to estimate the disease burden due to snakebites. methods and findings the global estimates were based on regional estimates that were, in turn, derived from data available for countries within a defined region. three main strategies were used to obtain primary data: electronic searching for publications on snakebite, extraction of relevant country-specific mortality data from databases maintained by united nations organizations, and identification of grey literature by discussion with key informants. countries were grouped into 21 distinct geographic regions that are as epidemiologically homogenous as possible, in line with the global burden of disease 2005 study (global burden project of the world bank). incidence rates for envenoming were extracted from publications and used to estimate the number of envenomings for individual countries; if no data were available for a particular country, the lowest incidence rate within a neighbouring country was used. where death registration data were reliable, reported deaths from snakebite were used; in other countries, deaths were estimated on the basis of observed mortality rates and the at-risk population. we estimate that, globally, at least 421,000 envenomings and 20,000 deaths occur each year due to snakebite. these figures may be as high as 1,841,000 envenomings and 94,000 deaths. based on the fact that envenoming occurs in about one in every four snakebites, between 1.2 million and 5.5 million snakebites could occur annually. conclusions snakebites cause considerable morbidity and mortality worldwide. the highest burden exists in south asia, southeast asia, and sub-saharan africa.",0
"behavioral and psychological symptoms of dementia (bpsd), also known as neuropsychiatric symptoms, represent a heterogeneous group of non-cognitive symptoms and behaviors occurring in subjects with dementia. bpsd constitute a major component of the dementia syndrome irrespective of its subtype. they are as clinically relevant as cognitive symptoms as they strongly correlate with the degree of functional and cognitive impairment. bpsd include agitation, aberrant motor behavior, anxiety, elation, irritability, depression, apathy, disinhibition, delusions, hallucinations, and sleep or appetite changes. it is estimated that bpsd affect up to 90% of all dementia subjects over the course of their illness, and is independently associated with poor outcomes, including distress among patients and caregivers, long-term hospitalization, misuse of medication, and increased health care costs. although these symptoms can be present individually it is more common that various psychopathological features co-occur simultaneously in the same patient. thus, categorization of bpsd in clusters taking into account their natural course, prognosis, and treatment response may be useful in the clinical practice. the pathogenesis of bpsd has not been clearly delineated but it is probably the result of a complex interplay of psychological, social, and biological factors. recent studies have emphasized the role of neurochemical, neuropathological, and genetic factors underlying the clinical manifestations of bpsd. a high degree of clinical expertise is crucial to appropriately recognize and manage the neuropsychiatric symptoms in a patient with dementia. combination of non-pharmacological and careful use of pharmacological interventions is the recommended therapeutic for managing bpsd. given the modest efficacy of current strategies, there is an urgent need to identify novel pharmacological targets and develop new non-pharmacological approaches to improve the adverse outcomes associated with bpsd.",0
"aims carotid-femoral pulse wave velocity (pwv), a direct measure of aortic stiffness, has become increasingly important for total cardiovascular (cv) risk estimation. its application as a routine tool for clinical patient evaluation has been hampered by the absence of reference values. the aim of the present study is to establish reference and normal values for pwv based on a large european population. methods and results we gathered data from 16 867 subjects and patients from 13 different centres across eight european countries, in which pwv and basic clinical parameters were measured. of these, 11 092 individuals were free from overt cv disease, non-diabetic and untreated by either anti-hypertensive or lipid-lowering drugs and constituted the reference value population, of which the subset with optimal/normal blood pressures (bps) (n = 1455) is the normal value population. prior to data pooling, pwv values were converted to a common standard using established conversion formulae. subjects were categorized by age decade and further subdivided according to bp categories. pulse wave velocity increased with age and bp category; the increase with age being more pronounced for higher bp categories and the increase with bp being more important for older subjects. the distribution of pwv with age and bp category is described and reference values for pwv are established. normal values are proposed based on the pwv values observed in the non-hypertensive subpopulation who had no additional cv risk factors. conclusion the present study is the first to establish reference and normal values for pwv, combining a sizeable european population after standardizing results for different methods of pwv measurement.",0
"immune checkpoint inhibitors (ici) targeting ctla-4 and the pd-1/pd-l1 axis have shown unprecedented clinical activity in several types of cancer and are rapidly transforming the practice of medical oncology. whereas cytotoxic chemotherapy and small molecule inhibitors ('targeted therapies') largely act on cancer cells directly, immune checkpoint inhibitors reinvigorate anti-tumour immune responses by disrupting co-inhibitory t-cell signalling. while resistance routinely develops in patients treated with conventional cancer therapies and targeted therapies, durable responses suggestive of long-lasting immunologic memory are commonly seen in large subsets of patients treated with ici. however, initial response appears to be a binary event, with most non-responders to single-agent ici therapy progressing at a rate consistent with the natural history of disease. in addition, late relapses are now emerging with longer follow-up of clinical trial populations, suggesting the emergence of acquired resistance. as robust biomarkers to predict clinical response and/or resistance remain elusive, the mechanisms underlying innate (primary) and acquired (secondary) resistance are largely inferred from pre-clinical studies and correlative clinical data. improved understanding of molecular and immunologic mechanisms of ici response (and resistance) may not only identify novel predictive and/or prognostic biomarkers, but also ultimately guide optimal combination/sequencing of ici therapy in the clinic. here we review the emerging clinical and pre-clinical data identifying novel mechanisms of innate and acquired resistance to immune checkpoint inhibition.",0
"serum samples from patients with meningococcal disease were examined for the presence of il-6, tnf-alpha, and lps. median serum concentration of il-6 was 1,000 times higher in patients with septic shock (189 ng/ml) than in patients with bacteriaemia, meningitis, or combined septic shock and meningitis. 11 of 21 patients with serum levels greater than 3.0 ng/ml died, whereas all 58 patients with serum levels at less than or equal to 3.0 ng/ml, survived. all four patients with serum il-6 levels greater than 750 ng/ml, died. il-1 was detected in serum from three patients who also had high serum levels of il-6, tnf-alpha, and lps, and rapidly fatal courses. il-6 appeared to be released into serum later than tnf-alpha, and was detected in serum for up to 36 h. the half-life of il-6 and tnf-alpha was calculated to be 103 +/- 27 min and 70 +/- 11 min, respectively. these data indicate that a complex pattern of cytokines exists in serum from patients with meningococcal septic shock, and that the release of il-6 and il-1, in addition to tnf-alpha, is associated with fatal outcome.",0
"two methods for simple and rapid plating of single hela cells, human, carcinomatous cells, are described. these result in growth and formation of colonies from each single cell. one of these procedures uses irradiated, non-multiplying ""feeder"" cells to condition the medium. the second requires more gentle handling of the cells, but otherwise is virtually the same as that used in plating bacteria on semisolid, nutrient media. by extension of these methods, it is possible to isolate single mutant colonies and grow pure clonal stocks of animal cells. these genetically uniform strains are much more homogeneous in their behavior than the parental hela cell population. growth curves obtained from developing colonies are highly reproducible. the most active mutant stocks so far isolated display a generation time of 18 to 20 hours. in pooled human serum hela cells assume a highly stretched, ameboid form, with marked motility; whereas growth of the same cells in a variety of non-human sera results in tightly packed, columnar, epithelial-like morphology. the two cell types possess volumes, nuclear cross-sections, plating efficiencies, and generation times which are identical within experimental error, but display widely different cross-sectional areas, suggesting that the basic change occurs in the cell surface. it is conceivable that this change may be related to that which enables the cells of a compact tumor to become invasive. animal cells subjected to the standard trypsinization procedures which involve mechanical trauma and repeated washings in incomplete media leak large amounts of p and suffer impaired ability to reproduce as isolated cells. application of the methods described in this paper as a tool for quantitative study of normal mammalian cell growth, physiology, genetics, and biochemistry, and the response of cells to drugs, viruses, high energy radiation, and other agents have been indicated.",0
"unlabelled sparky (goddard and kneller, sparky 3) remains the most popular software program for nmr data analysis, despite the fact that development of the package by its originators ceased in 2001. we have taken over the development of this package and describe nmrfam-sparky, which implements new functions reflecting advances in the biomolecular nmr field. nmrfam-sparky has been repackaged with current versions of python and tcl/tk, which support new tools for nmr peak simulation and graphical assignment determination. these tools, along with chemical shift predictions from the pacsy database, greatly accelerate protein side chain assignments. nmrfam-sparky supports automated data format interconversion for interfacing with a variety of web servers including, pecan , pine, talos-n, cs-rosetta, shiftx2 and ponderosa-c/s. availability and implementation the software package, along with binary and source codes, if desired, can be downloaded freely from instruction manuals and video tutorials can be found at contact whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu supplementary information supplementary data are available at bioinformatics online.",0
"i measured the rate of elongation at the barbed and pointed ends of actin filaments by electron microscopy with limulus sperm acrosomal processes as nuclei. with improvements in the mechanics of the assay, it was possible to measure growth rates from 0.05 to 280 s-1. at 22 degrees c in 1 mm mgcl2, 10 mm imidazole (ph 7), 0.2 mm atp with 1 mm egta or 50 microm cacl2 or with egta and 50 mm kcl, the elongation rates at both ends have a linear dependence on the atp-actin concentration from the critical concentration to 20 microm. consequently, over a wide range of subunit addition rates, the rate constants for association and dissociation of atp-actin are constant. this shows that the nucleotide composition at or near the end of the growing filament is either the same over this range of growth rates or has no detectable effect on the rate constants. under conditions where polymerization is fastest (mgcl2 + kcl + egta) the rate constants have these values: (table; see text) compared with atp-actin, adp-actin associates slower at both ends, dissociates faster from the barbed end, but dissociates slower from the pointed end. taking into account the events at both ends, these constants and a simple oosawa-type model account for the complex three-phase dependence of the rate of polymerization in bulk samples on the concentration of atp-actin monomers observed by carlier, m.-f., d. pantaloni, and e. d. korn (1985, j. biol. chem., 260:6565-6571). these constants can also be used to predict the reactions at steady state in atp. there will be slow subunit flux from the barbed end to the pointed end. there will also be minor fluctuations in length at the barbed end due to occasional rapid dissociation of strings of adp subunits but the pointed end will be relatively stable.",0
"psychophysiological research integrating heart rate variability (hrv) has increased during the last two decades, particularly given the fact that hrv is able to index cardiac vagal tone. cardiac vagal tone, which represents the contribution of the parasympathetic nervous system to cardiac regulation, is acknowledged to be linked with many phenomena relevant for psychophysiological research, including self-regulation at the cognitive, emotional, social, and health levels. the ease of hrv collection and measurement coupled with the fact it is relatively affordable, non-invasive and pain free makes it widely accessible to many researchers. this ease of access should not obscure the difficulty of interpretation of hrv findings that can be easily misconstrued, however, this can be controlled to some extent through correct methodological processes. standards of measurement were developed two decades ago by a task force within hrv research, and recent reviews updated several aspects of the task force paper. however, many methodological aspects related to hrv in psychophysiological research have to be considered if one aims to be able to draw sound conclusions, which makes it difficult to interpret findings and to compare results across laboratories. those methodological issues have mainly been discussed in separate outlets, making difficult to get a grasp on them, and thus this paper aims to address this issue. it will help to provide psychophysiological researchers with recommendations and practical advice concerning experimental designs, data analysis, and data reporting. this will ensure that researchers starting a project with hrv and cardiac vagal tone are well informed regarding methodological considerations in order for their findings to contribute to knowledge advancement in their field.",0
"background this paper describes the process and results of a refinement of a framework to characterize modifications to interventions. the original version did not fully capture several aspects of modification and adaptation that may be important to document and report. additionally, the earlier framework did not include a way to differentiate cultural adaptation from adaptations made for other reasons. reporting additional elements will allow for a more precise understanding of modifications, the process of modifying or adapting, and the relationship between different forms of modification and subsequent health and implementation outcomes. discussion we employed a multifaceted approach to develop the updated frame involving coding documents identified through a literature review, rapid coding of qualitative interviews, and a refinement process informed by multiple stakeholders. the updated frame expands upon stirman et al.'s original framework by adding components of modification to report: (1) when and how in the implementation process the modification was made, (2) whether the modification was planned/proactive (i.e., an adaptation) or unplanned/reactive, (3) who determined that the modification should be made, (4) what is modified, (5) at what level of delivery the modification is made, (6) type or nature of context or content-level modifications, (7) the extent to which the modification is fidelity-consistent, and (8) the reasons for the modification, including (a) the intent or goal of the modification (e.g., to reduce costs) and (b) contextual factors that influenced the decision. methods of using the framework to assess modifications are outlined, along with their strengths and weaknesses, and considerations for research to validate these measurement strategies. conclusion the updated frame includes consideration of when and how modifications occurred, whether it was planned or unplanned, relationship to fidelity, and reasons and goals for modification. this tool that can be used to support research on the timing, nature, goals and reasons for, and impact of modifications to evidence-based interventions.",0
"background neural stem cells are currently being investigated as potential therapies for neurodegenerative diseases, stroke, and trauma. however, concerns have been raised over the safety of this experimental therapeutic approach, including, for example, whether there is the potential for tumors to develop from transplanted stem cells. methods and findings a boy with ataxia telangiectasia (at) was treated with intracerebellar and intrathecal injection of human fetal neural stem cells. four years after the first treatment he was diagnosed with a multifocal brain tumor. the biopsied tumor was diagnosed as a glioneuronal neoplasm. we compared the tumor cells and the patient's peripheral blood cells by fluorescent in situ hybridization using x and y chromosome probes, by pcr for the amelogenin gene x- and y-specific alleles, by massarray for the atm patient specific mutation and for several snps, by pcr for polymorphic microsatellites, and by human leukocyte antigen (hla) typing. molecular and cytogenetic studies showed that the tumor was of nonhost origin suggesting it was derived from the transplanted neural stem cells. microsatellite and hla analysis demonstrated that the tumor is derived from at least two donors. conclusions this is the first report of a human brain tumor complicating neural stem cell therapy. the findings here suggest that neuronal stem/progenitor cells may be involved in gliomagenesis and provide the first example of a donor-derived brain tumor. further work is urgently needed to assess the safety of these therapies.",0
"the global burden of disease 2015 study aims to use all available data of sufficient quality to generate reliable and valid prevalence, incidence, and disability-adjusted life year (daly) estimates of oral conditions for the period of 1990 to 2015. since death as a direct result of oral diseases is rare, daly estimates were based on years lived with disability, which are estimated only on those persons with unmet need for dental care. we used our data to assess progress toward the federation dental international, world health organization, and international association for dental research's oral health goals of reducing the level of oral diseases and minimizing their impact by 2020. oral health has not improved in the last 25 y, and oral conditions remained a major public health challenge all over the world in 2015. due to demographic changes, including population growth and aging, the cumulative burden of oral conditions dramatically increased between 1990 and 2015. the number of people with untreated oral conditions rose from 2.5 billion in 1990 to 3.5 billion in 2015, with a 64% increase in dalys due to oral conditions throughout the world. clearly, oral diseases are highly prevalent in the globe, posing a very serious public health challenge to policy makers. greater efforts and potentially different approaches are needed if the oral health goal of reducing the level of oral diseases and minimizing their impact is to be achieved by 2020. despite some challenges with current measurement methodologies for oral diseases, measurable specific oral health goals should be developed to advance global public health.",0
"artificial intelligence (ai) has long promised to increase healthcare affordability, quality and accessibility but fda, until recently, had never authorized an autonomous ai diagnostic system. this pivotal trial of an ai system to detect diabetic retinopathy (dr) in people with diabetes enrolled 900 subjects, with no history of dr at primary care clinics, by comparing to wisconsin fundus photograph reading center (fprc) widefield stereoscopic photography and macular optical coherence tomography (oct), by fprc certified photographers, and fprc grading of early treatment diabetic retinopathy study severity scale (etdrs) and diabetic macular edema (dme). more than mild dr (mtmdr) was defined as etdrs level 35 or higher, and/or dme, in at least one eye. ai system operators underwent a standardized training protocol before study start. median age was 59 years (range, 22-84 years); among participants, 47.5% of participants were male; 16.1% were hispanic, 83.3% not hispanic; 28.6% african american and 63.4% were not; 198 (23.8%) had mtmdr. the ai system exceeded all pre-specified superiority endpoints at sensitivity of 87.2% (95% ci, 81.8-91.2%) (>85%), specificity of 90.7% (95% ci, 88.3-92.7%) (>82.5%), and imageability rate of 96.1% (95% ci, 94.6-97.3%), demonstrating ai's ability to bring specialty-level diagnostics to primary care settings. based on these results, fda authorized the system for use by health care providers to detect more than mild dr and diabetic macular edema, making it, the first fda authorized autonomous ai diagnostic system in any field of medicine, with the potential to help prevent vision loss in thousands of people with diabetes annually. clinicaltrials.gov nct02963441.",0
"secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. in recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. since 2011, the 'antibiotics and secondary metabolite analysis shell-antismash' ( has assisted researchers in this, both as a web server and a standalone tool. it has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (bgcs) in bacterial and fungal genome sequences. here, we present an entirely redesigned and extended version 5 of antismash. antismash 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal ripps, ras-ripps, polybrominated diphenyl ethers, c-nucleosides, ppy-like ketones and lipolanthines. for type ii polyketide synthase-encoding gene clusters, antismash 5 now offers more detailed predictions. the html output visualization has been redesigned to improve the navigation and visual representation of annotations. we have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. a new output file in the standard javascript object notation (json) format is aimed at downstream tools that process antismash results programmatically.",0
"background schizophrenia is one of the most common, burdensome, and costly psychiatric disorders in adults worldwide. antipsychotic drugs are its treatment of choice, but there is controversy about which agent should be used. we aimed to compare and rank antipsychotics by quantifying information from randomised controlled trials. methods we did a network meta-analysis of placebo-controlled and head-to-head randomised controlled trials and compared 32 antipsychotics. we searched embase, medline, psycinfo, pubmed, biosis, cochrane central register of controlled trials (central), who international clinical trials registry platform, and clinicaltrials.gov from database inception to jan 8, 2019. two authors independently selected studies and extracted data. we included randomised controlled trials in adults with acute symptoms of schizophrenia or related disorders. we excluded studies in patients with treatment resistance, first episode, predominant negative or depressive symptoms, concomitant medical illnesses, and relapse-prevention studies. our primary outcome was change in overall symptoms measured with standardised rating scales. we also extracted data for eight efficacy and eight safety outcomes. differences in the findings of the studies were explored in metaregressions and sensitivity analyses. effect size measures were standardised mean differences, mean differences, or risk ratios with 95% credible intervals (cris). confidence in the evidence was assessed using cinema (confidence in network meta-analysis). the study protocol is registered with prospero, number crd42014014919. findings we identified 54 417 citations and included 402 studies with data for 53 463 participants. effect size estimates suggested all antipsychotics reduced overall symptoms more than placebo (although not statistically significant for six drugs), with standardised mean differences ranging from -0·89 (95% cri -1·08 to -0·71) for clozapine to -0·03 (-0·59 to 0·52) for levomepromazine (40 815 participants). standardised mean differences compared with placebo for reduction of positive symptoms (31 179 participants) varied from -0·69 (95% cri -0·86 to -0·52) for amisulpride to -0·17 (-0·31 to -0·04) for brexpiprazole, for negative symptoms (32 015 participants) from -0·62 (-0·84 to -0·39; clozapine) to -0·10 (-0·45 to 0·25; flupentixol), for depressive symptoms (19 683 participants) from -0·90 (-1·36 to -0·44; sulpiride) to 0·04 (-0·39 to 0·47; flupentixol). risk ratios compared with placebo for all-cause discontinuation (42 672 participants) ranged from 0·52 (0·12 to 0·95; clopenthixol) to 1·15 (0·36 to 1·47; pimozide), for sedation (30 770 participants) from 0·92 (0·17 to 2·03; pimozide) to 10·20 (4·72 to 29·41; zuclopenthixol), for use of antiparkinson medication (24 911 participants) from 0·46 (0·19 to 0·88; clozapine) to 6·14 (4·81 to 6·55; pimozide). mean differences compared to placebo for weight gain (28 317 participants) ranged from -0·16 kg (-0·73 to 0·40; ziprasidone) to 3·21 kg (2·10 to 4·31; zotepine), for prolactin elevation (21 569 participants) from -77·05 ng/ml (-120·23 to -33·54; clozapine) to 48·51 ng/ml (43·52 to 53·51; paliperidone) and for qtc prolongation (15 467 participants) from -2·21 ms (-4·54 to 0·15; lurasidone) to 23·90 ms (20·56 to 27·33; sertindole). conclusions for the primary outcome did not substantially change after adjusting for possible effect moderators or in sensitivity analyses (eg, when excluding placebo-controlled studies). the confidence in evidence was often low or very low. interpretation there are some efficacy differences between antipsychotics, but most of them are gradual rather than discrete. differences in side-effects are more marked. these findings will aid clinicians in balancing risks versus benefits of those drugs available in their countries. they should consider the importance of each outcome, the patients' medical problems, and preferences. funding german ministry of education and research and national institute for health research.",0
"it was unknown whether plasma protein levels can be estimated based on dna methylation (dnam) levels, and if so, how the resulting surrogates can be consolidated into a powerful predictor of lifespan. we present here, seven dnam-based estimators of plasma proteins including those of plasminogen activator inhibitor 1 (pai-1) and growth differentiation factor 15. the resulting predictor of lifespan, dnam grimage (in units of years), is a composite biomarker based on the seven dnam surrogates and a dnam-based estimator of smoking pack-years. adjusting dnam grimage for chronological age generated novel measure of epigenetic age acceleration, ageaccelgrim .using large scale validation data from thousands of individuals, we demonstrate that dnam grimage stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death (cox regression p=2.0e-75), time-to-coronary heart disease (cox p=6.2e-24), time-to-cancer (p= 1.3e-12), its strong relationship with computed tomography data for fatty liver/excess visceral fat, and age-at-menopause (p=1.6e-12). ageaccelgrim is strongly associated with a host of age-related conditions including comorbidity count (p=3.45e-17). similarly, age-adjusted dnam pai-1 levels are associated with lifespan (p=5.4e-28), comorbidity count (p= 7.3e-56) and type 2 diabetes (p=2.0e-26). these dnam-based biomarkers show the expected relationship with lifestyle factors including healthy diet and educational attainment.overall, these epigenetic biomarkers are expected to find many applications including human anti-aging studies.",0
"mixed lineage kinase domain-like protein (mlkl) was identified to function downstream of receptor interacting protein 3 (rip3) in tumor necrosis factor-α (tnf)-induced necrosis (also called necroptosis). however, how mlkl functions to mediate necroptosis is unknown. by reconstitution of mlkl function in mlkl-knockout cells, we showed that the n-terminus of mlkl is required for its function in necroptosis. the oligomerization of mlkl in tnf-treated cells is essential for necroptosis, as artificially forcing mlkl together by using the hormone-binding domain (hbd*) triggers necroptosis. notably, forcing together the n-terminal domain (nd) but not the c-terminal kinase domain of mlkl causes necroptosis. further deletion analysis showed that the four-α-helix bundle of mlkl (1-130 amino acids) is sufficient to trigger necroptosis. both the hbd*-mediated and tnf-induced complexes of mlkl(nd) or mlkl are tetramers, and translocation of these complexes to lipid rafts of the plasma membrane precedes cell death. the homo-oligomerization is required for mlkl translocation and the signal sequence for plasma membrane location is located in the junction of the first and second α-helices of mlkl. the plasma membrane translocation of mlkl or mlkl(nd) leads to sodium influx, and depletion of sodium from the cell culture medium inhibits necroptosis. all of the above phenomena were not seen in apoptosis. thus, the mlkl oligomerization leads to translocation of mlkl to lipid rafts of plasma membrane, and the plasma membrane mlkl complex acts either by itself or via other proteins to increase the sodium influx, which increases osmotic pressure, eventually leading to membrane rupture.",0
"dna sequencing continues to decrease in cost with the illumina hiseq2000 generating up to 600 gb of paired-end 100 base reads in a ten-day run. here we present a protocol for community amplicon sequencing on the hiseq2000 and miseq illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. a critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. we show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the hiseq2000 versus the miseq) and across the sequenced regions of amplicons.",0
"contractile myocytes provide a test of the hypothesis that cells sense their mechanical as well as molecular microenvironment, altering expression, organization, and/or morphology accordingly. here, myoblasts were cultured on collagen strips attached to glass or polymer gels of varied elasticity. subsequent fusion into myotubes occurs independent of substrate flexibility. however, myosin/actin striations emerge later only on gels with stiffness typical of normal muscle (passive young's modulus, e approximately 12 kpa). on glass and much softer or stiffer gels, including gels emulating stiff dystrophic muscle, cells do not striate. in addition, myotubes grown on top of a compliant bottom layer of glass-attached myotubes (but not softer fibroblasts) will striate, whereas the bottom cells will only assemble stress fibers and vinculin-rich adhesions. unlike sarcomere formation, adhesion strength increases monotonically versus substrate stiffness with strongest adhesion on glass. these findings have major implications for in vivo introduction of stem cells into diseased or damaged striated muscle of altered mechanical composition.",0
"polybrominated diphenyl ethers (pbdes) are used as flame retardants in plastics (concentration, 5--30%) and in textile coatings. commercial products consist predominantly of penta-, octa-, and decabromodiphenyl ether mixtures, and global pbde production is about 40,000 tons per year. pbdes are bioaccumulated and biomagnified in the environment, and comparatively high levels are often found in aquatic biotopes from different parts of the world. during the mid-1970--1980s there was a substantial increase in the pbde levels with time in both sediments and aquatic biota, whereas the latest swedish data (pike and guillemot egg) may indicate that levels are at steady state or are decreasing. however, exponentially increasing pbde levels have been observed in mother's milk during 1972--1997. based on levels in food from 1999, the dietary intake of pbde in sweden has been estimated to be 0.05 microg per day. characteristic end points of animal toxicity are hepatotoxicity, embryotoxicity, and thyroid effects as well as maternal toxicity during gestation. recently, behavioral effects have been observed in mice on administration of pbdes during a critical period after birth. based on the critical effects reported in available studies, we consider the lowest-observed-adverse-effect level (loael) value of the pbde group to be 1 mg/kg/day (primarily based on effects of pentabdes). in conclusion, with the scientific knowledge of today and based on nordic intake data, the possible consumer health risk from pbdes appears limited, as a factor of over 10(6) separates the estimated present mean dietary intake from the suggested loael value. however, the presence of many and important data gaps, including those in carcinogenicity, reproduction, and developmental toxicity, as well as additional routes of exposure, make this conclusion only preliminary. moreover, the time trend of pbdes in human breast milk is alarming for the future.",0
"physiological changes occur in pregnancy to nurture the developing foetus and prepare the mother for labour and delivery. some of these changes influence normal biochemical values while others may mimic symptoms of medical disease. it is important to differentiate between normal physiological changes and disease pathology. this review highlights the important changes that take place during normal pregnancy.",0
"understanding the intentions of others while watching their actions is a fundamental building block of social behavior. the neural and functional mechanisms underlying this ability are still poorly understood. to investigate these mechanisms we used functional magnetic resonance imaging. twenty-three subjects watched three kinds of stimuli: grasping hand actions without a context, context only (scenes containing objects), and grasping hand actions performed in two different contexts. in the latter condition the context suggested the intention associated with the grasping action (either drinking or cleaning). actions embedded in contexts, compared with the other two conditions, yielded a significant signal increase in the posterior part of the inferior frontal gyrus and the adjacent sector of the ventral premotor cortex where hand actions are represented. thus, premotor mirror neuron areas-areas active during the execution and the observation of an action-previously thought to be involved only in action recognition are actually also involved in understanding the intentions of others. to ascribe an intention is to infer a forthcoming new goal, and this is an operation that the motor system does automatically.",0
"actions of cytochalasin b (cb) on cytoskeletons and motility of growth cones from cultured aplysia neurons were studied using a rapid flow perfusion chamber and digital video light microscopy. living growth cones were observed using differential interference contrast optics and were also fixed at various time points to assay actin filament (f-actin) and microtubule distributions. treatment with cb reversibly blocked motility and eliminated most of the phalloidin-stainable f-actin from the leading lamella. the loss of f-actin was nearly complete within 2-3 min of cb application and was largely reversed within 5-6 min of cb removal. the loss and recovery of f-actin were found to occur with a very distinctive spatial organization. within 20-30 s of cb application, f-actin networks receded from the entire peripheral margin of the lamella forming a band devoid of f-actin. this band widened as f-actin receded at rates of 3-6 microns/min. upon removal of cb, f-actin began to reappear within 20-30 s. the initial reappearance of f-actin took two forms: a coarse isotropic matrix of f-actin bundles throughout the lamella, and a denser matrix along the peripheral margin. the denser peripheral matrix then expanded in width, extending centrally to replace the coarse matrix at rates again between 3-6 microns/min. these results suggest that actin normally polymerizes at the leading edge and then flows rearward at a rate between 3-6 microns/min. cb treatment was also observed to alter the distribution of microtubules, assayed by antitubulin antibody staining. normally, microtubules are restricted to the neurite shaft and a central growth cone domain. within approximately 5 min after cb application, however, microtubules began extending into the lamellar region, often reaching the peripheral margin. upon removal of cb, the microtubules were restored to their former central localization. the timing of these microtubule redistributions is consistent with their being secondary to effects of cb on lamellar f-actin.",0
"we developed lomets, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on tm-score at a t-test significance level of 0.1%. moreover, side-chain and c-alpha (c(alpha)) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. these data can be easily used as constraints to guide the ab initio procedures such as tasser for further protein tertiary structure modeling. the lomets server is freely available to the academic community at",0
"the refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the protein data bank (pdb). the success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the pdb public archive . the pdb_redo procedure aims for 'constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. a web server for pdb_redo has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in refmac and partial model rebuilding. the goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the pdb. for this, additional steps were implemented in the pdb_redo pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in edstats and ligand validation as implemented in yasara. innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated coot scripts can guide users to subsequent model inspection and improvement. it is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the pdb.",0
"even at low-density lipoprotein cholesterol (ldl-c) goal, patients with cardiometabolic abnormalities remain at high risk of cardiovascular events. this paper aims (i) to critically appraise evidence for elevated levels of triglyceride-rich lipoproteins (trls) and low levels of high-density lipoprotein cholesterol (hdl-c) as cardiovascular risk factors, and (ii) to advise on therapeutic strategies for management. current evidence supports a causal association between elevated trl and their remnants, low hdl-c, and cardiovascular risk. this interpretation is based on mechanistic and genetic studies for trl and remnants, together with the epidemiological data suggestive of the association for circulating triglycerides and cardiovascular disease. for hdl, epidemiological, mechanistic, and clinical intervention data are consistent with the view that low hdl-c contributes to elevated cardiovascular risk; genetic evidence is unclear however, potentially reflecting the complexity of hdl metabolism. the panel believes that therapeutic targeting of elevated triglycerides (≥ 1.7 mmol/l or 150 mg/dl), a marker of trl and their remnants, and/or low hdl-c (<1.0 mmol/l or 40 mg/dl) may provide further benefit. the first step should be lifestyle interventions together with consideration of compliance with pharmacotherapy and secondary causes of dyslipidaemia. if inadequately corrected, adding niacin or a fibrate, or intensifying ldl-c lowering therapy may be considered. treatment decisions regarding statin combination therapy should take into account relevant safety concerns, i.e. the risk of elevation of blood glucose, uric acid or liver enzymes with niacin, and myopathy, increased serum creatinine and cholelithiasis with fibrates. these recommendations will facilitate reduction in the substantial cardiovascular risk that persists in patients with cardiometabolic abnormalities at ldl-c goal.",0
"background coronavirus disease 2019 (covid-19) is associated with immune dysregulation and hyperinflammation, including elevated interleukin-6 levels. the use of tocilizumab, a monoclonal antibody against the interleukin-6 receptor, has resulted in better outcomes in patients with severe covid-19 pneumonia in case reports and retrospective observational cohort studies. data are needed from randomized, placebo-controlled trials. methods in this phase 3 trial, we randomly assigned patients who were hospitalized with severe covid-19 pneumonia in a 2:1 ratio receive a single intravenous infusion of tocilizumab (at a dose of 8 mg per kilogram of body weight) or placebo. approximately one quarter of the participants received a second dose of tocilizumab or placebo 8 to 24 hours after the first dose. the primary outcome was clinical status at day 28 on an ordinal scale ranging from 1 (discharged or ready for discharge) to 7 (death) in the modified intention-to-treat population, which included all the patients who had received at least one dose of tocilizumab or placebo. results of the 452 patients who underwent randomization, 438 (294 in the tocilizumab group and 144 in the placebo group) were included in the primary and secondary analyses. the median value for clinical status on the ordinal scale at day 28 was 1.0 (95% confidence interval , 1.0 to 1.0) in the tocilizumab group and 2.0 (non-icu hospitalization without supplemental oxygen) (95% ci, 1.0 to 4.0) in the placebo group (between-group difference, -1.0; 95% ci, -2.5 to 0; p = 0.31 by the van elteren test). in the safety population, serious adverse events occurred in 103 of 295 patients (34.9%) in the tocilizumab group and in 55 of 143 patients (38.5%) in the placebo group. mortality at day 28 was 19.7% in the tocilizumab group and 19.4% in the placebo group (weighted difference, 0.3 percentage points; 95% ci, -7.6 to 8.2; nominal p = 0.94). conclusions in this randomized trial involving hospitalized patients with severe covid-19 pneumonia, the use of tocilizumab did not result in significantly better clinical status or lower mortality than placebo at 28 days. (funded by f. hoffmann-la roche and the department of health and human services; covacta clinicaltrials.gov number, nct04320615.).",0
"the diffusion rate of lipids in the cell membrane is reduced by a factor of 5-100 from that in artificial bilayers. this slowing mechanism has puzzled cell biologists for the last 25 yr. here we address this issue by studying the movement of unsaturated phospholipids in rat kidney fibroblasts at the single molecule level at the temporal resolution of 25 micros. the cell membrane was found to be compartmentalized: phospholipids are confined within 230-nm-diameter (phi) compartments for 11 ms on average before hopping to adjacent compartments. these 230-nm compartments exist within greater 750-nm-phi compartments where these phospholipids are confined for 0.33 s on average. the diffusion rate within 230-nm compartments is 5.4 microm2/s, which is nearly as fast as that in large unilamellar vesicles, indicating that the diffusion in the cell membrane is reduced not because diffusion per se is slow, but because the cell membrane is compartmentalized with regard to lateral diffusion of phospholipids. such compartmentalization depends on the actin-based membrane skeleton, but not on the extracellular matrix, extracellular domains of membrane proteins, or cholesterol-enriched rafts. we propose that various transmembrane proteins anchored to the actin-based membrane skeleton meshwork act as rows of pickets that temporarily confine phospholipids.",0
"high-throughput experimental technologies often identify dozens to hundreds of genes related to, or changed in, a biological or pathological process. from these genes one wants to identify biological pathways that may be involved and diseases that may be implicated. here, we report a web server, kobas 2.0, which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. it allows for both id mapping and cross-species sequence similarity mapping. it then performs statistical tests to identify statistically significantly enriched pathways and diseases. kobas 2.0 incorporates knowledge across 1327 species from 5 pathway databases (kegg pathway, pid, biocyc, reactome and panther) and 5 human disease databases (omim, kegg disease, fundo, gad and nhgri gwas catalog). kobas 2.0 can be accessed at",0
"cancer immunotherapy has transformed the treatment of cancer. however, increasing use of immune-based therapies, including the widely used class of agents known as immune checkpoint inhibitors, has exposed a discrete group of immune-related adverse events (iraes). many of these are driven by the same immunologic mechanisms responsible for the drugs' therapeutic effects, namely blockade of inhibitory mechanisms that suppress the immune system and protect body tissues from an unconstrained acute or chronic immune response. skin, gut, endocrine, lung and musculoskeletal iraes are relatively common, whereas cardiovascular, hematologic, renal, neurologic and ophthalmologic iraes occur much less frequently. the majority of iraes are mild to moderate in severity; however, serious and occasionally life-threatening iraes are reported in the literature, and treatment-related deaths occur in up to 2% of patients, varying by ici. immunotherapy-related iraes typically have a delayed onset and prolonged duration compared to adverse events from chemotherapy, and effective management depends on early recognition and prompt intervention with immune suppression and/or immunomodulatory strategies. there is an urgent need for multidisciplinary guidance reflecting broad-based perspectives on how to recognize, report and manage organ-specific toxicities until evidence-based data are available to inform clinical decision-making. the society for immunotherapy of cancer (sitc) established a multidisciplinary toxicity management working group, which met for a full-day workshop to develop recommendations to standardize management of iraes. here we present their consensus recommendations on managing toxicities associated with immune checkpoint inhibitor therapy.",0
"kegg ( is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. it also provides kegg mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. kegg mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. since the introduction of the kegg network database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. the network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. the kegg pathway maps are now integrated with network variation maps in the network database, as well as with conserved functional units of kegg modules and reaction modules in the module database. the ko database for functional orthologs continues to be improved and virus kos are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.",0
"background individuals with cancer, particularly those who are receiving systemic anticancer treatments, have been postulated to be at increased risk of mortality from covid-19. this conjecture has considerable effect on the treatment of patients with cancer and data from large, multicentre studies to support this assumption are scarce because of the contingencies of the pandemic. we aimed to describe the clinical and demographic characteristics and covid-19 outcomes in patients with cancer. methods in this prospective observational study, all patients with active cancer and presenting to our network of cancer centres were eligible for enrolment into the uk coronavirus cancer monitoring project (ukccmp). the ukccmp is the first covid-19 clinical registry that enables near real-time reports to frontline doctors about the effects of covid-19 on patients with cancer. eligible patients tested positive for severe acute respiratory syndrome coronavirus 2 on rt-pcr assay from a nose or throat swab. we excluded patients with a radiological or clinical diagnosis of covid-19, without a positive rt-pcr test. the primary endpoint was all-cause mortality, or discharge from hospital, as assessed by the reporting sites during the patient hospital admission. findings from march 18, to april 26, 2020, we analysed 800 patients with a diagnosis of cancer and symptomatic covid-19. 412 (52%) patients had a mild covid-19 disease course. 226 (28%) patients died and risk of death was significantly associated with advancing patient age (odds ratio 9·42 ; p interpretation mortality from covid-19 in cancer patients appears to be principally driven by age, gender, and comorbidities. we are not able to identify evidence that cancer patients on cytotoxic chemotherapy or other anticancer treatment are at an increased risk of mortality from covid-19 disease compared with those not on active treatment. funding university of birmingham, university of oxford.",0
"murine epidermal langerhans cells (lc) have been studied in tissue culture and compared to spleen dendritic cells (dc). lc comprised 3% of the starting cell suspensions and were distinguished from keratinocytes by cytology and reactivity with anti-ia and anti-mac-1 monoclonal antibodies. the lc were nonadherent, had a low buoyant density, did not proliferate, and could be enriched to 10-50% purity. lc continued to exhibit ia and mac-1 antigens for 4 d in culture. however, lc rapidly lost birbeck granules, fc receptors, f4/80 antigen, and cytochemical reactivity for nonspecific esterase and membrane atpase. as a result, the ultrastructure and phenotype of cultured lc became remarkably similar to lymphoid dc. stimulatory capacity for t cell proliferative responses (oxidative mitogenesis and the mixed leukocyte reaction) was monitored daily. initially, stimulatory capacity was very weak, even though lc expressed substantial levels of ia antigens. after 2-3 d in culture, lc had become 3-10 times more potent than spleen dc. 30 lc could induce significant responses in cultures of 3 x 10(5) responding t cells. removal of ia+ lc at the start of culture ablated the development of stimulatory activity, but exposure to 1,500 rad of ionizing irradiation did not. mixing experiments showed that contaminating ia- epidermal cells did not alter the function of ia+ stimulators. therefore, lc seem to be immunologically immature, but acquire many of the features of spleen dc during culture. we suggest that functioning lymphoid dc may, in general, be derived from less mature precursors located in nonlymphoid tissues.",0
"when internalized receptors and other cargo are destined for lysosomal degradation, they are ubiquitinated and sorted by the endosomal sorting complex required for transport (escrt) complexes 0, i, ii and iii into multivesicular bodies. multivesicular bodies are formed when cargo-rich patches of the limiting membrane of endosomes bud inwards by an unknown mechanism and are then cleaved to yield cargo-bearing intralumenal vesicles. the biogenesis of multivesicular bodies was reconstituted and visualized using giant unilamellar vesicles, fluorescent escrt-0, -i, -ii and -iii complexes, and a membrane-tethered fluorescent ubiquitin fusion as a model cargo. here we show that escrt-0 forms domains of clustered cargo but does not deform membranes. escrt-i and escrt-ii in combination deform the membrane into buds, in which cargo is confined. escrt-i and escrt-ii localize to the bud necks, and recruit escrt-0-ubiquitin domains to the buds. escrt-iii subunits localize to the bud neck and efficiently cleave the buds to form intralumenal vesicles. intralumenal vesicles produced in this reaction contain the model cargo but are devoid of escrts. the observations explain how the escrts direct membrane budding and scission from the cytoplasmic side of the bud without being consumed in the reaction.",0
"treatment of rheumatoid arthritis (ra) may differ among rheumatologists and currently, clear and consensual international recommendations on ra treatment are not available. in this paper recommendations for the treatment of ra with synthetic and biological disease-modifying antirheumatic drugs (dmards) and glucocorticoids (gcs) that also account for strategic algorithms and deal with economic aspects, are described. the recommendations are based on evidence from five systematic literature reviews (slrs) performed for synthetic dmards, biological dmards, gcs, treatment strategies and economic issues. the slr-derived evidence was discussed and summarised as an expert opinion in the course of a delphi-like process. levels of evidence, strength of recommendations and levels of agreement were derived. fifteen recommendations were developed covering an area from general aspects such as remission/low disease activity as treatment aim via the preference for methotrexate monotherapy with or without gcs vis-à-vis combination of synthetic dmards to the use of biological agents mainly in patients for whom synthetic dmards and tumour necrosis factor inhibitors had failed. cost effectiveness of the treatments was additionally examined. these recommendations are intended to inform rheumatologists, patients and other stakeholders about a european consensus on the management of ra with dmards and gcs as well as strategies to reach optimal outcomes of ra, based on evidence and expert opinion.",0
"osteoblasts and endothelium constitute functional niches that support haematopoietic stem cells in mammalian bone marrow. adult bone marrow also contains adipocytes, the number of which correlates inversely with the haematopoietic activity of the marrow. fatty infiltration of haematopoietic red marrow follows irradiation or chemotherapy and is a diagnostic feature in biopsies from patients with marrow aplasia. to explore whether adipocytes influence haematopoiesis or simply fill marrow space, we compared the haematopoietic activity of distinct regions of the mouse skeleton that differ in adiposity. here we show, by flow cytometry, colony-forming activity and competitive repopulation assay, that haematopoietic stem cells and short-term progenitors are reduced in frequency in the adipocyte-rich vertebrae of the mouse tail relative to the adipocyte-free vertebrae of the thorax. in lipoatrophic a-zip/f1 'fatless' mice, which are genetically incapable of forming adipocytes, and in mice treated with the peroxisome proliferator-activated receptor-gamma inhibitor bisphenol a diglycidyl ether, which inhibits adipogenesis, marrow engraftment after irradiation is accelerated relative to wild-type or untreated mice. these data implicate adipocytes as predominantly negative regulators of the bone-marrow microenvironment, and indicate that antagonizing marrow adipogenesis may enhance haematopoietic recovery in clinical bone-marrow transplantation.",0
"background stents are an alternative treatment to carotid endarterectomy for symptomatic carotid stenosis, but previous trials have not established equivalent safety and efficacy. we compared the safety of carotid artery stenting with that of carotid endarterectomy. methods the international carotid stenting study (icss) is a multicentre, international, randomised controlled trial with blinded adjudication of outcomes. patients with recently symptomatic carotid artery stenosis were randomly assigned in a 1:1 ratio to receive carotid artery stenting or carotid endarterectomy. randomisation was by telephone call or fax to a central computerised service and was stratified by centre with minimisation for sex, age, contralateral occlusion, and side of the randomised artery. patients and investigators were not masked to treatment assignment. patients were followed up by independent clinicians not directly involved in delivering the randomised treatment. the primary outcome measure of the trial is the 3-year rate of fatal or disabling stroke in any territory, which has not been analysed yet. the main outcome measure for the interim safety analysis was the 120-day rate of stroke, death, or procedural myocardial infarction. analysis was by intention to treat (itt). this study is registered, number isrctn25337470. findings the trial enrolled 1713 patients (stenting group, n=855; endarterectomy group, n=858). two patients in the stenting group and one in the endarterectomy group withdrew immediately after randomisation, and were not included in the itt analysis. between randomisation and 120 days, there were 34 (kaplan-meier estimate 4.0%) events of disabling stroke or death in the stenting group compared with 27 (3.2%) events in the endarterectomy group (hazard ratio 1.28, 95% ci 0.77-2.11). the incidence of stroke, death, or procedural myocardial infarction was 8.5% in the stenting group compared with 5.2% in the endarterectomy group (72 vs 44 events; hr 1.69, 1.16-2.45, p=0.006). risks of any stroke (65 vs 35 events; hr 1.92, 1.27-2.89) and all-cause death (19 vs seven events; hr 2.76, 1.16-6.56) were higher in the stenting group than in the endarterectomy group. three procedural myocardial infarctions were recorded in the stenting group, all of which were fatal, compared with four, all non-fatal, in the endarterectomy group. there was one event of cranial nerve palsy in the stenting group compared with 45 in the endarterectomy group. there were also fewer haematomas of any severity in the stenting group than in the endarterectomy group (31 vs 50 events; p=0.0197). interpretation completion of long-term follow-up is needed to establish the efficacy of carotid artery stenting compared with endarterectomy. in the meantime, carotid endarterectomy should remain the treatment of choice for patients suitable for surgery. funding medical research council, the stroke association, sanofi-synthélabo, european union.",0
"niemann-pick c disease (np-c) is a neurovisceral atypical lysosomal lipid storage disorder with an estimated minimal incidence of 1/120,000 live births. the broad clinical spectrum ranges from a neonatal rapidly fatal disorder to an adult-onset chronic neurodegenerative disease. the neurological involvement defines the disease severity in most patients but is typically preceded by systemic signs (cholestatic jaundice in the neonatal period or isolated spleno- or hepatosplenomegaly in infancy or childhood). the first neurological symptoms vary with age of onset: delay in developmental motor milestones (early infantile period), gait problems, falls, clumsiness, cataplexy, school problems (late infantile and juvenile period), and ataxia not unfrequently following initial psychiatric disturbances (adult form). the most characteristic sign is vertical supranuclear gaze palsy. the neurological disorder consists mainly of cerebellar ataxia, dysarthria, dysphagia, and progressive dementia. cataplexy, seizures and dystonia are other common features. np-c is transmitted in an autosomal recessive manner and is caused by mutations of either the npc1 (95% of families) or the npc2 genes. the exact functions of the npc1 and npc2 proteins are still unclear. np-c is currently described as a cellular cholesterol trafficking defect but in the brain, the prominently stored lipids are gangliosides. clinical examination should include comprehensive neurological and ophthalmological evaluations. the primary laboratory diagnosis requires living skin fibroblasts to demonstrate accumulation of unesterified cholesterol in perinuclear vesicles (lysosomes) after staining with filipin. pronounced abnormalities are observed in about 80% of the cases, mild to moderate alterations in the remainder (""variant"" biochemical phenotype). genotyping of patients is useful to confirm the diagnosis in the latter patients and essential for future prenatal diagnosis. the differential diagnosis may include other lipidoses; idiopathic neonatal hepatitis and other causes of cholestatic icterus should be considered in neonates, and conditions with cerebellar ataxia, dystonia, cataplexy and supranuclear gaze palsy in older children and adults. symptomatic management of patients is crucial. a first product, miglustat, has been granted marketing authorization in europe and several other countries for specific treatment of the neurological manifestations. the prognosis largely correlates with the age at onset of the neurological manifestations.",0
"natural products and traditional medicines are of great importance. such forms of medicine as traditional chinese medicine, ayurveda, kampo, traditional korean medicine, and unani have been practiced in some areas of the world and have blossomed into orderly-regulated systems of medicine. this study aims to review the literature on the relationship among natural products, traditional medicines, and modern medicine, and to explore the possible concepts and methodologies from natural products and traditional medicines to further develop drug discovery. the unique characteristics of theory, application, current role or status, and modern research of eight kinds of traditional medicine systems are summarized in this study. although only a tiny fraction of the existing plant species have been scientifically researched for bioactivities since 1805, when the first pharmacologically-active compound morphine was isolated from opium, natural products and traditional medicines have already made fruitful contributions for modern medicine. when used to develop new drugs, natural products and traditional medicines have their incomparable advantages, such as abundant clinical experiences, and their unique diversity of chemical structures and biological activities.",0
"when writing a manuscript, we often use words such as perfect, strong, good or weak to name the strength of the relationship between variables. however, it is unclear where a good relationship turns into a strong one. the same strength of r is named differently by several researchers. therefore, there is an absolute necessity to explicitly report the strength and direction of r while reporting correlation coefficients in manuscripts. this article aims to familiarize medical readers with several different correlation coefficients reported in medical manuscripts, clarify confounding aspects and summarize the naming practices for the strength of correlation coefficients.",0
"background pembrolizumab demonstrated robust antitumor activity and safety in the phase ib keynote-001 study (nct01295827) of advanced melanoma. five-year outcomes in all patients and treatment-naive patients are reported herein. patients whose disease progressed following initial response and who received a second course of pembrolizumab were also analyzed. patients and methods patients aged ≥18 years with previously treated or treatment-naive advanced/metastatic melanoma received pembrolizumab 2 mg/kg every 3 weeks, 10 mg/kg every 3 weeks, or 10 mg/kg every 2 weeks until disease progression, intolerable toxicity, or patient/investigator decision to withdraw. kaplan-meier estimates of overall survival (os) and progression-free survival (pfs) were calculated. objective response rate and pfs were based on immune-related response criteria by investigator assessment (data cut-off, september 1, 2017). results keynote-001 enrolled 655 patients with melanoma; median follow-up was 55 months. estimated 5-year os was 34% in all patients and 41% in treatment-naive patients; median os was 23.8 months (95% ci, 20.2-30.4) and 38.6 months (95% ci, 27.2-not reached), respectively. estimated 5-year pfs rates were 21% in all patients and 29% in treatment-naive patients; median pfs was 8.3 months (95% ci, 5.8-11.1) and 16.9 months (95% ci, 9.3-35.5), respectively. median response duration was not reached; 73% of all responses and 82% of treatment-naive responses were ongoing at data cut-off; the longest response was ongoing at 66 months. four patients whose disease progressed during observation subsequently received second-course pembrolizumab. one patient each achieved cr and partial response (after data cut-off). treatment-related aes (traes) occurred in 86% of patients and resulted in study discontinuation in 7.8%; 17% experienced grade 3/4 trae. conclusions this 5-year analysis of keynote-001 represents the longest follow-up for pembrolizumab to date and confirms the durable antitumor activity and tolerability of pembrolizumab in advanced melanoma. clinical trial registry clinicaltrials.gov, nct01295827.",0
"with the advance of sequencing technologies, whole exome sequencing has increasingly been used to identify mutations that cause human diseases, especially rare mendelian diseases. among the analysis steps, functional prediction (of being deleterious) plays an important role in filtering or prioritizing nonsynonymous snp (ns) for further analysis. unfortunately, different prediction algorithms use different information and each has its own strength and weakness. it has been suggested that investigators should use predictions from multiple algorithms instead of relying on a single one. however, querying predictions from different databases/web-servers for different algorithms is both tedious and time consuming, especially when dealing with a huge number of nss identified by exome sequencing. to facilitate the process, we developed dbnsfp (database for nonsynonymous snps' functional predictions). it compiles prediction scores from four new and popular algorithms (sift, polyphen2, lrt, and mutationtaster), along with a conservation score (phylop) and other related information, for every potential ns in the human genome (a total of 75,931,005). it is the first integrated database of functional predictions from multiple algorithms for the comprehensive collection of human nss. dbnsfp is freely available for download at",0
"background implementation science has progressed towards increased use of theoretical approaches to provide better understanding and explanation of how and why implementation succeeds or fails. the aim of this article is to propose a taxonomy that distinguishes between different categories of theories, models and frameworks in implementation science, to facilitate appropriate selection and application of relevant approaches in implementation research and practice and to foster cross-disciplinary dialogue among implementation researchers. discussion theoretical approaches used in implementation science have three overarching aims: describing and/or guiding the process of translating research into practice (process models); understanding and/or explaining what influences implementation outcomes (determinant frameworks, classic theories, implementation theories); and evaluating implementation (evaluation frameworks). this article proposes five categories of theoretical approaches to achieve three overarching aims. these categories are not always recognized as separate types of approaches in the literature. while there is overlap between some of the theories, models and frameworks, awareness of the differences is important to facilitate the selection of relevant approaches. most determinant frameworks provide limited ""how-to"" support for carrying out implementation endeavours since the determinants usually are too generic to provide sufficient detail for guiding an implementation process. and while the relevance of addressing barriers and enablers to translating research into practice is mentioned in many process models, these models do not identify or systematically structure specific determinants associated with implementation success. furthermore, process models recognize a temporal sequence of implementation endeavours, whereas determinant frameworks do not explicitly take a process perspective of implementation.",0
"pancreatic insulin-producing beta-cells have a long lifespan, such that in healthy conditions they replicate little during a lifetime. nevertheless, they show increased self-duplication after increased metabolic demand or after injury (that is, beta-cell loss). it is not known whether adult mammals can differentiate (regenerate) new beta-cells after extreme, total beta-cell loss, as in diabetes. this would indicate differentiation from precursors or another heterologous (non-beta-cell) source. here we show beta-cell regeneration in a transgenic model of diphtheria-toxin-induced acute selective near-total beta-cell ablation. if given insulin, the mice survived and showed beta-cell mass augmentation with time. lineage-tracing to label the glucagon-producing alpha-cells before beta-cell ablation tracked large fractions of regenerated beta-cells as deriving from alpha-cells, revealing a previously disregarded degree of pancreatic cell plasticity. such inter-endocrine spontaneous adult cell conversion could be harnessed towards methods of producing beta-cells for diabetes therapies, either in differentiation settings in vitro or in induced regeneration.",0
"there is considerable evidence that children and adolescents with autistic spectrum disorders (asd) are at increased risk of anxiety and anxiety disorders. however, it is less clear which of the specific dsm-iv anxiety disorders occur most in this population. the present study used meta-analytic techniques to help clarify this issue. a systematic review of the literature identified 31 studies involving 2,121 young people (aged <18 years) with asd, and where the presence of anxiety disorder was assessed using standardized questionnaires or diagnostic interviews. across studies, 39.6% of young people with asd had at least one comorbid dsm-iv anxiety disorder, the most frequent being specific phobia (29.8%) followed by ocd (17.4%) and social anxiety disorder (16.6%). associations were found between the specific anxiety disorders and asd subtype, age, iq, and assessment method (questionnaire versus interview). implications for the identification and treatment of anxiety in young people with asd are discussed.",0
"triglycerides are transported in plasma by specific triglyceride-rich lipoproteins; in epidemiological studies, increased triglyceride levels correlate with higher risk for coronary artery disease (cad). however, it is unclear whether this association reflects causal processes. we used 185 common variants recently mapped for plasma lipids (p < 5 × 10(-8) for each) to examine the role of triglycerides in risk for cad. first, we highlight loci associated with both low-density lipoprotein cholesterol (ldl-c) and triglyceride levels, and we show that the direction and magnitude of the associations with both traits are factors in determining cad risk. second, we consider loci with only a strong association with triglycerides and show that these loci are also associated with cad. finally, in a model accounting for effects on ldl-c and/or high-density lipoprotein cholesterol (hdl-c) levels, the strength of a polymorphism's effect on triglyceride levels is correlated with the magnitude of its effect on cad risk. these results suggest that triglyceride-rich lipoproteins causally influence risk for cad.",0
"listeria monocytogenes insertion mutants defective in hemolysin production were generated using the conjugative transposons tn916 and tn1545. all of the nonhemolytic mutants (hly-) lacked a secreted 58-kd polypeptide, presumedly hemolysin, and were avirulent in a mouse model. an intracellular multiplication assay was established in monolayers of mouse bone marrow-derived macrophages, the j774 macrophage-like cell line, the cl.7 embryonic mouse fibroblast cell line, and the henle 407 human epithelial cell line. the hly+ strain grew intracellularly in all of the tissue culture cells with a doubling time of approximately 60 min. in contrast, the hly- mutants failed to grow in the murine-derived tissue culture cells, but retained the ability to grow in the human tissue culture cells examined. hemolytic-positive revertants were selected after passage of the hly- mutants through monolayers of j774 cells. in each case, the hemolytic revertants possessed the 58-kd polypeptide, were capable of intracellular growth in tissue culture monolayers and were virulent for mice.",0
"background the global burden of sickle cell anaemia (sca) is set to rise as a consequence of improved survival in high-prevalence low- and middle-income countries and population migration to higher-income countries. the host of quantitative evidence documenting these changes has not been assembled at the global level. the purpose of this study is to estimate trends in the future number of newborns with sca and the number of lives that could be saved in under-five children with sca by the implementation of different levels of health interventions. methods and findings first, we calculated projected numbers of newborns with sca for each 5-y interval between 2010 and 2050 by combining estimates of national sca frequencies with projected demographic data. we then accounted for under-five mortality (u5m) projections and tested different levels of excess mortality for children with sca, reflecting the benefits of implementing specific health interventions for under-five patients in 2015, to assess the number of lives that could be saved with appropriate health care services. the estimated number of newborns with sca globally will increase from 305,800 (confidence interval : 238,400-398,800) in 2010 to 404,200 (ci: 242,500-657,600) in 2050. it is likely that nigeria (2010: 91,000 newborns with sca ; 2050: 140,800 ) and the democratic republic of the congo (2010: 39,700 ; 2050: 44,700 ) will remain the countries most in need of policies for the prevention and management of sca. we predict a decrease in the annual number of newborns with sca in india (2010: 44,400 ; 2050: 33,900 ). the implementation of basic health interventions (e.g., prenatal diagnosis, penicillin prophylaxis, and vaccination) for sca in 2015, leading to significant reductions in excess mortality among under-five children with sca, could, by 2050, prolong the lives of 5,302,900 newborns with sca. similarly, large-scale universal screening could save the lives of up to 9,806,000 (ci: 6,745,800-14,232,700) newborns with sca globally, 85% (ci: 81%-88%) of whom will be born in sub-saharan africa. the study findings are limited by the uncertainty in the estimates and the assumptions around mortality reductions associated with interventions. conclusions our quantitative approach confirms that the global burden of sca is increasing, and highlights the need to develop specific national policies for appropriate public health planning, particularly in low- and middle-income countries. further empirical collaborative epidemiological studies are vital to assess current and future health care needs, especially in nigeria, the democratic republic of the congo, and india.",0
"while covid-19 continues raging worldwide, effective vaccines are highly anticipated. however, vaccine hesitancy is widespread. survey results on uptake intentions vary and continue to change. this review compared trends and synthesized findings in vaccination receptivity over time across us and international polls, assessing survey design influences and evaluating context to inform policies and practices. data sources included academic literature (pubmed, embase, and psycinfo following prisma guidelines), news and official reports published by 20 october 2020. two researchers independently screened potential peer-reviewed articles and syndicated polls for eligibility; 126 studies and surveys were selected. declining vaccine acceptance (from >70% in march to <50% in october) with demographic, socioeconomic, and partisan divides was observed. perceived risk, concerns over vaccine safety and effectiveness, doctors' recommendations, and inoculation history were common factors. impacts of regional infection rates, gender, and personal covid-19 experience were inconclusive. unique covid-19 factors included political party orientation, doubts toward expedited development/approval process, and perceived political interference. many receptive participants preferred to wait until others have taken the vaccine; mandates could increase resistance. survey wording and answer options showed influence on responses. to achieve herd immunity, communication campaigns are immediately needed, focusing on transparency and restoring trust in health authorities.",0
"while severe acute respiratory syndrome coronavirus (sars-cov) was initially thought to enter cells through direct fusion with the plasma membrane, more recent evidence suggests that virus entry may also involve endocytosis. we have found that sars-cov enters cells via ph- and receptor-dependent endocytosis. treatment of cells with either sars-cov spike protein or spike-bearing pseudoviruses resulted in the translocation of angiotensin-converting enzyme 2 (ace2), the functional receptor of sars-cov, from the cell surface to endosomes. in addition, the spike-bearing pseudoviruses and early endosome antigen 1 were found to colocalize in endosomes. further analyses using specific endocytic pathway inhibitors and dominant-negative eps15 as well as caveolin-1 colocalization study suggested that virus entry was mediated by a clathrin- and caveolae-independent mechanism. moreover, cholesterol- and sphingolipid-rich lipid raft microdomains in the plasma membrane, which have been shown to act as platforms for many physiological signaling pathways, were shown to be involved in virus entry. endocytic entry of sars-cov may expand the cellular range of sars-cov infection, and our findings here contribute to the understanding of sars-cov pathogenesis, providing new information for anti-viral drug research.",0
"we report here a factor (b cell growth factor) found in induced supernatants of the mouse thymoma el4 that co-stimulates with anti-igm antibodies in short-term cultures of purified b lymphocytes to induce polyclonal b cell proliferation but not antibody-forming cell production. the factor is not mitogenic for resting b cells and interacts with anti-igm-activated b cells in a non-h-2-restricted manner. absorption studies and molecular weight analysis reveal the factor is distinct from interleukin 2. this factor synergises with antigen, interleukin 2, and an interleukin 2-free, b cell growth factor-free t cell supernatant that contains t cell-replacing factor to produce erythrocyte-specific plaque-forming cells in cultures of highly purified b cells.",0
"importance health care workers exposed to coronavirus disease 2019 (covid-19) could be psychologically stressed. objective to assess the magnitude of mental health outcomes and associated factors among health care workers treating patients exposed to covid-19 in china. design, settings, and participants this cross-sectional, survey-based, region-stratified study collected demographic data and mental health measurements from 1257 health care workers in 34 hospitals from january 29, 2020, to february 3, 2020, in china. health care workers in hospitals equipped with fever clinics or wards for patients with covid-19 were eligible. main outcomes and measures the degree of symptoms of depression, anxiety, insomnia, and distress was assessed by the chinese versions of the 9-item patient health questionnaire, the 7-item generalized anxiety disorder scale, the 7-item insomnia severity index, and the 22-item impact of event scale-revised, respectively. multivariable logistic regression analysis was performed to identify factors associated with mental health outcomes. results a total of 1257 of 1830 contacted individuals completed the survey, with a participation rate of 68.7%. a total of 813 (64.7%) were aged 26 to 40 years, and 964 (76.7%) were women. of all participants, 764 (60.8%) were nurses, and 493 (39.2%) were physicians; 760 (60.5%) worked in hospitals in wuhan, and 522 (41.5%) were frontline health care workers. a considerable proportion of participants reported symptoms of depression (634 ), anxiety (560 ), insomnia (427 ), and distress (899 ). nurses, women, frontline health care workers, and those working in wuhan, china, reported more severe degrees of all measurements of mental health symptoms than other health care workers (eg, median patient health questionnaire scores among physicians vs nurses: 4.0 vs 5.0 ; p = .007; median generalized anxiety disorder scale scores among men vs women: 2.0 vs 4.0 ; p conclusions and relevance in this survey of heath care workers in hospitals equipped with fever clinics or wards for patients with covid-19 in wuhan and other regions in china, participants reported experiencing psychological burden, especially nurses, women, those in wuhan, and frontline health care workers directly engaged in the diagnosis, treatment, and care for patients with covid-19.",0
"controversy still exists on the optimal surgical resection for potentially curable gastric cancer. much better long-term survival has been reported in retrospective/non-randomized studies with d2 resections that involve a radical extended regional lymphadenectomy than with the standard d1 resections. in this paper we report the long-term survival of patients entered into a randomized study, with follow-up to death or 3 years in 96% of patients and a median follow-up of 6.5 years. in this prospective trial d1 resection (removal of regional perigastric nodes) was compared with d2 resection (extended lymphadenectomy to include level 1 and 2 regional nodes). central randomization followed a staging laparotomy. out of 737 patients with histologically proven gastric adenocarcinoma registered, 337 patients were ineligible by staging laparotomy because of advanced disease and 400 were randomized. the 5-year survival rates were 35% for d1 resection and 33% for d2 resection (difference -2%, 95% ci = -12%-8%). there was no difference in the overall 5-year survival between the two arms (hr = 1.10, 95% ci 0.87-1.39, where hr > 1 implies a survival benefit to d1 surgery). survival based on death from gastric cancer as the event was similar in the d1 and d2 groups (hr = 1.05, 95% ci 0.79-1.39) as was recurrence-free survival (hr = 1.03, 95% ci 0.82-1.29). in a multivariate analysis, clinical stages ii and iii, old age, male sex and removal of spleen and pancreas were independently associated with poor survival. these findings indicate that the classical japanese d2 resection offers no survival advantage over d1 surgery. however, the possibility that d2 resection without pancreatico-splenectomy may be better than standard d1 resection cannot be dismissed by the results of this trial.",0
"interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. there are several weak and strong interactions that render stability to a protein structure or an assembly. protein interactions calculator (pic) is a server which, given the coordinate set of 3d structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. interactions are calculated on the basis of standard, published criteria. the identified interactions between residues can be visualized using a rasmol and jmol interface. the advantage with pic server is the easy availability of inter-residue interaction calculations in a single site. it also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. user can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.",0
"objective circulatory shock is a life-threatening syndrome resulting in multiorgan failure and a high mortality rate. the aim of this consensus is to provide support to the bedside clinician regarding the diagnosis, management and monitoring of shock. methods the european society of intensive care medicine invited 12 experts to form a task force to update a previous consensus (antonelli et al.: intensive care med 33:575-590, 2007). the same five questions addressed in the earlier consensus were used as the outline for the literature search and review, with the aim of the task force to produce statements based on the available literature and evidence. these questions were: (1) what are the epidemiologic and pathophysiologic features of shock in the intensive care unit? (2) should we monitor preload and fluid responsiveness in shock? (3) how and when should we monitor stroke volume or cardiac output in shock? (4) what markers of the regional and microcirculation can be monitored, and how can cellular function be assessed in shock? (5) what is the evidence for using hemodynamic monitoring to direct therapy in shock? four types of statements were used: definition, recommendation, best practice and statement of fact. results forty-four statements were made. the main new statements include: (1) statements on individualizing blood pressure targets; (2) statements on the assessment and prediction of fluid responsiveness; (3) statements on the use of echocardiography and hemodynamic monitoring. conclusions this consensus provides 44 statements that can be used at the bedside to diagnose, treat and monitor patients with shock.",0
"severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has caused a global pandemic with millions infected and more than 1 million fatalities. questions regarding the robustness, functionality, and longevity of the antibody response to the virus remain unanswered. here, on the basis of a dataset of 30,082 individuals screened at mount sinai health system in new york city, we report that the vast majority of infected individuals with mild-to-moderate covid-19 experience robust immunoglobulin g antibody responses against the viral spike protein. we also show that titers are relatively stable for at least a period of about 5 months and that anti-spike binding titers significantly correlate with neutralization of authentic sars-cov-2. our data suggest that more than 90% of seroconverters make detectable neutralizing antibody responses. these titers remain relatively stable for several months after infection.",0
"background sleep duration may be an important regulator of body weight and metabolism. an association between short habitual sleep time and increased body mass index (bmi) has been reported in large population samples. the potential role of metabolic hormones in this association is unknown. methods and findings study participants were 1,024 volunteers from the wisconsin sleep cohort study, a population-based longitudinal study of sleep disorders. participants underwent nocturnal polysomnography and reported on their sleep habits through questionnaires and sleep diaries. following polysomnography, morning, fasted blood samples were evaluated for serum leptin and ghrelin (two key opposing hormones in appetite regulation), adiponectin, insulin, glucose, and lipid profile. relationships among these measures, bmi, and sleep duration (habitual and immediately prior to blood sampling) were examined using multiple variable regressions with control for confounding factors. a u-shaped curvilinear association between sleep duration and bmi was observed. in persons sleeping less than 8 h (74.4% of the sample), increased bmi was proportional to decreased sleep. short sleep was associated with low leptin (p for slope = 0.01), with a predicted 15.5% lower leptin for habitual sleep of 5 h versus 8 h, and high ghrelin (p for slope = 0.008), with a predicted 14.9% higher ghrelin for nocturnal (polysomnographic) sleep of 5 h versus 8 h, independent of bmi. conclusion participants with short sleep had reduced leptin and elevated ghrelin. these differences in leptin and ghrelin are likely to increase appetite, possibly explaining the increased bmi observed with short sleep duration. in western societies, where chronic sleep restriction is common and food is widely available, changes in appetite regulatory hormones with sleep curtailment may contribute to obesity.",0
"in order to evaluate the efficacy of convalescent plasma therapy in the treatment of patients with severe acute respiratory syndrome (sars), 80 sars patients were given convalescent plasma at prince of wales hospital, hong kong, between 20 march and 26 may 2003. good outcome was defined as discharge by day 22 following the onset of sars symptoms. poor outcome was defined as death or hospitalization beyond 22 days. a higher day-22 discharge rate was observed among patients who were given convalescent plasma before day 14 of illness (58.3% vs 15.6%; p<0.001) and among those who were pcr positive and seronegative for coronavirus at the time of plasma infusion (66.7% vs 20%; p=0.001).",0
"fear is an adaptive response in the presence of danger. however, when threat is uncertain and continuous, as in the current coronavirus disease (covid-19) pandemic, fear can become chronic and burdensome. to identify predictors of fear of the coronavirus, we conducted an online survey (n = 439) three days after the world health organization declared the coronavirus outbreak a pandemic (i.e., between march 14 and 17, 2020). fear of the coronavirus was assessed with the newly developed fear of the coronavirus questionnaire (fcq) consisting of eight questions pertaining to different dimensions of fear (e.g., subjective worry, safety behaviors, preferential attention), and an open-ended question. the predictors included psychological vulnerability factors (i.e., intolerance of uncertainty, worry, and health anxiety), media exposure, and personal relevance (i.e., personal health, risk for loved ones, and risk control). we found four predictors for the fcq in a simultaneous regression analysis: health anxiety, regular media use, social media use, and risks for loved ones (r 2 = .37). furthermore, 16 different topics of concern were identified based participants' open-ended responses, including the health of loved ones, health care systems overload, and economic consequences. we discuss the relevance of our findings for managing people's fear of the coronavirus.",0
"bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the mechanisms of the disease processes at the molecular level over the last decades. to facilitate future research, it becomes necessary to form a database collectively presenting the virulence factors (vfs) of various medical significant bacterial pathogens. the aim of virulence factor database (vfdb) ( is to provide such a source for scientists to rapidly access to current knowledge about vfs from various bacterial pathogens. vfdb is comprehensive and user-friendly. one can search vfdb by browsing each genus or by typing keywords. furthermore, a blast search tool against all known vf-related genes is also available. vfdb provides a unified gateway to store, search, retrieve and update information about vfs from various bacterial pathogens.",0
"background effective antiviral therapy is important for tackling the coronavirus disease 2019 (covid-19) pandemic. we assessed the efficacy and safety of combined interferon beta-1b, lopinavir-ritonavir, and ribavirin for treating patients with covid-19. methods this was a multicentre, prospective, open-label, randomised, phase 2 trial in adults with covid-19 who were admitted to six hospitals in hong kong. patients were randomly assigned (2:1) to a 14-day combination of lopinavir 400 mg and ritonavir 100 mg every 12 h, ribavirin 400 mg every 12 h, and three doses of 8 million international units of interferon beta-1b on alternate days (combination group) or to 14 days of lopinavir 400 mg and ritonavir 100 mg every 12 h (control group). the primary endpoint was the time to providing a nasopharyngeal swab negative for severe acute respiratory syndrome coronavirus 2 rt-pcr, and was done in the intention-to-treat population. the study is registered with clinicaltrials.gov, nct04276688. findings between feb 10 and march 20, 2020, 127 patients were recruited; 86 were randomly assigned to the combination group and 41 were assigned to the control group. the median number of days from symptom onset to start of study treatment was 5 days (iqr 3-7). the combination group had a significantly shorter median time from start of study treatment to negative nasopharyngeal swab (7 days ) than the control group (12 days ; hazard ratio 4·37 , p=0·0010). adverse events included self-limited nausea and diarrhoea with no difference between the two groups. one patient in the control group discontinued lopinavir-ritonavir because of biochemical hepatitis. no patients died during the study. interpretation early triple antiviral therapy was safe and superior to lopinavir-ritonavir alone in alleviating symptoms and shortening the duration of viral shedding and hospital stay in patients with mild to moderate covid-19. future clinical study of a double antiviral therapy with interferon beta-1b as a backbone is warranted. funding the shaw-foundation, richard and carol yu, may tam mak mei yin, and sanming project of medicine.",0
"mammalian cell homeostasis during starvation depends on initiation of autophagy by endoplasmic reticulum-localized phosphatidylinositol 3-phosphate (ptdins(3)p) synthesis. formation of double-membrane autophagosomes that engulf cytosolic components requires the lc3-conjugating atg12-5-16l1 complex. the molecular mechanisms of atg12-5-16l1 recruitment and significance of ptdins(3)p synthesis at autophagosome formation sites are unknown. by identifying interacting partners of wipis, wd-repeat ptdins(3)p effector proteins, we found that atg16l1 directly binds wipi2b. mutation experiments and ectopic localization of wipi2b to plasma membrane show that wipi2b is a ptdins(3)p effector upstream of atg16l1 and is required for lc3 conjugation and starvation-induced autophagy through recruitment of the atg12-5-16l1 complex. atg16l1 mutants, which do not bind wipi2b but bind fip200, cannot rescue starvation-induced autophagy in atg16l1-deficient mefs. wipi2b is also required for autophagic clearance of pathogenic bacteria. wipi2b binds the membrane surrounding salmonella and recruits the atg12-5-16l1 complex, initiating lc3 conjugation, autophagosomal membrane formation, and engulfment of salmonella.",0
"hmmer is a software suite for protein sequence similarity searches using probabilistic methods. previously, hmmer has mainly been available only as a computationally intensive unix command-line tool, restricting its use. recent advances in the software, hmmer3, have resulted in a 100-fold speed gain relative to previous versions. it is now feasible to make efficient profile hidden markov model (profile hmm) searches via the web. a hmmer web server ( has been designed and implemented such that most protein database searches return within a few seconds. methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile hmm against a target sequence database, and for searching a protein sequence against pfam. the web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. all search methods are also available as restful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. we have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.",0
"sample size justification is an important consideration when planning a clinical trial, not only for the main trial but also for any preliminary pilot trial. when the outcome is a continuous variable, the sample size calculation requires an accurate estimate of the standard deviation of the outcome measure. a pilot trial can be used to get an estimate of the standard deviation, which could then be used to anticipate what may be observed in the main trial. however, an important consideration is that pilot trials often estimate the standard deviation parameter imprecisely. this paper looks at how we can choose an external pilot trial sample size in order to minimise the sample size of the overall clinical trial programme, that is, the pilot and the main trial together. we produce a method of calculating the optimal solution to the required pilot trial sample size when the standardised effect size for the main trial is known. however, as it may not be possible to know the standardised effect size to be used prior to the pilot trial, approximate rules are also presented. for a main trial designed with 90% power and two-sided 5% significance, we recommend pilot trial sample sizes per treatment arm of 75, 25, 15 and 10 for standardised effect sizes that are extra small (≤0.1), small (0.2), medium (0.5) or large (0.8), respectively.",0
"background many implementation efforts fail, even with highly developed plans for execution, because contextual factors can be powerful forces working against implementation in the real world. the consolidated framework for implementation research (cfir) is one of the most commonly used determinant frameworks to assess these contextual factors; however, it has been over 10 years since publication and there is a need for updates. the purpose of this project was to elicit feedback from experienced cfir users to inform updates to the framework. methods user feedback was obtained from two sources: (1) a literature review with a systematic search; and (2) a survey of authors who used the cfir in a published study. data were combined across both sources and reviewed to identify themes; a consensus approach was used to finalize all cfir updates. the va ann arbor healthcare system irb declared this study exempt from the requirements of 38 cfr 16 based on category 2. results the systematic search yielded 376 articles that contained the cfir in the title and/or abstract and 334 unique authors with contact information; 59 articles included feedback on the cfir. forty percent (n = 134/334) of authors completed the survey. the cfir received positive ratings on most framework sensibility items (e.g., applicability, usability), but respondents also provided recommendations for changes. overall, updates to the cfir include revisions to existing domains and constructs as well as the addition, removal, or relocation of constructs. these changes address important critiques of the cfir, including better centering innovation recipients and adding determinants to equity in implementation. conclusion the updates in the cfir reflect feedback from a growing community of cfir users. although there are many updates, constructs can be mapped back to the original cfir to ensure longitudinal consistency. we encourage users to continue critiquing the cfir, facilitating the evolution of the framework as implementation science advances.",0
"background bereavement is a universal experience, and its association with excess morbidity and mortality is well established. nevertheless, grief becomes a serious health concern for a relative few. for such individuals, intense grief persists, is distressing and disabling, and may meet criteria as a distinct mental disorder. at present, grief is not recognized as a mental disorder in the dsm-iv or icd-10. the goal of this study was to determine the psychometric validity of criteria for prolonged grief disorder (pgd) to enhance the detection and potential treatment of bereaved individuals at heightened risk of persistent distress and dysfunction. methods and findings a total of 291 bereaved respondents were interviewed three times, grouped as 0-6, 6-12, and 12-24 mo post-loss. item response theory (irt) analyses derived the most informative, unbiased pgd symptoms. combinatoric analyses identified the most sensitive and specific pgd algorithm that was then tested to evaluate its psychometric validity. criteria require reactions to a significant loss that involve the experience of yearning (e.g., physical or emotional suffering as a result of the desired, but unfulfilled, reunion with the deceased) and at least five of the following nine symptoms experienced at least daily or to a disabling degree: feeling emotionally numb, stunned, or that life is meaningless; experiencing mistrust; bitterness over the loss; difficulty accepting the loss; identity confusion; avoidance of the reality of the loss; or difficulty moving on with life. symptoms must be present at sufficiently high levels at least six mo from the death and be associated with functional impairment. conclusions the criteria set for pgd appear able to identify bereaved persons at heightened risk for enduring distress and dysfunction. the results support the psychometric validity of the criteria for pgd that we propose for inclusion in dsm-v and icd-11. please see later in the article for editors' summary.",0
"the human t-cell leukemia virus type 1 (htlv-1), identified as the first human oncogenic retrovirus 30 years ago, is not an ubiquitous virus. htlv-1 is present throughout the world, with clusters of high endemicity located often nearby areas where the virus is nearly absent. the main htlv-1 highly endemic regions are the southwestern part of japan, sub-saharan africa and south america, the caribbean area, and foci in middle east and australo-melanesia. the origin of this puzzling geographical or rather ethnic repartition is probably linked to a founder effect in some groups with the persistence of a high viral transmission rate. despite different socio-economic and cultural environments, the htlv-1 prevalence increases gradually with age, especially among women in all highly endemic areas. the three modes of htlv-1 transmission are mother to child, sexual transmission, and transmission with contaminated blood products. twenty years ago, de thé and bomford estimated the total number of htlv-1 carriers to be 10-20 millions people. at that time, large regions had not been investigated, few population-based studies were available and the assays used for htlv-1 serology were not enough specific. despite the fact that there is still a lot of data lacking in large areas of the world and that most of the htlv-1 studies concern only blood donors, pregnant women, or different selected patients or high-risk groups, we shall try based on the most recent data, to revisit the world distribution and the estimates of the number of htlv-1 infected persons. our best estimates range from 5-10 millions htlv-1 infected individuals. however, these results were based on only approximately 1.5 billion of individuals originating from known htlv-1 endemic areas with reliable available epidemiological data. correct estimates in other highly populated regions, such as china, india, the maghreb, and east africa, is currently not possible, thus, the current number of htlv-1 carriers is very probably much higher.",0
"jpred ( is a secondary structure prediction server powered by the jnet algorithm. jpred performs over 1000 predictions per week for users in more than 50 countries. the recently updated jnet algorithm provides a three-state (alpha-helix, beta-strand and coil) prediction of secondary structure at an accuracy of 81.5%. given either a single protein sequence or a multiple sequence alignment, jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility are made. the predictions are presented as coloured html, plain text, postscript, pdf and via the jalview alignment editor to allow flexibility in viewing and applying the data. the new jpred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests. functional improvements include batch submission of sequences, summary results via email and updates to the search databases. a new software pipeline will enable jnet/jpred to continue to be updated in sync with major updates to scop and uniprot and so ensures that jpred 3 will maintain high-accuracy predictions.",0
"background web-based and mobile health interventions (also called ""internet interventions"" or ""ehealth/mhealth interventions"") are tools or treatments, typically behaviorally based, that are operationalized and transformed for delivery via the internet or mobile platforms. these include electronic tools for patients, informal caregivers, healthy consumers, and health care providers. the ""consolidated standards of reporting trials"" (consort) was developed to improve the suboptimal reporting of randomized controlled trials (rcts). while broadly the consort statement can be applied to provide guidance on how ehealth and mhealth trials should be reported, rcts of web-based interventions pose very specific issues and challenges, in particular related to reporting sufficient details of the intervention to allow replication and theory-building. objective to develop a checklist, dubbed consort-ehealth (consolidated standards of reporting trials of electronic and mobile health applications and online telehealth), as an extension of the consort statement that provides guidance for authors of ehealth and mhealth interventions. methods a literature review was conducted, followed by a survey among ehealth experts and a workshop. results an instrument and checklist was constructed as an extension of the consort statement. the instrument has been adopted by the journal of medical internet research (jmir) and authors of ehealth rcts are required to submit an electronic checklist explaining how they addressed each subitem. conclusions consort-ehealth has the potential to improve reporting and provides a basis for evaluating the validity and applicability of ehealth trials. subitems describing how the intervention should be reported can also be used for non-rct evaluation reports. as part of the development process, an evaluation component is essential, therefore feedback from authors will be solicited, and a before-after study will evaluate whether reporting has been improved.",0
"diabetes is one of the most important comorbidities linked to the severity of all three known human pathogenic coronavirus infections, including severe acute respiratory syndrome coronavirus 2. patients with diabetes have an increased risk of severe complications including adult respiratory distress syndrome and multi-organ failure. depending on the global region, 20-50% of patients in the coronavirus disease 2019 (covid-19) pandemic had diabetes. given the importance of the link between covid-19 and diabetes, we have formed an international panel of experts in the field of diabetes and endocrinology to provide some guidance and practical recommendations for the management of diabetes during the pandemic. we aim to briefly provide insight into potential mechanistic links between the novel coronavirus infection and diabetes, present practical management recommendations, and elaborate on the differential needs of several patient groups.",0
"orthology assignment is ideally suited for functional inference. however, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. we, therefore, developed eggnog-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggnog database. to validate our method, we benchmarked gene ontology (go) predictions against two widely used homology-based approaches: blast and interproscan. orthology filters applied to blast results reduced the rate of false positive assignments by 11%, and increased the ratio of experimentally validated terms recovered over all terms assigned per protein by 15%. compared with interproscan, eggnog-mapper achieved similar proteome coverage and precision while predicting, on average, 41 more terms per protein and increasing the rate of experimentally validated terms recovered over total term assignments per protein by 35%. eggnog-mapper predictions scored within the top-5 methods in the three go categories using the cafa2 nk-partial benchmark. finally, we evaluated eggnog-mapper for functional annotation of metagenomics data, yielding better performance than interproscan. eggnog-mapper runs ∼15× faster than blast and at least 2.5× faster than interproscan. the tool is available standalone and as an online service at",0
"finding individual-level data for adequately-powered mendelian randomization analyses may be problematic. as publicly-available summarized data on genetic associations with disease outcomes from large consortia are becoming more abundant, use of published data is an attractive analysis strategy for obtaining precise estimates of the causal effects of risk factors on outcomes. we detail the necessary steps for conducting mendelian randomization investigations using published data, and present novel statistical methods for combining data on the associations of multiple (correlated or uncorrelated) genetic variants with the risk factor and outcome into a single causal effect estimate. a two-sample analysis strategy may be employed, in which evidence on the gene-risk factor and gene-outcome associations are taken from different data sources. these approaches allow the efficient identification of risk factors that are suitable targets for clinical intervention from published data, although the ability to assess the assumptions necessary for causal inference is diminished. methods and guidance are illustrated using the example of the causal effect of serum calcium levels on fasting glucose concentrations. the estimated causal effect of a 1 standard deviation (0.13 mmol/l) increase in calcium levels on fasting glucose (mm) using a single lead variant from the casr gene region is 0.044 (95 % credible interval -0.002, 0.100). in contrast, using our method to account for the correlation between variants, the corresponding estimate using 17 genetic variants is 0.022 (95 % credible interval 0.009, 0.035), a more clearly positive causal effect.",0
"objectives in this cross-sectional study, we tested the construct validity of a ""total svd score,"" which combines individual mri features of small-vessel disease (svd) in one measure, by testing associations with vascular risk factors and stroke subtype. methods we analyzed data from patients with lacunar or nondisabling cortical stroke from 2 prospective stroke studies. brain mri was rated for the presence of lacunes, white matter hyperintensities, cerebral microbleeds, and perivascular spaces independently. the presence of each svd feature was summed in an ordinal ""svd score"" (range 0-4). we tested associations with vascular risk factors, stroke subtype, and cerebral atrophy using ordinal regression analysis. results in 461 patients, multivariable analysis found that age (odds ratio 1.10, 95% confidence interval 1.08-1.12), male sex (or 1.58, 95% ci 1.10-2.29), hypertension (or 1.50, 95% ci 1.02-2.20), smoking (or 2.81, 95% ci 1.59-3.63), and lacunar stroke subtype (or 2.45, 95% ci 1.70-3.54) were significantly and independently associated with the total svd score. the score was not associated with cerebral atrophy. conclusions the total svd score may provide a more complete estimate of the full impact of svd on the brain, in a simple and pragmatic way. it could have potential for patient or risk stratification or early efficacy assessment in clinical trials of interventions to prevent svd progression and may (after further testing) have a useful role in clinical practice.",0
"cosmic ( curates comprehensive information on somatic mutations in human cancer. release v48 (july 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. key amongst these is tp53, now available through a collaboration with the iarc p53 database. in addition to data from the cancer genome project (cgp) at the sanger institute, uk, and the cancer genome atlas project (tcga), large systematic screens are also now curated. major website upgrades now make these data much more mineable, with many new selection filters and graphics. a biomart is now available allowing more automated data mining and integration with other biological databases. annotation of genomic features has become a significant focus; cosmic has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. with all genomic information recently updated to grch37, cosmic integrates many diverse types of mutation information and is making much closer links with ensembl and other data resources.",0
"we present vosviewer, a freely available computer program that we have developed for constructing and viewing bibliometric maps. unlike most computer programs that are used for bibliometric mapping, vosviewer pays special attention to the graphical representation of bibliometric maps. the functionality of vosviewer is especially useful for displaying large bibliometric maps in an easy-to-interpret way. the paper consists of three parts. in the first part, an overview of vosviewer's functionality for displaying bibliometric maps is provided. in the second part, the technical implementation of specific parts of the program is discussed. finally, in the third part, vosviewer's ability to handle large maps is demonstrated by using the program to construct and display a co-citation map of 5,000 major scientific journals.",0
"adoptive transfer of large numbers of tumor-reactive cd8(+) cytotoxic t lymphocytes (ctls) expanded and differentiated in vitro has shown promising clinical activity against cancer. however, such protocols are complicated by extensive ex vivo manipulations of tumor-reactive cells and have largely focused on cd8(+) ctls, with much less emphasis on the role and contribution of cd4(+) t cells. using a mouse model of advanced melanoma, we found that transfer of small numbers of naive tumor-reactive cd4(+) t cells into lymphopenic recipients induces substantial t cell expansion, differentiation, and regression of large established tumors without the need for in vitro manipulation. surprisingly, cd4(+) t cells developed cytotoxic activity, and tumor rejection was dependent on class ii-restricted recognition of tumors by tumor-reactive cd4(+) t cells. furthermore, blockade of the coinhibitory receptor ctl-associated antigen 4 (ctla-4) on the transferred cd4(+) t cells resulted in greater expansion of effector t cells, diminished accumulation of tumor-reactive regulatory t cells, and superior antitumor activity capable of inducing regression of spontaneous mouse melanoma. these findings suggest a novel potential therapeutic role for cytotoxic cd4(+) t cells and ctla-4 blockade in cancer immunotherapy, and demonstrate the potential advantages of differentiating tumor-reactive cd4(+) cells in vivo over current protocols favoring in vitro expansion and differentiation.",0
"motivation ld score regression is a reliable and efficient method of using genome-wide association study (gwas) summary-level results data to estimate the snp heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. because the method relies on summary level results data, ld score regression is computationally tractable even for very large sample sizes. however, publicly available gwas summary-level data are typically stored in different databases and have different formats, making it difficult to apply ld score regression to estimate genetic correlations across many different traits simultaneously. results in this manuscript, we describe ld hub - a centralized database of summary-level gwas results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the ld score regression analysis pipeline. to demonstrate functionality and validate our software, we replicated previously reported ld score regression analyses of 49 traits/diseases using ld hub; and estimated snp heritability and the genetic correlation across the different phenotypes. we also present new results obtained by uploading a recent atopic dermatitis gwas meta-analysis to examine the genetic correlation between the condition and other potentially related traits. in response to the growing availability of publicly accessible gwas summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the ld score regression methodology, provide a useful database for the public dissemination of gwas results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies. availability and implementation the web interface and instructions for using ld hub are available at contact: jie.zheng@bristol.ac.uksupplementary information: supplementary data are available at bioinformatics online.",0
"background & aims new york is the current epicenter of coronavirus disease 2019 (covid-19) pandemic. the underrepresented minorities, where the prevalence of obesity is higher, appear to be affected disproportionately. our objectives were to assess the characteristics and early outcomes of patients hospitalized with covid-19 in the bronx and investigate whether obesity is associated with worse outcomes independently from age, gender and other comorbidities. methods this retrospective study included the first 200 patients admitted to a tertiary medical center with covid-19. the electronic medical records were reviewed at least three weeks after admission. the primary endpoint was in-hospital mortality. results 200 patients were included (female sex: 102, african american: 102). the median bmi was 30 kg/m 2 . the median age was 64 years. hypertension (76%), hyperlipidemia (46.2%), and diabetes (39.5%) were the three most common comorbidities. fever (86%), cough (76.5%), and dyspnea (68%) were the three most common symptoms. 24% died during hospitalization (bmi 2 : 31.6%, bmi 25-34 kg/m 2 : 17.2%, bmi ≥ 35 kg/m 2 : 34.8%, p = 0.03). increasing age (analyzed in quartiles), male sex, bmi ≥ 35 kg/m 2 (reference: bmi 25-34 kg/m 2 ), heart failure, cad, and ckd or esrd were found to have a significant univariate association with mortality. the multivariate analysis demonstrated that bmi ≥ 35 kg/m 2 (reference: bmi 25-34 kg/m 2 , or: 3.78; 95% ci: 1.45-9.83; p = 0.006), male sex (or: 2.74; 95% ci: 1.25-5.98; p = 0.011) and increasing age (analyzed in quartiles, or: 1.73; 95% ci: 1.13-2.63; p = 0.011) were independently associated with higher in-hospital mortality. similarly, age, male sex, bmi ≥ 35 kg/m 2 and current or prior smoking were significant predictors for increasing oxygenation requirements in the multivariate analysis, while male sex, age and bmi ≥ 35 kg/m 2 were significant predictors in the multivariate analysis for the outcome of intubation. conclusions in this cohort of hospitalized patients with covid-19 in a minority-predominant population, severe obesity, increasing age, and male sex were independently associated with higher in-hospital mortality and in general worse in-hospital outcomes.",0
"inflammation is a biological response of the immune system that can be triggered by a variety of factors, including pathogens, damaged cells and toxic compounds. these factors may induce acute and/or chronic inflammatory responses in the heart, pancreas, liver, kidney, lung, brain, intestinal tract and reproductive system, potentially leading to tissue damage or disease. both infectious and non-infectious agents and cell damage activate inflammatory cells and trigger inflammatory signaling pathways, most commonly the nf-κb, mapk, and jak-stat pathways. here, we review inflammatory responses within organs, focusing on the etiology of inflammation, inflammatory response mechanisms, resolution of inflammation, and organ-specific inflammatory responses.",0
"the ongoing coronavirus disease 2019 (covid-19) outbreak expanded rapidly throughout china. major behavioral, clinical, and state interventions were undertaken to mitigate the epidemic and prevent the persistence of the virus in human populations in china and worldwide. it remains unclear how these unprecedented interventions, including travel restrictions, affected covid-19 spread in china. we used real-time mobility data from wuhan and detailed case data including travel history to elucidate the role of case importation in transmission in cities across china and to ascertain the impact of control measures. early on, the spatial distribution of covid-19 cases in china was explained well by human mobility data. after the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases were still indicative of local chains of transmission outside of wuhan. this study shows that the drastic control measures implemented in china substantially mitigated the spread of covid-19.",0
"kegg ( is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. each object (database entry) is identified by the kegg identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the url. the kegg pathway map viewer, the brite hierarchy viewer and the newly released kegg genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the url. together with an improved annotation procedure for ko (kegg orthology) assignment, an increasing number of eukaryotic genomes have been included in kegg for better representation of organisms in the taxonomic tree. multiple taxonomy files are generated for classification of kegg organisms and viruses, and the brite hierarchy viewer is used for taxonomy mapping, a variant of brite mapping in the new kegg mapper suite. the taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.",0
"c57bl/6 mice genetically deficient in interleukin 15 (il-15(-/-) mice) were generated by gene targeting. il-15(-/-) mice displayed marked reductions in numbers of thymic and peripheral natural killer (nk) t cells, memory phenotype cd8(+) t cells, and distinct subpopulations of intestinal intraepithelial lymphocytes (iels). the reduction but not absence of these populations in il-15(-/-) mice likely reflects an important role for il-15 for expansion and/or survival of these cells. il-15(-/-) mice lacked nk cells, as assessed by both immunophenotyping and functional criteria, indicating an obligate role for il-15 in the development and functional maturation of nk cells. specific defects associated with il-15 deficiency were reversed by in vivo administration of exogenous il-15. despite their immunological defects, il-15(-/-) mice remained healthy when maintained under specific pathogen-free conditions. however, il-15(-/-) mice are likely to have compromised host defense responses to various pathogens, as they were unable to mount a protective response to challenge with vaccinia virus. these data reveal critical roles for il-15 in the development of specific lymphoid lineages. moreover, the ability to rescue lymphoid defects in il-15(-/-) mice by il-15 administration represents a powerful means by which to further elucidate the biological roles of this cytokine.",0
"in the mammalian cerebral cortex the diversity of interneuronal subtypes underlies a division of labour subserving distinct modes of inhibitory control. a unique mode of inhibitory control may be provided by inhibitory neurons that specifically suppress the firing of other inhibitory neurons. such disinhibition could lead to the selective amplification of local processing and serve the important computational functions of gating and gain modulation. although several interneuron populations are known to target other interneurons to varying degrees, little is known about interneurons specializing in disinhibition and their in vivo function. here we show that a class of interneurons that express vasoactive intestinal polypeptide (vip) mediates disinhibitory control in multiple areas of neocortex and is recruited by reinforcement signals. by combining optogenetic activation with single-cell recordings, we examined the functional role of vip interneurons in awake mice, and investigated the underlying circuit mechanisms in vitro in auditory and medial prefrontal cortices. we identified a basic disinhibitory circuit module in which activation of vip interneurons transiently suppresses primarily somatostatin- and a fraction of parvalbumin-expressing inhibitory interneurons that specialize in the control of the input and output of principal cells, respectively. during the performance of an auditory discrimination task, reinforcement signals (reward and punishment) strongly and uniformly activated vip neurons in auditory cortex, and in turn vip recruitment increased the gain of a functional subpopulation of principal neurons. these results reveal a specific cell type and microcircuit underlying disinhibitory control in cortex and demonstrate that it is activated under specific behavioural conditions.",0
"background thrombosis and inflammation may contribute to the risk of death and complications among patients with coronavirus disease 2019 (covid-19). we hypothesized that therapeutic-dose anticoagulation may improve outcomes in noncritically ill patients who are hospitalized with covid-19. methods in this open-label, adaptive, multiplatform, controlled trial, we randomly assigned patients who were hospitalized with covid-19 and who were not critically ill (which was defined as an absence of critical care-level organ support at enrollment) to receive pragmatically defined regimens of either therapeutic-dose anticoagulation with heparin or usual-care pharmacologic thromboprophylaxis. the primary outcome was organ support-free days, evaluated on an ordinal scale that combined in-hospital death (assigned a value of -1) and the number of days free of cardiovascular or respiratory organ support up to day 21 among patients who survived to hospital discharge. this outcome was evaluated with the use of a bayesian statistical model for all patients and according to the baseline d-dimer level. results the trial was stopped when prespecified criteria for the superiority of therapeutic-dose anticoagulation were met. among 2219 patients in the final analysis, the probability that therapeutic-dose anticoagulation increased organ support-free days as compared with usual-care thromboprophylaxis was 98.6% (adjusted odds ratio, 1.27; 95% credible interval, 1.03 to 1.58). the adjusted absolute between-group difference in survival until hospital discharge without organ support favoring therapeutic-dose anticoagulation was 4.0 percentage points (95% credible interval, 0.5 to 7.2). the final probability of the superiority of therapeutic-dose anticoagulation over usual-care thromboprophylaxis was 97.3% in the high d-dimer cohort, 92.9% in the low d-dimer cohort, and 97.3% in the unknown d-dimer cohort. major bleeding occurred in 1.9% of the patients receiving therapeutic-dose anticoagulation and in 0.9% of those receiving thromboprophylaxis. conclusions in noncritically ill patients with covid-19, an initial strategy of therapeutic-dose anticoagulation with heparin increased the probability of survival to hospital discharge with reduced use of cardiovascular or respiratory organ support as compared with usual-care thromboprophylaxis. (attacc, activ-4a, and remap-cap clinicaltrials.gov numbers, nct04372589, nct04505774, nct04359277, and nct02735707.).",0
"scanprosite-- a new and improved version of the web-based tool for detecting prosite signature matches in protein sequences. for a number of prosite profiles, the tool now makes use of prorules--context-dependent annotation templates--to detect functional and structural intra-domain residues. the detection of those features enhances the power of function prediction based on profiles. both user-defined sequences and sequences from the uniprot knowledgebase can be matched against custom patterns, or against prosite signatures. to improve response times, matches of sequences from uniprotkb against prosite signatures are now retrieved from a pre-computed match database. several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.",0
"primary infection with virus can stimulate a vigorous cytotoxic t cell response. the magnitude of the antigen-specific component versus the bystander component of a primary t cell response remains controversial. in this study, we have used tetrameric major histocompatibility complex-peptide complexes to directly visualize antigen-specific cluster of differentration (cd)8+ t cells during the primary immune response to epstein-barr virus (ebv) infection in humans. we show that massive expansion of activated, antigen-specific t cells occurs during the primary response to this virus. in one individual, t cells specific for a single ebv epitope comprised 44% of the total cd8+ t cells within peripheral blood. the majority of the antigen-specific cells had an activated/memory phenotype, with expression of human histocompatibility leukocyte antigen (hla) dr, cd38, and cd45ro, downregulation of cd62 leukocyte (cd62l), and low levels of expression of cd45ra. after recovery from aim, the frequency of antigen-specific t cells fell in most donors studied, although populations of antigen-specific cells continued to be easily detectable for at least 3 yr.",0
"the clinician's guide to prevention and treatment of osteoporosis was developed by an expert committee of the national osteoporosis foundation (nof) in collaboration with a multispecialty council of medical experts in the field of bone health convened by nof. readers are urged to consult current prescribing information on any drug, device, or procedure discussed in this publication.",0
"mesenchymal stem cells (mscs) are defined as cells that undergo sustained in vitro growth and can give rise to multiple mesenchymal lineages. because mscs have only been isolated from tissue in culture, the equivalent cells have not been identified in vivo and little is known about their physiological roles or even their exact tissue location. in this study, we used phenotypic, morphological, and functional criteria to identify and prospectively isolate a subset of mscs (pdgfralpha+sca-1+cd45-ter119-) from adult mouse bone marrow. individual mscs generated colonies at a high frequency and could differentiate into hematopoietic niche cells, osteoblasts, and adipocytes after in vivo transplantation. naive mscs resided in the perivascular region in a quiescent state. this study provides the useful method needed to identify mscs as defined in vivo entities.",0
"although recent studies have revealed that heart cells are generated in adult mammals, the frequency of generation and the source of new heart cells are not yet known. some studies suggest a high rate of stem cell activity with differentiation of progenitors to cardiomyocytes. other studies suggest that new cardiomyocytes are born at a very low rate, and that they may be derived from the division of pre-existing cardiomyocytes. here we show, by combining two different pulse-chase approaches--genetic fate-mapping with stable isotope labelling, and multi-isotope imaging mass spectrometry--that the genesis of cardiomyocytes occurs at a low rate by the division of pre-existing cardiomyocytes during normal ageing, a process that increases adjacent to areas of myocardial injury. we found that cell cycle activity during normal ageing and after injury led to polyploidy and multinucleation, but also to new diploid, mononucleate cardiomyocytes. these data reveal pre-existing cardiomyocytes as the dominant source of cardiomyocyte replacement in normal mammalian myocardial homeostasis as well as after myocardial injury.",0
"background the knee injury and osteoarthritis outcome score (koos) is an extension of the western ontario and mcmaster universities osteoarthrtis index (womac), the most commonly used outcome instrument for assessment of patient-relevant treatment effects in osteoarthritis. koos was developed for younger and/or more active patients with knee injury and knee osteoarthritis and has in previous studies on these groups been the more responsive instrument compared to the womac. some patients eligible for total knee replacement have expectations of more demanding physical functions than required for daily living. this encouraged us to study the use of the knee injury and osteoarthritis outcome score (koos) to assess the outcome of total knee replacement. methods we studied the test-retest reliability, validity and responsiveness of the swedish version lk 1.0 of the koos when used to prospectively evaluate the outcome of 105 patients (mean age 71.3, 66 women) after total knee replacement. the follow-up rates at 6 and 12 months were 92% and 86%, respectively. results the intraclass correlation coefficients were over 0.75 for all subscales indicating sufficient test-retest reliability. bland-altman plots confirmed this finding. over 90% of the patients regarded improvement in the subscales pain, symptoms, activities of daily living, and knee-related quality of life to be extremely or very important when deciding to have their knee operated on indicating good content validity. the correlations found in comparison to the sf-36 indicated the koos measured expected constructs. the most responsive subscale was knee-related quality of life. the effect sizes of the five koos subscales at 12 months ranged from 1.08 to 3.54 and for the womac from 1.65 to 2.56. conclusion the knee injury and osteoarthritis outcome score (koos) is a valid, reliable, and responsive outcome measure in total joint replacement. in comparison to the womac, the koos improved validity and may be at least as responsive as the womac.",0
"background invasive fungal diseases (ifds) remain important causes of morbidity and mortality. the consensus definitions of the infectious diseases group of the european organization for research and treatment of cancer and the mycoses study group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. however, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. with newer diagnostic techniques available, it was clear that an update of these definitions was essential. methods to achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of ifd. a final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. there were several rounds of discussion before a final version of the manuscript was approved. results there is no change in the classifications of ""proven,"" ""probable,"" and ""possible"" ifd, although the definition of ""probable"" has been expanded and the scope of the category ""possible"" has been diminished. the category of proven ifd can apply to any patient, regardless of whether the patient is immunocompromised. the probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. conclusions these updated definitions of ifds should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.",0
"diagnostic accuracy studies are, like other clinical studies, at risk of bias due to shortcomings in design and conduct, and the results of a diagnostic accuracy study may not apply to other patient groups and settings. readers of study reports need to be informed about study design and conduct, in sufficient detail to judge the trustworthiness and applicability of the study findings. the stard statement (standards for reporting of diagnostic accuracy studies) was developed to improve the completeness and transparency of reports of diagnostic accuracy studies. stard contains a list of essential items that can be used as a checklist, by authors, reviewers and other readers, to ensure that a report of a diagnostic accuracy study contains the necessary information. stard was recently updated. all updated stard materials, including the checklist, are available at here, we present the stard 2015 explanation and elaboration document. through commented examples of appropriate reporting, we clarify the rationale for each of the 30 items on the stard 2015 checklist, and describe what is expected from authors in developing sufficiently informative study reports.",0
"a desirable but as yet unachieved property of a human immunodeficiency virus type 1 (hiv-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bnabs). one approach to the problem is to create trimeric mimics of the native envelope glycoprotein (env) spike that expose as many bnab epitopes as possible, while occluding those for non-neutralizing antibodies (non-nabs). here, we describe the design and properties of soluble, cleaved sosip.664 gp140 trimers based on the subtype a transmitted/founder strain, bg505. these trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. they are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (em). we used several techniques, including elisa and surface plasmon resonance (spr), to determine the relationship between the ability of monoclonal antibodies (mabs) to bind the soluble trimers and neutralize the corresponding virus. in general, the concordance was excellent, in that virtually all bnabs against multiple neutralizing epitopes on hiv-1 env were highly reactive with the bg505 sosip.664 gp140 trimers, including quaternary epitopes (ch01, pg9, pg16 and pgt145). conversely, non-nabs to the cd4-binding site, cd4-induced epitopes or gp41ecto did not react with the trimers, even when their epitopes were present on simpler forms of env (e.g. gp120 monomers or dissociated gp41 subunits). three non-neutralizing mabs to v3 epitopes did, however, react strongly with the trimers but only by elisa, and not at all by spr and to only a limited extent by em. these new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens.",0
"background alcohol and drug use can have negative consequences on the health, economy, productivity, and social aspects of communities. we aimed to use data from the global burden of diseases, injuries, and risk factors study (gbd) 2016 to calculate global and regional estimates of the prevalence of alcohol, amphetamine, cannabis, cocaine, and opioid dependence, and to estimate global disease burden attributable to alcohol and drug use between 1990 and 2016, and for 195 countries and territories within 21 regions, and within seven super-regions. we also aimed to examine the association between disease burden and socio-demographic index (sdi) quintiles. methods we searched pubmed, embase, and psycinfo databases for original epidemiological studies on alcohol and drug use published between jan 1, 1980, and sept 7, 2016, with out language restrictions, and used dismod-mr 2.1, a bayesian meta-regression tool, to estimate population-level prevalence of substance use disorders. we combined these estimates with disability weights to calculate years of life lived with disability (ylds), years of life lost (ylls), and disability-adjusted life-years (dalys) for 1990-2016. we also used a comparative assessment approach to estimate burden attributable to alcohol and drug use as risk factors for other health outcomes. findings globally, alcohol use disorders were the most prevalent of all substance use disorders, with 100·4 million estimated cases in 2016 (age-standardised prevalence 1320·8 cases per 100 000 people, 95% uncertainty interval 1181·2-1468·0). the most common drug use disorders were cannabis dependence (22·1 million cases; age-standardised prevalence 289·7 cases per 100 000 people, 95% ui 248·9-339·1) and opioid dependence (26·8 million cases; age-standardised prevalence 353·0 cases per 100 000 people, 309·9-405·9). globally, in 2016, 99·2 million dalys (95% ui 88·3-111·2) and 4·2% of all dalys (3·7-4·6) were attributable to alcohol use, and 31·8 million dalys (27·4-36·6) and 1·3% of all dalys (1·2-1·5) were attributable to drug use as a risk factor. the burden of disease attributable to alcohol and drug use varied substantially across geographical locations, and much of this burden was due to the effect of substance use on other health outcomes. contrasting patterns were observed for the association between total alcohol and drug-attributable burden and sdi: alcohol-attributable burden was highest in countries with a low sdi and middle-high middle sdi, whereas the burden due to drugs increased with higher s di level. interpretation alcohol and drug use are important contributors to global disease burden. effective interventions should be scaled up to prevent and reduce substance use disease burden. funding bill & melinda gates foundation and australian national health and medical research council.",0
"background a critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. the inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. the current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. results here we present krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. the html5 and javascript implementation enables fully interactive charts that can be explored with any modern web browser, without the need for installed software or plug-ins. this web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard web server. to illustrate krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. conclusions krona is both a powerful metagenomic visualization tool and a demonstration of the potential of html5 for highly accessible bioinformatic visualizations. its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. both the krona rendering code and conversion tools are freely available under a bsd open-source license, and available from:",0
"recent investigations provided evidence that the sphingomyelin signal transduction pathway mediates apoptosis for tumor necrosis factor alpha (tnf-alpha) in several hematopoietic and nonhematopoietic cells. in this pathway, tnf-receptor interaction initiates sphingomyelin hydrolysis to ceramide by a sphingomyelinase. ceramide acts as a second messenger stimulating a ceramide-activated serine/threonine protein kinase. the present studies show that ionizing radiation, like tnf, induces rapid sphingomyelin hydrolysis to ceramide and apoptosis in bovine aortic endothelial cells. elevation of ceramide with exogenous ceramide analogues was sufficient for induction of apoptosis. protein kinase c activation blocked both radiation-induced sphingomyelin hydrolysis and apoptosis, and apoptosis was restored by ceramide analogues added exogenously. ionizing radiation acted directly on membrane preparations devoid of nuclei, stimulating sphingomyelin hydrolysis enzymatically through a neutral sphingomyelinase. these studies provide the first conclusive evidence that apoptotic signaling can be generated by interaction of ionizing radiation with cellular membranes and suggest an alternative to the hypothesis that direct dna damage mediates radiation-induced cell kill.",0
"the emergence of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and its associated disease, covid-19, has demonstrated the devastating impact of a novel, infectious pathogen on a susceptible population. here, we explain the basic concepts of herd immunity and discuss its implications in the context of covid-19.",0
"talens are important new tools for genome engineering. fusions of transcription activator-like (tal) effectors of plant pathogenic xanthomonas spp. to the foki nuclease, talens bind and cleave dna in pairs. binding specificity is determined by customizable arrays of polymorphic amino acid repeats in the tal effectors. we present a method and reagents for efficiently assembling talen constructs with custom repeat arrays. we also describe design guidelines based on naturally occurring tal effectors and their binding sites. using software that applies these guidelines, in nine genes from plants, animals and protists, we found candidate cleavage sites on average every 35 bp. each of 15 sites selected from this set was cleaved in a yeast-based assay with talen pairs constructed with our reagents. we used two of the talen pairs to mutate hprt1 in human cells and adh1 in arabidopsis thaliana protoplasts. our reagents include a plasmid construct for making custom tal effectors and one for tal effector fusions to additional proteins of interest. using the former, we constructed de novo a functional analog of avrhah1 of xanthomonas gardneri. the complete plasmid set is available through the non-profit repository addgene and a web-based version of our software is freely accessible online.",0
"the world health organization (who) on march 11, 2020, has declared the novel coronavirus (covid-19) outbreak a global pandemic (1). at a news briefing , who director-general, dr. tedros adhanom ghebreyesus, noted that over the past 2 weeks, the number of cases outside china increased 13-fold and the number of countries with cases increased threefold. further increases are expected. he said that the who is ""deeply concerned both by the alarming levels of spread and severity and by the alarming levels of inaction,"" and he called on countries to take action now to contain the virus. ""we should double down,"" he said. ""we should be more aggressive."" .",0
"a new method for demonstrating cytochrome oxidase activity, based upon the oxidative polymerization of 3,3'-diaminobenzidine (dab) to an osmiophilic reaction product, has improved the localization of this enzyme over methods based upon the nadi reaction, in both the light and electron microscopes. the reaction product occurs in nondroplet form, which more accurately delineates the localization of cytochrome oxidase in mitochondria of heart, liver, and kidney. in electron microscopic preparations the excess reaction product is found to overflow into the intracristate spaces and into the outer compartment between inner and outer limiting mitochondrial membranes. this finding suggests that the enzymatic activity of cytochrome c is located on the inner surface of the intracristate space which is the outer surface of the inner mitochondrial membrane. succinic dehydrogenase activity has also been located at this site by using an osmiophilic ditetrazolium salt, tc-nbt. considered together, the sites of reactivity of both parts of the respiratory chain have implications for the chemiosomotic hypothesis of mitchell who suggests a mechanism of energy conservation during electron transport in the respiratory chain of the mitochondrion.",0
"many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using bayesian methods. this approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. the bglr r-package implements a large collection of bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (bayesian reproducing kernel hilbert spaces regressions, rkhs). the software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. the response can be continuous (censored or not) or categorical (either binary or ordinal). the algorithm is based on a gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled c and fortran routines. in this article we describe the methods implemented in bglr, present examples of the use of the package, and discuss practical issues emerging in real-data analysis.",0
"unlabelled this report describes the epidemiology, burden, and treatment of osteoporosis in the 27 countries of the european union (eu27). introduction osteoporosis is characterized by reduced bone mass and disruption of bone architecture, resulting in increased risk of fragility fractures which represent the main clinical consequence of the disease. fragility fractures are associated with substantial pain and suffering, disability and even death for affected patients and substantial costs to society. the aim of this report was to characterize the burden of osteoporosis in the eu27 in 2010 and beyond. methods the literature on fracture incidence and costs of fractures in the eu27 was reviewed and incorporated into a model estimating the clinical and economic burden of osteoporotic fractures in 2010. results twenty-two million women and 5.5 million men were estimated to have osteoporosis; and 3.5 million new fragility fractures were sustained, comprising 610,000 hip fractures, 520,000 vertebral fractures, 560,000 forearm fractures and 1,800,000 other fractures (i.e. fractures of the pelvis, rib, humerus, tibia, fibula, clavicle, scapula, sternum and other femoral fractures). the economic burden of incident and prior fragility fractures was estimated at 37 billion. incident fractures represented 66 % of this cost, long-term fracture care 29 % and pharmacological prevention 5 %. previous and incident fractures also accounted for 1,180,000 quality-adjusted life years lost during 2010. the costs are expected to increase by 25 % in 2025. the majority of individuals who have sustained an osteoporosis-related fracture or who are at high risk of fracture are untreated and the number of patients on treatment is declining. conclusions in spite of the high social and economic cost of osteoporosis, a substantial treatment gap and projected increase of the economic burden driven by the aging populations, the use of pharmacological interventions to prevent fractures has decreased in recent years, suggesting that a change in healthcare policy is warranted.",0
"background current diagnostic systems for mental disorders rely upon presenting signs and symptoms, with the result that current definitions do not adequately reflect relevant neurobiological and behavioral systems--impeding not only research on etiology and pathophysiology but also the development of new treatments. discussion the national institute of mental health began the research domain criteria (rdoc) project in 2009 to develop a research classification system for mental disorders based upon dimensions of neurobiology and observable behavior. rdoc supports research to explicate fundamental biobehavioral dimensions that cut across current heterogeneous disorder categories. we summarize the rationale, status and long-term goals of rdoc, outline challenges in developing a research classification system (such as construct validity and a suitable process for updating the framework) and discuss seven distinct differences in conception and emphasis from current psychiatric nosologies. summary future diagnostic systems cannot reflect ongoing advances in genetics, neuroscience and cognitive science until a literature organized around these disciplines is available to inform the revision efforts. the goal of the rdoc project is to provide a framework for research to transform the approach to the nosology of mental disorders.",0
"background depression and anxiety disorders are common and treatable with cognitive behavior therapy (cbt), but access to this therapy is limited. objective review evidence that computerized cbt for the anxiety and depressive disorders is acceptable to patients and effective in the short and longer term. method systematic reviews and data bases were searched for randomized controlled trials of computerized cognitive behavior therapy versus a treatment or control condition in people who met diagnostic criteria for major depression, panic disorder, social phobia or generalized anxiety disorder. number randomized, superiority of treatment versus control (hedges g) on primary outcome measure, risk of bias, length of follow up, patient adherence and satisfaction were extracted. principal findings 22 studies of comparisons with a control group were identified. the mean effect size superiority was 0.88 (nnt 2.13), and the benefit was evident across all four disorders. improvement from computerized cbt was maintained for a median of 26 weeks follow-up. acceptability, as indicated by adherence and satisfaction, was good. research probity was good and bias risk low. effect sizes were non-significantly higher in comparisons with waitlist than with active treatment control conditions. five studies comparing computerized cbt with traditional face-to-face cbt were identified, and both modes of treatment appeared equally beneficial. conclusions computerized cbt for anxiety and depressive disorders, especially via the internet, has the capacity to provide effective acceptable and practical health care for those who might otherwise remain untreated. trial registration australian new zealand clinical trials registry actrn12610000030077.",0
"background recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. however, assembly of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly. this results in regional duplication rather than consolidation into allelic variants and can cause issues with downstream analysis, for example variant discovery, or haplotype reconstruction using the diploid assembly with unpaired allelic contigs. results a new pipeline-purge haplotigs-was developed specifically for third-gen sequencing-based assemblies to automate the reassignment of allelic contigs, and to assist in the manual curation of genome assemblies. the pipeline uses a draft haplotype-fused assembly or a diploid assembly, read alignments, and repeat annotations to identify allelic variants in the primary assembly. the pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing, and compared with a similar tool. after processing with purge haplotigs, haploid assemblies were less duplicated with minimal impact on genome completeness, and diploid assemblies had more pairings of allelic contigs. conclusions purge haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. the implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. the software is available at under a permissive mit licence.",0
"the case study approach allows in-depth, multi-faceted explorations of complex issues in their real-life settings. the value of the case study approach is well recognised in the fields of business, law and policy, but somewhat less so in health services research. based on our experiences of conducting several health-related case studies, we reflect on the different types of case study design, the specific research questions this approach can help answer, the data sources that tend to be used, and the particular advantages and disadvantages of employing this methodological approach. the paper concludes with key pointers to aid those designing and appraising proposals for conducting case study research, and a checklist to help readers assess the quality of case study reports.",0
"background the sars-cov-2 omicron variant of concern was identified in south africa in november, 2021, and was associated with an increase in covid-19 cases. we aimed to assess the clinical severity of infections with the omicron variant using s gene target failure (sgtf) on the thermo fisher scientific taqpath covid-19 pcr test as a proxy. methods we did data linkages for national, south african covid-19 case data, sars-cov-2 laboratory test data, sars-cov-2 genome data, and covid-19 hospital admissions data. for individuals diagnosed with covid-19 via taqpath pcr tests, infections were designated as either sgtf or non-sgtf. the delta variant was identified by genome sequencing. using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with sgtf versus non-sgtf infections diagnosed between oct 1 and nov 30, 2021, and we further assessed disease severity by comparing sgtf-infected individuals diagnosed between oct 1 and nov 30, 2021, with delta variant-infected individuals diagnosed between april 1 and nov 9, 2021. findings from oct 1 (week 39), 2021, to dec 6 (week 49), 2021, 161 328 cases of covid-19 were reported in south africa. 38 282 people were diagnosed via taqpath pcr tests and 29 721 sgtf infections and 1412 non-sgtf infections were identified. the proportion of sgtf infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. after controlling for factors associated with hospitalisation, individuals with sgtf infections had significantly lower odds of admission than did those with non-sgtf infections (256 of 10 547 vs 121 of 948; adjusted odds ratio 0·2, 95% ci 0·1-0·3). after controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with sgtf versus non-sgtf infections (42 of 204 vs 45 of 113; aor 0·7, 95% ci 0·3-1·4). compared with individuals with earlier delta variant infections, sgtf-infected individuals had a significantly lower odds of severe disease (496 of 793 vs 57 of 244; aor 0·3, 95% ci 0·2-0·5), after controlling for factors associated with disease severity. interpretation our early analyses suggest a significantly reduced odds of hospitalisation among individuals with sgtf versus non-sgtf infections diagnosed during the same time period. sgtf-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. some of this reduced severity is probably a result of previous immunity. funding the south african medical research council, the south african national department of health, us centers for disease control and prevention, the african society of laboratory medicine, africa centers for disease control and prevention, the bill & melinda gates foundation, the wellcome trust, and the fleming fund.",0
"combination therapies exploit the chances for better efficacy, decreased toxicity, and reduced development of drug resistance and owing to these advantages, have become a standard for the treatment of several diseases and continue to represent a promising approach in indications of unmet medical need. in this context, studying the effects of a combination of drugs in order to provide evidence of a significant superiority compared to the single agents is of particular interest. research in this field has resulted in a large number of papers and revealed several issues. here, we propose an overview of the current methodological landscape concerning the study of combination effects. first, we aim to provide the minimal set of mathematical and pharmacological concepts necessary to understand the most commonly used approaches, divided into effect-based approaches and dose-effect-based approaches, and introduced in light of their respective practical advantages and limitations. then, we discuss six main common methodological issues that scientists have to face at each step of the development of new combination therapies. in particular, in the absence of a reference methodology suitable for all biomedical situations, the analysis of drug combinations should benefit from a collective, appropriate, and rigorous application of the concepts and methods reviewed here.",0
"the objective of this personal view is to compare transmissibility, hospitalisation, and mortality rates for severe acute respiratory syndrome coronavirus 2 (sars-cov-2) with those of other epidemic coronaviruses, such as severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov), and pandemic influenza viruses. the basic reproductive rate (r 0 ) for sars-cov-2 is estimated to be 2·5 (range 1·8-3·6) compared with 2·0-3·0 for sars-cov and the 1918 influenza pandemic, 0·9 for mers-cov, and 1·5 for the 2009 influenza pandemic. sars-cov-2 causes mild or asymptomatic disease in most cases; however, severe to critical illness occurs in a small proportion of infected individuals, with the highest rate seen in people older than 70 years. the measured case fatality rate varies between countries, probably because of differences in testing strategies. population-based mortality estimates vary widely across europe, ranging from zero to high. numbers from the first affected region in italy, lombardy, show an all age mortality rate of 154 per 100 000 population. differences are most likely due to varying demographic structures, among other factors. however, this new virus has a focal dissemination; therefore, some areas have a higher disease burden and are affected more than others for reasons that are still not understood. nevertheless, early introduction of strict physical distancing and hygiene measures have proven effective in sharply reducing r 0 and associated mortality and could in part explain the geographical differences.",0
"problem health-risk behaviors contribute to the leading causes of morbidity and mortality among youth and adults in the united states. in addition, significant health disparities exist among demographic subgroups of youth defined by sex, race/ethnicity, and grade in school and between sexual minority and nonsexual minority youth. population-based data on the most important health-related behaviors at the national, state, and local levels can be used to help monitor the effectiveness of public health interventions designed to protect and promote the health of youth at the national, state, and local levels. reporting period covered september 2016-december 2017. description of the system the youth risk behavior surveillance system (yrbss) monitors six categories of priority health-related behaviors among youth and young adults: 1) behaviors that contribute to unintentional injuries and violence; 2) tobacco use; 3) alcohol and other drug use; 4) sexual behaviors related to unintended pregnancy and sexually transmitted infections (stis), including human immunodeficiency virus (hiv) infection; 5) unhealthy dietary behaviors; and 6) physical inactivity. in addition, yrbss monitors the prevalence of other health-related behaviors, obesity, and asthma. yrbss includes a national school-based youth risk behavior survey (yrbs) conducted by cdc and state and large urban school district school-based yrbss conducted by state and local education and health agencies. starting with the 2015 yrbss cycle, a question to ascertain sexual identity and a question to ascertain sex of sexual contacts were added to the national yrbs questionnaire and to the standard yrbs questionnaire used by the states and large urban school districts as a starting point for their questionnaires. this report summarizes results from the 2017 national yrbs for 121 health-related behaviors and for obesity, overweight, and asthma by demographic subgroups defined by sex, race/ethnicity, and grade in school and by sexual minority status; updates the numbers of sexual minority students nationwide; and describes overall trends in health-related behaviors during 1991-2017. this reports also summarizes results from 39 state and 21 large urban school district surveys with weighted data for the 2017 yrbss cycle by sex and sexual minority status (where available). results results from the 2017 national yrbs indicated that many high school students are engaged in health-risk behaviors associated with the leading causes of death among persons aged 10-24 years in the united states. during the 30 days before the survey, 39.2% of high school students nationwide (among the 62.8% who drove a car or other vehicle during the 30 days before the survey) had texted or e-mailed while driving, 29.8% reported current alcohol use, and 19.8% reported current marijuana use. in addition, 14.0% of students had taken prescription pain medicine without a doctor's prescription or differently than how a doctor told them to use it one or more times during their life. during the 12 months before the survey, 19.0% had been bullied on school property and 7.4% had attempted suicide. many high school students are engaged in sexual risk behaviors that relate to unintended pregnancies and stis, including hiv infection. nationwide, 39.5% of students had ever had sexual intercourse and 9.7% had had sexual intercourse with four or more persons during their life. among currently sexually active students, 53.8% reported that either they or their partner had used a condom during their last sexual intercourse. results from the 2017 national yrbs also indicated many high school students are engaged in behaviors associated with chronic diseases, such as cardiovascular disease, cancer, and diabetes. nationwide, 8.8% of high school students had smoked cigarettes and 13.2% had used an electronic vapor product on at least 1 day during the 30 days before the survey. forty-three percent played video or computer games or used a computer for 3 or more hours per day on an average school day for something that was not school work and 15.4% had not been physically active for a total of at least 60 minutes on at least 1 day during the 7 days before the survey. further, 14.8% had obesity and 15.6% were overweight. the prevalence of most health-related behaviors varies by sex, race/ethnicity, and, particularly, sexual identity and sex of sexual contacts. specifically, the prevalence of many health-risk behaviors is significantly higher among sexual minority students compared with nonsexual minority students. nonetheless, analysis of long-term temporal trends indicates that the overall prevalence of most health-risk behaviors has moved in the desired direction. interpretation most high school students cope with the transition from childhood through adolescence to adulthood successfully and become healthy and productive adults. however, this report documents that some subgroups of students defined by sex, race/ethnicity, grade in school, and especially sexual minority status have a higher prevalence of many health-risk behaviors that might place them at risk for unnecessary or premature mortality, morbidity, and social problems (e.g., academic failure, poverty, and crime). public health action yrbss data are used widely to compare the prevalence of health-related behaviors among subpopulations of students; assess trends in health-related behaviors over time; monitor progress toward achieving 21 national health objectives; provide comparable state and large urban school district data; and take public health actions to decrease health-risk behaviors and improve health outcomes among youth. using this and other reports based on scientifically sound data is important for raising awareness about the prevalence of health-related behaviors among students in grades 9-12, especially sexual minority students, among decision makers, the public, and a wide variety of agencies and organizations that work with youth. these agencies and organizations, including schools and youth-friendly health care providers, can help facilitate access to critically important education, health care, and high-impact, evidence-based interventions.",0
"introduction despite significant improvements in intensive care medicine, the prognosis of acute renal failure (arf) remains poor, with mortality ranging from 40% to 65%. the aim of the present observational study was to analyze the influence of patient characteristics and fluid balance on the outcome of arf in intensive care unit (icu) patients. methods the data were extracted from the sepsis occurrence in acutely ill patients (soap) study, a multicenter observational cohort study to which 198 icus from 24 european countries contributed. all adult patients admitted to a participating icu between 1 and 15 may 2002, except those admitted for uncomplicated postoperative surveillance, were eligible for the study. for the purposes of this substudy, patients were divided into two groups according to whether they had arf. the groups were compared with respect to patient characteristics, fluid balance, and outcome. results of the 3,147 patients included in the soap study, 1,120 (36%) had arf at some point during their icu stay. sixty-day mortality rates were 36% in patients with arf and 16% in patients without arf (p conclusion in this large european multicenter study, a positive fluid balance was an important factor associated with increased 60-day mortality. outcome among patients treated with rrt was better when rrt was started early in the course of the icu stay.",0
"plasmacytoid dendritic cells (pdcs) have been identified as a potent secretor of the type i interferons (ifns) in response to cpg as well as several viruses. in this study, we examined the molecular mechanism of virus recognition by pdcs. first, we demonstrated that the cd11c+gr-1intb220+ pdcs from mouse bone marrow secreted high levels of ifn-alpha in response to either live or uv-inactivated herpes simplex virus-2 (hsv-2). next, we identified that ifn-alpha secretion by pdcs required the expression of the adaptor molecule myd88, suggesting the involvement of a toll-like receptor (tlr) in hsv-2 recognition. to test whether a tlr mediates hsv-2-induced ifn-alpha secretion from pdcs, various knockout mice were examined. these experiments revealed a clear requirement for tlr9 in this process. further, we demonstrated that purified hsv-2 dna can trigger ifn-alpha secretion from pdcs and that inhibitory cpg oligonucleotide treatment diminished hsv-induced ifn-alpha secretion by pdcs in a dose-dependent manner. the recognition of hsv-2 by tlr9 was mediated through an endocytic pathway that was inhibited by chloroquine or bafilomycin a1. the strict requirement for tlr9 in ifn-alpha secretion was further confirmed by the inoculation of hsv-2 in vivo. therefore, these results demonstrate a novel mechanism whereby the genomic dna of a virus can engage tlr9 and result in the secretion of ifn-alpha by pdcs.",0
"hippocampal place cells encode spatial information in rate and temporal codes. to examine the mechanisms underlying hippocampal coding, here we measured the intracellular dynamics of place cells by combining in vivo whole-cell recordings with a virtual-reality system. head-restrained mice, running on a spherical treadmill, interacted with a computer-generated visual environment to perform spatial behaviours. robust place-cell activity was present during movement along a virtual linear track. from whole-cell recordings, we identified three subthreshold signatures of place fields: an asymmetric ramp-like depolarization of the baseline membrane potential, an increase in the amplitude of intracellular theta oscillations, and a phase precession of the intracellular theta oscillation relative to the extracellularly recorded theta rhythm. these intracellular dynamics underlie the primary features of place-cell rate and temporal codes. the virtual-reality system developed here will enable new experimental approaches to study the neural circuits underlying navigation.",0
"we examined the ability of a set of cloned chicken ovalbumin (cova)-specific, id-restricted, t cell hybridomas to produce interleukin-2 in response to cova presented by the ia+ b cell lymphoma line, a20-2j. although viable a20-2j cells presented native, denatured, and fragmented cova more or less equally well, a20-2j cells that were glutaraldehyde-fixed could present only enzymatically or chemically fragmented cova. these results suggest that antigen fragmentation may be both necessary and sufficient to define accessory cell processing of soluble antigens so that they may be recognized in association with i-region molecules by t cells.",0
"background comparable data on the global and country-specific burden of neurological disorders and their trends are crucial for health-care planning and resource allocation. the global burden of diseases, injuries, and risk factors (gbd) study provides such information but does not routinely aggregate results that are of interest to clinicians specialising in neurological conditions. in this systematic analysis, we quantified the global disease burden due to neurological disorders in 2015 and its relationship with country development level. methods we estimated global and country-specific prevalence, mortality, disability-adjusted life-years (dalys), years of life lost (ylls), and years lived with disability (ylds) for various neurological disorders that in the gbd classification have been previously spread across multiple disease groupings. the more inclusive grouping of neurological disorders included stroke, meningitis, encephalitis, tetanus, alzheimer's disease and other dementias, parkinson's disease, epilepsy, multiple sclerosis, motor neuron disease, migraine, tension-type headache, medication overuse headache, brain and nervous system cancers, and a residual category of other neurological disorders. we also analysed results based on the socio-demographic index (sdi), a compound measure of income per capita, education, and fertility, to identify patterns associated with development and how countries fare against expected outcomes relative to their level of development. findings neurological disorders ranked as the leading cause group of dalys in 2015 (250·7 million, comprising 10·2% of global dalys) and the second-leading cause group of deaths (9·4 million], comprising 16·8% of global deaths). the most prevalent neurological disorders were tension-type headache (1505·9 ), migraine (958·8 million), medication overuse headache (58·5 ), and alzheimer's disease and other dementias (46·0 ). between 1990 and 2015, the number of deaths from neurological disorders increased by 36·7%, and the number of dalys by 7·4%. these increases occurred despite decreases in age-standardised rates of death and dalys of 26·1% and 29·7%, respectively; stroke and communicable neurological disorders were responsible for most of these decreases. communicable neurological disorders were the largest cause of dalys in countries with low sdi. stroke rates were highest at middle levels of sdi and lowest at the highest sdi. most of the changes in daly rates of neurological disorders with development were driven by changes in ylls. interpretation neurological disorders are an important cause of disability and death worldwide. globally, the burden of neurological disorders has increased substantially over the past 25 years because of expanding population numbers and ageing, despite substantial decreases in mortality rates from stroke and communicable neurological disorders. the number of patients who will need care by clinicians with expertise in neurological conditions will continue to grow in coming decades. policy makers and health-care providers should be aware of these trends to provide adequate services. funding bill & melinda gates foundation.",0
"unlabelled guidance is provided in a european setting on the assessment and treatment of postmenopausal women with or at risk from osteoporosis. introduction the european foundation for osteoporosis and bone disease (subsequently the international osteoporosis foundation) published guidelines for the diagnosis and management of osteoporosis in 1997. this manuscript updates these in a european setting. methods the following areas are reviewed: the role of bone mineral density measurement for the diagnosis of osteoporosis and assessment of fracture risk; general and pharmacological management of osteoporosis; monitoring of treatment; assessment of fracture risk; case finding strategies; investigation of patients; health economics of treatment. results and conclusions a platform is provided on which specific guidelines can be developed for national use.",0
"background in recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. a number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. in the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. these matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. with few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. results we start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. we demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. we have investigated patterns of amino acid substitution among homologous sequences from the three domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral pol proteins. conclusion this demonstrates that choosing protein models based on their source or method of construction may not be appropriate.",0
"glucocorticoids are released in response to stressful experiences and serve many beneficial homeostatic functions. however, dysregulation of glucocorticoids is associated with cognitive impairments and depressive illness. in the hippocampus, a brain region densely populated with receptors for stress hormones, stress and glucocorticoids strongly inhibit adult neurogenesis. decreased neurogenesis has been implicated in the pathogenesis of anxiety and depression, but direct evidence for this role is lacking. here we show that adult-born hippocampal neurons are required for normal expression of the endocrine and behavioural components of the stress response. using either transgenic or radiation methods to inhibit adult neurogenesis specifically, we find that glucocorticoid levels are slower to recover after moderate stress and are less suppressed by dexamethasone in neurogenesis-deficient mice than intact mice, consistent with a role for the hippocampus in regulation of the hypothalamic-pituitary-adrenal (hpa) axis. relative to controls, neurogenesis-deficient mice also showed increased food avoidance in a novel environment after acute stress, increased behavioural despair in the forced swim test, and decreased sucrose preference, a measure of anhedonia. these findings identify a small subset of neurons within the dentate gyrus that are critical for hippocampal negative control of the hpa axis and support a direct role for adult neurogenesis in depressive illness.",0
"the ki-67 antigen is used to evaluate the proliferative activity of breast cancer (bc); however, ki-67's role as a prognostic marker in bc is still undefined. in order to better define the prognostic value of ki-67/mib-1, we performed a meta-analysis of studies that evaluated the impact of ki-67/mib-1 on disease-free survival (dfs) and/or on overall survival (os) in early bc. sixty-eight studies were identified and 46 studies including 12 155 patients were evaluable for our meta-analysis; 38 studies were evaluable for the aggregation of results for dfs, and 35 studies for os. patients were considered to present positive tumours for the expression of ki-67/mib-1 according to the cut-off points defined by the authors. ki-67/mib-1 positivity is associated with higher probability of relapse in all patients (hr=1.93 (95% confidence interval (ci): 1.74-2.14); p<0.001), in node-negative patients (hr=2.31 (95% ci: 1.83-2.92); p<0.001) and in node-positive patients (hr=1.59 (95% ci: 1.35-1.87); p<0.001). furthermore, ki-67/mib-1 positivity is associated with worse survival in all patients (hr=1.95 (95% ci: 1.70-2.24; p<0.001)), node-negative patients (hr=2.54 (95% ci: 1.65-3.91); p<0.001) and node-positive patients (hr=2.33 (95% ci: 1.83-2.95); p<0.001). our meta-analysis suggests that ki-67/mib-1 positivity confers a higher risk of relapse and a worse survival in patients with early bc.",0
"the neuro-anatomical substrates of major depressive disorder (mdd) are still not well understood, despite many neuroimaging studies over the past few decades. here we present the largest ever worldwide study by the enigma (enhancing neuro imaging genetics through meta-analysis) major depressive disorder working group on cortical structural alterations in mdd. structural t1-weighted brain magnetic resonance imaging (mri) scans from 2148 mdd patients and 7957 healthy controls were analysed with harmonized protocols at 20 sites around the world. to detect consistent effects of mdd and its modulators on cortical thickness and surface area estimates derived from mri, statistical effects from sites were meta-analysed separately for adults and adolescents. adults with mdd had thinner cortical gray matter than controls in the orbitofrontal cortex (ofc), anterior and posterior cingulate, insula and temporal lobes (cohen's d effect sizes: -0.10 to -0.14). these effects were most pronounced in first episode and adult-onset patients (>21 years). compared to matched controls, adolescents with mdd had lower total surface area (but no differences in cortical thickness) and regional reductions in frontal regions (medial ofc and superior frontal gyrus) and primary and higher-order visual, somatosensory and motor areas (d: -0.26 to -0.57). the strongest effects were found in recurrent adolescent patients. this highly powered global effort to identify consistent brain abnormalities showed widespread cortical alterations in mdd patients as compared to controls and suggests that mdd may impact brain structure in a highly dynamic way, with different patterns of alterations at different stages of life.",0
"this review aims to outline the most up-to-date knowledge of pancreatic adenocarcinoma risk, diagnostics, treatment and outcomes, while identifying gaps that aim to stimulate further research in this understudied malignancy. pancreatic adenocarcinoma is a lethal condition with a rising incidence, predicted to become the second leading cause of cancer death in some regions. it often presents at an advanced stage, which contributes to poor five-year survival rates of 2%-9%, ranking firmly last amongst all cancer sites in terms of prognostic outcomes for patients. better understanding of the risk factors and symptoms associated with this disease is essential to inform both health professionals and the general population of potential preventive and/or early detection measures. the identification of high-risk patients who could benefit from screening to detect pre-malignant conditions such as pancreatic intraepithelial neoplasia, intraductal papillary mucinous neoplasms and mucinous cystic neoplasms is urgently required, however an acceptable screening test has yet to be identified. the management of pancreatic adenocarcinoma is evolving, with the introduction of new surgical techniques and medical therapies such as laparoscopic techniques and neo-adjuvant chemoradiotherapy, however this has only led to modest improvements in outcomes. the identification of novel biomarkers is desirable to move towards a precision medicine era, where pancreatic cancer therapy can be tailored to the individual patient, while unnecessary treatments that have negative consequences on quality of life could be prevented for others. research efforts must also focus on the development of new agents and delivery systems. overall, considerable progress is required to reduce the burden associated with pancreatic cancer. recent, renewed efforts to fund large consortia and research into pancreatic adenocarcinoma are welcomed, but further streams will be necessary to facilitate the momentum needed to bring breakthroughs seen for other cancer sites.",0
"in a significant fraction of breast cancer patients, distant metastases emerge after years or even decades of latency. how disseminated tumour cells (dtcs) are kept dormant, and what wakes them up, are fundamental problems in tumour biology. to address these questions, we used metastasis assays in mice and showed that dormant dtcs reside on microvasculature of lung, bone marrow and brain. we then engineered organotypic microvascular niches to determine whether endothelial cells directly influence breast cancer cell (bcc) growth. these models demonstrated that endothelial-derived thrombospondin-1 induces sustained bcc quiescence. this suppressive cue was lost in sprouting neovasculature; time-lapse analysis showed that sprouting vessels not only permit, but accelerate bcc outgrowth. we confirmed this surprising result in dormancy models and in zebrafish, and identified active tgf-β1 and periostin as tumour-promoting factors derived from endothelial tip cells. our work reveals that stable microvasculature constitutes a dormant niche, whereas sprouting neovasculature sparks micrometastatic outgrowth.",0
"functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. string is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. it weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. the most important new developments in string 8 over previous releases include a url-based programming interface, which can be used to query string from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures. version 8.0 of string covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. string can be reached at",0
"objectives to review the evidence for an association of white matter hyperintensities with risk of stroke, cognitive decline, dementia, and death. design systematic review and meta-analysis. data sources pubmed from 1966 to 23 november 2009. study selection prospective longitudinal studies that used magnetic resonance imaging and assessed the impact of white matter hyperintensities on risk of incident stroke, cognitive decline, dementia, and death, and, for the meta-analysis, studies that provided risk estimates for a categorical measure of white matter hyperintensities, assessing the impact of these lesions on risk of stroke, dementia, and death. data extraction population studied, duration of follow-up, method used to measure white matter hyperintensities, definition of the outcome, and measure of the association of white matter hyperintensities with the outcome. data synthesis 46 longitudinal studies evaluated the association of white matter hyperintensities with risk of stroke (n=12), cognitive decline (n=19), dementia (n=17), and death (n=10). 22 studies could be included in a meta-analysis (nine of stroke, nine of dementia, eight of death). white matter hyperintensities were associated with an increased risk of stroke (hazard ratio 3.3, 95% confidence interval 2.6 to 4.4), dementia (1.9, 1.3 to 2.8), and death (2.0, 1.6 to 2.7). an association of white matter hyperintensities with a faster decline in global cognitive performance, executive function, and processing speed was also suggested. conclusion white matter hyperintensities predict an increased risk of stroke, dementia, and death. therefore white matter hyperintensities indicate an increased risk of cerebrovascular events when identified as part of diagnostic investigations, and support their use as an intermediate marker in a research setting. their discovery should prompt detailed screening for risk factors of stroke and dementia.",0
"background a new betacoronavirus-middle east respiratory syndrome coronavirus (mers-cov)-has been identified in patients with severe acute respiratory infection. although related viruses infect bats, molecular clock analyses have been unable to identify direct ancestors of mers-cov. anecdotal exposure histories suggest that patients had been in contact with dromedary camels or goats. we investigated possible animal reservoirs of mers-cov by assessing specific serum antibodies in livestock. methods we took sera from animals in the middle east (oman) and from elsewhere (spain, netherlands, chile). cattle (n=80), sheep (n=40), goats (n=40), dromedary camels (n=155), and various other camelid species (n=34) were tested for specific serum igg by protein microarray using the receptor-binding s1 subunits of spike proteins of mers-cov, severe acute respiratory syndrome coronavirus, and human coronavirus oc43. results were confirmed by virus neutralisation tests for mers-cov and bovine coronavirus. findings 50 of 50 (100%) sera from omani camels and 15 of 105 (14%) from spanish camels had protein-specific antibodies against mers-cov spike. sera from european sheep, goats, cattle, and other camelids had no such antibodies. mers-cov neutralising antibody titres varied between 1/320 and 1/2560 for the omani camel sera and between 1/20 and 1/320 for the spanish camel sera. there was no evidence for cross-neutralisation by bovine coronavirus antibodies. interpretation mers-cov or a related virus has infected camel populations. both titres and seroprevalences in sera from different locations in oman suggest widespread infection. funding european union, european centre for disease prevention and control, deutsche forschungsgemeinschaft.",0
"authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of inter-est and their inter-pretation, but are also expected to archive in computer-readable cif format the experimental data on which the crystal-structure analysis is based. additionally, an iucr/ checkcif validation report will be required for the review of a submitted paper. such a validation report, automatically created from the deposited cif file, lists as alerts not only potential errors or unusual findings, but also suggestions for improvement along with inter-esting information on the structure at hand. major alerts for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the cif file. in addition, referees, readers and users of the data should be able to make their own judgment and inter-pretation of the underlying experimental data or perform their own calculations with the archived data. all the above is consistent with the fair (findable, accessible, inter-operable, and reusable) initiative . validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and inter-pretation pitfalls. the iucr web-based checkcif server provides such a validation report, based on data uploaded in cif format. alternatively, a locally installable checkcif version is available to be used iteratively during the structure-determination process. alerts come mostly as short single-line messages. there is also a short explanation of the alerts available through the iucr web server or with the locally installed platon / checkcif version. this paper provides additional background information on the checkcif procedure and additional details for a number of alerts along with options for how to act on them.",0
"protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. enzyme-catalyzed proximity labeling (pl) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. however, current pl methods require over 18 h of labeling time or utilize chemicals with limited cell permeability or high toxicity. we used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, turboid and miniturbo, which catalyze pl with much greater efficiency than bioid or bioid2, and enable 10-min pl in cells with non-toxic and easily deliverable biotin. furthermore, turboid extends biotin-based pl to flies and worms.",0
"an important part of characterizing any protein molecule is to determine its size and shape. sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. this review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. readers are reminded that the perrin equation is generally not a valid approach to determine the shape of proteins. instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum s, to estimate if a protein is globular or elongated. it is recalled that a gel filtration column fractionates proteins on the basis of their stokes radius, not molecular weight. the molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by siegel and monte. finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. a combination of hydrodynamics and electron microscopy is especially powerful.",0
"telomeres are specialized nucleoprotein structures, which protect chromosome ends and have been implicated in the ageing process. telomere shortening has been shown to contribute to a persistent dna damage response (ddr) during replicative senescence, the irreversible loss of division potential of somatic cells. similarly, persistent ddr foci can be found in stress-induced senescence, although their nature is not understood. here we show, using immuno-fluorescent in situ hybridization and chip, that up to half of the dna damage foci in stress-induced senescence are located at telomeres irrespective of telomerase activity. moreover, live-cell imaging experiments reveal that all persistent foci are associated with telomeres. finally, we report an age-dependent increase in frequencies of telomere-associated foci in gut and liver of mice, occurring irrespectively of telomere length. we conclude that telomeres are important targets for stress in vitro and in vivo and this has important consequences for the ageing process.",0
"autism spectrum disorders (asds) represent a formidable challenge for psychiatry and neuroscience because of their high prevalence, lifelong nature, complexity and substantial heterogeneity. facing these obstacles requires large-scale multidisciplinary efforts. although the field of genetics has pioneered data sharing for these reasons, neuroimaging had not kept pace. in response, we introduce the autism brain imaging data exchange (abide)-a grassroots consortium aggregating and openly sharing 1112 existing resting-state functional magnetic resonance imaging (r-fmri) data sets with corresponding structural mri and phenotypic information from 539 individuals with asds and 573 age-matched typical controls (tcs; 7-64 years) ( here, we present this resource and demonstrate its suitability for advancing knowledge of asd neurobiology based on analyses of 360 male subjects with asds and 403 male age-matched tcs. we focused on whole-brain intrinsic functional connectivity and also survey a range of voxel-wise measures of intrinsic functional brain architecture. whole-brain analyses reconciled seemingly disparate themes of both hypo- and hyperconnectivity in the asd literature; both were detected, although hypoconnectivity dominated, particularly for corticocortical and interhemispheric functional connectivity. exploratory analyses using an array of regional metrics of intrinsic brain function converged on common loci of dysfunction in asds (mid- and posterior insula and posterior cingulate cortex), and highlighted less commonly explored regions such as the thalamus. the survey of the abide r-fmri data sets provides unprecedented demonstrations of both replication and novel discovery. by pooling multiple international data sets, abide is expected to accelerate the pace of discovery setting the stage for the next generation of asd studies.",0
"iq-tree ( last accessed february 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. since the release of version 1 in 2014, we have continuously expanded iq-tree to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. here, we describe notable features of iq-tree version 2 and highlight the key advantages over other software.",0
"improving approaches for hematopoietic stem cell (hsc) and hematopoietic progenitor cell (hpc) mobilization is clinically important because increased numbers of these cells are needed for enhanced transplantation. chemokine stromal cell derived factor-1 (also known as cxcl12) is believed to be involved in retention of hscs and hpcs in bone marrow. amd3100, a selective antagonist of cxcl12 that binds to its receptor, cxcr4, was evaluated in murine and human systems for mobilizing capacity, alone and in combination with granulocyte colony-stimulating factor (g-csf). amd3100 induced rapid mobilization of mouse and human hpcs and synergistically augmented g-csf-induced mobilization of hpcs. amd3100 also mobilized murine long-term repopulating (ltr) cells that engrafted primary and secondary lethally-irradiated mice, and human cd34(+) cells that can repopulate nonobese diabetic-severe combined immunodeficiency (scid) mice. amd3100 synergized with g-csf to mobilize murine ltr cells and human scid repopulating cells (srcs). human cd34(+) cells isolated after treatment with g-csf plus amd3100 expressed a phenotype that was characteristic of highly engrafting mouse hscs. synergy of amd3100 and g-csf in mobilization was due to enhanced numbers and perhaps other characteristics of the mobilized cells. these results support the hypothesis that the cxcl12-cxcr4 axis is involved in marrow retention of hscs and hpcs, and demonstrate the clinical potential of amd3100 for hsc mobilization.",0
"background cancer is one of the leading causes of death globally, but its burden is not uniform. globocan 2020 has newly updated the estimates of cancer burden. this study summarizes the most recent changing profiles of cancer burden worldwide and in china and compares the cancer data of china with those of other regions. methods we conducted a descriptive secondary analysis of the globocan 2020 data. to depict the changing global profile of the leading cancer types in 2020 compared with 2018, we extracted the numbers of cases and deaths in 2018 from globocan 2018. we also obtained cancer incidence and mortality from the 2015 national cancer registry report in china when sorting the leading cancer types by new cases and deaths. for the leading cancer types according to sex in china, we summarized the estimated numbers of incidence and mortality, and calculated china's percentage of the global new cases and deaths. results breast cancer displaced lung cancer to become the most leading diagnosed cancer worldwide in 2020. lung, liver, stomach, breast, and colon cancers were the top five leading causes of cancer-related death, among which liver cancer changed from the third-highest cancer mortality in 2018 to the second-highest in 2020. china accounted for 24% of newly diagnosed cases and 30% of the cancer-related deaths worldwide in 2020. among the 185 countries included in the database, china's age-standardized incidence rate (204.8 per 100,000) ranked 65th and the age-standardized mortality rate (129.4 per 100,000) ranked 13th. the two rates were above the global average. lung cancer remained the most common cancer type and the leading cause of cancer death in china. however, breast cancer became the most frequent cancer type among women if the incidence was stratified by sex. incidences of colorectal cancer and breast cancer increased rapidly. the leading causes of cancer death varied minimally in ranking from 2015 to 2020 in china. gastrointestinal cancers, including stomach, colorectal, liver, and esophageal cancers, contributed to a massive burden of cancer for both sexes. conclusions the burden of breast cancer is increasing globally. china is undergoing cancer transition with an increasing burden of lung cancer, gastrointestinal cancer, and breast cancers. the mortality rate of cancer in china is high. comprehensive strategies are urgently needed to target china's changing profiles of the cancer burden.",0
"effect sizes are the most important outcome of empirical studies. most articles on effect sizes highlight their importance to communicate the practical significance of results. for scientists themselves, effect sizes are most useful because they facilitate cumulative science. effect sizes can be used to determine the sample size for follow-up studies, or examining effects across studies. this article aims to provide a practical primer on how to calculate and report effect sizes for t-tests and anova's such that effect sizes can be used in a-priori power analyses and meta-analyses. whereas many articles about effect sizes focus on between-subjects designs and address within-subjects designs only briefly, i provide a detailed overview of the similarities and differences between within- and between-subjects designs. i suggest that some research questions in experimental psychology examine inherently intra-individual effects, which makes effect sizes that incorporate the correlation between measures the best summary of the results. finally, a supplementary spreadsheet is provided to make it as easy as possible for researchers to incorporate effect size calculations into their workflow.",0
"the aim of the uniprot knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. in this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. the number of sequences in uniprotkb has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. we continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. in addition, the scientific community continues their contributions of publications and annotations to uniprot entries of their interest. finally, we describe our new website ( designed to enhance our users' experience and make our data easily accessible to the research community. this interface includes access to alphafold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins.",0
"cell migration underlies tissue formation, maintenance, and regeneration as well as pathological conditions such as cancer invasion. structural and molecular determinants of both tissue environment and cell behavior define whether cells migrate individually (through amoeboid or mesenchymal modes) or collectively. using a multiparameter tuning model, we describe how dimension, density, stiffness, and orientation of the extracellular matrix together with cell determinants-including cell-cell and cell-matrix adhesion, cytoskeletal polarity and stiffness, and pericellular proteolysis-interdependently control migration mode and efficiency. motile cells integrate variable inputs to adjust interactions among themselves and with the matrix to dictate the migration mode. the tuning model provides a matrix of parameters that control cell movement as an adaptive and interconvertible process with relevance to different physiological and pathological contexts.",0
"the gwas catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. the scope of the catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. as of september 2018, the catalog contains 5687 gwas comprising 71673 variant-trait associations from 3567 publications. new content includes 284 full p-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. in the last 12 months, the catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. we have improved data access with the release of a new restful api to support high-throughput programmatic access, an improved web interface and a new summary statistics database. summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. this format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. availability:",0
"resting-state fmri (rs-fmri) has been drawing more and more attention in recent years. however, a publicly available, systematically integrated and easy-to-use tool for rs-fmri data processing is still lacking. we developed a toolkit for the analysis of rs-fmri data, namely the resting-state fmri data analysis toolkit (rest). rest was developed in matlab with graphical user interface (gui). after data preprocessing with spm or afni, a few analytic methods can be performed in rest, including functional connectivity analysis based on linear correlation, regional homogeneity, amplitude of low frequency fluctuation (alff), and fractional alff. a few additional functions were implemented in rest, including a dicom sorter, linear trend removal, bandpass filtering, time course extraction, regression of covariates, image calculator, statistical analysis, and slice viewer (for result visualization, multiple comparison correction, etc.). rest is an open-source package and is freely available at",0
"purpose copy-number analysis to detect disease-causing losses and gains across the genome is recommended for the evaluation of individuals with neurodevelopmental disorders and/or multiple congenital anomalies, as well as for fetuses with ultrasound abnormalities. in the decade that this analysis has been in widespread clinical use, tremendous strides have been made in understanding the effects of copy-number variants (cnvs) in both affected individuals and the general population. however, continued broad implementation of array and next-generation sequencing-based technologies will expand the types of cnvs encountered in the clinical setting, as well as our understanding of their impact on human health. methods to assist clinical laboratories in the classification and reporting of cnvs, irrespective of the technology used to identify them, the american college of medical genetics and genomics has developed the following professional standards in collaboration with the national institutes of health (nih)-funded clinical genome resource (clingen) project. results this update introduces a quantitative, evidence-based scoring framework; encourages the implementation of the five-tier classification system widely used in sequence variant classification; and recommends ""uncoupling"" the evidence-based classification of a variant from its potential implications for a particular individual. conclusion these professional standards will guide the evaluation of constitutional cnvs and encourage consistency and transparency across clinical laboratories.",0
"summary varsome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants. availability and implementation varsome is freely available at supplementary information supplementary data are available at bioinformatics online.",0
"in this paper we describe a method for retrospective estimation and correction of eddy current (ec)-induced distortions and subject movement in diffusion imaging. in addition a susceptibility-induced field can be supplied and will be incorporated into the calculations in a way that accurately reflects that the two fields (susceptibility- and ec-induced) behave differently in the presence of subject movement. the method is based on registering the individual volumes to a model free prediction of what each volume should look like, thereby enabling its use on high b-value data where the contrast is vastly different in different volumes. in addition we show that the linear ec-model commonly used is insufficient for the data used in the present paper (high spatial and angular resolution data acquired with stejskal-tanner gradients on a 3t siemens verio, a 3t siemens connectome skyra or a 7t siemens magnetome scanner) and that a higher order model performs significantly better. the method is already in extensive practical use and is used by four major projects (the wu-uminn hcp, the mgh hcp, the uk biobank and the whitehall studies) to correct for distortions and subject movement.",0
"here we report the simons genome diversity project data set: high quality genomes from 300 individuals from 142 diverse populations. these genomes include at least 5.8 million base pairs that are not present in the human reference genome. our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-africans compared to africans since divergence. we show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. we also demonstrate that indigenous australians, new guineans and andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-africans.",0
"here we present primer3plus, a new web interface to the popular primer3 primer design program as an enhanced alternative for the cgi- scripts that come with primer3. primer3 consists of a command line program and a web interface. the web interface is one large form showing all of the possible options. this makes the interface powerful, but at the same time confusing for occasional users. primer3plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. it focuses on the task at hand, and hides detailed settings from the user until these are needed. we also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. settings and designed primer sequences can be stored locally for later use. primer3plus supports a range of common sequence formats, such as fasta. finally, primers selected by primer3plus can be sent to an order form, allowing tight integration into laboratory ordering systems. moreover, the open architecture of primer3plus allows easy expansion or integration of external software packages. the primer3plus perl source code is available under gpl license from sourceforge. primer3plus is available at",0
"mental disorders are among the strongest predictors of suicide attempts. however, little is known regarding which disorders that are uniquely associated with suicidal behavior because of high levels of psychiatric comorbidity. we examined the unique associations between individual disorders and subsequent suicidal behavior (suicide ideation, plans and attempts) using data from the national comorbidity survey replication, a nationally representative household survey of 9282 us adults. results revealed that approximately 80% of suicide attempters in the united states have a temporally prior mental disorder. anxiety, mood, impulse-control and substance use disorders all significantly predict subsequent suicide attempts in bivariate analyses (odds ratios (or)=2.7-6.7); however, these associations decrease substantially in multivariate analyses controlling for comorbidity (or=1.5-2.3) but remain statistically significant in most cases. disaggregation of the observed effects reveals that depression predicts suicide ideation, but not suicide plans or attempts among those with ideation. instead, disorders characterized by severe anxiety/agitation (for example, post-traumatic stress disorder) and poor impulse control (for example, conduct disorder, substance use disorders) predict which suicide ideators who go on to make a plan or attempt. these results advance understanding of the unique associations between mental disorders and different forms of suicidal behavior. future research must further delineate the mechanisms through which people come to think about suicide and progress from suicidal thoughts to attempts.",0
"background most genes in arabidopsis thaliana are members of gene families. how do the members of gene families arise, and how are gene family copy numbers maintained? some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. results our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in arabidopsis thaliana, identify large internal segmental duplications in arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. examples of six gene families exemplifying characteristic modes are described. distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. both gene family size and duplication by distance closely follow power-law distributions. conclusions combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. these differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.",0
"model selection using likelihood-based criteria (e.g., aic) is one of the first steps in phylogenetic analysis. one must select both a substitution matrix and a model for rates across sites. a simple method is to test all combinations and select the best one. we describe heuristics to avoid these extensive calculations. runtime is divided by ∼2 with results remaining nearly the same, and the method performs well compared with prottest and jmodeltest2. our software, ""smart model selection"" (sms), is implemented in the phyml environment and available using two interfaces: command-line (to be integrated in pipelines) and a web server (",0
"treatment of sheep erythrocytes with suitable concentrations of tannic acid render them capable of adsorbing certain protein molecules from solution in saline. red cells which have adsorbed proteins in this way are agglutinated after washing by the homologous antiprotein sera, even by high dilutions. through hemagglutination sera can be titrated for antibodies against antigens adsorbed on the cells exposed to tannic acid. furthermore, small amounts of the antigens can be detected through their power to inhibit hemagglutination of the treated cells.",0
"the molecular interaction database (mint, is a public repository for protein-protein interactions (ppi) reported in peer-reviewed journals. the database grows steadily over the years and at september 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. the web interface allows the users to search, visualize and download interactions data. mint is one of the members of the international molecular exchange consortium (imex) and adopts the molecular interaction ontology of the proteomics standard initiative (psi-mi) standards for curation and data exchange. mint data are freely accessible and downloadable at we report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.",0
"objective to determine whether there is a link between hypoglycaemia and mortality among participants in the action to control cardiovascular risk in diabetes (accord) trial. design retrospective epidemiological analysis of data from the accord trial. setting diabetes clinics, research clinics, and primary care clinics. participants patients were eligible for the accord study if they had type 2 diabetes, a glycated haemoglobin (haemoglobin a(1c)) concentration of 7.5% or more during screening, and were aged 40-79 years with established cardiovascular disease or 55-79 years with evidence of subclinical disease or two additional cardiovascular risk factors. intervention intensive (haemoglobin a(1c) outcome measures symptomatic, severe hypoglycaemia, manifest as either blood glucose concentration of less than 2.8 mmol/l ( results 10 194 of the 10 251 participants enrolled in the accord study who had at least one assessment for hypoglycaemia during regular follow-up for vital status were included in this analysis. unadjusted annual mortality among patients in the intensive glucose control arm was 2.8% in those who had one or more episodes of hypoglycaemia requiring any assistance compared with 1.2% for those with no episodes (53 deaths per 1924 person years and 201 deaths per 16 315 person years, respectively; adjusted hazard ratio (hr) 1.41, 95% ci 1.03 to 1.93). a similar pattern was seen among participants in the standard glucose control arm (3.7% (21 deaths per 564 person years) v 1.0% (176 deaths per 17 297 person years); adjusted hr 2.30, 95% ci 1.46 to 3.65). on the other hand, among participants with at least one hypoglycaemic episode requiring any assistance, a non-significantly lower risk of death was seen in those in the intensive arm compared with those in the standard arm (adjusted hr 0.74, 95% 0.46 to 1.23). a significantly lower risk was observed in the intensive arm compared with the standard arm in participants who had experienced at least one hypoglycaemic episode requiring medical assistance (adjusted hr 0.55, 95% ci 0.31 to 0.99). of the 451 deaths that occurred in accord up to the time when the intensive treatment arm was closed, one death was adjudicated as definitely related to hypoglycaemia. conclusion symptomatic, severe hypoglycaemia was associated with an increased risk of death within each study arm. however, among participants who experienced at least one episode of hypoglycaemia, the risk of death was lower in such participants in the intensive arm than in the standard arm. symptomatic, severe hypoglycaemia does not appear to account for the difference in mortality between the two study arms up to the time when the accord intensive glycaemia arm was discontinued. trial registration nct00000620.",0
"improvements in a method for the specific microscopic localization of antigen in tissue cells are described. this method employs antibody labelled with fluorescein isocyanate as a histochemical stain, the specific antigen-antibody precipitate being made visible under the fluorescence microscope. two isomeric series derived from nitrofluorescein are described.",0
"background as the most stable and experimentally accessible epigenetic mark, dna methylation is of great interest to the research community. the landscape of dna methylation across tissues, through development and in disease pathogenesis is not yet well characterized. thus there is a need for rapid and cost effective methods for assessing genome-wide levels of dna methylation. the illumina infinium humanmethylation450 (450k) beadchip is a very useful addition to the available methods for dna methylation analysis but its complex design, incorporating two different assay methods, requires careful consideration. accordingly, several normalization schemes have been published. we have taken advantage of known dna methylation patterns associated with genomic imprinting and x-chromosome inactivation (xci), in addition to the performance of snp genotyping assays present on the array, to derive three independent metrics which we use to test alternative schemes of correction and normalization. these metrics also have potential utility as quality scores for datasets. results the standard index of dna methylation at any specific cpg site is β = m/(m + u + 100) where m and u are methylated and unmethylated signal intensities, respectively. betas (βs) calculated from raw signal intensities (the default genomestudio behavior) perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement, even in highly consistent data, by all three metrics. the commonly used procedure of normalizing betas is inferior to the separate normalization of m and u, and it is also advantageous to normalize type i and type ii assays separately. more elaborate manipulation of quantiles proves to be counterproductive. conclusions careful selection of preprocessing steps can minimize variance and thus improve statistical power, especially for the detection of the small absolute dna methylation changes likely associated with complex disease phenotypes. for the convenience of the research community we have created a user-friendly r software package called watermelon, downloadable from bioconductor, compatible with the existing methylumi, minfi and ima packages, that allows others to utilize the same normalization methods and data quality tests on 450k data.",0
"chemokines dictate regional trafficking of functionally distinct t cell subsets. in rodents and humans, a unique subset of cd4(+)cd25(+) cytotoxic t lymphocyte antigen (ctla)-4(+) regulatory t cells (treg) has been proposed to control peripheral tolerance. however, the molecular basis of immune suppression and the trafficking properties of treg cells are still unknown. here, we determined the chemotactic response profile and chemokine receptor expression of human blood-borne cd4(+)cd25(+) treg cells. these treg cells were found to vigorously respond to several inflammatory and lymphoid chemokines. treg cells specifically express the chemokine receptors ccr4 and ccr8 and represent a major subset of circulating cd4(+) t cells responding to the chemokines macrophage-derived chemokine (mdc)/ccl22, thymus and activation-regulated chemokine (tarc)/ccl17, i-309/ccl1, and to the virokine vmip-i (ligands of ccr4 and ccr8). blood-borne cd4(+) t cells that migrate in response to ccl1 and ccl22 exhibit a reduced alloproliferative response, dependent on the increased frequency of treg cells in the migrated population. importantly, mature dendritic cells preferentially attract treg cells among circulating cd4(+) t cells, by secretion of ccr4 ligands ccl17 and ccl22. overall, these results suggest that ccr4 and/or ccr8 may guide treg cells to sites of antigen presentation in secondary lymphoid tissues and inflamed areas to attenuate t cell activation.",0
"topcons ( is a widely used web server for consensus prediction of membrane protein topology. we hereby present a major update to the server, with some substantial improvements, including the following: (i) topcons can now efficiently separate signal peptides from transmembrane regions. (ii) the server can now differentiate more successfully between globular and membrane proteins. (iii) the server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. for most proteins, the final prediction is produced in a matter of seconds. (iv) the user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. indicatively, the user can now scan the entire human proteome in a few days. (v) for proteins with homology to a known 3d structure, the homology-inferred topology is also displayed. (vi) finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and topcons is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions.",0
"we demonstrate the additive manufacturing of complex three-dimensional (3d) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. these structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. this process, termed freeform reversible embedding of suspended hydrogels, enables 3d printing of hydrated materials with an elastic modulus <500 kpa including alginate, collagen, and fibrin. computer-aided design models of 3d optical, computed tomography, and magnetic resonance imaging data were 3d printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3d internal and external anatomical architectures.",0
"us hospital discharges for which clostridium difficile-associated disease (cdad) was listed as any diagnosis doubled from 82,000 (95% confidence interval 71,000-94,000) or 31/100,000 population in 1996 to 178,000 (95% ci 151,000-205,000) or 61/100,000 in 2003; this increase was significant between 2000 and 2003 (slope of linear trend 9.48; 95% ci 6.16-12.80, p = 0.01). the overall rate during this period was severalfold higher in persons >65 years of age (228/100,000) than in the age group with the next highest rate, 45-64 years (40/100,000; p < or = 0.001). cdad appears to be increasing rapidly in the united states and is disproportionately affecting older persons. clinicians should be aware of the increasing risk for cdad and make efforts to control transmission of c. difficile and prevent disease.",0
"jaspar ( is an open-access database storing curated, non-redundant transcription factor (tf) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. for this 2016 release, we expanded the jaspar core collection with 494 new tf binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). the introduced profiles represent an 83% expansion and 10% update when compared to the previous release. we updated the structural annotation of the tf dna binding domains (dbds) following a published hierarchical structural classification. in addition, we introduced 130 transcription factor flexible models trained on chip-seq data for vertebrates, which capture dinucleotide dependencies within tf binding sites. this new jaspar release is accompanied by a new web tool to infer jaspar tf binding profiles recognized by a given tf protein sequence. moreover, we provide the users with a ruby module complementing the jaspar api to ease programmatic access and use of the jaspar collection of profiles. finally, we provide the jaspar2016 r/bioconductor data package with the data of this release.",0
"metabolic syndrome is defined by a constellation of interconnected physiological, biochemical, clinical, and metabolic factors that directly increases the risk of cardiovascular disease, type 2 diabetes mellitus, and all cause mortality. insulin resistance, visceral adiposity, atherogenic dyslipidemia, endothelial dysfunction, genetic susceptibility, elevated blood pressure, hypercoagulable state, and chronic stress are the several factors which constitute the syndrome. chronic inflammation is known to be associated with visceral obesity and insulin resistance which is characterized by production of abnormal adipocytokines such as tumor necrosis factor α , interleukin-1 (il-1), il-6, leptin, and adiponectin. the interaction between components of the clinical phenotype of the syndrome with its biological phenotype (insulin resistance, dyslipidemia, etc.) contributes to the development of a proinflammatory state and further a chronic, subclinical vascular inflammation which modulates and results in atherosclerotic processes. lifestyle modification remains the initial intervention of choice for such population. modern lifestyle modification therapy combines specific recommendations on diet and exercise with behavioural strategies. pharmacological treatment should be considered for those whose risk factors are not adequately reduced with lifestyle changes. this review provides summary of literature related to the syndrome's definition, epidemiology, underlying pathogenesis, and treatment approaches of each of the risk factors comprising metabolic syndrome.",0
"until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. with technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. these data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. for a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. here, we present a bayesian markov chain monte carlo method for the multispecies coalescent. our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. the inference is made possible by multilocus data from multiple individuals per species. using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. these simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. finally, we compare our new method to both an existing method (best 2.2) with similar goals and the supermatrix (concatenation) method. we demonstrate that both best and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms best in divergence time and population size estimation.",0
"a highly multiplexed cytometric imaging approach, termed co-detection by indexing (codex), is used here to create multiplexed datasets of normal and lupus (mrl/lpr) murine spleens. codex iteratively visualizes antibody binding events using dna barcodes, fluorescent dntp analogs, and an in situ polymerization-based indexing procedure. an algorithmic pipeline for single-cell antigen quantification in tightly packed tissues was developed and used to overlay well-known morphological features with de novo characterization of lymphoid tissue architecture at a single-cell and cellular neighborhood levels. we observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. by comparing normal murine spleen to spleens from animals with systemic autoimmune disease (mrl/lpr), extensive and previously uncharacterized splenic cell-interaction dynamics in the healthy versus diseased state was observed. the fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples.",0
"the tumor-permissive and immunosuppressive characteristics of tumor-associated macrophages (tam) have fueled interest in therapeutically targeting these cells. in this context, the colony-stimulating factor 1 (csf1)/colony-stimulating factor 1 receptor (csf1r) axis has gained the most attention, and various approaches targeting either the ligands or the receptor are currently in clinical development. emerging data on the tolerability of csf1/csf1r-targeting agents suggest a favorable safety profile, making them attractive combination partners for both standard treatment modalities and immunotherapeutic agents. the specificity of these agents and their potent blocking activity has been substantiated by impressive response rates in diffuse-type tenosynovial giant cell tumors, a benign connective tissue disorder driven by csf1 in an autocrine fashion. in the malignant disease setting, data on the clinical activity of immunotherapy combinations with csf1/csf1r-targeting agents are pending. as our knowledge of macrophage biology expands, it becomes apparent that the complex phenotypic and functional properties of macrophages are heavily influenced by a continuum of survival, differentiation, recruitment, and polarization signals within their specific tissue environment. thus, the role of macrophages in regulating tumorigenesis and the impact of depleting and/or reprogramming tam as therapeutic approaches for cancer patients may vary greatly depending on organ-specific characteristics of these cells. we review the currently available clinical safety and efficacy data with csf1/csf1r-targeting agents and provide a comprehensive overview of ongoing clinical studies. furthermore, we discuss the local tissue macrophage and tumor-type specificities and their potential impact on csf1/csf1r-targeting treatment strategies for the future.",0
"a substantial body of evidence supports that the gut microbiota plays a pivotal role in the regulation of metabolic, endocrine and immune functions. in recent years, there has been growing recognition of the involvement of the gut microbiota in the modulation of multiple neurochemical pathways through the highly interconnected gut-brain axis. although amazing scientific breakthroughs over the last few years have expanded our knowledge on the communication between microbes and their hosts, the underpinnings of microbiota-gut-brain crosstalk remain to be determined. short-chain fatty acids (scfas), the main metabolites produced in the colon by bacterial fermentation of dietary fibers and resistant starch, are speculated to play a key role in neuro-immunoendocrine regulation. however, the underlying mechanisms through which scfas might influence brain physiology and behavior have not been fully elucidated. in this review, we outline the current knowledge about the involvement of scfas in microbiota-gut-brain interactions. we also highlight how the development of future treatments for central nervous system (cns) disorders can take advantage of the intimate and mutual interactions of the gut microbiota with the brain by exploring the role of scfas in the regulation of neuro-immunoendocrine function.",0
"background assessing the burden of covid-19 on the basis of medically attended case numbers is suboptimal given its reliance on testing strategy, changing case definitions, and disease presentation. population-based serosurveys measuring anti-severe acute respiratory syndrome coronavirus 2 (anti-sars-cov-2) antibodies provide one method for estimating infection rates and monitoring the progression of the epidemic. here, we estimate weekly seroprevalence of anti-sars-cov-2 antibodies in the population of geneva, switzerland, during the epidemic. methods the serocov-pop study is a population-based study of former participants of the bus santé study and their household members. we planned a series of 12 consecutive weekly serosurveys among randomly selected participants from a previous population-representative survey, and their household members aged 5 years and older. we tested each participant for anti-sars-cov-2-igg antibodies using a commercially available elisa. we estimated seroprevalence using a bayesian logistic regression model taking into account test performance and adjusting for the age and sex of geneva's population. here we present results from the first 5 weeks of the study. findings between april 6 and may 9, 2020, we enrolled 2766 participants from 1339 households, with a demographic distribution similar to that of the canton of geneva. in the first week, we estimated a seroprevalence of 4·8% (95% ci 2·4-8·0, n=341). the estimate increased to 8·5% (5·9-11·4, n=469) in the second week, to 10·9% (7·9-14·4, n=577) in the third week, 6·6% (4·3-9·4, n=604) in the fourth week, and 10·8% (8·2-13·9, n=775) in the fifth week. individuals aged 5-9 years (relative risk 0·32 ) and those older than 65 years (rr 0·50 ) had a significantly lower risk of being seropositive than those aged 20-49 years. after accounting for the time to seroconversion, we estimated that for every reported confirmed case, there were 11·6 infections in the community. interpretation these results suggest that most of the population of geneva remained uninfected during this wave of the pandemic, despite the high prevalence of covid-19 in the region (5000 reported clinical cases over funding swiss federal office of public health, swiss school of public health (corona immunitas research program), fondation de bienfaisance du groupe pictet, fondation ancrage, fondation privée des hôpitaux universitaires de genève, and center for emerging viral diseases.",0
"although the th17 subset and its signature cytokine, interleukin (il)-17a (il-17), are implicated in certain autoimmune diseases, their role in cancer remains to be further explored. il-17 has been shown to be elevated in several types of cancer, but how it might contribute to tumor growth is still unclear. we show that growth of b16 melanoma and mb49 bladder carcinoma is reduced in il-17(-/-) mice but drastically accelerated in ifn-gamma(-/-) mice, contributed to by elevated intratumoral il-17, indicating a role of il-17 in promoting tumor growth. adoptive transfer studies and analysis of the tumor microenvironment suggest that cd4(+) t cells are the predominant source of il-17. enhancement of tumor growth by il-17 involves direct effects on tumor cells and tumor-associated stromal cells, which bear il-17 receptors. il-17 induces il-6 production, which in turn activates oncogenic signal transducer and activator of transcription (stat) 3, up-regulating prosurvival and proangiogenic genes. the th17 response can thus promote tumor growth, in part via an il-6-stat3 pathway.",0
"interproscan is a tool that combines different protein signature recognition methods from the interpro consortium member databases into one resource. at the time of writing there are 10 distinct publicly available databases in the application. protein as well as dna sequences can be analysed. a web-based version is accessible for academic and commercial organizations from the ebi ( in addition, a standalone perl version and a soap web service are also available to the users. various output formats are supported and include text tables, xml documents, as well as various graphs to help interpret the results.",0
"a qualitative description design is particularly relevant where information is required directly from those experiencing the phenomenon under investigation and where time and resources are limited. nurses and midwives often have clinical questions suitable to a qualitative approach but little time to develop an exhaustive comprehension of qualitative methodological approaches. qualitative description research is sometimes considered a less sophisticated approach for epistemological reasons. another challenge when considering qualitative description design is differentiating qualitative description from other qualitative approaches. this article provides a systematic and robust journey through the philosophical, ontological, and epistemological perspectives, which evidences the purpose of qualitative description research. methods and rigor issues underpinning qualitative description research are also appraised to provide the researcher with a systematic approach to conduct research utilizing this approach. the key attributes and value of qualitative description research in the health care professions will be highlighted with the aim of extending its usage.",0
"background the global burden of diseases, injuries, and risk factors study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. by providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. methods we used the comparative risk assessment framework developed for previous iterations of the global burden of disease study to estimate attributable deaths, disability-adjusted life-years (dalys), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. this study included 388 risk-outcome pairs that met world cancer research fund-defined criteria for convincing or probable evidence. we extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. we used statistical models to pool data, adjust for bias, and incorporate covariates. we developed a metric that allows comparisons of exposure across risk factors-the summary exposure value. using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and dalys that could be attributed to a given risk. we decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific daly rates. we characterised risk exposure in relation to a socio-demographic index (sdi). findings between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. global exposure for several occupational risks, high body-mass index (bmi), and drug use increased by more than 25% over the same period. all risks jointly evaluated in 2015 accounted for 57·8% (95% ci 56·6-58·8) of global deaths and 41·2% (39·8-42·8) of dalys. in 2015, the ten largest contributors to global dalys among level 3 risks were high systolic blood pressure (211·8 million global dalys), smoking (148·6 million ), high fasting plasma glucose (143·1 million ), high bmi (120·1 million ), childhood undernutrition (113·3 million ), ambient particulate matter (103·1 million ), high total cholesterol (88·7 million ), household air pollution (85·6 million ), alcohol use (85·0 million ), and diets high in sodium (83·0 million ). from 1990 to 2015, attributable dalys declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted daly rates rather than reductions in exposure drove these declines. rising exposure contributed to notable increases in attributable dalys from high bmi, high fasting plasma glucose, occupational carcinogens, and drug use. environmental risks and childhood undernutrition declined steadily with sdi; low physical activity, high bmi, and high fasting plasma glucose increased with sdi. in 119 countries, metabolic risks, such as high bmi and fasting plasma glucose, contributed the most attributable dalys in 2015. regionally, smoking still ranked among the leading five risk factors for attributable dalys in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-saharan africa. interpretation declines in some key environmental risks have contributed to declines in critical infectious diseases. some risks appear to be invariant to sdi. increasing risks, including high bmi, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. some highly preventable risks, such as smoking, remain major causes of attributable dalys, even as exposure is declining. public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. funding bill & melinda gates foundation.",0
"the precise spatio-temporal dynamics of protein activity are often critical in determining cell behaviour, yet for most proteins they remain poorly understood; it remains difficult to manipulate protein activity at precise times and places within living cells. protein activity has been controlled by light, through protein derivatization with photocleavable moieties or using photoreactive small-molecule ligands. however, this requires use of toxic ultraviolet wavelengths, activation is irreversible, and/or cell loading is accomplished via disruption of the cell membrane (for example, through microinjection). here we have developed a new approach to produce genetically encoded photoactivatable derivatives of rac1, a key gtpase regulating actin cytoskeletal dynamics in metazoan cells. rac1 mutants were fused to the photoreactive lov (light oxygen voltage) domain from phototropin, sterically blocking rac1 interactions until irradiation unwound a helix linking lov to rac1. photoactivatable rac1 (pa-rac1) could be reversibly and repeatedly activated using 458- or 473-nm light to generate precisely localized cell protrusions and ruffling. localized rac activation or inactivation was sufficient to produce cell motility and control the direction of cell movement. myosin was involved in rac control of directionality but not in rac-induced protrusion, whereas pak was required for rac-induced protrusion. pa-rac1 was used to elucidate rac regulation of rhoa in cell motility. rac and rho coordinate cytoskeletal behaviours with seconds and submicrometre precision. their mutual regulation remains controversial, with data indicating that rac inhibits and/or activates rho. rac was shown to inhibit rhoa in mouse embryonic fibroblasts, with inhibition modulated at protrusions and ruffles. a pa-rac crystal structure and modelling revealed lov-rac interactions that will facilitate extension of this photoactivation approach to other proteins.",0
"background the full range of long-term health consequences of covid-19 in patients who are discharged from hospital is largely unclear. the aim of our study was to comprehensively compare consequences between 6 months and 12 months after symptom onset among hospital survivors with covid-19. methods we undertook an ambidirectional cohort study of covid-19 survivors who had been discharged from jin yin-tan hospital (wuhan, china) between jan 7 and may 29, 2020. at 6-month and 12-month follow-up visit, survivors were interviewed with questionnaires on symptoms and health-related quality of life (hrqol), and received a physical examination, a 6-min walking test, and laboratory tests. they were required to report their health-care use after discharge and work status at the 12-month visit. survivors who had completed pulmonary function tests or had lung radiographic abnormality at 6 months were given the corresponding tests at 12 months. non-covid-19 participants (controls) matched for age, sex, and comorbidities were interviewed and completed questionnaires to assess prevalent symptoms and hrqol. the primary outcomes were symptoms, modified british medical research council (mmrc) score, hrqol, and distance walked in 6 min (6mwd). multivariable adjusted logistic regression models were used to evaluate the risk factors of 12-month outcomes. findings 1276 covid-19 survivors completed both visits. the median age of patients was 59·0 years (iqr 49·0-67·0) and 681 (53%) were men. the median follow-up time was 185·0 days (iqr 175·0-198·0) for the 6-month visit and 349·0 days (337·0-361·0) for the 12-month visit after symptom onset. the proportion of patients with at least one sequelae symptom decreased from 68% (831/1227) at 6 months to 49% (620/1272) at 12 months (p interpretation most covid-19 survivors had a good physical and functional recovery during 1-year follow-up, and had returned to their original work and life. the health status in our cohort of covid-19 survivors at 12 months was still lower than that in the control population. funding chinese academy of medical sciences innovation fund for medical sciences, the national natural science foundation of china, the national key research and development program of china, major projects of national science and technology on new drug creation and development of pulmonary tuberculosis, the china evergrande group, jack ma foundation, sino biopharmaceutical, ping an insurance (group), and new sunshine charity foundation.",0
"analogous to checklists of recommendations such as the consort statement (for randomized trials), or the quorum statement (for systematic reviews), which are designed to ensure the quality of reports in the medical literature, a checklist of recommendations for authors is being presented by the journal of medical internet research (jmir) in an effort to ensure complete descriptions of web-based surveys. papers on web-based surveys reported according to the cherries statement will give readers a better understanding of the sample (self-)selection and its possible differences from a ""representative"" sample. it is hoped that author adherence to the checklist will increase the usefulness of such reports.",0
"vascular contributions to dementia and alzheimer's disease are increasingly recognized 1-6 . recent studies have suggested that breakdown of the blood-brain barrier (bbb) is an early biomarker of human cognitive dysfunction 7 , including the early clinical stages of alzheimer's disease 5,8-10 . the e4 variant of apolipoprotein e (apoe4), the main susceptibility gene for alzheimer's disease 11-14 , leads to accelerated breakdown of the bbb and degeneration of brain capillary pericytes 15-19 , which maintain bbb integrity 20-22 . it is unclear, however, whether the cerebrovascular effects of apoe4 contribute to cognitive impairment. here we show that individuals bearing apoe4 (with the ε3/ε4 or ε4/ε4 alleles) are distinguished from those without apoe4 (ε3/ε3) by breakdown of the bbb in the hippocampus and medial temporal lobe. this finding is apparent in cognitively unimpaired apoe4 carriers and more severe in those with cognitive impairment, but is not related to amyloid-β or tau pathology measured in cerebrospinal fluid or by positron emission tomography 23 . high baseline levels of the bbb pericyte injury biomarker soluble pdgfrβ 7,8 in the cerebrospinal fluid predicted future cognitive decline in apoe4 carriers but not in non-carriers, even after controlling for amyloid-β and tau status, and were correlated with increased activity of the bbb-degrading cyclophilin a-matrix metalloproteinase-9 pathway 19 in cerebrospinal fluid. our findings suggest that breakdown of the bbb contributes to apoe4-associated cognitive decline independently of alzheimer's disease pathology, and might be a therapeutic target in apoe4 carriers.",0
"objective to analyse the available evidence on cardiovascular safety of non-steroidal anti-inflammatory drugs. design network meta-analysis. data sources bibliographic databases, conference proceedings, study registers, the food and drug administration website, reference lists of relevant articles, and reports citing relevant articles through the science citation index (last update july 2009). manufacturers of celecoxib and lumiracoxib provided additional data. study selection all large scale randomised controlled trials comparing any non-steroidal anti-inflammatory drug with other non-steroidal anti-inflammatory drugs or placebo. two investigators independently assessed eligibility. data extraction the primary outcome was myocardial infarction. secondary outcomes included stroke, death from cardiovascular disease, and death from any cause. two investigators independently extracted data. data synthesis 31 trials in 116 429 patients with more than 115 000 patient years of follow-up were included. patients were allocated to naproxen, ibuprofen, diclofenac, celecoxib, etoricoxib, rofecoxib, lumiracoxib, or placebo. compared with placebo, rofecoxib was associated with the highest risk of myocardial infarction (rate ratio 2.12, 95% credibility interval 1.26 to 3.56), followed by lumiracoxib (2.00, 0.71 to 6.21). ibuprofen was associated with the highest risk of stroke (3.36, 1.00 to 11.6), followed by diclofenac (2.86, 1.09 to 8.36). etoricoxib (4.07, 1.23 to 15.7) and diclofenac (3.98, 1.48 to 12.7) were associated with the highest risk of cardiovascular death. conclusions although uncertainty remains, little evidence exists to suggest that any of the investigated drugs are safe in cardiovascular terms. naproxen seemed least harmful. cardiovascular risk needs to be taken into account when prescribing any non-steroidal anti-inflammatory drug.",0
"objective to determine whether moderate hypothermia after hypoxic-ischaemic encephalopathy in neonates improves survival and neurological outcome at 18 months of age. design a meta-analysis was performed using a fixed effect model. risk ratios, risk difference, and number needed to treat, plus 95% confidence intervals, were measured. data sources studies were identified from the cochrane central register of controlled trials, the oxford database of perinatal trials, pubmed, previous reviews, and abstracts. review methods reports that compared whole body cooling or selective head cooling with normal care in neonates with hypoxic-ischaemic encephalopathy and that included data on death or disability and on specific neurological outcomes of interest to patients and clinicians were selected. results we found three trials, encompassing 767 infants, that included information on death and major neurodevelopmental disability after at least 18 months' follow-up. we also identified seven other trials with mortality information but no appropriate neurodevelopmental data. therapeutic hypothermia significantly reduced the combined rate of death and severe disability in the three trials with 18 month outcomes (risk ratio 0.81, 95% confidence interval 0.71 to 0.93, p=0.002; risk difference -0.11, 95% ci -0.18 to -0.04), with a number needed to treat of nine (95% ci 5 to 25). hypothermia increased survival with normal neurological function (risk ratio 1.53, 95% ci 1.22 to 1.93, p conclusions in infants with hypoxic-ischaemic encephalopathy, moderate hypothermia is associated with a consistent reduction in death and neurological impairment at 18 months.",0
"background there is evidence that genes and their protein products are organized into functional modules according to cellular processes and pathways. gene co-expression networks have been used to describe the relationships between gene transcripts. ample literature exists on how to detect biologically meaningful modules in networks but there is a need for methods that allow one to study the relationships between modules. results we show that network methods can also be used to describe the relationships between co-expression modules and present the following methodology. first, we describe several methods for detecting modules that are shared by two or more networks (referred to as consensus modules). we represent the gene expression profiles of each module by an eigengene. second, we propose a method for constructing an eigengene network, where the edges are undirected but maintain information on the sign of the co-expression information. third, we propose methods for differential eigengene network analysis that allow one to assess the preservation of network properties across different data sets. we illustrate the value of eigengene networks in studying the relationships between consensus modules in human and chimpanzee brains; the relationships between consensus modules in brain, muscle, liver, and adipose mouse tissues; and the relationships between male-female mouse consensus modules and clinical traits. in some applications, we find that module eigengenes can be organized into higher level clusters which we refer to as meta-modules. conclusion eigengene networks can be effective and biologically meaningful tools for studying the relationships between modules of a gene co-expression network. the proposed methods may reveal a higher order organization of the transcriptome. r software tutorials, the data, and supplementary material can be found at the following webpage:",0
"background the scale-up of tobacco control, especially after the adoption of the framework convention for tobacco control, is a major public health success story. nonetheless, smoking remains a leading risk for early death and disability worldwide, and therefore continues to require sustained political commitment. the global burden of diseases, injuries, and risk factors study (gbd) offers a robust platform through which global, regional, and national progress toward achieving smoking-related targets can be assessed. methods we synthesised 2818 data sources with spatiotemporal gaussian process regression and produced estimates of daily smoking prevalence by sex, age group, and year for 195 countries and territories from 1990 to 2015. we analysed 38 risk-outcome pairs to generate estimates of smoking-attributable mortality and disease burden, as measured by disability-adjusted life-years (dalys). we then performed a cohort analysis of smoking prevalence by birth-year cohort to better understand temporal age patterns in smoking. we also did a decomposition analysis, in which we parsed out changes in all-cause smoking-attributable dalys due to changes in population growth, population ageing, smoking prevalence, and risk-deleted daly rates. finally, we explored results by level of development using the socio-demographic index (sdi). findings worldwide, the age-standardised prevalence of daily smoking was 25·0% (95% uncertainty interval 24·2-25·7) for men and 5·4% (5·1-5·7) for women, representing 28·4% (25·8-31·1) and 34·4% (29·4-38·6) reductions, respectively, since 1990. a greater percentage of countries and territories achieved significant annualised rates of decline in smoking prevalence from 1990 to 2005 than in between 2005 and 2015; however, only four countries had significant annualised increases in smoking prevalence between 2005 and 2015 (congo and azerbaijan for men and kuwait and timor-leste for women). in 2015, 11·5% of global deaths (6·4 million ) were attributable to smoking worldwide, of which 52·2% took place in four countries (china, india, the usa, and russia). smoking was ranked among the five leading risk factors by dalys in 109 countries and territories in 2015, rising from 88 geographies in 1990. in terms of birth cohorts, male smoking prevalence followed similar age patterns across levels of sdi, whereas much more heterogeneity was found in age patterns for female smokers by level of development. while smoking prevalence and risk-deleted daly rates mostly decreased by sex and sdi quintile, population growth, population ageing, or a combination of both, drove rises in overall smoking-attributable dalys in low-sdi to middle-sdi geographies between 2005 and 2015. interpretation the pace of progress in reducing smoking prevalence has been heterogeneous across geographies, development status, and sex, and as highlighted by more recent trends, maintaining past rates of decline should not be taken for granted, especially in women and in low-sdi to middle-sdi countries. beyond the effect of the tobacco industry and societal mores, a crucial challenge facing tobacco control initiatives is that demographic forces are poised to heighten smoking's global toll, unless progress in preventing initiation and promoting cessation can be substantially accelerated. greater success in tobacco control is possible but requires effective, comprehensive, and adequately implemented and enforced policies, which might in turn require global and national levels of political commitment beyond what has been achieved during the past 25 years. funding bill & melinda gates foundation and bloomberg philanthropies.",0
"background in a previous paper, we introduced muscle, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing muscle to achieve the highest scores reported to date on four alignment accuracy benchmarks. here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. we introduce a new option, muscle-fast, designed for high-throughput applications. we also describe a new protocol for evaluating objective functions that align two profiles. results we compare the speed and accuracy of muscle with clustalw, progressive poa and the mafft script fftns1, the fastest previously published program known to the author. accuracy is measured using four benchmarks: balibase, prefab, sabmark and smart. we test three variants that offer highest accuracy (muscle with default settings), highest speed (muscle-fast), and a carefully chosen compromise between the two (muscle-prog). we find muscle-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to clustalw in times that are typically two to three orders of magnitude less. muscle-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. conclusions muscle offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. muscle is freely available at",0
"the interactive tree of life ( is an online tool for the display, manipulation and annotation of phylogenetic and other trees. it is freely available and open to everyone. itol version 5 introduces a completely new tree display engine, together with numerous new features. for example, a new dataset type has been added (meme motifs), while annotation options have been expanded for several existing ones. node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. support for tree and dataset scales has been extended, providing fine control over line and label styles. unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. the user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users.",0
"molecular interactions between protein complexes and dna mediate essential gene-regulatory functions. uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (chip-seq) has recently become the focus of intense interest. we here introduce quantitative enrichment of sequence tags (quest), a powerful statistical framework based on the kernel density estimation approach, which uses chip-seq data to determine positions where protein complexes contact dna. using quest, we discovered several thousand binding sites for the human transcription factors srf, gabp and nrsf at an average resolution of about 20 base pairs. meme motif-discovery tool-based analyses of the quest-identified sequences revealed dna binding by cofactors of srf, providing evidence that cofactor binding specificity can be obtained from chip-seq data. by combining quest analyses with gene ontology (go) annotations and expression data, we illustrate how general functions of transcription factors can be inferred.",0
"background understanding what constitutes an important difference on a hrql measure is critical to its interpretation. the aim of this study was to provide a range of estimates of minimally important differences (mids) in eq-5d scores in cancer and to determine if estimates are comparable in lung cancer. methods a retrospective analysis was conducted on cross-sectional data collected from 534 cancer patients, 50 of whom were lung cancer patients. a range of minimally important differences (mids) in eq-5d index-based utility (uk and us) scores and vas scores were estimated using both anchor-based and distribution-based (1/2 standard deviation and standard error of the measure) approaches. groups were anchored using eastern cooperative oncology group performance status (ps) ratings and fact-g total score-based quintiles. results for uk-utility scores, mid estimates based on ps ranged from 0.10 to 0.12 both for all cancers and for lung cancer subgroup. using fact-g quintiles, mids were 0.09 to 0.10 for all cancers, and 0.07 to 0.08 for lung cancer. for us-utility scores, mids ranged from 0.07 to 0.09 grouped by ps for all cancers and for lung cancer; when based on fact-g quintiles, mids were 0.06 to 0.07 in all cancers and 0.05 to 0.06 in lung cancer. mids for vas scores were similar for lung and all cancers, ranging from 8 to 12 (ps) and 7 to 10 (fact-g quintiles). discussion important differences in eq-5d utility and vas scores were similar for all cancers and lung cancer, with the lower end of the range of estimates closer to the mid, i.e. 0.08 for uk-index scores, 0.06 for us-index scores, and 7 for vas scores.",0
"perceptual events derive their significance to an animal from their meaning about the world, that is from the information they carry about their causes. the brain should thus be able to efficiently infer the causes underlying our sensory events. here we use multisensory cue combination to study causal inference in perception. we formulate an ideal-observer model that infers whether two sensory cues originate from the same location and that also estimates their location(s). this model accurately predicts the nonlinear integration of cues by human subjects in two auditory-visual localization tasks. the results show that indeed humans can efficiently infer the causal structure as well as the location of causes. by combining insights from the study of causal inference with the ideal-observer approach to sensory cue combination, we show that the capacity to infer causal structure is not limited to conscious, high-level cognition; it is also performed continually and effortlessly in perception.",0
"background the direct repeat locus of the mycobacterium tuberculosis complex (mtc) is a member of the crispr (clustered regularly interspaced short palindromic repeats) sequences family. spoligotyping is the widely used pcr-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. it is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) unique events polymorphism (uep) (2) insertion-sequence-mediated genetic recombination. genetic convergence, although rare, was also previously demonstrated. three previous international spoligotype databases had partly revealed the global and local geographical structures of mtc bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. results the fourth international spoligotyping database, spoldb4, describes 1939 shared-types (sts) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. the spoldb4 update adds 26 new potentially phylogeographically-specific mtc genotype families. it provides a clearer picture of the current mtc genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. indeed, an independent naïve-bayes mixture-model analysis has validated main of the previous supervised spoldb3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand mtc population structure. updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. our results suggests the existence of fine geographical genetic clines within mtc populations, that could mirror the passed and present homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global tb epidemiologic network. conclusion our results broaden the knowledge of the global phylogeography of the mtc complex. spoldb4 should be a very useful tool to better define the identity of a given mtc clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. the building and mining of extended mtc polymorphic genetic databases is in progress.",0
"studies published between 1986 and 1999 indicated that rotavirus causes approximately 22% (range 17%-28%) of childhood diarrhea hospitalizations. from 2000 to 2004, this proportion increased to 39% (range 29%-45%). application of this proportion to the recent world health organization estimates of diarrhea-related childhood deaths gave an estimated 611,000 (range 454,000-705,000) rotavirus-related deaths.",0
"background hydroxychloroquine and chloroquine have been proposed as treatments for coronavirus disease 2019 (covid-19) on the basis of in vitro activity and data from uncontrolled studies and small, randomized trials. methods in this randomized, controlled, open-label platform trial comparing a range of possible treatments with usual care in patients hospitalized with covid-19, we randomly assigned 1561 patients to receive hydroxychloroquine and 3155 to receive usual care. the primary outcome was 28-day mortality. results the enrollment of patients in the hydroxychloroquine group was closed on june 5, 2020, after an interim analysis determined that there was a lack of efficacy. death within 28 days occurred in 421 patients (27.0%) in the hydroxychloroquine group and in 790 (25.0%) in the usual-care group (rate ratio, 1.09; 95% confidence interval , 0.97 to 1.23; p = 0.15). consistent results were seen in all prespecified subgroups of patients. the results suggest that patients in the hydroxychloroquine group were less likely to be discharged from the hospital alive within 28 days than those in the usual-care group (59.6% vs. 62.9%; rate ratio, 0.90; 95% ci, 0.83 to 0.98). among the patients who were not undergoing mechanical ventilation at baseline, those in the hydroxychloroquine group had a higher frequency of invasive mechanical ventilation or death (30.7% vs. 26.9%; risk ratio, 1.14; 95% ci, 1.03 to 1.27). there was a small numerical excess of cardiac deaths (0.4 percentage points) but no difference in the incidence of new major cardiac arrhythmia among the patients who received hydroxychloroquine. conclusions among patients hospitalized with covid-19, those who received hydroxychloroquine did not have a lower incidence of death at 28 days than those who received usual care. (funded by uk research and innovation and national institute for health research and others; recovery isrctn number, isrctn50189673; clinicaltrials.gov number, nct04381936.).",0
"ancient dna makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. here we report a genome-wide scan for selection using ancient dna, capitalizing on the largest ancient dna data set yet assembled: 230 west eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. the new samples include, to our knowledge, the first genome-wide ancient dna from anatolian neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of europe's first farmers. we also report a transect of the steppe region in samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. we detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.",0
"introduction frequent assessments of rheumatoid arthritis (ra) disease activity allow timely adaptation of therapy, which is essential in preventing disease progression. however, values of acute phase reactants (aprs) are needed to calculate current composite activity indices, such as the disease activity score (das)28, the das28-crp (i.e. the das28 using c-reactive protein instead of erythrocyte sedimentation rate) and the simplified disease activity index (sdai). we hypothesized that aprs make limited contribution to the sdai, and that an sdai-modification eliminating aprs - termed the clinical disease activity index (cdai; i.e. the sum of tender and swollen joint counts and patient and physician global assessments ) - would have comparable validity in clinical cohorts. method data sources comprised an observational cohort of 767 ra patients (average disease duration 8.1 +/- 10.6 years), and an independent inception cohort of 106 patients (disease duration 11.5 +/- 12.5 weeks) who were followed prospectively. results our clinically based hypothesis was statistically supported: aprs accounted only for 15% of the das28, and for 5% of the sdai and the das28-crp. in both cohorts the cdai correlated strongly with das28 (r = 0.89-0.90) and comparably to the correlation of sdai with das28 (r = 0.90-0.91). in additional analyses, the cdai when compared to the sdai and the das28 agreed with a weighted kappa of 0.70 and 0.79, respectively, and comparably to the agreement between das28 and das28-crp. all three scores correlated similarly with health assessment questionnaire (haq) scores (r = 0.45-0.47). the average changes in all scores were greater in patients with better american college of rheumatology response (p conclusion aprs add little information on top (and independent) of the combination of clinical variables included in the sdai. a purely clinical score is a valid measure of disease activity and will have its greatest merits in clinical practice rather than research, where aprs are usually always available. the cdai may facilitate immediate and consistent treatment decisions and help to improve patient outcomes in the longer term.",0
"dengue is a systemic viral infection transmitted between humans by aedes mosquitoes. for some patients, dengue is a life-threatening illness. there are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. the contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. we then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. we predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). this infection total is more than three times the dengue burden estimate of the world health organization. stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. the most notable differences are discussed. these new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. we anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.",0
"pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden markov models. the current release of pfam (22.0) contains 9318 protein families. pfam is now based not only on the uniprotkb sequence database, but also on ncbi genpept and on sequences from selected metagenomics projects. pfam is available on the web from the consortium members using a new, consistent and improved website design in the uk ( the usa ( and sweden ( as well as from mirror sites in france ( and south korea (",0
"objective available evidence supports the emerging hypothesis that metabolic syndrome may be associated with the risk of some common cancers. we did a systematic review and meta-analysis to assess the association between metabolic syndrome and risk of cancer at different sites. research design and methods we conducted an electronic search for articles published through october 2011 without restrictions and by reviewing reference lists from retrieved articles. every included study was to report risk estimates with 95% cis for the association between metabolic syndrome and cancer. results we analyzed 116 datasets from 43 articles, including 38,940 cases of cancer. in cohort studies in men, the presence of metabolic syndrome was associated with liver (relative risk 1.43, p conclusions metabolic syndrome is associated with increased risk of common cancers; for some cancers, the risk differs betweens sexes, populations, and definitions of metabolic syndrome.",0
"we sequenced the genomes of a ∼7,000-year-old farmer from germany and eight ∼8,000-year-old hunter-gatherers from luxembourg and sweden. we analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day europeans derive from at least three highly differentiated populations: west european hunter-gatherers, who contributed ancestry to all europeans but not to near easterners; ancient north eurasians related to upper palaeolithic siberians, who contributed to both europeans and near easterners; and early european farmers, who were mainly of near eastern origin but also harboured west european hunter-gatherer related ancestry. we model these populations' deep relationships and show that early european farmers had ∼44% ancestry from a 'basal eurasian' population that split before the diversification of other non-african lineages.",0
"here, we use single-molecule techniques to study the aggregation of α-synuclein, the protein whose misfolding and deposition is associated with parkinson's disease. we identify a conformational change from the initially formed oligomers to stable, more compact proteinase-k-resistant oligomers as the key step that leads ultimately to fibril formation. the oligomers formed as a result of the structural conversion generate much higher levels of oxidative stress in rat primary neurons than do the oligomers formed initially, showing that they are more damaging to cells. the structural conversion is remarkably slow, indicating a high kinetic barrier for the conversion and suggesting that there is a significant period of time for the cellular protective machinery to operate and potentially for therapeutic intervention, prior to the onset of cellular damage. in the absence of added soluble protein, the assembly process is reversed and fibrils disaggregate to form stable oligomers, hence acting as a source of cytotoxic species.",0
"importance clinical outcomes for glioblastoma remain poor. treatment with immune checkpoint blockade has shown benefits in many cancer types. to our knowledge, data from a randomized phase 3 clinical trial evaluating a programmed death-1 (pd-1) inhibitor therapy for glioblastoma have not been reported. objective to determine whether single-agent pd-1 blockade with nivolumab improves survival in patients with recurrent glioblastoma compared with bevacizumab. design, setting, and participants in this open-label, randomized, phase 3 clinical trial, 439 patients with glioblastoma at first recurrence following standard radiation and temozolomide therapy were enrolled, and 369 were randomized. patients were enrolled between september 2014 and may 2015. the median follow-up was 9.5 months at data cutoff of january 20, 2017. the study included 57 multicenter, multinational clinical sites. interventions patients were randomized 1:1 to nivolumab 3 mg/kg or bevacizumab 10 mg/kg every 2 weeks until confirmed disease progression, unacceptable toxic effects, or death. main outcomes and measures the primary end point was overall survival (os). results a total of 369 patients were randomized to nivolumab (n = 184) or bevacizumab (n = 185). the mgmt promoter was methylated in 23.4% (43/184; nivolumab) and 22.7% (42/185; bevacizumab), unmethylated in 32.1% (59/184; nivolumab) and 36.2% (67/185; bevacizumab), and not reported in remaining patients. at median follow-up of 9.5 months, median os (mos) was comparable between groups: nivolumab, 9.8 months (95% ci, 8.2-11.8); bevacizumab, 10.0 months (95% ci, 9.0-11.8); hr, 1.04 (95% ci, 0.83-1.30); p = .76. the 12-month os was 42% in both groups. the objective response rate was higher with bevacizumab (23.1%; 95% ci, 16.7%-30.5%) vs nivolumab (7.8%; 95% ci, 4.1%-13.3%). grade 3/4 treatment-related adverse events (traes) were similar between groups (nivolumab, 33/182 ; bevacizumab, 25/165 ), with no unexpected neurological traes or deaths due to traes. conclusions and relevance although the primary end point was not met in this randomized clinical trial, mos was comparable between nivolumab and bevacizumab in the overall patient population with recurrent glioblastoma. the safety profile of nivolumab in patients with glioblastoma was consistent with that in other tumor types. trial registration clinicaltrials.gov identifier: nct02017717.",0
"postsynaptic densities (psds) have been isolated from cerebral cortex, midbrain, cerebellum, and brain stem by the triton x-100 method previously used in the isolation of cerebral psds (cohen et al., 1977, j. cell biol. 74:181). these psds have been compared in protein composition, protein phosphorylation, and morphology. thin-section electron microscopy revealed that cerebral cortex and midbrain psds were identical, being approximately 57 nm thick and composed of apparent aggregates 20-30 nm in diameter. isolated cerebellar psds appeared thinner (33 nm) than cerebral cortex psds and lacked the apparent 20- to 30-nm aggregates, but had a latticelike structure. in unidirectional and rotary-shadowed replicas, the cerebrum and midbrain psds were circular in shape with a large central perforation or hole in the center of them. cerebellum psds did not have a large perforation, but did have numerous smaller perforations in a lattice like structure. filaments (6-9 nm) were observed connecting possible 20- to 30-nm aggregates in cerebrum psds and were also observed radiating from one side of the psd. both cerebral cortex and midbrain psds exhibited identical protein patterns on sds gel electrophoresis. in comparison, cerebellar psds (a) lacked the major 51,000 mr protein, (b) contained two times less calmodulin, and (c) contained a unique protein at 73,000 mr. calcium plus calmodulin stimulated the phosphorylation of the 51,000 and 62,000 mr bands in both cerebral cortex and midbrain psds. in cerebellar psds, only the 58,000 and 62,000 mr bands were phosphorylated. in the psds from all brain regions, camp stimulated the phosphorylation of protein ia (73,000 mr), protein ib (68.000 mr), and a 60,000 mr protein, although cerebrum and midbrain psds contained very much higher levels of phosphorylated protein than did the cerebellum. on the basis of the morphological criteria, it is possible that psds isolated from cerebrum and midbrain were derived from the gray type i, or asymmetric, synapses, whereas cerebellum psds were derived from the gray type ii, or symmetric, synapses. since there is some evidence that the type i synapses are involved in excitatory mechanisms while the type ii are involved in inhibitory mechanisms, the role of the psd and of some of its proteins in these synaptic responses is discussed.",0
"salmonella species are known to initiate infection of mammalian hosts by penetrating the intestinal epithelium of the small bowel. these bacteria preferentially interact with peyer's patches which are collections of lymphoid follicles making up the gut-associated lymphoid tissue. we infected murine ligated intestinal loops with invasive and noninvasive salmonella typhimurium strains for 30, 60, 120, and 180 min and examined the infected tissue by transmission electron microscopy. within 30 min, we found that invasive s. typhimurium exclusively entered m cells found within the follicle-associated epithelium (fae) of the peyer's patches. initially, interactions between invasive bacteria and enterocytes adjacent to the m cells were not found. invasion of m cells was associated with the ability of the bacteria to invade tissue culture cells. s. typhimurium mutants, which were noninvasive for tissue culture cells, could not be found in ligated loops associated with m cells or enterocytes after incubations of 30, 60, 120, or 180 min. at 60 min, internalized invasive s. typhimurium were cytotoxic for the m cells. destruction of an m cell formed a gap in the fae which allowed organisms to invade enterocytes adjacent to the dead cell. later in the infection process (120 and 180 min), the presence of bacteria beneath the fae correlated with changes in the cytoarchitecture of the lymphoid follicle. in addition, replicating salmonella began to enter both the apical and basolateral surfaces of enterocytes adjacent to infected m cells.",0
"a t helper cell type 1-mediated colitis develops in severe combined immunodeficient mice after transfer of cd45rb(high) cd4(+) t cells and can be prevented by cotransfer of the cd45rb(low) subset. the immune-suppressive activities of the cd45rb(low) t cell population can be reversed in vivo by administration of an anti-transforming growth factor beta antibody. here we show that interleukin (il)-10 is an essential mediator of the regulatory functions of the cd45rb(low) population. this population isolated from il-10-deficient (il-10(-/-)) mice was unable to protect from colitis and when transferred alone to immune-deficient recipients induced colitis. treatment with an anti-murine il-10 receptor monoclonal antibody abrogated inhibition of colitis mediated by wild-type (wt) cd45rb(low) cd4(+) cells, suggesting that il-10 was necessary for the effector function of the regulatory t cell population. inhibition of colitis by wt regulatory t cells was not dependent on il-10 production by progeny of the cd45rb(high) cd4(+) cells, as cd45rb(low) cd4(+) cells from wt mice were able to inhibit colitis induced by il-10(-/-) cd45rb(high) cd4(+) cells. these findings provide the first clear evidence that il-10 plays a nonredundant role in the functioning of regulatory t cells that control inflammatory responses towards intestinal antigens.",0
"inflammasomes are a family of cytosolic multiprotein complexes that initiate innate immune responses to pathogenic microbes by activating the caspase 1 protease. although genetic data support a critical role for inflammasomes in immune defence and inflammatory diseases, the molecular basis by which individual inflammasomes respond to specific stimuli remains poorly understood. the inflammasome that contains the nlrc4 (nlr family, card domain containing 4) protein was previously shown to be activated in response to two distinct bacterial proteins, flagellin and prgj, a conserved component of pathogen-associated type iii secretion systems. however, direct binding between nlrc4 and flagellin or prgj has never been demonstrated. a homologue of nlrc4, naip5 (nlr family, apoptosis inhibitory protein 5), has been implicated in activation of nlrc4 (refs 7-11), but is widely assumed to have only an auxiliary role, as naip5 is often dispensable for nlrc4 activation. however, naip5 is a member of a small multigene family, raising the possibility of redundancy and functional specialization among naip genes. here we show in mice that different naip paralogues determine the specificity of the nlrc4 inflammasome for distinct bacterial ligands. in particular, we found that activation of endogenous nlrc4 by bacterial prgj requires naip2, a previously uncharacterized member of the naip gene family, whereas naip5 and naip6 activate nlrc4 specifically in response to bacterial flagellin. we dissected the biochemical mechanism underlying the requirement for naip proteins by use of a reconstituted nlrc4 inflammasome system. we found that naip proteins control ligand-dependent oligomerization of nlrc4 and that the naip2-nlrc4 complex physically associates with prgj but not flagellin, whereas naip5-nlrc4 associates with flagellin but not prgj. our results identify naips as immune sensor proteins and provide biochemical evidence for a simple receptor-ligand model for activation of the naip-nlrc4 inflammasomes.",0
"cd4(+)cd25(+) regulatory t (t(r)) cells can inhibit a variety of autoimmune and inflammatory diseases, but the precise mechanisms by which they suppress immune responses in vivo remain unresolved. here, we have used helicobacter hepaticus infection of t cell-reconstituted recombination-activating gene (rag)(-/-) mice as a model to study the ability of cd4(+)cd25(+) t(r) cells to inhibit bacterially triggered intestinal inflammation. h. hepaticus infection elicited both t cell-mediated and t cell-independent intestinal inflammation, both of which were inhibited by adoptively transferred cd4(+)cd25(+) t(r) cells. t cell-independent pathology was accompanied by activation of the innate immune system that was also inhibited by cd4(+)cd25(+) t(r) cells. suppression of innate immune pathology was dependent on t cell-derived interleukin 10 and also on the production of transforming growth factor beta. thus, cd4(+)cd25(+) t(r) cells do not only suppress adaptive t cell responses, but are also able to control pathology mediated by innate immune mechanisms.",0
"determinants of membrane targeting of rho proteins were investigated in live cells with green fluorescent fusion proteins expressed with or without rho-guanine nucleotide dissociation inhibitor (gdi)alpha. the hypervariable region determined to which membrane compartment each protein was targeted. targeting was regulated by binding to rhogdi alpha in the case of rhoa, rac1, rac2, and cdc42hs but not rhob or tc10. although rhob localized to the plasma membrane (pm), golgi, and motile peri-golgi vesicles, tc10 localized to pms and endosomes. inhibition of palmitoylation mislocalized h-ras, rhob, and tc10 to the endoplasmic reticulum. although overexpressed cdc42hs and rac2 were observed predominantly on endomembrane, rac1 was predominantly at the pm. rhoa was cytosolic even when expressed at levels in vast excess of rhogdi alpha. oncogenic dbl stimulated translocation of green fluorescent protein (gfp)-rac1, gfp-cdc42hs, and gfp-rhoa to lamellipodia. rhogdi binding to gfp-cdc42hs was not affected by substituting farnesylation for geranylgeranylation. a palmitoylation site inserted into rhoa blocked rhogdi alpha binding. mutations that render rhoa, cdc42hs, or rac1, either constitutively active or dominant negative abrogated binding to rhogdi alpha and redirected expression to both pms and internal membranes. thus, despite the common essential feature of the caax (prenylation, aax tripeptide proteolysis, and carboxyl methylation) motif, the subcellular localizations of rho gtpases, like their functions, are diverse and dynamic.",0
"an envelope of tails test was used to show that the delayed rectifier k+ current (ik) of guinea pig ventricular myocytes results from the activation of two outward k+ currents. one current was specifically blocked by the benzenesulfonamide antiarrhythmic agent, e-4031 (ic50 = 397 nm). the drug-sensitive current, ""ikr"" exhibits prominent rectification and activates very rapidly relative to the slowly activating drug-insensitive current, ""iks."" iks was characterized by a delayed onset of activation that occurs over a voltage range typical of the classically described cardiac ik. fully activated iks, measured as tail current after 7.5-s test pulses, was 11.4 times larger than the fully activated ikr. ikr was also blocked by d-sotalol (100 microm), a less potent benzenesulfonamide class iii antiarrhythmic agent. the activation curve of ikr had a steep slope (+7.5 mv) and a negative half-point (-21.5 mv) relative to the activation curve of iks (slope = +12.7 mv, half-point = +15.7 mv). the reversal potential (erev) of ikr (-93 mv) was similar to ek (-94 mv for o = 4 mm), whereas erev of iks was -77 mv. the time constants for activation and deactivation of ikr made up a bell-shaped function of membrane potential, peaking between -30 and -40 mv (170 ms). the slope conductance of the linear portion of the fully activated ikr-v relation was 22.5 s/f. inward rectification of this relation occurred at potentials greater than -50 mv, resulting in a voltage-dependent decrease in peak ikr at test potentials greater than 0 mv. peak ikr at 0 mv averaged 0.8 pa/pf (n = 21). although the magnitude of ikr was small relative to fully activated iks, the two currents were of similar magnitude when measured during a relatively short pulse protocol (225 ms) at membrane potentials (-20 to +20 mv) typical of the plateau phase of cardiac action potentials.",0
"on march 11, 2020, the world health organization declared coronavirus disease 2019 (covid-19) a pandemic (1). as of march 28, 2020, a total of 571,678 confirmed covid-19 cases and 26,494 deaths have been reported worldwide (2). reports from china and italy suggest that risk factors for severe disease include older age and the presence of at least one of several underlying health conditions (3,4). u.s. older adults, including those aged ≥65 years and particularly those aged ≥85 years, also appear to be at higher risk for severe covid-19-associated outcomes; however, data describing underlying health conditions among u.s. covid-19 patients have not yet been reported (5). as of march 28, 2020, u.s. states and territories have reported 122,653 u.s. covid-19 cases to cdc, including 7,162 (5.8%) for whom data on underlying health conditions and other known risk factors for severe outcomes from respiratory infections were reported. among these 7,162 cases, 2,692 (37.6%) patients had one or more underlying health condition or risk factor, and 4,470 (62.4%) had none of these conditions reported. the percentage of covid-19 patients with at least one underlying health condition or risk factor was higher among those requiring intensive care unit (icu) admission (358 of 457, 78%) and those requiring hospitalization without icu admission (732 of 1,037, 71%) than that among those who were not hospitalized (1,388 of 5,143, 27%). the most commonly reported conditions were diabetes mellitus, chronic lung disease, and cardiovascular disease. these preliminary findings suggest that in the united states, persons with underlying health conditions or other recognized risk factors for severe outcomes from respiratory infections appear to be at a higher risk for severe disease from covid-19 than are persons without these conditions.",0
"hand washing and maintaining social distance are the main measures recommended by the world health organization (who) to avoid contracting covid-19. unfortunately, these measured do not prevent infection by inhalation of small droplets exhaled by an infected person that can travel distance of meters or tens of meters in the air and carry their viral content. science explains the mechanisms of such transport and there is evidence that this is a significant route of infection in indoor environments. despite this, no countries or authorities consider airborne spread of covid-19 in their regulations to prevent infections transmission indoors. it is therefore extremely important, that the national authorities acknowledge the reality that the virus spreads through air, and recommend that adequate control measures be implemented to prevent further spread of the sars-cov-2 virus, in particularly removal of the virus-laden droplets from indoor air by ventilation.",0
"summary the rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in r. the user may (i) transfer annotation tracks to and from a genome browser and (ii) create and manipulate browser views to focus on a particular set of annotations in a specific genomic region. currently, the ucsc genome browser is supported. availability the package is freely available from a quick-start vignette is included with the package.",0
"background the study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. results to address these challenges, we present metawrap, a modular pipeline software for shotgun metagenomic data analysis. metawrap deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. metawrap is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. it includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. metawrap's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. finally, metawrap comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. conclusions metawrap is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. the bin refinement and reassembly modules of metawrap consistently outperform other binning approaches. each module of metawrap is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. metawrap is open-source software available at .",0
"oscillatory neuronal activity may provide a mechanism for dynamic network coordination. rhythmic neuronal interactions can be quantified using multiple metrics, each with their own advantages and disadvantages. this tutorial will review and summarize current analysis methods used in the field of invasive and non-invasive electrophysiology to study the dynamic connections between neuronal populations. first, we review metrics for functional connectivity, including coherence, phase synchronization, phase-slope index, and granger causality, with the specific aim to provide an intuition for how these metrics work, as well as their quantitative definition. next, we highlight a number of interpretational caveats and common pitfalls that can arise when performing functional connectivity analysis, including the common reference problem, the signal to noise ratio problem, the volume conduction problem, the common input problem, and the sample size bias problem. these pitfalls will be illustrated by presenting a set of matlab-scripts, which can be executed by the reader to simulate each of these potential problems. we discuss how these issues can be addressed using current methods.",0
"the emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. these datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. the impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates' recent diversification. gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. the software is freely available for download at github.com/sanger-pathogens/gubbins, implemented in python and c and supported on linux and mac os x.",0
"mass spectrometry (ms) instruments and experimental protocols are rapidly advancing, but the software tools to analyse tandem mass spectra are lagging behind. we present a database search tool ms-gf+ that is sensitive (it identifies more peptides than most other database search tools) and universal (it works well for diverse types of spectra, different configurations of ms instruments and different experimental protocols). we benchmark ms-gf+ using diverse spectral data sets: (i) spectra of varying fragmentation methods; (ii) spectra of multiple enzyme digests; (iii) spectra of phosphorylated peptides; and (iv) spectra of peptides with unusual fragmentation propensities produced by a novel alpha-lytic protease. for all these data sets, ms-gf+ significantly increases the number of identified peptides compared with commonly used methods for peptide identifications. we emphasize that although ms-gf+ is not specifically designed for any particular experimental set-up, it improves on the performance of tools specifically designed for these applications (for example, specialized tools for phosphoproteomics).",0
"many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. we developed the r package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. data can be imported from several formats including genalex formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. new functions include calculation of bruvo's distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. while functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. a manual with documentation and examples is provided. poppr is open source and major releases are available on cran: more supporting documentation and tutorials can be found under 'resources' at:",0
"the psipred workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. here, we present the work we have completed to update the psipred protein analysis workbench and make it ready for the next 20 years. the main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. we additionally discuss any new software, the new hardware infrastructure, our webservices and web site. lastly we survey updates to some of the key predictive algorithms available through our website.",0
"background as mortality rates decline, life expectancy increases, and populations age, non-fatal outcomes of diseases and injuries are becoming a larger component of the global burden of disease. the global burden of diseases, injuries, and risk factors study 2016 (gbd 2016) provides a comprehensive assessment of prevalence, incidence, and years lived with disability (ylds) for 328 causes in 195 countries and territories from 1990 to 2016. methods we estimated prevalence and incidence for 328 diseases and injuries and 2982 sequelae, their non-fatal consequences. we used dismod-mr 2.1, a bayesian meta-regression tool, as the main method of estimation, ensuring consistency between incidence, prevalence, remission, and cause of death rates for each condition. for some causes, we used alternative modelling strategies if incidence or prevalence needed to be derived from other data. ylds were estimated as the product of prevalence and a disability weight for all mutually exclusive sequelae, corrected for comorbidity and aggregated to cause level. we updated the socio-demographic index (sdi), a summary indicator of income per capita, years of schooling, and total fertility rate. gbd 2016 complies with the guidelines for accurate and transparent health estimates reporting (gather). findings globally, low back pain, migraine, age-related and other hearing loss, iron-deficiency anaemia, and major depressive disorder were the five leading causes of ylds in 2016, contributing 57·6 million (95% uncertainty interval 40·8-75·9 million ), 45·1 million (29·0-62·8 million ), 36·3 million (25·3-50·9 million ), 34·7 million (23·0-49·6 million ), and 34·1 million (23·5-46·0 million ) of total ylds, respectively. age-standardised rates of ylds for all causes combined decreased between 1990 and 2016 by 2·7% (95% ui 2·3-3·1). despite mostly stagnant age-standardised rates, the absolute number of ylds from non-communicable diseases has been growing rapidly across all sdi quintiles, partly because of population growth, but also the ageing of populations. the largest absolute increases in total numbers of ylds globally were between the ages of 40 and 69 years. age-standardised yld rates for all conditions combined were 10·4% (95% ui 9·0-11·8) higher in women than in men. iron-deficiency anaemia, migraine, alzheimer's disease and other dementias, major depressive disorder, anxiety, and all musculoskeletal disorders apart from gout were the main conditions contributing to higher yld rates in women. men had higher age-standardised rates of substance use disorders, diabetes, cardiovascular diseases, cancers, and all injuries apart from sexual violence. globally, we noted much less geographical variation in disability than has been documented for premature mortality. in 2016, there was a less than two times difference in age-standardised yld rates for all causes between the location with the lowest rate (china, 9201 ylds per 100 000, 95% ui 6862-11943) and highest rate (yemen, 14 774 ylds per 100 000, 11 018-19 228). interpretation the decrease in death rates since 1990 for most causes has not been matched by a similar decline in age-standardised yld rates. for many large causes, yld rates have either been stagnant or have increased for some causes, such as diabetes. as populations are ageing, and the prevalence of disabling disease generally increases steeply with age, health systems will face increasing demand for services that are generally costlier than the interventions that have led to declines in mortality in childhood or for the major causes of mortality in adults. up-to-date information about the trends of disease and how this varies between countries is essential to plan for an adequate health-system response. funding bill & melinda gates foundation, and the national institute on aging and the national institute of mental health of the national institutes of health.",0
"a novel method has been developed for the preparation of nearly pure separate cultures of astrocytes and oligodendrocytes. the method is based on (a) the absence of viable neurons in cultures prepared from postnatal rat cerebra, (b) the stratification of astrocytes and oligodendrocytes in culture, and (c) the selective detachment of the overlying oligodendrocytes when exposed to sheer forces generated by shaking the cultures on an orbital shaker for 15--18 h at 37 degrees c. preparations appear greater than 98% pure and contain approximately 1-2 x 10(7) viable cells (20--40 mg of cell protein). three methods were used to characterize these two culture t ypes. first, electron microscopic examination was used to identify the cells in each preparation (mixed and separated cultures of astrocytes and oligodendrocytes) and to assess the purity of each preparation. second, two oligodendroglial cell markers, 2',3'-cyclic nucleotide 3'-phosphohydrolase (ec 3.1.4.37) and glycerol phosphate dehydrogenase (ec 1.1.1.8) were monitored. third, the regulation of cyclic amp accumulation in each culture type was examined. in addition to these studies, we examined the influence of brain extract and dibutyryl camp on the gross morphology and ultrastructure of each preparation. these agents induced astroglial process formation without any apparent morphological effect on oligodendrocytes. collectively, the results indicate that essentially pure cultures of astrocytes and of oligodendrocytes can be prepared and maintained. these preparations should significantly aid in efforts to examine the biochemistry, physiology, and pharmacology of these two major classes of central nervous system cells.",0
"a major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. this relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. here, we describe the drosophila melanogaster genetic reference panel (dgrp), a community resource for analysis of population genomics and quantitative traits. the dgrp consists of fully sequenced inbred lines derived from a natural population. population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the x chromosome, evidence for positive and negative selection, and rapid evolution of the x chromosome. many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. the dgrp facilitates genotype-phenotype mapping using the power of drosophila genetics.",0
"rdp4 is the latest version of recombination detection program (rdp), a windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. rdp4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 mb) than those that could be analysed by older versions of the program. rdp4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. other novelties in rdp4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of 'recombination aware' phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. the key feature of rdp4 that differentiates it from other recombination detection tools is its flexibility. it can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.",0
"in recent years, there has been a growing interest in researching and developing new antimicrobial agents from various sources to combat microbial resistance. therefore, a greater attention has been paid to antimicrobial activity screening and evaluating methods. several bioassays such as disk-diffusion, well diffusion and broth or agar dilution are well known and commonly used, but others such as flow cytofluorometric and bioluminescent methods are not widely used because they require specified equipment and further evaluation for reproducibility and standardization, even if they can provide rapid results of the antimicrobial agent's effects and a better understanding of their impact on the viability and cell damage inflicted to the tested microorganism. in this review article, an exhaustive list of in vitro antimicrobial susceptibility testing methods and detailed information on their advantages and limitations are reported.",0
"the prevention and treatment of prevalent infectious diseases and tumors should benefit from improvements in the induction of antigen-specific t cell immunity. to assess the potential of antigen targeting to dendritic cells to improve immunity, we incorporated ovalbumin protein into a monoclonal antibody to the dec-205 receptor, an endocytic receptor that is abundant on these cells in lymphoid tissues. simultaneously, we injected agonistic alpha-cd40 antibody to mature the dendritic cells. we found that a single low dose of antibody-conjugated ovalbumin initiated immunity from the naive cd4+ and cd8+ t cell repertoire. unexpectedly, the alphadec-205 antigen conjugates, given s.c., targeted to dendritic cells systemically and for long periods, and ovalbumin peptide was presented on mhc class i for 2 weeks. this was associated with stronger cd8+ t cell-mediated immunity relative to other forms of antigen delivery, even when the latter was given at a thousand times higher doses. in parallel, the mice showed enhanced resistance to an established rapidly growing tumor and to viral infection at a mucosal site. by better harnessing the immunizing functions of maturing dendritic cells, antibody-mediated antigen targeting via the dec-205 receptor increases the efficiency of vaccination for t cell immunity, including systemic and mucosal resistance in disease models.",0
"background nvx-cov2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (rsars-cov-2) nanoparticle vaccine composed of trimeric full-length sars-cov-2 spike glycoproteins and matrix-m1 adjuvant. methods we initiated a randomized, placebo-controlled, phase 1-2 trial to evaluate the safety and immunogenicity of the rsars-cov-2 vaccine (in 5-μg and 25-μg doses, with or without matrix-m1 adjuvant, and with observers unaware of trial-group assignments) in 131 healthy adults. in phase 1, vaccination comprised two intramuscular injections, 21 days apart. the primary outcomes were reactogenicity; laboratory values (serum chemistry and hematology), according to food and drug administration toxicity scoring, to assess safety; and igg anti-spike protein response (in enzyme-linked immunosorbent assay units). secondary outcomes included unsolicited adverse events, wild-type virus neutralization (microneutralization assay), and t-cell responses (cytokine staining). igg and microneutralization assay results were compared with 32 (igg) and 29 (neutralization) convalescent serum samples from patients with covid-19, most of whom were symptomatic. we performed a primary analysis at day 35. results after randomization, 83 participants were assigned to receive the vaccine with adjuvant and 25 without adjuvant, and 23 participants were assigned to receive placebo. no serious adverse events were noted. reactogenicity was absent or mild in the majority of participants, more common with adjuvant, and of short duration (mean, ≤2 days). one participant had mild fever that lasted 1 day. unsolicited adverse events were mild in most participants; there were no severe adverse events. the addition of adjuvant resulted in enhanced immune responses, was antigen dose-sparing, and induced a t helper 1 (th1) response. the two-dose 5-μg adjuvanted regimen induced geometric mean anti-spike igg (63,160 elisa units) and neutralization (3906) responses that exceeded geometric mean responses in convalescent serum from mostly symptomatic covid-19 patients (8344 and 983, respectively). conclusions at 35 days, nvx-cov2373 appeared to be safe, and it elicited immune responses that exceeded levels in covid-19 convalescent serum. the matrix-m1 adjuvant induced cd4+ t-cell responses that were biased toward a th1 phenotype. (funded by the coalition for epidemic preparedness innovations; clinicaltrials.gov number, nct04368988).",0
"one of our era's greatest scourges is air pollution, on account not only of its impact on climate change but also its impact on public and individual health due to increasing morbidity and mortality. there are many pollutants that are major factors in disease in humans. among them, particulate matter (pm), particles of variable but very small diameter, penetrate the respiratory system via inhalation, causing respiratory and cardiovascular diseases, reproductive and central nervous system dysfunctions, and cancer. despite the fact that ozone in the stratosphere plays a protective role against ultraviolet irradiation, it is harmful when in high concentration at ground level, also affecting the respiratory and cardiovascular system. furthermore, nitrogen oxide, sulfur dioxide, volatile organic compounds (vocs), dioxins, and polycyclic aromatic hydrocarbons (pahs) are all considered air pollutants that are harmful to humans. carbon monoxide can even provoke direct poisoning when breathed in at high levels. heavy metals such as lead, when absorbed into the human body, can lead to direct poisoning or chronic intoxication, depending on exposure. diseases occurring from the aforementioned substances include principally respiratory problems such as chronic obstructive pulmonary disease (copd), asthma, bronchiolitis, and also lung cancer, cardiovascular events, central nervous system dysfunctions, and cutaneous diseases. last but not least, climate change resulting from environmental pollution affects the geographical distribution of many infectious diseases, as do natural disasters. the only way to tackle this problem is through public awareness coupled with a multidisciplinary approach by scientific experts; national and international organizations must address the emergence of this threat and propose sustainable solutions.",0
"environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. this will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.",0
"eating disorders are relatively rare among the general population. this review discusses the literature on the incidence, prevalence and mortality rates of eating disorders. we searched online medline/pubmed, embase and psycinfo databases for articles published in english using several keyterms relating to eating disorders and epidemiology. anorexia nervosa is relatively common among young women. while the overall incidence rate remained stable over the past decades, there has been an increase in the high risk-group of 15-19 year old girls. it is unclear whether this reflects earlier detection of anorexia nervosa cases or an earlier age at onset. the occurrence of bulimia nervosa might have decreased since the early nineties of the last century. all eating disorders have an elevated mortality risk; anorexia nervosa the most striking. compared with the other eating disorders, binge eating disorder is more common among males and older individuals.",0
"the december, 2019 coronavirus disease outbreak has seen many countries ask people who have potentially come into contact with the infection to isolate themselves at home or in a dedicated quarantine facility. decisions on how to apply quarantine should be based on the best available evidence. we did a review of the psychological impact of quarantine using three electronic databases. of 3166 papers found, 24 are included in this review. most reviewed studies reported negative psychological effects including post-traumatic stress symptoms, confusion, and anger. stressors included longer quarantine duration, infection fears, frustration, boredom, inadequate supplies, inadequate information, financial loss, and stigma. some researchers have suggested long-lasting effects. in situations where quarantine is deemed necessary, officials should quarantine individuals for no longer than required, provide clear rationale for quarantine and information about protocols, and ensure sufficient supplies are provided. appeals to altruism by reminding the public about the benefits of quarantine to wider society can be favourable.",0
"cofilin is an actin depolymerizing protein found widely distributed in animals and plants. we have used electron cryomicroscopy and helical reconstruction to identify its binding site on actin filaments. cofilin binds filamentous (f)-actin cooperatively by bridging two longitudinally associated actin subunits. the binding site is centered axially at subdomain 2 of the lower actin subunit and radially at the cleft between subdomains 1 and 3 of the upper actin subunit. our work has revealed a totally unexpected (and unique) property of cofilin, namely, its ability to change filament twist. as a consequence of this change in twist, filaments decorated with cofilin have much shorter 'actin crossovers' ( approximately 75% of those normally observed in f-actin structures). although their binding sites are distinct, cofilin and phalloidin do not bind simultaneously to f-actin. this is the first demonstration of a protein that excludes another actin-binding molecule by changing filament twist. alteration of f-actin structure by cofilin/adf appears to be a novel mechanism through which the actin cytoskeleton may be regulated or remodeled.",0
"while metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaspades addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. we benchmark metaspades against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.",0
"objective to systematically review associations between intake of saturated fat and trans unsaturated fat and all cause mortality, cardiovascular disease (cvd) and associated mortality, coronary heart disease (chd) and associated mortality, ischemic stroke, and type 2 diabetes. design systematic review and meta-analysis. data sources medline, embase, cochrane central registry of controlled trials, evidence-based medicine reviews, and cinahl from inception to 1 may 2015, supplemented by bibliographies of retrieved articles and previous reviews. eligibility criteria for selecting studies observational studies reporting associations of saturated fat and/or trans unsaturated fat (total, industrially manufactured, or from ruminant animals) with all cause mortality, chd/cvd mortality, total chd, ischemic stroke, or type 2 diabetes. data extraction and synthesis two reviewers independently extracted data and assessed study risks of bias. multivariable relative risks were pooled. heterogeneity was assessed and quantified. potential publication bias was assessed and subgroup analyses were undertaken. the grade approach was used to evaluate quality of evidence and certainty of conclusions. results for saturated fat, three to 12 prospective cohort studies for each association were pooled (five to 17 comparisons with 90,501-339,090 participants). saturated fat intake was not associated with all cause mortality (relative risk 0.99, 95% confidence interval 0.91 to 1.09), cvd mortality (0.97, 0.84 to 1.12), total chd (1.06, 0.95 to 1.17), ischemic stroke (1.02, 0.90 to 1.15), or type 2 diabetes (0.95, 0.88 to 1.03). there was no convincing lack of association between saturated fat and chd mortality (1.15, 0.97 to 1.36; p=0.10). for trans fats, one to six prospective cohort studies for each association were pooled (two to seven comparisons with 12,942-230,135 participants). total trans fat intake was associated with all cause mortality (1.34, 1.16 to 1.56), chd mortality (1.28, 1.09 to 1.50), and total chd (1.21, 1.10 to 1.33) but not ischemic stroke (1.07, 0.88 to 1.28) or type 2 diabetes (1.10, 0.95 to 1.27). industrial, but not ruminant, trans fats were associated with chd mortality (1.18 (1.04 to 1.33) v 1.01 (0.71 to 1.43)) and chd (1.42 (1.05 to 1.92) v 0.93 (0.73 to 1.18)). ruminant trans-palmitoleic acid was inversely associated with type 2 diabetes (0.58, 0.46 to 0.74). the certainty of associations between saturated fat and all outcomes was ""very low."" the certainty of associations of trans fat with chd outcomes was ""moderate"" and ""very low"" to ""low"" for other associations. conclusions saturated fats are not associated with all cause mortality, cvd, chd, ischemic stroke, or type 2 diabetes, but the evidence is heterogeneous with methodological limitations. trans fats are associated with all cause mortality, total chd, and chd mortality, probably because of higher levels of intake of industrial trans fats than ruminant trans fats. dietary guidelines must carefully consider the health effects of recommendations for alternative macronutrients to replace trans fats and saturated fats.",0
"all patients with carcinoma of the breast seen in this unit since 1970 were reviewed to study the incidence, prognosis, morbidity and response to treatment of bone metastases. the biological characteristics of the primary tumour were compared in patients relapsing first in bone or liver. sixty-nine percent of patients dying with breast cancer had bone metastases and bone was the commonest site of first distant relapse. bone relapse was more common in receptor positive or well differentiated (grade 1) tumours. the median survival was 24 months in those with disease apparently confined to the skeleton compared with 3 months after first relapse in liver. ten percent of patients with breast cancer developed hypercalcaemia. all had metastatic disease and 85% had widespread skeletal involvement. fifteen percent of patients with disease confined to the skeleton developed hypercalcaemia. the response in bone to primary endocrine therapy, and chemotherapy, was apparently less than the overall response achieved. a large proportion had apparently static disease reflecting the insensitivity of the uicc assessment criteria. the duration of survival in these patients was similar to responding patients, suggesting a tumour response may occur in the absence of discernable radiological evidence of healing.",0
"no scientific conclusion follows automatically from a statistically non-significant result, yet people routinely use non-significant results to guide conclusions about the status of theories (or the effectiveness of practices). to know whether a non-significant result counts against a theory, or if it just indicates data insensitivity, researchers must use one of: power, intervals (such as confidence or credibility intervals), or else an indicator of the relative evidence for one theory over another, such as a bayes factor. i argue bayes factors allow theory to be linked to data in a way that overcomes the weaknesses of the other approaches. specifically, bayes factors use the data themselves to determine their sensitivity in distinguishing theories (unlike power), and they make use of those aspects of a theory's predictions that are often easiest to specify (unlike power and intervals, which require specifying the minimal interesting value in order to address theory). bayes factors provide a coherent approach to determining whether non-significant results support a null hypothesis over a theory, or whether the data are just insensitive. they allow accepting and rejecting the null hypothesis to be put on an equal footing. concrete examples are provided to indicate the range of application of a simple online bayes calculator, which reveal both the strengths and weaknesses of bayes factors.",0
"the idea of two separate attention networks in the human brain for the voluntary deployment of attention and the reorientation to unexpected events, respectively, has inspired an enormous amount of research over the past years. in this review, we will reconcile these theoretical ideas on the dorsal and ventral attentional system with recent empirical findings from human neuroimaging experiments and studies in stroke patients. we will highlight how novel methods-such as the analysis of effective connectivity or the combination of neurostimulation with functional magnetic resonance imaging-have contributed to our understanding of the functionality and interaction of the two systems. we conclude that neither of the two networks controls attentional processes in isolation and that the flexible interaction between both systems enables the dynamic control of attention in relation to top-down goals and bottom-up sensory stimulation. we discuss which brain regions potentially govern this interaction according to current task demands.",0
"the emergence of the novel human coronavirus sars-cov-2 in wuhan, china has caused a worldwide epidemic of respiratory disease (covid-19). vaccines and targeted therapeutics for treatment of this disease are currently lacking. here we report a human monoclonal antibody that neutralizes sars-cov-2 (and sars-cov) in cell culture. this cross-neutralizing antibody targets a communal epitope on these viruses and may offer potential for prevention and treatment of covid-19.",0
"what happens in early, still undetectable human malignancies is unknown because direct observations are impractical. here we present and validate a 'big bang' model, whereby tumors grow predominantly as a single expansion producing numerous intermixed subclones that are not subject to stringent selection and where both public (clonal) and most detectable private (subclonal) alterations arise early during growth. genomic profiling of 349 individual glands from 15 colorectal tumors showed an absence of selective sweeps, uniformly high intratumoral heterogeneity (ith) and subclone mixing in distant regions, as postulated by our model. we also verified the prediction that most detectable ith originates from early private alterations and not from later clonal expansions, thus exposing the profile of the primordial tumor. moreover, some tumors appear 'born to be bad', with subclone mixing indicative of early malignant potential. this new model provides a quantitative framework to interpret tumor growth dynamics and the origins of ith, with important clinical implications.",0
"structural similarity between viral t cell epitopes and self-peptides could lead to the induction of an autoaggressive t cell response. based on the structural requirements for both mhc class ii binding and tcr recognition of an immunodominant myelin basic protein (mbp) peptide, criteria for a data base search were developed in which the degeneracy of amino acid side chains required for mhc class ii binding and the conservation of those required for t cell activation were considered. a panel of 129 peptides that matched the molecular mimicry motif was tested on seven mbp-specific t cell clones from multiple sclerosis patients. seven viral and one bacterial peptide efficiently activated three of these clones. only one peptide could have been identified as a molecular mimic by sequence alignment. the observation that a single t cell receptor can recognize quite distinct but structurally related peptides from multiple pathogens has important implications for understanding the pathogenesis of autoimmunity.",0
"the research field of systems biology has greatly advanced and, as a result, the concept of network pharmacology has been developed. this advancement, in turn, has shifted the paradigm from a ""one-target, one-drug"" mode to a ""network-target, multiple-component-therapeutics"" mode. network pharmacology is more effective for establishing a ""compound-protein/gene-disease"" network and revealing the regulation principles of small molecules in a high-throughput manner. this approach makes it very powerful for the analysis of drug combinations, especially traditional chinese medicine (tcm) preparations. in this work, we first summarized the databases and tools currently used for tcm research. second, we focused on several representative applications of network pharmacology for tcm research, including studies on tcm compatibility, tcm target prediction, and tcm network toxicology research. third, we compared the general statistics of several current tcm databases and evaluated and compared the search results of these databases based on 10 famous herbs. in summary, network pharmacology is a rational approach for tcm studies, and with the development of tcm research, powerful and comprehensive tcm databases have emerged but need further improvements. additionally, given that several diseases could be treated by tcms, with the mediation of gut microbiota, future studies should focus on both the microbiome and tcms to better understand and treat microbiome-related diseases.",0
"background the cutaneous manifestations of covid-19 disease are poorly characterized. objectives to describe the cutaneous manifestations of covid-19 disease and to relate them to other clinical findings. methods we carried out a nationwide case collection survey of images and clinical data. using a consensus we described five clinical patterns. we later described the association of these patterns with patient demographics, the timing in relation to symptoms of the disease, the severity and the prognosis. results the lesions may be classified as acral areas of erythema with vesicles or pustules (pseudo-chilblain) (19%), other vesicular eruptions (9%), urticarial lesions (19%), maculopapular eruptions (47%) and livedo or necrosis (6%). vesicular eruptions appear early in the course of the disease (15% before other symptoms). the pseudo-chilblain pattern frequently appears late in the evolution of the covid-19 disease (59% after other symptoms), while the rest tend to appear with other symptoms of covid-19. the severity of covid-19 shows a gradient from less severe disease in acral lesions to more severe in the latter groups. the results are similar for confirmed and suspected cases, in terms of both clinical and epidemiological findings. alternative diagnoses are discussed but seem unlikely for the most specific patterns (pseudo-chilblain and vesicular). conclusions we provide a description of the cutaneous manifestations associated with covid-19 infection. these may help clinicians approach patients with the disease and recognize cases presenting with few symptoms. what is already known about this topic? previous descriptions of cutaneous manifestations of covid-19 were case reports and mostly lacked illustrations. what does this study add? we describe a large, representative sample of patients with unexplained skin manifestations and a diagnosis of covid-19, using a consensus method to define morphological patterns associated with covid-19. we describe five clinical patterns associated with different patient demographics, timing and prognosis, and provide illustrations of these patterns to allow for easy recognition.",0
"we present a www server for augustus, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden markov model, a probabilistic model of a sequence and its gene structure. the web server allows the user to impose constraints on the predicted gene structure. a constraint can specify the position of a splice site, a translation initiation site or a stop codon. furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence. the number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure. the result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. the specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction. the web interface and the downloadable stand-alone program are available free of charge at",0
"in immature thymocytes, t cell receptor for antigen (tcr) mobilization leads to an active t cell suicide process, apoptosis, which is involved in the selection of the t cell repertoire. we have proposed that inappropriate induction of such a cell death program in the mature cd4+ t cell population could account for both early qualitative and late quantitative cd4+ t lymphocyte defects of human immunodeficiency virus (hiv)-infected individuals (ameisen, j.c., and a. capron. 1991. immunol. today. 4:102). here, we report that the selective failure of cd4+ t cells from 59 clinically asymptomatic hiv-infected individuals to proliferate in vitro to tcr mobilization by major histocompatibility complex class ii-dependent superantigens and to pokeweed mitogen (pwm) is due to an active cd4+ t cell death process, with the biochemical and ultrastructural features of apoptosis. activation-induced cell death occurred only in the cd4+ t cell population from hiv-infected asymptomatic individuals and was not observed in t cells from any of 58 hiv-seronegative controls, including nine patients with other acute or chronic infectious diseases. activation-induced cd4+ t cell death was prevented by cycloheximide, cyclosporin a, and a cd28 monoclonal antibody (mab). the cd28 mab not only prevented apoptosis but also restored t cell proliferation to stimuli, including pwm, superantigens, and the tetanus and influenza recall antigens. these findings may have implications for the understanding of the pathogenesis of acquired immune deficiency syndrome and for the design of specific therapeutic strategies.",0
"background the burden of cardiovascular diseases (cvds) remains unclear in many regions of the world. objectives the gbd (global burden of disease) 2015 study integrated data on disease incidence, prevalence, and mortality to produce consistent, up-to-date estimates for cardiovascular burden. methods cvd mortality was estimated from vital registration and verbal autopsy data. cvd prevalence was estimated using modeling software and data from health surveys, prospective cohorts, health system administrative data, and registries. years lived with disability (yld) were estimated by multiplying prevalence by disability weights. years of life lost (yll) were estimated by multiplying age-specific cvd deaths by a reference life expectancy. a sociodemographic index (sdi) was created for each location based on income per capita, educational attainment, and fertility. results in 2015, there were an estimated 422.7 million cases of cvd (95% uncertainty interval: 415.53 to 427.87 million cases) and 17.92 million cvd deaths (95% uncertainty interval: 17.59 to 18.28 million cvd deaths). declines in the age-standardized cvd death rate occurred between 1990 and 2015 in all high-income and some middle-income countries. ischemic heart disease was the leading cause of cvd health lost globally, as well as in each world region, followed by stroke. as sdi increased beyond 0.25, the highest cvd mortality shifted from women to men. cvd mortality decreased sharply for both sexes in countries with an sdi >0.75. conclusions cvds remain a major cause of health loss for all regions of the world. sociodemographic change over the past 25 years has been associated with dramatic declines in cvd in regions with very high sdi, but only a gradual decrease or no change in most regions. future updates of the gbd study can be used to guide policymakers who are focused on reducing the overall burden of noncommunicable disease and achieving specific global health targets for cvd.",0
"background bisphenol a (bpa) and 4-tertiary-octylphenol (top) are industrial chemicals used in the manufacture of polycarbonate plastics and epoxy resins (bpa) and nonionic surfactants (top). these products are in widespread use in the united states. objectives we aimed to assess exposure to bpa and top in the u.s. general population. methods we measured the total (free plus conjugated) urinary concentrations of bpa and top in 2,517 participants > or = 6 years of age in the 2003-2004 national health and nutrition examination survey using automated solid-phase extraction coupled to isotope dilution-high-performance liquid chromatography-tandem mass spectrometry. results bpa and top were detected in 92.6% and 57.4% of the persons, respectively. least square geometric mean (lsgm) concentrations of bpa were significantly lower in mexican americans than in non-hispanic blacks (p = 0.006) and non-hispanic whites (p = 0.007); lsgm concentrations for non-hispanic blacks and non-hispanic whites were not statistically different (p = 0.21). females had statistically higher bpa lsgm concentrations than males (p = 0.043). children had higher concentrations than adolescents (p $45,000/year). conclusions urine concentrations of total bpa differed by race/ethnicity, age, sex, and household income. these first u.s. population representative concentration data for urinary bpa and top should help guide public health research priorities, including studies of exposure pathways, potential health effects, and risk assessment.",0
"background covid-19 pandemic has the potential to significantly affect the mental health of healthcare workers (hcws), who stand in the frontline of this crisis. it is, therefore, an immediate priority to monitor rates of mood, sleep and other mental health issues in order to understand mediating factors and inform tailored interventions. the aim of this review is to synthesize and analyze existing evidence on the prevalence of depression, anxiety and insomnia among hcws during the covid-19 outbreak. methods a systematic search of literature databases was conducted up to april 17th, 2020. two reviewers independently assessed full-text articles according to predefined criteria. risk of bias for each individual study was assessed and data pooled using random-effects meta-analyses to estimate the prevalence of specific mental health problems. the review protocol is registered in prospero and is available online. findings thirteen studies were included in the analysis with a combined total of 33,062 participants. anxiety was assessed in 12 studies, with a pooled prevalence of 23·2% and depression in 10 studies, with a prevalence rate of 22·8%. a subgroup analysis revealed gender and occupational differences with female hcps and nurses exhibiting higher rates of affective symptoms compared to male and medical staff respectively. finally, insomnia prevalence was estimated at 38·9% across 5 studies. interpretation early evidence suggests that a considerable proportion of hcws experience mood and sleep disturbances during this outbreak, stressing the need to establish ways to mitigate mental health risks and adjust interventions under pandemic conditions.",0
"background covid-19 pandemic and lockdown has brought about a sense of fear and anxiety around the globe. this phenomenon has led to short term as well as long term psychosocial and mental health implications for children and adolescents. the quality and magnitude of impact on minors is determined by many vulnerability factors like developmental age, educational status, pre-existing mental health condition, being economically underprivileged or being quarantined due to infection or fear of infection. aims this paper is aimed at narratively reviewing various articles related to mental-health aspects of children and adolescents impacted by covid-19 pandemic and enforcement of nationwide or regional lockdowns to prevent further spread of infection. methodology we conducted a review and collected articles and advisories on mental health aspects of children and adolescents during the covid-19 pandemic. we selected articles and thematically organized them. we put up their major findings under the thematic areas of impact on young children, school and college going students, children and adolescents with mental health challenges, economically underprivileged children, impact due to quarantine and separation from parents and the advisories of international organizations. we have also provided recommendations to the above. conclusion there is a pressing need for planning longitudinal and developmental studies, and implementing evidence based elaborative plan of action to cater to the psycho social and mental health needs of the vulnerable children and adolescents during pandemic as well as post pandemic. there is a need to ameliorate children and adolescents' access to mental health support services geared towards providing measures for developing healthy coping mechanisms during the current crisis. for this innovative child and adolescent mental health policies policies with direct and digital collaborative networks of psychiatrists, psychologists, paediatricians, and community volunteers are deemed necessary.",0
"interleukin (il)-6 is produced at the site of inflammation and plays a key role in the acute phase response as defined by a variety of clinical and biological features such as the production of acute phase proteins. il-6 in combination with its soluble receptor sil-6ralpha, dictates the transition from acute to chonic inflammation by changing the nature of leucocyte infiltrate (from polymorphonuclear neutrophils to monocyte/macrophages). in addition, il-6 exerts stimulatory effects on t- and b-cells, thus favoring chronic inflammatory responses. strategies targeting il-6 and il-6 signaling led to effective prevention and treatment of models of rheumatoid arthritis and other chronic inflammatory diseases.",0
"methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. busco estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. here, we present new functionalities and major improvements of the busco software, as well as the renewal and expansion of the underlying data sets in sync with the orthodb v10 release. among the major novelties, busco now enables phylogenetic placement of the input sequence to automatically select the most appropriate busco data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. a newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. busco is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.",0
"macrophages are a heterogeneous population of immune cells playing several and diverse functions in homeostatic and immune responses. the broad spectrum of macrophage functions depends on both heterogeneity and plasticity of these cells, which are highly specialized in sensing the microenvironment and modify their properties accordingly. although it is clear that macrophage phenotypes are difficult to categorize and should be seen as plastic and adaptable, they can be simplified into two extremes: a pro-inflammatory (m1) and an anti-inflammatory/pro-resolving (m2) profile. based on this definition, m1 macrophages are able to start and sustain inflammatory responses, secreting pro-inflammatory cytokines, activating endothelial cells, and inducing the recruitment of other immune cells into the inflamed tissue; on the other hand, m2 macrophages promote the resolution of inflammation, phagocytose apoptotic cells, drive collagen deposition, coordinate tissue integrity, and release anti-inflammatory mediators. dramatic switches in cell metabolism accompany these phenotypic and functional changes of macrophages. in particular, m1 macrophages rely mainly on glycolysis and present two breaks on the tca cycle that result in accumulation of itaconate (a microbicide compound) and succinate. excess of succinate leads to hypoxia inducible factor 1α (hif1α) stabilization that, in turn, activates the transcription of glycolytic genes, thus sustaining the glycolytic metabolism of m1 macrophages. on the contrary, m2 cells are more dependent on oxidative phosphorylation (oxphos), their tca cycle is intact and provides the substrates for the complexes of the electron transport chain (etc). moreover, pro- and anti-inflammatory macrophages are characterized by specific pathways that regulate the metabolism of lipids and amino acids and affect their responses. all these metabolic adaptations are functional to support macrophage activities as well as to sustain their polarization in specific contexts. the aim of this review is to discuss recent findings linking macrophage functions and metabolism.",0
"background the sars-cov-2 delta (b.1.617.2) variant was first detected in england in march, 2021. it has since rapidly become the predominant lineage, owing to high transmissibility. it is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (b.1.1.7) variant. we aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. methods this cohort study was done among all patients with covid-19 in england between march 29 and may 23, 2021, who were identified as being infected with either the alpha or delta sars-cov-2 variant through whole-genome sequencing. individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from public health england's second generation surveillance system and covid-19-associated deaths dataset; the national immunisation management system; and nhs digital secondary uses services and emergency care data set). the risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. stratified cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. findings individual-level data on 43 338 covid-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years ) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio 2·26 ). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted hr 1·45 ). most patients were unvaccinated (32 078 across both groups). the hrs for vaccinated patients with the delta variant versus the alpha variant (adjusted hr for hospital admission 1·94 and for hospital admission or emergency care attendance 1·58 ) were similar to the hrs for unvaccinated patients (2·32 and 1·43 ; p=0·82 for both) but the precision for the vaccinated subgroup was low. interpretation this large national study found a higher hospital admission or emergency care attendance risk for patients with covid-19 infected with the delta variant compared with the alpha variant. results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. funding medical research council; uk research and innovation; department of health and social care; and national institute for health research.",0
"an essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. however, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein-protein interaction information can be error-prone and require considerable effort to annotate. here, we present an update on the online database resource search tool for the retrieval of interacting genes (string); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. interactions in string are provided with a confidence score, and accessory information such as protein domains and 3d structures is made available, all within a stable and consistent identifier space. new features in string include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. version 9.0 of string covers more than 1100 completely sequenced organisms; the resource can be reached at",0
"colitis-associated cancer (cac) is a major complication of inflammatory bowel diseases. we show that components of the inflammasome are protective during acute and recurring colitis and cac in the dextran sulfate sodium (dss) and azoxymethane + dss models. mice lacking the inflammasome adaptor protein pycard (asc) and caspase-1 demonstrate increased disease outcome, morbidity, histopathology, and polyp formation. the increased tumor burden is correlated with attenuated levels of il-1beta and il-18 at the tumor site. to decipher the nucleotide-binding domain, leucine-rich-repeat-containing (nlr) component that is involved in colitis and cac, we assessed nlrp3 and nlrc4 deficient mice. nlrp3(-/-) mice showed an increase in acute and recurring colitis and cac, although the disease outcome was less severe in nlrp3(-/-) mice than in pycard(-/-) or casp1(-/-) animals. no significant differences were observed in disease progression or outcome in nlrc4(-/-) mice compared with similarly treated wild-type animals. bone marrow reconstitution experiments show that nlrp3 gene expression and function in hematopoietic cells, rather than intestinal epithelial cells or stromal cells, is responsible for protection against increased tumorigenesis. these data suggest that the inflammasome functions as an attenuator of colitis and cac.",0
"objective it has been argued that the relationship between depression and diabetes is bi-directional, but this hypothesis has not been explicitly tested. this systematic review examines the bi-directional prospective relationships between depression and type 2 diabetes. research design and methods a search was conducted using medline for publications from 1950 through 2007. reviewers assessed the eligibility of each report by exposure/outcome measurement and study design. only comparative prospective studies of depression and type 2 diabetes that excluded prevalent cases of depression (for diabetes predicting depression) or diabetes (for depression predicting diabetes) were included. two sets of pooled risk estimates were calculated using random effects: depression predicting type 2 diabetes and type 2 diabetes predicting depression. results of 42 full-text publications reviewed, 13 met eligibility for depression predicting onset of diabetes, representing 6,916 incident cases. seven met criteria for diabetes predicting onset of depression, representing 6,414 incident cases. the pooled relative risk (rr) for incident depression associated with baseline diabetes was 1.15 (95% ci 1.02-1.30). the rr for incident diabetes associated with baseline depression was 1.60 (1.37-1.88). conclusions depression is associated with a 60% increased risk of type 2 diabetes. type 2 diabetes is associated with only modest increased risk of depression. future research should focus on identifying mechanisms linking these conditions.",0
"rare diseases, an emerging global public health priority, require an evidence-based estimate of the global point prevalence to inform public policy. we used the publicly available epidemiological data in the orphanet database to calculate such a prevalence estimate. overall, orphanet contains information on 6172 unique rare diseases; 71.9% of which are genetic and 69.9% which are exclusively pediatric onset. global point prevalence was calculated using rare disease prevalence data for predefined geographic regions from the 'orphanet epidemiological file' ( of the 5304 diseases defined by point prevalence, 84.5% of those analysed have a point prevalence of <1/1 000 000. however 77.3-80.7% of the population burden of rare diseases is attributable to the 4.2% (n = 149) diseases in the most common prevalence range (1-5 per 10 000). consequently national definitions of 'rare diseases' (ranging from prevalence of 5 to 80 per 100 000) represent a variable number of rare disease patients despite sharing the majority of rare disease in their scope. our analysis yields a conservative, evidence-based estimate for the population prevalence of rare diseases of 3.5-5.9%, which equates to 263-446 million persons affected globally at any point in time. this figure is derived from data from 67.6% of the prevalent rare diseases; using the european definition of 5 per 10 000; and excluding rare cancers, infectious diseases, and poisonings. future registry research and the implementation of rare disease codification in healthcare systems will further refine the estimates.",0
"the consolidated standards of reporting trials (consort) statement is a guideline designed to improve the transparency and quality of the reporting of randomised controlled trials (rcts). in this article we present an extension to that statement for randomised pilot and feasibility trials conducted in advance of a future definitive rct. the checklist applies to any randomised study in which a future definitive rct, or part of it, is conducted on a smaller scale, regardless of its design (eg, cluster, factorial, crossover) or the terms used by authors to describe the study (eg, pilot, feasibility, trial, study). the extension does not directly apply to internal pilot studies built into the design of a main trial, non-randomised pilot and feasibility studies, or phase ii studies, but these studies all have some similarities to randomised pilot and feasibility studies and so many of the principles might also apply. the development of the extension was motivated by the growing number of studies described as feasibility or pilot studies and by research that has identified weaknesses in their reporting and conduct. we followed recommended good practice to develop the extension, including carrying out a delphi survey, holding a consensus meeting and research team meetings, and piloting the checklist. the aims and objectives of pilot and feasibility randomised studies differ from those of other randomised trials. consequently, although much of the information to be reported in these trials is similar to those in randomised controlled trials (rcts) assessing effectiveness and efficacy, there are some key differences in the type of information and in the appropriate interpretation of standard consort reporting items. we have retained some of the original consort statement items, but most have been adapted, some removed, and new items added. the new items cover how participants were identified and consent obtained; if applicable, the prespecified criteria used to judge whether or how to proceed with a future definitive rct; if relevant, other important unintended consequences; implications for progression from pilot to future definitive rct, including any proposed amendments; and ethical approval or approval by a research review committee confirmed with a reference number. this article includes the 26 item checklist, a separate checklist for the abstract, a template for a consort flowchart for these studies, and an explanation of the changes made and supporting examples. we believe that routine use of this proposed extension to the consort statement will result in improvements in the reporting of pilot trials. editor's note: in order to encourage its wide dissemination this article is freely accessible on the bmj and pilot and feasibility studies journal websites.",0
"introduction the spread of novel corona virus (covid-19) across the globe and the associated morbidity and mortality challenged the nations by several means. one such underrecognized and unaddressed area is the mental health issues medical staff develop during the pandemic. materials and methods this review aimed to review the literature about mental health problems faced by health care workers (hcw) during the covid-19 pandemic. literature search was conducted in the following databases: pubmed, google scholar, cochrane library, embase. all types of articles published in the last 4 months (january 2020-april 2020) which were relevant to the subject of the review were searched. a total of 23 articles were selected by initial screening and 6 articles were included in the final review. results review of all the 6 articles showed that current research focused on assessing several aspects of mental health affected in hcw due to covid-19. several sociodemographic variables like gender, profession, age, place of work, department of work and psychological variables like poor social support, self-efficacy were associated with increased stress, anxiety, depressive symptoms, insomnia in hcw. there is increasing evidence that suggests that covid-19 can be an independent risk factor for stress in hcw. conclusion regular screening of medical personnel involved in treating, diagnosing patients with covid-19 should be done for evaluating stress, depression and anxiety by using multidisciplinary psychiatry teams.",0
"introduction worldwide, more than 20 million patients undergo groin hernia repair annually. the many different approaches, treatment indications and a significant array of techniques for groin hernia repair warrant guidelines to standardize care, minimize complications, and improve results. the main goal of these guidelines is to improve patient outcomes, specifically to decrease recurrence rates and reduce chronic pain, the most frequent problems following groin hernia repair. they have been endorsed by all five continental hernia societies, the international endo hernia society and the european association for endoscopic surgery. methods an expert group of international surgeons (the herniasurge group) and one anesthesiologist pain expert was formed. the group consisted of members from all continents with specific experience in hernia-related research. care was taken to include surgeons who perform different types of repair and had preferably performed research on groin hernia surgery. during the group's first meeting, evidence-based medicine (ebm) training occurred and 166 key questions (kq) were formulated. ebm rules were followed in complete literature searches (including a complete search by the dutch cochrane database) to january 1, 2015 and to july 1, 2015 for level 1 publications. the articles were scored by teams of two or three according to oxford, sign and grade methodologies. during five 2-day meetings, results were discussed with the working group members leading to 136 statements and 88 recommendations. recommendations were graded as ""strong"" (recommendations) or ""weak"" (suggestions) and by consensus in some cases upgraded. in the results and summary section below, the term ""should"" refers to a recommendation. the agree ii instrument was used to validate the guidelines. an external review was performed by three international experts. they recommended the guidelines with high scores. the risk factors for inguinal hernia (ih) include: family history, previous contra-lateral hernia, male gender, age, abnormal collagen metabolism, prostatectomy, and low body mass index. peri-operative risk factors for recurrence include poor surgical techniques, low surgical volumes, surgical inexperience and local anesthesia. these should be considered when treating ih patients. ih diagnosis can be confirmed by physical examination alone in the vast majority of patients with appropriate signs and symptoms. rarely, ultrasound is necessary. less commonly still, a dynamic mri or ct scan or herniography may be needed. the ehs classification system is suggested to stratify ih patients for tailored treatment, research and audit. symptomatic groin hernias should be treated surgically. asymptomatic or minimally symptomatic male ih patients may be managed with ""watchful waiting"" since their risk of hernia-related emergencies is low. the majority of these individuals will eventually require surgery; therefore, surgical risks and the watchful waiting strategy should be discussed with patients. surgical treatment should be tailored to the surgeon's expertise, patient- and hernia-related characteristics and local/national resources. furthermore, patient health-related, life style and social factors should all influence the shared decision-making process leading up to hernia management. mesh repair is recommended as first choice, either by an open procedure or a laparo-endoscopic repair technique. one standard repair technique for all groin hernias does not exist. it is recommended that surgeons/surgical services provide both anterior and posterior approach options. lichtenstein and laparo-endoscopic repair are best evaluated. many other techniques need further evaluation. provided that resources and expertise are available, laparo-endoscopic techniques have faster recovery times, lower chronic pain risk and are cost effective. there is discussion concerning laparo-endoscopic management of potential bilateral hernias (occult hernia issue). after patient consent, during tapp, the contra-lateral side should be inspected. this is not suggested during unilateral tep repair. after appropriate discussions with patients concerning results tissue repair (first choice is the shouldice technique) can be offered. day surgery is recommended for the majority of groin hernia repair provided aftercare is organized. surgeons should be aware of the intrinsic characteristics of the meshes they use. use of so-called low-weight mesh may have slight short-term benefits like reduced postoperative pain and shorter convalescence, but are not associated with better longer-term outcomes like recurrence and chronic pain. mesh selection on weight alone is not recommended. the incidence of erosion seems higher with plug versus flat mesh. it is suggested not to use plug repair techniques. the use of other implants to replace the standard flat mesh in the lichtenstein technique is currently not recommended. in almost all cases, mesh fixation in tep is unnecessary. in both tep and tapp it is recommended to fix mesh in m3 hernias (large medial) to reduce recurrence risk. antibiotic prophylaxis in average-risk patients in low-risk environments is not recommended in open surgery. in laparo-endoscopic repair it is never recommended. local anesthesia in open repair has many advantages, and its use is recommended provided the surgeon is experienced in this technique. general anesthesia is suggested over regional in patients aged 65 and older as it might be associated with fewer complications like myocardial infarction, pneumonia and thromboembolism. perioperative field blocks and/or subfascial/subcutaneous infiltrations are recommended in all cases of open repair. patients are recommended to resume normal activities without restrictions as soon as they feel comfortable. provided expertise is available, it is suggested that women with groin hernias undergo laparo-endoscopic repair in order to decrease the risk of chronic pain and avoid missing a femoral hernia. watchful waiting is suggested in pregnant women as groin swelling most often consists of self-limited round ligament varicosities. timely mesh repair by a laparo-endoscopic approach is suggested for femoral hernias provided expertise is available. all complications of groin hernia management are discussed in an extensive chapter on the topic. overall, the incidence of clinically significant chronic pain is in the 10-12% range, decreasing over time. debilitating chronic pain affecting normal daily activities or work ranges from 0.5 to 6%. chronic postoperative inguinal pain (cpip) is defined as bothersome moderate pain impacting daily activities lasting at least 3 months postoperatively and decreasing over time. cpip risk factors include: young age, female gender, high preoperative pain, early high postoperative pain, recurrent hernia and open repair. for cpip the focus should be on nerve recognition in open surgery and, in selected cases, prophylactic pragmatic nerve resection (planned resection is not suggested). it is suggested that cpip management be performed by multi-disciplinary teams. it is also suggested that cpip be managed by a combination of pharmacological and interventional measures and, if this is unsuccessful, followed by, in selected cases (triple) neurectomy and (in selected cases) mesh removal. for recurrent hernia after anterior repair, posterior repair is recommended. if recurrence occurs after a posterior repair, an anterior repair is recommended. after a failed anterior and posterior approach, management by a specialist hernia surgeon is recommended. risk factors for hernia incarceration/strangulation include: female gender, femoral hernia and a history of hospitalization related to groin hernia. it is suggested that treatment of emergencies be tailored according to patient- and hernia-related factors, local expertise and resources. learning curves vary between different techniques. probably about 100 supervised laparo-endoscopic repairs are needed to achieve the same results as open mesh surgery like lichtenstein. it is suggested that case load per surgeon is more important than center volume. it is recommended that minimum requirements be developed to certify individuals as expert hernia surgeon. the same is true for the designation ""hernia center"". from a cost-effectiveness perspective, day-case laparoscopic ih repair with minimal use of disposables is recommended. the development and implementation of national groin hernia registries in every country (or region, in the case of small country populations) is suggested. they should include patient follow-up data and account for local healthcare structures. a dissemination and implementation plan of the guidelines will be developed by global (herniasurge), regional (international societies) and local (national chapters) initiatives through internet websites, social media and smartphone apps. an overarching plan to improve access to safe ih surgery in low-resource settings (lrss) is needed. it is suggested that this plan contains simple guidelines and a sustainability strategy, independent of international aid. it is suggested that in lrss the focus be on performing high-volume lichtenstein repair under local anesthesia using low-cost mesh. three chapters discuss future research, guidelines for general practitioners and guidelines for patients. conclusions the herniasurge group has developed these extensive and inclusive guidelines for the management of adult groin hernia patients. it is hoped that they will lead to better outcomes for groin hernia patients wherever they live. more knowledge, better training, national audit and specialization in groin hernia management will standardize care for these patients, lead to more effective and efficient healthcare and provide direction for future research.",0
"objective the outbreak of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has caused more than 26 million cases of corona virus disease (covid-19) in the world so far. to control the spread of the disease, screening large numbers of suspected cases for appropriate quarantine and treatment are a priority. pathogenic laboratory testing is typically the gold standard, but it bears the burden of significant false negativity, adding to the urgent need of alternative diagnostic methods to combat the disease. based on covid-19 radiographic changes in ct images, this study hypothesized that artificial intelligence methods might be able to extract specific graphical features of covid-19 and provide a clinical diagnosis ahead of the pathogenic test, thus saving critical time for disease control. methods we collected 1065 ct images of pathogen-confirmed covid-19 cases along with those previously diagnosed with typical viral pneumonia. we modified the inception transfer-learning model to establish the algorithm, followed by internal and external validation. results the internal validation achieved a total accuracy of 89.5% with a specificity of 0.88 and sensitivity of 0.87. the external testing dataset showed a total accuracy of 79.3% with a specificity of 0.83 and sensitivity of 0.67. in addition, in 54 covid-19 images, the first two nucleic acid test results were negative, and 46 were predicted as covid-19 positive by the algorithm, with an accuracy of 85.2%. conclusion these results demonstrate the proof-of-principle for using artificial intelligence to extract radiological features for timely and accurate covid-19 diagnosis. key points • the study evaluated the diagnostic performance of a deep learning algorithm using ct images to screen for covid-19 during the influenza season. • as a screening method, our model achieved a relatively high sensitivity on internal and external ct image datasets. • the model was used to distinguish between covid-19 and other typical viral pneumonia, both of which have quite similar radiologic characteristics.",0
"dynamic remodeling of the extracellular matrix (ecm) is essential for development, wound healing and normal organ homeostasis. life-threatening pathological conditions arise when ecm remodeling becomes excessive or uncontrolled. in this perspective, we focus on how ecm remodeling contributes to fibrotic diseases and cancer, which both present challenging obstacles with respect to clinical treatment, to illustrate the importance and complexity of cell-ecm interactions in the pathogenesis of these conditions. fibrotic diseases, which include pulmonary fibrosis, systemic sclerosis, liver cirrhosis and cardiovascular disease, account for over 45% of deaths in the developed world. ecm remodeling is also crucial for tumor malignancy and metastatic progression, which ultimately cause over 90% of deaths from cancer. here, we discuss current methodologies and models for understanding and quantifying the impact of environmental cues provided by the ecm on disease progression, and how improving our understanding of ecm remodeling in these pathological conditions is crucial for uncovering novel therapeutic targets and treatment strategies. this can only be achieved through the use of appropriate in vitro and in vivo models to mimic disease, and with technologies that enable accurate monitoring, imaging and quantification of the ecm.",0
"background the main associations of body-mass index (bmi) with overall and cause-specific mortality can best be assessed by long-term prospective follow-up of large numbers of people. the prospective studies collaboration aimed to investigate these associations by sharing data from many studies. methods collaborative analyses were undertaken of baseline bmi versus mortality in 57 prospective studies with 894 576 participants, mostly in western europe and north america (61% male, mean recruitment age 46 years, median recruitment year 1979 , mean bmi 25 kg/m(2)). the analyses were adjusted for age, sex, smoking status, and study. to limit reverse causality, the first 5 years of follow-up were excluded, leaving 66 552 deaths of known cause during a mean of 8 (sd 6) further years of follow-up (mean age at death 67 years): 30 416 vascular; 2070 diabetic, renal or hepatic; 22 592 neoplastic; 3770 respiratory; 7704 other. findings in both sexes, mortality was lowest at about 22.5-25 kg/m(2). above this range, positive associations were recorded for several specific causes and inverse associations for none, the absolute excess risks for higher bmi and smoking were roughly additive, and each 5 kg/m(2) higher bmi was on average associated with about 30% higher overall mortality (hazard ratio per 5 kg/m(2) 1.29 ): 40% for vascular mortality (hr 1.41 ); 60-120% for diabetic, renal, and hepatic mortality (hrs 2.16 , 1.59 , and 1.82 , respectively); 10% for neoplastic mortality (hr 1.10 ); and 20% for respiratory and for all other mortality (hrs 1.20 and 1.20 , respectively). below the range 22.5-25 kg/m(2), bmi was associated inversely with overall mortality, mainly because of strong inverse associations with respiratory disease and lung cancer. these inverse associations were much stronger for smokers than for non-smokers, despite cigarette consumption per smoker varying little with bmi. interpretation although other anthropometric measures (eg, waist circumference, waist-to-hip ratio) could well add extra information to bmi, and bmi to them, bmi is in itself a strong predictor of overall mortality both above and below the apparent optimum of about 22.5-25 kg/m(2). the progressive excess mortality above this range is due mainly to vascular disease and is probably largely causal. at 30-35 kg/m(2), median survival is reduced by 2-4 years; at 40-45 kg/m(2), it is reduced by 8-10 years (which is comparable with the effects of smoking). the definite excess mortality below 22.5 kg/m(2) is due mainly to smoking-related diseases, and is not fully explained.",0
"it has long been recognized that an increase of reactive oxygen species (ros) can modify the cell-signaling proteins and have functional consequences, which successively mediate pathological processes such as atherosclerosis, diabetes, unchecked growth, neurodegeneration, inflammation, and aging. while numerous articles have demonstrated the impacts of ros on various signaling pathways and clarify the mechanism of action of cell-signaling proteins, their influence on the level of intracellular ros, and their complex interactions among multiple ros associated signaling pathways, the systemic summary is necessary. in this review paper, we particularly focus on the pattern of the generation and homeostasis of intracellular ros, the mechanisms and targets of ros impacting on cell-signaling proteins (nf-κb, mapks, keap1-nrf2-are, and pi3k-akt), ion channels and transporters (ca(2+) and mptp), and modifying protein kinase and ubiquitination/proteasome system.",0
"china has been severely affected by coronavirus disease 2019(covid-19) since december, 2019. we aimed to assess the mental health burden of chinese public during the outbreak, and to explore the potential influence factors. using a web-based cross-sectional survey, we collected data from 7,236 self-selected volunteers assessed with demographic information, covid-19 related knowledge, generalized anxiety disorder (gad), depressive symptoms, and sleep quality. the overall prevalence of gad, depressive symptoms, and sleep quality of the public were 35.1%, 20.1%, and 18.2%, respectively. younger people reported a significantly higher prevalence of gad and depressive symptoms than older people. compared with other occupational group, healthcare workers were more likely to have poor sleep quality. multivariate logistic regression showed that age (< 35 years) and time spent focusing on the covid-19 (≥ 3 hours per day) were associated with gad, and healthcare workers were at high risk for poor sleep quality. our study identified a major mental health burden of the public during the covid-19 outbreak. younger people, people spending too much time thinking about the outbreak, and healthcare workers were at high risk of mental illness. continuous surveillance of the psychological consequences for outbreaks should become routine as part of preparedness efforts worldwide.",0
"a number of compounds related to tea(+) (tetraethylammoniumion) were injected into squid axons and their effects on g(k) (the potassium conductance) were determined. in most of these ions a quaternary nitrogen is surrounded by three ethyl groups and a fourth group that is very hydrophobic. several of the ions cause inactivation of g(k), a type of ionic gating that is not normally seen in squid axon; i.e., after depolarization g(k) increases and then spontaneously decreases to a small fraction of its peak value even though the depolarization is maintained. observations on the mechanism of this gating show that (a) qa (quaternary ammonium) ions only enter k(+) channels that have open activation gates (the normal permeability gates). (b) the activation gates of qa-occluded channels do not close readily. (c) hyperpolarization helps to clear qa ions from the channels. (d) raising the external k(+) concentration also helps to clear qa ions from the channels. observations (c) and (d) strongly suggest that k(+) ions traverse the membrane by way of pores, and they cannot be explained by the usual type of carrier model. the data suggest that a k(+) pore has two distinct parts: a wide inner mouth that can accept a hydrated k(+) ion or a tea(+)-like ion, and a narrower portion that can accept a dehydrated or partially dehydrated k(+) ion, but not tea(+).",0
"imaging biomarkers (ibs) are integral to the routine management of patients with cancer. ibs used daily in oncology include clinical tnm stage, objective response and left ventricular ejection fraction. other ct, mri, pet and ultrasonography biomarkers are used extensively in cancer research and drug development. new ibs need to be established either as useful tools for testing research hypotheses in clinical trials and research studies, or as clinical decision-making tools for use in healthcare, by crossing 'translational gaps' through validation and qualification. important differences exist between ibs and biospecimen-derived biomarkers and, therefore, the development of ibs requires a tailored 'roadmap'. recognizing this need, cancer research uk (cruk) and the european organisation for research and treatment of cancer (eortc) assembled experts to review, debate and summarize the challenges of ib validation and qualification. this consensus group has produced 14 key recommendations for accelerating the clinical translation of ibs, which highlight the role of parallel (rather than sequential) tracks of technical (assay) validation, biological/clinical validation and assessment of cost-effectiveness; the need for ib standardization and accreditation systems; the need to continually revisit ib precision; an alternative framework for biological/clinical validation of ibs; and the essential requirements for multicentre studies to qualify ibs for clinical use.",0
"the increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. the kegg resource ( provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (kegg genes) and the chemical space (kegg ligand), and wiring diagrams of interaction networks and reaction networks (kegg pathway). a fourth component, kegg brite, has been formally added to the kegg suite of databases. this reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. in accordance with the new chemical genomics initiatives, the scope of kegg ligand has been significantly expanded to cover both endogenous and exogenous molecules. specifically, rpair contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. additionally, drug information is now stored separately and linked to new kegg drug structure maps.",0
"liposomes, sphere-shaped vesicles consisting of one or more phospholipid bilayers, were first described in the mid-60s. today, they are a very useful reproduction, reagent, and tool in various scientific disciplines, including mathematics and theoretical physics, biophysics, chemistry, colloid science, biochemistry, and biology. since then, liposomes have made their way to the market. among several talented new drug delivery systems, liposomes characterize an advanced technology to deliver active molecules to the site of action, and at present, several formulations are in clinical use. research on liposome technology has progressed from conventional vesicles to 'second-generation liposomes', in which long-circulating liposomes are obtained by modulating the lipid composition, size, and charge of the vesicle. liposomes with modified surfaces have also been developed using several molecules, such as glycolipids or sialic acid. this paper summarizes exclusively scalable techniques and focuses on strengths, respectively, limitations in respect to industrial applicability and regulatory requirements concerning liposomal drug formulations based on fda and emea documents.",0
"next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (gasterosteus aculeatus). we used illumina-sequenced rad tags to identify and type over 45,000 single nucleotide polymorphisms (snps) in each of 100 individuals from two oceanic and three freshwater populations. overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. some of these genomic regions co-localize with previously identified qtl for stickleback phenotypic variation identified using laboratory mapping crosses. in addition, we have identified several novel regions showing parallel differentiation across independent populations. annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. this study represents the first high-density snp-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. these data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance.",0
"recent studies suggest that a shared neural ensemble may link distinct memories encoded close in time. according to the memory allocation hypothesis, learning triggers a temporary increase in neuronal excitability that biases the representation of a subsequent memory to the neuronal ensemble encoding the first memory, such that recall of one memory increases the likelihood of recalling the other memory. here we show in mice that the overlap between the hippocampal ca1 ensembles activated by two distinct contexts acquired within a day is higher than when they are separated by a week. several findings indicate that this overlap of neuronal ensembles links two contextual memories. first, fear paired with one context is transferred to a neutral context when the two contexts are acquired within a day but not across a week. second, the first memory strengthens the second memory within a day but not across a week. older mice, known to have lower ca1 excitability, do not show the overlap between ensembles, the transfer of fear between contexts, or the strengthening of the second memory. finally, in aged mice, increasing cellular excitability and activating a common ensemble of ca1 neurons during two distinct context exposures rescued the deficit in linking memories. taken together, these findings demonstrate that contextual memories encoded close in time are linked by directing storage into overlapping ensembles. alteration of these processes by ageing could affect the temporal structure of memories, thus impairing efficient recall of related information.",0
"in this article, the 2010 european league against rheumatism (eular) recommendations for the management of rheumatoid arthritis (ra) with synthetic and biological disease-modifying antirheumatic drugs (sdmards and bdmards, respectively) have been updated. the 2013 update has been developed by an international task force, which based its decisions mostly on evidence from three systematic literature reviews (one each on sdmards, including glucocorticoids, bdmards and safety aspects of dmard therapy); treatment strategies were also covered by the searches. the evidence presented was discussed and summarised by the experts in the course of a consensus finding and voting process. levels of evidence and grades of recommendations were derived and levels of agreement (strengths of recommendations) were determined. fourteen recommendations were developed (instead of 15 in 2010). some of the 2010 recommendations were deleted, and others were amended or split. the recommendations cover general aspects, such as attainment of remission or low disease activity using a treat-to-target approach, and the need for shared decision-making between rheumatologists and patients. the more specific items relate to starting dmard therapy using a conventional sdmard (csdmard) strategy in combination with glucocorticoids, followed by the addition of a bdmard or another csdmard strategy (after stratification by presence or absence of adverse risk factors) if the treatment target is not reached within 6 months (or improvement not seen at 3 months). tumour necrosis factor inhibitors (adalimumab, certolizumab pegol, etanercept, golimumab, infliximab, biosimilars), abatacept, tocilizumab and, under certain circumstances, rituximab are essentially considered to have similar efficacy and safety. if the first bdmard strategy fails, any other bdmard may be used. the recommendations also address tofacitinib as a targeted sdmard (tsdmard), which is recommended, where licensed, after use of at least one bdmard. biosimilars are also addressed. these recommendations are intended to inform rheumatologists, patients, national rheumatology societies and other stakeholders about eular's most recent consensus on the management of ra with sdmards, glucocorticoids and bdmards. they are based on evidence and expert opinion and intended to improve outcome in patients with ra.",0
"functional genomics technologies have been widely adopted in the biological research of both model and non-model species. an efficient functional annotation of dna or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. we present the blast2go suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of dna or protein sequences based on the gene ontology vocabulary. the most outstanding blast2go features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive go-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. we used the blast2go framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.",0
"impedance and potential measurements have been made on a number of artificial membranes. impedance changes were determined as functions of current and of the composition of the environmental solutions. it was shown that rectification is present in asymmetrical systems and that it increases with the membrane potential. the behavior in pairs of solutions of the same salt at different concentrations has formed the basis for the studies although a few experiments with different salts at the same concentrations gave results consistent with the conclusions drawn. a theoretical picture has been presented based on the use of the general kinetic equations for ion motion under the influence of diffusion and electrical forces and on a consideration of possible membrane structures. the equations have been solved for two very simple cases; one based on the assumption of microscopic electroneutrality, and the other on the assumption of a constant electric field. the latter was found to give better results than the former in interpreting the data on potentials and rectification, showing agreement, however, of the right order of magnitude only. although the indications are that a careful treatment of boundary conditions may result in better agreement with experiment, no attempt has been made to carry this through since the data now available are not sufficiently complete or reproducible. applications of the second theoretical case to the squid giant axon have been made showing qualitative agreement with the rectification properties and very good agreement with the membrane potential data.",0
"most common human traits and diseases have a polygenic pattern of inheritance: dna sequence variants at many genetic loci influence the phenotype. genome-wide association (gwa) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. the large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. first, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (p = 0.016) and that underlie skeletal growth defects (p < 0.001). second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that gwa studies can identify large numbers of loci that implicate biologically relevant genes and pathways.",0
"background health literacy concerns the capacities of people to meet the complex demands of health in modern society. in spite of the growing attention for the concept among european health policymakers, researchers and practitioners, information about the status of health literacy in europe remains scarce. this article presents selected findings from the first european comparative survey on health literacy in populations. m ethods the european health literacy survey (hls-eu) was conducted in eight countries: austria, bulgaria, germany, greece, ireland, the netherlands, poland and spain (n = 1000 per country, n = 8000 total sample). data collection was based on eurobarometer standards and the implementation of the hls-eu-q (questionnaire) in computer-assisted or paper-assisted personal interviews. r esults the hls-eu-q constructed four levels of health literacy: insufficient, problematic, sufficient and excellent. at least 1 in 10 (12%) respondents showed insufficient health literacy and almost 1 in 2 (47%) had limited (insufficient or problematic) health literacy. however, the distribution of levels differed substantially across countries (29-62%). subgroups within the population, defined by financial deprivation, low social status, low education or old age, had higher proportions of people with limited health literacy, suggesting the presence of a social gradient which was also confirmed by raw bivariate correlations and a multivariate linear regression model. discussion limited health literacy represents an important challenge for health policies and practices across europe, but to a different degree for different countries. the social gradient in health literacy must be taken into account when developing public health strategies to improve health equity in europe.",0
"in this report, we have addressed two questions concerning immunological memory: the way in which naive and memory t cells recirculate through the body, and the intrinsic rate of division within the naive and memory populations. we identified naive and memory t cells in sheep by their cell surface phenotype and their ability to respond to recall antigen. memory t cells were cd2hi, cd58hi, cd44hi, cd11ahi, and cd45r-, as pertains in man. t cells that crossed from blood to the tissues of the hind leg and accumulated in the popliteal afferent lymph were all of memory phenotype. conversely, t cells in efferent lymph, 90% of which entered the lymph node (ln) via high endothelial venules (hev), were mostly of the naive phenotype (cd2lo, cd58lo, cd44lo, cd11alo, and cd45r+). the marked enrichment of these two phenotypes in different recirculatory compartments indicated that memory t cells selectively traffic from blood to peripheral tissues to ln (via afferent lymph), whereas naive t cells selectively traffic from blood to ln (via hev). we argue that the differential use of these two recirculation pathways probably optimizes lymphocyte interactions with antigen. the nonrandom distribution of t cell subsets in various recirculatory compartments may be related to the relative proportion of memory cells in each subset. in particular, gamma/delta t cells in blood were almost exclusively of memory phenotype, and accumulated preferentially in afferent, but not in efferent, lymph. finally, using the bromo-deoxyuridine labeling technique, we found that at least a sizeable proportion of memory t cells, whether in blood or afferent lymph, were a dividing population of cells, whereas naive t cells were a nondividing population. this result supports an alternative model of lymphocyte memory that assumes that maintenance of memory requires persistent antigenic stimulation.",0
"background cross-sectional studies with binary outcomes analyzed by logistic regression are frequent in the epidemiological literature. however, the odds ratio can importantly overestimate the prevalence ratio, the measure of choice in these studies. also, controlling for confounding is not equivalent for the two measures. in this paper we explore alternatives for modeling data of such studies with techniques that directly estimate the prevalence ratio. methods we compared cox regression with constant time at risk, poisson regression and log-binomial regression against the standard mantel-haenszel estimators. models with robust variance estimators in cox and poisson regressions and variance corrected by the scale parameter in poisson regression were also evaluated. results three outcomes, from a cross-sectional study carried out in pelotas, brazil, with different levels of prevalence were explored: weight-for-age deficit (4%), asthma (31%) and mother in a paid job (52%). unadjusted cox/poisson regression and poisson regression with scale parameter adjusted by deviance performed worst in terms of interval estimates. poisson regression with scale parameter adjusted by chi2 showed variable performance depending on the outcome prevalence. cox/poisson regression with robust variance, and log-binomial regression performed equally well when the model was correctly specified. conclusions cox or poisson regression with robust variance and log-binomial regression provide correct estimates and are a better alternative for the analysis of cross-sectional studies with binary outcomes than logistic regression, since the prevalence ratio is more interpretable and easier to communicate to non-specialists than the odds ratio. however, precautions are needed to avoid estimation problems in specific situations.",0
"parkinson's disease is the second most common neurodegenerative disorder. growing evidence indicates a causative role of misfolded forms of the protein α-synuclein in the pathogenesis of parkinson's disease. intraneuronal aggregates of α-synuclein occur in lewy bodies and lewy neurites, the cytopathological hallmarks of parkinson's disease and related disorders called synucleinopathies. α-synuclein has long been defined as a 'natively unfolded' monomer of about 14 kda (ref. 6) that is believed to acquire α-helical secondary structure only upon binding to lipid vesicles. this concept derives from the widespread use of recombinant bacterial expression protocols for in vitro studies, and of overexpression, sample heating and/or denaturing gels for cell culture and tissue studies. in contrast, we report that endogenous α-synuclein isolated and analysed under non-denaturing conditions from neuronal and non-neuronal cell lines, brain tissue and living human cells occurs in large part as a folded tetramer of about 58 kda. several methods, including analytical ultracentrifugation, scanning transmission electron microscopy and in vitro cell crosslinking confirmed the occurrence of the tetramer. native, cell-derived α-synuclein showed α-helical structure without lipid addition and had much greater lipid-binding capacity than the recombinant α-synuclein studied heretofore. whereas recombinantly expressed monomers readily aggregated into amyloid-like fibrils in vitro, native human tetramers underwent little or no amyloid-like aggregation. on the basis of these findings, we propose that destabilization of the helically folded tetramer precedes α-synuclein misfolding and aggregation in parkinson's disease and other human synucleinopathies, and that small molecules that stabilize the physiological tetramer could reduce α-synuclein pathogenicity.",0
"background the 'hawthorne effect' may be an important factor affecting the generalisability of clinical research to routine practice, but has been little studied. hawthorne effects have been reported in previous clinical trials in dementia but to our knowledge, no attempt has been made to quantify them. our aim was to compare minimal follow-up to intensive follow-up in participants in a placebo controlled trial of ginkgo biloba for treating mild-moderate dementia. methods participants in a dementia trial were randomised to intensive follow-up (with comprehensive assessment visits at baseline and two, four and six months post randomisation) or minimal follow-up (with an abbreviated assessment at baseline and a full assessment at six months). our primary outcomes were cognitive functioning (adas-cog) and participant and carer-rated quality of life (qol-ad). results we recruited 176 participants, mainly through general practices. the main analysis was based on intention to treat (itt), with available data. in the ancova model with baseline score as a co-variate, follow-up group had a significant effect on outcome at six months on the adas-cog score (n = 140; mean difference = -2.018; 95%ci -3.914, -0.121; p = 0.037 favouring the intensive follow-up group), and on participant-rated quality of life score (n = 142; mean difference = -1.382; 95%ci -2.642, -0.122; p = 0.032 favouring minimal follow-up group). there was no significant difference on carer quality of life. conclusion we found that more intensive follow-up of individuals in a placebo-controlled clinical trial of ginkgo biloba for treating mild-moderate dementia resulted in a better outcome than minimal follow-up, as measured by their cognitive functioning. trial registration current controlled trials: isrctn45577048.",0
"mendelian randomization (mr) uses genetic variants as instrumental variables to infer whether a risk factor causally affects a health outcome. meta-analysis has been used historically in mr to combine results from separate epidemiological studies, with each study using a small but select group of genetic variants. in recent years, it has been used to combine genome-wide association study (gwas) summary data for large numbers of genetic variants. heterogeneity among the causal estimates obtained from multiple genetic variants points to a possible violation of the necessary instrumental variable assumptions. in this article, we provide a basic introduction to mr and the instrumental variable theory that it relies upon. we then describe how random effects models, meta-regression, and robust regression are being used to test and adjust for heterogeneity in order to improve the rigor of the mr approach.",0
"on 5 february 2020, in yokohama, japan, a cruise ship hosting 3,711 people underwent a 2-week quarantine after a former passenger was found with covid-19 post-disembarking. as at 20 february, 634 persons on board tested positive for the causative virus. we conducted statistical modelling to derive the delay-adjusted asymptomatic proportion of infections, along with the infections' timeline. the estimated asymptomatic proportion was 17.9% (95% credible interval (cri): 15.5-20.2%). most infections occurred before the quarantine start.",0
"background a potential association between the use of angiotensin-receptor blockers (arbs) and angiotensin-converting-enzyme (ace) inhibitors and the risk of coronavirus disease 2019 (covid-19) has not been well studied. methods we carried out a population-based case-control study in the lombardy region of italy. a total of 6272 case patients in whom infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was confirmed between february 21 and march 11, 2020, were matched to 30,759 beneficiaries of the regional health service (controls) according to sex, age, and municipality of residence. information about the use of selected drugs and patients' clinical profiles was obtained from regional databases of health care use. odds ratios and 95% confidence intervals for associations between drugs and infection, with adjustment for confounders, were estimated by means of logistic regression. results among both case patients and controls, the mean (±sd) age was 68±13 years, and 37% were women. the use of ace inhibitors and arbs was more common among case patients than among controls, as was the use of other antihypertensive and non-antihypertensive drugs, and case patients had a worse clinical profile. use of arbs or ace inhibitors did not show any association with covid-19 among case patients overall (adjusted odds ratio, 0.95 for arbs and 0.96 for ace inhibitors) or among patients who had a severe or fatal course of the disease (adjusted odds ratio, 0.83 for arbs and 0.91 for ace inhibitors), and no association between these variables was found according to sex. conclusions in this large, population-based study, the use of ace inhibitors and arbs was more frequent among patients with covid-19 than among controls because of their higher prevalence of cardiovascular disease. however, there was no evidence that ace inhibitors or arbs affected the risk of covid-19.",0
"neural responses are typically characterized by computing the mean firing rate, but response variability can exist across trials. many studies have examined the effect of a stimulus on the mean response, but few have examined the effect on response variability. we measured neural variability in 13 extracellularly recorded datasets and one intracellularly recorded dataset from seven areas spanning the four cortical lobes in monkeys and cats. in every case, stimulus onset caused a decline in neural variability. this occurred even when the stimulus produced little change in mean firing rate. the variability decline was observed in membrane potential recordings, in the spiking of individual neurons and in correlated spiking variability measured with implanted 96-electrode arrays. the variability decline was observed for all stimuli tested, regardless of whether the animal was awake, behaving or anaesthetized. this widespread variability decline suggests a rather general property of cortex, that its state is stabilized by an input.",0
"background spinal cord injury (sci) is a traumatic event that impacts a patient's physical, psychological, and social well-being and places substantial financial burden on health care systems. to determine the true impact of sci, this systematic review aims to summarize literature reporting on either the incidence or prevalence of sci. methods a systematic search was conducted using pubmed, medline, medline in process, embase, cochrane controlled trial register, and cochrane database of systematic reviews to identify relevant literature published through june 2013. we sought studies that provided regional, provincial/state, or national data on the incidence of sci or reported estimates of disease prevalence. the level of evidence of each study was rated using a scale that evaluated study design, methodology, sampling bias, and precision of estimates. results the initial search yielded 5,874 articles, 48 of which met the inclusion criteria. forty-four studies estimated the incidence of sci and nine reported the prevalence, with five discussing both. of the incidence studies, 14 provided figures at a regional, ten at a state or provincial level and 21 at a national level. the prevalence of sci was highest in the united states of america (906 per million) and lowest in the rhone-alpes region, france (250 per million) and helsinki, finland (280 per million). with respect to states and provinces in north america, the crude annual incidence of sci was highest in alaska (83 per million) and mississippi (77 per million) and lowest in alabama (29.4 per million), despite a large percentage of violence injuries (21.2%). annual incidences were above 50 per million in the hualien county in taiwan (56.1 per million), the central portugal region (58 per million), and olmsted county in minnesota (54.8 per million) and were lower than 20 per million in taipei, taiwan (14.6 per million), the rhone-alpes region in france (12.7 per million), aragon, spain (12.1 per million), southeast turkey (16.9 per million), and stockholm, sweden (19.5 per million). the highest national incidence was 49.1 per million in new zealand, and the lowest incidences were in fiji (10.0 per million) and spain (8.0 per million). the majority of studies showed a high male-to-female ratio and an age of peak incidence of younger than 30 years old. traffic accidents were typically the most common cause of sci, followed by falls in the elderly population. conclusion this review demonstrates that the incidence, prevalence, and causation of sci differs between developing and developed countries and suggests that management and preventative strategies need to be tailored to regional trends. the rising aging population in westernized countries also indicates that traumatic sci secondary to falls may become an increasing public health challenge and that incidence among the elderly may rise with increasing life expectancy.",0
"glioblastoma multiforme (gbm) is one of the most malignant types of central nervous system tumors. despite advances in treatment modalities it remains largely incurable. the objective of our review is to provide a holistic picture of gbm epidemiology, etiology, pathogenesis, clinical findings and treatment. a literature search was conducted for gbm at pubmed and google scholar, with relevant key words like glioblastoma multiforme, pathogenesis, signs and symptoms, treatment etc., and papers published until 2015 were reviewed. it was found that radiation and certain genetic syndromes are the only risk factors identified to date for gbm. depending on the tumor site patients may present to the clinic with varying symptoms. to confirm the presence and the extent of tumor, various invasive and non-invasive imaging techniques require employment. the literature survey revealed the pathogenesis to involve aberrations of multiple signaling pathways through multiple genetic mutations and altered gene expression. although several treatment options are available, including surgery, along with adjuvant chemo- and radio-therapy, the disease has a poor prognosis and patients generally succumb within 14 months of diagnosis.",0
"the human liver is usually perceived as a non-immunological organ engaged primarily in metabolic, nutrient storage and detoxification activities. however, we now know that the healthy liver is also a site of complex immunological activity mediated by a diverse immune cell repertoire as well as non-hematopoietic cell populations. in the non-diseased liver, metabolic and tissue remodeling functions require elements of inflammation. this inflammation, in combination with regular exposure to dietary and microbial products, creates the potential for excessive immune activation. in this complex microenvironment, the hepatic immune system tolerates harmless molecules while at the same time remaining alert to possible infectious agents, malignant cells or tissue damage. upon appropriate immune activation to challenge by pathogens or tissue damage, mechanisms to resolve inflammation are essential to maintain liver homeostasis. failure to clear 'dangerous' stimuli or regulate appropriately activated immune mechanisms leads to pathological inflammation and disrupted tissue homeostasis characterized by the progressive development of fibrosis, cirrhosis and eventual liver failure. hepatic inflammatory mechanisms therefore have a spectrum of roles in the healthy adult liver; they are essential to maintain tissue and organ homeostasis and, when dysregulated, are key drivers of the liver pathology associated with chronic infection, autoimmunity and malignancy. in this review, we explore the changing perception of inflammation and inflammatory mediators in normal liver homeostasis and propose targeting of liver-specific immune regulation pathways as a therapeutic approach to treat liver disease.",0
"the impact of missing data on quantitative research can be serious, leading to biased estimates of parameters, loss of information, decreased statistical power, increased standard errors, and weakened generalizability of findings. in this paper, we discussed and demonstrated three principled missing data methods: multiple imputation, full information maximum likelihood, and expectation-maximization algorithm, applied to a real-world data set. results were contrasted with those obtained from the complete data set and from the listwise deletion method. the relative merits of each method are noted, along with common features they share. the paper concludes with an emphasis on the importance of statistical assumptions, and recommendations for researchers. quality of research will be enhanced if (a) researchers explicitly acknowledge missing data problems and the conditions under which they occurred, (b) principled methods are employed to handle missing data, and (c) the appropriate treatment of missing data is incorporated into review standards of manuscripts submitted for publication.",0
"a phase iii randomised study, comparing treatment with fluorouracil, epidoxorubicin and methotrexate (femtx) with the best supportive care, was conducted in patients with unresectable or metastatic gastric cancer. during the period from july 1986 to june 1992, 41 patients were randomised to receive femtx or best supportive care. mtx was given in a dose of 1500 mg m-2 intravenously (i.v.) followed after 1 h by 5-fu 1500 mg m-2 i.v. on day 1; leucovorin rescue was started after 24 h (30 mg orally every 6 h for 48 h) and epidoxorubicin 60 mg m-2 i.v. was administered on day 15. in addition both groups received tablets containing vitamins a and e. response rates for femtx were as follows: complete response (cr), 19% (4/21); partial response (pr), 10% (2/21); no change (nc), 33% (7/21); and progressive disease (pd), 24% (5/21). response rates in the control group were: nc, 20% (4/20); and pd, 80% (16/20). increased pain was observed in one patient in the treated group and in 11 patients in the control group within the first 2 months. who grade iii/iv toxicity in the chemotherapy group was as follows: nausea/vomiting 40%, diarrhoea 10%, stomatitis 15%, leucopenia 50% and thrombocytopenia 10%. one possible treatment-related death was due to sepsis. the median time to progression in the femtx group was 5.4 months , but only 1.7 months in the control group (95% ci 1.2-2.7 months) (p = 0.0013). similarly, the femtx group displayed significantly (p = 0.0006) prolonged survival compared with the control group, i.e. median survival 12.3 months (95% ci 7.1-15.6 months) vs 3.1 months (95% ci 1.6-4.6 months). in conclusion, femtx combined with vitamin a and e is a fairly well-tolerated treatment, giving a response rate of 29% in patients with advanced gastric cancer, and also prolonging patients' survival. it can be used as a reference treatment in testing new investigational combinations.",0
"background accurate and up-to-date assessment of demographic metrics is crucial for understanding a wide range of social, economic, and public health issues that affect populations worldwide. the global burden of diseases, injuries, and risk factors study (gbd) 2019 produced updated and comprehensive demographic assessments of the key indicators of fertility, mortality, migration, and population for 204 countries and territories and selected subnational locations from 1950 to 2019. methods 8078 country-years of vital registration and sample registration data, 938 surveys, 349 censuses, and 238 other sources were identified and used to estimate age-specific fertility. spatiotemporal gaussian process regression (st-gpr) was used to generate age-specific fertility rates for 5-year age groups between ages 15 and 49 years. with extensions to age groups 10-14 and 50-54 years, the total fertility rate (tfr) was then aggregated using the estimated age-specific fertility between ages 10 and 54 years. 7417 sources were used for under-5 mortality estimation and 7355 for adult mortality. st-gpr was used to synthesise data sources after correction for known biases. adult mortality was measured as the probability of death between ages 15 and 60 years based on vital registration, sample registration, and sibling histories, and was also estimated using st-gpr. hiv-free life tables were then estimated using estimates of under-5 and adult mortality rates using a relational model life table system created for gbd, which closely tracks observed age-specific mortality rates from complete vital registration when available. independent estimates of hiv-specific mortality generated by an epidemiological analysis of hiv prevalence surveys and antenatal clinic serosurveillance and other sources were incorporated into the estimates in countries with large epidemics. annual and single-year age estimates of net migration and population for each country and territory were generated using a bayesian hierarchical cohort component model that analysed estimated age-specific fertility and mortality rates along with 1250 censuses and 747 population registry years. we classified location-years into seven categories on the basis of the natural rate of increase in population (calculated by subtracting the crude death rate from the crude birth rate) and the net migration rate. we computed healthy life expectancy (hale) using years lived with disability (ylds) per capita, life tables, and standard demographic methods. uncertainty was propagated throughout the demographic estimation process, including fertility, mortality, and population, with 1000 draw-level estimates produced for each metric. findings the global tfr decreased from 2·72 (95% uncertainty interval 2·66-2·79) in 2000 to 2·31 (2·17-2·46) in 2019. global annual livebirths increased from 134·5 million (131·5-137·8) in 2000 to a peak of 139·6 million (133·0-146·9) in 2016. global livebirths then declined to 135·3 million (127·2-144·1) in 2019. of the 204 countries and territories included in this study, in 2019, 102 had a tfr lower than 2·1, which is considered a good approximation of replacement-level fertility. all countries in sub-saharan africa had tfrs above replacement level in 2019 and accounted for 27·1% (95% ui 26·4-27·8) of global livebirths. global life expectancy at birth increased from 67·2 years (95% ui 66·8-67·6) in 2000 to 73·5 years (72·8-74·3) in 2019. the total number of deaths increased from 50·7 million (49·5-51·9) in 2000 to 56·5 million (53·7-59·2) in 2019. under-5 deaths declined from 9·6 million (9·1-10·3) in 2000 to 5·0 million (4·3-6·0) in 2019. global population increased by 25·7%, from 6·2 billion (6·0-6·3) in 2000 to 7·7 billion (7·5-8·0) in 2019. in 2019, 34 countries had negative natural rates of increase; in 17 of these, the population declined because immigration was not sufficient to counteract the negative rate of decline. globally, hale increased from 58·6 years (56·1-60·8) in 2000 to 63·5 years (60·8-66·1) in 2019. hale increased in 202 of 204 countries and territories between 2000 and 2019. interpretation over the past 20 years, fertility rates have been dropping steadily and life expectancy has been increasing, with few exceptions. much of this change follows historical patterns linking social and economic determinants, such as those captured by the gbd socio-demographic index, with demographic outcomes. more recently, several countries have experienced a combination of low fertility and stagnating improvement in mortality rates, pushing more populations into the late stages of the demographic transition. tracking demographic change and the emergence of new patterns will be essential for global health monitoring. funding bill & melinda gates foundation.",0
"prosite consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. it is complemented by prorule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. prosite is largely used for the annotation of domain features of uniprotkb/swiss-prot entries. among the 983 (dna-binding) domains, repeats and zinc fingers present in swiss-prot (release 57.8 of 22 september 2009), 696 ( approximately 70%) are annotated with prosite descriptors using information from prorule. in order to allow better functional characterization of domains, prosite developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. here, we describe amsa, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of scanprosite to vital-it, a cluster of 633 cpus, and the adoption of the distributed annotation system (das) to facilitate prosite data integration and interchange with other sources. the latest version of prosite (release 20.54, of 22 september 2009) contains 1308 patterns, 863 profiles and 869 prorules. prosite is accessible at:",0
"the mismatch negativity (mmn) is a brain response to violations of a rule, established by a sequence of sensory stimuli (typically in the auditory domain) . the mmn reflects the brain's ability to perform automatic comparisons between consecutive stimuli and provides an electrophysiological index of sensory learning and perceptual accuracy. although the mmn has been studied extensively, the neurophysiological mechanisms underlying the mmn are not well understood. several hypotheses have been put forward to explain the generation of the mmn; amongst these accounts, the ""adaptation hypothesis"" and the ""model adjustment hypothesis"" have received the most attention. this paper presents a review of studies that focus on neuronal mechanisms underlying the mmn generation, discusses the two major explanatory hypotheses, and proposes predictive coding as a general framework that attempts to unify both.",0
"microglia are the immune cells of the brain. in the absence of pathological insult, their highly motile processes continually survey the brain parenchyma and transiently contact synaptic elements. aside from monitoring, their physiological roles at synapses are not known. to gain insight into possible roles of microglia in the modification of synaptic structures, we used immunocytochemical electron microscopy, serial section electron microscopy with three-dimensional reconstructions, and two-photon in vivo imaging to characterize microglial interactions with synapses during normal and altered sensory experience, in the visual cortex of juvenile mice. during normal visual experience, most microglial processes displayed direct apposition with multiple synapse-associated elements, including synaptic clefts. microglial processes were also distinctively surrounded by pockets of extracellular space. in terms of dynamics, microglial processes localized to the vicinity of small and transiently growing dendritic spines, which were typically lost over 2 d. when experience was manipulated through light deprivation and reexposure, microglial processes changed their morphology, showed altered distributions of extracellular space, displayed phagocytic structures, apposed synaptic clefts more frequently, and enveloped synapse-associated elements more extensively. while light deprivation induced microglia to become less motile and changed their preference of localization to the vicinity of a subset of larger dendritic spines that persistently shrank, light reexposure reversed these behaviors. taken together, these findings reveal different modalities of microglial interactions with synapses that are subtly altered by sensory experience. these findings suggest that microglia may actively contribute to the experience-dependent modification or elimination of a specific subset of synapses in the healthy brain.",0
"the genome sequence archive (gsa) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. considering explosive data growth with diverse data types, here we present the gsa family by expanding into a set of resources for raw data archive with different purposes, namely, gsa ( gsa for human (gsa-human, and open archive for miscellaneous data (omix, compared with the 2017 version, gsa has been significantly updated in data model, online functionalities, and web interfaces. gsa-human, as a new partner of gsa, is a data repository specialized in human genetics-related data with controlled access and security. omix, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.",0
"cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. these processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. we developed algorithms to decipher this narrative and applied them to 21 breast cancers. mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.",0
"in an adaptive immune response, naive t cells proliferate during infection and generate long-lived memory cells that undergo secondary expansion after a repeat encounter with the same pathogen. although natural killer (nk) cells have traditionally been classified as cells of the innate immune system, they share many similarities with cytotoxic t lymphocytes. we use a mouse model of cytomegalovirus infection to show that, like t cells, nk cells bearing the virus-specific ly49h receptor proliferate 100-fold in the spleen and 1,000-fold in the liver after infection. after a contraction phase, ly49h-positive nk cells reside in lymphoid and non-lymphoid organs for several months. these self-renewing 'memory' nk cells rapidly degranulate and produce cytokines on reactivation. adoptive transfer of these nk cells into naive animals followed by viral challenge results in a robust secondary expansion and protective immunity. these findings reveal properties of nk cells that were previously attributed only to cells of the adaptive immune system.",0
"objective to systematically tabulate published and unpublished sources of reliable glycemic index (gi) values. research design and methods a literature search identified 205 articles published between 1981 and 2007. unpublished data were also included where the data quality could be verified. the data were separated into two lists: the first representing more precise data derived from testing healthy subjects and the second primarily from individuals with impaired glucose metabolism. results the tables, which are available in the online-only appendix, list the gi of over 2,480 individual food items. dairy products, legumes, and fruits were found to have a low gi. breads, breakfast cereals, and rice, including whole grain, were available in both high and low gi versions. the correlation coefficient for 20 staple foods tested in both healthy and diabetic subjects was r = 0.94 (p conclusions these tables improve the quality and quantity of gi data available for research and clinical practice.",0
"background the coronavirus disease 2019 (covid-19) is profoundly affecting life around the globe. isolation, contact restrictions and economic shutdown impose a complete change to the psychosocial environment in affected countries. these measures have the potential to threaten the mental health of children and adolescents significantly. even though the current crisis can bring with it opportunities for personal growth and family cohesion, disadvantages may outweigh these benefits. anxiety, lack of peer contact and reduced opportunities for stress regulation are main concerns. another main threat is an increased risk for parental mental illness, domestic violence and child maltreatment. especially for children and adolescents with special needs or disadvantages, such as disabilities, trauma experiences, already existing mental health problems, migrant background and low socioeconomic status, this may be a particularly challenging time. to maintain regular and emergency child and adolescent psychiatric treatment during the pandemic is a major challenge but is necessary for limiting long-term consequences for the mental health of children and adolescents. urgent research questions comprise understanding the mental health effects of social distancing and economic pressure, identifying risk and resilience factors, and preventing long-term consequences, including-but not restricted to-child maltreatment. the efficacy of telepsychiatry is another highly relevant issue is to evaluate the efficacy of telehealth and perfect its applications to child and adolescent psychiatry. conclusion there are numerous mental health threats associated with the current pandemic and subsequent restrictions. child and adolescent psychiatrists must ensure continuity of care during all phases of the pandemic. covid-19-associated mental health risks will disproportionately hit children and adolescents who are already disadvantaged and marginalized. research is needed to assess the implications of policies enacted to contain the pandemic on mental health of children and adolescents, and to estimate the risk/benefit ratio of measures such as home schooling, in order to be better prepared for future developments.",0
"the purpose of the study was to assess a large representative sample of cancer patients on distress levels, common psychosocial problems, and awareness and use of psychosocial support services. a total of 3095 patients were assessed over a 4-week period with the brief symptom inventory-18 (bsi-18), a common problems checklist, and on awareness and use of psychosocial resources. full data was available on 2776 patients. on average, patients were 60 years old, caucasian (78.3%), and middle class. approximately, half were attending for follow-up care. types of cancer varied, with the largest groups being breast (23.5%), prostate (16.9%), colorectal (7.5%), and lung (5.8%) cancer patients. overall, 37.8% of all patients met criteria for general distress in the clinical range. a higher proportion of men met case criteria for somatisation, and more women for depression. there were no gender differences in anxiety or overall distress severity. minority patients were more likely to be distressed, as were those with lower income, cancers other than prostate, and those currently on active treatment. lung, pancreatic, head and neck, hodgkin's disease, and brain cancer patients were the most distressed. almost half of all patients who met distress criteria had not sought professional psychosocial support nor did they intend to in the future. in conclusion, distress is very common in cancer patients across diagnoses and across the disease trajectory. many patients who report high levels of distress are not taking advantage of available supportive resources. barriers to such use, and factors predicting distress and use of psychosocial care, require further exploration.",0
"how different is local cortical circuitry from a random network? to answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. analysis of this dataset revealed several nonrandom features in synaptic connectivity. we confirmed previous reports that bidirectional connections are more common than expected in a random network. we found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. we also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. we found that the distribution of synaptic connection strength differs significantly from the poisson distribution and can be fitted by a lognormal distribution. such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. in addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. such a skeleton is likely to play an important role in network dynamics and should be investigated further.",0
"amyotrophic lateral sclerosis (als) is a paralytic and usually fatal disorder caused by motor-neuron degeneration in the brain and spinal cord. most cases of als are sporadic but about 5-10% are familial. mutations in superoxide dismutase 1 (sod1), tar dna-binding protein (tardbp, also known as tdp43) and fused in sarcoma (fus, also known as translocated in liposarcoma (tls)) account for approximately 30% of classic familial als. mutations in several other genes have also been reported as rare causes of als or als-like syndromes. the causes of the remaining cases of familial als and of the vast majority of sporadic als are unknown. despite extensive studies of previously identified als-causing genes, the pathogenic mechanism underlying motor-neuron degeneration in als remains largely obscure. dementia, usually of the frontotemporal lobar type, may occur in some als cases. it is unclear whether als and dementia share common aetiology and pathogenesis in als/dementia. here we show that mutations in ubqln2, which encodes the ubiquitin-like protein ubiquilin 2, cause dominantly inherited, chromosome-x-linked als and als/dementia. we describe novel ubiquilin 2 pathology in the spinal cords of als cases and in the brains of als/dementia cases with or without ubqln2 mutations. ubiquilin 2 is a member of the ubiquilin family, which regulates the degradation of ubiquitinated proteins. functional analysis showed that mutations in ubqln2 lead to an impairment of protein degradation. therefore, our findings link abnormalities in ubiquilin 2 to defects in the protein degradation pathway, abnormal protein aggregation and neurodegeneration, indicating a common pathogenic mechanism that can be exploited for therapeutic intervention.",0
"problem/condition autism spectrum disorder (asd). period covered 2012. description of system the autism and developmental disabilities monitoring (addm) network is an active surveillance system that provides estimates of the prevalence and characteristics of asd among children aged 8 years whose parents or guardians reside in 11 addm network sites in the united states (arkansas, arizona, colorado, georgia, maryland, missouri, new jersey, north carolina, south carolina, utah, and wisconsin). surveillance to determine asd case status is conducted in two phases. the first phase consists of screening and abstracting comprehensive evaluations performed by professional service providers in the community. data sources identified for record review are categorized as either 1) education source type, including developmental evaluations to determine eligibility for special education services or 2) health care source type, including diagnostic and developmental evaluations. the second phase involves the review of all abstracted evaluations by trained clinicians to determine asd surveillance case status. a child meets the surveillance case definition for asd if one or more comprehensive evaluations of that child completed by a qualified professional describes behaviors that are consistent with the diagnostic and statistical manual of mental disorders, fourth edition, text revision diagnostic criteria for any of the following conditions: autistic disorder, pervasive developmental disorder-not otherwise specified (including atypical autism), or asperger disorder. this report provides asd prevalence estimates for children aged 8 years living in catchment areas of the addm network sites in 2012, overall and stratified by sex, race/ethnicity, and the type of source records (education and health records versus health records only). in addition, this report describes the proportion of children with asd with a score consistent with intellectual disability on a standardized intellectual ability test, the age at which the earliest known comprehensive evaluation was performed, the proportion of children with a previous asd diagnosis, the specific type of asd diagnosis, and any special education eligibility classification. results for 2012, the combined estimated prevalence of asd among the 11 addm network sites was 14.6 per 1,000 (one in 68) children aged 8 years. estimated prevalence was significantly higher among boys aged 8 years (23.6 per 1,000) than among girls aged 8 years (5.3 per 1,000). estimated asd prevalence was significantly higher among non-hispanic white children aged 8 years (15.5 per 1,000) compared with non-hispanic black children (13.2 per 1,000), and hispanic (10.1 per 1,000) children aged 8 years. estimated prevalence varied widely among the 11 addm network sites, ranging from 8.2 per 1,000 children aged 8 years (in the area of the maryland site where only health care records were reviewed) to 24.6 per 1,000 children aged 8 years (in new jersey, where both education and health care records were reviewed). estimated prevalence was higher in surveillance sites where education records and health records were reviewed compared with sites where health records only were reviewed (17.1 per 1,000 and 10.7 per 1,000 children aged 8 years, respectively; p interpretation overall estimated asd prevalence was 14.6 per 1,000 children aged 8 years in the addm network sites in 2012. the higher estimated prevalence among sites that reviewed both education and health records suggests the role of special education systems in providing comprehensive evaluations and services to children with developmental disabilities. disparities by race/ethnicity in estimated asd prevalence, particularly for hispanic children, as well as disparities in the age of earliest comprehensive evaluation and presence of a previous asd diagnosis or classification, suggest that access to treatment and services might be lacking or delayed for some children. public health action the addm network will continue to monitor the prevalence and characteristics of asd among children aged 8 years living in selected sites across the united states. recommendations from the addm network include enhancing strategies to 1) lower the age of first evaluation of asd by community providers in accordance with the healthy people 2020 goal that children with asd are evaluated by age 36 months and begin receiving community-based support and services by age 48 months; 2) reduce disparities by race/ethnicity in identified asd prevalence, the age of first comprehensive evaluation, and presence of a previous asd diagnosis or classification; and 3) assess the effect on asd prevalence of the revised asd diagnostic criteria published in the diagnostic and statistical manual of mental disorders, fifth edition.",0
"background non-pharmaceutical interventions have been implemented to reduce transmission of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) in the uk. projecting the size of an unmitigated epidemic and the potential effect of different control measures has been crucial to support evidence-based policy making during the early stages of the epidemic. this study assesses the potential impact of different control measures for mitigating the burden of covid-19 in the uk. methods we used a stochastic age-structured transmission model to explore a range of intervention scenarios, tracking 66·4 million people aggregated to 186 county-level administrative units in england, wales, scotland, and northern ireland. the four base interventions modelled were school closures, physical distancing, shielding of people aged 70 years or older, and self-isolation of symptomatic cases. we also modelled the combination of these interventions, as well as a programme of intensive interventions with phased lockdown-type restrictions that substantially limited contacts outside of the home for repeated periods. we simulated different triggers for the introduction of interventions, and estimated the impact of varying adherence to interventions across counties. for each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (ie, admission to the intensive care units ) treatment, and deaths, and compared the effect of each intervention on the basic reproduction number, r 0 . findings we projected a median unmitigated burden of 23 million (95% prediction interval 13-30) clinical cases and 350 000 deaths (170 000-480 000) due to covid-19 in the uk by december, 2021. we found that the four base interventions were each likely to decrease r 0 , but not sufficiently to prevent icu demand from exceeding health service capacity. the combined intervention was more effective at reducing r 0 , but only lockdown periods were sufficient to bring r 0 near or below 1; the most stringent lockdown scenario resulted in a projected 120 000 cases (46 000-700 000) and 50 000 deaths (9300-160 000). intensive interventions with lockdown periods would need to be in place for a large proportion of the coming year to prevent health-care demand exceeding availability. interpretation the characteristics of sars-cov-2 mean that extreme measures are probably required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in icus. funding medical research council.",0
"background conventional systematic review techniques have limitations when the aim of a review is to construct a critical analysis of a complex body of literature. this article offers a reflexive account of an attempt to conduct an interpretive review of the literature on access to healthcare by vulnerable groups in the uk methods: this project involved the development and use of the method of critical interpretive synthesis (cis). this approach is sensitised to the processes of conventional systematic review methodology and draws on recent advances in methods for interpretive synthesis. results many analyses of equity of access have rested on measures of utilisation of health services, but these are problematic both methodologically and conceptually. a more useful means of understanding access is offered by the synthetic construct of candidacy. candidacy describes how people's eligibility for healthcare is determined between themselves and health services. it is a continually negotiated property of individuals, subject to multiple influences arising both from people and their social contexts and from macro-level influences on allocation of resources and configuration of services. health services are continually constituting and seeking to define the appropriate objects of medical attention and intervention, while at the same time people are engaged in constituting and defining what they understand to be the appropriate objects of medical attention and intervention. access represents a dynamic interplay between these simultaneous, iterative and mutually reinforcing processes. by attending to how vulnerabilities arise in relation to candidacy, the phenomenon of access can be better understood, and more appropriate recommendations made for policy, practice and future research. discussion by innovating with existing methods for interpretive synthesis, it was possible to produce not only new methods for conducting what we have termed critical interpretive synthesis, but also a new theoretical conceptualisation of access to healthcare. this theoretical account of access is distinct from models already extant in the literature, and is the result of combining diverse constructs and evidence into a coherent whole. both the method and the model should be evaluated in other contexts.",0
"this study aimed to review the literature describing and quantifying time lags in the health research translation process. papers were included in the review if they quantified time lags in the development of health interventions. the study identified 23 papers. few were comparable as different studies use different measures, of different things, at different time points. we concluded that the current state of knowledge of time lags is of limited use to those responsible for r&d and knowledge transfer who face difficulties in knowing what they should or can do to reduce time lags. this effectively 'blindfolds' investment decisions and risks wasting effort. the study concludes that understanding lags first requires agreeing models, definitions and measures, which can be applied in practice. a second task would be to develop a process by which to gather these data.",0
"background infertility affects an estimated 15% of couples globally, amounting to 48.5 million couples. males are found to be solely responsible for 20-30% of infertility cases and contribute to 50% of cases overall. however, this number does not accurately represent all regions of the world. indeed, on a global level, there is a lack of accurate statistics on rates of male infertility. our report examines major regions of the world and reports rates of male infertility based on data on female infertility. methods our search consisted of systematic reviews, meta-analyses, and population-based studies by searching the terms ""epidemiology, male infertility, and prevalence."" we identified 16 articles for detailed study. we typically used the assumption that 50% of all cases of infertility are due to female factors alone, 20-30% are due to male factors alone, and the remaining 20-30% are due to a combination of male and female factors. therefore, in regions of the world where male factor or rates of male infertility were not reported, we used this assumption to calculate general rates of male factor infertility. results our calculated data showed that the distribution of infertility due to male factor ranged from 20% to 70% and that the percentage of infertile men ranged from 2·5% to 12%. infertility rates were highest in africa and central/eastern europe. additionally, according to a variety of sources, rates of male infertility in north america, australia, and central and eastern europe varied from 4 5-6%, 9%, and 8-12%, respectively. conclusion this study demonstrates a novel and unique way to calculate the distribution of male infertility around the world. according to our results, at least 30 million men worldwide are infertile with the highest rates in africa and eastern europe. results indicate further research is needed regarding etiology and treatment, reduce stigma & cultural barriers, and establish a more precise calculation.",0
"thirty years have elapsed since the emergence of the classification of carbohydrate-active enzymes in sequence-based families that became the cazy database over 20 years ago, freely available for browsing and download at in the era of large scale sequencing and high-throughput biology, it is important to examine the position of this specialist database that is deeply rooted in human curation. the three primary tasks of the cazy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by genbank and the protein data bank and (iii) to capture and present functional information for each family. the cazy website is updated once a month. here we briefly summarize the increase in novel families and the annotations conducted during the last 8 years. we present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations. most importantly we highlight the considerable amount of work that accompanies the analysis and report of biochemical data from the literature.",0
"dopamine signaling is implicated in reinforcement learning, but the neural substrates targeted by dopamine are poorly understood. we bypassed dopamine signaling itself and tested how optogenetic activation of dopamine d1 or d2 receptor–expressing striatal projection neurons influenced reinforcement learning in mice. stimulating d1 receptor–expressing neurons induced persistent reinforcement, whereas stimulating d2 receptor–expressing neurons induced transient punishment, indicating that activation of these circuits is sufficient to modify the probability of performing future actions.",0
"summary multiple sequence alignments are central to many areas of bioinformatics. it has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. here, we present trimal, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimal can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. these include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. moreover, trimal can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. availability trimal has been written in c++, it is portable to all platforms. trimal is freely available for download ( and can be used online through the phylemon web server ( supplementary material is available at",0
"severe acute respiratory syndrome-corona virus-2, which causes coronavirus disease 2019 (covid-19), is highly contagious. airway management of patients with covid-19 is high risk to staff and patients. we aimed to develop principles for airway management of patients with covid-19 to encourage safe, accurate and swift performance. this consensus statement has been brought together at short notice to advise on airway management for patients with covid-19, drawing on published literature and immediately available information from clinicians and experts. recommendations on the prevention of contamination of healthcare workers, the choice of staff involved in airway management, the training required and the selection of equipment are discussed. the fundamental principles of airway management in these settings are described for: emergency tracheal intubation; predicted or unexpected difficult tracheal intubation; cardiac arrest; anaesthetic care; and tracheal extubation. we provide figures to support clinicians in safe airway management of patients with covid-19. the advice in this document is designed to be adapted in line with local workplace policies.",0
"background high body-mass index (bmi) predisposes to several site-specific cancers, but a large-scale systematic and detailed characterisation of patterns of risk across all common cancers adjusted for potential confounders has not previously been undertaken. we aimed to investigate the links between bmi and the most common site-specific cancers. methods with primary care data from individuals in the clinical practice research datalink with bmi data, we fitted cox models to investigate associations between bmi and 22 of the most common cancers, adjusting for potential confounders. we fitted linear then non-linear (spline) models; investigated effect modification by sex, menopausal status, smoking, and age; and calculated population effects. findings 5·24 million individuals were included; 166,955 developed cancers of interest. bmi was associated with 17 of 22 cancers, but effects varied substantially by site. each 5 kg/m(2) increase in bmi was roughly linearly associated with cancers of the uterus (hazard ratio 1·62, 99% ci 1·56-1·69; p interpretation bmi is associated with cancer risk, with substantial population-level effects. the heterogeneity in the effects suggests that different mechanisms are associated with different cancer sites and different patient subgroups. funding national institute for health research, wellcome trust, and medical research council.",0
"unlabelled parkinson's disease (pd) is the second most common neurodegenerative disorder of aging. the pathological hallmark of pd is neuronal inclusions termed lewy bodies whose main component is alpha-synuclein protein. the finding of these lewy bodies in the intestinal enteric nerves led to the hypothesis that the intestine might be an early site of pd disease in response to an environmental toxin or pathogen. one potential mechanism for environmental toxin(s) and proinflammatory luminal products to gain access to mucosal neuronal tissue and promote oxidative stress is compromised intestinal barrier integrity. however, the role of intestinal permeability in pd has never been tested. we hypothesized that pd subjects might exhibit increased intestinal permeability to proinflammatory bacterial products in the intestine. to test our hypothesis we evaluated intestinal permeability in subjects newly diagnosed with pd and compared their values to healthy subjects. in addition, we obtained intestinal biopsies from both groups and used immunohistochemistry to assess bacterial translocation, nitrotyrosine (oxidative stress), and alpha-synuclein. we also evaluated serum markers of endotoxin exposure including lps binding protein (lbp). our data show that our pd subjects exhibit significantly greater intestinal permeability (gut leakiness) than controls. in addition, this intestinal hyperpermeability significantly correlated with increased intestinal mucosa staining for e. coli bacteria, nitrotyrosine, and alpha-synuclein as well as serum lbp levels in pd subjects. these data represent not only the first demonstration of abnormal intestinal permeability in pd subjects but also the first correlation of increased intestinal permeability in pd with intestinal alpha-synuclein (the hallmark of pd), as well as staining for gram negative bacteria and tissue oxidative stress. our study may thus shed new light on pd pathogenesis as well as provide a new method for earlier diagnosis of pd and suggests potential therapeutic targets in pd subjects. trial registration clinicaltrials.gov nct01155492.",0
"chemotactic factors are postulated to direct emigration of lymphocytes from the blood stream into sites of inflammation. members of a family of chemotactic cytokines, termed chemokines, have been shown to attract lymphocytes but efficacy, i.e., the maximal percentage of attracted cells, has been low. we have identified a highly efficacious lymphocyte chemotactic activity in the supernatants of the murine bone marrow stroma cell line ms-5 which attracts 10-fold more lymphocytes in vitro than currently described lymphocyte chemoattractants. purification of this chemotactic activity revealed identity to stromal cell-derived factor 1 (sdf-1). sdf-1 acts on lymphocytes and monocytes but not neutrophils in vitro and is both a highly efficacious and highly potent mononuclear cell attractant in vivo. in addition, sdf-1 induces intracellular actin polymerization in lymphocytes, a process that is thought to be a prerequisite for cell motility. since sdf-1 is expressed constitutively in a broad range of tissues it may have a role in immune surveillance and in basal extravasation of lymphocytes and monocytes rather than in inflammation.",0
"antibodies against the t3-antigen receptor complex can activate the human t cell line, jurkat, to produce interleukin 2 (2-5). this activation is initiated by a receptor-mediated increase in the concentration of free cytoplasmic calcium ions i (3, 4). in this communication, we investigate the mechanism by which the receptor complex increases i can occur when extracellular ca2+ is depleted by egta. perturbation of the t cell antigen receptor, therefore, generates a signal which mobilizes ca2+ from intracellular stores. as inositol trisphosphate appears to function as such a signal for certain hormone receptors, we measured the levels of inositol trisphosphate and of the other inositol phosphate compounds in jurkat. antibodies to either the antigen receptor heterodimer or t3 determinants result in marked elevations of all three inositol phosphates. these changes in inositol phosphates are not secondary to the receptor-mediated increases in i as demonstrated by the inability of the ca2+ ionophore, ionomycin, to affect the levels of any of these compounds. in concentrations between 0.1 and 1 microm, purified inositol trisphosphate releases ca2+ from permeabilized jurkat cells. taken together, these data indicate that, during activation, perturbation of the t3-antigen receptor complex generates inositol trisphosphate. this compound functions as an intracellular signal to release ca2+ from intracellular stores, leading to increases in i.",0
"bisphenol a (bpa) is used to manufacture polycarbonate plastic and epoxy resins, which are used in baby bottles, as protective coatings on food containers, and for composites and sealants in dentistry. 4-nonylphenol (np) is used to make nonylphenol ethoxylates, nonionic surfactants applied as emulsifying, wetting, dispersing, or stabilizing agents in industrial, agricultural, and domestic consumer products. the potential for human exposure to bpa and np is high because of their widespread use. we measured bpa and np in archived urine samples from a reference population of 394 adults in the united states using isotope-dilution gas chromatography/mass spectrometry. the concentration ranges of bpa and np were similar to those observed in other human populations. bpa was detected in 95% of the samples examined at concentrations > or = 0.1 microg/l urine; the geometric mean and median concentrations were 1.33 microg/l (1.36 microg/g creatinine) and 1.28 microg/l (1.32 microg/g creatinine), respectively; the 95th percentile concentration was 5.18 microg/l (7.95 microg/g creatinine). np was detected in 51% of the samples examined > or = 0.1 microg/l. the median and 95th percentile concentrations were < 0.1 microg/l and 1.57 microg/l (1.39 microg/g creatinine), respectively. the frequent detection of bpa suggests widespread exposure to this compound in residents of the united states. the lower frequency of detection of np than of bpa could be explained by a lower exposure of humans to np, by different pharmacokinetic factors (i.e., absorption, distribution, metabolism, elimination), by the fact that 4-n-nonylphenol--the measured np isomer--represents a small percentage of the np used in commercial mixtures, or a combination of all of the above. additional research is needed to determine the best urinary biomarker(s) to assess exposure to np. despite the sample population's nonrepresentativeness of the u.s. population (although sample weights were used to improve the extent to which the results represent the u.s. population) and relatively small size, this study provides the first reference range of human internal dose levels of bpa and np in a demographically diverse human population.",0
"interleukin 10 (il-10) and viral il-10 (v-il-10) strongly reduced antigen-specific proliferation of human t cells and cd4+ t cell clones when monocytes were used as antigen-presenting cells. in contrast, il-10 and v-il-10 did not affect the proliferative responses to antigens presented by autologous epstein-barr virus-lymphoblastoid cell line (ebv-lcl). inhibition of antigen-specific t cell responses was associated with downregulation of constitutive, as well as interferon gamma- or il-4-induced, class ii mhc expression on monocytes by il-10 and v-il-10, resulting in the reduction in antigen-presenting capacity of these cells. in contrast, il-10 and v-il-10 had no effect on class ii major histocompatibility complex (mhc) expression on ebv-lcl. the reduced antigen-presenting capacity of monocytes correlated with a decreased capacity to mobilize intracellular ca2+ in the responder t cell clones. the diminished antigen-presenting capacities of monocytes were not due to inhibitory effects of il-10 and v-il-10 on antigen processing, since the proliferative t cell responses to antigenic peptides, which did not require processing, were equally well inhibited. furthermore, the inhibitory effects of il-10 and v-il-10 on antigen-specific proliferative t cell responses could not be neutralized by exogenous il-2 or il-4. although il-10 and v-il-10 suppressed il-1 alpha, il-1 beta, tumor necrosis factor alpha (tnf-alpha), and il-6 production by monocytes, it was excluded that these cytokines played a role in antigen-specific t cell proliferation, since normal antigen-specific responses were observed in the presence of neutralizing anti-il-1, -il-6, and -tnf-alpha mabs. furthermore, addition of saturating concentrations of il-1 alpha, il-1 beta, il-6, and tnf-alpha to the cultures had no effect on the reduced proliferative t cell responses in the presence of il-10, or v-il-10. collectively, our data indicate that il-10 and v-il-10 can completely prevent antigen-specific t cell proliferation by inhibition of the antigen-presenting capacity of monocytes through downregulation of class ii mhc antigens on monocytes.",0
"background our objective was to develop an instrument to assess the methodological quality of systematic reviews, building upon previous tools, empirical evidence and expert consensus. methods a 37-item assessment tool was formed by combining 1) the enhanced overview quality assessment questionnaire (oqaq), 2) a checklist created by sacks, and 3) three additional items recently judged to be of methodological importance. this tool was applied to 99 paper-based and 52 electronic systematic reviews. exploratory factor analysis was used to identify underlying components. the results were considered by methodological experts using a nominal group technique aimed at item reduction and design of an assessment tool with face and content validity. results the factor analysis identified 11 components. from each component, one item was selected by the nominal group. the resulting instrument was judged to have face and content validity. conclusion a measurement tool for the 'assessment of multiple systematic reviews' (amstar) was developed. the tool consists of 11 items and has good face and content validity for measuring the methodological quality of systematic reviews. additional studies are needed with a focus on the reproducibility and construct validity of amstar, before strong recommendations can be made on its use.",0
"the international union of basic and clinical pharmacology/british pharmacological society (iuphar/bps) guide to pharmacology ( is a new open access resource providing pharmacological, chemical, genetic, functional and pathophysiological data on the targets of approved and experimental drugs. created under the auspices of the iuphar and the bps, the portal provides concise, peer-reviewed overviews of the key properties of a wide range of established and potential drug targets, with in-depth information for a subset of important targets. the resource is the result of curation and integration of data from the iuphar database (iuphar-db) and the published bps 'guide to receptors and channels' (grac) compendium. the data are derived from a global network of expert contributors, and the information is extensively linked to relevant databases, including chembl, drugbank, ensembl, pubchem, uniprot and pubmed. each of the ∼6000 small molecule and peptide ligands is annotated with manually curated 2d chemical structures or amino acid sequences, nomenclature and database links. future expansion of the resource will complete the coverage of all the targets of currently approved drugs and future candidate targets, alongside educational resources to guide scientists and students in pharmacological principles and techniques.",0
"the characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. the national institutes of health human microbiome project has provided one of the broadest such characterizations so far. here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. we applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. this study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.",0
"objective we conducted a systematic review and meta-analysis to estimate the pooled prevalence of depression, anxiety, insomnia, ptsd, and psychological distress (pd) related to covid-19 among affected populations. methods we searched articles in medline, embase, apa psycinfo, cinahl, scopus, and web of science. random-effects meta-analyses on the proportions of individuals with symptoms of depression, anxiety, insomnia, ptsd, and pd were generated and between-group differences for gender, healthcare workers (hcws), and regions where studies were conducted. results a total of 2189 articles were screened, 136 full-text articles were assessed for eligibility. fifty-five peer-reviewed studies met inclusion criteria for the meta-analysis (n=189,159). the prevalence of depression (k=46) was 15.97% (95%ci, 13.24-19.13). the prevalence of anxiety (k=54) was 15.15% (95%ci, 12.29-18.54). the prevalence of insomnia (k=14) was 23.87% (95%ci, 15.74-34.48). the prevalence of ptsd (k=13) was 21.94% (95%ci, 9.37-43.31). finally, the prevalence of psychological distress (k=19) was 13.29% (95%ci, 8.80-19.57). between-group differences were only found in hcws (z=2.69, p conclusions findings suggest that the short-term mental health consequences of covid-19 are equally high across affected countries, and across gender. however, reports of insomnia are significantly higher among hcws than the general population.",0
"introduction covid-19 may predispose to both venous and arterial thromboembolism due to excessive inflammation, hypoxia, immobilisation and diffuse intravascular coagulation. reports on the incidence of thrombotic complications are however not available. methods we evaluated the incidence of the composite outcome of symptomatic acute pulmonary embolism (pe), deep-vein thrombosis, ischemic stroke, myocardial infarction or systemic arterial embolism in all covid-19 patients admitted to the icu of 2 dutch university hospitals and 1 dutch teaching hospital. results we studied 184 icu patients with proven covid-19 pneumonia of whom 23 died (13%), 22 were discharged alive (12%) and 139 (76%) were still on the icu on april 5th 2020. all patients received at least standard doses thromboprophylaxis. the cumulative incidence of the composite outcome was 31% (95%ci 20-41), of which ctpa and/or ultrasonography confirmed vte in 27% (95%ci 17-37%) and arterial thrombotic events in 3.7% (95%ci 0-8.2%). pe was the most frequent thrombotic complication (n = 25, 81%). age (adjusted hazard ratio (ahr) 1.05/per year, 95%ci 1.004-1.01) and coagulopathy, defined as spontaneous prolongation of the prothrombin time > 3 s or activated partial thromboplastin time > 5 s (ahr 4.1, 95%ci 1.9-9.1), were independent predictors of thrombotic complications. conclusion the 31% incidence of thrombotic complications in icu patients with covid-19 infections is remarkably high. our findings reinforce the recommendation to strictly apply pharmacological thrombosis prophylaxis in all covid-19 patients admitted to the icu, and are strongly suggestive of increasing the prophylaxis towards high-prophylactic doses, even in the absence of randomized evidence.",0
"background the international standard radiotherapy schedule for breast cancer treatment delivers a high total dose in 25 small daily doses (fractions). however, a lower total dose delivered in fewer, larger fractions (hypofractionation) is hypothesised to be at least as safe and effective as the standard treatment. we tested two dose levels of a 13-fraction schedule against the standard regimen with the aim of measuring the sensitivity of normal and malignant tissues to fraction size. methods between 1998 and 2002, 2236 women with early breast cancer (pt1-3a pn0-1 m0) at 17 centres in the uk were randomly assigned after primary surgery to receive 50 gy in 25 fractions of 2.0 gy versus 41.6 gy or 39 gy in 13 fractions of 3.2 gy or 3.0 gy over 5 weeks. women were eligible if they were aged over 18 years, did not have an immediate surgical reconstruction, and were available for follow-up. randomisation method was computer generated and was not blinded. the protocol-specified principal endpoints were local-regional tumour relapse, defined as reappearance of cancer at irradiated sites, late normal tissue effects, and quality of life. analysis was by intention to treat. this study is registered as an international standard randomised controlled trial, number isrctn59368779. findings 749 women were assigned to the 50 gy group, 750 to the 41.6 gy group, and 737 to the 39 gy group. after a median follow up of 5.1 years (iqr 4.4-6.0) the rate of local-regional tumour relapse at 5 years was 3.6% (95% ci 2.2-5.1) after 50 gy, 3.5% (95% ci 2.1-4.3) after 41.6 gy, and 5.2% (95% ci 3.5-6.9) after 39 gy. the estimated absolute differences in 5-year local-regional relapse rates compared with 50 gy were 0.2% (95% ci -1.3% to 2.6%) after 41.6 gy and 0.9% (95% ci -0.8% to 3.7%) after 39 gy. photographic and patient self-assessments suggested lower rates of late adverse effects after 39 gy than with 50 gy, with an hr for late change in breast appearance (photographic) of 0.69 (95% ci 0.52-0.91, p=0.01). from a planned meta-analysis with the pilot trial, the adjusted estimates of alpha/beta value for tumour control was 4.6 gy (95% ci 1.1-8.1) and for late change in breast appearance (photographic) was 3.4 gy (95% ci 2.3-4.5). interpretation the data are consistent with the hypothesis that breast cancer and the dose-limiting normal tissues respond similarly to change in radiotherapy fraction size. 41.6 gy in 13 fractions was similar to the control regimen of 50 gy in 25 fractions in terms of local-regional tumour control and late normal tissue effects, a result consistent with the result of start trial b. a lower total dose in a smaller number of fractions could offer similar rates of tumour control and normal tissue damage as the international standard fractionation schedule of 50 gy in 25 fractions.",0
"very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. we conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). we identify 3 variants associated with subjective well-being, 2 variants associated with depressive symptoms, and 11 variants associated with neuroticism, including 2 inversion polymorphisms. the two loci associated with depressive symptoms replicate in an independent depression sample. joint analyses that exploit the high genetic correlations between the phenotypes (|ρ^| ≈ 0.8) strengthen the overall credibility of the findings and allow us to identify additional variants. across our phenotypes, loci regulating expression in central nervous system and adrenal or pancreas tissues are strongly enriched for association.",0
"the classic diathesis-stress framework, which views some individuals as particularly vulnerable to adversity, informs virtually all psychiatric research on behavior-gene-environment (g x e) interaction. an alternative framework of 'differential susceptibility' is proposed, one which regards those most susceptible to adversity because of their genetic make up as simultaneously most likely to benefit from supportive or enriching experiences-or even just the absence of adversity. recent g x e findings consistent with this perspective and involving monoamine oxidase-a, 5-httlpr (5-hydroxytryptamine-linked polymorphic region polymorphism) and dopamine receptor d4 (drd4) are reviewed for illustrative purposes. results considered suggest that putative 'vulnerability genes' or 'risk alleles' might, at times, be more appropriately conceptualized as 'plasticity genes', because they seem to make individuals more susceptible to environmental influences-for better and for worse.",0
"background bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. the prevalence of bacterial infection in patients infected with sars-cov-2 is not well understood. aims to determine the prevalence of bacterial co-infection (at presentation) and secondary infection (after presentation) in patients with covid-19. sources we performed a systematic search of medline, ovid epub and embase databases for english language literature from 2019 to april 16, 2020. studies were included if they (a) evaluated patients with confirmed covid-19 and (b) reported the prevalence of acute bacterial infection. content data were extracted by a single reviewer and cross-checked by a second reviewer. the main outcome was the proportion of covid-19 patients with an acute bacterial infection. any bacteria detected from non-respiratory-tract or non-bloodstream sources were excluded. of 1308 studies screened, 24 were eligible and included in the rapid review representing 3338 patients with covid-19 evaluated for acute bacterial infection. in the meta-analysis, bacterial co-infection (estimated on presentation) was identified in 3.5% of patients (95%ci 0.4-6.7%) and secondary bacterial infection in 14.3% of patients (95%ci 9.6-18.9%). the overall proportion of covid-19 patients with bacterial infection was 6.9% (95%ci 4.3-9.5%). bacterial infection was more common in critically ill patients (8.1%, 95%ci 2.3-13.8%). the majority of patients with covid-19 received antibiotics (71.9%, 95%ci 56.1 to 87.7%). implications bacterial co-infection is relatively infrequent in hospitalized patients with covid-19. the majority of these patients may not require empirical antibacterial treatment.",0
"the alzheimer disease genetics consortium (adgc) performed a genome-wide association study of late-onset alzheimer disease using a three-stage design consisting of a discovery stage (stage 1) and two replication stages (stages 2 and 3). both joint analysis and meta-analysis approaches were used. we obtained genome-wide significant results at ms4a4a (rs4938933; stages 1 and 2, meta-analysis p (p(m)) = 1.7 × 10(-9), joint analysis p (p(j)) = 1.7 × 10(-9); stages 1, 2 and 3, p(m) = 8.2 × 10(-12)), cd2ap (rs9349407; stages 1, 2 and 3, p(m) = 8.6 × 10(-9)), epha1 (rs11767557; stages 1, 2 and 3, p(m) = 6.0 × 10(-10)) and cd33 (rs3865444; stages 1, 2 and 3, p(m) = 1.6 × 10(-9)). we also replicated previous associations at cr1 (rs6701713; p(m) = 4.6 × 10(-10), p(j) = 5.2 × 10(-11)), clu (rs1532278; p(m) = 8.3 × 10(-8), p(j) = 1.9 × 10(-8)), bin1 (rs7561528; p(m) = 4.0 × 10(-14), p(j) = 5.2 × 10(-14)) and picalm (rs561655; p(m) = 7.0 × 10(-11), p(j) = 1.0 × 10(-10)), but not at exoc3l2, to late-onset alzheimer's disease susceptibility.",0
"gastric cancer remains one of the most common and deadly cancers worldwide, especially among older males. based on globocan 2018 data, stomach cancer is the 5 th most common neoplasm and the 3 rd most deadly cancer, with an estimated 783,000 deaths in 2018. gastric cancer incidence and mortality are highly variable by region and highly dependent on diet and helicobacter pylori infection. while strides in preventing and treating h. pylori infection have decreased the overall incidence of gastric cancer, they have also contributed to an increase in the incidence of cardia gastric cancer, a rare subtype of the neoplasm that has grown 7-fold in the past decades. a better understanding of the etiology and risk factors of the disease can help reach a consensus in approaching h. pylori infection. dietary modification, smoking cessation, and exercise hold promise in preventing gastric cancer, while genetic testing is enabling earlier diagnosis and thus greater survival.",0
"background many interventions found to be effective in health services research studies fail to translate into meaningful patient care outcomes across multiple contexts. health services researchers recognize the need to evaluate not only summative outcomes but also formative outcomes to assess the extent to which implementation is effective in a specific setting, prolongs sustainability, and promotes dissemination into other settings. many implementation theories have been published to help promote effective implementation. however, they overlap considerably in the constructs included in individual theories, and a comparison of theories reveals that each is missing important constructs included in other theories. in addition, terminology and definitions are not consistent across theories. we describe the consolidated framework for implementation research (cfir) that offers an overarching typology to promote implementation theory development and verification about what works where and why across multiple contexts. methods we used a snowball sampling approach to identify published theories that were evaluated to identify constructs based on strength of conceptual or empirical support for influence on implementation, consistency in definitions, alignment with our own findings, and potential for measurement. we combined constructs across published theories that had different labels but were redundant or overlapping in definition, and we parsed apart constructs that conflated underlying concepts. results the cfir is composed of five major domains: intervention characteristics, outer setting, inner setting, characteristics of the individuals involved, and the process of implementation. eight constructs were identified related to the intervention (e.g., evidence strength and quality), four constructs were identified related to outer setting (e.g., patient needs and resources), 12 constructs were identified related to inner setting (e.g., culture, leadership engagement), five constructs were identified related to individual characteristics, and eight constructs were identified related to process (e.g., plan, evaluate, and reflect). we present explicit definitions for each construct. conclusion the cfir provides a pragmatic structure for approaching complex, interacting, multi-level, and transient states of constructs in the real world by embracing, consolidating, and unifying key constructs from published implementation theories. it can be used to guide formative evaluations and build the implementation knowledge base across multiple studies and settings.",0
"in recent decades, the biomedical applications of mesenchymal stem cells (mscs) have attracted increasing attention. mscs are easily extracted from the bone marrow, fat, and synovium, and differentiate into various cell lineages according to the requirements of specific biomedical applications. as mscs do not express significant histocompatibility complexes and immune stimulating molecules, they are not detected by immune surveillance and do not lead to graft rejection after transplantation. these properties make them competent biomedical candidates, especially in tissue engineering. we present a brief overview of msc extraction methods and subsequent potential for differentiation, and a comprehensive overview of their preclinical and clinical applications in regenerative medicine, and discuss future challenges.",0
"hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. they assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. the substrate binding and release cycle is driven by the switching of hsp70 between the low-affinity atp bound state and the high-affinity adp bound state. thus, atp binding and hydrolysis are essential in vitro and in vivo for the chaperone activity of hsp70 proteins. this atpase cycle is controlled by co-chaperones of the family of j-domain proteins, which target hsp70s to their substrates, and by nucleotide exchange factors, which determine the lifetime of the hsp70-substrate complex. additional co-chaperones fine-tune this chaperone cycle. for specific tasks the hsp70 cycle is coupled to the action of other chaperones, such as hsp90 and hsp100.",0
"three independent variants with a profound reduction of cell surface h-2 have been selected from the c57bl/6 mouse-derived rbl-5 and el-4 t lymphomas. after subcutaneous inoculation of low cell doses in syngeneic mice, the h-2- variants failed to grow out, whereas the h-2+ control lines showed progressive growth. no difference in growth rate or cloning efficiency was detectable in tissue culture. the in vivo difference in tumor outgrowth was analyzed in detail for one of the h-2-low lines. the outgrowth difference remained after the h-2-low variant and the control line had been injected subcutaneously in opposite flanks of the same mouse, and it was not dependent upon activity of mature t cells, since the same result was seen in athymic nude mice. the difference was partially sensitive to irradiation of the hosts. when mice were pretreated with anti-asialo gm1 antiserum, known to depress natural killer (nk) cell activity, the difference in outgrowth was abolished, and both the control line and the h-2- variant showed progressive growth in vivo. experiments comparing the distribution and survival of isotope-prelabeled variant and wild type cells indicated that a rapid elimination of the former took place within 24 h after intravenous injection. these differences in tumor elimination were not seen in mice treated with anti-asialo gm1 antiserum. we conclude that the reduced tumorigenicity of sublines with impaired h-2 expression is largely, if not exclusively due to rapid elimination by nk cells. these findings may reflect an inverse, indirect relation between factors controlling h-2 expression and nk sensitivity. another possible explanation is that major histocompatibility complex (mhc)-encoded gene products are directly involved in a regulatory signal in the nk cell system. according to this interpretation, immunological selectivity in the nk cell system would be achieved by the failure to recognize self-mhc, irrespective of the presence of foreign antigens, i.e. by detection of no-self rather than of nonself. this may also explain previous observations on h-2-linked hybrid resistance against lymphoid grafts and changes in h-2 phenotypes associated with tumor progression.",0
"background lower respiratory infections are a leading cause of morbidity and mortality around the world. the global burden of diseases, injuries, and risk factors (gbd) study 2016, provides an up-to-date analysis of the burden of lower respiratory infections in 195 countries. this study assesses cases, deaths, and aetiologies spanning the past 26 years and shows how the burden of lower respiratory infection has changed in people of all ages. methods we used three separate modelling strategies for lower respiratory infections in gbd 2016: a bayesian hierarchical ensemble modelling platform (cause of death ensemble model), which uses vital registration, verbal autopsy data, and surveillance system data to predict mortality due to lower respiratory infections; a compartmental meta-regression tool (dismod-mr), which uses scientific literature, population representative surveys, and health-care data to predict incidence, prevalence, and mortality; and modelling of counterfactual estimates of the population attributable fraction of lower respiratory infection episodes due to streptococcus pneumoniae, haemophilus influenzae type b, influenza, and respiratory syncytial virus. we calculated each modelled estimate for each age, sex, year, and location. we modelled the exposure level in a population for a given risk factor using dismod-mr and a spatio-temporal gaussian process regression, and assessed the effectiveness of targeted interventions for each risk factor in children younger than 5 years. we also did a decomposition analysis of the change in lri deaths from 2000-16 using the risk factors associated with lri in gbd 2016. findings in 2016, lower respiratory infections caused 652 572 deaths (95% uncertainty interval 586 475-720 612) in children younger than 5 years (under-5s), 1 080 958 deaths (943 749-1 170 638) in adults older than 70 years, and 2 377 697 deaths (2 145 584-2 512 809) in people of all ages, worldwide. streptococcus pneumoniae was the leading cause of lower respiratory infection morbidity and mortality globally, contributing to more deaths than all other aetiologies combined in 2016 (1 189 937 deaths, 95% ui 690 445-1 770 660). childhood wasting remains the leading risk factor for lower respiratory infection mortality among children younger than 5 years, responsible for 61·4% of lower respiratory infection deaths in 2016 (95% ui 45·7-69·6). interventions to improve wasting, household air pollution, ambient particulate matter pollution, and expanded antibiotic use could avert one under-5 death due to lower respiratory infection for every 4000 children treated in the countries with the highest lower respiratory infection burden. interpretation our findings show substantial progress in the reduction of lower respiratory infection burden, but this progress has not been equal across locations, has been driven by decreases in several primary risk factors, and might require more effort among elderly adults. by highlighting regions and populations with the highest burden, and the risk factors that could have the greatest effect, funders, policy makers, and programme implementers can more effectively reduce lower respiratory infections among the world's most susceptible populations. funding bill & melinda gates foundation.",0
"the dose of foreign antigen can influence whether a cell-mediated or humoral class of immune response is elicited, and this may be largely accounted for by the development of cd4+ t helper cells (th) producing distinct sets of cytokines. the ability of antigen dose to direct the development of a th1 or th2 phenotype from naive cd4+ t cells, however, has not been demonstrated. in this report, we show that the antigen dose used in primary cultures could directly affect th phenotype development from naive do11.10 tcr-alpha beta-transgenic cd4+ t cells when dendritic cells or activated b cells were used as the antigen-presenting cells. consistent with our previous findings, midrange peptide doses (0.3-0.6 microm) directed the development of th0/th1-like cells, which produced moderate amounts of interferon gamma (ifn-gamma). as the peptide dose was increased, development of th1-like cells producing increased amounts of ifn-gamma was initially observed. at very high (> 10 microm) and very low (< 0.05 microm) doses of antigenic peptide, however, a dramatic switch to development of th2-like cells that produced increasing amounts of interleukin 4 (il-4) and diminishing levels of ifn-gamma was observed. this was true even when highly purified naive, high buoyant density cd4+ lecam-1hi t cells were used, ruling out a possible contribution from contaminating ""memory"" phenotype cd4+ t cells. neutralizing anti-il-4 antibodies completely inhibited the development of this th2-like phenotype at both high and low antigen doses, demonstrating a requirement for endogenous il-4. our findings suggest that the antigen dose may affect the levels of endogenous cytokines such as il-4 in primary cultures, resulting in the development of distinct th cell phenotypes.",0
"in recent years remarkable progress has been made towards the understanding of proposed hallmarks of cancer development and treatment. however with its increasing incidence, the clinical management of cancer continues to be a challenge for the 21st century. treatment modalities comprise of radiation therapy, surgery, chemotherapy, immunotherapy and hormonal therapy. radiation therapy remains an important component of cancer treatment with approximately 50% of all cancer patients receiving radiation therapy during their course of illness; it contributes towards 40% of curative treatment for cancer. the main goal of radiation therapy is to deprive cancer cells of their multiplication (cell division) potential. celebrating a century of advances since marie curie won her second nobel prize for her research into radium, 2011 has been designated the year of radiation therapy in the uk. over the last 100 years, ongoing advances in the techniques of radiation treatment and progress made in understanding the biology of cancer cell responses to radiation will endeavor to increase the survival and reduce treatment side effects for cancer patients. in this review, principles, application and advances in radiation therapy with their biological end points are discussed.",0
"individual differences in cognitive paradigms are increasingly employed to relate cognition to brain structure, chemistry, and function. however, such efforts are often unfruitful, even with the most well established tasks. here we offer an explanation for failures in the application of robust cognitive paradigms to the study of individual differences. experimental effects become well established - and thus those tasks become popular - when between-subject variability is low. however, low between-subject variability causes low reliability for individual differences, destroying replicable correlations with other factors and potentially undermining published conclusions drawn from correlational relationships. though these statistical issues have a long history in psychology, they are widely overlooked in cognitive psychology and neuroscience today. in three studies, we assessed test-retest reliability of seven classic tasks: eriksen flanker, stroop, stop-signal, go/no-go, posner cueing, navon, and spatial-numerical association of response code (snarc). reliabilities ranged from 0 to .82, being surprisingly low for most tasks given their common use. as we predicted, this emerged from low variance between individuals rather than high measurement variance. in other words, the very reason such tasks produce robust and easily replicable experimental effects - low between-participant variability - makes their use as correlational tools problematic. we demonstrate that taking such reliability estimates into account has the potential to qualitatively change theoretical conclusions. the implications of our findings are that well-established approaches in experimental psychology and neuropsychology may not directly translate to the study of individual differences in brain structure, chemistry, and function, and alternative metrics may be required.",0
"presymptomatic transmission of sars-cov-2, the virus that causes coronavirus disease 2019 (covid-19), might pose challenges for disease control. the first case of covid-19 in singapore was detected on january 23, 2020, and by march 16, a total of 243 cases had been confirmed, including 157 locally acquired cases. clinical and epidemiologic findings of all covid-19 cases in singapore through march 16 were reviewed to determine whether presymptomatic transmission might have occurred. presymptomatic transmission was defined as the transmission of sars-cov-2 from an infected person (source patient) to a secondary patient before the source patient developed symptoms, as ascertained by exposure and symptom onset dates, with no evidence that the secondary patient had been exposed to anyone else with covid-19. seven covid-19 epidemiologic clusters in which presymptomatic transmission likely occurred were identified, and 10 such cases within these clusters accounted for 6.4% of the 157 locally acquired cases. in the four clusters for which the date of exposure could be determined, presymptomatic transmission occurred 1-3 days before symptom onset in the presymptomatic source patient. to account for the possibility of presymptomatic transmission, officials developing contact tracing protocols should strongly consider including a period before symptom onset. evidence of presymptomatic transmission of sars-cov-2 underscores the critical role social distancing, including avoidance of congregate settings, plays in controlling the covid-19 pandemic.",0
"establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history and will help to facilitate the development of new approaches for disease-gene discovery. large-scale surveys of human genetic variation have reported signatures of recent explosive population growth, notable for an excess of rare genetic variants, suggesting that many mutations arose recently. to more quantitatively assess the distribution of mutation ages, we resequenced 15,336 genes in 6,515 individuals of european american and african american ancestry and inferred the age of 1,146,401 autosomal single nucleotide variants (snvs). we estimate that approximately 73% of all protein-coding snvs and approximately 86% of snvs predicted to be deleterious arose in the past 5,000-10,000 years. the average age of deleterious snvs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious snvs than other genes. furthermore, european americans had an excess of deleterious variants in essential and mendelian disease genes compared to african americans, consistent with weaker purifying selection due to the out-of-africa dispersal. our results better delimit the historical details of human protein-coding variation, show the profound effect of recent human history on the burden of deleterious snvs segregating in contemporary populations, and provide important practical information that can be used to prioritize variants in disease-gene discovery.",0
"urinary bladder cancer (ubc) is a common disease worldwide. at any point in time 2.7 million people have a history of ubc. the incidence of ubc varies over the world with highest rates in developed communities. but the burden of ubc will increase in less developed areas of the world. these changes can be attributed to global changes in exposure to risk factors for ubc and growth and aging of the world population.",0
"we studied the capacity of cultured mouse peritoneal macrophages to generate superoxide anion (o(2-)), the initial product of conversion of oxygen to microbicidal species, during phagocytosis of opsonized zymosan or upon contact with the membrane-active agent phorbel myristate acetate (pma). macrophages from mice infected with bacille calmette-guerin (bcg) or injected intraperitoneally with thioglycollate broth or endotoxin, released up to 12 times more o(2-) than did resident peritoneal macrophages, depending upon the cell type and whether the stimulus was zymosan or pma. there was little if any o(2-) release from resting (unstimulated) macrophages. the density of cells on culture dishes was an important variable since crowding of the dish markedly reduced the efficiency of o(2-) production. the enhanced o(2-) release of chemically elicited and infection-activated macrophages was noted after stimulation with a wide range of concentrations of pma and zymosan, at all time points studied (up to 120 min), and with cells maintained for 140 rain to 16 days in culture. the o(2-) response of resident cells improved twofold to zymosan and ninefold to pma during the first 3 days in culture. the capacity to release o~ appears to be limited to actively phagocytic cell types: murine macrophage-like tumor lines and cultured human monocytes released o(2-) when stimulated by pma or zymosan, fibroblast and endothelial lines and embryo-derived cells did not. activity of superoxide dismutase, which removes o(2-), was not detectable in culture supernates of any cell type, and thus, differences in detectable o(2-) could not be attributed to variations in the release of this enzyme. we conclude that the phagocytosis- associated respiratory burst is significantly enhanced in mononuclear phagocytes obtained ai~r chemical inflammation or bcg infection. increased capacity to generate o(2-) and other oxygen radicals during phagocytosis could contribute to the improved microbicidal and tumoricidal activity of activated macrophages.",0
"small amounts of pge inhibit mitogen-induced thymidine incorporation in human peripheral lymphocytes. the 50% inhibitory concentration is approximately 10(-7) m, and this is reduced to approximately 10(-8) m when endogenous pge production is blocked. pge inhibits pha- and con a-stimulated cultures much better than pwm cultures, suggesting a differential effect of pge on t-cell vs. b-cell function. in vitro blockade of pg synthesis results in approximately 50% increase in thymidine incorporation in pha cultures. pge is produced endogenously in pha cultures by glass adherent suppressor cells.",0
"molecular self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components. dna has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra. templated self-assembly of dna into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase 'scaffold strand' that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide 'staple strands'. here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. we demonstrate the design and assembly of nanostructures approximating six shapes-monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross-with precisely controlled dimensions ranging from 10 to 100 nm. we also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. we anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale.",0
"the evolution of macrophages has made them primordial for both development and immunity. their functions range from the shaping of body plans to the ingestion and elimination of apoptotic cells and pathogens. cytokines are small soluble proteins that confer instructions and mediate communication among immune and non-immune cells. a portfolio of cytokines is central to the role of macrophages as sentries of the innate immune system that mediate the transition from innate to adaptive immunity. in concert with other mediators, cytokines bias the fate of macrophages into a spectrum of inflammation-promoting ""classically activated,"" to anti-inflammatory or ""alternatively activated"" macrophages. deregulated cytokine secretion is implicated in several disease states ranging from chronic inflammation to allergy. macrophages release cytokines via a series of beautifully orchestrated pathways that are spatiotemporally regulated. at the molecular level, these exocytic cytokine secretion pathways are coordinated by multi-protein complexes that guide cytokines from their point of synthesis to their ports of exit into the extracellular milieu. these trafficking proteins, many of which were discovered in yeast and commemorated in the 2013 nobel prize in physiology or medicine, coordinate the organelle fusion steps that are responsible for cytokine release. this review discusses the functions of cytokines secreted by macrophages, and summarizes what is known about their release mechanisms. this information will be used to delve into how selected pathogens subvert cytokine release for their own survival.",0
"the novel coronavirus disease 2019 (covid-19), originated in wuhan city of china, has spread rapidly around the world, sending billions of people into lockdown. the world health organization (who) declared the coronavirus epidemic a pandemic. in light of rising concern about the current covid-19 pandemic, a growing number of universities across the world have either postponed or canceled all campus events such as workshops, conferences, sports, and other activities. universities are taking intensive measures to prevent and protect all students and staff members from the highly infectious disease. faculty members are already in the process of transitioning to online teaching platforms. in this review, the author will highlight the potential impact of the terrible covid-19 outbreak on the education and mental health of students and academic staff.",0
"cells of the dendritic family display some unique properties that confer to them the capacity to sensitize naive t cells in vitro and in vivo. in the mouse, two subclasses of dendritic cells (dcs) have been described that differ by their cd8alpha expression and their localization in lymphoid organs. the physiologic function of both cell populations remains obscure. studies conducted in vitro have suggested that cd8alpha+ dcs could play a role in the regulation of immune responses, whereas conventional cd8alpha- dcs would be more stimulatory. we report here that both subclasses of dcs efficiently prime antigen-specific t cells in vivo, and direct the development of distinct t helper (th) populations. antigen-pulsed cd8alpha+ and cd8alpha- dcs are separated after overnight culture in recombinant granulocyte/macrophage colony-stimulating factor and injected into the footpads of syngeneic mice. administration of cd8alpha- dcs induces a th2-type response, whereas injection of cd8alpha+ dcs leads to th1 differentiation. we further show that interleukin 12 plays a critical role in th1 development by cd8alpha+ dcs. these findings suggest that the nature of the dc that presents the antigen to naive t cells may dictate the class selection of the adaptative immune response.",0
"sleep plays a vital role in brain function and systemic physiology across many body systems. problems with sleep are widely prevalent and include deficits in quantity and quality of sleep; sleep problems that impact the continuity of sleep are collectively referred to as sleep disruptions. numerous factors contribute to sleep disruption, ranging from lifestyle and environmental factors to sleep disorders and other medical conditions. sleep disruptions have substantial adverse short- and long-term health consequences. a literature search was conducted to provide a nonsystematic review of these health consequences (this review was designed to be nonsystematic to better focus on the topics of interest due to the myriad parameters affected by sleep). sleep disruption is associated with increased activity of the sympathetic nervous system and hypothalamic-pituitary-adrenal axis, metabolic effects, changes in circadian rhythms, and proinflammatory responses. in otherwise healthy adults, short-term consequences of sleep disruption include increased stress responsivity, somatic pain, reduced quality of life, emotional distress and mood disorders, and cognitive, memory, and performance deficits. for adolescents, psychosocial health, school performance, and risk-taking behaviors are impacted by sleep disruption. behavioral problems and cognitive functioning are associated with sleep disruption in children. long-term consequences of sleep disruption in otherwise healthy individuals include hypertension, dyslipidemia, cardiovascular disease, weight-related issues, metabolic syndrome, type 2 diabetes mellitus, and colorectal cancer. all-cause mortality is also increased in men with sleep disturbances. for those with underlying medical conditions, sleep disruption may diminish the health-related quality of life of children and adolescents and may worsen the severity of common gastrointestinal disorders. as a result of the potential consequences of sleep disruption, health care professionals should be cognizant of how managing underlying medical conditions may help to optimize sleep continuity and consider prescribing interventions that minimize sleep disruption.",0
"chimeric antigen receptor (car)-t cell therapy is a revolutionary new pillar in cancer treatment. although treatment with car-t cells has produced remarkable clinical responses with certain subsets of b cell leukemia or lymphoma, many challenges limit the therapeutic efficacy of car-t cells in solid tumors and hematological malignancies. barriers to effective car-t cell therapy include severe life-threatening toxicities, modest anti-tumor activity, antigen escape, restricted trafficking, and limited tumor infiltration. in addition, the host and tumor microenvironment interactions with car-t cells critically alter car-t cell function. furthermore, a complex workforce is required to develop and implement these treatments. in order to overcome these significant challenges, innovative strategies and approaches to engineer more powerful car-t cells with improved anti-tumor activity and decreased toxicity are necessary. in this review, we discuss recent innovations in car-t cell engineering to improve clinical efficacy in both hematological malignancy and solid tumors and strategies to overcome limitations of car-t cell therapy in both hematological malignancy and solid tumors.",0
"bone regeneration is a complex, well-orchestrated physiological process of bone formation, which can be seen during normal fracture healing, and is involved in continuous remodelling throughout adult life. however, there are complex clinical conditions in which bone regeneration is required in large quantity, such as for skeletal reconstruction of large bone defects created by trauma, infection, tumour resection and skeletal abnormalities, or cases in which the regenerative process is compromised, including avascular necrosis, atrophic non-unions and osteoporosis. currently, there is a plethora of different strategies to augment the impaired or 'insufficient' bone-regeneration process, including the 'gold standard' autologous bone graft, free fibula vascularised graft, allograft implantation, and use of growth factors, osteoconductive scaffolds, osteoprogenitor cells and distraction osteogenesis. improved 'local' strategies in terms of tissue engineering and gene therapy, or even 'systemic' enhancement of bone repair, are under intense investigation, in an effort to overcome the limitations of the current methods, to produce bone-graft substitutes with biomechanical properties that are as identical to normal bone as possible, to accelerate the overall regeneration process, or even to address systemic conditions, such as skeletal disorders and osteoporosis.",0
"the mummer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. since the last major release of mummer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. despite its broad utility, mummer3 has limitations that can make it difficult to use for large genomes and for the very large sequence data sets that are common today. in this paper we describe mummer4, a substantially improved version of mummer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of mummer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. with a theoretical limit on the input size of 141tbp, mummer4 can now work with input sequences of any biologically realistic length. we show that as a result of these enhancements, the nucmer program in mummer4 is easily able to handle alignments of large genomes; we illustrate this with an alignment of the human and chimpanzee genomes, which allows us to compute that the two species are 98% identical across 96% of their length. with the enhancements described here, mummer4 can also be used to efficiently align reads to reference genomes, although it is less sensitive and accurate than the dedicated read aligners. the nucmer aligner in mummer4 can now be called from scripting languages such as perl, python and ruby. these improvements make mumer4 one the most versatile genome alignment packages available.",0
"(myo)fibroblasts are key players for maintaining skin homeostasis and for orchestrating physiological tissue repair. (myo)fibroblasts are embedded in a sophisticated extracellular matrix (ecm) that they secrete, and a complex and interactive dialogue exists between (myo)fibroblasts and their microenvironment. in addition to the secretion of the ecm, (myo)fibroblasts, by secreting matrix metalloproteinases and tissue inhibitors of metalloproteinases, are able to remodel this ecm. (myo)fibroblasts and their microenvironment form an evolving network during tissue repair, with reciprocal actions leading to cell differentiation, proliferation, quiescence, or apoptosis, and actions on growth factor bioavailability by binding, sequestration, and activation. in addition, the (myo)fibroblast phenotype is regulated by mechanical stresses to which they are subjected and thus by mechanical signaling. in pathological situations (excessive scarring or fibrosis), or during aging, this dialogue between the (myo)fibroblasts and their microenvironment may be altered or disrupted, leading to repair defects or to injuries with damaged and/or cosmetic skin alterations such as wrinkle development. the intimate dialogue between the (myo)fibroblasts and their microenvironment therefore represents a fascinating domain that must be better understood in order not only to characterize new therapeutic targets and drugs able to prevent or treat pathological developments but also to interfere with skin alterations observed during normal aging or premature aging induced by a deleterious environment.",0
"diffusion imaging in python (dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dmri) experiments. dmri is an application of mri that can be used to measure structural features of brain white matter. many methods have been developed to use dmri data to model the local configuration of white matter nerve fiber bundles and infer the trajectory of bundles connecting different parts of the brain. dipy gathers implementations of many different methods in dmri, including: diffusion signal pre-processing; reconstruction of diffusion distributions in individual voxels; fiber tractography and fiber track post-processing, analysis and visualization. dipy aims to provide transparent implementations for all the different steps of dmri analysis with a uniform programming interface. we have implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography. in addition, cutting edge novel reconstruction techniques are implemented, such as constrained spherical deconvolution and diffusion spectrum imaging (dsi) with deconvolution, as well as methods for probabilistic tracking and original methods for tractography clustering. many additional utility functions are provided to calculate various statistics, informative visualizations, as well as file-handling routines to assist in the development and use of novel techniques. in contrast to many other scientific software projects, dipy is not being developed by a single research group. rather, it is an open project that encourages contributions from any scientist/developer through github and open discussions on the project mailing list. consequently, dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing.",0
"the dials project is a collaboration between diamond light source, lawrence berkeley national laboratory and ccp4 to develop a new software suite for the analysis of crystallographic x-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. the design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.",0
"sweetclover was harvested at the early blooming stage and wilted for 0, 8, or 30 hours ( dm 27. 36% , 38. 69% or 44. 98% , respectively) , and was ensiled with sugar at a rate of 1. 0% , 1. 5% or 2. 0%. haylage (dm 44. 98% ) without additives had lower ammonia nitrogen content and higher wsc and cp contents. sugar addition resulted in higher ammonia nitrogen content, butyric acid production, and cp content reduction; it promoted bad fermentation of the silage.",0
"large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of dna sequence changes. here we describe the aggregation and analysis of high-quality exome (protein-coding region) dna sequence data for 60,706 individuals of diverse ancestries generated as part of the exome aggregation consortium (exac). this catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. we have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.",0
"caveolae are specialized invaginations of the plasma membrane which have been proposed to play a role in diverse cellular processes such as endocytosis and signal transduction. we have developed an assay to determine the fraction of internal versus plasma membrane caveolae. the gpi-anchored protein, alkaline phosphatase, was clustered in caveolae after antibody-induced crosslinking at low temperature and then, after various treatments, the relative amount of alkaline phosphatase on the cell surface was determined. using this assay we were able to show a time- and temperature-dependent decrease in cell-surface alkaline phosphatase activity which was dependent on antibody-induced clustering. the decrease in cell surface alkaline phosphatase activity was greatly accelerated by the phosphatase inhibitor, okadaic acid, but not by a protein kinase c activator. internalization of clustered alkaline phosphatase in the presence or absence of okadaic acid was blocked by cytochalasin d and by the kinase inhibitor staurosporine. electron microscopy confirmed that okadaic acid induced removal of caveolae from the cell surface. in the presence of hypertonic medium this was followed by the redistribution of groups of caveolae to the center of the cell close to the microtubule-organizing center. this process was reversible, blocked by cytochalasin d, and the centralization of the caveolar clusters was shown to be dependent on an intact microtubule network. although the exact mechanism of internalization remains unknown, the results show that caveolae are dynamic structures which can be internalized into the cell. this process may be regulated by kinase activity and require an intact actin network.",0
"modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. in an attempt to expand the range of applicability, a new method called pm7 has been developed. pm7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. the resulting method was tested by modeling crystal structures and heats of formation of solids. two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the nddo formalism were rectified. average unsigned errors (aues) in geometry and δhf for pm7 were reduced relative to pm6; for simple gas-phase organic systems, the aue in bond lengths decreased by about 5% and the aue in δhf decreased by about 10%; for organic solids, the aue in δhf dropped by 60% and the reduction was 33.3% for geometries. a two-step process (pm7-ts) for calculating the heights of activation barriers has been developed. using pm7-ts, the aue in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol(-1) in pm6 and 10.8 kcal/mol(-1) in pm7 to 3.8 kcal/mol(-1). the origins of the errors in nddo methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. this conclusion provides insight into how these methods can be improved.",0
"neonatal necrotizing enterocolitis is the most important cause of acquired gastrointestinal morbidity or mortality among low birthweight infants. prematurity alone is probably the only identifiable risk factor. although the etiology is unknown nec has many similarities to an infectious disease. proper staging helps improve reporting and the management of nec.",0
"microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. in 2011, we developed antismash, a web-based analysis platform that automates this process. here, we present the highly improved antismash 2.0 release, available at for the new version, antismash was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antismash 2.0 now supports input of multiple related sequences simultaneously (multi-fasta/genbank/embl), which allows the analysis of draft genomes comprising multiple contigs. moreover, direct analysis of protein sequences is now possible. antismash 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. the algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. the antismash clusterblast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. the new features currently make antismash 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms.",0
"by aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. however, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. to address these issues we have developed magma, a novel tool for gene and gene-set analysis. the gene analysis is based on a multiple regression model, to provide better statistical performance. the gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. this gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. simulations and an analysis of crohn's disease data are used to evaluate the performance of magma and to compare it to a number of other gene and gene-set analysis tools. the results show that magma has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with crohn's disease while maintaining a correct type 1 error rate. moreover, the magma analysis of the crohn's disease data was found to be considerably faster as well.",0
"using biochemical assays to determine the activation state of rho-like gtpases, we show that the guanine nucleotide exchange factor tiam1 functions as a specific activator of rac but not cdc42 or rho in nih3t3 fibroblasts. activation of rac by tiam1 induces an epithelial-like morphology with functional cadherin-based adhesions and inhibits migration of fibroblasts. this epithelial phenotype is characterized by rac-mediated effects on rho activity. transient pdgf-induced as well as sustained rac activation by tiam1 or v12rac downregulate rho activity. we found that cdc42 also downregulates rho activity. neither v14rho or n19rho affects rac activity, suggesting unidirectional signaling from rac towards rho. downregulation of rho activity occurs independently of rac- induced cytoskeletal changes and cell spreading. moreover, rac effector mutants that are defective in mediating cytoskeleton changes or jun kinase activation both downregulate rho activity, suggesting that neither of these rac signaling pathways are involved in the regulation of rho. restoration of rho activity in tiam1-expressing cells by expression of v14rho results in reversion of the epithelioid phenotype towards a migratory, fibroblastoid morphology. we conclude that rac signaling is able to antagonize rho activity directly at the gtpase level, and that the reciprocal balance between rac and rho activity determines cellular morphology and migratory behavior in nih3t3 fibroblasts.",0
"objective to describe the promise and potential of big data analytics in healthcare. methods the paper describes the nascent field of big data analytics in healthcare, discusses the benefits, outlines an architectural framework and methodology, describes examples reported in the literature, briefly discusses the challenges, and offers conclusions. results the paper provides a broad overview of big data analytics for healthcare researchers and practitioners. conclusions big data analytics in healthcare is evolving into a promising field for providing insight from very large data sets and improving outcomes while reducing costs. its potential is great; however there remain challenges to overcome.",0
"from the moment of conception, we begin to age. a decay of cellular structures, gene regulation, and dna sequence ages cells and organisms. dna methylation patterns change with increasing age and contribute to age related disease. here we identify 88 sites in or near 80 genes for which the degree of cytosine methylation is significantly correlated with age in saliva of 34 male identical twin pairs between 21 and 55 years of age. furthermore, we validated sites in the promoters of three genes and replicated our results in a general population sample of 31 males and 29 females between 18 and 70 years of age. the methylation of three sites--in the promoters of the edaradd, tom1l1, and nptx2 genes--is linear with age over a range of five decades. using just two cytosines from these loci, we built a regression model that explained 73% of the variance in age, and is able to predict the age of an individual with an average accuracy of 5.2 years. in forensic science, such a model could estimate the age of a person, based on a biological sample alone. furthermore, a measurement of relevant sites in the genome could be a tool in routine medical screening to predict the risk of age-related diseases and to tailor interventions based on the epigenetic bio-age instead of the chronological age.",0
"neuromyelitis optica (nmo) is an inflammatory demyelinating disease that selectively affects optic nerves and spinal cord. it is considered a severe variant of multiple sclerosis (ms), and frequently is misdiagnosed as ms, but prognosis and optimal treatments differ. a serum immunoglobulin g autoantibody (nmo-igg) serves as a specific marker for nmo. here we show that nmo-igg binds selectively to the aquaporin-4 water channel, a component of the dystroglycan protein complex located in astrocytic foot processes at the blood-brain barrier. nmo may represent the first example of a novel class of autoimmune channelopathy.",0
"background the burden of ischaemic and haemorrhagic stroke varies between regions and over time. with differences in prognosis, prevalence of risk factors, and treatment strategies, knowledge of stroke pathological type is important for targeted region-specific health-care planning for stroke and could inform priorities for type-specific prevention strategies. we used data from the global burden of diseases, injuries, and risk factors study 2010 (gbd 2010) to estimate the global and regional burden of first-ever ischaemic and haemorrhagic stroke during 1990-2010. methods we searched medline, embase, lilacs, scopus, pubmed, science direct, global health database, the who library, and regional databases from 1990 to 2012 to identify relevant studies published between 1990 and 2010. we applied the gbd 2010 analytical technique (dismod-mr) to calculate regional and country-specific estimates for ischaemic and haemorrhagic stroke incidence, mortality, mortality-to-incidence ratio, and disability-adjusted life-years (dalys) lost, by age group (aged findings we included 119 studies (58 from high-income countries and 61 from low-income and middle-income countries). worldwide, the burden of ischaemic and haemorrhagic stroke increased significantly between 1990 and 2010 in terms of the absolute number of people with incident ischaemic and haemorrhagic stroke (37% and 47% increase, respectively), number of deaths (21% and 20% increase), and dalys lost (18% and 14% increase). in the past two decades in high-income countries, incidence of ischaemic stroke reduced significantly by 13% (95% ci 6-18), mortality by 37% (19-39), dalys lost by 34% (16-36), and mortality-to-incidence ratios by 21% (10-27). for haemorrhagic stroke, incidence reduced significantly by 19% (1-15), mortality by 38% (32-43), dalys lost by 39% (32-44), and mortality-to-incidence ratios by 27% (19-35). by contrast, in low-income and middle-income countries, we noted a significant increase of 22% (5-30) in incidence of haemorrhagic stroke and a 6% (-7 to 18) non-significant increase in the incidence of ischaemic stroke. mortality rates for ischaemic stroke fell by 14% (9-19), dalys lost by 17% (-11 to 21%), and mortality-to-incidence ratios by 16% (-12 to 22). for haemorrhagic stroke in low-income and middle-income countries, mortality rates reduced by 23% (-18 to 25%), dalys lost by 25% (-21 to 28), and mortality-to-incidence ratios by 36% (-34 to 28). interpretation although age-standardised mortality rates for ischaemic and haemorrhagic stroke have decreased in the past two decades, the absolute number of people who have these stroke types annually, and the number with related deaths and dalys lost, is increasing, with most of the burden in low-income and middle-income countries. further study is needed in these countries to identify which subgroups of the population are at greatest risk and who could be targeted for preventive efforts.",0
"during the inflammatory response that drives atherogenesis, macrophages accumulate progressively in the expanding arterial wall. the observation that circulating monocytes give rise to lesional macrophages has reinforced the concept that monocyte infiltration dictates macrophage buildup. recent work has indicated, however, that macrophage accumulation does not depend on monocyte recruitment in some inflammatory contexts. we therefore revisited the mechanism underlying macrophage accumulation in atherosclerosis. in murine atherosclerotic lesions, we found that macrophages turn over rapidly, after 4 weeks. replenishment of macrophages in these experimental atheromata depends predominantly on local macrophage proliferation rather than monocyte influx. the microenvironment orchestrates macrophage proliferation through the involvement of scavenger receptor a (sr-a). our study reveals macrophage proliferation as a key event in atherosclerosis and identifies macrophage self-renewal as a therapeutic target for cardiovascular disease.",0
"a therapeutic strategy that can eliminate primary tumours, inhibit metastases, and prevent tumour relapses is developed herein by combining adjuvant nanoparticle-based photothermal therapy with checkpoint-blockade immunotherapy. indocyanine green (icg), a photothermal agent, and imiquimod (r837), a toll-like-receptor-7 agonist, are co-encapsulated by poly(lactic-co-glycolic) acid (plga). the formed plga-icg-r837 nanoparticles composed purely by three clinically approved components can be used for near-infrared laser-triggered photothermal ablation of primary tumours, generating tumour-associated antigens, which in the presence of r837-containing nanoparticles as the adjuvant can show vaccine-like functions. in combination with the checkpoint-blockade using anti-cytotoxic t-lymphocyte antigen-4 (ctla4), the generated immunological responses will be able to attack remaining tumour cells in mice, useful in metastasis inhibition, and may potentially be applicable for various types of tumour models. furthermore, such strategy offers a strong immunological memory effect, which can provide protection against tumour rechallenging post elimination of their initial tumours.",0
"introduction the emerge (electronic medical records and genomics) network is an nhgri-supported consortium of five institutions to explore the utility of dna repositories coupled to electronic medical record (emr) systems for advancing discovery in genome science. emerge also includes a special emphasis on the ethical, legal and social issues related to these endeavors. organization the five sites are supported by an administrative coordinating center. setting of network goals is initiated by working groups: (1) genomics, (2) informatics, and (3) consent & community consultation, which also includes active participation by investigators outside the emerge funded sites, and (4) return of results oversight committee. the steering committee, comprised of site pis and representatives and nhgri staff, meet three times per year, once per year with the external scientific panel. current progress the primary site-specific phenotypes for which samples have undergone genome-wide association study (gwas) genotyping are cataract and hdl, dementia, electrocardiographic qrs duration, peripheral arterial disease, and type 2 diabetes. a gwas is also being undertaken for resistant hypertension in ≈ 2,000 additional samples identified across the network sites, to be added to data available for samples already genotyped. funded by arra supplements, secondary phenotypes have been added at all sites to leverage the genotyping data, and hypothyroidism is being analyzed as a cross-network phenotype. results are being posted in dbgap. other key emerge activities include evaluation of the issues associated with cross-site deployment of common algorithms to identify cases and controls in emrs, data privacy of genomic and clinically-derived data, developing approaches for large-scale meta-analysis of gwas data across five sites, and a community consultation and consent initiative at each site. future activities plans are underway to expand the network in diversity of populations and incorporation of gwas findings into clinical care. summary by combining advanced clinical informatics, genome science, and community consultation, emerge represents a first step in the development of data-driven approaches to incorporate genomic information into routine healthcare delivery.",0
"the accuracy of multiple sequence alignment program mafft has been improved. the new version (5.3) of mafft offers new iterative refinement options, h-ins-i, f-ins-i and g-ins-i, in which pairwise alignment information are incorporated into objective function. these new options of mafft showed higher accuracy than currently available methods including tcoffee version 2 and clustal w in benchmark tests consisting of alignments of >50 sequences. like the previously available options, the new options of mafft can handle hundreds of sequences on a standard desktop computer. we also examined the effect of the number of homologues included in an alignment. for a multiple alignment consisting of approximately 8 sequences with low similarity, the accuracy was improved (2-10 percentage points) when the sequences were aligned together with dozens of their close homologues (e-value < 10(-5)-10(-20)) collected from a database. such improvement was generally observed for most methods, but remarkably large for the new options of mafft proposed here. thus, we made a ruby script, maffte.rb, which aligns the input sequences together with their close homologues collected from swissprot using ncbi-blast.",0
"introduction we recently reported a high cumulative incidence of thrombotic complications in critically ill patients with covid-19 admitted to the intensive care units (icus) of three dutch hospitals. in answering questions raised regarding our study, we updated our database and repeated all analyses. methods we re-evaluated the incidence of the composite outcome of symptomatic acute pulmonary embolism (pe), deep-vein thrombosis, ischemic stroke, myocardial infarction and/or systemic arterial embolism in all covid-19 patients admitted to the icus of 2 dutch university hospitals and 1 dutch teaching hospital from icu admission to death, icu discharge or april 22nd 2020, whichever came first. results we studied the same 184 icu patients as reported on previously, of whom a total of 41 died (22%) and 78 were discharged alive (43%). the median follow-up duration increased from 7 to 14 days. all patients received pharmacological thromboprophylaxis. the cumulative incidence of the composite outcome, adjusted for competing risk of death, was 49% (95% confidence interval 41-57%). the majority of thrombotic events were pe (65/75; 87%). in the competing risk model, chronic anticoagulation therapy at admission was associated with a lower risk of the composite outcome (hazard ratio 0.29, 95%ci 0.091-0.92). patients diagnosed with thrombotic complications were at higher risk of all-cause death (hr 5.4; 95%ci 2.4-12). use of therapeutic anticoagulation was not associated with all-cause death (hr 0.79, 95%ci 0.35-1.8). conclusion in this updated analysis, we confirm the very high cumulative incidence of thrombotic complications in critically ill patients with covid-19 pneumonia.",0
"background middle east respiratory syndrome (mers) is a new human disease caused by a novel coronavirus (cov). clinical data on mers-cov infections are scarce. we report epidemiological, demographic, clinical, and laboratory characteristics of 47 cases of mers-cov infections, identify knowledge gaps, and define research priorities. methods we abstracted and analysed epidemiological, demographic, clinical, and laboratory data from confirmed cases of sporadic, household, community, and health-care-associated mers-cov infections reported from saudi arabia between sept 1, 2012, and june 15, 2013. cases were confirmed as having mers-cov by real-time rt-pcr. findings 47 individuals (46 adults, one child) with laboratory-confirmed mers-cov disease were identified; 36 (77%) were male (male:female ratio 3·3:1). 28 patients died, a 60% case-fatality rate. the case-fatality rate rose with increasing age. only two of the 47 cases were previously healthy; most patients (45 ) had underlying comorbid medical disorders, including diabetes (32 ), hypertension (16 ), chronic cardiac disease (13 ), and chronic renal disease (23 ). common symptoms at presentation were fever (46 ), fever with chills or rigors (41 ), cough (39 ), shortness of breath (34 ), and myalgia (15 ). gastrointestinal symptoms were also frequent, including diarrhoea (12 ), vomiting (ten ), and abdominal pain (eight ). all patients had abnormal findings on chest radiography, ranging from subtle to extensive unilateral and bilateral abnormalities. laboratory analyses showed raised concentrations of lactate dehydrogenase (23 ) and aspartate aminotransferase (seven ) and thrombocytopenia (17 ) and lymphopenia (16 ). interpretation disease caused by mers-cov presents with a wide range of clinical manifestations and is associated with substantial mortality in admitted patients who have medical comorbidities. major gaps in our knowledge of the epidemiology, community prevalence, and clinical spectrum of infection and disease need urgent definition. funding none.",0
"background pain is an enormous problem globally. estimates suggest that 20% of adults suffer from pain globally and 10% are newly diagnosed with chronic pain each year. nevertheless, the problem of pain has primarily been regarded as a medical problem, and has been little addressed by the field of public health. discussion despite the ubiquity of pain, whether acute, chronic or intermittent, public health scholars and practitioners have not addressed this issue as a public health problem. the importance of viewing pain through a public health lens allows one to understand pain as a multifaceted, interdisciplinary problem for which many of the causes are the social determinants of health. addressing pain as a global public health issue will also aid in priority setting and formulating public health policy to address this problem, which, like most other chronic non-communicable diseases, is growing both in absolute numbers and in its inequitable distribution across the globe. summary the prevalence, incidence, and vast social and health consequences of global pain requires that the public health community give due attention to this issue. doing so will mean that health care providers and public health professionals will have a more comprehensive understanding of pain and the appropriate public health and social policy responses to this problem.",0
"type 2 diabetes (t2d) is a major comorbidity of covid-19. however, the impact of blood glucose (bg) control on the degree of required medical interventions and on mortality in patients with covid-19 and t2d remains uncertain. thus, we performed a retrospective, multi-centered study of 7,337 cases of covid-19 in hubei province, china, among which 952 had pre-existing t2d. we found that subjects with t2d required more medical interventions and had a significantly higher mortality (7.8% versus 2.7%; adjusted hazard ratio , 1.49) and multiple organ injury than the non-diabetic individuals. further, we found that well-controlled bg (glycemic variability within 3.9 to 10.0 mmol/l) was associated with markedly lower mortality compared to individuals with poorly controlled bg (upper limit of glycemic variability exceeding 10.0 mmol/l) (adjusted hr, 0.14) during hospitalization. these findings provide clinical evidence correlating improved glycemic control with better outcomes in patients with covid-19 and pre-existing t2d.",0
"peroxisome proliferator-activated receptors are expressed in many tissues, including adipocytes, hepatocytes, muscles and endothelial cells; however, the affinity depends on the isoform of ppar, and different distribution and expression profiles, which ultimately lead to different clinical outcomes. because they play an important role in lipid and glucose homeostasis, they are called lipid and insulin sensors. their actions are limited to specific tissue types and thus, reveal a characteristic influence on target cells. pparα mainly influences fatty acid metabolism and its activation lowers lipid levels, while pparγ is mostly involved in the regulation of the adipogenesis, energy balance, and lipid biosynthesis. pparβ/δ participates in fatty acid oxidation, mostly in skeletal and cardiac muscles, but it also regulates blood glucose and cholesterol levels. many natural and synthetic ligands influence the expression of these receptors. synthetic ligands are widely used in the treatment of dyslipidemia (e.g. fibrates--pparα activators) or in diabetes mellitus (e.g. thiazolidinediones--pparγ agonists). new generation drugs--pparα/γ dual agonists--reveal hypolipemic, hypotensive, antiatherogenic, anti-inflammatory and anticoagulant action while the overexpression of pparβ/δ prevents the development of obesity and reduces lipid accumulation in cardiac cells, even during a high-fat diet. precise data on the expression and function of natural ppar agonists on glucose and lipid metabolism are still missing, mostly because the same ligand influences several receptors and a number of reports have provided conflicting results. to date, we know that ppars have the capability to accommodate and bind a variety of natural and synthetic lipophilic acids, such as essential fatty acids, eicosanoids, phytanic acid and palmitoylethanolamide. a current understanding of the effects of ppars, their molecular mechanisms and the role of these receptors in nutrition and therapeutic treatment are delineated in this paper.",0
"pulsenet, the national molecular subtyping network for foodborne disease surveillance, was established by the centers for disease control and prevention and several state health department laboratories to facilitate subtyping bacterial foodborne pathogens for epidemiologic purposes. pulsenet, which began in 1996 with 10 laboratories typing a single pathogen (escherichia coli o157:h7), now includes 46 state and 2 local public health laboratories and the food safety laboratories of the u.s. food and drug administration and the u.s. department of agriculture. four foodborne pathogens (e. coli o157:h7; nontyphoidal salmonella serotypes, listeria monocytogenes and shigella) are being subtyped, and other bacterial, viral, and parasitic organisms will be added soon.",0
"pulse-chase experiments have revealed that cyclin, the auxiliary protein of dna polymerase-delta, is stable during the transition from growth to quiescence in 3t3 cells. immunoblotting together with immunofluorescence analysis has shown that the amount of cyclin after 24 h of quiescence is 30-40% of that of growing cells and that it presents a nucleoplasmic staining. immunofluorescence studies show the existence of two populations of cyclin during the s phase, one that is nucleoplasmic as in quiescent cells and is easily extracted by detergent, and another that is associated to specific nuclear structures. by using antibromodeoxyuridine immunofluorescence to detect the sites of dna synthesis, it was shown that the staining patterns of the replicon clusters and their order of appearance throughout the s phase are identical to those observed for cyclin. two-dimensional gel analysis of triton-extracted cells show that 20-30% of cyclin remains associated with the replicon clusters. this population of cyclin could not be released from the nucleus using high-salt extractions. this demonstrates that cyclin is tightly associated to the sites of dna replication and that it must have a fundamental role in dna synthesis in eukaryotic cells.",0
"objective to assess the effect of decreased sodium intake on blood pressure, related cardiovascular diseases, and potential adverse effects such as changes in blood lipids, catecholamine levels, and renal function. design systematic review and meta-analysis. data sources cochrane central register of controlled trials, medline, embase, who international clinical trials registry platform, the latin american and caribbean health science literature database, and the reference lists of previous reviews. study selection randomised controlled trials and prospective cohort studies in non-acutely ill adults and children assessing the relations between sodium intake and blood pressure, renal function, blood lipids, and catecholamine levels, and in non-acutely ill adults all cause mortality, cardiovascular disease, stroke, and coronary heart disease. study appraisal and synthesis potential studies were screened independently and in duplicate and study characteristics and outcomes extracted. when possible we conducted a meta-analysis to estimate the effect of lower sodium intake using the inverse variance method and a random effects model. we present results as mean differences or risk ratios, with 95% confidence intervals. results we included 14 cohort studies and five randomised controlled trials reporting all cause mortality, cardiovascular disease, stroke, or coronary heart disease; and 37 randomised controlled trials measuring blood pressure, renal function, blood lipids, and catecholamine levels in adults. nine controlled trials and one cohort study in children reporting on blood pressure were also included. in adults a reduction in sodium intake significantly reduced resting systolic blood pressure by 3.39 mm hg (95% confidence interval 2.46 to 4.31) and resting diastolic blood pressure by 1.54 mm hg (0.98 to 2.11). when sodium intake was 0.05). there were insufficient randomised controlled trials to assess the effects of reduced sodium intake on mortality and morbidity. the associations in cohort studies between sodium intake and all cause mortality, incident fatal and non-fatal cardiovascular disease, and coronary heart disease were non-significant (p>0.05). increased sodium intake was associated with an increased risk of stroke (risk ratio 1.24, 95% confidence interval 1.08 to 1.43), stroke mortality (1.63, 1.27 to 2.10), and coronary heart disease mortality (1.32, 1.13 to 1.53). in children, a reduction in sodium intake significantly reduced systolic blood pressure by 0.84 mm hg (0.25 to 1.43) and diastolic blood pressure by 0.87 mm hg (0.14 to 1.60). conclusions high quality evidence in non-acutely ill adults shows that reduced sodium intake reduces blood pressure and has no adverse effect on blood lipids, catecholamine levels, or renal function, and moderate quality evidence in children shows that a reduction in sodium intake reduces blood pressure. lower sodium intake is also associated with a reduced risk of stroke and fatal coronary heart disease in adults. the totality of evidence suggests that most people will likely benefit from reducing sodium intake.",0
"haplotype phasing is a fundamental problem in medical and population genetics. phasing is generally performed via statistical phasing in a genotyped cohort, an approach that can yield high accuracy in very large cohorts but attains lower accuracy in smaller cohorts. here we instead explore the paradigm of reference-based phasing. we introduce a new phasing algorithm, eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the haplotype reference consortium; hrc) using a new data structure based on the positional burrows-wheeler transform. we demonstrate that eagle2 attains a ∼20× speedup and ∼10% increase in accuracy compared to reference-based phasing using shapeit2. on european-ancestry samples, eagle2 with the hrc panel achieves >2× the accuracy of 1000 genomes-based phasing. eagle2 is open source and freely available for hrc-based phasing via the sanger imputation service and the michigan imputation server.",0
"the mission of the universal protein resource (uniprot) ( is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. it integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. uniprot comprises four major components, each optimized for different uses, the uniprot archive, the uniprot knowledgebase, the uniprot reference clusters and the uniprot metagenomic and environmental sequence database. uniprot is produced by the uniprot consortium, which consists of groups from the european bioinformatics institute (ebi), the sib swiss institute of bioinformatics (sib) and the protein information resource (pir). uniprot is updated and distributed every 4 weeks and can be accessed online for searches or downloads.",0
"background the quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. results with our years of experience in manually curating genomes for the joint genome institute, we developed a new gene prediction algorithm called prodigal (prokaryotic dynamic programming gene-finding algorithm). with prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. we compared the results of prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. conclusion we built a fast, lightweight, open source gene prediction program called prodigal prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.",0
"eosinophil accumulation is a prominent feature of allergic inflammatory reactions, such as those occurring in the lung of the allergic asthmatic, but the endogenous chemoattractants involved have not been identified. we have investigated this in an established model of allergic inflammation, using in vivo systems both to generate and assay relevant activity. bronchoalveolar lavage (bal) fluid was taken from sensitized guinea pigs at intervals after aerosol challenge with ovalbumin. bal fluid was injected intradermally in unsensitized assay guinea pigs and the accumulation of intravenously injected 111in-eosinophils was measured. activity was detected at 30 min after allergen challenge, peaking from 3 to 6 h and declining to low levels by 24 h. 3-h bal fluid was purified using high performance liquid chromatography techniques in conjunction with the skin assay. microsequencing revealed a novel protein from the c-c branch of the platelet factor 4 superfamily of chemotactic cytokines. the protein, ""eotaxin,"" exhibits homology of 53% with human mcp-1, 44% with guinea pig mcp-1, 31% with human mip-1 alpha, and 26% with human rantes. laser desorption time of flight mass analysis gave four different signals (8.15, 8.38, 8.81, and 9.03 kd), probably reflecting differential o-glycosylation. eotaxin was highly potent, inducing substantial 111in-eosinophil accumulation at a 1-2 pmol dose in the skin, but did not induce significant 111in-neutrophil accumulation. eotaxin was a potent stimulator of both guinea pig and human eosinophils in vitro. human recombinant rantes, mip-1 alpha, and mcp-1 were all inactive in inducing 111in-eosinophil accumulation in guinea pig skin; however, evidence was obtained that eotaxin shares a binding site with rantes on guinea pig eosinophils. this is the first description of a potent eosinophil chemoattractant cytokine generated in vivo and suggests the possibility that similar molecules may be important in the human asthmatic lung.",0
"motivation emergence of genetic data coupled to longitudinal electronic medical records (emrs) offers the possibility of phenome-wide association scans (phewas) for disease-gene associations. we propose a novel method to scan phenomic data for genetic associations using international classification of disease (icd9) billing codes, which are available in most emr systems. we have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent icd9 codes derived from emr data. as a proof of concept of this algorithm, we genotyped the first 6005 european-americans accrued into biovu, vanderbilt's dna biobank, at five single nucleotide polymorphisms (snps) with previously reported disease associations: atrial fibrillation, crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. the phewas software generated cases and control populations across all icd9 code groups for each of these five snps, and disease-snp associations were analyzed. the primary outcome of this study was replication of seven previously known snp-disease associations for these snps. results four of seven known snp-disease associations using the phewas algorithm were replicated with p-values between 2.8 x 10(-6) and 0.011. the phewas algorithm also identified 19 previously unknown statistical associations between these snps and diseases at p availability the phewas software and code translation table are freely available at",0
"background public health is a priority for the chinese government. evidence-based decision making for health at the province level in china, which is home to a fifth of the global population, is of paramount importance. this analysis uses data from the global burden of diseases, injuries, and risk factors study (gbd) 2017 to help inform decision making and monitor progress on health at the province level. methods we used the methods in gbd 2017 to analyse health patterns in the 34 province-level administrative units in china from 1990 to 2017. we estimated all-cause and cause-specific mortality, years of life lost (ylls), years lived with disability (ylds), disability-adjusted life-years (dalys), summary exposure values (sevs), and attributable risk. we compared the observed results with expected values estimated based on the socio-demographic index (sdi). findings stroke and ischaemic heart disease were the leading causes of death and dalys at the national level in china in 2017. age-standardised dalys per 100 000 population decreased by 33·1% (95% uncertainty interval 29·8 to 37·4) for stroke and increased by 4·6% (-3·3 to 10·7) for ischaemic heart disease from 1990 to 2017. age-standardised stroke, ischaemic heart disease, lung cancer, chronic obstructive pulmonary disease, and liver cancer were the five leading causes of ylls in 2017. musculoskeletal disorders, mental health disorders, and sense organ diseases were the three leading causes of ylds in 2017, and high systolic blood pressure, smoking, high-sodium diet, and ambient particulate matter pollution were among the leading four risk factors contributing to deaths and dalys. all provinces had higher than expected dalys per 100 000 population for liver cancer, with the observed to expected ratio ranging from 2·04 to 6·88. the all-cause age-standardised dalys per 100 000 population were lower than expected in all provinces in 2017, and among the top 20 level 3 causes were lower than expected for ischaemic heart disease, alzheimer's disease, headache disorder, and low back pain. the largest percentage change at the national level in age-standardised sevs among the top ten leading risk factors was in high body-mass index (185%, 95% ui 113·1 to 247·7]), followed by ambient particulate matter pollution (88·5%, 66·4 to 116·4). interpretation china has made substantial progress in reducing the burden of many diseases and disabilities. strategies targeting chronic diseases, particularly in the elderly, should be prioritised in the expanding chinese health-care system. funding china national key research and development program and bill & melinda gates foundation.",0
"introduction in the beginning of 2020, an unexpected outbreak due to a new corona virus made the headlines all over the world. exponential growth in the number of those affected makes this virus such a threat. the current meta-analysis aimed to estimate the prevalence of underlying disorders in hospitalized covid-19 patients. methods a comprehensive systematic search was performed on pubmed, scopus, web of science, and google scholar, to find articles published until 15 february 2020. all relevant articles that reported clinical characteristics and epidemiological information of hospitalized covid-19 patients were included in the analysis. results the data of 76993 patients presented in 10 articles were included in this study. according to the meta-analysis, the pooled prevalence of hypertension, cardiovascular disease, smoking history and diabetes in people infected with sars-cov-2 were estimated as 16.37% (95%ci: 10.15%-23.65%), 12.11% (95%ci 4.40%-22.75%), 7.63% (95%ci 3.83%-12.43%) and 7.87% (95%ci 6.57%-9.28%), respectively. conclusion according to the findings of the present study, hypertension, cardiovascular diseases, diabetes mellitus, smoking, chronic obstructive pulmonary disease (copd), malignancy, and chronic kidney disease were among the most prevalent underlying diseases among hospitalized covid-19 patients, respectively.",0
"background guidelines differ about the value of assessment of adiposity measures for cardiovascular disease risk prediction when information is available for other risk factors. we studied the separate and combined associations of body-mass index (bmi), waist circumference, and waist-to-hip ratio with risk of first-onset cardiovascular disease. methods we used individual records from 58 cohorts to calculate hazard ratios (hrs) per 1 sd higher baseline values (4.56 kg/m(2) higher bmi, 12.6 cm higher waist circumference, and 0.083 higher waist-to-hip ratio) and measures of risk discrimination and reclassification. serial adiposity assessments were used to calculate regression dilution ratios. results individual records were available for 221,934 people in 17 countries (14,297 incident cardiovascular disease outcomes; 1.87 million person-years at risk). serial adiposity assessments were made in up to 63,821 people (mean interval 5.7 years ). in people with bmi of 20 kg/m(2) or higher, hrs for cardiovascular disease were 1.23 (95% ci 1.17-1.29) with bmi, 1.27 (1.20-1.33) with waist circumference, and 1.25 (1.19-1.31) with waist-to-hip ratio, after adjustment for age, sex, and smoking status. after further adjustment for baseline systolic blood pressure, history of diabetes, and total and hdl cholesterol, corresponding hrs were 1.07 (1.03-1.11) with bmi, 1.10 (1.05-1.14) with waist circumference, and 1.12 (1.08-1.15) with waist-to-hip ratio. addition of information on bmi, waist circumference, or waist-to-hip ratio to a cardiovascular disease risk prediction model containing conventional risk factors did not importantly improve risk discrimination (c-index changes of -0.0001, -0.0001, and 0.0008, respectively), nor classification of participants to categories of predicted 10-year risk (net reclassification improvement -0.19%, -0.05%, and -0.05%, respectively). findings were similar when adiposity measures were considered in combination. reproducibility was greater for bmi (regression dilution ratio 0.95, 95% ci 0.93-0.97) than for waist circumference (0.86, 0.83-0.89) or waist-to-hip ratio (0.63, 0.57-0.70). interpretation bmi, waist circumference, and waist-to-hip ratio, whether assessed singly or in combination, do not importantly improve cardiovascular disease risk prediction in people in developed countries when additional information is available for systolic blood pressure, history of diabetes, and lipids. funding british heart foundation and uk medical research council.",0
"recurrent microdeletions and microduplications of a 600-kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders. we report the association of 16p11.2 microduplications with schizophrenia in two large cohorts. the microduplication was detected in 12/1,906 (0.63%) cases and 1/3,971 (0.03%) controls (p = 1.2 x 10(-5), or = 25.8) from the initial cohort, and in 9/2,645 (0.34%) cases and 1/2,420 (0.04%) controls (p = 0.022, or = 8.3) of the replication cohort. the 16p11.2 microduplication was associated with a 14.5-fold increased risk of schizophrenia (95% ci (3.3, 62)) in the combined sample. a meta-analysis of datasets for multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia (p = 4.8 x 10(-7)), bipolar disorder (p = 0.017) and autism (p = 1.9 x 10(-7)). in contrast, the reciprocal microdeletion was associated only with autism and developmental disorders (p = 2.3 x 10(-13)). head circumference was larger in patients with the microdeletion than in patients with the microduplication (p = 0.0007).",0
"the universal protein resource (uniprot) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. formed by uniting the swiss-prot, trembl and pir protein database activities, the uniprot consortium produces three layers of protein sequence databases: the uniprot archive (uniparc), the uniprot knowledgebase (uniprot) and the uniprot reference (uniref) databases. the uniprot knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. this centrepiece consists of two sections: uniprot/swiss-prot, with fully, manually curated entries; and uniprot/trembl, enriched with automated classification and annotation. during 2004, tens of thousands of knowledgebase records got manually annotated or updated; we introduced a new comment line topic: toxic dose to store information on the acute toxicity of a toxin; the uniprot keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. furthermore, we introduced a new documentation file of the strains and their synonyms. many new database cross-references were introduced and we started to make use of digital object identifiers. we also achieved in collaboration with the macromolecular structure database group at ebi an improved integration with structural databases by residue level mapping of sequences from the protein data bank entries onto corresponding uniprot entries. for convenient sequence searches we provide the uniref non-redundant sequence databases. the comprehensive uniparc database stores the complete body of publicly available protein sequence data. the uniprot databases can be accessed online ( or downloaded in several formats (ftp://ftp.uniprot.org/pub). new releases are published every two weeks.",0
"cases of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection in manaus, brazil, resurged in late 2020 despite previously high levels of infection. genome sequencing of viruses sampled in manaus between november 2020 and january 2021 revealed the emergence and circulation of a novel sars-cov-2 variant of concern. lineage p.1 acquired 17 mutations, including a trio in the spike protein (k417t, e484k, and n501y) associated with increased binding to the human ace2 (angiotensin-converting enzyme 2) receptor. molecular clock analysis shows that p.1 emergence occurred around mid-november 2020 and was preceded by a period of faster molecular evolution. using a two-category dynamical model that integrates genomic and mortality data, we estimate that p.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-p.1) infection provides 54 to 79% of the protection against infection with p.1 that it provides against non-p.1 lineages. enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.",0
"background medical image segmentation is an important image processing step. comparing images to evaluate the quality of segmentation is an essential part of measuring progress in this research area. some of the challenges in evaluating medical segmentation are: metric selection, the use in the literature of multiple definitions for certain metrics, inefficiency of the metric calculation implementations leading to difficulties with large volumes, and lack of support for fuzzy segmentation by existing metrics. result first we present an overview of 20 evaluation metrics selected based on a comprehensive literature review. for fuzzy segmentation, which shows the level of membership of each voxel to multiple classes, fuzzy definitions of all metrics are provided. we present a discussion about metric properties to provide a guide for selecting evaluation metrics. finally, we propose an efficient evaluation tool implementing the 20 selected metrics. the tool is optimized to perform efficiently in terms of speed and required memory, also if the image size is extremely large as in the case of whole body mri or ct volume segmentation. an implementation of this tool is available as an open source project. conclusion we propose an efficient evaluation tool for 3d medical image segmentation using 20 evaluation metrics and provide guidelines for selecting a subset of these metrics that is suitable for the data and the segmentation task.",0
"neuronal connectivity is fundamental to information processing in the brain. therefore, understanding the mechanisms of sensory processing requires uncovering how connection patterns between neurons relate to their function. on a coarse scale, long-range projections can preferentially link cortical regions with similar responses to sensory stimuli. but on the local scale, where dendrites and axons overlap substantially, the functional specificity of connections remains unknown. here we determine synaptic connectivity between nearby layer 2/3 pyramidal neurons in vitro, the response properties of which were first characterized in mouse visual cortex in vivo. we found that connection probability was related to the similarity of visually driven neuronal activity. neurons with the same preference for oriented stimuli connected at twice the rate of neurons with orthogonal orientation preferences. neurons responding similarly to naturalistic stimuli formed connections at much higher rates than those with uncorrelated responses. bidirectional synaptic connections were found more frequently between neuronal pairs with strongly correlated visual responses. our results reveal the degree of functional specificity of local synaptic connections in the visual cortex, and point to the existence of fine-scale subnetworks dedicated to processing related sensory information.",0
"protein aggregates and damaged organelles are tagged with ubiquitin chains to trigger selective autophagy. to initiate mitophagy, the ubiquitin kinase pink1 phosphorylates ubiquitin to activate the ubiquitin ligase parkin, which builds ubiquitin chains on mitochondrial outer membrane proteins, where they act to recruit autophagy receptors. using genome editing to knockout five autophagy receptors in hela cells, here we show that two receptors previously linked to xenophagy, ndp52 and optineurin, are the primary receptors for pink1- and parkin-mediated mitophagy. pink1 recruits ndp52 and optineurin, but not p62, to mitochondria to activate mitophagy directly, independently of parkin. once recruited to mitochondria, ndp52 and optineurin recruit the autophagy factors ulk1, dfcp1 and wipi1 to focal spots proximal to mitochondria, revealing a function for these autophagy receptors upstream of lc3. this supports a new model in which pink1-generated phospho-ubiquitin serves as the autophagy signal on mitochondria, and parkin then acts to amplify this signal. this work also suggests direct and broader roles for ubiquitin phosphorylation in other autophagy pathways.",0
"sewage, a complex mixture of organic and inorganic chemicals, is considered to be a major source of environmental pollution. a random screen of 20 organic man-made chemicals present in liquid effluents revealed that half appeared able to interact with the estradiol receptor. this was demonstrated by their ability to inhibit binding of 17 beta-estradiol to the fish estrogen receptor. further studies, using mammalian estrogen screens in vitro, revealed that the two phthalate esters butylbenzyl phthalate (bbp) and di-n-butylphthalate (dbp) and a food antioxidant, butylated hydroxyanisole (bha) were estrogenic; however, they were all less estrogenic than the environmental estrogen octylphenol. phthalate esters, used in the production of various plastics (including pvc), are among the most common industrial chemicals. their ubiquity in the environment and tendency to bioconcentrate in animal fat are well known. neither bbp nor dbp were able to act as antagonists, indicating that, in the presence of endogenous estrogens, their overall effect would be cumulative. recently, it has been suggested that environmental estrogens may be etiological agents in several human diseases, including disorders of the male reproductive tract and breast and testicular cancers. the current finding that some phthalate compounds and some food additives are weakly estrogenic in vitro, needs to be supported by further studies on their effects in vivo before any conclusions can be made regarding their possible role in the development of these conditions.",0
"approximately one-third of all mammalian genes are essential for life. phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. as part of the international mouse phenotyping consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. using a standardized phenotyping platform that incorporates high-resolution 3d imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. in addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.",0
"the unique immunomodulatory properties of mesenchymal stem cells (mscs) make them an invaluable cell type for the repair of tissue/ organ damage caused by chronic inflammation or autoimmune disorders. although they hold great promise in the treatment of immune disorders such as graft versus host disease (gvhd) and allergic disorders, there remain many challenges to overcome before their widespread clinical application. an understanding of the biological properties of mscs will clarify the mechanisms of msc-based transplantation for immunomodulation. in this review, we summarize the preclinical and clinical studies of mscs from different adult tissues, discuss the current hurdles to their use and propose the future development of pluripotent stem cell-derived mscs as an approach to immunomodulation therapy.",0
"the transcription factor nf-κb regulates multiple aspects of innate and adaptive immune functions and serves as a pivotal mediator of inflammatory responses. nf-κb induces the expression of various pro-inflammatory genes, including those encoding cytokines and chemokines, and also participates in inflammasome regulation. in addition, nf-κb plays a critical role in regulating the survival, activation and differentiation of innate immune cells and inflammatory t cells. consequently, deregulated nf-κb activation contributes to the pathogenic processes of various inflammatory diseases. in this review, we will discuss the activation and function of nf-κb in association with inflammatory diseases and highlight the development of therapeutic strategies based on nf-κb inhibition.",0
"importance coronavirus disease 2019 (covid-19) continues to cause considerable morbidity and mortality worldwide. case reports of hospitalized patients suggest that covid-19 prominently affects the cardiovascular system, but the overall impact remains unknown. objective to evaluate the presence of myocardial injury in unselected patients recently recovered from covid-19 illness. design, setting, and participants in this prospective observational cohort study, 100 patients recently recovered from covid-19 illness were identified from the university hospital frankfurt covid-19 registry between april and june 2020. exposure recent recovery from severe acute respiratory syndrome coronavirus 2 infection, as determined by reverse transcription-polymerase chain reaction on swab test of the upper respiratory tract. main outcomes and measures demographic characteristics, cardiac blood markers, and cardiovascular magnetic resonance (cmr) imaging were obtained. comparisons were made with age-matched and sex-matched control groups of healthy volunteers (n = 50) and risk factor-matched patients (n = 57). results of the 100 included patients, 53 (53%) were male, and the mean (sd) age was 49 (14) years. the median (iqr) time interval between covid-19 diagnosis and cmr was 71 (64-92) days. of the 100 patients recently recovered from covid-19, 67 (67%) recovered at home, while 33 (33%) required hospitalization. at the time of cmr, high-sensitivity troponin t (hstnt) was detectable (greater than 3 pg/ml) in 71 patients recently recovered from covid-19 (71%) and significantly elevated (greater than 13.9 pg/ml) in 5 patients (5%). compared with healthy controls and risk factor-matched controls, patients recently recovered from covid-19 had lower left ventricular ejection fraction, higher left ventricle volumes, and raised native t1 and t2. a total of 78 patients recently recovered from covid-19 (78%) had abnormal cmr findings, including raised myocardial native t1 (n = 73), raised myocardial native t2 (n = 60), myocardial late gadolinium enhancement (n = 32), or pericardial enhancement (n = 22). there was a small but significant difference between patients who recovered at home vs in the hospital for native t1 mapping (median , 1119 ms vs 1141 ms; p = .008) and hstnt (4.2 pg/dl vs 6.3 pg/dl; p = .002) but not for native t2 mapping. none of these measures were correlated with time from covid-19 diagnosis (native t1: r = 0.07; p = .47; native t2: r = 0.14; p = .15; hstnt: r = -0.07; p = .50). high-sensitivity troponin t was significantly correlated with native t1 mapping (r = 0.33; p conclusions and relevance in this study of a cohort of german patients recently recovered from covid-19 infection, cmr revealed cardiac involvement in 78 patients (78%) and ongoing myocardial inflammation in 60 patients (60%), independent of preexisting conditions, severity and overall course of the acute illness, and time from the original diagnosis. these findings indicate the need for ongoing investigation of the long-term cardiovascular consequences of covid-19.",0
"the abcd study is recruiting and following the brain development and health of over 10,000 9-10 year olds through adolescence. the imaging component of the study was developed by the abcd data analysis and informatics center (daic) and the abcd imaging acquisition workgroup. imaging methods and assessments were selected, optimized and harmonized across all 21 sites to measure brain structure and function relevant to adolescent development and addiction. this article provides an overview of the imaging procedures of the abcd study, the basis for their selection and preliminary quality assurance and results that provide evidence for the feasibility and age-appropriateness of procedures and generalizability of findings to the existent literature.",0
"acetylcholinesterase is involved in the termination of impulse transmission by rapid hydrolysis of the neurotransmitter acetylcholine in numerous cholinergic pathways in the central and peripheral nervous systems. the enzyme inactivation, induced by various inhibitors, leads to acetylcholine accumulation, hyperstimulation of nicotinic and muscarinic receptors, and disrupted neurotransmission. hence, acetylcholinesterase inhibitors, interacting with the enzyme as their primary target, are applied as relevant drugs and toxins. this review presents an overview of toxicology and pharmacology of reversible and irreversible acetylcholinesterase inactivating compounds. in the case of reversible inhibitors being commonly applied in neurodegenerative disorders treatment, special attention is paid to currently approved drugs (donepezil, rivastigmine and galantamine) in the pharmacotherapy of alzheimer's disease, and toxic carbamates used as pesticides. subsequently, mechanism of irreversible acetylcholinesterase inhibition induced by organophosphorus compounds (insecticides and nerve agents), and their specific and nonspecific toxic effects are described, as well as irreversible inhibitors having pharmacological implementation. in addition, the pharmacological treatment of intoxication caused by organophosphates is presented, with emphasis on oxime reactivators of the inhibited enzyme activity administering as causal drugs after the poisoning. besides, organophosphorus and carbamate insecticides can be detoxified in mammals through enzymatic hydrolysis before they reach targets in the nervous system. carboxylesterases most effectively decompose carbamates, whereas the most successful route of organophosphates detoxification is their degradation by corresponding phosphotriesterases.",0
"tight junctions (tjs) in endothelial cells are thought to determine vascular permeability. recently, claudin-1 to -15 were identified as major components of tj strands. among these, claudin-5 (also called transmembrane protein deleted in velo-cardio-facial syndrome ) was expressed ubiquitously, even in organs lacking epithelial tissues, suggesting the possible involvement of this claudin species in endothelial tjs. we then obtained a claudin-6-specific polyclonal antibody and a polyclonal antibody that recognized both claudin-5/tmvcf and claudin-6. in the brain and lung, immunofluorescence microscopy with these polyclonal antibodies showed that claudin-5/tmvcf was exclusively concentrated at cell-cell borders of endothelial cells of all segments of blood vessels, but not at those of epithelial cells. immunoreplica electron microscopy revealed that claudin-5/tmvcf was a component of tj strands. in contrast, in the kidney, the claudin-5/tmvcf signal was restricted to endothelial cells of arteries, but was undetectable in those of veins and capillaries. in addition, in all other tissues we examined, claudin-5/tmvcf was specifically detected in endothelial cells of some segments of blood vessels, but not in epithelial cells. furthermore, when claudin-5/tmvcf cdna was introduced into mouse l fibroblasts, tj strands were reconstituted that resembled those in endothelial cells in vivo, i.e., the extracellular face-associated tjs. these findings indicated that claudin-5/tmvcf is an endothelial cell-specific component of tj strands.",0
"recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. here we analyze a broad set of functional elements, including cell type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (gwas) of 17 complex diseases and traits with an average sample size of 73,599. to enable this analysis, we introduce a new method, stratified ld score regression, for partitioning heritability from gwas summary statistics while accounting for linked markers. this new method is computationally tractable at very large sample sizes and leverages genome-wide information. our findings include a large enrichment of heritability in conserved regions across many traits, a very large immunological disease-specific enrichment of heritability in fantom5 enhancers and many cell type-specific enrichments, including significant enrichment of central nervous system cell types in the heritability of body mass index, age at menarche, educational attainment and smoking behavior.",0
"background bcg vaccination provides incomplete protection against tuberculosis in infants. a new vaccine, modified vaccinia ankara virus expressing antigen 85a (mva85a), was designed to enhance the protective efficacy of bcg. we aimed to assess safety, immunogenicity, and efficacy of mva85a against tuberculosis and mycobacterium tuberculosis infection in infants. methods in our double-blind, randomised, placebo-controlled phase 2b trial, we enrolled healthy infants (aged 4–6 months) without hiv infection who had previously received bcg vaccination. we randomly allocated infants (1:1), according to an independently generated sequence with block sizes of four, to receive one intradermal dose of mva85a or an equal volume of candida skin test antigen as placebo at a clinical facility in a rural region near cape town, south africa. we actively followed up infants every 3 months for up to 37 months. the primary study outcome was safety (incidence of adverse and serious adverse events) in all vaccinated participants, but we also assessed efficacy in a protocol-defined group of participants who received at least one dose of allocated vaccine. the primary efficacy endpoint was incident tuberculosis incorporating microbiological, radiological, and clinical criteria, and the secondary efficacy endpoint was m tuberculosis infection according to quantiferon tb gold in-tube conversion (cellestis, australia). this trial was registered with the south african national clinical trials register (doh-27-0109-2654) and with clinicaltrials.gov on july 31, 2009, number nct00953927. findings between july 15, 2009, and may 4, 2011, we enrolled 2797 infants (1399 allocated mva85a and 1398 allocated placebo). median follow-up in the per-protocol population was 24·6 months (iqr 19·2–28·1), and did not differ between groups. more infants who received mva85a than controls had at least one local adverse event (1251 of 1399 mva85a recipients and 628 of 1396 controls who received the allocated intervention) but the numbers of infants with systemic adverse events (1120 and 1059 ) or serious adverse events (257 and 258 (18%) did not differ between groups. none of the 648 serious adverse events in these 515 infants was related to mva85a. 32 (2%) of 1399 mva85a recipients met the primary efficacy endpoint (tuberculosis incidence of 1·15 per 100 person-years ; with conversion in 178 of 1398 infants ) as did 39 (3%) of 1395 controls (1·39 per 100 person-years ; with conversion in 171 of 1394 infants ). efficacy against tuberculosis was 17·3% (95% ci −31·9 to 48·2) and against m tuberculosis infection was −3·8% (–28·1 to 15·9). interpretation mva85a was well tolerated and induced modest cell-mediated immune responses. reasons for the absence of mva85a efficacy against tuberculosis or m tuberculosis infection in infants need exploration. funding aeras, wellcome trust, and oxford-emergent tuberculosis consortium (oetc).",0
"the role of lipid rafts in t cell antigen receptor (tcr) signaling was investigated using fluorescence microscopy. lipid rafts labeled with cholera toxin b subunit (ct-b) and cross-linked into patches displayed characteristics of rafts isolated biochemically, including detergent resistance and colocalization with raft-associated proteins. lck, lat, and the tcr all colocalized with lipid patches, although tcr association was sensitive to nonionic detergent. aggregation of the tcr by anti-cd3 mab cross-linking also caused coaggregation of raft-associated proteins. however, the protein tyrosine phosphatase cd45 did not colocalize to either ct-b or cd3 patches. cross-linking of either cd3 or ct-b strongly induced tyrosine phosphorylation and recruitment of a zap-70(sh2)(2)-green fluorescent protein (gfp) fusion protein to the lipid patches. also, ct-b patching induced signaling events analagous to tcr stimulation, with the same dependence on expression of key tcr signaling molecules. targeting of lck to rafts was necessary for these events, as a nonraft- associated transmembrane lck chimera, which did not colocalize with tcr patches, could not reconstitute ct-b-induced signaling. thus, our results indicate a mechanism whereby tcr engagement promotes aggregation of lipid rafts, which facilitates colocalization of lck, lat, and the tcr whilst excluding cd45, thereby triggering protein tyrosine phosphorylation.",0
"we analyzed the interaction between human peripheral blood natural killer (nk) cells and monocyte-derived immature dendritic cells (dc). fresh nk cells were activated, as indicated by the induced expression of the cd69 antigen, and their cytolytic activity was strongly augmented by contact with lipopolysaccharide (lps)-treated mature dc, or with immature dc in the presence of the maturation stimuli lps, mycobacterium tuberculosis or interferon (ifn)-alpha. reciprocally, fresh nk cells cultured with immature dc in the presence of the maturation stimuli strongly enhanced dc maturation and interleukin (il)-12 production. il-2--activated nk cells directly induced maturation of dc and enhanced their ability to stimulate allogeneic naive cd4(+) t cells. the effects of nk cells were cell contact dependent, although the secretion of ifn-gamma and tnf also contributed to dc maturation. within peripheral blood lymphocytes the reciprocal activating interaction with dc was restricted to nk cells, because the other lymphocyte subsets were neither induced to express cd69, nor induced to mature in contact with dc. these data demonstrated for the first time a bidirectional cross talk between nk cells and dc, in which nk cells activated by il-2 or by mature dc induce dc maturation.",0
"the emergence of the highly transmissible b.1.1.529 omicron variant of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is concerning for antibody countermeasure efficacy because of the number of mutations in the spike protein. in this study, we tested a panel of anti-receptor-binding domain monoclonal antibodies (mabs) corresponding to those in clinical use by vir biotechnology (s309, the parent mab of vir-7831 (sotrovimab)), astrazeneca (cov2-2196 and cov2-2130, the parent mabs of azd8895 and azd1061), regeneron (regn10933 and regn10987), eli lilly (ly-cov555 and ly-cov016) and celltrion (ct-p59) for their ability to neutralize an infectious b.1.1.529 omicron isolate. several mabs (ly-cov555, ly-cov016, regn10933, regn10987 and ct-p59) completely lost neutralizing activity against b.1.1.529 virus in both vero-tmprss2 and vero-hace2-tmprss2 cells, whereas others were reduced (cov2-2196 and cov2-2130 combination, ~12-fold decrease) or minimally affected (s309). our results suggest that several, but not all, of the antibodies in clinical use might lose efficacy against the b.1.1.529 omicron variant.",0
"we describe the results of a systematic study, using electron microscopy, of the effects of ionic strength on the morphology of chromatin and of h1-depleted chromatin. with increasing ionic strength, chromatin folds up progressively from a filament of nucleosomes at approximately 1 mm monovalent salt through some intermediate higher-order helical structures (thoma, f., and t. koller, 1977, cell 12:101-107) with a fairly constant pitch but increasing numbers of nucleosomes per turn, until finally at 60 mm (or else in approximately 0.3 mm mg++) a thick fiber of 250 a diameter is formed, corresponding to a structurally well-organized but not perfectly regular superhelix or solenoid of pitch approximately 110 a as described by finch and klug (1976, proc. natl. acad. sci. u.s.a. 73:1897-1901). the numbers of nucleosomes per turn of the helical structures agree well with those which can be calculated from the light-scattering data of campbell et al. (1978, nucleic acids res. 5:1571-1580). h1-depleted chromatin also condenses with increasing ionic strength but not so densely as chromatin and not into a definite structure with a well-defined fiber direction. at very low ionic strengths, nucleosomes are present in chromatin but not in h1-depleted chromatin which has the form of an unravelled filament. at somewhat higher ionic strengths (greater than 5 mm triethanolamine chloride), nucleosomes are visible in both types of specimen but the fine details are different. in chromatin containing h1, the dna enters and leaves the nucleosome on the same side but in chromatin depleted of h1 the entrance and exit points are much more random and more or less on opposite sides of the nucleosome. we conclude that h1 stabilizes the nucleosome and is located in the region of the exit and entry points of the dna. this result is correlated with biochemical and x-ray crystallographic results on the internal structure of the nucleosome core to give a picture of a nucleosome in which h1 is bound to the unique region on a complete two-turn, 166 base pair particle (fig. 15). in the formation of higher-order structures, these regions on neighboring nucleosomes come closer together so that an h1 polymer may be formed in the center of the superhelical structures.",0
"circulating tumor dna (ctdna) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctdna detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. here we introduce cancer personalized profiling by deep sequencing (capp-seq), an economical and ultrasensitive method for quantifying ctdna. we implemented capp-seq for non-small-cell lung cancer (nsclc) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. we detected ctdna in 100% of patients with stage ii-iv nsclc and in 50% of patients with stage i, with 96% specificity for mutant allele fractions down to ∼0.02%. levels of ctdna were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctdna levels allowed for earlier response assessment than radiographic approaches. finally, we evaluated biopsy-free tumor screening and genotyping with capp-seq. we envision that capp-seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.",0
"purpose of review mendelian randomization (mr) is a strategy for evaluating causality in observational epidemiological studies. mr exploits the fact that genotypes are not generally susceptible to reverse causation and confounding, due to their fixed nature and mendel's first and second laws of inheritance. mr has the potential to provide information on causality in many situations where randomized controlled trials are not possible, but the results of mr studies must be interpreted carefully to avoid drawing erroneous conclusions. recent findings in this review, we outline the principles behind mr, as well as assumptions and limitations of the method. extensions to the basic approach are discussed, including two-sample mr, bidirectional mr, two-step mr, multivariable mr, and factorial mr. we also consider some new applications and recent developments in the methodology, including its ability to inform drug development, automation of the method using tools such as mr-base, and phenome-wide and hypothesis-free mr. summary in conjunction with the growing availability of large-scale genomic databases, higher level of automation and increased robustness of the methods, mr promises to be a valuable strategy to examine causality in complex biological/omics networks, inform drug development and prioritize intervention targets for disease prevention in the future.",0
"in addition to the previously characterized viruses bk and jc, three new human polyomaviruses (pys) have been recently identified: kiv, wuv, and merkel cell py (mcv). using an elisa employing recombinant vp1 capsid proteins, we have determined the seroprevalence of kiv, wuv, and mcv, along with bkv and jcv, and the monkey viruses sv40 and lpv. soluble vp1 proteins were used to assess crossreactivity between viruses. we found the seroprevalence (+/- 1%) in healthy adult blood donors (1501) was sv40 (9%), bkv (82%), jcv (39%), lpv (15%), kiv (55%), wuv (69%), mcv strain 350 (25%), and mcv strain 339 (42%). competition assays detected no sero-crossreactivity between the vp1 proteins of lpv or mcv or between wuv and kiv. there was considerable sero-crossreactivity between sv40 and bkv, and to a lesser extent, between sv40 and jcv vp1 proteins. after correcting for crossreactivity, the sv40 seroprevalence was approximately 2%. the seroprevalence in children under 21 years of age (n = 721) for all pys was similar to that of the adult population, suggesting that primary exposure to these viruses likely occurs in childhood.",0
"animals respond to stress by activating a wide array of behavioral and physiological responses that are collectively referred to as the stress response. corticotropin-releasing factor (crf) plays a central role in the stress response by regulating the hypothalamic-pituitary-adrenal (hpa) axis. in response to stress, crf initiates a cascade of events that culminate in the release of glucocorticoids from the adrenal cortex. as a result of the great number of physiological and behavioral effects exerted by glucocorticoids, several mechanisms have evolved to control hpa axis activation and integrate the stress response. glucocorticoid feedback inhibition plays a prominent role in regulating the magnitude and duration of glucocorticoid release. in addition to glucocorticoid feedback, the hpa axis is regulated at the level of the hypothalamus by a diverse group of afferent projections from limbic, midbrain, and brain stem nuclei. the stress response is also mediated in part by brain stem noradrenergic neurons, sympathetic andrenomedullary circuits, and parasympathetic systems. in summary, the aim of this review is to discuss the role of the hpa axis in the integration of adaptive responses to stress. we also identify and briefly describe the major neuronal and endocrine systems that contribute to the regulation of the hpa axis and the maintenance of homeostasis in the face of aversive stimuli.",0
"acute lung injury in humans is characterized histopathologically by neutrophilic alveolitis, injury of the alveolar epithelium and endothelium, hyaline membrane formation, and microvascular thrombi. different animal models of experimental lung injury have been used to investigate mechanisms of lung injury. most are based on reproducing in animals known risk factors for ards, such as sepsis, lipid embolism secondary to bone fracture, acid aspiration, ischemia-reperfusion of pulmonary or distal vascular beds, and other clinical risks. however, none of these models fully reproduces the features of human lung injury. the goal of this review is to summarize the strengths and weaknesses of existing models of lung injury. we review the specific features of human ards that should be modeled in experimental lung injury and then discuss specific characteristics of animal species that may affect the pulmonary host response to noxious stimuli. we emphasize those models of lung injury that are based on reproducing risk factors for human ards in animals and discuss the advantages and disadvantages of each model and the extent to which each model reproduces human ards. the present review will help guide investigators in the design and interpretation of animal studies of acute lung injury.",0
"subpopulations of thymus-derived t lymphocytes bearing receptors for either igm or igg molecules were isolated from human peripheral blood. those with receptors for igm (t.m) provided help in a cell dose-dependent fashion for the pokeweed mitogen-induced differentiation of b lymphocytes in vitro, whereas cells with receptors for igg (t.g) did not. t.g cells, on the hand, efficiently suppressed the differentiation and proliferation of b cells in the pokeweed system in the presence of helper t.m cells. this suppressive activity of t.g cells required prior interaction of the t.g cells with immune complexes. the helper activity of t.m cells was relatively radioresistant while the suppressor activity of t.g cells was radiosensitive. the results indicate that helper and suppressor functions of human t lymphocytes in this model system are mediated by different subpopulations of t cells which can be distinguished by their ability to bind igm or igg immune complexes, respectively.",0
"objective to individuate a novel sex-specific index, based on waist circumference, bmi, triglycerides, and hdl cholesterol, indirectly expressing visceral fat function. research design and methods visceral adiposity index (vai) was first modeled on 315 nonobese healthy subjects. using two multiple logistic regression models, vai was retrospectively validated in 1,498 primary care patients in comparison to classical cardio- and cerebrovascular risk factors. results all components of metabolic syndrome increased significantly across vai quintiles. vai was independently associated with both cardiovascular (odd ratio 2.45; 95% ci 1.52-3.95; p conclusions our study suggests vai is a valuable indicator of ""visceral adipose function"" and insulin sensitivity, and its increase is strongly associated with cardiometabolic risk.",0
"metabolomic discovery of biomarkers of type 2 diabetes (t2d) risk may reveal etiological pathways and help to identify individuals at risk for disease. we prospectively investigated the association between serum metabolites measured by targeted metabolomics and risk of t2d in the european prospective investigation into cancer and nutrition (epic)-potsdam (27,548 adults) among all incident cases of t2d (n = 800, mean follow-up 7 years) and a randomly drawn subcohort (n = 2,282). flow injection analysis tandem mass spectrometry was used to quantify 163 metabolites, including acylcarnitines, amino acids, hexose, and phospholipids, in baseline serum samples. serum hexose; phenylalanine; and diacyl-phosphatidylcholines c32:1, c36:1, c38:3, and c40:5 were independently associated with increased risk of t2d and serum glycine; sphingomyelin c16:1; acyl-alkyl-phosphatidylcholines c34:3, c40:6, c42:5, c44:4, and c44:5; and lysophosphatidylcholine c18:2 with decreased risk. variance of the metabolites was largely explained by two metabolite factors with opposing risk associations (factor 1 relative risk in extreme quintiles 0.31 , factor 2 3.82 ). the metabolites significantly improved t2d prediction compared with established risk factors. they were further linked to insulin sensitivity and secretion in the tübingen family study and were partly replicated in the independent kora (cooperative health research in the region of augsburg) cohort. the data indicate that metabolic alterations, including sugar metabolites, amino acids, and choline-containing phospholipids, are associated early on with a higher risk of t2d.",0
"the success of genome-wide association (gwa) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (snp) genotyping for the identification of quantitative trait loci (qtl) and for marker-assisted selection in model and agricultural species. a cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 snp loci to support gwa applications in cattle is described. a novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. the assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 snp are polymorphic within individual breeds (average minor allele frequency (maf) ranging from 0.24 to 0.27). the assay also identified 79 putative copy number variants in cattle. utility for gwa was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. the combination of snp selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. aspects of the approach can be exploited in species which lack an available genome sequence. the bovinesnp50 assay described here is commercially available from illumina and provides a robust platform for mapping disease genes and qtl in cattle.",0
"several types of cells store proteins in secretory vesicles from which they are released by an appropriate stimulus. it might be expected that the secretory vesicles in different cell types use similar molecular machinery. here we describe a transmembrane glycoprotein (mr approximately 100,000) that is present in secretory vesicles in all neurons and endocrine cells studied, in species from elasmobranch fish to mammals, and in neural and endocrine cell lines. it was detected by cross-reactivity with monoclonal antibodies raised to highly purified cholinergic synaptic vesicles from the electric organ of fish. by immunoprecipitation of intact synaptic vesicles and electron microscopic immunoperoxidase labeling, we have shown that the antigenic determinant is on the cytoplasmic face of the synaptic vesicles. however, the electrophoretic mobility of the antigen synthesized in the presence of tunicamycin is reduced to mr approximately 62,000, which suggests that the antigen is glycosylated and must therefore span the vesicle membrane.",0
"post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. however, proteome-wide analysis of endogenous ubiquitylation remains a challenging task, and almost always has relied on cells expressing affinity tagged ubiquitin. here we combine single-step immunoenrichment of ubiquitylated peptides with peptide fractionation and high-resolution mass spectrometry to investigate endogenous ubiquitylation sites. we precisely map 11,054 endogenous putative ubiquitylation sites (diglycine-modified lysines) on 4,273 human proteins. the presented data set covers 67% of the known ubiquitylation sites and contains 10,254 novel sites on proteins with diverse cellular functions including cell signaling, receptor endocytosis, dna replication, dna damage repair, and cell cycle progression. our method enables site-specific quantification of ubiquitylation in response to cellular perturbations and is applicable to any cell type or tissue. global quantification of ubiquitylation in cells treated with the proteasome inhibitor mg-132 discovers sites that are involved in proteasomal degradation, and suggests a nonproteasomal function for almost half of all sites. surprisingly, ubiquitylation of about 15% of sites decreased more than twofold within four hours of mg-132 treatment, showing that inhibition of proteasomal function can dramatically reduce ubiquitylation on many sites with non-proteasomal functions. comparison of ubiquitylation sites with acetylation sites reveals an extensive overlap between the lysine residues targeted by these two modifications. however, the crosstalk between these two post-translational modifications is significantly less frequent on sites that show increased ubiquitylation upon proteasome inhibition. taken together, we report the largest site-specific ubiquitylation dataset in human cells, and for the first time demonstrate proteome-wide, site-specific quantification of endogenous putative ubiquitylation sites.",0
"cannabidiol is a component of marijuana that does not activate cannabinoid receptors, but moderately inhibits the degradation of the endocannabinoid anandamide. we previously reported that an elevation of anandamide levels in cerebrospinal fluid inversely correlated to psychotic symptoms. furthermore, enhanced anandamide signaling let to a lower transition rate from initial prodromal states into frank psychosis as well as postponed transition. in our translational approach, we performed a double-blind, randomized clinical trial of cannabidiol vs amisulpride, a potent antipsychotic, in acute schizophrenia to evaluate the clinical relevance of our initial findings. either treatment was safe and led to significant clinical improvement, but cannabidiol displayed a markedly superior side-effect profile. moreover, cannabidiol treatment was accompanied by a significant increase in serum anandamide levels, which was significantly associated with clinical improvement. the results suggest that inhibition of anandamide deactivation may contribute to the antipsychotic effects of cannabidiol potentially representing a completely new mechanism in the treatment of schizophrenia.",0
"previous studies have indicated that endotoxin and other bacterial and protozoal products can stimulate macrophages to produce a factor that can suppress the activity of the enzyme lipoprotein lipase (lpl), in vivo and in vitro. in the present report we describe the purification of this factor, cachectin, to apparent homogeneity from the conditioned medium of endotoxin-stimulated raw 264.7 cells. the isolated protein has an isoelectric point of 4.7 and a subunit molecular weight of 17,000. although cachectin's isoelectric point and molecular weight are similar to those described for interleukin 1, pure cachectin has no leukocyte-activating factor (laf) activity. cachectin at a concentration of 10(-11) m has the ability to suppress the lpl activity of the 3t3-l1 adipocyte cell line by 80%. binding studies using radio-labeled cachectin and 3t3-l1 adipocytes and c2 myotubules revealed approximately 10(4) high-affinity receptors per cell on both cell types (ka, 3 x 10(9]. cachectin receptors were also present on liver membranes but were absent on erythrocytes and lymphocytes. the isolation of cachectin and characterization of its receptor should facilitate further investigations into the role of cachectin and other macrophage mediators in the metabolic derangements that occur during infection and cachexia.",0
"the primary mission of universal protein resource (uniprot) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. uniprot is produced by the uniprot consortium which consists of groups from the european bioinformatics institute (ebi), the swiss institute of bioinformatics (sib) and the protein information resource (pir). uniprot is comprised of four major components, each optimized for different uses: the uniprot archive, the uniprot knowledgebase, the uniprot reference clusters and the uniprot metagenomic and environmental sequence database. uniprot is updated and distributed every 4 weeks and can be accessed online for searches or download at",0
"mesenchymal stem cells (mscs) are partially defined by their ability to differentiate into tissues including bone, cartilage and adipose in vitro, but it is their trophic, paracrine and immunomodulatory functions that may have the greatest therapeutic impact in vivo. unlike pharmaceutical treatments that deliver a single agent at a specific dose, mscs are site regulated and secrete bioactive factors and signals at variable concentrations in response to local microenvironmental cues. significant progress has been made in understanding the biochemical and metabolic mechanisms and feedback associated with msc response. the anti-inflammatory and immunomodulatory capacity of msc may be paramount in the restoration of localized or systemic conditions for normal healing and tissue regeneration. allogeneic msc treatments, categorized as a drug by regulatory agencies, have been widely pursued, but new studies demonstrate the efficacy of autologous msc therapies, even for individuals affected by a disease state. safety and regulatory concerns surrounding allogeneic cell preparations make autologous and minimally manipulated cell therapies an attractive option for many regenerative, anti-inflammatory and autoimmune applications.",0
"the contribution of rare and low-frequency variants to human traits is largely unexplored. here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. in extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (apob), adiponectin (adipoq) and low-density lipoprotein cholesterol (ldlr and rgag1) from single-marker and rare variant aggregation tests. we describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results.",0
"the generation of invasiveness in transformed cells represents an essential step of tumor progression. we show here, first, that nontransformed madin-darby canine kidney (mdck) epithelial cells acquire invasive properties when intercellular adhesion is specifically inhibited by the addition of antibodies against the cell adhesion molecule uvomorulin; the separated cells then invade collagen gels and embryonal heart tissue. second, mdck cells transformed with harvey and moloney sarcoma viruses are constitutively invasive, and they were found not to express uvomorulin at their cell surface. these data suggest that the loss of adhesive function of uvomorulin (which is identical to e-cadherin and homologous to l-cam) is a critical step in the promotion of epithelial cells to a more malignant, i.e., invasive, phenotype. similar modulation of intercellular adhesion might also occur during invasion of carcinoma cells in vivo.",0
"misinformation about covid-19 is a major threat to public health. using five national samples from the uk ( n = 1050 and n = 1150), ireland ( n = 700), the usa ( n = 700), spain ( n = 700) and mexico ( n = 700), we examine predictors of belief in the most common statements about the virus that contain misinformation. we also investigate the prevalence of belief in covid-19 misinformation across different countries and the role of belief in such misinformation in predicting relevant health behaviours. we find that while public belief in misinformation about covid-19 is not particularly common, a substantial proportion views this type of misinformation as highly reliable in each country surveyed. in addition, a small group of participants find common factual information about the virus highly unreliable. we also find that increased susceptibility to misinformation negatively affects people's self-reported compliance with public health guidance about covid-19, as well as people's willingness to get vaccinated against the virus and to recommend the vaccine to vulnerable friends and family. across all countries surveyed, we find that higher trust in scientists and having higher numeracy skills were associated with lower susceptibility to coronavirus-related misinformation. taken together, these results demonstrate a clear link between susceptibility to misinformation and both vaccine hesitancy and a reduced likelihood to comply with health guidance measures, and suggest that interventions which aim to improve critical thinking and trust in science may be a promising avenue for future research.",0
"therapeutic monoclonal antibodies targeting immune checkpoints (icps) have changed the treatment landscape of many tumors. however, response rate remains relatively low in most cases. a major factor involved in initial resistance to icp inhibitors is the lack or paucity of tumor t cell infiltration, characterizing the so-called ""cold tumors."" in this review, we describe the main mechanisms involved in the absence of t cell infiltration, including lack of tumor antigens, defect in antigen presentation, absence of t cell activation and deficit of homing into the tumor bed. we discuss then the different therapeutic approaches that could turn cold into hot tumors. in this way, specific therapies are proposed according to their mechanism of action. in addition, ''supra-physiological'' therapies, such as t cell recruiting bispecific antibodies and chimeric antigen receptor (car) t cells, may be active regardless of the mechanism involved, especially in mhc class i negative tumors. the determination of the main factors implicated in the lack of preexisting tumor t cell infiltration is crucial for the development of adapted algorithms of treatments for cold tumors.",0
"in microorganisms, noise in gene expression gives rise to cell-to-cell variability in protein concentrations. in mammalian cells, protein levels also vary and individual cells differ widely in their responsiveness to uniform physiological stimuli. in the case of apoptosis mediated by trail (tumour necrosis factor (tnf)-related apoptosis-inducing ligand) it is common for some cells in a clonal population to die while others survive-a striking divergence in cell fate. among cells that die, the time between trail exposure and caspase activation is highly variable. here we image sister cells expressing reporters of caspase activation and mitochondrial outer membrane permeabilization after exposure to trail. we show that naturally occurring differences in the levels or states of proteins regulating receptor-mediated apoptosis are the primary causes of cell-to-cell variability in the timing and probability of death in human cell lines. protein state is transmitted from mother to daughter, giving rise to transient heritability in fate, but protein synthesis promotes rapid divergence so that sister cells soon become no more similar to each other than pairs of cells chosen at random. our results have implications for understanding 'fractional killing' of tumour cells after exposure to chemotherapy, and for variability in mammalian signal transduction in general.",0
"objective to determine the efficacy and safety of liraglutide (a glucagon-like peptide-1 receptor agonist) when added to metformin and rosiglitazone in type 2 diabetes. research design and methods this 26-week, double-blind, placebo-controlled, parallel-group trial randomized 533 subjects (1:1:1) to once-daily liraglutide (1.2 or 1.8 mg) or liraglutide placebo in combination with metformin (1 g twice daily) and rosiglitazone (4 mg twice daily). subjects had type 2 diabetes, a1c 7-11% (previous oral antidiabetes drug monotherapy >or=3 months) or 7-10% (previous oad combination therapy >or=3 months), and bmi results mean a1c values decreased significantly more in the liraglutide groups versus placebo (mean +/- se -1.5 +/- 0.1% for both 1.2 and 1.8 mg liraglutide and -0.5 +/- 0.1% for placebo). fasting plasma glucose decreased by 40, 44, and 8 mg/dl for 1.2 and 1.8 mg and placebo, respectively, and 90-min postprandial glucose decreased by 47, 49, and 14 mg/dl, respectively (p conclusions liraglutide combined with metformin and a thiazolidinedione is a well-tolerated combination therapy for type 2 diabetes, providing significant improvements in glycemic control.",0
"background the sars-cov-2 variant of concern, omicron, appears to be less severe than delta. we aim to quantify the differences in symptom prevalence, risk of hospital admission, and symptom duration among the vaccinated population. methods in this prospective longitudinal observational study, we collected data from participants who were self-reporting test results and symptoms in the zoe covid app (previously known as the covid symptoms study app). eligible participants were aged 16-99 years, based in the uk, with a body-mass index between 15 and 55 kg/m 2 , had received at least two doses of any sars-cov-2 vaccine, were symptomatic, and logged a positive symptomatic pcr or lateral flow result for sars-cov-2 during the study period. the primary outcome was the likelihood of developing a given symptom (of the 32 monitored in the app) or hospital admission within 7 days before or after the positive test in participants infected during omicron prevalence compared with those infected during delta prevalence. findings between june 1, 2021, and jan 17, 2022, we identified 63 002 participants who tested positive for sars-cov-2 and reported symptoms in the zoe app. these patients were matched 1:1 for age, sex, and vaccination dose, across two periods (june 1 to nov 27, 2021, delta prevalent at >70%; n=4990, and dec 20, 2021, to jan 17, 2022, omicron prevalent at >70%; n=4990). loss of smell was less common in participants infected during omicron prevalence than during delta prevalence (16·7% vs 52·7%, odds ratio 0·17; 95% ci 0·16-0·19, p interpretation the prevalence of symptoms that characterise an omicron infection differs from those of the delta sars-cov-2 variant, apparently with less involvement of the lower respiratory tract and reduced probability of hospital admission. our data indicate a shorter period of illness and potentially of infectiousness which should impact work-health policies and public health advice. funding wellcome trust, zoe, national institute for health research, chronic disease research foundation, national institutes of health, and medical research council.",0
"background we conducted meta-analyses examining the effects of endurance, dynamic resistance, combined endurance and resistance training, and isometric resistance training on resting blood pressure (bp) in adults. the aims were to quantify and compare bp changes for each training modality and identify patient subgroups exhibiting the largest bp changes. methods and results randomized controlled trials lasting ≥4 weeks investigating the effects of exercise on bp in healthy adults (age ≥18 years) and published in a peer-reviewed journal up to february 2012 were included. random effects models were used for analyses, with data reported as weighted means and 95% confidence interval. we included 93 trials, involving 105 endurance, 29 dynamic resistance, 14 combined, and 5 isometric resistance groups, totaling 5223 participants (3401 exercise and 1822 control). systolic bp (sbp) was reduced after endurance (-3.5 mm hg ), dynamic resistance (-1.8 mm hg ), and isometric resistance (-10.9 mm hg ) but not after combined training. reductions in diastolic bp (dbp) were observed after endurance (-2.5 mm hg ), dynamic resistance (-3.2 mm hg ), isometric resistance (-6.2 mm hg ), and combined (-2.2 mm hg ) training. bp reductions after endurance training were greater (p conclusion endurance, dynamic resistance, and isometric resistance training lower sbp and dbp, whereas combined training lowers only dbp. data from a small number of isometric resistance training studies suggest this form of training has the potential for the largest reductions in sbp.",0
"background implicit biases involve associations outside conscious awareness that lead to a negative evaluation of a person on the basis of irrelevant characteristics such as race or gender. this review examines the evidence that healthcare professionals display implicit biases towards patients. methods pubmed, psychinfo, psycharticle and cinahl were searched for peer-reviewed articles published between 1st march 2003 and 31st march 2013. two reviewers assessed the eligibility of the identified papers based on precise content and quality criteria. the references of eligible papers were examined to identify further eligible studies. results forty two articles were identified as eligible. seventeen used an implicit measure (implicit association test in fifteen and subliminal priming in two), to test the biases of healthcare professionals. twenty five articles employed a between-subjects design, using vignettes to examine the influence of patient characteristics on healthcare professionals' attitudes, diagnoses, and treatment decisions. the second method was included although it does not isolate implicit attitudes because it is recognised by psychologists who specialise in implicit cognition as a way of detecting the possible presence of implicit bias. twenty seven studies examined racial/ethnic biases; ten other biases were investigated, including gender, age and weight. thirty five articles found evidence of implicit bias in healthcare professionals; all the studies that investigated correlations found a significant positive relationship between level of implicit bias and lower quality of care. discussion the evidence indicates that healthcare professionals exhibit the same levels of implicit bias as the wider population. the interactions between multiple patient characteristics and between healthcare professional and patient characteristics reveal the complexity of the phenomenon of implicit bias and its influence on clinician-patient interaction. the most convincing studies from our review are those that combine the iat and a method measuring the quality of treatment in the actual world. correlational evidence indicates that biases are likely to influence diagnosis and treatment decisions and levels of care in some circumstances and need to be further investigated. our review also indicates that there may sometimes be a gap between the norm of impartiality and the extent to which it is embraced by healthcare professionals for some of the tested characteristics. conclusions our findings highlight the need for the healthcare profession to address the role of implicit biases in disparities in healthcare. more research in actual care settings and a greater homogeneity in methods employed to test implicit biases in healthcare is needed.",0
"background many patients with several concurrent medical conditions (multimorbidity) are seen in the primary care setting. a thorough understanding of outcomes associated with multimorbidity would benefit primary care workers of all disciplines. the purpose of this systematic review was to clarify the relationship between the presence of multimorbidity and the quality of life (qol) or health-related quality of life (hrqol) of patients seen, or likely to be seen, in the primary care setting. methods medline and embase electronic databases were screened using the following search terms for the reference period 1990 to 2003: multimorbidity, comorbidity, chronic disease, and their spelling variations, along with quality of life and health-related quality of life. only descriptive studies relevant to primary care were selected. results of 753 articles screened, 108 were critically assessed for compliance with study inclusion and exclusion criteria. thirty of these studies were ultimately selected for this review, including 7 in which the relationship between multimorbidity or comorbidity and qol or hrqol was the main outcome measure. major limitations of these studies include the lack of a uniform definition for multimorbidity or comorbidity and the absence of assessment of disease severity. the use of self-reported diagnoses may also be a weakness. the frequent exclusion of psychiatric diagnoses and presence of potential confounding variables are other limitations. nonetheless, we did find an inverse relationship between the number of medical conditions and qol related to physical domains. for social and psychological dimensions of qol, some studies reveal a similar inverse relationship in patients with 4 or more diagnoses. conclusions our findings confirm the existence of an inverse relationship between multimorbidity or comorbidy and qol. however, additional studies are needed to clarify this relationship, including the various dimensions of qol affected. those studies must employ a clear definition of multimorbidity or comorbidity and valid ways to measure these concepts in a primary care setting. pursuit of this research will help to better understand the impact of chronic diseases on patients.",0
"background obesity, typically quantified in terms of body mass index (bmi) exceeding threshold values, is considered a leading cause of premature death worldwide. for given body size (bmi), it is recognized that risk is also affected by body shape, particularly as a marker of abdominal fat deposits. waist circumference (wc) is used as a risk indicator supplementary to bmi, but the high correlation of wc with bmi makes it hard to isolate the added value of wc. methods and findings we considered a usa population sample of 14,105 non-pregnant adults (age ≥ 18) from the national health and nutrition examination survey (nhanes) 1999-2004 with follow-up for mortality averaging 5 yr (828 deaths). we developed a body shape index (absi) based on wc adjusted for height and weight: absi ≡ wc/(bmi(2/3)height(1/2)). absi had little correlation with height, weight, or bmi. death rates increased approximately exponentially with above average baseline absi (overall regression coefficient of +33% per standard deviation of absi [95% confidence interval: +20%-+48%), whereas elevated death rates were found for both high and low values of bmi and wc. 22% (8%-41%) of the population mortality hazard was attributable to high absi, compared to 15% (3%-30%) for bmi and 15% (4%-29%) for wc. the association of death rate with absi held even when adjusted for other known risk factors including smoking, diabetes, blood pressure, and serum cholesterol. absi correlation with mortality hazard held across the range of age, sex, and bmi, and for both white and black ethnicities (but not for mexican ethnicity), and was not weakened by excluding deaths from the first 3 yr of follow-up. conclusions body shape, as measured by absi, appears to be a substantial risk factor for premature mortality in the general population derivable from basic clinical measurements. absi expresses the excess risk from high wc in a convenient form that is complementary to bmi and to other known risk factors.",0
"in this brief report, we offer a concise overview on current cancer epidemiology garnered from the official databases of world health organization and american cancer society and provide recent information on frequency, mortality, and survival expectancy of the 15 leading types of cancers worldwide. overall, cancer poses the highest clinical, social, and economic burden in terms of cause-specific disability-adjusted life years (dalys) among all human diseases. the overall 0-74 years risk of developing cancer is 20.2% (22.4% in men and 18.2% in women, respectively). a total number of 18 million new cases have been diagnosed in 2018, the most frequent of which are lung (2.09 million cases), breast (2.09 million cases), and prostate (1.28 million cases) cancers. beside sex-specific malignancies, the ratio of frequency between men and women is >1 for all cancers, except thyroid (i.e., 0.30). as concerns mortality, cancer is the second worldwide cause of death (8.97 million deaths) after ischemic heart disease, but will likely become the first in 2060 (~18.63 million deaths). lung, liver, and stomach are the three most deadly cancers in the general population, while lung and breast cancers are the leading causes of cancer related-mortality in men and women, respectively. prostate and thyroid cancers have the best prognosis, with 5-year survival ~100%, while esophagus, liver, and especially pancreas cancers have the worst prognosis, typically <20% at 5 years. we hope that this report will provide fertile ground for addressing health-care interventions aimed at preventing, diagnosing, and managing cancer around the world.",0
"drug development is a lengthy and costly process that proceeds through several stages from target identification to lead discovery and optimization, preclinical validation and clinical trials culminating in approval for clinical use. an important step in this process is high-throughput screening (hts) of small compound libraries for lead identification. currently, the majority of cell-based hts is being carried out on cultured cells propagated in two-dimensions (2d) on plastic surfaces optimized for tissue culture. at the same time, compelling evidence suggests that cells cultured in these non-physiological conditions are not representative of cells residing in the complex microenvironment of a tissue. this discrepancy is thought to be a significant contributor to the high failure rate in drug discovery, where only a low percentage of drugs investigated ever make it through the gamut of testing and approval to the market. thus, three-dimensional (3d) cell culture technologies that more closely resemble in vivo cell environments are now being pursued with intensity as they are expected to accommodate better precision in drug discovery. here we will review common approaches to 3d culture, discuss the significance of 3d cultures in drug resistance and drug repositioning and address some of the challenges of applying 3d cell cultures to high-throughput drug discovery.",0
"astrocytes are specialized glial cells that outnumber neurons by over fivefold. they contiguously tile the entire central nervous system (cns) and exert many essential complex functions in the healthy cns. astrocytes respond to all forms of cns insults through a process referred to as reactive astrogliosis, which has become a pathological hallmark of cns structural lesions. substantial progress has been made recently in determining functions and mechanisms of reactive astrogliosis and in identifying roles of astrocytes in cns disorders and pathologies. a vast molecular arsenal at the disposal of reactive astrocytes is being defined. transgenic mouse models are dissecting specific aspects of reactive astrocytosis and glial scar formation in vivo. astrocyte involvement in specific clinicopathological entities is being defined. it is now clear that reactive astrogliosis is not a simple all-or-none phenomenon but is a finely gradated continuum of changes that occur in context-dependent manners regulated by specific signaling events. these changes range from reversible alterations in gene expression and cell hypertrophy with preservation of cellular domains and tissue structure, to long-lasting scar formation with rearrangement of tissue structure. increasing evidence points towards the potential of reactive astrogliosis to play either primary or contributing roles in cns disorders via loss of normal astrocyte functions or gain of abnormal effects. this article reviews (1) astrocyte functions in healthy cns, (2) mechanisms and functions of reactive astrogliosis and glial scar formation, and (3) ways in which reactive astrocytes may cause or contribute to specific cns disorders and lesions.",0
"the human brain has often been viewed as outstanding among mammalian brains: the most cognitively able, the largest-than-expected from body size, endowed with an overdeveloped cerebral cortex that represents over 80% of brain mass, and purportedly containing 100 billion neurons and 10x more glial cells. such uniqueness was seemingly necessary to justify the superior cognitive abilities of humans over larger-brained mammals such as elephants and whales. however, our recent studies using a novel method to determine the cellular composition of the brain of humans and other primates as well as of rodents and insectivores show that, since different cellular scaling rules apply to the brains within these orders, brain size can no longer be considered a proxy for the number of neurons in the brain. these studies also showed that the human brain is not exceptional in its cellular composition, as it was found to contain as many neuronal and non-neuronal cells as would be expected of a primate brain of its size. additionally, the so-called overdeveloped human cerebral cortex holds only 19% of all brain neurons, a fraction that is similar to that found in other mammals. in what regards absolute numbers of neurons, however, the human brain does have two advantages compared to other mammalian brains: compared to rodents, and probably to whales and elephants as well, it is built according to the very economical, space-saving scaling rules that apply to other primates; and, among economically built primate brains, it is the largest, hence containing the most neurons. these findings argue in favor of a view of cognitive abilities that is centered on absolute numbers of neurons, rather than on body size or encephalization, and call for a re-examination of several concepts related to the exceptionality of the human brain.",0
"the intervertebral disc is a cartilaginous structure that resembles articular cartilage in its biochemistry, but morphologically it is clearly different. it shows degenerative and ageing changes earlier than does any other connective tissue in the body. it is believed to be important clinically because there is an association of disc degeneration with back pain. current treatments are predominantly conservative or, less commonly, surgical; in many cases there is no clear diagnosis and therapy is considered inadequate. new developments, such as genetic and biological approaches, may allow better diagnosis and treatments in the future.",0
"vascular contributions to cognitive impairment are increasingly recognized 1-5 as shown by neuropathological 6,7 , neuroimaging 4,8-11 , and cerebrospinal fluid biomarker 4,12 studies. moreover, small vessel disease of the brain has been estimated to contribute to approximately 50% of all dementias worldwide, including those caused by alzheimer's disease (ad) 3,4,13 . vascular changes in ad have been typically attributed to the vasoactive and/or vasculotoxic effects of amyloid-β (aβ) 3,11,14 , and more recently tau 15 . animal studies suggest that aβ and tau lead to blood vessel abnormalities and blood-brain barrier (bbb) breakdown 14-16 . although neurovascular dysfunction 3,11 and bbb breakdown develop early in ad 1,4,5,8-10,12,13 , how they relate to changes in the ad classical biomarkers aβ and tau, which also develop before dementia 17 , remains unknown. to address this question, we studied brain capillary damage using a novel cerebrospinal fluid biomarker of bbb-associated capillary mural cell pericyte, soluble platelet-derived growth factor receptor-β 8,18 , and regional bbb permeability using dynamic contrast-enhanced magnetic resonance imaging 8-10 . our data show that individuals with early cognitive dysfunction develop brain capillary damage and bbb breakdown in the hippocampus irrespective of alzheimer's aβ and/or tau biomarker changes, suggesting that bbb breakdown is an early biomarker of human cognitive dysfunction independent of aβ and tau.",0
"objective to determine the clinical manifestations, risk factors, and maternal and perinatal outcomes in pregnant and recently pregnant women with suspected or confirmed coronavirus disease 2019 (covid-19). design living systematic review and meta-analysis. data sources medline, embase, cochrane database, who covid-19 database, china national knowledge infrastructure (cnki), and wanfang databases from 1 december 2019 to 6 october 2020, along with preprint servers, social media, and reference lists. study selection cohort studies reporting the rates, clinical manifestations (symptoms, laboratory and radiological findings), risk factors, and maternal and perinatal outcomes in pregnant and recently pregnant women with suspected or confirmed covid-19. data extraction at least two researchers independently extracted the data and assessed study quality. random effects meta-analysis was performed, with estimates pooled as odds ratios and proportions with 95% confidence intervals. all analyses will be updated regularly. results 192 studies were included. overall, 10% (95% confidence interval 7% to 12%; 73 studies, 67 271 women) of pregnant and recently pregnant women attending or admitted to hospital for any reason were diagnosed as having suspected or confirmed covid-19. the most common clinical manifestations of covid-19 in pregnancy were fever (40%) and cough (41%). compared with non-pregnant women of reproductive age, pregnant and recently pregnant women with covid-19 were less likely to have symptoms (odds ratio 0.28, 95% confidence interval 0.13 to 0.62; i2=42.9%) or report symptoms of fever (0.49, 0.38 to 0.63; i2=40.8%), dyspnoea (0.76, 0.67 to 0.85; i2=4.4%) and myalgia (0.53, 0.36 to 0.78; i2=59.4%). the odds of admission to an intensive care unit (odds ratio 2.13, 1.53 to 2.95; i2=71.2%), invasive ventilation (2.59, 2.28 to 2.94; i2=0%) and need for extra corporeal membrane oxygenation (2.02, 1.22 to 3.34; i2=0%) were higher in pregnant and recently pregnant than non-pregnant reproductive aged women. overall, 339 pregnant women (0.02%, 59 studies, 41 664 women) with confirmed covid-19 died from any cause. increased maternal age (odds ratio 1.83, 1.27 to 2.63; i2=43.4%), high body mass index (2.37, 1.83 to 3.07; i2=0%), any pre-existing maternal comorbidity (1.81, 1.49 to 2.20; i2=0%), chronic hypertension (2.0, 1.14 to 3.48; i2=0%), pre-existing diabetes (2.12, 1.62 to 2.78; i2=0%), and pre-eclampsia (4.21, 1.27 to 14.0; i2=0%) were associated with severe covid-19 in pregnancy. in pregnant women with covid-19, increased maternal age, high body mass index, non-white ethnicity, any pre-existing maternal comorbidity including chronic hypertension and diabetes, and pre-eclampsia were associated with serious complications such as admission to an intensive care unit, invasive ventilation and maternal death. compared to pregnant women without covid-19, those with the disease had increased odds of maternal death (odds ratio 2.85, 1.08 to 7.52; i2=0%), of needing admission to the intensive care unit (18.58, 7.53 to 45.82; i2=0%), and of preterm birth (1.47, 1.14 to 1.91; i2=18.6%). the odds of admission to the neonatal intensive care unit (4.89, 1.87 to 12.81, i2=96.2%) were higher in babies born to mothers with covid-19 versus those without covid-19. conclusion pregnant and recently pregnant women with covid-19 attending or admitted to the hospitals for any reason are less likely to manifest symptoms such as fever, dyspnoea, and myalgia, and are more likely to be admitted to the intensive care unit or needing invasive ventilation than non-pregnant women of reproductive age. pre-existing comorbidities, non-white ethnicity, chronic hypertension, pre-existing diabetes, high maternal age, and high body mass index are risk factors for severe covid-19 in pregnancy. pregnant women with covid-19 versus without covid-19 are more likely to deliver preterm and could have an increased risk of maternal death and of being admitted to the intensive care unit. their babies are more likely to be admitted to the neonatal unit. systematic review registration prospero crd42020178076. readers' note this article is a living systematic review that will be updated to reflect emerging evidence. updates may occur for up to two years from the date of original publication. this version is update 1 of the original article published on 1 september 2020 (bmj 2020;370:m3320), and previous updates can be found as data supplements ( when citing this paper please consider adding the update number and date of access for clarity.",0
"diabetic retinopathy (dr) is the most common complication of diabetes mellitus (dm). it has long been recognized as a microvascular disease. the diagnosis of dr relies on the detection of microvascular lesions. the treatment of dr remains challenging. the advent of anti-vascular endothelial growth factor (vegf) therapy demonstrated remarkable clinical benefits in dr patients; however, the majority of patients failed to achieve clinically-significant visual improvement. therefore, there is an urgent need for the development of new treatments. laboratory and clinical evidence showed that in addition to microvascular changes, inflammation and retinal neurodegeneration may contribute to diabetic retinal damage in the early stages of dr. further investigation of the underlying molecular mechanisms may provide targets for the development of new early interventions. here, we present a review of the current understanding and new insights into pathophysiology in dr, as well as clinical treatments for dr patients. recent laboratory findings and related clinical trials are also reviewed.",0
"the usage and control of recent modifications of the program package xds for the processing of rotation images are described in the context of previous versions. new features include automatic determination of spot size and reflecting range and recognition and assignment of crystal symmetry. moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement.",0
"metabolomics is increasingly being applied towards the identification of biomarkers for disease diagnosis, prognosis and risk prediction. unfortunately among the many published metabolomic studies focusing on biomarker discovery, there is very little consistency and relatively little rigor in how researchers select, assess or report their candidate biomarkers. in particular, few studies report any measure of sensitivity, specificity, or provide receiver operator characteristic (roc) curves with associated confidence intervals. even fewer studies explicitly describe or release the biomarker model used to generate their roc curves. this is surprising given that for biomarker studies in most other biomedical fields, roc curve analysis is generally considered the standard method for performance assessment. because the ultimate goal of biomarker discovery is the translation of those biomarkers to clinical practice, it is clear that the metabolomics community needs to start ""speaking the same language"" in terms of biomarker analysis and reporting-especially if it wants to see metabolite markers being routinely used in the clinic. in this tutorial, we will first introduce the concept of roc curves and describe their use in single biomarker analysis for clinical chemistry. this includes the construction of roc curves, understanding the meaning of area under roc curves (auc) and partial auc, as well as the calculation of confidence intervals. the second part of the tutorial focuses on biomarker analyses within the context of metabolomics. this section describes different statistical and machine learning strategies that can be used to create multi - metabolite biomarker models and explains how these models can be assessed using roc curves. in the third part of the tutorial we discuss common issues and potential pitfalls associated with different analysis methods and provide readers with a list of nine recommendations for biomarker analysis and reporting. to help readers test, visualize and explore the concepts presented in this tutorial, we also introduce a web-based tool called roccet (roc curve explorer & tester, roccet was originally developed as a teaching aid but it can also serve as a training and testing resource to assist metabolomics researchers build biomarker models and conduct a range of common roc curve analyses for biomarker studies.",0
"smart (simple modular architecture research tool) is an online resource ( for the identification and annotation of protein domains and the analysis of protein domain architectures. smart version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version. the current release introduces several novel features and a streamlined user interface resulting in a faster and more comfortable workflow. the underlying protein databases were greatly expanded, resulting in a 2-fold increase in number of annotated domains and features. the database of completely sequenced genomes now includes 1133 species, compared to 630 in the previous release. domain architecture analysis results can now be exported and visualized through the itol phylogenetic tree viewer. 'metasmart' was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets. an advanced full text search engine was implemented, covering the complete annotations for smart and pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information.",0
"objective to estimate the serial interval of novel coronavirus (covid-19) from information on 28 infector-infectee pairs. methods we collected dates of illness onset for primary cases (infectors) and secondary cases (infectees) from published research articles and case investigation reports. we subjectively ranked the credibility of the data and performed analyses on both the full dataset (n = 28) and a subset of pairs with highest certainty in reporting (n = 18). in addition, we adjust for right truncation of the data as the epidemic is still in its growth phase. results accounting for right truncation and analyzing all pairs, we estimated the median serial interval at 4.0 days (95% credible interval : 3.1, 4.9). limiting our data to only the most certain pairs, the median serial interval was estimated at 4.6 days (95% cri: 3.5, 5.9). conclusions the serial interval of covid-19 is close to or shorter than its median incubation period. this suggests that a substantial proportion of secondary transmission may occur prior to illness onset. the covid-19 serial interval is also shorter than the serial interval of severe acute respiratory syndrome (sars), indicating that calculations made using the sars serial interval may introduce bias.",0
"background there is currently a lack of information about the uses, benefits, and limitations of social media for health communication among the general public, patients, and health professionals from primary research. objective to review the current published literature to identify the uses, benefits, and limitations of social media for health communication among the general public, patients, and health professionals, and identify current gaps in the literature to provide recommendations for future health communication research. methods this paper is a review using a systematic approach. a systematic search of the literature was conducted using nine electronic databases and manual searches to locate peer-reviewed studies published between january 2002 and february 2012. results the search identified 98 original research studies that included the uses, benefits, and/or limitations of social media for health communication among the general public, patients, and health professionals. the methodological quality of the studies assessed using the downs and black instrument was low; this was mainly due to the fact that the vast majority of the studies in this review included limited methodologies and was mainly exploratory and descriptive in nature. seven main uses of social media for health communication were identified, including focusing on increasing interactions with others, and facilitating, sharing, and obtaining health messages. the six key overarching benefits were identified as (1) increased interactions with others, (2) more available, shared, and tailored information, (3) increased accessibility and widening access to health information, (4) peer/social/emotional support, (5) public health surveillance, and (6) potential to influence health policy. twelve limitations were identified, primarily consisting of quality concerns and lack of reliability, confidentiality, and privacy. conclusions social media brings a new dimension to health care as it offers a medium to be used by the public, patients, and health professionals to communicate about health issues with the possibility of potentially improving health outcomes. social media is a powerful tool, which offers collaboration between users and is a social interaction mechanism for a range of individuals. although there are several benefits to the use of social media for health communication, the information exchanged needs to be monitored for quality and reliability, and the users' confidentiality and privacy need to be maintained. eight gaps in the literature and key recommendations for future health communication research were provided. examples of these recommendations include the need to determine the relative effectiveness of different types of social media for health communication using randomized control trials and to explore potential mechanisms for monitoring and enhancing the quality and reliability of health communication using social media. further robust and comprehensive evaluation and review, using a range of methodologies, are required to establish whether social media improves health communication practice both in the short and long terms.",0
"the hypothesis that fasl expression by tumor cells may impair the in vivo efficacy of antitumor immune responses, through a mechanism known as 'fas tumor counterattack,' has been recently questioned, becoming the object of an intense debate based on conflicting results. here we definitely show that fasl is indeed detectable in the cytoplasm of melanoma cells and its expression is confined to multivesicular bodies that contain melanosomes. in these structures fasl colocalizes with both melanosomal (i.e., gp100) and lysosomal (i.e., cd63) antigens. isolated melanosomes express fasl, as detected by western blot and cytofluorimetry, and they can exert fas-mediated apoptosis in jurkat cells. we additionally show that melanosome-containing multivesicular bodies degranulate extracellularly and release fasl-bearing microvesicles, that coexpress both gp100 and cd63 and retain their functional activity in triggering fas-dependent apoptosis of lymphoid cells. hence our data provide evidence for a novel mechanism potentially operating in fas tumor counterattack through the secretion of subcellular particles expressing functional fasl. such vesicles may form a sort of front line hindering lymphocytes and other immunocompetent cells from entering neoplastic lesions and exert their antitumor activity.",0
"inference about the causal structure that induces correlations between two traits can be achieved by combining genetic associations with a mediation-based approach, as is done in the causal inference test (cit). however, we show that measurement error in the phenotypes can lead to the cit inferring the wrong causal direction, and that increasing sample sizes has the adverse effect of increasing confidence in the wrong answer. this problem is likely to be general to other mediation-based approaches. here we introduce an extension to mendelian randomisation, a method that uses genetic associations in an instrumentation framework, that enables inference of the causal direction between traits, with some advantages. first, it can be performed using only summary level data from genome-wide association studies; second, it is less susceptible to bias in the presence of measurement error or unmeasured confounding. we apply the method to infer the causal direction between dna methylation and gene expression levels. our results demonstrate that, in general, dna methylation is more likely to be the causal factor, but this result is highly susceptible to bias induced by systematic differences in measurement error between the platforms, and by horizontal pleiotropy. we emphasise that, where possible, implementing mr and appropriate sensitivity analyses alongside other approaches such as cit is important to triangulate reliable conclusions about causality.",0
"background the use of mobile apps for health and well being promotion has grown exponentially in recent years. yet, there is currently no app-quality assessment tool beyond ""star""-ratings. objective the objective of this study was to develop a reliable, multidimensional measure for trialling, classifying, and rating the quality of mobile health apps. methods a literature search was conducted to identify articles containing explicit web or app quality rating criteria published between january 2000 and january 2013. existing criteria for the assessment of app quality were categorized by an expert panel to develop the new mobile app rating scale (mars) subscales, items, descriptors, and anchors. there were sixty well being apps that were randomly selected using an itunes search for mars rating. there were ten that were used to pilot the rating procedure, and the remaining 50 provided data on interrater reliability. results there were 372 explicit criteria for assessing web or app quality that were extracted from 25 published papers, conference proceedings, and internet resources. there were five broad categories of criteria that were identified including four objective quality scales: engagement, functionality, aesthetics, and information quality; and one subjective quality scale; which were refined into the 23-item mars. the mars demonstrated excellent internal consistency (alpha = .90) and interrater reliability intraclass correlation coefficient (icc = .79). conclusions the mars is a simple, objective, and reliable tool for classifying and assessing the quality of mobile health apps. it can also be used to provide a checklist for the design and development of new high quality health apps.",0
"alzheimer's disease (ad) is associated with neurodegeneration in vulnerable limbic and heteromodal regions of the cerebral cortex, detectable in vivo using magnetic resonance imaging. it is not clear whether abnormalities of cortical anatomy in ad can be reliably measured across different subject samples, how closely they track symptoms, and whether they are detectable prior to symptoms. an exploratory map of cortical thinning in mild ad was used to define regions of interest that were applied in a hypothesis-driven fashion to other subject samples. results demonstrate a reliably quantifiable in vivo signature of abnormal cortical anatomy in ad, which parallels known regional vulnerability to ad neuropathology. thinning in vulnerable cortical regions relates to symptom severity even in the earliest stages of clinical symptoms. furthermore, subtle thinning is present in asymptomatic older controls with brain amyloid binding as detected with amyloid imaging. the reliability and clinical validity of ad-related cortical thinning suggests potential utility as an imaging biomarker. this ""disease signature"" approach to cortical morphometry, in which disease effects are mapped across the cortical mantle and then used to define rois for hypothesis-driven analyses, may provide a powerful methodological framework for studies of neuropsychiatric diseases.",0
"combination immune checkpoint blockade has demonstrated promising benefit in lung cancer, but predictors of response to combination therapy are unknown. using whole-exome sequencing to examine non-small-cell lung cancer (nsclc) treated with pd-1 plus ctla-4 blockade, we found that high tumor mutation burden (tmb) predicted improved objective response, durable benefit, and progression-free survival. tmb was independent of pd-l1 expression and the strongest feature associated with efficacy in multivariable analysis. the low response rate in tmb low nsclcs demonstrates that combination immunotherapy does not overcome the negative predictive impact of low tmb. this study demonstrates the association between tmb and benefit to combination immunotherapy in nsclc. tmb should be incorporated in future trials examining pd-(l)1 with ctla-4 blockade in nsclc.",0
"the human lymphocyte function-associated antigen-1 (lfa-1), the complement receptor-associated okm1 molecule, and a previously undescribed molecule termed p150,95, have been found to be structurally and antigenically related. each antigen contains an alpha- and beta-subunit noncovalently associated in an alpha 1 beta 1-structure as shown by cross-linking experiments. lfa-1, okm1, and p150,95 alpha-subunit designations and their molecular weights are alpha l = 177,000 mr, alpha m = 165,000 mr, and alpha x = 150,000 mr, respectively. the beta-subunits are all = 95,000 mr. some mab precipitated only lfa-1, others only okm1, and another precipitates all three antigens. the specificity of these mab for particular subunits was examined after subunit dissociation by high ph. mab specific for lfa-1 or okm1 bind to the alpha l- or alpha m-subunits, respectively, while the cross-reactive mab binds to the beta-subunits. coprecipitation experiments with intact alpha 1 beta 1-complexes showed anti-alpha and anti-beta mab can precipitate the same molecules. in two-dimensional (2d) isoelectric focusing-sds-page, the alpha subunits of the three antigens are distinct, while the beta-subunits are identical. biosynthesis experiments showed alpha l, alpha m, and alpha x are synthesized from distinct precursors, as is beta. the three antigens differ in expression on lymphocytes, granulocytes, and monocytes. during maturation of the monoblast-like u937 line, alpha m and alpha x are upregulated and alpha l is downregulated. some mab to the alpha subunit of okm1 inhibited the complement receptor type three. lfa-1, okm1, and p150,95 constitute a novel family of functionally important human leukocyte antigens that share a common beta-subunit.",0
"background the treatment of perinatal depression is a public-health priority because of its high prevalence and association with disability and poor infant development. we integrated a cognitive behaviour therapy-based intervention into the routine work of community-based primary health workers in rural pakistan and assessed the effect of this intervention on maternal depression and infant outcomes. methods we randomly assigned 40 union council clusters in rural rawalpindi, pakistan, in equal numbers to intervention or control. married women (aged 16-45 years) in their third trimester of pregnancy with perinatal depression were eligible to participate. in the intervention group, primary health workers were trained to deliver the psychological intervention, whereas in the control group untrained health workers made an equal number of visits to the depressed mothers. the primary outcomes were infant weight and height at 6 months and 12 months, and secondary outcome was maternal depression. the interviewers were unaware of what group the participants were assigned to. analysis was by intention to treat. the study is registered as isrctn65316374. findings the number of clusters per group was 20, with 463 mothers in the intervention group and 440 in the control group. at 6 months, 97 (23%) of 418 and 211 (53%) of 400 mothers in the intervention and control groups, respectively, met the criteria for major depression (adjusted odds ratio (or) 0.22, 95% ci 0.14 to 0.36, p interpretation this psychological intervention delivered by community-based primary health workers has the potential to be integrated into health systems in resource-poor settings.",0
"innatedb ( is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. in this article, we provide details of recent updates and improvements to the database. innatedb now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). in addition, the innatedb team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. more recently, innatedb has also initiated the curation of allergy- and asthma-related interactions. furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to innatedb interaction data using proteomics standards initiative common query interface, enhanced gene ontology analysis for innate immunity, and the availability of new network visualizations tools. finally, the recent integration of bovine data makes innatedb the first integrated network analysis platform for this agriculturally important model organism.",0
"the meme suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as dna binding sites and protein interaction domains. the popular meme motif discovery algorithm is now complemented by the glam2 algorithm which allows discovery of motifs containing gaps. three sequence scanning algorithms--mast, fimo and glam2scan--allow scanning numerous dna and protein sequence databases for motifs discovered by meme and glam2. transcription factor motifs (including those discovered using meme) can be compared with motifs in many popular motif databases using the motif database scanning algorithm tomtom. transcription factor motifs can be further analyzed for putative function by association with gene ontology (go) terms using the motif-go term association tool gomo. meme output now contains sequence logos for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (mast, fimo and tomtom), or to gomo, for further analysis. glam2 output similarly contains buttons for further analysis using glam2scan and for rerunning glam2 with different parameters. all of the motif-based tools are now implemented as web services via opal. source code, binaries and a web server are freely available for noncommercial use at",0
"one of the characteristics of the central nervous system is the lack of a classical lymphatic drainage system. although it is now accepted that the central nervous system undergoes constant immune surveillance that takes place within the meningeal compartment, the mechanisms governing the entrance and exit of immune cells from the central nervous system remain poorly understood. in searching for t-cell gateways into and out of the meninges, we discovered functional lymphatic vessels lining the dural sinuses. these structures express all of the molecular hallmarks of lymphatic endothelial cells, are able to carry both fluid and immune cells from the cerebrospinal fluid, and are connected to the deep cervical lymph nodes. the unique location of these vessels may have impeded their discovery to date, thereby contributing to the long-held concept of the absence of lymphatic vasculature in the central nervous system. the discovery of the central nervous system lymphatic system may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.",0
"this article reviews the development of the immune response through neonatal, infant and adult life, including pregnancy, ending with the decline in old age. a picture emerges of a child born with an immature, innate and adaptive immune system, which matures and acquires memory as he or she grows. it then goes into decline in old age. these changes are considered alongside the risks of different types of infection, autoimmune disease and malignancy.",0
"background as microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. in particular, the earth microbiome project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types. findings features of emperor include: ability to visualize gradients and categorical data, visualize different principal coordinates axes, present the data in the form of parallel coordinates, show taxa as well as environmental samples, dynamically adjust the size and transparency of the spheres representing the communities on a per-category basis, dynamically scale the axes according to the fraction of variance each explains, show, hide or recolor points according to arbitrary metadata including that compliant with the mixs family of standards developed by the genomic standards consortium, display jackknifed-resampled data to assess statistical confidence in clustering, perform coordinate comparisons (useful for procrustes analysis plots), and greatly reduce loading times and overall memory footprint compared with existing approaches. additionally, ease of sharing, given emperor's small output file size, enables agile collaboration by allowing users to embed these visualizations via emails or web pages without the need for extra plugins. conclusions here we present emperor, an open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3d visualizations of microbial community data, such as the widely used principal coordinates plots. emperor includes a rich set of controllers to modify features as a function of the metadata. by being specifically tailored to the requirements of microbial ecologists, emperor thus increases the speed with which insight can be gained from large microbiome datasets.",0
"we report a new method for in situ localization of dna sequences that allows excellent preservation of nuclear and chromosomal ultrastructure and direct, in vivo observations. 256 direct repeats of the lac operator were added to vector constructs used for transfection and served as a tag for labeling by lac repressor. this system was first characterized by visualization of chromosome homogeneously staining regions (hsrs) produced by gene amplification using a dihydrofolate reductase (dhfr) expression vector with methotrexate selection. using electron microscopy, most hsrs showed approximately 100-nm fibers, as described previously for the bulk, large-scale chromatin organization in these cells, and by light microscopy, distinct, large-scale chromatin fibers could be traced in vivo up to 5 microns in length. subsequent experiments demonstrated the potential for more general applications of this labeling technology. single and multiple copies of the integrated vector could be detected in living cho cells before gene amplification, and detection of a single 256 lac operator repeat and its stability during mitosis was demonstrated by its targeted insertion into budding yeast cells by homologous recombination. in both cho cells and yeast, use of the green fluorescent protein-lac repressor protein allowed extended, in vivo observations of the operator-tagged chromosomal dna. future applications of this technology should facilitate structural, functional, and genetic analysis of chromatin organization, chromosome dynamics, and nuclear architecture.",0
"socioeconomic disparities are associated with differences in cognitive development. the extent to which this translates to disparities in brain structure is unclear. we investigated relationships between socioeconomic factors and brain morphometry, independently of genetic ancestry, among a cohort of 1,099 typically developing individuals between 3 and 20 years of age. income was logarithmically associated with brain surface area. among children from lower income families, small differences in income were associated with relatively large differences in surface area, whereas, among children from higher income families, similar income increments were associated with smaller differences in surface area. these relationships were most prominent in regions supporting language, reading, executive functions and spatial skills; surface area mediated socioeconomic differences in certain neurocognitive abilities. these data imply that income relates most strongly to brain structure among the most disadvantaged children.",0
"healthy biological systems exhibit complex patterns of variability that can be described by mathematical chaos. heart rate variability (hrv) consists of changes in the time intervals between consecutive heartbeats called interbeat intervals (ibis). a healthy heart is not a metronome. the oscillations of a healthy heart are complex and constantly changing, which allow the cardiovascular system to rapidly adjust to sudden physical and psychological challenges to homeostasis. this article briefly reviews current perspectives on the mechanisms that generate 24 h, short-term (~5 min), and ultra-short-term (<5 min) hrv, the importance of hrv, and its implications for health and performance. the authors provide an overview of widely-used hrv time-domain, frequency-domain, and non-linear metrics. time-domain indices quantify the amount of hrv observed during monitoring periods that may range from ~2 min to 24 h. frequency-domain values calculate the absolute or relative amount of signal energy within component bands. non-linear measurements quantify the unpredictability and complexity of a series of ibis. the authors survey published normative values for clinical, healthy, and optimal performance populations. they stress the importance of measurement context, including recording period length, subject age, and sex, on baseline hrv values. they caution that 24 h, short-term, and ultra-short-term normative values are not interchangeable. they encourage professionals to supplement published norms with findings from their own specialized populations. finally, the authors provide an overview of hrv assessment strategies for clinical and optimal performance interventions.",0
"objective to establish the mechanism of the phenotypic switch of adipose tissue macrophages (atms) from an alternatively activated (m2a) to a classically activated (m1) phenotype with obesity. research design and methods atms from lean and obese (high-fat diet-fed) c57bl/6 mice were analyzed by a combination of flow cytometry, immunofluorescence, and expression analysis for m2a and m1 genes. pulse labeling of atms with pkh26 assessed the recruitment rate of atms to spatially distinct regions. results resident atms in lean mice express the m2a marker macrophage galactose n-acetyl-galactosamine specific lectin 1 (mgl1) and localize to interstitial spaces between adipocytes independent of ccr2 and ccl2. with diet-induced obesity, mgl1(+) atms remain in interstitial spaces, whereas a population of mgl1(-)ccr2(+) atms with high m1 and low m2a gene expression is recruited to clusters surrounding necrotic adipocytes. pulse labeling showed that the rate of recruitment of new macrophages to mgl1(-) atm clusters is significantly faster than that of interstitial mgl1(+) atms. this recruitment is attenuated in ccr2(-/-) mice. m2a- and m1-polarized macrophages produced different effects on adipogenesis and adipocyte insulin sensitivity in vitro. conclusions the shift in the m2a/m1 atm balance is generated by spatial and temporal differences in the recruitment of distinct atm subtypes. the obesity-induced switch in atm activation state is coupled to the localized recruitment of an inflammatory atm subtype to macrophage clusters from the circulation and not to the conversion of resident m2a macrophages to m1 atms in situ.",0
"background lack of appropriate reporting of methodological details has previously been shown to distort risk of bias assessments in randomized controlled trials. the same might be true for observational studies. the goal of this study was to compare the newcastle-ottawa scale (nos) assessment for risk of bias between reviewers and authors of cohort studies included in a published systematic review on risk factors for severe outcomes in patients infected with influenza. methods cohort studies included in the systematic review and published between 2008-2011 were included. the corresponding or first authors completed a survey covering all nos items. results were compared with the nos assessment applied by reviewers of the systematic review. inter-rater reliability was calculated using kappa (k) statistics. results authors of 65/182 (36%) studies completed the survey. the overall nos score was significantly higher (p conclusions differences in assessment and low agreement between reviewers and authors suggest the need to contact authors for information not published in studies when applying the nos in systematic reviews.",0
"background profile hidden markov models (profile-hmms) are sensitive tools for remote protein homology detection, but the main scoring algorithms, viterbi or forward, require considerable time to search large sequence databases. results we have designed a series of database filtering steps, hmmerhead, that are applied prior to the scoring algorithms, as implemented in the hmmer package, in an effort to reduce search time. using this heuristic, we obtain a 20-fold decrease in forward and a 6-fold decrease in viterbi search time with a minimal loss in sensitivity relative to the unfiltered approaches. we then implemented an iterative profile-hmm search method, jackhmmer, which employs the hmmerhead heuristic. due to our search heuristic, we eliminated the subdatabase creation that is common in current iterative profile-hmm approaches. on our benchmark, jackhmmer detects 14% more remote protein homologs than sam's iterative method t2k. conclusions our search heuristic, hmmerhead, significantly reduces the time needed to score a profile-hmm against large sequence databases. this search heuristic allowed us to implement an iterative profile-hmm search method, jackhmmer, which detects significantly more remote protein homologs than sam's t2k and ncbi's psi-blast.",0
"opioid receptors mediate the actions of endogenous and exogenous opioids on many physiological processes, including the regulation of pain, respiratory drive, mood, and--in the case of κ-opioid receptor (κ-or)--dysphoria and psychotomimesis. here we report the crystal structure of the human κ-or in complex with the selective antagonist jdtic, arranged in parallel dimers, at 2.9 å resolution. the structure reveals important features of the ligand-binding pocket that contribute to the high affinity and subtype selectivity of jdtic for the human κ-or. modelling of other important κ-or-selective ligands, including the morphinan-derived antagonists norbinaltorphimine and 5'-guanidinonaltrindole, and the diterpene agonist salvinorin a analogue rb-64, reveals both common and distinct features for binding these diverse chemotypes. analysis of site-directed mutagenesis and ligand structure-activity relationships confirms the interactions observed in the crystal structure, thereby providing a molecular explanation for κ-or subtype selectivity, and essential insights for the design of compounds with new pharmacological properties targeting the human κ-or.",0
"the mitotic checkpoint prevents cells with unaligned chromosomes from prematurely exiting mitosis by inhibiting the anaphase-promoting complex/cyclosome (apc/c) from targeting key proteins for ubiquitin-mediated proteolysis. we have examined the mechanism by which the checkpoint inhibits the apc/c by purifying an apc/c inhibitory factor from hela cells. we call this factor the mitotic checkpoint complex (mcc) as it consists of hbubr1, hbub3, cdc20, and mad2 checkpoint proteins in near equal stoichiometry. mcc inhibitory activity is 3,000-fold greater than that of recombinant mad2, which has also been shown to inhibit apc/c in vitro. surprisingly, mcc is not generated from kinetochores, as it is also present and active in interphase cells. however, only apc/c isolated from mitotic cells was sensitive to inhibition by mcc. we found that the majority of the apc/c in mitotic lysates is associated with the mcc, and this likely contributes to the lag in ubiquitin ligase activity. importantly, chromosomes can suppress the reactivation of apc/c. chromosomes did not affect the inhibitory activity of mcc or the stimulatory activity of cdc20. we propose that the preformed interphase pool of mcc allows for rapid inhibition of apc/c when cells enter mitosis. unattached kinetochores then target the apc/c for sustained inhibition by the mcc.",0
"objective preexposure prophylaxis (prep) offers a promising new approach to hiv prevention. this systematic review and meta-analysis evaluated the evidence for use of oral prep containing tenofovir disoproxil fumarate as an additional hiv prevention strategy in populations at substantial risk for hiv based on hiv acquisition, adverse events, drug resistance, sexual behavior, and reproductive health outcomes. design rigorous systematic review and meta-analysis. methods a comprehensive search strategy reviewed three electronic databases and conference abstracts through april 2015. pooled effect estimates were calculated using random-effects meta-analysis. results eighteen studies were included, comprising data from 39 articles and six conference abstracts. across populations and prep regimens, prep significantly reduced the risk of hiv acquisition compared with placebo. trials with prep use more than 70% demonstrated the highest prep effectiveness (risk ratio = 0.30, 95% confidence interval: 0.21-0.45, p conclusion prep is protective against hiv infection across populations, presents few significant safety risks, and there is no evidence of behavioral risk compensation. the effective and cost-effective use of prep will require development of best practices for fostering uptake and adherence among people at substantial hiv risk.",0
"the inflammatory nature of atherosclerosis is well established but the agent(s) that incite inflammation in the artery wall remain largely unknown. germ-free animals are susceptible to atherosclerosis, suggesting that endogenous substances initiate the inflammation. mature atherosclerotic lesions contain macroscopic deposits of cholesterol crystals in the necrotic core, but their appearance late in atherogenesis had been thought to disqualify them as primary inflammatory stimuli. however, using a new microscopic technique, we revealed that minute cholesterol crystals are present in early diet-induced atherosclerotic lesions and that their appearance in mice coincides with the first appearance of inflammatory cells. other crystalline substances can induce inflammation by stimulating the caspase-1-activating nlrp3 (nalp3 or cryopyrin) inflammasome, which results in cleavage and secretion of interleukin (il)-1 family cytokines. here we show that cholesterol crystals activate the nlrp3 inflammasome in phagocytes in vitro in a process that involves phagolysosomal damage. similarly, when injected intraperitoneally, cholesterol crystals induce acute inflammation, which is impaired in mice deficient in components of the nlrp3 inflammasome, cathepsin b, cathepsin l or il-1 molecules. moreover, when mice deficient in low-density lipoprotein receptor (ldlr) were bone-marrow transplanted with nlrp3-deficient, asc (also known as pycard)-deficient or il-1alpha/beta-deficient bone marrow and fed on a high-cholesterol diet, they had markedly decreased early atherosclerosis and inflammasome-dependent il-18 levels. minimally modified ldl can lead to cholesterol crystallization concomitant with nlrp3 inflammasome priming and activation in macrophages. although there is the possibility that oxidized ldl activates the nlrp3 inflammasome in vivo, our results demonstrate that crystalline cholesterol acts as an endogenous danger signal and its deposition in arteries or elsewhere is an early cause rather than a late consequence of inflammation. these findings provide new insights into the pathogenesis of atherosclerosis and indicate new potential molecular targets for the therapy of this disease.",0
"network meta-analysis synthesizes direct and indirect evidence in a network of trials that compare multiple interventions and has the potential to rank the competing treatments according to the studied outcome. despite its usefulness network meta-analysis is often criticized for its complexity and for being accessible only to researchers with strong statistical and computational skills. the evaluation of the underlying model assumptions, the statistical technicalities and presentation of the results in a concise and understandable way are all challenging aspects in the network meta-analysis methodology. in this paper we aim to make the methodology accessible to non-statisticians by presenting and explaining a series of graphical tools via worked examples. to this end, we provide a set of stata routines that can be easily employed to present the evidence base, evaluate the assumptions, fit the network meta-analysis model and interpret its results.",0
"a new coronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), has recently emerged to cause a human pandemic. although molecular diagnostic tests were rapidly developed, serologic assays are still lacking, yet urgently needed. validated serologic assays are needed for contact tracing, identifying the viral reservoir, and epidemiologic studies. we developed serologic assays for detection of sars-cov-2 neutralizing, spike protein-specific, and nucleocapsid-specific antibodies. using serum samples from patients with pcr-confirmed sars-cov-2 infections, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial elisas. we demonstrated that most pcr-confirmed sars-cov-2-infected persons seroconverted by 2 weeks after disease onset. we found that commercial s1 igg or iga elisas were of lower specificity, and sensitivity varied between the 2 assays; the iga elisa showed higher sensitivity. overall, the validated assays described can be instrumental for detection of sars-cov-2-specific antibodies for diagnostic, seroepidemiologic, and vaccine evaluation studies.",0
"the reactome knowledgebase ( provides molecular details of signal transduction, transport, dna replication, metabolism and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. over the last two years we redeveloped major components of the reactome web interface to improve usability, responsiveness and data visualization. a new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. the analysis module can now be accessed through a restful interface, facilitating its inclusion in third party applications. a new overview module allows the visualization of analysis results on a genome-wide reactome pathway hierarchy using a single screen page. the search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.",0
"acidic extracellular ph is a major feature of tumor tissue, extracellular acidification being primarily considered to be due to lactate secretion from anaerobic glycolysis. clinicopathological evidence shows that transporters and pumps contribute to h+ secretion, such as the na+/h+ exchanger, the h+-lactate co-transporter, monocarboxylate transporters, and the proton pump (h+-atpase); these may also be associated with tumor metastasis. an acidic extracellular ph not only activates secreted lysosomal enzymes that have an optimal ph in the acidic range, but induces the expression of certain genes of pro-metastatic factors through an intracellular signaling cascade that is different from hypoxia. in addition to lactate, co2 from the pentose phosphate pathway is an alternative source of acidity, showing that hypoxia and extracellular acidity are, while being independent from each other, deeply associated with the cellular microenvironment. in this article, the importance of an acidic extracellular ph as a microenvironmental factor participating in tumor progression is reviewed.",0
"new developments in the program package atsas (version 2.4) for the processing and analysis of isotropic small-angle x-ray and neutron scattering data are described. they include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. the new atsas release includes installers for current major platforms (windows, linux and mac osx) and provides improved indexed user documentation. the web-related developments, including a user discussion forum and a widened online access to run atsas programs, are also presented.",0
"mutations in park8, encoding for the multidomain leucine-rich repeat kinase 2 (lrrk2) protein, comprise the predominant genetic cause of parkinson's disease (pd). g2019s, the most common amino acid substitution activates the kinase two- to threefold. this has motivated the development of lrrk2 kinase inhibitors; however, poor consensus on physiological lrrk2 substrates has hampered clinical development of such therapeutics. we employ a combination of phosphoproteomics, genetics, and pharmacology to unambiguously identify a subset of rab gtpases as key lrrk2 substrates. lrrk2 directly phosphorylates these both in vivo and in vitro on an evolutionary conserved residue in the switch ii domain. pathogenic lrrk2 variants mapping to different functional domains increase phosphorylation of rabs and this strongly decreases their affinity to regulatory proteins including rab gdp dissociation inhibitors (gdis). our findings uncover a key class of bona-fide lrrk2 substrates and a novel regulatory mechanism of rabs that connects them to pd.",0
"mtor (mammalian target of rapamycin) signalling and macroautophagy (henceforth autophagy) regulate numerous pathological and physiological processes, including cellular responses to altered nutrient levels. however, the mechanisms regulating mtor and autophagy remain incompletely understood. lysosomes are dynamic intracellular organelles intimately involved both in the activation of mtor complex 1 (mtorc1) signalling and in degrading autophagic substrates. here we report that lysosomal positioning coordinates anabolic and catabolic responses with changes in nutrient availability by orchestrating early plasma-membrane signalling events, mtorc1 signalling and autophagy. activation of mtorc1 by nutrients correlates with its presence on peripheral lysosomes that are physically close to the upstream signalling modules, whereas starvation causes perinuclear clustering of lysosomes, driven by changes in intracellular ph. lysosomal positioning regulates mtorc1 signalling, which in turn influences autophagosome formation. lysosome positioning also influences autophagosome-lysosome fusion rates, and thus controls autophagic flux by acting at both the initiation and termination stages of the process. our findings provide a physiological role for the dynamic state of lysosomal positioning in cells as a coordinator of mtorc1 signalling with autophagic flux.",0
"background although macrophages (mphi) are known as essential players in wound healing, their contribution to recovery from spinal cord injury (sci) is a subject of debate. the difficulties in distinguishing between different mphi subpopulations at the lesion site have further contributed to the controversy and led to the common view of mphi as functionally homogenous. given the massive accumulation in the injured spinal cord of activated resident microglia, which are the native immune occupants of the central nervous system (cns), the recruitment of additional infiltrating monocytes from the peripheral blood seems puzzling. a key question that remains is whether the infiltrating monocyte-derived mphi contribute to repair, or represent an unavoidable detrimental response. the hypothesis of the current study is that a specific population of infiltrating monocyte-derived mphi is functionally distinct from the inflammatory resident microglia and is essential for recovery from sci. methods and findings we inflicted sci in adult mice, and tested the effect of infiltrating monocyte-derived mphi on the recovery process. adoptive transfer experiments and bone marrow chimeras were used to functionally distinguish between the resident microglia and the infiltrating monocyte-derived mphi. we followed the infiltration of the monocyte-derived mphi to the injured site and characterized their spatial distribution and phenotype. increasing the naïve monocyte pool by either adoptive transfer or cns-specific vaccination resulted in a higher number of spontaneously recruited cells and improved recovery. selective ablation of infiltrating monocyte-derived mphi following sci while sparing the resident microglia, using either antibody-mediated depletion or conditional ablation by diphtheria toxin, impaired recovery. reconstitution of the peripheral blood with monocytes resistant to ablation restored the lost motor functions. importantly, the infiltrating monocyte-derived mphi displayed a local anti-inflammatory beneficial role, which was critically dependent upon their expression of interleukin 10. conclusions the results of this study attribute a novel anti-inflammatory role to a unique subset of infiltrating monocyte-derived mphi in sci recovery, which cannot be provided by the activated resident microglia. according to our results, limited recovery following sci can be attributed in part to the inadequate, untimely, spontaneous recruitment of monocytes. this process is amenable to boosting either by active vaccination with a myelin-derived altered peptide ligand, which indicates involvement of adaptive immunity in monocyte recruitment, or by augmenting the naïve monocyte pool in the peripheral blood. thus, our study sheds new light on the long-held debate regarding the contribution of mphi to recovery from cns injuries, and has potentially far-reaching therapeutic implications.",0
"while traditional models of language comprehension have focused on the left posterior temporal cortex as the neurological basis for language comprehension, lesion and functional imaging studies indicate the involvement of an extensive network of cortical regions. however, the full extent of this network and the white matter pathways that contribute to it remain to be characterized. in an earlier voxel-based lesion-symptom mapping analysis of data from aphasic patients (dronkers et al., 2004), several brain regions in the left hemisphere were found to be critical for language comprehension: the left posterior middle temporal gyrus, the anterior part of brodmann's area 22 in the superior temporal gyrus (anterior stg/ba22), the posterior superior temporal sulcus (sts) extending into brodmann's area 39 (sts/ba39), the orbital part of the inferior frontal gyrus (ba47), and the middle frontal gyrus (ba46). here, we investigated the white matter pathways associated with these regions using diffusion tensor imaging from healthy subjects. we also used resting-state functional magnetic resonance imaging data to assess the functional connectivity profiles of these regions. fiber tractography and functional connectivity analyses indicated that the left mtg, anterior stg/ba22, sts/ba39, and ba47 are part of a richly interconnected network that extends to additional frontal, parietal, and temporal regions in the two hemispheres. the inferior occipito-frontal fasciculus, the arcuate fasciculus, and the middle and inferior longitudinal fasciculi, as well as transcallosal projections via the tapetum were found to be the most prominent white matter pathways bridging the regions important for language comprehension. the left mtg showed a particularly extensive structural and functional connectivity pattern which is consistent with the severity of the impairments associated with mtg lesions and which suggests a central role for this region in language comprehension.",0
"background increases in mental health problems have been observed during the covid-19 pandemic. the objectives were to examine the extent to which mental health symptoms changed during the pandemic in 2020, whether changes were persistent or short lived, and if changes were symptom specific. methods systematic review and meta-analysis of longitudinal cohort studies examining changes in mental health among the same group of participants before vs. during the pandemic in 2020. results sixty-five studies were included. compared to pre-pandemic outbreak, there was an overall increase in mental health symptoms observed during march-april 2020 (smc = .102 ) that significantly declined over time and became non-significant (may-july smc = .067 . compared to measures of anxiety (smc = 0.13, p = 0.02) and general mental health (smc = -.03, p = 0.65), increases in depression and mood disorder symptoms tended to be larger and remained significantly elevated in may-july . in primary analyses increases were most pronounced among samples with physical health conditions and there was no evidence of any change in symptoms among samples with a pre-existing mental health condition. limitations there was a high degree of unexplained heterogeneity observed (i 2 s > 90%), indicating that change in mental health was highly variable across samples. conclusions there was a small increase in mental health symptoms soon after the outbreak of the covid-19 pandemic that decreased and was comparable to pre-pandemic levels by mid-2020 among most population sub-groups and symptom types.",0
"programmed death 1 (pd-1) is an inhibitory molecule expressed on activated t cells; however, the biological context in which pd-1 controls t cell tolerance remains unclear. using two-photon laser-scanning microscopy, we show here that unlike naive or activated islet antigen-specific t cells, tolerized islet antigen-specific t cells moved freely and did not swarm around antigen-bearing dendritic cells (dcs) in pancreatic lymph nodes. inhibition of t cell antigen receptor (tcr)-driven stop signals depended on continued interactions between pd-1 and its ligand, pd-l1, as antibody blockade of pd-1 or pd-l1 resulted in lower t cell motility, enhanced t cell-dc contacts and caused autoimmune diabetes. blockade of the immunomodulatory receptor ctla-4 did not alter t cell motility or abrogate tolerance. thus, pd-1-pd-l1 interactions maintain peripheral tolerance by mechanisms fundamentally distinct from those of ctla-4.",0
"panther (protein analysis through evolutionary relationships, is a widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. recent development has been focused in three main areas: genome coverage, functional information ('annotation') coverage and accuracy, and improved genomic data analysis tools. the latest version of panther, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life. phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events. functional annotations are regularly updated using the models generated by the gene ontology phylogenetic annotation project. for the data analysis tools, panther has expanded the number of different 'functional annotation sets' available for functional enrichment testing, allowing analyses to access all gene ontology annotations--updated monthly from the gene ontology database--in addition to the annotations that have been inferred through evolutionary relationships. the prowler (data browser) has been updated to enable users to more efficiently browse the entire database, and to create custom gene lists using the multiple axes of classification in panther.",0
"experimental autoimmune uveitis (eau) represents autoimmune uveitis in humans. we examined the role of the interleukin (il)-23-il-17 and il-12-t helper cell (th)1 pathways in the pathogenesis of eau. il-23 but not il-12 was necessary to elicit disease by immunization with the retinal antigen (ag) interphotoreceptor retinoid-binding protein (irbp) in complete freund's adjuvant. il-17 played a dominant role in this model; its neutralization prevented or reversed disease, and th17 effector cells induced eau in the absence of interferon (ifn)-gamma. in a transfer model, however, a polarized th1 line could induce severe eau independently of host il-17. furthermore, induction of eau with irbp-pulsed mature dendritic cells required generation of an ifn-gamma-producing effector response, and an il-17 response by itself was insufficient to elicit pathology. finally, genetic deficiency of il-17 did not abrogate eau susceptibility. thus, autoimmune pathology can develop in the context of either a th17 or a th1 effector response depending on the model. the data suggest that the dominant effector phenotype may be determined at least in part by conditions present during initial exposure to ag, including the quality/quantity of toll-like receptor stimulation and/or type of ag-presenting cells. these data also raise the possibility that the nonredundant requirement for il-23 in eau may extend beyond its role in promoting the th17 effector response and help provide a balance in the current th1 versus th17 paradigm.",0
"data-independent acquisition (dia) in liquid chromatography (lc) coupled to tandem mass spectrometry (ms/ms) provides comprehensive untargeted acquisition of molecular data. we provide an open-source software pipeline, which we call ms-dial, for dia-based identification and quantification of small molecules by mass spectral deconvolution. for a reversed-phase lc-ms/ms analysis of nine algal strains, ms-dial using an enriched lipidblast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains.",0
"objective to provide an update to the original surviving sepsis campaign clinical management guidelines, ""surviving sepsis campaign guidelines for management of severe sepsis and septic shock,"" published in 2004. design modified delphi method with a consensus conference of 55 international experts, several subsequent meetings of subgroups and key individuals, teleconferences, and electronic-based discussion among subgroups and among the entire committee. this process was conducted independently of any industry funding. methods we used the grade system to guide assessment of quality of evidence from high (a) to very low (d) and to determine the strength of recommendations. a strong recommendation indicates that an intervention's desirable effects clearly outweigh its undesirable effects (risk, burden, cost), or clearly do not. weak recommendations indicate that the tradeoff between desirable and undesirable effects is less clear. the grade of strong or weak is considered of greater clinical importance than a difference in letter level of quality of evidence. in areas without complete agreement, a formal process of resolution was developed and applied. recommendations are grouped into those directly targeting severe sepsis, recommendations targeting general care of the critically ill patient that are considered high priority in severe sepsis, and pediatric considerations. results key recommendations, listed by category, include: early goal-directed resuscitation of the septic patient during the first 6 hrs after recognition (1c); blood cultures prior to antibiotic therapy (1c); imaging studies performed promptly to confirm potential source of infection (1c); administration of broad-spectrum antibiotic therapy within 1 hr of diagnosis of septic shock (1b) and severe sepsis without septic shock (1d); reassessment of antibiotic therapy with microbiology and clinical data to narrow coverage, when appropriate (1c); a usual 7-10 days of antibiotic therapy guided by clinical response (1d); source control with attention to the balance of risks and benefits of the chosen method (1c); administration of either crystalloid or colloid fluid resuscitation (1b); fluid challenge to restore mean circulating filling pressure (1c); reduction in rate of fluid administration with rising filing pressures and no improvement in tissue perfusion (1d); vasopressor preference for norepinephrine or dopamine to maintain an initial target of mean arterial pressure > or = 65 mm hg (1c); dobutamine inotropic therapy when cardiac output remains low despite fluid resuscitation and combined inotropic/vasopressor therapy (1c); stress-dose steroid therapy given only in septic shock after blood pressure is identified to be poorly responsive to fluid and vasopressor therapy (2c); recombinant activated protein c in patients with severe sepsis and clinical assessment of high risk for death (2b except 2c for post-operative patients). in the absence of tissue hypoperfusion, coronary artery disease, or acute hemorrhage, target a hemoglobin of 7-9 g/dl (1b); a low tidal volume (1b) and limitation of inspiratory plateau pressure strategy (1c) for acute lung injury (ali)/acute respiratory distress syndrome (ards); application of at least a minimal amount of positive end-expiratory pressure in acute lung injury (1c); head of bed elevation in mechanically ventilated patients unless contraindicated (1b); avoiding routine use of pulmonary artery catheters in ali/ards (1a); to decrease days of mechanical ventilation and icu length of stay, a conservative fluid strategy for patients with established ali/ards who are not in shock (1c); protocols for weaning and sedation/analgesia (1b); using either intermittent bolus sedation or continuous infusion sedation with daily interruptions or lightening (1b); avoidance of neuromuscular blockers, if at all possible (1b); institution of glycemic control (1b) targeting a blood glucose conclusion there was strong agreement among a large cohort of international experts regarding many level 1 recommendations for the best current care of patients with severe sepsis. evidenced-based recommendations regarding the acute management of sepsis and septic shock are the first step toward improved outcomes for this important group of critically ill patients.",0
"objective the efficacy and safety of adding liraglutide (a glucagon-like peptide-1 receptor agonist) to metformin were compared with addition of placebo or glimepiride to metformin in subjects previously treated with oral antidiabetes (oad) therapy. research design and methods in this 26-week, double-blind, double-dummy, placebo- and active-controlled, parallel-group trial, 1,091 subjects were randomly assigned (2:2:2:1:2) to once-daily liraglutide (either 0.6, 1.2, or 1.8 mg/day injected subcutaneously), to placebo, or to glimepiride (4 mg once daily). all treatments were in combination therapy with metformin (1g twice daily). enrolled subjects (aged 25-79 years) had type 2 diabetes, a1c of 7-11% (previous oad monotherapy for > or =3 months) or 7-10% (previous oad combination therapy for > or =3 months), and bmi results a1c values were significantly reduced in all liraglutide groups versus the placebo group (p conclusions in subjects with type 2 diabetes, once-daily liraglutide induced similar glycemic control, reduced body weight, and lowered the occurrence of hypoglycemia compared with glimepiride, when both had background therapy of metformin.",0
"curcumin is a constituent (up to ∼5%) of the traditional medicine known as turmeric. interest in the therapeutic use of turmeric and the relative ease of isolation of curcuminoids has led to their extensive investigation. curcumin has recently been classified as both a pains (pan-assay interference compounds) and an imps (invalid metabolic panaceas) candidate. the likely false activity of curcumin in vitro and in vivo has resulted in >120 clinical trials of curcuminoids against several diseases. no double-blinded, placebo controlled clinical trial of curcumin has been successful. this manuscript reviews the essential medicinal chemistry of curcumin and provides evidence that curcumin is an unstable, reactive, nonbioavailable compound and, therefore, a highly improbable lead. on the basis of this in-depth evaluation, potential new directions for research on curcuminoids are discussed.",0
"study objective to determine the relationship between delirium in the intensive care unit (icu) and outcomes including length of stay in the hospital. design a prospective cohort study. setting the adult medical icu of a tertiary care, university-based medical center. participants the study population consisted of 48 patients admitted to the icu, 24 of whom received mechanical ventilation. measurements all patients were evaluated for the development and persistence of delirium on a daily basis by a geriatric or psychiatric specialist with expertise in delirium assessment using the diagnostic statistical manual iv (dsm-iv) criteria of the american psychiatric association, the reference standard for delirium ratings. primary outcomes measured were length of stay in the icu and hospital. results the mean onset of delirium was 2.6 days (s.d.+/-1.7), and the mean duration was 3.4+/-1.9 days. of the 48 patients, 39 (81.3%) developed delirium, and of these 29 (60.4%) developed the complication while still in the icu. the duration of delirium was associated with length of stay in the icu ( r=0.65, p=0.0001) and in the hospital ( r=0.68, p conclusions in this patient cohort, the majority of patients developed delirium in the icu, and delirium was the strongest independent determinant of length of stay in the hospital. further study and monitoring of delirium in the icu and the risk factors for its development are warranted.",0
"objective to determine whether there is an association between healthcare professionals' wellbeing and burnout, with patient safety. design systematic research review. data sources psychinfo (1806 to july 2015), medline (1946 to july 2015), embase (1947 to july 2015) and scopus (1823 to july 2015) were searched, along with reference lists of eligible articles. eligibility criteria for selecting studies quantitative, empirical studies that included i) either a measure of wellbeing or burnout, and ii) patient safety, in healthcare staff populations. results forty-six studies were identified. sixteen out of the 27 studies that measured wellbeing found a significant correlation between poor wellbeing and worse patient safety, with six additional studies finding an association with some but not all scales used, and one study finding a significant association but in the opposite direction to the majority of studies. twenty-one out of the 30 studies that measured burnout found a significant association between burnout and patient safety, whilst a further four studies found an association between one or more (but not all) subscales of the burnout measures employed, and patient safety. conclusions poor wellbeing and moderate to high levels of burnout are associated, in the majority of studies reviewed, with poor patient safety outcomes such as medical errors, however the lack of prospective studies reduces the ability to determine causality. further prospective studies, research in primary care, conducted within the uk, and a clearer definition of healthcare staff wellbeing are needed. implications this review illustrates the need for healthcare organisations to consider improving employees' mental health as well as creating safer work environments when planning interventions to improve patient safety. systematic review registration prospero registration number: crd42015023340.",0
"a hyperinflammatory syndrome (his) may cause a life-threatening acute respiratory distress syndrome (ards) in patients with covid-19 pneumonia. a prospective series of 100 consecutive patients admitted to the spedali civili university hospital in brescia (italy) between march 9th and march 20th with confirmed covid-19 pneumonia and ards requiring ventilatory support was analyzed to determine whether intravenous administration of tocilizumab (tcz), a monoclonal antibody that targets the interleukin 6 (il-6) receptor, was associated with improved outcome. tocilizumab was administered at a dosage of 8 mg/kg by two consecutive intravenous infusions 12 h apart. a third infusion was optional based on clinical response. the outcome measure was an improvement in acute respiratory failure assessed by means of the brescia covid respiratory severity score (bcrss 0 to 8, with higher scores indicating higher severity) at 24-72 h and 10 days after tocilizumab administration. out of 100 treated patients (88 m, 12 f; median age: 62 years), 43 received tcz in the intensive care unit (icu), while 57 in the general ward as no icu beds were available. of these 57 patients, 37 (65%) improved and suspended noninvasive ventilation (niv) (median bcrss: 1 ), 7 (12%) patients remained stable in niv, and 13 (23%) patients worsened (10 died, 3 were admitted to icu). of the 43 patients treated in the icu, 32 (74%) improved (17 of them were taken off the ventilator and were discharged to the ward), 1 (2%) remained stable (bcrss: 5) and 10 (24%) died (all of them had bcrss≥7 before tcz). overall at 10 days, the respiratory condition was improved or stabilized in 77 (77%) patients, of whom 61 showed a significant clearing of diffuse bilateral opacities on chest x-ray and 15 were discharged from the hospital. respiratory condition worsened in 23 (23%) patients, of whom 20 (20%) died. all the patients presented with lymphopenia and high levels of c-reactive protein (crp), fibrinogen, ferritin and il-6 indicating a his. during the 10-day follow-up, three cases of severe adverse events were recorded: two patients developed septic shock and died, one had gastrointestinal perforation requiring urgent surgery and was alive at day 10. in conclusion, our series showed that covid-19 pneumonia with ards was characterized by his. the response to tcz was rapid, sustained, and associated with significant clinical improvement.",0
"schizophrenia is a complex, heterogeneous behavioural and cognitive syndrome that seems to originate from disruption of brain development caused by genetic or environmental factors, or both. dysfunction of dopaminergic neurotransmission contributes to the genesis of psychotic symptoms, but evidence also points to a widespread and variable involvement of other brain areas and circuits. disturbances of synaptic function might underlie abnormalities of neuronal connectivity that possibly involves interneurons, but the precise nature, location, and timing of these events are uncertain. at present, treatment mainly consists of antipsychotic drugs combined with psychological therapies, social support, and rehabilitation, but a pressing need for more effective treatments and delivery of services exists. advances in genomics, epidemiology, and neuroscience have led to great progress in understanding the disorder, and the opportunities for further scientific breakthrough are numerous--but so are the challenges.",0
"candida species are the most common cause of opportunistic fungal infection worldwide. here we report the genome sequences of six candida species and compare these and related pathogens and non-pathogens. there are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. surprisingly, key components of the mating and meiosis pathways are missing from several species. these include major differences at the mating-type loci (mtl); lodderomyces elongisporus lacks mtl, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. analysis of the cug leucine-to-serine genetic-code change reveals that 99% of ancestral cug codons were erased and new ones arose elsewhere. lastly, we revise the candida albicans gene catalogue, identifying many new genes.",0
"functional brain networks detected in task-free (""resting-state"") functional magnetic resonance imaging (fmri) have a small-world architecture that reflects a robust functional organization of the brain. here, we examined whether this functional organization is disrupted in alzheimer's disease (ad). task-free fmri data from 21 ad subjects and 18 age-matched controls were obtained. wavelet analysis was applied to the fmri data to compute frequency-dependent correlation matrices. correlation matrices were thresholded to create 90-node undirected-graphs of functional brain networks. small-world metrics (characteristic path length and clustering coefficient) were computed using graph analytical methods. in the low frequency interval 0.01 to 0.05 hz, functional brain networks in controls showed small-world organization of brain activity, characterized by a high clustering coefficient and a low characteristic path length. in contrast, functional brain networks in ad showed loss of small-world properties, characterized by a significantly lower clustering coefficient (p<0.01), indicative of disrupted local connectivity. clustering coefficients for the left and right hippocampus were significantly lower (p<0.01) in the ad group compared to the control group. furthermore, the clustering coefficient distinguished ad participants from the controls with a sensitivity of 72% and specificity of 78%. our study provides new evidence that there is disrupted organization of functional brain networks in ad. small-world metrics can characterize the functional organization of the brain in ad, and our findings further suggest that these network measures may be useful as an imaging-based biomarker to distinguish ad from healthy aging.",0
"obesity is the accumulation of abnormal or excessive fat that may interfere with the maintenance of an optimal state of health. the excess of macronutrients in the adipose tissues stimulates them to release inflammatory mediators such as tumor necrosis factor α and interleukin 6, and reduces production of adiponectin, predisposing to a pro-inflammatory state and oxidative stress. the increased level of interleukin 6 stimulates the liver to synthesize and secrete c-reactive protein. as a risk factor, inflammation is an imbedded mechanism of developed cardiovascular diseases including coagulation, atherosclerosis, metabolic syndrome, insulin resistance, and diabetes mellitus. it is also associated with development of non-cardiovascular diseases such as psoriasis, depression, cancer, and renal diseases. on the other hand, a reduced level of adiponectin, a significant predictor of cardiovascular mortality, is associated with impaired fasting glucose, leading to type-2 diabetes development, metabolic abnormalities, coronary artery calcification, and stroke. finally, managing obesity can help reduce the risks of cardiovascular diseases and poor outcome via inhibiting inflammatory mechanisms.",0
"importance increasing numbers of confirmed cases and mortality rates of coronavirus disease 2019 (covid-19) are occurring in several countries and continents. information regarding the impact of cardiovascular complication on fatal outcome is scarce. objective to evaluate the association of underlying cardiovascular disease (cvd) and myocardial injury with fatal outcomes in patients with covid-19. design, setting, and participants this retrospective single-center case series analyzed patients with covid-19 at the seventh hospital of wuhan city, china, from january 23, 2020, to february 23, 2020. analysis began february 25, 2020. main outcomes and measures demographic data, laboratory findings, comorbidities, and treatments were collected and analyzed in patients with and without elevation of troponin t (tnt) levels. results among 187 patients with confirmed covid-19, 144 patients (77%) were discharged and 43 patients (23%) died. the mean (sd) age was 58.50 (14.66) years. overall, 66 (35.3%) had underlying cvd including hypertension, coronary heart disease, and cardiomyopathy, and 52 (27.8%) exhibited myocardial injury as indicated by elevated tnt levels. the mortality during hospitalization was 7.62% (8 of 105) for patients without underlying cvd and normal tnt levels, 13.33% (4 of 30) for those with underlying cvd and normal tnt levels, 37.50% (6 of 16) for those without underlying cvd but elevated tnt levels, and 69.44% (25 of 36) for those with underlying cvd and elevated tnts. patients with underlying cvd were more likely to exhibit elevation of tnt levels compared with the patients without cvd (36 vs 16 ). plasma tnt levels demonstrated a high and significantly positive linear correlation with plasma high-sensitivity c-reactive protein levels (β = 0.530, p conclusions and relevance myocardial injury is significantly associated with fatal outcome of covid-19, while the prognosis of patients with underlying cvd but without myocardial injury is relatively favorable. myocardial injury is associated with cardiac dysfunction and arrhythmias. inflammation may be a potential mechanism for myocardial injury. aggressive treatment may be considered for patients at high risk of myocardial injury.",0
"background global, regional, and national estimates of prevalence of and tends in infertility are needed to target prevention and treatment efforts. by applying a consistent algorithm to demographic and reproductive surveys available from developed and developing countries, we estimate infertility prevalence and trends, 1990 to 2010, by country and region. methods and findings we accessed and analyzed household survey data from 277 demographic and reproductive health surveys using a consistent algorithm to calculate infertility. we used a demographic infertility measure with live birth as the outcome and a 5-y exposure period based on union status, contraceptive use, and desire for a child. we corrected for biases arising from the use of incomplete information on past union status and contraceptive use. we used a bayesian hierarchical model to estimate prevalence of and trends in infertility in 190 countries and territories. in 2010, among women 20-44 y of age who were exposed to the risk of pregnancy, 1.9% (95% uncertainty interval 1.7%, 2.2%) were unable to attain a live birth (primary infertility). out of women who had had at least one live birth and were exposed to the risk of pregnancy, 10.5% (9.5%, 11.7%) were unable to have another child (secondary infertility). infertility prevalence was highest in south asia, sub-saharan africa, north africa/middle east, and central/eastern europe and central asia. levels of infertility in 2010 were similar to those in 1990 in most world regions, apart from declines in primary and secondary infertility in sub-saharan africa and primary infertility in south asia (posterior probability ≥0.99). although there were no statistically significant changes in the prevalence of infertility in most regions amongst women who were exposed to the risk of pregnancy, reduced child-seeking behavior resulted in a reduction of primary infertility among all women from 1.6% to 1.5% (pp=0.90) and a reduction of secondary infertility among all women from 3.9% to 3.0% (pp>0.99) from 1990 to 2010. due to population growth, however, the absolute number of couples affected by infertility increased from 42.0 million (39.6 million, 44.8 million) in 1990 to 48.5 million (45.0 million, 52.6 million) in 2010. limitations of the study include gaps in survey data for some countries and the use of proxies to determine exposure to pregnancy. conclusions we analyzed demographic and reproductive household survey data to reveal global patterns and trends in infertility. independent from population growth and worldwide declines in the preferred number of children, we found little evidence of changes in infertility over two decades, apart from in the regions of sub-saharan africa and south asia. further research is needed to identify the etiological causes of these patterns and trends.",0
"prolonged symptom duration and disability are common in adults hospitalized with severe coronavirus disease 2019 (covid-19). characterizing return to baseline health among outpatients with milder covid-19 illness is important for understanding the full spectrum of covid-19-associated illness and tailoring public health messaging, interventions, and policy. during april 15-june 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (rt-pcr) test for sars-cov-2, the virus that causes covid-19, at an outpatient visit at one of 14 u.s. academic health care systems in 13 states. interviews were conducted 14-21 days after the test date. respondents were asked about demographic characteristics, baseline chronic medical conditions, symptoms present at the time of testing, whether those symptoms had resolved by the interview date, and whether they had returned to their usual state of health at the time of interview. among 292 respondents, 94% (274) reported experiencing one or more symptoms at the time of testing; 35% of these symptomatic respondents reported not having returned to their usual state of health by the date of the interview (median = 16 days from testing date), including 26% among those aged 18-34 years, 32% among those aged 35-49 years, and 47% among those aged ≥50 years. among respondents reporting cough, fatigue, or shortness of breath at the time of testing, 43%, 35%, and 29%, respectively, continued to experience these symptoms at the time of the interview. these findings indicate that covid-19 can result in prolonged illness even among persons with milder outpatient illness, including young adults. effective public health messaging targeting these groups is warranted. preventative measures, including social distancing, frequent handwashing, and the consistent and correct use of face coverings in public, should be strongly encouraged to slow the spread of sars-cov-2.",0
"the principal component analysis (pca) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. the same applies to creating heatmaps: it is possible to add conditional formatting for excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. we present a web tool called clustvis that aims to have an intuitive user interface. users can upload data from a simple delimited text file that can be created in a spreadsheet program. it is possible to modify data processing methods and the final appearance of the pca and heatmap plots by using drop-down menus, text boxes, sliders etc. appropriate defaults are given to reduce the time needed by the user to specify input parameters. as an output, users can download pca plot and heatmap in one of the preferred file formats. this web server is freely available at",0
"antigen presentation by host dendritic cells (dc) is critical for the initiation of adaptive immune responses. we have previously demonstrated in immunogenic murine tumor models that bone marrow (bm)-derived dc pulsed ex vivo with synthetic tumor-associated peptides, naturally expressed by tumor cells, serve as effective antitumor vaccines, protecting animals against an otherwise lethal tumor challenge (mayordomo, j.i., t. zorina, w.j. storkus, c. celluzzi, l.d. falo, c.j. melief, t. ildstad, w.m. kast, a.b. deleo, and m.t. lotze. 1995. nature med. 1:1297-1302). however, t cell-defined epitopes have not been identified for most human cancers. to explore the utility of this approach in the treatment of tumors expressing as yet uncharacterized epitopes, syngeneic granulocyte/macrophage colony-stimulating factor-stimulated and bm-derived dc, pulsed with unfractionated acid-eluted tumor peptides (storkus, w.j., h.j. zeh iii, r.d. salter, and m.t. lotze. 1993. j. immunother. 14:94-103) were used to treat mice bearing spontaneous, established tumors. the adoptive transfer of 5 x 10(5) tumor peptide-pulsed dc dramatically suppressed the growth of weakly immunogenic tumors in day 4 to day 8 established mca205 (h-2b) and ts/a (h-2d) tumor models, when applied in three biweekly intravenous injections. using the immunogenic c3 (h-2b) tumor model in b6 mice, tumor peptide-pulsed dc therapy resulted in the erradication of established d14 tumors and long-term survival in 100% of treated animals. the dc-driven antitumor immune response was primarily cell mediated since the transfer of spleen cells, but not sera, from immunized mice efficiently protected sublethally irradiated naive mice against a subsequent tumor challenge. furthermore, depletion of either cd4+ or cd8+ t cells from tumor-bearing mice before therapy totally suppressed the therapeutic efficacy of dc pulsed with tumor-derived peptides. costimulation of the host cell-mediated antitumor immunity was critical since inoculation of the chimeric fusion protein ctla4-ig virtually abrogated the therapeutic effects of peptide-pulsed dc in vivo. the analysis of the cytokine pattern in the draining lymph nodes and spleens of tumor-bearing mice immunized with dc pulsed with tumor-eluted peptides revealed a marked upregulation of interleukin (il) 4 and interferon (ifn) gamma production, as compared with mice immunized with dc alone or dc pulsed with irrelevant peptides. dc-induced antitumor effects were completely blocked by coadministration of neutralizing monoclonal antibody directed against t helper cell 1-associated cytokines (such as il-12, tumor necrosis factor alpha, ifn-gamma), and eventually, but not initially, blocked by anti-mil-4 mab. based on these results, we believe that dc pulsed with acid-eluted peptides derived from autologous tumors represents a novel approach to the treatment of established, weakly immunogenic tumors, and serves as a basis for designing clinical trials in cancer patients.",0
"the immuno polymorphism database (ipd) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. through the ipd project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the major histocompatibility complex in a number of different species. we have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to ipd for online publication. ipd consists of five core databases, with the imgt/hla database as the primary database. through the work of the various nomenclature committees, the hla informatics group and in collaboration with the european bioinformatics institute we are able to provide public access to this data through the website the ipd project continues to develop with new tools being added to address scientific developments, such as next generation sequencing, and to address user feedback and requests. regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.",0
"the chi-square statistic is a non-parametric (distribution free) tool designed to analyze group differences when the dependent variable is measured at a nominal level. like all non-parametric statistics, the chi-square is robust with respect to the distribution of the data. specifically, it does not require equality of variances among the study groups or homoscedasticity in the data. it permits evaluation of both dichotomous independent variables, and of multiple group studies. unlike many other non-parametric and some parametric statistics, the calculations needed to compute the chi-square provide considerable information about how each of the groups performed in the study. this richness of detail allows the researcher to understand the results and thus to derive more detailed information from this statistic than from many others. the chi-square is a significance statistic, and should be followed with a strength statistic. the cramer's v is the most common strength test used to test the data when a significant chi-square result has been obtained. advantages of the chi-square include its robustness with respect to distribution of the data, its ease of computation, the detailed information that can be derived from the test, its use in studies for which parametric assumptions cannot be met, and its flexibility in handling data from both two group and multiple group studies. limitations include its sample size requirements, difficulty of interpretation when there are large numbers of categories (20 or more) in the independent or dependent variables, and tendency of the cramer's v to produce relative low correlation measures, even for highly significant results.",0
"guidelines for use of wild mammal species in research are updated from sikes et al. (2011) . these guidelines cover current professional techniques and regulations involving the use of mammals in research and teaching; they also incorporate new resources, procedural summaries, and reporting requirements. included are details on capturing, marking, housing, and humanely killing wild mammals. it is recommended that institutional animal care and use committees (iacucs), regulatory agencies, and investigators use these guidelines as a resource for protocols involving wild mammals, whether studied in the field or in captivity. these guidelines were prepared and approved by the american society of mammalogists (asm), in consultation with professional veterinarians experienced in wildlife research and iacucs, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals. the current version of these guidelines and any subsequent modifications are available online on the animal care and use committee page of the asm website ( ). additional resources pertaining to the use of wild animals in research are available at: .",0
"background neurological disorders are now the leading source of disability globally, and ageing is increasing the burden of neurodegenerative disorders, including parkinson's disease. we aimed to determine the global burden of parkinson's disease between 1990 and 2016 to identify trends and to enable appropriate public health, medical, and scientific responses. methods through a systematic analysis of epidemiological studies, we estimated global, regional, and country-specific prevalence and years of life lived with disability for parkinson's disease from 1990 to 2016. we estimated the proportion of mild, moderate, and severe parkinson's disease on the basis of studies that used the hoehn and yahr scale and assigned disability weights to each level. we jointly modelled prevalence and excess mortality risk in a natural history model to derive estimates of deaths due to parkinson's disease. death counts were multiplied by values from the global burden of disease study's standard life expectancy to compute years of life lost. disability-adjusted life-years (dalys) were computed as the sum of years lived with disability and years of life lost. we also analysed results based on the socio-demographic index, a compound measure of income per capita, education, and fertility. findings in 2016, 6·1 million (95% uncertainty interval 5·0-7·3) individuals had parkinson's disease globally, compared with 2·5 million (2·0-3·0) in 1990. this increase was not solely due to increasing numbers of older people, because age-standardised prevalence rates increased by 21·7% (95% ui 18·1-25·3) over the same period (compared with an increase of 74·3%, 95% ui 69·2-79·6, for crude prevalence rates). parkinson's disease caused 3·2 million (95% ui 2·6-4·0) dalys and 211 296 deaths (95% ui 167 771-265 160) in 2016. the male-to-female ratios of age-standardised prevalence rates were similar in 2016 (1·40, 95% ui 1·36-1·43) and 1990 (1·37, 1·34-1·40). from 1990 to 2016, age-standardised prevalence, daly rates, and death rates increased for all global burden of disease regions except for southern latin america, eastern europe, and oceania. in addition, age-standardised daly rates generally increased across the socio-demographic index. interpretation over the past generation, the global burden of parkinson's disease has more than doubled as a result of increasing numbers of older people, with potential contributions from longer disease duration and environmental factors. demographic and potentially other factors are poised to increase the future burden of parkinson's disease substantially. funding bill & melinda gates foundation.",0
"lymphocytes from balb/c or c57b6/6 mice that develop killer activity to alloantigens belong to the numerically small ly-23 subclass of peripheral t cells, distinguished by selective expression of ly-23 determinants on their surfaces. the maturation of these cells to killer cells can be amplified by ly-1+ cells, which do not themselves contribute to the killer cell pool. this amplification was abolished by escluding ia(""beta"")+ cells from the stimulator population during mixed lymphocyte culture (mcl), suggesting that amplification is due to selective recognition of i region antigens by l-1+ cells, a conclusion already drawn from our previous evidence that ia differences activate ly-1+ cells but not ly-23+ cells. these and other experiments indicate that amplification of killer cell production in vitro by ly-1+ cells is not due to their conversion to ly-23+ cells during mlc, but to their ability to recognize major histocompatibility complex determinants not recognized by ly-23+ cells.",0
"diabetes is a complex metabolic disorder affecting the glucose status of the human body. chronic hyperglycaemia related to diabetes is associated with end organ failure. the clinical relationship between diabetes and atherosclerotic cardiovascular disease is well established. this makes therapeutic approaches that simultaneously target diabetes and atherosclerotic disease an attractive area for research. the majority of people with diabetes fall into two broad pathogenetic categories, type 1 or type 2 diabetes. the role of obesity, adipose tissue, gut microbiota and pancreatic beta cell function in diabetes are under intensive scrutiny with several clinical trials to have been completed while more are in development. the emerging role of inflammation in both type 1 and type 2 diabetes (t1d and t1d) pathophysiology and associated metabolic disorders, has generated increasing interest in targeting inflammation to improve prevention and control of the disease. after an extensive review of the possible mechanisms that drive the metabolic pattern in t1d and t2d and the inflammatory pathways that are involved, it becomes ever clearer that future research should focus on a model of combined suppression for various inflammatory response pathways.",0
"elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. to date, identification of common genetic variants influencing blood pressure has proven challenging. we tested 2.5 million genotyped and imputed snps for association with systolic and diastolic blood pressure in 34,433 subjects of european ancestry from the global bpgen consortium and followed up findings with direct genotyping (n ≤ 71,225 european ancestry, n ≤ 12,889 indian asian ancestry) and in silico comparison (charge consortium, n = 29,136). we identified association between systolic or diastolic blood pressure and common variants in eight regions near the cyp17a1 (p = 7 × 10(-24)), cyp1a2 (p = 1 × 10(-23)), fgf5 (p = 1 × 10(-21)), sh2b3 (p = 3 × 10(-18)), mthfr (p = 2 × 10(-13)), c10orf107 (p = 1 × 10(-9)), znf652 (p = 5 × 10(-9)) and plcd3 (p = 1 × 10(-8)) genes. all variants associated with continuous blood pressure were associated with dichotomous hypertension. these associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.",0
"the short chain fatty acids (scfas) acetate (c(2)), propionate (c(3)) and butyrate (c(4)) are the main metabolic products of anaerobic bacteria fermentation in the intestine. in addition to their important role as fuel for intestinal epithelial cells, scfas modulate different processes in the gastrointestinal (gi) tract such as electrolyte and water absorption. these fatty acids have been recognized as potential mediators involved in the effects of gut microbiota on intestinal immune function. scfas act on leukocytes and endothelial cells through at least two mechanisms: activation of gpcrs (gpr41 and gpr43) and inhibiton of histone deacetylase (hdac). scfas regulate several leukocyte functions including production of cytokines (tnf-α, il-2, il-6 and il-10), eicosanoids and chemokines (e.g., mcp-1 and cinc-2). the ability of leukocytes to migrate to the foci of inflammation and to destroy microbial pathogens also seems to be affected by the scfas. in this review, the latest research that describes how scfas regulate the inflammatory process is presented. the effects of these fatty acids on isolated cells (leukocytes, endothelial and intestinal epithelial cells) and, particularly, on the recruitment and activation of leukocytes are discussed. therapeutic application of these fatty acids for the treatment of inflammatory pathologies is also highlighted.",0
"background the assessment of calibration performance of risk prediction models based on regression or more flexible machine learning algorithms receives little attention. main text herein, we argue that this needs to change immediately because poorly calibrated algorithms can be misleading and potentially harmful for clinical decision-making. we summarize how to avoid poor calibration at algorithm development and how to assess calibration at algorithm validation, emphasizing balance between model complexity and the available sample size. at external validation, calibration curves require sufficiently large samples. algorithm updating should be considered for appropriate support of clinical practice. conclusion efforts are required to avoid poor calibration when developing prediction models, to evaluate calibration when validating models, and to update models when indicated. the ultimate aim is to optimize the utility of predictive analytics for shared decision-making and patient counseling.",0
"as the size of functional and structural mri datasets expands, it becomes increasingly important to establish a baseline from which diagnostic relevance may be determined, a processing strategy that efficiently prepares data for analysis, and a statistical approach that identifies important effects in a manner that is both robust and reproducible. in this paper, we introduce a multivariate analytic approach that optimizes sensitivity and reduces unnecessary testing. we demonstrate the utility of this mega-analytic approach by identifying the effects of age and gender on the resting-state networks (rsns) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). data were collected on the same scanner, preprocessed using an automated analysis pipeline based in spm, and studied using group independent component analysis. rsns were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. these findings, along with the analysis approach and statistical framework described here, provide a useful baseline for future investigations of brain networks in health and disease.",0
"antigen injection into animals causes antigen-specific t cells to become activated and, rapidly thereafter, die. this antigen-induced death is inhibited by inflammation. to find out how inflammation has this effect, various cytokines were tested for their ability to interfere with the rapid death of activated t cells. t cells were activated in vivo, isolated, and cultured with the test reagents. two groups of cytokines were active, members of the interleukin 2 family and the interferons (ifns) alpha and beta. this activity of ifn-alpha/beta has not been described previously. it was due to direct effects of the ifns on the t cells and was not mediated by induction of a second cytokine such as interleukin 15. ifn-gamma did not slow the death of activated t cells, and therefore the activity of ifn-alpha/beta was not mediated only by activation of stat 1, a protein that is affected by both classes of ifn. ifn-alpha/beta did not raise the levels of bcl-2 or bcl-xl in t cells. therefore, their activity was distinct from that of members of the interleukin 2 family or cd28 engagement. since ifn-alpha/beta are very efficiently generated in response to viral and bacterial infections, these molecules may be among the signals that the immune system uses to prevent activated t cell death during infections.",0
"background it is unclear whether more timely cancer diagnosis brings favourable outcomes, with much of the previous evidence, in some cancers, being equivocal. we set out to determine whether there is an association between time to diagnosis, treatment and clinical outcomes, across all cancers for symptomatic presentations. methods systematic review of the literature and narrative synthesis. results we included 177 articles reporting 209 studies. these studies varied in study design, the time intervals assessed and the outcomes reported. study quality was variable, with a small number of higher-quality studies. heterogeneity precluded definitive findings. the cancers with more reports of an association between shorter times to diagnosis and more favourable outcomes were breast, colorectal, head and neck, testicular and melanoma. conclusions this is the first review encompassing many cancer types, and we have demonstrated those cancers in which more evidence of an association between shorter times to diagnosis and more favourable outcomes exists, and where it is lacking. we believe that it is reasonable to assume that efforts to expedite the diagnosis of symptomatic cancer are likely to have benefits for patients in terms of improved survival, earlier-stage diagnosis and improved quality of life, although these benefits vary between cancers.",0
"human blood mononuclear leukocytes stimulated with toxoplasma antigen, concanavalin a, mezerein plus lentil lectin, or staphylococcal enterotoxin a secreted a factor (macrophage-activating factor, or maf) that enhanced the capacity of human macrophages to release h2o2 and to kill toxoplasmas. the same lymphoid supernatants contained ifn gamma but not ifn alpha or ifn beta. the maf activity of six of seven unfractionated supernatants was completely eliminated by a monoclonal antibody that neutralizes ifn gamma, and maf in the remaining supernatant was almost completely neutralized. native ifn gamma partially purified by two independent protocols to specific activities of 1 x 10(6) and 10(7) u/mg protein was enriched in maf activity at least as much as in antiviral activity. the capacity of macrophages to secrete h2o2 after incubation in partially purified native ifn gamma (mean peak stimulation, 8.8-fold) was greater than with unpurified lymphokines (3.8-fold) and sometimes equaled or exceeded the capacity of freshly harvested monocytes. the maf activity of the partially purified native ifn gamma preparations was abolished by monoclonal anti-ifn gamma. finally, ifn gamma of greater than 99% estimated purity was isolated (at genentech, inc.) from bacteria transformed with the cloned human gene for this lymphokine. recombinant ifn gamma had potent maf activity, stimulating the peroxide-releasing capacity of macrophages an average of 19.8-fold at peak response and enhancing their ability to kill toxoplasmas from 2.6 +/- 1.3% for untreated cells to 54 +/- 0.4% for treated cells. attainment of 50% of the maximal elevation in peroxide-releasing capacity required a geometric mean concentration of 0.1 antiviral u/ml of recombinant ifn gamma, which is estimated to be approximately 6 picomolar for this preparation. peroxide secretory capacity and toxoplasmacidal activity of macrophages peaked 2-4 d after exposure to ifn gamma. peroxide-secretory capacity remained elevated during at least 6 d of continuous exposure, but the effect of ifn gamma was reversed within about 3 d of its removal. activation was usually but not invariably accompanied by characteristic changes in cell morphology. thus, ifn gamma activates human macrophage oxidative metabolism and antimicrobial activity, and appeared to be the only factor consistently capable of doing so in the diverse lk preparations tested.",0
"preeclampsia is a serious complication of pregnancy in which the fetus receives an inadequate supply of blood due to failure of trophoblast invasion. there is evidence that the condition has an immunological basis. the only known polymorphic histocompatibility antigens on the fetal trophoblast are hla-c molecules. we tested the idea that recognition of these molecules by killer immunoglobulin receptors (kirs) on maternal decidual nk cells is a key factor in the development of preeclampsia. striking differences were observed when these polymorphic ligand: receptor pairs were considered in combination. mothers lacking most or all activating kir (aa genotype) when the fetus possessed hla-c belonging to the hla-c2 group were at a greatly increased risk of preeclampsia. this was true even if the mother herself also had hla-c2, indicating that neither nonself nor missing-self discrimination was operative. thus, this interaction between maternal kir and trophoblast appears not to have an immune function, but instead plays a physiological role related to placental development. different human populations have a reciprocal relationship between aa frequency and hla-c2 frequency, suggesting selection against this combination. in light of our findings, reproductive success may have been a factor in the evolution and maintenance of human hla-c and kir polymorphisms.",0
"background the global burden of diseases, injuries, and risk factors study (gbd) 2016 provides an up-to-date analysis of the burden of diarrhoea in 195 countries. this study assesses cases, deaths, and aetiologies in 1990-2016 and assesses how the burden of diarrhoea has changed in people of all ages. methods we modelled diarrhoea mortality with a bayesian hierarchical modelling platform that evaluates a wide range of covariates and model types on the basis of vital registration and verbal autopsy data. we modelled diarrhoea incidence with a compartmental meta-regression tool that enforces an association between incidence and prevalence, and relies on scientific literature, population representative surveys, and health-care data. diarrhoea deaths and episodes were attributed to 13 pathogens by use of a counterfactual population attributable fraction approach. diarrhoea risk factors are also based on counterfactual estimates of risk exposure and the association between the risk and diarrhoea. each modelled estimate accounted for uncertainty. findings in 2016, diarrhoea was the eighth leading cause of death among all ages (1 655 944 deaths, 95% uncertainty interval 1 244 073-2 366 552) and the fifth leading cause of death among children younger than 5 years (446 000 deaths, 390 894-504 613). rotavirus was the leading aetiology for diarrhoea mortality among children younger than 5 years (128 515 deaths, 105 138-155 133) and among all ages (228 047 deaths, 183 526-292 737). childhood wasting (low weight-for-height score), unsafe water, and unsafe sanitation were the leading risk factors for diarrhoea, responsible for 80·4% (95% ui 68·2-85·0), 72·1% (34·0-91·4), and 56·4% (49·3-62·7) of diarrhoea deaths in children younger than 5 years, respectively. prevention of wasting in 1762 children (95% ui 1521-2170) could avert one death from diarrhoea. interpretation substantial progress has been made globally in reducing the burden of diarrhoeal diseases, driven by decreases in several primary risk factors. however, this reduction has not been equal across locations, and burden among adults older than 70 years requires attention. funding bill & melinda gates foundation.",0
"extensive evidence suggests that the human ability to adaptively implement a wide variety of tasks is preferentially a result of the operation of a fronto-parietal brain network (fpn). we hypothesized that this network's adaptability is made possible by flexible hubs: brain regions that rapidly update their pattern of global functional connectivity according to task demands. using recent advances in characterizing brain network organization and dynamics, we identified mechanisms consistent with the flexible hub theory. we found that the fpn's brain-wide functional connectivity pattern shifted more than those of other networks across a variety of task states and that these connectivity patterns could be used to identify the current task. furthermore, these patterns were consistent across practiced and novel tasks, suggesting that reuse of flexible hub connectivity patterns facilitates adaptive (novel) task performance. together, these findings support a central role for fronto-parietal flexible hubs in cognitive control and adaptive implementation of task demands.",0
"activated rhoa, a ras-related gtp-binding protein, stimulates the appearance of stress fibers, focal adhesions, and tyrosine phosphorylation in quiescent cells (ridley, a.j., and a. hall, 1992. cell. 70:389-399). the pathway by which rho triggers these events has not been elucidated. many of the agents that activate rho (e.g., vasopressin, endothelin, lysophosphatidic acid) stimulate the contractility of smooth muscle and other cells. we have investigated whether rho's induction of stress fibers, focal adhesions, and tyrosine phosphorylation is the result of its stimulation of contractility. we demonstrate that stimulation of fibroblasts with lysophosphatidic acid, which activates rho, induces myosin light chain phosphorylation. this precedes the formation of stress fibers and focal adhesions and is accompanied by increased contractility. inhibition of contractility by several different mechanisms leads to inhibition of rho-induced stress fibers, focal adhesions, and tyrosine phosphorylation. in addition, when contractility is inhibited, integrins disperse from focal adhesions as stress fibers and focal adhesions disassemble. conversely, upon stimulation of contractility, diffusely distributed integrins are aggregated into focal adhesions. these results suggest that activated rho stimulates contractility, driving the formation of stress fibers and focal adhesions and elevating tyrosine phosphorylation. a model is proposed to account for how contractility could promote these events.",0
"clinvar ( at the national center for biotechnology information (ncbi) is a freely available archive for interpretations of clinical significance of variants for reported conditions. the database includes germline and somatic variants of any size, type or genomic location. interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, omim®, genereviews™, uniprot, expert panels and practice guidelines. in ncbi's variation submission portal, submitters upload batch submissions or use the submission wizard for single submissions. each submitted interpretation is assigned an accession number prefixed with scv. clinvar staff review validation reports with data types such as hgvs (human genome variation society) expressions; however, clinical significance is reported directly from submitters. interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with rcv. clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. clinvar uses data standards, such as hgvs nomenclature for variants and medgen identifiers for conditions. the data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. programmatic access for clinvar records is available through ncbi's e-utilities. future development includes providing a variant-centric xml archive and a web page for details of scv submissions.",0
"specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. inspired by molecular modeling, we replaced the n,n-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. this addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. the novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the uv and visible range.",0
"the transfac database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database transcompel on composite elements have been further enhanced on various levels. a new web interface with different search options and integrated versions of match and patch provides increased functionality for transfac. the list of databases which are linked to the common gene table of transfac and transcompel has been extended by: ensembl, unigene, entrezgene, humanpsd and transpro. standard gene names from hgnc, mgi and rgd, are included for human, mouse and rat genes, respectively. with the help of interproscan, pfam, smart and prosite domains are assigned automatically to the protein sequences of the transcription factors. transcompel contains now, in addition to the compel table, a separate table for detailed information on the experimental evidence on which the composite elements are based. finally, for transfac, in respect of data growth, in particular the gain of drosophila transcription factor binding sites (by courtesy of the drosophila dnase i footprint database) and of arabidopsis factors (by courtesy of datf, database of arabidopsis transcription factors) has to be stressed. the here described public releases, transfac 7.0 and transcompel 7.0, are accessible under",0
"glycolysis has long been considered as the major metabolic process for energy production and anabolic growth in cancer cells. although such a view has been instrumental for the development of powerful imaging tools that are still used in the clinics, it is now clear that mitochondria play a key role in oncogenesis. besides exerting central bioenergetic functions, mitochondria provide indeed building blocks for tumor anabolism, control redox and calcium homeostasis, participate in transcriptional regulation, and govern cell death. thus, mitochondria constitute promising targets for the development of novel anticancer agents. however, tumors arise, progress, and respond to therapy in the context of an intimate crosstalk with the host immune system, and many immunological functions rely on intact mitochondrial metabolism. here, we review the cancer cell-intrinsic and cell-extrinsic mechanisms through which mitochondria influence all steps of oncogenesis, with a focus on the therapeutic potential of targeting mitochondrial metabolism for cancer therapy.",0
"background in the era of evidence based medicine, with systematic reviews as its cornerstone, adequate quality assessment tools should be available. there is currently a lack of a systematically developed and evaluated tool for the assessment of diagnostic accuracy studies. the aim of this project was to combine empirical evidence and expert opinion in a formal consensus method to develop a tool to be used in systematic reviews to assess the quality of primary studies of diagnostic accuracy. methods we conducted a delphi procedure to develop the quality assessment tool by refining an initial list of items. members of the delphi panel were experts in the area of diagnostic research. the results of three previously conducted reviews of the diagnostic literature were used to generate a list of potential items for inclusion in the tool and to provide an evidence base upon which to develop the tool. results a total of nine experts in the field of diagnostics took part in the delphi procedure. the delphi procedure consisted of four rounds, after which agreement was reached on the items to be included in the tool which we have called quadas. the initial list of 28 items was reduced to fourteen items in the final tool. items included covered patient spectrum, reference standard, disease progression bias, verification bias, review bias, clinical review bias, incorporation bias, test execution, study withdrawals, and indeterminate results. the quadas tool is presented together with guidelines for scoring each of the items included in the tool. conclusions this project has produced an evidence based quality assessment tool to be used in systematic reviews of diagnostic accuracy studies. further work to determine the usability and validity of the tool continues.",0
"development of strategies for mitigating the severity of a new influenza pandemic is now a top global public health priority. influenza prevention and containment strategies can be considered under the broad categories of antiviral, vaccine and non-pharmaceutical (case isolation, household quarantine, school or workplace closure, restrictions on travel) measures. mathematical models are powerful tools for exploring this complex landscape of intervention strategies and quantifying the potential costs and benefits of different options. here we use a large-scale epidemic simulation to examine intervention options should initial containment of a novel influenza outbreak fail, using great britain and the united states as examples. we find that border restrictions and/or internal travel restrictions are unlikely to delay spread by more than 2-3 weeks unless more than 99% effective. school closure during the peak of a pandemic can reduce peak attack rates by up to 40%, but has little impact on overall attack rates, whereas case isolation or household quarantine could have a significant impact, if feasible. treatment of clinical cases can reduce transmission, but only if antivirals are given within a day of symptoms starting. given enough drugs for 50% of the population, household-based prophylaxis coupled with reactive school closure could reduce clinical attack rates by 40-50%. more widespread prophylaxis would be even more logistically challenging but might reduce attack rates by over 75%. vaccine stockpiled in advance of a pandemic could significantly reduce attack rates even if of low efficacy. estimates of policy effectiveness will change if the characteristics of a future pandemic strain differ substantially from those seen in past pandemics.",0
"background traumatic brain injury (tbi) is a leading cause of death and disability. a reliable prediction of outcome on admission is of great clinical relevance. we aimed to develop prognostic models with readily available traditional and novel predictors. methods and findings prospectively collected individual patient data were analyzed from 11 studies. we considered predictors available at admission in logistic regression models to predict mortality and unfavorable outcome according to the glasgow outcome scale at 6 mo after injury. prognostic models were developed in 8,509 patients with severe or moderate tbi, with cross-validation by omission of each of the 11 studies in turn. external validation was on 6,681 patients from the recent medical research council corticosteroid randomisation after significant head injury (mrc crash) trial. we found that the strongest predictors of outcome were age, motor score, pupillary reactivity, and ct characteristics, including the presence of traumatic subarachnoid hemorrhage. a prognostic model that combined age, motor score, and pupillary reactivity had an area under the receiver operating characteristic curve (auc) between 0.66 and 0.84 at cross-validation. this performance could be improved (auc increased by approximately 0.05) by considering ct characteristics, secondary insults (hypotension and hypoxia), and laboratory parameters (glucose and hemoglobin). external validation confirmed that the discriminative ability of the model was adequate (auc 0.80). outcomes were systematically worse than predicted, but less so in 1,588 patients who were from high-income countries in the crash trial. conclusions prognostic models using baseline characteristics provide adequate discrimination between patients with good and poor 6 mo outcomes after tbi, especially if ct and laboratory findings are considered in addition to traditional predictors. the model predictions may support clinical practice and research, including the design and analysis of randomized controlled trials.",0
"objectives to assess the incidence of and risks for congestive heart failure, myocardial infarction, pericardial disease, and valvular abnormalities among adult survivors of childhood and adolescent cancers. design retrospective cohort study. setting 26 institutions that participated in the childhood cancer survivor study. participants 14,358 five year survivors of cancer diagnosed under the age of 21 with leukaemia, brain cancer, hodgkin's lymphoma, non-hodgkin's lymphoma, kidney cancer, neuroblastoma, soft tissue sarcoma, or bone cancer between 1970 and 1986. comparison group included 3899 siblings of cancer survivors. main outcome measures participants or their parents (in participants aged less than 18 years) completed a questionnaire collecting information on demographic characteristics, height, weight, health habits, medical conditions, and surgical procedures occurring since diagnosis. the main outcome measures were the incidence of and risk factors for congestive heart failure, myocardial infarction, pericardial disease, and valvular abnormalities in survivors of cancer compared with siblings. results survivors of cancer were significantly more likely than siblings to report congestive heart failure (hazard ratio (hr) 5.9, 95% confidence interval 3.4 to 9.6; p conclusion survivors of childhood and adolescent cancer are at substantial risk for cardiovascular disease. healthcare professionals must be aware of these risks when caring for this growing population.",0
"by using the two criteria (a) high density of immunoglobulin determinants on the cell surface and (b) presence of receptors for c'3 on the cell surface for defining bone marrow-derived lymphocytes, it is indirectly shown that all or at least a major population of human thymus-derived lymphocytes under certain conditions will form nonimmune rosettes with sheep red blood cells (srbc). almost all thymocytes tested from two different donors formed rosettes. the srbc rosettes are not formed by virtue of immunoglobulin receptors and form only around living cells. positive bivalent ions are required for rosette formation since edta will block rosette formation. sodium iodoacetate will also block rosette formation demonstrating the dependence on an intact glycolytic pathway. rosette formation is temperature dependent and will not appear at 37 degrees c. trypsin treatment of lymphocytes will abolish their srbc-binding ability which cannot be restored by treating them with fresh donor serum or fetal calf serum, but which will reappear after culturing the lymphocytes. it is suggested that these rosettes are formed by a rapidly released or metabolized receptor substance on the living cell surface which behaves as a trypsin-sensitive structure produced by the cells themselves.",0
"recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. here we present merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. by comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, merqury estimates base-level accuracy and completeness. for trios, merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. we demonstrate on both human and plant genomes that merqury is a fast and robust method for assembly validation.",0
"background diabetes is one of the leading causes of death and disability worldwide, and affects people regardless of country, age group, or sex. using the most recent evidentiary and analytical framework from the global burden of diseases, injuries, and risk factors study (gbd), we produced location-specific, age-specific, and sex-specific estimates of diabetes prevalence and burden from 1990 to 2021, the proportion of type 1 and type 2 diabetes in 2021, the proportion of the type 2 diabetes burden attributable to selected risk factors, and projections of diabetes prevalence through 2050. methods estimates of diabetes prevalence and burden were computed in 204 countries and territories, across 25 age groups, for males and females separately and combined; these estimates comprised lost years of healthy life, measured in disability-adjusted life-years (dalys; defined as the sum of years of life lost and years lived with disability ). we used the cause of death ensemble model (codem) approach to estimate deaths due to diabetes, incorporating 25 666 location-years of data from vital registration and verbal autopsy reports in separate total (including both type 1 and type 2 diabetes) and type-specific models. other forms of diabetes, including gestational and monogenic diabetes, were not explicitly modelled. total and type 1 diabetes prevalence was estimated by use of a bayesian meta-regression modelling tool, dismod-mr 2.1, to analyse 1527 location-years of data from the scientific literature, survey microdata, and insurance claims; type 2 diabetes estimates were computed by subtracting type 1 diabetes from total estimates. mortality and prevalence estimates, along with standard life expectancy and disability weights, were used to calculate ylls, ylds, and dalys. when appropriate, we extrapolated estimates to a hypothetical population with a standardised age structure to allow comparison in populations with different age structures. we used the comparative risk assessment framework to estimate the risk-attributable type 2 diabetes burden for 16 risk factors falling under risk categories including environmental and occupational factors, tobacco use, high alcohol use, high body-mass index (bmi), dietary factors, and low physical activity. using a regression framework, we forecast type 1 and type 2 diabetes prevalence through 2050 with socio-demographic index (sdi) and high bmi as predictors, respectively. findings in 2021, there were 529 million (95% uncertainty interval 500-564) people living with diabetes worldwide, and the global age-standardised total diabetes prevalence was 6·1% (5·8-6·5). at the super-region level, the highest age-standardised rates were observed in north africa and the middle east (9·3% ) and, at the regional level, in oceania (12·3% ). nationally, qatar had the world's highest age-specific prevalence of diabetes, at 76·1% (73·1-79·5) in individuals aged 75-79 years. total diabetes prevalence-especially among older adults-primarily reflects type 2 diabetes, which in 2021 accounted for 96·0% (95·1-96·8) of diabetes cases and 95·4% (94·9-95·9) of diabetes dalys worldwide. in 2021, 52·2% (25·5-71·8) of global type 2 diabetes dalys were attributable to high bmi. the contribution of high bmi to type 2 diabetes dalys rose by 24·3% (18·5-30·4) worldwide between 1990 and 2021. by 2050, more than 1·31 billion (1·22-1·39) people are projected to have diabetes, with expected age-standardised total diabetes prevalence rates greater than 10% in two super-regions: 16·8% (16·1-17·6) in north africa and the middle east and 11·3% (10·8-11·9) in latin america and caribbean. by 2050, 89 (43·6%) of 204 countries and territories will have an age-standardised rate greater than 10%. interpretation diabetes remains a substantial public health issue. type 2 diabetes, which makes up the bulk of diabetes cases, is largely preventable and, in some cases, potentially reversible if identified and managed early in the disease course. however, all evidence indicates that diabetes prevalence is increasing worldwide, primarily due to a rise in obesity caused by multiple factors. preventing and controlling type 2 diabetes remains an ongoing challenge. it is essential to better understand disparities in risk factor profiles and diabetes burden across populations, to inform strategies to successfully control diabetes risk factors within the context of multiple and complex drivers. funding bill & melinda gates foundation.",0
"objectives the aim of this study was to develop a critical appraisal (ca) tool that addressed study design and reporting quality as well as the risk of bias in cross-sectional studies (csss). in addition, the aim was to produce a help document to guide the non-expert user through the tool. design an initial scoping review of the published literature and key epidemiological texts was undertaken prior to the formation of a delphi panel to establish key components for a ca tool for csss. a consensus of 80% was required from the delphi panel for any component to be included in the final tool. results an initial list of 39 components was identified through examination of existing resources. an international delphi panel of 18 medical and veterinary experts was established. after 3 rounds of the delphi process, the appraisal tool for cross-sectional studies (axis tool) was developed by consensus and consisted of 20 components. a detailed explanatory document was also developed with the tool, giving expanded explanation of each question and providing simple interpretations and examples of the epidemiological concepts being examined in each question to aid non-expert users. conclusions ca of the literature is a vital step in evidence synthesis and therefore evidence-based decision-making in a number of different disciplines. the axis tool is therefore unique and was developed in a way that it can be used across disciplines to aid the inclusion of csss in systematic reviews, guidelines and clinical decision-making.",0
"a severe acute respiratory syndrome coronavirus 2 (sars-cov-2) variant, voc 202012/01 (lineage b.1.1.7), emerged in southeast england in september 2020 and is rapidly spreading toward fixation. using a variety of statistical and dynamic modeling approaches, we estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants. a fitted two-strain dynamic transmission model shows that voc 202012/01 will lead to large resurgences of covid-19 cases. without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine rollout, covid-19 hospitalizations and deaths across england in the first 6 months of 2021 were projected to exceed those in 2020. voc 202012/01 has spread globally and exhibits a similar transmission increase (59 to 74%) in denmark, switzerland, and the united states.",0
"this paper presents an overview of how to run the ccp4 programs for data reduction (scala, pointless and ctruncate) through the ccp4 graphical interface ccp4i and points out some issues that need to be considered, together with a few examples. it covers determination of the point-group symmetry of the diffraction data (the laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multiple data sets on a common indexing system when there are alternatives, the scaling step itself, which produces a large set of data-quality indicators, estimation of |f| from intensity and finally examination of intensity statistics to detect crystal pathologies such as twinning. an appendix outlines the scoring schemes used by the program pointless to assign probabilities to possible laue and space groups.",0
"the carbohydrate-active enzymes database (cazy; provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3d structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. functional and 3d structural information is added and curated on a regular basis based on the available literature. in addition to the use of the database by enzymologists seeking curated information on cazymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of cazy. the past few years have seen the expansion of the cazy classification scheme to new families, the development of subfamilies in several families and the power of cazy for the analysis of genomes and metagenomes. this article outlines the changes that have occurred in cazy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of cazymes.",0
"phenix.refine is a program within the phenix package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. it has several automation features and is also highly flexible. several hundred parameters enable extensive customizations for complex use cases. multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. an intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. x-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the phenix suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwpdb. this paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.",0
"tissue damage causes inflammation, by recruiting leukocytes and activating them to release proinflammatory mediators. we show that high-mobility group box 1 protein (hmgb1) orchestrates both processes by switching among mutually exclusive redox states. reduced cysteines make hmgb1 a chemoattractant, whereas a disulfide bond makes it a proinflammatory cytokine and further cysteine oxidation to sulfonates by reactive oxygen species abrogates both activities. we show that leukocyte recruitment and activation can be separated. a nonoxidizable hmgb1 mutant in which serines replace all cysteines (3s-hmgb1) does not promote cytokine production, but is more effective than wild-type hmgb1 in recruiting leukocytes in vivo. boxa, a hmgb1 inhibitor, interferes with leukocyte recruitment but not with activation. we detected the different redox forms of hmgb1 ex vivo within injured muscle. hmgb1 is completely reduced at first and disulfide-bonded later. thus, hmgb1 orchestrates both key events in sterile inflammation, leukocyte recruitment and their induction to secrete inflammatory cytokines, by adopting mutually exclusive redox states.",0
"pubchem ( is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. in the past two years, pubchem made substantial improvements. data from more than 100 new data sources were added to pubchem, including chemical-literature links from thieme chemistry, chemical and physical property links from springermaterials, and patent links from the world intellectual properties organization (wipo). pubchem's homepage and individual record pages were updated to help users find desired information faster. this update involved a data model change for the data objects used by these pages as well as by programmatic users. several new services were introduced, including the pubchem periodic table and element pages, pathway pages, and knowledge panels. additionally, in response to the coronavirus disease 2019 (covid-19) outbreak, pubchem created a special data collection that contains pubchem data related to covid-19 and the severe acute respiratory syndrome coronavirus 2 (sars-cov-2).",0
"background mobile health interventions could have beneficial effects on health care delivery processes. we aimed to conduct a systematic review of controlled trials of mobile technology interventions to improve health care delivery processes. methods and findings we searched for all controlled trials of mobile technology based health interventions using medline, embase, psycinfo, global health, web of science, cochrane library, uk nhs hta (jan 1990-sept 2010). two authors independently extracted data on allocation concealment, allocation sequence, blinding, completeness of follow-up, and measures of effect. we calculated effect estimates and we used random effects meta-analysis to give pooled estimates. we identified 42 trials. none of the trials had low risk of bias. seven trials of health care provider support reported 25 outcomes regarding appropriate disease management, of which 11 showed statistically significant benefits. one trial reported a statistically significant improvement in nurse/surgeon communication using mobile phones. two trials reported statistically significant reductions in correct diagnoses using mobile technology photos compared to gold standard. the pooled effect on appointment attendance using text message (short message service or sms) reminders versus no reminder was increased, with a relative risk (rr) of 1.06 (95% ci 1.05-1.07, i(2) = 6%). the pooled effects on the number of cancelled appointments was not significantly increased rr 1.08 (95% ci 0.89-1.30). there was no difference in attendance using sms reminders versus other reminders (rr 0.98, 95% ci 0.94-1.02, respectively). to address the limitation of the older search, we also reviewed more recent literature. conclusions the results for health care provider support interventions on diagnosis and management outcomes are generally consistent with modest benefits. trials using mobile technology-based photos reported reductions in correct diagnoses when compared to the gold standard. sms appointment reminders have modest benefits and may be appropriate for implementation. high quality trials measuring clinical outcomes are needed. please see later in the article for the editors' summary.",0
"alzheimer's disease is a progressive neurodegenerative disease most often associated with memory deficits and cognitive decline, although less common clinical presentations are increasingly recognized. the cardinal pathological features of the disease have been known for more than one hundred years, and today the presence of these amyloid plaques and neurofibrillary tangles are still required for a pathological diagnosis. alzheimer's disease is the most common cause of dementia globally. there remain no effective treatment options for the great majority of patients, and the primary causes of the disease are unknown except in a small number of familial cases driven by genetic mutations. confounding efforts to develop effective diagnostic tools and disease-modifying therapies is the realization that alzheimer's disease is a mixed proteinopathy (amyloid and tau) frequently associated with other age-related processes such as cerebrovascular disease and lewy body disease. defining the relationships between and interdependence of various co-pathologies remains an active area of investigation. this review outlines etiologically-linked pathologic features of alzheimer's disease, as well as those that are inevitable findings of uncertain significance, such as granulovacuolar degeneration and hirano bodies. other disease processes that are frequent, but not inevitable, are also discussed, including pathologic processes that can clinically mimic alzheimer's disease. these include cerebrovascular disease, lewy body disease, tdp-43 proteinopathies and argyrophilic grain disease. the purpose of this review is to provide an overview of alzheimer's disease pathology, its defining pathologic substrates and the related pathologies that can affect diagnosis and treatment.",0
"bcl-2 belongs to a family of apoptosis-regulatory proteins which incorporate into the outer mitochondrial as well as nuclear membranes. the mechanism by which the proto-oncogene product bcl-2 inhibits apoptosis is thus far elusive. we and others have shown previously that the first biochemical alteration detectable in cells undergoing apoptosis, well before nuclear changes become manifest, is a collapse of the mitochondrial inner membrane potential (delta psi m), suggesting the involvement of mitochondrial products in the apoptotic cascade. here we show that mitochondria contain a pre-formed approximately 50-kd protein which is released upon delta psi m disruption and which, in a cell-free in vitro system, causes isolated nuclei to undergo apoptotic changes such as chromatin condensation and internucleosomal dna fragmentation. this apoptosis-inducing factor (aif) is blocked by n-benzyloxycarbonyl-val-ala-asp.fluoromethylketone (z-vad.fmk), an antagonist of interleukin-1 beta-converting enzyme (ice)-like proteases that is also an efficient inhibitor of apoptosis in cells. we have tested the effect of bcl-2 on the formation, release, and action of aif. when preventing mitochondrial permeability transition (which accounts for the pre-apoptotic delta psi m disruption in cells), bcl-2 hyperexpressed in the outer mitochondrial membrane also impedes the release of aif from isolated mitochondria in vitro. in contrast, bcl-2 does not affect the formation of aif, which is contained in comparable quantities in control mitochondria and in mitochondria from bcl-2-hyperexpressing cells. furthermore, the presence of bcl-2 in the nuclear membrane does not interfere with the action of aif on the nucleus, nor does bcl-2 hyperexpression protect cells against aif. it thus appears that bcl-2 prevents apoptosis by favoring the retention of an apoptogenic protease in mitochondria.",0
"background nonlinear regression, like linear regression, assumes that the scatter of data around the ideal curve follows a gaussian or normal distribution. this assumption leads to the familiar goal of regression: to minimize the sum of the squares of the vertical or y-value distances between the points and the curve. outliers can dominate the sum-of-the-squares calculation, and lead to misleading results. however, we know of no practical method for routinely identifying outliers when fitting curves with nonlinear regression. results we describe a new method for identifying outliers when fitting data with nonlinear regression. we first fit the data using a robust form of nonlinear regression, based on the assumption that scatter follows a lorentzian distribution. we devised a new adaptive method that gradually becomes more robust as the method proceeds. to define outliers, we adapted the false discovery rate approach to handling multiple comparisons. we then remove the outliers, and analyze the data using ordinary least-squares regression. because the method combines robust regression and outlier removal, we call it the rout method. when analyzing simulated data, where all scatter is gaussian, our method detects (falsely) one or more outlier in only about 1-3% of experiments. when analyzing data contaminated with one or several outliers, the rout method performs well at outlier identification, with an average false discovery rate less than 1%. conclusion our method, which combines a new method of robust nonlinear regression with a new method of outlier identification, identifies outliers from nonlinear curve fits with reasonable power and few false positives.",0
"many different types of cancer show a high incidence of tp53 mutations, leading to the expression of mutant p53 proteins. there is growing evidence that these mutant p53s have both lost wild-type p53 tumor suppressor activity and gained functions that help to contribute to malignant progression. understanding the functions of mutant p53 will help in the development of new therapeutic approaches that may be useful in a broad range of cancer types.",0
"the pandemic of 2019 coronavirus disease (covid-19) has burdened an unprecedented psychological stress on people around the world, especially the medical workforce. the study focuses on assess the psychological status of them. the authors conducted a single-center, cross-sectional survey via online questionnaires. occurrence of fear, anxiety and depression were measured by the numeric rating scale (nrs) on fear, hamilton anxiety scale (hama), and hamilton depression scale (hamd), respectively. a total of 2299 eligible participants were enrolled from the authors' institution, including 2042 medical staff and 257 administrative staff. the severity of fear, anxiety and depression were significantly different between two groups. furthermore, as compared to the non-clinical staff, front line medical staff with close contact with infected patients, including working in the departments of respiratory, emergency, infectious disease, and icu, showed higher scores on fear scale, hama and hamd, and they were 1.4 times more likely to feel fear, twice more likely to suffer anxiety and depression. the medical staff especially working in above-mentioned departments made them more susceptible to psychological disorders. effective strategies toward to improving the mental health should be provided to these individuals.",0
"large numbers and large quantities of endocrine-disrupting chemicals have been released into the environment since world war ii. many of these chemicals can disturb development of the endocrine system and of the organs that respond to endocrine signals in organisms indirectly exposed during prenatal and/or early postnatal life; effects of exposure during development are permanent and irreversible. the risk to the developing organism can also stem from direct exposure of the offspring after birth or hatching. in addition, transgenerational exposure can result from the exposure of the mother to a chemical at any time throughout her life before producing offspring due to persistence of endocrine-disrupting chemicals in body fat, which is mobilized during egg laying or pregnancy and lactation. mechanisms underlying the disruption of the development of vital systems, such as the endocrine, reproductive, and immune systems, are discussed with reference to wildlife, laboratory animals, and humans.",0
"background along with its high infectivity and fatality rates, the 2019 corona virus disease (covid-19) has caused universal psychosocial impact by causing mass hysteria, economic burden and financial losses. mass fear of covid-19, termed as ""coronaphobia"", has generated a plethora of psychiatric manifestations across the different strata of the society. so, this review has been undertaken to define psychosocial impact of covid-19. methods pubmed and googlescholar are searched with the following key terms- ""covid-19"", ""sars-cov2"", ""pandemic"", ""psychology"", ""psychosocial"", ""psychitry"", ""marginalized"", ""telemedicine"", ""mental health"", ""quarantine"", ""infodemic"", ""social media"" and"" ""internet"". few news paper reports related to covid-19 and psychosocial impacts have also been added as per context. results disease itself multiplied by forced quarantine to combat covid-19 applied by nationwide lockdowns can produce acute panic, anxiety, obsessive behaviors, hoarding, paranoia, and depression, and post-traumatic stress disorder (ptsd) in the long run. these have been fueled by an ""infodemic"" spread via different platforms of social media. outbursts of racism, stigmatization, and xenophobia against particular communities are also being widely reported. nevertheless, frontline healthcare workers are at higher-risk of contracting the disease as well as experiencing adverse psychological outcomes in form of burnout, anxiety, fear of transmitting infection, feeling of incompatibility, depression, increased substance-dependence, and ptsd. community-based mitigation programs to combat covid-19 will disrupt children's usual lifestyle and may cause florid mental distress. the psychosocial aspects of older people, their caregivers, psychiatric patients and marginalized communities are affected by this pandemic in different ways and need special attention. conclusion for better dealing with these psychosocial issues of different strata of the society, psychosocial crisis prevention and intervention models should be urgently developed by the government, health care personnel and other stakeholders. apt application of internet services, technology and social media to curb both pandemic and infodemic needs to be instigated. psychosocial preparedness by setting up mental organizations specific for future pandemics is certainly necessary.",0
"background an ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (sars-cov-2) started in december, 2019, in wuhan, china. information about critically ill patients with sars-cov-2 infection is scarce. we aimed to describe the clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia. methods in this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with sars-cov-2 pneumonia who were admitted to the intensive care unit (icu) of wuhan jin yin-tan hospital (wuhan, china) between late december, 2019, and jan 26, 2020. demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected. data were compared between survivors and non-survivors. the primary outcome was 28-day mortality, as of feb 9, 2020. secondary outcomes included incidence of sars-cov-2-related acute respiratory distress syndrome (ards) and the proportion of patients requiring mechanical ventilation. findings of 710 patients with sars-cov-2 pneumonia, 52 critically ill adult patients were included. the mean age of the 52 patients was 59·7 (sd 13·3) years, 35 (67%) were men, 21 (40%) had chronic illness, 51 (98%) had fever. 32 (61·5%) patients had died at 28 days, and the median duration from admission to the intensive care unit (icu) to death was 7 (iqr 3-11) days for non-survivors. compared with survivors, non-survivors were older (64·6 years vs 51·9 years ), more likely to develop ards (26 patients vs 9 patients), and more likely to receive mechanical ventilation (30 patients vs 7 patients), either invasively or non-invasively. most patients had organ function damage, including 35 (67%) with ards, 15 (29%) with acute kidney injury, 12 (23%) with cardiac injury, 15 (29%) with liver dysfunction, and one (2%) with pneumothorax. 37 (71%) patients required mechanical ventilation. hospital-acquired infection occurred in seven (13·5%) patients. interpretation the mortality of critically ill patients with sars-cov-2 pneumonia is considerable. the survival time of the non-survivors is likely to be within 1-2 weeks after icu admission. older patients (>65 years) with comorbidities and ards are at increased risk of death. the severity of sars-cov-2 pneumonia poses great strain on critical care resources in hospitals, especially if they are not adequately staffed or resourced. funding none.",0
"many genetic variations are single nucleotide polymorphisms (snps). non-synonymous snps are 'neutral' if the resulting point-mutated protein is not functionally discernible from the wild type and 'non-neutral' otherwise. the ability to identify non-neutral substitutions could significantly aid targeting disease causing detrimental mutations, as well as snps that increase the fitness of particular phenotypes. here, we introduced comprehensive data sets to assess the performance of methods that predict snp effects. along we introduced snap (screening for non-acceptable polymorphisms), a neural network-based method for the prediction of the functional effects of non-synonymous snps. snap needs only sequence information as input, but benefits from functional and structural annotations, if available. in a cross-validation test on over 80,000 mutants, snap identified 80% of the non-neutral substitutions at 77% accuracy and 76% of the neutral substitutions at 80% accuracy. this constituted an important improvement over other methods; the improvement rose to over ten percentage points for mutants for which existing methods disagreed. possibly even more importantly snap introduced a well-calibrated measure for the reliability of each prediction. this measure will allow users to focus on the most accurate predictions and/or the most severe effects. available at",0
"objective to evaluate the breadth, validity, and presence of biases of the associations of vitamin d with diverse outcomes. design umbrella review of the evidence across systematic reviews and meta-analyses of observational studies of plasma 25-hydroxyvitamin d or 1,25-dihydroxyvitamin d concentrations and randomised controlled trials of vitamin d supplementation. data sources medline, embase, and screening of citations and references. eligibility criteria three types of studies were eligible for the umbrella review: systematic reviews and meta-analyses that examined observational associations between circulating vitamin d concentrations and any clinical outcome; and meta-analyses of randomised controlled trials assessing supplementation with vitamin d or active compounds (both established and newer compounds of vitamin d). results 107 systematic literature reviews and 74 meta-analyses of observational studies of plasma vitamin d concentrations and 87 meta-analyses of randomised controlled trials of vitamin d supplementation were identified. the relation between vitamin d and 137 outcomes has been explored, covering a wide range of skeletal, malignant, cardiovascular, autoimmune, infectious, metabolic, and other diseases. ten outcomes were examined by both meta-analyses of observational studies and meta-analyses of randomised controlled trials, but the direction of the effect and level of statistical significance was concordant only for birth weight (maternal vitamin d status or supplementation). on the basis of the available evidence, an association between vitamin d concentrations and birth weight, dental caries in children, maternal vitamin d concentrations at term, and parathyroid hormone concentrations in patients with chronic kidney disease requiring dialysis is probable, but further studies and better designed trials are needed to draw firmer conclusions. in contrast to previous reports, evidence does not support the argument that vitamin d only supplementation increases bone mineral density or reduces the risk of fractures or falls in older people. conclusions despite a few hundred systematic reviews and meta-analyses, highly convincing evidence of a clear role of vitamin d does not exist for any outcome, but associations with a selection of outcomes are probable.",0
"parkinson's disease (pd) is a prevalent neurodegenerative disorder. recent identification of genes linked to familial forms of pd such as parkin and pink1 (pten-induced putative kinase 1) has revealed that ubiquitylation and mitochondrial integrity are key factors in disease pathogenesis. however, the exact mechanism underlying the functional interplay between parkin-catalyzed ubiquitylation and pink1-regulated mitochondrial quality control remains an enigma. in this study, we show that pink1 is rapidly and constitutively degraded under steady-state conditions in a mitochondrial membrane potential-dependent manner and that a loss in mitochondrial membrane potential stabilizes pink1 mitochondrial accumulation. furthermore, pink1 recruits parkin from the cytoplasm to mitochondria with low membrane potential to initiate the autophagic degradation of damaged mitochondria. interestingly, the ubiquitin ligase activity of parkin is repressed in the cytoplasm under steady-state conditions; however, pink1-dependent mitochondrial localization liberates the latent enzymatic activity of parkin. some pathogenic mutations of pink1 and parkin interfere with the aforementioned events, suggesting an etiological importance. these results provide crucial insight into the pathogenic mechanisms of pd.",0
"using age-adjusted incidence rates and proportional incidence ratios, the risks of prostate cancer and breast cancer in three racial/ethnic groups - spanish-surnamed whites, other whites and japanese - were studied in los angeles county native residents and compared with those in immigrants and representative 'homeland' populations. an algorithm based on social security numbers was developed and utilised to estimate age at immigration for non-us-born los angeles county cancer patients. for prostate cancer, the incidence rates in los angeles county were much higher than those in the homelands for each racial/ethnic group. however, prostate cancer rates of immigrants were similar to those of us-born patients in the spanish-surnamed white and japanese populations, regardless of age at immigration. for breast cancer, the incidence rates in los angeles county were also high compared with those in the homelands. however, the timing of immigration to the us was important in determining breast cancer risk. when social security numbers indicated that migration occurred later in life, rates for breast cancer were substantially lower than when migration occurred early, although they were still much higher than in the homeland populations. these findings suggest that environmental factors in early life rather than in later life are important in the etiology of breast cancer and that later life events can substantially impact the likelihood of developing clinically detectable prostate cancer.",0
"depletion of immune elements before adoptive cell transfer (act) can dramatically improve the antitumor efficacy of transferred cd8+ t cells, but the specific mechanisms that contribute to this enhanced immunity remain poorly defined. elimination of cd4+cd25+ regulatory t (t reg) cells has been proposed as a key mechanism by which lymphodepletion augments act-based immunotherapy. we found that even in the genetic absence of t reg cells, a nonmyeloablative regimen substantially augmented cd8+ t cell reactivity to self-tissue and tumor. surprisingly, enhanced antitumor efficacy and autoimmunity was caused by increased function rather than increased numbers of tumor-reactive t cells, as would be expected by homeostatic mechanisms. the gammac cytokines il-7 and il-15 were required for augmenting t cell functionality and antitumor activity. removal of gammac cytokine-responsive endogenous cells using antibody or genetic means resulted in the enhanced antitumor responses similar to those seen after nonmyeloablative conditioning. these data indicate that lymphodepletion removes endogenous cellular elements that act as sinks for cytokines that are capable of augmenting the activity of self/tumor-reactive cd8+ t cells. thus, the restricted availability of homeostatic cytokines can be a contributing factor to peripheral tolerance, as well as a limiting resource for the effectiveness of tumor-specific t cells.",0
"inflammatory bowel disease (ibd) is a complex multifactorial disease of unknown etiology. thus, dozens of different animal models of ibd have been developed in past decades. animal models of ibd are valuable and indispensable tools that provide a wide range of options for investigating involvement of various factors into the pathogenesis of ibd and to evaluate different therapeutic options. however, the dextran sulphate sodium (dss-) induced colitis model has some advantages when compared to other animal models of colitis. it is well appreciated and widely used model of inflammatory bowel disease because of its simplicity. it has many similarities to human ibd, which are mentioned in the paper. in spite of its simplicity and wide applicability, there are also traps that need to be taken into account when using dss model. as demonstrated in the present paper, various factors may affect susceptibility to dss-induced lesions and modify results.",0
"background the quality and quantity of individuals' social relationships has been linked not only to mental health but also to both morbidity and mortality. objectives this meta-analytic review was conducted to determine the extent to which social relationships influence risk for mortality, which aspects of social relationships are most highly predictive, and which factors may moderate the risk. data extraction data were extracted on several participant characteristics, including cause of mortality, initial health status, and pre-existing health conditions, as well as on study characteristics, including length of follow-up and type of assessment of social relationships. results across 148 studies (308,849 participants), the random effects weighted average effect size was or = 1.50 (95% ci 1.42 to 1.59), indicating a 50% increased likelihood of survival for participants with stronger social relationships. this finding remained consistent across age, sex, initial health status, cause of death, and follow-up period. significant differences were found across the type of social measurement evaluated (p conclusions the influence of social relationships on risk for mortality is comparable with well-established risk factors for mortality. please see later in the article for the editors' summary.",0
"radiomics is a quantitative approach to medical imaging, which aims at enhancing the existing data available to clinicians by means of advanced mathematical analysis. through mathematical extraction of the spatial distribution of signal intensities and pixel interrelationships, radiomics quantifies textural information by using analysis methods from the field of artificial intelligence. various studies from different fields in imaging have been published so far, highlighting the potential of radiomics to enhance clinical decision-making. however, the field faces several important challenges, which are mainly caused by the various technical factors influencing the extracted radiomic features.the aim of the present review is twofold: first, we present the typical workflow of a radiomics analysis and deliver a practical ""how-to"" guide for a typical radiomics analysis. second, we discuss the current limitations of radiomics, suggest potential improvements, and summarize relevant literature on the subject.",0
"the nhgri-ebi gwas catalog ( is a fair knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (gwas) data to >200 000 users per year from academic research, healthcare and industry. the catalog contains variant-trait associations and supporting metadata for >45 000 published gwas across >5000 human traits, and >40 000 full p-value summary statistics datasets. content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. gwas data volume has vastly increased in recent years. we have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. the scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based gwas, gene-based analyses and copy number variation analyses. community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in gwas. interoperability of the catalog has been enhanced through links to other resources including the polygenic score catalog and the international mouse phenotyping consortium, refinements to gwas trait annotation, and the development of a standard format for gwas data.",0
"the metacyc database (metacyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. the majority of metacyc pathways are small-molecule metabolic pathways that have been experimentally determined. metacyc contains more than 2400 pathways derived from >46,000 publications, and is the largest curated collection of metabolic pathways. biocyc (biocyc.org) is a collection of 5700 organism-specific pathway/genome databases (pgdbs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. the biocyc website offers a variety of tools for querying and analyzing pgdbs, including omics viewers and tools for comparative analysis. this article provides an update of new developments in metacyc and biocyc during the last two years, including addition of gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.",0
"the hmmer website, available at provides access to the protein homology search algorithms found in the hmmer software suite. since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. the continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. the taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. the repertoire of profile hidden markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from cath-gene3d, pirsf, superfamily and tigrfams. finally, we discuss the relocation of the hmmer webserver to the european bioinformatics institute and the potential impact that this will have.",0
"promotion of good mental health, prevention, and early intervention before/at the onset of mental disorders improve outcomes. however, the range and peak ages at onset for mental disorders are not fully established. to provide robust, global epidemiological estimates of age at onset for mental disorders, we conducted a prisma/moose-compliant systematic review with meta-analysis of birth cohort/cross-sectional/cohort studies, representative of the general population, reporting age at onset for any icd/dsm-mental disorders, identified in pubmed/web of science (up to 16/05/2020) (prospero:crd42019143015). co-primary outcomes were the proportion of individuals with onset of mental disorders before age 14, 18, 25, and peak age at onset, for any mental disorder and across international classification of diseases 11 diagnostic blocks. median age at onset of specific disorders was additionally investigated. across 192 studies (n = 708,561) included, the proportion of individuals with onset of any mental disorders before the ages of 14, 18, 25 were 34.6%, 48.4%, 62.5%, and peak age was 14.5 years (k = 14, median = 18, interquartile range (iqr) = 11-34). for diagnostic blocks, the proportion of individuals with onset of disorder before the age of 14, 18, 25 and peak age were as follows: neurodevelopmental disorders: 61.5%, 83.2%, 95.8%, 5.5 years (k = 21, median=12, iqr = 7-16), anxiety/fear-related disorders: 38.1%, 51.8%, 73.3%, 5.5 years (k = 73, median = 17, iqr = 9-25), obsessive-compulsive/related disorders: 24.6%, 45.1%, 64.0%, 14.5 years (k = 20, median = 19, iqr = 14-29), feeding/eating disorders/problems: 15.8%, 48.1%, 82.4%, 15.5 years (k = 11, median = 18, iqr = 15-23), conditions specifically associated with stress disorders: 16.9%, 27.6%, 43.1%, 15.5 years (k = 16, median = 30, iqr = 17-48), substance use disorders/addictive behaviours: 2.9%, 15.2%, 48.8%, 19.5 years (k = 58, median = 25, iqr = 20-41), schizophrenia-spectrum disorders/primary psychotic states: 3%, 12.3%, 47.8%, 20.5 years (k = 36, median = 25, iqr = 20-34), personality disorders/related traits: 1.9%, 9.6%, 47.7%, 20.5 years (k = 6, median = 25, iqr = 20-33), and mood disorders: 2.5%, 11.5%, 34.5%, 20.5 years (k = 79, median = 31, iqr = 21-46). no significant difference emerged by sex, or definition of age of onset. median age at onset for specific mental disorders mapped on a time continuum, from phobias/separation anxiety/autism spectrum disorder/attention deficit hyperactivity disorder/social anxiety (8-13 years) to anorexia nervosa/bulimia nervosa/obsessive-compulsive/binge eating/cannabis use disorders (17-22 years), followed by schizophrenia, personality, panic and alcohol use disorders (25-27 years), and finally post-traumatic/depressive/generalized anxiety/bipolar/acute and transient psychotic disorders (30-35 years), with overlap among groups and no significant clustering. these results inform the timing of good mental health promotion/preventive/early intervention, updating the current mental health system structured around a child/adult service schism at age 18.",0
"sweden has a long tradition of recording cause of death data. the swedish cause of death register is a high quality virtually complete register of all deaths in sweden since 1952. although originally created for official statistics, it is a highly important data source for medical research since it can be linked to many other national registers, which contain data on social and health factors in the swedish population. for the appropriate use of this register, it is fundamental to understand its origins and composition. in this paper we describe the origins and composition of the swedish cause of death register, set out the key strengths and weaknesses of the register, and present the main causes of death across age groups and over time in sweden. this paper provides a guide and reference to individuals and organisations interested in data from the swedish cause of death register.",0
"graph theory is a valuable framework to study the organization of functional and anatomical connections in the brain. its use for comparing network topologies, however, is not without difficulties. graph measures may be influenced by the number of nodes (n) and the average degree (k) of the network. the explicit form of that influence depends on the type of network topology, which is usually unknown for experimental data. direct comparisons of graph measures between empirical networks with different n and/or k can therefore yield spurious results. we list benefits and pitfalls of various approaches that intend to overcome these difficulties. we discuss the initial graph definition of unweighted graphs via fixed thresholds, average degrees or edge densities, and the use of weighted graphs. for instance, choosing a threshold to fix n and k does eliminate size and density effects but may lead to modifications of the network by enforcing (ignoring) non-significant (significant) connections. opposed to fixing n and k, graph measures are often normalized via random surrogates but, in fact, this may even increase the sensitivity to differences in n and k for the commonly used clustering coefficient and small-world index. to avoid such a bias we tried to estimate the n,k-dependence for empirical networks, which can serve to correct for size effects, if successful. we also add a number of methods used in social sciences that build on statistics of local network structures including exponential random graph models and motif counting. we show that none of the here-investigated methods allows for a reliable and fully unbiased comparison, but some perform better than others.",0
"1. sera from individuals acutely ill with lobar pneumonia possess the capacity to precipitate in high titre a non-protein somatic fraction derived from pneumococci (fraction c). following crisis the reaction is no longer demonstrable. 2. sera obtained from cases of pneumococcus pneumonia during illness and convalescence have been tested for antibodies specifically reactive with three chemically distinct constituents of pneumococcus. the results, when correlated with the course of disease, demonstrate differences in the occurrence of each qualitatively distinct antibody. 3. the precipitation of pneumococcus fraction c is not limited to the sera of individuals ill with pneumococcus infection. but in the few other cases available for comparative tests, definite reactions have been obtained only in streptococcus and staphylococcus infections and in acute rheumatic fever.",0
"healthcare workers (hcws) found the 2003 outbreak of severe acute respiratory syndrome (sars) to be stressful, but the long-term impact is not known. from 13 to 26 months after the sars outbreak, 769 hcws at 9 toronto hospitals that treated sars patients and 4 hamilton hospitals that did not treat sars patients completed a survey of several adverse outcomes. toronto hcws reported significantly higher levels of burnout (p = 0.019), psychological distress (p<0.001), and posttraumatic stress (p<0.001). toronto workers were more likely to have reduced patient contact and work hours and to report behavioral consequences of stress. variance in adverse outcomes was explained by a protective effect of the perceived adequacy of training and support and by a provocative effect of maladaptive coping style and other individual factors. the results reinforce the value of effective staff support and training in preparation for future outbreaks.",0
"background most successful computational approaches for protein function prediction integrate multiple genomics and proteomics data sources to make inferences about the function of unknown proteins. the most accurate of these algorithms have long running times, making them unsuitable for real-time protein function prediction in large genomes. as a result, the predictions of these algorithms are stored in static databases that can easily become outdated. we propose a new algorithm, genemania, that is as accurate as the leading methods, while capable of predicting protein function in real-time. results we use a fast heuristic algorithm, derived from ridge regression, to integrate multiple functional association networks and predict gene function from a single process-specific network using label propagation. our algorithm is efficient enough to be deployed on a modern webserver and is as accurate as, or more so than, the leading methods on the mousefunc i benchmark and a new yeast function prediction benchmark; it is robust to redundant and irrelevant data and requires, on average, less than ten seconds of computation time on tasks from these benchmarks. conclusion genemania is fast enough to predict gene function on-the-fly while achieving state-of-the-art accuracy. a prototype version of a genemania-based webserver is available at",0
"we have prepared an mab specific for a human cell surface component (termed anti-fas mab). anti-fas shows cell-killing activity that is indistinguishable from the cytolytic activity of tnf. fas antigen was characterized by western blotting, indicating that fas antigen is a cell surface protein with a molecular weight of 200,000, which is different from the molecular weight of tnf-r. fas antigen, however, is co-downregulated with the tnf-r when cells sensitive to the cytolytic activity of tnf are incubated with either tnf or anti-fas. in contrast, fas antigen on cells insensitive to tnf is not co-downregulated with the tnf-r. we suggest that the cell-killing activity of tnf is mediated by fas antigen associated with the tnf-r.",0
"grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. in addition, most of the tools are not scalable to large datasets. here we introduce automated software called metabat that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. metabat outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. it automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. metabat is open source software and available at",0
"stereological principles provide efficient and reliable tools for the determination of quantitative parameters of tissue structure on sections. some principles which allow the estimation of volumetric ratios, surface areas, surface-to-volume ratios, thicknesses of tissue or cell sheets, and the number of structures are reviewed and presented in general form; means for their practical application in electron microscopy are outlined. the systematic and statistical errors involved in such measurements are discussed.",0
"mitochondria are highly dynamic organelles undergoing coordinated cycles of fission and fusion, referred as 'mitochondrial dynamics', in order to maintain their shape, distribution and size. their transient and rapid morphological adaptations are crucial for many cellular processes such as cell cycle, immunity, apoptosis and mitochondrial quality control. mutations in the core machinery components and defects in mitochondrial dynamics have been associated with numerous human diseases. these dynamic transitions are mainly ensured by large gtpases belonging to the dynamin family. mitochondrial fission is a multi-step process allowing the division of one mitochondrion in two daughter mitochondria. it is regulated by the recruitment of the gtpase dynamin-related protein 1 (drp1) by adaptors at actin- and endoplasmic reticulum-mediated mitochondrial constriction sites. drp1 oligomerization followed by mitochondrial constriction leads to the recruitment of dynamin 2 to terminate membrane scission. inner mitochondrial membrane constriction has been proposed to be an independent process regulated by calcium influx. mitochondrial fusion is driven by a two-step process with the outer mitochondrial membrane fusion mediated by mitofusins 1 and 2 followed by inner membrane fusion, mediated by optic atrophy 1. in addition to the role of membrane lipid composition, several members of the machinery can undergo post-translational modifications modulating these processes. understanding the molecular mechanisms controlling mitochondrial dynamics is crucial to decipher how mitochondrial shape meets the function and to increase the knowledge on the molecular basis of diseases associated with morphology defects. this article will describe an overview of the molecular mechanisms that govern mitochondrial fission and fusion in mammals.",0
"we present model-based analysis of chip-seq data, macs, which analyzes data generated by short read sequencers such as solexa's genome analyzer. macs empirically models the shift size of chip-seq tags, and uses it to improve the spatial resolution of predicted binding sites. macs also uses a dynamic poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. macs compares favorably to existing chip-seq peak-finding algorithms, and is freely available.",0
"background accurate assessment is required to assess current and changing physical activity levels, and to evaluate the effectiveness of interventions designed to increase activity levels. this study systematically reviewed the literature to determine the extent of agreement between subjectively (self-report e.g. questionnaire, diary) and objectively (directly measured; e.g. accelerometry, doubly labeled water) assessed physical activity in adults. methods eight electronic databases were searched to identify observational and experimental studies of adult populations. searching identified 4,463 potential articles. initial screening found that 293 examined the relationship between self-reported and directly measured physical activity and met the eligibility criteria. data abstraction was completed for 187 articles, which described comparable data and/or comparisons, while 76 articles lacked comparable data or comparisons, and a further 30 did not meet the review's eligibility requirements. a risk of bias assessment was conducted for all articles from which data was abstracted. results correlations between self-report and direct measures were generally low-to-moderate and ranged from -0.71 to 0.96. no clear pattern emerged for the mean differences between self-report and direct measures of physical activity. trends differed by measure of physical activity employed, level of physical activity measured, and the gender of participants. results of the risk of bias assessment indicated that 38% of the studies had lower quality scores. conclusion the findings suggest that the measurement method may have a significant impact on the observed levels of physical activity. self-report measures of physical activity were both higher and lower than directly measured levels of physical activity, which poses a problem for both reliance on self-report measures and for attempts to correct for self-report - direct measure differences. this review reveals the need for valid, accurate and reliable measures of physical activity in evaluating current and changing physical activity levels, physical activity interventions, and the relationships between physical activity and health outcomes.",0
"background while the covid-19 pandemic will increase mortality due to the virus, it is also likely to increase mortality indirectly. in this study, we estimate the additional maternal and under-5 child deaths resulting from the potential disruption of health systems and decreased access to food. methods we modelled three scenarios in which the coverage of essential maternal and child health interventions is reduced by 9·8-51·9% and the prevalence of wasting is increased by 10-50%. although our scenarios are hypothetical, we sought to reflect real-world possibilities, given emerging reports of the supply-side and demand-side effects of the pandemic. we used the lives saved tool to estimate the additional maternal and under-5 child deaths under each scenario, in 118 low-income and middle-income countries. we estimated additional deaths for a single month and extrapolated for 3 months, 6 months, and 12 months. findings our least severe scenario (coverage reductions of 9·8-18·5% and wasting increase of 10%) over 6 months would result in 253 500 additional child deaths and 12 200 additional maternal deaths. our most severe scenario (coverage reductions of 39·3-51·9% and wasting increase of 50%) over 6 months would result in 1 157 000 additional child deaths and 56 700 additional maternal deaths. these additional deaths would represent an increase of 9·8-44·7% in under-5 child deaths per month, and an 8·3-38·6% increase in maternal deaths per month, across the 118 countries. across our three scenarios, the reduced coverage of four childbirth interventions (parenteral administration of uterotonics, antibiotics, and anticonvulsants, and clean birth environments) would account for approximately 60% of additional maternal deaths. the increase in wasting prevalence would account for 18-23% of additional child deaths and reduced coverage of antibiotics for pneumonia and neonatal sepsis and of oral rehydration solution for diarrhoea would together account for around 41% of additional child deaths. interpretation our estimates are based on tentative assumptions and represent a wide range of outcomes. nonetheless, they show that, if routine health care is disrupted and access to food is decreased (as a result of unavoidable shocks, health system collapse, or intentional choices made in responding to the pandemic), the increase in child and maternal deaths will be devastating. we hope these numbers add context as policy makers establish guidelines and allocate resources in the days and months to come. funding bill & melinda gates foundation, global affairs canada.",0
"across scientific disciplines, there is a rapidly growing recognition of the need for more statistically robust, transparent approaches to data visualization. complementary to this, many scientists have called for plotting tools that accurately and transparently convey key aspects of statistical effects and raw data with minimal distortion. previously common approaches, such as plotting conditional mean or median barplots together with error-bars have been criticized for distorting effect size, hiding underlying patterns in the raw data, and obscuring the assumptions upon which the most commonly used statistical tests are based. here we describe a data visualization approach which overcomes these issues, providing maximal statistical information while preserving the desired 'inference at a glance' nature of barplots and other similar visualization devices. these ""raincloud plots"" can visualize raw data, probability density, and key summary statistics such as median, mean, and relevant confidence intervals in an appealing and flexible format with minimal redundancy. in this tutorial paper, we provide basic demonstrations of the strength of raincloud plots and similar approaches, outline potential modifications for their optimal use, and provide open-source code for their streamlined implementation in r, python and matlab ( readers can investigate the r and python tutorials interactively in the browser using binder by project jupyter.",0
"brominated flame retardants (bfrs) have routinely been added to consumer products for several decades in a successful effort to reduce fire-related injury and property damage. recently, concern for this emerging class of chemicals has risen because of the occurrence of several classes of bfrs in the environment and in human biota. the widespread production and use of bfrs; strong evidence of increasing contamination of the environment, wildlife, and people; and limited knowledge of potential effects heighten the importance of identifying emerging issues associated with the use of bfrs. in this article, we briefly review scientific issues associated with the use of tetrabromobisphenol a, hexabromocyclododecane, and three commercial mixtures of polybrominated diphenyl ethers and discuss data gaps. overall, the toxicology database is very limited; the current literature is incomplete and often conflicting. available data, however, raise concern over the use of certain classes of brominated flame retardants.",0
"four melanoma proteins, mart-1, gp100, tyrosinase, and tyrosinase-related protein-1 (gp75) were evaluated for recognition by hla-a2-restricted melanoma-specific cytotoxic t lymphocytes (ctls) derived from the tumor-infiltrating lymphocytes (til) of 10 different patients. 9 of 10 til recognized mart-1, 4 recognized gp100 (including 3 that also recognized mart-1), but none of the til recognized tyrosinase or gp75. based on the known hla-a2.1 peptide binding motifs, 23 peptides from mart-1 were synthesized in an attempt to identify the epitopes recognized by til. three peptides were recognized by til when pulsed on t2 target cells. one of the 9-mer peptides, aagigiltv, was most effective in sensitizing the t2 cells for til lysis. this peptide was recognized by 9 of 10 hla-a2-restricted melanoma-specific ctls. therefore, this peptide appears to be a very common immunogenic epitope for hla-a2-restricted melanoma-specific til and may be useful for the development of immunotherapeutic strategies.",0
"the environment for tree exploration (ete) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. here, we present ete v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. the new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the ncbi taxonomy database. ete is freely available at",0
"background leptospirosis, a spirochaetal zoonosis, occurs in diverse epidemiological settings and affects vulnerable populations, such as rural subsistence farmers and urban slum dwellers. although leptospirosis is a life-threatening disease and recognized as an important cause of pulmonary haemorrhage syndrome, the lack of global estimates for morbidity and mortality has contributed to its neglected disease status. methodology/principal findings we conducted a systematic review of published morbidity and mortality studies and databases to extract information on disease incidence and case fatality ratios. linear regression and monte carlo modelling were used to obtain age and gender-adjusted estimates of disease morbidity for countries and global burden of disease (gbd) and who regions. we estimated mortality using models that incorporated age and gender-adjusted disease morbidity and case fatality ratios. the review identified 80 studies on disease incidence from 34 countries that met quality criteria. in certain regions, such as africa, few quality assured studies were identified. the regression model, which incorporated country-specific variables of population structure, life expectancy at birth, distance from the equator, tropical island, and urbanization, accounted for a significant proportion (r(2) = 0.60) of the variation in observed disease incidence. we estimate that there were annually 1.03 million cases (95% ci 434,000-1,750,000) and 58,900 deaths (95% ci 23,800-95,900) due to leptospirosis worldwide. a large proportion of cases (48%, 95% ci 40-61%) and deaths (42%, 95% ci 34-53%) were estimated to occur in adult males with age of 20-49 years. highest estimates of disease morbidity and mortality were observed in gbd regions of south and southeast asia, oceania, caribbean, andean, central, and tropical latin america, and east sub-saharan africa. conclusions/significance leptospirosis is among the leading zoonotic causes of morbidity worldwide and accounts for numbers of deaths, which approach or exceed those for other causes of haemorrhagic fever. highest morbidity and mortality were estimated to occur in resource-poor countries, which include regions where the burden of leptospirosis has been underappreciated.",0
"purpose covid-19 (coronavirus disease 2019) is a public health emergency of international concern. as of this time, there is no known effective pharmaceutical treatment, although it is much needed for patient contracting the severe form of the disease. the aim of this systematic review was to summarize the evidence regarding chloroquine for the treatment of covid-19. methods pubmed, embase, and three trial registries were searched for studies on the use of chloroquine in patients with covid-19. results we included six articles (one narrative letter, one in-vitro study, one editorial, expert consensus paper, two national guideline documents) and 23 ongoing clinical trials in china. chloroquine seems to be effective in limiting the replication of sars-cov-2 (virus causing covid-19) in vitro. conclusions there is rationale, pre-clinical evidence of effectiveness and evidence of safety from long-time clinical use for other indications to justify clinical research on chloroquine in patients with covid-19. however, clinical use should either adhere to the monitored emergency use of unregistered interventions (meuri) framework or be ethically approved as a trial as stated by the world health organization. safety data and data from high-quality clinical trials are urgently needed.",0
"medulloblastoma, a small blue cell malignancy of the cerebellum, is a major cause of morbidity and mortality in pediatric oncology. current mechanisms for clinical prognostication and stratification include clinical factors (age, presence of metastases, and extent of resection) as well as histological subgrouping (classic, desmoplastic, and large cell/anaplastic histology). transcriptional profiling studies of medulloblastoma cohorts from several research groups around the globe have suggested the existence of multiple distinct molecular subgroups that differ in their demographics, transcriptomes, somatic genetic events, and clinical outcomes. variations in the number, composition, and nature of the subgroups between studies brought about a consensus conference in boston in the fall of 2010. discussants at the conference came to a consensus that the evidence supported the existence of four main subgroups of medulloblastoma (wnt, shh, group 3, and group 4). participants outlined the demographic, transcriptional, genetic, and clinical differences between the four subgroups. while it is anticipated that the molecular classification of medulloblastoma will continue to evolve and diversify in the future as larger cohorts are studied at greater depth, herein we outline the current consensus nomenclature, and the differences between the medulloblastoma subgroups.",0
"prediction models are developed to aid health care providers in estimating the probability or risk that a specific disease or condition is present (diagnostic models) or that a specific event will occur in the future (prognostic models), to inform their decision making. however, the overwhelming evidence shows that the quality of reporting of prediction model studies is poor. only with full and clear reporting of information on all aspects of a prediction model can risk of bias and potential usefulness of prediction models be adequately assessed. the transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (tripod) initiative developed a set of recommendations for the reporting of studies developing, validating, or updating a prediction model, whether for diagnostic or prognostic purposes. this article describes how the tripod statement was developed. an extensive list of items based on a review of the literature was created, which was reduced after a web-based survey and revised during a 3-day meeting in june 2011 with methodologists, health care professionals, and journal editors. the list was refined during several meetings of the steering group and in e-mail discussions with the wider group of tripod contributors. the resulting tripod statement is a checklist of 22 items, deemed essential for transparent reporting of a prediction model study. the tripod statement aims to improve the transparency of the reporting of a prediction model study regardless of the study methods used. the tripod statement is best used in conjunction with the tripod explanation and elaboration document. to aid the editorial process and readers of prediction model studies, it is recommended that authors include a completed checklist in their submission (also available at",0
"abiotic stresses are one of the major constraints to crop production and food security worldwide. the situation has aggravated due to the drastic and rapid changes in global climate. heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. it is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. a wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. a better understanding of plant responses to these stresses has pragmatic implication for remedies and management. a comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. a side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. a holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.",0
"the envelope spike (s) proteins of mers-cov and sars-cov determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. here, we present high-resolution structures of the trimeric mers-cov and sars-cov s proteins in its pre-fusion conformation by single particle cryo-electron microscopy. the overall structures resemble that from other coronaviruses including hku1, mhv and nl63 reported recently, with the exception of the receptor binding domain (rbd). we captured two states of the rbd with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible rbd readily recognized by the receptor. further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, hr1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.",0
"high-resolution information on climatic conditions is essential to many applications in environmental and ecological sciences. here we present the chelsa (climatologies at high resolution for the earth's land surface areas) data of downscaled model output temperature and precipitation estimates of the era-interim climatic reanalysis to a high resolution of 30 arc sec. the temperature algorithm is based on statistical downscaling of atmospheric temperatures. the precipitation algorithm incorporates orographic predictors including wind fields, valley exposition, and boundary layer height, with a subsequent bias correction. the resulting data consist of a monthly temperature and precipitation climatology for the years 1979-2013. we compare the data derived from the chelsa algorithm with other standard gridded products and station data from the global historical climate network. we compare the performance of the new climatologies in species distribution modelling and show that we can increase the accuracy of species range predictions. we further show that chelsa climatological data has a similar accuracy as other products for temperature, but that its predictions of precipitation patterns are better.",0
"our study aimed to investigate the immediate impact of the covid-19 pandemic on mental health and quality of life among local chinese residents aged ≥18 years in liaoning province, mainland china. an online survey was distributed through a social media platform between january and february 2020. participants completed a modified validated questionnaire that assessed the impact of event scale (ies), indicators of negative mental health impacts, social and family support, and mental health-related lifestyle changes. a total of 263 participants (106 males and 157 females) completed the study. the mean age of the participants was 37.7 ± 14.0 years, and 74.9% had a high level of education. the mean ies score in the participants was 13.6 ± 7.7, reflecting a mild stressful impact. only 7.6% of participants had an ies score ≥26. the majority of participants (53.3%) did not feel helpless due to the pandemic. on the other hand, 52.1% of participants felt horrified and apprehensive due to the pandemic. additionally, the majority of participants (57.8-77.9%) received increased support from friends and family members, increased shared feeling and caring with family members and others. in conclusion, the covid-19 pandemic was associated with mild stressful impact in our sample, even though the covid-19 pandemic is still ongoing. these findings would need to be verified in larger population studies.",0
"aim the aim of this study was to evaluate the benefits and safety of long-term i.v. iron therapy in iron-deficient patients with heart failure (hf). methods and results confirm-hf was a multi-centre, double-blind, placebo-controlled trial that enrolled 304 ambulatory symptomatic hf patients with left ventricular ejection fraction ≤45%, elevated natriuretic peptides, and iron deficiency (ferritin conclusion treatment of symptomatic, iron-deficient hf patients with fcm over a 1-year period resulted in sustainable improvement in functional capacity, symptoms, and qol and may be associated with risk reduction of hospitalization for worsening hf (clinicaltrials.gov number nct01453608).",0
"the role of coated vesicles during the absorption of horseradish peroxidase was investigated in the epithelium of the rat vas deferens by electron microscopy and cytochemistry. peroxidase was introduced into the vas lumen in vivo. tissue was excised at selected intervals, fixed in formaldehyde-glutaraldehyde, sectioned without freezing, incubated in karnovsky's medium, postfixed in oso(4), and processed for electron microscopy. some controls and peroxidase-perfused specimens were incubated with tpp,(1) gp, and cmp. attention was focused on the golgi complex, apical multivesicular bodies, and two populations of coated vesicles; large (> 1000 a) ones concentrated in the apical cytoplasm and small (<750 a) ones found primarily in the golgi region. 10 min after peroxidase injection, the tracer is found adhering to the surface plasmalemma, concentrated in bristle-coated invaginations, and within large coated vesicles. after 20-45 min, it is present in large smooth vesicles, apical multivesicular bodies, and dense bodies. peroxidase is not seen in small coated vesicles at any interval. counts of small coated vesicles reveal that during peroxidase absorption they first increase in number in the golgi region and later, in the apical cytoplasm. in both control and peroxidase-perfused specimens incubated with tpp, reaction product is seen in several golgi cisternae and in small coated vesicles in the golgi region. with gp, reaction product is seen in one to two golgi cisternae, multivesicular bodies, dense bodies, and small coated vesicles present in the golgi region or near multivesicular bodies. the results demonstrate that (a) this epithelium functions in the absorption of protein from the duct lumen, (b) large coated vesicles serve as heterophagosomes to transport absorbed protein to lysosomes, and (c) some small coated vesicles serve as primary lysosomes to transport hydrolytic enzymes from the golgi complex to multivesicular bodies.",0
"these guidelines provide an up-date of previous ifcn report on ""non-invasive electrical and magnetic stimulation of the brain, spinal cord and roots: basic principles and procedures for routine clinical application"" (rossini et al., 1994). a new committee, composed of international experts, some of whom were in the panel of the 1994 ""report"", was selected to produce a current state-of-the-art review of non-invasive stimulation both for clinical application and research in neuroscience. since 1994, the international scientific community has seen a rapid increase in non-invasive brain stimulation in studying cognition, brain-behavior relationship and pathophysiology of various neurologic and psychiatric disorders. new paradigms of stimulation and new techniques have been developed. furthermore, a large number of studies and clinical trials have demonstrated potential therapeutic applications of non-invasive brain stimulation, especially for tms. recent guidelines can be found in the literature covering specific aspects of non-invasive brain stimulation, such as safety (rossi et al., 2009), methodology (groppa et al., 2012) and therapeutic applications (lefaucheur et al., 2014). this up-dated review covers theoretical, physiological and practical aspects of non-invasive stimulation of brain, spinal cord, nerve roots and peripheral nerves in the light of more updated knowledge, and include some recent extensions and developments.",0
"background the framework method is becoming an increasingly popular approach to the management and analysis of qualitative data in health research. however, there is confusion about its potential application and limitations. discussion the article discusses when it is appropriate to adopt the framework method and explains the procedure for using it in multi-disciplinary health research teams, or those that involve clinicians, patients and lay people. the stages of the method are illustrated using examples from a published study. summary used effectively, with the leadership of an experienced qualitative researcher, the framework method is a systematic and flexible approach to analysing qualitative data and is appropriate for use in research teams even where not all members have previous experience of conducting qualitative research.",0
"noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. the main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. in recent time, the use of extrinsic fluorescent dyes such as ans, bis-ans, nile red, thioflavin t and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. the intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization.",0
"summary aliview is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. aliview handles alignments of unlimited size in the formats most commonly used, i.e. fasta, phylip, nexus, clustal and msf. the intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. aliview also works as an easy-to-use alignment editor for small as well as large datasets. availability and implementation aliview is released as open-source software under the gnu general public license, version 3.0 (gplv3), and is available at github ( the program is cross-platform and extensively tested on linux, mac os x and windows systems. downloads and help are available at contact anders.larsson@ebc.uu.se supplementary information supplementary data are available at bioinformatics online.",0
"the number of cancer cases caused by being obese is estimated to be 20% with the increased risk of malignancies being influenced by diet, weight change, and body fat distribution together with physical activity. reports from the international agency for research into cancer and the world cancer research fund (wcrf) have shown that the strongest evidence exists for an association of obesity with the following cancer types: endometrial, esophageal adenocarcinoma, colorectal, postmenopausal breast, prostate, and renal, whereas the less common malignancies are leukemia, non-hodgkin's lymphoma, multiple myeloma, malignant melanoma, and thyroid tumours. to be able to develop novel methods in prevention and treatment, we first must understand the underlying processes which link cancer to obesity. four main systems have been identified as potential producers of cancer in obesity: insulin, insulin-like growth factor-i, sex steroids, and adipokines. various novel candidate mechanisms have been proposed: chronic inflammation, oxidative stress, crosstalk between tumour cells and surrounding adipocytes, migrating adipose stromal cells, obesity-induced hypoxia, shared genetic susceptibility, and the functional defeat of immune function. herein, we review the major pathogenic links between obesity and susceptibility to cancer.",0
"the epidermal growth factor receptor (egfr) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. a map of molecular interactions of the egfr signaling system is a valuable resource for research in this area. in this paper, we present a comprehensive pathway map of egfr signaling and other related pathways. the map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. the map is created using celldesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in systems biology markup language (sbml).",0
"background selection of relevant genes for sample classification is a common task in most gene expression studies, where researchers try to identify the smallest possible set of genes that can still achieve good predictive performance (for instance, for future use with diagnostic purposes in clinical practice). many gene selection approaches use univariate (gene-by-gene) rankings of gene relevance and arbitrary thresholds to select the number of genes, can only be applied to two-class problems, and use gene selection ranking criteria unrelated to the classification algorithm. in contrast, random forest is a classification algorithm well suited for microarray data: it shows excellent performance even when most predictive variables are noise, can be used when the number of variables is much larger than the number of observations and in problems involving more than two classes, and returns measures of variable importance. thus, it is important to understand the performance of random forest with microarray data and its possible use for gene selection. results we investigate the use of random forest for classification of microarray data (including multi-class problems) and propose a new method of gene selection in classification problems based on random forest. using simulated and nine microarray data sets we show that random forest has comparable performance to other classification methods, including dlda, knn, and svm, and that the new gene selection procedure yields very small sets of genes (often smaller than alternative methods) while preserving predictive accuracy. conclusion because of its performance and features, random forest and gene selection using random forest should probably become part of the ""standard tool-box"" of methods for class prediction and gene selection with microarray data.",0
"hydrogel products constitute a group of polymeric materials, the hydrophilic structure of which renders them capable of holding large amounts of water in their three-dimensional networks. extensive employment of these products in a number of industrial and environmental areas of application is considered to be of prime importance. as expected, natural hydrogels were gradually replaced by synthetic types due to their higher water absorption capacity, long service life, and wide varieties of raw chemical resources. literature on this subject was found to be expanding, especially in the scientific areas of research. however, a number of publications and technical reports dealing with hydrogel products from the engineering points of view were examined to overview technological aspects covering this growing multidisciplinary field of research. the primary objective of this article is to review the literature concerning classification of hydrogels on different bases, physical and chemical characteristics of these products, and technical feasibility of their utilization. it also involved technologies adopted for hydrogel production together with process design implications, block diagrams, and optimized conditions of the preparation process. an innovated category of recent generations of hydrogel materials was also presented in some details.",0
"medical imaging has enormous potential for early disease prediction, but is impeded by the difficulty and expense of acquiring data sets before symptom onset. uk biobank aims to address this problem directly by acquiring high-quality, consistently acquired imaging data from 100,000 predominantly healthy participants, with health outcomes being tracked over the coming decades. the brain imaging includes structural, diffusion and functional modalities. along with body and cardiac imaging, genetics, lifestyle measures, biological phenotyping and health records, this imaging is expected to enable discovery of imaging markers of a broad range of diseases at their earliest stages, as well as provide unique insight into disease mechanisms. we describe uk biobank brain imaging and present results derived from the first 5,000 participants' data release. although this covers just 5% of the ultimate cohort, it has already yielded a rich range of associations between brain imaging and other measures collected by uk biobank.",0
"background depressive disorders were a leading cause of burden in the global burden of disease (gbd) 1990 and 2000 studies. here, we analyze the burden of depressive disorders in gbd 2010 and present severity proportions, burden by country, region, age, sex, and year, as well as burden of depressive disorders as a risk factor for suicide and ischemic heart disease. methods and findings burden was calculated for major depressive disorder (mdd) and dysthymia. a systematic review of epidemiological data was conducted. the data were pooled using a bayesian meta-regression. disability weights from population survey data quantified the severity of health loss from depressive disorders. these weights were used to calculate years lived with disability (ylds) and disability adjusted life years (dalys). separate dalys were estimated for suicide and ischemic heart disease attributable to depressive disorders. depressive disorders were the second leading cause of ylds in 2010. mdd accounted for 8.2% (5.9%-10.8%) of global ylds and dysthymia for 1.4% (0.9%-2.0%). depressive disorders were a leading cause of dalys even though no mortality was attributed to them as the underlying cause. mdd accounted for 2.5% (1.9%-3.2%) of global dalys and dysthymia for 0.5% (0.3%-0.6%). there was more regional variation in burden for mdd than for dysthymia; with higher estimates in females, and adults of working age. whilst burden increased by 37.5% between 1990 and 2010, this was due to population growth and ageing. mdd explained 16 million suicide dalys and almost 4 million ischemic heart disease dalys. this attributable burden would increase the overall burden of depressive disorders from 3.0% (2.2%-3.8%) to 3.8% (3.0%-4.7%) of global dalys. conclusions gbd 2010 identified depressive disorders as a leading cause of burden. mdd was also a contributor of burden allocated to suicide and ischemic heart disease. these findings emphasize the importance of including depressive disorders as a public-health priority and implementing cost-effective interventions to reduce its burden. please see later in the article for the editors' summary.",0
"background and purpose covid-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2). apart from respiratory complications, acute cerebrovascular disease (cvd) has been observed in some patients with covid-19. therefore, we described the clinical characteristics, laboratory features, treatment and outcomes of cvd complicating sars-cov-2 infection. materials and methods demographic and clinical characteristics, laboratory findings, treatments and clinical outcomes were collected and analysed. clinical characteristics and laboratory findings of patients with covid-19 with or without new-onset cvd were compared. results of 219 patients with covid-19, 10 (4.6%) developed acute ischaemic stroke and 1 (0.5%) had intracerebral haemorrhage. covid-19 with new onset of cvd were significantly older (75.7±10.8 years vs 52.1±15.3 years, p conclusion acute cvd is not uncommon in covid-19. our findings suggest that older patients with risk factors are more likely to develop cvd. the development of cvd is an important negative prognostic factor which requires further study to identify optimal management strategy to combat the covid-19 outbreak.",0
"aerosol generating procedures (agps) may expose health care workers (hcws) to pathogens causing acute respiratory infections (aris), but the risk of transmission of aris from agps is not fully known. we sought to determine the clinical evidence for the risk of transmission of aris to hcws caring for patients undergoing agps compared with the risk of transmission to hcws caring for patients not undergoing agps. we searched pubmed, embase, medline, cinahl, the cochrane library, university of york crd databases, euroscan, lilacs, indian medlars, index medicus for se asia, international health technology agencies and the internet in all languages for articles from 01/01/1990 to 22/10/2010. independent reviewers screened abstracts using pre-defined criteria, obtained full-text articles, selected relevant studies, and abstracted data. disagreements were resolved by consensus. the outcome of interest was risk of ari transmission. the quality of evidence was rated using the grade system. we identified 5 case-control and 5 retrospective cohort studies which evaluated transmission of sars to hcws. procedures reported to present an increased risk of transmission included tracheal intubation , non-invasive ventilation , tracheotomy and manual ventilation before intubation . other intubation associated procedures, endotracheal aspiration, suction of body fluids, bronchoscopy, nebulizer treatment, administration of o2, high flow o2, manipulation of o2 mask or bipap mask, defibrillation, chest compressions, insertion of nasogastric tube, and collection of sputum were not significant. our findings suggest that some procedures potentially capable of generating aerosols have been associated with increased risk of sars transmission to hcws or were a risk factor for transmission, with the most consistent association across multiple studies identified with tracheal intubation.",0
"background respiratory syncytial virus (rsv) is the most common cause of acute lower respiratory infection in young children. we previously estimated that in 2015, 33·1 million episodes of rsv-associated acute lower respiratory infection occurred in children aged 0-60 months, resulting in a total of 118 200 deaths worldwide. since then, several community surveillance studies have been done to obtain a more precise estimation of rsv associated community deaths. we aimed to update rsv-associated acute lower respiratory infection morbidity and mortality at global, regional, and national levels in children aged 0-60 months for 2019, with focus on overall mortality and narrower infant age groups that are targeted by rsv prophylactics in development. methods in this systematic analysis, we expanded our global rsv disease burden dataset by obtaining new data from an updated search for papers published between jan 1, 2017, and dec 31, 2020, from medline, embase, global health, cinahl, web of science, lilacs, opengrey, cnki, wanfang, and chongqingvip. we also included unpublished data from rsv gen collaborators. eligible studies reported data for children aged 0-60 months with rsv as primary infection with acute lower respiratory infection in community settings, or acute lower respiratory infection necessitating hospital admission; reported data for at least 12 consecutive months, except for in-hospital case fatality ratio (cfr) or for where rsv seasonality is well-defined; and reported incidence rate, hospital admission rate, rsv positive proportion in acute lower respiratory infection hospital admission, or in-hospital cfr. studies were excluded if case definition was not clearly defined or not consistently applied, rsv infection was not laboratory confirmed or based on serology alone, or if the report included fewer than 50 cases of acute lower respiratory infection. we applied a generalised linear mixed-effects model (glmm) to estimate rsv-associated acute lower respiratory infection incidence, hospital admission, and in-hospital mortality both globally and regionally (by country development status and by world bank income classification) in 2019. we estimated country-level rsv-associated acute lower respiratory infection incidence through a risk-factor based model. we developed new models (through glmm) that incorporated the latest rsv community mortality data for estimating overall rsv mortality. this review was registered in prospero (crd42021252400). findings in addition to 317 studies included in our previous review, we identified and included 113 new eligible studies and unpublished data from 51 studies, for a total of 481 studies. we estimated that globally in 2019, there were 33·0 million rsv-associated acute lower respiratory infection episodes (uncertainty range 25·4-44·6 million), 3·6 million rsv-associated acute lower respiratory infection hospital admissions (2·9-4·6 million), 26 300 rsv-associated acute lower respiratory infection in-hospital deaths (15 100-49 100), and 101 400 rsv-attributable overall deaths (84 500-125 200) in children aged 0-60 months. in infants aged 0-6 months, we estimated that there were 6·6 million rsv-associated acute lower respiratory infection episodes (4·6-9·7 million), 1·4 million rsv-associated acute lower respiratory infection hospital admissions (1·0-2·0 million), 13 300 rsv-associated acute lower respiratory infection in-hospital deaths (6800-28 100), and 45 700 rsv-attributable overall deaths (38 400-55 900). 2·0% of deaths in children aged 0-60 months (ur 1·6-2·4) and 3·6% of deaths in children aged 28 days to 6 months (3·0-4·4) were attributable to rsv. more than 95% of rsv-associated acute lower respiratory infection episodes and more than 97% of rsv-attributable deaths across all age bands were in low-income and middle-income countries (lmics). interpretation rsv contributes substantially to morbidity and mortality burden globally in children aged 0-60 months, especially during the first 6 months of life and in lmics. we highlight the striking overall mortality burden of rsv disease worldwide, with one in every 50 deaths in children aged 0-60 months and one in every 28 deaths in children aged 28 days to 6 months attributable to rsv. for every rsv-associated acute lower respiratory infection in-hospital death, we estimate approximately three more deaths attributable to rsv in the community. rsv passive immunisation programmes targeting protection during the first 6 months of life could have a substantial effect on reducing rsv disease burden, although more data are needed to understand the implications of the potential age-shifts in peak rsv burden to older age when these are implemented. funding eu innovative medicines initiative respiratory syncytial virus consortium in europe (resceu).",0
"summary the sequence alignment/map (sam) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 mbp) produced by different sequencing platforms. it is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 genomes project are released. samtools implements various utilities for post-processing alignments in the sam format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. availability",0
"in anatomic pathology, immunohistochemistry (ihc) serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. however, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. this instigated us to design a simple method of automated digital ihc image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. as a first step, we adopted the spectral deconvolution method of dab/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the dab color spectra. then the dab stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703) of dab stained ihc images including sample images taken from human protein atlas web resource. the ihc profiler plugin developed is compatible with the open resource digital image analysis software, imagej, which creates a pixel-by-pixel analysis profile of a digital ihc image and further assigns a score in a four tier system. a comparison study between manual pathological analysis and ihc profiler resolved in a match of 88.6% (p<0.0001, ci = 95%). this new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. we foresee that this method will minimize the problem of inter-observer variations across labs and further help in worldwide patient stratification potentially benefitting various multinational clinical trial initiatives.",0
"the purpose of this paper is to give an overview of the recent surgical intraoperational applications of indocyanine green fluorescence imaging methods, the basics of the technology, and instrumentation used. well over 200 papers describing this technique in clinical setting are reviewed. in addition to the surgical applications, other recent medical applications of icg are briefly examined.",0
"when archie cochrane reproached the medical profession for not having critical summaries of all randomised controlled trials, about 14 reports of trials were being published per day. there are now 75 trials, and 11 systematic reviews of trials, per day and a plateau in growth has not yet been reached. although trials, reviews, and health technology assessments have undoubtedly had major impacts, the staple of medical literature synthesis remains the non-systematic narrative review. only a small minority of trial reports are being analysed in up-to-date systematic reviews. given the constraints, archie cochrane's vision will not be achieved without some serious changes in course. to meet the needs of patients, clinicians, and policymakers, unnecessary trials need to be reduced, and systematic reviews need to be prioritised. streamlining and innovation in methods of systematic reviewing are necessary to enable valid answers to be found for most patient questions. finally, clinicians and patients require open access to these important resources.",0
"there is considerable variability in the susceptibility of smokers to develop chronic obstructive pulmonary disease (copd). the only known genetic risk factor is severe deficiency of alpha(1)-antitrypsin, which is present in 1-2% of individuals with copd. we conducted a genome-wide association study (gwas) in a homogenous case-control cohort from bergen, norway (823 copd cases and 810 smoking controls) and evaluated the top 100 single nucleotide polymorphisms (snps) in the family-based international copd genetics network (icgn; 1891 caucasian individuals from 606 pedigrees) study. the polymorphisms that showed replication were further evaluated in 389 subjects from the us national emphysema treatment trial (nett) and 472 controls from the normative aging study (nas) and then in a fourth cohort of 949 individuals from 127 extended pedigrees from the boston early-onset copd population. logistic regression models with adjustments of covariates were used to analyze the case-control populations. family-based association analyses were conducted for a diagnosis of copd and lung function in the family populations. two snps at the alpha-nicotinic acetylcholine receptor (chrna 3/5) locus were identified in the genome-wide association study. they showed unambiguous replication in the icgn family-based analysis and in the nett case-control analysis with combined p-values of 1.48 x 10(-10), (rs8034191) and 5.74 x 10(-10) (rs1051730). furthermore, these snps were significantly associated with lung function in both the icgn and boston early-onset copd populations. the c allele of the rs8034191 snp was estimated to have a population attributable risk for copd of 12.2%. the association of hedgehog interacting protein (hhip) locus on chromosome 4 was also consistently replicated, but did not reach genome-wide significance levels. genome-wide significant association of the hhip locus with lung function was identified in the framingham heart study (wilk et al., companion article in this issue of plos genetics; doi:10.1371/journal.pgen.1000429). the chrna 3/5 and the hhip loci make a significant contribution to the risk of copd. chrna3/5 is the same locus that has been implicated in the risk of lung cancer.",0
"most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. in the kegg database resource ( diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. disease information is computerized in two forms: pathway maps and gene/molecule lists. the kegg pathway database contains pathway maps for the molecular systems in both normal and perturbed states. in the kegg disease database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. the kegg drug database contains chemical structures and/or chemical components of all drugs in japan, including crude drugs and tcm (traditional chinese medicine) formulas, and drugs in the usa and europe. this database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. the new disease/drug information resource named kegg medicus can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.",0
"background mobile phone health apps may now seem to be ubiquitous, yet much remains unknown with regard to their usage. information is limited with regard to important metrics, including the percentage of the population that uses health apps, reasons for adoption/nonadoption, and reasons for noncontinuance of use. objective the purpose of this study was to examine health app use among mobile phone owners in the united states. methods we conducted a cross-sectional survey of 1604 mobile phone users throughout the united states. the 36-item survey assessed sociodemographic characteristics, history of and reasons for health app use/nonuse, perceived effectiveness of health apps, reasons for stopping use, and general health status. results a little over half (934/1604, 58.23%) of mobile phone users had downloaded a health-related mobile app. fitness and nutrition were the most common categories of health apps used, with most respondents using them at least daily. common reasons for not having downloaded apps were lack of interest, cost, and concern about apps collecting their data. individuals more likely to use health apps tended to be younger, have higher incomes, be more educated, be latino/hispanic, and have a body mass index (bmi) in the obese range (all p conclusions these findings suggest that while many individuals use health apps, a substantial proportion of the population does not, and that even among those who use health apps, many stop using them. these data suggest that app developers need to better address consumer concerns, such as cost and high data entry burden, and that clinical trials are necessary to test the efficacy of health apps to broaden their appeal and adoption.",0
"many athletes, coaches, and support staff are taking an increasingly scientific approach to both designing and monitoring training programs. appropriate load monitoring can aid in determining whether an athlete is adapting to a training program and in minimizing the risk of developing non-functional overreaching, illness, and/or injury. in order to gain an understanding of the training load and its effect on the athlete, a number of potential markers are available for use. however, very few of these markers have strong scientific evidence supporting their use, and there is yet to be a single, definitive marker described in the literature. research has investigated a number of external load quantifying and monitoring tools, such as power output measuring devices, time-motion analysis, as well as internal load unit measures, including perception of effort, heart rate, blood lactate, and training impulse. dissociation between external and internal load units may reveal the state of fatigue of an athlete. other monitoring tools used by high-performance programs include heart rate recovery, neuromuscular function, biochemical/hormonal/immunological assessments, questionnaires and diaries, psychomotor speed, and sleep quality and quantity. the monitoring approach taken with athletes may depend on whether the athlete is engaging in individual or team sport activity; however, the importance of individualization of load monitoring cannot be over emphasized. detecting meaningful changes with scientific and statistical approaches can provide confidence and certainty when implementing change. appropriate monitoring of training load can provide important information to athletes and coaches; however, monitoring systems should be intuitive, provide efficient data analysis and interpretation, and enable efficient reporting of simple, yet scientifically valid, feedback.",0
"we demonstrate the successful application of exome sequencing to discover a gene for an autosomal dominant disorder, kabuki syndrome (omim%147920). we subjected the exomes of ten unrelated probands to massively parallel sequencing. after filtering against existing snp databases, there was no compelling candidate gene containing previously unknown variants in all affected individuals. less stringent filtering criteria allowed for the presence of modest genetic heterogeneity or missing data but also identified multiple candidate genes. however, genotypic and phenotypic stratification highlighted mll2, which encodes a trithorax-group histone methyltransferase: seven probands had newly identified nonsense or frameshift mutations in this gene. follow-up sanger sequencing detected mll2 mutations in two of the three remaining individuals with kabuki syndrome (cases) and in 26 of 43 additional cases. in families where parental dna was available, the mutation was confirmed to be de novo (n = 12) or transmitted (n = 2) in concordance with phenotype. our results strongly suggest that mutations in mll2 are a major cause of kabuki syndrome.",0
"dormant solid tumors were produced in vivo by prevention of neovascularization. when small fragments of anaplastic brown-pearce carcinoma were implanted directly on the iris in susceptible rabbits, they always vascularized. a characteristic growth pattern, consisting of prevascular, vascular, and late phases, was observed, which terminated with destruction of the eye within 2 wk. the beginning of exponential volume increase was shown to coincide with vascularization of the implant, as demonstrated by perfusion with intravenous fluorescein and by histologic sections. in contrast, implants placed in the anterior chamber, at a distance from the iris, did not become vascularized. after initial growth into spheroids, they remained arrested at a small size comparable to prevascular iris implants, for periods as long as 6 wk. although dormant in terms of expansion, these avascular tumors contained a population of viable and mitotically active tumor cells. when reimplanted on the iris, vascularization was followed by rapid, invasive growth. these observations suggest that neovascularization is a necessary condition for malignant growth of a solid tumor. when a small mass of tumor cells is prevented from eliciting new vessel ingrowth from surrounding host tissues, population dormancy results. these data suggest that the specific blockade of tumor-induced angiogenesis may be an effective means of controlling neoplastic growth.",0
"background mendelian randomization (mr) is being increasingly used to strengthen causal inference in observational studies. availability of summary data of genetic associations for a variety of phenotypes from large genome-wide association studies (gwas) allows straightforward application of mr using summary data methods, typically in a two-sample design. in addition to the conventional inverse variance weighting (ivw) method, recently developed summary data mr methods, such as the mr-egger and weighted median approaches, allow a relaxation of the instrumental variable assumptions. methods here, a new method - the mode-based estimate (mbe) - is proposed to obtain a single causal effect estimate from multiple genetic instruments. the mbe is consistent when the largest number of similar (identical in infinite samples) individual-instrument causal effect estimates comes from valid instruments, even if the majority of instruments are invalid. we evaluate the performance of the method in simulations designed to mimic the two-sample summary data setting, and demonstrate its use by investigating the causal effect of plasma lipid fractions and urate levels on coronary heart disease risk. results the mbe presented less bias and lower type-i error rates than other methods under the null in many situations. its power to detect a causal effect was smaller compared with the ivw and weighted median methods, but was larger than that of mr-egger regression, with sample size requirements typically smaller than those available from gwas consortia. conclusions the mbe relaxes the instrumental variable assumptions, and should be used in combination with other approaches in sensitivity analyses.",0
"there is considerable interest in the structural and functional properties of the angular gyrus (ag). located in the posterior part of the inferior parietal lobule, the ag has been shown in numerous meta-analysis reviews to be consistently activated in a variety of tasks. this review discusses the involvement of the ag in semantic processing, word reading and comprehension, number processing, default mode network, memory retrieval, attention and spatial cognition, reasoning, and social cognition. this large functional neuroimaging literature depicts a major role for the ag in processing concepts rather than percepts when interfacing perception-to-recognition-to-action. more specifically, the ag emerges as a cross-modal hub where converging multisensory information is combined and integrated to comprehend and give sense to events, manipulate mental representations, solve familiar problems, and reorient attention to relevant information. in addition, this review discusses recent findings that point to the existence of multiple subdivisions in the ag. this spatial parcellation can serve as a framework for reporting ag activations with greater definition. this review also acknowledges that the role of the ag cannot comprehensibly be identified in isolation but needs to be understood in parallel with the influence from other regions. several interesting questions that warrant further investigations are finally emphasized.",0
"background a commonly reported problem with the conduct of multicentre randomised controlled trials (rcts) is that recruitment is often slower or more difficult than expected, with many trials failing to reach their planned sample size within the timescale and funding originally envisaged. the aim of this study was to explore factors that may have been associated with good and poor recruitment in a cohort of multicentre trials funded by two public bodies: the uk medical research council (mrc) and the health technology assessment (hta) programme. methods the cohort of trials was identified from the administrative databases held by the two funding bodies. 114 trials that recruited participants between 1994 and 2002 met the inclusion criteria. the full scientific applications and subsequent trial reports submitted by the trial teams to the funders provided the principal data sources. associations between trial characteristics and recruitment success were tested using the chi-squared test, or fisher's exact test where appropriate. results less than a third (31%) of the trials achieved their original recruitment target and half (53%) were awarded an extension. the proportion achieving targets did not appear to improve over time. the overall start to recruitment was delayed in 47 (41%) trials and early recruitment problems were identified in 77 (63%) trials. the inter-relationship between trial features and recruitment success was complex. a variety of strategies were employed to try to increase recruitment, but their success could not be assessed. conclusion recruitment problems are complex and challenging. many of the trials in the cohort experienced recruitment difficulties. trials often required extended recruitment periods (sometimes supported by additional funds). while this is of continuing concern, success in addressing the trial question may be more important than recruitment alone.",0
"dendritic cells, the professional antigen-presenting cells (apc) involved in t cell priming, express cd40, a molecule which triggering plays a key role in b cell growth and differentiation as well as monocyte activation. herein we demonstrate that dendritic langerhans cells (d-lc) generated by culturing cord blood cd34+ progenitor cells with granulocyte/macrophage colony-stimulating and tumor necrosis factor alpha (tnf-alpha) express functional cd40 at a density higher than that found on b cells. culturing d-lc on cd40-ligand (cd40l) transfected l cells allowed d-lc survival as 50 +/- 15% of seeded cells were recovered after 4 d while only 5% survived over control l cells. cd40 activation induced important morphological changes with a reduction of cytoplasmic content and a remarkable increase of dendrite development as well as an altered phenotype. in particular, cd40 triggering induced maintenance of high levels of major histocompatibility complex class ii antigens and upregulation of accessory molecules such as cd58, cd80 (b7-1) and cd86 (b7-2). cd40 engagement also seems to turn on d-lc maturation as illustrated by upregulation of cd25, a molecule usually expressed on interdigitating dendritic cells of secondary lymphoid organs. finally, cd40 activated d-lc secreted a limited set of cytokines (tnf-alpha, il-8, and macrophage inflammatory protein 1 alpha ) whereas a similar activation induced elutriated monocytes to secrete il-1 alpha, il-1 beta, il-6, il-8, il-10, tnf-alpha, and mip-1 alpha. as d-lc activated t cells upregulated cd40l, it is likely that cd40 activation of d-lc observed herein with a fibroblast cell line stably expressing cd40l, mimics physiological interactions between dendritic cells and t cells.",0
"dietary restriction extends healthy lifespan in diverse organisms and reduces fecundity. it is widely assumed to induce adaptive reallocation of nutrients from reproduction to somatic maintenance, aiding survival of food shortages in nature. if this were the case, long life under dietary restriction and high fecundity under full feeding would be mutually exclusive, through competition for the same limiting nutrients. here we report a test of this idea in which we identified the nutrients producing the responses of lifespan and fecundity to dietary restriction in drosophila. adding essential amino acids to the dietary restriction condition increased fecundity and decreased lifespan, similar to the effects of full feeding, with other nutrients having little or no effect. however, methionine alone was necessary and sufficient to increase fecundity as much as did full feeding, but without reducing lifespan. reallocation of nutrients therefore does not explain the responses to dietary restriction. lifespan was decreased by the addition of amino acids, with an interaction between methionine and other essential amino acids having a key role. hence, an imbalance in dietary amino acids away from the ratio optimal for reproduction shortens lifespan during full feeding and limits fecundity during dietary restriction. reduced activity of the insulin/insulin-like growth factor signalling pathway extends lifespan in diverse organisms, and we find that it also protects against the shortening of lifespan with full feeding. in other organisms, including mammals, it may be possible to obtain the benefits to lifespan of dietary restriction without incurring a reduction in fecundity, through a suitable balance of nutrients in the diet.",0
"background over the past few decades, scientific research has been focused on developing peptide/protein-based therapies to treat various diseases. with the several advantages over small molecules, including high specificity, high penetration, ease of manufacturing, peptides have emerged as promising therapeutic molecules against many diseases. however, one of the bottlenecks in peptide/protein-based therapy is their toxicity. therefore, in the present study, we developed in silico models for predicting toxicity of peptides and proteins. description we obtained toxic peptides having 35 or fewer residues from various databases for developing prediction models. non-toxic or random peptides were obtained from swissprot and trembl. it was observed that certain residues like cys, his, asn, and pro are abundant as well as preferred at various positions in toxic peptides. we developed models based on machine learning technique and quantitative matrix using various properties of peptides for predicting toxicity of peptides. the performance of dipeptide-based model in terms of accuracy was 94.50% with mcc 0.88. in addition, various motifs were extracted from the toxic peptides and this information was combined with dipeptide-based model for developing a hybrid model. in order to evaluate the over-optimization of the best model based on dipeptide composition, we evaluated its performance on independent datasets and achieved accuracy around 90%. based on above study, a web server, toxinpred has been developed, which would be helpful in predicting (i) toxicity or non-toxicity of peptides, (ii) minimum mutations in peptides for increasing or decreasing their toxicity, and (iii) toxic regions in proteins. conclusion toxinpred is a unique in silico method of its kind, which will be useful in predicting toxicity of peptides/proteins. in addition, it will be useful in designing least toxic peptides and discovering toxic regions in proteins. we hope that the development of toxinpred will provide momentum to peptide/protein-based drug discovery (",0
"since their discovery in the 1960s, liposomes have been studied in depth, and they continue to constitute a field of intense research. liposomes are valued for their biological and technological advantages, and are considered to be the most successful drug-carrier system known to date. notable progress has been made, and several biomedical applications of liposomes are either in clinical trials, are about to be put on the market, or have already been approved for public use. in this review, we briefly analyze how the efficacy of liposomes depends on the nature of their components and their size, surface charge, and lipidic organization. moreover, we discuss the influence of the physicochemical properties of liposomes on their interaction with cells, half-life, ability to enter tissues, and final fate in vivo. finally, we describe some strategies developed to overcome limitations of the ""first-generation"" liposomes, and liposome-based drugs on the market and in clinical trials.",0
"a key component of genetic architecture is the allelic spectrum influencing trait variability. for autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. individual risk-associated genes have been identified from rare variation, especially de novo mutations. from this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial impact en masse. at issue is how much of an impact relative to rare variation this common variation has. using a unique epidemiological sample from sweden, new methods that distinguish total narrow-sense heritability from that due to common variation and synthesis of results from other studies, we reach several conclusions about autism's genetic architecture: its narrow-sense heritability is ∼52.4%, with most due to common variation, and rare de novo mutations contribute substantially to individual liability, yet their contribution to variance in liability, 2.6%, is modest compared to that for heritable variation.",0
"severe acute respiratory syndrome coronavirus 2 causes direct damage to the airway epithelium, enabling aspergillus invasion. reports of covid-19-associated pulmonary aspergillosis have raised concerns about it worsening the disease course of covid-19 and increasing mortality. additionally, the first cases of covid-19-associated pulmonary aspergillosis caused by azole-resistant aspergillus have been reported. this article constitutes a consensus statement on defining and managing covid-19-associated pulmonary aspergillosis, prepared by experts and endorsed by medical mycology societies. covid-19-associated pulmonary aspergillosis is proposed to be defined as possible, probable, or proven on the basis of sample validity and thus diagnostic certainty. recommended first-line therapy is either voriconazole or isavuconazole. if azole resistance is a concern, then liposomal amphotericin b is the drug of choice. our aim is to provide definitions for clinical research and up-to-date recommendations for clinical management of the diagnosis and treatment of covid-19-associated pulmonary aspergillosis.",0
"faecal microbiota transplantation (fmt) is an important therapeutic option for clostridium difficile infection. promising findings suggest that fmt may play a role also in the management of other disorders associated with the alteration of gut microbiota. although the health community is assessing fmt with renewed interest and patients are becoming more aware, there are technical and logistical issues in establishing such a non-standardised treatment into the clinical practice with safety and proper governance. in view of this, an evidence-based recommendation is needed to drive the practical implementation of fmt. in this european consensus conference, 28 experts from 10 countries collaborated, in separate working groups and through an evidence-based process, to provide statements on the following key issues: fmt indications; donor selection; preparation of faecal material; clinical management and faecal delivery and basic requirements for implementing an fmt centre. statements developed by each working group were evaluated and voted by all members, first through an electronic delphi process, and then in a plenary consensus conference. the recommendations were released according to best available evidence, in order to act as guidance for physicians who plan to implement fmt, aiming at supporting the broad availability of the procedure, discussing other issues relevant to fmt and promoting future clinical research in the area of gut microbiota manipulation. this consensus report strongly recommends the implementation of fmt centres for the treatment of c. difficile infection as well as traces the guidelines of technicality, regulatory, administrative and laboratory requirements.",0
"the molecular evolutionary genetics analysis (mega) software has matured to contain a large collection of methods and tools of computational molecular evolution. here, we describe new additions that make mega a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. they are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive node calibrations editor, and an extended tree explorer to display timetrees. also added is a bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. the computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. these enhancements will improve the user experience, quality of results, and the pace of biological discovery. natively compiled graphical user interface and command-line versions of mega11 are available for microsoft windows, linux, and macos from",0
"background the prominence of sedentary behavior research in health science has grown rapidly. with this growth there is increasing urgency for clear, common and accepted terminology and definitions. such standardization is difficult to achieve, especially across multi-disciplinary researchers, practitioners, and industries. the sedentary behavior research network (sbrn) undertook a terminology consensus project to address this need. method first, a literature review was completed to identify key terms in sedentary behavior research. these key terms were then reviewed and modified by a steering committee formed by sbrn. next, sbrn members were invited to contribute to this project and interested participants reviewed and provided feedback on the proposed list of terms and draft definitions through an online survey. finally, a conceptual model and consensus definitions (including caveats and examples for all age groups and functional abilities) were finalized based on the feedback received from the 87 sbrn member participants who responded to the original invitation and survey. results consensus definitions for the terms physical inactivity, stationary behavior, sedentary behavior, standing, screen time, non-screen-based sedentary time, sitting, reclining, lying, sedentary behavior pattern, as well as how the terms bouts, breaks, and interruptions should be used in this context are provided. conclusion it is hoped that the definitions resulting from this comprehensive, transparent, and broad-based participatory process will result in standardized terminology that is widely supported and adopted, thereby advancing future research, interventions, policies, and practices related to sedentary behaviors.",0
"the consensus algorithm for the medical management of type 2 diabetes was published in august 2006 with the expectation that it would be updated, based on the availability of new interventions and new evidence to establish their clinical role. the authors continue to endorse the principles used to develop the algorithm and its major features. we are sensitive to the risks of changing the algorithm cavalierly or too frequently, without compelling new information. an update to the consensus algorithm published in january 2008 specifically addressed safety issues surrounding the thiazolidinediones. in this revision, we focus on the new classes of medications that now have more clinical data and experience.",0
"jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. the f-box protein coronatine insensitive 1 (coi1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor jaz proteins. despite its importance, the mechanism of jasmonate perception remains unclear. here we present structural and pharmacological data to show that the true arabidopsis jasmonate receptor is a complex of both coi1 and jaz. coi1 contains an open pocket that recognizes the bioactive hormone (3r,7s)-jasmonoyl-l-isoleucine (ja-ile) with high specificity. high-affinity hormone binding requires a bipartite jaz degron sequence consisting of a conserved α-helix for coi1 docking and a loop region to trap the hormone in its binding pocket. in addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both coi1 and jaz adjacent to the ligand. our results unravel the mechanism of jasmonate perception and highlight the ability of f-box proteins to evolve as multi-component signalling hubs.",0
"cytotoxic t lymphocyte-associated antigen 4 (ctla-4) is a critical negative regulator of immune responses. uniquely among known inhibitory receptors, its genetic ablation results in a fulminating and fatal lymphoproliferative disorder. this central regulatory role led to the development of antibodies designed to block ctla-4 activity in vivo, aiming to enhance immune responses against cancer. despite their preclinical efficacy and promising clinical activity against late stage metastatic melanoma, the critical cellular targets for their activity remains unclear. in particular, debate has focused on whether the effector t cell (t(eff)) or regulatory t cell (t reg cell) compartment is the primary target of antibody-mediated blockade. we developed a mouse expressing human instead of mouse ctla-4, allowing us to evaluate the independent contributions of ctla-4 blockade of each t cell compartment during cancer immunotherapy in an in vivo model of mouse melanoma. the data show that although blockade on effector cells significantly improves tumor protection, unicompartmental blockade on regulatory cells completely fails to enhance antitumor responses. however, concomitant blockade of both compartments leads to a synergistic effect and maximal antitumor activity. we conclude that the combination of direct enhancement of t(eff) cell function and concomitant inhibition of t reg cell activity through blockade of ctla-4 on both cell types is essential for mediating the full therapeutic effects of anti-ctla-4 antibodies during cancer immunotherapy.",0
"braf and nras are common targets for somatic mutations in benign and malignant neoplasms that arise from melanocytes situated in epithelial structures, and lead to constitutive activation of the mitogen-activated protein (map) kinase pathway. however, braf and nras mutations are absent in a number of other melanocytic neoplasms in which the equivalent oncogenic events are currently unknown. here we report frequent somatic mutations in the heterotrimeric g protein alpha-subunit, gnaq, in blue naevi (83%) and ocular melanoma of the uvea (46%). the mutations occur exclusively in codon 209 in the ras-like domain and result in constitutive activation, turning gnaq into a dominant acting oncogene. our results demonstrate an alternative route to map kinase activation in melanocytic neoplasia, providing new opportunities for therapeutic intervention.",0
"background motivation is a critical factor in supporting sustained exercise, which in turn is associated with important health outcomes. accordingly, research on exercise motivation from the perspective of self-determination theory (sdt) has grown considerably in recent years. previous reviews have been mostly narrative and theoretical. aiming at a more comprehensive review of empirical data, this article examines the empirical literature on the relations between key sdt-based constructs and exercise and physical activity behavioral outcomes. methods this systematic review includes 66 empirical studies published up to june 2011, including experimental, cross-sectional, and prospective studies that have measured exercise causality orientations, autonomy/need support and need satisfaction, exercise motives (or goal contents), and exercise self-regulations and motivation. we also studied sdt-based interventions aimed at increasing exercise behavior. in all studies, actual or self-reported exercise/physical activity, including attendance, was analyzed as the dependent variable. findings are summarized based on quantitative analysis of the evidence. results the results show consistent support for a positive relation between more autonomous forms of motivation and exercise, with a trend towards identified regulation predicting initial/short-term adoption more strongly than intrinsic motivation, and intrinsic motivation being more predictive of long-term exercise adherence. the literature is also consistent in that competence satisfaction and more intrinsic motives positively predict exercise participation across a range of samples and settings. mixed evidence was found concerning the role of other types of motives (e.g., health/fitness and body-related), and also the specific nature and consequences of introjected regulation. the majority of studies have employed descriptive (i.e., non-experimental) designs but similar results are found across cross-sectional, prospective, and experimental designs. conclusion overall, the literature provides good evidence for the value of sdt in understanding exercise behavior, demonstrating the importance of autonomous (identified and intrinsic) regulations in fostering physical activity. nevertheless, there remain some inconsistencies and mixed evidence with regard to the relations between specific sdt constructs and exercise. particular limitations concerning the different associations explored in the literature are discussed in the context of refining the application of sdt to exercise and physical activity promotion, and integrating these with avenues for future research.",0
"the imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. we present a mixed effects model of evolution (meme) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. using empirical and simulated data, we demonstrate the superior performance of meme over older models under a broad range of scenarios. we find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated.",0
"the blood vessels of cancerous tumours are leaky and poorly organized. this can increase the interstitial fluid pressure inside tumours and reduce blood supply to them, which impairs drug delivery. anti-angiogenic therapies--which 'normalize' the abnormal blood vessels in tumours by making them less leaky--have been shown to improve the delivery and effectiveness of chemotherapeutics with low molecular weights, but it remains unclear whether normalizing tumour vessels can improve the delivery of nanomedicines. here, we show that repairing the abnormal vessels in mammary tumours, by blocking vascular endothelial growth factor receptor-2, improves the delivery of smaller nanoparticles (diameter, 12 nm) while hindering the delivery of larger nanoparticles (diameter, 125 nm). using a mathematical model, we show that reducing the sizes of pores in the walls of vessels through normalization decreases the interstitial fluid pressure in tumours, thus allowing small nanoparticles to enter them more rapidly. however, increased steric and hydrodynamic hindrances, also associated with smaller pores, make it more difficult for large nanoparticles to enter tumours. our results further suggest that smaller (∼12 nm) nanomedicines are ideal for cancer therapy due to their superior tumour penetration.",0
"background local recurrence rates in operable rectal cancer are improved by radiotherapy (with or without chemotherapy) and surgical techniques such as total mesorectal excision. however, the contributions of surgery and radiotherapy to outcomes are unclear. we assessed the effect of the involvement of the circumferential resection margin and the plane of surgery achieved. methods in this prospective study, the plane of surgery achieved and the involvement of the circumferential resection margin were assessed by local pathologists, using a standard pathological protocol in 1156 patients with operable rectal cancer from the cr07 and ncic-ctg co16 trial, which compared short-course (5 days) preoperative radiotherapy and selective postoperative chemoradiotherapy, between march, 1998, and august, 2005. all analyses were by intention to treat. this trial is registered, number isrctn 28785842. findings 128 patients (11%) had involvement of the circumferential resection margin, and the plane of surgery achieved was classified as good (mesorectal) in 604 (52%), intermediate (intramesorectal) in 398 (34%), and poor (muscularis propria plane) in 154 (13%). we found that both a negative circumferential resection margin and a superior plane of surgery achieved were associated with low local recurrence rates. hazard ratio (hr) was 0.32 (95% ci 0.16-0.63, p=0.0011) with 3-year local recurrence rates of 6% (5-8%) and 17% (10-26%) for patients who were negative and positive for circumferential resection margin, respectively. for plane of surgery achieved, hrs for mesorectal and intramesorectal groups compared with the muscularis propria group were 0.32 (0.16-0.64) and 0.48 (0.25-0.93), respectively. at 3 years, the estimated local recurrence rates were 4% (3-6%) for mesorectal, 7% (5-11%) for intramesorectal, and 13% (8-21%) for muscularis propria groups. the benefit of short-course preoperative radiotherapy did not differ in the three plane of surgery groups (p=0.30 for trend). patients in the short-course preoperative radiotherapy group who had a resection in the mesorectal plane had a 3-year local recurrence rate of only 1%. interpretation in rectal cancer, the plane of surgery achieved is an important prognostic factor for local recurrence. short-course preoperative radiotherapy reduced the rate of local recurrence for all three plane of surgery groups, almost abolishing local recurrence in short-course preoperative radiotherapy patients who had a resection in the mesorectal plane. the plane of surgery achieved should therefore be assessed and reported routinely.",0
"physiological conversion of the maternal spiral arteries is key to a successful human pregnancy. it involves loss of smooth muscle and the elastic lamina from the vessel wall as far as the inner third of the myometrium, and is associated with a 5-10-fold dilation at the vessel mouth. failure of conversion accompanies common complications of pregnancy, such as early-onset preeclampsia and fetal growth restriction. here, we model the effects of terminal dilation on inflow of blood into the placental intervillous space at term, using dimensions in the literature derived from three-dimensional reconstructions. we observe that dilation slows the rate of flow from 2 to 3m/s in the non-dilated part of an artery of 0.4-0.5mm diameter to approximately 10 cm/s at the 2.5mm diameter mouth, depending on the exact radius and viscosity. this rate predicts a transit time through the intervillous space of approximately 25s, which matches observed times closely. the model shows that in the absence of conversion blood will enter the intervillous space as a turbulent jet at rates of 1-2m/s. we speculate that the high momentum will damage villous architecture, rupturing anchoring villi and creating echogenic cystic lesions as evidenced by ultrasound. the retention of smooth muscle will also increase the risk of spontaneous vasoconstriction and ischaemia-reperfusion injury, generating oxidative stress. dilation has a surprisingly modest impact on total blood flow, and so we suggest the placental pathology associated with deficient conversion is dominated by rheological consequences rather than chronic hypoxia.",0
"background understanding the epidemiology and clinical course of multisystem inflammatory syndrome in children (mis-c) and its temporal association with coronavirus disease 2019 (covid-19) is important, given the clinical and public health implications of the syndrome. methods we conducted targeted surveillance for mis-c from march 15 to may 20, 2020, in pediatric health centers across the united states. the case definition included six criteria: serious illness leading to hospitalization, an age of less than 21 years, fever that lasted for at least 24 hours, laboratory evidence of inflammation, multisystem organ involvement, and evidence of infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) based on reverse-transcriptase polymerase chain reaction (rt-pcr), antibody testing, or exposure to persons with covid-19 in the past month. clinicians abstracted the data onto standardized forms. results we report on 186 patients with mis-c in 26 states. the median age was 8.3 years, 115 patients (62%) were male, 135 (73%) had previously been healthy, 131 (70%) were positive for sars-cov-2 by rt-pcr or antibody testing, and 164 (88%) were hospitalized after april 16, 2020. organ-system involvement included the gastrointestinal system in 171 patients (92%), cardiovascular in 149 (80%), hematologic in 142 (76%), mucocutaneous in 137 (74%), and respiratory in 131 (70%). the median duration of hospitalization was 7 days (interquartile range, 4 to 10); 148 patients (80%) received intensive care, 37 (20%) received mechanical ventilation, 90 (48%) received vasoactive support, and 4 (2%) died. coronary-artery aneurysms (z scores ≥2.5) were documented in 15 patients (8%), and kawasaki's disease-like features were documented in 74 (40%). most patients (171 ) had elevations in at least four biomarkers indicating inflammation. the use of immunomodulating therapies was common: intravenous immune globulin was used in 144 (77%), glucocorticoids in 91 (49%), and interleukin-6 or 1ra inhibitors in 38 (20%). conclusions multisystem inflammatory syndrome in children associated with sars-cov-2 led to serious and life-threatening illness in previously healthy children and adolescents. (funded by the centers for disease control and prevention.).",0
"saturation has attained widespread acceptance as a methodological principle in qualitative research. it is commonly taken to indicate that, on the basis of the data that have been collected or analysed hitherto, further data collection and/or analysis are unnecessary. however, there appears to be uncertainty as to how saturation should be conceptualized, and inconsistencies in its use. in this paper, we look to clarify the nature, purposes and uses of saturation, and in doing so add to theoretical debate on the role of saturation across different methodologies. we identify four distinct approaches to saturation, which differ in terms of the extent to which an inductive or a deductive logic is adopted, and the relative emphasis on data collection, data analysis, and theorizing. we explore the purposes saturation might serve in relation to these different approaches, and the implications for how and when saturation will be sought. in examining these issues, we highlight the uncertain logic underlying saturation-as essentially a predictive statement about the unobserved based on the observed, a judgement that, we argue, results in equivocation, and may in part explain the confusion surrounding its use. we conclude that saturation should be operationalized in a way that is consistent with the research question(s), and the theoretical position and analytic framework adopted, but also that there should be some limit to its scope, so as not to risk saturation losing its coherence and potency if its conceptualization and uses are stretched too widely.",0
"the information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. however, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. to provide the community with a resource free of these hurdles, we have developed disgenet ( one of the largest available collections of genes and variants involved in human diseases. disgenet integrates data from expert curated repositories, gwas catalogues, animal models and the scientific literature. disgenet data are homogeneously annotated with controlled vocabularies and community-driven ontologies. additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. the information is accessible through a web interface, a cytoscape app, an rdf sparql endpoint, scripts in several programming languages and an r package. disgenet is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.",0
"eggnog is a public resource that provides orthologous groups (ogs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. developments since the latest public release include changes to the algorithm for creating ogs across taxonomic levels, making nested groups hierarchically consistent. this allows for a better propagation of functional terms across nested ogs and led to the novel annotation of 95 890 previously uncharacterized ogs, increasing overall annotation coverage from 67% to 72%. the functional annotations of ogs have been expanded to also provide gene ontology terms, kegg pathways and smart/pfam domains for each group. moreover, eggnog now provides pairwise orthology relationships within ogs based on analysis of phylogenetic trees. we have also incorporated a framework for quickly mapping novel sequences to ogs based on precomputed hmm profiles. finally, eggnog version 4.5 incorporates a novel data set spanning 2605 viral ogs, covering 5228 proteins from 352 viral proteomes. all data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. the new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggnog v4.5 is available at",0
"reactome ( is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. a new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated reactome pathway datasets for species including arabidopsis, oryza sativa (rice), drosophila and gallus gallus (chicken). reactome's data content and software can all be freely used and redistributed under open source terms.",0
"a prerequisite for many studies of neurons in culture is a means of determining their original identity. we needed such a technique to study the interactions in vitro between a class of spinal cord neurons, sympathetic preganglionic neurons, and their normal target, neurons from the sympathetic chain. here, we describe how we use two highly fluorescent carbocyanine dyes, which differ in color but are otherwise similar, to identify neurons in culture. the long carbon chain carbocyanine dyes we use are lipid-soluble and so become incorporated into the plasma membrane. neurons can be labeled either retrogradely or during dissociation. some of the labeled membrane gradually becomes internalized and retains its fluorescence, allowing identification of cells for several weeks in culture. these dyes do not affect the survival, development, or basic physiological properties of neurons and do not spread detectably from labeled to unlabeled neurons. it seems likely that cells become retrogradely labeled mainly by lateral diffusion of dye in the plane of the membrane. if so, carbocyanine dyes may be most useful for retrograde labeling over relatively short distances. an additional feature of carbocyanine labeling is that neuronal processes are brightly fluorescent for the first few days in culture, presumably because dye rapidly diffuses into newly inserted membrane. we have used carbocyanine dyes to identify sympathetic preganglionic neurons in culture. our results indicate that preganglionic neurons can survive in the absence of their target cells and that several aspects of their differentiation in the absence of target appear normal.",0
"recent advances in hardware and software have enabled increasingly long molecular dynamics (md) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. recent modifications to the amber and charmm protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the amber ff99sb force field. first, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on protein data bank statistics. second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. finally, we used microsecond-timescale md simulations in explicit solvent to validate the resulting force field against a large set of experimental nmr measurements that directly probe side-chain conformations. the new force field, which we have termed amber ff99sb-ildn, exhibits considerably better agreement with the nmr data.",0
"scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. it is released under the liberal modified bsd open source license, provides a well-documented api in the python programming language, and is developed by an active, international team of collaborators. in this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. more information can be found on the project homepage,",0
"uk biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. it is currently in the process of bringing back 100,000 of the original participants for brain, heart and body mri, carotid ultrasound and low-dose bone/fat x-ray. the brain imaging component covers 6 modalities (t1, t2 flair, susceptibility weighted mri, resting fmri, task fmri and diffusion mri). raw and processed data from the first 10,000 imaged subjects has recently been released for general research access. to help convert this data into useful summary information we have developed an automated processing and qc (quality control) pipeline that is available for use by other researchers. in this paper we describe the pipeline in detail, following a brief overview of uk biobank brain imaging and the acquisition protocol. we also describe several quantitative investigations carried out as part of the development of both the imaging protocol and the processing pipeline.",0
"nuclear domain 10 (nd10), also referred to as nuclear bodies, are discrete interchromosomal accumulations of several proteins including promyelocytic leukemia protein (pml) and sp100. in this study, we investigated the mechanism of nd10 assembly by identifying proteins that are essential for this process using cells lines that lack individual nd10-associated proteins. we identified the adapter protein daxx and bml, the recq helicase missing in bloom syndrome, as new nd10-associated proteins. pml, but not blm or sp100, was found to be responsible for the proper localization of all other nd10-associated proteins since they are dispersed in pml-/- cells. introducing pml into this cell line by transient expression or fusion with pml-producing cells recruited nd10-associated proteins into de novo formed nd10 attesting to pmls essential nature in nd10 formation. in the absence of pml, daxx is highly enriched in condensed chromatin. its recruitment to nd10 from condensed chromatin requires a small ubiquitin-related modifier (sumo-1) modification of pml and reflects the interaction between the cooh-terminal domain of daxx and pml. the segregation of daxx from condensed chromatin in the absence of pml to nd10 by increased accumulation of sumo-1-modified pml suggests the presence of a variable equilibrium between these two nuclear sites. our findings identify the basic requirements for nd10 formation and suggest a dynamic mechanism for protein recruitment to these nuclear domains controlled by the sumo-1 modification state of pml.",0
"magnetic resonance imaging (mri) has transformed our understanding of the human brain through well-replicated mapping of abilities to specific structures (for example, lesion studies) and functions 1-3 (for example, task functional mri (fmri)). mental health research and care have yet to realize similar advances from mri. a primary challenge has been replicating associations between inter-individual differences in brain structure or function and complex cognitive or mental health phenotypes (brain-wide association studies (bwas)). such bwas have typically relied on sample sizes appropriate for classical brain mapping 4 (the median neuroimaging study sample size is about 25), but potentially too small for capturing reproducible brain-behavioural phenotype associations 5,6 . here we used three of the largest neuroimaging datasets currently available-with a total sample size of around 50,000 individuals-to quantify bwas effect sizes and reproducibility as a function of sample size. bwas associations were smaller than previously thought, resulting in statistically underpowered studies, inflated effect sizes and replication failures at typical sample sizes. as sample sizes grew into the thousands, replication rates began to improve and effect size inflation decreased. more robust bwas effects were detected for functional mri (versus structural), cognitive tests (versus mental health questionnaires) and multivariate methods (versus univariate). smaller than expected brain-phenotype associations and variability across population subsamples can explain widespread bwas replication failures. in contrast to non-bwas approaches with larger effects (for example, lesions, interventions and within-person), bwas reproducibility requires samples with thousands of individuals.",0
"it is well-known that deficiency or over exposure to various elements has noticeable effects on human health. the effect of an element is determined by several characteristics, including absorption, metabolism, and degree of interaction with physiological processes. iron is an essential element for almost all living organisms as it participates in a wide variety of metabolic processes, including oxygen transport, deoxyribonucleic acid (dna) synthesis, and electron transport. however, as iron can form free radicals, its concentration in body tissues must be tightly regulated because in excessive amounts, it can lead to tissue damage. disorders of iron metabolism are among the most common diseases of humans and encompass a broad spectrum of diseases with diverse clinical manifestations, ranging from anemia to iron overload, and possibly to neurodegenerative diseases. in this review, we discuss the latest progress in studies of iron metabolism and bioavailability, and our current understanding of human iron requirement and consequences and causes of iron deficiency. finally, we discuss strategies for prevention of iron deficiency.",0
"alkylphenols are widely used as plastic additives and surfactants. we report the identification of an alkylphenol, nonylphenol, as an estrogenic substance released from plastic centrifuge tubes. this compound was extracted with methanol, purified by flash chromatography and reverse-phase high performance liquid chromatography, and identified by gas chromatography-mass spectrometry. nonylphenol induced both cell proliferation and progesterone receptor in human estrogen-sensitive mcf7 breast tumor cells. nonylphenol also triggered mitotic activity in rat endometrium; this result confirms the reliability of the mcf7 cell proliferation bioassay. the estrogenic properties of alkylphenols, specifically nonylphenols, indicate that the use of plasticware containing these chemicals in experimental and diagnostic tests may lead to spurious results, and these compounds as well as alkylphenol polyethoxylates may also be potentially harmful to exposed humans and the environment at large.",0
"phenolic compounds are an important class of plant secondary metabolites which play crucial physiological roles throughout the plant life cycle. phenolics are produced under optimal and suboptimal conditions in plants and play key roles in developmental processes like cell division, hormonal regulation, photosynthetic activity, nutrient mineralization, and reproduction. plants exhibit increased synthesis of polyphenols such as phenolic acids and flavonoids under abiotic stress conditions, which help the plant to cope with environmental constraints. phenylpropanoid biosynthetic pathway is activated under abiotic stress conditions (drought, heavy metal, salinity, high/low temperature, and ultraviolet radiations) resulting in accumulation of various phenolic compounds which, among other roles, have the potential to scavenge harmful reactive oxygen species. deepening the research focuses on the phenolic responses to abiotic stress is of great interest for the scientific community. in the present article, we discuss the biochemical and molecular mechanisms related to the activation of phenylpropanoid metabolism and we describe phenolic-mediated stress tolerance in plants. an attempt has been made to provide updated and brand-new information about the response of phenolics under a challenging environment.",0
"the 2019 novel coronavirus disease (covid-19), with a starting point in china, has spread rapidly among people living in other countries and is approaching approximately 101,917,147 cases worldwide according to the statistics of world health organization. there are a limited number of covid-19 test kits available in hospitals due to the increasing cases daily. therefore, it is necessary to implement an automatic detection system as a quick alternative diagnosis option to prevent covid-19 spreading among people. in this study, five pre-trained convolutional neural network-based models (resnet50, resnet101, resnet152, inceptionv3 and inception-resnetv2) have been proposed for the detection of coronavirus pneumonia-infected patient using chest x-ray radiographs. we have implemented three different binary classifications with four classes (covid-19, normal (healthy), viral pneumonia and bacterial pneumonia) by using five-fold cross-validation. considering the performance results obtained, it has been seen that the pre-trained resnet50 model provides the highest classification performance (96.1% accuracy for dataset-1, 99.5% accuracy for dataset-2 and 99.7% accuracy for dataset-3) among other four used models.",0
"background the treatment of noncommunicable diseases (ncd), like coronary heart disease or type 2 diabetes mellitus, causes rising costs for the health system. physical activity is supposed to reduce the risk for these diseases. results of cross-sectional studies showed that physical activity is associated with better health, and that physical activity could prevent the development of these diseases. the purpose of this review is to summarize existing evidence for the long-term (>5 years) relationship between physical activity and weight gain, obesity, coronary heart disease, type 2 diabetes mellitus, alzheimer's disease and dementia. methods fifteen longitudinal studies with at least 5-year follow up times and a total of 288,724 subjects (>500 participants in each study), aged between 18 and 85 years, were identified using digital databases. only studies published in english, about healthy adults at baseline, intentional physical activity and the listed ncds were included. results the results of these studies show that physical activity appears to have a positive long-term influence on all selected diseases. conclusions this review revealed a paucity of long-term studies on the relationship between physical activity and the incidence of ncd.",0
"mendelian randomization (mr) is a method for estimating the causal relationship between an exposure and an outcome using a genetic factor as an instrumental variable (iv) for the exposure. in the traditional mr setting, data on the iv, exposure, and outcome are available for all participants. however, obtaining complete exposure data may be difficult in some settings, due to high measurement costs or lack of appropriate biospecimens. we used simulated data sets to assess statistical power and bias for mr when exposure data are available for a subset (or an independent set) of participants. we show that obtaining exposure data for a subset of participants is a cost-efficient strategy, often having negligible effects on power in comparison with a traditional complete-data analysis. the size of the subset needed to achieve maximum power depends on iv strength, and maximum power is approximately equal to the power of traditional iv estimators. weak ivs are shown to lead to bias towards the null when the subsample is small and towards the confounded association when the subset is relatively large. various approaches for confidence interval calculation are considered. these results have important implications for reducing the costs and increasing the feasibility of mr studies.",0
"e- and n-cadherin are calcium-dependent cell adhesion molecules that mediate cell-cell adhesion and also modulate cell migration and tumor invasiveness. the loss of e-cadherin-mediated adhesion has been shown to play an important role in the transition of epithelial tumors from a benign to an invasive state. however, recent evidence indicates that another member of the cadherin family, n-cadherin, is expressed in highly invasive tumor cell lines that lacked e-cadherin expression. these findings have raised the possibility that n-cadherin contributes to the invasive phenotype. to determine whether n-cadherin promotes invasion and metastasis, we transfected a weakly metastatic and e-cadherin-expressing breast cancer cell line, mcf-7, with n-cadherin and analyzed the effects on cell migration, invasion, and metastasis. transfected cells expressed both e- and n-cadherin and exhibited homotypic cell adhesion from both molecules. in vitro, n-cadherin-expressing cells migrated more efficiently, showed an increased invasion of matrigel, and adhered more efficiently to monolayers of endothelial cells. all cells produced low levels of the matrix metalloproteinase mmp-9, which was dramatically upregulated by treatment with fgf-2 only in n-cadherin-expressing cells. migration and invasion of matrigel were also greatly enhanced by this treatment. when injected into the mammary fat pad of nude mice, n-cadherin-expressing cells, but not control mcf-7 cells, metastasized widely to the liver, pancreas, salivary gland, omentum, lung, lymph nodes, and lumbar spinal muscle. the expression of both e- and n-cadherin was maintained both in the primary tumors and metastatic lesions. these results demonstrate that n-cadherin promotes motility, invasion, and metastasis even in the presence of the normally suppressive e-cadherin. the increase in mmp-9 production by n-cadherin-expressing cells in response to a growth factor may endow them with a greater ability to penetrate matrix protein barriers, while the increase in their adherence to endothelium may improve their ability to enter and exit the vasculature, two properties that may be responsible for metastasis of n-cadherin-expressing cells.",0
"background venn diagrams are commonly used to display list comparison. in biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. they thus allow the comparison between different experimental conditions or between different methods. however, when the number of input lists exceeds four, the diagram becomes difficult to read. alternative layouts and dynamic display features can improve its use and its readability. results jvenn is a new javascript library. it processes lists and produces venn diagrams. it handles up to six input lists and presents results using classical or edwards-venn layouts. user interactions can be controlled and customized. finally, jvenn can easily be embeded in a web page, allowing to have dynamic venn diagrams. conclusions jvenn is an open source component for web environments helping scientists to analyze their data. the library package, which comes with full documentation and an example, is freely available at",0
"crop domestications are long-term selection experiments that have greatly advanced human civilization. the domestication of cultivated rice (oryza sativa l.) ranks as one of the most important developments in history. however, its origins and domestication processes are controversial and have long been debated. here we generate genome sequences from 446 geographically diverse accessions of the wild rice species oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. in the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. in-depth analyses of the domestication sweeps and genome-wide patterns reveal that oryza sativa japonica rice was first domesticated from a specific population of o. rufipogon around the middle area of the pearl river in southern china, and that oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into south east and south asia. the domestication-associated traits are analysed through high-resolution genetic mapping. this study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.",0
"background public trust in immunization is an increasingly important global health issue. losses in confidence in vaccines and immunization programmes can lead to vaccine reluctance and refusal, risking disease outbreaks and challenging immunization goals in high- and low-income settings. national and international immunization stakeholders have called for better monitoring of vaccine confidence to identify emerging concerns before they evolve into vaccine confidence crises. methods we perform a large-scale, data-driven study on worldwide attitudes to immunizations. this survey - which we believe represents the largest survey on confidence in immunization to date - examines perceptions of vaccine importance, safety, effectiveness, and religious compatibility among 65,819 individuals across 67 countries. hierarchical models are employed to probe relationships between individual- and country-level socio-economic factors and vaccine attitudes obtained through the four-question, likert-scale survey. findings overall sentiment towards vaccinations is positive across all 67 countries, however there is wide variability between countries and across world regions. vaccine-safety related sentiment is particularly negative in the european region, which has seven of the ten least confident countries, with 41% of respondents in france and 36% of respondents in bosnia & herzegovina reporting that they disagree that vaccines are safe (compared to a global average of 13%). the oldest age group (65+) and roman catholics (amongst all faiths surveyed) are associated with positive views on vaccine sentiment, while the western pacific region reported the highest level of religious incompatibility with vaccines. countries with high levels of schooling and good access to health services are associated with lower rates of positive sentiment, pointing to an emerging inverse relationship between vaccine sentiments and socio-economic status. conclusions regular monitoring of vaccine attitudes - coupled with monitoring of local immunization rates - at the national and sub-national levels can identify populations with declining confidence and acceptance. these populations should be prioritized to further investigate the drivers of negative sentiment and to inform appropriate interventions to prevent adverse public health outcomes.",0
"autophagy, as a type ii programmed cell death, plays crucial roles with autophagy-related (atg) proteins in cancer. up to now, the dual role of autophagy both in cancer progression and inhibition remains controversial, in which the numerous atg proteins and their core complexes including ulk1/2 kinase core complex, autophagy-specific class iii pi3k complex, atg9a trafficking system, atg12 and lc3 ubiquitin-like conjugation systems, give multiple activities of autophagy pathway and are involved in autophagy initiation, nucleation, elongation, maturation, fusion and degradation. autophagy plays a dynamic tumor-suppressive or tumor-promoting role in different contexts and stages of cancer development. in the early tumorigenesis, autophagy, as a survival pathway and quality-control mechanism, prevents tumor initiation and suppresses cancer progression. once the tumors progress to late stage and are established and subjected to the environmental stresses, autophagy, as a dynamic degradation and recycling system, contributes to the survival and growth of the established tumors and promotes aggressiveness of the cancers by facilitating metastasis. this indicates that regulation of autophagy can be used as effective interventional strategies for cancer therapy.",0
"the bayesian evolutionary analysis by sampling trees (beast) software package has become a primary tool for bayesian phylogenetic and phylodynamic inference from genetic sequence data. beast unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using markov chain monte carlo integration. a convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.",0
"background obesity is associated with vitamin d deficiency, and both are areas of active public health concern. we explored the causality and direction of the relationship between body mass index (bmi) and 25-hydroxyvitamin d using genetic markers as instrumental variables (ivs) in bi-directional mendelian randomization (mr) analysis. methods and findings we used information from 21 adult cohorts (up to 42,024 participants) with 12 bmi-related snps (combined in an allelic score) to produce an instrument for bmi and four snps associated with 25(oh)d (combined in two allelic scores, separately for genes encoding its synthesis or metabolism) as an instrument for vitamin d. regression estimates for the ivs (allele scores) were generated within-study and pooled by meta-analysis to generate summary effects. associations between vitamin d scores and bmi were confirmed in the genetic investigation of anthropometric traits (giant) consortium (n = 123,864). each 1 kg/m(2) higher bmi was associated with 1.15% lower 25(oh)d (p = 6.52×10⁻²⁷). the bmi allele score was associated both with bmi (p = 6.30×10⁻⁶²) and 25(oh)d (-0.06% , p = 0.004) in the cohorts that underwent meta-analysis. the two vitamin d allele scores were strongly associated with 25(oh)d (p≤8.07×10⁻⁵⁷ for both scores) but not with bmi (synthesis score, p = 0.88; metabolism score, p = 0.08) in the meta-analysis. a 10% higher genetically instrumented bmi was associated with 4.2% lower 25(oh)d concentrations (iv ratio: -4.2 , p = 0.005). no association was seen for genetically instrumented 25(oh)d with bmi, a finding that was confirmed using data from the giant consortium (p≥0.57 for both vitamin d scores). conclusions on the basis of a bi-directional genetic approach that limits confounding, our study suggests that a higher bmi leads to lower 25(oh)d, while any effects of lower 25(oh)d increasing bmi are likely to be small. population level interventions to reduce bmi are expected to decrease the prevalence of vitamin d deficiency.",0
"background pregnancy is a time of increased vulnerability for the development of anxiety and depression. this systematic review aims to identify the main risk factors involved in the onset of antenatal anxiety and depression. methods a systematic literature analysis was conducted, using pubmed, psychinfo, and the cochrane library. original papers were included if they were written in english and published between 1st january 2003 and 31st august 2015, while literature reviews and meta-analyses were consulted regardless of publication date. a final number of 97 papers were selected. results the most relevant factors associated with antenatal depression or anxiety were: lack of partner or of social support; history of abuse or of domestic violence; personal history of mental illness; unplanned or unwanted pregnancy; adverse events in life and high perceived stress; present/past pregnancy complications; and pregnancy loss. limitations the review does not include a meta-analysis, which may have added additional information about the differential impact of each risk factor. moreover, it does not specifically examine factors that may influence different types of anxiety disorders, or the recurrence or persistence of depression or anxiety from pregnancy to the postpartum period. conclusions the results show the complex aetiology of antenatal depression and anxiety. the administration of a screening tool to identify women at risk of anxiety and depression during pregnancy should be universal practice in order to promote the long-term wellbeing of mothers and babies, and the knowledge of specific risk factors may help creating such screening tool targeting women at higher risk.",0
"background long-term retention of patients in africa's rapidly expanding antiretroviral therapy (art) programs for hiv/aids is essential for these programs' success but has received relatively little attention. in this paper we present a systematic review of patient retention in art programs in sub-saharan africa. methods and findings we searched medline, other literature databases, conference abstracts, publications archives, and the ""gray literature"" (project reports available online) between 2000 and 2007 for reports on the proportion of adult patients retained (i.e., remaining in care and on art) after 6 mo or longer in sub-saharan african, non-research art programs, with and without donor support. estimated retention rates at 6, 12, and 24 mo were calculated and plotted for each program. retention was also estimated using kaplan-meier curves. in sensitivity analyses we considered best-case, worst-case, and midpoint scenarios for retention at 2 y; the best-case scenario assumed no further attrition beyond that reported, while the worst-case scenario assumed that attrition would continue in a linear fashion. we reviewed 32 publications reporting on 33 patient cohorts (74,192 patients, 13 countries). for all studies, the weighted average follow-up period reported was 9.9 mo, after which 77.5% of patients were retained. loss to follow-up and death accounted for 56% and 40% of attrition, respectively. weighted mean retention rates as reported were 79.1%, 75.0% and 61.6 % at 6, 12, and 24 mo, respectively. of those reporting 24 mo of follow-up, the best program retained 85% of patients and the worst retained 46%. attrition was higher in studies with shorter reporting periods, leading to monthly weighted mean attrition rates of 3.3%/mo, 1.9%/mo, and 1.6%/month for studies reporting to 6, 12, and 24 months, respectively, and suggesting that overall patient retention may be overestimated in the published reports. in sensitivity analyses, estimated retention rates ranged from 24% in the worse case to 77% in the best case at the end of 2 y, with a plausible midpoint scenario of 50%. conclusions since the inception of large-scale art access early in this decade, art programs in africa have retained about 60% of their patients at the end of 2 y. loss to follow-up is the major cause of attrition, followed by death. better patient tracing procedures, better understanding of loss to follow-up, and earlier initiation of art to reduce mortality are needed if retention is to be improved. retention varies widely across programs, and programs that have achieved higher retention rates can serve as models for future improvements.",0
"background rehabilitation has often been seen as a disability-specific service needed by only few of the population. despite its individual and societal benefits, rehabilitation has not been prioritised in countries and is under-resourced. we present global, regional, and country data for the number of people who would benefit from rehabilitation at least once during the course of their disabling illness or injury. methods to estimate the need for rehabilitation, data from the global burden of diseases, injuries, and risk factors study 2019 were used to calculate the prevalence and years of life lived with disability (ylds) of 25 diseases, impairments, or bespoke aggregations of sequelae that were selected as amenable to rehabilitation. all analyses were done at the country level and then aggregated to seven regions: world bank high-income countries and the six who regions (ie, africa, the americas, southeast asia, europe, eastern mediterranean, and western pacific). findings globally, in 2019, 2·41 billion (95% uncertainty interval 2·34-2·50) individuals had conditions that would benefit from rehabilitation, contributing to 310 million ylds. this number had increased by 63% from 1990 to 2019. regionally, the western pacific had the highest need of rehabilitation services (610 million people and 83 million ylds ). the disease area that contributed most to prevalence was musculoskeletal disorders (1·71 billion people ), with low back pain being the most prevalent condition in 134 of the 204 countries analysed. interpretation to our knowledge, this is the first study to produce a global estimate of the need for rehabilitation services and to show that at least one in every three people in the world needs rehabilitation at some point in the course of their illness or injury. this number counters the common view of rehabilitation as a service required by only few people. we argue that rehabilitation needs to be brought close to communities as an integral part of primary health care to reach more people in need. funding bill & melinda gates foundation.",0
"although cell-matrix adhesive interactions are known to regulate stem cell differentiation, the underlying mechanisms, in particular for direct three-dimensional encapsulation within hydrogels, are poorly understood. here, we demonstrate that in covalently crosslinked hyaluronic acid (ha) hydrogels, the differentiation of human mesenchymal stem cells (hmscs) is directed by the generation of degradation-mediated cellular traction, independently of cell morphology or matrix mechanics. hmscs within ha hydrogels of equivalent elastic moduli that permit (restrict) cell-mediated degradation exhibited high (low) degrees of cell spreading and high (low) tractions, and favoured osteogenesis (adipogenesis). moreover, switching the permissive hydrogel to a restrictive state through delayed secondary crosslinking reduced further hydrogel degradation, suppressed traction, and caused a switch from osteogenesis to adipogenesis in the absence of changes to the extended cellular morphology. furthermore, inhibiting tension-mediated signalling in the permissive environment mirrored the effects of delayed secondary crosslinking, whereas upregulating tension induced osteogenesis even in the restrictive environment.",0
"background chest ct is used to assess the severity of lung involvement in coronavirus disease 2019 (covid-19). purpose to determine the changes in chest ct findings associated with covid-19 from initial diagnosis until patient recovery. materials and methods this retrospective review included patients with real-time polymerase chain reaction-confirmed covid-19 who presented between january 12, 2020, and february 6, 2020. patients with severe respiratory distress and/or oxygen requirement at any time during the disease course were excluded. repeat chest ct was performed at approximately 4-day intervals. each of the five lung lobes was visually scored on a scale of 0 to 5, with 0 indicating no involvement and 5 indicating more than 75% involvement. the total ct score was determined as the sum of lung involvement, ranging from 0 (no involvement) to 25 (maximum involvement). results twenty-one patients (six men and 15 women aged 25-63 years) with confirmed covid-19 were evaluated. a total of 82 chest ct scans were obtained in these patients, with a mean interval (±standard deviation) of 4 days ± 1 (range, 1-8 days). all patients were discharged after a mean hospitalization period of 17 days ± 4 (range, 11-26 days). maximum lung involved peaked at approximately 10 days (with a calculated total ct score of 6) from the onset of initial symptoms ( r 2 = 0.25, p p = .002); scans obtained in stage 3 (9-13 days) showed consolidation (19 of 21 scans ) and a peak in the total ct score (mean, 7 ± 4); and scans obtained in stage 4 (≥14 days) showed gradual resolution of consolidation (15 of 20 scans ) and a decrease in the total ct score (mean, 6 ± 4) without crazy-paving pattern. conclusion in patients recovering from coronavirus disease 2019 (without severe respiratory distress during the disease course), lung abnormalities on chest ct scans showed greatest severity approximately 10 days after initial onset of symptoms. © rsna, 2020.",0
"background a multisystem inflammatory syndrome in children (mis-c) is associated with coronavirus disease 2019. the new york state department of health (nysdoh) established active, statewide surveillance to describe hospitalized patients with the syndrome. methods hospitals in new york state reported cases of kawasaki's disease, toxic shock syndrome, myocarditis, and potential mis-c in hospitalized patients younger than 21 years of age and sent medical records to the nysdoh. we carried out descriptive analyses that summarized the clinical presentation, complications, and outcomes of patients who met the nysdoh case definition for mis-c between march 1 and may 10, 2020. results as of may 10, 2020, a total of 191 potential cases were reported to the nysdoh. of 95 patients with confirmed mis-c (laboratory-confirmed acute or recent severe acute respiratory syndrome coronavirus 2 infection) and 4 with suspected mis-c (met clinical and epidemiologic criteria), 53 (54%) were male; 31 of 78 (40%) were black, and 31 of 85 (36%) were hispanic. a total of 31 patients (31%) were 0 to 5 years of age, 42 (42%) were 6 to 12 years of age, and 26 (26%) were 13 to 20 years of age. all presented with subjective fever or chills; 97% had tachycardia, 80% had gastrointestinal symptoms, 60% had rash, 56% had conjunctival injection, and 27% had mucosal changes. elevated levels of c-reactive protein, d-dimer, and troponin were found in 100%, 91%, and 71% of the patients, respectively; 62% received vasopressor support, 53% had evidence of myocarditis, 80% were admitted to an intensive care unit, and 2 died. the median length of hospital stay was 6 days. conclusions the emergence of multisystem inflammatory syndrome in children in new york state coincided with widespread sars-cov-2 transmission; this hyperinflammatory syndrome with dermatologic, mucocutaneous, and gastrointestinal manifestations was associated with cardiac dysfunction.",0
"escherichia coli o157:h7 causes 73,000 illnesses in the united states annually. we reviewed e. coli o157 outbreaks reported to centers for disease control and prevention (cdc) to better understand the epidemiology of e. coli o157. e. coli o157 outbreaks (>or=2 cases of e. coli o157 infection with a common epidemiologic exposure) reported to cdc from 1982 to 2002 were reviewed. in that period, 49 states reported 350 outbreaks, representing 8,598 cases, 1,493 (17%) hospitalizations, 354 (4%) hemolytic uremic syndrome cases, and 40 (0.5%) deaths. transmission route for 183 (52%) was foodborne, 74 (21%) unknown, 50 (14%) person-to-person, 31 (9%) waterborne, 11 (3%) animal contact, and 1 (0.3%) laboratory-related. the food vehicle for 75 (41%) foodborne outbreaks was ground beef, and for 38 (21%) outbreaks, produce.",0
"objective to develop robis, a new tool for assessing the risk of bias in systematic reviews (rather than in primary studies). study design and setting we used four-stage approach to develop robis: define the scope, review the evidence base, hold a face-to-face meeting, and refine the tool through piloting. results robis is currently aimed at four broad categories of reviews mainly within health care settings: interventions, diagnosis, prognosis, and etiology. the target audience of robis is primarily guideline developers, authors of overviews of systematic reviews (""reviews of reviews""), and review authors who might want to assess or avoid risk of bias in their reviews. the tool is completed in three phases: (1) assess relevance (optional), (2) identify concerns with the review process, and (3) judge risk of bias. phase 2 covers four domains through which bias may be introduced into a systematic review: study eligibility criteria; identification and selection of studies; data collection and study appraisal; and synthesis and findings. phase 3 assesses the overall risk of bias in the interpretation of review findings and whether this considered limitations identified in any of the phase 2 domains. signaling questions are included to help judge concerns with the review process (phase 2) and the overall risk of bias in the review (phase 3); these questions flag aspects of review design related to the potential for bias and aim to help assessors judge risk of bias in the review process, results, and conclusions. conclusions robis is the first rigorously developed tool designed specifically to assess the risk of bias in systematic reviews.",0
"summary a combination of bisulfite treatment of dna and high-throughput sequencing (bs-seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. bismark is a flexible tool for the time-efficient analysis of bs-seq data which performs both read mapping and methylation calling in a single convenient step. its output discriminates between cytosines in cpg, chg and chh context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed. availability and implementation bismark is released under the gnu gplv3+ licence. the source code is freely available from",0
"background apoptosis is a form of programmed cell death that is regulated by the bcl-2 family and caspase family of proteins. the caspase cascade responsible for executing cell death following cytochrome c release is well described; however the distinct roles of caspases-9, -3 and -7 during this process are not completely defined. results here we demonstrate several unique functions for each of these caspases during cell death. specific inhibition of caspase-9 allows for efficient release of cytochrome c, but blocks changes in mitochondrial morphology and ros production. we show that caspase-9 can cleave bid into tbid at amino acid 59 and that this cleavage of bid is required for ros production following serum withdrawal. we also demonstrate that caspase-3-deficient mefs are less sensitive to intrinsic cell death stimulation, yet have higher ros production. in contrast, caspase-7-deficient mefs are not resistance to intrinsic cell death, but remain attached to the ecm. conclusions taken together, these data suggest that caspase-9 is required for mitochondrial morphological changes and ros production by cleaving and activating bid into tbid. after activation by caspase-9, caspase-3 inhibits ros production and is required for efficient execution of apoptosis, while effector caspase-7 is required for apoptotic cell detachment.",0
"the in vitro differentiation of homogeneous populations of monocyte-like cells from the unstimulated mouse peritoneal cavity is described. under the conditions employed, a progressive increase in cell size occurs without significant cell division. this process is characterized morphologically by the accumulation of phase-dense and neutral red-positive granules, mitochondria, and lipid droplets. the phase-dense granules react strongly for acid phosphatase. biochemical determinations indicate marked increases in the total content and specific activity of acid phosphatase, cathepsin, and beta-glucuronidase. the production of acid phosphatase is more rapid and extensive than that of the other two hydrolases. from these data it appears that the conversion of a monocyte-like cell to a mature macrophage is accompanied by the formation of increased numbers of lysosome-like cytoplasmic organelles. mouse peritoneal phagocytes stimulated in vivo with a bacterial lipopolysaccharide undergo a similar series of morphological and biochemical events.",0
"background & aims recent data on the coronavirus disease 2019 (covid-19) outbreak caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has begun to shine light on the impact of the disease on the liver. but no studies to date have systematically described liver test abnormalities in patients with covid-19. we evaluated the clinical characteristics of covid-19 in patients with abnormal liver test results. methods clinical records and laboratory results were obtained from 417 patients with laboratory-confirmed covid-19 who were admitted to the only referral hospital in shenzhen, china from january 11 to february 21, 2020 and followed up to march 7, 2020. information on clinical features of patients with abnormal liver tests were collected for analysis. results of 417 patients with covid-19, 318 (76.3%) had abnormal liver test results and 90 (21.5%) had liver injury during hospitalization. the presence of abnormal liver tests became more pronounced during hospitalization within 2 weeks, with 49 (23.4%), 31 (14.8%), 24 (11.5%) and 51 (24.4%) patients having alanine aminotransferase, aspartate aminotransferase, total bilirubin and gamma-glutamyl transferase levels elevated to more than 3× the upper limit of normal, respectively. patients with abnormal liver tests of hepatocellular type or mixed type at admission had higher odds of progressing to severe disease (odds ratios 2.73; 95% ci 1.19-6.3, and 4.44, 95% ci 1.93-10.23, respectively). the use of lopinavir/ritonavir was also found to lead to increased odds of liver injury (or from 4.44 to 5.03, both p conclusion patients with abnormal liver tests were at higher risk of progressing to severe disease. the detrimental effects on liver injury mainly related to certain medications used during hospitalization, which should be monitored and evaluated frequently. lay summary data on liver tests in patients with covid-19 are scarce. we observed a high prevalence of liver test abnormalities and liver injury in 417 patients with covid-19 admitted to our referral center, and the prevalence increased substantially during hospitalization. the presence of abnormal liver tests and liver injury were associated with the progression to severe pneumonia. the detrimental effects on liver injury were related to certain medications used during hospitalization, which warrants frequent monitoring and evaluation for these patients.",0
"background severe acute respiratory syndrome (sars) is caused by a newly discovered coronavirus (sars-cov). no effective prophylactic or post-exposure therapy is currently available. results we report, however, that chloroquine has strong antiviral effects on sars-cov infection of primate cells. these inhibitory effects are observed when the cells are treated with the drug either before or after exposure to the virus, suggesting both prophylactic and therapeutic advantage. in addition to the well-known functions of chloroquine such as elevations of endosomal ph, the drug appears to interfere with terminal glycosylation of the cellular receptor, angiotensin-converting enzyme 2. this may negatively influence the virus-receptor binding and abrogate the infection, with further ramifications by the elevation of vesicular ph, resulting in the inhibition of infection and spread of sars cov at clinically admissible concentrations. conclusion chloroquine is effective in preventing the spread of sars cov in cell culture. favorable inhibition of virus spread was observed when the cells were either treated with chloroquine prior to or after sars cov infection. in addition, the indirect immunofluorescence assay described herein represents a simple and rapid method for screening sars-cov antiviral compounds.",0
"background while the patient and public involvement (ppi) evidence base has expanded over the past decade, the quality of reporting within papers is often inconsistent, limiting our understanding of how it works, in what context, for whom, and why. objective to develop international consensus on the key items to report to enhance the quality, transparency, and consistency of the ppi evidence base. to collaboratively involve patients as research partners at all stages in the development of gripp2. methods the equator method for developing reporting guidelines was used. the original gripp (guidance for reporting involvement of patients and the public) checklist was revised, based on updated systematic review evidence. a three round delphi survey was used to develop consensus on items to be included in the guideline. a subsequent face-to-face meeting produced agreement on items not reaching consensus during the delphi process. results 143 participants agreed to participate in round one, with an 86% (123/143) response for round two and a 78% (112/143) response for round three. the delphi survey identified the need for long form (lf) and short form (sf) versions. gripp2-lf includes 34 items on aims, definitions, concepts and theory, methods, stages and nature of involvement, context, capture or measurement of impact, outcomes, economic assessment, and reflections and is suitable for studies where the main focus is ppi. gripp2-sf includes five items on aims, methods, results, outcomes, and critical perspective and is suitable for studies where ppi is a secondary focus. conclusions gripp2-lf and gripp2-sf represent the first international evidence based, consensus informed guidance for reporting patient and public involvement in research. both versions of gripp2 aim to improve the quality, transparency, and consistency of the international ppi evidence base, to ensure ppi practice is based on the best evidence. in order to encourage its wide dissemination this article is freely accessible on the bmj and research involvement and engagement journal websites.",0
"unlabelled the red queen said, 'it takes all the running you can do, to keep in the same place.' lewis carrol motivation newly solved protein structures are routinely scanned against structures already in the protein data bank (pdb) using internet servers. in favourable cases, comparing 3d structures may reveal biologically interesting similarities that are not detectable by comparing sequences. the number of known structures continues to grow exponentially. sensitive-thorough but slow-search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the pdb than seconds in a day. the brute-force solution would be to distribute the individual comparisons on a massively parallel computer. a frugal solution, as implemented in the dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. this note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a pc. availability the dali server for protein structure database searching at is running dalilite v.3. the software can be downloaded for academic use from",0
"macrophages exposed to macrophage colony-stimulating factor acquire the capacity to suppress t cell proliferation; this effect is associated with de novo expression of the tryptophan-catabolizing enzyme indoleamine 2,3-dioxygenase (ido). we have purified ido and tested its activity in in vitro models of t cell activation. ido was able to inhibit proliferation of cd4(+) t lymphocytes, cd8(+) t lymphocytes, and natural killer (nk) cells; proliferation of b lymphocytes was not affected. the inhibitory role of tryptophan and of its catabolites was then tested. in the presence of tryptophan, only l-kynurenine and picolinic acid inhibit cell proliferation. in a tryptophan-free medium cell proliferation was not affected. in the absence of tryptophan inhibition induced by l-kynurenine and picolinic acid was observed at concentrations below the lowest concentration that was effective in the presence of tryptophan, and quinolinic acid acquired some inhibitory capacity. inhibition of cell proliferation induced by the tryptophan catabolites resulting from ido activity was selective, applying only to cells undergoing activation. resting cells were not affected and could subsequently activate normally. we suggest that ido exerts its effect on cell proliferation by (i) starting the cascade of biochemical reactions that produce the three catabolites and by (ii) enhancing their inhibitory potential by depriving the extracellular microenvironment of tryptophan.",0
"background tumor associated fibroblasts (taf), are essential for tumor progression providing both a functional and structural supportive environment. taf, known as activated fibroblasts, have an established biological impact on tumorigenesis as matrix synthesizing or matrix degrading cells, contractile cells, and even blood vessel associated cells. the production of growth factors, cytokines, chemokines, matrix-degrading enzymes, and immunomodulatory mechanisms by these cells augment tumor progression by providing a suitable environment. there are several suggested origins of the taf including tissue-resident, circulating, and epithelial-to-mesenchymal-transitioned cells. methodology/principal findings we provide evidence that taf are derived from mesenchymal stem cells (msc) that acquire a taf phenotype following exposure to or systemic recruitment into adenocarcinoma xenograft models including breast, pancreatic, and ovarian. we define the msc derived taf in a xenograft ovarian carcinoma model by the immunohistochemical presence of 1) fibroblast specific protein and fibroblast activated protein; 2) markers phenotypically associated with aggressiveness, including tenascin-c, thrombospondin-1, and stromelysin-1; 3) production of pro-tumorigenic growth factors including hepatocyte growth factor, epidermal growth factor, and interleukin-6; and 4) factors indicative of vascularization, including alpha-smooth muscle actin, desmin, and vascular endothelial growth factor. we demonstrate that under long-term tumor conditioning in vitro, msc express taf-like proteins. additionally, human msc but not murine msc stimulated tumor growth primarily through the paracrine production of secreted il6. conclusions/significance our results suggest the dependence of in vitro skov-3 tumor cell proliferation is due to the presence of tumor-stimulated msc secreted il6. the subsequent taf phenotype arises from the msc which ultimately promotes tumor growth through the contribution of microvascularization, stromal networks, and the production of tumor-stimulating paracrine factors.",0
"background there is increasing awareness that meta-analyses require a sufficiently large information size to detect or reject an anticipated intervention effect. the required information size in a meta-analysis may be calculated from an anticipated a priori intervention effect or from an intervention effect suggested by trials with low-risk of bias. methods information size calculations need to consider the total model variance in a meta-analysis to control type i and type ii errors. here, we derive an adjusting factor for the required information size under any random-effects model meta-analysis. results we devise a measure of diversity (d2) in a meta-analysis, which is the relative variance reduction when the meta-analysis model is changed from a random-effects into a fixed-effect model. d2 is the percentage that the between-trial variability constitutes of the sum of the between-trial variability and a sampling error estimate considering the required information size. d2 is different from the intuitively obvious adjusting factor based on the common quantification of heterogeneity, the inconsistency (i2), which may underestimate the required information size. thus, d2 and i2 are compared and interpreted using several simulations and clinical examples. in addition we show mathematically that diversity is equal to or greater than inconsistency, that is d2 >or= i2, for all meta-analyses. conclusion we conclude that d2 seems a better alternative than i2 to consider model variation in any random-effects meta-analysis despite the choice of the between trial variance estimator that constitutes the model. furthermore, d2 can readily adjust the required information size in any random-effects model meta-analysis.",0
"ly alloantigens coded by two unlinked genetic loci (ly-1 and ly-2/ly-3) are expressed on lymphoid cells undergoing thymus-dependent differentiation. peripheral thy-1+ cells from c57bl/6 mice can be divided into three subclasses on the basis of differential expression of ly-1, ly-2, and ly-3; about 50% express all three ly antigens (ly -123+), about 33% only ly-1 (ly-1+), and about 6-8% ly-2 and ly-3 (ly-23+). cells of the ly-123+ subclasses are the first peripheral thy-1+ cells to appear in ontogeny, and are reduced in the periphery shortly after adult thymectomy. in contrast, ly-1+ and ly-23+ subclasses appear later in the peripheral tissues than do ly-123+ cells, and are resistant to the early effects of adult thymectomymperiheral lymphoid populations depleted of ly-1+ cells and ly-123+ cells (and thereby enriched for ly-23+ cells) were incapable of developing significant helper activity to srbc but generated substantial levels of cytotoxic activity to allogeneic target cells. the same lymphoid populations, depleted of ly-23+ cells and ly-123+ cells (and thereby enriched for ly-1+ cells), produced substantial helper responses but were unable to generate appreciable levels of killer activity. these experiments imply that commitment of t cells to participate exclusively in either helper or cytotoxic function is a differentiative process that takes place before they encounter antigen, and is accompanied by exclusion of different ly groups, lu-23 or ly-1 respectively, from tl+ly-123+ t-cell precursors. it is yet to be decided whether the tl-phase by ly-123+ subclass is a transitional form or a separately differentiated subclass with a discrete immunologic function.",0
"background: this document provides evidence-based clinical practice guidelines on the management of adult patients with community-acquired pneumonia. methods: a multidisciplinary panel conducted pragmatic systematic reviews of the relevant research and applied grading of recommendations, assessment, development, and evaluation methodology for clinical recommendations. results: the panel addressed 16 specific areas for recommendations spanning questions of diagnostic testing, determination of site of care, selection of initial empiric antibiotic therapy, and subsequent management decisions. although some recommendations remain unchanged from the 2007 guideline, the availability of results from new therapeutic trials and epidemiological investigations led to revised recommendations for empiric treatment strategies and additional management decisions. conclusions: the panel formulated and provided the rationale for recommendations on selected diagnostic and treatment strategies for adult patients with community-acquired pneumonia.",0
"chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (cnv). a recent report of nonrecurrent duplications associated with pelizaeus-merzbacher disease identified three distinctive characteristics. first, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. second, junctions at endpoints show microhomology of 2-5 base pairs (bp). third, endpoints occur near pre-existing low copy repeats (lcrs). using these observations and evidence from dna repair in other organisms, we derive a model of microhomology-mediated break-induced replication (mmbir) for the origin of cnv and, ultimately, of lcrs. we propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (bir). under these circumstances, single-strand 3' tails from broken replication forks will anneal with microhomology on any single-stranded dna nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.",0
"mendelian randomization analyses are often performed using summarized data. the causal estimate from a one-sample analysis (in which data are taken from a single data source) with weak instrumental variables is biased in the direction of the observational association between the risk factor and outcome, whereas the estimate from a two-sample analysis (in which data on the risk factor and outcome are taken from non-overlapping datasets) is less biased and any bias is in the direction of the null. when using genetic consortia that have partially overlapping sets of participants, the direction and extent of bias are uncertain. in this paper, we perform simulation studies to investigate the magnitude of bias and type 1 error rate inflation arising from sample overlap. we consider both a continuous outcome and a case-control setting with a binary outcome. for a continuous outcome, bias due to sample overlap is a linear function of the proportion of overlap between the samples. so, in the case of a null causal effect, if the relative bias of the one-sample instrumental variable estimate is 10% (corresponding to an f parameter of 10), then the relative bias with 50% sample overlap is 5%, and with 30% sample overlap is 3%. in a case-control setting, if risk factor measurements are only included for the control participants, unbiased estimates are obtained even in a one-sample setting. however, if risk factor data on both control and case participants are used, then bias is similar with a binary outcome as with a continuous outcome. consortia releasing publicly available data on the associations of genetic variants with continuous risk factors should provide estimates that exclude case participants from case-control samples.",0
"background associations of c-reactive protein (crp) concentration with risk of major diseases can best be assessed by long-term prospective follow-up of large numbers of people. we assessed the associations of crp concentration with risk of vascular and non-vascular outcomes under different circumstances. methods we meta-analysed individual records of 160 309 people without a history of vascular disease (ie, 1.31 million person-years at risk, 27 769 fatal or non-fatal disease outcomes) from 54 long-term prospective studies. within-study regression analyses were adjusted for within-person variation in risk factor levels. results log(e) crp concentration was linearly associated with several conventional risk factors and inflammatory markers, and nearly log-linearly with the risk of ischaemic vascular disease and non-vascular mortality. risk ratios (rrs) for coronary heart disease per 1-sd higher log(e) crp concentration (three-fold higher) were 1.63 (95% ci 1.51-1.76) when initially adjusted for age and sex only, and 1.37 (1.27-1.48) when adjusted further for conventional risk factors; 1.44 (1.32-1.57) and 1.27 (1.15-1.40) for ischaemic stroke; 1.71 (1.53-1.91) and 1.55 (1.37-1.76) for vascular mortality; and 1.55 (1.41-1.69) and 1.54 (1.40-1.68) for non-vascular mortality. rrs were largely unchanged after exclusion of smokers or initial follow-up. after further adjustment for fibrinogen, the corresponding rrs were 1.23 (1.07-1.42) for coronary heart disease; 1.32 (1.18-1.49) for ischaemic stroke; 1.34 (1.18-1.52) for vascular mortality; and 1.34 (1.20-1.50) for non-vascular mortality. interpretation crp concentration has continuous associations with the risk of coronary heart disease, ischaemic stroke, vascular mortality, and death from several cancers and lung disease that are each of broadly similar size. the relevance of crp to such a range of disorders is unclear. associations with ischaemic vascular disease depend considerably on conventional risk factors and other markers of inflammation. funding british heart foundation, uk medical research council, bupa foundation, and glaxosmithkline.",0
"the scurfy mutant mouse strain suffers from a fatal lymphoproliferative disease leading to early death within 3-4 wk of age. a frame-shift mutation of the forkhead box transcription factor foxp3 has been identified as the molecular cause of this multiorgan autoimmune disease. foxp3 is a central control element in the development and function of regulatory t cells (t reg cells), which are necessary for the maintenance of self-tolerance. however, it is unclear whether dysfunction or a lack of t reg cells is etiologically involved in scurfy pathogenesis and its human correlate, the ipex syndrome. we describe the generation of bacterial artificial chromosome-transgenic mice termed ""depletion of regulatory t cell"" (dereg) mice expressing a diphtheria toxin (dt) receptor-enhanced green fluorescent protein fusion protein under the control of the foxp3 gene locus, allowing selective and efficient depletion of foxp3+ t reg cells by dt injection. ablation of foxp3+ t reg cells in newborn dereg mice led to the development of scurfy-like symptoms with splenomegaly, lymphadenopathy, insulitis, and severe skin inflammation. thus, these data provide experimental evidence that the absence of foxp3+ t reg cells is indeed sufficient to induce a scurfy-like phenotype. furthermore, dereg mice will allow a more precise definition of the function of foxp3+ t reg cells in immune reactions in vivo.",0
"the outbreak of a novel coronavirus (2019-ncov) represents a pandemic threat that has been declared a public health emergency of international concern. the cov spike (s) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. to facilitate medical countermeasure development, we determined a 3.5-angstrom-resolution cryo-electron microscopy structure of the 2019-ncov s trimer in the prefusion conformation. the predominant state of the trimer has one of the three receptor-binding domains (rbds) rotated up in a receptor-accessible conformation. we also provide biophysical and structural evidence that the 2019-ncov s protein binds angiotensin-converting enzyme 2 (ace2) with higher affinity than does severe acute respiratory syndrome (sars)-cov s. additionally, we tested several published sars-cov rbd-specific monoclonal antibodies and found that they do not have appreciable binding to 2019-ncov s, suggesting that antibody cross-reactivity may be limited between the two rbds. the structure of 2019-ncov s should enable the rapid development and evaluation of medical countermeasures to address the ongoing public health crisis.",0
"echo planar imaging (epi) is an mri technique of particular value to neuroscience, with its use for virtually all functional mri (fmri) and diffusion imaging of fiber connections in the human brain. epi generates a single 2d image in a fraction of a second; however, it requires 2-3 seconds to acquire multi-slice whole brain coverage for fmri and even longer for diffusion imaging. here we report on a large reduction in epi whole brain scan time at 3 and 7 tesla, without significantly sacrificing spatial resolution, and while gaining functional sensitivity. the multiplexed-epi (m-epi) pulse sequence combines two forms of multiplexing: temporal multiplexing (m) utilizing simultaneous echo refocused (sir) epi and spatial multiplexing (n) with multibanded rf pulses (mb) to achieve m×n images in an epi echo train instead of the normal single image. this resulted in an unprecedented reduction in epi scan time for whole brain fmri performed at 3 tesla, permitting trs of 400 ms and 800 ms compared to a more conventional 2.5 sec tr, and 2-4 times reductions in scan time for hardi imaging of neuronal fibertracks. the simultaneous se refocusing of sir imaging at 7 tesla advantageously reduced sar by using fewer rf refocusing pulses and by shifting fat signal out of the image plane so that fat suppression pulses were not required. in preliminary studies of resting state functional networks identified through independent component analysis, the 6-fold higher sampling rate increased the peak functional sensitivity by 60%. the novel m-epi pulse sequence resulted in a significantly increased temporal resolution for whole brain fmri, and as such, this new methodology can be used for studying non-stationarity in networks and generally for expanding and enriching the functional information.",0
"pd-catalyzed cross-coupling reactions that form c-n bonds have become useful methods to synthesize anilines and aniline derivatives, an important class of compounds throughout chemical research. a key factor in the widespread adoption of these methods has been the continued development of reliable and versatile catalysts that function under operationally simple, user-friendly conditions. this review provides an overview of pd-catalyzed n-arylation reactions found in both basic and applied chemical research from 2008 to the present. selected examples of c-n cross-coupling reactions between nine classes of nitrogen-based coupling partners and (pseudo)aryl halides are described for the synthesis of heterocycles, medicinally relevant compounds, natural products, organic materials, and catalysts.",0
"ferroptosis is a mode of regulated cell death that depends on iron. cells die from the toxic accumulation of lipid reactive oxygen species. ferroptosis is tightly linked to a variety of human diseases, such as cancers and degenerative diseases. the ferroptotic process is complicated and consists of a wide range of metabolites and biomolecules. although great progress has been achieved, the mechanism of ferroptosis remains enigmatic. we have currently entered an era of extensive knowledge advancement, and thus, it is important to find ways to organize and utilize data efficiently. we have observed a high-quality knowledge base of ferroptosis research is lacking. in this study, we downloaded 784 ferroptosis articles from the pubmed database. ferroptosis regulators and markers and associated diseases were extracted from these articles and annotated. in summary, 253 regulators (including 108 drivers, 69 suppressors, 35 inducers and 41 inhibitors), 111 markers and 95 ferroptosis-disease associations were found. we then developed ferrdb, the first manually curated database for regulators and markers of ferroptosis and ferroptosis-disease associations. the database has a user-friendly interface, and it will be updated every 6 months to offer long-term service. ferrdb is expected to help researchers acquire insights into ferroptosis.database url:",0
"importance the coronavirus disease 2019 (covid-19) pandemic and the policies to contain it have been a near ubiquitous exposure in the us with unknown effects on depression symptoms. objective to estimate the prevalence of and risk factors associated with depression symptoms among us adults during vs before the covid-19 pandemic. design, setting, and participants this nationally representative survey study used 2 population-based surveys of us adults aged 18 or older. during covid-19, estimates were derived from the covid-19 and life stressors impact on mental health and well-being study, conducted from march 31, 2020, to april 13, 2020. before covid-19 estimates were derived from the national health and nutrition examination survey, conducted from 2017 to 2018. data were analyzed from april 15 to 20, 2020. exposures the covid-19 pandemic and outcomes associated with the measures to mitigate it. main outcomes and measures depression symptoms, defined using the patient health questionnaire-9 cutoff of 10 or higher. categories of depression symptoms were defined as none (score, 0-4), mild (score, 5-9), moderate (score, 10-14), moderately severe (score, 15-19), and severe (score, ≥20). results a total of 1470 participants completed the covid-19 and life stressors impact on mental health and well-being survey (completion rate, 64.3%), and after removing those with missing data, the final during-covid-19 sample included 1441 participants (619 participants aged 18-39 years; 723 men; 933 non-hispanic white). the pre-covid-19 sample included 5065 participants (1704 participants aged 18-39 years; 2588 women; 1790 non-hispanic white). depression symptom prevalence was higher in every category during covid-19 compared with before (mild: 24.6% vs 16.2% ; moderate: 14.8% vs 5.7% ; moderately severe: 7.9% vs 2.1% ; severe: 5.1% vs 0.7% ). higher risk of depression symptoms during covid-19 was associated with having lower income (odds ratio, 2.37 ), having less than $5000 in savings (odds ratio, 1.52 ), and exposure to more stressors (odds ratio, 3.05 ). conclusions and relevance these findings suggest that prevalence of depression symptoms in the us was more than 3-fold higher during covid-19 compared with before the covid-19 pandemic. individuals with lower social resources, lower economic resources, and greater exposure to stressors (eg, job loss) reported a greater burden of depression symptoms. post-covid-19 plans should account for the probable increase in mental illness to come, particularly among at-risk populations.",0
"acetylated-low density lipoprotein (ac-ldl) is taken up by macrophages and endothelial cells via the ""scavenger cell pathway"" of ldl metabolism. in this report, aortic and microvascular endothelial cells internalized and degraded 7-15 times more -ac-ldl than did smooth muscle cells or pericytes. bound -ac-ldl was displaced by unlabeled ac-ldl, but not unmodified ldl. the ability to identify endothelial cells based on their increased metabolism of ac-ldl was examined using ac-ldl labeled with the fluorescent probe 1,1'-dioctadecyl-3,3,3',3'-tetramethyl-indocarbocyanine perchlorate (dil-ac-ldl). when cells were incubated with 10 micrograms/ml dil-ac-ldl for 4 h at 37 degrees c and subsequently examined by fluorescence microscopy, capillary and aortic endothelial cells were brilliantly fluorescent whereas the fluorescent intensity of retinal pericytes and smooth muscle cells was only slightly above background levels. dil-ac-ldl at the concentration used for labeling cells had no effect on endothelial cell growth rate. when primary cultures of bovine adrenal capillary cells were labeled with 10 micrograms/ml of dil-ac-ldl for 4 h at 37 degrees c, then trypsinized and subjected to fluorescence-activated cell sorting, pure cultures of capillary endothelial cells could be obtained. utilizing this method, large numbers of early passage microvascular endothelial cells can be obtained in significantly less time than with conventional methods.",0
"kegg ( is a database of biological systems that integrates genomic, chemical and systemic functional information. kegg provides a reference knowledge base for linking genomes to life through the process of pathway mapping, which is to map, for example, a genomic or transcriptomic content of genes to kegg reference pathways to infer systemic behaviors of the cell or the organism. in addition, kegg provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of brite mapping. kegg brite is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. kegg pathway is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. in addition, smaller pathway modules are defined and stored in kegg module that also contains other functional units and complexes. the kegg resource is being expanded to suit the needs for practical applications. kegg drug contains all approved drugs in the us and japan, and kegg disease is a new database linking disease genes, pathways, drugs and diagnostic markers.",0
"background coronavirus disease 2019 (covid-19), formerly known as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and 2019 novel coronavirus (2019-ncov), was first identified in december 2019 in wuhan city, china. structural equation modeling (sem) is a multivariate analysis method to determine the structural relationship between measured variables. this observational study aimed to use sem to determine the effects of social support on sleep quality and function of medical staff who treated patients with covid-19 in january and february 2020 in wuhan, china. material and methods a one-month cross-sectional observational study included 180 medical staff who treated patients with covid-19 infection. levels of anxiety, self-efficacy, stress, sleep quality, and social support were measured using the and the self-rating anxiety scale (sas), the general self-efficacy scale (gses), the stanford acute stress reaction (sasr) questionnaire, the pittsburgh sleep quality index (psqi), and the social support rate scale (ssrs), respectively. pearson's correlation analysis and sem identified the interactions between these factors. results levels of social support for medical staff were significantly associated with self-efficacy and sleep quality and negatively associated with the degree of anxiety and stress. levels of anxiety were significantly associated with the levels of stress, which negatively impacted self-efficacy and sleep quality. anxiety, stress, and self-efficacy were mediating variables associated with social support and sleep quality. conclusions sem showed that medical staff in china who were treating patients with covid-19 infection during january and february 2020 had levels of anxiety, stress, and self-efficacy that were dependent on sleep quality and social support.",0
"since the initial covid-19 outbreak in china, much attention has focused on people with diabetes because of poor prognosis in those with the infection. initial reports were mainly on people with type 2 diabetes, although recent surveys have shown that individuals with type 1 diabetes are also at risk of severe covid-19. the reason for worse prognosis in people with diabetes is likely to be multifactorial, thus reflecting the syndromic nature of diabetes. age, sex, ethnicity, comorbidities such as hypertension and cardiovascular disease, obesity, and a pro-inflammatory and pro-coagulative state all probably contribute to the risk of worse outcomes. glucose-lowering agents and anti-viral treatments can modulate the risk, but limitations to their use and potential interactions with covid-19 treatments should be carefully assessed. finally, severe acute respiratory syndrome coronavirus 2 infection itself might represent a worsening factor for people with diabetes, as it can precipitate acute metabolic complications through direct negative effects on β-cell function. these effects on β-cell function might also cause diabetic ketoacidosis in individuals with diabetes, hyperglycaemia at hospital admission in individuals with unknown history of diabetes, and potentially new-onset diabetes.",0
"objective disease containment of covid-19 has necessitated widespread social isolation. we aimed to establish what is known about how loneliness and disease containment measures impact on the mental health in children and adolescents. method for this rapid review, we searched medline, psycinfo, and web of science for articles published between january 1, 1946, and march 29, 2020. of the articles, 20% were double screened using predefined criteria, and 20% of data was double extracted for quality assurance. results a total of 83 articles (80 studies) met inclusion criteria. of these, 63 studies reported on the impact of social isolation and loneliness on the mental health of previously healthy children and adolescents (n = 51,576; mean age 15.3 years). in all, 61 studies were observational, 18 were longitudinal, and 43 were cross-sectional studies assessing self-reported loneliness in healthy children and adolescents. one of these studies was a retrospective investigation after a pandemic. two studies evaluated interventions. studies had a high risk of bias, although longitudinal studies were of better methodological quality. social isolation and loneliness increased the risk of depression, and possibly anxiety at the time at which loneliness was measured and between 0.25 and 9 years later. duration of loneliness was more strongly correlated with mental health symptoms than intensity of loneliness. conclusion children and adolescents are probably more likely to experience high rates of depression and most likely anxiety during and after enforced isolation ends. this may increase as enforced isolation continues. clinical services should offer preventive support and early intervention where possible and be prepared for an increase in mental health problems.",0
"amplitude decorrelation measurement is sensitive to transverse flow and immune to phase noise in comparison to doppler and other phase-based approaches. however, the high axial resolution of oct makes it very sensitive to the pulsatile bulk motion noise in the axial direction. to overcome this limitation, we developed split-spectrum amplitude-decorrelation angiography (ssada) to improve the signal-to-noise ratio (snr) of flow detection. the full oct spectrum was split into several narrower bands. inter-b-scan decorrelation was computed using the spectral bands separately and then averaged. the ssada algorithm was tested on in vivo images of the human macula and optic nerve head. it significantly improved both snr for flow detection and connectivity of microvascular network when compared to other amplitude-decorrelation algorithms.",0
"a tight junction-enriched membrane fraction has been used as immunogen to generate a monoclonal antiserum specific for this intercellular junction. hybridomas were screened for their ability to both react on an immunoblot and localize to the junctional complex region on frozen sections of unfixed mouse liver. a stable hybridoma line has been isolated that secretes an antibody (r26.4c) that localizes in thin section images of isolated mouse liver plasma membranes to the points of membrane contact at the tight junction. this antibody recognizes a polypeptide of approximately 225,000 d, detectable in whole liver homogenates as well as in the tight junction-enriched membrane fraction. r26.4c localizes to the junctional complex region of a number of other epithelia, including colon, kidney, and testis, and to arterial endothelium, as assayed by immunofluorescent staining of cryostat sections of whole tissue. this antibody also stains the junctional complex region in confluent monolayers of the madin-darby canine kidney epithelial cell line. immunoblot analysis of madin-darby canine kidney cells demonstrates the presence of a polypeptide similar in molecular weight to that detected in liver, suggesting that this protein is potentially a ubiquitous component of all mammalian tight junctions. the 225-kd tight junction-associated polypeptide is termed ""zo-1.""",0
"objective the mental health toll of covid-19 on healthcare workers (hcw) is not yet fully described. we characterized distress, coping, and preferences for support among nyc hcws during the covid-19 pandemic. methods this was a cross-sectional web survey of physicians, advanced practice providers, residents/fellows, and nurses, conducted during a peak of inpatient admissions for covid-19 in nyc (april 9th-april 24th 2020) at a large medical center in nyc (n = 657). results positive screens for psychological symptoms were common; 57% for acute stress, 48% for depressive, and 33% for anxiety symptoms. for each, a higher percent of nurses/advanced practice providers screened positive vs. attending physicians, though housestaff's rates for acute stress and depression did not differ from either. sixty-one percent of participants reported increased sense of meaning/purpose since the covid-19 outbreak. physical activity/exercise was the most common coping behavior (59%), and access to an individual therapist with online self-guided counseling (33%) garnered the most interest. conclusions nyc hcws, especially nurses and advanced practice providers, are experiencing covid-19-related psychological distress. participants reported using empirically-supported coping behaviors, and endorsed indicators of resilience, but they also reported interest in additional wellness resources. programs developed to mitigate stress among hcws during the covid-19 pandemic should integrate hcw preferences.",0
"background health system planning requires careful assessment of chronic kidney disease (ckd) epidemiology, but data for morbidity and mortality of this disease are scarce or non-existent in many countries. we estimated the global, regional, and national burden of ckd, as well as the burden of cardiovascular disease and gout attributable to impaired kidney function, for the global burden of diseases, injuries, and risk factors study 2017. we use the term ckd to refer to the morbidity and mortality that can be directly attributed to all stages of ckd, and we use the term impaired kidney function to refer to the additional risk of ckd from cardiovascular disease and gout. methods the main data sources we used were published literature, vital registration systems, end-stage kidney disease registries, and household surveys. estimates of ckd burden were produced using a cause of death ensemble model and a bayesian meta-regression analytical tool, and included incidence, prevalence, years lived with disability, mortality, years of life lost, and disability-adjusted life-years (dalys). a comparative risk assessment approach was used to estimate the proportion of cardiovascular diseases and gout burden attributable to impaired kidney function. findings globally, in 2017, 1·2 million (95% uncertainty interval 1·2 to 1·3) people died from ckd. the global all-age mortality rate from ckd increased 41·5% (95% ui 35·2 to 46·5) between 1990 and 2017, although there was no significant change in the age-standardised mortality rate (2·8%, -1·5 to 6·3). in 2017, 697·5 million (95% ui 649·2 to 752·0) cases of all-stage ckd were recorded, for a global prevalence of 9·1% (8·5 to 9·8). the global all-age prevalence of ckd increased 29·3% (95% ui 26·4 to 32·6) since 1990, whereas the age-standardised prevalence remained stable (1·2%, -1·1 to 3·5). ckd resulted in 35·8 million (95% ui 33·7 to 38·0) dalys in 2017, with diabetic nephropathy accounting for almost a third of dalys. most of the burden of ckd was concentrated in the three lowest quintiles of socio-demographic index (sdi). in several regions, particularly oceania, sub-saharan africa, and latin america, the burden of ckd was much higher than expected for the level of development, whereas the disease burden in western, eastern, and central sub-saharan africa, east asia, south asia, central and eastern europe, australasia, and western europe was lower than expected. 1·4 million (95% ui 1·2 to 1·6) cardiovascular disease-related deaths and 25·3 million (22·2 to 28·9) cardiovascular disease dalys were attributable to impaired kidney function. interpretation kidney disease has a major effect on global health, both as a direct cause of global morbidity and mortality and as an important risk factor for cardiovascular disease. ckd is largely preventable and treatable and deserves greater attention in global health policy decision making, particularly in locations with low and middle sdi. funding bill & melinda gates foundation.",0
"background the summit of independent european vaccination experts (sieve) recommended in 2007 that efforts be made to improve healthcare workers' knowledge and beliefs about vaccines, and their attitudes towards them, to increase vaccination coverage. the aim of the study was to compile and analyze the areas of disagreement in the existing evidence about the relationship between healthcare workers' knowledge, beliefs and attitudes about vaccines and their intentions to vaccinate the populations they serve. methods we conducted a systematic search in four electronic databases for studies published in any of seven different languages between february 1998 and june 2009. we included studies conducted in developed countries that used statistical methods to relate or associate the variables included in our research question. two independent reviewers verified that the studies met the inclusion criteria, assessed the quality of the studies and extracted their relevant characteristics. the data were descriptively analyzed. results of the 2354 references identified in the initial search, 15 studies met the inclusion criteria. the diversity in the study designs and in the methods used to measure the variables made it impossible to integrate the results, and each study had to be assessed individually. all the studies found an association in the direction postulated by the sieve experts: among healthcare workers, higher awareness, beliefs that are more aligned with scientific evidence and more favorable attitudes toward vaccination were associated with greater intentions to vaccinate. all the studies included were cross-sectional; thus, no causal relationship between the variables was established. conclusion the results suggest that interventions aimed at improving healthcare workers' knowledge, beliefs and attitudes about vaccines should be encouraged, and their impact on vaccination coverage should be assessed.",0
"most theories of motor cortex have assumed that neural activity represents movement parameters. this view derives from what is known about primary visual cortex, where neural activity represents patterns of light. yet it is unclear how well the analogy between motor and visual cortex holds. single-neuron responses in motor cortex are complex, and there is marked disagreement regarding which movement parameters are represented. a better analogy might be with other motor systems, where a common principle is rhythmic neural activity. here we find that motor cortex responses during reaching contain a brief but strong oscillatory component, something quite unexpected for a non-periodic behaviour. oscillation amplitude and phase followed naturally from the preparatory state, suggesting a mechanistic role for preparatory neural activity. these results demonstrate an unexpected yet surprisingly simple structure in the population response. this underlying structure explains many of the confusing features of individual neural responses.",0
"recent advances in understanding the cellular and molecular signaling pathways and global transcriptional regulators of adult mesenchymal stem cells have provided new insights into their biology and potential clinical applications, particularly for tissue repair and regeneration. this review focuses on these advances, specifically in the context of self-renewal and regulation of lineage-specific differentiation of mesenchymal stem cells. in addition we review recent research on the concept of stem cell niche, and its relevance to adult mesenchymal stem cells.",0
"the cytokine interleukin-1β (il-1β) is a key mediator of the inflammatory response. essential for the host-response and resistance to pathogens, it also exacerbates damage during chronic disease and acute tissue injury. it is not surprising therefore that there is a huge level of interest in how this protein is produced and exported from cells. however, the mechanism of il-1β release has proven to be elusive. it does not follow the conventional er-golgi route of secretion. a literature full of disparate observations arising from numerous experimental systems, has contributed to a complicated mix of diverse proposals. here we summarise these observations and propose that secretion of il-1β occurs on a continuum, dependent upon stimulus strength and the extracellular il-1β requirement.",0
"background transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. while there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. therefore, there is a considerable demand for computational identification of transposable elements. ltr retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (ltrs). results we have developed a software tool ltrharvest for the de novo detection of full length ltr retrotransposons in large sequence sets. ltrharvest efficiently delivers high quality annotations based on known ltr transposon features like length, distance, and sequence motifs. a quality validation of ltrharvest against a gold standard annotation for saccharomyces cerevisae and drosophila melanogaster shows a sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. this is comparable or slightly better than annotations for previous software tools. the main advantage of ltrharvest over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software. conclusion ltrharvest is an efficient software tool delivering high quality annotation of ltr retrotransposons. it can, for example, process the largest human chromosome in approx. 8 minutes on a linux pc with 4 gb of memory. its flexibility and small space and run-time requirements makes ltrharvest a very competitive candidate for future ltr retrotransposon annotation projects. moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of ltr retrotransposons.",0
"dammif , a revised implementation of the ab - initio shape-determination program dammin for small-angle scattering data, is presented. the program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. symmetry and anisometry constraints can be imposed on the particle shape, similar to dammin . in equivalent conditions, dammif is 25-40 times faster than dammin on a single cpu. the possibility to utilize multiple cpus is added to dammif . the application is available in binary form for major platforms.",0
"the development of magnetic resonance imaging (mri) techniques has defined modern neuroimaging. since its inception, tens of thousands of studies using techniques such as functional mri and diffusion weighted imaging have allowed for the non-invasive study of the brain. despite the fact that mri is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. this renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. to solve this problem, we have developed the brain imaging data structure (bids), a standard for organizing and describing mri datasets. the bids standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.",0
"background regularly updated data on stroke and its pathological types, including data on their incidence, prevalence, mortality, disability, risk factors, and epidemiological trends, are important for evidence-based stroke care planning and resource allocation. the global burden of diseases, injuries, and risk factors study (gbd) aims to provide a standardised and comprehensive measurement of these metrics at global, regional, and national levels. methods we applied gbd 2019 analytical tools to calculate stroke incidence, prevalence, mortality, disability-adjusted life-years (dalys), and the population attributable fraction (paf) of dalys (with corresponding 95% uncertainty intervals ) associated with 19 risk factors, for 204 countries and territories from 1990 to 2019. these estimates were provided for ischaemic stroke, intracerebral haemorrhage, subarachnoid haemorrhage, and all strokes combined, and stratified by sex, age group, and world bank country income level. findings in 2019, there were 12·2 million (95% ui 11·0-13·6) incident cases of stroke, 101 million (93·2-111) prevalent cases of stroke, 143 million (133-153) dalys due to stroke, and 6·55 million (6·00-7·02) deaths from stroke. globally, stroke remained the second-leading cause of death (11·6% of total deaths) and the third-leading cause of death and disability combined (5·7% of total dalys) in 2019. from 1990 to 2019, the absolute number of incident strokes increased by 70·0% (67·0-73·0), prevalent strokes increased by 85·0% (83·0-88·0), deaths from stroke increased by 43·0% (31·0-55·0), and dalys due to stroke increased by 32·0% (22·0-42·0). during the same period, age-standardised rates of stroke incidence decreased by 17·0% (15·0-18·0), mortality decreased by 36·0% (31·0-42·0), prevalence decreased by 6·0% (5·0-7·0), and dalys decreased by 36·0% (31·0-42·0). however, among people younger than 70 years, prevalence rates increased by 22·0% (21·0-24·0) and incidence rates increased by 15·0% (12·0-18·0). in 2019, the age-standardised stroke-related mortality rate was 3·6 (3·5-3·8) times higher in the world bank low-income group than in the world bank high-income group, and the age-standardised stroke-related daly rate was 3·7 (3·5-3·9) times higher in the low-income group than the high-income group. ischaemic stroke constituted 62·4% of all incident strokes in 2019 (7·63 million ), while intracerebral haemorrhage constituted 27·9% (3·41 million ) and subarachnoid haemorrhage constituted 9·7% (1·18 million ). in 2019, the five leading risk factors for stroke were high systolic blood pressure (contributing to 79·6 million dalys or 55·5% of total stroke dalys), high body-mass index (34·9 million dalys or 24·3% ), high fasting plasma glucose (28·9 million dalys or 20·2% ), ambient particulate matter pollution (28·7 million dalys or 20·1% ), and smoking (25·3 million dalys or 17·6% ). interpretation the annual number of strokes and deaths due to stroke increased substantially from 1990 to 2019, despite substantial reductions in age-standardised rates, particularly among people older than 70 years. the highest age-standardised stroke-related mortality and daly rates were in the world bank low-income group. the fastest-growing risk factor for stroke between 1990 and 2019 was high body-mass index. without urgent implementation of effective primary prevention strategies, the stroke burden will probably continue to grow across the world, particularly in low-income countries. funding bill & melinda gates foundation.",0
"background breast cancer is the most commonly diagnosed cancer worldwide, and its burden has been rising over the past decades. in this article, we examine and describe the global burden of breast cancer in 2020 and predictions for the year 2040. methods estimates of new female breast cancer cases and deaths in 2020 were abstracted from the globocan database. age-standardized incidence and mortality rates were calculated per 100,000 females by country, world region, and level of human development. predicted cases and deaths were computed based on global demographic projections for the year 2040. results over 2.3 million new cases and 685,000 deaths from breast cancer occurred in 2020. large geographic variation across countries and world regions exists, with incidence rates ranging from conclusion breast cancer is the most common cancer worldwide and continues to have a large impact on the global number of cancer deaths. global efforts are needed to counteract its growing burden, especially in transitioning countries where incidence is rising rapidly, and mortality rates remain high.",0
"zinc is a free public resource for ligand discovery. the database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. the web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and cas number. small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. the database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org.",0
"background since the first case of a novel coronavirus (covid-19) infection pneumonia was detected in wuhan, china, a series of confirmed cases of the covid-19 were found in beijing. we analyzed the data of 262 confirmed cases to determine the clinical and epidemiological characteristics of covid-19 in beijing. methods we collected patients who were transferred by beijing emergency medical service to the designated hospitals. the information on demographic, epidemiological, clinical, laboratory test for the covid-19 virus, diagnostic classification, cluster case and outcome were obtained. furthermore we compared the characteristics between severe and common confirmed cases which including mild cases, no-pneumonia cases and asymptomatic cases, and we also compared the features between covid-19 and 2003 sars. findings by feb 10, 2020, 262 patients were transferred from the hospitals across beijing to the designated hospitals for special treatment of the covid-19 infected by beijing emergency medical service. among of 262 patients, 46 (17.6%) were severe cases, 216 (82.4%) were common cases, which including 192 (73.3%) mild cases, 11(4.2%) non-pneumonia cases and 13 (5.0%) asymptomatic cases respectively. the median age of patients was 47.5 years old and 48.5% were male. 192 (73.3%) patients were residents of beijing, 50 (26.0%) of which had been to wuhan, 116 (60.4%) had close contact with confirmed cases, 21 (10.9%) had no contact history. the most common symptoms at the onset of illness were fever (82.1%), cough (45.8%), fatigue (26.3%), dyspnea (6.9%) and headache (6.5%). the median incubation period was 6.7 days, the interval time from between illness onset and seeing a doctor was 4.5 days. as of feb 10, 17.2% patients have discharged and 81.7% patients remain in hospital in our study, the fatality of covid-19 infection in beijing was 0.9%. interpretation on the basis of this study, we provided the ratio of the covid-19 infection on the severe cases to the mild, asymptomatic and non-pneumonia cases in beijing. population was generally susceptible, and with a relatively low fatality rate. the measures to prevent transmission was very successful at early stage, the next steps on the covid-19 infection should be focused on early isolation of patients and quarantine for close contacts in families and communities in beijing. funding beijing municipal science and technology commission and ministry of science and technology.",0
"italy is one of the major covid-19 hotspots. to reduce the spread of the infections and the pressure on italian healthcare systems, since march 10, 2020, italy has been under a total lockdown, forcing people into home confinement. here we present data from 1,310 people living in the italian territory (m age = 23.91 ± 3.60 years, 880 females, 501 workers, 809 university students), who completed an online survey from march 24 to march 28, 2020. in the survey, we asked participants to think about their use of digital media before going to bed, their sleep pattern and their subjective experience of time in the previous week (march 17-23, which was the second week of the lockdown) and up to the first week of february (february 3-10, before any restriction in any italian area). during the lockdown, people increased the usage of digital media near bedtime, but this change did not affect sleep habits. nevertheless, during home confinement, sleep timing markedly changed, with people going to bed and waking up later, and spending more time in bed, but, paradoxically, also reporting a lower sleep quality. the increase in sleep difficulties was stronger for people with a higher level of depression, anxiety and stress symptomatology, and associated with the feeling of elongation of time. considering that the lockdown is likely to continue for weeks, research data are urgently needed to support decision making, to build public awareness and to provide timely and supportive psychosocial interventions.",0
"microglia are the resident macrophage population of the central nervous system (cns). adequate microglial function is crucial for a healthy cns. microglia are not only the first immune sentinels of infection, contributing to both innate and adaptive immune responses locally, but are also involved in the maintenance of brain homeostasis. emerging data are showing new and fundamental roles for microglia in the control of neuronal proliferation and differentiation, as well as in the formation of synaptic connections. while microglia have been studied for decades, a long history of experimental misinterpretation meant that their true origins remained debated. however, recent studies on microglial origin indicate that these cells in fact arise early during development from progenitors in the embryonic yolk sac (ys) that seed the brain rudiment and, remarkably, appear to persist there into adulthood. here, we review the history of microglial cells and discuss the latest advances in our understanding of their origin, differentiation, and homeostasis, which provides new insights into their roles in health and disease.",0
"although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. because many drug-target combinations exist, it would be useful to explore possible interactions computationally. here we compared 3,665 us food and drug administration (fda)-approved and investigational drugs against hundreds of targets, defining each target by its ligands. chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. thirty were tested experimentally, including the antagonism of the beta(1) receptor by the transporter inhibitor prozac, the inhibition of the 5-hydroxytryptamine (5-ht) transporter by the ion channel drug vadilex, and antagonism of the histamine h(4) receptor by the enzyme inhibitor rescriptor. overall, 23 new drug-target associations were confirmed, five of which were potent (<100 nm). the physiological relevance of one, the drug n,n-dimethyltryptamine (dmt) on serotonergic receptors, was confirmed in a knockout mouse. the chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs.",0
"purpose this article introduces the new 5-level eq-5d (eq-5d-5l) health status measure. methods eq-5d currently measures health using three levels of severity in five dimensions. a euroqol group task force was established to find ways of improving the instrument's sensitivity and reducing ceiling effects by increasing the number of severity levels. the study was performed in the united kingdom and spain. severity labels for 5 levels in each dimension were identified using response scaling. focus groups were used to investigate the face and content validity of the new versions, including hypothetical health states generated from those versions. results selecting labels at approximately the 25th, 50th, and 75th centiles produced two alternative 5-level versions. focus group work showed a slight preference for the wording 'slight-moderate-severe' problems, with anchors of 'no problems' and 'unable to do' in the eq-5d functional dimensions. similar wording was used in the pain/discomfort and anxiety/depression dimensions. hypothetical health states were well understood though participants stressed the need for the internal coherence of health states. conclusions a 5-level version of the eq-5d has been developed by the euroqol group. further testing is required to determine whether the new version improves sensitivity and reduces ceiling effects.",0
"current day concentrations of ambient air pollution have been associated with a range of adverse health effects, particularly mortality and morbidity due to cardiovascular and respiratory diseases. in this review, we summarize the evidence from epidemiological studies on long-term exposure to fine and coarse particles, nitrogen dioxide (no2) and elemental carbon on mortality from all-causes, cardiovascular disease and respiratory disease. we also summarize the findings on potentially susceptible subgroups across studies. we identified studies through a search in the databases medline and scopus and previous reviews until january 2013 and performed a meta-analysis if more than five studies were available for the same exposure metric.",0
"a major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (ra). here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of european and asian ancestries (29,880 ra cases and 73,758 controls), by evaluating ∼10 million single-nucleotide polymorphisms. we discovered 42 novel ra risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2 - 4). we devised an in silico pipeline using established bioinformatics methods based on functional annotation, cis-acting expression quantitative trait loci and pathway analyses--as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes--to identify 98 biological candidate genes at these 101 risk loci. we demonstrate that these genes are the targets of approved therapies for ra, and further suggest that drugs approved for other indications may be repurposed for the treatment of ra. together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to ra pathogenesis, and provides empirical evidence that the genetics of ra can provide important information for drug discovery.",0
"the unpredictability and uncertainty of the covid-19 pandemic; the associated lockdowns, physical distancing, and other containment strategies; and the resulting economic breakdown could increase the risk of mental health problems and exacerbate health inequalities. preliminary findings suggest adverse mental health effects in previously healthy people and especially in people with pre-existing mental health disorders. despite the heterogeneity of worldwide health systems, efforts have been made to adapt the delivery of mental health care to the demands of covid-19. mental health concerns have been addressed via the public mental health response and by adapting mental health services, mostly focusing on infection control, modifying access to diagnosis and treatment, ensuring continuity of care for mental health service users, and paying attention to new cases of mental ill health and populations at high risk of mental health problems. sustainable adaptations of delivery systems for mental health care should be developed by experts, clinicians, and service users, and should be specifically designed to mitigate disparities in health-care provision. thorough and continuous assessment of health and service-use outcomes in mental health clinical practice will be crucial for defining which practices should be further developed and which discontinued. for this position paper, an international group of clinicians, mental health experts, and users of mental health services has come together to reflect on the challenges for mental health that covid-19 poses. the interconnectedness of the world made society vulnerable to this infection, but it also provides the infrastructure to address previous system failings by disseminating good practices that can result in sustained, efficient, and equitable delivery of mental health-care delivery. thus, the covid-19 pandemic could be an opportunity to improve mental health services.",0
"transposable elements (tes) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. using this approach, about half of the human genome has been previously identified as tes and low-complexity repeats. we recently developed a highly sensitive alternative de novo strategy, p-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo ""clouds""). we show here that p-clouds predicts >840 mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. to investigate this remarkable difference, we conducted detailed analyses of the ability of both p-clouds and a commonly used conventional approach, repeatmasker (rm), to detect different sized fragments of the highly abundant human alu and mir sines. rm can have surprisingly low sensitivity for even moderately long fragments, in contrast to p-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. we further developed ""element-specific"" p-clouds (esps) to identify novel alu and mir sine elements, and using it we identified ∼100 mb of previously unannotated human elements. esp estimates of new mir sequences are in good agreement with rm-based predictions of the amount that rm missed. these results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.",0
"objectives to develop recommendations for the management of adult and paediatric lupus nephritis (ln). methods the available evidence was systematically reviewed using the pubmed database. a modified delphi method was used to compile questions, elicit expert opinions and reach consensus. results immunosuppressive treatment should be guided by renal biopsy, and aiming for complete renal response (proteinuria conclusions recommendations for the management of ln were developed using an evidence-based approach followed by expert consensus.",0
"antibodies are a potential therapy for severe acute respiratory syndrome coronavirus 2 (sars-cov-2), but the risk of the virus evolving to escape them remains unclear. here we map how all mutations to the receptor binding domain (rbd) of sars-cov-2 affect binding by the antibodies in the regn-cov2 cocktail and the antibody ly-cov016. these complete maps uncover a single amino acid mutation that fully escapes the regn-cov2 cocktail, which consists of two antibodies, regn10933 and regn10987, targeting distinct structural epitopes. the maps also identify viral mutations that are selected in a persistently infected patient treated with regn-cov2 and during in vitro viral escape selections. finally, the maps reveal that mutations escaping the individual antibodies are already present in circulating sars-cov-2 strains. these complete escape maps enable interpretation of the consequences of mutations observed during viral surveillance.",0
"free radicals are common outcome of normal aerobic cellular metabolism. in-built antioxidant system of body plays its decisive role in prevention of any loss due to free radicals. however, imbalanced defense mechanism of antioxidants, overproduction or incorporation of free radicals from environment to living system leads to serious penalty leading to neuro-degeneration. neural cells suffer functional or sensory loss in neurodegenerative diseases. apart from several other environmental or genetic factors, oxidative stress (os) leading to free radical attack on neural cells contributes calamitous role to neuro-degeneration. though, oxygen is imperative for life, imbalanced metabolism and excess reactive oxygen species (ros) generation end into a range of disorders such as alzheimer's disease, parkinson's disease, aging and many other neural disorders. toxicity of free radicals contributes to proteins and dna injury, inflammation, tissue damage and subsequent cellular apoptosis. antioxidants are now being looked upon as persuasive therapeutic against solemn neuronal loss, as they have capability to combat by neutralizing free radicals. diet is major source of antioxidants, as well as medicinal herbs are catching attention to be commercial source of antioxidants at present. recognition of upstream and downstream antioxidant therapy to oxidative stress has been proved an effective tool in alteration of any neuronal damage as well as free radical scavenging. antioxidants have a wide scope to sequester metal ions involved in neuronal plaque formation to prevent oxidative stress. in addition, antioxidant therapy is vital in scavenging free radicals and ros preventing neuronal degeneration in post-oxidative stress scenario.",0
"the mammalian target of rapamycin (mtor), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. here we report co-crystal structures of a complex of truncated mtor and mammalian lethal with sec13 protein 8 (mlst8) with an atp transition state mimic and with atp-site inhibitors. the structures reveal an intrinsically active kinase conformation, with catalytic residues and a catalytic mechanism remarkably similar to canonical protein kinases. the active site is highly recessed owing to the fkbp12-rapamycin-binding (frb) domain and an inhibitory helix protruding from the catalytic cleft. mtor-activating mutations map to the structural framework that holds these elements in place, indicating that the kinase is controlled by restricted access. in vitro biochemistry shows that the frb domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. rapamycin-fkbp12 inhibits the kinase by directly blocking substrate recruitment and by further restricting active-site access. the structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.",0
"blood pressure is a heritable trait influenced by several biological pathways and responsive to environmental stimuli. over one billion people worldwide have hypertension (≥140 mm hg systolic blood pressure or ≥90 mm hg diastolic blood pressure). even small increments in blood pressure are associated with an increased risk of cardiovascular events. this genome-wide association study of systolic and diastolic blood pressure, which used a multi-stage design in 200,000 individuals of european descent, identified sixteen novel loci: six of these loci contain genes previously known or suspected to regulate blood pressure (gucy1a3-gucy1b3, npr3-c5orf23, adm, furin-fes, gosr2, gnas-edn3); the other ten provide new clues to blood pressure physiology. a genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke and coronary artery disease, but not kidney disease or kidney function. we also observed associations with blood pressure in east asian, south asian and african ancestry individuals. our findings provide new insights into the genetics and biology of blood pressure, and suggest potential novel therapeutic pathways for cardiovascular disease prevention.",0
"there is a need to assess the contribution of mood disorder, especially anxiety and depression, in order to understand the experience of suffering in the setting of medical practice. most physicians are aware of this aspect of the illness of their patients but many feel incompetent to provide the patient with reliable information. the hospital anxiety and depression scale, or hads, was designed to provide a simple yet reliable tool for use in medical practice. the term 'hospital' in its title suggests that it is only valid in such a setting but many studies conducted throughout the world have confirmed that it is valid when used in community settings and primary care medical practice. it should be emphasised that self-assessment scales are only valid for screening purposes; definitive diagnosis must rest on the process of clinical examination.",0
"background healthy life expectancy (hale) and disability-adjusted life-years (dalys) provide summary measures of health across geographies and time that can inform assessments of epidemiological patterns and health system performance, help to prioritise investments in research and development, and monitor progress toward the sustainable development goals (sdgs). we aimed to provide updated hale and dalys for geographies worldwide and evaluate how disease burden changes with development. methods we used results from the global burden of diseases, injuries, and risk factors study 2015 (gbd 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive hale and dalys by sex for 195 countries and territories from 1990 to 2015. we calculated dalys by summing years of life lost (ylls) and years of life lived with disability (ylds) for each geography, age group, sex, and year. we estimated hale using the sullivan method, which draws from age-specific death rates and ylds per capita. we then assessed how observed levels of dalys and hale differed from expected trends calculated with the socio-demographic index (sdi), a composite indicator constructed from measures of income per capita, average years of schooling, and total fertility rate. findings total global dalys remained largely unchanged from 1990 to 2015, with decreases in communicable, neonatal, maternal, and nutritional (group 1) disease dalys offset by increased dalys due to non-communicable diseases (ncds). much of this epidemiological transition was caused by changes in population growth and ageing, but it was accelerated by widespread improvements in sdi that also correlated strongly with the increasing importance of ncds. both total dalys and age-standardised daly rates due to most group 1 causes significantly decreased by 2015, and although total burden climbed for the majority of ncds, age-standardised daly rates due to ncds declined. nonetheless, age-standardised daly rates due to several high-burden ncds (including osteoarthritis, drug use disorders, depression, diabetes, congenital birth defects, and skin, oral, and sense organ diseases) either increased or remained unchanged, leading to increases in their relative ranking in many geographies. from 2005 to 2015, hale at birth increased by an average of 2·9 years (95% uncertainty interval 2·9-3·0) for men and 3·5 years (3·4-3·7) for women, while hale at age 65 years improved by 0·85 years (0·78-0·92) and 1·2 years (1·1-1·3), respectively. rising sdi was associated with consistently higher hale and a somewhat smaller proportion of life spent with functional health loss; however, rising sdi was related to increases in total disability. many countries and territories in central america and eastern sub-saharan africa had increasingly lower rates of disease burden than expected given their sdi. at the same time, a subset of geographies recorded a growing gap between observed and expected levels of dalys, a trend driven mainly by rising burden due to war, interpersonal violence, and various ncds. interpretation health is improving globally, but this means more populations are spending more time with functional health loss, an absolute expansion of morbidity. the proportion of life spent in ill health decreases somewhat with increasing sdi, a relative compression of morbidity, which supports continued efforts to elevate personal income, improve education, and limit fertility. our analysis of dalys and hale and their relationship to sdi represents a robust framework on which to benchmark geography-specific health performance and sdg progress. country-specific drivers of disease burden, particularly for causes with higher-than-expected dalys, should inform financial and research investments, prevention efforts, health policies, and health system improvement initiatives for all countries along the development continuum. funding bill & melinda gates foundation.",0
"brain anatomical networks are sparse, complex, and have economical small-world properties. we investigated the efficiency and cost of human brain functional networks measured using functional magnetic resonance imaging (fmri) in a factorial design: two groups of healthy old (n = 11; mean age = 66.5 years) and healthy young (n = 15; mean age = 24.7 years) volunteers were each scanned twice in a no-task or ""resting"" state following placebo or a single dose of a dopamine receptor antagonist (sulpiride 400 mg). functional connectivity between 90 cortical and subcortical regions was estimated by wavelet correlation analysis, in the frequency interval 0.06-0.11 hz, and thresholded to construct undirected graphs. these brain functional networks were small-world and economical in the sense of providing high global and local efficiency of parallel information processing for low connection cost. efficiency was reduced disproportionately to cost in older people, and the detrimental effects of age on efficiency were localised to frontal and temporal cortical and subcortical regions. dopamine antagonism also impaired global and local efficiency of the network, but this effect was differentially localised and did not interact with the effect of age. brain functional networks have economical small-world properties-supporting efficient parallel information transfer at relatively low cost-which are differently impaired by normal aging and pharmacological blockade of dopamine transmission.",0
"background narrative reviews are the commonest type of articles in the medical literature. however, unlike systematic reviews and randomized controlled trials (rct) articles, for which formal instruments exist to evaluate quality, there is currently no instrument available to assess the quality of narrative reviews. in response to this gap, we developed sanra, the scale for the assessment of narrative review articles. methods a team of three experienced journal editors modified or deleted items in an earlier sanra version based on face validity, item-total correlations, and reliability scores from previous tests. we deleted an item which addressed a manuscript's writing and accessibility due to poor inter-rater reliability. the six items which form the revised scale are rated from 0 (low standard) to 2 (high standard) and cover the following topics: explanation of (1) the importance and (2) the aims of the review, (3) literature search and (4) referencing and presentation of (5) evidence level and (6) relevant endpoint data. for all items, we developed anchor definitions and examples to guide users in filling out the form. the revised scale was tested by the same editors (blinded to each other's ratings) in a group of 30 consecutive non-systematic review manuscripts submitted to a general medical journal. results raters confirmed that completing the scale is feasible in everyday editorial work. the mean sum score across all 30 manuscripts was 6.0 out of 12 possible points (sd 2.6, range 1-12). corrected item-total correlations ranged from 0.33 (item 3) to 0.58 (item 6), and cronbach's alpha was 0.68 (internal consistency). the intra-class correlation coefficient (average measure) was 0.77 (inter-rater reliability). raters often disagreed on items 1 and 4. conclusions sanra's feasibility, inter-rater reliability, homogeneity of items, and internal consistency are sufficient for a scale of six items. further field testing, particularly of validity, is desirable. we recommend rater training based on the ""explanations and instructions"" document provided with sanra. in editorial decision-making, sanra may complement journal-specific evaluation of manuscripts-pertaining to, e.g., audience, originality or difficulty-and may contribute to improving the standard of non-systematic reviews.",0
"the principles of shared decision making are well documented but there is a lack of guidance about how to accomplish the approach in routine clinical practice. our aim here is to translate existing conceptual descriptions into a three-step model that is practical, easy to remember, and can act as a guide to skill development. achieving shared decision making depends on building a good relationship in the clinical encounter so that information is shared and patients are supported to deliberate and express their preferences and views during the decision making process. to accomplish these tasks, we propose a model of how to do shared decision making that is based on choice, option and decision talk. the model has three steps: a) introducing choice, b) describing options, often by integrating the use of patient decision support, and c) helping patients explore preferences and make decisions. this model rests on supporting a process of deliberation, and on understanding that decisions should be influenced by exploring and respecting ""what matters most"" to patients as individuals, and that this exploration in turn depends on them developing informed preferences.",0
"it is well established that autism spectrum disorders (asd) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing asd in families with no previous history of asd or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic asd, including 189 new trios and 20 that were previously reported. additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop asd. moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. in proband exomes, recurrent protein-altering mutations were observed in two genes: chd8 and ntng1. mutation screening of six candidate genes in 1,703 asd probands identified additional de novo, protein-altering mutations in grin2b, lamc3 and scn1a. combined with copy number variant (cnv) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.",0
"drugbank ( is a comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms and their targets. since it was first described in 2006, drugbank has rapidly evolved, both in response to user requests and in response to changing trends in drug research and development. previous versions of drugbank have been widely used to facilitate drug and in silico drug target discovery. the latest update, drugbank 4.0, has been further expanded to contain data on drug metabolism, absorption, distribution, metabolism, excretion and toxicity (admet) and other kinds of quantitative structure activity relationships (qsar) information. these enhancements are intended to facilitate research in xenobiotic metabolism (both prediction and characterization), pharmacokinetics, pharmacodynamics and drug design/discovery. for this release, >1200 drug metabolites (including their structures, names, activity, abundance and other detailed data) have been added along with >1300 drug metabolism reactions (including metabolizing enzymes and reaction types) and dozens of drug metabolism pathways. another 30 predicted or measured admet parameters have been added to each drugcard, bringing the average number of quantitative admet values for food and drug administration-approved drugs close to 40. referential nuclear magnetic resonance and ms spectra have been added for almost 400 drugs as well as spectral and mass matching tools to facilitate compound identification. this expanded collection of drug information is complemented by a number of new or improved search tools, including one that provides a simple analyses of drug-target, -enzyme and -transporter associations to provide insight on drug-drug interactions.",0
"introduction mortality rates are used as global measures of a population's health status and as indicators for public health efforts and medical treatments. elevated mortality rates among individuals with mental illness have been reported in various studies, but very little focus has been placed on interstate comparisons and congruency of mortality and causes of death among public mental health clients. methods using age-adjusted death rates, standardized mortality ratios, and years of potential life lost, we compared the mortality of public mental health clients in eight states with the mortality of their state general populations. the data used in our study were submitted by public mental health agencies in eight states (arizona, missouri, oklahoma, rhode island, texas, utah, vermont, and virginia) for 1997 through 2000 during the sixteen-state study on mental health performance measures, a multistate study federally funded by the center for mental health services in collaboration with the national association of state mental health program directors. results in all eight states, we found that public mental health clients had a higher relative risk of death than the general populations of their states. deceased public mental health clients had died at much younger ages and lost decades of potential life when compared with their living cohorts nationwide. clients with major mental illness diagnoses died at younger ages and lost more years of life than people with non-major mental illness diagnoses. most mental health clients died of natural causes similar to the leading causes of death found nationwide, including heart disease, cancer, and cerebrovascular, respiratory, and lung diseases. conclusion mental health and physical health are intertwined; both types of care should be provided and linked together within health care delivery systems. research to track mortality and primary care should be increased to provide information for additional action, treatment modification, diagnosis-specific risk, and evidence-based practices.",0
"background systematic reviews and meta-analyses of test accuracy studies are increasingly being recognised as central in guiding clinical practice. however, there is currently no dedicated and comprehensive software for meta-analysis of diagnostic data. in this article, we present meta-disc, a windows-based, user-friendly, freely available (for academic use) software that we have developed, piloted, and validated to perform diagnostic meta-analysis. results meta-disc a) allows exploration of heterogeneity, with a variety of statistics including chi-square, i-squared and spearman correlation tests, b) implements meta-regression techniques to explore the relationships between study characteristics and accuracy estimates, c) performs statistical pooling of sensitivities, specificities, likelihood ratios and diagnostic odds ratios using fixed and random effects models, both overall and in subgroups and d) produces high quality figures, including forest plots and summary receiver operating characteristic curves that can be exported for use in manuscripts for publication. all computational algorithms have been validated through comparison with different statistical tools and published meta-analyses. meta-disc has a graphical user interface with roll-down menus, dialog boxes, and online help facilities. conclusion meta-disc is a comprehensive and dedicated test accuracy meta-analysis software. it has already been used and cited in several meta-analyses published in high-ranking journals. the software is publicly available at",0
"pyroptosis is a lytic type of cell death that is initiated by inflammatory caspases. these caspases are activated within multi-protein inflammasome complexes that assemble in response to pathogens and endogenous danger signals. pyroptotic cell death has been proposed to proceed via the formation of a plasma membrane pore, but the underlying molecular mechanism has remained unclear. recently, gasdermin d (gsdmd), a member of the ill-characterized gasdermin protein family, was identified as a caspase substrate and an essential mediator of pyroptosis. gsdmd is thus a candidate for pyroptotic pore formation. here, we characterize gsdmd function in live cells and in vitro we show that the n-terminal fragment of caspase-1-cleaved gsdmd rapidly targets the membrane fraction of macrophages and that it induces the formation of a plasma membrane pore. in vitro, the n-terminal fragment of caspase-1-cleaved recombinant gsdmd tightly binds liposomes and forms large permeability pores. visualization of liposome-inserted gsdmd at nanometer resolution by cryo-electron and atomic force microscopy shows circular pores with variable ring diameters around 20 nm. overall, these data demonstrate that gsdmd is the direct and final executor of pyroptotic cell death.",0
"the basic morphological properties of liver cells are defined in the form of a morphometric model to permit integrated quantitative characterization of functionally important parameters. stereologic methods which allow efficient and reliable quantitative evaluation of sectioned liver tissue are presented. material, obtained by a rigorous three-stage sampling procedure from five normal rat livers, is systematically subjected to this analysis at four levels of magnification. this yields quantitative data which are expressed as ""densities,"" i.e. content per 1 ml of tissue, as ""specific dimensions"" related to 100 g body weight, and as absolute dimensions per average ""mononuclear"" hepatocyte. base line data relating to the normal rat liver are presented for the entire spectrum of parameters. as examples, 1 ml of liver tissue contains 169 x 10(6) hepatocyte nuclei, some 90 x 10(6) nuclei of other cells, and 280 x 10(9) mitochondria. hepatocyte cytoplasm accounts for 77% of liver volume, and the mitochondria for 18%. the surface area of endoplasmic reticulum membranes in 1 ml of liver tissue measures 11 m(2) of which are (2/3) of the rough form carrying some 2 x 10(13) ribosomes. the surface area of mitochondrial cristae in the unit volume is estimated at 6 m(2). the validity and applicability of the method are discussed, and the data are compared with available information from other studies.",0
"since sars-cov-2, the novel coronavirus that causes coronavirus disease 2019 (covid-19), was first detected in december 2019 (1), approximately 1.3 million cases have been reported worldwide (2), including approximately 330,000 in the united states (3). to conduct population-based surveillance for laboratory-confirmed covid-19-associated hospitalizations in the united states, the covid-19-associated hospitalization surveillance network (covid-net) was created using the existing infrastructure of the influenza hospitalization surveillance network (flusurv-net) (4) and the respiratory syncytial virus hospitalization surveillance network (rsv-net). this report presents age-stratified covid-19-associated hospitalization rates for patients admitted during march 1-28, 2020, and clinical data on patients admitted during march 1-30, 2020, the first month of u.s. surveillance. among 1,482 patients hospitalized with covid-19, 74.5% were aged ≥50 years, and 54.4% were male. the hospitalization rate among patients identified through covid-net during this 4-week period was 4.6 per 100,000 population. rates were highest (13.8) among adults aged ≥65 years. among 178 (12%) adult patients with data on underlying conditions as of march 30, 2020, 89.3% had one or more underlying conditions; the most common were hypertension (49.7%), obesity (48.3%), chronic lung disease (34.6%), diabetes mellitus (28.3%), and cardiovascular disease (27.8%). these findings suggest that older adults have elevated rates of covid-19-associated hospitalization and the majority of persons hospitalized with covid-19 have underlying medical conditions. these findings underscore the importance of preventive measures (e.g., social distancing, respiratory hygiene, and wearing face coverings in public settings where social distancing measures are difficult to maintain) † to protect older adults and persons with underlying medical conditions, as well as the general public. in addition, older adults and persons with serious underlying medical conditions should avoid contact with persons who are ill and immediately contact their health care provider(s) if they have symptoms consistent with covid-19 ( (5). ongoing monitoring of hospitalization rates, clinical characteristics, and outcomes of hospitalized patients will be important to better understand the evolving epidemiology of covid-19 in the united states and the clinical spectrum of disease, and to help guide planning and prioritization of health care system resources.",0
"a valid comparison of the magnitude of two correlations requires researchers to directly contrast the correlations using an appropriate statistical test. in many popular statistics packages, however, tests for the significance of the difference between correlations are missing. to close this gap, we introduce cocor, a free software package for the r programming language. the cocor package covers a broad range of tests including the comparisons of independent and dependent correlations with either overlapping or nonoverlapping variables. the package also includes an implementation of zou's confidence interval for all of these comparisons. the platform independent cocor package enhances the r statistical computing environment and is available for scripting. two different graphical user interfaces-a plugin for rkward and a web interface-make cocor a convenient and user-friendly tool.",0
"background severe malaria is a major cause of childhood death and often the main reason for paediatric hospital admission in sub-saharan africa. quinine is still the established treatment of choice, although evidence from asia suggests that artesunate is associated with a lower mortality. we compared parenteral treatment with either artesunate or quinine in african children with severe malaria. methods this open-label, randomised trial was undertaken in 11 centres in nine african countries. children ( findings 5425 children were enrolled; 2712 were assigned to artesunate and 2713 to quinine. all patients were analysed for the primary outcome. 230 (8·5%) patients assigned to artesunate treatment died compared with 297 (10·9%) assigned to quinine treatment (odds ratio stratified for study site 0·75, 95% ci 0·63-0·90; relative reduction 22·5%, 95% ci 8·1-36·9; p=0·0022). incidence of neurological sequelae did not differ significantly between groups, but the development of coma (65/1832 with artesunate vs 91/1768 with quinine; or 0·69 95% ci 0·49-0·95; p=0·0231), convulsions (224/2712 vs 273/2713 ; or 0·80, 0·66-0·97; p=0·0199), and deterioration of the coma score (166/2712 vs 208/2713 ; or 0·78, 0·64-0·97; p=0·0245) were all significantly less frequent in artesunate recipients than in quinine recipients. post-treatment hypoglycaemia was also less frequent in patients assigned to artesunate than in those assigned to quinine (48/2712 vs 75/2713 ; or 0·63, 0·43-0·91; p=0·0134). artesunate was well tolerated, with no serious drug-related adverse effects. interpretation artesunate substantially reduces mortality in african children with severe malaria. these data, together with a meta-analysis of all trials comparing artesunate and quinine, strongly suggest that parenteral artesunate should replace quinine as the treatment of choice for severe falciparum malaria worldwide. funding the wellcome trust.",0
"background people with diabetes can suffer from diverse complications that seriously erode quality of life. diabetes, costing the united states more than $174 billion per year in 2007, is expected to take an increasingly large financial toll in subsequent years. accurate projections of diabetes burden are essential to policymakers planning for future health care needs and costs. methods using data on prediabetes and diabetes prevalence in the united states, forecasted incidence, and current us census projections of mortality and migration, the authors constructed a series of dynamic models employing systems of difference equations to project the future burden of diabetes among us adults. a three-state model partitions the us population into no diabetes, undiagnosed diabetes, and diagnosed diabetes. a four-state model divides the state of ""no diabetes"" into high-risk (prediabetes) and low-risk (normal glucose) states. a five-state model incorporates an intervention designed to prevent or delay diabetes in adults at high risk. results the authors project that annual diagnosed diabetes incidence (new cases) will increase from about 8 cases per 1,000 in 2008 to about 15 in 2050. assuming low incidence and relatively high diabetes mortality, total diabetes prevalence (diagnosed and undiagnosed cases) is projected to increase from 14% in 2010 to 21% of the us adult population by 2050. however, if recent increases in diabetes incidence continue and diabetes mortality is relatively low, prevalence will increase to 33% by 2050. a middle-ground scenario projects a prevalence of 25% to 28% by 2050. intervention can reduce, but not eliminate, increases in diabetes prevalence. conclusions these projected increases are largely attributable to the aging of the us population, increasing numbers of members of higher-risk minority groups in the population, and people with diabetes living longer. effective strategies will need to be undertaken to moderate the impact of these factors on national diabetes burden. our analysis suggests that widespread implementation of reasonably effective preventive interventions focused on high-risk subgroups of the population can considerably reduce, but not eliminate, future increases in diabetes prevalence.",0
"background health literacy concerns the knowledge and competences of persons to meet the complex demands of health in modern society. although its importance is increasingly recognised, there is no consensus about the definition of health literacy or about its conceptual dimensions, which limits the possibilities for measurement and comparison. the aim of the study is to review definitions and models on health literacy to develop an integrated definition and conceptual model capturing the most comprehensive evidence-based dimensions of health literacy. methods a systematic literature review was performed to identify definitions and conceptual frameworks of health literacy. a content analysis of the definitions and conceptual frameworks was carried out to identify the central dimensions of health literacy and develop an integrated model. results the review resulted in 17 definitions of health literacy and 12 conceptual models. based on the content analysis, an integrative conceptual model was developed containing 12 dimensions referring to the knowledge, motivation and competencies of accessing, understanding, appraising and applying health-related information within the healthcare, disease prevention and health promotion setting, respectively. conclusions based upon this review, a model is proposed integrating medical and public health views of health literacy. the model can serve as a basis for developing health literacy enhancing interventions and provide a conceptual basis for the development and validation of measurement tools, capturing the different dimensions of health literacy within the healthcare, disease prevention and health promotion settings.",0
"infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is initiated by virus binding to the ace2 cell-surface receptors 1-4 , followed by fusion of the virus and cell membranes to release the virus genome into the cell. both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein 5-7 . as with other class-i membrane-fusion proteins, the spike protein is post-translationally cleaved, in this case by furin, into the s1 and s2 components that remain associated after cleavage 8-10 . fusion activation after receptor binding is proposed to involve the exposure of a second proteolytic site (s2'), cleavage of which is required for the release of the fusion peptide 11,12 . here we analyse the binding of ace2 to the furin-cleaved form of the sars-cov-2 spike protein using cryo-electron microscopy. we classify ten different molecular species, including the unbound, closed spike trimer, the fully open ace2-bound trimer and dissociated monomeric s1 bound to ace2. the ten structures describe ace2-binding events that destabilize the spike trimer, progressively opening up, and out, the individual s1 components. the opening process reduces s1 contacts and unshields the trimeric s2 core, priming the protein for fusion activation and dissociation of ace2-bound s1 monomers. the structures also reveal refolding of an s1 subdomain after ace2 binding that disrupts interactions with s2, which involves asp614 13-15 and leads to the destabilization of the structure of s2 proximal to the secondary (s2') cleavage site.",0
"background reduced tor signaling has been shown to significantly increase lifespan in a variety of organisms , , , . it was recently demonstrated that long-term treatment with rapamycin, an inhibitor of the mtor pathway, or ablation of the mtor target p70s6k extends lifespan in mice, possibly by delaying aging. whether inhibition of the mtor pathway would delay or prevent age-associated disease such as ad remained to be determined. methodology/principal findings we used rapamycin administration and behavioral tools in a mouse model of ad as well as standard biochemical and immunohistochemical measures in brain tissue to provide answers for this question. here we show that long-term inhibition of mtor by rapamycin prevented ad-like cognitive deficits and lowered levels of abeta(42), a major toxic species in ad, in the pdapp transgenic mouse model. these data indicate that inhibition of the mtor pathway can reduce abeta(42) levels in vivo and block or delay ad in mice. as expected from the inhibition of mtor, autophagy was increased in neurons of rapamycin-treated transgenic, but not in non-transgenic, pdapp mice, suggesting that the reduction in abeta and the improvement in cognitive function are due in part to increased autophagy, possibly as a response to high levels of abeta. conclusions/significance our data suggest that inhibition of mtor by rapamycin, an intervention that extends lifespan in mice, can slow or block ad progression in a transgenic mouse model of the disease. rapamycin, already used in clinical settings, may be a potentially effective therapeutic agent for the treatment of ad.",0
"tau protein from mammalian brain promotes microtubule polymerization in vitro and is induced during nerve cell differentiation. however, the effects of tau or any other microtubule-associated protein on tubulin assembly within cells are presently unknown. we have tested tau protein activity in vivo by microinjection into a cell type that has no endogenous tau protein. immunofluorescence shows that tau protein microinjected into fibroblast cells associates specifically with microtubules. the injected tau protein increases tubulin polymerization and stabilizes microtubules against depolymerization. this increased polymerization does not, however, cause major changes in cell morphology or microtubule arrangement. thus, tau protein acts in vivo primarily to induce tubulin assembly and stabilize microtubules, activities that may be necessary, but not sufficient, for neuronal morphogenesis.",0
"we describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (scnas) that drive cancer growth. by separating scna profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. we additionally describe a probabilistic method for defining the boundaries of selected-for scna regions with user-defined confidence. here we detail this revised computational approach, gistic2.0, and validate its performance in real and simulated datasets.",0
"estimates of foodborne illness can be used to direct food safety policy and interventions. we used data from active and passive surveillance and other sources to estimate that each year 31 major pathogens acquired in the united states caused 9.4 million episodes of foodborne illness (90% credible interval 6.6-12.7 million), 55,961 hospitalizations (90% cri 39,534-75,741), and 1,351 deaths (90% cri 712-2,268). most (58%) illnesses were caused by norovirus, followed by nontyphoidal salmonella spp. (11%), clostridium perfringens (10%), and campylobacter spp. (9%). leading causes of hospitalization were nontyphoidal salmonella spp. (35%), norovirus (26%), campylobacter spp. (15%), and toxoplasma gondii (8%). leading causes of death were nontyphoidal salmonella spp. (28%), t. gondii (24%), listeria monocytogenes (19%), and norovirus (11%). these estimates cannot be compared with prior (1999) estimates to assess trends because different methods were used. additional data and more refined methods can improve future estimates.",0
"background in december 2019, the coronavirus disease 2019 (covid-19) outbreak occurred in wuhan. data on the clinical characteristics and outcomes of patients with severe covid-19 are limited. objective we sought to evaluate the severity on admission, complications, treatment, and outcomes of patients with covid-19. methods patients with covid-19 admitted to tongji hospital from january 26, 2020, to february 5, 2020, were retrospectively enrolled and followed-up until march 3, 2020. potential risk factors for severe covid-19 were analyzed by a multivariable binary logistic model. cox proportional hazard regression model was used for survival analysis in severe patients. results we identified 269 (49.1%) of 548 patients as severe cases on admission. older age, underlying hypertension, high cytokine levels (il-2r, il-6, il-10, and tnf-α), and high lactate dehydrogenase level were significantly associated with severe covid-19 on admission. the prevalence of asthma in patients with covid-19 was 0.9%, markedly lower than that in the adult population of wuhan. the estimated mortality was 1.1% in nonsevere patients and 32.5% in severe cases during the average 32 days of follow-up period. survival analysis revealed that male sex, older age, leukocytosis, high lactate dehydrogenase level, cardiac injury, hyperglycemia, and high-dose corticosteroid use were associated with death in patients with severe covid-19. conclusions patients with older age, hypertension, and high lactate dehydrogenase level need careful observation and early intervention to prevent the potential development of severe covid-19. severe male patients with heart injury, hyperglycemia, and high-dose corticosteroid use may have a high risk of death.",0
"objectives to assess the overall effect of vitamin d supplementation on risk of acute respiratory tract infection, and to identify factors modifying this effect. design systematic review and meta-analysis of individual participant data (ipd) from randomised controlled trials. data sources medline, embase, the cochrane central register of controlled trials, web of science, clinicaltrials.gov, and the international standard randomised controlled trials number registry from inception to december 2015. eligibility criteria for study selection randomised, double blind, placebo controlled trials of supplementation with vitamin d 3 or vitamin d 2 of any duration were eligible for inclusion if they had been approved by a research ethics committee and if data on incidence of acute respiratory tract infection were collected prospectively and prespecified as an efficacy outcome. results 25 eligible randomised controlled trials (total 11 321 participants, aged 0 to 95 years) were identified. ipd were obtained for 10 933 (96.6%) participants. vitamin d supplementation reduced the risk of acute respiratory tract infection among all participants (adjusted odds ratio 0.88, 95% confidence interval 0.81 to 0.96; p for heterogeneity conclusions vitamin d supplementation was safe and it protected against acute respiratory tract infection overall. patients who were very vitamin d deficient and those not receiving bolus doses experienced the most benefit. systematic review registration prospero crd42014013953.",0
"background coronavirus disease 2019 (covid-19) occurs after exposure to severe acute respiratory syndrome coronavirus 2 (sars-cov-2). for persons who are exposed, the standard of care is observation and quarantine. whether hydroxychloroquine can prevent symptomatic infection after sars-cov-2 exposure is unknown. methods we conducted a randomized, double-blind, placebo-controlled trial across the united states and parts of canada testing hydroxychloroquine as postexposure prophylaxis. we enrolled adults who had household or occupational exposure to someone with confirmed covid-19 at a distance of less than 6 ft for more than 10 minutes while wearing neither a face mask nor an eye shield (high-risk exposure) or while wearing a face mask but no eye shield (moderate-risk exposure). within 4 days after exposure, we randomly assigned participants to receive either placebo or hydroxychloroquine (800 mg once, followed by 600 mg in 6 to 8 hours, then 600 mg daily for 4 additional days). the primary outcome was the incidence of either laboratory-confirmed covid-19 or illness compatible with covid-19 within 14 days. results we enrolled 821 asymptomatic participants. overall, 87.6% of the participants (719 of 821) reported a high-risk exposure to a confirmed covid-19 contact. the incidence of new illness compatible with covid-19 did not differ significantly between participants receiving hydroxychloroquine (49 of 414 ) and those receiving placebo (58 of 407 ); the absolute difference was -2.4 percentage points (95% confidence interval, -7.0 to 2.2; p = 0.35). side effects were more common with hydroxychloroquine than with placebo (40.1% vs. 16.8%), but no serious adverse reactions were reported. conclusions after high-risk or moderate-risk exposure to covid-19, hydroxychloroquine did not prevent illness compatible with covid-19 or confirmed infection when used as postexposure prophylaxis within 4 days after exposure. (funded by david baszucki and jan ellison baszucki and others; clinicaltrials.gov number, nct04308668.).",0
"functional magnetic resonance imaging (fmri) studies typically collapse data from many subjects, but brain functional organization varies between individuals. here we establish that this individual variability is both robust and reliable, using data from the human connectome project to demonstrate that functional connectivity profiles act as a 'fingerprint' that can accurately identify subjects from a large group. identification was successful across scan sessions and even between task and rest conditions, indicating that an individual's connectivity profile is intrinsic, and can be used to distinguish that individual regardless of how the brain is engaged during imaging. characteristic connectivity patterns were distributed throughout the brain, but the frontoparietal network emerged as most distinctive. furthermore, we show that connectivity profiles predict levels of fluid intelligence: the same networks that were most discriminating of individuals were also most predictive of cognitive behavior. results indicate the potential to draw inferences about single subjects on the basis of functional connectivity fmri.",0
"cdd, the conserved domain database, is part of ncbi's entrez query and retrieval system and is also accessible via cdd provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. pre-computed annotation is available via entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing rps-blast to rapidly identify putative matches. cdd incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3d) structure and the published literature. to this date, the majority of protein 3d structures are represented by models tracked by cdd, and cdd curators are characterizing novel families that emerge from protein structure determination efforts.",0
"objective the antidiabetic properties of metformin are mediated through its ability to activate the amp-activated protein kinase (ampk). activation of ampk can suppress tumor formation and inhibit cell growth in addition to lowering blood glucose levels. we tested the hypothesis that metformin reduces the risk of cancer in people with type 2 diabetes. research design and methods in an observational cohort study using record-linkage databases and based in tayside, scotland, u.k., we identified people with type 2 diabetes who were new users of metformin in 1994-2003. we also identified a set of diabetic comparators, individually matched to the metformin users by year of diabetes diagnosis, who had never used metformin. in a survival analysis we calculated hazard ratios for diagnosis of cancer, adjusted for baseline characteristics of the two groups using cox regression. results cancer was diagnosed among 7.3% of 4,085 metformin users compared with 11.6% of 4,085 comparators, with median times to cancer of 3.5 and 2.6 years, respectively (p conclusions these results suggest that metformin use may be associated with a reduced risk of cancer. a randomized trial is needed to assess whether metformin is protective in a population at high risk for cancer.",0
"the aim of the uniprot knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. in this article, we describe significant updates that we have made over the last two years to the resource. the number of sequences in uniprotkb has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. we have adopted new methods of assessing proteome completeness and quality. we continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented association-rule-based annotator (arba). we have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to uniprot entries. we describe how uniprotkb responded to the covid-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. uniprot resources are available under a cc-by (4.0) license via the web at",0
"a new connective tissue protein, which we call fibrillin, has been isolated from the medium of human fibroblast cell cultures. electrophoresis of the disulfide bond-reduced protein gave a single band with an estimated molecular mass of 350,000 d. this 350-kd protein appeared to possess intrachain disulfide bonds. it could be stained with periodic acid-schiff reagent, and after metabolic labeling, it contained glucosamine. it could not be labeled with sulfate. it was resistant to digestion by bacterial collagenase. using mabs specific for fibrillin, we demonstrated its widespread distribution in the connective tissue matrices of skin, lung, kidney, vasculature, cartilage, tendon, muscle, cornea, and ciliary zonule. electron microscopic immunolocalization with colloidal gold conjugates specified its location to a class of extracellular structural elements described as microfibrils. these microfibrils possessed a characteristic appearance and averaged 10 nm in diameter. microfibrils around the amorphous cores of the elastic fiber system as well as bundles of microfibrils without elastin cores were labeled equally well with antibody. immunolocalization suggested that fibrillin is arrayed periodically along the individual microfibril and that individual microfibrils may be aligned within bundles. the periodicity of the epitope appeared to match the interstitial collagen band periodicity. in contrast, type vi collagen, which has been proposed as a possible microfibrillar component, was immunolocalized with a specific mab to small diameter microfilaments that interweave among the large, banded collagen fibers; it was not associated with the system of microfibrils identified by the presence of fibrillin.",0
"neutralizing antibodies have become an important tool in treating infectious diseases. recently, two separate approaches yielded successful antibody treatments for ebola-one from genetically humanized mice and the other from a human survivor. here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) spike protein, which yielded a large collection of fully human antibodies that were characterized for binding, neutralization, and three-dimensional structure. on the basis of these criteria, we selected pairs of highly potent individual antibodies that simultaneously bind the receptor binding domain of the spike protein, thereby providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single-antibody treatment.",0
"background tuberculosis (tb) is a major contributor to the global burden of disease and has received considerable attention in recent years, particularly in low- and middle-income countries where it is closely associated with hiv/aids. poor adherence to treatment is common despite various interventions aimed at improving treatment completion. lack of a comprehensive and holistic understanding of barriers to and facilitators of, treatment adherence is currently a major obstacle to finding effective solutions. the aim of this systematic review of qualitative studies was to understand the factors considered important by patients, caregivers and health care providers in contributing to tb medication adherence. methods and findings we searched 19 electronic databases (1966-february 2005) for qualitative studies on patients', caregivers', or health care providers' perceptions of adherence to preventive or curative tb treatment with the free text terms ""tuberculosis and (adherence or compliance or concordance)"". we supplemented our search with citation searches and by consulting experts. for included studies, study quality was assessed using a predetermined checklist and data were extracted independently onto a standard form. we then followed noblit and hare's method of meta-ethnography to synthesize the findings, using both reciprocal translation and line-of-argument synthesis. we screened 7,814 citations and selected 44 articles that met the prespecified inclusion criteria. the synthesis offers an overview of qualitative evidence derived from these multiple international studies. we identified eight major themes across the studies: organisation of treatment and care; interpretations of illness and wellness; the financial burden of treatment; knowledge, attitudes, and beliefs about treatment; law and immigration; personal characteristics and adherence behaviour; side effects; and family, community, and household support. our interpretation of the themes across all studies produced a line-of-argument synthesis describing how four major factors interact to affect adherence to tb treatment: structural factors, including poverty and gender discrimination; the social context; health service factors; and personal factors. the findings of this study are limited by the quality and foci of the included studies. conclusions adherence to the long course of tb treatment is a complex, dynamic phenomenon with a wide range of factors impacting on treatment-taking behaviour. patients' adherence to their medication regimens was influenced by the interaction of a number of these factors. the findings of our review could help inform the development of patient-centred interventions and of interventions to address structural barriers to treatment adherence.",0
"the generation and efficient maintenance of antigen-specific memory t cells is essential for long-lasting immunological protection. in this study, we examined the role of interleukin (il)-15 in the generation and maintenance of virus-specific memory cd8 t cells using mice deficient in either il-15 or the il-15 receptor alpha chain. both cytokine- and receptor-deficient mice made potent primary cd8 t cell responses to infection with lymphocytic choriomeningitis virus (lcmv), effectively cleared the virus and generated a pool of antigen-specific memory cd8 t cells that were phenotypically and functionally similar to memory cd8 t cells present in il-15(+/+) mice. however, longitudinal analysis revealed a slow attrition of virus-specific memory cd8 t cells in the absence of il-15 signals. this loss of cd8 t cells was due to a severe defect in the proliferative renewal of antigen-specific memory cd8 t cells in il-15(-/-) mice. taken together, these results show that il-15 is not essential for the generation of memory cd8 t cells, but is required for homeostatic proliferation to maintain populations of memory cells over long periods of time.",0
"rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (wgs) for these purposes poses significant challenges. here we present srst2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (mlst) from wgs data. using >900 genomes from common pathogens, we show srst2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. we include validation of srst2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. in the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, srst2 represents a powerful tool for rapidly extracting clinically useful information from raw wgs data. source code is available from",0
"introduction the lack of a standard definition for acute kidney injury has resulted in a large variation in the reported incidence and associated mortality. rifle, a newly developed international consensus classification for acute kidney injury, defines three grades of severity--risk (class r), injury (class i) and failure (class f)--but has not yet been evaluated in a clinical series. methods we performed a retrospective cohort study, in seven intensive care units in a single tertiary care academic center, on 5,383 patients admitted during a one year period (1 july 2000-30 june 2001). results acute kidney injury occurred in 67% of intensive care unit admissions, with maximum rifle class r, class i and class f in 12%, 27% and 28%, respectively. of the 1,510 patients (28%) that reached a level of risk, 840 (56%) progressed. patients with maximum rifle class r, class i and class f had hospital mortality rates of 8.8%, 11.4% and 26.3%, respectively, compared with 5.5% for patients without acute kidney injury. additionally, acute kidney injury (hazard ratio, 1.7; 95% confidence interval, 1.28-2.13; p conclusion in this general intensive care unit population, acute kidney 'risk, injury, failure', as defined by the newly developed rifle classification, is associated with increased hospital mortality and resource use. patients with rifle class r are indeed at high risk of progression to class i or class f. patients with rifle class i or class f incur a significantly increased length of stay and an increased risk of inhospital mortality compared with those who do not progress past class r or those who never develop acute kidney injury, even after adjusting for baseline severity of illness, case mix, race, gender and age.",0
"removal of apoptotic cells is essential for maintenance of tissue homeostasis, organogenesis, remodeling, development, and maintenance of the immune system, protection against neoplasia, and resolution of inflammation. the mechanisms of this removal involve recognition of the apoptotic cell surface and initiation of phagocytic uptake into a variety of cell types. here we provide evidence that c1q and mannose binding lectin (mbl), a member of the collectin family of proteins, bind to apoptotic cells and stimulate ingestion of these by ligation on the phagocyte surface of the multifunctional protein, calreticulin (also known as the cc1qr), which in turn is bound to the endocytic receptor protein cd91, also known as the alpha-2-macroglobulin receptor. use of these proteins provides another example of apoptotic cell clearance mediated by pattern recognition molecules of the innate immune system. ingestion of the apoptotic cells through calreticulin/cd91 stimulation is further shown to involve the process of macropinocytosis, implicated as a primitive and relatively nonselective uptake mechanism for c1q- and mbl-enhanced engulfment of whole, intact apoptotic cells, as well as cell debris and foreign organisms to which these molecules may bind.",0
"trends in incidence or mortality rates over a specified time interval are usually described by the conventional annual per cent change (capc), under the assumption of a constant rate of change. when this assumption does not hold over the entire time interval, the trend may be characterized using the annual per cent changes from segmented analysis (sapcs). this approach assumes that the change in rates is constant over each time partition defined by the transition points, but varies among different time partitions. different groups (e.g. racial subgroups), however, may have different transition points and thus different time partitions over which they have constant rates of change, making comparison of sapcs problematic across groups over a common time interval of interest (e.g. the past 10 years). we propose a new measure, the average annual per cent change (aapc), which uses sapcs to summarize and compare trends for a specific time period. the advantage of the proposed aapc is that it takes into account the trend transitions, whereas capc does not and can lead to erroneous conclusions. in addition, when the trend is constant over the entire time interval of interest, the aapc has the advantage of reducing to both capc and sapc. moreover, because the estimated aapc is based on the segmented analysis over the entire data series, any selected subinterval within a single time partition will yield the same aapc estimate--that is it will be equal to the estimated sapc for that time partition. the capc, however, is re-estimated using data only from that selected subinterval; thus, its estimate may be sensitive to the subinterval selected. the aapc estimation has been incorporated into the segmented regression (free) software joinpoint, which is used by many registries throughout the world for characterizing trends in cancer rates.",0
"periodontitis is a common chronic inflammatory disease characterised by destruction of the supporting structures of the teeth (the periodontal ligament and alveolar bone). it is highly prevalent (severe periodontitis affects 10-15% of adults) and has multiple negative impacts on quality of life. epidemiological data confirm that diabetes is a major risk factor for periodontitis; susceptibility to periodontitis is increased by approximately threefold in people with diabetes. there is a clear relationship between degree of hyperglycaemia and severity of periodontitis. the mechanisms that underpin the links between these two conditions are not completely understood, but involve aspects of immune functioning, neutrophil activity, and cytokine biology. there is emerging evidence to support the existence of a two-way relationship between diabetes and periodontitis, with diabetes increasing the risk for periodontitis, and periodontal inflammation negatively affecting glycaemic control. incidences of macroalbuminuria and end-stage renal disease are increased twofold and threefold, respectively, in diabetic individuals who also have severe periodontitis compared to diabetic individuals without severe periodontitis. furthermore, the risk of cardiorenal mortality (ischaemic heart disease and diabetic nephropathy combined) is three times higher in diabetic people with severe periodontitis than in diabetic people without severe periodontitis. treatment of periodontitis is associated with hba(1c) reductions of approximately 0.4%. oral and periodontal health should be promoted as integral components of diabetes management.",0
"kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic dna sequences. previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. using exact alignment of k-mers, kraken achieves classification accuracy comparable to the fastest blast program. in its fastest mode, kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than megablast and 11 times faster than the abundance estimation program metaphlan. kraken is available at",0
"background during the covid-19 pandemic general medical complications have received the most attention, whereas only few studies address the potential direct effect on mental health of sars-cov-2 and the neurotropic potential. furthermore, the indirect effects of the pandemic on general mental health are of increasing concern, particularly since the sars-cov-1 epidemic (2002-2003) was associated with psychiatric complications. methods we systematically searched the database pubmed including studies measuring psychiatric symptoms or morbidities associated with covid-19 among infected patients and among none infected groups the latter divided in psychiatric patients, health care workers and non-health care workers. results a total of 43 studies were included. out of these, only two studies evaluated patients with confirmed covid-19 infection, whereas 41 evaluated the indirect effect of the pandemic (2 on patients with preexisting psychiatric disorders, 20 on medical health care workers, and 19 on the general public). 18 of the studies were case-control studies/compared to norm, while 25 of the studies had no control groups. the two studies investigating covid-19 patients found a high level of post-traumatic stress symptoms (ptss) (96.2%) and significantly higher level of depressive symptoms (p = 0.016). patients with preexisting psychiatric disorders reported worsening of psychiatric symptoms. studies investigating health care workers found increased depression/depressive symptoms, anxiety, psychological distress and poor sleep quality. studies of the general public revealed lower psychological well-being and higher scores of anxiety and depression compared to before covid-19, while no difference when comparing these symptoms in the initial phase of the outbreak to four weeks later. a variety of factors were associated with higher risk of psychiatric symptoms and/or low psychological well-being including female gender, poor-self-related health and relatives with covid-19. conclusion research evaluating the direct neuropsychiatric consequences and the indirect effects on mental health is highly needed to improve treatment, mental health care planning and for preventive measures during potential subsequent pandemics.",0
"as part of a world health organization-led effort to update the empirical evidence base for the leishmaniases, national experts provided leishmaniasis case data for the last 5 years and information regarding treatment and control in their respective countries and a comprehensive literature review was conducted covering publications on leishmaniasis in 98 countries and three territories (see 'leishmaniasis country profiles text s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17, s18, s19, s20, s21, s22, s23, s24, s25, s26, s27, s28, s29, s30, s31, s32, s33, s34, s35, s36, s37, s38, s39, s40, s41, s42, s43, s44, s45, s46, s47, s48, s49, s50, s51, s52, s53, s54, s55, s56, s57, s58, s59, s60, s61, s62, s63, s64, s65, s66, s67, s68, s69, s70, s71, s72, s73, s74, s75, s76, s77, s78, s79, s80, s81, s82, s83, s84, s85, s86, s87, s88, s89, s90, s91, s92, s93, s94, s95, s96, s97, s98, s99, s100, s101'). additional information was collated during meetings conducted at who regional level between 2007 and 2011. two questionnaires regarding epidemiology and drug access were completed by experts and national program managers. visceral and cutaneous leishmaniasis incidence ranges were estimated by country and epidemiological region based on reported incidence, underreporting rates if available, and the judgment of national and international experts. based on these estimates, approximately 0.2 to 0.4 cases and 0.7 to 1.2 million vl and cl cases, respectively, occur each year. more than 90% of global vl cases occur in six countries: india, bangladesh, sudan, south sudan, ethiopia and brazil. cutaneous leishmaniasis is more widely distributed, with about one-third of cases occurring in each of three epidemiological regions, the americas, the mediterranean basin, and western asia from the middle east to central asia. the ten countries with the highest estimated case counts, afghanistan, algeria, colombia, brazil, iran, syria, ethiopia, north sudan, costa rica and peru, together account for 70 to 75% of global estimated cl incidence. mortality data were extremely sparse and generally represent hospital-based deaths only. using an overall case-fatality rate of 10%, we reach a tentative estimate of 20,000 to 40,000 leishmaniasis deaths per year. although the information is very poor in a number of countries, this is the first in-depth exercise to better estimate the real impact of leishmaniasis. these data should help to define control strategies and reinforce leishmaniasis advocacy.",0
"typing of dna from 94 unrelated children with celiac disease (cd) with hla-dqa1 and -dqb1 allele-specific oligonucleotide probes revealed that all but one (i.e., 98.9%) may share a particular combination of a dqa1 and a dqb1 gene. these genes are arranged in cis position on the dr3dqw2 haplotype and in trans position in dr5dqw7/dr7dqw2 heterozygous individuals. thus, most cd patients may share the same cis- or trans-encoded hla-dq alpha/beta heterodimer.",0
"many unknowns exist about human immune responses to the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) virus. sars-cov-2-reactive cd4 + t cells have been reported in unexposed individuals, suggesting preexisting cross-reactive t cell memory in 20 to 50% of people. however, the source of those t cells has been speculative. using human blood samples derived before the sars-cov-2 virus was discovered in 2019, we mapped 142 t cell epitopes across the sars-cov-2 genome to facilitate precise interrogation of the sars-cov-2-specific cd4 + t cell repertoire. we demonstrate a range of preexisting memory cd4 + t cells that are cross-reactive with comparable affinity to sars-cov-2 and the common cold coronaviruses human coronavirus (hcov)-oc43, hcov-229e, hcov-nl63, and hcov-hku1. thus, variegated t cell memory to coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity observed in coronavirus disease 2019 (covid-19) disease.",0
"we demonstrate that all-trans retinoic acid (ra) induces foxp3(+) adaptive t regulatory cells (a-tregs) to acquire a gut-homing phenotype (alpha 4 beta 7(+) cc chemokine receptor 9(+)) and the capacity to home to the lamina propria of the small intestine. under conditions that favor the differentiation of a-tregs (transforming growth factor-beta1 and interleukin 2) in vitro, the inclusion of ra induces nearly all activated cd4(+) t cells to express foxp3 and greatly increases the accumulation of these cells. in the absence of ra, a-treg differentiation is abruptly impaired by proficient antigen presenting cells or through direct co-stimulation. in the presence of ra, a-treg generation occurs even in the presence of high levels of co-stimulation, with ra attenuating co-stimulation from interfering from foxp3 induction. the recognition that ra induces gut imprinting, together with our finding that it enhances a-treg conversion, differentiation, and expansion, indicates that ra production in vivo may drive both the imprinting and a-treg development in the face of overt inflammation.",0
"background improving the design and implementation of evidence-based practice depends on successful behaviour change interventions. this requires an appropriate method for characterising interventions and linking them to an analysis of the targeted behaviour. there exists a plethora of frameworks of behaviour change interventions, but it is not clear how well they serve this purpose. this paper evaluates these frameworks, and develops and evaluates a new framework aimed at overcoming their limitations. methods a systematic search of electronic databases and consultation with behaviour change experts were used to identify frameworks of behaviour change interventions. these were evaluated according to three criteria: comprehensiveness, coherence, and a clear link to an overarching model of behaviour. a new framework was developed to meet these criteria. the reliability with which it could be applied was examined in two domains of behaviour change: tobacco control and obesity. results nineteen frameworks were identified covering nine intervention functions and seven policy categories that could enable those interventions. none of the frameworks reviewed covered the full range of intervention functions or policies, and only a minority met the criteria of coherence or linkage to a model of behaviour. at the centre of a proposed new framework is a 'behaviour system' involving three essential conditions: capability, opportunity, and motivation (what we term the 'com-b system'). this forms the hub of a 'behaviour change wheel' (bcw) around which are positioned the nine intervention functions aimed at addressing deficits in one or more of these conditions; around this are placed seven categories of policy that could enable those interventions to occur. the bcw was used reliably to characterise interventions within the english department of health's 2010 tobacco control strategy and the national institute of health and clinical excellence's guidance on reducing obesity. conclusions interventions and policies to change behaviour can be usefully characterised by means of a bcw comprising: a 'behaviour system' at the hub, encircled by intervention functions and then by policy categories. research is needed to establish how far the bcw can lead to more efficient design of effective interventions.",0
"with the aim to provide a resource for functional and evolutionary study of plant transcription factors (tfs), we updated the plant tf database planttfdb to version 3.0 ( after refining the tf classification pipeline, we systematically identified 129 288 tfs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. besides the abundant annotation provided in the previous version, we generated more annotations for identified tfs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from uniprot, tair and ncbi generif, as well as references to provide clues for functional studies of tfs. to help identify evolutionary relationship among identified tfs, we assigned 69 450 tfs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for tfs within the same families or same orthologous groups, respectively. in addition, we set up a tf prediction server in this version for users to identify tfs from their own sequences.",0
"pseudomonas aeruginosa causes severe and persistent infections in immune compromised individuals and cystic fibrosis sufferers. the infection is hard to eradicate as p. aeruginosa has developed strong resistance to most conventional antibiotics. the problem is further compounded by the ability of the pathogen to form biofilm matrix, which provides bacterial cells a protected environment withstanding various stresses including antibiotics. quorum sensing (qs), a cell density-based intercellular communication system, which plays a key role in regulation of the bacterial virulence and biofilm formation, could be a promising target for developing new strategies against p. aeruginosa infection. the qs network of p. aeruginosa is organized in a multi-layered hierarchy consisting of at least four interconnected signaling mechanisms. evidence is accumulating that the qs regulatory network not only responds to bacterial population changes but also could react to environmental stress cues. this plasticity should be taken into consideration during exploration and development of anti-qs therapeutics.",0
"drosophila olfactory sensory neurons (osns) each express two odorant receptors (ors): a divergent member of the or family and the highly conserved, broadly expressed receptor or83b. or83b is essential for olfaction in vivo and enhances or function in vitro, but the molecular mechanism by which it acts is unknown. here we demonstrate that or83b heterodimerizes with conventional ors early in the endomembrane system in osns, couples these complexes to the conserved ciliary trafficking pathway, and is essential to maintain the or/or83b complex within the sensory cilia, where odor signal transduction occurs. the or/or83b complex is necessary and sufficient to promote functional reconstitution of odor-evoked signaling in sensory neurons that normally respond only to carbon dioxide. unexpectedly, unlike all known vertebrate and nematode chemosensory receptors, we find that drosophila ors and or83b adopt a novel membrane topology with their n-termini and the most conserved loops in the cytoplasm. these loops mediate direct association of ors with or83b. our results reveal that or83b is a universal and integral part of the functional or in drosophila. this atypical heteromeric and topological design appears to be an insect-specific solution for odor recognition, making the or/or83b complex an attractive target for the development of highly selective insect repellents to disrupt olfactory-mediated host-seeking behaviors of insect disease vectors.",0
"droplet digital polymerase chain reaction (ddpcr) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddpcr measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. this novel ddpcr format offers a simple workflow capable of generating highly stable partitioning of dna molecules. in this study, we assessed key performance parameters of the ddpcr system. a linear ddpcr response to dna concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target dna copy number per ddpcr. analysis of simplex and duplex assays targeting two distinct loci in the lambda dna genome using the ddpcr platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital pcr (cdpcr). a relative expanded uncertainty under 5% was achieved for copy number concentration using ddpcr. this level of uncertainty is much lower than values typically observed for quantification of specific dna target sequences using currently commercially available real-time and digital cdpcr technologies.",0
"the novel coronavirus pneumonia, namely covid-19, has become a global public health problem. previous studies have found that air pollution is a risk factor for respiratory infection by carrying microorganisms and affecting body's immunity. this study aimed to explore the relationship between ambient air pollutants and the infection caused by the novel coronavirus. daily confirmed cases, air pollution concentration and meteorological variables in 120 cities were obtained from january 23, 2020 to february 29, 2020 in china. we applied a generalized additive model to investigate the associations of six air pollutants (pm 2.5 , pm 10 , so 2 , co, no 2 and o 3 ) with covid-19 confirmed cases. we observed significantly positive associations of pm 2.5 , pm 10 , no 2 and o 3 in the last two weeks with newly covid-19 confirmed cases. a 10-μg/m 3 increase (lag0-14) in pm 2.5 , pm 10 , no 2 , and o 3 was associated with a 2.24% (95% ci: 1.02 to 3.46), 1.76% (95% ci: 0.89 to 2.63), 6.94% (95% ci: 2.38 to 11.51), and 4.76% (95% ci: 1.99 to 7.52) increase in the daily counts of confirmed cases, respectively. however, a 10-μg/m 3 increase (lag0-14) in so 2 was associated with a 7.79% decrease (95% ci: -14.57 to -1.01) in covid-19 confirmed cases. our results indicate that there is a significant relationship between air pollution and covid-19 infection, which could partially explain the effect of national lockdown and provide implications for the control and prevention of this novel disease.",0
"situations in which rewards are unexpectedly obtained or withheld represent opportunities for new learning. often, this learning includes identifying cues that predict reward availability. unexpected rewards strongly activate midbrain dopamine neurons. this phasic signal is proposed to support learning about antecedent cues by signaling discrepancies between actual and expected outcomes, termed a reward prediction error. however, it is unknown whether dopamine neuron prediction error signaling and cue-reward learning are causally linked. to test this hypothesis, we manipulated dopamine neuron activity in rats in two behavioral procedures, associative blocking and extinction, that illustrate the essential function of prediction errors in learning. we observed that optogenetic activation of dopamine neurons concurrent with reward delivery, mimicking a prediction error, was sufficient to cause long-lasting increases in cue-elicited reward-seeking behavior. our findings establish a causal role for temporally precise dopamine neuron signaling in cue-reward learning, bridging a critical gap between experimental evidence and influential theoretical frameworks.",0
"purpose a classification for primary and incisional abdominal wall hernias is needed to allow comparison of publications and future studies on these hernias. it is important to know whether the populations described in different studies are comparable. methods several members of the ehs board and some invitees gathered for 2 days to discuss the development of an ehs classification for primary and incisional abdominal wall hernias. results to distinguish primary and incisional abdominal wall hernias, a separate classification based on localisation and size as the major risk factors was proposed. further data are needed to define the optimal size variable for classification of incisional hernias in order to distinguish subgroups with differences in outcome. conclusions a classification for primary abdominal wall hernias and a division into subgroups for incisional abdominal wall hernias, concerning the localisation of the hernia, was formulated.",0
"in this paper we review the associations between maternal and child undernutrition with human capital and risk of adult diseases in low-income and middle-income countries. we analysed data from five long-standing prospective cohort studies from brazil, guatemala, india, the philippines, and south africa and noted that indices of maternal and child undernutrition (maternal height, birthweight, intrauterine growth restriction, and weight, height, and body-mass index at 2 years according to the new who growth standards) were related to adult outcomes (height, schooling, income or assets, offspring birthweight, body-mass index, glucose concentrations, blood pressure). we undertook systematic reviews of studies from low-income and middle-income countries for these outcomes and for indicators related to blood lipids, cardiovascular disease, lung and immune function, cancers, osteoporosis, and mental illness. undernutrition was strongly associated, both in the review of published work and in new analyses, with shorter adult height, less schooling, reduced economic productivity, and--for women--lower offspring birthweight. associations with adult disease indicators were not so clear-cut. increased size at birth and in childhood were positively associated with adult body-mass index and to a lesser extent with blood pressure values, but not with blood glucose concentrations. in our new analyses and in published work, lower birthweight and undernutrition in childhood were risk factors for high glucose concentrations, blood pressure, and harmful lipid profiles once adult body-mass index and height were adjusted for, suggesting that rapid postnatal weight gain--especially after infancy--is linked to these conditions. the review of published works indicates that there is insufficient information about long-term changes in immune function, blood lipids, or osteoporosis indicators. birthweight is positively associated with lung function and with the incidence of some cancers, and undernutrition could be associated with mental illness. we noted that height-for-age at 2 years was the best predictor of human capital and that undernutrition is associated with lower human capital. we conclude that damage suffered in early life leads to permanent impairment, and might also affect future generations. its prevention will probably bring about important health, educational, and economic benefits. chronic diseases are especially common in undernourished children who experience rapid weight gain after infancy.",0
"molecular replacement (mr) generally becomes more difficult as the number of components in the asymmetric unit requiring separate mr models (i.e. the dimensionality of the search) increases. when the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. maximum-likelihood mr functions enable complex asymmetric units to be built up from individual components with a ;tree search with pruning' approach. this method, as implemented in the automated search procedure of the program phaser, has been very successful in solving many previously intractable mr problems. however, there are a number of cases in which the automated search procedure of phaser is suboptimal or encounters difficulties. these include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying b factors. two case studies are presented to illustrate how phaser can be used to best advantage in the standard ;automated mr' mode and two case studies are used to show how to modify the automated search strategy for problematic cases.",0
"the ongoing pandemic spread of a new human coronavirus, sars-cov-2, which is associated with severe pneumonia/disease (covid-19), has resulted in the generation of tens of thousands of virus genome sequences. the rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of sars-cov-2. here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. by focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of sars-cov-2.",0
"peripheral blood neutrophils form highly decondensed chromatin structures, termed neutrophil extracellular traps (nets), that have been implicated in innate immune response to bacterial infection. neutrophils express high levels of peptidylarginine deiminase 4 (pad4), which catalyzes histone citrullination. however, whether pad4 or histone citrullination plays a role in chromatin structure in neutrophils is unclear. in this study, we show that the hypercitrullination of histones by pad4 mediates chromatin decondensation. histone hypercitrullination is detected on highly decondensed chromatin in hl-60 granulocytes and blood neutrophils. the inhibition of pad4 decreases histone hypercitrullination and the formation of net-like structures, whereas pad4 treatment of hl-60 cells facilitates these processes. the loss of heterochromatin and multilobular nuclear structures is detected in hl-60 granulocytes after pad4 activation. importantly, citrullination of biochemically defined avian nucleosome arrays inhibits their compaction by the linker histone h5 to form higher order chromatin structures. together, these results suggest that histone hypercitrullination has important functions in chromatin decondensation in granulocytes/neutrophils.",0
"background greater use of antibiotics during the past 50 years has exerted selective pressure on susceptible bacteria and may have favoured the survival of resistant strains. existing information on antibiotic resistance patterns from pathogens circulating among community-based patients is substantially less than from hospitalized patients on whom guidelines are often based. we therefore chose to assess the relationship between the antibiotic resistance pattern of bacteria circulating in the community and the consumption of antibiotics in the community. methods both gray literature and published scientific literature in english and other european languages was examined. multiple regression analysis was used to analyse whether studies found a positive relationship between antibiotic consumption and resistance. a subsequent meta-analysis and meta-regression was conducted for studies for which a common effect size measure (odds ratio) could be calculated. results electronic searches identified 974 studies but only 243 studies were considered eligible for inclusion by the two independent reviewers who extracted the data. a binomial test revealed a positive relationship between antibiotic consumption and resistance (p conclusions using a large set of studies we found that antibiotic consumption is associated with the development of antibiotic resistance. a subsequent meta-analysis, with a subsample of the studies, generated several significant predictors. countries in southern europe produced a stronger link between consumption and resistance than other regions so efforts at reducing antibiotic consumption may need to be strengthened in this area. increased consumption of antibiotics may not only produce greater resistance at the individual patient level but may also produce greater resistance at the community, country, and regional levels, which can harm individual patients.",0
"while interactions between cd28 and members of the b7 family costimulate and enhance t cell responses, recent evidence indicates that the cd28 homologue ctla-4 plays a downregulatory role. the mechanism by which this occurs is not clear, but it has been suggested that ctla-4 terminates ongoing responses of activated t cells, perhaps by induction of apoptosis. here we demonstrate that ctla-4 engagement by antibody cross-linking or binding to b7 inhibits proliferation and accumulation of the primary t cell growth factor, il-2, by cells stimulated with anti-cd3 and anti-cd28. this inhibition is not a result of enhanced cell death. rather it appears to result from restriction of transition from the g1 to the s phase of the cell cycle. our observation that upregulation of both the il-2r alpha chain and the cd69 activation antigen are inhibited by ctla-4 engagement supplies further evidence that ctla-4 restricts the progression of t cells to an activated state. together this data demonstrates that ctla-4 can regulate t cell activation in the absence of induction of apoptotic cell death.",0
"background effective prevention is needed to combat the worldwide epidemic of type 2 diabetes. we investigated the long-term extent of beneficial effects of lifestyle intervention and metformin on diabetes prevention, originally shown during the 3-year diabetes prevention program (dpp), and assessed whether these interventions reduced diabetes-associated microvascular complications. methods the dpp (1996-2001) was a randomised trial comparing an intensive lifestyle intervention or masked metformin with placebo in a cohort selected to be at very high risk of developing diabetes. all participants were offered lifestyle training at the end of the dpp. 2776 (88%) of the surviving dpp cohort were followed up in the dpp outcomes study (dppos, sept 1, 2002, to jan 2, 2014) and analysed by intention to treat on the basis of their original dpp assignment. during dppos, the original lifestyle intervention group was offered lifestyle reinforcement semi-annually and the metformin group received unmasked metformin. the primary outcomes were the development of diabetes and the prevalence of microvascular disease. for the assessment of microvascular disease, we used an aggregate microvascular outcome, composed of nephropathy, retinopathy, and neuropathy. findings during a mean follow-up of 15 years, diabetes incidence was reduced by 27% in the lifestyle intervention group (hazard ratio 0·73, 95% ci 0·65-0·83; p interpretation lifestyle intervention or metformin significantly reduced diabetes development over 15 years. there were no overall differences in the aggregate microvascular outcome between treatment groups; however, those who did not develop diabetes had a lower prevalence of microvascular complications than those who did develop diabetes. this result supports the importance of diabetes prevention. funding national institute of diabetes and digestive and kidney diseases.",0
"the hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. we reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. we confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. however, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.",0
"population isolates such as those in finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency 1,2 . finngen aims to study the genome and national health register data of 500,000 finnish individuals. given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, finngen is enriched for disease end points. here we analyse data from 224,737 participants from finngen and study 15 diseases that have previously been investigated in large genome-wide association studies (gwass). we also include meta-analyses of biobank data from estonia and the united kingdom. we identified 30 new associations, primarily low-frequency variants, enriched in the finnish population. a gwas of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (pws), p -11 ) at 2,496 (771 pws) independent loci with 807 (247 pws) end points. among these, fine-mapping implicated 148 (73 pws) coding variants associated with 83 (42 pws) end points. moreover, 91 (47 pws) had an allele frequency of <5% in non-finnish european individuals, of which 62 (32 pws) were enriched by more than twofold in finland. these findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.",0
"background the outbreak of 2019 novel coronavirus disease (covid-19) in wuhan, china, has spread rapidly worldwide. in the early stage, we encountered a small but meaningful number of patients who were unintentionally scheduled for elective surgeries during the incubation period of covid-19. we intended to describe their clinical characteristics and outcomes. methods we retrospectively analyzed the clinical data of 34 patients underwent elective surgeries during the incubation period of covid-19 at renmin hospital, zhongnan hospital, tongji hospital and central hospital in wuhan, from january 1 to february 5, 2020. findings of the 34 operative patients, the median age was 55 years (iqr, 43-63), and 20 (58·8%) patients were women. all patients developed covid-19 pneumonia shortly after surgery with abnormal findings on chest computed tomographic scans. common symptoms included fever (31 ), fatigue (25 ) and dry cough (18 ). 15 (44·1%) patients required admission to intensive care unit (icu) during disease progression, and 7 patients (20·5%) died after admission to icu. compared with non-icu patients, icu patients were older, were more likely to have underlying comorbidities, underwent more difficult surgeries, as well as more severe laboratory abnormalities (eg, hyperleukocytemia, lymphopenia). the most common complications in non-survivors included ards, shock, arrhythmia and acute cardiac injury. interpretation in this retrospective cohort study of 34 operative patients with confirmed covid-19, 15 (44·1%) patients needed icu care, and the mortality rate was 20·5%. funding national natural science foundation of china.",0
"frozen brain specimens from patients with multiple sclerosis (ms) and other neurologic diseases were analyzed using immunocytochemical techniques for the presence of tnf. in brain lesions in ms, and subacute sclerosing panencephalitis, tnf+ cells were demonstrated. at the lesion site in ms, tnf+ staining is associated with both astrocytes and macrophages. these observations were not made in alzheimer's disease or normal brain tissue. the presence of tnf in ms lesions suggests a significant role for cytokines and the immune response in disease progression.",0
"background it is widely claimed that racial and ethnic minorities, especially in the us, are less willing than non-minority individuals to participate in health research. yet, there is a paucity of empirical data to substantiate this claim. methods and findings we performed a comprehensive literature search to identify all published health research studies that report consent rates by race or ethnicity. we found 20 health research studies that reported consent rates by race or ethnicity. these 20 studies reported the enrollment decisions of over 70,000 individuals for a broad range of research, from interviews to drug treatment to surgical trials. eighteen of the twenty studies were single-site studies conducted exclusively in the us or multi-site studies where the majority of sites (i.e., at least 2/3) were in the us. of the remaining two studies, the concorde study was conducted at 74 sites in the united kingdom, ireland, and france, while the delta study was conducted at 152 sites in europe and 23 sites in australia and new zealand. for the three interview or non-intervention studies, african-americans had a nonsignificantly lower overall consent rate than non-hispanic whites (82.2% versus 83.5%; odds ratio = 0.92; 95% confidence interval 0.84-1.02). for these same three studies, hispanics had a nonsignificantly higher overall consent rate than non-hispanic whites (86.1% versus 83.5%; or = 1.37; 95% ci 0.94-1.98). for the ten clinical intervention studies, african-americans' overall consent rate was nonsignificantly higher than that of non-hispanic whites (45.3% versus 41.8%; or = 1.06; 95% ci 0.78-1.45). for these same ten studies, hispanics had a statistically significant higher overall consent rate than non-hispanic whites (55.9% versus 41.8%; or = 1.33; 95% ci 1.08-1.65). for the seven surgery trials, which report all minority groups together, minorities as a group had a nonsignificantly higher overall consent rate than non-hispanic whites (65.8% versus 47.8%; or = 1.26; 95% ci 0.89-1.77). given the preponderance of us sites, the vast majority of these individuals from minority groups were african-americans or hispanics from the us. conclusions we found very small differences in the willingness of minorities, most of whom were african-americans and hispanics in the us, to participate in health research compared to non-hispanic whites. these findings, based on the research enrollment decisions of over 70,000 individuals, the vast majority from the us, suggest that racial and ethnic minorities in the us are as willing as non-hispanic whites to participate in health research. hence, efforts to increase minority participation in health research should focus on ensuring access to health research for all groups, rather than changing minority attitudes.",0
"several methods for absolute structure refinement were tested using single-crystal x-ray diffraction data collected using cu kα radiation for 23 crystals with no element heavier than oxygen: conventional refinement using an inversion twin model, estimation using intensity quotients in shelxl2012, estimation using bayesian methods in platon, estimation using restraints consisting of numerical intensity differences in crystals and estimation using differences and quotients in topas-academic where both quantities were coded in terms of other structural parameters and implemented as restraints. the conventional refinement approach yielded accurate values of the flack parameter, but with standard uncertainties ranging from 0.15 to 0.77. the other methods also yielded accurate values of the flack parameter, but with much higher precision. absolute structure was established in all cases, even for a hydrocarbon. the procedures in which restraints are coded explicitly in terms of other structural parameters enable the flack parameter to correlate with these other parameters, so that it is determined along with those parameters during refinement.",0
"an expert working group of the european association for palliative care has revised and updated its guidelines on the use of morphine in the management of cancer pain. the revised recommendations presented here give guidance on the use of morphine and the alternative strong opioid analgesics which have been introduced in many parts of the world in recent years. practical strategies for dealing with difficult situations are described presenting a consensus view where supporting evidence is lacking. the strength of the evidence on which each recommendation is based is indicated.",0
"recent progress in massively parallel sequencing platforms has enabled genome-wide characterization of dna-associated proteins using the combination of chromatin immunoprecipitation and sequencing (chip-seq). although a variety of methods exist for analysis of the established alternative chip microarray (chip-chip), few approaches have been described for processing chip-seq data. to fill this gap, we propose an analysis pipeline specifically designed to detect protein-binding positions with high accuracy. using previously reported data sets for three transcription factors, we illustrate methods for improving tag alignment and correcting for background signals. we compare the sensitivity and spatial precision of three peak detection algorithms with published methods, demonstrating gains in spatial precision when an asymmetric distribution of tags on positive and negative strands is considered. we also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.",0
"background the results of randomized controlled trials (rcts) on time-to-event outcomes that are usually reported are median time to events and cox hazard ratio. these do not constitute the sufficient statistics required for meta-analysis or cost-effectiveness analysis, and their use in secondary analyses requires strong assumptions that may not have been adequately tested. in order to enhance the quality of secondary data analyses, we propose a method which derives from the published kaplan meier survival curves a close approximation to the original individual patient time-to-event data from which they were generated. methods we develop an algorithm that maps from digitised curves back to km data by finding numerical solutions to the inverted km equations, using where available information on number of events and numbers at risk. the reproducibility and accuracy of survival probabilities, median survival times and hazard ratios based on reconstructed km data was assessed by comparing published statistics (survival probabilities, medians and hazard ratios) with statistics based on repeated reconstructions by multiple observers. results the validation exercise established there was no material systematic error and that there was a high degree of reproducibility for all statistics. accuracy was excellent for survival probabilities and medians, for hazard ratios reasonable accuracy can only be obtained if at least numbers at risk or total number of events are reported. conclusion the algorithm is a reliable tool for meta-analysis and cost-effectiveness analyses of rcts reporting time-to-event data. it is recommended that all rcts should report information on numbers at risk and total number of events alongside km curves.",0
"global climate change and associated adverse abiotic stress conditions, such as drought, salinity, heavy metals, waterlogging, extreme temperatures, oxygen deprivation, etc., greatly influence plant growth and development, ultimately affecting crop yield and quality, as well as agricultural sustainability in general. plant cells produce oxygen radicals and their derivatives, so-called reactive oxygen species (ros), during various processes associated with abiotic stress. moreover, the generation of ros is a fundamental process in higher plants and employs to transmit cellular signaling information in response to the changing environmental conditions. one of the most crucial consequences of abiotic stress is the disturbance of the equilibrium between the generation of ros and antioxidant defense systems triggering the excessive accumulation of ros and inducing oxidative stress in plants. notably, the equilibrium between the detoxification and generation of ros is maintained by both enzymatic and nonenzymatic antioxidant defense systems under harsh environmental stresses. although this field of research has attracted massive interest, it largely remains unexplored, and our understanding of ros signaling remains poorly understood. in this review, we have documented the recent advancement illustrating the harmful effects of ros, antioxidant defense system involved in ros detoxification under different abiotic stresses, and molecular cross-talk with other important signal molecules such as reactive nitrogen, sulfur, and carbonyl species. in addition, state-of-the-art molecular approaches of ros-mediated improvement in plant antioxidant defense during the acclimation process against abiotic stresses have also been discussed.",0
"objective to examine the clinical evidence reporting the prevalence of sarcopenia and the effect of nutrition and exercise interventions from studies using the consensus definition of sarcopenia proposed by the european working group on sarcopenia in older people (ewgsop). methods pubmed and dialog databases were searched (january 2000-october 2013) using pre-defined search terms. prevalence studies and intervention studies investigating muscle mass plus strength or function outcome measures using the ewgsop definition of sarcopenia, in well-defined populations of adults aged ≥50 years were selected. results prevalence of sarcopenia was, with regional and age-related variations, 1-29% in community-dwelling populations, 14-33% in long-term care populations and 10% in the only acute hospital-care population examined. moderate quality evidence suggests that exercise interventions improve muscle strength and physical performance. the results of nutrition interventions are equivocal due to the low number of studies and heterogeneous study design. essential amino acid (eaa) supplements, including ∼2.5 g of leucine, and β-hydroxy β-methylbutyric acid (hmb) supplements, show some effects in improving muscle mass and function parameters. protein supplements have not shown consistent benefits on muscle mass and function. conclusion prevalence of sarcopenia is substantial in most geriatric settings. well-designed, standardised studies evaluating exercise or nutrition interventions are needed before treatment guidelines can be developed. physicians should screen for sarcopenia in both community and geriatric settings, with diagnosis based on muscle mass and function. supervised resistance exercise is recommended for individuals with sarcopenia. eaa (with leucine) and hmb may improve muscle outcomes.",0
"motivation biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. with the progress in natural language processing (nlp), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. however, directly applying the advancements in nlp to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. in this article, we investigate how the recently introduced pre-trained language model bert can be adapted for biomedical corpora. results we introduce biobert (bidirectional encoder representations from transformers for biomedical text mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. with almost the same architecture across tasks, biobert largely outperforms bert and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. while bert obtains performance comparable to that of previous state-of-the-art models, biobert significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% f1 score improvement), biomedical relation extraction (2.80% f1 score improvement) and biomedical question answering (12.24% mrr improvement). our analysis results show that pre-training bert on biomedical corpora helps it to understand complex biomedical texts. availability and implementation we make the pre-trained weights of biobert freely available at and the source code for fine-tuning biobert available at",0
"background bisulfite sequencing is a powerful technique to study dna cytosine methylation. bisulfite treatment followed by pcr amplification specifically converts unmethylated cytosines to thymine. coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. however, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple cpg heterogeneous methylation. results we developed an efficient bisulfite reads mapping algorithm bsmap to address the above issues. bsmap combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. compared with existing bisulfite mapping approaches, bsmap is faster, more sensitive and more flexible. conclusion bsmap is the first general-purpose bisulfite mapping software. it is able to map high-throughput bisulfite reads at whole genome level with feasible memory and cpu usage. it is freely available under gpl v3 license at",0
"mendelian randomisation analyses use genetic variants as instrumental variables (ivs) to estimate causal effects of modifiable risk factors on disease outcomes. genetic variants typically explain a small proportion of the variability in risk factors; hence mendelian randomisation analyses can require large sample sizes. however, an increasing number of genetic variants have been found to be robustly associated with disease-related outcomes in genome-wide association studies. use of multiple instruments can improve the precision of iv estimates, and also permit examination of underlying iv assumptions. we discuss the use of multiple genetic variants in mendelian randomisation analyses with continuous outcome variables where all relationships are assumed to be linear. we describe possible violations of iv assumptions, and how multiple instrument analyses can be used to identify them. we present an example using four adiposity-associated genetic variants as ivs for the causal effect of fat mass on bone density, using data on 5509 children enrolled in the alspac birth cohort study. we also use simulation studies to examine the effect of different sets of ivs on precision and bias. when each instrument independently explains variability in the risk factor, use of multiple instruments increases the precision of iv estimates. however, inclusion of weak instruments could increase finite sample bias. missing data on multiple genetic variants can diminish the available sample size, compared with single instrument analyses. in simulations with additive genotype-risk factor effects, iv estimates using a weighted allele score had similar properties to estimates using multiple instruments. under the correct conditions, multiple instrument analyses are a promising approach for mendelian randomisation studies. further research is required into multiple imputation methods to address missing data issues in iv estimation.",0
"the web-based software tool genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. genevestigator v3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and arabidopsis. in addition to improved querying features, genevestigator v3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. being a reference expression database with user-friendly tools, genevestigator v3 facilitates discovery research and hypothesis validation.",0
"the human brain is a complex system whose topological organization can be represented using connectomics. recent studies have shown that human connectomes can be constructed using various neuroimaging technologies and further characterized using sophisticated analytic strategies, such as graph theory. these methods reveal the intriguing topological architectures of human brain networks in healthy populations and explore the changes throughout normal development and aging and under various pathological conditions. however, given the huge complexity of this methodology, toolboxes for graph-based network visualization are still lacking. here, using matlab with a graphical user interface (gui), we developed a graph-theoretical network visualization toolbox, called brainnet viewer, to illustrate human connectomes as ball-and-stick models. within this toolbox, several combinations of defined files with connectome information can be loaded to display different combinations of brain surface, nodes and edges. in addition, display properties, such as the color and size of network elements or the layout of the figure, can be adjusted within a comprehensive but easy-to-use settings panel. moreover, brainnet viewer draws the brain surface, nodes and edges in sequence and displays brain networks in multiple views, as required by the user. the figure can be manipulated with certain interaction functions to display more detailed information. furthermore, the figures can be exported as commonly used image file formats or demonstration video for further use. brainnet viewer helps researchers to visualize brain networks in an easy, flexible and quick manner, and this software is freely available on the nitrc website (",0
"the immune system of patients infected by sars-cov-2 is severely impaired. detailed investigation of t cells and cytokine production in patients affected by covid-19 pneumonia are urgently required. here we show that, compared with healthy controls, covid-19 patients' t cell compartment displays several alterations involving naïve, central memory, effector memory and terminally differentiated cells, as well as regulatory t cells and pd1 + cd57 + exhausted t cells. significant alterations exist also in several lineage-specifying transcription factors and chemokine receptors. terminally differentiated t cells from patients proliferate less than those from healthy controls, whereas their mitochondria functionality is similar in cd4 + t cells from both groups. patients display significant increases of proinflammatory or anti-inflammatory cytokines, including t helper type-1 and type-2 cytokines, chemokines and galectins; their lymphocytes produce more tumor necrosis factor (tnf), interferon-γ, interleukin (il)-2 and il-17, with the last observation implying that blocking il-17 could provide a novel therapeutic strategy for covid-19.",0
"the anatomy of language has been investigated with pet or fmri for more than 20 years. here i attempt to provide an overview of the brain areas associated with heard speech, speech production and reading. the conclusions of many hundreds of studies were considered, grouped according to the type of processing, and reported in the order that they were published. many findings have been replicated time and time again leading to some consistent and undisputable conclusions. these are summarised in an anatomical model that indicates the location of the language areas and the most consistent functions that have been assigned to them. the implications for cognitive models of language processing are also considered. in particular, a distinction can be made between processes that are localized to specific structures (e.g. sensory and motor processing) and processes where specialisation arises in the distributed pattern of activation over many different areas that each participate in multiple functions. for example, phonological processing of heard speech is supported by the functional integration of auditory processing and articulation; and orthographic processing is supported by the functional integration of visual processing, articulation and semantics. future studies will undoubtedly be able to improve the spatial precision with which functional regions can be dissociated but the greatest challenge will be to understand how different brain regions interact with one another in their attempts to comprehend and produce language.",0
"background a quality assessment tool for diagnostic accuracy studies, named quadas, has recently been developed. although quadas has been used in several systematic reviews, it has not been formally validated. the objective was to evaluate the validity and usefulness of quadas. methods three reviewers independently rated the quality of 30 studies using quadas. we assessed the proportion of agreements between each reviewer and the final consensus rating. this was done for all quadas items combined and for each individual item. twenty reviewers who had used quadas in their reviews completed a short structured questionnaire on their experience of quadas. results over all items, the agreements between each reviewer and the final consensus rating were 91%, 90% and 85%. the results for individual quadas items varied between 50% and 100% with a median value of 90%. items related to uninterpretable test results and withdrawals led to the most disagreements. the feedback on the content of the tool was generally positive with only small numbers of reviewers reporting problems with coverage, ease of use, clarity of instructions and validity. conclusion major modifications to the content of quadas itself are not necessary. the evaluation highlighted particular difficulties in scoring the items on uninterpretable results and withdrawals. revised guidelines for scoring these items are proposed. it is essential that reviewers tailor guidelines for scoring items to their review, and ensure that all reviewers are clear on how to score studies. reviewers should consider whether all quadas items are relevant to their review, and whether additional quality items should be assessed as part of their review.",0
"protein structure homology modelling has become a routine technique to generate 3d models for proteins when experimental structures are not available. fully automated servers such as swiss-model with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. here, we describe the latest version of the swiss-model expert system for protein structure modelling. the swiss-model template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. the improved swiss-model pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. the accuracy of the models generated by swiss-model is continuously evaluated by the cameo system. the new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. in cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. swiss-model is available at",0
"the medial prefrontal cortex (mpfc) and especially anterior cingulate cortex is central to higher cognitive function and many clinical disorders, yet its basic function remains in dispute. various competing theories of mpfc have treated effects of errors, conflict, error likelihood, volatility and reward, using findings from neuroimaging and neurophysiology in humans and monkeys. no single theory has been able to reconcile and account for the variety of findings. here we show that a simple model based on standard learning rules can simulate and unify an unprecedented range of known effects in mpfc. the model reinterprets many known effects and suggests a new view of mpfc, as a region concerned with learning and predicting the likely outcomes of actions, whether good or bad. cognitive control at the neural level is then seen as a result of evaluating the probable and actual outcomes of one's actions.",0
"this paper describes various components of the macromolecular crystallographic refinement program refmac5, which is distributed as part of the ccp4 suite. refmac5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of sad/siras experimental diffraction data. to ensure chemical and structural integrity of the refined model, refmac5 offers several classes of restraints and choices of model parameterization. reliable models at resolutions at least as low as 4 å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local ncs restraints, `jelly-body' restraints and the use of novel long-range restraints on atomic displacement parameters (adps) based on the kullback-leibler divergence. refmac5 additionally offers tls parameterization and, when high-resolution data are available, fast refinement of anisotropic adps. refinement in the presence of twinning is performed in a fully automated fashion. refmac5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.",0
"background projections of future mortality and life expectancy are needed to plan for health and social services and pensions. our aim was to forecast national age-specific mortality and life expectancy using an approach that takes into account the uncertainty related to the choice of forecasting model. methods we developed an ensemble of 21 forecasting models, all of which probabilistically contributed towards the final projections. we applied this approach to project age-specific mortality to 2030 in 35 industrialised countries with high-quality vital statistics data. we used age-specific death rates to calculate life expectancy at birth and at age 65 years, and probability of dying before age 70 years, with life table methods. findings life expectancy is projected to increase in all 35 countries with a probability of at least 65% for women and 85% for men. there is a 90% probability that life expectancy at birth among south korean women in 2030 will be higher than 86·7 years, the same as the highest worldwide life expectancy in 2012, and a 57% probability that it will be higher than 90 years. projected female life expectancy in south korea is followed by those in france, spain, and japan. there is a greater than 95% probability that life expectancy at birth among men in south korea, australia, and switzerland will surpass 80 years in 2030, and a greater than 27% probability that it will surpass 85 years. of the countries studied, the usa, japan, sweden, greece, macedonia, and serbia have some of the lowest projected life expectancy gains for both men and women. the female life expectancy advantage over men is likely to shrink by 2030 in every country except mexico, where female life expectancy is predicted to increase more than male life expectancy, and in chile, france, and greece where the two sexes will see similar gains. more than half of the projected gains in life expectancy at birth in women will be due to enhanced longevity above age 65 years. interpretation there is more than a 50% probability that by 2030, national female life expectancy will break the 90 year barrier, a level that was deemed unattainable by some at the turn of the 21st century. our projections show continued increases in longevity, and the need for careful planning for health and social services and pensions. funding uk medical research council and us environmental protection agency.",0
"bone mineral density (bmd) is the most widely used predictor of fracture risk. we performed the largest meta-analysis to date on lumbar spine and femoral neck bmd, including 17 genome-wide association studies and 32,961 individuals of european and east asian ancestry. we tested the top bmd-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. we identified 56 loci (32 new) associated with bmd at genome-wide significance (p < 5 × 10(-8)). several of these factors cluster within the rank-rankl-opg, mesenchymal stem cell differentiation, endochondral ossification and wnt signaling pathways. however, we also discovered loci that were localized to genes not known to have a role in bone biology. fourteen bmd-associated loci were also associated with fracture risk (p < 5 × 10(-4), bonferroni corrected), of which six reached p < 5 × 10(-8), including at 18p11.21 (fam210a), 7q21.3 (slc25a13), 11q13.2 (lrp5), 4q22.1 (mepe), 2p16.2 (sptbn1) and 10q21.1 (dkk1). these findings shed light on the genetic architecture and pathophysiological mechanisms underlying bmd variation and fracture susceptibility.",0
"stigma is a well-documented barrier to health seeking behavior, engagement in care and adherence to treatment across a range of health conditions globally. in order to halt the stigmatization process and mitigate the harmful consequences of health-related stigma (i.e. stigma associated with health conditions), it is critical to have an explicit theoretical framework to guide intervention development, measurement, research, and policy. existing stigma frameworks typically focus on one health condition in isolation and often concentrate on the psychological pathways occurring among individuals. this tendency has encouraged a siloed approach to research on health-related stigmas, focusing on individuals, impeding both comparisons across stigmatized conditions and research on innovations to reduce health-related stigma and improve health outcomes. we propose the health stigma and discrimination framework, which is a global, crosscutting framework based on theory, research, and practice, and demonstrate its application to a range of health conditions, including leprosy, epilepsy, mental health, cancer, hiv, and obesity/overweight. we also discuss how stigma related to race, gender, sexual orientation, class, and occupation intersects with health-related stigmas, and examine how the framework can be used to enhance research, programming, and policy efforts. research and interventions inspired by a common framework will enable the field to identify similarities and differences in stigma processes across diseases and will amplify our collective ability to respond effectively and at-scale to a major driver of poor health outcomes globally.",0
"the aldehydes introduced in this paper and the more appropriate concentrations for their general use as fixatives are: 4 to 6.5 per cent glutaraldehyde, 4 per cent glyoxal, 12.5 per cent hydroxyadipaldehyde, 10 per cent crotonaldehyde, 5 per cent pyruvic aldehyde, 10 per cent acetaldehyde, and 5 per cent methacrolein. these were prepared as cacodylate- or phosphate-buffered solutions (0.1 to 0.2 m, ph 6.5 to 7.6) that, with the exception of glutaraldehyde, contained sucrose (0.22 to 0.55 m). after fixation of from 0.5 hour to 24 hours, the blocks were stored in cold (4 degrees c) buffer (0.1 m) plus sucrose (0.22 m). this material was used for enzyme histochemistry, for electron microscopy (both with and without a second fixation with 1 or 2 per cent osmium tetroxide) after epon embedding, and for the combination of the two techniques. after fixation in aldehyde, membranous differentiations of the cell were not apparent and the nuclear structure differed from that commonly observed with osmium tetroxide. a postfixation in osmium tetroxide, even after long periods of storage, developed an image that-notable in the case of glutaraldehyde-was largely indistinguishable from that of tissues fixed under optimal conditions with osmium tetroxide alone. aliesterase, acetylcholinesterase, alkaline phosphatase, acid phosphatase, 5-nucleotidase, adenosine triphosphatase, and dpnh and tpnh diaphorase activities were demonstrable histochemically after most of the fixatives. cytochrome oxidase, succinic dehydrogenase, and glucose-6-phosphatase were retained after hydroxyaldipaldehyde and, to a lesser extent, after glyoxal fixation. the final product of the activity of several of the above-mentioned enzymes was localized in relation to the fine structure. for this purpose the double fixation procedure was used, selecting in each case the appropriate aldehyde.",0
"zhou et al. (nature) and hoffmann et al. (cell) identify ace2 as a sars-cov-2 receptor, and the latter show its entry mechanism depends on cellular serine protease tmprss2. these results may explain proinflammatory cytokine release via the associated angiotestin ii pathway and a possible therapeutic target via the il-6-stat3 axis.",0
"development of functional nanoparticles can be encumbered by unanticipated material properties and biological events, which can affect nanoparticle effectiveness in complex, physiologically relevant systems. despite the advances in bottom-up nanoengineering and surface chemistry, reductionist functionalization approaches remain inadequate in replicating the complex interfaces present in nature and cannot avoid exposure of foreign materials. here we report on the preparation of polymeric nanoparticles enclosed in the plasma membrane of human platelets, which are a unique population of cellular fragments that adhere to a variety of disease-relevant substrates. the resulting nanoparticles possess a right-side-out unilamellar membrane coating functionalized with immunomodulatory and adhesion antigens associated with platelets. compared to uncoated particles, the platelet membrane-cloaked nanoparticles have reduced cellular uptake by macrophage-like cells and lack particle-induced complement activation in autologous human plasma. the cloaked nanoparticles also display platelet-mimicking properties such as selective adhesion to damaged human and rodent vasculatures as well as enhanced binding to platelet-adhering pathogens. in an experimental rat model of coronary restenosis and a mouse model of systemic bacterial infection, docetaxel and vancomycin, respectively, show enhanced therapeutic efficacy when delivered by the platelet-mimetic nanoparticles. the multifaceted biointerfacing enabled by the platelet membrane cloaking method provides a new approach in developing functional nanoparticles for disease-targeted delivery.",0
"mendelian randomization is the use of genetic instrumental variables to obtain causal inferences from observational data. two recent developments for combining information on multiple uncorrelated instrumental variables (ivs) into a single causal estimate are as follows: (i) allele scores, in which individual-level data on the ivs are aggregated into a univariate score, which is used as a single iv, and (ii) a summary statistic method, in which causal estimates calculated from each iv using summarized data are combined in an inverse-variance weighted meta-analysis. to avoid bias from weak instruments, unweighted and externally weighted allele scores have been recommended. here, we propose equivalent approaches using summarized data and also provide extensions of the methods for use with correlated ivs. we investigate the impact of different choices of weights on the bias and precision of estimates in simulation studies. we show that allele score estimates can be reproduced using summarized data on genetic associations with the risk factor and the outcome. estimates from the summary statistic method using external weights are biased towards the null when the weights are imprecisely estimated; in contrast, allele score estimates are unbiased. with equal or external weights, both methods provide appropriate tests of the null hypothesis of no causal effect even with large numbers of potentially weak instruments. we illustrate these methods using summarized data on the causal effect of low-density lipoprotein cholesterol on coronary heart disease risk. it is shown that a more precise causal estimate can be obtained using multiple genetic variants from a single gene region, even if the variants are correlated.",0
"misinterpretation and abuse of statistical tests, confidence intervals, and statistical power have been decried for decades, yet remain rampant. a key problem is that there are no interpretations of these concepts that are at once simple, intuitive, correct, and foolproof. instead, correct use and interpretation of these statistics requires an attention to detail which seems to tax the patience of working scientists. this high cognitive demand has led to an epidemic of shortcut definitions and interpretations that are simply wrong, sometimes disastrously so-and yet these misinterpretations dominate much of the scientific literature. in light of this problem, we provide definitions and a discussion of basic statistics that are more general and critical than typically found in traditional introductory expositions. our goal is to provide a resource for instructors, researchers, and consumers of statistics whose knowledge of statistical theory and technique may be limited but who wish to avoid and spot misinterpretations. we emphasize how violation of often unstated analysis protocols (such as selecting analyses for presentation based on the p values they produce) can lead to small p values even if the declared test hypothesis is correct, and can lead to large p values even if that hypothesis is incorrect. we then provide an explanatory list of 25 misinterpretations of p values, confidence intervals, and power. we conclude with guidelines for improving statistical interpretation and reporting.",0
"background class i major histocompatibility complex (mhc) molecules bind, and present to t cells, short peptides derived from intracellular processing of proteins. the peptide repertoire of a specific molecule is to a large extent determined by the molecular structure accommodating so-called main anchor positions of the presented peptide. these receptors are extremely polymorphic, and much of the polymorphism influences the peptide-binding repertoire. however, despite this polymorphism, class i molecules can be clustered into sets of molecules that bind largely overlapping peptide repertoires. almost a decade ago we introduced this concept of clustering human leukocyte antigen (hla) alleles and defined nine different groups, denominated as supertypes, on the basis of their main anchor specificity. the utility of this original supertype classification, as well several other subsequent arrangements derived by others, has been demonstrated in a large number of epitope identification studies. results following our original approach, in the present report we provide an updated classification of hla-a and -b class i alleles into supertypes. the present analysis incorporates the large amount of class i mhc binding data and sequence information that has become available in the last decade. as a result, over 80% of the 945 different hla-a and -b alleles examined to date can be assigned to one of the original nine supertypes. a few alleles are expected to be associated with repertoires that overlap multiple supertypes. interestingly, the current analysis did not identify any additional supertype specificities. conclusion as a result of this updated analysis, hla supertype associations have been defined for over 750 different hla-a and -b alleles. this information is expected to facilitate epitope identification and vaccine design studies, as well as investigations into disease association and correlates of immunity. in addition, the approach utilized has been made more transparent, allowing others to utilize the classification approach going forward.",0
"despite years of research and hundreds of reports on tumour markers in oncology, the number of markers that have emerged as clinically useful is pitifully small. often initially reported studies of a marker show great promise, but subsequent studies on the same or related markers yield inconsistent conclusions or stand in direct contradiction to the promising results. it is imperative that we attempt to understand the reasons that multiple studies of the same marker lead to differing conclusions. a variety of methodological problems have been cited to explain these discrepancies. unfortunately, many tumour marker studies have not been reported in a rigorous fashion, and published articles often lack sufficient information to allow adequate assessment of the quality of the study or the generalisability of the study results. the development of guidelines for the reporting of tumour marker studies was a major recommendation of the us national cancer institute and the european organisation for research and treatment of cancer (nci-eortc) first international meeting on cancer diagnostics in 2000. similar to the successful consort initiative for randomised trials and the stard statement for diagnostic studies, we suggest guidelines to provide relevant information about the study design, preplanned hypotheses, patient and specimen characteristics, assay methods, and statistical analysis methods. in addition, the guidelines suggest helpful presentations of data and important elements to include in discussions. the goal of these guidelines is to encourage transparent and complete reporting so that the relevant information will be available to others to help them to judge the usefulness of the data and understand the context in which the conclusions apply.",0
"metaboanalyst ( is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. it supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. first introduced in 2009, metaboanalyst has experienced more than a 50x growth in user traffic (>50 000 jobs processed each month). in order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. the result is metaboanalyst 3.0. by completely re-implementing the metaboanalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. in addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms.",0
"with mounting data on its accuracy and prognostic value, cardiovascular magnetic resonance (cmr) is becoming an increasingly important diagnostic tool with growing utility in clinical routine. given its versatility and wide range of quantitative parameters, however, agreement on specific standards for the interpretation and post-processing of cmr studies is required to ensure consistent quality and reproducibility of cmr reports. this document addresses this need by providing consensus recommendations developed by the task force for post processing of the society for cardiovascular mr (scmr). the aim of the task force is to recommend requirements and standards for image interpretation and post processing enabling qualitative and quantitative evaluation of cmr images. furthermore, pitfalls of cmr image analysis are discussed where appropriate.",0
"background the aim of the study was to evaluate if physical functions usually associated with a younger population were of importance for an older population, and to construct an outcome measure for hip osteoarthritis with improved responsiveness compared to the western ontario mcmaster osteoarthritis score (womac lk 3.0). methods a 40 item questionnaire (hip disability and osteoarthritis outcome score, hoos) was constructed to assess patient-relevant outcomes in five separate subscales (pain, symptoms, activity of daily living, sport and recreation function and hip related quality of life). the hoos contains all womac lk 3.0 questions in unchanged form. the hoos was distributed to 90 patients with primary hip osteoarthritis (mean age 71.5, range 49-85, 41 females) assigned for total hip replacement for osteoarthritis preoperatively and at six months follow-up. results the hoos met set criteria of validity and responsiveness. it was more responsive than womac regarding the subscales pain (srm 2.11 vs. 1.83) and other symptoms (srm 1.83 vs. 1.28). the responsiveness (srm) for the two added subscales sport and recreation and quality of life were 1.29 and 1.65, respectively. patients 66 years of age (range 67-85) (pain srm 2.60 vs. 1.97, other symptoms srm 3.0 vs. 1.60, activity of daily living srm 2.51 vs. 1.52, sport and recreation function srm 1.53 vs. 1.21 and hip related quality of life srm 1.95 vs. 1.57). conclusion the hoos 2.0 appears to be useful for the evaluation of patient-relevant outcome after thr and is more responsive than the womac lk 3.0. the added subscales sport and recreation function and hip related quality of life were highly responsive for this group of patients, with the responsiveness being highest for those younger than 66.",0
"development, differentiation and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of regulated transcriptional factors to their cognate genomic sites. the mechanism whereby a given regulatory factor selects a limited number of in vivo targets from a myriad of potential genomic binding sites is undetermined. here we show that up to 95% of de novo genomic binding by the glucocorticoid receptor, a paradigmatic ligand-activated transcription factor, is targeted to preexisting foci of accessible chromatin. factor binding invariably potentiates chromatin accessibility. cell-selective glucocorticoid receptor occupancy patterns appear to be comprehensively predetermined by cell-specific differences in baseline chromatin accessibility patterns, with secondary contributions from local sequence features. the results define a framework for understanding regulatory factor-genome interactions and provide a molecular basis for the tissue selectivity of steroid pharmaceuticals and other agents that intersect the living genome.",0
"background the influence of social relationships on morbidity is widely accepted, but the size of the risk to cardiovascular health is unclear. objective we undertook a systematic review and meta-analysis to investigate the association between loneliness or social isolation and incident coronary heart disease (chd) and stroke. methods sixteen electronic databases were systematically searched for longitudinal studies set in high-income countries and published up until may 2015. two independent reviewers screened studies for inclusion and extracted data. we assessed quality using a component approach and pooled data for analysis using random effects models. results of the 35 925 records retrieved, 23 papers met inclusion criteria for the narrative review. they reported data from 16 longitudinal datasets, for a total of 4628 chd and 3002 stroke events recorded over follow-up periods ranging from 3 to 21 years. reports of 11 chd studies and 8 stroke studies provided data suitable for meta-analysis. poor social relationships were associated with a 29% increase in risk of incident chd (pooled relative risk: 1.29, 95% ci 1.04 to 1.59) and a 32% increase in risk of stroke (pooled relative risk: 1.32, 95% ci 1.04 to 1.68). subgroup analyses did not identify any differences by gender. conclusions our findings suggest that deficiencies in social relationships are associated with an increased risk of developing chd and stroke. future studies are needed to investigate whether interventions targeting loneliness and social isolation can help to prevent two of the leading causes of death and disability in high-income countries. study registration number crd42014010225.",0
"the acronym eskape includes six nosocomial pathogens that exhibit multidrug resistance and virulence: enterococcus faecium, staphylococcus aureus, klebsiella pneumoniae, acinetobacter baumannii, pseudomonas aeruginosa , and enterobacter spp. persistent use of antibiotics has provoked the emergence of multidrug resistant (mdr) and extensively drug resistant (xdr) bacteria, which render even the most effective drugs ineffective. extended spectrum β-lactamase (esbl) and carbapenemase producing gram negative bacteria have emerged as an important therapeutic challenge. development of novel therapeutics to treat drug resistant infections, especially those caused by eskape pathogens is the need of the hour. alternative therapies such as use of antibiotics in combination or with adjuvants, bacteriophages, antimicrobial peptides, nanoparticles, and photodynamic light therapy are widely reported. many reviews published till date describe these therapies with respect to the various agents used, their dosage details and mechanism of action against mdr pathogens but very few have focused specifically on eskape. the objective of this review is to describe the alternative therapies reported to treat eskape infections, their advantages and limitations, potential application in vivo , and status in clinical trials. the review further highlights the importance of a combinatorial approach, wherein two or more therapies are used in combination in order to overcome their individual limitations, additional studies on which are warranted, before translating them into clinical practice. these advances could possibly give an alternate solution or extend the lifetime of current antimicrobials.",0
"objective to assess the relation between the level of habitual salt intake and stroke or total cardiovascular disease outcome. design systematic review and meta-analysis of prospective studies published 1966-2008. data sources medline (1966-2008), embase (from 1988), amed (from 1985), cinahl (from 1982), psychinfo (from 1985), and the cochrane library. review methods for each study, relative risks and 95% confidence intervals were extracted and pooled with a random effect model, weighting for the inverse of the variance. heterogeneity, publication bias, subgroup, and meta-regression analyses were performed. criteria for inclusion were prospective adult population study, assessment of salt intake as baseline exposure, assessment of either stroke or total cardiovascular disease as outcome, follow-up of at least three years, indication of number of participants exposed and number of events across different salt intake categories. results there were 19 independent cohort samples from 13 studies, with 177 025 participants (follow-up 3.5-19 years) and over 11 000 vascular events. higher salt intake was associated with greater risk of stroke (pooled relative risk 1.23, 95% confidence interval 1.06 to 1.43; p=0.007) and cardiovascular disease (1.14, 0.99 to 1.32; p=0.07), with no significant evidence of publication bias. for cardiovascular disease, sensitivity analysis showed that the exclusion of a single study led to a pooled estimate of 1.17 (1.02 to 1.34; p=0.02). the associations observed were greater the larger the difference in sodium intake and the longer the follow-up. conclusions high salt intake is associated with significantly increased risk of stroke and total cardiovascular disease. because of imprecision in measurement of salt intake, these effect sizes are likely to be underestimated. these results support the role of a substantial population reduction in salt intake for the prevention of cardiovascular disease.",0
"an analysis of the activity of compounds tested in pre-clinical in vivo and in vitro assays by the national cancer institute's developmental therapeutics program was performed. for 39 agents with both xenograft data and phase ii clinical trials results available, in vivo activity in a particular histology in a tumour model did not closely correlate with activity in the same human cancer histology, casting doubt on the correspondence of the pre-clinical models to clinical results. however, for compounds with in vivo activity in at least one-third of tested xenograft models, there was correlation with ultimate activity in at least some phase ii trials. thus, an efficient means of predicting activity in vivo models remains desirable for compounds with anti-proliferative activity in vitro. for 564 compounds tested in the hollow fibre assay which were also tested against in vivo tumour models, the likelihood of finding xenograft activity in at least one-third of the in vivo models tested rose with increasing intraperitoneal hollow fibre activity, from 8% for all compounds tested to 20% in agents with evidence of response in more than 6 intraperitoneal fibres (p< 0.0001). intraperitoneal hollow fibre activity was also found to be a better predictor of xenograft activity than either subcutaneous hollow fibre activity or intraperitoneal plus subcutaneous activity combined. since hollow fibre activity was a useful indicator of potential in vivo response, correlates with hollow fibre activity were examined for 2304 compounds tested in both the nci 60 cell line in vitro cancer drug screen and hollow fibre assay. a positive correlation was found for histologic selectivity between in vitro and hollow fibre responses. the most striking correlation was between potency in the 60 cell line screen and hollow fibre activity; 56% of compounds with mean 50% growth inhibition below 10(-7.5) m were active in more than 6 intraperitoneal fibres whereas only 4% of compounds with a potency of 10(-4) m achieved the same level of hollow fibre activity (p< 0.0001). structural parameters of the drugs analysed included compound molecular weight and hydrogen-bonding factors, both of which were found to be predictive of hollow fibre activity.",0
"summary the database for annotation, visualization and integrated discovery (david), which can be freely accessed at is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. it has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. however, the current web interface does not support programmatic access to david, and the uniform resource locator (url)-based application programming interface (api) has a limit on url size and is stateless in nature as it uses url request and response messages to communicate with the server, without keeping any state-related details. david-ws (web service) has been developed to automate user tasks by providing stateful web services to access david programmatically without the need for human interactions. availability the web service and sample clients (written in java, perl, python and matlab) are made freely available under the david license at",0
"unlabelled a fracture risk assessment tool (frax) is developed based on the use of clinical risk factors with or without bone mineral density tests applied to the uk. introduction the aim of this study was to apply an assessment tool for the prediction of fracture in men and women with the use of clinical risk factors (crfs) for fracture with and without the use of femoral neck bone mineral density (bmd). the clinical risk factors, identified from previous meta-analyses, comprised body mass index (bmi, as a continuous variable), a prior history of fracture, a parental history of hip fracture, use of oral glucocorticoids, rheumatoid arthritis and other secondary causes of osteoporosis, current smoking, and alcohol intake 3 or more units daily. methods four models were constructed to compute fracture probabilities based on the epidemiology of fracture in the uk. the models comprised the ten-year probability of hip fracture, with and without femoral neck bmd, and the ten-year probability of a major osteoporotic fracture, with and without bmd. for each model fracture and death hazards were computed as continuous functions. results each clinical risk factor contributed to fracture probability. in the absence of bmd, hip fracture probability in women with a fixed bmi (25 kg/m(2)) ranged from 0.2% at the age of 50 years for women without crf's to 22% at the age of 80 years with a parental history of hip fracture (approximately 100-fold range). in men, the probabilities were lower, as was the range (0.1 to 11% in the examples above). for a major osteoporotic fracture the probabilities ranged from 3.5% to 31% in women, and from 2.8% to 15% in men in the example above. the presence of one or more risk factors increased probabilities in an incremental manner. the differences in probabilities between men and women were comparable at any given t-score and age, except in the elderly where probabilities were higher in women than in men due to the higher mortality of the latter. conclusion the models provide a framework which enhances the assessment of fracture risk in both men and women by the integration of clinical risk factors alone and/or in combination with bmd.",0
"human disease associated with influenza a subtype h5n1 re-emerged in january, 2003, for the first time since an outbreak in hong kong in 1997. patients with h5n1 disease had unusually high serum concentrations of chemokines (eg, interferon induced protein-10 and monokine induced by interferon gamma ). taken together with a previous report that h5n1 influenza viruses induce large amounts of proinflammatory cytokines from macrophage cultures in vitro, our findings suggest that cytokine dysfunction contributes to the pathogenesis of h5n1 disease. development of vaccines against influenza a (h5n1) virus should be made a priority.",0
"erplab toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (erp) data in the matlab environment. erplab is closely integrated with eeglab, a popular open-source toolbox that provides many eeg preprocessing steps and an excellent user interface design. erplab adds to eeglab's eeg processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. erplab also provides robust tools for averaging eeg segments together to create averaged erps, for creating difference waves and other recombinations of erp waveforms through algebraic expressions, for filtering and re-referencing the averaged erps, for plotting erp waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. erplab's tools can be accessed either from an easy-to-learn graphical user interface or from matlab scripts, and a command history function makes it easy for users with no programming experience to write scripts. consequently, erplab provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex erp experiments. several forms of documentation are available, including a detailed user's guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.",0
"the obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. the disease is the result not only of several environmental risk factors, but also of genetic predisposition. to take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of sardinia. initial analysis suggested that several snps in the fto and pfkp genes were associated with increased bmi, hip circumference, and weight. within the fto gene, rs9930506 showed the strongest association with bmi (p = 8.6 x10(-7)), hip circumference (p = 3.4 x 10(-8)), and weight (p = 9.1 x 10(-7)). in sardinia, homozygotes for the rare ""g"" allele of this snp (minor allele frequency = 0.46) were 1.3 bmi units heavier than homozygotes for the common ""a"" allele. within the pfkp gene, rs6602024 showed very strong association with bmi (p = 4.9 x 10(-6)). homozygotes for the rare ""a"" allele of this snp (minor allele frequency = 0.12) were 1.8 bmi units heavier than homozygotes for the common ""g"" allele. to replicate our findings, we genotyped these two snps in the gennet study. in european americans (n = 1,496) and in hispanic americans (n = 839), we replicated significant association between rs9930506 in the fto gene and bmi (p-value for meta-analysis of european american and hispanic american follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). we did not replicate association between rs6602024 and obesity-related traits in the gennet sample, although we found that in european americans, hispanic americans, and african americans, homozygotes for the rare ""a"" allele were, on average, 1.0-3.0 bmi units heavier than homozygotes for the more common ""g"" allele. in summary, we have completed a whole genome-association scan for three obesity-related quantitative traits and report that common genetic variants in the fto gene are associated with substantial changes in bmi, hip circumference, and body weight. these changes could have a significant impact on the risk of obesity-related morbidity in the general population.",0
"since 2004 the european bioinformatics institute (embl-ebi) has provided access to a wide range of databases and analysis tools via web services interfaces. this comprises services to search across the databases available from the embl-ebi and to explore the network of cross-references present in the data (e.g. eb-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. fasta and ncbi blast), multiple sequence alignment (e.g. clustal omega and muscle), pairwise sequence alignment and protein functional analysis (e.g. interproscan and phobius). the rest/soap web services ( interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. to get users started using the web services, sample clients are provided covering a range of programming languages and popular web service tool kits, and a brief guide to web services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. users of the web services are informed of improvements and updates via a range of methods.",0
"we are at the beginning of a genomic revolution in which all known species are planned to be sequenced. accessing such data for comparative analyses is crucial in this new age of data-driven biology. here, we introduce an improved version of diamond that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard blastp.",0
"motivated by the rapid spread of coronavirus disease 2019 (covid-19) in mainland china, we use a global metapopulation disease transmission model to project the impact of travel limitations on the national and international spread of the epidemic. the model is calibrated on the basis of internationally reported cases and shows that, at the start of the travel ban from wuhan on 23 january 2020, most chinese cities had already received many infected travelers. the travel quarantine of wuhan delayed the overall epidemic progression by only 3 to 5 days in mainland china but had a more marked effect on the international scale, where case importations were reduced by nearly 80% until mid-february. modeling results also indicate that sustained 90% travel restrictions to and from mainland china only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community.",0
"the structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. a number of existing practical methods predict protonation equilibrium pk constants of macromolecules based upon their atomic resolution protein data bank (pdb) structures; the calculations are often performed within the framework of the continuum electrostatics model. unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort. our web server provides access to a tool that automates this process, allowing both experts and novices to quickly obtain estimates of pks as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates. protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified ph; the output is in the pqr (pdb + charges + radii) format. in addition, corresponding coordinate and topology files are generated in the format supported by the molecular modeling package amber. the server is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers; it can also be used as an educational tool in biochemistry courses.",0
"observational epidemiological studies are prone to confounding, reverse causation and various biases and have generated findings that have proved to be unreliable indicators of the causal effects of modifiable exposures on disease outcomes. mendelian randomization (mr) is a method that utilizes genetic variants that are robustly associated with such modifiable exposures to generate more reliable evidence regarding which interventions should produce health benefits. the approach is being widely applied, and various ways to strengthen inference given the known potential limitations of mr are now available. developments of mr, including two-sample mr, bidirectional mr, network mr, two-step mr, factorial mr and multiphenotype mr, are outlined in this review. the integration of genetic information into population-based epidemiological studies presents translational opportunities, which capitalize on the investment in genomic discovery research.",0
"polygenic scores have recently been used to summarise genetic effects among an ensemble of markers that do not individually achieve significance in a large-scale association study. markers are selected using an initial training sample and used to construct a score in an independent replication sample by forming the weighted sum of associated alleles within each subject. association between a trait and this composite score implies that a genetic signal is present among the selected markers, and the score can then be used for prediction of individual trait values. this approach has been used to obtain evidence of a genetic effect when no single markers are significant, to establish a common genetic basis for related disorders, and to construct risk prediction models. in some cases, however, the desired association or prediction has not been achieved. here, the power and predictive accuracy of a polygenic score are derived from a quantitative genetics model as a function of the sizes of the two samples, explained genetic variance, selection thresholds for including a marker in the score, and methods for weighting effect sizes in the score. expressions are derived for quantitative and discrete traits, the latter allowing for case/control sampling. a novel approach to estimating the variance explained by a marker panel is also proposed. it is shown that published studies with significant association of polygenic scores have been well powered, whereas those with negative results can be explained by low sample size. it is also shown that useful levels of prediction may only be approached when predictors are estimated from very large samples, up to an order of magnitude greater than currently available. therefore, polygenic scores currently have more utility for association testing than predicting complex traits, but prediction will become more feasible as sample sizes continue to grow.",0
"cancer has been characterized as a heterogeneous disease consisting of many different subtypes. the early diagnosis and prognosis of a cancer type have become a necessity in cancer research, as it can facilitate the subsequent clinical management of patients. the importance of classifying cancer patients into high or low risk groups has led many research teams, from the biomedical and the bioinformatics field, to study the application of machine learning (ml) methods. therefore, these techniques have been utilized as an aim to model the progression and treatment of cancerous conditions. in addition, the ability of ml tools to detect key features from complex datasets reveals their importance. a variety of these techniques, including artificial neural networks (anns), bayesian networks (bns), support vector machines (svms) and decision trees (dts) have been widely applied in cancer research for the development of predictive models, resulting in effective and accurate decision making. even though it is evident that the use of ml methods can improve our understanding of cancer progression, an appropriate level of validation is needed in order for these methods to be considered in the everyday clinical practice. in this work, we present a review of recent ml approaches employed in the modeling of cancer progression. the predictive models discussed here are based on various supervised ml techniques as well as on different input features and data samples. given the growing trend on the application of ml methods in cancer research, we present here the most recent publications that employ these techniques as an aim to model cancer risk or patient outcomes.",0
"background the true causes of the obesity epidemic are not well understood and there are few longitudinal population-based data published examining this issue. the objective of this analysis was to examine trends in occupational physical activity during the past 5 decades and explore how these trends relate to concurrent changes in body weight in the u.s. methodology/principal findings analysis of energy expenditure for occupations in u.s. private industry since 1960 using data from the u.s. bureau of labor statistics. mean body weight was derived from the u.s. national health and nutrition examination surveys (nhanes). in the early 1960's almost half the jobs in private industry in the u.s. required at least moderate intensity physical activity whereas now less than 20% demand this level of energy expenditure. since 1960 the estimated mean daily energy expenditure due to work related physical activity has dropped by more than 100 calories in both women and men. energy balance model predicted weights based on change in occupation-related daily energy expenditure since 1960 for each nhanes examination period closely matched the actual change in weight for 40-50 year old men and women. for example from 1960-62 to 2003-06 we estimated that the occupation-related daily energy expenditure decreased by 142 calories in men. given a baseline weight of 76.9 kg in 1960-02, we estimated that a 142 calories reduction would result in an increase in mean weight to 89.7 kg, which closely matched the mean nhanes weight of 91.8 kg in 2003-06. the results were similar for women. conclusion over the last 50 years in the u.s. we estimate that daily occupation-related energy expenditure has decreased by more than 100 calories, and this reduction in energy expenditure accounts for a significant portion of the increase in mean u.s. body weights for women and men.",0
"in epithelial tissues, the lineage relationship between normal progenitor cells and cell type(s) of origin for cancer has been poorly understood. here we show that a known regulator of prostate epithelial differentiation, the homeobox gene nkx3-1, marks a stem cell population that functions during prostate regeneration. genetic lineage-marking demonstrates that rare luminal cells that express nkx3-1 in the absence of testicular androgens (castration-resistant nkx3-1-expressing cells, carns) are bipotential and can self-renew in vivo, and single-cell transplantation assays show that carns can reconstitute prostate ducts in renal grafts. functional assays of nkx3-1 mutant mice in serial prostate regeneration suggest that nkx3-1 is required for stem cell maintenance. furthermore, targeted deletion of the pten tumour suppressor gene in carns results in rapid carcinoma formation after androgen-mediated regeneration. these observations indicate that carns represent a new luminal stem cell population that is an efficient target for oncogenic transformation in prostate cancer.",0
"introduction multimorbidity is a major concern in primary care. nevertheless, evidence of prevalence and patterns of multimorbidity, and their determinants, are scarce. the aim of this study is to systematically review studies of the prevalence, patterns and determinants of multimorbidity in primary care. methods systematic review of literature published between 1961 and 2013 and indexed in ovid (cinahl, psychinfo, medline and embase) and web of knowledge. studies were selected according to eligibility criteria of addressing prevalence, determinants, and patterns of multimorbidity and using a pretested proforma in primary care. the quality and risk of bias were assessed using strobe criteria. two researchers assessed the eligibility of studies for inclusion (kappa= 0.86). results we identified 39 eligible publications describing studies that included a total of 70,057,611 patients in 12 countries. the number of health conditions analysed per study ranged from 5 to 335, with multimorbidity prevalence ranging from 12.9% to 95.1%. all studies observed a significant positive association between multimorbidity and age (odds ratio , 1.26 to 227.46), and lower socioeconomic status (or, 1.20 to 1.91). positive associations with female gender and mental disorders were also observed. the most frequent patterns of multimorbidity included osteoarthritis together with cardiovascular and/or metabolic conditions. conclusions well-established determinants of multimorbidity include age, lower socioeconomic status and gender. the most prevalent conditions shape the patterns of multimorbidity. however, the limitations of the current evidence base means that further and better designed studies are needed to inform policy, research and clinical practice, with the goal of improving health-related quality of life for patients with multimorbidity. standardization of the definition and assessment of multimorbidity is essential in order to better understand this phenomenon, and is a necessary immediate step.",0
"humoral responses in coronavirus disease 2019 (covid-19) are often of limited durability, as seen with other human coronavirus epidemics. to address the underlying etiology, we examined post mortem thoracic lymph nodes and spleens in acute sars-cov-2 infection and observed the absence of germinal centers and a striking reduction in bcl-6 + germinal center b cells but preservation of aid + b cells. absence of germinal centers correlated with an early specific block in bcl-6 + t fh cell differentiation together with an increase in t-bet + t h1 cells and aberrant extra-follicular tnf-α accumulation. parallel peripheral blood studies revealed loss of transitional and follicular b cells in severe disease and accumulation of sars-cov-2-specific ""disease-related"" b cell populations. these data identify defective bcl-6 + t fh cell generation and dysregulated humoral immune induction early in covid-19 disease, providing a mechanistic explanation for the limited durability of antibody responses in coronavirus infections, and suggest that achieving herd immunity through natural infection may be difficult.",0
"background decision curve analysis is a novel method for evaluating diagnostic tests, prediction models and molecular markers. it combines the mathematical simplicity of accuracy measures, such as sensitivity and specificity, with the clinical applicability of decision analytic approaches. most critically, decision curve analysis can be applied directly to a data set, and does not require the sort of external data on costs, benefits and preferences typically required by traditional decision analytic techniques. methods in this paper we present several extensions to decision curve analysis including correction for overfit, confidence intervals, application to censored data (including competing risk) and calculation of decision curves directly from predicted probabilities. all of these extensions are based on straightforward methods that have previously been described in the literature for application to analogous statistical techniques. results simulation studies showed that repeated 10-fold crossvalidation provided the best method for correcting a decision curve for overfit. the method for applying decision curves to censored data had little bias and coverage was excellent; for competing risk, decision curves were appropriately affected by the incidence of the competing risk and the association between the competing risk and the predictor of interest. calculation of decision curves directly from predicted probabilities led to a smoothing of the decision curve. conclusion decision curve analysis can be easily extended to many of the applications common to performance measures for prediction models. software to implement decision curve analysis is provided.",0
"background infections due to antibiotic-resistant bacteria are threatening modern health care. however, estimating their incidence, complications, and attributable mortality is challenging. we aimed to estimate the burden of infections caused by antibiotic-resistant bacteria of public health concern in countries of the eu and european economic area (eea) in 2015, measured in number of cases, attributable deaths, and disability-adjusted life-years (dalys). methods we estimated the incidence of infections with 16 antibiotic resistance-bacterium combinations from european antimicrobial resistance surveillance network (ears-net) 2015 data that was country-corrected for population coverage. we multiplied the number of bloodstream infections (bsis) by a conversion factor derived from the european centre for disease prevention and control point prevalence survey of health-care-associated infections in european acute care hospitals in 2011-12 to estimate the number of non-bsis. we developed disease outcome models for five types of infection on the basis of systematic reviews of the literature. findings from ears-net data collected between jan 1, 2015, and dec 31, 2015, we estimated 671 689 (95% uncertainty interval 583 148-763 966) infections with antibiotic-resistant bacteria, of which 63·5% (426 277 of 671 689) were associated with health care. these infections accounted for an estimated 33 110 (28 480-38 430) attributable deaths and 874 541 (768 837-989 068) dalys. the burden for the eu and eea was highest in infants (aged interpretation our results present the health burden of five types of infection with antibiotic-resistant bacteria expressed, for the first time, in dalys. the estimated burden of infections with antibiotic-resistant bacteria in the eu and eea is substantial compared with that of other infectious diseases, and has increased since 2007. our burden estimates provide useful information for public health decision-makers prioritising interventions for infectious diseases. funding european centre for disease prevention and control.",0
"mycobacterium tuberculosis represents a world-wide health risk and immunosuppression is a particular problem in m. tuberculosis infections. although macrophages are primarily infected, dendritic cells (dcs) are important in inducing cellular immune responses against m. tuberculosis. we hypothesized that dcs represent a target for m. tuberculosis and that the observed immuno-suppression results from modulation of dc functions. we demonstrate that the dc-specific c-type lectin dc-sign is an important receptor on dcs that captures and internalizes intact mycobacterium bovis bacillus calmette-guérin (bcg) through the mycobacterial cell wall component manlam. antibodies against dc-sign block m. bovis bcg infection of dcs. manlam is also secreted by m. tuberculosis-infected macrophages and has been implicated as a virulence factor. strikingly, manlam binding to dc-sign prevents mycobacteria- or lps-induced dc maturation. both mycobacteria and lps induce dc maturation through toll-like receptor (tlr) signaling, suggesting that dc-sign, upon binding of manlam, interferes with tlr-mediated signals. blocking antibodies against dc-sign reverse the manlam-mediated immunosuppressive effects. our results suggest that m. tuberculosis targets dc-sign both to infect dcs and to down-regulate dc-mediated immune responses. moreover, we demonstrate that dc-sign has a broader pathogen recognition profile than previously shown, suggesting that dc-sign may represent a molecular target for clinical intervention in infections other than hiv-1.",0
"a fundamental question in cancer biology is whether cells with tumorigenic potential are common or rare within human cancers. studies on diverse cancers, including melanoma, have indicated that only rare human cancer cells (0.1-0.0001%) form tumours when transplanted into non-obese diabetic/severe combined immunodeficiency (nod/scid) mice. however, the extent to which nod/scid mice underestimate the frequency of tumorigenic human cancer cells has been uncertain. here we show that modified xenotransplantation assay conditions, including the use of more highly immunocompromised nod/scid interleukin-2 receptor gamma chain null (il2rg(-/-)) mice, can increase the detection of tumorigenic melanoma cells by several orders of magnitude. in limiting dilution assays, approximately 25% of unselected melanoma cells from 12 different patients, including cells from primary and metastatic melanomas obtained directly from patients, formed tumours under these more permissive conditions. in single-cell transplants, an average of 27% of unselected melanoma cells from four different patients formed tumours. modifications to xenotransplantation assays can therefore dramatically increase the detectable frequency of tumorigenic cells, demonstrating that they are common in some human cancers.",0
"background some patients awaken from coma (that is, open the eyes) but remain unresponsive (that is, only showing reflex movements without response to command). this syndrome has been coined vegetative state. we here present a new name for this challenging neurological condition: unresponsive wakefulness syndrome (abbreviated uws). discussion many clinicians feel uncomfortable when referring to patients as vegetative. indeed, to most of the lay public and media vegetative state has a pejorative connotation and seems inappropriately to refer to these patients as being vegetable-like. some political and religious groups have hence felt the need to emphasize these vulnerable patients' rights as human beings. moreover, since its first description over 35 years ago, an increasing number of functional neuroimaging and cognitive evoked potential studies have shown that physicians should be cautious to make strong claims about awareness in some patients without behavioral responses to command. given these concerns regarding the negative associations intrinsic to the term vegetative state as well as the diagnostic errors and their potential effect on the treatment and care for these patients (who sometimes never recover behavioral signs of consciousness but often recover to what was recently coined a minimally conscious state) we here propose to replace the name. conclusion since after 35 years the medical community has been unsuccessful in changing the pejorative image associated with the words vegetative state, we think it would be better to change the term itself. we here offer physicians the possibility to refer to this condition as unresponsive wakefulness syndrome or uws. as this neutral descriptive term indicates, it refers to patients showing a number of clinical signs (hence syndrome) of unresponsiveness (that is, without response to commands) in the presence of wakefulness (that is, eye opening).",0
"background mortality of patients with coronavirus disease 2019 (covid-19), acute respiratory distress syndrome (ards), and systemic inflammation is high. in areas of pandemic outbreak, the number of patients can exceed maximum capacity of intensive care units (icus), and, thus, these individuals often receive non-invasive ventilation outside of the icu. effective treatments for this population are needed urgently. anakinra is a recombinant interleukin-1 receptor antagonist that might be beneficial in this patient population. methods we conducted a retrospective cohort study at the san raffaele hospital in milan, italy. we included consecutive patients (aged ≥18 years) with covid-19, moderate-to-severe ards, and hyperinflammation (defined as serum c-reactive protein ≥100 mg/l, ferritin ≥900 ng/ml, or both) who were managed with non-invasive ventilation outside of the icu and who received standard treatment of 200 mg hydroxychloroquine twice a day orally and 400 mg lopinavir with 100 mg ritonavir twice a day orally. we compared survival, mechanical ventilation-free survival, changes in c-reactive protein, respiratory function, and clinical status in a cohort of patients who received additional treatment with anakinra (either 5 mg/kg twice a day intravenously or 100 mg twice a day subcutaneously ) with a retrospective cohort of patients who did not receive anakinra (referred to as the standard treatment group). all outcomes were assessed at 21 days. this study is part of the covid-19 biobank study, which is registered with clinicaltrials.gov, nct04318366. findings between march 17 and march 27, 2020, 29 patients received high-dose intravenous anakinra, non-invasive ventilation, and standard treatment. between march 10 and march 17, 2020, 16 patients received non-invasive ventilation and standard treatment only and comprised the comparison group for this study. a further seven patients received low-dose subcutaneous anakinra in addition to non-invasive ventilation and standard treatment; however, anakinra treatment was interrupted after 7 days because of a paucity of effects on serum c-reactive protein and clinical status. at 21 days, treatment with high-dose anakinra was associated with reductions in serum c-reactive protein and progressive improvements in respiratory function in 21 (72%) of 29 patients; five (17%) patients were on mechanical ventilation and three (10%) died. in the standard treatment group, eight (50%) of 16 patients showed respiratory improvement at 21 days; one (6%) patient was on mechanical ventilation and seven (44%) died. at 21 days, survival was 90% in the high-dose anakinra group and 56% in the standard treatment group (p=0·009). mechanical ventilation-free survival was 72% in the anakinra group versus 50% in the standard treatment group (p=0·15). bacteraemia occurred in four (14%) of 29 patients receiving high-dose anakinra and two (13%) of 16 patients receiving standard treatment. discontinuation of anakinra was not followed by inflammatory relapses. interpretation in this retrospective cohort study of patients with covid-19 and ards managed with non-invasive ventilation outside of the icu, treatment with high-dose anakinra was safe and associated with clinical improvement in 72% of patients. confirmation of efficacy will require controlled trials. funding none.",0
"the architecture of the junctional sarcoplasmic reticulum (sr) and transverse tubule (t tubule) membranes and the morphology of the two major proteins isolated from these membranes, the ryanodine receptor (or foot protein) and the dihydropyridine receptor, have been examined in detail. evidence for a direct interaction between the foot protein and a protein component of the junctional t tubule membrane is presented. comparisons between freeze-fracture images of the junctional sr and rotary-shadowed images of isolated triads and of the isolated foot protein, show that the foot protein has two domains. one is the large hydrophilic foot which spans the junctional gap and is composed of four subunits. the other is a hydrophobic domain which presumably forms the sr ca2+-release channel and which also has a fourfold symmetry. freeze-fracture images of the junctional t tubule membranes demonstrate the presence of diamond-shaped clusters of particles that correspond exactly in position to the subunits of the feet protein. these results suggest the presence of a large junctional complex spanning the two junctional membranes and intervening gap. this junctional complex is an ideal candidate for a mechanical coupling hypothesis of excitation-contraction coupling at the triadic junction.",0
"the functional assessment of chronic illness therapy (facit) measurement system is a collection of health-related quality of life (hrqol) questionnaires targeted to the management of chronic illness. the measurement system, under development since 1987, began with the creation of a generic core questionnaire called the functional assessment of cancer therapy-general (fact-g). the fact-g (now in version 4) is a 27-item compilation of general questions divided into four primary qol domains: physical well-being, social/family well-being, emotional well-being, and functional well-being. it is appropriate for use with patients with any form of cancer, and extensions of it have been used and validated in other chronic illness condition (e.g., hiv/aids; multiple sclerosis; parkinson's disease; rheumatoid arthritis), and in the general population. the facit measurement system now includes over 400 questions, some of which have been translated into more than 45 languages. assessment of any one patient is tailored so that the most-relevant questions are asked and administration time for any one assessment is usually less than 15 minutes. this is accomplished both by the use of specific subscales for relevant domains of hrqol, or computerized adaptive testing (cat) of selected symptoms and functional areas. facit questionnaires can be administered by self-report (paper or computer) or interview (face-to-face or telephone). available scoring, normative data and information on meaningful change now allow one to interpret results in the context of a growing literature base.",0
"bayesian inference of phylogeny using markov chain monte carlo (mcmc) plays a central role in understanding evolutionary history from molecular sequence data. visualizing and analyzing the mcmc-generated samples from the posterior distribution is a key step in any non-trivial bayesian inference. we present the software package tracer (version 1.7) for visualizing and analyzing the mcmc trace files generated through bayesian phylogenetic inference. tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. tracer is open-source and available at",0
"background quantifying sexually transmitted infection (sti) prevalence and incidence is important for planning interventions and advocating for resources. the world health organization (who) periodically estimates global and regional prevalence and incidence of four curable stis: chlamydia, gonorrhoea, trichomoniasis and syphilis. methods and findings who's 2012 estimates were based upon literature reviews of prevalence data from 2005 through 2012 among general populations for genitourinary infection with chlamydia, gonorrhoea, and trichomoniasis, and nationally reported data on syphilis seroprevalence among antenatal care attendees. data were standardized for laboratory test type, geography, age, and high risk subpopulations, and combined using a bayesian meta-analytic approach. regional incidence estimates were generated from prevalence estimates by adjusting for average duration of infection. in 2012, among women aged 15-49 years, the estimated global prevalence of chlamydia was 4.2% (95% uncertainty interval (ui): 3.7-4.7%), gonorrhoea 0.8% (0.6-1.0%), trichomoniasis 5.0% (4.0-6.4%), and syphilis 0.5% (0.4-0.6%); among men, estimated chlamydia prevalence was 2.7% (2.0-3.6%), gonorrhoea 0.6% (0.4-0.9%), trichomoniasis 0.6% (0.4-0.8%), and syphilis 0.48% (0.3-0.7%). these figures correspond to an estimated 131 million new cases of chlamydia (100-166 million), 78 million of gonorrhoea (53-110 million), 143 million of trichomoniasis (98-202 million), and 6 million of syphilis (4-8 million). prevalence and incidence estimates varied by region and sex. conclusions estimates of the global prevalence and incidence of chlamydia, gonorrhoea, trichomoniasis, and syphilis in adult women and men remain high, with nearly one million new infections with curable sti each day. the estimates highlight the urgent need for the public health community to ensure that well-recognized effective interventions for sti prevention, screening, diagnosis, and treatment are made more widely available. improved estimation methods are needed to allow use of more varied data and generation of estimates at the national level.",0
"a system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. the string database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. the associations in string include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. in the latest version 10.5 of string, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular cytoscape software framework. further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. the string resource is available online, at",0
"there is an urgent need to improve the infrastructure supporting the reuse of scholarly data. a diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the fair data principles. the intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. distinct from peer initiatives that focus on the human scholar, the fair principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. this comment is the first formal publication of the fair principles, and includes the rationale behind them, and some exemplar implementations in the community.",0
"the outbreak of covid-19 in china in december 2019 has been identified as a pandemic and a health emergency of global concern. our objective was to investigate the prevalence and predictors of posttraumatic stress symptoms (ptss) in china hardest-hit areas during covid-19 outbreak, especially exploring the gender difference existing in ptss. one month after the december 2019 covid-19 outbreak in wuhan china, we surveyed ptss and sleep qualities among 285 residents in wuhan and surrounding cities using the ptsd checklist for dsm-5 (pcl-5) and 4 items from the pittsburgh sleep quality index (psqi). hierarchical regression analysis and non-parametric test were used to analyze the data. results indicated that the prevalence of ptss in china hardest-hit areas a month after the covid-19 outbreak was 7%. women reported significant higher ptss in the domains of re-experiencing, negative alterations in cognition or mood, and hyper-arousal. participants with better sleep quality or less frequency of early awakenings reported lower ptss. professional and effective mental health services should be designed in order to aid the psychological wellbeing of the population in affected areas, especially those living in hardest-hit areas, females and people with poor sleep quality.",0
"the variable domain of an immunoglobulin (ig) sequence is encoded by multiple genes, including the variable (v) gene, the diversity (d) gene and the joining (j) gene. analysis of ig sequences typically requires identification of each gene, as well as a comparison of sequence variations in the context of defined regions. general purpose tools, such as the blast program, have only limited use for such tasks, as the rearranged nature of an ig sequence and the variable length of each gene requires multiple rounds of blast searches for a single ig sequence. additionally, manual assembly of different genes is difficult and error-prone. to address these issues and to facilitate other common tasks in analysing ig sequences, we have developed the sequence analysis tool igblast ( with this tool, users can view the matches to the germline v, d and j genes, details at rearrangement junctions, the delineation of ig v domain framework regions and complementarity determining regions. igblast has the capability to analyse nucleotide and protein sequences and can process sequences in batches. furthermore, igblast allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline v gene.",0
"we conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest's edge, subject to the degrading effects of fragmentation. a synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. these findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.",0
"background the burden of inflammatory bowel disease (ibd) is rising globally, with substantial variation in levels and trends of disease in different countries and regions. understanding these geographical differences is crucial for formulating effective strategies for preventing and treating ibd. we report the prevalence, mortality, and overall burden of ibd in 195 countries and territories between 1990 and 2017, based on data from the global burden of diseases, injuries, and risk factors study (gbd) 2017. methods we modelled mortality due to ibd using a standard cause of death ensemble model including data mainly from vital registrations. to estimate the non-fatal burden, we used data presented in primary studies, hospital discharges, and claims data, and used dismod-mr 2.1, a bayesian meta-regression tool, to ensure consistency between measures. mortality, prevalence, years of life lost (ylls) due to premature death, years lived with disability (ylds), and disability-adjusted life-years (dalys) were estimated. all of the estimates were reported as numbers and rates per 100 000 population, with 95% uncertainty intervals (ui). findings in 2017, there were 6·8 million (95% ui 6·4-7·3) cases of ibd globally. the age-standardised prevalence rate increased from 79·5 (75·9-83·5) per 100 000 population in 1990 to 84·3 (79·2-89·9) per 100 000 population in 2017. the age-standardised death rate decreased from 0·61 (0·55-0·69) per 100 000 population in 1990 to 0·51 (0·42-0·54) per 100 000 population in 2017. at the gbd regional level, the highest age-standardised prevalence rate in 2017 occurred in high-income north america (422·0 per 100 000) and the lowest age-standardised prevalence rates were observed in the caribbean (6·7 per 100 000 population). high socio-demographic index (sdi) locations had the highest age-standardised prevalence rate, while low sdi regions had the lowest age-standardised prevalence rate. at the national level, the usa had the highest age-standardised prevalence rate (464·5 per 100 000 population), followed by the uk (449·6 per 100 000). vanuatu had the highest age-standardised death rate in 2017 (1·8 per 100 000 population) and singapore had the lowest (0·08 per 100 000 population). the total ylds attributed to ibd almost doubled over the study period, from 0·56 million (0·39-0·77) in 1990 to 1·02 million (0·71-1·38) in 2017. the age-standardised rate of dalys decreased from 26·5 (21·0-33·0) per 100 000 population in 1990 to 23·2 (19·1-27·8) per 100 000 population in 2017. interpretation the prevalence of ibd increased substantially in many regions from 1990 to 2017, which might pose a substantial social and economic burden on governments and health systems in the coming years. our findings can be useful for policy makers developing strategies to tackle ibd, including the education of specialised personnel to address the burden of this complex disease. funding bill & melinda gates foundation.",0
"background many promising technological innovations in health and social care are characterized by nonadoption or abandonment by individuals or by failed attempts to scale up locally, spread distantly, or sustain the innovation long term at the organization or system level. objective our objective was to produce an evidence-based, theory-informed, and pragmatic framework to help predict and evaluate the success of a technology-supported health or social care program. methods the study had 2 parallel components: (1) secondary research (hermeneutic systematic review) to identify key domains, and (2) empirical case studies of technology implementation to explore, test, and refine these domains. we studied 6 technology-supported programs-video outpatient consultations, global positioning system tracking for cognitive impairment, pendant alarm services, remote biomarker monitoring for heart failure, care organizing software, and integrated case management via data sharing-using longitudinal ethnography and action research for up to 3 years across more than 20 organizations. data were collected at micro level (individual technology users), meso level (organizational processes and systems), and macro level (national policy and wider context). analysis and synthesis was aided by sociotechnically informed theories of individual, organizational, and system change. the draft framework was shared with colleagues who were introducing or evaluating other technology-supported health or care programs and refined in response to feedback. results the literature review identified 28 previous technology implementation frameworks, of which 14 had taken a dynamic systems approach (including 2 integrative reviews of previous work). our empirical dataset consisted of over 400 hours of ethnographic observation, 165 semistructured interviews, and 200 documents. the final nonadoption, abandonment, scale-up, spread, and sustainability (nasss) framework included questions in 7 domains: the condition or illness, the technology, the value proposition, the adopter system (comprising professional staff, patient, and lay caregivers), the organization(s), the wider (institutional and societal) context, and the interaction and mutual adaptation between all these domains over time. our empirical case studies raised a variety of challenges across all 7 domains, each classified as simple (straightforward, predictable, few components), complicated (multiple interacting components or issues), or complex (dynamic, unpredictable, not easily disaggregated into constituent components). programs characterized by complicatedness proved difficult but not impossible to implement. those characterized by complexity in multiple nasss domains rarely, if ever, became mainstreamed. the framework showed promise when applied (both prospectively and retrospectively) to other programs. conclusions subject to further empirical testing, nasss could be applied across a range of technological innovations in health and social care. it has several potential uses: (1) to inform the design of a new technology; (2) to identify technological solutions that (perhaps despite policy or industry enthusiasm) have a limited chance of achieving large-scale, sustained adoption; (3) to plan the implementation, scale-up, or rollout of a technology program; and (4) to explain and learn from program failures.",0
"background the knowledge that persistent human papillomavirus (hpv) infection is the main cause of cervical cancer has resulted in the development of prophylactic vaccines to prevent hpv infection and hpv assays that detect nucleic acids of the virus. who has launched a global initiative to scale up preventive, screening, and treatment interventions to eliminate cervical cancer as a public health problem during the 21st century. therefore, our study aimed to assess the existing burden of cervical cancer as a baseline from which to assess the effect of this initiative. methods for this worldwide analysis, we used data of cancer estimates from 185 countries from the global cancer observatory 2018 database. we used a hierarchy of methods dependent on the availability and quality of the source information from population-based cancer registries to estimate incidence of cervical cancer. for estimation of cervical cancer mortality, we used the who mortality database. countries were grouped in 21 subcontinents and were also categorised as high-resource or lower-resource countries, on the basis of their human development index. we calculated the number of cervical cancer cases and deaths in a given country, directly age-standardised incidence and mortality rate of cervical cancer, indirectly standardised incidence ratio and mortality ratio, cumulative incidence and mortality rate, and average age at diagnosis. findings approximately 570 000 cases of cervical cancer and 311 000 deaths from the disease occurred in 2018. cervical cancer was the fourth most common cancer in women, ranking after breast cancer (2·1 million cases), colorectal cancer (0·8 million) and lung cancer (0·7 million). the estimated age-standardised incidence of cervical cancer was 13·1 per 100 000 women globally and varied widely among countries, with rates ranging from less than 2 to 75 per 100 000 women. cervical cancer was the leading cause of cancer-related death in women in eastern, western, middle, and southern africa. the highest incidence was estimated in eswatini, with approximately 6·5% of women developing cervical cancer before age 75 years. china and india together contributed more than a third of the global cervical burden, with 106 000 cases in china and 97 000 cases in india, and 48 000 deaths in china and 60 000 deaths in india. globally, the average age at diagnosis of cervical cancer was 53 years, ranging from 44 years (vanuatu) to 68 years (singapore). the global average age at death from cervical cancer was 59 years, ranging from 45 years (vanuatu) to 76 years (martinique). cervical cancer ranked in the top three cancers affecting women younger than 45 years in 146 (79%) of 185 countries assessed. interpretation cervical cancer continues to be a major public health problem affecting middle-aged women, particularly in less-resourced countries. the global scale-up of hpv vaccination and hpv-based screening-including self-sampling-has potential to make cervical cancer a rare disease in the decades to come. our study could help shape and monitor the initiative to eliminate cervical cancer as a major public health problem. funding belgian foundation against cancer, dg research and innovation of the european commission, and the bill & melinda gates foundation.",0
"background thrombosis and inflammation may contribute to morbidity and mortality among patients with coronavirus disease 2019 (covid-19). we hypothesized that therapeutic-dose anticoagulation would improve outcomes in critically ill patients with covid-19. methods in an open-label, adaptive, multiplatform, randomized clinical trial, critically ill patients with severe covid-19 were randomly assigned to a pragmatically defined regimen of either therapeutic-dose anticoagulation with heparin or pharmacologic thromboprophylaxis in accordance with local usual care. the primary outcome was organ support-free days, evaluated on an ordinal scale that combined in-hospital death (assigned a value of -1) and the number of days free of cardiovascular or respiratory organ support up to day 21 among patients who survived to hospital discharge. results the trial was stopped when the prespecified criterion for futility was met for therapeutic-dose anticoagulation. data on the primary outcome were available for 1098 patients (534 assigned to therapeutic-dose anticoagulation and 564 assigned to usual-care thromboprophylaxis). the median value for organ support-free days was 1 (interquartile range, -1 to 16) among the patients assigned to therapeutic-dose anticoagulation and was 4 (interquartile range, -1 to 16) among the patients assigned to usual-care thromboprophylaxis (adjusted proportional odds ratio, 0.83; 95% credible interval, 0.67 to 1.03; posterior probability of futility [defined as an odds ratio conclusions in critically ill patients with covid-19, an initial strategy of therapeutic-dose anticoagulation with heparin did not result in a greater probability of survival to hospital discharge or a greater number of days free of cardiovascular or respiratory organ support than did usual-care pharmacologic thromboprophylaxis. (remap-cap, activ-4a, and attacc clinicaltrials.gov numbers, nct02735707, nct04505774, nct04359277, and nct04372589.).",0
"dynamic causal modeling (dcm) is a generic bayesian framework for inferring hidden neuronal states from measurements of brain activity. it provides posterior estimates of neurobiologically interpretable quantities such as the effective strength of synaptic connections among neuronal populations and their context-dependent modulation. dcm is increasingly used in the analysis of a wide range of neuroimaging and electrophysiological data. given the relative complexity of dcm, compared to conventional analysis techniques, a good knowledge of its theoretical foundations is needed to avoid pitfalls in its application and interpretation of results. by providing good practice recommendations for dcm, in the form of ten simple rules, we hope that this article serves as a helpful tutorial for the growing community of dcm users.",0
"the diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit earth is among the most fundamental questions in science. yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. this approach was validated against well-known taxa, and when applied to all domains of life, it predicts ~8.7 million (± 1.3 million se) eukaryotic species globally, of which ~2.2 million (± 0.18 million se) are marine. in spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86% of existing species on earth and 91% of species in the ocean still await description. renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on earth is to be closed.",0
"pfam is a database of protein families that currently contains 7973 entries (release 18.0). a recent development in pfam has enabled the grouping of related families into clans. pfam clans are described in detail, together with the new associated web pages. improvements to the range of pfam web tools and the first set of pfam web services that allow programmatic access to the database and associated tools are also presented. pfam is available on the web in the uk ( the usa ( france ( and sweden (",0
"we describe the direct detection of dna methylation, without bisulfite conversion, through single-molecule, real-time (smrt) sequencing. in smrt sequencing, dna polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands. the arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the dna template, including n6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine. measurement of polymerase kinetics is an intrinsic part of smrt sequencing and does not adversely affect determination of primary dna sequence. the various modifications affect polymerase kinetics differently, allowing discrimination between them. we used these kinetic signatures to identify adenine methylation in genomic samples and found that, in combination with circular consensus sequencing, they can enable single-molecule identification of epigenetic modifications with base-pair resolution. this method is amenable to long read lengths and will likely enable mapping of methylation patterns in even highly repetitive genomic regions.",0
"background ct may play a central role in the diagnosis and management of coronavirus disease 2019 (covid-19) pneumonia. purpose to perform a longitudinal study to analyze the serial ct findings over time in patients with covid-19 pneumonia. materials and methods during january 16 to february 17, 2020, 90 patients (33 men, 57 women; mean age, 45 years) with covid-19 pneumonia were prospectively enrolled and followed up until being discharged, death, or the end of the study. a total of 366 ct scans were acquired and reviewed by two groups of radiologists for the patterns and distribution of lung abnormalities, total ct scores, and number of zones involved. those features were analyzed for temporal change. results ct scores and number of zones involved progressed rapidly, peaked during illness days 6-11 (median ct score, 5; median number of zones involved, five), and were followed by persistence of high levels. the predominant pattern of abnormalities after symptom onset was ground-glass opacity (35 of 78 scans to 49 of 79 scans in different periods). the percentage of mixed pattern peaked on illness days 12-17 (30 of 78 scans ) and became the second most predominant pattern thereafter. pure ground-glass opacity was the most prevalent subtype of ground-glass opacity after symptom onset (20 of 50 scans to 20 of 28 scans ). the percentage of ground-glass opacity with irregular linear opacity peaked on illness days 6-11 (14 of 50 scans ) and became the second most prevalent subtype thereafter. the distribution of lesions was predominantly bilateral and subpleural. sixty-six of the 70 patients discharged (94%) had residual disease on final ct scans (median ct score, 4; median number of zones involved, four), with ground-glass opacity (42 of 70 patients ) and pure ground-glass opacity (31 of 42 patients ) the most common pattern and subtype. conclusion the extent of lung abnormalities at ct peaked during illness days 6-11. the temporal changes of the diverse ct manifestations followed a specific pattern, which might indicate the progression and recovery of the illness. © rsna, 2020 online supplemental material is available for this article.",0
"type 2 diabetes is a global public health crisis that threatens the economies of all nations, particularly developing countries. fueled by rapid urbanization, nutrition transition, and increasingly sedentary lifestyles, the epidemic has grown in parallel with the worldwide rise in obesity. asia's large population and rapid economic development have made it an epicenter of the epidemic. asian populations tend to develop diabetes at younger ages and lower bmi levels than caucasians. several factors contribute to accelerated diabetes epidemic in asians, including the ""normal-weight metabolically obese"" phenotype; high prevalence of smoking and heavy alcohol use; high intake of refined carbohydrates (e.g., white rice); and dramatically decreased physical activity levels. poor nutrition in utero and in early life combined with overnutrition in later life may also play a role in asia's diabetes epidemic. recent advances in genome-wide association studies have contributed substantially to our understanding of diabetes pathophysiology, but currently identified genetic loci are insufficient to explain ethnic differences in diabetes risk. nonetheless, interactions between westernized diet and lifestyle and genetic background may accelerate the growth of diabetes in the context of rapid nutrition transition. epidemiologic studies and randomized clinical trials show that type 2 diabetes is largely preventable through diet and lifestyle modifications. translating these findings into practice, however, requires fundamental changes in public policies, the food and built environments, and health systems. to curb the escalating diabetes epidemic, primary prevention through promotion of a healthy diet and lifestyle should be a global public policy priority.",0
"susceptibility to systemic meningococcal disease is related to a selective deficiency of humoral antibodies to pathogenic strains of meningococci. in a study of the age-specific incidence of meningococcal meningitis in the united states, it was found that the proportion of individuals with serum bactericidal activity to meningococci of serogroups a, b, and c was reciprocally related to the incidence of disease. the prevalence of bactericidal activity was highest at birth and among adults, and lowest in infants between 6 and 24 months of age. sera from 51 of 54 prospective cases of meningococcal disease among military recruits were deficient in antibodies to homologous and heterologous strains of pathogenic meningococci as determined by serum bactericidal activity and indirect immunofluorescence. such sera, however, could support the bactericidal activity of purified human gamma globulin (cohn fraction ii), and such individuals could respond immunologically to infection with meningococci. the implication is that susceptible persons are deficient in antimeningococcal antibodies because they have not received significant exposure to meningococcal antigens in the past. the fate of individuals who lack bactericidal antibodies to pathogenic meningococci was determined during an outbreak of group c meningitis among military recruits. the incidence of disease was found to be primarily associated with the incidence of exposure of susceptibles to the pathogenic strains. whereas 81.5% of the presumed susceptibles acquired a meningococcal strain, only 24.1% acquired an organism similar to the prevalent disease-producing strains. of the exposed susceptibles, 38.5% developed systemic meningococcal disease.",0
"proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (md) simulations, especially in studies of lipid bilayers. the use of the charmm36 force field (c36 ff) in different md simulation programs can result in disagreements with published simulations performed with charmm due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. in this study, we systematically test the use of the c36 lipid ff in namd, gromacs, amber, openmm, and charmm/openmm. a wide range of lennard-jones (lj) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. md simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (dppc) bilayer were used to obtain the optimal protocol for each program. md simulations with all programs were found to reasonably match the dppc bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in charmm as well as from experiments. the optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. amber compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the lj potential versus a force-based switching function used to smooth the lj potential as it approaches the cutoff distance. the optimal simulation protocol for each program has been implemented in charmm-gui. this protocol is expected to be applicable to the remainder of the additive c36 ff including the proteins, nucleic acids, carbohydrates, and small molecules.",0
"background spain is one of the european countries most affected by the covid-19 pandemic. serological surveys are a valuable tool to assess the extent of the epidemic, given the existence of asymptomatic cases and little access to diagnostic tests. this nationwide population-based study aims to estimate the seroprevalence of sars-cov-2 infection in spain at national and regional level. methods 35 883 households were selected from municipal rolls using two-stage random sampling stratified by province and municipality size, with all residents invited to participate. from april 27 to may 11, 2020, 61 075 participants (75·1% of all contacted individuals within selected households) answered a questionnaire on history of symptoms compatible with covid-19 and risk factors, received a point-of-care antibody test, and, if agreed, donated a blood sample for additional testing with a chemiluminescent microparticle immunoassay. prevalences of igg antibodies were adjusted using sampling weights and post-stratification to allow for differences in non-response rates based on age group, sex, and census-tract income. using results for both tests, we calculated a seroprevalence range maximising either specificity (positive for both tests) or sensitivity (positive for either test). findings seroprevalence was 5·0% (95% ci 4·7-5·4) by the point-of-care test and 4·6% (4·3-5·0) by immunoassay, with a specificity-sensitivity range of 3·7% (3·3-4·0; both tests positive) to 6·2% (5·8-6·6; either test positive), with no differences by sex and lower seroprevalence in children younger than 10 years ( 10%) and lower in coastal areas ( interpretation the majority of the spanish population is seronegative to sars-cov-2 infection, even in hotspot areas. most pcr-confirmed cases have detectable antibodies, but a substantial proportion of people with symptoms compatible with covid-19 did not have a pcr test and at least a third of infections determined by serology were asymptomatic. these results emphasise the need for maintaining public health measures to avoid a new epidemic wave. funding spanish ministry of health, institute of health carlos iii, and spanish national health system.",0
"although experience-dependent structural changes have been found in adult gray matter, there is little evidence for such changes in white matter. using diffusion imaging, we detected a localized increase in fractional anisotropy, a measure of microstructure, in white matter underlying the intraparietal sulcus following training of a complex visuo-motor skill. this provides, to the best of our knowledge, the first evidence for training-related changes in white-matter structure in the healthy human adult brain.",0
"certain g-rich dna sequences readily form four-stranded structures called g-quadruplexes. these sequence motifs are located in telomeres as a repeated unit, and elsewhere in the genome, where their function is currently unknown. it has been proposed that g-quadruplexes may be directly involved in gene regulation at the level of transcription. in support of this hypothesis, we show that the promoter regions (1 kb upstream of the transcription start site tss) of genes are significantly enriched in quadruplex motifs relative to the rest of the genome, with >40% of human gene promoters containing one or more quadruplex motif. furthermore, these promoter quadruplexes strongly associate with nuclease hypersensitive sites identified throughout the genome via biochemical measurement. regions of the human genome that are both nuclease hypersensitive and within promoters show a remarkable (230-fold) enrichment of quadruplex elements, compared to the rest of the genome. these quadruplex motifs identified in promoter regions also show an interesting structural bias towards more stable forms. these observations support the proposal that promoter g-quadruplexes are directly involved in the regulation of gene expression.",0
"the coronavirus disease 2019 (covid-19) pandemic is having a profound effect on all aspects of society, including mental health and physical health. we explore the psychological, social, and neuroscientific effects of covid-19 and set out the immediate priorities and longer-term strategies for mental health science research. these priorities were informed by surveys of the public and an expert panel convened by the uk academy of medical sciences and the mental health research charity, mq: transforming mental health, in the first weeks of the pandemic in the uk in march, 2020. we urge uk research funding agencies to work with researchers, people with lived experience, and others to establish a high level coordination group to ensure that these research priorities are addressed, and to allow new ones to be identified over time. the need to maintain high-quality research standards is imperative. international collaboration and a global perspective will be beneficial. an immediate priority is collecting high-quality data on the mental health effects of the covid-19 pandemic across the whole population and vulnerable groups, and on brain function, cognition, and mental health of patients with covid-19. there is an urgent need for research to address how mental health consequences for vulnerable groups can be mitigated under pandemic conditions, and on the impact of repeated media consumption and health messaging around covid-19. discovery, evaluation, and refinement of mechanistically driven interventions to address the psychological, social, and neuroscientific aspects of the pandemic are required. rising to this challenge will require integration across disciplines and sectors, and should be done together with people with lived experience. new funding will be required to meet these priorities, and it can be efficiently leveraged by the uk's world-leading infrastructure. this position paper provides a strategy that may be both adapted for, and integrated with, research efforts in other countries.",0
"a pathological hallmark of alzheimer's disease is an accumulation of insoluble plaque containing the amyloid-beta peptide of 40-42 amino acid residues. prefibrillar, soluble oligomers of amyloid-beta have been recognized to be early and key intermediates in alzheimer's-disease-related synaptic dysfunction. at nanomolar concentrations, soluble amyloid-beta oligomers block hippocampal long-term potentiation, cause dendritic spine retraction from pyramidal cells and impair rodent spatial memory. soluble amyloid-beta oligomers have been prepared from chemical syntheses, transfected cell culture supernatants, transgenic mouse brain and human alzheimer's disease brain. together, these data imply a high-affinity cell-surface receptor for soluble amyloid-beta oligomers on neurons-one that is central to the pathophysiological process in alzheimer's disease. here we identify the cellular prion protein (prp(c)) as an amyloid-beta-oligomer receptor by expression cloning. amyloid-beta oligomers bind with nanomolar affinity to prp(c), but the interaction does not require the infectious prp(sc) conformation. synaptic responsiveness in hippocampal slices from young adult prp null mice is normal, but the amyloid-beta oligomer blockade of long-term potentiation is absent. anti-prp antibodies prevent amyloid-beta-oligomer binding to prp(c) and rescue synaptic plasticity in hippocampal slices from oligomeric amyloid-beta. thus, prp(c) is a mediator of amyloid-beta-oligomer-induced synaptic dysfunction, and prp(c)-specific pharmaceuticals may have therapeutic potential for alzheimer's disease.",0
"detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. here, we test the ability of the profile hidden markov model method hmmer3 to correctly assign homologous sequences to >13,000 manually curated families from the pfam database. we identify problem families using protein regions that match two or more pfam families not currently annotated as related in pfam. we find that hmmer3 e-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils. these results support the continued use of manually curated inclusion thresholds in the pfam database, especially on the subset of families that have been identified as problematic in experiments such as these. they also highlight the need for developing new methods that can correct for this particular type of compositional bias.",0
"in recent years, there has been an increased focus on placing patients at the center of health care research and evaluating clinical care in order to improve their experience and ensure that research is both robust and of maximum value for the use of medicinal products, therapy, or health services. this paper provides an overview of patients' involvement in clinical research and service evaluation along with its benefits and limitations. we describe and discuss patient-reported outcomes (pros) and patient-reported outcome measures (proms), including the trends in current research. both the patient-reported experiences measures (prems) and patient and public involvement (ppi) initiative for including patients in the research processes are also outlined. pros provide reports from patients about their own health, quality of life, or functional status associated with the health care or treatment they have received. proms are tools and/or instruments used to report pros. patient report experiences through the use of prems, such as satisfaction scales, providing insight into the patients' experience with their care or a health service. there is increasing international attention regarding the use of prems as a quality indicator of patient care and safety. this reflects the ongoing health service commitment of involving patients and the public within the wider context of the development and evaluation of health care service delivery and quality improvement.",0
"in the last 20 years, atrial fibrillation (af) has become one of the most important public health problems and a significant cause of increasing health care costs in western countries. the prevalence of af is increasing due to our greater ability to treat chronic cardiac and noncardiac diseases, and the improved ability to suspect and diagnose af. at the present time, the prevalence of af (2%) is double that reported in the last decade. the prevalence of af varies with age and sex. af is present in 0.12%-0.16% of those younger than 49 years, in 3.7%-4.2% of those aged 60-70 years, and in 10%-17% of those aged 80 years or older. in addition, it occurs more frequently in males, with a male to female ratio of 1.2:1. the incidence of af ranges between 0.21 and 0.41 per 1,000 person/years. permanent af occurs in approximately 50% of patients, and paroxysmal and persistent af in 25% each. af is frequently associated with cardiac disease and comorbidities. the most common concomitant diseases are coronary artery disease, valvular heart disease, and cardiomyopathy. the most common comorbidities are hypertension, diabetes, heart failure, chronic obstructive pulmonary disease, renal failure, stroke, and cognitive disturbance. paroxysmal af occurs in younger patients and with a reduced burden of both cardiac disease and comorbidities. generally, the history of af is long, burdened by frequent recurrences, and associated with symptoms (in two thirds of patients). patients with af have a five-fold and two-fold higher risk of stroke and death, respectively. we estimate that the number of patients with af in 2030 in europe will be 14-17 million and the number of new cases of af per year at 120,000-215,000. given that af is associated with significant morbidity and mortality, this increasing number of individuals with af will have major public health implications.",0
"triangulation is the practice of obtaining more reliable answers to research questions through integrating results from several different approaches, where each approach has different key sources of potential bias that are unrelated to each other. with respect to causal questions in aetiological epidemiology, if the results of different approaches all point to the same conclusion, this strengthens confidence in the finding. this is particularly the case when the key sources of bias of some of the approaches would predict that findings would point in opposite directions if they were due to such biases. where there are inconsistencies, understanding the key sources of bias of each approach can help to identify what further research is required to address the causal question. the aim of this paper is to illustrate how triangulation might be used to improve causal inference in aetiological epidemiology. we propose a minimum set of criteria for use in triangulation in aetiological epidemiology, summarize the key sources of bias of several approaches and describe how these might be integrated within a triangulation framework. we emphasize the importance of being explicit about the expected direction of bias within each approach, whenever this is possible, and seeking to identify approaches that would be expected to bias the true causal effect in different directions. we also note the importance, when comparing results, of taking account of differences in the duration and timing of exposures. we provide three examples to illustrate these points.",0
"background many newly detected point mutations are located in protein-coding regions of the human genome. knowledge of their effects on the protein's 3d structure provides insight into the protein's mechanism, can aid the design of further experiments, and eventually can lead to the development of new medicines and diagnostic tools. results in this article we describe hope, a fully automatic program that analyzes the structural and functional effects of point mutations. hope collects information from a wide range of information sources including calculations on the 3d coordinates of the protein by using what if web services, sequence annotations from the uniprot database, and predictions by das services. homology models are built with yasara. data is stored in a database and used in a decision scheme to identify the effects of a mutation on the protein's 3d structure and function. hope builds a report with text, figures, and animations that is easy to use and understandable for (bio)medical researchers. conclusions we tested hope by comparing its output to the results of manually performed projects. in all straightforward cases hope performed similar to a trained bioinformatician. the use of 3d structures helps optimize the results in terms of reliability and details. hope's results are easy to understand and are presented in a way that is attractive for researchers without an extensive bioinformatics background.",0
"use of the rotterdam symptom checklist (rscl) to measure psychological and physical distress as experienced by cancer patients, is discussed in this paper. the stability of the structure of the rscl was assessed in principal component analyses in three studies: one concerning cancer patients during either chemotherapy or follow-up (n = 86), one done in patients undergoing chemotherapy for advanced ovarian cancer (n = 56), and the third dealing with cancer patients under treatment, disease-free 'patients', and 'normal' controls (n = 611). the psychological dimension proved to be stable across populations. a scale based on this factor was highly reliable (cronbach's alpha 0.88-0.94). the physical distress is reflected by several dimensions in a homogeneous population (pain, fatigue, gastrointestinal complaints) and undimensionally in a heterogeneous population. reliability of the physical distress scales is good (0.71-0.88). the current components of the rscl and the use of individual and disease specific symptoms are discussed.",0
"stroke is ranked as the second leading cause of death worldwide with an annual mortality rate of about 5.5 million. not only does the burden of stroke lie in the high mortality but the high morbidity also results in up to 50% of survivors being chronically disabled. thus stroke is a disease of immense public health importance with serious economic and social consequences. the public health burden of stroke is set to rise over future decades because of demographic transitions of populations, particularly in developing countries. this paper provides an overview of stroke in the 21 st century from a public health perspective.",0
"we have defined a signal responsible for the morphological differentiation of human umbilical vein and human dermal microvascular endothelial cells in vitro. we find that human umbilical vein endothelial cells deprived of growth factors undergo morphological differentiation with tube formation after 6-12 wk, and that human dermal microvascular endothelial cells differentiate after 1 wk of growth factor deprivation. here, we report that morphological differentiation of both types of endothelial cells is markedly accelerated by culture on a reconstituted gel composed of basement membrane proteins. under these conditions, tube formation begins in 1-2 h and is complete by 24 h. the tubes are maintained for greater than 2 wk. little or no proliferation occurs under these conditions, although the cells, when trypsinized and replated on fibronectin-coated tissue culture dishes, resume division. ultrastructurally, the tubes possess a lumen surrounded by endothelial cells attached to one another by junctional complexes. the cells possess weibel-palade bodies and factor viii-related antigens, and take up acetylated low density lipoproteins. tubule formation does not occur on tissue culture plastic coated with laminin or collagen iv, either alone or in combination, or on an agarose or a collagen i gel. however, endothelial cells cultured on a collagen i gel supplemented with laminin form tubules, while supplementation with collagen iv induces a lesser degree of tubule formation. preincubation of endothelial cells with antibodies to laminin prevented tubule formation while antibodies to collagen iv were less inhibitory. preincubation of endothelial cells with synthetic peptides derived from the laminin b1 chain that bind to the laminin cell surface receptor or incorporation of these peptides into the gel matrix blocked tubule formation, whereas control peptides did not. these observations indicate that endothelial cells can rapidly differentiate on a basement membrane-like matrix and that laminin is the principal factor in inducing this change.",0
"background liver cirrhosis is a major yet largely preventable and underappreciated cause of global health loss. variations in cirrhosis mortality at the country level reflect differences in prevalence of risk factors such as alcohol use and hepatitis b and c infection. we estimated annual age-specific mortality from liver cirrhosis in 187 countries between 1980 and 2010. methods we systematically collected vital registration and verbal autopsy data on liver cirrhosis mortality for the period 1980 to 2010. we corrected for misclassification of deaths, which included deaths attributed to improbable or nonfatal causes. we used ensemble models to estimate liver cirrhosis mortality with uncertainty by age, sex, country and year. we used out-of-sample predictive validity to select the optimal model. results global liver cirrhosis deaths increased from around 676,000 (95% uncertainty interval: 452,863 to 1,004,530) in 1980 to over 1 million (1,029,042; 670,216 to 1,554,530) in 2010 (about 2% of the global total). over the same period, the age-standardized cirrhosis mortality rate decreased by 22%. this was largely driven by decreasing cirrhosis mortality rates in china, the us and countries in western europe. in 2010, egypt, followed by moldova, had the highest age-standardized cirrhosis mortality rates, 72.7 and 71.2 deaths per 100,000, respectively, while iceland had the lowest. in egypt, almost one-fifth (18.1%) of all deaths in males 45- to 54-years old were due to liver cirrhosis. liver cirrhosis mortality in mexico is the highest in latin america. in france and italy, liver cirrhosis mortality fell by 50% to 60%; conversely, in the united kingdom, mortality increased by about one-third. mortality from liver cirrhosis was also comparatively high in central asia countries, particularly mongolia, uzbekistan and kyrgyzstan, and in parts of sub-saharan africa, notably gabon. conclusions liver cirrhosis is a significant cause of global health burden, with more than one million deaths in 2010. our study identifies areas with high and/or rapidly increasing mortality where preventive measures to control and reduce liver cirrhosis risk factors should be urgently strengthened.",0
"t cell expansion and memory formation are generally more effective when elicited by live organisms than by inactivated vaccines. elucidation of the underlying mechanisms is important for vaccination and therapeutic strategies. we show that the massive expansion of antigen-specific cd8 t cells that occurs in response to viral infection is critically dependent on the direct action of type i interferons (ifn-is) on cd8 t cells. by examining the response to infection with lymphocytic choriomeningitis virus using ifn-i receptor-deficient (ifn-ir(0)) and -sufficient cd8 t cells adoptively transferred into normal ifn-ir wild-type hosts, we show that the lack of direct cd8 t cell contact with ifn-i causes >99% reduction in their capacity to expand and generate memory cells. the diminished expansion of ifn-ir(0) cd8 t cells was not caused by a defect in proliferation but by poor survival during the antigen-driven proliferation phase. thus, ifn-ir signaling in cd8 t cells is critical for the generation of effector and memory cells in response to viral infection.",0
"background published work assessing psychosocial stress (job strain) as a risk factor for coronary heart disease is inconsistent and subject to publication bias and reverse causation bias. we analysed the relation between job strain and coronary heart disease with a meta-analysis of published and unpublished studies. methods we used individual records from 13 european cohort studies (1985-2006) of men and women without coronary heart disease who were employed at time of baseline assessment. we measured job strain with questions from validated job-content and demand-control questionnaires. we extracted data in two stages such that acquisition and harmonisation of job strain measure and covariables occurred before linkage to records for coronary heart disease. we defined incident coronary heart disease as the first non-fatal myocardial infarction or coronary death. findings 30,214 (15%) of 197,473 participants reported job strain. in 1·49 million person-years at risk (mean follow-up 7·5 years ), we recorded 2358 events of incident coronary heart disease. after adjustment for sex and age, the hazard ratio for job strain versus no job strain was 1·23 (95% ci 1·10-1·37). this effect estimate was higher in published (1·43, 1·15-1·77) than unpublished (1·16, 1·02-1·32) studies. hazard ratios were likewise raised in analyses addressing reverse causality by exclusion of events of coronary heart disease that occurred in the first 3 years (1·31, 1·15-1·48) and 5 years (1·30, 1·13-1·50) of follow-up. we noted an association between job strain and coronary heart disease for sex, age groups, socioeconomic strata, and region, and after adjustments for socioeconomic status, and lifestyle and conventional risk factors. the population attributable risk for job strain was 3·4%. interpretation our findings suggest that prevention of workplace stress might decrease disease incidence; however, this strategy would have a much smaller effect than would tackling of standard risk factors, such as smoking. funding finnish work environment fund, the academy of finland, the swedish research council for working life and social research, the german social accident insurance, the danish national research centre for the working environment, the bupa foundation, the ministry of social affairs and employment, the medical research council, the wellcome trust, and the us national institutes of health.",0
"horizontal pleiotropy occurs when the variant has an effect on disease outside of its effect on the exposure in mendelian randomization (mr). violation of the 'no horizontal pleiotropy' assumption can cause severe bias in mr. we developed the mendelian randomization pleiotropy residual sum and outlier (mr-presso) test to identify horizontal pleiotropic outliers in multi-instrument summary-level mr testing. we showed using simulations that the mr-presso test is best suited when horizontal pleiotropy occurs in <50% of instruments. next we applied the mr-presso test, along with several other mr tests, to complex traits and diseases and found that horizontal pleiotropy (i) was detectable in over 48% of significant causal relationships in mr; (ii) introduced distortions in the causal estimates in mr that ranged on average from -131% to 201%; (iii) induced false-positive causal relationships in up to 10% of relationships; and (iv) could be corrected in some but not all instances.",0
"the nucleoids of escherichia coli, independently of the physiological state of the bacteria, are shown to be preserved as a fine-stranded fibrillar nucleoplasm by an oso(4) fixation under defined conditions: acetate-veronal buffer ph 6, presence of ca(++) and amino acids, stabilization with uranyl-acetate before dehydration. the same fixation procedure applied to the dna of vegetative phage reveals a pool of homogeneous fibrillar structure very similar to the nucleoplasm. the ""versene test,"" which produces a coarse coagulation of these plasms, emphasizes the similar behaviour of the pool and the nucleoids. the heads of mature phage are preserved in their true polyhedral shape by the standard fixation procedure, although they may be badly distorted when fixed under different conditions. lanthanum nitrate and uranyl-acetate are shown to increase markedly the contrast of both phage and cytoplasm. the consequences of the fibrillar structure of the genetic material are discussed in relation to the probable division process.",0
"metastatic cancer is a major cause of death and is associated with poor treatment efficacy. a better understanding of the characteristics of late-stage cancer is required to help adapt personalized treatments, reduce overtreatment and improve outcomes. here we describe the largest, to our knowledge, pan-cancer study of metastatic solid tumour genomes, including whole-genome sequencing data for 2,520 pairs of tumour and normal tissue, analysed at median depths of 106× and 38×, respectively, and surveying more than 70 million somatic variants. the characteristic mutations of metastatic lesions varied widely, with mutations that reflect those of the primary tumour types, and with high rates of whole-genome duplication events (56%). individual metastatic lesions were relatively homogeneous, with the vast majority (96%) of driver mutations being clonal and up to 80% of tumour-suppressor genes being inactivated bi-allelically by different mutational mechanisms. although metastatic tumour genomes showed similar mutational landscape and driver genes to primary tumours, we find characteristics that could contribute to responsiveness to therapy or resistance in individual patients. we implement an approach for the review of clinically relevant associations and their potential for actionability. for 62% of patients, we identify genetic variants that may be used to stratify patients towards therapies that either have been approved or are in clinical trials. this demonstrates the importance of comprehensive genomic tumour profiling for precision medicine in cancer.",0
"allele-specific copy number analysis (ascn) from next generation sequencing (ngs) data can greatly extend the utility of ngs beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (loh), allele-specific gains/amplifications. in addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of 'actionable' mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret ngs-based cancer gene copy number data in the context of clinical sequencing. we developed facets, an ascn tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. it is a fully integrated stand-alone pipeline that includes sequencing bam file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. we demonstrate the application of facets using the cancer genome atlas (tcga) whole-exome sequencing of lung adenocarcinoma samples. we also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.",0
"background literature searches underlie the foundations of systematic reviews and related review types. yet, the literature searching component of systematic reviews and related review types is often poorly reported. guidance for literature search reporting has been diverse, and, in many cases, does not offer enough detail to authors who need more specific information about reporting search methods and information sources in a clear, reproducible way. this document presents the prisma-s (preferred reporting items for systematic reviews and meta-analyses literature search extension) checklist, and explanation and elaboration. methods the checklist was developed using a 3-stage delphi survey process, followed by a consensus conference and public review process. results the final checklist includes 16 reporting items, each of which is detailed with exemplar reporting and rationale. conclusions the intent of prisma-s is to complement the prisma statement and its extensions by providing a checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of a search is completely reported and therefore reproducible.",0
"orthodb ( provides evolutionary and functional annotations of orthologs. this update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. these include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. orthodb relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. since orthologs are the most likely candidates to retain functions of their ancestor gene, orthodb is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. optional registered-user sessions allow on-line busco assessments of gene set completeness and mapping of the uploaded data to orthodb to enable further interactive exploration of related annotations and generation of comparative charts. the accelerating expansion of genomics data continues to add valuable information, and orthodb strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. the data can be browsed online, downloaded or assessed via rest api or sparql rdf compatible with both uniprot and ensembl.",0
"the human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. the resulting human brainnetome atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. additionally, we further mapped the delineated structures to mental processes by reference to the brainmap database. it thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. the human brainnetome atlas will be made freely available for download at so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states.",0
"unlabelled easyfig is a python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. blast comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures. availability easyfig is freely available (under a gpl license) for download (for mac os x, unix and microsoft windows) from the sourceforge web site:",0
"alkali (li(+), na(+), k(+), rb(+), and cs(+)) and halide (f(-), cl(-), br(-), and i(-)) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. to properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. a good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. at present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. in this work, we describe our efforts to build better models of the monovalent ions within the pairwise coulombic and 6-12 lennard-jones framework, where the models are tuned to balance crystal and solution properties in ewald simulations with specific choices of well-known water models. although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. the applied methodology is general and can be extended to other ions and to polarizable force-field models. our starting point centered on observations from long simulations of biomolecules in salt solution with the amber force fields where salt crystals formed well below their solubility limit. the likely cause of the artifact in the amber parameters relates to the naive mixing of the smith and dang chloride parameters with amber-adapted aqvist cation parameters. to provide a more appropriate balance, we reoptimized the parameters of the lennard-jones potential for the ions and specific choices of water models. to validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (le) and lattice constants (lc) of alkali halide salt crystals. this is the first effort that systematically scans across the lennard-jones space (well depth and radius) while balancing ion properties like le and lc across all pair combinations of the alkali ions and halide ions. the optimization across the entire monovalent series avoids systematic deviations. the ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically tip3p, tip4p ew, and spc/e. in addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.",0
"size distributions of expiratory droplets expelled during coughing and speaking and the velocities of the expiration air jets of healthy volunteers were measured. droplet size was measured using the interferometric mie imaging (imi) technique while the particle image velocimetry (piv) technique was used for measuring air velocity. these techniques allowed measurements in close proximity to the mouth and avoided air sampling losses. the average expiration air velocity was 11.7 m/s for coughing and 3.9 m/s for speaking. under the experimental setting, evaporation and condensation effects had negligible impact on the measured droplet size. the geometric mean diameter of droplets from coughing was 13.5 μm and it was 16.0 μm for speaking (counting 1-100). the estimated total number of droplets expelled ranged from 947 to 2085 per cough and 112-6720 for speaking. the estimated droplet concentrations for coughing ranged from 2.4 to 5.2 cm -3 per cough and 0.004-0.223 cm -3 for speaking.",0
"importance covid-19 is associated with clinically significant symptoms despite resolution of the acute infection (i.e., post-covid-19 syndrome). fatigue and cognitive impairment are amongst the most common and debilitating symptoms of post-covid-19 syndrome. objective to quantify the proportion of individuals experiencing fatigue and cognitive impairment 12 or more weeks following covid-19 diagnosis, and to characterize the inflammatory correlates and functional consequences of post-covid-19 syndrome. data sources systematic searches were conducted without language restrictions from database inception to june 8, 2021 on pubmed/medline, the cochrane library, psycinfo, embase, web of science, google/google scholar, and select reference lists. study selection primary research articles which evaluated individuals at least 12 weeks after confirmed covid-19 diagnosis and specifically reported on fatigue, cognitive impairment, inflammatory parameters, and/or functional outcomes were selected. data extraction & synthesis two reviewers independently extracted published summary data and assessed methodological quality and risk of bias. a meta-analysis of proportions was conducted to pool freeman-tukey double arcsine transformed proportions using the random-effects restricted maximum-likelihood model. main outcomes & measures the co-primary outcomes were the proportions of individuals reporting fatigue and cognitive impairment, respectively, 12 or more weeks following covid-19 infection. the secondary outcomes were inflammatory correlates and functional consequences associated with post-covid-19 syndrome. results the literature search yielded 10,979 studies, and 81 studies were selected for inclusion. the fatigue meta-analysis comprised 68 studies, the cognitive impairment meta-analysis comprised 43 studies, and 48 studies were included in the narrative synthesis. meta-analysis revealed that the proportion of individuals experiencing fatigue 12 or more weeks following covid-19 diagnosis was 0.32 (95% ci, 0.27, 0.37; p 2 = 99.1%). the proportion of individuals exhibiting cognitive impairment was 0.22 (95% ci, 0.17, 0.28; p 2 = 98.0). moreover, narrative synthesis revealed elevations in proinflammatory markers and considerable functional impairment in a subset of individuals. conclusions & relevance a significant proportion of individuals experience persistent fatigue and/or cognitive impairment following resolution of acute covid-19. the frequency and debilitating nature of the foregoing symptoms provides the impetus to characterize the underlying neurobiological substrates and how to best treat these phenomena. study registration prospero (crd42021256965).",0
"background major depression is one of the leading causes of disability worldwide, yet epidemiologic data are not available for many countries, particularly low- to middle-income countries. in this paper, we present data on the prevalence, impairment and demographic correlates of depression from 18 high and low- to middle-income countries in the world mental health survey initiative. methods major depressive episodes (mde) as defined by the diagnostic and statistical manual of mental disorders, fourth edition (dms-iv) were evaluated in face-to-face interviews using the world health organization composite international diagnostic interview (cidi). data from 18 countries were analyzed in this report (n = 89,037). all countries surveyed representative, population-based samples of adults. results the average lifetime and 12-month prevalence estimates of dsm-iv mde were 14.6% and 5.5% in the ten high-income and 11.1% and 5.9% in the eight low- to middle-income countries. the average age of onset ascertained retrospectively was 25.7 in the high-income and 24.0 in low- to middle-income countries. functional impairment was associated with recency of mde. the female: male ratio was about 2:1. in high-income countries, younger age was associated with higher 12-month prevalence; by contrast, in several low- to middle-income countries, older age was associated with greater likelihood of mde. the strongest demographic correlate in high-income countries was being separated from a partner, and in low- to middle-income countries, was being divorced or widowed. conclusions mde is a significant public-health concern across all regions of the world and is strongly linked to social conditions. future research is needed to investigate the combination of demographic risk factors that are most strongly associated with mde in the specific countries included in the wmh.",0
"we examined the effectiveness of cytotoxic t lymphocyte-associated antigen 4 (ctla-4) blockade, alone or in combination with a granulocyte/macrophage colony-stimulating factor (gm-csf)-expressing tumor cell vaccine, on rejection of the highly tumorigenic, poorly immunogenic murine melanoma b16-bl6. recently established tumors could be eradicated in 80% (68/85) of the cases using combination treatment, whereas each treatment by itself showed little or no effect. tumor rejection was dependent on cd8(+) and nk1.1(+) cells but occurred irrespective of the presence of cd4(+) t cells. mice surviving a primary challenge rejected a secondary challenge with b16-bl6 or the parental b16-f0 line. the same treatment regimen was found to be therapeutically effective against outgrowth of preestablished b16-f10 lung metastases, inducing long-term survival. of all mice surviving b16-bl6 or b16-f10 tumors after combination treatment, 56% (38/68) developed depigmentation, starting at the site of vaccination or challenge and in most cases progressing to distant locations. depigmentation was found to occur in cd4-depleted mice, strongly suggesting that the effect was mediated by ctls. this study shows that ctla-4 blockade provides a powerful tool to enhance t cell activation and memory against a poorly immunogenic spontaneous murine tumor and that this may involve recruitment of autoreactive t cells.",0
"we demonstrate the first successful application of exome sequencing to discover the gene for a rare mendelian disorder of unknown cause, miller syndrome (mim%263750). for four affected individuals in three independent kindreds, we captured and sequenced coding regions to a mean coverage of 40x and sufficient depth to call variants at approximately 97% of each targeted exome. filtering against public snp databases and eight hapmap exomes for genes with two previously unknown variants in each of the four individuals identified a single candidate gene, dhodh, which encodes a key enzyme in the pyrimidine de novo biosynthesis pathway. sanger sequencing confirmed the presence of dhodh mutations in three additional families with miller syndrome. exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.",0
"this study identifies a dendritic cell (dc) subset that constitutively transports apoptotic intestinal epithelial cell remnants to t cell areas of mesenteric lymph nodes in vivo. rat intestinal lymph contains two dc populations. both populations have typical dc morphology, are major histocompatibility complex class ii(hi), and express ox62, cd11c, and b7. cd4(+)/ox41(+) dcs are strong antigen-presenting cells (apcs). cd4(-)/ox41(-) dcs are weak apcs and contain cytoplasmic apoptotic dna, epithelial cell-restricted cytokeratins, and nonspecific esterase (nse)(+) inclusions, not seen in ox41(+) dcs. identical patterns of nse electrophoretic variants exist in cd4(-)/ox41(-) dcs, intestinal epithelial cells, and mesenteric node dcs but not in other dc populations, macrophages, or tissues. terminal deoxynucleotidyl transferase-mediated dutp-biotin nick-end labeling (tunel)-positive dcs and strongly nse(+) dcs are present in intestinal lamina propria. peyer's patches and mesenteric but not other lymph nodes contain many strongly nse(+) dcs in interfollicular and t cell areas. similar dcs are seen in the ileum and in t cell areas of mesenteric nodes in gnotobiotic rats. these results show that a distinct dc subset constitutively endocytoses and transports apoptotic cells to t cell areas and suggest a role for these dcs in inducing and maintaining peripheral self-tolerance.",0
"b cell maturation is a very selective process that requires finely tuned differentiation and survival signals. b cell activation factor from the tnf family (baff) is a tnf family member that binds to b cells and potentiates b cell receptor (bcr)-mediated proliferation. a role for baff in b cell survival was suggested by the observation of reduced peripheral b cell numbers in mice treated with reagents blocking baff, and high bcl-2 levels detected in b cells from baff transgenic (tg) mice. we tested in vitro the survival effect of baff on lymphocytes derived from primary and secondary lymphoid organs. baff induced survival of a subset of splenic immature b cells, referred to as transitional type 2 (t2) b cells. baff treatment allowed t2 b cells to survive and differentiate into mature b cells in response to signals through the bcr. the t2 and the marginal zone (mz) b cell compartments were particularly enlarged in baff tg mice. immature transitional b cells are targets for negative selection, a feature thought to promote self-tolerance. these findings support a model in which excessive baff-mediated survival of peripheral immature b cells contributes to the emergence and maturation of autoreactive b cells, skewed towards the mz compartment. this work provides new clues on mechanisms regulating b cell maturation and tolerance.",0
"certain junctions between ependymal cells, between astrocytes, and between some electrically coupled neurons have heretofore been regarded as tight, pentalaminar occlusions of the intercellular cleft. these junctions are now redefined in terms of their configuration after treatment of brain tissue in uranyl acetate before dehydration. instead of a median dense lamina, they are bisected by a median gap 20-30 a wide which is continuous with the rest of the interspace. the patency of these ""gap junctions"" is further demonstrated by the penetration of horseradish peroxidase or lanthanum into the median gap, the latter tracer delineating there a polygonal substructure. however, either tracer can circumvent gap junctions because they are plaque-shaped rather than complete, circumferential belts. tight junctions, which retain a pentalaminar appearance after uranyl acetate block treatment, are restricted primarily to the endothelium of parenchymal capillaries and the epithelium of the choroid plexus. they form rows of extensive, overlapping occlusions of the interspace and are neither circumvented nor penetrated by peroxidase and lanthanum. these junctions are morphologically distinguishable from the ""labile"" pentalaminar appositions which appear or disappear according to the preparative method and which do not interfere with the intercellular movement of tracers. therefore, the interspaces of the brain are generally patent, allowing intercellular movement of colloidal materials. endothelial and epithelial tight junctions occlude the interspaces between blood and parenchyma or cerebral ventricles, thereby constituting a structural basis for the blood-brain and blood-cerebrospinal fluid barriers.",0
"glutathione (gsh) plays an important role in a multitude of cellular processes, including cell differentiation, proliferation, and apoptosis, and disturbances in gsh homeostasis are involved in the etiology and progression of many human diseases including cancer. while gsh deficiency, or a decrease in the gsh/glutathione disulphide (gssg) ratio, leads to an increased susceptibility to oxidative stress implicated in the progression of cancer, elevated gsh levels increase the antioxidant capacity and the resistance to oxidative stress as observed in many cancer cells. the present review highlights the role of gsh and related cytoprotective effects in the susceptibility to carcinogenesis and in the sensitivity of tumors to the cytotoxic effects of anticancer agents.",0
"when experts are immersed in a task, do their brains prioritize task-related activity? most efforts to understand neural activity during well-learned tasks focus on cognitive computations and task-related movements. we wondered whether task-performing animals explore a broader movement landscape and how this impacts neural activity. we characterized movements using video and other sensors and measured neural activity using widefield and two-photon imaging. cortex-wide activity was dominated by movements, especially uninstructed movements not required for the task. some uninstructed movements were aligned to trial events. accounting for them revealed that neurons with similar trial-averaged activity often reflected utterly different combinations of cognitive and movement variables. other movements occurred idiosyncratically, accounting for trial-by-trial fluctuations that are often considered 'noise'. this held true throughout task-learning and for extracellular neuropixels recordings that included subcortical areas. our observations argue that animals execute expert decisions while performing richly varied, uninstructed movements that profoundly shape neural activity.",0
"background lowering ldl cholesterol with statin regimens reduces the risk of myocardial infarction, ischaemic stroke, and the need for coronary revascularisation in people without kidney disease, but its effects in people with moderate-to-severe kidney disease are uncertain. the sharp trial aimed to assess the efficacy and safety of the combination of simvastatin plus ezetimibe in such patients. methods this randomised double-blind trial included 9270 patients with chronic kidney disease (3023 on dialysis and 6247 not) with no known history of myocardial infarction or coronary revascularisation. patients were randomly assigned to simvastatin 20 mg plus ezetimibe 10 mg daily versus matching placebo. the key prespecified outcome was first major atherosclerotic event (non-fatal myocardial infarction or coronary death, non-haemorrhagic stroke, or any arterial revascularisation procedure). all analyses were by intention to treat. this trial is registered at clinicaltrials.gov, nct00125593, and isrctn54137607. findings 4650 patients were assigned to receive simvastatin plus ezetimibe and 4620 to placebo. allocation to simvastatin plus ezetimibe yielded an average ldl cholesterol difference of 0·85 mmol/l (se 0·02; with about two-thirds compliance) during a median follow-up of 4·9 years and produced a 17% proportional reduction in major atherosclerotic events (526 simvastatin plus ezetimibe vs 619 placebo; rate ratio 0·83, 95% ci 0·74-0·94; log-rank p=0·0021). non-significantly fewer patients allocated to simvastatin plus ezetimibe had a non-fatal myocardial infarction or died from coronary heart disease (213 vs 230 ; rr 0·92, 95% ci 0·76-1·11; p=0·37) and there were significant reductions in non-haemorrhagic stroke (131 vs 174 ; rr 0·75, 95% ci 0·60-0·94; p=0·01) and arterial revascularisation procedures (284 vs 352 ; rr 0·79, 95% ci 0·68-0·93; p=0·0036). after weighting for subgroup-specific reductions in ldl cholesterol, there was no good evidence that the proportional effects on major atherosclerotic events differed from the summary rate ratio in any subgroup examined, and, in particular, they were similar in patients on dialysis and those who were not. the excess risk of myopathy was only two per 10,000 patients per year of treatment with this combination (9 vs 5 ). there was no evidence of excess risks of hepatitis (21 vs 18 ), gallstones (106 vs 106 ), or cancer (438 vs 439 , p=0·89) and there was no significant excess of death from any non-vascular cause (668 vs 612 , p=0·13). interpretation reduction of ldl cholesterol with simvastatin 20 mg plus ezetimibe 10 mg daily safely reduced the incidence of major atherosclerotic events in a wide range of patients with advanced chronic kidney disease. funding merck/schering-plough pharmaceuticals; australian national health and medical research council; british heart foundation; uk medical research council.",0
"background an integrative theoretical framework, developed for cross-disciplinary implementation and other behaviour change research, has been applied across a wide range of clinical situations. this study tests the validity of this framework. methods validity was investigated by behavioural experts sorting 112 unique theoretical constructs using closed and open sort tasks. the extent of replication was tested by discriminant content validation and fuzzy cluster analysis. results there was good support for a refinement of the framework comprising 14 domains of theoretical constructs (average silhouette value 0.29): 'knowledge', 'skills', 'social/professional role and identity', 'beliefs about capabilities', 'optimism', 'beliefs about consequences', 'reinforcement', 'intentions', 'goals', 'memory, attention and decision processes', 'environmental context and resources', 'social influences', 'emotions', and 'behavioural regulation'. conclusions the refined theoretical domains framework has a strengthened empirical base and provides a method for theoretically assessing implementation problems, as well as professional and other health-related behaviours as a basis for intervention development.",0
"identifying genetic correlations between complex traits and diseases can provide useful etiological insights and help prioritize likely causal relationships. the major challenges preventing estimation of genetic correlation from genome-wide association study (gwas) data with current methods are the lack of availability of individual-level genotype data and widespread sample overlap among meta-analyses. we circumvent these difficulties by introducing a technique-cross-trait ld score regression-for estimating genetic correlation that requires only gwas summary statistics and is not biased by sample overlap. we use this method to estimate 276 genetic correlations among 24 traits. the results include genetic correlations between anorexia nervosa and schizophrenia, anorexia and obesity, and educational attainment and several diseases. these results highlight the power of genome-wide analyses, as there currently are no significantly associated snps for anorexia nervosa and only three for educational attainment.",0
"on the basis of their surface markers, t lymphocytes are divided into subsets of ""naive"" and ""memory cells"". we have defined the interrelationship and relative life spans of naive and memory t cells by examining the surface markers on murine t cells incorporating bromodeoxyuridine, a dna precursor, given in the drinking water. three findings are reported. first, using a new method we show that the release of newly formed naive t cells from the unmanipulated thymus is very low (confirming the findings of others with surgical approaches). second, in thymectomized mice, t cells with a naive phenotype remain in interphase for prolonged periods; however, some of these cells divide and retain (or regain) their ""naive"" markers. third, most t cells with a memory phenotype divide rapidly, but others remain in interphase for many weeks. collectively, the data indicate that long-lived t cells have multiple phenotypes and contain a mixture of memory cells, naive (virgin) cells, and memory cells masquerading as naive cells.",0
"it is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. consurf ( and conseq ( are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical bayesian inference, starting from protein structure and sequence, respectively. here, we present the new version of the consurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. in addition, the new version of consurf calculates the evolutionary rates for nucleic acid sequences. the new version is freely available at:",0
"hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize this knowledge. results from individual studies can be inconsistent, and comparing published data is further complicated by a lack of standard processing and analysis methods. here we introduce the microbiomehd database, which includes 28 published case-control gut microbiome studies spanning ten diseases. we perform a cross-disease meta-analysis of these studies using standardized methods. we find consistent patterns characterizing disease-associated microbiome changes. some diseases are associated with over 50 genera, while most show only 10-15 genus-level changes. some diseases are marked by the presence of potentially pathogenic microbes, whereas others are characterized by a depletion of health-associated bacteria. furthermore, we show that about half of genera associated with individual studies are bacteria that respond to more than one disease. thus, many associations found in case-control studies are likely not disease-specific but rather part of a non-specific, shared response to health and disease.",0
"background consumer-wearable activity trackers are electronic devices used for monitoring fitness- and other health-related metrics. the purpose of this systematic review was to summarize the evidence for validity and reliability of popular consumer-wearable activity trackers (fitbit and jawbone) and their ability to estimate steps, distance, physical activity, energy expenditure, and sleep. methods searches included only full-length english language studies published in pubmed, embase, sportdiscus, and google scholar through july 31, 2015. two people reviewed and abstracted each included study. results in total, 22 studies were included in the review (20 on adults, 2 on youth). for laboratory-based studies using step counting or accelerometer steps, the correlation with tracker-assessed steps was high for both fitbit and jawbone (pearson or intraclass correlation coefficients (cc) > =0.80). only one study assessed distance for the fitbit, finding an over-estimate at slower speeds and under-estimate at faster speeds. two field-based studies compared accelerometry-assessed physical activity to the trackers, with one study finding higher correlation (spearman cc 0.86, fitbit) while another study found a wide range in correlation (intraclass cc 0.36-0.70, fitbit and jawbone). using several different comparison measures (indirect and direct calorimetry, accelerometry, self-report), energy expenditure was more often under-estimated by either tracker. total sleep time and sleep efficiency were over-estimated and wake after sleep onset was under-estimated comparing metrics from polysomnography to either tracker using a normal mode setting. no studies of intradevice reliability were found. interdevice reliability was reported on seven studies using the fitbit, but none for the jawbone. walking- and running-based fitbit trials indicated consistently high interdevice reliability for steps (pearson and intraclass cc 0.76-1.00), distance (intraclass cc 0.90-0.99), and energy expenditure (pearson and intraclass cc 0.71-0.97). when wearing two fitbits while sleeping, consistency between the devices was high. conclusion this systematic review indicated higher validity of steps, few studies on distance and physical activity, and lower validity for energy expenditure and sleep. the evidence reviewed indicated high interdevice reliability for steps, distance, energy expenditure, and sleep for certain fitbit models. as new activity trackers and features are introduced to the market, documentation of the measurement properties can guide their use in research settings.",0
"objectives this study aims to (1) elucidate whether the hawthorne effect exists, (2) explore under what conditions, and (3) estimate the size of any such effect. study design and setting this systematic review summarizes and evaluates the strength of available evidence on the hawthorne effect. an inclusive definition of any form of research artifact on behavior using this label, and without cointerventions, was adopted. results nineteen purposively designed studies were included, providing quantitative data on the size of the effect in eight randomized controlled trials, five quasiexperimental studies, and six observational evaluations of reporting on one's behavior by answering questions or being directly observed and being aware of being studied. although all but one study was undertaken within health sciences, study methods, contexts, and findings were highly heterogeneous. most studies reported some evidence of an effect, although significant biases are judged likely because of the complexity of the evaluation object. conclusion consequences of research participation for behaviors being investigated do exist, although little can be securely known about the conditions under which they operate, their mechanisms of effects, or their magnitudes. new concepts are needed to guide empirical studies.",0
"meta-analysis in the presence of unexplained heterogeneity is frequently undertaken by using a random-effects model, in which the effects underlying different studies are assumed to be drawn from a normal distribution. here we discuss the justification and interpretation of such models, by addressing in turn the aims of estimation, prediction and hypothesis testing. a particular issue that we consider is the distinction between inference on the mean of the random-effects distribution and inference on the whole distribution. we suggest that random-effects meta-analyses as currently conducted often fail to provide the key results, and we investigate the extent to which distribution-free, classical and bayesian approaches can provide satisfactory methods. we conclude that the bayesian approach has the advantage of naturally allowing for full uncertainty, especially for prediction. however, it is not without problems, including computational intensity and sensitivity to a priori judgements. we propose a simple prediction interval for classical meta-analysis and offer extensions to standard practice of bayesian meta-analysis, making use of an example of studies of 'set shifting' ability in people with eating disorders.",0
"naive cd4(+) t cell differentiation into distinct subsets of t helper (th) cells is a pivotal process in the initiation of the adaptive immune response. allergens predominantly stimulate th2 cells, causing allergic inflammation. however, why allergens induce th2 cell differentiation is not well understood. here we show that group 2 innate lymphoid cells (ilc2s) are required to mount a robust th2 cell response to the protease-allergen papain. intranasal administration of papain stimulated ilc2s and th2 cells, causing allergic lung inflammation and elevated immunoglobulin e titers. this process was severely impaired in ilc2-deficient mice. whereas interleukin-4 (il-4) was dispensable for papain-induced th2 cell differentiation, ilc2-derived il-13 was critical as it promoted migration of activated lung dendritic cells into the draining lymph node where they primed naive t cells to differentiate into th2 cells. papain-induced ilc2 activation and th2 cell differentiation was il-33-dependent, suggesting a common pathway in the initiation of th2 cell responses to allergen.",0
"fibroblasts are the major mesenchymal cell type in connective tissue and deposit the collagen and elastic fibres of the extracellular matrix (ecm). even within a single tissue, fibroblasts exhibit considerable functional diversity, but it is not known whether this reflects the existence of a differentiation hierarchy or is a response to different environmental factors. here we show, using transplantation assays and lineage tracing in mice, that the fibroblasts of skin connective tissue arise from two distinct lineages. one forms the upper dermis, including the dermal papilla that regulates hair growth and the arrector pili muscle, which controls piloerection. the other forms the lower dermis, including the reticular fibroblasts that synthesize the bulk of the fibrillar ecm, and the preadipocytes and adipocytes of the hypodermis. the upper lineage is required for hair follicle formation. in wounded adult skin, the initial wave of dermal repair is mediated by the lower lineage and upper dermal fibroblasts are recruited only during re-epithelialization. epidermal β-catenin activation stimulates the expansion of the upper dermal lineage, rendering wounds permissive for hair follicle formation. our findings explain why wounding is linked to formation of ecm-rich scar tissue that lacks hair follicles. they also form a platform for discovering fibroblast lineages in other tissues and for examining fibroblast changes in ageing and disease.",0
"background an outbreak of coronavirus disease 2019 (covid-19) occurred in wuhan, china; the epidemic is more widespread than initially estimated, with cases now confirmed in multiple countries. aims the aim of this meta-analysis was to assess the prevalence of comorbidities in the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infected patients and the risk of underlying diseases in severe patients compared to non-severe patients. methods a literature search was conducted using the databases pubmed, embase, and web of science through february 25, 2020. odds ratios (ors) and 95% confidence intervals (cis) were pooled using random-effects models. results seven studies were included in the meta-analysis, including 1 576 infected patients. the results showed the most prevalent clinical symptom was fever (91.3%, 95% ci: 86-97%), followed by cough (67.7%, 95% ci: 59-76%), fatigue (51.0%, 95% ci: 34-68%) and dyspnea (30.4%, 95% ci: 21-40%). the most prevalent comorbidities were hypertension (21.1%, 95% ci: 13.0-27.2%) and diabetes (9.7%, 95% ci: 7.2-12.2%), followed by cardiovascular disease (8.4%, 95% ci: 3.8-13.8%) and respiratory system disease (1.5%, 95% ci: 0.9-2.1%). when compared between severe and non-severe patients, the pooled or of hypertension, respiratory system disease, and cardiovascular disease were 2.36 (95% ci: 1.46-3.83), 2.46 (95% ci: 1.76-3.44) and 3.42 (95% ci: 1.88-6.22) respectively. conclusion we assessed the prevalence of comorbidities in the covid-19 patients and found that underlying disease, including hypertension, respiratory system disease and cardiovascular disease, may be risk factors for severe patients compared with non-severe patients.",0
"objectives to describe new who 2020 guidelines on physical activity and sedentary behaviour. methods the guidelines were developed in accordance with who protocols. an expert guideline development group reviewed evidence to assess associations between physical activity and sedentary behaviour for an agreed set of health outcomes and population groups. the assessment used and systematically updated recent relevant systematic reviews; new primary reviews addressed additional health outcomes or subpopulations. results the new guidelines address children, adolescents, adults, older adults and include new specific recommendations for pregnant and postpartum women and people living with chronic conditions or disability. all adults should undertake 150-300 min of moderate-intensity, or 75-150 min of vigorous-intensity physical activity, or some equivalent combination of moderate-intensity and vigorous-intensity aerobic physical activity, per week. among children and adolescents, an average of 60 min/day of moderate-to-vigorous intensity aerobic physical activity across the week provides health benefits. the guidelines recommend regular muscle-strengthening activity for all age groups. additionally, reducing sedentary behaviours is recommended across all age groups and abilities, although evidence was insufficient to quantify a sedentary behaviour threshold. conclusion these 2020 who guidelines update previous who recommendations released in 2010. they reaffirm messages that some physical activity is better than none, that more physical activity is better for optimal health outcomes and provide a new recommendation on reducing sedentary behaviours. these guidelines highlight the importance of regularly undertaking both aerobic and muscle strengthening activities and for the first time, there are specific recommendations for specific populations including for pregnant and postpartum women and people living with chronic conditions or disability. these guidelines should be used to inform national health policies aligned with the who global action plan on physical activity 2018-2030 and to strengthen surveillance systems that track progress towards national and global targets.",0
"to understand the genetic heterogeneity underlying developmental delay, we compared copy number variants (cnvs) in 15,767 children with intellectual disability and various congenital defects (cases) to cnvs in 8,329 unaffected adult controls. we estimate that ∼14.2% of disease in these children is caused by cnvs >400 kb. we observed a greater enrichment of cnvs in individuals with craniofacial anomalies and cardiovascular defects compared to those with epilepsy or autism. we identified 59 pathogenic cnvs, including 14 new or previously weakly supported candidates, refined the critical interval for several genomic disorders, such as the 17q21.31 microdeletion syndrome, and identified 940 candidate dosage-sensitive genes. we also developed methods to opportunistically discover small, disruptive cnvs within the large and growing diagnostic array datasets. this evolving cnv morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders.",0
"this study investigated regional variations in the contribution made by different human papilloma (hpv) types to invasive cervical cancer (icc). a total of 85 studies using polymerase chain reaction to estimate hpv prevalence in icc were identified. data on hpv prevalence were extracted separately for squamous cell carcinoma (scc) and for adeno- and adenosquamous-carcinoma (adc). a total of 10 058 cases (8550 scc, 1508 adc) were included in pooled analyses. the most common hpv types in icc were, in order of decreasing prevalence, hpv16, 18, 45, 31, 33, 58, 52, 35, 59, 56, 6, 51, 68, 39, 82, 73, 66 and 70. in scc, hpv16 was the predominant type (46-63%) followed by hpv18 (10-14%), 45 (2-8%), 31 (2-7%) and 33 (3-5%) in all regions except asia, where hpv types 58 (6%) and 52 (4%) were more frequently identified. in adc, hpv prevalence was significantly lower (76.4%) than in scc (87.3%), and hpv18 was the predominant type in every region (37-41%), followed by 16 (26-36%) and 45 (5-7%). the overall detection of hpv dna was similar in different regions (83-89%). a majority of icc was associated with hpv16 or 18 in all regions, but approximately a quarter of all icc cases were associated with one of 16 other hpv types, their distribution varying by region.",0
"brain networks or 'connectomes' include a minority of highly connected hub nodes that are functionally valuable, because their topological centrality supports integrative processing and adaptive behaviours. recent studies also suggest that hubs have higher metabolic demands and longer-distance connections than other brain regions, and therefore could be considered biologically costly. assuming that hubs thus normally combine both high topological value and high biological cost, we predicted that pathological brain lesions would be concentrated in hub regions. to test this general hypothesis, we first identified the hubs of brain anatomical networks estimated from diffusion tensor imaging data on healthy volunteers (n = 56), and showed that computational attacks targeted on hubs disproportionally degraded the efficiency of brain networks compared to random attacks. we then prepared grey matter lesion maps, based on meta-analyses of published magnetic resonance imaging data on more than 20 000 subjects and 26 different brain disorders. magnetic resonance imaging lesions that were common across all brain disorders were more likely to be located in hubs of the normal brain connectome (p < 10(-4), permutation test). specifically, nine brain disorders had lesions that were significantly more likely to be located in hubs (p < 0.05, permutation test), including schizophrenia and alzheimer's disease. both these disorders had significantly hub-concentrated lesion distributions, although (almost completely) distinct subsets of cortical hubs were lesioned in each disorder: temporal lobe hubs specifically were associated with higher lesion probability in alzheimer's disease, whereas in schizophrenia lesions were concentrated in both frontal and temporal cortical hubs. these results linking pathological lesions to the topological centrality of nodes in the normal diffusion tensor imaging connectome were generally replicated when hubs were defined instead by the meta-analysis of more than 1500 task-related functional neuroimaging studies of healthy volunteers to create a normative functional co-activation network. we conclude that the high cost/high value hubs of human brain networks are more likely to be anatomically abnormal than non-hubs in many (if not all) brain disorders.",0
"we present a major update of the hocomoco collection that consists of patterns describing dna binding specificities for human and mouse transcription factors. in this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (tf) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred tfs with previously unknown binding specificities. this was achieved by systematic motif discovery from more than five thousand chip-seq experiments uniformly processed within the biouml framework with several chip-seq peak calling tools and aggregated in the gtrd database. hocomoco v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. an interactive interface and bulk downloads are available on the web: and in this release, we complement hocomoco by molotool (motif location toolbox, that applies hocomoco models for visualization of binding sites in short dna sequences.",0
"the genetic make-up of an individual contributes to the susceptibility and response to viral infection. although environmental, clinical and social factors have a role in the chance of exposure to sars-cov-2 and the severity of covid-19 1,2 , host genetics may also be important. identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for sars-cov-2 infection and outcomes. we formed a global network of researchers to investigate the role of human genetics in sars-cov-2 infection and covid-19 severity. here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with covid-19 from 46 studies across 19 countries. we report 13 genome-wide significant loci that are associated with sars-cov-2 infection or severe manifestations of covid-19. several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases 3-7 . they also represent potentially actionable mechanisms in response to infection. mendelian randomization analyses support a causal role for smoking and body-mass index for severe covid-19 although not for type ii diabetes. the identification of novel host genetic factors associated with covid-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. this working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.",0
"apoptosis, the cell's natural mechanism for death, is a promising target for anticancer therapy. both the intrinsic and extrinsic pathways use caspases to carry out apoptosis through the cleavage of hundreds of proteins. in cancer, the apoptotic pathway is typically inhibited through a wide variety of means including overexpression of antiapoptotic proteins and under-expression of proapoptotic proteins. many of these changes cause intrinsic resistance to the most common anticancer therapy, chemotherapy. promising new anticancer therapies are plant-derived compounds that exhibit anticancer activity through activating the apoptotic pathway.",0
"exosomes are membrane vesicles secreted by hematopoietic cells upon fusion of late multivesicular endosomes with the plasma membrane. dendritic cell (dc)-derived exosomes induce potent antitumor immune responses in mice, resulting in the regression of established tumors (zitvogel, l., a. regnault, a. lozier, j. wolfers, c. flament, d. tenza, p. ricciardi-castagnoli, g. raposo, and s. amigorena. 1998. nat. med. 4:594-600). to unravel the molecular basis of exosome-induced immune stimulation, we now analyze the regulation of their production during dc maturation and characterize extensively their protein composition by peptide mass mapping. exosomes contain several cytosolic proteins (including annexin ii, heat shock cognate protein hsc73, and heteromeric g protein gi2alpha), as well as different integral or peripherally associated membrane proteins (major histocompatibility complex class ii, mac-1 integrin, cd9, milk fat globule-egf-factor viii ). mfg-e8, the major exosomal component, binds integrins expressed by dcs and macrophages, suggesting that it may be involved in exosome targeting to these professional antigen-presenting cells. another exosome component is hsc73, a cytosolic heat shock protein (hsp) also present in dc endocytic compartments. hsc73 was shown to induce antitumor immune responses in vivo, and therefore could be involved in the exosome's potent antitumor effects. finally, exosome production is downregulated upon dc maturation, indicating that in vivo, exosomes are produced by immature dcs in peripheral tissues. thus, dc-derived exosomes accumulate a defined subset of cellular proteins reflecting their endosomal biogenesis and accounting for their biological function.",0
"assessing mitochondrial dysfunction requires definition of the dysfunction to be investigated. usually, it is the ability of the mitochondria to make atp appropriately in response to energy demands. where other functions are of interest, tailored solutions are required. dysfunction can be assessed in isolated mitochondria, in cells or in vivo, with different balances between precise experimental control and physiological relevance. there are many methods to measure mitochondrial function and dysfunction in these systems. generally, measurements of fluxes give more information about the ability to make atp than do measurements of intermediates and potentials. for isolated mitochondria, the best assay is mitochondrial respiratory control: the increase in respiration rate in response to adp. for intact cells, the best assay is the equivalent measurement of cell respiratory control, which reports the rate of atp production, the proton leak rate, the coupling efficiency, the maximum respiratory rate, the respiratory control ratio and the spare respiratory capacity. measurements of membrane potential provide useful additional information. measurement of both respiration and potential during appropriate titrations enables the identification of the primary sites of effectors and the distribution of control, allowing deeper quantitative analyses. many other measurements in current use can be more problematic, as discussed in the present review.",0
"background choosing a suitable sample size in qualitative research is an area of conceptual debate and practical uncertainty. that sample size principles, guidelines and tools have been developed to enable researchers to set, and justify the acceptability of, their sample size is an indication that the issue constitutes an important marker of the quality of qualitative research. nevertheless, research shows that sample size sufficiency reporting is often poor, if not absent, across a range of disciplinary fields. methods a systematic analysis of single-interview-per-participant designs within three health-related journals from the disciplines of psychology, sociology and medicine, over a 15-year period, was conducted to examine whether and how sample sizes were justified and how sample size was characterised and discussed by authors. data pertinent to sample size were extracted and analysed using qualitative and quantitative analytic techniques. results our findings demonstrate that provision of sample size justifications in qualitative health research is limited; is not contingent on the number of interviews; and relates to the journal of publication. defence of sample size was most frequently supported across all three journals with reference to the principle of saturation and to pragmatic considerations. qualitative sample sizes were predominantly - and often without justification - characterised as insufficient (i.e., 'small') and discussed in the context of study limitations. sample size insufficiency was seen to threaten the validity and generalizability of studies' results, with the latter being frequently conceived in nomothetic terms. conclusions we recommend, firstly, that qualitative health researchers be more transparent about evaluations of their sample size sufficiency, situating these within broader and more encompassing assessments of data adequacy. secondly, we invite researchers critically to consider how saturation parameters found in prior methodological studies and sample size community norms might best inform, and apply to, their own project and encourage that data adequacy is best appraised with reference to features that are intrinsic to the study at hand. finally, those reviewing papers have a vital role in supporting and encouraging transparent study-specific reporting.",0
"for determination of the physiological role and mechanism of vacuolar proteolysis in the yeast saccharomyces cerevisiae, mutant cells lacking proteinase a, b, and carboxypeptidase y were transferred from a nutrient medium to a synthetic medium devoid of various nutrients and morphological changes of their vacuoles were investigated. after incubation for 1 h in nutrient-deficient media, a few spherical bodies appeared in the vacuoles and moved actively by brownian movement. these bodies gradually increased in number and after 3 h they filled the vacuoles almost completely. during their accumulation, the volume of the vacuolar compartment also increased. electron microscopic examination showed that these bodies were surrounded by a unit membrane which appeared thinner than any other intracellular membrane. the contents of the bodies were morphologically indistinguishable from the cytosol; these bodies contained cytoplasmic ribosomes, rer, mitochondria, lipid granules and glycogen granules, and the density of the cytoplasmic ribosomes in the bodies was almost the same as that of ribosomes in the cytosol. the diameter of the bodies ranged from 400 to 900 nm. vacuoles that had accumulated these bodies were prepared by a modification of the method of ohsumi and anraku (ohsumi, y., and y. anraku. 1981. j. biol. chem. 256:2079-2082). the isolated vacuoles contained ribosomes and showed latent activity of the cytosolic enzyme glucose-6-phosphate dehydrogenase. these results suggest that these bodies sequestered the cytosol in the vacuoles. we named these spherical bodies ""autophagic bodies."" accumulation of autophagic bodies in the vacuoles was induced not only by nitrogen starvation, but also by depletion of nutrients such as carbon and single amino acids that caused cessation of the cell cycle. genetic analysis revealed that the accumulation of autophagic bodies in the vacuoles was the result of lack of the prb1 product proteinase b, and disruption of the prb1 gene confirmed this result. in the presence of pmsf, wild-type cells accumulated autophagic bodies in the vacuoles under nutrient-deficient conditions in the same manner as did multiple protease-deficient mutants or cells with a disrupted prb1 gene. as the autophagic bodies disappeared rapidly after removal of pmsf from cultures of normal cells, they must be an intermediate in the normal autophagic process. this is the first report that nutrient-deficient conditions induce extensive autophagic degradation of cytosolic components in the vacuoles of yeast cells.",0
"background dna methylation levels change with age. recent studies have identified biomarkers of chronological age based on dna methylation levels. it is not yet known whether dna methylation age captures aspects of biological age. results here we test whether differences between people's chronological ages and estimated ages, dna methylation age, predict all-cause mortality in later life. the difference between dna methylation age and chronological age (δage) was calculated in four longitudinal cohorts of older people. meta-analysis of proportional hazards models from the four cohorts was used to determine the association between δage and mortality. a 5-year higher δage is associated with a 21% higher mortality risk, adjusting for age and sex. after further adjustments for childhood iq, education, social class, hypertension, diabetes, cardiovascular disease, and apoe e4 status, there is a 16% increased mortality risk for those with a 5-year higher δage. a pedigree-based heritability analysis of δage was conducted in a separate cohort. the heritability of δage was 0.43. conclusions dna methylation-derived measures of accelerated aging are heritable traits that predict mortality independently of health status, lifestyle factors, and known genetic factors.",0
"the effects exerted on the in vitro development of antigen-specific t cell lines and t cell clones by addition or neutralization of interleukin 12 (il-12) in lymphocyte bulk culture were examined. t cell lines specific for dermatophagoides pteronyssinus group i (der p i) derived in the presence of il-12 exhibited reduced ability to produce il-4 and increased ability to produce interferon gamma (ifn-gamma), and developed into der p i-specific cd4+ t cell clones showing a t helper type 0 (th0)- or th1-, instead of th2-, like cytokine profile. in contrast, purified protein derivative (ppd)-specific t cell lines derived in the presence of anti-il-12 antibody exhibited an increased ability to produce il-4 and developed into ppd-specific cd4+ t cell clones showing a th0-, instead of th1-, like profile. the influence of il-12 on the cytokine secretion profile of der p i-specific t cell lines was not prevented by addition to lymphocyte bulk cultures of anti-ifn-gamma antibody, but could be at least partially inhibited by the removal from bulk cultures of cd16+ cells. thus, il-12 and cd16+ cells appear to have inhibitory effects on the development of il-4-producing cells and to play an inductive role in promoting th1-like responses.",0
"background the use of positive psychological interventions may be considered as a complementary strategy in mental health promotion and treatment. the present article constitutes a meta-analytical study of the effectiveness of positive psychology interventions for the general public and for individuals with specific psychosocial problems. methods we conducted a systematic literature search using pubmed, psychinfo, the cochrane register, and manual searches. forty articles, describing 39 studies, totaling 6,139 participants, met the criteria for inclusion. the outcome measures used were subjective well-being, psychological well-being and depression. positive psychology interventions included self-help interventions, group training and individual therapy. results the standardized mean difference was 0.34 for subjective well-being, 0.20 for psychological well-being and 0.23 for depression indicating small effects for positive psychology interventions. at follow-up from three to six months, effect sizes are small, but still significant for subjective well-being and psychological well-being, indicating that effects are fairly sustainable. heterogeneity was rather high, due to the wide diversity of the studies included. several variables moderated the impact on depression: interventions were more effective if they were of longer duration, if recruitment was conducted via referral or hospital, if interventions were delivered to people with certain psychosocial problems and on an individual basis, and if the study design was of low quality. moreover, indications for publication bias were found, and the quality of the studies varied considerably. conclusions the results of this meta-analysis show that positive psychology interventions can be effective in the enhancement of subjective well-being and psychological well-being, as well as in helping to reduce depressive symptoms. additional high-quality peer-reviewed studies in diverse (clinical) populations are needed to strengthen the evidence-base for positive psychology interventions.",0
"the accumulation of misfolded proteins is a fundamental pathogenic process in neurodegenerative diseases. however, the factors that trigger aggregation of α-synuclein (α-syn), the principal component of the intraneuronal inclusions known as lewy bodies (lbs), and lewy neurites (lns), which characterize parkinson's disease (pd) and dementia with lbs (dlb), are poorly understood. we show here that in young asymptomatic α-syn transgenic (tg) mice, intracerebral injections of brain homogenates derived from older tg mice exhibiting α-syn pathology accelerate both the formation of intracellular lb/ln-like inclusions and the onset of neurological symptoms in recipient animals. pathological α-syn propagated along major central nervous system (cns) pathways to regions far beyond injection sites and reduced survival with a highly reproducible interval from injection to death in inoculated animals. importantly, inoculation with α-syn amyloid fibrils assembled from recombinant human α-syn induced identical consequences. furthermore, we show for the first time that synthetic α-syn fibrils are wholly sufficient to initiate pd-like lbs/lns and to transmit disease in vivo. thus, our data point to a prion-like cascade in synucleinopathies whereby cell-cell transmission and propagation of misfolded α-syn underlie the cns spread of lbs/lns. these findings open up new avenues for understanding the progression of pd and for developing novel therapeutics.",0
"reactive oxygen species- (ros-) induced lipid peroxidation plays a critical role in cell death including apoptosis, autophagy, and ferroptosis. this fundamental and conserved mechanism is based on an excess of ros which attacks biomembranes, propagates lipid peroxidation chain reactions, and subsequently induces different types of cell death. a highly evolved sophisticated antioxidant system exists that acts to protect the cells from oxidative damage. in this review, we discussed how ros propagate lipid peroxidation chain reactions and how the products of lipid peroxidation initiate apoptosis and autophagy in current models. we also discussed the mechanism of lipid peroxidation during ferroptosis, and we summarized lipid peroxidation in pathological conditions of critical illness. we aim to bring a more global and integrative sight to know how different ros-induced lipid peroxidation occurs among apoptosis, autophagy, and ferroptosis.",0
"genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. we conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. we identified 29 additional risk loci (p < 5 × 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. after annotating associated regions using grail, expression quantitative trait loci data and correlations with non-synonymous snps, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including il1r2, il8ra-il8rb, il7r, il12b, dap, prdm1, jak2, irf5, gna12 and lsp1. the total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between crohn's disease and ulcerative colitis.",0
"aims we previously reported that in the empa-reg outcome(®) trial, empagliflozin added to standard of care reduced the risk of 3-point major adverse cardiovascular events, cardiovascular and all-cause death, and hospitalization for heart failure in patients with type 2 diabetes and high cardiovascular risk. we have now further investigated heart failure outcomes in all patients and in subgroups, including patients with or without baseline heart failure. methods and results patients were randomized to receive empagliflozin 10 mg, empagliflozin 25 mg, or placebo. seven thousand and twenty patients were treated; 706 (10.1%) had heart failure at baseline. heart failure hospitalization or cardiovascular death occurred in a significantly lower percentage of patients treated with empagliflozin than with placebo [hazard ratio, hr: 0.66 (95% confidence interval: 0.55-0.79); p conclusion in patients with type 2 diabetes and high cardiovascular risk, empagliflozin reduced heart failure hospitalization and cardiovascular death, with a consistent benefit in patients with and without baseline heart failure.",0
"quantitative measurements of environmental factors greatly improve the quality of epidemiologic studies but can pose challenges because of the presence of upper or lower detection limits or interfering compounds, which do not allow for precise measured values. we consider the regression of an environmental measurement (dependent variable) on several covariates (independent variables). various strategies are commonly employed to impute values for interval-measured data, including assignment of one-half the detection limit to nondetected values or of ""fill-in"" values randomly selected from an appropriate distribution. on the basis of a limited simulation study, we found that the former approach can be biased unless the percentage of measurements below detection limits is small (5-10%). the fill-in approach generally produces unbiased parameter estimates but may produce biased variance estimates and thereby distort inference when 30% or more of the data are below detection limits. truncated data methods (e.g., tobit regression) and multiple imputation offer two unbiased approaches for analyzing measurement data with detection limits. if interest resides solely on regression parameters, then tobit regression can be used. if individualized values for measurements below detection limits are needed for additional analysis, such as relative risk regression or graphical display, then multiple imputation produces unbiased estimates and nominal confidence intervals unless the proportion of missing data is extreme. we illustrate various approaches using measurements of pesticide residues in carpet dust in control subjects from a case-control study of non-hodgkin lymphoma.",0
"hunger is a complex behavioural state that elicits intense food seeking and consumption. these behaviours are rapidly recapitulated by activation of starvation-sensitive agrp neurons, which present an entry point for reverse-engineering neural circuits for hunger. here we mapped synaptic interactions of agrp neurons with multiple cell populations in mice and probed the contribution of these distinct circuits to feeding behaviour using optogenetic and pharmacogenetic techniques. an inhibitory circuit with paraventricular hypothalamus (pvh) neurons substantially accounted for acute agrp neuron-evoked eating, whereas two other prominent circuits were insufficient. within the pvh, we found that agrp neurons target and inhibit oxytocin neurons, a small population that is selectively lost in prader-willi syndrome, a condition involving insatiable hunger. by developing strategies for evaluating molecularly defined circuits, we show that agrp neuron suppression of oxytocin neurons is critical for evoked feeding. these experiments reveal a new neural circuit that regulates hunger state and pathways associated with overeating disorders.",0
"human angiotensin-converting enzyme 2 (ace2) is a functional receptor for sars coronavirus (sars-cov). here we identify the sars-cov spike (s)-protein-binding site on ace2. we also compare s proteins of sars-cov isolated during the 2002-2003 sars outbreak and during the much less severe 2003-2004 outbreak, and from palm civets, a possible source of sars-cov found in humans. all three s proteins bound to and utilized palm-civet ace2 efficiently, but the latter two s proteins utilized human ace2 markedly less efficiently than did the s protein obtained during the earlier human outbreak. the lower affinity of these s proteins could be complemented by altering specific residues within the s-protein-binding site of human ace2 to those of civet ace2, or by altering s-protein residues 479 and 487 to residues conserved during the 2002-2003 outbreak. collectively, these data describe molecular interactions important to the adaptation of sars-cov to human cells, and provide insight into the severity of the 2002-2003 sars epidemic.",0
"background despite growing recognition of neglectful, abusive, and disrespectful treatment of women during childbirth in health facilities, there is no consensus at a global level on how these occurrences are defined and measured. this mixed-methods systematic review aims to synthesize qualitative and quantitative evidence on the mistreatment of women during childbirth in health facilities to inform the development of an evidence-based typology of the phenomenon. methods and findings we searched pubmed, cinahl, and embase databases and grey literature using a predetermined search strategy to identify qualitative, quantitative, and mixed-methods studies on the mistreatment of women during childbirth across all geographical and income-level settings. we used a thematic synthesis approach to synthesize the qualitative evidence and assessed the confidence in the qualitative review findings using the cerqual approach. in total, 65 studies were included from 34 countries. qualitative findings were organized under seven domains: (1) physical abuse, (2) sexual abuse, (3) verbal abuse, (4) stigma and discrimination, (5) failure to meet professional standards of care, (6) poor rapport between women and providers, and (7) health system conditions and constraints. due to high heterogeneity of the quantitative data, we were unable to conduct a meta-analysis; instead, we present descriptions of study characteristics, outcome measures, and results. additional themes identified in the quantitative studies are integrated into the typology. conclusions this systematic review presents a comprehensive, evidence-based typology of the mistreatment of women during childbirth in health facilities, and demonstrates that mistreatment can occur at the level of interaction between the woman and provider, as well as through systemic failures at the health facility and health system levels. we propose this typology be adopted to describe the phenomenon and be used to develop measurement tools and inform future research, programs, and interventions.",0
"background reliable estimates of populations affected by diseases are necessary to guide efficient allocation of public health resources. sickle haemoglobin (hbs) is the most common and clinically significant haemoglobin structural variant, but no contemporary estimates exist of the global populations affected. moreover, the precision of available national estimates of heterozygous (as) and homozygous (ss) neonates is unknown. we aimed to provide evidence-based estimates at various scales, with uncertainty measures. methods using a database of sickle haemoglobin surveys, we created a contemporary global map of hbs allele frequency distribution within a bayesian geostatistical model. the pairing of this map with demographic data enabled calculation of global, regional, and national estimates of the annual number of as and ss neonates. subnational estimates were also calculated in data-rich areas. findings our map shows subnational spatial heterogeneities and high allele frequencies across most of sub-saharan africa, the middle east, and india, as well as gene flow following migrations to western europe and the eastern coast of the americas. accounting for local heterogeneities and demographic factors, we estimated that the global number of neonates affected by hbs in 2010 included 5,476,000 (iqr 5,291,000-5,679,000) as neonates and 312,000 (294,000-330,000) ss neonates. these global estimates are higher than previous conservative estimates. important differences predicted at the national level are discussed. interpretation hbs will have an increasing effect on public health systems. our estimates can help countries and the international community gauge the need for appropriate diagnoses and genetic counselling to reduce the number of neonates affected. similar mapping and modelling methods could be used for other inherited disorders. funding the wellcome trust.",0
"studying the metabolism of immune cells in recent years has emphasized the tight link existing between the metabolic state and the phenotype of these cells. macrophages in particular are a good example of this phenomenon. whether the macrophage obtains its energy through glycolysis or through oxidative metabolism can give rise to different phenotypes. classically activated or m1 macrophages are key players of the first line of defense against bacterial infections and are known to obtain energy through glycolysis. alternatively activated or m2 macrophages on the other hand are involved in tissue repair and wound healing and use oxidative metabolism to fuel their longer-term functions. metabolic intermediates, however, are not just a source of energy but can be directly implicated in a particular macrophage phenotype. in m1 macrophages, the krebs cycle intermediate succinate regulates hif1α, which is responsible for driving the sustained production of the pro-inflammatory cytokine il1β. in m2 macrophages, the sedoheptulose kinase carbohydrate kinase-like protein is critical for regulating the pentose phosphate pathway. the potential to target these events and impact on disease is an exciting prospect.",0
"key amino acid positions that are important for maintaining the 3d structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, dna or other proteins, are often under strong evolutionary constraints. thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. consurf ( is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. we present here version 3.0 of consurf. this new version includes an empirical bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. moreover, consurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.",0
"by centralizing many of the tasks associated with the upkeep of scientific software, sbgrid allows researchers to spend more of their time on research.",0
"background asthma is a major cause of disability, health resource utilization and poor quality of life world-wide. we set out to generate estimates of the global burden of asthma in adults, which may inform the development of strategies to address this common disease. methods the world health survey (whs) was developed and implemented by the world health organization in 2002-2003. a total of 178,215 individuals from 70 countries aged 18 to 45 years responded to questions related to asthma and related symptoms. the prevalence of asthma was based on responses to questions relating to self-reported doctor diagnosed asthma, clinical/treated asthma, and wheezing in the last 12 months. results the global prevalence rates of doctor diagnosed asthma, clinical/treated asthma and wheezing in adults were 4.3%, 4.5%, and 8.6% respectively, and varied by as much as 21-fold amongst the 70 countries. australia reported the highest rate of doctor diagnosed, clinical/treated asthma, and wheezing (21.0%, 21.5%, and 27.4%). amongst those with clinical/treated asthma, almost 24% were current smokers, half reported wheezing, and 20% had never been treated for asthma. conclusions this study provides a global estimate of the burden of asthma in adults, and suggests that asthma continues to be a major public health concern worldwide. the high prevalence of smoking remains a major barrier to combating the global burden of asthma. while the highest prevalence rates were observed in resource-rich countries, resource-poor nations were also significantly affected, posing a barrier to development as it stretches further the demands of non-communicable diseases.",0
"unified, structured vocabularies and classifications freely provided by the gene ontology (go) consortium are widely accepted in most of the large scale gene annotation projects. consequently, many tools have been created for use with the go ontologies. wego (web gene ontology annotation plot) is a simple but useful tool for visualizing, comparing and plotting go annotation results. different from other commercial software for creating chart, wego is designed to deal with the directed acyclic graph structure of go to facilitate histogram creation of go annotation results. wego has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. it has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. wego, along with the two other tools, namely external to go query and go archive query, are freely available for all users at there are two available mirror sites at and any suggestions are welcome at wego@genomics.org.cn.",0
"prediction of clinical outcome in cancer is usually achieved by histopathological evaluation of tissue samples obtained during surgical resection of the primary tumor. traditional tumor staging (ajcc/uicc-tnm classification) summarizes data on tumor burden (t), presence of cancer cells in draining and regional lymph nodes (n) and evidence for metastases (m). however, it is now recognized that clinical outcome can significantly vary among patients within the same stage. the current classification provides limited prognostic information, and does not predict response to therapy. recent literature has alluded to the importance of the host immune system in controlling tumor progression. thus, evidence supports the notion to include immunological biomarkers, implemented as a tool for the prediction of prognosis and response to therapy. accumulating data, collected from large cohorts of human cancers, has demonstrated the impact of immune-classification, which has a prognostic value that may add to the significance of the ajcc/uicc tnm-classification. it is therefore imperative to begin to incorporate the 'immunoscore' into traditional classification, thus providing an essential prognostic and potentially predictive tool. introduction of this parameter as a biomarker to classify cancers, as part of routine diagnostic and prognostic assessment of tumors, will facilitate clinical decision-making including rational stratification of patient treatment. equally, the inherent complexity of quantitative immunohistochemistry, in conjunction with protocol variation across laboratories, analysis of different immune cell types, inconsistent region selection criteria, and variable ways to quantify immune infiltration, all underline the urgent requirement to reach assay harmonization. in an effort to promote the immunoscore in routine clinical settings, an international task force was initiated. this review represents a follow-up of the announcement of this initiative, and of the j transl med. editorial from january 2012. immunophenotyping of tumors may provide crucial novel prognostic information. the results of this international validation may result in the implementation of the immunoscore as a new component for the classification of cancer, designated tnm-i (tnm-immune).",0
"to identify endocytic receptors that allow dendritic cells (dcs) to capture and present antigens on major histocompatibility complex (mhc) class i products in vivo, we evaluated dec-205, which is abundant on dcs in lymphoid tissues. ovalbumin (ova) protein, when chemically coupled to monoclonal alphadec-205 antibody, was presented by cd11c+ lymph node dcs, but not by cd11c- cells, to ova-specific, cd4+ and cd8+ t cells. receptor-mediated presentation was at least 400 times more efficient than unconjugated ova and, for mhc class i, the dcs had to express transporter of antigenic peptides (tap) transporters. when alphadec-205:ova was injected subcutaneously, ova protein was identified over a 4-48 h period in dcs, primarily in the lymph nodes draining the injection site. in vivo, the ova protein was selectively presented by dcs to tcr transgenic cd8+ cells, again at least 400 times more effectively than soluble ova and in a tap-dependent fashion. targeting of alphadec-205:ova to dcs in the steady state initially induced 4-7 cycles of t cell division, but the t cells were then deleted and the mice became specifically unresponsive to rechallenge with ova in complete freund's adjuvant. in contrast, simultaneous delivery of a dc maturation stimulus via cd40, together with alphadec-205:ova, induced strong immunity. the cd8+ t cells responding in the presence of agonistic alphacd40 antibody produced large amounts of interleukin 2 and interferon gamma, acquired cytolytic function in vivo, emigrated in large numbers to the lung, and responded vigorously to ova rechallenge. therefore, dec-205 provides an efficient receptor-based mechanism for dcs to process proteins for mhc class i presentation in vivo, leading to tolerance in the steady state and immunity after dc maturation.",0
"influx of ca(2+) through store-operated ca(2+) channels (socs) is a central component of receptor-evoked ca(2+) signals. orai channels are socs that are gated by stim1, a ca(2+) sensor located in the er but how it gates and regulates the orai channels is unknown. here, we report the molecular basis for gating of orais by stim1. all orai channels are fully activated by the conserved stim1 amino acid fragment 344-442, which we termed soar (the stim1 orai activating region). soar acts in combination with stim1 (450-485) to regulate the strength of interaction with orai1. activation of orai1 by soar recapitulates all the kinetic properties of orai1 activation by stim1. however, mutations of stim1 within soar prevent activation of orai1 but not co-clustering of stim1 and orai1 in response to ca(2+) store depletion, indicating that stim1-orai1 co-clustering is not sufficient for orai1 activation. an intact carboxy terminus alpha-helicial region of orai is required for activation by soar. deleting most of the orai1 amino terminus impaired orai1 activation by stim1, but orai1(delta1-73) interacted with and was fully activated by soar. accordingly, the characteristic inward rectification of orai is mediated by an interaction between the polybasic stim1 (672-685) and a pro-rich region in the n terminus of orai1. hence, the essential properties of orai1 function can be rationalized by interactions with discrete regions of stim1.",0
"heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. unlike existing non-commercial heat map packages, which either lack graphical interfaces or are specialized for only one or two kinds of heat maps, heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. more specifically, heatmapper allows users to generate, cluster and visualize: (i) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; (ii) pairwise distance maps; (iii) correlation maps; (iv) image overlay heat maps; (v) latitude and longitude heat maps and (vi) geopolitical (choropleth) heat maps. heatmapper offers a number of simple and intuitive customization options for facile adjustments to each heat map's appearance and plotting parameters. heatmapper also allows users to interactively explore their numeric data values by hovering their cursor over each heat map cell, or by using a searchable/sortable data table view. heat map data can be easily uploaded to heatmapper in text, excel or tab delimited formatted tables and the resulting heat map images can be easily downloaded in common formats including png, jpg and pdf. heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, environmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geologists, educators and students. heatmapper is available at",0
"background the syntheses of multiple qualitative studies can pull together data across different contexts, generate new theoretical or conceptual models, identify research gaps, and provide evidence for the development, implementation and evaluation of health interventions. this study aims to develop a framework for reporting the synthesis of qualitative health research. methods we conducted a comprehensive search for guidance and reviews relevant to the synthesis of qualitative research, methodology papers, and published syntheses of qualitative health research in medline, embase, cinahl and relevant organisational websites to may 2011. initial items were generated inductively from guides to synthesizing qualitative health research. the preliminary checklist was piloted against forty published syntheses of qualitative research, purposively selected to capture a range of year of publication, methods and methodologies, and health topics. we removed items that were duplicated, impractical to assess, and rephrased items for clarity. results the enhancing transparency in reporting the synthesis of qualitative research (entreq) statement consists of 21 items grouped into five main domains: introduction, methods and methodology, literature search and selection, appraisal, and synthesis of findings. conclusions the entreq statement can help researchers to report the stages most commonly associated with the synthesis of qualitative health research: searching and selecting qualitative research, quality appraisal, and methods for synthesising qualitative findings. the synthesis of qualitative research is an expanding and evolving methodological area and we would value feedback from all stakeholders for the continued development and extension of the entreq statement.",0
"unlabelled genome-wide association studies (gwas) have revealed hundreds of loci associated with common human genetic diseases and traits. we have developed a web-based plotting tool that provides fast visual display of gwas results in a publication-ready format. locuszoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (ld) and recombination patterns and the positions of genes in the region. availability locuszoom can be accessed from a web interface at users may generate a single plot using a web form, or many plots using batch mode. the software utilizes ld information from hapmap phase ii (ceu, yri and jpt+chb) or 1000 genomes (ceu) and gene information from the ucsc browser, and will accept snp identifiers in dbsnp or 1000 genomes format. single plots are generated in approximately 20 s. source code and associated databases are available for download and local installation, and full documentation is available online.",0
"objective to determine the prevalence of people with diabetes who meet hemoglobin a1c (a1c), blood pressure (bp), and ldl cholesterol (abc) recommendations and their current statin use, factors associated with goal achievement, and changes in the proportion achieving goals between 1988 and 2010. research design and methods data were cross-sectional from the national health and nutrition examination surveys (nhanes) from 1988-1994, 1999-2002, 2003-2006, and 2007-2010. participants were 4,926 adults aged ≥ 20 years who self-reported a previous diagnosis of diabetes and completed the household interview and physical examination (n = 1,558 for valid ldl levels). main outcome measures were a1c, bp, and ldl cholesterol, in accordance with the american diabetes association recommendations, and current use of statins. results in 2007-2010, 52.5% of people with diabetes achieved a1c conclusions despite significant improvement during the past decade, achieving the abc goals remains suboptimal among adults with diabetes, particularly in some minority groups. substantial opportunity exists to further improve diabetes control and, thus, to reduce diabetes-related morbidity and mortality.",0
"dna barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. we provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). we utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. we find that the lowest overall error for species identification is 4%. in contrast, barcoding performs poorly in incompletely sampled groups. here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. whereas proponents envision a ""barcoding gap"" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. moreover, error rates double if only traditionally recognized species are analyzed. thus, dna barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. however, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. the promise of barcoding will be realized only if based on solid taxonomic foundations.",0
"in the absence of perfusable vascular networks, three-dimensional (3d) engineered tissues densely populated with cells quickly develop a necrotic core. yet the lack of a general approach to rapidly construct such networks remains a major challenge for 3d tissue culture. here, we printed rigid 3d filament networks of carbohydrate glass, and used them as a cytocompatible sacrificial template in engineered tissues containing living cells to generate cylindrical networks that could be lined with endothelial cells and perfused with blood under high-pressure pulsatile flow. because this simple vascular casting approach allows independent control of network geometry, endothelialization and extravascular tissue, it is compatible with a wide variety of cell types, synthetic and natural extracellular matrices, and crosslinking strategies. we also demonstrated that the perfused vascular channels sustained the metabolic function of primary rat hepatocytes in engineered tissue constructs that otherwise exhibited suppressed function in their core.",0
"objective the colonic microbiota ferment dietary fibres, producing short chain fatty acids. recent evidence suggests that the short chain fatty acid propionate may play an important role in appetite regulation. we hypothesised that colonic delivery of propionate would increase peptide yy (pyy) and glucagon like peptide-1 (glp-1) secretion in humans, and reduce energy intake and weight gain in overweight adults. design to investigate whether propionate promotes pyy and glp-1 secretion, a primary cultured human colonic cell model was developed. to deliver propionate specifically to the colon, we developed a novel inulin-propionate ester. an acute randomised, controlled cross-over study was used to assess the effects of this inulin-propionate ester on energy intake and plasma pyy and glp-1 concentrations. the long-term effects of inulin-propionate ester on weight gain were subsequently assessed in a randomised, controlled 24-week study involving 60 overweight adults. results propionate significantly stimulated the release of pyy and glp-1 from human colonic cells. acute ingestion of 10 g inulin-propionate ester significantly increased postprandial plasma pyy and glp-1 and reduced energy intake. over 24 weeks, 10 g/day inulin-propionate ester supplementation significantly reduced weight gain, intra-abdominal adipose tissue distribution, intrahepatocellular lipid content and prevented the deterioration in insulin sensitivity observed in the inulin-control group. conclusions these data demonstrate for the first time that increasing colonic propionate prevents weight gain in overweight adult humans. trial registration number nct00750438.",0
"oxidative stress is a component of many diseases, including atherosclerosis, chronic obstructive pulmonary disease, alzheimer disease and cancer. although numerous small molecules evaluated as antioxidants have exhibited therapeutic potential in preclinical studies, clinical trial results have been disappointing. a greater understanding of the mechanisms through which antioxidants act and where and when they are effective may provide a rational approach that leads to greater pharmacological success. here, we review the relationships between oxidative stress, redox signalling and disease, the mechanisms through which oxidative stress can contribute to pathology, how antioxidant defences work, what limits their effectiveness and how antioxidant defences can be increased through physiological signalling, dietary components and potential pharmaceutical intervention.",0
"autophagy maintains cell, tissue and organism homeostasis through degradation. complex post-translational modulation of the atg (autophagy-related) proteins adds additional entry points for crosstalk with other cellular processes and helps define cell-type-specific regulations of autophagy. beyond the simplistic view of a process exclusively dedicated to the turnover of cellular components, recent data have uncovered unexpected functions for autophagy and the autophagy-related genes, such as regulation of metabolism, membrane transport and modulation of host defenses--indicating the novel frontiers lying ahead.",0
"chemokine receptors serve as coreceptors for hiv entry into cd4+ cells. their expression is thought to determine the tropism of viral strains for different cell types, and also to influence susceptibility to infection and rates of disease progression. of the chemokine receptors, ccr5 is the most important for viral transmission, since ccr5 is the principal receptor for primary, macrophage-tropic viruses, and individuals homozygous for a defective ccr5 allele (delta32/delta32) are highly resistant to infection with hiv-1. in this study, ccr5-specific mabs were generated using transfectants expressing high levels of ccr5. the specificity of these mabs was confirmed using a broad panel of chemokine receptor transfectants, and by their non-reactivity with t cells from delta32/delta32 individuals. ccr5 showed a distinct pattern of expression, being abundant on long-term activated, il-2-stimulated t cells, on a subset of effector/memory t cells in blood, and on tissue macrophages. a comparison of normal and ccr5 delta32 heterozygotes revealed markedly reduced expression of ccr5 on t cells from the heterozygotes. there was considerable individual to individual variability in the expression of ccr5 on blood t cells, that related to factors other than ccr5 genotype. low expression of ccr5 correlated with the reduced infectability of t cells with macrophage-tropic hiv-1, in vitro. anti-ccr5 mabs inhibited the infection of pbmc by macrophage-tropic hiv-1 in vitro, but did not inhibit infection by t cell-tropic virus. anti-ccr5 mabs were poor inhibitors of chemokine binding, indicating that hiv-1 and ligands bind to separate, but overlapping regions of ccr5. these results illustrate many of the important biological features of ccr5, and demonstrate the feasibility of blocking macrophage-tropic hiv-1 entry into cells with an anti-ccr5 reagent.",0
"diagnostic accuracy relates to the ability of a test to discriminate between the target condition and health. this discriminative potential can be quantified by the measures of diagnostic accuracy such as sensitivity and specificity, predictive values, likelihood ratios, the area under the roc curve, youden's index and diagnostic odds ratio. different measures of diagnostic accuracy relate to the different aspects of diagnostic procedure: while some measures are used to assess the discriminative property of the test, others are used to assess its predictive ability. measures of diagnostic accuracy are not fixed indicators of a test performance, some are very sensitive to the disease prevalence, while others to the spectrum and definition of the disease. furthermore, measures of diagnostic accuracy are extremely sensitive to the design of the study. studies not meeting strict methodological standards usually over- or under-estimate the indicators of test performance as well as they limit the applicability of the results of the study. stard initiative was a very important step toward the improvement the quality of reporting of studies of diagnostic accuracy. stard statement should be included into the instructions to authors by scientific journals and authors should be encouraged to use the checklist whenever reporting their studies on diagnostic accuracy. such efforts could make a substantial difference in the quality of reporting of studies of diagnostic accuracy and serve to provide the best possible evidence to the best for the patient care. this brief review outlines some basic definitions and characteristics of the measures of diagnostic accuracy.",0
"jaspar ( is an open-access database of curated, non-redundant transcription factor (tf)-binding profiles stored as position frequency matrices (pfms) for tfs across multiple species in six taxonomic groups. in this 8th release of jaspar, the core collection has been expanded with 245 new pfms (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 pfms were updated (125 for vertebrates, 28 for plants and 3 for insects). these new profiles represent an 18% expansion compared to the previous release. jaspar 2020 comes with a novel collection of unvalidated tf-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. this collection has a dedicated web form to engage the community in the curation of unvalidated tf-binding profiles. moreover, we created a q&a forum to ease the communication between the user community and jaspar curators. finally, we updated the genomic tracks, inference tool, and tf-binding profile similarity clusters. all the data is available through the jaspar website, its associated restful api, and through the jaspar2020 r/bioconductor package.",0
"pancreatic cancer is the seventh leading cause of cancer-related deaths worldwide. however, its toll is higher in more developed countries. reasons for vast differences in mortality rates of pancreatic cancer are not completely clear yet, but it may be due to lack of appropriate diagnosis, treatment and cataloging of cancer cases. because patients seldom exhibit symptoms until an advanced stage of the disease, pancreatic cancer remains one of the most lethal malignant neoplasms that caused 432,242 new deaths in 2018 (globocan 2018 estimates). globally, 458,918 new cases of pancreatic cancer have been reported in 2018, and 355,317 new cases are estimated to occur until 2040. despite advancements in the detection and management of pancreatic cancer, the 5-year survival rate still stands at 9% only. to date, the causes of pancreatic carcinoma are still insufficiently known, although certain risk factors have been identified, such as tobacco smoking, diabetes mellitus, obesity, dietary factors, alcohol abuse, age, ethnicity, family history and genetic factors, helicobacter pylori infection , non-o blood group and chronic pancreatitis. in general population, screening of large groups is not considered useful to detect the disease at its early stage, although newer techniques and the screening of tightly targeted groups (especially of those with family history), are being evaluated. primary prevention is considered of utmost importance. up-to-date statistics on pancreatic cancer occurrence and outcome along with a better understanding of the etiology and identifying the causative risk factors are essential for the primary prevention of this disease.",0
"background a primary focus of self-care interventions for chronic illness is the encouragement of an individual's behavior change necessitating knowledge sharing, education, and understanding of the condition. the use of the internet to deliver web-based interventions to patients is increasing rapidly. in a 7-year period (1996 to 2003), there was a 12-fold increase in medline citations for ""web-based therapies."" the use and effectiveness of web-based interventions to encourage an individual's change in behavior compared to non-web-based interventions have not been substantially reviewed. objective this meta-analysis was undertaken to provide further information on patient/client knowledge and behavioral change outcomes after web-based interventions as compared to outcomes seen after implementation of non-web-based interventions. methods the medline, cinahl, cochrane library, embase, eric, and psychinfo databases were searched for relevant citations between the years 1996 and 2003. identified articles were retrieved, reviewed, and assessed according to established criteria for quality and inclusion/exclusion in the study. twenty-two articles were deemed appropriate for the study and selected for analysis. effect sizes were calculated to ascertain a standardized difference between the intervention (web-based) and control (non-web-based) groups by applying the appropriate meta-analytic technique. homogeneity analysis, forest plot review, and sensitivity analyses were performed to ascertain the comparability of the studies. results aggregation of participant data revealed a total of 11,754 participants (5,841 women and 5,729 men). the average age of participants was 41.5 years. in those studies reporting attrition rates, the average drop out rate was 21% for both the intervention and control groups. for the five web-based studies that reported usage statistics, time spent/session/person ranged from 4.5 to 45 minutes. session logons/person/week ranged from 2.6 logons/person over 32 weeks to 1008 logons/person over 36 weeks. the intervention designs included one-time web-participant health outcome studies compared to non-web participant health outcomes, self-paced interventions, and longitudinal, repeated measure intervention studies. longitudinal studies ranged from 3 weeks to 78 weeks in duration. the effect sizes for the studied outcomes ranged from -.01 to .75. broad variability in the focus of the studied outcomes precluded the calculation of an overall effect size for the compared outcome variables in the web-based compared to the non-web-based interventions. homogeneity statistic estimation also revealed widely differing study parameters (q(w16) = 49.993, p conclusions the effect size comparisons in the use of web-based interventions compared to non-web-based interventions showed an improvement in outcomes for individuals using web-based interventions to achieve the specified knowledge and/or behavior change for the studied outcome variables. these outcomes included increased exercise time, increased knowledge of nutritional status, increased knowledge of asthma treatment, increased participation in healthcare, slower health decline, improved body shape perception, and 18-month weight loss maintenance.",0
"the production of ros (reactive oxygen species) by mammalian mitochondria is important because it underlies oxidative damage in many pathologies and contributes to retrograde redox signalling from the organelle to the cytosol and nucleus. superoxide (o2(*-)) is the proximal mitochondrial ros, and in the present review i outline the principles that govern o2(*-) production within the matrix of mammalian mitochondria. the flux of o2(*-) is related to the concentration of potential electron donors, the local concentration of o2 and the second-order rate constants for the reactions between them. two modes of operation by isolated mitochondria result in significant o2(*-) production, predominantly from complex i: (i) when the mitochondria are not making atp and consequently have a high deltap (protonmotive force) and a reduced coq (coenzyme q) pool; and (ii) when there is a high nadh/nad+ ratio in the mitochondrial matrix. for mitochondria that are actively making atp, and consequently have a lower deltap and nadh/nad+ ratio, the extent of o2(*-) production is far lower. the generation of o2(*-) within the mitochondrial matrix depends critically on deltap, the nadh/nad+ and coqh2/coq ratios and the local o2 concentration, which are all highly variable and difficult to measure in vivo. consequently, it is not possible to estimate o2(*-) generation by mitochondria in vivo from o2(*-)-production rates by isolated mitochondria, and such extrapolations in the literature are misleading. even so, the description outlined here facilitates the understanding of factors that favour mitochondrial ros production. there is a clear need to develop better methods to measure mitochondrial o2(*-) and h2o2 formation in vivo, as uncertainty about these values hampers studies on the role of mitochondrial ros in pathological oxidative damage and redox signalling.",0
"the universal protein resource (uniprot) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. the uniprot knowledgebase (uniprotkb), comprising the manually annotated uniprotkb/swiss-prot section and the automatically annotated uniprotkb/trembl section, is the preeminent storehouse of protein annotation. the extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. the uniprot reference clusters (uniref) speed similarity searches via sequence space compression by merging sequences that are 100% (uniref100), 90% (uniref90) or 50% (uniref50) identical. finally, the uniprot archive (uniparc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. uniprot databases continue to grow in size and in availability of information. recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. new download availability includes all major releases of uniprotkb, sequence collections by taxonomic division and complete proteomes. a bibliography mapping service has been added, and an id mapping service will be available soon. uniprot databases can be accessed online at or downloaded at ftp://ftp.uniprot.org/pub/databases/.",0
"background the gap between research and practice or policy is often described as a problem. to identify new barriers of and facilitators to the use of evidence by policymakers, and assess the state of research in this area, we updated a systematic review. methods systematic review. we searched online databases including medline, embase, socsci abstracts, cds, dare, psychlit, cochrane library, nhseed, hta, pais, ibss (search dates: july 2000 - september 2012). studies were included if they were primary research or systematic reviews about factors affecting the use of evidence in policy. studies were coded to extract data on methods, topic, focus, results and population. results 145 new studies were identified, of which over half were published after 2010. thirteen systematic reviews were included. compared with the original review, a much wider range of policy topics was found. although still primarily in the health field, studies were also drawn from criminal justice, traffic policy, drug policy, and partnership working. the most frequently reported barriers to evidence uptake were poor access to good quality relevant research, and lack of timely research output. the most frequently reported facilitators were collaboration between researchers and policymakers, and improved relationships and skills. there is an increasing amount of research into new models of knowledge transfer, and evaluations of interventions such as knowledge brokerage. conclusions timely access to good quality and relevant research evidence, collaborations with policymakers and relationship- and skills-building with policymakers are reported to be the most important factors in influencing the use of evidence. although investigations into the use of evidence have spread beyond the health field and into more countries, the main barriers and facilitators remained the same as in the earlier review. few studies provide clear definitions of policy, evidence or policymaker. nor are empirical data about policy processes or implementation of policy widely available. it is therefore difficult to describe the role of evidence and other factors influencing policy. future research and policy priorities should aim to illuminate these concepts and processes, target the factors identified in this review, and consider new methods of overcoming the barriers described.",0
"background and objectives the tumor microenvironment has been widely implicated in tumorigenesis because it harbors tumor cells that interact with surrounding cells through the circulatory and lymphatic systems to influence the development and progression of cancer. in addition, nonmalignant cells in the tumor microenvironment play critical roles in all the stages of carcinogenesis by stimulating and facilitating uncontrolled cell proliferation. aim this study aims to explore the concept of the tumor microenvironment by conducting a critical review of previous studies on the topic. materials and methods: this review relies on evidence presented in previous studies related to the topic. the articles included in this review were obtained from different medical and health databases. results and discussion the tumor microenvironment has received significant attention in the cancer literature, with a particular focus on its role in tumor development and progression. previous studies have identified various components of the tumor microenvironment that influence malignant behavior and progression. in addition to malignant cells, adipocytes, fibroblasts, tumor vasculature, lymphocytes, dendritic cells, and cancer-associated fibroblasts are present in the tumor microenvironment. each of these cell types has unique immunological capabilities that determine whether the tumor will survive and affect neighboring cells. conclusion the tumor microenvironment harbors cancer stem cells and other molecules that contribute to tumor development and progression. consequently, targeting and manipulating the cells and factors in the tumor microenvironment during cancer treatment can help control malignancies and achieve positive health outcomes.",0
"in this report, we show that cross-presentation of self-antigens can lead to the peripheral deletion of autoreactive cd8(+) t cells. we had previously shown that transfer of ovalbumin (ova)-specific cd8(+) t cells (ot-i cells) into rat insulin promoter-membrane-bound form of ova transgenic mice, which express the model autoantigen ova in the proximal tubular cells of the kidneys, the beta cells of the pancreas, the thymus, and the testis of male mice, led to the activation of ot-i cells in the draining lymph nodes. this was due to class i-restricted cross-presentation of exogenous ova on a bone marrow-derived antigen presenting cell (apc) population. here, we show that adoptively transferred or thymically derived ot-i cells activated by cross-presentation are deleted from the peripheral pool of recirculating lymphocytes. such deletion only required antigen recognition on a bone marrow-derived population, suggesting that cells of the professional apc class may be tolerogenic under these circumstances. our results provide a mechanism by which the immune system can induce cd8(+) t cell tolerance to autoantigens that are expressed outside the recirculation pathway of naive t cells.",0
"the advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. we propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of dna donated by the other individuals. results of this ""chromosome painting"" can be summarized as a ""coancestry matrix,"" which directly reveals key information about ancestral relationships among individuals. if markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard principal components analysis (pca) and model-based approaches such as structure in a unified manner. furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using pca. in parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over pca in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. we analyse human genome diversity panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. we present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. the software used for this article, chromopainter and finestructure, is available from",0
"objective severe acute respiratory syndrome (sars) was the first massive infectious disease outbreak of the 21st century. however, it is unlikely that this outbreak will be the last. this study aimed to evaluate the long-term psychiatric morbidities in survivors of sars. method this is a cohort study designed to investigate psychiatric complications among sars survivors treated in the united christian hospital 30 months after the sars outbreak. psychiatric morbidities were assessed by the structured clinical interview for dsm-iv, the impact of events scale-revised and the hospital anxiety and depression scale. functional outcomes were assessed by the medical outcomes study 36-item short-form health survey. results ninety subjects were recruited, yielding a response rate of 96.8%. post-sars cumulative incidence of dsm-iv psychiatric disorders was 58.9%. current prevalence for any psychiatric disorder at 30 months post-sars was 33.3%. one-fourth of the patients had post-traumatic stress disorder (ptsd), and 15.6% had depressive disorders. conclusion the outbreak of sars can be regarded as a mental health catastrophe. ptsd was the most prevalent long-term psychiatric condition, followed by depressive disorders. our results highlight the need to enhance preparedness and competence of health care professionals in detecting and managing the psychological sequelae of future comparable infectious disease outbreaks.",0
"dengue is currently regarded globally as the most important mosquito-borne viral disease. a history of symptoms compatible with dengue can be traced back to the chin dynasty of 265-420 ad. the virus and its vectors have now become widely distributed throughout tropical and subtropical regions of the world, particularly over the last half-century. significant geographic expansion has been coupled with rapid increases in incident cases, epidemics, and hyperendemicity, leading to the more severe forms of dengue. transmission of dengue is now present in every world health organization (who) region of the world and more than 125 countries are known to be dengue endemic. the true impact of dengue globally is difficult to ascertain due to factors such as inadequate disease surveillance, misdiagnosis, and low levels of reporting. currently available data likely grossly underestimates the social, economic, and disease burden. estimates of the global incidence of dengue infections per year have ranged between 50 million and 200 million; however, recent estimates using cartographic approaches suggest this number is closer to almost 400 million. the expansion of dengue is expected to increase due to factors such as the modern dynamics of climate change, globalization, travel, trade, socioeconomics, settlement and also viral evolution. no vaccine or specific antiviral therapy currently exists to address the growing threat of dengue. prompt case detection and appropriate clinical management can reduce the mortality from severe dengue. effective vector control is the mainstay of dengue prevention and control. surveillance and improved reporting of dengue cases is also essential to gauge the true global situation as indicated in the objectives of the who global strategy for dengue prevention and control, 2012-2020. more accurate data will inform the prioritization of research, health policy, and financial resources toward reducing this poorly controlled disease. the objective of this paper is to review historical and current epidemiology of dengue worldwide and, additionally, reflect on some potential reasons for expansion of dengue into the future.",0
"murine l929 fibrosarcoma cells treated with tumor necrosis factor (tnf) rapidly die in a necrotic way, due to excessive formation of reactive oxygen intermediates. we investigated the role of caspases in the necrotic cell death pathway. when the cytokine response modifier a (crma), a serpin-like caspase inhibitor of viral origin, was stably overexpressed in l929 cells, the latter became 1,000-fold more sensitive to tnf-mediated cell death. in addition, tnf sensitization was also observed when the cells were pretreated with ac-yvad-cmk or zdevd-fmk, which inhibits caspase-1- and caspase-3-like proteases, respectively. zvad-fmk and zd-fmk, two broad-spectrum inhibitors of caspases, also rendered the cells more sensitive, since the half-maximal dose for tnf-mediated necrosis decreased by a factor of 1,000. the presence of zvad-fmk also resulted in a more rapid increase of tnf-mediated production of oxygen radicals. zvad-fmk-dependent sensitization of tnf cytotoxicity could be completely inhibited by the oxygen radical scavenger butylated hydroxyanisole. these results indicate an involvement of caspases in protection against tnf-induced formation of oxygen radicals and necrosis.",0
"sars-cov-2 enters cells using its spike protein, which is also the main target of neutralizing antibodies. therefore, assays to measure how antibodies and sera affect spike-mediated viral infection are important for studying immunity. because sars-cov-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with spike. such pseudotyping has now been described for single-cycle lentiviral, retroviral, and vesicular stomatitis virus (vsv) particles, but the reagents and protocols are not widely available. here, we detailed how to effectively pseudotype lentiviral particles with sars-cov-2 spike and infect 293t cells engineered to express the sars-cov-2 receptor, ace2. we also made all the key experimental reagents available in the bei resources repository of atcc and the nih. furthermore, we demonstrated how these pseudotyped lentiviral particles could be used to measure the neutralizing activity of human sera or plasma against sars-cov-2 in convenient luciferase-based assays, thereby providing a valuable complement to elisa-based methods that measure antibody binding rather than neutralization.",0
"background within systematic reviews, when searching for relevant references, it is advisable to use multiple databases. however, searching databases is laborious and time-consuming, as syntax of search strategies are database specific. we aimed to determine the optimal combination of databases needed to conduct efficient searches in systematic reviews and whether the current practice in published reviews is appropriate. while previous studies determined the coverage of databases, we analyzed the actual retrieval from the original searches for systematic reviews. methods since may 2013, the first author prospectively recorded results from systematic review searches that he performed at his institution. pubmed was used to identify systematic reviews published using our search strategy results. for each published systematic review, we extracted the references of the included studies. using the prospectively recorded results and the studies included in the publications, we calculated recall, precision, and number needed to read for single databases and databases in combination. we assessed the frequency at which databases and combinations would achieve varying levels of recall (i.e., 95%). for a sample of 200 recently published systematic reviews, we calculated how many had used enough databases to ensure 95% recall. results a total of 58 published systematic reviews were included, totaling 1746 relevant references identified by our database searches, while 84 included references had been retrieved by other search methods. sixteen percent of the included references (291 articles) were only found in a single database; embase produced the most unique references (n = 132). the combination of embase, medline, web of science core collection, and google scholar performed best, achieving an overall recall of 98.3 and 100% recall in 72% of systematic reviews. we estimate that 60% of published systematic reviews do not retrieve 95% of all available relevant references as many fail to search important databases. other specialized databases, such as cinahl or psycinfo, add unique references to some reviews where the topic of the review is related to the focus of the database. conclusions optimal searches in systematic reviews should search at least embase, medline, web of science, and google scholar as a minimum requirement to guarantee adequate and efficient coverage.",0
"crispr (clustered regularly interspaced short palindromic repeats) arrays and their associated (cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. crisprcasfinder allows the identification of both crispr arrays and cas proteins. the program includes: (i) an improved crispr array detection tool facilitating expert validation based on a rating system, (ii) prediction of crispr orientation and (iii) a cas protein detection and typing tool updated to match the latest classification scheme of these systems. crisprcasfinder can either be used online or as a standalone tool compatible with linux operating system. all third-party software packages employed by the program are freely available. crisprcasfinder is available at",0
"neopterin, a compound derived from gtp, represents a precursor molecule of biopterin that is an essential cofactor in neurotransmitter synthesis. we have recently reported that in vivo as well as in vitro immune responses are accompanied by an increased release of neopterin and that this phenomenon can be used for the biochemical monitoring of diseases accompanied by hyperimmune stimulation. this article deals with the cellular origin and the control of this immune response-associated neopterin release in vitro. using highly purified or monoclonal cellular reagents we demonstrate that macrophages (m phi) stimulated with supernatants from activated t cells release large amounts of neopterin into culture supernatants. further experiments involving induction of neopterin release from m phi with various human recombinant interferons (ifns) or neutralization of the effect of t cell supernatants with various monoclonal anti-ifn antibodies revealed immune ifn as the active principle. it thus appears that a metabolic pathway so far exclusively known in context with the generation of an essential cofactor of neurotransmitter-synthesis during immune responses is also activated in m phi under stringent control by immune ifn-like lymphokines.",0
"hospital-acquired infections with staphylococcus aureus, especially methicillin-resistant s. aureus (mrsa) infections, are a major cause of illness and death and impose serious economic costs on patients and hospitals. however, the recent magnitude and trend of these infections have not been reported. we used national hospitalization and resistance data to estimate the annual number of hospitalizations and deaths associated with s. aureus and mrsa from 1999 through 2005. during this period, the estimated number of s. aureus-related hospitalizations increased 62%, from 294,570 to 477,927, and the estimated number of mrsa-related hospitalizations more than doubled, from 127,036 to 278,203. our findings suggest that s. aureus and mrsa should be considered a national priority for disease control.",0
"programmed death-1 (pd-1) receptor, an inhibitory costimulatory molecule found on activated t cells, has been demonstrated to play a role in the regulation of immune responses and peripheral tolerance. we investigated the role of this pathway in the development of autoimmune diabetes. pd-1 or pd-l1 but not pd-l2 blockade rapidly precipitated diabetes in prediabetic female nonobese diabetic (nod) mice regardless of age (from 1 to 10-wk-old), although it was most pronounced in the older mice. by contrast, cytotoxic t lymphocyte-associated antigen 4 (ctla-4) blockade induced disease only in neonates. male nod mice also developed diabetes after pd-1-pd-l1 pathway blockade, but nor mice, congenic to nod but resistant to the development of diabetes, did not. insulitis scores were significantly higher and frequency of interferon gamma-producing gad-reactive splenocytes was increased after pd-1-pd-l1 pathway blockade compared with controls. interestingly, pd-l1 but not pd-l2 was found to be expressed on inflamed islets of nod mice. these data demonstrate a central role for pd-1-pd-l1 interaction in the regulation of induction and progression of autoimmune diabetes in the nod mouse and provide the rationale to develop new therapies to target this costimulatory pathway in this disease.",0
"aims to investigate the range of methods used to validate diagnoses in the general practice research database (gprd), to summarize findings and to assess the quality of these validations. methods a systematic literature review was performed by searching pubmed and embase for publications using gprd data published between 1987 and april 2008. additional publications were identified from conference proceedings, back issues of relevant journals, bibliographies of retrieved publications and relevant websites. publications that reported attempts to validate disease diagnoses recorded in the gprd were included. results we identified 212 publications, often validating more than one diagnosis. in total, 357 validations investigating 183 different diagnoses met our inclusion criteria. of these, 303 (85%) utilized data from outside the gprd to validate diagnoses. the remainder utilized only data recorded in the database. the median proportion of cases with a confirmed diagnosis was 89% (range 24-100%). details of validation methods and results were often incomplete. conclusions a number of methods have been used to assess validity. overall, estimates of validity were high. however, the quality of reporting of the validations was often inadequate to permit a clear interpretation. not all methods provided a quantitative estimate of validity and most methods considered only the positive predictive value of a set of diagnostic codes in a highly selected group of cases. we make recommendations for methodology and reporting to strengthen further the use of the gprd in research.",0
"programmed cell death 1 (pd-1) is a negative costimulatory receptor critical for the suppression of t cell activation in vitro and in vivo. single cell imaging elucidated a molecular mechanism of pd-1-mediated suppression. pd-1 becomes clustered with t cell receptors (tcrs) upon binding to its ligand pd-l1 and is transiently associated with the phosphatase shp2 (src homology 2 domain-containing tyrosine phosphatase 2). these negative costimulatory microclusters induce the dephosphorylation of the proximal tcr signaling molecules. this results in the suppression of t cell activation and blockade of the tcr-induced stop signal. in addition to pd-1 clustering, pd-1-tcr colocalization within microclusters is required for efficient pd-1-mediated suppression. this inhibitory mechanism also functions in pd-1(hi) t cells generated in vivo and can be overridden by a neutralizing anti-pd-l1 antibody. therefore, pd-1 microcluster formation is important for regulation of t cell activation.",0
"evidencemodeler (evm) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. evm, when combined with the program to assemble spliced alignments (pasa), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. our experiments on both rice and human genome sequences demonstrate that evm produces automated gene structure annotation approaching the quality of manual curation.",0
"fastme provides distance algorithms to infer phylogenies. fastme is based on balanced minimum evolution, which is the very principle of neighbor joining (nj). fastme improves over nj by performing topological moves using fast, sophisticated algorithms. the first version of fastme only included nearest neighbor interchange. the new 2.0 version also includes subtree pruning and regrafting, while remaining as fast as nj and providing a number of facilities: distance estimation for dna and proteins with various models and options, bootstrapping, and parallel computations. fastme is available using several interfaces: command-line (to be integrated in pipelines), phylip-like, and a web server (",0
"engineered transcription activator–like effector nucleases (talens) have shown promise as facile and broadly applicable genome editing tools. however, no publicly available high-throughput method for constructing talens has been published, and large-scale assessments of the success rate and targeting range of the technology remain lacking. here we describe the fast ligation-based automatable solid-phase high-throughput (flash) system, a rapid and cost-effective method for large-scale assembly of talens. we tested 48 flash-assembled talen pairs in a human cell–based egfp reporter system and found that all 48 possessed efficient gene-modification activities. we also used flash to assemble talens for 96 endogenous human genes implicated in cancer and/or epigenetic regulation and found that 84 pairs were able to efficiently introduce targeted alterations. our results establish the robustness of talen technology and demonstrate that flash facilitates high-throughput genome editing at a scale not currently possible with other genome modification technologies.",0
"background following publication of the prisma statement, the uk centre for reviews and dissemination (crd) at the university of york in england began to develop an international prospective register of systematic reviews with health-related outcomes. the objectives were to reduce unplanned duplication of reviews and provide transparency in the review process, with the aim of minimizing reporting bias. methods an international advisory group was formed and a consultation undertaken to establish the key items necessary for inclusion in the register and to gather views on various aspects of functionality. this article describes the development of the register, now called prospero, and the process of registration. results prospero offers free registration and free public access to a unique prospective register of systematic reviews across all areas of health from all around the world. the dedicated web-based interface is electronically searchable and available to all prospective registrants. at the moment, inclusion in prospero is restricted to systematic reviews of the effects of interventions and strategies to prevent, diagnose, treat, and monitor health conditions, for which there is a health-related outcome.ideally, registration should take place before the researchers have started formal screening against inclusion criteria but reviews are eligible as long as they have not progressed beyond the point of completing data extraction.the required dataset captures the key attributes of review design as well as the administrative details necessary for registration.submitted registration forms are checked against the scope for inclusion in prospero and for clarity of content before being made publicly available on the register, rejected, or returned to the applicant for clarification.the public records include an audit trail of major changes to planned methods, details of when the review has been completed, and links to resulting publications when provided by the authors. conclusions there has been international support and an enthusiastic response to the principle of prospective registration of protocols for systematic reviews and to the development of prospero.in october 2011, prospero contained 200 records of systematic reviews being undertaken in 26 countries around the world on a diverse range of interventions.",0
"mapping the pathways that give rise to metastasis is one of the key challenges of breast cancer research. recently, several large-scale studies have shed light on this problem through analysis of gene expression profiles to identify markers correlated with metastasis. here, we apply a protein-network-based approach that identifies markers not as individual genes but as subnetworks extracted from protein interaction databases. the resulting subnetworks provide novel hypotheses for pathways involved in tumor progression. although genes with known breast cancer mutations are typically not detected through analysis of differential expression, they play a central role in the protein network by interconnecting many differentially expressed genes. we find that the subnetwork markers are more reproducible than individual marker genes selected without network information, and that they achieve higher accuracy in the classification of metastatic versus non-metastatic tumors.",0
"background menarche and menopause mark the onset and cessation, respectively, of ovarian activity associated with reproduction, and affect breast cancer risk. our aim was to assess the strengths of their effects and determine whether they depend on characteristics of the tumours or the affected women. methods individual data from 117 epidemiological studies, including 118 964 women with invasive breast cancer and 306 091 without the disease, none of whom had used menopausal hormone therapy, were included in the analyses. we calculated adjusted relative risks (rrs) associated with menarche and menopause for breast cancer overall, and by tumour histology and by oestrogen receptor expression. findings breast cancer risk increased by a factor of 1·050 (95% ci 1·044-1·057; p interpretation the effects of menarche and menopause on breast cancer risk might not be acting merely by lengthening women's total number of reproductive years. endogenous ovarian hormones are more relevant for oestrogen receptor-positive disease than for oestrogen receptor-negative disease and for lobular than for ductal tumours. funding cancer research uk.",0
"as modern humans migrated out of africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. these diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. one of the most celebrated examples in humans is the adaptation of tibetans to the hypoxic environment of the high-altitude tibetan plateau. a hypoxia pathway gene, epas1, was previously identified as having the most extreme signature of positive selection in tibetans, and was shown to be associated with differences in haemoglobin concentration at high altitude. re-sequencing the region around epas1 in 40 tibetan and 40 han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of dna from denisovan or denisovan-related individuals into humans. scanning a larger set of worldwide populations, we find that the selected haplotype is only found in denisovans and in tibetans, and at very low frequency among han chinese. furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between tibetans and denisovans was caused by incomplete ancestral lineage sorting rather than introgression. our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.",0
"infectious diseases have for centuries ranked with wars and famine as major challenges to human progress and survival. they remain among the leading causes of death and disability worldwide. against a constant background of established infections, epidemics of new and old infectious diseases periodically emerge, greatly magnifying the global burden of infections. studies of these emerging infections reveal the evolutionary properties of pathogenic microorganisms and the dynamic relationships between microorganisms, their hosts and the environment.",0
"in this paper we present keratin expression data that lend strong support to a model of corneal epithelial maturation in which the stem cells are located in the limbus, the transitional zone between cornea and conjunctiva. using a new monoclonal antibody, ae5, which is highly specific for a 64,000-mol-wt corneal keratin, designated rk3, we demonstrate that this keratin is localized in all cell layers of rabbit corneal epithelium, but only in the suprabasal layers of the limbal epithelium. analysis of cultured corneal keratinocytes showed that they express sequentially three major keratin pairs. early cultures consisting of a monolayer of ""basal"" cells express mainly the 50/58k keratins, exponentially growing cells synthesize additional 48/56k keratins, and postconfluent, heavily stratified cultures begin to express the 55/64k corneal keratins. cell separation experiments showed that basal cells isolated from postconfluent cultures contain predominantly the 50/58k pair, whereas suprabasal cells contain additional 55/64k and 48/56k pairs. basal cells of the older, postconfluent cultures, however, can become ae5 positive, indicating that suprabasal location is not a prerequisite for the expression of the 64k keratin. taken together, these results suggest that the acidic 55k and basic 64k keratins represent markers for an advanced stage of corneal epithelial differentiation. the fact that epithelial basal cells of central cornea but not those of the limbus possess the 64k keratin therefore indicates that corneal basal cells are in a more differentiated state than limbal basal cells. these findings, coupled with the known centripetal migration of corneal epithelial cells, strongly suggest that corneal epithelial stem cells are located in the limbus, and that corneal basal cells correspond to ""transient amplifying cells"" in the scheme of ""stem cells----transient amplifying cells----terminally differentiated cells.""",0
"we analyzed 43 ctx-m-15-producing escherichia coli isolates and 6 plasmids encoding the blactx-m-15 gene from canada, india, kuwait, france, switzerland, portugal, and spain. most isolates belonged to phylogroups b2 (50%) and d (25%). an ec-b2 strain of clonal complex sequence type (st) 131 was detected in all countries; other b2 isolates corresponded to st28, st405, st354, and st695 from specific areas. ec-d strains were clonally unrelated but isolates from 3 countries belonged to st405. all ctx-m-15 plasmids corresponded to incfii group with overrepresentation of 3 hpai-digested plasmid dna profiles (a, b and c; 85-120kb, similarity > or =70%). plasmid a was detected in ec-b2 strains (st131, st354, or st405), plasmid c was detected in b2 and d strains, and plasmid b was confined to worldwide-disseminated st131. most plasmids contained blaoxa-1, aac(6')-ib-cr, and blatem-1. worldwide dissemination of ctx-m-15 seems to be determined by clonal complexes st131 and st405 and multidrug-resistant incfii plasmids.",0
"rebase is a comprehensive and fully curated database of information about the components of restriction-modification (rm) systems. it contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. all genomes that are completely sequenced are analyzed for rm system components, and with the advent of pacbio sequencing, the recognition sequences of dna methyltransferases (mtases) are appearing rapidly. thus, type i and type iii systems can now be characterized in terms of recognition specificity merely by dna sequencing. the contents of rebase may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). monthly updates are also available via email.",0
"the role of mitochondria in cell metabolism and survival is controlled by calcium signals that are commonly transmitted at the close associations between mitochondria and endoplasmic reticulum (er). however, the physical linkage of the er-mitochondria interface and its relevance for cell function remains elusive. we show by electron tomography that er and mitochondria are adjoined by tethers that are approximately 10 nm at the smooth er and approximately 25 nm at the rough er. limited proteolysis separates er from mitochondria, whereas expression of a short ""synthetic linker"" (<5 nm) leads to tightening of the associations. although normal connections are necessary and sufficient for proper propagation of er-derived calcium signals to the mitochondria, tightened connections, synthetic or naturally observed under apoptosis-inducing conditions, make mitochondria prone to ca2+ overloading and ensuing permeability transition. these results reveal an unexpected dependence of cell function and survival on the maintenance of proper spacing between the er and mitochondria.",0
"transient receptor potential (trp) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian trp channel, trpv1, at 3.4 å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. like voltage-gated channels, trpv1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (s5-s6) and the intervening pore loop, which is flanked by s1-s4 voltage-sensor-like domains. trpv1 has a wide extracellular 'mouth' with a short selectivity filter. the conserved 'trp domain' interacts with the s4-s5 linker, consistent with its contribution to allosteric modulation. subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. these observations provide a structural blueprint for understanding unique aspects of trp channel function.",0
"neurons are metabolically active cells with high energy demands at locations distant from the cell body. as a result, these cells are particularly dependent on mitochondrial function, as reflected by the observation that diseases of mitochondrial dysfunction often have a neurodegenerative component. recent discoveries have highlighted that neurons are reliant particularly on the dynamic properties of mitochondria. mitochondria are dynamic organelles by several criteria. they engage in repeated cycles of fusion and fission, which serve to intermix the lipids and contents of a population of mitochondria. in addition, mitochondria are actively recruited to subcellular sites, such as the axonal and dendritic processes of neurons. finally, the quality of a mitochondrial population is maintained through mitophagy, a form of autophagy in which defective mitochondria are selectively degraded. we review the general features of mitochondrial dynamics, incorporating recent findings on mitochondrial fusion, fission, transport and mitophagy. defects in these key features are associated with neurodegenerative disease. charcot-marie-tooth type 2a, a peripheral neuropathy, and dominant optic atrophy, an inherited optic neuropathy, result from a primary deficiency of mitochondrial fusion. moreover, several major neurodegenerative diseases--including parkinson's, alzheimer's and huntington's disease--involve disruption of mitochondrial dynamics. remarkably, in several disease models, the manipulation of mitochondrial fusion or fission can partially rescue disease phenotypes. we review how mitochondrial dynamics is altered in these neurodegenerative diseases and discuss the reciprocal interactions between mitochondrial fusion, fission, transport and mitophagy.",0
"schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. here we present analysis of the 363 megabase nuclear genome of the blood fluke. it encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. as the first sequenced flatworm, and a representative of the lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. our analysis has been informed by the need to find new drug targets. the deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. the information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.",0
"mesenchymal stem cells (mscs) were officially named more than 25 years ago to represent a class of cells from human and mammalian bone marrow and periosteum that could be isolated and expanded in culture while maintaining their in vitro capacity to be induced to form a variety of mesodermal phenotypes and tissues. the in vitro capacity to form bone, cartilage, fat, etc., became an assay for identifying this class of multipotent cells and around which several companies were formed in the 1990s to medically exploit the regenerative capabilities of mscs. today, there are hundreds of clinics and hundreds of clinical trials using human mscs with very few, if any, focusing on the in vitro multipotential capacities of these cells. unfortunately, the fact that mscs are called ""stem cells"" is being used to infer that patients will receive direct medical benefit, because they imagine that these cells will differentiate into regenerating tissue-producing cells. such a stem cell treatment will presumably cure the patient of their medically relevant difficulties ranging from osteoarthritic (bone-on-bone) knees to various neurological maladies including dementia. i now urge that we change the name of mscs to medicinal signaling cells to more accurately reflect the fact that these cells home in on sites of injury or disease and secrete bioactive factors that are immunomodulatory and trophic (regenerative) meaning that these cells make therapeutic drugs in situ that are medicinal. it is, indeed, the patient's own site-specific and tissue-specific resident stem cells that construct the new tissue as stimulated by the bioactive factors secreted by the exogenously supplied mscs. stem cells translational medicine 2017;6:1445-1451.",0
"purpose given incomplete data reporting by race, we used data on covid-19 cases and deaths in u.s. counties to describe racial disparities in covid-19 disease and death and associated determinants. methods using publicly available data (accessed april 13, 2020), predictors of covid-19 cases and deaths were compared between disproportionately (≥13%) black and all other ( results nearly 90% of disproportionately black counties (656/677) reported a case and 49% (330/677) reported a death versus 81% (1987/2465) and 28% (684/2465), respectively, for all other counties. counties with higher proportions of black people have higher prevalence of comorbidities and greater air pollution. counties with higher proportions of black residents had more covid-19 diagnoses (rate ratio (rr): 1.24, 95% confidence interval: 1.17-1.33) and deaths (rr: 1.18, 95% confidence interval: 1.00-1.40), after adjusting for county-level characteristics such as age, poverty, comorbidities, and epidemic duration. covid-19 deaths were higher in disproportionally black rural and small metro counties. the population attributable fraction of covid-19 diagnosis due to lack of health insurance was 3.3% for counties with less than 13% black residents and 4.2% for counties with greater than or equal to 13% black residents. conclusions nearly 20% of u.s. counties are disproportionately black, and they accounted for 52% of covid-19 diagnoses and 58% of covid-19 deaths nationally. county-level comparisons can both inform covid-19 responses and identify epidemic hot spots. social conditions, structural racism, and other factors elevate risk for covid-19 diagnoses and deaths in black communities.",0
"projections for the period 1995-2029 suggest that the number of men dying from mesothelioma in western europe each year will almost double over the next 20 years, from 5000 in 1998 to about 9000 around 2018, and then decline, with a total of about a quarter of a million deaths over the next 35 years. the highest risk will be suffered by men born around 1945-50, of whom about 1 in 150 will die of mesothelioma. asbestos use in western europe remained high until 1980, and substantial quantities are still used in several european countries. these projections are based on the fit of a simple age and birth cohort model to male pleural cancer mortality from 1970 to 1989 for six countries (britain, france, germany, italy, the netherlands and switzerland) which together account for three-quarters of the population of western europe. the model was tested by comparing observed and predicted numbers of deaths for the period 1990-94. the ratio of mesothelioma to recorded pleural cancer mortality has been 1.6:1 in britain but was assumed to be 1:1 in other countries.",0
"kaks_calculator is a software package that calculates nonsynonymous (ka) and synonymous (ks) substitution rates through model selection and model averaging. since existing methods for this estimation adopt their specific mutation (substitution) models that consider different evolutionary features, leading to diverse estimates, kaks_calculator implements a set of candidate models in a maximum likelihood framework and adopts the akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. in addition, several existing methods for calculating ka and ks are also incorporated into this software.",0
"recent epidemiological surveys conducted in general populations have found that the lifetime prevalence of depression is in the range of 10% to 15%. mood disorders, as defined by the world mental health and the diagnostic and statistical manual of mental disorders, 4th edition, have a 12-month prevalence which varies from 3% in japan to over 9% in the us. a recent american survey found the prevalence of current depression to be 9% and the rate of current major depression to be 3.4%. all studies of depressive disorders have stressed the importance of the mortality and morbidity associated with depression. the mortality risk for suicide in depressed patients is more than 20-fold greater than in the general population. recent studies have also shown the importance of depression as a risk factor for cardiovascular death. the risk of cardiac mortality after an initial myocardial infarction is greater in patients with depression and related to the severity of the depressive episode. greater severity of depressive symptoms has been found to be associated with significantly higher risk of all-cause mortality including cardiovascular death and stroke. in addition to mortality, functional impairment and disability associated with depression have been consistently reported. depression increases the risk of decreased workplace productivity and absenteeism resulting in lowered income or unemployment. absenteeism and presenteeism (being physically present at work but functioning suboptimally) have been estimated to result in a loss of $36.6 billion per year in the us. worldwide projections by the world health organization for the year 2030 identify unipolar major depression as the leading cause of disease burden. this article is a brief overview of how depression affects the quality of life of the subject and is also a huge burden for both the family of the depressed patient and for society at large.",0
"background quantifying the burden of parasitic diseases in relation to other diseases and injuries requires reliable estimates of prevalence for each disease and an analytic framework within which to estimate attributable morbidity and mortality. here we use data included in the global atlas of helminth infection to derive new global estimates of numbers infected with intestinal nematodes (soil-transmitted helminths, sth: ascaris lumbricoides, trichuris trichiura and the hookworms) and use disability-adjusted life years (dalys) to estimate disease burden. methods prevalence data for 6,091 locations in 118 countries were sourced and used to estimate age-stratified mean prevalence for sub-national administrative units via a combination of model-based geostatistics (for sub-saharan africa) and empirical approaches (for all other regions). geographical variation in infection prevalence within these units was approximated using modelled logit-normal distributions, and numbers of individuals with infection intensities above given thresholds estimated for each species using negative binomial distributions and age-specific worm/egg burden thresholds. finally, age-stratified prevalence estimates for each level of infection intensity were incorporated into the global burden of disease study 2010 analytic framework to estimate the global burden of morbidity and mortality associated with each sth infection. results globally, an estimated 438.9 million people (95% credible interval (ci), 406.3 - 480.2 million) were infected with hookworm in 2010, 819.0 million (95% ci, 771.7 - 891.6 million) with a. lumbricoides and 464.6 million (95% ci, 429.6 - 508.0 million) with t. trichiura. of the 4.98 million years lived with disability (ylds) attributable to sth, 65% were attributable to hookworm, 22% to a. lumbricoides and the remaining 13% to t. trichiura. the vast majority of sth infections (67%) and ylds (68%) occurred in asia. when considering ylds relative to total populations at risk however, the burden distribution varied more considerably within major global regions than between them. conclusion improvements in the cartography of helminth infection, combined with mathematical modelling approaches, have resulted in the most comprehensive contemporary estimates for the public health burden of sth. these numbers form an important benchmark upon which to evaluate future scale-up of major control efforts.",0
"introduction acute kidney injury (aki) can evolve quickly and clinical measures of function often fail to detect aki at a time when interventions are likely to provide benefit. identifying early markers of kidney damage has been difficult due to the complex nature of human aki, in which multiple etiologies exist. the objective of this study was to identify and validate novel biomarkers of aki. methods we performed two multicenter observational studies in critically ill patients at risk for aki - discovery and validation. the top two markers from discovery were validated in a second study (sapphire) and compared to a number of previously described biomarkers. in the discovery phase, we enrolled 522 adults in three distinct cohorts including patients with sepsis, shock, major surgery, and trauma and examined over 300 markers. in the sapphire validation study, we enrolled 744 adult subjects with critical illness and without evidence of aki at enrollment; the final analysis cohort was a heterogeneous sample of 728 critically ill patients. the primary endpoint was moderate to severe aki (kdigo stage 2 to 3) within 12 hours of sample collection. results moderate to severe aki occurred in 14% of sapphire subjects. the two top biomarkers from discovery were validated. urine insulin-like growth factor-binding protein 7 (igfbp7) and tissue inhibitor of metalloproteinases-2 (timp-2), both inducers of g1 cell cycle arrest, a key mechanism implicated in aki, together demonstrated an auc of 0.80 (0.76 and 0.79 alone). urine · was significantly superior to all previously described markers of aki (p 0.72. furthermore, · significantly improved risk stratification when added to a nine-variable clinical model when analyzed using cox proportional hazards model, generalized estimating equation, integrated discrimination improvement or net reclassification improvement. finally, in sensitivity analyses · remained significant and superior to all other markers regardless of changes in reference creatinine method. conclusions two novel markers for aki have been identified and validated in independent multicenter cohorts. both markers are superior to existing markers, provide additional information over clinical variables and add mechanistic insight into aki. trial registration clinicaltrials.gov number nct01209169.",0
"the electronic medical records and genomics network is a national human genome research institute-funded consortium engaged in the development of methods and best practices for using the electronic medical record as a tool for genomic research. now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from electronic medical records can be used successfully for genomic research. current work is advancing knowledge in multiple disciplines at the intersection of genomics and health-care informatics, particularly for electronic phenotyping, genome-wide association studies, genomic medicine implementation, and the ethical and regulatory issues associated with genomics research and returning results to study participants. here, we describe the evolution, accomplishments, opportunities, and challenges of the network from its inception as a five-group consortium focused on genotype-phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting toward the implementation of genomic medicine.",0
"cognitive control is defined by a set of neural processes that allow us to interact with our complex environment in a goal-directed manner. humans regularly challenge these control processes when attempting to simultaneously accomplish multiple goals (multitasking), generating interference as the result of fundamental information processing limitations. it is clear that multitasking behaviour has become ubiquitous in today's technologically dense world, and substantial evidence has accrued regarding multitasking difficulties and cognitive control deficits in our ageing population. here we show that multitasking performance, as assessed with a custom-designed three-dimensional video game (neuroracer), exhibits a linear age-related decline from 20 to 79 years of age. by playing an adaptive version of neuroracer in multitasking training mode, older adults (60 to 85 years old) reduced multitasking costs compared to both an active control group and a no-contact control group, attaining levels beyond those achieved by untrained 20-year-old participants, with gains persisting for 6 months. furthermore, age-related deficits in neural signatures of cognitive control, as measured with electroencephalography, were remediated by multitasking training (enhanced midline frontal theta power and frontal-posterior theta coherence). critically, this training resulted in performance benefits that extended to untrained cognitive control abilities (enhanced sustained attention and working memory), with an increase in midline frontal theta power predicting the training-induced boost in sustained attention and preservation of multitasking improvement 6 months later. these findings highlight the robust plasticity of the prefrontal cognitive control system in the ageing brain, and provide the first evidence, to our knowledge, of how a custom-designed video game can be used to assess cognitive abilities across the lifespan, evaluate underlying neural mechanisms, and serve as a powerful tool for cognitive enhancement.",0
"the overall size and composition of the pool of naive and memory t cells are tightly regulated by homeostatic mechanisms. recent work has shown that homeostasis of naive t cells is controlled by two factors, self-major histocompatibility complex (mhc)/peptide ligands and a cytokine, interleukin (il)-7. in particular, contact with these two factors is required for naive cd4+ and cd8+ cells to undergo ""homeostatic"" proliferation, i.e., proliferation induced as a consequence of severe t cell depletion. in contrast to naive t cells, the factors that drive memory t cells to undergo homeostatic proliferation are poorly understood. to address this issue, purified memory phenotype cd4+ and cd8+ cells from normal mice were adoptively transferred into various gene-knockout mice rendered t cell-deficient by sublethal irradiation. three findings are reported. first, unlike naive t cells, homeostatic proliferation of memory t cells is largely mhc independent. second, memory cd8+ cells can utilize either il-7 or il-15 to undergo homeostatic proliferation; however, in the absence of both il-7 and il-15, homeostatic proliferation fails to occur. third, unlike memory cd8+ cells, homeostatic proliferation of memory cd4+ cells is independent of il-7 and il-15 (also il-4). thus, the homeostatic proliferation mechanisms that control memory cd8+ cells and memory cd4+ cells are quite distinct.",0
"additive manufacturing (am) alias 3d printing translates computer-aided design (cad) virtual 3d models into physical objects. by digital slicing of cad, 3d scan, or tomography data, am builds objects layer by layer without the need for molds or machining. am enables decentralized fabrication of customized objects on demand by exploiting digital information storage and retrieval via the internet. the ongoing transition from rapid prototyping to rapid manufacturing prompts new challenges for mechanical engineers and materials scientists alike. because polymers are by far the most utilized class of materials for am, this review focuses on polymer processing and the development of polymers and advanced polymer systems specifically for am. am techniques covered include vat photopolymerization (stereolithography), powder bed fusion (sls), material and binder jetting (inkjet and aerosol 3d printing), sheet lamination (lom), extrusion (fdm, 3d dispensing, 3d fiber deposition, and 3d plotting), and 3d bioprinting. the range of polymers used in am encompasses thermoplastics, thermosets, elastomers, hydrogels, functional polymers, polymer blends, composites, and biological systems. aspects of polymer design, additives, and processing parameters as they relate to enhancing build speed and improving accuracy, functionality, surface finish, stability, mechanical properties, and porosity are addressed. selected applications demonstrate how polymer-based am is being exploited in lightweight engineering, architecture, food processing, optics, energy technology, dentistry, drug delivery, and personalized medicine. unparalleled by metals and ceramics, polymer-based am plays a key role in the emerging am of advanced multifunctional and multimaterial systems including living biological systems as well as life-like synthetic systems.",0
"mitochondria are renowned for their central bioenergetic role in eukaryotic cells, where they act as powerhouses to generate adenosine triphosphate from oxidation of nutrients. at the same time, these organelles are highly dynamic and undergo fusion, fission, transport, and degradation. each of these dynamic processes is critical for maintaining a healthy mitochondrial population. given the central metabolic function of mitochondria, it is not surprising that mitochondrial dynamics and bioenergetics reciprocally influence each other. we review the dynamic properties of mitochondria, with an emphasis on how these processes respond to cellular signaling events and how they affect metabolism.",0
"cigarette smoking remains the leading cause of preventable disease and death in the united states (1). the prevalence of current cigarette smoking among u.s. adults has declined over the past several decades, with a prevalence of 13.7% in 2018 (2). however, a variety of combustible, noncombustible, and electronic tobacco products are available in the united states (1,3). to assess recent national estimates of tobacco product use among u.s. adults aged ≥18 years, cdc analyzed data from the 2019 national health interview survey (nhis). in 2019, an estimated 50.6 million u.s. adults (20.8%) reported currently using any tobacco product, including cigarettes (14.0%), e-cigarettes (4.5%), cigars (3.6%), smokeless tobacco (2.4%), and pipes* (1.0%). † most current tobacco product users (80.5%) reported using combustible products (cigarettes, cigars, or pipes), and 18.6% reported using two or more tobacco products. § the prevalence of any current tobacco product use was higher among males; adults aged ≤65 years; non-hispanic american indian/alaska native (ai/an) adults; those whose highest level of educational attainment was a general educational development (ged) certificate; those with an annual household income <$35,000; lesbian, gay, or bisexual (lgb) adults; uninsured adults and those with medicaid; those with a disability; or those with mild, moderate, or severe generalized anxiety disorder. e-cigarette use was highest among adults aged 18-24 years (9.3%), with over half (56.0%) of these young adults reporting that they had never smoked cigarettes. implementing comprehensive, evidence-based, population level interventions (e.g., tobacco price increases, comprehensive smoke-free policies, high-impact antitobacco media campaigns, and barrier-free cessation coverage), in coordination with regulation of the manufacturing, marketing, and sale of all tobacco products, can reduce tobacco-related disease and death in the united states (1,4). as part of a comprehensive approach, targeted interventions are also warranted to reach subpopulations with the highest prevalence of use, which might vary by tobacco product type.",0
"programmed cell death (pcd) plays a key role in developmental biology and in maintenance of the steady state in continuously renewing tissues. currently, its existence is inferred mainly from gel electrophoresis of a pooled dna extract as pcd was shown to be associated with dna fragmentation. based on this observation, we describe here the development of a method for the in situ visualization of pcd at the single-cell level, while preserving tissue architecture. conventional histological sections, pretreated with protease, were nick end labeled with biotinylated poly du, introduced by terminal deoxy-transferase, and then stained using avidin-conjugated peroxidase. the reaction is specific, only nuclei located at positions where pcd is expected are stained. the initial screening includes: small and large intestine, epidermis, lymphoid tissues, ovary, and other organs. a detailed analysis revealed that the process is initiated at the nuclear periphery, it is relatively short (1-3 h from initiation to cell elimination) and that pcd appears in tissues in clusters. the extent of tissue-pcd revealed by this method is considerably greater than apoptosis detected by nuclear morphology, and thus opens the way for a variety of studies.",0
"background mendelian randomization (mr) is a powerful tool in epidemiology that can be used to estimate the causal effect of an exposure on an outcome in the presence of unobserved confounding, by utilizing genetic variants that are instrumental variables (ivs) for the exposure. this has been extended to multivariable mr (mvmr) to estimate the effect of two or more exposures on an outcome. methods and results we use simulations and theory to clarify the interpretation of estimated effects in a mvmr analysis under a range of underlying scenarios, where a secondary exposure acts variously as a confounder, a mediator, a pleiotropic pathway and a collider. we then describe how instrument strength and validity can be assessed for an mvmr analysis in the single-sample setting, and develop tests to assess these assumptions in the popular two-sample summary data setting. we illustrate our methods using data from uk biobank to estimate the effect of education and cognitive ability on body mass index. conclusion mvmr analysis consistently estimates the direct causal effect of an exposure, or exposures, of interest and provides a powerful tool for determining causal effects in a wide range of scenarios with either individual- or summary-level data.",0
"the spike glycoprotein (s) of recently identified middle east respiratory syndrome coronavirus (mers-cov) targets the cellular receptor, dipeptidyl peptidase 4 (dpp4). sequence comparison and modeling analysis have revealed a putative receptor-binding domain (rbd) on the viral spike, which mediates this interaction. we report the 3.0 å-resolution crystal structure of mers-cov rbd bound to the extracellular domain of human dpp4. our results show that mers-cov rbd consists of a core and a receptor-binding subdomain. the receptor-binding subdomain interacts with dpp4 β-propeller but not its intrinsic hydrolase domain. mers-cov rbd and related sars-cov rbd share a high degree of structural similarity in their core subdomains, but are notably divergent in the receptor-binding subdomain. mutagenesis studies have identified several key residues in the receptor-binding subdomain that are critical for viral binding to dpp4 and entry into the target cell. the atomic details at the interface between mers-cov rbd and dpp4 provide structural understanding of the virus and receptor interaction, which can guide development of therapeutics and vaccines against mers-cov infection.",0
"an animal model to study human infectious diseases should accurately reproduce the various aspects of disease. domestic pigs (sus scrofa domesticus) are closely related to humans in terms of anatomy, genetics and physiology, and represent an excellent animal model to study various microbial infectious diseases. indeed, experiments in pigs are much more likely to be predictive of therapeutic treatments in humans than experiments in rodents. in this review, we highlight the numerous advantages of the pig model for infectious disease research and vaccine development and document a few examples of human microbial infectious diseases for which the use of pigs as animal models has contributed to the acquisition of new knowledge to improve both animal and human health.",0
"background the degree of myocardial injury, as reflected by troponin elevation, and associated outcomes among u.s. hospitalized patients with coronavirus disease-2019 (covid-19) are unknown. objectives the purpose of this study was to describe the degree of myocardial injury and associated outcomes in a large hospitalized cohort with laboratory-confirmed covid-19. methods patients with covid-19 admitted to 1 of 5 mount sinai health system hospitals in new york city between february 27, 2020, and april 12, 2020, with troponin-i (normal value results the median age was 66.4 years, with 59.6% men. cardiovascular disease (cvd), including coronary artery disease, atrial fibrillation, and heart failure, was more prevalent in patients with higher troponin concentrations, as were hypertension and diabetes. a total of 506 (18.5%) patients died during hospitalization. in all, 985 (36%) patients had elevated troponin concentrations. after adjusting for disease severity and relevant clinical factors, even small amounts of myocardial injury (e.g., troponin i >0.03 to 0.09 ng/ml; n = 455; 16.6%) were significantly associated with death (adjusted hazard ratio: 1.75; 95% ci: 1.37 to 2.24; p 0.09 ng/dl; n = 530; 19.4%) were significantly associated with higher risk (adjusted hr: 3.03; 95% ci: 2.42 to 3.80; p conclusions myocardial injury is prevalent among patients hospitalized with covid-19; however, troponin concentrations were generally present at low levels. patients with cvd are more likely to have myocardial injury than patients without cvd. troponin elevation among patients hospitalized with covid-19 is associated with higher risk of mortality.",0
"protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modifications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the 'ubiquitin code'. ubiquitin can be ubiquitinated on seven lysine (lys) residues or on the n-terminus, leading to polyubiquitin chains that can encompass complex topologies. alternatively or in addition, ubiquitin lys residues can be modified by ubiquitin-like molecules (such as sumo or nedd8). finally, ubiquitin can also be acetylated on lys, or phosphorylated on ser, thr or tyr residues, and each modification has the potential to dramatically alter the signaling outcome. while the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. we here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. we then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on ser65-phosphorylation and its role in mitophagy and parkin activation.",0
"yolk proteins are thought to enter certain eggs by a process akin to micropinocytosis but the detailed mechanism has not been previously depicted. in this study the formation of protein yolk was investigated in the mosquito aedes aegypti l. ovaries were fixed in phosphate-buffered osmium tetroxide, for electron microscopy, before and at intervals after a meal of blood. the deposition of protein yolk in the oocyte was correlated with a 15-fold increase in 140 mmicro pit-like depressions on the oocyte surface. these pits form by invagination of the oocyte cell membrane. they have a 20 mmicro bristle coat on their convex cytoplasmic side. they also show a layer of protein on their concave extracellular side which we propose accumulates by selective adsorption from the extraoocyte space. the pits, by pinching off from the cell membrane become bristle-coated vesicles which carry the adsorbed protein into the oocyte. these vesicles lose the coat and then fuse to form small crystalline yolk droplets, which subsequently coalesce to form the large proteid yolk bodies of the mature oocyte. preliminary radioautographs, and certain morphological features of the fat body, ovary, and midgut, suggest that the midgut is the principal site of yolk protein synthesis in the mosquito.",0
"in the nonobese diabetic (nod) mouse model of type 1 diabetes, the immune system recognizes many autoantigens expressed in pancreatic islet beta cells. to silence autoimmunity, we used dendritic cells (dcs) from nod mice to expand cd25+ cd4+ suppressor t cells from bdc2.5 mice, which are specific for a single islet autoantigen. the expanded t cells were more suppressive in vitro than their freshly isolated counterparts, indicating that dcs from autoimmune mice can increase the number and function of antigen-specific, cd25+ cd4+ regulatory t cells. importantly, only 5,000 expanded cd25+ cd4+ bdc2.5 t cells could block autoimmunity caused by diabetogenic t cells in nod mice, whereas 10(5) polyclonal, cd25+ cd4+ t cells from nod mice were inactive. when islets were examined in treated mice, insulitis development was blocked at early (3 wk) but not later (11 wk) time points. the expanded cd25+ cd4+ bdc2.5 t cells were effective even if administered 14 d after the diabetogenic t cells. our data indicate that dcs can generate cd25+ cd4+ t cells that suppress autoimmune disease in vivo. this might be harnessed as a new avenue for immunotherapy, especially because cd25+ cd4+ regulatory cells responsive to a single autoantigen can inhibit diabetes mediated by reactivity to multiple antigens.",0
"existing long-read assemblers require thousands of central processing unit hours to assemble a human genome and are being outpaced by sequencing technologies in terms of both throughput and cost. we developed a long-read assembler wtdbg2 ( that is 2-17 times as fast as published tools while achieving comparable contiguity and accuracy. it paves the way for population-scale long-read assembly in future.",0
"importance the global burden of diseases, injuries, and risk factors study 2019 (gbd 2019) provided systematic estimates of incidence, morbidity, and mortality to inform local and international efforts toward reducing cancer burden. objective to estimate cancer burden and trends globally for 204 countries and territories and by sociodemographic index (sdi) quintiles from 2010 to 2019. evidence review the gbd 2019 estimation methods were used to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life years (dalys) in 2019 and over the past decade. estimates are also provided by quintiles of the sdi, a composite measure of educational attainment, income per capita, and total fertility rate for those younger than 25 years. estimates include 95% uncertainty intervals (uis). findings in 2019, there were an estimated 23.6 million (95% ui, 22.2-24.9 million) new cancer cases (17.2 million when excluding nonmelanoma skin cancer) and 10.0 million (95% ui, 9.36-10.6 million) cancer deaths globally, with an estimated 250 million (235-264 million) dalys due to cancer. since 2010, these represented a 26.3% (95% ui, 20.3%-32.3%) increase in new cases, a 20.9% (95% ui, 14.2%-27.6%) increase in deaths, and a 16.0% (95% ui, 9.3%-22.8%) increase in dalys. among 22 groups of diseases and injuries in the gbd 2019 study, cancer was second only to cardiovascular diseases for the number of deaths, years of life lost, and dalys globally in 2019. cancer burden differed across sdi quintiles. the proportion of years lived with disability that contributed to dalys increased with sdi, ranging from 1.4% (1.1%-1.8%) in the low sdi quintile to 5.7% (4.2%-7.1%) in the high sdi quintile. while the high sdi quintile had the highest number of new cases in 2019, the middle sdi quintile had the highest number of cancer deaths and dalys. from 2010 to 2019, the largest percentage increase in the numbers of cases and deaths occurred in the low and low-middle sdi quintiles. conclusions and relevance the results of this systematic analysis suggest that the global burden of cancer is substantial and growing, with burden differing by sdi. these results provide comprehensive and comparable estimates that can potentially inform efforts toward equitable cancer control around the world.",0
"background for women with oestrogen receptor (er)-positive early breast cancer, treatment with tamoxifen for 5 years substantially reduces the breast cancer mortality rate throughout the first 15 years after diagnosis. we aimed to assess the further effects of continuing tamoxifen to 10 years instead of stopping at 5 years. methods in the worldwide adjuvant tamoxifen: longer against shorter (atlas) trial, 12,894 women with early breast cancer who had completed 5 years of treatment with tamoxifen were randomly allocated to continue tamoxifen to 10 years or stop at 5 years (open control). allocation (1:1) was by central computer, using minimisation. after entry (between 1996 and 2005), yearly follow-up forms recorded any recurrence, second cancer, hospital admission, or death. we report effects on breast cancer outcomes among the 6846 women with er-positive disease, and side-effects among all women (with positive, negative, or unknown er status). long-term follow-up still continues. this study is registered, number isrctn19652633. findings among women with er-positive disease, allocation to continue tamoxifen reduced the risk of breast cancer recurrence (617 recurrences in 3428 women allocated to continue vs 711 in 3418 controls, p=0·002), reduced breast cancer mortality (331 deaths vs 397 deaths, p=0·01), and reduced overall mortality (639 deaths vs 722 deaths, p=0·01). the reductions in adverse breast cancer outcomes appeared to be less extreme before than after year 10 (recurrence rate ratio 0·90 during years 5–9 and 0·75 in later years; breast cancer mortality rr 0·97 during years 5–9 and 0·71 in later years). the cumulative risk of recurrence during years 5–14 was 21·4% for women allocated to continue versus 25·1% for controls; breast cancer mortality during years 5–14 was 12·2% for women allocated to continue versus 15·0% for controls (absolute mortality reduction 2·8%). treatment allocation seemed to have no effect on breast cancer outcome among 1248 women with er-negative disease, and an intermediate effect among 4800 women with unknown er status. among all 12,894 women, mortality without recurrence from causes other than breast cancer was little affected (691 deaths without recurrence in 6454 women allocated to continue versus 679 deaths in 6440 controls; rr 0·99 ; p=0·84). for the incidence (hospitalisation or death) rates of specific diseases, rrs were as follows: pulmonary embolus 1·87 (95% ci 1·13–3·07, p=0·01 ), stroke 1·06 (0·83–1·36), ischaemic heart disease 0·76 (0·60–0·95, p=0·02), and endometrial cancer 1·74 (1·30–2·34, p=0·0002). the cumulative risk of endometrial cancer during years 5–14 was 3·1% (mortality 0·4%) for women allocated to continue versus 1·6% (mortality 0·2%) for controls (absolute mortality increase 0·2%). interpretation for women with er-positive disease, continuing tamoxifen to 10 years rather than stopping at 5 years produces a further reduction in recurrence and mortality, particularly after year 10. these results, taken together with results from previous trials of 5 years of tamoxifen treatment versus none, suggest that 10 years of tamoxifen treatment can approximately halve breast cancer mortality during the second decade after diagnosis. funding cancer research uk, uk medical research council, astrazeneca uk, us army, eu-biomed.",0
"little is known about the regulation of nonapoptotic cell death. using massive insertional mutagenesis of haploid kbm7 cells we identified nine genes involved in small-molecule-induced nonapoptotic cell death, including mediators of fatty acid metabolism (acsl4) and lipid remodeling (lpcat3) in ferroptosis. one novel compound, cil56, triggered cell death dependent upon the rate-limiting de novo lipid synthetic enzyme acc1. these results provide insight into the genetic regulation of cell death and highlight the central role of lipid metabolism in nonapoptotic cell death.",0
"chronic kidney disease (ckd) is a global health burden with a high economic cost to health systems and is an independent risk factor for cardiovascular disease (cvd). all stages of ckd are associated with increased risks of cardiovascular morbidity, premature mortality, and/or decreased quality of life. ckd is usually asymptomatic until later stages and accurate prevalence data are lacking. thus we sought to determine the prevalence of ckd globally, by stage, geographical location, gender and age. a systematic review and meta-analysis of observational studies estimating ckd prevalence in general populations was conducted through literature searches in 8 databases. we assessed pooled data using a random effects model. of 5,842 potential articles, 100 studies of diverse quality were included, comprising 6,908,440 patients. global mean(95%ci) ckd prevalence of 5 stages 13·4%(11·7-15·1%), and stages 3-5 was 10·6%(9·2-12·2%). weighting by study quality did not affect prevalence estimates. ckd prevalence by stage was stage-1 (egfr>90+acr>30): 3·5% (2·8-4·2%); stage-2 (egfr 60-89+acr>30): 3·9% (2·7-5·3%); stage-3 (egfr 30-59): 7·6% (6·4-8·9%); stage-4 = (egfr 29-15): 0·4% (0·3-0·5%); and stage-5 (egfr<15): 0·1% (0·1-0·1%). ckd has a high global prevalence with a consistent estimated global ckd prevalence of between 11 to 13% with the majority stage 3. future research should evaluate intervention strategies deliverable at scale to delay the progression of ckd and improve cvd outcomes.",0
"panther (protein analysis through evolutionary relationships, is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. we report the improvements we have made to the resource during the past two years. for evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages. we have refined many protein family boundaries, and have aligned panther with the merops resource for protease and protease inhibitor families. for functional classifications, we have developed an entirely new panther go-slim, containing over four times as many gene ontology terms as our previous go-slim, as well as curated associations of genes to these terms. lastly, we have made substantial improvements to the enrichment analysis tools available on the panther website: users can now analyze over 900 different genomes, using updated statistical tests with false discovery rate corrections for multiple testing. the overrepresentation test is also available as a web service, for easy addition to third-party sites.",0
"in the last few years, the deep learning (dl) computing paradigm has been deemed the gold standard in the machine learning (ml) community. moreover, it has gradually become the most widely used computational approach in the field of ml, thus achieving outstanding results on several complex cognitive tasks, matching or even beating those provided by human performance. one of the benefits of dl is the ability to learn massive amounts of data. the dl field has grown fast in the last few years and it has been extensively used to successfully address a wide range of traditional applications. more importantly, dl has outperformed well-known ml techniques in many domains, e.g., cybersecurity, natural language processing, bioinformatics, robotics and control, and medical information processing, among many others. despite it has been contributed several works reviewing the state-of-the-art on dl, all of them only tackled one aspect of the dl, which leads to an overall lack of knowledge about it. therefore, in this contribution, we propose using a more holistic approach in order to provide a more suitable starting point from which to develop a full understanding of dl. specifically, this review attempts to provide a more comprehensive survey of the most important aspects of dl and including those enhancements recently added to the field. in particular, this paper outlines the importance of dl, presents the types of dl techniques and networks. it then presents convolutional neural networks (cnns) which the most utilized dl network type and describes the development of cnns architectures together with their main features, e.g., starting with the alexnet network and closing with the high-resolution network (hr.net). finally, we further present the challenges and suggested solutions to help researchers understand the existing research gaps. it is followed by a list of the major dl applications. computational tools including fpga, gpu, and cpu are summarized along with a description of their influence on dl. the paper ends with the evolution matrix, benchmark datasets, and summary and conclusion.",0
"background the global burden of cholera is largely unknown because the majority of cases are not reported. the low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories, as well as social, political, and economic disincentives for reporting. we previously estimated 2.8 million cases and 91,000 deaths annually due to cholera in 51 endemic countries. a major limitation in our previous estimate was that the endemic and non-endemic countries were defined based on the countries' reported cholera cases. we overcame the limitation with the use of a spatial modelling technique in defining endemic countries, and accordingly updated the estimates of the global burden of cholera. methods/principal findings countries were classified as cholera endemic, cholera non-endemic, or cholera-free based on whether a spatial regression model predicted an incidence rate over a certain threshold in at least three of five years (2008-2012). the at-risk populations were calculated for each country based on the percent of the country without sustainable access to improved sanitation facilities. incidence rates from population-based published studies were used to calculate the estimated annual number of cases in endemic countries. the number of annual cholera deaths was calculated using inverse variance-weighted average case-fatality rate (cfrs) from literature-based cfr estimates. we found that approximately 1.3 billion people are at risk for cholera in endemic countries. an estimated 2.86 million cholera cases (uncertainty range: 1.3m-4.0m) occur annually in endemic countries. among these cases, there are an estimated 95,000 deaths (uncertainty range: 21,000-143,000). conclusion/significance the global burden of cholera remains high. sub-saharan africa accounts for the majority of this burden. our findings can inform programmatic decision-making for cholera control.",0
"current methods for annotating and interpreting human genetic variation tend to exploit a single information type (for example, conservation) and/or are restricted in scope (for example, to missense changes). here we describe combined annotation-dependent depletion (cadd), a method for objectively integrating many diverse annotations into a single measure (c score) for each variant. we implement cadd as a support vector machine trained to differentiate 14.7 million high-frequency human-derived alleles from 14.7 million simulated variants. we precompute c scores for all 8.6 billion possible human single-nucleotide variants and enable scoring of short insertions-deletions. c scores correlate with allelic diversity, annotations of functionality, pathogenicity, disease severity, experimentally measured regulatory effects and complex trait associations, and they highly rank known pathogenic variants within individual genomes. the ability of cadd to prioritize functional, deleterious and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current single-annotation method.",0
"purpose to update the world society of the abdominal compartment syndrome (wsacs) consensus definitions and management statements relating to intra-abdominal hypertension (iah) and the abdominal compartment syndrome (acs). methods we conducted systematic or structured reviews to identify relevant studies relating to iah or acs. updated consensus definitions and management statements were then derived using a modified delphi method and the grading of recommendations, assessment, development, and evaluation (grade) guidelines, respectively. quality of evidence was graded from high (a) to very low (d) and management statements from strong recommendations (desirable effects clearly outweigh potential undesirable ones) to weaker suggestions (potential risks and benefits of the intervention are less clear). results in addition to reviewing the consensus definitions proposed in 2006, the wsacs defined the open abdomen, lateralization of the abdominal musculature, polycompartment syndrome, and abdominal compliance, and proposed an open abdomen classification system. recommendations included intra-abdominal pressure (iap) measurement, avoidance of sustained iah, protocolized iap monitoring and management, decompressive laparotomy for overt acs, and negative pressure wound therapy and efforts to achieve same-hospital-stay fascial closure among patients with an open abdomen. suggestions included use of medical therapies and percutaneous catheter drainage for treatment of iah/acs, considering the association between body position and iap, attempts to avoid a positive fluid balance after initial patient resuscitation, use of enhanced ratios of plasma to red blood cells and prophylactic open abdominal strategies, and avoidance of routine early biologic mesh use among patients with open abdominal wounds. no recommendations were possible regarding monitoring of abdominal perfusion pressure or the use of diuretics, renal replacement therapies, albumin, or acute component-parts separation. conclusion although iah and acs are common and frequently associated with poor outcomes, the overall quality of evidence available to guide development of recommendations was generally low. appropriately designed intervention trials are urgently needed for patients with iah and acs.",0
"the distribution of actin and tubulin during the cell cycle of the budding yeast saccharomyces was mapped by immunofluorescence using fixed cells from which the walls had been removed by digestion. the intranuclear mitotic spindle was shown clearly by staining with a monoclonal antitubulin; the presence of extensive bundles of cytoplasmic microtubules is reported. in cells containing short spindles still entirely within the mother cells, one of the bundles of cytoplasmic microtubules nearly always extended to (or into) the bud. two independent reagents (anti-yeast actin and fluorescent phalloidin) revealed an unusual distribution of actin: it was present as a set of cortical dots or patches and also as distinct fibers that were presumably bundles of actin filaments. double labeling showed that at no stage in the cell cycle do the distributions of actin and tubulin coincide for any significant length, and, in particular, that the mitotic spindle did not stain detectably for actin. however, both microtubule and actin staining patterns change in a characteristic way during the cell cycle. in particular, the actin dots clustered in rings about the bases of very small buds and at the sites on unbudded cells at which bud emergence was apparently imminent. later in the budding cycle, the actin dots were present largely in the buds and, in many strains, primarily at the tips of these buds. at about the time of cytokinesis the actin dots clustered in the neck region between the separating cells. these aspects of actin distribution suggest that it may have a role in the localized deposition of new cell wall material.",0
"the cambridge structural database (csd) contains a complete record of all published organic and metal-organic small-molecule crystal structures. the database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. as well as structures that are made public to support scientific articles, it includes many structures published directly as csd communications. all structures are processed both computationally and by expert structural chemistry editors prior to entering the database. a key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. this important step helps ensure that data is widely discoverable and readily reusable. content is further enriched through selective inclusion of additional experimental data. entries are available to anyone through free csd community web services. linking services developed and maintained by the ccdc, combined with the use of standard identifiers, facilitate discovery from other resources. data can also be accessed through ccdc and third party software applications and through an application programming interface.",0
"thalidomide selectively inhibits the production of human monocyte tumor necrosis factor alpha (tnf-alpha) when these cells are triggered with lipopolysaccharide and other agonists in culture. 40% inhibition occurs at the clinically achievable dose of the drug of 1 micrograms/ml. in contrast, the amount of total protein and individual proteins labeled with methionine and expressed on sds-page are not influenced. the amounts of interleukin 1 beta (il-1 beta), il-6, and granulocyte/macrophage colony-stimulating factor produced by monocytes remain unaltered. the selectivity of this drug may be useful in determining the role of tnf-alpha in vivo and modulating its toxic effects in a clinical setting.",0
"importance detailed information about the association of covid-19 with outcomes in pregnant individuals compared with not-infected pregnant individuals is much needed. objective to evaluate the risks associated with covid-19 in pregnancy on maternal and neonatal outcomes compared with not-infected, concomitant pregnant individuals. design, setting, and participants in this cohort study that took place from march to october 2020, involving 43 institutions in 18 countries, 2 unmatched, consecutive, not-infected women were concomitantly enrolled immediately after each infected woman was identified, at any stage of pregnancy or delivery, and at the same level of care to minimize bias. women and neonates were followed up until hospital discharge. exposures covid-19 in pregnancy determined by laboratory confirmation of covid-19 and/or radiological pulmonary findings or 2 or more predefined covid-19 symptoms. main outcomes and measures the primary outcome measures were indices of (maternal and severe neonatal/perinatal) morbidity and mortality; the individual components of these indices were secondary outcomes. models for these outcomes were adjusted for country, month entering study, maternal age, and history of morbidity. results a total of 706 pregnant women with covid-19 diagnosis and 1424 pregnant women without covid-19 diagnosis were enrolled, all with broadly similar demographic characteristics (mean age, 30.2 years). overweight early in pregnancy occurred in 323 women (48.6%) with covid-19 diagnosis and 554 women (40.2%) without. women with covid-19 diagnosis were at higher risk for preeclampsia/eclampsia (relative risk , 1.76; 95% ci, 1.27-2.43), severe infections (rr, 3.38; 95% ci, 1.63-7.01), intensive care unit admission (rr, 5.04; 95% ci, 3.13-8.10), maternal mortality (rr, 22.3; 95% ci, 2.88-172), preterm birth (rr, 1.59; 95% ci, 1.30-1.94), medically indicated preterm birth (rr, 1.97; 95% ci, 1.56-2.51), severe neonatal morbidity index (rr, 2.66; 95% ci, 1.69-4.18), and severe perinatal morbidity and mortality index (rr, 2.14; 95% ci, 1.66-2.75). fever and shortness of breath for any duration was associated with increased risk of severe maternal complications (rr, 2.56; 95% ci, 1.92-3.40) and neonatal complications (rr, 4.97; 95% ci, 2.11-11.69). asymptomatic women with covid-19 diagnosis remained at higher risk only for maternal morbidity (rr, 1.24; 95% ci, 1.00-1.54) and preeclampsia (rr, 1.63; 95% ci, 1.01-2.63). among women who tested positive (98.1% by real-time polymerase chain reaction), 54 (13%) of their neonates tested positive. cesarean delivery (rr, 2.15; 95% ci, 1.18-3.91) but not breastfeeding (rr, 1.10; 95% ci, 0.66-1.85) was associated with increased risk for neonatal test positivity. conclusions and relevance in this multinational cohort study, covid-19 in pregnancy was associated with consistent and substantial increases in severe maternal morbidity and mortality and neonatal complications when pregnant women with and without covid-19 diagnosis were compared. the findings should alert pregnant individuals and clinicians to implement strictly all the recommended covid-19 preventive measures.",0
"recombinant mouse interleukin 10 (il-10) was exceedingly potent at suppressing the ability of mouse peritoneal macrophages (m phi) to release tumor necrosis factor alpha (tnf-alpha). the ic50 of il-10 for the suppression of tnf-alpha release induced by 0.5 microgram/ml lipopolysaccharide was 0.04 +/- 0.03 u/ml, with as little as 1 u/ml suppressing tnf-alpha production by a factor of 21.4 +/- 2.5. at 10 u/ml, il-10 markedly suppressed m phi release of reactive oxygen intermediates (roi) (ic50 3.7 +/- 1.8 u/ml), but only weakly inhibited m phi release of reactive nitrogen intermediates (rni). since tnf-alpha is a t cell growth and differentiation factor, whereas roi and rni are known to inhibit lymphocyte function, it is possible that m phi exposed to low concentrations of il-10 suppress lymphocytes. m phi deactivated by higher concentrations of il-10 might be permissive for the growth of microbial pathogens and tumor cells, as tnf-alpha, roi, and rni are major antimicrobial and tumoricidal products of m phi. il-10's effects on m phi overlap with but are distinct from the effects of the two previously described cytokines that suppress the function of mouse m phi, transforming growth factor beta and macrophage deactivation factor. based on results with neutralizing antibodies, all three m phi suppressor factors appear to act independently.",0
"statin-associated muscle symptoms (sams) are one of the principal reasons for statin non-adherence and/or discontinuation, contributing to adverse cardiovascular outcomes. this european atherosclerosis society (eas) consensus panel overviews current understanding of the pathophysiology of statin-associated myopathy, and provides guidance for diagnosis and management of sams. statin-associated myopathy, with significant elevation of serum creatine kinase (ck), is a rare but serious side effect of statins, affecting 1 per 1000 to 1 per 10 000 people on standard statin doses. statin-associated muscle symptoms cover a broader range of clinical presentations, usually with normal or minimally elevated ck levels, with a prevalence of 7-29% in registries and observational studies. preclinical studies show that statins decrease mitochondrial function, attenuate energy production, and alter muscle protein degradation, thereby providing a potential link between statins and muscle symptoms; controlled mechanistic and genetic studies in humans are necessary to further understanding. the panel proposes to identify sams by symptoms typical of statin myalgia (i.e. muscle pain or aching) and their temporal association with discontinuation and response to repetitive statin re-challenge. in people with sams, the panel recommends the use of a maximally tolerated statin dose combined with non-statin lipid-lowering therapies to attain recommended low-density lipoprotein cholesterol targets. the panel recommends a structured work-up to identify individuals with clinically relevant sams generally to at least three different statins, so that they can be offered therapeutic regimens to satisfactorily address their cardiovascular risk. further research into the underlying pathophysiological mechanisms may offer future therapeutic potential.",0
"introduction alzheimer's disease (ad) is increasing in frequency as the global population ages. five drugs are approved for treatment of ad, including four cholinesterase inhibitors and an n-methyl-d-aspartate (nmda)-receptor antagonist. we have an urgent need to find new therapies for ad. methods we examined clinicaltrials.gov, a public website that records ongoing clinical trials. we examined the decade of 2002 to 2012, to better understand ad-drug development. we reviewed trials by sponsor, sites, drug mechanism of action, duration, number of patients required, and rate of success in terms of advancement from one phase to the next. we also reviewed the current ad therapy pipeline. results during the 2002 to 2012 observation period, 413 ad trials were performed: 124 phase 1 trials, 206 phase 2 trials, and 83 phase 3 trials. seventy-eight percent were sponsored by pharmaceutical companies. the united states of america (u.s.) remains the single world region with the greatest number of trials; cumulatively, more non-u.s. than u.s. trials are performed. the largest number of registered trials addressed symptomatic agents aimed at improving cognition (36.6%), followed by trials of disease-modifying small molecules (35.1%) and trials of disease-modifying immunotherapies (18%). the mean length of trials increases from phase 2 to phase 3, and the number of participants in trials increases between phase 2 and phase 3. trials of disease-modifying agents are larger and longer than those for symptomatic agents. a very high attrition rate was found, with an overall success rate during the 2002 to 2012 period of 0.4% (99.6% failure). conclusions the clinicaltrials.gov database demonstrates that relatively few clinical trials are undertaken for ad therapeutics, considering the magnitude of the problem. the success rate for advancing from one phase to another is low, and the number of compounds progressing to regulatory review is among the lowest found in any therapeutic area. the ad drug-development ecosystem requires support.",0
"this paper introduces isolde, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. isolde combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. in addition, common validation tasks are accelerated and visualized in real time. using the recently described 3.8 å resolution cryo-em structure of the eukaryotic minichromosome maintenance (mcm) helicase complex as a case study, it is demonstrated how isolde can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. a detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.",0
"both the programmed death (pd) 1-pd-ligand (pd-l) pathway and regulatory t (t reg) cells are instrumental to the maintenance of peripheral tolerance. we demonstrate that pd-l1 has a pivotal role in regulating induced t reg (it reg) cell development and sustaining it reg cell function. pd-l1(-/-) antigen-presenting cells minimally convert naive cd4 t cells to it reg cells, showing the essential role of pd-l1 for it reg cell induction. pd-l1-coated beads induce it reg cells in vitro, indicating that pd-l1 itself regulates it reg cell development. furthermore, pd-l1 enhances and sustains foxp3 expression and the suppressive function of it reg cells. the obligatory role for pd-l1 in controlling it reg cell development and function in vivo is illustrated by a marked reduction in it reg cell conversion and rapid onset of a fatal inflammatory phenotype in pd-l1(-/-)pd-l2(-/-) rag(-/-) recipients of naive cd4 t cells. pd-l1 it reg cell development is mediated through the down-regulation of phospho-akt, mtor, s6, and erk2 and concomitant with the up-regulation of pten, all key signaling molecules which are critical for it reg cell development. thus, pd-l1 can inhibit t cell responses by promoting both the induction and maintenance of it reg cells. these studies define a novel mechanism for it reg cell development and function, as well as a new strategy for controlling t reg cell plasticity.",0
"background hundreds of studies of maternity care interventions have been published, too many for most people involved in providing maternity care to identify and consider when making decisions. it became apparent that systematic reviews of individual studies were required to appraise, summarise and bring together existing studies in a single place. however, decision makers are increasingly faced by a plethora of such reviews and these are likely to be of variable quality and scope, with more than one review of important topics. systematic reviews (or overviews) of reviews are a logical and appropriate next step, allowing the findings of separate reviews to be compared and contrasted, providing clinical decision makers with the evidence they need. methods the methods used to identify and appraise published and unpublished reviews systematically, drawing on our experiences and good practice in the conduct and reporting of systematic reviews are described. the process of identifying and appraising all published reviews allows researchers to describe the quality of this evidence base, summarise and compare the review's conclusions and discuss the strength of these conclusions. results methodological challenges and possible solutions are described within the context of (i) sources, (ii) study selection, (iii) quality assessment (i.e. the extent of searching undertaken for the reviews, description of study selection and inclusion criteria, comparability of included studies, assessment of publication bias and assessment of heterogeneity), (iv) presentation of results, and (v) implications for practice and research. conclusion conducting a systematic review of reviews highlights the usefulness of bringing together a summary of reviews in one place, where there is more than one review on an important topic. the methods described here should help clinicians to review and appraise published reviews systematically, and aid evidence-based clinical decision-making.",0
"hic-pro is an optimized and flexible pipeline for processing hi-c data from raw reads to normalized contact maps. hic-pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. it includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for hi-c contact maps. in addition, hic-pro can use phased genotype data to build allele-specific contact maps. we applied hic-pro to different hi-c datasets, demonstrating its ability to easily process large data in a reasonable time. source code and documentation are available at .",0
"the transcription factor nuclear factor erythroid 2-related factor 2 (nrf2) is a key regulator of the cellular antioxidant response, controlling the expression of genes that counteract oxidative and electrophilic stresses. many pathological conditions are linked to imbalances in redox homeostasis, illustrating the important role of antioxidant defense systems in preventing the pathogenic effects associated with the accumulation of reactive species. in particular, it is becoming increasingly apparent that the accumulation of lipid peroxides has an important role in driving the pathogenesis of multiple disease states. a key example of this is the recent discovery of a novel form of cell death termed ferroptosis. ferroptosis is an iron-dependent, lipid peroxidation-driven cell death cascade that has become a key target in the development of anti-cancer therapies, as well as the prevention of neurodegenerative and cardiovascular diseases. in this review, we will provide a brief overview of lipid peroxidation, as well as key components involved in the ferroptotic cascade. we will also highlight the role of the nrf2 signaling pathway in mediating lipid peroxidation and ferroptosis, focusing on established nrf2 target genes that mitigate these pathways, as well as the relevance of the nrf2-lipid peroxidation-ferroptosis axis in disease.",0
"objective to develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19). design prospective observational cohort study. setting international severe acute respiratory and emerging infections consortium (isaric) world health organization (who) clinical characterisation protocol uk (ccp-uk) study (performed by the isaric coronavirus clinical characterisation consortium-isaric-4c) in 260 hospitals across england, scotland, and wales. model training was performed on a cohort of patients recruited between 6 february and 20 may 2020, with validation conducted on a second cohort of patients recruited after model development between 21 may and 29 june 2020 . participants: adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction. main outcome measure in-hospital mortality. results 35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). the final 4c mortality score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and c reactive protein (score range 0-21 points). the 4c score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73). conclusions an easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. the 4c mortality score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. the score should be further validated to determine its applicability in other populations. study registration isrctn66726260.",0
"the ccp4 (collaborative computational project, number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by x-ray crystallography. the suite is designed to be flexible, allowing users a number of methods of achieving their aims. the programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. structure solution by macromolecular crystallography is becoming increasingly automated and the ccp4 suite includes several automation pipelines. after giving a brief description of the evolution of ccp4 over the last 30 years, an overview of the current suite is given. while detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package.",0
"the nhgri-ebi gwas catalog has provided data from published genome-wide association studies since 2008. in 2015, the database was redesigned and relocated to embl-ebi. the new infrastructure includes a new graphical user interface ( ontology supported search functionality and an improved curation interface. these developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. the range of available catalog data has also been extended with structured ancestry and recruitment information added for all studies. the infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.",0
"macrophages (mphi) are prominent components of solid tumors and exhibit distinct phenotypes in different microenvironments. we have recently found that tumors can alter the normal developmental process of mphi to trigger transient activation of monocytes in peritumoral stroma. we showed that a fraction of monocytes/mphi in peritumoral stroma, but not in cancer nests, expresses surface pd-l1 (also termed b7-h1) molecules in tumors from patients with hepatocellular carcinoma (hcc). monocytes activated by tumors strongly express pd-l1 proteins with kinetics similar to their activation status, and significant correlations were found between the levels of pd-l1(+) and hla-dr(high) on tumor-infiltrating monocytes. autocrine tumor necrosis factor alpha and interleukin 10 released from activated monocytes stimulated monocyte expression of pd-l1. the pd-l1(+) monocytes effectively suppressed tumor-specific t cell immunity and contributed to the growth of human tumors in vivo; the effect could be reversed by blocking pd-l1 on those monocytes. moreover, we found that pd-l1 expression on tumor-infiltrating monocytes increased with disease progression, and the intensity of the protein was associated with high mortality and reduced survival in the hcc patients. thus, expression of pd-l1 on activated monocytes/mphi may represent a novel mechanism that links the proinflammatory response to immune tolerance in the tumor milieu.",0
"in cells treated with brefeldin a (bfa), movement of newly synthesized membrane proteins from the endoplasmic reticulum (er) to the golgi apparatus was blocked. surprisingly, the glycoproteins retained in the er were rapidly processed by cis/medial golgi enzymes but not by trans golgi enzymes. an explanation for these observations was provided from morphological studies at both the light and electron microscopic levels using markers for the cis/medial and trans golgi. they revealed a rapid and dramatic redistribution to the er of components of the cis/medial but not the trans golgi in response to treatment with bfa. upon removal of bfa, the morphology of the golgi apparatus was rapidly reestablished and proteins normally transported out of the er were efficiently and rapidly sorted to their final destinations. these results suggest that bfa disrupts a dynamic membrane-recycling pathway between the er and cis/medial golgi, effectively blocking membrane transport out of but not back to the er.",0
"the gastrointestinal tract is a specialized organ in which dynamic interactions between host cells and the complex environment occur in addition to food digestion. together with the chemical barrier of the mucosal layer and the cellular immune system, the epithelial cell layer performs a pivotal role as the first physical barrier against external factors and maintains a symbiotic relationship with commensal bacteria. the tight junction proteins, including occludin, claudins, and zonula occludens, are crucial for the maintenance of epithelial barrier integrity. to allow the transport of essential molecules and restrict harmful substances, the intracellular signaling transduction system and a number of extracellular stimuli such as cytokines, small gtpases, and post-translational modifications dynamically modulate the tight junction protein complexes. an imbalance in these regulations leads to compromised barrier integrity and is linked with pathological conditions. despite the obscurity of the causal relationship, the loss of barrier integrity is considered to contribute to inflammatory bowel disease, obesity, and metabolic disorders. the elucidation of the role of diseases in barrier integrity and the underlying regulatory mechanisms have improved our understanding of the intestinal barrier to allow the development of novel and potent therapeutic approaches.",0
"the mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions. studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks. in this report, we combine resting state functional connectivity mri (rs-fcmri), graph analysis, community detection, and spring-embedding visualization techniques to analyze four separate networks defined in earlier studies. as we have previously reported, we find, across development, a trend toward 'segregation' (a general decrease in correlation strength) between regions close in anatomical space and 'integration' (an increased correlation strength) between selected regions distant in space. the generalization of these earlier trends across multiple networks suggests that this is a general developmental principle for changes in functional connectivity that would extend to large-scale graph theoretic analyses of large-scale brain networks. communities in children are predominantly arranged by anatomical proximity, while communities in adults predominantly reflect functional relationships, as defined from adult fmri studies. in sum, over development, the organization of multiple functional networks shifts from a local anatomical emphasis in children to a more ""distributed"" architecture in young adults. we argue that this ""local to distributed"" developmental characterization has important implications for understanding the development of neural systems underlying cognition. further, graph metrics (e.g., clustering coefficients and average path lengths) are similar in child and adult graphs, with both showing ""small-world""-like properties, while community detection by modularity optimization reveals stable communities within the graphs that are clearly different between young children and young adults. these observations suggest that early school age children and adults both have relatively efficient systems that may solve similar information processing problems in divergent ways.",0
"hepatic natural killer (nk) cells mediate antigen-specific contact hypersensitivity (chs) in mice deficient in t cells and b cells. we report here that hepatic nk cells, but not splenic or naive nk cells, also developed specific memory of vaccines containing antigens from influenza, vesicular stomatitis virus (vsv) or human immunodeficiency virus type 1 (hiv-1). adoptive transfer of virus-sensitized nk cells into naive recipient mice enhanced the survival of the mice after lethal challenge with the sensitizing virus but not after lethal challenge with a different virus. nk cell memory of haptens and viruses depended on cxcr6, a chemokine receptor on hepatic nk cells that was required for the persistence of memory nk cells but not for antigen recognition. thus, hepatic nk cells can develop adaptive immunity to structurally diverse antigens, an activity that requires nk cell-expressed cxcr6.",0
"the release of the 1000th complete microbial genome will occur in the next two to three years. in anticipation of this milestone, the fellowship for interpretation of genomes (fig) launched the project to annotate 1000 genomes. the project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. an annotation environment was created where populated subsystems are curated and projected to new genomes. a portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. tools were also developed to resolve conflicts between populated subsystems. the seed is the first annotation environment that supports this model of annotation. here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. the initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. this data comes from 173 subsystems and 383 different organisms.",0
"dendritic spines are small actin-rich protrusions from neuronal dendrites that form the postsynaptic part of most excitatory synapses and are major sites of information processing and storage in the brain. changes in the shape and size of dendritic spines are correlated with the strength of excitatory synaptic connections and heavily depend on remodeling of its underlying actin cytoskeleton. emerging evidence suggests that most signaling pathways linking synaptic activity to spine morphology influence local actin dynamics. therefore, specific mechanisms of actin regulation are integral to the formation, maturation, and plasticity of dendritic spines and to learning and memory.",0
"stem cells sense and respond to the mechanical properties of the extracellular matrix. however, both the extent to which extracellular-matrix mechanics affect stem-cell fate in three-dimensional microenvironments and the underlying biophysical mechanisms are unclear. we demonstrate that the commitment of mesenchymal stem-cell populations changes in response to the rigidity of three-dimensional microenvironments, with osteogenesis occurring predominantly at 11-30 kpa. in contrast to previous two-dimensional work, however, cell fate was not correlated with morphology. instead, matrix stiffness regulated integrin binding as well as reorganization of adhesion ligands on the nanoscale, both of which were traction dependent and correlated with osteogenic commitment of mesenchymal stem-cell populations. these findings suggest that cells interpret changes in the physical properties of adhesion substrates as changes in adhesion-ligand presentation, and that cells themselves can be harnessed as tools to mechanically process materials into structures that feed back to manipulate their fate.",0
"assessing whether long-term exposure to air pollution increases the severity of covid-19 health outcomes, including death, is an important public health objective. limitations in covid-19 data availability and quality remain obstacles to conducting conclusive studies on this topic. at present, publicly available covid-19 outcome data for representative populations are available only as area-level counts. therefore, studies of long-term exposure to air pollution and covid-19 outcomes using these data must use an ecological regression analysis, which precludes controlling for individual-level covid-19 risk factors. we describe these challenges in the context of one of the first preliminary investigations of this question in the united states, where we found that higher historical pm 2.5 exposures are positively associated with higher county-level covid-19 mortality rates after accounting for many area-level confounders. motivated by this study, we lay the groundwork for future research on this important topic, describe the challenges, and outline promising directions and opportunities.",0
"the health benefits of dietary fiber have long been appreciated. higher intakes of dietary fiber are linked to less cardiovascular disease and fiber plays a role in gut health, with many effective laxatives actually isolated fiber sources. higher intakes of fiber are linked to lower body weights. only polysaccharides were included in dietary fiber originally, but more recent definitions have included oligosaccharides as dietary fiber, not based on their chemical measurement as dietary fiber by the accepted total dietary fiber (tdf) method, but on their physiological effects. inulin, fructo-oligosaccharides, and other oligosaccharides are included as fiber in food labels in the us. additionally, oligosaccharides are the best known ""prebiotics"", ""a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microflora that confers benefits upon host well-bring and health."" to date, all known and suspected prebiotics are carbohydrate compounds, primarily oligosaccharides, known to resist digestion in the human small intestine and reach the colon where they are fermented by the gut microflora. studies have provided evidence that inulin and oligofructose (of), lactulose, and resistant starch (rs) meet all aspects of the definition, including the stimulation of bifidobacterium, a beneficial bacterial genus. other isolated carbohydrates and carbohydrate-containing foods, including galactooligosaccharides (gos), transgalactooligosaccharides (tos), polydextrose, wheat dextrin, acacia gum, psyllium, banana, whole grain wheat, and whole grain corn also have prebiotic effects.",0
"as of 29 february 2020 there were 79,394 confirmed cases and 2,838 deaths from covid-19 in mainland china. of these, 48,557 cases and 2,169 deaths occurred in the epicenter, wuhan. a key public health priority during the emergence of a novel pathogen is estimating clinical severity, which requires properly adjusting for the case ascertainment rate and the delay between symptoms onset and death. using public and published information, we estimate that the overall symptomatic case fatality risk (the probability of dying after developing symptoms) of covid-19 in wuhan was 1.4% (0.9-2.1%), which is substantially lower than both the corresponding crude or naïve confirmed case fatality risk (2,169/48,557 = 4.5%) and the approximator 1 of deaths/deaths + recoveries (2,169/2,169 + 17,572 = 11%) as of 29 february 2020. compared to those aged 30-59 years, those aged below 30 and above 59 years were 0.6 (0.3-1.1) and 5.1 (4.2-6.1) times more likely to die after developing symptoms. the risk of symptomatic infection increased with age (for example, at ~4% per year among adults aged 30-60 years).",0
"background ending the global tobacco epidemic is a defining challenge in global health. timely and comprehensive estimates of the prevalence of smoking tobacco use and attributable disease burden are needed to guide tobacco control efforts nationally and globally. methods we estimated the prevalence of smoking tobacco use and attributable disease burden for 204 countries and territories, by age and sex, from 1990 to 2019 as part of the global burden of diseases, injuries, and risk factors study. we modelled multiple smoking-related indicators from 3625 nationally representative surveys. we completed systematic reviews and did bayesian meta-regressions for 36 causally linked health outcomes to estimate non-linear dose-response risk curves for current and former smokers. we used a direct estimation approach to estimate attributable burden, providing more comprehensive estimates of the health effects of smoking than previously available. findings globally in 2019, 1·14 billion (95% uncertainty interval 1·13-1·16) individuals were current smokers, who consumed 7·41 trillion (7·11-7·74) cigarette-equivalents of tobacco in 2019. although prevalence of smoking had decreased significantly since 1990 among both males (27·5% reduction) and females (37·7% reduction) aged 15 years and older, population growth has led to a significant increase in the total number of smokers from 0·99 billion (0·98-1·00) in 1990. globally in 2019, smoking tobacco use accounted for 7·69 million (7·16-8·20) deaths and 200 million (185-214) disability-adjusted life-years, and was the leading risk factor for death among males (20·2% of male deaths). 6·68 million of 7·69 million deaths attributable to smoking tobacco use were among current smokers. interpretation in the absence of intervention, the annual toll of 7·69 million deaths and 200 million disability-adjusted life-years attributable to smoking will increase over the coming decades. substantial progress in reducing the prevalence of smoking tobacco use has been observed in countries from all regions and at all stages of development, but a large implementation gap remains for tobacco control. countries have a clear and urgent opportunity to pass strong, evidence-based policies to accelerate reductions in the prevalence of smoking and reap massive health benefits for their citizens. funding bloomberg philanthropies and the bill & melinda gates foundation.",0
"from the earliest stages of embryonic development, cells of epithelial and mesenchymal origin contribute to the structure and function of developing organs. however, these phenotypes are not always permanent, and instead, under the appropriate conditions, epithelial and mesenchymal cells convert between these two phenotypes. these processes, termed epithelial-mesenchymal transition (emt), or the reverse mesenchymal-epithelial transition (met), are required for complex body patterning and morphogenesis. in addition, epithelial plasticity and the acquisition of invasive properties without the full commitment to a mesenchymal phenotype are critical in development, particularly during branching morphogenesis in the mammary gland. recent work in cancer has identified an analogous plasticity of cellular phenotypes whereby epithelial cancer cells acquire mesenchymal features that permit escape from the primary tumor. because local invasion is thought to be a necessary first step in metastatic dissemination, emt and epithelial plasticity are hypothesized to contribute to tumor progression. similarities between developmental and oncogenic emt have led to the identification of common contributing pathways, suggesting that the reactivation of developmental pathways in breast and other cancers contributes to tumor progression. for example, developmental emt regulators including snail/slug, twist, six1, and cripto, along with developmental signaling pathways including tgf-beta and wnt/beta-catenin, are misexpressed in breast cancer and correlate with poor clinical outcomes. this review focuses on the parallels between epithelial plasticity/emt in the mammary gland and other organs during development, and on a selection of developmental emt regulators that are misexpressed specifically during breast cancer.",0
"routinely collected health data, obtained for administrative and clinical purposes without specific a priori research goals, are increasingly used for research. the rapid evolution and availability of these data have revealed issues not addressed by existing reporting guidelines, such as strengthening the reporting of observational studies in epidemiology (strobe). the reporting of studies conducted using observational routinely collected health data (record) statement was created to fill these gaps. record was created as an extension to the strobe statement to address reporting items specific to observational studies using routinely collected health data. record consists of a checklist of 13 items related to the title, abstract, introduction, methods, results, and discussion section of articles, and other information required for inclusion in such research reports. this document contains the checklist and explanatory and elaboration information to enhance the use of the checklist. examples of good reporting for each record checklist item are also included herein. this document, as well as the accompanying website and message board ( will enhance the implementation and understanding of record. through implementation of record, authors, journals editors, and peer reviewers can encourage transparency of research reporting.",0
"transforming growth factor beta (tgf-beta) is a potent chemoattractant in vitro for human dermal fibroblasts. intact disulfide and perhaps the dimeric structure of tgf-beta is essential for its ability to stimulate chemotactic migration of fibroblasts, since reduction with 2-me results in a marked loss of its potency as a chemoattractant. although epidermal growth factor (egf) appears to be capable of modulating some effects of tgf-beta, it does not alter the chemotactic response of fibroblasts to tgf-beta. specific polyvalent rabbit antibodies to homogeneously pure tgf-beta block its chemotactic activity but has no effect on the other chemoattractants tested (platelet-derived growth factor, fibronectin, and denatured type i collagen). since tgf-beta is secreted by a variety of neoplastic and normal cells including platelets, monocytes/macrophages, and lymphocytes, it may play a critical role in vivo in embryogenesis, host response to tumors, and the repair response that follows damage to tissues by immune and nonimmune reactions.",0
"more than one in three adults worldwide is either overweight or obese. epidemiological studies indicate that the location and distribution of excess fat, rather than general adiposity, are more informative for predicting risk of obesity sequelae, including cardiometabolic disease and cancer. we performed a genome-wide association study meta-analysis of body fat distribution, measured by waist-to-hip ratio (whr) adjusted for body mass index (whradjbmi), and identified 463 signals in 346 loci. heritability and variant effects were generally stronger in women than men, and we found approximately one-third of all signals to be sexually dimorphic. the 5% of individuals carrying the most whradjbmi-increasing alleles were 1.62 times more likely than the bottom 5% to have a whr above the thresholds used for metabolic syndrome. these data, made publicly available, will inform the biology of body fat distribution and its relationship with disease.",0
"retinal dystrophies, known in man, dog, mouse, and rat, involve progressive loss of photoreceptor cells with onset during or soon after the developmental period. functional (electroretinogram), chemical (rhodopsin analyses) and morphological (light and electron microscopy) data obtained in the rat indicated two main processes: (a) overproduction of rhodopsin and an associated abnormal lamellar tissue component, (b) progressive loss of photoreceptor cells. the first abnormality recognized was the appearance of swirling sheets or bundles of extracellular lamellae between normally developing retinal rods and pigment epithelium; membrane thickness and spacing resembled that in normal outer segments. rhodopsin content reached twice normal values, was present in both rods and extracellular lamellae, and was qualitatively normal, judged by absorption maximum and products of bleaching. photoreceptors attained virtually adult form and erg function. then rod inner segments and nuclei began degenerating; the erg lost sensitivity and showed selective depression of the a-wave at high luminances. outer segments and lamellae gradually degenerated and rhodopsin content decreased. no phagocytosis was seen, though pigment cells partially dedifferentiated and many migrated through the outer segment-debris zone toward the retina. eventually photoreceptor cells and the b-wave of the erg entirely disappeared. rats kept in darkness retained electrical activity, rhodopsin content, rod structure, and extracellular lamellae longer than litter mates in light.",0
"background the american cancer society, the centers for disease control and prevention (cdc), the national cancer institute (nci), and the north american association of central cancer registries (naaccr) collaborate annually to provide updated information on cancer occurrence and trends in the united states. this year's report includes trends in lung cancer incidence and death rates, tobacco use, and tobacco control by state of residence. methods information on invasive cancers was obtained from the nci, cdc, and naaccr and information on mortality from the cdc's national center for health statistics. annual percentage changes in the age-standardized incidence and death rates (2000 us population standard) for all cancers combined and for the top 15 cancers were estimated by joinpoint analysis of long-term (1975-2005) trends and by least squares linear regression of short-term (1996-2005) trends. all statistical tests were two-sided. results both incidence and death rates from all cancers combined decreased statistically significantly (p conclusions although the decrease in overall cancer incidence and death rates is encouraging, large state and regional differences in lung cancer trends among women underscore the need to maintain and strengthen many state tobacco control programs.",0
"aim to compare the effects of combining liraglutide (0.6, 1.2 or 1.8 mg/day) or rosiglitazone 4 mg/day (all n >or= 228) or placebo (n = 114) with glimepiride (2-4 mg/day) on glycaemic control, body weight and safety in type 2 diabetes. methods in total, 1041 adults (mean +/- sd), age 56 +/- 10 years, weight 82 +/- 17 kg and glycated haemoglobin (hba(1c)) 8.4 +/- 1.0% at 116 sites in 21 countries were stratified based on previous oral glucose-lowering mono : combination therapies (30 : 70%) to participate in a five-arm, 26-week, double-dummy, randomized study. results liraglutide (1.2 or 1.8 mg) produced greater reductions in hba(1c) from baseline, (-1.1%, baseline 8.5%) compared with placebo (+0.2%, p conclusions liraglutide added to glimepiride was well tolerated and provided improved glycaemic control and favourable weight profile.",0
"during its february 2015 meeting, the advisory committee on immunization practices (acip) recommended 9-valent human papillomavirus (hpv) vaccine (9vhpv) (gardasil 9, merck and co., inc.) as one of three hpv vaccines that can be used for routine vaccination. hpv vaccine is recommended for routine vaccination at age 11 or 12 years. acip also recommends vaccination for females aged 13 through 26 years and males aged 13 through 21 years not vaccinated previously. vaccination is also recommended through age 26 years for men who have sex with men and for immunocompromised persons (including those with hiv infection) if not vaccinated previously. 9vhpv is a noninfectious, virus-like particle (vlp) vaccine. similar to quadrivalent hpv vaccine (4vhpv), 9vhpv contains hpv 6, 11, 16, and 18 vlps. in addition, 9vhpv contains hpv 31, 33, 45, 52, and 58 vlps. 9vhpv was approved by the food and drug administration (fda) on december 10, 2014, for use in females aged 9 through 26 years and males aged 9 through 15 years. for these recommendations, acip reviewed additional data on 9vhpv in males aged 16 through 26 years. 9vhpv and 4vhpv are licensed for use in females and males. bivalent hpv vaccine (2vhpv), which contains hpv 16, 18 vlps, is licensed for use in females. this report summarizes evidence considered by acip in recommending 9vhpv as one of three hpv vaccines that can be used for vaccination and provides recommendations for vaccine use.",0
"background prostate cancer might have high radiation-fraction sensitivity that would give a therapeutic advantage to hypofractionated treatment. we present a pre-planned analysis of the efficacy and side-effects of a randomised trial comparing conventional and hypofractionated radiotherapy after 5 years follow-up. methods chhip is a randomised, phase 3, non-inferiority trial that recruited men with localised prostate cancer (pt1b-t3an0m0). patients were randomly assigned (1:1:1) to conventional (74 gy delivered in 37 fractions over 7·4 weeks) or one of two hypofractionated schedules (60 gy in 20 fractions over 4 weeks or 57 gy in 19 fractions over 3·8 weeks) all delivered with intensity-modulated techniques. most patients were given radiotherapy with 3-6 months of neoadjuvant and concurrent androgen suppression. randomisation was by computer-generated random permuted blocks, stratified by national comprehensive cancer network (nccn) risk group and radiotherapy treatment centre, and treatment allocation was not masked. the primary endpoint was time to biochemical or clinical failure; the critical hazard ratio (hr) for non-inferiority was 1·208. analysis was by intention to treat. long-term follow-up continues. the chhip trial is registered as an international standard randomised controlled trial, number isrctn97182923. findings between oct 18, 2002, and june 17, 2011, 3216 men were enrolled from 71 centres and randomly assigned (74 gy group, 1065 patients; 60 gy group, 1074 patients; 57 gy group, 1077 patients). median follow-up was 62·4 months (iqr 53·9-77·0). the proportion of patients who were biochemical or clinical failure free at 5 years was 88·3% (95% ci 86·0-90·2) in the 74 gy group, 90·6% (88·5-92·3) in the 60 gy group, and 85·9% (83·4-88·0) in the 57 gy group. 60 gy was non-inferior to 74 gy (hr 0·84 , pni=0·0018) but non-inferiority could not be claimed for 57 gy compared with 74 gy (hr 1·20 , pni=0·48). long-term side-effects were similar in the hypofractionated groups compared with the conventional group. there were no significant differences in either the proportion or cumulative incidence of side-effects 5 years after treatment using three clinician-reported as well as patient-reported outcome measures. the estimated cumulative 5 year incidence of radiation therapy oncology group (rtog) grade 2 or worse bowel and bladder adverse events was 13·7% (111 events) and 9·1% (66 events) in the 74 gy group, 11·9% (105 events) and 11·7% (88 events) in the 60 gy group, 11·3% (95 events) and 6·6% (57 events) in the 57 gy group, respectively. no treatment-related deaths were reported. interpretation hypofractionated radiotherapy using 60 gy in 20 fractions is non-inferior to conventional fractionation using 74 gy in 37 fractions and is recommended as a new standard of care for external-beam radiotherapy of localised prostate cancer. funding cancer research uk, department of health, and the national institute for health research cancer research network.",0
"background the emergence of the covid-19 and its consequences has led to fears, worries, and anxiety among individuals worldwide. the present study developed the fear of covid-19 scale (fcv-19s) to complement the clinical efforts in preventing the spread and treating of covid-19 cases. methods the sample comprised 717 iranian participants. the items of the fcv-19s were constructed based on extensive review of existing scales on fears, expert evaluations, and participant interviews. several psychometric tests were conducted to ascertain its reliability and validity properties. results after panel review and corrected item-total correlation testing, seven items with acceptable corrected item-total correlation (0.47 to 0.56) were retained and further confirmed by significant and strong factor loadings (0.66 to 0.74). also, other properties evaluated using both classical test theory and rasch model were satisfactory on the seven-item scale. more specifically, reliability values such as internal consistency ( α = .82) and test-retest reliability (icc = .72) were acceptable. concurrent validity was supported by the hospital anxiety and depression scale (with depression, r = 0.425 and anxiety, r = 0.511) and the perceived vulnerability to disease scale (with perceived infectability, r = 0.483 and germ aversion, r = 0.459). conclusion the fear of covid-19 scale, a seven-item scale, has robust psychometric properties. it is reliable and valid in assessing fear of covid-19 among the general population and will also be useful in allaying covid-19 fears among individuals.",0
"we address the diffusion of information about the covid-19 with a massive data analysis on twitter, instagram, youtube, reddit and gab. we analyze engagement and interest in the covid-19 topic and provide a differential assessment on the evolution of the discourse on a global scale for each platform and their users. we fit information spreading with epidemic models characterizing the basic reproduction number for each social media platform. moreover, we identify information spreading from questionable sources, finding different volumes of misinformation in each platform. however, information from both reliable and questionable sources do not present different spreading patterns. finally, we provide platform-dependent numerical estimates of rumors' amplification.",0
"sp1-like proteins and krüppel-like factors (klfs) are highly related zinc-finger proteins that are important components of the eukaryotic cellular transcriptional machinery. by regulating the expression of a large number of genes that have gc-rich promoters, sp1-like/klf transcription regulators may take part in virtually all facets of cellular function, including cell proliferation, apoptosis, differentiation, and neoplastic transformation. individual members of the sp1-like/klf family can function as activators or repressors depending on which promoter they bind and the coregulators with which they interact. a long-standing research aim has been to define the mechanisms by which sp1-like factors and klfs regulate gene expression and cellular function in a cell- and promoter-specific manner. most members of this family have been identified in mammals, with at least 21 sp1-like/klf proteins encoded in the human genome, and members are also found in frogs, worms and flies. sp1-like/klf proteins have highly conserved carboxy-terminal zinc-finger domains that function in dna binding. the amino terminus, containing the transcription activation domain, can vary significantly between family members.",0
"currently, the number of patients with coronavirus disease 2019 (covid-19) has increased rapidly, but relationship between comorbidity and patients with covid-19 still not clear. the aim was to explore whether the presence of common comorbidities increases covid-19 patients' risk. a literature search was performed using the electronic platforms (pubmed, cochrane library, embase, and other databases) to obtain relevant research studies published up to march 1, 2020. relevant data of research endpoints in each study were extracted and merged. all data analysis was performed using stata12.0 software. a total of 1558 patients with covid-19 in 6 studies were enrolled in our meta-analysis eventually. hypertension (or: 2.29, p<0.001), diabetes (or: 2.47, p<0.001), chronic obstructive pulmonary disease (copd) (or: 5.97, p<0.001), cardiovascular disease (or: 2.93, p<0.001), and cerebrovascular disease (or:3.89, p=0.002)were independent risk factors associated with covid-19 patients. the meta-analysis revealed no correlation between increased risk of covid-19 and liver disease, malignancy, or renal disease. hypertension, diabetes, copd, cardiovascular disease, and cerebrovascular disease are major risk factors for patients with covid-19. knowledge of these risk factors can be a resource for clinicians in the early appropriate medical management of patients with covid-19.",0
"the endogenous cellular and molecular mechanisms that control acute inflammation and its resolution are of wide interest. using self-resolving inflammatory exudates and lipidomics, we have identified a new pathway involving biosynthesis of potent antiinflammatory and proresolving mediators from the essential fatty acid docosahexaenoic acid (dha) by macrophages (mphis). during the resolution of mouse peritonitis, exudates accumulated both 17-hydroxydocosahexaenoic acid, a known marker of 17s-d series resolvin (rv) and protectin biosynthesis, and 14s-hydroxydocosa-4z,7z,10z,12e,16z,19z-hexaenoic acid from endogenous dha. addition of either dha or 14s-hydroperoxydocosa-4z,7z,10z,12e,16z,19z-hexaenoic acid to activated mphis converted these substrates to novel dihydroxy-containing products that possessed potent antiinflammatory and proresolving activity with a potency similar to resolvin e1, 5s,12r,18r-trihydroxyeicosa-6z,8e,10e,14z,16e-pentaenoic acid, and protectin d1, 10r,17s-dihydroxydocosa-4z,7z,11e,13e,15z,19z-hexaenoic acid. stable isotope incorporation, intermediate trapping, and characterization of physical and biological properties of the products demonstrated a novel 14-lipoxygenase pathway, generating bioactive 7,14-dihydroxydocosa-4z,8,10,12,16z,19z-hexaenoic acid, coined mphi mediator in resolving inflammation (maresin), which enhances resolution. these findings suggest that maresins and this new metabolome may be involved in some of the beneficial actions of dha and mphis in tissue homeostasis, inflammation resolution, wound healing, and host defense.",0
"dynactin is a multisubunit complex that plays an accessory role in cytoplasmic dynein function. overexpression in mammalian cells of one dynactin subunit, dynamitin, disrupts the complex, resulting in dissociation of cytoplasmic dynein from prometaphase kinetochores, with consequent perturbation of mitosis (echeverri, c.j., b.m. paschal, k.t. vaughan, and r.b. vallee. 1996. j. cell biol. 132:617-634). based on these results, dynactin was proposed to play a role in linking cytoplasmic dynein to kinetochores and, potentially, to membrane organelles. the current study reports on the dynamitin interphase phenotype. in dynamitin-overexpressing cells, early endosomes (labeled with antitransferrin receptor), as well as late endosomes and lysosomes (labeled with anti-lysosome-associated membrane protein-1 ), were redistributed to the cell periphery. this redistribution was disrupted by nocodazole, implicating an underlying plus end-directed microtubule motor activity. the golgi stack, monitored using sialyltransferase, galactosyltransferase, and n-acetylglucosaminyltransferase i, was dramatically disrupted into scattered structures that colocalized with components of the intermediate compartment (ergic-53 and erd-2). the disrupted golgi elements were revealed by em to represent short stacks similar to those formed by microtubule-depolymerizing agents. golgi-to-er traffic of stack markers induced by brefeldin a was not inhibited by dynamitin overexpression. time-lapse observations of dynamitin-overexpressing cells recovering from brefeldin a treatment revealed that the scattered golgi elements do not undergo microtubule-based transport as seen in control cells, but rather, remain stationary at or near their er exit sites. these results indicate that dynactin is specifically required for ongoing centripetal movement of endocytic organelles and components of the intermediate compartment. results similar to those of dynamitin overexpression were obtained by microinjection with antidynein intermediate chain antibody, consistent with a role for dynactin in mediating interactions of cytoplasmic dynein with specific membrane organelles. these results suggest that dynamitin plays a pivotal role in regulating organelle movement at the level of motor-cargo binding.",0
"assessment of alzheimer's disease (ad)-related neurofibrillary pathology requires a procedure that permits a sufficient differentiation between initial, intermediate, and late stages. the gradual deposition of a hyperphosphorylated tau protein within select neuronal types in specific nuclei or areas is central to the disease process. the staging of ad-related neurofibrillary pathology originally described in 1991 was performed on unconventionally thick sections (100 mum) using a modern silver technique and reflected the progress of the disease process based chiefly on the topographic expansion of the lesions. to better meet the demands of routine laboratories this procedure is revised here by adapting tissue selection and processing to the needs of paraffin-embedded sections (5-15 mum) and by introducing a robust immunoreaction (at8) for hyperphosphorylated tau protein that can be processed on an automated basis. it is anticipated that this revised methodological protocol will enable a more uniform application of the staging procedure.",0
"integrins are cell adhesion receptors that are evolutionary old and that play important roles during developmental and pathological processes. the integrin family is composed of 24 alphabeta heterodimeric members that mediate the attachment of cells to the extracellular matrix (ecm) but that also take part in specialized cell-cell interactions. only a subset of integrins (8 out of 24) recognizes the rgd sequence in the native ligands. in some ecm molecules, such as collagen and certain laminin isoforms, the rgd sequences are exposed upon denaturation or proteolytic cleavage, allowing cells to bind these ligands by using rgd-binding receptors. proteolytic cleavage of ecm proteins might also generate fragments with novel biological activity such as endostatin, tumstatin, and endorepellin. nine integrin chains contain an alphai domain, including the collagen-binding integrins alpha1beta1, alpha2beta1, alpha10beta1, and alpha11beta1. the collagen-binding integrins recognize the triple-helical gfoger sequence in the major collagens, but their ability to recognize these sequences in vivo is dependent on the fibrillar status and accessibility of the interactive domains in the fibrillar collagens. the current review summarizes some basic facts about the integrin family including a historical perspective, their structure, and their ligand-binding properties.",0
"genome-wide association studies have been successful in identifying single nucleotide polymorphisms (snps) associated with a large number of phenotypes. however, an associated snp is likely part of a larger region of linkage disequilibrium. this makes it difficult to precisely identify the snps that have a biological link with the phenotype. we have systematically investigated the association of multiple types of encode data with disease-associated snps and show that there is significant enrichment for functional snps among the currently identified associations. this enrichment is strongest when integrating multiple sources of functional information and when highest confidence disease-associated snps are used. we propose an approach that integrates multiple types of functional data generated by the encode consortium to help identify ""functional snps"" that may be associated with the disease phenotype. our approach generates putative functional annotations for up to 80% of all previously reported associations. we show that for most associations, the functional snp most strongly supported by experimental evidence is a snp in linkage disequilibrium with the reported association rather than the reported snp itself. our results show that the experimental data sets generated by the encode consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes.",0
"multiple imputation is commonly used to impute missing data, and is typically more efficient than complete cases analysis in regression analysis when covariates have missing values. imputation may be performed using a regression model for the incomplete covariates on other covariates and, importantly, on the outcome. with a survival outcome, it is a common practice to use the event indicator d and the log of the observed event or censoring time t in the imputation model, but the rationale is not clear.we assume that the survival outcome follows a proportional hazards model given covariates x and z. we show that a suitable model for imputing binary or normal x is a logistic or linear regression on the event indicator d, the cumulative baseline hazard h(0)(t), and the other covariates z. this result is exact in the case of a single binary covariate; in other cases, it is approximately valid for small covariate effects and/or small cumulative incidence. if we do not know h(0)(t), we approximate it by the nelson-aalen estimator of h(t) or estimate it by cox regression.we compare the methods using simulation studies. we find that using logt biases covariate-outcome associations towards the null, while the new methods have lower bias. overall, we recommend including the event indicator and the nelson-aalen estimator of h(t) in the imputation model.",0
"high-throughput sequencing of circulating tumor dna (ctdna) promises to facilitate personalized cancer therapy. however, low quantities of cell-free dna (cfdna) in the blood and sequencing artifacts currently limit analytical sensitivity. to overcome these limitations, we introduce an approach for integrated digital error suppression (ides). our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfdna molecules. individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (capp-seq) by about threefold, and synergize when combined to yield ∼15-fold improvements. as a result, ides-enhanced capp-seq facilitates noninvasive variant detection across hundreds of kilobases. applied to non-small cell lung cancer (nsclc) patients, our method enabled biopsy-free profiling of egfr kinase domain mutations with 92% sensitivity and >99.99% specificity at the variant level, and with 90% sensitivity and 96% specificity at the patient level. in addition, our approach allowed monitoring of nsclc ctdna down to 4 in 10(5) cfdna molecules. we anticipate that ides will aid the noninvasive genotyping and detection of ctdna in research and clinical settings.",0
"radiomics extracts and mines large number of medical imaging features quantifying tumor phenotypic characteristics. highly accurate and reliable machine-learning approaches can drive the success of radiomic applications in clinical care. in this radiomic study, fourteen feature selection methods and twelve classification methods were examined in terms of their performance and stability for predicting overall survival. a total of 440 radiomic features were extracted from pre-treatment computed tomography (ct) images of 464 lung cancer patients. to ensure the unbiased evaluation of different machine-learning methods, publicly available implementations along with reported parameter configurations were used. furthermore, we used two independent radiomic cohorts for training (n = 310 patients) and validation (n = 154 patients). we identified that wilcoxon test based feature selection method wlcx (stability = 0.84 ± 0.05, auc = 0.65 ± 0.02) and a classification method random forest rf (rsd = 3.52%, auc = 0.66 ± 0.03) had highest prognostic performance with high stability against data perturbation. our variability analysis indicated that the choice of classification method is the most dominant source of performance variation (34.21% of total variance). identification of optimal machine-learning methods for radiomic applications is a crucial step towards stable and clinically relevant radiomic biomarkers, providing a non-invasive way of quantifying and monitoring tumor-phenotypic characteristics in clinical practice.",0
"in this review we describe and discuss several approaches to selecting higher plants as candidates for drug development with the greatest possibility of success. we emphasize the role of information derived from various systems of traditional medicine (ethnomedicine) and its utility for drug discovery purposes. we have identified 122 compounds of defined structure, obtained from only 94 species of plants, that are used globally as drugs and demonstrate that 80% of these have had an ethnomedical use identical or related to the current use of the active elements of the plant. we identify and discuss advantages and disadvantages of using plants as starting points for drug development, specifically those used in traditional medicine.",0
"we provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from south africa's severe acute respiratory syndrome coronavirus 2 (sars-cov-2) epidemic to date. although we found no evidence of increased reinfection risk associated with circulation of the beta (b.1.351) or delta (b.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the omicron (b.1.1.529) variant in previously infected individuals in south africa. reinfections occurring between 1 november 2021 and 31 january 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-november 2021.",0
"pluripotent stem cells provide a potential solution to current epidemic rates of heart failure by providing human cardiomyocytes to support heart regeneration. studies of human embryonic-stem-cell-derived cardiomyocytes (hesc-cms) in small-animal models have shown favourable effects of this treatment. however, it remains unknown whether clinical-scale hesc-cm transplantation is feasible, safe or can provide sufficient myocardial regeneration. here we show that hesc-cms can be produced at a clinical scale (more than one billion cells per batch) and cryopreserved with good viability. using a non-human primate model of myocardial ischaemia followed by reperfusion, we show that cryopreservation and intra-myocardial delivery of one billion hesc-cms generates extensive remuscularization of the infarcted heart. the hesc-cms showed progressive but incomplete maturation over a 3-month period. grafts were perfused by host vasculature, and electromechanical junctions between graft and host myocytes were present within 2 weeks of engraftment. importantly, grafts showed regular calcium transients that were synchronized to the host electrocardiogram, indicating electromechanical coupling. in contrast to small-animal models, non-fatal ventricular arrhythmias were observed in hesc-cm-engrafted primates. thus, hesc-cms can remuscularize substantial amounts of the infarcted monkey heart. comparable remuscularization of a human heart should be possible, but potential arrhythmic complications need to be overcome.",0
"the coefficient of determination r 2 quantifies the proportion of variance explained by a statistical model and is an important summary statistic of biological interest. however, estimating r 2 for generalized linear mixed models (glmms) remains challenging. we have previously introduced a version of r 2 that we called for poisson and binomial glmms, but not for other distributional families. similarly, we earlier discussed how to estimate intra-class correlation coefficients (iccs) using poisson and binomial glmms. in this paper, we generalize our methods to all other non-gaussian distributions, in particular to negative binomial and gamma distributions that are commonly used for modelling biological data. while expanding our approach, we highlight two useful concepts for biologists, jensen's inequality and the delta method, both of which help us in understanding the properties of glmms. jensen's inequality has important implications for biologically meaningful interpretation of glmms, whereas the delta method allows a general derivation of variance associated with non-gaussian distributions. we also discuss some special considerations for binomial glmms with binary or proportion data. we illustrate the implementation of our extension by worked examples from the field of ecology and evolution in the r environment. however, our method can be used across disciplines and regardless of statistical environments.",0
"background ovarian cancer has a poor prognosis, with just 40% of patients surviving 5 years. we designed this trial to establish the effect of early detection by screening on ovarian cancer mortality. methods in this randomised controlled trial, we recruited postmenopausal women aged 50-74 years from 13 centres in national health service trusts in england, wales, and northern ireland. exclusion criteria were previous bilateral oophorectomy or ovarian malignancy, increased risk of familial ovarian cancer, and active non-ovarian malignancy. the trial management system confirmed eligibility and randomly allocated participants in blocks of 32 using computer-generated random numbers to annual multimodal screening (mms) with serum ca125 interpreted with use of the risk of ovarian cancer algorithm, annual transvaginal ultrasound screening (uss), or no screening, in a 1:1:2 ratio. the primary outcome was death due to ovarian cancer by dec 31, 2014, comparing mms and uss separately with no screening, ascertained by an outcomes committee masked to randomisation group. all analyses were by modified intention to screen, excluding the small number of women we discovered after randomisation to have a bilateral oophorectomy, have ovarian cancer, or had exited the registry before recruitment. investigators and participants were aware of screening type. this trial is registered with clinicaltrials.gov, number nct00058032. findings between june 1, 2001, and oct 21, 2005, we randomly allocated 202,638 women: 50,640 (25·0%) to mms, 50,639 (25·0%) to uss, and 101,359 (50·0%) to no screening. 202,546 (>99·9%) women were eligible for analysis: 50,624 (>99·9%) women in the mms group, 50,623 (>99·9%) in the uss group, and 101,299 (>99·9%) in the no screening group. screening ended on dec 31, 2011, and included 345,570 mms and 327,775 uss annual screening episodes. at a median follow-up of 11·1 years (iqr 10·0-12·0), we diagnosed ovarian cancer in 1282 (0·6%) women: 338 (0·7%) in the mms group, 314 (0·6%) in the uss group, and 630 (0·6%) in the no screening group. of these women, 148 (0·29%) women in the mms group, 154 (0·30%) in the uss group, and 347 (0·34%) in the no screening group had died of ovarian cancer. the primary analysis using a cox proportional hazards model gave a mortality reduction over years 0-14 of 15% (95% ci -3 to 30; p=0·10) with mms and 11% (-7 to 27; p=0·21) with uss. the royston-parmar flexible parametric model showed that in the mms group, this mortality effect was made up of 8% (-20 to 31) in years 0-7 and 23% (1-46) in years 7-14, and in the uss group, of 2% (-27 to 26) in years 0-7 and 21% (-2 to 42) in years 7-14. a prespecified analysis of death from ovarian cancer of mms versus no screening with exclusion of prevalent cases showed significantly different death rates (p=0·021), with an overall average mortality reduction of 20% (-2 to 40) and a reduction of 8% (-27 to 43) in years 0-7 and 28% (-3 to 49) in years 7-14 in favour of mms. interpretation although the mortality reduction was not significant in the primary analysis, we noted a significant mortality reduction with mms when prevalent cases were excluded. we noted encouraging evidence of a mortality reduction in years 7-14, but further follow-up is needed before firm conclusions can be reached on the efficacy and cost-effectiveness of ovarian cancer screening. funding medical research council, cancer research uk, department of health, the eve appeal.",0
"systematic reviews and meta-analyses are essential to summarise evidence relating to efficacy and safety of healthcare interventions accurately and reliably. the clarity and transparency of these reports, however, are not optimal. poor reporting of systematic reviews diminishes their value to clinicians, policy makers, and other users. since the development of the quorom (quality of reporting of meta-analysis) statement-a reporting guideline published in 1999-there have been several conceptual, methodological, and practical advances regarding the conduct and reporting of systematic reviews and meta-analyses. also, reviews of published systematic reviews have found that key information about these studies is often poorly reported. realising these issues, an international group that included experienced authors and methodologists developed prisma (preferred reporting items for systematic reviews and meta-analyses) as an evolution of the original quorom guideline for systematic reviews and meta-analyses of evaluations of health care interventions. the prisma statement consists of a 27-item checklist and a four-phase flow diagram. the checklist includes items deemed essential for transparent reporting of a systematic review. in this explanation and elaboration document, we explain the meaning and rationale for each checklist item. for each item, we include an example of good reporting and, where possible, references to relevant empirical studies and methodological literature. the prisma statement, this document, and the associated website ( should be helpful resources to improve reporting of systematic reviews and meta-analyses.",0
"the use of herbal medicinal products and supplements has increased tremendously over the past three decades with not less than 80% of people worldwide relying on them for some part of primary healthcare. although therapies involving these agents have shown promising potential with the efficacy of a good number of herbal products clearly established, many of them remain untested and their use are either poorly monitored or not even monitored at all. the consequence of this is an inadequate knowledge of their mode of action, potential adverse reactions, contraindications, and interactions with existing orthodox pharmaceuticals and functional foods to promote both safe and rational use of these agents. since safety continues to be a major issue with the use of herbal remedies, it becomes imperative, therefore, that relevant regulatory authorities put in place appropriate measures to protect public health by ensuring that all herbal medicines are safe and of suitable quality. this review discusses toxicity-related issues and major safety concerns arising from the use of herbal medicinal products and also highlights some important challenges associated with effective monitoring of their safety.",0
"wolbachia are intracellular bacteria found in many species of arthropods and nematodes. they manipulate the reproduction of their arthropod hosts in various ways, may play a role in host speciation and have potential applications in biological pest control. estimates suggest that at least 20% of all insect species are infected with wolbachia. these estimates result from several wolbachia screenings in which numerous species were tested for infection; however, tests were mostly performed on only one to two individuals per species. the actual percent of species infected will depend on the distribution of infection frequencies among species. we present a meta-analysis that estimates percentage of infected species based on data on the distribution of infection levels among species. we used a beta-binomial model that describes the distribution of infection frequencies of wolbachia, shedding light on the overall infection rate as well as on the infection frequency within species. our main findings are that (1) the proportion of wolbachia-infected species is estimated to be 66%, and that (2) within species the infection frequency follows a 'most-or-few' infection pattern in a sense that the wolbachia infection frequency within one species is typically either very high (>90%) or very low (<10%).",0
"cardiovascular diseases (cvds), principally ischemic heart disease (ihd) and stroke, are the leading cause of global mortality and a major contributor to disability. this paper reviews the magnitude of total cvd burden, including 13 underlying causes of cardiovascular death and 9 related risk factors, using estimates from the global burden of disease (gbd) study 2019. gbd, an ongoing multinational collaboration to provide comparable and consistent estimates of population health over time, used all available population-level data sources on incidence, prevalence, case fatality, mortality, and health risks to produce estimates for 204 countries and territories from 1990 to 2019. prevalent cases of total cvd nearly doubled from 271 million (95% uncertainty interval : 257 to 285 million) in 1990 to 523 million (95% ui: 497 to 550 million) in 2019, and the number of cvd deaths steadily increased from 12.1 million (95% ui:11.4 to 12.6 million) in 1990, reaching 18.6 million (95% ui: 17.1 to 19.7 million) in 2019. the global trends for disability-adjusted life years (dalys) and years of life lost also increased significantly, and years lived with disability doubled from 17.7 million (95% ui: 12.9 to 22.5 million) to 34.4 million (95% ui:24.9 to 43.6 million) over that period. the total number of dalys due to ihd has risen steadily since 1990, reaching 182 million (95% ui: 170 to 194 million) dalys, 9.14 million (95% ui: 8.40 to 9.74 million) deaths in the year 2019, and 197 million (95% ui: 178 to 220 million) prevalent cases of ihd in 2019. the total number of dalys due to stroke has risen steadily since 1990, reaching 143 million (95% ui: 133 to 153 million) dalys, 6.55 million (95% ui: 6.00 to 7.02 million) deaths in the year 2019, and 101 million (95% ui: 93.2 to 111 million) prevalent cases of stroke in 2019. cardiovascular diseases remain the leading cause of disease burden in the world. cvd burden continues its decades-long rise for almost all countries outside high-income countries, and alarmingly, the age-standardized rate of cvd has begun to rise in some locations where it was previously declining in high-income countries. there is an urgent need to focus on implementing existing cost-effective policies and interventions if the world is to meet the targets for sustainable development goal 3 and achieve a 30% reduction in premature mortality due to noncommunicable diseases.",0
"developments in genomic techniques have provided insight into the remarkable genetic complexity of malignant tumours. there is increasing evidence that solid tumours may comprise of subpopulations of cells with distinct genomic alterations within the same tumour, a phenomenon termed intra-tumour heterogeneity. intra-tumour heterogeneity is likely to have implications for cancer therapeutics and biomarker discovery, particularly in the era of targeted treatment, and evidence for a relationship between intra-tumoural heterogeneity and clinical outcome is emerging. our understanding of the processes that exacerbate intra-tumoural heterogeneity, both iatrogenic and tumour specific, is likely to increase with the development and more widespread implementation of advanced sequencing technologies, and adaptation of clinical trial design to include comprehensive tissue collection protocols. the current evidence for intra-tumour heterogeneity and its relevance to cancer therapeutics will be presented in this mini-review.",0
"hybrid myeloma cell lines secreting monoclonal antibodies to tubulin have been prepared using rat myelomas and spleen cells from rats immunized with yeast tubulin. a comparison between the results obtained with the rat myeloma y3-ag 1.2.3., which secretes a light chain, and a new line, yb2/o, which does not, shows that they are both excellent parental lines and that the second produces hybrids with no myeloma chain components. the antitubulin antibodies in the serum of rats bearing two of the hybrid myeloma tumors gave titers of up to 1:10(6) from which large amounts of monoclonal antibodies could be easily purified. they recognized tubulin from yeast as well as from birds and mammals. the two antibodies gave clear immunofluorescent staining of yeast mitotic spindles as well as the interphase microtubule network of tissue culture cells. some difference in the pattern of immunofluorescence staining of yeast cells and nuclei was observed between the two antibodies. the purified antibodies could be conjugated to colloidal gold particles and used for direct labeling of yeast microtubules for electron microscopy.",0
"short-chain fatty acids (scfas) are bacterial fermentation products, which are chemically composed by a carboxylic acid moiety and a small hydrocarbon chain. among them, acetic, propionic and butyric acids are the most studied, presenting, respectively, two, three and four carbons in their chemical structure. these metabolites are found in high concentrations in the intestinal tract, from where they are uptaken by intestinal epithelial cells (iecs). the scfas are partially used as a source of atp by these cells. in addition, these molecules act as a link between the microbiota and the immune system by modulating different aspects of iecs and leukocytes development, survival and function through activation of g protein coupled receptors (ffar2, ffar3, gpr109a and olfr78) and by modulation of the activity of enzymes and transcription factors including the histone acetyltransferase and deacetylase and the hypoxia-inducible factor. considering that, it is not a surprise, the fact that these molecules and/or their targets are suggested to have an important role in the maintenance of intestinal homeostasis and that changes in components of this system are associated with pathological conditions including inflammatory bowel disease, obesity and others. the aim of this review is to present a clear and updated description of the effects of the scfas derived from bacteria on host immune system, as well as the molecular mechanisms involved on them.",0
"by reaching near-atomic resolution for a wide range of specimens, single-particle cryo-em structure determination is transforming structural biology. however, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. here, we present an implementation of the relion image processing software that uses graphics processors (gpus) to address the most computationally intensive steps of its cryo-em structure determination workflow. both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. memory requirements on gpus have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. this enables high-resolution cryo-em structure determination in a matter of days on a single workstation.",0
"the early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. the ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour dna (ctdna) has not yet been demonstrated. here we use a tumour-specific phylogenetic approach to profile the ctdna of the first 100 tracerx (tracking non-small-cell lung cancer evolution through therapy (rx)) study participants, including one patient who was also recruited to the peace (posthumous evaluation of advanced cancer environment) post-mortem study. we identify independent predictors of ctdna release and analyse the tumour-volume detection limit. through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. finally, we show that phylogenetic ctdna profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctdna-driven therapeutic studies.",0
"background this study aims to review the literature regarding the barriers to sampling, recruitment, participation, and retention of members of socioeconomically disadvantaged groups in health research and strategies for increasing the amount of health research conducted with socially disadvantaged groups. methods a systematic review with narrative synthesis was conducted. searches of electronic databases medline, psychinfo, embase, social science index via web of knowledge and cinhal were conducted for english language articles published up to may 2013. qualitative and quantitative studies as well as literature reviews were included. articles were included if they reported attempts to increase disadvantaged group participation in research, or the barriers to research with disadvantaged groups. groups of interest were those described as socially, culturally or financially disadvantaged compared to the majority of society. eligible articles were categorised according to five phases of research: 1) sampling, 2) recruitment and gaining consent, 3) data collection and measurement, 4) intervention delivery and uptake, and 5) retention and attrition. results in total, 116 papers from 115 studies met inclusion criteria and 31 previous literature reviews were included. a comprehensive summation of the major barriers to working with various disadvantaged groups is provided, along with proposed strategies for addressing each of the identified types of barriers. most studies of strategies to address the barriers were of a descriptive nature and only nine studies reported the results of randomised trials. conclusions to tackle the challenges of research with socially disadvantaged groups, and increase their representation in health and medical research, researchers and research institutions need to acknowledge extended timeframes, plan for higher resourcing costs and operate via community partnerships.",0
"background foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. to our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. methods and findings we synthesized data on the number of foodborne illnesses, sequelae, deaths, and disability adjusted life years (dalys), for all diseases with sufficient data to support global and regional estimates, by age and region. the data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. we sought relevant data circa 2010, and included sources from 1990-2012. the number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. to estimate mortality for mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal salmonella enterica infections, we excluded cases attributed to hiv infection. we excluded stillbirths in our estimates. we estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval 1.5-2.9 billion) cases, over one million (95% ui 0.89-1.4 million) deaths, and 78.7 million (95% ui 65.0-97.7 million) dalys in 2010. to estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. waterborne transmission of disease was not included. we estimate that 29% (95% ui 23-36%) of cases caused by diseases in our study, or 582 million (95% ui 401-922 million), were transmitted by contaminated food, resulting in 25.2 million (95% ui 17.5-37.0 million) dalys. norovirus was the leading cause of foodborne illness causing 125 million (95% ui 70-251 million) cases, while campylobacter spp. caused 96 million (95% ui 52-177 million) foodborne illnesses. of all foodborne diseases, diarrheal and invasive infections due to non-typhoidal s. enterica infections resulted in the highest burden, causing 4.07 million (95% ui 2.49-6.27 million) dalys. regionally, dalys per 100,000 population were highest in the african region followed by the south east asian region. considerable burden of foodborne disease is borne by children less than five years of age. major limitations of our study include data gaps, particularly in middle- and high-mortality countries, and uncertainty around the proportion of diseases that were foodborne. conclusions foodborne diseases result in a large disease burden, particularly in children. although it is known that diarrheal diseases are a major burden in children, we have demonstrated for the first time the importance of contaminated food as a cause. there is a need to focus food safety interventions on preventing foodborne diseases, particularly in low- and middle-income settings.",0
"activation in lectin-free interleukin 2 (il-2) containing supernatants of peripheral blood mononuclear leukocytes (pbl) from cancer patients or normal individuals resulted in expression of cytotoxicity toward 20 of 21 natural killer (nk)-resistant fresh solid tumor cells tested. fresh solid tumor cells were resistant to nk-mediated lysis in 10 autologous patients' pbl-tumor interactions, and from 17 normal individuals tested against 13 allogeneic fresh tumors. culture of pbl in il-2 for 2-3 d was required for the lymphokine activated killers (lak) to be expressed, and lytic activity toward a variety of nk-resistant fresh and cultured tumor targets developed in parallel. autologous il-2 was functional in lak activation, as well as interferon-depleted il-2 preparations. irradiation of responder pbl before culture in il-2 prevented lak development. precursors of lak were present in pbl depleted of adherent cells and in nk-void thoracic duct lymphocytes, suggesting that the precursor is neither a monocyte nor an nk cell. lak effectors expressed the serologically defined t cell markers of okt.3, leu-1, and 4f2, but did not express the monocyte/nk marker okm-1. lysis of autologous fresh solid tumors by lak from cancer patients' pbl was demonstrated in 85% of the patient-fresh tumor combinations. our data present evidence that the lak system is a phenomenon distinct from either nk or ctl systems that probably accounts for a large number of reported nonclassical cytotoxicities. the biological role of lak cells is not yet known, although it is suggested that these cells may be functional in immune surveillance against human solid tumors.",0
"functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. in this paper, we describe the blast2go suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (go) vocabulary. blast2go optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the go hierarchy, and the quality of the original annotations. the tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. the application supports interpro, enzyme codes, kegg pathways, go direct acyclic graphs (dags), and goslim. blast2go is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.",0
"the clinical efficacy and safety of a drug is determined by its activity profile across many proteins in the proteome. however, designing drugs with a specific multi-target profile is both complex and difficult. therefore methods to design drugs rationally a priori against profiles of several proteins would have immense value in drug discovery. here we describe a new approach for the automated design of ligands against profiles of multiple drug targets. the method is demonstrated by the evolution of an approved acetylcholinesterase inhibitor drug into brain-penetrable ligands with either specific polypharmacology or exquisite selectivity profiles for g-protein-coupled receptors. overall, 800 ligand-target predictions of prospectively designed ligands were tested experimentally, of which 75% were confirmed to be correct. we also demonstrate target engagement in vivo. the approach can be a useful source of drug leads when multi-target profiles are required to achieve either selectivity over other drug targets or a desired polypharmacology.",0
"objective to explore evidence on the links between patient experience and clinical safety and effectiveness outcomes. design systematic review. setting a wide range of settings within primary and secondary care including hospitals and primary care centres. participants a wide range of demographic groups and age groups. primary and secondary outcome measures a broad range of patient safety and clinical effectiveness outcomes including mortality, physical symptoms, length of stay and adherence to treatment. results this study, summarising evidence from 55 studies, indicates consistent positive associations between patient experience, patient safety and clinical effectiveness for a wide range of disease areas, settings, outcome measures and study designs. it demonstrates positive associations between patient experience and self-rated and objectively measured health outcomes; adherence to recommended clinical practice and medication; preventive care (such as health-promoting behaviour, use of screening services and immunisation); and resource use (such as hospitalisation, length of stay and primary-care visits). there is some evidence of positive associations between patient experience and measures of the technical quality of care and adverse events. overall, it was more common to find positive associations between patient experience and patient safety and clinical effectiveness than no associations. conclusions the data presented display that patient experience is positively associated with clinical effectiveness and patient safety, and support the case for the inclusion of patient experience as one of the central pillars of quality in healthcare. it supports the argument that the three dimensions of quality should be looked at as a group and not in isolation. clinicians should resist sidelining patient experience as too subjective or mood-oriented, divorced from the 'real' clinical work of measuring safety and effectiveness.",0
"since 2002, beta coronaviruses (cov) have caused three zoonotic outbreaks, sars-cov in 2002-2003, mers-cov in 2012, and the newly emerged sars-cov-2 in late 2019. however, little is currently known about the biology of sars-cov-2. here, using sars-cov-2 s protein pseudovirus system, we confirm that human angiotensin converting enzyme 2 (hace2) is the receptor for sars-cov-2, find that sars-cov-2 enters 293/hace2 cells mainly through endocytosis, that pikfyve, tpc2, and cathepsin l are critical for entry, and that sars-cov-2 s protein is less stable than sars-cov s. polyclonal anti-sars s1 antibodies t62 inhibit entry of sars-cov s but not sars-cov-2 s pseudovirions. further studies using recovered sars and covid-19 patients' sera show limited cross-neutralization, suggesting that recovery from one infection might not protect against the other. our results present potential targets for development of drugs and vaccines for sars-cov-2.",0
"background visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. new visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. results blast ring image generator (brig) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. the output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where blast matches are coloured on a sliding scale indicating a defined percentage identity. images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. in addition, brig supports the mapping of unassembled sequencing reads against one or more central reference sequences. many types of custom data and annotations can be shown using brig, making it a versatile approach for visualising a range of genomic comparison data. brig is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and blast comparisons automatically. conclusions there is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. here we present brig, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. brig is freely available for all operating systems at",0
"background imagej is an image analysis program extensively used in the biological sciences and beyond. due to its ease of use, recordable macro language, and extensible plug-in architecture, imagej enjoys contributions from non-programmers, amateur programmers, and professional developers alike. enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. however, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. results we rewrote the entire imagej codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. this next-generation imagej, called ""imagej2"" in places where the distinction matters, provides a host of new functionality. it separates concerns, fully decoupling the data model from the user interface. it emphasizes integration with external applications to maximize interoperability. its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. the redesigned data model supports arbitrarily large, n-dimensional datasets, which are increasingly common in modern image acquisition. despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic imagej interface, allowing users and developers to migrate to these new methods at their own pace. conclusions scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. imagej has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for imagej's development. the described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.",0
"background despite high vaccine coverage and effectiveness, the incidence of symptomatic infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has been increasing in israel. whether the increasing incidence of infection is due to waning immunity after the receipt of two doses of the bnt162b2 vaccine is unclear. methods we conducted a 6-month longitudinal prospective study involving vaccinated health care workers who were tested monthly for the presence of anti-spike igg and neutralizing antibodies. linear mixed models were used to assess the dynamics of antibody levels and to determine predictors of antibody levels at 6 months. results the study included 4868 participants, with 3808 being included in the linear mixed-model analyses. the level of igg antibodies decreased at a consistent rate, whereas the neutralizing antibody level decreased rapidly for the first 3 months with a relatively slow decrease thereafter. although igg antibody levels were highly correlated with neutralizing antibody titers (spearman's rank correlation between 0.68 and 0.75), the regression relationship between the igg and neutralizing antibody levels depended on the time since receipt of the second vaccine dose. six months after receipt of the second dose, neutralizing antibody titers were substantially lower among men than among women (ratio of means, 0.64; 95% confidence interval , 0.55 to 0.75), lower among persons 65 years of age or older than among those 18 to less than 45 years of age (ratio of means, 0.58; 95% ci, 0.48 to 0.70), and lower among participants with immunosuppression than among those without immunosuppression (ratio of means, 0.30; 95% ci, 0.20 to 0.46). conclusions six months after receipt of the second dose of the bnt162b2 vaccine, humoral response was substantially decreased, especially among men, among persons 65 years of age or older, and among persons with immunosuppression.",0
"unlabelled i-mutant2.0 is a support vector machine (svm)-based tool for the automatic prediction of protein stability changes upon single point mutations. i-mutant2.0 predictions are performed starting either from the protein structure or, more importantly, from the protein sequence. this latter task, to the best of our knowledge, is exploited for the first time. the method was trained and tested on a data set derived from protherm, which is presently the most comprehensive available database of thermodynamic experimental data of free energy changes of protein stability upon mutation under different conditions. i-mutant2.0 can be used both as a classifier for predicting the sign of the protein stability change upon mutation and as a regression estimator for predicting the related deltadeltag values. acting as a classifier, i-mutant2.0 correctly predicts (with a cross-validation procedure) 80% or 77% of the data set, depending on the usage of structural or sequence information, respectively. when predicting deltadeltag values associated with mutations, the correlation of predicted with expected/experimental values is 0.71 (with a standard error of 1.30 kcal/mol) and 0.62 (with a standard error of 1.45 kcal/mol) when structural or sequence information are respectively adopted. our web interface allows the selection of a predictive mode that depends on the availability of the protein structure and/or sequence. in this latter case, the web server requires only pasting of a protein sequence in a raw format. we therefore introduce i-mutant2.0 as a unique and valuable helper for protein design, even when the protein structure is not yet known with atomic resolution. availability",0
"during the last decade the field of cancer immunotherapy has witnessed impressive progress. highly effective immunotherapies such as immune checkpoint inhibition, and t-cell engaging therapies like bispecific t-cell engaging (bite) single-chain antibody constructs and chimeric antigen receptor (car) t cells have shown remarkable efficacy in clinical trials and some of these agents have already received regulatory approval. however, along with growing experience in the clinical application of these potent immunotherapeutic agents comes the increasing awareness of their inherent and potentially fatal adverse effects, most notably the cytokine release syndrome (crs). this review provides a comprehensive overview of the mechanisms underlying crs pathophysiology, risk factors, clinical presentation, differential diagnoses, and prognostic factors. in addition, based on the current evidence we give practical guidance to the management of the cytokine release syndrome.",0
"accurate estimation of the contrast transfer function (ctf) is critical for a near-atomic resolution cryo electron microscopy (cryoem) reconstruction. here, a gpu-accelerated computer program, gctf, for accurate and robust, real-time ctf determination is presented. the main target of gctf is to maximize the cross-correlation of a simulated ctf with the logarithmic amplitude spectra (las) of observed micrographs after background subtraction. novel approaches in gctf improve both speed and accuracy. in addition to gpu acceleration (e.g. 10-50×), a fast '1-dimensional search plus 2-dimensional refinement (1s2r)' procedure further speeds up gctf. based on the global ctf determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves ctf parameters of all particles for subsequent image processing. novel diagnosis method using equiphase averaging (epa) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. gctf is an independent program and the outputs can be easily imported into other cryoem software such as relion (scheres, 2012) and frealign (grigorieff, 2007). the results from several representative datasets are shown and discussed in this paper.",0
"high concentrations of airborne particles have been associated with increased pulmonary and cardiovascular mortality, with indications of a specific toxicologic role for ultrafine particles (ufps; particles < 0.1 microm). within hours after the respiratory system is exposed to ufps, the ufps may appear in many compartments of the body, including the liver, heart, and nervous system. to date, the mechanisms by which ufps penetrate boundary membranes and the distribution of ufps within tissue compartments of their primary and secondary target organs are largely unknown. we combined different experimental approaches to study the distribution of ufps in lungs and their uptake by cells. in the in vivo experiments, rats inhaled an ultrafine titanium dioxide aerosol of 22 nm count median diameter. the intrapulmonary distribution of particles was analyzed 1 hr or 24 hr after the end of exposure, using energy-filtering transmission electron microscopy for elemental microanalysis of individual particles. in an in vitro study, we exposed pulmonary macrophages and red blood cells to fluorescent polystyrene microspheres (1, 0.2, and 0.078 microm) and assessed particle uptake by confocal laser scanning microscopy. inhaled ultrafine titanium dioxide particles were found on the luminal side of airways and alveoli, in all major lung tissue compartments and cells, and within capillaries. particle uptake in vitro into cells did not occur by any of the expected endocytic processes, but rather by diffusion or adhesive interactions. particles within cells are not membrane bound and hence have direct access to intracellular proteins, organelles, and dna, which may greatly enhance their toxic potential.",0
"summary multiple sequence alignment (msa) is an important step in comparative sequence analyses. parallelization is a key technique for reducing the time required for large-scale sequence analyses. the three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the mafft msa program were parallelized using the posix threads library. two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default. availability the parallelized version of mafft is available at this version currently supports the linux operating system only.",0
"early detection and effective treatment of severe covid-19 patients remain major challenges. here, we performed proteomic and metabolomic profiling of sera from 46 covid-19 and 53 control individuals. we then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. the model was validated using 10 independent patients, 7 of which were correctly classified. targeted proteomics and metabolomics assays were employed to further validate this molecular classifier in a second test cohort of 19 covid-19 patients, leading to 16 correct assignments. we identified molecular changes in the sera of covid-19 patients compared to other groups implicating dysregulation of macrophage, platelet degranulation, complement system pathways, and massive metabolic suppression. this study revealed characteristic protein and metabolite changes in the sera of severe covid-19 patients, which might be used in selection of potential blood biomarkers for severity evaluation.",0
"matrix metalloproteinase (mmp)-1, mmp-8 and mmp-13 are interstitial collagenases that degrade type ii collagen in cartilage; this is a committed step in the progression of rheumatoid arthritis and osteoarthritis. of these enzymes, the expression of mmp-1 and mmp-13 is substantially increased in response to il-1 and tumor necrosis factor-alpha, and elevated levels of these collagenases are observed in arthritic tissues. therefore, cytokine-mediated mmp-1 and mmp-13 gene regulation is an important issue in arthritis research. in this review, we discuss current models of mmp-1 and mmp-13 transcriptional regulation, with a focus on signaling intermediates and transcription factors that may be future targets for the development of new arthritis drugs.",0
"background : mr-egger regression has recently been proposed as a method for mendelian randomization (mr) analyses incorporating summary data estimates of causal effect from multiple individual variants, which is robust to invalid instruments. it can be used to test for directional pleiotropy and provides an estimate of the causal effect adjusted for its presence. mr-egger regression provides a useful additional sensitivity analysis to the standard inverse variance weighted (ivw) approach that assumes all variants are valid instruments. both methods use weights that consider the single nucleotide polymorphism (snp)-exposure associations to be known, rather than estimated. we call this the `no measurement error' (nome) assumption. causal effect estimates from the ivw approach exhibit weak instrument bias whenever the genetic variants utilized violate the nome assumption, which can be reliably measured using the f-statistic. the effect of nome violation on mr-egger regression has yet to be studied. methods an adaptation of the i2 statistic from the field of meta-analysis is proposed to quantify the strength of nome violation for mr-egger. it lies between 0 and 1, and indicates the expected relative bias (or dilution) of the mr-egger causal estimate in the two-sample mr context. we call it igx2 . the method of simulation extrapolation is also explored to counteract the dilution. their joint utility is evaluated using simulated data and applied to a real mr example. results in simulated two-sample mr analyses we show that, when a causal effect exists, the mr-egger estimate of causal effect is biased towards the null when nome is violated, and the stronger the violation (as indicated by lower values of igx2 ), the stronger the dilution. when additionally all genetic variants are valid instruments, the type i error rate of the mr-egger test for pleiotropy is inflated and the causal effect underestimated. simulation extrapolation is shown to substantially mitigate these adverse effects. we demonstrate our proposed approach for a two-sample summary data mr analysis to estimate the causal effect of low-density lipoprotein on heart disease risk. a high value of igx2 close to 1 indicates that dilution does not materially affect the standard mr-egger analyses for these data. conclusions : care must be taken to assess the nome assumption via the igx2 statistic before implementing standard mr-egger regression in the two-sample summary data context. if igx2 is sufficiently low (less than 90%), inferences from the method should be interpreted with caution and adjustment methods considered.",0
"we describe the biochemical properties and cell surface distributions of three human t cell antigens (leu-1, leu-2a, and leu-2b) which we postulate to be the homologues of the lyt-1, lyt-2, and lyt-3 antigens that distinguish functional t cell subsets in the mouse. leu-l, like lyt-1, is on all thymocytes and peripheral t cells and is present in greater amounts on the helper/inducer subset than on the cytotoxic/suppressor subset. both antigens increase in parallel fashion during t cell maturation in the thymus and each antigen is carried on a single 67,000-molecular weight (relative) (m(r)) polypeptide chain. surprisingly, leu-1 and lyt-1 each are also expressed in readily detectable amounts on some b celi ieukemias but not detectably so on normal b cells. leu-2a and leu-2b are antigens found only on suppressor/cytotoxic cells in the human and are very similar to the murine lyt-2 and lyt-3 antigens. in both species, the two antigens are on the same disulfide- linked multimeric molecules. disulfide-bond reduction in both species yields subunits of similar size and charge. lyt-3 and leu-2b are extremely sensitive to trypsin digestion on viable cells whereas lyt-2 and leu-2a are much less so. a different membrane antigen, leu-3, is an exclusive marker of the helper/inducer subset in man. no mouse homologue for this 55,000-m(r) protein is known. the maintenance of the homologous molecules on functionally distinct t cell subpopulations in two evolutionarily distant species suggests that the lyt and leu antigens perform essential functions for the cells on which they are found.",0
"osteoarthritis is a highly prevalent and debilitating joint disorder. there is no effective medical therapy for the condition because of limited understanding of its pathogenesis. we show that transforming growth factor β1 (tgf-β1) is activated in subchondral bone in response to altered mechanical loading in an anterior cruciate ligament transection (aclt) mouse model of osteoarthritis. tgf-β1 concentrations are also high in subchondral bone from humans with osteoarthritis. high concentrations of tgf-β1 induced formation of nestin-positive mesenchymal stem cell (msc) clusters, leading to formation of marrow osteoid islets accompanied by high levels of angiogenesis. we found that transgenic expression of active tgf-β1 in osteoblastic cells induced osteoarthritis, whereas inhibition of tgf-β activity in subchondral bone attenuated the degeneration of articular cartilage. in particular, knockout of the tgf-β type ii receptor (tβrii) in nestin-positive mscs led to less development of osteoarthritis relative to wild-type mice after aclt. thus, high concentrations of active tgf-β1 in subchondral bone seem to initiate the pathological changes of osteoarthritis, and inhibition of this process could be a potential therapeutic approach to treating this disease.",0
"unlabelled guidance is provided in a european setting on the assessment and treatment of postmenopausal women at risk of fractures due to osteoporosis. introduction the international osteoporosis foundation and european society for clinical and economic aspects of osteoporosis and osteoarthritis published guidance for the diagnosis and management of osteoporosis in 2008. this manuscript updates these in a european setting. methods systematic literature reviews. results the following areas are reviewed: the role of bone mineral density measurement for the diagnosis of osteoporosis and assessment of fracture risk, general and pharmacological management of osteoporosis, monitoring of treatment, assessment of fracture risk, case finding strategies, investigation of patients and health economics of treatment. conclusions a platform is provided on which specific guidelines can be developed for national use.",0
"advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. here, we present protox-ii that incorporates molecular similarity, pharmacophores, fragment propensities and machine-learning models for the prediction of various toxicity endpoints; such as acute toxicity, hepatotoxicity, cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity, adverse outcomes pathways (tox21) and toxicity targets. the predictive models are built on data from both in vitro assays (e.g. tox21 assays, ames bacterial mutation assays, hepg2 cytotoxicity assays, immunotoxicity assays) and in vivo cases (e.g. carcinogenicity, hepatotoxicity). the models have been validated on independent external sets and have shown strong performance. protox-ii provides a freely available webserver for in silico toxicity prediction for toxicologists, regulatory agencies, computational and medicinal chemists, and all users without login at the webserver takes a two-dimensional chemical structure as an input and reports the possible toxicity profile of the chemical for 33 models with confidence scores, and an overall toxicity radar chart along with three most similar compounds with known acute toxicity.",0
"background implementation outcome measures are essential for monitoring and evaluating the success of implementation efforts. yet, currently available measures lack conceptual clarity and have largely unknown reliability and validity. this study developed and psychometrically assessed three new measures: the acceptability of intervention measure (aim), intervention appropriateness measure (iam), and feasibility of intervention measure (fim). methods thirty-six implementation scientists and 27 mental health professionals assigned 31 items to the constructs and rated their confidence in their assignments. the wilcoxon one-sample signed rank test was used to assess substantive and discriminant content validity. exploratory and confirmatory factor analysis (efa and cfa) and cronbach alphas were used to assess the validity of the conceptual model. three hundred twenty-six mental health counselors read one of six randomly assigned vignettes depicting a therapist contemplating adopting an evidence-based practice (ebp). participants used 15 items to rate the therapist's perceptions of the acceptability, appropriateness, and feasibility of adopting the ebp. cfa and cronbach alphas were used to refine the scales, assess structural validity, and assess reliability. analysis of variance (anova) was used to assess known-groups validity. finally, half of the counselors were randomly assigned to receive the same vignette and the other half the opposite vignette; and all were asked to re-rate acceptability, appropriateness, and feasibility. pearson correlation coefficients were used to assess test-retest reliability and linear regression to assess sensitivity to change. results all but five items exhibited substantive and discriminant content validity. a trimmed cfa with five items per construct exhibited acceptable model fit (cfi = 0.98, rmsea = 0.08) and high factor loadings (0.79 to 0.94). the alphas for 5-item scales were between 0.87 and 0.89. scale refinement based on measure-specific cfas and cronbach alphas using vignette data produced 4-item scales (α's from 0.85 to 0.91). a three-factor cfa exhibited acceptable fit (cfi = 0.96, rmsea = 0.08) and high factor loadings (0.75 to 0.89), indicating structural validity. anova showed significant main effects, indicating known-groups validity. test-retest reliability coefficients ranged from 0.73 to 0.88. regression analysis indicated each measure was sensitive to change in both directions. conclusions the aim, iam, and fim demonstrate promising psychometric properties. predictive validity assessment is planned.",0
"background health literacy has become an increasingly important concept in public health. we sought to develop a comprehensive measure of health literacy capable of diagnosing health literacy needs across individuals and organisations by utilizing perspectives from the general population, patients, practitioners and policymakers. methods using a validity-driven approach we undertook grounded consultations (workshops and interviews) to identify broad conceptually distinct domains. questionnaire items were developed directly from the consultation data following a strict process aiming to capture the full range of experiences of people currently engaged in healthcare through to people in the general population. psychometric analyses included confirmatory factor analysis (cfa) and item response theory. cognitive interviews were used to ensure questions were understood as intended. items were initially tested in a calibration sample from community health, home care and hospital settings (n=634) and then in a replication sample (n=405) comprising recent emergency department attendees. results initially 91 items were generated across 6 scales with agree/disagree response options and 5 scales with difficulty in undertaking tasks response options. cognitive testing revealed that most items were well understood and only some minor re-wording was required. psychometric testing of the calibration sample identified 34 poorly performing or conceptually redundant items and they were removed resulting in 10 scales. these were then tested in a replication sample and refined to yield 9 final scales comprising 44 items. a 9-factor cfa model was fitted to these items with no cross-loadings or correlated residuals allowed. given the very restricted nature of the model, the fit was quite satisfactory: χ²wlsmv(866 d.f.) = 2927, p conclusions the hlq covers 9 conceptually distinct areas of health literacy to assess the needs and challenges of a wide range of people and organisations. given the validity-driven approach, the hlq is likely to be useful in surveys, intervention evaluation, and studies of the needs and capabilities of individuals.",0
"cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. castp ( is an online tool that locates and measures pockets and voids on 3d protein structures. this new version of castp includes annotated functional information of specific residues on the protein structure. the annotations are derived from the protein data bank (pdb), swiss-prot, as well as online mendelian inheritance in man (omim), the latter contains information on the variant single nucleotide polymorphisms (snps) that are known to cause disease. these annotated residues are mapped to surface pockets, interior voids or other regions of the pdb structures. we use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in swiss-prot, omim and entries in pdb. the updated castp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.",0
"acute respiratory distress syndrome (ards), the most severe form of acute lung injury, is a devastating clinical syndrome with a high mortality rate (30-60%) (refs 1-3). predisposing factors for ards are diverse and include sepsis, aspiration, pneumonias and infections with the severe acute respiratory syndrome (sars) coronavirus. at present, there are no effective drugs for improving the clinical outcome of ards. angiotensin-converting enzyme (ace) and ace2 are homologues with different key functions in the renin-angiotensin system. ace cleaves angiotensin i to generate angiotensin ii, whereas ace2 inactivates angiotensin ii and is a negative regulator of the system. ace2 has also recently been identified as a potential sars virus receptor and is expressed in lungs. here we report that ace2 and the angiotensin ii type 2 receptor (at2) protect mice from severe acute lung injury induced by acid aspiration or sepsis. however, other components of the renin-angiotensin system, including ace, angiotensin ii and the angiotensin ii type 1a receptor (at1a), promote disease pathogenesis, induce lung oedemas and impair lung function. we show that mice deficient for ace show markedly improved disease, and also that recombinant ace2 can protect mice from severe acute lung injury. our data identify a critical function for ace2 in acute lung injury, pointing to a possible therapy for a syndrome affecting millions of people worldwide every year.",0
"in a study comparing the effects of two treatments, the propensity score is the probability of assignment to one treatment conditional on a subject's measured baseline covariates. propensity-score matching is increasingly being used to estimate the effects of exposures using observational data. in the most common implementation of propensity-score matching, pairs of treated and untreated subjects are formed whose propensity scores differ by at most a pre-specified amount (the caliper width). there has been a little research into the optimal caliper width. we conducted an extensive series of monte carlo simulations to determine the optimal caliper width for estimating differences in means (for continuous outcomes) and risk differences (for binary outcomes). when estimating differences in means or risk differences, we recommend that researchers match on the logit of the propensity score using calipers of width equal to 0.2 of the standard deviation of the logit of the propensity score. when at least some of the covariates were continuous, then either this value, or one close to it, minimized the mean square error of the resultant estimated treatment effect. it also eliminated at least 98% of the bias in the crude estimator, and it resulted in confidence intervals with approximately the correct coverage rates. furthermore, the empirical type i error rate was approximately correct. when all of the covariates were binary, then the choice of caliper width had a much smaller impact on the performance of estimation of risk differences and differences in means.",0
"background there is major concern about the impact of the global covid-19 outbreak on mental health. several studies suggest that mental health deteriorated in many countries before and during enforced isolation (ie, lockdown), but it remains unknown how mental health has changed week by week over the course of the covid-19 pandemic. this study aimed to explore the trajectories of anxiety and depression over the 20 weeks after lockdown was announced in england, and compare the growth trajectories by individual characteristics. methods in this prospective longitudinal observational study, we analysed data from the ucl covid-19 social study, a panel study weighted to population proportions, which collects information on anxiety (using the generalised anxiety disorder assessment) and depressive symptoms (using the patient health questionnaire) weekly in the uk since march 21, 2020. we included data from adults living in england who had at least three repeated measures between march 23 and aug 9, 2020. analyses were done using latent growth models, which were fitted to account for sociodemographic and health covariates. findings between march 23, and aug 9, data from over 70 000 adults were collected in the ucl covid-19 social study. when including participants living in england with three follow-up measures and no missing values, our analytic sample consisted of 36 520 participants. the average depression score was 6·6 (sd=6·0, range 0-27) and the average anxiety score 5·7 (sd=5·6, range 0-21) in week 1. anxiety and depression levels both declined across the first 20 weeks following the introduction of lockdown in england (b=-1·93, se=0·26, p interpretation these data suggest that the highest levels of depression and anxiety occurred in the early stages of lockdown but declined fairly rapidly, possibly because individuals adapted to circumstances. our findings emphasise the importance of supporting individuals in the lead-up to future lockdowns to try to reduce distress, and highlight that groups already at risk for poor mental health before the pandemic have remained at risk throughout lockdown and its aftermath. funding nuffield foundation, uk research and innovation, wellcome trust.",0
"phage search tool (phast) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. it accepts either raw dna sequence data or partially annotated genbank formatted data and rapidly performs a number of database comparisons as well as phage 'cornerstone' feature identification steps to locate, annotate and display prophage sequences and prophage features. relative to other prophage identification tools, phast is up to 40 times faster and up to 15% more sensitive. it is also able to process and annotate both raw dna sequence data and genbank files, provide richly annotated tables on prophage features and prophage 'quality' and distinguish between intact and incomplete prophage. phast also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. phast is available at (",0
"the distribution of actin in wild-type cells and in morphogenetic mutants of the budding yeast saccharomyces cerevisiae was explored by staining cells with fluorochrome-labeled phallotoxins after fixing and permeabilizing the cells by several methods. the actin appeared to be localized in a set of cortical spots or patches, as well as in a network of cytoplasmic fibers. bundles of filaments that may possibly correspond to the fibers visualized by fluorescence were observed with the electron microscope. the putative actin spots were concentrated in small and medium-sized buds and at what were apparently the sites of incipient bud formation on unbudded cells, whereas the putative actin fibers were generally oriented along the long axes of the mother-bud pairs. in several morphogenetic mutants that form multiple, abnormally elongated buds, the actin patches were conspicuously clustered at the tips of most buds, and actin fibers were clearly oriented along the long axes of the buds. there was a strong correlation between the occurrence of active growth at particular bud tips and clustering of actin spots at those same tips. near the end of the cell cycle in wild-type cells, actin appeared to concentrate (as a cluster of spots or a band) in the neck region connecting the mother cell to its bud. observations made using indirect immunofluorescence with a monoclonal anti-yeast-tubulin antibody on the morphogenetic mutant cdc4 (which forms multiple, abnormally elongated buds while the nuclear cycle is arrested) revealed the surprising occurrence of multiple bundles of cytoplasmic microtubules emanating from the one duplicated spindle-pole body per cell. it seems that most or all of the buds contain one or more of these bundles of microtubules, which often can be seen to extend to the very tips of the buds. these observations are consistent with the hypotheses that actin, tubulin, or both may be involved in the polarization of growth and localization of cell-wall deposition that occurs during the yeast cell cycle.",0
"we present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (ngs) data-mitochondrial baiting and iterative mapping (mitobim). the method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. we demonstrate the efficiency of the approach in case studies using real ngs data sets of the two monogenean ectoparasites species gyrodactylus thymalli and gyrodactylus derjavinoides including their respective teleost hosts european grayling (thymallus thymallus) and rainbow trout (oncorhynchus mykiss). mitobim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic dna derived ngs data sets in <24 h using a standard desktop computer. the approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range pcr. we furthermore demonstrate the applicability of mitobim for metagenomic/pooled data sets using simulated data. mitobim is an easy to use tool even for biologists with modest bioinformatics experience. the software is made available as open source pipeline under the mit license at",0
"genome-wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for mendelian randomization investigations. we demonstrate how such coefficients from multiple variants can be combined in a mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. the bias and efficiency of estimates based on summarized data are compared to those based on individual-level data in simulation studies. we investigate the impact of gene-gene interactions, linkage disequilibrium, and 'weak instruments' on these estimates. both an inverse-variance weighted average of variant-specific associations and a likelihood-based approach for summarized data give similar estimates and precision to the two-stage least squares method for individual-level data, even when there are gene-gene interactions. however, these summarized data methods overstate precision when variants are in linkage disequilibrium. if the p-value in a linear regression of the risk factor for each variant is less than 1×10⁻⁵, then weak instrument bias will be small. we use these methods to estimate the causal association of low-density lipoprotein cholesterol (ldl-c) on coronary artery disease using published data on five genetic variants. a 30% reduction in ldl-c is estimated to reduce coronary artery disease risk by 67% (95% ci: 54% to 76%). we conclude that mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual-level data, although the necessary assumptions cannot be so fully assessed.",0
"background scoping studies are an increasingly popular approach to reviewing health research evidence. in 2005, arksey and o'malley published the first methodological framework for conducting scoping studies. while this framework provides an excellent foundation for scoping study methodology, further clarifying and enhancing this framework will help support the consistency with which authors undertake and report scoping studies and may encourage researchers and clinicians to engage in this process. discussion we build upon our experiences conducting three scoping studies using the arksey and o'malley methodology to propose recommendations that clarify and enhance each stage of the framework. recommendations include: clarifying and linking the purpose and research question (stage one); balancing feasibility with breadth and comprehensiveness of the scoping process (stage two); using an iterative team approach to selecting studies (stage three) and extracting data (stage four); incorporating a numerical summary and qualitative thematic analysis, reporting results, and considering the implications of study findings to policy, practice, or research (stage five); and incorporating consultation with stakeholders as a required knowledge translation component of scoping study methodology (stage six). lastly, we propose additional considerations for scoping study methodology in order to support the advancement, application and relevance of scoping studies in health research. summary specific recommendations to clarify and enhance this methodology are outlined for each stage of the arksey and o'malley framework. continued debate and development about scoping study methodology will help to maximize the usefulness and rigor of scoping study findings within healthcare research and practice.",0
"the immunogenicity of long-surviving, enhanced (as x aug)f1 renal allografts retransplanted into secondary as recipients was restored by the injection of small numbers of donor strain dendritic cells derived from afferent lymph. whereas 1 x 10(4) to 5 x 10(4) dendritic cells were able to trigger an acute rejection response, neither the passenger volume of donor strain blood nor 5 x 10(6) t or b lymphocytes were able to do so, thereby demonstrating more than a 100-fold difference in immunogenic potency. it is concluded that intrarenal dendritic cells provide the major immunogenic stimulus of a kidney allograft. these results suggest that the antigenic strength of major histocompatibility complex-incompatible tissue correlates with the content of donor strain dendritic cells. they also provide further evidence that antigens of the major histocompatibility complex behave like conventional antigens unless they are on the surface of allogeneic dendritic cells.",0
"computerized clinical decision support systems, or cdss, represent a paradigm shift in healthcare today. cdss are used to augment clinicians in their complex decision-making processes. since their first use in the 1980s, cdss have seen a rapid evolution. they are now commonly administered through electronic medical records and other computerized clinical workflows, which has been facilitated by increasing global adoption of electronic medical records with advanced capabilities. despite these advances, there remain unknowns regarding the effect cdss have on the providers who use them, patient outcomes, and costs. there have been numerous published examples in the past decade(s) of cdss success stories, but notable setbacks have also shown us that cdss are not without risks. in this paper, we provide a state-of-the-art overview on the use of clinical decision support systems in medicine, including the different types, current use cases with proven efficacy, common pitfalls, and potential harms. we conclude with evidence-based recommendations for minimizing risk in cdss design, implementation, evaluation, and maintenance.",0
"the paradoxical coexistence of spontaneous tumor antigen-specific immune responses with progressive disease in cancer patients furthers the need to dissect the molecular pathways involved in tumor-induced t cell dysfunction. in patients with advanced melanoma, we have previously shown that the cancer-germline antigen ny-eso-1 stimulates spontaneous ny-eso-1-specific cd8(+) t cells that up-regulate pd-1 expression. we also observed that pd-1 regulates ny-eso-1-specific cd8(+) t cell expansion upon chronic antigen stimulation. in the present study, we show that a fraction of pd-1(+) ny-eso-1-specific cd8(+) t cells in patients with advanced melanoma up-regulates tim-3 expression and that tim-3(+)pd-1(+) ny-eso-1-specific cd8(+) t cells are more dysfunctional than tim-3(-)pd-1(+) and tim-3(-)pd-1(-) ny-eso-1-specific cd8(+) t cells, producing less ifn-γ, tnf, and il-2. tim-3-tim-3l blockade enhanced cytokine production by ny-eso-1-specific cd8(+) t cells upon short ex vivo stimulation with cognate peptide, thus enhancing their functional capacity. in addition, tim-3-tim-3l blockade enhanced cytokine production and proliferation of ny-eso-1-specific cd8(+) t cells upon prolonged antigen stimulation and acted in synergy with pd-1-pd-l1 blockade. collectively, our findings support the use of tim-3-tim-3l blockade together with pd-1-pd-l1 blockade to reverse tumor-induced t cell exhaustion/dysfunction in patients with advanced melanoma.",0
"biological pathways are structured in complex networks of interacting genes. solving the architecture of such networks may provide valuable information, such as how microorganisms cause disease. here we present a method (tn-seq) for accurately determining quantitative genetic interactions on a genome-wide scale in microorganisms. tn-seq is based on the assembly of a saturated mariner transposon insertion library. after library selection, changes in frequency of each insertion mutant are determined by sequencing the flanking regions en masse. these changes are used to calculate each mutant's fitness. using this approach, we determined fitness for each gene of streptococcus pneumoniae, a causative agent of pneumonia and meningitis. a genome-wide screen for genetic interactions of five query genes identified both alleviating and aggravating interactions that could be divided into seven distinct categories. owing to the wide activity of the mariner transposon, tn-seq has the potential to contribute to the exploration of complex pathways across many different species.",0
"background since the inception of the go annotation project, a variety of tools have been developed that support exploring and searching the go database. in particular, a variety of tools that perform go enrichment analysis are currently available. most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set. a few tools also exist that support analyzing ranked lists. the latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results. results gorilla is a web-based application that identifies enriched go terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. this is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression). gorilla employs a flexible threshold statistical approach to discover go terms that are significantly enriched at the top of a ranked gene list. building on a complete theoretical characterization of the underlying distribution, called mhg, gorilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations. this enables rigorous statistical analysis of thousand of genes and thousands of go terms in order of seconds. the output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched go terms. conclusion gorilla is an efficient go analysis tool with unique features that make a useful addition to the existing repertoire of go enrichment tools. gorilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation. gorilla is publicly available at:",0
"the proteomexchange (px) consortium of proteomics resources ( was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. we give an overview of the current consortium activities and describe the advances of the past few years. augmenting the px founding members (pride and peptideatlas, including the passel resource), two new members have joined the consortium: massive and jpost. proteomecentral remains as the common data access portal, providing the ability to search for data sets in all participating px resources, now with enhanced data visualization components.we describe the updated submission guidelines, now expanded to include four members instead of two. as demonstrated by data submission statistics, px is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. more than 4500 data sets have been submitted to the various px resources since 2012. human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. data reprocessing activities are becoming more prominent, with both massive and peptideatlas releasing the results of reprocessed data sets. finally, we outline the upcoming advances for proteomexchange.",0
"objective to examine the global prevalence and major risk factors for diabetic retinopathy (dr) and vision-threatening diabetic retinopathy (vtdr) among people with diabetes. research design and methods a pooled analysis using individual participant data from population-based studies around the world was performed. a systematic literature review was conducted to identify all population-based studies in general populations or individuals with diabetes who had ascertained dr from retinal photographs. studies provided data for dr end points, including any dr, proliferative dr, diabetic macular edema, and vtdr, and also major systemic risk factors. pooled prevalence estimates were directly age-standardized to the 2010 world diabetes population aged 20-79 years. results a total of 35 studies (1980-2008) provided data from 22,896 individuals with diabetes. the overall prevalence was 34.6% (95% ci 34.5-34.8) for any dr, 6.96% (6.87-7.04) for proliferative dr, 6.81% (6.74-6.89) for diabetic macular edema, and 10.2% (10.1-10.3) for vtdr. all dr prevalence end points increased with diabetes duration, hemoglobin a(1c), and blood pressure levels and were higher in people with type 1 compared with type 2 diabetes. conclusions there are approximately 93 million people with dr, 17 million with proliferative dr, 21 million with diabetic macular edema, and 28 million with vtdr worldwide. longer diabetes duration and poorer glycemic and blood pressure control are strongly associated with dr. these data highlight the substantial worldwide public health burden of dr and the importance of modifiable risk factors in its occurrence. this study is limited by data pooled from studies at different time points, with different methodologies and population characteristics.",0
"arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the amova framework. arlequin 3 introduces a completely new graphical interface written in c++, a more robust semantic analysis of input files, and two new methods: a bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from dna sequence polymorphism. arlequin can handle several data types like dna sequences, microsatellite data, or standard multi-locus genotypes. a windows version of the software is freely available on",0
"motivation microsatellites are a widely-used marker system in plant genetics and forensics. the development of reliable microsatellite markers from resequencing data is challenging. results we extended misa, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. we improved compound microsatellite detection and added the possibility to display and export misa results in gff3 format for downstream analysis. availability and implementation misa-web can be accessed under the website provides tutorials, usage note as well as download links to the source code. contact scholz@ipk-gatersleben.de.",0
"background association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (qtl) and provides relatively high resolution in terms of defining the genome position of a gene or qtl. seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. in this study, a genome-wide association study (gwas) was performed to identify quantitative trait loci (qtl) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content. results a total of 55,159 single nucleotide polymorphisms (snps) were genotyped using various methods including illumina infinium and goldengate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (ld) in heterochromatic and euchromatic regions. in euchromatic regions, the mean ld (r2) rapidly declined to 0.2 within 360 kbp, whereas the mean ld declined to 0.2 at 9,600 kbp in heterochromatic regions. the gwas results identified 40 snps in 17 different genomic regions significantly associated with seed protein. of these, the five snps with the highest associations and seven adjacent snps were located in the 27.6-30.0 mbp region of gm20. a major seed protein qtl has been previously mapped to the same location and potential candidate genes have recently been identified in this region. the gwas results also detected 25 snps in 13 different genomic regions associated with seed oil. of these markers, seven snps had a significant association with both protein and oil. conclusions this research indicated that gwas not only identified most of the previously reported qtl controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these qtl. the narrower gwas-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s).",0
"covid-19 (corona virus disease 2019) has significantly resulted in a large number of psychological consequences. the aim of this study is to explore the impacts of covid-19 on people's mental health, to assist policy makers to develop actionable policies, and help clinical practitioners (e.g., social workers, psychiatrists, and psychologists) provide timely services to affected populations. we sample and analyze the weibo posts from 17,865 active weibo users using the approach of online ecological recognition (oer) based on several machine-learning predictive models. we calculated word frequency, scores of emotional indicators (e.g., anxiety, depression, indignation, and oxford happiness) and cognitive indicators (e.g., social risk judgment and life satisfaction) from the collected data. the sentiment analysis and the paired sample t-test were performed to examine the differences in the same group before and after the declaration of covid-19 on 20 january, 2020. the results showed that negative emotions (e.g., anxiety, depression and indignation) and sensitivity to social risks increased, while the scores of positive emotions (e.g., oxford happiness) and life satisfaction decreased. people were concerned more about their health and family, while less about leisure and friends. the results contribute to the knowledge gaps of short-term individual changes in psychological conditions after the outbreak. it may provide references for policy makers to plan and fight against covid-19 effectively by improving stability of popular feelings and urgently prepare clinical practitioners to deliver corresponding therapy foundations for the risk groups and affected people.",0
"background coronavirus disease 2019 (covid-19) was declared a pandemic in march 2020. several prophylactic vaccines against covid-19 are currently in development, yet little is known about people's acceptability of a covid-19 vaccine. methods we conducted an online survey of adults ages 18 and older in the united states (n = 2,006) in may 2020. multivariable relative risk regression identified correlates of participants' willingness to get a covid-19 vaccine (i.e., vaccine acceptability). results overall, 69% of participants were willing to get a covid-19 vaccine. participants were more likely to be willing to get vaccinated if they thought their healthcare provider would recommend vaccination (rr = 1.73, 95% ci: 1.49-2.02) or if they were moderate (rr = 1.09, 95% ci: 1.02-1.16) or liberal (rr = 1.14, 95% ci: 1.07-1.22) in their political leaning. participants were also more likely to be willing to get vaccinated if they reported higher levels of perceived likelihood getting a covid-19 infection in the future (rr = 1.05, 95% ci: 1.01-1.09), perceived severity of covid-19 infection (rr = 1.08, 95% ci: 1.04-1.11), or perceived effectiveness of a covid-19 vaccine (rr = 1.46, 95% ci: 1.40-1.52). participants were less likely to be willing to get vaccinated if they were non-latinx black (rr = 0.81, 95% ci: 0.74-0.90) or reported a higher level of perceived potential vaccine harms (rr = 0.95, 95% ci: 0.92-0.98). conclusions many adults are willing to get a covid-19 vaccine, though acceptability should be monitored as vaccine development continues. our findings can help guide future efforts to increase covid-19 vaccine acceptability (and uptake if a vaccine becomes available).",0
"background usually the researchers performing meta-analysis of continuous outcomes from clinical trials need their mean value and the variance (or standard deviation) in order to pool data. however, sometimes the published reports of clinical trials only report the median, range and the size of the trial. methods in this article we use simple and elementary inequalities and approximations in order to estimate the mean and the variance for such trials. our estimation is distribution-free, i.e., it makes no assumption on the distribution of the underlying data. results we found two simple formulas that estimate the mean using the values of the median (m), low and high end of the range (a and b, respectively), and n (the sample size). using simulations, we show that median can be used to estimate mean when the sample size is larger than 25. for smaller samples our new formula, devised in this paper, should be used. we also estimated the variance of an unknown sample using the median, low and high end of the range, and the sample size. our estimate is performing as the best estimate in our simulations for very small samples (n 70), the formula range/6 gives the best estimator for the standard deviation (variance). we also include an illustrative example of the potential value of our method using reports from the cochrane review on the role of erythropoietin in anemia due to malignancy. conclusion using these formulas, we hope to help meta-analysts use clinical trials in their analysis even when not all of the information is available and/or reported.",0
"taxol (generic name paclitaxel) is a microtubule-stabilizing drug that is approved by the food and drug administration for the treatment of ovarian, breast, and lung cancer, as well as kaposi's sarcoma. it is used off-label to treat gastroesophageal, endometrial, cervical, prostate, and head and neck cancers, in addition to sarcoma, lymphoma, and leukemia. paclitaxel has long been recognized to induce mitotic arrest, which leads to cell death in a subset of the arrested population. however, recent evidence demonstrates that intratumoral concentrations of paclitaxel are too low to cause mitotic arrest and result in multipolar divisions instead. it is hoped that this insight can now be used to develop a biomarker to identify the ∼50% of patients that will benefit from paclitaxel therapy. here i discuss the history of paclitaxel and our recently evolved understanding of its mechanism of action.",0
"background few data are available on the rate and characteristics of thromboembolic complications in hospitalized patients with covid-19. methods we studied consecutive symptomatic patients with laboratory-proven covid-19 admitted to a university hospital in milan, italy (13.02.2020-10.04.2020). the primary outcome was any thromboembolic complication, including venous thromboembolism (vte), ischemic stroke, and acute coronary syndrome (acs)/myocardial infarction (mi). secondary outcome was overt disseminated intravascular coagulation (dic). results we included 388 patients (median age 66 years, 68% men, 16% requiring intensive care ). thromboprophylaxis was used in 100% of icu patients and 75% of those on the general ward. thromboembolic events occurred in 28 (7.7% of closed cases; 95%ci 5.4%-11.0%), corresponding to a cumulative rate of 21% (27.6% icu, 6.6% general ward). half of the thromboembolic events were diagnosed within 24 h of hospital admission. forty-four patients underwent vte imaging tests and vte was confirmed in 16 (36%). computed tomography pulmonary angiography (ctpa) was performed in 30 patients, corresponding to 7.7% of total, and pulmonary embolism was confirmed in 10 (33% of ctpa). the rate of ischemic stroke and acs/mi was 2.5% and 1.1%, respectively. overt dic was present in 8 (2.2%) patients. conclusions the high number of arterial and, in particular, venous thromboembolic events diagnosed within 24 h of admission and the high rate of positive vte imaging tests among the few covid-19 patients tested suggest that there is an urgent need to improve specific vte diagnostic strategies and investigate the efficacy and safety of thromboprophylaxis in ambulatory covid-19 patients.",0
"time series regression studies have been widely used in environmental epidemiology, notably in investigating the short-term associations between exposures such as air pollution, weather variables or pollen, and health outcomes such as mortality, myocardial infarction or disease-specific hospital admissions. typically, for both exposure and outcome, data are available at regular time intervals (e.g. daily pollution levels and daily mortality counts) and the aim is to explore short-term associations between them. in this article, we describe the general features of time series data, and we outline the analysis process, beginning with descriptive analysis, then focusing on issues in time series regression that differ from other regression methods: modelling short-term fluctuations in the presence of seasonal and long-term patterns, dealing with time varying confounding factors and modelling delayed ('lagged') associations between exposure and outcome. we finish with advice on model checking and sensitivity analysis, and some common extensions to the basic model.",0
"the interactions between the l. pneumophila phagosome and monocyte lysosomes were investigated by prelabeling the lysosomes with thorium dioxide, an electron-opaque colloidal marker, and by acid phosphatase cytochemistry. phagosomes containing live l. pneumophila did not fuse with secondary lysosomes at 1 h after entry into monocytes or at 4 or 8 h after entry by which time the ribosome-lined l. pneumophila replicative vacuole had formed. in contrast, the majority of phagosomes containing formalin-killed l. pneumophila, live streptococcus pneumoniae, and live escherichia coli had fused with secondary lysosomes by 1 h after entry into monocytes. erythromycin, a potent inhibitor of bacterial protein synthesis, at a concentration that completely inhibits l. pneumophila intracellular multiplication, had no influence on fusion of l. pneumophila phagosomes with secondary lysosomes. however, coating live l. pneumophila with antibody or with antibody and complement partially overcame the inhibition of fusion. also activating the monocytes promoted fusion of a small proportion of phagosomes containing live l. pneumophila with secondary lysosomes. acid phosphatase cytochemistry revealed that phagosomes containing live l. pneumophila did not fuse with either primary or secondary lysosomes. in contrast to phagosomes containing live bacteria, the majority of phagosomes containing formalin-killed l. pneumophila were fused with lysosomes by acid phosphatase cytochemistry. the capacity of l. pneumophila to inhibit phagosome-lysosome fusion may be a critical mechanism by which the bacterium resists monocyte microbicidal effects.",0
"background behaviour change interventions are effective in supporting individuals in achieving temporary behaviour change. behaviour change maintenance, however, is rarely attained. the aim of this review was to identify and synthesise current theoretical explanations for behaviour change maintenance to inform future research and practice. methods potentially relevant theories were identified through systematic searches of electronic databases (ovid medline, embase, psycinfo). in addition, an existing database of 80 theories was searched, and 25 theory experts were consulted. theories were included if they formulated hypotheses about behaviour change maintenance. included theories were synthesised thematically to ascertain overarching explanations for behaviour change maintenance. initial theoretical themes were cross-validated. findings one hundred and seventeen behaviour theories were identified, of which 100 met the inclusion criteria. five overarching, interconnected themes representing theoretical explanations for behaviour change maintenance emerged. theoretical explanations of behaviour change maintenance focus on the differential nature and role of motives, self-regulation, resources (psychological and physical), habits, and environmental and social influences from initiation to maintenance. discussion there are distinct patterns of theoretical explanations for behaviour change and for behaviour change maintenance. the findings from this review can guide the development and evaluation of interventions promoting maintenance of health behaviours and help in the development of an integrated theory of behaviour change maintenance.",0
"accurate pathological diagnosis is crucial for optimal management of patients with cancer. for the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. here we present a comprehensive approach for the dna methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. we show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. for broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology.",0
"contracting granulation tissues contain fibroblasts that develop characteristics typical of smooth muscle: (a) they contain an extensive cytoplasmic fibrillar system. (b) they show immunofluorescent labeling of their cytoplasm with human anti-smooth muscle serum. (c) the nuclei show complicated folds and indentations, indicative of cellular contraction. (d) there are cell-to-cell and cell-to-stroma attachments. (e) it is possible to extract similar quantities of actomyosin (having the same adenosine triphosphatase activity) from granulation tissue and from pregnant rat uterus. (f) strips of granulation tissue, when tested pharmacologically in vitro, behave similarly to smooth muscle. all these data support the view that, under certain conditions, fibroblasts can differentiate into a cell type structurally and functionally similar to smooth muscle and that this cell, the ""myo-fibroblast,"" plays an important role in connective tissue contraction.",0
"we have recently characterized three yeast gene products (vps35p, vps29p, and vps30p) as candidate components of the sorting machinery required for the endosome-to-golgi retrieval of the vacuolar protein sorting receptor vps10p (seaman, m.n.j., e.g. marcusson, j.-l. cereghino, and s.d. emr. 1997. j. cell biol. 137:79-92). by genetic and biochemical means we now show that vps35p and vps29p interact and form part of a multimeric membrane-associated complex that also contains vps26p, vps17p, and vps5p. this complex, designated here as the retromer complex, assembles from two distinct subcomplexes comprising (a) vps35p, vps29p, and vps26p; and (b) vps5p and vps17p. density gradient fractionation of golgi/endosomal/vesicular membranes reveals that vps35p cofractionates with vps5p/vps17p in a vesicle-enriched dense membrane fraction. furthermore, gel filtration analysis indicates that vps35p and vps5p are present on a population of vesicles and tubules slightly larger than copi/coatomer-coated vesicles. we also show by immunogold em that vps5p is localized to discrete regions at the rims of the prevacuolar endosome where vesicles appear to be budding. size fractionation of cytosolic and recombinant vps5p reveals that vps5p can self-assemble in vitro, suggesting that vps5p may provide the mechanical impetus to drive vesicle formation. based on these findings we propose a model in which vps35p/vps29p/vps26p function to select cargo for retrieval, and vps5p/vps17p assemble onto the membrane to promote vesicle formation. conservation of the yeast retromer complex components in higher eukaryotes suggests an important general role for this complex in endosome-to-golgi retrieval.",0
"background reporting standards, such as prisma aim to ensure that the methods and results of systematic reviews are described in sufficient detail to allow full transparency. flow diagrams in evidence syntheses allow the reader to rapidly understand the core procedures used in a review and examine the attrition of irrelevant records throughout the review process. recent research suggests that use of flow diagrams in systematic reviews is poor and of low quality and called for standardised templates to facilitate better reporting in flow diagrams. the increasing options for interactivity provided by the internet gives us an opportunity to support easy-to-use evidence synthesis tools, and here we report on the development of a tool for the production of prisma 2020-compliant systematic review flow diagrams. methods and findings we developed a free-to-use, open source r package and web-based shiny app to allow users to design prisma flow diagrams for their own systematic reviews. our tool allows users to produce standardised visualisations that transparently document the methods and results of a systematic review process in a variety of formats. in addition, we provide the opportunity to produce interactive, web-based flow diagrams (exported as html files), that allow readers to click on boxes of the diagram and navigate to further details on methods, results or data files. we provide an interactive example here; conclusions we have developed a user-friendly tool for producing prisma 2020-compliant flow diagrams for users with coding experience and, importantly, for users without prior experience in coding by making use of shiny ( this free-to-use tool will make it easier to produce clear and prisma 2020-compliant systematic review flow diagrams. significantly, users can also produce interactive flow diagrams for the first time, allowing readers of their reviews to smoothly and swiftly explore and navigate to further details of the methods and results of a review. we believe this tool will increase use of prisma flow diagrams, improve the compliance and quality of flow diagrams, and facilitate strong science communication of the methods and results of systematic reviews by making use of interactivity. we encourage the systematic review community to make use of the tool, and provide feedback to streamline and improve their usability and efficiency.",0
"oligodendrocyte precursors (ops) continue to proliferate and generate myelinating oligodendrocytes (ols) well into adulthood. it is not known whether adult-born ols ensheath previously unmyelinated axons or remodel existing myelin. we quantified op division and ol production in different regions of the adult mouse cns including the 4-month-old optic nerve, in which practically all axons are already myelinated. even there, all ops were dividing and generating new ols and myelin at a rate higher than can be explained by first-time myelination of naked axons. we conclude that adult-born ols in the optic nerve are engaged in myelin remodeling, either replacing ols that die in service or intercalating among existing myelin sheaths. the latter would predict that average internode length should decrease with age. consistent with that, we found that adult-born ols elaborated much shorter but many more internodes than ols generated during early postnatal life.",0
"effects of silica, diamond dust, and carrageenan on mouse macrophages were studied by phase-contrast cine-micrography, electron microscopy, histochemical techniques for lysosomal enzymes and measurements of the release of lysosomal enzymes into the culture medium. all added materials were rapidly taken up into phagosomes, to which lysosomes became attached. in all cases lysosomal enzymes were discharged into the phagosomes to form secondary lysosomes. within 24 hr most of the silica particles and enzyme had escaped from the secondary lysosomes and lysosomal enzymes were found in the culture media. most macrophages were killed by this time. with nontoxic particles (diamond dust, aluminium-coated silica, or silica in the presence of the protective agent polyvinyl-pyridine-n-oxide, pvpno) ingested particles and lysosomal enzymes were retained within the secondary lysosomes for a much longer time, and cytotoxic effects were considerably delayed or absent altogether. it is concluded that silica particles are toxic because they are efficiently taken up by macrophages and can then react relatively rapidly with the membranes surrounding the secondary lysosomes. the particles and lytic enzymes can then escape into the cytoplasm, producing general damage, and thence into the culture medium. it is suggested that hydrogen bonding of silicic acid with lipid and protein constituents of the membrane accounts for the induced permeability. protective agents such as pvpno are retamed in lysosomes and preferentially form hydrogen bonds with silicic acid. carrageenan is demonstrable within macrophages by its metachromatic reaction. it brings about release of enzymes from secondary lysosomes, but much more slowly than does silica. silica released from killed macrophages is as cytotoxic as the original preparation. it is suggested that repeated cycles of macrophage killing in vivo leads to the mobilization of fibroblasts and fibrogenesis characterizing the disease silicosis.",0
"the basolateral amygdala (bla) has a crucial role in emotional learning irrespective of valence. the bla projection to the nucleus accumbens (nac) is thought to modulate cue-triggered motivated behaviours, but our understanding of the interaction between these two brain regions has been limited by the inability to manipulate neural-circuit elements of this pathway selectively during behaviour. to circumvent this limitation, we used in vivo optogenetic stimulation or inhibition of glutamatergic fibres from the bla to the nac, coupled with intracranial pharmacology and ex vivo electrophysiology. here we show that optical stimulation of the pathway from the bla to the nac in mice reinforces behavioural responding to earn additional optical stimulation of these synaptic inputs. optical stimulation of these glutamatergic fibres required intra-nac dopamine d1-type receptor signalling, but not d2-type receptor signalling. brief optical inhibition of fibres from the bla to the nac reduced cue-evoked intake of sucrose, demonstrating an important role of this specific pathway in controlling naturally occurring reward-related behaviour. moreover, although optical stimulation of glutamatergic fibres from the medial prefrontal cortex to the nac also elicited reliable excitatory synaptic responses, optical self-stimulation behaviour was not observed by activation of this pathway. these data indicate that whereas the bla is important for processing both positive and negative affect, the glutamatergic pathway from the bla to the nac, in conjunction with dopamine signalling in the nac, promotes motivated behavioural responding. thus, optogenetic manipulation of anatomically distinct synaptic inputs to the nac reveals functionally distinct properties of these inputs in controlling reward-seeking behaviours.",0
"to extend understanding of the genetic architecture and molecular basis of type 2 diabetes (t2d), we conducted a meta-analysis of genetic variants on the metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of european descent. we identified ten previously unreported t2d susceptibility loci, including two showing sex-differentiated association. genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to t2d. exploration of the enlarged set of susceptibility loci implicates several processes, including crebbp-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.",0
"irritable bowel syndrome (ibs) is a functional condition of the bowel that is diagnosed using clinical criteria. this paper discusses the nature of the diagnostic process for ibs and how this impacts epidemiological measurements. depending on the diagnostic criteria employed, ibs affects around 11% of the population globally. around 30% of people who experience the symptoms of ibs will consult physicians for their ibs symptoms. these people do not have significantly different abdominal symptoms to those who do not consult, but they do have greater levels of anxiety and lower quality of life. internationally, there is a female predominance in the prevalence of ibs. there is 25% less ibs diagnosed in those over 50 years and there is no association with socioeconomic status. ibs aggregates within families and the genetic and sociological factors potentially underlying this are reviewed. patients diagnosed with ibs are highly likely to have other functional disease and have more surgery than the general population. there is no evidence that ibs is associated with an increased mortality risk. the epidemiological evidence surrounding these aspects of the natural history is discussed.",0
"two seemingly unrelated experimental treatments inhibit receptor mediated endocytosis: (a) depletion of intracellular k+ (larkin, j. m., m. s. brown, j. l. goldstein, and r. g. w. anderson. 1983. cell. 33:273-285); and (b) treatment with hypertonic media (daukas, g., and s. h. zigmond. 1985. j. cell biol. 101:1673-1679). since the former inhibits the formation of clathrin-coated pits (larkin, j. m., w. d. donzell, and r. g. w. anderson, 1986. j. cell biol. 103:2619-2627), we were interested in determining whether hypertonic treatment has the same effect, and if so, why. fibroblasts (human or chicken) were incubated in normal saline made hypertonic with 0.45 m sucrose, then broken open by sonication and freeze-etched to generate replicas of their inner membrane surfaces. whereas untreated cells display typical geodesic lattices of clathrin under each coated pit, hypertonic cells display in addition a number of empty clathrin ""microcages"". at first, these appear around the edges of normal coated pit lattices. with further time in hypertonic medium, however, normal lattices largely disappear and are replaced by accumulations of microcages. concomitantly, low density lipoprotein (ldl) receptors lose their normal clustered distribution and become dispersed all over the cell surface, as seen by fluorescence microscopy and freeze-etch electron microscopy of ldl attached to the cell surface. upon return to normal medium at 37 degrees c, these changes promptly reverse. within 2 min, small clusters of ldl reappear on the surfaces of cells and normal clathrin lattices begin to reappear inside; the size and number of these receptor/clathrin complexes returns to normal over the next 10 min. thus, in spite of their seeming unrelatedness, both k+ depletion and hypertonic treatment cause coated pits to disappear, and both induce abnormal clathrin polymerization into empty microcages. this suggests that in both cases, an abnormal formation of microcages inhibits endocytosis by rendering clathrin unavailable for assembly into normal coated pits.",0
"the dali server ( is a network service for comparing protein structures in 3d. in favourable cases, comparing 3d structures may reveal biologically interesting similarities that are not detectable by comparing sequences. the dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. the latest update of the server provides enhanced analytics for the study of sequence and structure conservation. the server performs three types of structure comparisons: (i) protein data bank (pdb) search compares one query structure against those in the pdb and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. structural superimpositions are visualized using the java-free webgl viewer pv. the structural alignment view is enhanced by sequence similarity searches against uniprot. the combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. in the stack, each structure is structurally aligned to the query protein and represented by a sequence logo.",0
"motivation species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. yet, gene trees often differ from species trees, creating challenges to species tree estimation. one of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ils), which is modelled by the multi-species coalescent. while many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. results we present astral, a fast method for estimating species trees from multiple genes. astral is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy-improving on mp-est and the population tree from bucky, two statistically consistent leading coalescent-based methods. astral is often more accurate than concatenation using maximum likelihood, except when ils levels are low or there are too few gene trees. availability and implementation astral is available in open source form at datasets studied in this article are available at supplementary information supplementary data are available at bioinformatics online.",0
"epigenetic mechanisms integrate genetic and environmental causes of disease, but comprehensive genome-wide analyses of epigenetic modifications have not yet demonstrated robust association with common diseases. using illumina humanmethylation450 arrays on 354 anti-citrullinated protein antibody-associated rheumatoid arthritis cases and 337 controls, we identified two clusters within the major histocompatibility complex (mhc) region whose differential methylation potentially mediates genetic risk for rheumatoid arthritis. to reduce confounding factors that have hampered previous epigenome-wide studies, we corrected for cellular heterogeneity by estimating and adjusting for cell-type proportions in our blood-derived dna samples and used mediation analysis to filter out associations likely to be a consequence of disease. four cpgs also showed an association between genotype and variance of methylation. the associations for both clusters replicated at least one cpg (p < 0.01), with the rest showing suggestive association, in monocyte cell fractions in an independent cohort of 12 cases and 12 controls. thus, dna methylation is a potential mediator of genetic risk.",0
"data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like r or python for the generation of plots and tables. it is widely recognized that data analyses should ideally be conducted in a reproducible way. reproducibility enables technical validation and regeneration of results on the original or even new data. however, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. we postulate that it is equally important to ensure adaptability and transparency. the former describes the ability to modify the analysis to answer extended or slightly different research questions. the latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. we show how the popular workflow management system snakemake can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.",0
"this paper develops a method for appraising health status in elderly people. a frailty index was defined as the proportion of accumulated deficits (symptoms, signs, functional impairments, and laboratory abnormalities). it serves as an individual state variable, reflecting severity of illness and proximity to death. in a representative database of elderly canadians we found that deficits accumulated at 3% per year, and show a gamma distribution, typical for systems with redundant components that can be used in case of failure of a given subsystem. of note, the slope of the index is insensitive to the individual nature of the deficits, and serves as an important prognostic factor for life expectancy. the formula for estimating an individual's life span given the frailty index value is presented. for different patterns of cognitive impairments the average within-group index value increases with the severity of the cognitive impairment, and the relative variability of the index is significantly reduced. finally, the statistical distribution of the frailty index sharply differs between well groups (gamma distribution) and morbid groups (normal distribution). this pattern reflects an increase in uncompensated deficits in impaired organisms, which would lead to illness of various etiologies, and ultimately to increased mortality. the accumulation of deficits is as an example of a macroscopic variable, i.e., one that reflects general properties of aging at the level of the whole organism rather than any given functional deficiency. in consequence, we propose that it may be used as a proxy measure of aging.",0
"background chest ct is used in the diagnosis of coronavirus disease 2019 (covid-19) and is an important complement to reverse-transcription polymerase chain reaction (rt-pcr) tests. purpose to investigate the diagnostic value and consistency of chest ct as compared with rt-pcr assay in covid-19. materials and methods this study included 1014 patients in wuhan, china, who underwent both chest ct and rt-pcr tests between january 6 and february 6, 2020. with use of rt-pcr as the reference standard, the performance of chest ct in the diagnosis of covid-19 was assessed. in addition, for patients with multiple rt-pcr assays, the dynamic conversion of rt-pcr results (negative to positive, positive to negative) was analyzed as compared with serial chest ct scans for those with a time interval between rt-pcr tests of 4 days or more. results of the 1014 patients, 601 of 1014 (59%) had positive rt-pcr results and 888 of 1014 (88%) had positive chest ct scans. the sensitivity of chest ct in suggesting covid-19 was 97% (95% confidence interval: 95%, 98%; 580 of 601 patients) based on positive rt-pcr results. in the 413 patients with negative rt-pcr results, 308 of 413 (75%) had positive chest ct findings. of those 308 patients, 48% (103 of 308) were considered as highly likely cases and 33% (103 of 308) as probable cases. at analysis of serial rt-pcr assays and ct scans, the mean interval between the initial negative to positive rt-pcr results was 5.1 days ± 1.5; the mean interval between initial positive to subsequent negative rt-pcr results was 6.9 days ± 2.3. of the 1014 patients, 60% (34 of 57) to 93% (14 of 15) had initial positive ct scans consistent with covid-19 before (or parallel to) the initial positive rt-pcr results. twenty-four of 57 patients (42%) showed improvement on follow-up chest ct scans before the rt-pcr results turned negative. conclusion chest ct has a high sensitivity for diagnosis of coronavirus disease 2019 (covid-19). chest ct may be considered as a primary tool for the current covid-19 detection in epidemic areas. © rsna, 2020 online supplemental material is available for this article. a translation of this abstract in farsi is available in the supplement. ترجمه چکیده این مقاله به فارسی، در ضمیمه موجود است.",0
"the history of human population size is important for understanding human evolution. various studies have found evidence for a founder event (bottleneck) in east asian and european populations, associated with the human dispersal out-of-africa event around 60 thousand years (kyr) ago. however, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially markovian coalescent model applied to the complete diploid genome sequences of a chinese male (yh), a korean male (sjk), three european individuals (j. c. venter, na12891 and na12878 (ref. 9)) and two yoruba males (na18507 (ref. 10) and na19239). we infer that european and chinese populations had very similar population-size histories before 10-20 kyr ago. both populations experienced a severe bottleneck 10-60 kyr ago, whereas african populations experienced a milder bottleneck from which they recovered earlier. all three populations have an elevated effective population size between 60 and 250 kyr ago, possibly due to population substructure. we also infer that the differentiation of genetically modern humans may have started as early as 100-120 kyr ago, but considerable genetic exchanges may still have occurred until 20-40 kyr ago.",0
"small-molecule protein kinase inhibitors are widely used to elucidate cellular signaling pathways and are promising therapeutic agents. owing to evolutionary conservation of the atp-binding site, most kinase inhibitors that target this site promiscuously inhibit multiple kinases. interpretation of experiments that use these compounds is confounded by a lack of data on the comprehensive kinase selectivity of most inhibitors. here we used functional assays to profile the activity of 178 commercially available kinase inhibitors against a panel of 300 recombinant protein kinases. quantitative analysis revealed complex and often unexpected interactions between protein kinases and kinase inhibitors, with a wide spectrum of promiscuity. many off-target interactions occur with seemingly unrelated kinases, revealing how large-scale profiling can identify multitargeted inhibitors of specific, diverse kinases. the results have implications for drug development and provide a resource for selecting compounds to elucidate kinase function and for interpreting the results of experiments involving kinase inhibitors.",0
"the 63,632 drug overdose deaths in the united states in 2016 represented a 21.4% increase from 2015; two thirds of these deaths involved an opioid (1). from 2015 to 2016, drug overdose deaths increased in all drug categories examined; the largest increase occurred among deaths involving synthetic opioids other than methadone (synthetic opioids), which includes illicitly manufactured fentanyl (imf) (1). since 2013, driven largely by imf, including fentanyl analogs (2-4), the current wave of the opioid overdose epidemic has been marked by increases in deaths involving synthetic opioids. imf has contributed to increases in overdose deaths, with geographic differences reported (1). cdc examined state-level changes in death rates involving all drug overdoses in 50 states and the district of columbia (dc) and those involving synthetic opioids in 20 states, during 2013-2017. in addition, changes in death rates from 2016 to 2017 involving all opioids and opioid subcategories,* were examined by demographics, county urbanization levels, and by 34 states and dc. among 70,237 drug overdose deaths in 2017, 47,600 (67.8%) involved an opioid. † from 2013 to 2017, drug overdose death rates increased in 35 of 50 states and dc, and significant increases in death rates involving synthetic opioids occurred in 15 of 20 states, likely driven by imf (2,3). from 2016 to 2017, overdose deaths involving all opioids and synthetic opioids increased, but deaths involving prescription opioids and heroin remained stable. the opioid overdose epidemic continues to worsen and evolve because of the continuing increase in deaths involving synthetic opioids. provisional data from 2018 indicate potential improvements in some drug overdose indicators; § however, analysis of final data from 2018 is necessary for confirmation. more timely and comprehensive surveillance data are essential to inform efforts to prevent and respond to opioid overdoses; intensified prevention and response measures are urgently needed to curb deaths involving prescription and illicit opioids, specifically imf.",0
"the bcl-2 family of proteins controls cell death primarily by direct binding interactions that regulate mitochondrial outer membrane permeabilization (momp) leading to the irreversible release of intermembrane space proteins, subsequent caspase activation and apoptosis. the affinities and relative abundance of the bcl-2 family proteins dictate the predominate interactions between anti-apoptotic and pro-apoptotic bcl-2 family proteins that regulate momp. we highlight the core mechanisms of bcl-2 family regulation of momp with an emphasis on how the interactions between the bcl-2 family proteins govern cell fate. we address the critical importance of both the concentration and affinities of bcl-2 family proteins and show how differences in either can greatly change the outcome. further, we explain the importance of using full-length bcl-2 family proteins (versus truncated versions or peptides) to parse out the core mechanisms of momp regulation by the bcl-2 family. finally, we discuss how post-translational modifications and differing intracellular localizations alter the mechanisms of apoptosis regulation by bcl-2 family proteins. successful therapeutic intervention of momp regulation in human disease requires an understanding of the factors that mediate the major binding interactions between bcl-2 family proteins in cells.",0
"the human gene mutation database (hgmd ® ) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. at the time of writing (march 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. with new mutation entries currently accumulating at a rate exceeding 17,000 per annum, hgmd represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. the public version of hgmd ( ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (hgmd professional) is available to academic, clinical and commercial users under license via qiagen inc.",0
"introduction epidemiological studies have shown that weaker grip strength in later life is associated with disability, morbidity, and mortality. grip strength is a key component of the sarcopenia and frailty phenotypes and yet it is unclear how individual measurements should be interpreted. our objective was to produce cross-sectional centile values for grip strength across the life course. a secondary objective was to examine the impact of different aspects of measurement protocol. methods we combined 60,803 observations from 49,964 participants (26,687 female) of 12 general population studies in great britain. we produced centile curves for ages 4 to 90 and investigated the prevalence of weak grip, defined as strength at least 2.5 sds below the gender-specific peak mean. we carried out a series of sensitivity analyses to assess the impact of dynamometer type and measurement position (seated or standing). results our results suggested three overall periods: an increase to peak in early adult life, maintenance through to midlife, and decline from midlife onwards. males were on average stronger than females from adolescence onwards: males' peak median grip was 51 kg between ages 29 and 39, compared to 31 kg in females between ages 26 and 42. weak grip strength, defined as strength at least 2.5 sds below the gender-specific peak mean, increased sharply with age, reaching a prevalence of 23% in males and 27% in females by age 80. sensitivity analyses suggested our findings were robust to differences in dynamometer type and measurement position. conclusion this is the first study to provide normative data for grip strength across the life course. these centile values have the potential to inform the clinical assessment of grip strength which is recognised as an important part of the identification of people with sarcopenia and frailty.",0
"although attention plays a ubiquitous role in perception and cognition, researchers lack a simple way to measure a person's overall attentional abilities. because behavioral measures are diverse and difficult to standardize, we pursued a neuromarker of an important aspect of attention, sustained attention, using functional magnetic resonance imaging. to this end, we identified functional brain networks whose strength during a sustained attention task predicted individual differences in performance. models based on these networks generalized to previously unseen individuals, even predicting performance from resting-state connectivity alone. furthermore, these same models predicted a clinical measure of attention--symptoms of attention deficit hyperactivity disorder--from resting-state connectivity in an independent sample of children and adolescents. these results demonstrate that whole-brain functional network strength provides a broadly applicable neuromarker of sustained attention.",0
"basal keratinocytes attach to the underlying dermal stroma through an ultrastructurally unique and complex basement membrane zone. electron-dense plaques along the basal surface plasma membrane, termed hemidesmosomes, appear to attach directly to the lamina densa of the basement membrane through fine strands, called anchoring filaments. the lamina densa is secured to the stroma through a complex of type vii collagen containing anchoring fibrils and anchoring plaques. we have identified what we believe is a novel antigen unique to this tissue region. the mabs to this antigen localize to the anchoring filaments, just below the basal-dense plate of the hemidesmosomes. in cell culture, the antigen is deposited upon the culture substate by growing and migrating human keratinocytes. addition of mab to the cultures causes the cells to round and detach, but does not impair them metabolically. skin fragments incubated with antibody extensively de-epithelialize. these findings strongly suggest that this antigen is intimately involved in attachment of keratinocytes to the basement membrane. this antigen was isolated from keratinocyte cultures by immunoaffinity chromatography. two molecules are observed. the most intact species contains three nonidentical chains, 165, 155, and 140 kd linked by interchain disulfide bonds. the second and more abundant species contains the 165- and 140-kd chains, but the 155-kd chain has been proteolytically cleaved to 105 kd. likewise, two rotary-shadowed images are observed. the larger of the two, presumably corresponding to the most intact form, appears as an asymmetric 107-nm-long rod, with a single globule at one end and two smaller globules at the other. the more abundant species, presumably the proteolytically cleaved form, lacks the distal small globule. we propose the name ""kalinin"" for this new molecule.",0
"at 4 degrees c transferrin bound to receptors on the reticulocyte plasma membrane, and at 37 degrees c receptor-mediated endocytosis of transferrin occurred. uptake at 37 degrees c exceeded binding at 4 degrees c by 2.5-fold and saturated after 20-30 min. during uptake at 37 degrees c, bound transferrin was internalized into a trypsin-resistant space. trypsinization at 4 degrees c destroyed surface receptors, but with subsequent incubation at 37 degrees c, surface receptors rapidly appeared (albeit in reduced numbers), and uptake occurred at a decreased level. after endocytosis, transferrin was released, apparently intact, into the extracellular space. at 37 degrees c colloidal gold-transferrin (autf) clustered in coated pits and then appeared inside various intracellular membrane-bounded compartments. small vesicles and tubules were labeled after short (5-10 min) incubations at 37 degrees c. larger multivesicular endosomes became heavily labeled after longer (20-35 min) incubations. multivesicular endosomes apparently fused with the plasma membrane and released their contents by exocytosis. none of these organelles appeared to be lysosomal in nature, and 98% of intracellular autf was localized in acid phosphatase-negative compartments. autf, like transferrin, was released with subsequent incubation at 37 degrees c. freeze-dried and freeze-fractured reticulocytes confirmed the distribution of autf in reticulocytes and revealed the presence of clathrin-coated patches amidst the spectrin coating the inner surface of the plasma membrane. these data suggest that transferrin is internalized via coated pits and vesicles and demonstrate that transferrin and its receptor are recycled back to the plasma membrane after endocytosis.",0
"jaspar ( is an open-access database of curated, non-redundant transcription factor (tf)-binding profiles stored as position frequency matrices (pfms) and tf flexible models (tffms) for tfs across multiple species in six taxonomic groups. in the 2018 release of jaspar, the core collection has been expanded with 322 new pfms (60 for vertebrates and 262 for plants) and 33 pfms were updated (24 for vertebrates, 8 for plants and 1 for insects). these new profiles represent a 30% expansion compared to the 2016 release. in addition, we have introduced 316 tffms (95 for vertebrates, 218 for plants and 3 for insects). this release incorporates clusters of similar pfms in each taxon and each tf class per taxon. the jaspar 2018 core vertebrate collection of pfms was used to predict tf-binding sites in the human genome. the predictions are made available to the scientific community through a ucsc genome browser track data hub. finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. all the underlying data can be retrieved programmatically using a restful api and through the jaspar 2018 r/bioconductor package.",0
"liposomes are the first nano drug delivery systems that have been successfully translated into real-time clinical applications. these closed bilayer phospholipid vesicles have witnessed many technical advances in recent years since their first development in 1965. delivery of therapeutics by liposomes alters their biodistribution profile, which further enhances the therapeutic index of various drugs. extensive research is being carried out using these nano drug delivery systems in diverse areas including the delivery of anti-cancer, anti-fungal, anti-inflammatory drugs and therapeutic genes. the significant contribution of liposomes as drug delivery systems in the healthcare sector is known by many clinical products, e.g., doxil ® , ambisome ® , depodur™, etc. this review provides a detailed update on liposomal technologies e.g., depofoam™ technology, stealth technology, etc., the formulation aspects of clinically used products and ongoing clinical trials on liposomes.",0
"intercellular adhesion molecule-1 (icam-1) on the surface of cultured umbilical vein and saphenous vein endothelial cells was upregulated between 2.5- and 40-fold by ril-1, rtnf, lps and rifn gamma corresponding to up to 5 x 10(6) sites/cell. endothelial cell icam-1 was a single band of 90 kd in sds-page. purified endothelial cell icam-1 reconstituted into liposomes and bound to plastic was an excellent substrate for both jy b lymphoblastoid cell and t lymphoblast adhesion. adhesion to endothelial cell icam-1 in planar membranes was blocked completely by monoclonal antibodies to lymphocyte function associated antigen-1 (lfa-1) or icam-1. adhesion to artificial membranes was most sensitive to icam-1 density within the physiological range found on resting and stimulated endothelial cells. adhesion of jy b lymphoblastoid cells, normal and genetically lfa-1 deficient t lymphoblasts and resting peripheral blood lymphocytes to endothelial cell monolayers was also assayed. in summary, lfa-1 dependent (60-90% of total adhesion) and lfa-1-independent basal adhesion was observed and the use of both adhesion pathways by different interacting cell pairs was increased by monokine or lipopolysaccharide stimulation of endothelial cells. the lfa-1-dependent adhesion could be further subdivided into an lfa-1/icam-1-dependent component which was increased by cytokines and a basal lfa-1-dependent, icam-1-independent component which did not appear to be affected by cytokines. we conclude that icam-1 is a regulated ligand for lymphocyte-endothelial cell adhesion, but at least two other major adhesion pathways exist.",0
"responding to an outbreak of a novel coronavirus in december 2019, china banned travel to and from wuhan city on 23 january 2020 and implemented a national emergency response. we investigated the spread and control of covid-19 using a data set that included case reports, human movement, and public health interventions. the wuhan shutdown was associated with the delayed arrival of covid-19 in other cities by 2.91 days. cities that implemented control measures preemptively reported fewer cases on average (13.0) in the first week of their outbreaks compared with cities that started control later (20.6). suspending intracity public transport, closing entertainment venues, and banning public gatherings were associated with reductions in case incidence. the national emergency response appears to have delayed the growth and limited the size of the covid-19 epidemic in china, averting hundreds of thousands of cases by 19 february (day 50).",0
"summary more and more cancer studies use next-generation sequencing (ngs) data to detect various types of genomic variation. however, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (loh). here, we present the tool control-freec that enables automatic calculation of copy number and allelic content profiles from ngs data, and consequently predicts regions of genomic alteration such as gains, losses and loh. taking as input aligned reads, control-freec constructs copy number and b-allele frequency profiles. the profiles are then normalized, segmented and analyzed in order to assign genotype status (copy number and allelic content) to each genomic region. when a matched normal sample is provided, control-freec discriminates somatic from germline events. control-freec is able to analyze overdiploid tumor samples and samples contaminated by normal cells. low mappability regions can be excluded from the analysis using provided mappability tracks. availability c++ source code is available at: contact freec@curie.fr supplementary information supplementary data are available at bioinformatics online.",0
"background the global burden of diseases, injuries, and risk factors study 2015 (gbd 2015) provides an up-to-date analysis of the burden of diarrhoeal diseases. this study assesses cases, deaths, and aetiologies spanning the past 25 years and informs the changing picture of diarrhoeal disease worldwide. methods we estimated diarrhoeal mortality by age, sex, geography, and year using the cause of death ensemble model (codem), a modelling platform shared across most causes of death in the gbd 2015 study. we modelled diarrhoeal morbidity, including incidence and prevalence, using a meta-regression platform called dismod-mr. we estimated aetiologies for diarrhoeal diseases using a counterfactual approach that incorporates the aetiology-specific risk of diarrhoeal disease and the prevalence of the aetiology in diarrhoea episodes. we used the socio-demographic index, a summary indicator derived from measures of income per capita, educational attainment, and fertility, to assess trends in diarrhoeal mortality. the two leading risk factors for diarrhoea-childhood malnutrition and unsafe water, sanitation, and hygiene-were used in a decomposition analysis to establish the relative contribution of changes in diarrhoea disability-adjusted life-years (dalys). findings globally, in 2015, we estimate that diarrhoea was a leading cause of death among all ages (1·31 million deaths, 95% uncertainty interval 1·23 million to 1·39 million), as well as a leading cause of dalys because of its disproportionate impact on young children (71·59 million dalys, 66·44 million to 77·21 million). diarrhoea was a common cause of death among children under 5 years old (499 000 deaths, 95% ui 447 000-558 000). the number of deaths due to diarrhoea decreased by an estimated 20·8% (95% ui 15·4-26·1) from 2005 to 2015. rotavirus was the leading cause of diarrhoea deaths (199 000, 95% ui 165 000-241 000), followed by shigella spp (164 300, 85 000-278 700) and salmonella spp (90 300, 95% ui 34 100-183 100). among children under 5 years old, the three aetiologies responsible for the most deaths were rotavirus, cryptosporidium spp, and shigella spp. improvements in safe water and sanitation have decreased diarrhoeal dalys by 13·4%, and reductions in childhood undernutrition have decreased diarrhoeal dalys by 10·0% between 2005 and 2015. interpretation at the global level, deaths due to diarrhoeal diseases have decreased substantially in the past 25 years, although progress has been faster in some countries than others. diarrhoea remains a largely preventable disease and cause of death, and continued efforts to improve access to safe water, sanitation, and childhood nutrition will be important in reducing the global burden of diarrhoea. funding bill & melinda gates foundation.",0
"several studies have shown that global crop production needs to double by 2050 to meet the projected demands from rising population, diet shifts, and increasing biofuels consumption. boosting crop yields to meet these rising demands, rather than clearing more land for agriculture has been highlighted as a preferred solution to meet this goal. however, we first need to understand how crop yields are changing globally, and whether we are on track to double production by 2050. using ∼2.5 million agricultural statistics, collected for ∼13,500 political units across the world, we track four key global crops-maize, rice, wheat, and soybean-that currently produce nearly two-thirds of global agricultural calories. we find that yields in these top four crops are increasing at 1.6%, 1.0%, 0.9%, and 1.3% per year, non-compounding rates, respectively, which is less than the 2.4% per year rate required to double global production by 2050. at these rates global production in these crops would increase by ∼67%, ∼42%, ∼38%, and ∼55%, respectively, which is far below what is needed to meet projected demands in 2050. we present detailed maps to identify where rates must be increased to boost crop production and meet rising demands.",0
"motivation the blast software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. numerous research studies have suggested that preprocessing the database instead would give better performance. however, production usage of sequence comparison methods that preprocess the database has been limited to programs such as blat and ssaha that are designed to find matches when query and database subsequences are highly similar. results we developed a new version of the megablast module of blast that does the initial phase of finding short seeds for matches by searching a database index. we also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. we show that the new 'indexed megablast' is faster than the 'non-indexed' version for most practical uses. we show that indexed megablast is faster than miblast, another implementation of blast nucleotide searching with a preprocessed database, for most of the 200 queries we tested. to deploy indexed megablast as part of ncbi'sweb blast service, the storage of databases and the queueing mechanism were modified, so that some machines are now dedicated to serving queries for a specific database. the response time for such web queries is now faster than it was when each computer handled queries for multiple databases. availability the code for indexed megablast is part of the blastn program in the ncbi c++ toolkit. the preprocessor program makembindex is also in the toolkit. indexed megablast has been used in production on ncbi's web blast service to search one version of the human and mouse genomes since october 2007. the linux command-line executables for blastn and makembindex, documentation, and some query sets used to carry out the tests described below are available in the directory: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast supplementary information supplementary data are available at bioinformatics online.",0
"the number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. to interact with this increasing body of data, we have developed phytozome ( a comparative hub for plant genome and gene family data and analysis. phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the joint genome institute, as well as selected species sequenced elsewhere. through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.",0
"the causes of antimicrobial resistance (amr) in developing countries are complex and may be rooted in practices of health care professionals and patients' behavior towards the use of antimicrobials as well as supply chains of antimicrobials in the population. some of these factors may include inappropriate prescription practices, inadequate patient education, limited diagnostic facilities, unauthorized sale of antimicrobials, lack of appropriate functioning drug regulatory mechanisms, and non-human use of antimicrobials such as in animal production. considering that these factors in developing countries may vary from those in developed countries, intervention efforts in developing countries need to address the context and focus on the root causes specific to this part of the world. here, we describe these health-seeking behaviors that lead to the threat of amr and healthcare practices that drive the development of amr in developing countries and we discuss alternatives for disease prevention as well as other treatment options worth exploring.",0
"background isolation of cases and contact tracing is used to control outbreaks of infectious diseases, and has been used for coronavirus disease 2019 (covid-19). whether this strategy will achieve control depends on characteristics of both the pathogen and the response. here we use a mathematical model to assess if isolation and contact tracing are able to control onwards transmission from imported cases of covid-19. methods we developed a stochastic transmission model, parameterised to the covid-19 outbreak. we used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a severe acute respiratory syndrome coronavirus 2 (sars-cov-2)-like pathogen. we considered scenarios that varied in the number of initial cases, the basic reproduction number (r 0 ), the delay from symptom onset to isolation, the probability that contacts were traced, the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. we assumed isolation prevented all further transmission in the model. outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. we measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort. findings simulated outbreaks starting with five initial cases, an r 0 of 1·5, and 0% transmission before symptom onset could be controlled even with low contact tracing probability; however, the probability of controlling an outbreak decreased with the number of initial cases, when r 0 was 2·5 or 3·5 and with more transmission before symptom onset. across different initial numbers of cases, the majority of scenarios with an r 0 of 1·5 were controllable with less than 50% of contacts successfully traced. to control the majority of outbreaks, for r 0 of 2·5 more than 70% of contacts had to be traced, and for an r 0 of 3·5 more than 90% of contacts had to be traced. the delay between symptom onset and isolation had the largest role in determining whether an outbreak was controllable when r 0 was 1·5. for r 0 values of 2·5 or 3·5, if there were 40 initial cases, contact tracing and isolation were only potentially feasible when less than 1% of transmission occurred before symptom onset. interpretation in most scenarios, highly effective contact tracing and case isolation is enough to control a new outbreak of covid-19 within 3 months. the probability of control decreases with long delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. this model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts. funding wellcome trust, global challenges research fund, and health data research uk.",0
"clinvar ( is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the national institutes of health. interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. clinvar aggregates data by variant-disease pairs, and by variant (or set of variants). data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive xml report. clinvar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). clinvar continues to make improvements to its search and retrieval functions. several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.",0
"aims/hypothesis type 2 diabetes is regarded as inevitably progressive, with irreversible beta cell failure. the hypothesis was tested that both beta cell failure and insulin resistance can be reversed by dietary restriction of energy intake. methods eleven people with type 2 diabetes (49.5 ± 2.5 years, bmi 33.6 ± 1.2 kg/m(2), nine male and two female) were studied before and after 1, 4 and 8 weeks of a 2.5 mj (600 kcal)/day diet. basal hepatic glucose output, hepatic and peripheral insulin sensitivity and beta cell function were measured. pancreas and liver triacylglycerol content was measured using three-point dixon magnetic resonance imaging. an age-, sex- and weight-matched group of eight non-diabetic participants was studied. results after 1 week of restricted energy intake, fasting plasma glucose normalised in the diabetic group (from 9.2 ± 0.4 to 5.9 ± 0.4 mmol/l; p = 0.003). insulin suppression of hepatic glucose output improved from 43 ± 4% to 74 ± 5% (p = 0.003 vs baseline; controls 68 ± 5%). hepatic triacylglycerol content fell from 12.8 ± 2.4% in the diabetic group to 2.9 ± 0.2% by week 8 (p = 0.003). the first-phase insulin response increased during the study period (0.19 ± 0.02 to 0.46 ± 0.07 nmol min(-1) m(-2); p conclusions/interpretation normalisation of both beta cell function and hepatic insulin sensitivity in type 2 diabetes was achieved by dietary energy restriction alone. this was associated with decreased pancreatic and liver triacylglycerol stores. the abnormalities underlying type 2 diabetes are reversible by reducing dietary energy intake.",0
"neuroplasticity can be defined as the ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function and connections. major advances in the understanding of neuroplasticity have to date yielded few established interventions. to advance the translation of neuroplasticity research towards clinical applications, the national institutes of health blueprint for neuroscience research sponsored a workshop in 2009. basic and clinical researchers in disciplines from central nervous system injury/stroke, mental/addictive disorders, paediatric/developmental disorders and neurodegeneration/ageing identified cardinal examples of neuroplasticity, underlying mechanisms, therapeutic implications and common denominators. promising therapies that may enhance training-induced cognitive and motor learning, such as brain stimulation and neuropharmacological interventions, were identified, along with questions of how best to use this body of information to reduce human disability. improved understanding of adaptive mechanisms at every level, from molecules to synapses, to networks, to behaviour, can be gained from iterative collaborations between basic and clinical researchers. lessons can be gleaned from studying fields related to plasticity, such as development, critical periods, learning and response to disease. improved means of assessing neuroplasticity in humans, including biomarkers for predicting and monitoring treatment response, are needed. neuroplasticity occurs with many variations, in many forms, and in many contexts. however, common themes in plasticity that emerge across diverse central nervous system conditions include experience dependence, time sensitivity and the importance of motivation and attention. integration of information across disciplines should enhance opportunities for the translation of neuroplasticity and circuit retraining research into effective clinical therapies.",0
"background tumour-infiltrating lymphocytes (tils) are often found in tumours, presumably reflecting an immune response against the tumour. we carried out a systematic review and meta-analysis, aiming to establish pooled estimates for survival outcomes based on the presence of tils in cancer. methods a pubmed and embase literature search was designed. studies were included, in which the prognostic significance of intratumoural cd3+, cd4+, cd8+, and foxp3+ lymphocytes, as well as ratios between these subsets, were determined in solid tumours. results in pooled analysis, cd3+ tils had a positive effect on survival with a hazard ratio (hr) of 0.58 (95% confidence interval (ci) 0.43-0.78) for death, as did cd8+ tils with a hr of 0.71 (95% ci 0.62-0.82). foxp3+ regulatory tils were not linked to overall survival, with a hr of 1.19 (95% ci 0.84-1.67). the cd8/foxp3 ratio produced a more impressive hr (risk of death: hr 0.48, 95% ci 0.34-0.68), but was used in relatively few studies. sample size and follow-up time seemed to influence study outcomes. conclusion any future studies should be carefully designed, to prevent overestimating the effect of tils on prognosis. in this context, ratios between til subsets may be more informative.",0
"the frequency with which scientists fabricate and falsify data, or commit other forms of scientific misconduct is a matter of controversy. many surveys have asked scientists directly whether they have committed or know of a colleague who committed research misconduct, but their results appeared difficult to compare and synthesize. this is the first meta-analysis of these surveys. to standardize outcomes, the number of respondents who recalled at least one incident of misconduct was calculated for each question, and the analysis was limited to behaviours that distort scientific knowledge: fabrication, falsification, ""cooking"" of data, etc... survey questions on plagiarism and other forms of professional misconduct were excluded. the final sample consisted of 21 surveys that were included in the systematic review, and 18 in the meta-analysis. a pooled weighted average of 1.97% (n = 7, 95%ci: 0.86-4.45) of scientists admitted to have fabricated, falsified or modified data or results at least once--a serious form of misconduct by any standard--and up to 33.7% admitted other questionable research practices. in surveys asking about the behaviour of colleagues, admission rates were 14.12% (n = 12, 95% ci: 9.91-19.72) for falsification, and up to 72% for other questionable research practices. meta-regression showed that self reports surveys, surveys using the words ""falsification"" or ""fabrication"", and mailed surveys yielded lower percentages of misconduct. when these factors were controlled for, misconduct was reported more frequently by medical/pharmacological researchers than others. considering that these surveys ask sensitive questions and have other limitations, it appears likely that this is a conservative estimate of the true prevalence of scientific misconduct.",0
"current tandem mass spectral libraries for lipid annotations in metabolomics are limited in size and diversity. we provide a freely available computer-generated tandem mass spectral library of 212,516 spectra covering 119,200 compounds from 26 lipid compound classes, including phospholipids, glycerolipids, bacterial lipoglycans and plant glycolipids. we show platform independence by using tandem mass spectra from 40 different mass spectrometer types including low-resolution and high-resolution instruments.",0
"family caregivers of people with dementia, often called the invisible second patients, are critical to the quality of life of the care recipients. the effects of being a family caregiver, though sometimes positive, are generally negative, with high rates of burden and psychological morbidity as well as social isolation, physical ill-health, and financial hardship. caregivers vulnerable to adverse effects can be identified, as can factors which ameliorate or exacerbate burden and strain. psychosocial interventions have been demonstrated to reduce caregiver burden and depression and delay nursing home admission. comprehensive management of the patient with dementia includes building a partnership between health professionals and family caregivers, referral to alzheimer's associations, and psychosocial interventions where indicated.",0
"background the past decade has seen considerable interest in the development and evaluation of complex interventions to improve health. such interventions can only have a significant impact on health and health care if they are shown to be effective when tested, are capable of being widely implemented and can be normalised into routine practice. to date, there is still a problematic gap between research and implementation. the normalisation process theory (npt) addresses the factors needed for successful implementation and integration of interventions into routine work (normalisation). discussion in this paper, we suggest that the npt can act as a sensitising tool, enabling researchers to think through issues of implementation while designing a complex intervention and its evaluation. the need to ensure trial procedures that are feasible and compatible with clinical practice is not limited to trials of complex interventions, and npt may improve trial design by highlighting potential problems with recruitment or data collection, as well as ensuring the intervention has good implementation potential. summary the npt is a new theory which offers trialists a consistent framework that can be used to describe, assess and enhance implementation potential. we encourage trialists to consider using it in their next trial.",0
"bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. for this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. recently, large datasets of protein-small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. here, we introduce swisstargetprediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2d and 3d similarity measures with known ligands. predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. swisstargetprediction is accessible free of charge and without login requirement at",0
"human coronaviruses (hcv) in two serogroups represented by hcv-229e and hcv-oc43 are an important cause of upper respiratory tract infections. here we report that human aminopeptidase n, a cell-surface metalloprotease on intestinal, lung and kidney epithelial cells, is a receptor for human coronavirus strain hcv-229e, but not for hcv-oc43. a monoclonal antibody, rbs, blocked hcv-229e virus infection of human lung fibroblasts, immunoprecipitated aminopeptidase n and inhibited its enzymatic activity. hcv-229e-resistant murine fibroblasts became susceptible after transfection with complementary dna encoding human aminopeptidase n. by contrast, infection of human cells with hcv-oc43 was not inhibited by antibody rbs and expression of aminopeptidase n did not enhance hcv-oc43 replication in mouse cells. a mutant aminopeptidase lacking the catalytic site of the enzyme did not bind hcv-229e or rbs and did not render murine cells susceptible to hcv-229e infection, suggesting that the virus-binding site may lie at or near the active site of the human aminopeptidase molecule.",0
"only mature b lymphocytes can enter the lymphoid follicles of spleen and lymph nodes and thus efficiently participate in the immune response. mature, long-lived b lymphocytes derive from short-lived precursors generated in the bone marrow. we show that selection into the mature pool is an active process and takes place in the spleen. two populations of splenic b cells were identified as precursors for mature b cells. transitional b cells of type 1 (t1) are recent immigrants from the bone marrow. they develop into the transitional b cells of type 2 (t2), which are cycling and found exclusively in the primary follicles of the spleen. mature b cells can be generated from t1 or t2 b cells. mice with genetic deletions of elements participating in the b cell receptor signaling cascade display developmental arrest at the t1 or t2 stage. the analysis of these defects showed that the development of t2 and mature b cells from t1 precursors requires defined qualitative and quantitative signals derived from the b cell receptor and that the induction of longevity and maturation requires different signals.",0
"background in december 2020, israel began a mass vaccination campaign against coronavirus disease 2019 (covid-19) by administering the bnt162b2 vaccine, which led to a sharp curtailing of the outbreak. after a period with almost no cases of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection, a resurgent covid-19 outbreak began in mid-june 2021. possible reasons for the resurgence were reduced vaccine effectiveness against the delta (b.1.617.2) variant and waning immunity. the extent of waning immunity of the vaccine against the delta variant in israel is unclear. methods we used data on confirmed infection and severe disease collected from an israeli national database for the period of july 11 to 31, 2021, for all israeli residents who had been fully vaccinated before june 2021. we used a poisson regression model to compare rates of confirmed sars-cov-2 infection and severe covid-19 among persons vaccinated during different time periods, with stratification according to age group and with adjustment for possible confounding factors. results among persons 60 years of age or older, the rate of infection in the july 11-31 period was higher among persons who became fully vaccinated in january 2021 (when they were first eligible) than among those fully vaccinated 2 months later, in march (rate ratio, 1.6; 95% confidence interval , 1.3 to 2.0). among persons 40 to 59 years of age, the rate ratio for infection among those fully vaccinated in february (when they were first eligible), as compared with 2 months later, in april, was 1.7 (95% ci, 1.4 to 2.1). among persons 16 to 39 years of age, the rate ratio for infection among those fully vaccinated in march (when they were first eligible), as compared with 2 months later, in may, was 1.6 (95% ci, 1.3 to 2.0). the rate ratio for severe disease among persons fully vaccinated in the month when they were first eligible, as compared with those fully vaccinated in march, was 1.8 (95% ci, 1.1 to 2.9) among persons 60 years of age or older and 2.2 (95% ci, 0.6 to 7.7) among those 40 to 59 years of age; owing to small numbers, the rate ratio could not be calculated among persons 16 to 39 years of age. conclusions these findings indicate that immunity against the delta variant of sars-cov-2 waned in all age groups a few months after receipt of the second dose of vaccine.",0
"from october 4 to november 2, 2001, the first 10 confirmed cases of inhalational anthrax caused by intentional release of bacillus anthracis were identified in the united states. epidemiologic investigation indicated that the outbreak, in the district of columbia, florida, new jersey, and new york, resulted from intentional delivery of b. anthracis spores through mailed letters or packages. we describe the clinical presentation and course of these cases of bioterrorism-related inhalational anthrax. the median age of patients was 56 years (range 43 to 73 years), 70% were male, and except for one, all were known or believed to have processed, handled, or received letters containing b. anthracis spores. the median incubation period from the time of exposure to onset of symptoms, when known (n=6), was 4 days (range 4 to 6 days). symptoms at initial presentation included fever or chills (n=10), sweats (n=7), fatigue or malaise (n=10), minimal or nonproductive cough (n=9), dyspnea (n=8), and nausea or vomiting (n=9). the median white blood cell count was 9.8 x 10(3)/mm(3) (range 7.5 to 13.3), often with increased neutrophils and band forms. nine patients had elevated serum transaminase levels, and six were hypoxic. all 10 patients had abnormal chest x-rays; abnormalities included infiltrates (n=7), pleural effusion (n=8), and mediastinal widening (seven patients). computed tomography of the chest was performed on eight patients, and mediastinal lymphadenopathy was present in seven. with multidrug antibiotic regimens and supportive care, survival of patients (60%) was markedly higher (<15%) than previously reported.",0
"photosensitive caged compounds have enhanced our ability to address the complexity of biological systems by generating effectors with remarkable spatial/temporal resolutions. the caging effect is typically removed by photolysis with ultraviolet light to liberate the bioactive species. although this technique has been successfully applied to many biological problems, it suffers from a number of intrinsic drawbacks. for example, it requires dedicated efforts to design and synthesize a precursor compound for each effector. the ultraviolet light may cause damage to biological samples and is suitable only for in vitro studies because of its quick attenuation in tissue. here we address these issues by developing a platform based on the photothermal effect of gold nanocages. gold nanocages represent a class of nanostructures with hollow interiors and porous walls. they can have strong absorption (for the photothermal effect) in the near-infrared while maintaining a compact size. when the surface of a gold nanocage is covered with a smart polymer, the pre-loaded effector can be released in a controllable fashion using a near-infrared laser. this system works well with various effectors without involving sophisticated syntheses, and is well suited for in vivo studies owing to the high transparency of soft tissue in the near-infrared region.",0
"misclassification of exposure is a well-recognized inherent limitation of epidemiologic studies of disease and the environment. for many agents of interest, exposures take place over time and in multiple locations; accurately estimating the relevant exposures for an individual participant in epidemiologic studies is often daunting, particularly within the limits set by feasibility, participant burden, and cost. researchers have taken steps to deal with the consequences of measurement error by limiting the degree of error through a study's design, estimating the degree of error using a nested validation study, and by adjusting for measurement error in statistical analyses. in this paper, we address measurement error in observational studies of air pollution and health. because measurement error may have substantial implications for interpreting epidemiologic studies on air pollution, particularly the time-series analyses, we developed a systematic conceptual formulation of the problem of measurement error in epidemiologic studies of air pollution and then considered the consequences within this formulation. when possible, we used available relevant data to make simple estimates of measurement error effects. this paper provides an overview of measurement errors in linear regression, distinguishing two extremes of a continuum-berkson from classical type errors, and the univariate from the multivariate predictor case. we then propose one conceptual framework for the evaluation of measurement errors in the log-linear regression used for time-series studies of particulate air pollution and mortality and identify three main components of error. we present new simple analyses of data on exposures of particulate matter < 10 microm in aerodynamic diameter from the particle total exposure assessment methodology study. finally, we summarize open questions regarding measurement error and suggest the kind of additional data necessary to address them.",0
"cell lines are invaluable biomedical research tools, and recent literature has emphasized the importance of genotype authentication and characterization. in the present study, 24 out of 27 cell line identities were confirmed by short tandem repeat profiling. the molecular phenotypes of the 24 colon cancer cell lines were examined, and microsatellite instability (msi) and cpg island methylator phenotype (cimp) were determined, using the bethesda panel mononucleotide repeat loci and two epimarker panels, respectively. furthermore, the braf, kras and pik3ca oncogenes were analyzed for mutations in known hotspots, while the entire coding sequences of the pten and tp53 tumor suppressors were investigated. nine cell lines showed msi. thirteen and nine cell lines were found to be cimp positive, using the issa panel and the weisenberger et al. panel, respectively. the latter was found to be superior for cimp classification of colon cancer cell lines. seventeen cell lines harbored disrupting tp53 mutations. altogether, 20/24 cell lines had the mitogen-activated protein kinase pathway activating mutually exclusive kras or braf mutations. pik3ca and pten mutations leading to hyperactivation of the phosphoinositide 3-kinase/akt pathway were observed in 13/24 cell lines. interestingly, in four cell lines there were no mutations in neither braf, kras, pik3ca nor in pten. in conclusion, this study presents molecular features of a large number of colon cancer cell lines to aid the selection of suitable in vitro models for descriptive and functional research.",0
"biologic monitoring (i.e., biomonitoring) is used to assess human exposures to environmental and workplace chemicals. urinary biomonitoring data typically are adjusted to a constant creatinine concentration to correct for variable dilutions among spot samples. traditionally, this approach has been used in population groups without much diversity. the inclusion of multiple demographic groups in studies using biomonitoring for exposure assessment has increased the variability in the urinary creatinine levels in these study populations. our objectives were to document the normal range of urinary creatinine concentrations among various demographic groups, evaluate the impact that variations in creatinine concentrations can have on classifying exposure status of individuals in epidemiologic studies, and recommend an approach using multiple regression to adjust for variations in creatinine in multivariate analyses. we performed a weighted multivariate analysis of urinary creatinine concentrations in 22,245 participants of the third national health and nutrition examination survey (1988-1994) and established reference ranges (10th-90th percentiles) for each demographic and age category. significant predictors of urinary creatinine concentration included age group, sex, race/ethnicity, body mass index, and fat-free mass. time of day that urine samples were collected made a small but statistically significant difference in creatinine concentrations. for an individual, the creatinine-adjusted concentration of an analyte should be compared with a ""reference"" range derived from persons in a similar demographic group (e.g., children with children, adults with adults). for multiple regression analysis of population groups, we recommend that the analyte concentration (unadjusted for creatinine) should be included in the analysis with urinary creatinine added as a separate independent variable. this approach allows the urinary analyte concentration to be appropriately adjusted for urinary creatinine and the statistical significance of other variables in the model to be independent of effects of creatinine concentration.",0
"parametric mapping techniques provide a non-invasive tool for quantifying tissue alterations in myocardial disease in those eligible for cardiovascular magnetic resonance (cmr). parametric mapping with cmr now permits the routine spatial visualization and quantification of changes in myocardial composition based on changes in t1, t2, and t2*(star) relaxation times and extracellular volume (ecv). these changes include specific disease pathways related to mainly intracellular disturbances of the cardiomyocyte (e.g., iron overload, or glycosphingolipid accumulation in anderson-fabry disease); extracellular disturbances in the myocardial interstitium (e.g., myocardial fibrosis or cardiac amyloidosis from accumulation of collagen or amyloid proteins, respectively); or both (myocardial edema with increased intracellular and/or extracellular water). parametric mapping promises improvements in patient care through advances in quantitative diagnostics, inter- and intra-patient comparability, and relatedly improvements in treatment. there is a multitude of technical approaches and potential applications. this document provides a summary of the existing evidence for the clinical value of parametric mapping in the heart as of mid 2017, and gives recommendations for practical use in different clinical scenarios for scientists, clinicians, and cmr manufacturers.",0
"preprocessing of functional magnetic resonance imaging (fmri) involves numerous steps to clean and standardize the data before statistical analysis. generally, researchers create ad hoc preprocessing workflows for each dataset, building upon a large inventory of available tools. the complexity of these workflows has snowballed with rapid advances in acquisition and processing. we introduce fmriprep, an analysis-agnostic tool that addresses the challenge of robust and reproducible preprocessing for fmri data. fmriprep automatically adapts a best-in-breed workflow to the idiosyncrasies of virtually any dataset, ensuring high-quality preprocessing without manual intervention. by introducing visual assessment checkpoints into an iterative integration framework for software testing, we show that fmriprep robustly produces high-quality results on a diverse fmri data collection. additionally, fmriprep introduces less uncontrolled spatial smoothness than observed with commonly used preprocessing tools. fmriprep equips neuroscientists with an easy-to-use and transparent preprocessing workflow, which can help ensure the validity of inference and the interpretability of results.",0
"background vitamin d deficiency has been described as being pandemic, but serum 25-hydroxyvitamin d distribution data for the european union are of very variable quality. the nih-led international vitamin d standardization program (vdsp) has developed protocols for standardizing existing 25(oh)d values from national health/nutrition surveys. objective this study applied vdsp protocols to serum 25(oh)d data from representative childhood/teenage and adult/older adult european populations, representing a sizable geographical footprint, to better quantify the prevalence of vitamin d deficiency in europe. design the vdsp protocols were applied in 14 population studies by using certified liquid chromatography-tandem mass spectrometry on biobanked sera. these data were combined with standardized serum 25(oh)d data from 4 previously standardized studies (for a total n= 55,844). prevalence estimates of vitamin d deficiency were generated on the basis of standardized 25(oh)d data. results an overall pooled estimate, irrespective of age group, ethnic mix, and latitude of study populations, showed that 13.0% of the 55,844 european individuals had serum 25(oh)d concentrations conclusions vitamin d deficiency is evident throughout the european population at prevalence rates that are concerning and that require action from a public health perspective. what direction these strategies take will depend on european policy but should aim to ensure vitamin d intakes that are protective against vitamin d deficiency in the majority of the european population.",0
"aims the aims of the study were, first, to critically evaluate lipoprotein(a) as a cardiovascular risk factor and, second, to advise on screening for elevated plasma lp(a), on desirable levels, and on therapeutic strategies. methods and results the robust and specific association between elevated lp(a) levels and increased cardiovascular disease (cvd)/coronary heart disease (chd) risk, together with recent genetic findings, indicates that elevated lp(a), like elevated ldl-cholesterol, is causally related to premature cvd/chd. the association is continuous without a threshold or dependence on ldl- or non-hdl-cholesterol levels. mechanistically, elevated lp(a) levels may either induce a prothrombotic/anti-fibrinolytic effect as apolipoprotein(a) resembles both plasminogen and plasmin but has no fibrinolytic activity, or may accelerate atherosclerosis because, like ldl, the lp(a) particle is cholesterol-rich, or both. we advise that lp(a) be measured once, using an isoform-insensitive assay, in subjects at intermediate or high cvd/chd risk with premature cvd, familial hypercholesterolaemia, a family history of premature cvd and/or elevated lp(a), recurrent cvd despite statin treatment, ≥3% 10-year risk of fatal cvd according to european guidelines, and/or ≥10% 10-year risk of fatal + non-fatal chd according to us guidelines. as a secondary priority after ldl-cholesterol reduction, we recommend a desirable level for lp(a) conclusion we recommend screening for elevated lp(a) in those at intermediate or high cvd/chd risk, a desirable level <50 mg/dl as a function of global cardiovascular risk, and use of niacin for lp(a) and cvd/chd risk reduction.",0
"major depressive disorder affects around 16 per cent of the world population at some point in their lives. despite the availability of numerous monoaminergic-based antidepressants, most patients require several weeks, if not months, to respond to these treatments, and many patients never attain sustained remission of their symptoms. the non-competitive, glutamatergic nmdar (n-methyl-d-aspartate receptor) antagonist (r,s)-ketamine exerts rapid and sustained antidepressant effects after a single dose in patients with depression, but its use is associated with undesirable side effects. here we show that the metabolism of (r,s)-ketamine to (2s,6s;2r,6r)-hydroxynorketamine (hnk) is essential for its antidepressant effects, and that the (2r,6r)-hnk enantiomer exerts behavioural, electroencephalographic, electrophysiological and cellular antidepressant-related actions in mice. these antidepressant actions are independent of nmdar inhibition but involve early and sustained activation of ampars (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors). we also establish that (2r,6r)-hnk lacks ketamine-related side effects. our data implicate a novel mechanism underlying the antidepressant properties of (r,s)-ketamine and have relevance for the development of next-generation, rapid-acting antidepressants.",0
"a likelihood-based approach to density modification is developed that can be applied to a wide variety of cases where some information about the electron density at various points in the unit cell is available. the key to the approach consists of developing likelihood functions that represent the probability that a particular value of electron density is consistent with prior expectations for the electron density at that point in the unit cell. these likelihood functions are then combined with likelihood functions based on experimental observations and with others containing any prior knowledge about structure factors to form a combined likelihood function for each structure factor. a simple and general approach to maximizing the combined likelihood function is developed. it is found that this likelihood-based approach yields greater phase improvement in model and real test cases than either conventional solvent flattening and histogram matching or a recent reciprocal-space solvent-flattening procedure .",0
"polymorphonuclear leukocyte (pmn) locomotion and chemotaxis have been evaluated by direct microscopic observation of individual cells in thin slide-cover slip preparations, and also by observations on populations of cells migrating into a millipore filter. the direct microscopic method used the polarity of the locomoting pmns (broad, advancing lamellipodium and knoblike constriction at the rear) to record the direction of movement. the boyden chamber millipore assay was made more reliable by following the front of cells advancing into the filter, rather than counting the number of cells on the lower filter surface. special modifications of the millipore assay were necessary in order to distinguish between influences on rate of locomotion and true chemotaxis. in both systems the results indicate that under certain conditions leukocytes, and in particular pmns, release into the medium a factor stimulating locomotion and exerting chemotactic action on pmns in the vicinity. this cell-derived factor appears not to require serum factors for its release or action.",0
"the prevalence of depression may be affected by changes in psychiatric practices and the availability of online mental health information in the past two decades. this study aimed to evaluate the aggregate prevalence of depression in communities from different countries between 1994 and 2014 and to explore the variations in prevalence stratified by geographical, methodological and socio-economic factors. a total of 90 studies were identified and met the inclusion criteria (n = 1,112,573 adults) with 68 studies on single point prevalence, 9 studies on one-year prevalence, and 13 studies on lifetime prevalence of depression. a random-effects model meta-analysis that was performed to calculate the aggregate point, one-year and lifetime prevalence of depression calculated prevalences of 12.9%, 7.2% and 10.8% respectively. point prevalence of depression was significantly higher in women (14.4%), countries with a medium human development index (hdi) (29.2%), studies published from 2004 to 2014 (15.4%) and when using self-reporting instruments (17.3%) to assess depression. heterogeneity was identified by meta-regression and subgroup analysis, and response rate, percentage of women and year of publication, respectively, were determined contribute to depression prevalence. this meta-analysis allows benchmarking of the prevalence of depression during the era when online health information emerged, facilitating future comparisons.",0
"diet is a major lifestyle-related risk factor of various chronic diseases. dietary intake can be assessed by subjective report and objective observation. subjective assessment is possible using open-ended surveys such as dietary recalls or records, or using closed-ended surveys including food frequency questionnaires. each method has inherent strengths and limitations. continued efforts to improve the accuracy of dietary intake assessment and enhance its feasibility in epidemiological studies have been made. this article reviews common dietary assessment methods and their feasibility in epidemiological studies.",0
"a new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-em) single-particle analysis is presented. the motion within the sample is modelled through the use of gaussian process regression. this allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. this formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative b factors to that damage in a robust way. the method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. the new method has been implemented as bayesian polishing in relion -3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.",0
"bone remodeling depends on the precise coordination of bone resorption and subsequent bone formation. disturbances of this process are associated with skeletal diseases, such as camurati-engelmann disease (ced). we show using in vitro and in vivo models that active tgf-beta1 released during bone resorption coordinates bone formation by inducing migration of bone marrow stromal cells, also known as bone mesenchymal stem cells, to the bone resorptive sites and that this process is mediated through a smad signaling pathway. analyzing mice carrying a ced-derived mutant tgfb1 (encoding tgf-beta1), which show the typical progressive diaphyseal dysplasia seen in the human disease, we found high levels of active tgf-beta1 in the bone marrow. treatment with a tgf-beta type i receptor inhibitor partially rescued the uncoupled bone remodeling and prevented the fractures. thus, as tgf-beta1 functions to couple bone resorption and formation, modulation of tgf-beta1 activity could be an effective treatment for bone remodeling diseases.",0
"the outbreak of coronavirus disease 2019 (covid-19) has posed a serious threat to global public health, calling for the development of safe and effective prophylactics and therapeutics against infection of its causative agent, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), also known as 2019 novel coronavirus (2019-ncov). the cov spike (s) protein plays the most important roles in viral attachment, fusion and entry, and serves as a target for development of antibodies, entry inhibitors and vaccines. here, we identified the receptor-binding domain (rbd) in sars-cov-2 s protein and found that the rbd protein bound strongly to human and bat angiotensin-converting enzyme 2 (ace2) receptors. sars-cov-2 rbd exhibited significantly higher binding affinity to ace2 receptor than sars-cov rbd and could block the binding and, hence, attachment of sars-cov-2 rbd and sars-cov rbd to ace2-expressing cells, thus inhibiting their infection to host cells. sars-cov rbd-specific antibodies could cross-react with sars-cov-2 rbd protein, and sars-cov rbd-induced antisera could cross-neutralize sars-cov-2, suggesting the potential to develop sars-cov rbd-based vaccines for prevention of sars-cov-2 and sars-cov infection.",0
"background the estimation of individual ancestry from genetic data has become essential to applied population genetics and genetic epidemiology. software programs for calculating ancestry estimates have become essential tools in the geneticist's analytic arsenal. results here we describe four enhancements to admixture, a high-performance tool for estimating individual ancestries and population allele frequencies from snp (single nucleotide polymorphism) data. first, admixture can be used to estimate the number of underlying populations through cross-validation. second, individuals of known ancestry can be exploited in supervised learning to yield more precise ancestry estimates. third, by penalizing small admixture coefficients for each individual, one can encourage model parsimony, often yielding more interpretable results for small datasets or datasets with large numbers of ancestral populations. finally, by exploiting multiple processors, large datasets can be analyzed even more rapidly. conclusions the enhancements we have described make admixture a more accurate, efficient, and versatile tool for ancestry estimation.",0
"the cardiovascular complications of acute coronavirus disease 2019 (covid-19) are well described, but the post-acute cardiovascular manifestations of covid-19 have not yet been comprehensively characterized. here we used national healthcare databases from the us department of veterans affairs to build a cohort of 153,760 individuals with covid-19, as well as two sets of control cohorts with 5,637,647 (contemporary controls) and 5,859,411 (historical controls) individuals, to estimate risks and 1-year burdens of a set of pre-specified incident cardiovascular outcomes. we show that, beyond the first 30 d after infection, individuals with covid-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease. these risks and burdens were evident even among individuals who were not hospitalized during the acute phase of the infection and increased in a graded fashion according to the care setting during the acute phase (non-hospitalized, hospitalized and admitted to intensive care). our results provide evidence that the risk and 1-year burden of cardiovascular disease in survivors of acute covid-19 are substantial. care pathways of those surviving the acute episode of covid-19 should include attention to cardiovascular health and disease.",0
"objective to explore and evaluate the most common factors causing therapeutic non-compliance. methods a qualitative review was undertaken by a literature search of the medline database from 1970 to 2005 to identify studies evaluating the factors contributing to therapeutic non-compliance. results a total of 102 articles was retrieved and used in the review from the 2095 articles identified by the literature review process. from the literature review, it would appear that the definition of therapeutic compliance is adequately resolved. the preliminary evaluation revealed a number of factors that contributed to therapeutic non-compliance. these factors could be categorized to patient-centered factors, therapy-related factors, social and economic factors, healthcare system factors, and disease factors. for some of these factors, the impact on compliance was not unequivocal, but for other factors, the impact was inconsistent and contradictory. conclusion there are numerous studies on therapeutic noncompliance over the years. the factors related to compliance may be better categorized as ""soft"" and ""hard"" factors as the approach in countering their effects may differ. the review also highlights that the interaction of the various factors has not been studied systematically. future studies need to address this interaction issue, as this may be crucial to reducing the level of non-compliance in general, and to enhancing the possibility of achieving the desired healthcare outcomes.",0
"objective to establish whether there is any change in mortality from infection with a new variant of sars-cov-2, designated a variant of concern (voc-202012/1) in december 2020, compared with circulating sars-cov-2 variants. design matched cohort study. setting community based (pillar 2) covid-19 testing centres in the uk using the taqpath assay (a proxy measure of voc-202012/1 infection). participants 54 906 matched pairs of participants who tested positive for sars-cov-2 in pillar 2 between 1 october 2020 and 29 january 2021, followed-up until 12 february 2021. participants were matched on age, sex, ethnicity, index of multiple deprivation, lower tier local authority region, and sample date of positive specimens, and differed only by detectability of the spike protein gene using the taqpath assay. main outcome measure death within 28 days of the first positive sars-cov-2 test result. results the mortality hazard ratio associated with infection with voc-202012/1 compared with infection with previously circulating variants was 1.64 (95% confidence interval 1.32 to 2.04) in patients who tested positive for covid-19 in the community. in this comparatively low risk group, this represents an increase in deaths from 2.5 to 4.1 per 1000 detected cases. conclusions the probability that the risk of mortality is increased by infection with voc-202012/01 is high. if this finding is generalisable to other populations, infection with voc-202012/1 has the potential to cause substantial additional mortality compared with previously circulating variants. healthcare capacity planning and national and international control policies are all impacted by this finding, with increased mortality lending weight to the argument that further coordinated and stringent measures are justified to reduce deaths from sars-cov-2.",0
"a method for the specific histochemical demonstration of antibody in cells and parts of cells is described. it consists of carrying out a two stage immunological reaction on frozen sections of tissues: (a) allowing reaction between antibody in the tissue and dilute antigen applied in vitro, and (b) the detection of those areas where this antigen has been specifically absorbed by means of a precipitin reaction carried out with fluorescein-labelled antibody. examination under the fluorescence microscope reveals the yellow-green fluorescence of fluorescein over those areas where a precipitate has formed. a study of the hyperimmune rabbit on the first few days after the last of a series of intravenous antigen injections reveals that antibody against human gamma-globulin or ovalbumin is present in groups of plasma cells in the red pulp of the spleen, the medullary areas of lymph nodes, the submucosa of the ileum, and the portal connective tissue of the liver. because of extensive non-specific reactions, the bone marrow could not be examined. small amounts of antibody were occasionally visible in cells in the lymphoid follicles of the spleen and lymph nodes, so that a minor contribution by lymphocytes to antibody synthesis cannot be excluded.",0
"the vascular endothelium provides the crucial interface between the blood compartment and tissues, and displays a series of remarkable properties that normally maintain homeostasis. this tightly regulated palette of functions includes control of haemostasis, fibrinolysis, vasomotion, inflammation, oxidative stress, vascular permeability, and structure. while these functions participate in the moment-to-moment regulation of the circulation and coordinate many host defence mechanisms, they can also contribute to disease when their usually homeostatic and defensive functions over-reach and turn against the host. sars-cov-2, the aetiological agent of covid-19, causes the current pandemic. it produces protean manifestations ranging from head to toe, wreaking seemingly indiscriminate havoc on multiple organ systems including the lungs, heart, brain, kidney, and vasculature. this essay explores the hypothesis that covid-19, particularly in the later complicated stages, represents an endothelial disease. cytokines, protein pro-inflammatory mediators, serve as key danger signals that shift endothelial functions from the homeostatic into the defensive mode. the endgame of covid-19 usually involves a cytokine storm, a phlogistic phenomenon fed by well-understood positive feedback loops that govern cytokine production and overwhelm counter-regulatory mechanisms. the concept of covid-19 as an endothelial disease provides a unifying pathophysiological picture of this raging infection, and also provides a framework for a rational treatment strategy at a time when we possess an indeed modest evidence base to guide our therapeutic attempts to confront this novel pandemic.",0
"class i-restricted presentation is usually associated with cytoplasmic degradation of cellular proteins and is often considered inaccessible to exogenous antigens. nonetheless, certain exogenous elements can gain entry into this so-called endogenous pathway by a mechanism termed cross-presentation. this is known to be effective for class i-restricted cytotoxic t lymphocyte (ctl) cross-priming directed against a variety of exogenous tumor, viral, and minor transplantation antigens. the related effect of cross-tolerance can also effectively eliminate responses to selected self components. in both cases, this presentation appears to require the active involvement of a bone marrow-derived antigen presenting cell (apc). here, we show that ctl induction by cross-priming with cell-associated ovalbumin requires the active involvement of cd4+ helper t cells. importantly, this cd4+ population is only effective when both the helper and ctl determinants are recognized on the same apc. moreover, we would argue that the cognitive nature of this event suggests that the cd4+ t cell actively modifies the apc, converting it into an effective stimulator for the successful priming of the ctl precursor.",0
"global declines in insects have sparked wide interest among scientists, politicians, and the general public. loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. here, we used a standardized protocol to measure total insect biomass using malaise traps, deployed over 27 years in 63 nature protection areas in germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. our analysis estimates a seasonal decline of 76%, and mid-summer decline of 82% in flying insect biomass over the 27 years of study. we show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. this yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the european landscape.",0
"background anti-pd1/pd-l1 directed immune checkpoint inhibitors (ici) are widely used to treat patients with advanced non-small-cell lung cancer (nsclc). the activity of ici across nsclc harboring oncogenic alterations is poorly characterized. the aim of our study was to address the efficacy of ici in the context of oncogenic addiction. patients and methods we conducted a retrospective study for patients receiving ici monotherapy for advanced nsclc with at least one oncogenic driver alteration. anonymized data were evaluated for clinicopathologic characteristics and outcomes for ici therapy: best response (recist 1.1), progression-free survival (pfs), and overall survival (os) from ici initiation. the primary end point was pfs under ici. secondary end points were best response (recist 1.1) and os from ici initiation. results we studied 551 patients treated in 24 centers from 10 countries. the molecular alterations involved kras (n = 271), egfr (n = 125), braf (n = 43), met (n = 36), her2 (n = 29), alk (n = 23), ret (n = 16), ros1 (n = 7), and multiple drivers (n = 1). median age was 60 years, gender ratio was 1 : 1, never/former/current smokers were 28%/51%/21%, respectively, and the majority of tumors were adenocarcinoma. the objective response rate by driver alteration was: kras = 26%, braf = 24%, ros1 = 17%, met = 16%, egfr = 12%, her2 = 7%, ret = 6%, and alk = 0%. in the entire cohort, median pfs was 2.8 months, os 13.3 months, and the best response rate 19%. in a subgroup analysis, median pfs (in months) was 2.1 for egfr, 3.2 for kras, 2.5 for alk, 3.1 for braf, 2.5 for her2, 2.1 for ret, and 3.4 for met. in certain subgroups, pfs was positively associated with pd-l1 expression (kras, egfr) and with smoking status (braf, her2). conclusions : ici induced regression in some tumors with actionable driver alterations, but clinical activity was lower compared with the kras group and the lack of response in the alk group was notable. patients with actionable tumor alterations should receive targeted therapies and chemotherapy before considering immunotherapy as a single agent.",0
"background there is convincing preclinical evidence that early decompression in the setting of spinal cord injury (sci) improves neurologic outcomes. however, the effect of early surgical decompression in patients with acute sci remains uncertain. our objective was to evaluate the relative effectiveness of early ( methods we performed a multicenter, international, prospective cohort study (surgical timing in acute spinal cord injury study: stascis) in adults aged 16-80 with cervical sci. enrolment occurred between 2002 and 2009 at 6 north american centers. the primary outcome was ordinal change in asia impairment scale (ais) grade at 6 months follow-up. secondary outcomes included assessments of complications rates and mortality. findings a total of 313 patients with acute cervical sci were enrolled. of these, 182 underwent early surgery, at a mean of 14.2(± 5.4) hours, with the remaining 131 having late surgery, at a mean of 48.3(± 29.3) hours. of the 222 patients with follow-up available at 6 months post injury, 19.8% of patients undergoing early surgery showed a ≥ 2 grade improvement in ais compared to 8.8% in the late decompression group (or = 2.57, 95% ci:1.11,5.97). in the multivariate analysis, adjusted for preoperative neurological status and steroid administration, the odds of at least a 2 grade ais improvement were 2.8 times higher amongst those who underwent early surgery as compared to those who underwent late surgery (or = 2.83, 95% ci:1.10,7.28). during the 30 day post injury period, there was 1 mortality in both of the surgical groups. complications occurred in 24.2% of early surgery patients and 30.5% of late surgery patients (p = 0.21). conclusion decompression prior to 24 hours after sci can be performed safely and is associated with improved neurologic outcome, defined as at least a 2 grade ais improvement at 6 months follow-up.",0
"background mammographically dense breast tissue is one of the greatest risk factors for developing breast carcinoma. despite the strong clinical correlation, breast density has not been causally linked to tumorigenesis, largely because no animal model has existed for studying breast tissue density. importantly, regions of high breast density are associated with increased stromal collagen. thus, the influence of the extracellular matrix on breast carcinoma development and the underlying molecular mechanisms are not understood. methods to study the effects of collagen density on mammary tumor formation and progression, we utilized a bi-transgenic tumor model with increased stromal collagen in mouse mammary tissue. imaging of the tumors and tumor-stromal interface in live tumor tissue was performed with multiphoton laser-scanning microscopy to generate multiphoton excitation and spectrally resolved fluorescent lifetimes of endogenous fluorophores. second harmonic generation was utilized to image stromal collagen. results herein we demonstrate that increased stromal collagen in mouse mammary tissue significantly increases tumor formation approximately three-fold (p conclusion this study provides the first data causally linking increased stromal collagen to mammary tumor formation and metastasis, and demonstrates that fundamental differences arise and persist in epithelial tumor cells that progressed within collagen-dense microenvironments. furthermore, the imaging techniques and signature identified in this work may provide useful diagnostic tools to rapidly assess fresh tissue biopsies.",0
"the perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the international committee on taxonomy of viruses (ictv). there are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. here we present sequence demarcation tool (sdt), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. sdt can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ictv approved taxonomic demarcation criteria. besides a graphical interface version of the program for windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).",0
"aims/hypothesis coronavirus disease-2019 (covid-19) is a life-threatening infection caused by the severe acute respiratory syndrome coronavirus-2 (sars-cov-2) virus. diabetes has rapidly emerged as a major comorbidity for covid-19 severity. however, the phenotypic characteristics of diabetes in covid-19 patients are unknown. methods we conducted a nationwide multicentre observational study in people with diabetes hospitalised for covid-19 in 53 french centres in the period 10-31 march 2020. the primary outcome combined tracheal intubation for mechanical ventilation and/or death within 7 days of admission. age- and sex-adjusted multivariable logistic regressions were performed to assess the prognostic value of clinical and biological features with the endpoint. ors are reported for a 1 sd increase after standardisation. results the current analysis focused on 1317 participants: 64.9% men, mean age 69.8 ± 13.0 years, median bmi 28.4 (25th-75th percentile: 25.0-32.7) kg/m 2 ; with a predominance of type 2 diabetes (88.5%). microvascular and macrovascular diabetic complications were found in 46.8% and 40.8% of cases, respectively. the primary outcome was encountered in 29.0% (95% ci 26.6, 31.5) of participants, while 10.6% (9.0, 12.4) died and 18.0% (16.0, 20.2) were discharged on day 7. in univariate analysis, characteristics prior to admission significantly associated with the primary outcome were sex, bmi and previous treatment with renin-angiotensin-aldosterone system (raas) blockers, but not age, type of diabetes, hba 1c , diabetic complications or glucose-lowering therapies. in multivariable analyses with covariates prior to admission, only bmi remained positively associated with the primary outcome (or 1.28 ). on admission, dyspnoea (or 2.10 ), as well as lymphocyte count (or 0.67 ), c-reactive protein (or 1.93 ) and ast (or 2.23 ) levels were independent predictors of the primary outcome. finally, age (or 2.48 ), treated obstructive sleep apnoea (or 2.80 ), and microvascular (or 2.14 ) and macrovascular complications (or 2.54 ) were independently associated with the risk of death on day 7. conclusions/interpretations in people with diabetes hospitalised for covid-19, bmi, but not long-term glucose control, was positively and independently associated with tracheal intubation and/or death within 7 days. trial registration clinicaltrials.gov nct04324736.",0
"unlabelled sambamba is a high-performance robust tool and library for working with sam, bam and cram sequence alignment files; the most common file formats for aligned next generation sequencing data. sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability. availability and implementation sambamba is free and open source software, available under a gplv2 license. sambamba can be downloaded and installed from v0.5.0 was released with doi:10.5281/zenodo.13200.",0
"a key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. for model systems such as drosophila and c. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. for this purpose, we designed a software application, trakem2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. we address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. the output is a neural circuit of 3d arbors and synapses, encoded in neuroml and other formats, ready for analysis.",0
"many children younger than 5 years in developing countries are exposed to multiple risks, including poverty, malnutrition, poor health, and unstimulating home environments, which detrimentally affect their cognitive, motor, and social-emotional development. there are few national statistics on the development of young children in developing countries. we therefore identified two factors with available worldwide data--the prevalence of early childhood stunting and the number of people living in absolute poverty--to use as indicators of poor development. we show that both indicators are closely associated with poor cognitive and educational performance in children and use them to estimate that over 200 million children under 5 years are not fulfilling their developmental potential. most of these children live in south asia and sub-saharan africa. these disadvantaged children are likely to do poorly in school and subsequently have low incomes, high fertility, and provide poor care for their children, thus contributing to the intergenerational transmission of poverty.",0
"profile hidden markov models (profile hmms) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. however, practical use of profile hmm methods has been hindered by the computational expense of existing software implementations. here i describe an acceleration heuristic for profile hmms, the ""multiple segment viterbi"" (msv) algorithm. the msv algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast smith/waterman alignment. msv scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an msv score and thus facilitating its use as a heuristic filter. i also describe a 20-fold acceleration of the standard profile hmm forward/backward algorithms using a method i call ""sparse rescaling"". these methods are assembled in a pipeline in which high-scoring msv hits are passed on for reanalysis with the full hmm forward/backward algorithm. this accelerated pipeline is implemented in the freely available hmmer3 software package. performance benchmarks show that the use of the heuristic msv filter sacrifices negligible sensitivity compared to unaccelerated profile hmm searches. hmmer3 is substantially more sensitive and 100- to 1000-fold faster than hmmer2. hmmer3 is now about as fast as blast for protein searches.",0
"although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (gwa) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. they are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. here we demonstrate the power of this approach by carrying out a gwa study of 107 phenotypes in arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. our results are dramatically different from those of human gwa studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. however, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. our study demonstrates the feasibility of gwa studies in a. thaliana and suggests that the approach will be appropriate for many other organisms.",0
"objective to assess post-discharge persistent symptoms and health-related quality of life (hrqol) of patients hospitalized in a covid-19 ward unit more than 100 days after their admission. methods all eligible patients were contacted by phone by trained physicians and were asked to answer to a dedicated questionnaire. patients managed in hospital ward without needing intensive care were compared with those who were transferred in intensive care units (icu). results we included 120 patients after a mean (±sd) of 110.9 (±11.1) days following admission. the most frequently reported persistent symptoms were fatigue (55%), dyspnoea (42%), loss of memory (34%), concentration and sleep disorders (28% and 30.8%, respectively). comparisons between ward- and icu patients led to no statistically significant differences regarding those symptoms. in both group, eq-5d (mobility, self-care, pain, anxiety or depression, usual activity) was altered with a slight difference in pain in the icu group. conclusion most patients requiring hospitalization for covid-19 still have persistent symptoms. while there were few differences between hrqol between ward and icu patients, our findings must be confirmed in larger cohorts, including more severe patients.",0
"the innate immune system detects infection by using germline-encoded receptors that are specific for conserved microbial molecules. the recognition of microbial ligands leads to the production of cytokines, such as type i interferons (ifns), that are essential for successful pathogen elimination. cytosolic detection of pathogen-derived dna is one major mechanism of inducing ifn production, and this process requires signalling through tank binding kinase 1 (tbk1) and its downstream transcription factor, ifn-regulatory factor 3 (irf3). in addition, a transmembrane protein called sting (stimulator of ifn genes; also known as mita, eris, mpys and tmem173) functions as an essential signalling adaptor, linking the cytosolic detection of dna to the tbk1-irf3 signalling axis. recently, unique nucleic acids called cyclic dinucleotides, which function as conserved signalling molecules in bacteria, have also been shown to induce a sting-dependent type i ifn response. however, a mammalian sensor of cyclic dinucleotides has not been identified. here we report evidence that sting itself is an innate immune sensor of cyclic dinucleotides. we demonstrate that sting binds directly to radiolabelled cyclic diguanylate monophosphate (c-di-gmp), and we show that unlabelled cyclic dinucleotides, but not other nucleotides or nucleic acids, compete with c-di-gmp for binding to sting. furthermore, we identify mutations in sting that selectively affect the response to cyclic dinucleotides without affecting the response to dna. thus, sting seems to function as a direct sensor of cyclic dinucleotides, in addition to its established role as a signalling adaptor in the ifn response to cytosolic dna. cyclic dinucleotides have shown promise as novel vaccine adjuvants and immunotherapeutics, and our results provide insight into the mechanism by which cyclic dinucleotides are sensed by the innate immune system.",0
"objectives the phase iii radiate study examined the efficacy and safety of tocilizumab, an anti-il-6 receptor monoclonal antibody in patients with rheumatoid arthritis (ra) refractory to tumour necrosis factor (tnf) antagonist therapy. methods 499 patients with inadequate response to one or more tnf antagonists were randomly assigned to receive 8 mg/kg or 4 mg/kg tocilizumab or placebo (control) intravenously every 4 weeks with stable methotrexate for 24 weeks. acr20 responses, secondary efficacy and safety endpoints were assessed. results acr20 was achieved at 24 weeks by 50.0%, 30.4% and 10.1% of patients in the 8 mg/kg, 4 mg/kg and control groups, respectively (less than p conclusion tocilizumab plus methotrexate is effective in achieving rapid and sustained improvements in signs and symptoms of ra in patients with inadequate response to tnf antagonists and has a manageable safety profile. trial registration number nct00106522.",0
"asian rice, oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. here we show the results of a genome-wide association study based on genotyping 44,100 snp variants across 413 diverse accessions of o. sativa collected from 82 countries that were systematically phenotyped for 34 traits. using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. this work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.",0
"summary here we describe nanopack, a set of tools developed for visualization and processing of long-read sequencing data from oxford nanopore technologies and pacific biosciences. availability and implementation the nanopack tools are written in python3 and released under the gnu gpl3.0 license. the source code can be found at together with links to separate scripts and their documentation. the scripts are compatible with linux, mac os and the ms windows 10 subsystem for linux and are available as a graphical user interface, a web service at and command line tools. supplementary information supplementary data are available at bioinformatics online.",0
"people with covid-19 might have sustained postinfection sequelae. known by a variety of names, including long covid or long-haul covid, and listed in the icd-10 classification as post-covid-19 condition since september, 2020, this occurrence is variable in its expression and its impact. the absence of a globally standardised and agreed-upon definition hampers progress in characterisation of its epidemiology and the development of candidate treatments. in a who-led delphi process, we engaged with an international panel of 265 patients, clinicians, researchers, and who staff to develop a consensus definition for this condition. 14 domains and 45 items were evaluated in two rounds of the delphi process to create a final consensus definition for adults: post-covid-19 condition occurs in individuals with a history of probable or confirmed sars-cov-2 infection, usually 3 months from the onset, with symptoms that last for at least 2 months and cannot be explained by an alternative diagnosis. common symptoms include, but are not limited to, fatigue, shortness of breath, and cognitive dysfunction, and generally have an impact on everyday functioning. symptoms might be new onset following initial recovery from an acute covid-19 episode or persist from the initial illness. symptoms might also fluctuate or relapse over time. a separate definition might be applicable for children. although the consensus definition is likely to change as knowledge increases, this common framework provides a foundation for ongoing and future studies of epidemiology, risk factors, clinical characteristics, and therapy.",0
"we report on solid-state mesoscopic heterojunction solar cells employing nanoparticles (nps) of methyl ammonium lead iodide (ch(3)nh(3))pbi(3) as light harvesters. the perovskite nps were produced by reaction of methylammonium iodide with pbi(2) and deposited onto a submicron-thick mesoscopic tio(2) film, whose pores were infiltrated with the hole-conductor spiro-meotad. illumination with standard am-1.5 sunlight generated large photocurrents (j(sc)) exceeding 17 ma/cm(2), an open circuit photovoltage (v(oc)) of 0.888 v and a fill factor (ff) of 0.62 yielding a power conversion efficiency (pce) of 9.7%, the highest reported to date for such cells. femto second laser studies combined with photo-induced absorption measurements showed charge separation to proceed via hole injection from the excited (ch(3)nh(3))pbi(3) nps into the spiro-meotad followed by electron transfer to the mesoscopic tio(2) film. the use of a solid hole conductor dramatically improved the device stability compared to (ch(3)nh(3))pbi(3) -sensitized liquid junction cells.",0
"background measurement of changes in health across locations is useful to compare and contrast changing epidemiological patterns against health system performance and identify specific needs for resource allocation in research, policy development, and programme decision making. using the global burden of diseases, injuries, and risk factors study 2016, we drew from two widely used summary measures to monitor such changes in population health: disability-adjusted life-years (dalys) and healthy life expectancy (hale). we used these measures to track trends and benchmark progress compared with expected trends on the basis of the socio-demographic index (sdi). methods we used results from the global burden of diseases, injuries, and risk factors study 2016 for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive hale and dalys by sex for 195 countries and territories from 1990 to 2016. we calculated dalys by summing years of life lost and years of life lived with disability for each location, age group, sex, and year. we estimated hale using age-specific death rates and years of life lived with disability per capita. we explored how dalys and hale differed from expected trends when compared with the sdi: the geometric mean of income per person, educational attainment in the population older than age 15 years, and total fertility rate. findings the highest globally observed hale at birth for both women and men was in singapore, at 75·2 years (95% uncertainty interval 71·9-78·6) for females and 72·0 years (68·8-75·1) for males. the lowest for females was in the central african republic (45·6 years ) and for males was in lesotho (41·5 years ). from 1990 to 2016, global hale increased by an average of 6·24 years (5·97-6·48) for both sexes combined. global hale increased by 6·04 years (5·74-6·27) for males and 6·49 years (6·08-6·77) for females, whereas hale at age 65 years increased by 1·78 years (1·61-1·93) for males and 1·96 years (1·69-2·13) for females. total global dalys remained largely unchanged from 1990 to 2016 (-2·3% ), with decreases in communicable, maternal, neonatal, and nutritional (cmnn) disease dalys offset by increased dalys due to non-communicable diseases (ncds). the exemplars, calculated as the five lowest ratios of observed to expected age-standardised daly rates in 2016, were nicaragua, costa rica, the maldives, peru, and israel. the leading three causes of dalys globally were ischaemic heart disease, cerebrovascular disease, and lower respiratory infections, comprising 16·1% of all dalys. total dalys and age-standardised daly rates due to most cmnn causes decreased from 1990 to 2016. conversely, the total daly burden rose for most ncds; however, age-standardised daly rates due to ncds declined globally. interpretation at a global level, dalys and hale continue to show improvements. at the same time, we observe that many populations are facing growing functional health loss. rising sdi was associated with increases in cumulative years of life lived with disability and decreases in cmnn dalys offset by increased ncd dalys. relative compression of morbidity highlights the importance of continued health interventions, which has changed in most locations in pace with the gross domestic product per person, education, and family planning. the analysis of dalys and hale and their relationship to sdi represents a robust framework with which to benchmark location-specific health performance. country-specific drivers of disease burden, particularly for causes with higher-than-expected dalys, should inform health policies, health system improvement initiatives, targeted prevention efforts, and development assistance for health, including financial and research investments for all countries, regardless of their level of sociodemographic development. the presence of countries that substantially outperform others suggests the need for increased scrutiny for proven examples of best practices, which can help to extend gains, whereas the presence of underperforming countries suggests the need for devotion of extra attention to health systems that need more robust support. funding bill & melinda gates foundation.",0
"motivation fast and accurate quality control is essential for studies involving next-generation sequencing data. whilst numerous tools exist to quantify qc metrics, there is no common approach to flexibly integrate these across tools and large sample sets. assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. results we present multiqc, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. multiqc can plot data from many common bioinformatics tools and is built to allow easy extension and customization. availability and implementation multiqc is available with an gnu gplv3 license on github, the python package index and bioconda. documentation and example reports are available at contact phil.ewels@scilifelab.se.",0
"the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) virus is causing a global pandemic, and cases continue to rise. most infected individuals experience mildly symptomatic coronavirus disease 2019 (covid-19), but it is unknown whether this can induce persistent immune memory that could contribute to immunity. we performed a longitudinal assessment of individuals recovered from mild covid-19 to determine whether they develop and sustain multifaceted sars-cov-2-specific immunological memory. recovered individuals developed sars-cov-2-specific immunoglobulin (igg) antibodies, neutralizing plasma, and memory b and memory t cells that persisted for at least 3 months. our data further reveal that sars-cov-2-specific igg memory b cells increased over time. additionally, sars-cov-2-specific memory lymphocytes exhibited characteristics associated with potent antiviral function: memory t cells secreted cytokines and expanded upon antigen re-encounter, whereas memory b cells expressed receptors capable of neutralizing virus when expressed as monoclonal antibodies. therefore, mild covid-19 elicits memory lymphocytes that persist and display functional hallmarks of antiviral immunity.",0
"innate immune cells must be able to distinguish between direct binding to microbes and detection of components shed from the surface of microbes located at a distance. dectin-1 (also known as clec7a) is a pattern-recognition receptor expressed by myeloid phagocytes (macrophages, dendritic cells and neutrophils) that detects β-glucans in fungal cell walls and triggers direct cellular antimicrobial activity, including phagocytosis and production of reactive oxygen species (ros). in contrast to inflammatory responses stimulated upon detection of soluble ligands by other pattern-recognition receptors, such as toll-like receptors (tlrs), these responses are only useful when a cell comes into direct contact with a microbe and must not be spuriously activated by soluble stimuli. in this study we show that, despite its ability to bind both soluble and particulate β-glucan polymers, dectin-1 signalling is only activated by particulate β-glucans, which cluster the receptor in synapse-like structures from which regulatory tyrosine phosphatases cd45 and cd148 (also known as ptprc and ptprj, respectively) are excluded (supplementary fig. 1). the 'phagocytic synapse' now provides a model mechanism by which innate immune receptors can distinguish direct microbial contact from detection of microbes at a distance, thereby initiating direct cellular antimicrobial responses only when they are required.",0
"background bmi is known to be strongly associated with all-cause mortality, but few studies have been large enough to reliably examine associations between bmi and a comprehensive range of cause-specific mortality outcomes. methods in this population-based cohort study, we used uk primary care data from the clinical practice research datalink (cprd) linked to national mortality registration data and fitted adjusted cox regression models to examine associations between bmi and all-cause mortality, and between bmi and a comprehensive range of cause-specific mortality outcomes (recorded by international classification of diseases, 10th revision codes). we included all individuals with bmi data collected at age 16 years and older and with subsequent follow-up time available. follow-up began at whichever was the latest of: start of cprd research-standard follow up, the 5-year anniversary of the first bmi record, or on jan 1, 1998 (start date for death registration data); follow-up ended at death or on march 8, 2016. fully adjusted models were stratified by sex and adjusted for baseline age, smoking, alcohol use, diabetes, index of multiple deprivation, and calendar period. models were fitted in both never-smokers only and the full study population. we also did an extensive range of sensitivity analyses. the expected age of death for men and women aged 40 years at baseline, by bmi category, was estimated from a poisson model including bmi, age, and sex. findings 3 632 674 people were included in the full study population; the following results are from the analysis of never-smokers, which comprised 1 969 648 people and 188 057 deaths. bmi had a j-shaped association with overall mortality; the estimated hazard ratio per 5 kg/m 2 increase in bmi was 0·81 (95% ci 0·80-0·82) below 25 kg/m 2 and 1·21 (1·20-1·22) above this point. bmi was associated with all cause of death categories except for transport-related accidents, but the shape of the association varied. most causes, including cancer, cardiovascular diseases, and respiratory diseases, had a j-shaped association with bmi, with lowest risk occurring in the range 21-25 kg/m 2 . for mental and behavioural, neurological, and accidental (non-transport-related) causes, bmi was inversely associated with mortality up to 24-27 kg/m 2 , with little association at higher bmis; for deaths from self-harm or interpersonal violence, an inverse linear association was observed. associations between bmi and mortality were stronger at younger ages than at older ages, and the bmi associated with lowest mortality risk was higher in older individuals than in younger individuals. compared with individuals of healthy weight (bmi 18·5-24·9 kg/m 2 ), life expectancy from age 40 years was 4·2 years shorter in obese (bmi ≥30·0 kg/m 2 ) men and 3·5 years shorter in obese women, and 4·3 years shorter in underweight (bmi 2 ) men and 4·5 years shorter in underweight women. when smokers were included in analyses, results for most causes of death were broadly similar, although marginally stronger associations were seen among people with lower bmi, suggesting slight residual confounding by smoking. interpretation bmi had j-shaped associations with overall mortality and most specific causes of death; for mental and behavioural, neurological, and external causes, lower bmi was associated with increased mortality risk. funding wellcome trust.",0
"mitochondria are signaling organelles that regulate a wide variety of cellular functions and can dictate cell fate. multiple mechanisms contribute to communicate mitochondrial fitness to the rest of the cell. recent evidence confers a new role for tca cycle intermediates, generally thought to be important for biosynthetic purposes, as signaling molecules with functions controlling chromatin modifications, dna methylation, the hypoxic response, and immunity. this review summarizes the mechanisms by which the abundance of different tca cycle metabolites controls cellular function and fate in different contexts. we will focus on how these metabolites mediated signaling can affect physiology and disease.",0
"previously we reported that fine particle mass (particulate matter 2.5 microm; pm(2.5)), which is primarily from combustion sources, but not coarse particle mass, which is primarily from crustal sources, was associated with daily mortality in six eastern u.s. cities (1). in this study, we used the elemental composition of size-fractionated particles to identify several distinct source-related fractions of fine particles and examined the association of these fractions with daily mortality in each of the six cities. using specific rotation factor analysis for each city, we identified a silicon factor classified as soil and crustal material, a lead factor classified as motor vehicle exhaust, a selenium factor representing coal combustion, and up to two additional factors. we extracted daily counts of deaths from national center for health statistics records and estimated city-specific associations of mortality with each source factor by poisson regression, adjusting for time trends, weather, and the other source factors. combined effect estimates were calculated as the inverse variance weighted mean of the city-specific estimates. in the combined analysis, a 10 microg/m(3) increase in pm(2.5) from mobile sources accounted for a 3.4% increase in daily mortality , and the equivalent increase in fine particles from coal combustion sources accounted for a 1.1% increase [ci, 0.3-2.0%). pm(2.5) crustal particles were not associated with daily mortality. these results indicate that combustion particles in the fine fraction from mobile and coal combustion sources, but not fine crustal particles, are associated with increased mortality.",0
"transcatheter arterial chemoembolization (tace) offers a survival benefit to patients with intermediate hepatocellular carcinoma (hcc). a widely accepted tace regimen includes administration of doxorubicin-oil emulsion followed by gelatine sponge-conventional tace. recently, a drug-eluting bead (dc bead) has been developed to enhance tumor drug delivery and reduce systemic availability. this randomized trial compares conventional tace (ctace) with tace with dc bead for the treatment of cirrhotic patients with hcc. two hundred twelve patients with child-pugh a/b cirrhosis and large and/or multinodular, unresectable, n0, m0 hccs were randomized to receive tace with dc bead loaded with doxorubicin or ctace with doxorubicin. randomization was stratified according to child-pugh status (a/b), performance status (ecog 0/1), bilobar disease (yes/no), and prior curative treatment (yes/no). the primary endpoint was tumor response (easl) at 6 months following independent, blinded review of mri studies. the drug-eluting bead group showed higher rates of complete response, objective response, and disease control compared with the ctace group (27% vs. 22%, 52% vs. 44%, and 63% vs. 52%, respectively). the hypothesis of superiority was not met (one-sided p = 0.11). however, patients with child-pugh b, ecog 1, bilobar disease, and recurrent disease showed a significant increase in objective response (p = 0.038) compared to ctace. dc bead was associated with improved tolerability, with a significant reduction in serious liver toxicity (p < 0.001) and a significantly lower rate of doxorubicin-related side effects (p = 0.0001). tace with dc bead and doxorubicin is safe and effective in the treatment of hcc and offers a benefit to patients with more advanced disease.",0
"significance: chronic wounds include, but are not limited, to diabetic foot ulcers, venous leg ulcers, and pressure ulcers. they are a challenge to wound care professionals and consume a great deal of healthcare resources around the globe. this review discusses the pathophysiology of complex chronic wounds and the means and modalities currently available to achieve healing in such patients. recent advances: although often difficult to treat, an understanding of the underlying pathophysiology and specific attention toward managing these perturbations can often lead to successful healing. critical issues: overcoming the factors that contribute to delayed healing are key components of a comprehensive approach to wound care and present the primary challenges to the treatment of chronic wounds. when wounds fail to achieve sufficient healing after 4 weeks of standard care, reassessment of underlying pathology and consideration of the need for advanced therapeutic agents should be undertaken. however, selection of an appropriate therapy is often not evidence based. future directions: basic tenets of care need to be routinely followed, and a systematic evaluation of patients and their wounds will also facilitate appropriate care. underlying pathologies, which result in the failure of these wounds to heal, differ among various types of chronic wounds. a better understanding of the differences between various types of chronic wounds at the molecular and cellular levels should improve our treatment approaches, leading to better healing rates, and facilitate the development of new more effective therapies. more evidence for the efficacy of current and future advanced wound therapies is required for their appropriate use.",0
"multifactorial mechanisms underlying late-onset alzheimer's disease (load) are poorly characterized from an integrative perspective. here spatiotemporal alterations in brain amyloid-β deposition, metabolism, vascular, functional activity at rest, structural properties, cognitive integrity and peripheral proteins levels are characterized in relation to load progression. we analyse over 7,700 brain images and tens of plasma and cerebrospinal fluid biomarkers from the alzheimer's disease neuroimaging initiative (adni). through a multifactorial data-driven analysis, we obtain dynamic load-abnormality indices for all biomarkers, and a tentative temporal ordering of disease progression. imaging results suggest that intra-brain vascular dysregulation is an early pathological event during disease development. cognitive decline is noticeable from initial load stages, suggesting early memory deficit associated with the primary disease factors. high abnormality levels are also observed for specific proteins associated with the vascular system's integrity. although still subjected to the sensitivity of the algorithms and biomarkers employed, our results might contribute to the development of preventive therapeutic interventions.",0
"immunotherapy has revolutionized cancer treatment, but efficacy remains limited in most clinical settings. cancer is a systemic disease that induces many functional and compositional changes to the immune system as a whole. immunity is regulated by interactions of diverse cell lineages across tissues. therefore, an improved understanding of tumour immunology must assess the systemic immune landscape beyond the tumour microenvironment (tme). importantly, the peripheral immune system is required to drive effective natural and therapeutically induced antitumour immune responses. in fact, emerging evidence suggests that immunotherapy drives new immune responses rather than the reinvigoration of pre-existing immune responses. however, new immune responses in individuals burdened with tumours are compromised even beyond the tme. herein, we aim to comprehensively outline the current knowledge of systemic immunity in cancer.",0
"the gtpases rac1, rhoa and cdc42 act together to control cytoskeleton dynamics. recent biosensor studies have shown that all three gtpases are activated at the front of migrating cells, and biochemical evidence suggests that they may regulate one another: cdc42 can activate rac1 (ref. 8), and rac1 and rhoa are mutually inhibitory. however, their spatiotemporal coordination, at the seconds and single-micrometre dimensions typical of individual protrusion events, remains unknown. here we examine gtpase coordination in mouse embryonic fibroblasts both through simultaneous visualization of two gtpase biosensors and using a 'computational multiplexing' approach capable of defining the relationships between multiple protein activities visualized in separate experiments. we found that rhoa is activated at the cell edge synchronous with edge advancement, whereas cdc42 and rac1 are activated 2 micro-m behind the edge with a delay of 40 s. this indicates that rac1 and rhoa operate antagonistically through spatial separation and precise timing, and that rhoa has a role in the initial events of protrusion, whereas rac1 and cdc42 activate pathways implicated in reinforcement and stabilization of newly expanded protrusions.",0
"background in order to more effectively promote fruit and vegetable intake among children and adolescents, insight into determinants of intake is necessary. we conducted a review of the literature for potential determinants of fruit and vegetable intake in children and adolescents. methods papers were identified from medline and psycinfo by using all combinations of the search terms: ""fruit(s) or vegetable(s)"" and ""children or adolescents"". quantitative research examining determinants of fruit and/or vegetable intake among children and adolescents aged 6-18 years were included. the selection and review process was conducted according to a four-step protocol resulting in information on country, population, design, methodology, theoretical basis, instrument used for measuring intake, statistical analysis, included independent variables, and effect sizes. results ninety-eight papers were included. a large number of potential determinants have been studied among children and adolescents. however, for many presumed determinants convincing evidence is lacking, mostly because of paucity of studies. the determinants best supported by evidence are: age, gender, socio-economic position, preferences, parental intake, and home availability/accessibility. girls and younger children tend to have a higher or more frequent intake than boys and older children. socio-economic position, preferences, parental intake, and home availability/accessibility are all consistently positively associated with intake. conclusion the determinants most consistently supported by evidence are gender, age, socio-economic position, preferences, parental intake and home availability/accessibility. there is a need for internationally comparative, longitudinal, theory-based and multi-level studies taking both personal and environmental factors into account. this paper is published as part of the special pro children series in the international journal of behavioral nutrition and physical activity. please see for the relevant editorial.",0
"background hydroxychloroquine has been widely administered to patients with covid-19 without robust evidence supporting its use. methods we examined the association between hydroxychloroquine use and intubation or death at a large medical center in new york city. data were obtained regarding consecutive patients hospitalized with covid-19, excluding those who were intubated, died, or discharged within 24 hours after presentation to the emergency department (study baseline). the primary end point was a composite of intubation or death in a time-to-event analysis. we compared outcomes in patients who received hydroxychloroquine with those in patients who did not, using a multivariable cox model with inverse probability weighting according to the propensity score. results of 1446 consecutive patients, 70 patients were intubated, died, or discharged within 24 hours after presentation and were excluded from the analysis. of the remaining 1376 patients, during a median follow-up of 22.5 days, 811 (58.9%) received hydroxychloroquine (600 mg twice on day 1, then 400 mg daily for a median of 5 days); 45.8% of the patients were treated within 24 hours after presentation to the emergency department, and 85.9% within 48 hours. hydroxychloroquine-treated patients were more severely ill at baseline than those who did not receive hydroxychloroquine (median ratio of partial pressure of arterial oxygen to the fraction of inspired oxygen, 223 vs. 360). overall, 346 patients (25.1%) had a primary end-point event (180 patients were intubated, of whom 66 subsequently died, and 166 died without intubation). in the main analysis, there was no significant association between hydroxychloroquine use and intubation or death (hazard ratio, 1.04, 95% confidence interval, 0.82 to 1.32). results were similar in multiple sensitivity analyses. conclusions in this observational study involving patients with covid-19 who had been admitted to the hospital, hydroxychloroquine administration was not associated with either a greatly lowered or an increased risk of the composite end point of intubation or death. randomized, controlled trials of hydroxychloroquine in patients with covid-19 are needed. (funded by the national institutes of health.).",0
"background qualitative systematic reviews are increasing in popularity in evidence based health care. difficulties have been reported in conducting literature searches of qualitative research using the pico search tool. an alternative search tool, entitled spider, was recently developed for more effective searching of qualitative research, but remained untested beyond its development team. methods in this article we tested the 'spider' search tool in a systematic narrative review of qualitative literature investigating the health care experiences of people with multiple sclerosis. identical search terms were combined into the pico or spider search tool and compared across ovid medline, ovid embase and ebsco cinahl plus databases. in addition, we added to this method by comparing initial spider and pico tools to a modified version of pico with added qualitative search terms (picos). results results showed a greater number of hits from the pico searches, in comparison to the spider searches, with greater sensitivity. spider searches showed greatest specificity for every database. the modified pico demonstrated equal or higher sensitivity than spider searches, and equal or lower specificity than spider searches. the modified pico demonstrated lower sensitivity and greater specificity than pico searches. conclusions the recommendations for practice are therefore to use the pico tool for a fully comprehensive search but the picos tool where time and resources are limited. based on these limited findings the spider tool would not be recommended due to the risk of not identifying relevant papers, but has potential due to its greater specificity.",0
"background there is a growing recognition of the value of synthesising qualitative research in the evidence base in order to facilitate effective and appropriate health care. in response to this, methods for undertaking these syntheses are currently being developed. thematic analysis is a method that is often used to analyse data in primary qualitative research. this paper reports on the use of this type of analysis in systematic reviews to bring together and integrate the findings of multiple qualitative studies. methods we describe thematic synthesis, outline several steps for its conduct and illustrate the process and outcome of this approach using a completed review of health promotion research. thematic synthesis has three stages: the coding of text 'line-by-line'; the development of 'descriptive themes'; and the generation of 'analytical themes'. while the development of descriptive themes remains 'close' to the primary studies, the analytical themes represent a stage of interpretation whereby the reviewers 'go beyond' the primary studies and generate new interpretive constructs, explanations or hypotheses. the use of computer software can facilitate this method of synthesis; detailed guidance is given on how this can be achieved. results we used thematic synthesis to combine the studies of children's views and identified key themes to explore in the intervention studies. most interventions were based in school and often combined learning about health benefits with 'hands-on' experience. the studies of children's views suggested that fruit and vegetables should be treated in different ways, and that messages should not focus on health warnings. interventions that were in line with these suggestions tended to be more effective. thematic synthesis enabled us to stay 'close' to the results of the primary studies, synthesising them in a transparent way, and facilitating the explicit production of new concepts and hypotheses. conclusion we compare thematic synthesis to other methods for the synthesis of qualitative research, discussing issues of context and rigour. thematic synthesis is presented as a tried and tested method that preserves an explicit and transparent link between conclusions and the text of primary studies; as such it preserves principles that have traditionally been important to systematic reviewing.",0
"antimicrobial resistance (amr) has developed as one of the major urgent threats to public health causing serious issues to successful prevention and treatment of persistent diseases. in spite of different actions taken in recent decades to tackle this issue, the trends of global amr demonstrate no signs of slowing down. misusing and overusing different antibacterial agents in the health care setting as well as in the agricultural industry are considered the major reasons behind the emergence of antimicrobial resistance. in addition, the spontaneous evolution, mutation of bacteria, and passing the resistant genes through horizontal gene transfer are significant contributors to antimicrobial resistance. many studies have demonstrated the disastrous financial consequences of amr including extremely high healthcare costs due to an increase in hospital admissions and drug usage. the literature review, which included articles published after the year 2012, was performed using scopus, pubmed and google scholar with the utilization of keyword searches. results indicated that the multifactorial threat of antimicrobial resistance has resulted in different complex issues affecting countries across the globe. these impacts found in the sources are categorized into three different levels: patient, healthcare, and economic. although gaps in knowledge about amr and areas for improvement are obvious, there is not any clearly understood progress to put an end to the persistent trends of antimicrobial resistance.",0
"coronavirus disease 2019 (covid-19) outbreak, first reported in wuhan, china, has rapidly swept around the world just within a month, causing global public health emergency. in diagnosis, chest computed tomography (ct) manifestations can supplement parts of limitations of real-time reverse transcription polymerase chain reaction (rt-pcr) assay. based on a comprehensive literature review and the experience in the frontline, we aim to review the typical and relatively atypical ct manifestations with representative covid-19 cases at our hospital, and hope to strengthen the recognition of these features with radiologists and help them make a quick and accurate diagnosis.key points• ground glass opacities, consolidation, reticular pattern, and crazy paving pattern are typical ct manifestations of covid-19.• emerging atypical ct manifestations, including airway changes, pleural changes, fibrosis, nodules, etc., were demonstrated in covid-19 patients.• ct manifestations may associate with the progression and prognosis of covid-19.",0
"background the introduction of evidence-based programs and practices into healthcare settings has been the subject of an increasing amount of research in recent years. while a number of studies have examined initial implementation efforts, less research has been conducted to determine what happens beyond that point. there is increasing recognition that the extent to which new programs are sustained is influenced by many different factors and that more needs to be known about just what these factors are and how they interact. to understand the current state of the research literature on sustainability, our team took stock of what is currently known in this area and identified areas in which further research would be particularly helpful. this paper reviews the methods that have been used, the types of outcomes that have been measured and reported, findings from studies that reported long-term implementation outcomes, and factors that have been identified as potential influences on the sustained use of new practices, programs, or interventions. we conclude with recommendations and considerations for future research. methods two coders identified 125 studies on sustainability that met eligibility criteria. an initial coding scheme was developed based on constructs identified in previous literature on implementation. additional codes were generated deductively. related constructs among factors were identified by consensus and collapsed under the general categories. studies that described the extent to which programs or innovations were sustained were also categorized and summarized. results although ""sustainability"" was the term most commonly used in the literature to refer to what happened after initial implementation, not all the studies that were reviewed actually presented working definitions of the term. most study designs were retrospective and naturalistic. approximately half of the studies relied on self-reports to assess sustainability or elements that influence sustainability. approximately half employed quantitative methodologies, and the remainder employed qualitative or mixed methodologies. few studies that investigated sustainability outcomes employed rigorous methods of evaluation (e.g., objective evaluation, judgement of implementation quality or fidelity). among those that did, a small number reported full sustainment or high fidelity. very little research has examined the extent, nature, or impact of adaptations to the interventions or programs once implemented. influences on sustainability included organizational context, capacity, processes, and factors related to the new program or practice themselves. conclusions clearer definitions and research that is guided by the conceptual literature on sustainability are critical to the development of the research in the area. further efforts to characterize the phenomenon and the factors that influence it will enhance the quality of future research. careful consideration must also be given to interactions among influences at multiple levels, as well as issues such as fidelity, modification, and changes in implementation over time. while prospective and experimental designs are needed, there is also an important role for qualitative research in efforts to understand the phenomenon, refine hypotheses, and develop strategies to promote sustainment.",0
"genome-wide association studies (gwas) have now identified at least 2,000 common variants that appear associated with common diseases or related traits ( hundreds of which have been convincingly replicated. it is generally thought that the associated markers reflect the effect of a nearby common (minor allele frequency >0.05) causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites. we propose as an alternative explanation that variants much less common than the associated one may create ""synthetic associations"" by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for gwas findings. here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. we show that they are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies. we also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations, in the latter case extending over a 2.5-mb interval encompassing scores of ""blocks"" of associated variants. in conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of gwas signals.",0
"neutrophils are the most abundant leukocytes in the circulation, and have been regarded as first line of defense in the innate arm of the immune system. they capture and destroy invading microorganisms, through phagocytosis and intracellular degradation, release of granules, and formation of neutrophil extracellular traps after detecting pathogens. neutrophils also participate as mediators of inflammation. the classical view for these leukocytes is that neutrophils constitute a homogenous population of terminally differentiated cells with a unique function. however, evidence accumulated in recent years, has revealed that neutrophils present a large phenotypic heterogeneity and functional versatility, which place neutrophils as important modulators of both inflammation and immune responses. indeed, the roles played by neutrophils in homeostatic conditions as well as in pathological inflammation and immune processes are the focus of a renovated interest in neutrophil biology. in this review, i present the concept of neutrophil phenotypic and functional heterogeneity and describe several neutrophil subpopulations reported to date. i also discuss the role these subpopulations seem to play in homeostasis and disease.",0
"amigo is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data. amigo can be used online at the gene ontology (go) website to access the data provided by the go consortium; it can also be downloaded and installed to browse local ontologies and annotations. amigo is free open source software developed and maintained by the go consortium.",0
"heme oxygenase 1 (ho-1) inhibits apoptosis by regulating cellular prooxidant iron. we now show that there is an additional mechanism by which ho-1 inhibits apoptosis, namely by generating the gaseous molecule carbon monoxide (co). overexpression of ho-1, or induction of ho-1 expression by heme, protects endothelial cells (ecs) from apoptosis. when ho-1 enzymatic activity is blocked by tin protoporphyrin (snppix) or the action of co is inhibited by hemoglobin (hb), ho-1 no longer prevents ec apoptosis while these reagents do not affect the antiapoptotic action of bcl-2. exposure of ecs to exogenous co, under inhibition of ho-1 activity by snppix, substitutes ho-1 in preventing ec apoptosis. the mechanism of action of ho-1/co is dependent on the activation of the p38 mitogen-activated protein kinase (mapk) signaling transduction pathway. expression of ho-1 or exposure of ecs to exogenous co enhanced p38 mapk activation by tnf-alpha. specific inhibition of p38 mapk activation by the pyridinyl imidazol sb203580 or through overexpression of a p38 mapk dominant negative mutant abrogated the antiapoptotic effect of ho-1. taken together, these data demonstrate that the antiapoptotic effect of ho-1 in ecs is mediated by co and more specifically via the activation of p38 mapk by co.",0
"solubility, the phenomenon of dissolution of solute in solvent to give a homogenous system, is one of the important parameters to achieve desired concentration of drug in systemic circulation for desired (anticipated) pharmacological response. low aqueous solubility is the major problem encountered with formulation development of new chemical entities as well as for the generic development. more than 40% nces (new chemical entities) developed in pharmaceutical industry are practically insoluble in water. solubility is a major challenge for formulation scientist. any drug to be absorbed must be present in the form of solution at the site of absorption. various techniques are used for the enhancement of the solubility of poorly soluble drugs which include physical and chemical modifications of drug and other methods like particle size reduction, crystal engineering, salt formation, solid dispersion, use of surfactant, complexation, and so forth. selection of solubility improving method depends on drug property, site of absorption, and required dosage form characteristics.",0
"background skilled attendance at childbirth is crucial for decreasing maternal and neonatal mortality, yet many women in low- and middle-income countries deliver outside of health facilities, without skilled help. the main conceptual framework in this field implicitly looks at home births with complications. we expand this to include ""preventive"" facility delivery for uncomplicated childbirth, and review the kinds of determinants studied in the literature, their hypothesized mechanisms of action and the typical findings, as well as methodological difficulties encountered. methods we searched pubmed and ovid databases for reviews and ascertained relevant articles from these and other sources. twenty determinants identified were grouped under four themes: (1) sociocultural factors, (2) perceived benefit/need of skilled attendance, (3) economic accessibility and (4) physical accessibility. results there is ample evidence that higher maternal age, education and household wealth and lower parity increase use, as does urban residence. facility use in the previous delivery and antenatal care use are also highly predictive of health facility use for the index delivery, though this may be due to confounding by service availability and other factors. obstetric complications also increase use but are rarely studied. quality of care is judged to be essential in qualitative studies but is not easily measured in surveys, or without linking facility records with women. distance to health facilities decreases use, but is also difficult to determine. challenges in comparing results between studies include differences in methods, context-specificity and the substantial overlap between complex variables. conclusion studies of the determinants of skilled attendance concentrate on sociocultural and economic accessibility variables and neglect variables of perceived benefit/need and physical accessibility. to draw valid conclusions, it is important to consider as many influential factors as possible in any analysis of delivery service use. the increasing availability of georeferenced data provides the opportunity to link health facility data with large-scale household data, enabling researchers to explore the influences of distance and service quality.",0
"the carbohydrate-active enzyme (cazy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. as of september 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. these families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. protein biochemical information is continuously curated based on the available literature and structural information. over 6400 proteins have assigned ec numbers and 700 proteins have a pdb structure. the classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. this resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. more recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. the cazy resource resides at url:",0
"summary genalex: genetic analysis in excel is a cross-platform package for population genetic analyses that runs within microsoft excel. genalex offers analysis of diploid codominant, haploid and binary genetic loci and dna sequences. both frequency-based (f-statistics, heterozygosity, hwe, population assignment, relatedness) and distance-based (amova, pcoa, mantel tests, multivariate spatial autocorrelation) analyses are provided. new features include calculation of new estimators of population structure: g'(st), g''(st), jost's d(est) and f'(st) through amova, shannon information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. export to more than 30 other data formats is provided. teaching tutorials and expanded step-by-step output options are included. the comprehensive guide has been fully revised. availability and implementation genalex is written in vba and provided as a microsoft excel add-in (compatible with excel 2003, 2007, 2010 on pc; excel 2004, 2011 on macintosh). genalex, and supporting documentation and tutorials are freely available at: contact rod.peakall@anu.edu.au.",0
"background overweight and obese persons are at risk of a number of medical conditions which can lead to further morbidity and mortality. the primary objective of this study is to provide an estimate of the incidence of each co-morbidity related to obesity and overweight using a meta-analysis. methods a literature search for the twenty co-morbidities identified in a preliminary search was conducted in medline and embase (jan 2007). studies meeting the inclusion criteria (prospective cohort studies of sufficient size reporting risk estimate based on the incidence of disease) were extracted. study-specific unadjusted relative risks (rrs) on the log scale comparing overweight with normal and obese with normal were weighted by the inverse of their corresponding variances to obtain a pooled rr with 95% confidence intervals (ci). results a total of 89 relevant studies were identified. the review found evidence for 18 co-morbidities which met the inclusion criteria. the meta-analysis determined statistically significant associations for overweight with the incidence of type ii diabetes, all cancers except esophageal (female), pancreatic and prostate cancer, all cardiovascular diseases (except congestive heart failure), asthma, gallbladder disease, osteoarthritis and chronic back pain. we noted the strongest association between overweight defined by body mass index (bmi) and the incidence of type ii diabetes in females (rr = 3.92 (95% ci: 3.10-4.97)). statistically significant associations with obesity were found with the incidence of type ii diabetes, all cancers except esophageal and prostate cancer, all cardiovascular diseases, asthma, gallbladder disease, osteoarthritis and chronic back pain. obesity defined by bmi was also most strongly associated with the incidence of type ii diabetes in females (12.41 (9.03-17.06)). conclusion both overweight and obesity are associated with the incidence of multiple co-morbidities including type ii diabetes, cancer and cardiovascular diseases. maintenance of a healthy weight could be important in the prevention of the large disease burden in the future. further studies are needed to explore the biological mechanisms that link overweight and obesity with these co-morbidities.",0
"tuberculosis caused 20% of all human deaths in the western world between the seventeenth and nineteenth centuries and remains a cause of high mortality in developing countries. in analogy to other crowd diseases, the origin of human tuberculosis has been associated with the neolithic demographic transition, but recent studies point to a much earlier origin. we analyzed the whole genomes of 259 m. tuberculosis complex (mtbc) strains and used this data set to characterize global diversity and to reconstruct the evolutionary history of this pathogen. coalescent analyses indicate that mtbc emerged about 70,000 years ago, accompanied migrations of anatomically modern humans out of africa and expanded as a consequence of increases in human population density during the neolithic period. this long coevolutionary history is consistent with mtbc displaying characteristics indicative of adaptation to both low and high host densities.",0
"background in systematic reviews and meta-analysis, researchers often pool the results of the sample mean and standard deviation from a set of similar clinical trials. a number of the trials, however, reported the study using the median, the minimum and maximum values, and/or the first and third quartiles. hence, in order to combine results, one may have to estimate the sample mean and standard deviation for such trials. methods in this paper, we propose to improve the existing literature in several directions. first, we show that the sample standard deviation estimation in hozo et al.'s method (bmc med res methodol 5:13, 2005) has some serious limitations and is always less satisfactory in practice. inspired by this, we propose a new estimation method by incorporating the sample size. second, we systematically study the sample mean and standard deviation estimation problem under several other interesting settings where the interquartile range is also available for the trials. results we demonstrate the performance of the proposed methods through simulation studies for the three frequently encountered scenarios, respectively. for the first two scenarios, our method greatly improves existing methods and provides a nearly unbiased estimate of the true sample standard deviation for normal data and a slightly biased estimate for skewed data. for the third scenario, our method still performs very well for both normal data and skewed data. furthermore, we compare the estimators of the sample mean and standard deviation under all three scenarios and present some suggestions on which scenario is preferred in real-world applications. conclusions in this paper, we discuss different approximation methods in the estimation of the sample mean and standard deviation and propose some new estimation methods to improve the existing literature. we conclude our work with a summary table (an excel spread sheet including all formulas) that serves as a comprehensive guidance for performing meta-analysis in different situations.",0
"a subset of cd4+cd11c-cd3- blood cells was recently shown to develop into dendritic cells when cultured with monocyte conditioned medium. here, we demonstrate that cd4+ cd11c-cd3- cells, isolated from tonsils, correspond to the so-called plasmacytoid t cells, an obscure cell type that has long been observed by pathologists within secondary lymphoid tissues. they express cd45ra, but not markers specific for known lymphoid- or myeloid-derived cell types. they undergo rapid apoptosis in culture, unless rescued by il-3. further addition of cd40-ligand results in their differentiation into dendritic cells that express low levels of myeloid antigens cd13 and cd33.",0
"background most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. results treefinder is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. in this paper the main features of treefinder (version of april 2004) are described. treefinder is written in ansi c and java and implements powerful statistical approaches for inferring gene tree and related analyzes. in addition, it provides a user-friendly graphical interface and a phylogenetic programming language. conclusions treefinder is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.",0
"introduction biomarkers can be useful for identifying or ruling out sepsis, identifying patients who may benefit from specific therapies or assessing the response to therapy. methods we used an electronic search of the pubmed database using the key words ""sepsis"" and ""biomarker"" to identify clinical and experimental studies which evaluated a biomarker in sepsis. results the search retrieved 3370 references covering 178 different biomarkers. conclusions many biomarkers have been evaluated for use in sepsis. most of the biomarkers had been tested clinically, primarily as prognostic markers in sepsis; relatively few have been used for diagnosis. none has sufficient specificity or sensitivity to be routinely employed in clinical practice. pct and crp have been most widely used, but even these have limited ability to distinguish sepsis from other inflammatory conditions or to predict outcome.",0
"ovarian cancer (oc) is the seventh most commonly diagnosed cancer among women in the world and the tenth most common in china. epithelial oc is the most predominant pathologic subtype, with five major histotypes that differ in origination, pathogenesis, molecular alterations, risk factors, and prognosis. genetic susceptibility is manifested by rare inherited mutations with high to moderate penetrance. genome-wide association studies have additionally identified 29 common susceptibility alleles for oc, including 14 subtype-specific alleles. several reproductive and hormonal factors may lower risk, including parity, oral contraceptive use, and lactation, while others such as older age at menopause and hormone replacement therapy confer increased risks. these associations differ by histotype, especially for mucinous oc, likely reflecting differences in etiology. endometrioid and clear cell oc share a similar, unique pattern of associations with increased risks among women with endometriosis and decreased risks associated with tubal ligation. oc risks associated with other gynecological conditions and procedures, such as hysterectomy, pelvic inflammatory disease, and polycystic ovarian syndrome, are less clear. other possible risk factors include environmental and lifestyle factors such as asbestos and talc powder exposures, and cigarette smoking. the epidemiology provides clues on etiology, primary prevention, early detection, and possibly even therapeutic strategies.",0
"background today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. at the same time, several different inference techniques are routinely employed instead of relying on just one. in view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. a tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures. results we developed treegraph 2, a gui-based graphical editor for phylogenetic trees (available from it allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. the program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. these node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. treegraph 2 outputs various graphic formats such as svg, pdf, or png, useful for tree figures in both publications and presentations. conclusion treegraph 2 is a user-friendly, fully documented application to produce ready-to-publish trees. it can display any number of annotations in several ways, and permits easily importing and combining them. additionally, a great number of editing- and formatting-operations is available.",0
"we present an implementation of generalized born implicit solvent all-atom classical molecular dynamics (md) within the amber program package that runs entirely on cuda enabled nvidia graphics processing units (gpus). we discuss the algorithms that are used to exploit the processing power of the gpus and show the performance that can be achieved in comparison to simulations on conventional cpu clusters. the implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (spdp), or everything is computed in single precision (spsp) or double precision (dpdp). in addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent md simulations. we show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. the numerical noise due to rounding errors within the spsp precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. we recommend the use of the mixed-precision spdp model since the numerical results obtained are comparable with those of the full double precision dpdp model and the reference double precision cpu implementation but at significantly reduced computational cost. our implementation provides performance for gb simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers.",0
"background there are specific guidelines regarding the level of physical activity (pa) required to provide health benefits. however, the research underpinning these pa guidelines does not address the element of social health. furthermore, there is insufficient evidence about the levels or types of pa associated specifically with psychological health. this paper first presents the results of a systematic review of the psychological and social health benefits of participation in sport by children and adolescents. secondly, the information arising from the systematic review has been used to develop a conceptual model. methods a systematic review of 14 electronic databases was conducted in june 2012, and studies published since 1990 were considered for inclusion. studies that addressed mental and/or social health benefits from participation in sport were included. results a total of 3668 publications were initially identified, of which 30 met the selection criteria. there were many different psychological and social health benefits reported, with the most commonly being improved self-esteem, social interaction followed by fewer depressive symptoms. sport may be associated with improved psychosocial health above and beyond improvements attributable to participation in pa. specifically, team sport seems to be associated with improved health outcomes compared to individual activities, due to the social nature of the participation. a conceptual model, health through sport, is proposed. the model depicts the relationship between psychological, psychosocial and social health domains, and their positive associations with sport participation, as reported in the literature. however, it is acknowledged that the capacity to determine the existence and direction of causal links between participation and health is limited by the fact that the majority of studies identified (n=21) were cross-sectional. conclusion it is recommended that community sport participation is advocated as a form of leisure time pa for children and adolescents, in an effort to not only improve physical health in relation to such matters as the obesity crisis, but also to enhance psychological and social health outcomes. it is also recommended that the causal link between participation in sport and psychosocial health be further investigated and the conceptual model of health through sport tested.",0
"human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. we find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. these data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. this may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost.",0
"after an infection, t cells that carry the cd8 marker are activated and undergo a characteristic kinetic sequence of rapid expansion, subsequent contraction and formation of memory cells. the pool of naive t-cell clones is diverse and contains cells bearing t-cell antigen receptors (tcrs) that differ in their affinity for the same antigen. how these differences in affinity affect the function and the response kinetics of individual t-cell clones was previously unknown. here we show that during the in vivo response to microbial infection, even very weak tcr-ligand interactions are sufficient to activate naive t cells, induce rapid initial proliferation and generate effector and memory cells. the strength of the tcr-ligand interaction critically affects when expansion stops, when the cells exit lymphoid organs and when contraction begins; that is, strongly stimulated t cells contract and exit lymphoid organs later than weakly stimulated cells. our data challenge the prevailing view that strong tcr ligation is a prerequisite for cd8(+) t-cell activation. instead, very weak interactions are sufficient for activation, but strong tcr ligation is required to sustain t-cell expansion. we propose that in response to microbial challenge, t-cell clones with a broad range of avidities for foreign ligands are initially recruited, and that the pool of t cells subsequently matures in affinity owing to the more prolonged expansion of high-affinity t-cell clones.",0
"background people of sub saharan africa (ssa) and south asians(sa) ethnic minorities living in europe have higher risk of stroke than native europeans(eu). study objective is to provide an assessment of gender specific absolute differences in office systolic(sbp) and diastolic(dbp) blood pressure(bp) levels between ssa, sa, and eu. methods and findings we performed a systematic review and meta-analysis of observational studies conducted in europe that examined bp in non-selected adult ssa, sa and eu subjects. medline, pubmed, embase, web of science, and scopus were searched from their inception through january 31st 2015, for relevant articles. outcome measures were mean sbp and dbp differences between minorities and eu, using a random effects model and tested for heterogeneity. twenty-one studies involving 9,070 ssa, 18,421 sa, and 130,380 eu were included. compared with eu, ssa had higher values of both sbp (3.38 mmhg, 95% ci 1.28 to 5.48 mmhg; and 6.00 mmhg, 95% ci 2.22 to 9.78 in men and women respectively) and dbp (3.29 mmhg, 95% ci 1.80 to 4.78; 5.35 mmhg, 95% ci 3.04 to 7.66). sa had lower sbp than eu(-4.57 mmhg, 95% ci -6.20 to -2.93; -2.97 mmhg, 95% ci -5.45 to -0.49) but similar dbp values. meta-analysis by subgroup showed that sa originating from countries where islam is the main religion had lower sbp and dbp values than eu. in multivariate meta-regression analyses, sbp difference between minorities and eu populations, was influenced by panethnicity and diabetes prevalence. conclusions 1) the higher bp in ssa is maintained over decades, suggesting limited efficacy of prevention strategies in such group in europe;2) the lower bp in muslim populations suggests that yet untapped lifestyle and behavioral habits may reveal advantages towards the development of hypertension;3) the additive effect of diabetes, emphasizes the need of new strategies for the control of hypertension in groups at high prevalence of diabetes.",0
"two intermingled hypothalamic neuron populations specified by expression of agouti-related peptide (agrp) or pro-opiomelanocortin (pomc) positively and negatively influence feeding behavior, respectively, possibly by reciprocally regulating downstream melanocortin receptors. however, the sufficiency of these neurons to control behavior and the relationship of their activity to the magnitude and dynamics of feeding are unknown. to measure this, we used channelrhodopsin-2 for cell type-specific photostimulation. activation of only 800 agrp neurons in mice evoked voracious feeding within minutes. the behavioral response increased with photoexcitable neuron number, photostimulation frequency and stimulus duration. conversely, pomc neuron stimulation reduced food intake and body weight, which required melanocortin receptor signaling. however, agrp neuron-mediated feeding was not dependent on suppressing this melanocortin pathway, indicating that agrp neurons directly engage feeding circuits. furthermore, feeding was evoked selectively over drinking without training or prior photostimulus exposure, which suggests that agrp neurons serve a dedicated role coordinating this complex behavior.",0
"the european working group on sarcopenia in older people (ewgsop) developed a practical clinical definition and consensus diagnostic criteria for age-related sarcopenia. ewgsop included representatives from four participant organisations, i.e. the european geriatric medicine society, the european society for clinical nutrition and metabolism, the international association of gerontology and geriatrics-european region and the international association of nutrition and aging. these organisations endorsed the findings in the final document. the group met and addressed the following questions, using the medical literature to build evidence-based answers: (i) what is sarcopenia? (ii) what parameters define sarcopenia? (iii) what variables reflect these parameters, and what measurement tools and cut-off points can be used? (iv) how does sarcopenia relate to cachexia, frailty and sarcopenic obesity? for the diagnosis of sarcopenia, ewgsop recommends using the presence of both low muscle mass + low muscle function (strength or performance). ewgsop variously applies these characteristics to further define conceptual stages as 'presarcopenia', 'sarcopenia' and 'severe sarcopenia'. ewgsop reviewed a wide range of tools that can be used to measure the specific variables of muscle mass, muscle strength and physical performance. our paper summarises currently available data defining sarcopenia cut-off points by age and gender; suggests an algorithm for sarcopenia case finding in older individuals based on measurements of gait speed, grip strength and muscle mass; and presents a list of suggested primary and secondary outcome domains for research. once an operational definition of sarcopenia is adopted and included in the mainstream of comprehensive geriatric assessment, the next steps are to define the natural course of sarcopenia and to develop and define effective treatment.",0
"medical research is developing an ever greater need for comprehensive high-quality data generation to realize the promises of personalized health care based on molecular biomarkers. the nucleic acid proximity-based methods proximity ligation and proximity extension assays have, with their dual reporters, shown potential to relieve the shortcomings of antibodies and their inherent cross-reactivity in multiplex protein quantification applications. the aim of the present study was to develop a robust 96-plex immunoassay based on the proximity extension assay (pea) for improved high throughput detection of protein biomarkers. this was enabled by: (1) a modified design leading to a reduced number of pipetting steps compared to the existing pea protocol, as well as improved intra-assay precision; (2) a new enzymatic system that uses a hyper-thermostabile enzyme, pwo, for uniting the two probes allowing for room temperature addition of all reagents and improved the sensitivity; (3) introduction of an inter-plate control and a new normalization procedure leading to improved inter-assay precision (reproducibility). the multiplex proximity extension assay was found to perform well in complex samples, such as serum and plasma, and also in xenografted mice and resuspended dried blood spots, consuming only 1 µl sample per test. all-in-all, the development of the current multiplex technique is a step toward robust high throughput protein marker discovery and research.",0
"background recent data suggest that complications and death from coronavirus disease 2019 (covid-19) may be related to high viral loads. methods in this ongoing, double-blind, phase 1-3 trial involving nonhospitalized patients with covid-19, we investigated two fully human, neutralizing monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 (sars-cov-2) spike protein, used in a combined cocktail (regn-cov2) to reduce the risk of the emergence of treatment-resistant mutant virus. patients were randomly assigned (1:1:1) to receive placebo, 2.4 g of regn-cov2, or 8.0 g of regn-cov2 and were prospectively characterized at baseline for endogenous immune response against sars-cov-2 (serum antibody-positive or serum antibody-negative). key end points included the time-weighted average change in viral load from baseline (day 1) through day 7 and the percentage of patients with at least one covid-19-related medically attended visit through day 29. safety was assessed in all patients. results data from 275 patients are reported. the least-squares mean difference (combined regn-cov2 dose groups vs. placebo group) in the time-weighted average change in viral load from day 1 through day 7 was -0.56 log 10 copies per milliliter (95% confidence interval , -1.02 to -0.11) among patients who were serum antibody-negative at baseline and -0.41 log 10 copies per milliliter (95% ci, -0.71 to -0.10) in the overall trial population. in the overall trial population, 6% of the patients in the placebo group and 3% of the patients in the combined regn-cov2 dose groups reported at least one medically attended visit; among patients who were serum antibody-negative at baseline, the corresponding percentages were 15% and 6% (difference, -9 percentage points; 95% ci, -29 to 11). the percentages of patients with hypersensitivity reactions, infusion-related reactions, and other adverse events were similar in the combined regn-cov2 dose groups and the placebo group. conclusions in this interim analysis, the regn-cov2 antibody cocktail reduced viral load, with a greater effect in patients whose immune response had not yet been initiated or who had a high viral load at baseline. safety outcomes were similar in the combined regn-cov2 dose groups and the placebo group. (funded by regeneron pharmaceuticals and the biomedical and advanced research and development authority of the department of health and human services; clinicaltrials.gov number, nct04425629.).",0
"the mission of uniprot is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. uniprot is comprised of four major components, each optimized for different uses: the uniprot archive, the uniprot knowledgebase, the uniprot reference clusters and the uniprot metagenomic and environmental sequence database. a key development at uniprot is the provision of complete, reference and representative proteomes. uniprot is updated and distributed every 4 weeks and can be accessed online for searches or download at",0
"carl moons and colleagues provide a checklist and background explanation for critically appraising and extracting data from systematic reviews of prognostic and diagnostic prediction modelling studies. please see later in the article for the editors' summary.",0
"importance the increasing burden due to cancer and other noncommunicable diseases poses a threat to human development, which has resulted in global political commitments reflected in the sustainable development goals as well as the world health organization (who) global action plan on non-communicable diseases. to determine if these commitments have resulted in improved cancer control, quantitative assessments of the cancer burden are required. objective to assess the burden for 29 cancer groups over time to provide a framework for policy discussion, resource allocation, and research focus. evidence review cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (dalys) were evaluated for 195 countries and territories by age and sex using the global burden of disease study estimation methods. levels and trends were analyzed over time, as well as by the sociodemographic index (sdi). changes in incident cases were categorized by changes due to epidemiological vs demographic transition. findings in 2016, there were 17.2 million cancer cases worldwide and 8.9 million deaths. cancer cases increased by 28% between 2006 and 2016. the smallest increase was seen in high sdi countries. globally, population aging contributed 17%; population growth, 12%; and changes in age-specific rates, -1% to this change. the most common incident cancer globally for men was prostate cancer (1.4 million cases). the leading cause of cancer deaths and dalys was tracheal, bronchus, and lung cancer (1.2 million deaths and 25.4 million dalys). for women, the most common incident cancer and the leading cause of cancer deaths and dalys was breast cancer (1.7 million incident cases, 535 000 deaths, and 14.9 million dalys). in 2016, cancer caused 213.2 million dalys globally for both sexes combined. between 2006 and 2016, the average annual age-standardized incidence rates for all cancers combined increased in 130 of 195 countries or territories, and the average annual age-standardized death rates decreased within that timeframe in 143 of 195 countries or territories. conclusions and relevance large disparities exist between countries in cancer incidence, deaths, and associated disability. scaling up cancer prevention and ensuring universal access to cancer care are required for health equity and to fulfill the global commitments for noncommunicable disease and cancer control.",0
"a consensus conference on cardio-renal syndromes (crs) was held in venice italy, in september 2008 under the auspices of the acute dialysis quality initiative (adqi). the following topics were matter of discussion after a systematic literature review and the appraisal of the best available evidence: definition/classification system; epidemiology; diagnostic criteria and biomarkers; prevention/protection strategies; management and therapy. the umbrella term crs was used to identify a disorder of the heart and kidneys whereby acute or chronic dysfunction in one organ may induce acute or chronic dysfunction in the other organ. different syndromes were identified and classified into five subtypes. acute crs (type 1): acute worsening of heart function (ahf-acs) leading to kidney injury and/or dysfunction. chronic cardio-renal syndrome (type 2): chronic abnormalities in heart function (chf-chd) leading to kidney injury and/or dysfunction. acute reno-cardiac syndrome (type 3): acute worsening of kidney function (aki) leading to heart injury and/or dysfunction. chronic reno-cardiac syndrome (type 4): chronic kidney disease leading to heart injury, disease, and/or dysfunction. secondary crs (type 5): systemic conditions leading to simultaneous injury and/or dysfunction of heart and kidney. consensus statements concerning epidemiology, diagnosis, prevention, and management strategies are discussed in the paper for each of the syndromes.",0
"the reactome knowledgebase ( provides molecular details of signal transduction, transport, dna replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogues from tumor cells. to support the continued brisk growth in the size and complexity of reactome, we have implemented a graph database, improved performance of data analysis tools, and designed new data structures and strategies to boost diagram viewer performance. to make our website more accessible to human users, we have improved pathway display and navigation by implementing interactive enhanced high level diagrams (ehlds) with an associated icon library, and subpathway highlighting and zooming, in a simplified and reorganized web site with adaptive design. to encourage re-use of our content, we have enabled export of pathway diagrams as 'powerpoint' files.",0
"cellular microvesicles and nanovesicles (exosomes) are involved in many disease processes and have major potential as biomarkers. however, developments in this area are constrained by limitations in the technology available for their measurement. here we report on the use of fluorescence nanoparticle tracking analysis (nta) to rapidly size and phenotype cellular vesicles. in this system vesicles are visualized by light scattering using a light microscope. a video is taken, and the nta software tracks the brownian motion of individual vesicles and calculates their size and total concentration. using human placental vesicles and plasma, we have demonstrated that nta can measure cellular vesicles as small as ≈ 50 nm and is far more sensitive than conventional flow cytometry (lower limit ≈ 300 nm). by combining nta with fluorescence measurement we have demonstrated that vesicles can be labeled with specific antibody-conjugated quantum dots, allowing their phenotype to be determined. from the clinical editor the authors of this study utilized fluorescence nanoparticle tracking analysis (nta) to rapidly size and phenotype cellular vesicles, demonstrating that nta is far more sensitive than conventional flow cytometry.",0
"endscript 2 is a friendly web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. this major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3d visualization. it takes advantage of the new version 3 of espript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. from a single pdb entry or file, endscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. all this information and more are now mapped on interactive 3d pymol representations. thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune endscript to their needs. endscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool web servers, with both 2d and 3d representations. endscript 2 and espript 3 are freely available at and respectively.",0
"neuromyelitis optica (nmo) is an inflammatory cns syndrome distinct from multiple sclerosis (ms) that is associated with serum aquaporin-4 immunoglobulin g antibodies (aqp4-igg). prior nmo diagnostic criteria required optic nerve and spinal cord involvement but more restricted or more extensive cns involvement may occur. the international panel for nmo diagnosis (ipnd) was convened to develop revised diagnostic criteria using systematic literature reviews and electronic surveys to facilitate consensus. the new nomenclature defines the unifying term nmo spectrum disorders (nmosd), which is stratified further by serologic testing (nmosd with or without aqp4-igg). the core clinical characteristics required for patients with nmosd with aqp4-igg include clinical syndromes or mri findings related to optic nerve, spinal cord, area postrema, other brainstem, diencephalic, or cerebral presentations. more stringent clinical criteria, with additional neuroimaging findings, are required for diagnosis of nmosd without aqp4-igg or when serologic testing is unavailable. the ipnd also proposed validation strategies and achieved consensus on pediatric nmosd diagnosis and the concepts of monophasic nmosd and opticospinal ms.",0
"amyloid-β (aβ) plaque deposition in specific brain regions is a pathological hallmark of alzheimer's disease. however, the mechanism underlying the regional vulnerability to aβ deposition in alzheimer's disease is unknown. herein, we provide evidence that endogenous neuronal activity regulates the regional concentration of interstitial fluid (isf) aβ, which drives local aβ aggregation. using in vivo microdialysis, we show that isf aβ concentrations in several brain regions of app transgenic mice before plaque deposition were commensurate with the degree of subsequent plaque deposition and with the concentration of lactate, a marker of neuronal activity. furthermore, unilateral vibrissal stimulation increased isf aβ, and unilateral vibrissal deprivation decreased isf aβ and lactate, in contralateral barrel cortex. long-term unilateral vibrissal deprivation decreased amyloid plaque formation and growth. our results suggest a mechanism to account for the vulnerability of specific brain regions to aβ deposition in alzheimer's disease.",0
"we sought to understand the relationship between reactive oxygen species (ros) and the mitochondrial permeability transition (mpt) in cardiac myocytes based on the observation of increased ros production at sites of spontaneously deenergized mitochondria. we devised a new model enabling incremental ros accumulation in individual mitochondria in isolated cardiac myocytes via photoactivation of tetramethylrhodamine derivatives, which also served to report the mitochondrial transmembrane potential, deltapsi. this ros accumulation reproducibly triggered abrupt (and sometimes reversible) mitochondrial depolarization. this phenomenon was ascribed to mpt induction because (a) bongkrekic acid prevented it and (b) mitochondria became permeable for calcein ( approximately 620 daltons) concurrently with depolarization. these photodynamically produced ""triggering"" ros caused the mpt induction, as the ros scavenger trolox prevented it. the time required for triggering ros to induce the mpt was dependent on intrinsic cellular ros-scavenging redox mechanisms, particularly glutathione. mpt induction caused by triggering ros coincided with a burst of mitochondrial ros generation, as measured by dichlorofluorescein fluorescence, which we have termed mitochondrial ""ros-induced ros release"" (rirr). this mpt induction/rirr phenomenon in cardiac myocytes often occurred synchronously and reversibly among long chains of adjacent mitochondria demonstrating apparent cooperativity. the observed link between mpt and rirr could be a fundamental phenomenon in mitochondrial and cell biology.",0
"background based on previous findings, we hypothesised that radiotherapy to the prostate would improve overall survival in men with metastatic prostate cancer, and that the benefit would be greatest in patients with a low metastatic burden. we aimed to compare standard of care for metastatic prostate cancer, with and without radiotherapy. methods we did a randomised controlled phase 3 trial at 117 hospitals in switzerland and the uk. eligible patients had newly diagnosed metastatic prostate cancer. we randomly allocated patients open-label in a 1:1 ratio to standard of care (control group) or standard of care and radiotherapy (radiotherapy group). randomisation was stratified by hospital, age at randomisation, nodal involvement, who performance status, planned androgen deprivation therapy, planned docetaxel use (from december, 2015), and regular aspirin or non-steroidal anti-inflammatory drug use. standard of care was lifelong androgen deprivation therapy, with up-front docetaxel permitted from december, 2015. men allocated radiotherapy received either a daily (55 gy in 20 fractions over 4 weeks) or weekly (36 gy in six fractions over 6 weeks) schedule that was nominated before randomisation. the primary outcome was overall survival, measured as the number of deaths; this analysis had 90% power with a one-sided α of 2·5% for a hazard ratio (hr) of 0·75. secondary outcomes were failure-free survival, progression-free survival, metastatic progression-free survival, prostate cancer-specific survival, and symptomatic local event-free survival. analyses used cox proportional hazards and flexible parametric models, adjusted for stratification factors. the primary outcome analysis was by intention to treat. two prespecified subgroup analyses tested the effects of prostate radiotherapy by baseline metastatic burden and radiotherapy schedule. this trial is registered with clinicaltrials.gov, number nct00268476. findings between jan 22, 2013, and sept 2, 2016, 2061 men underwent randomisation, 1029 were allocated the control and 1032 radiotherapy. allocated groups were balanced, with a median age of 68 years (iqr 63-73) and median amount of prostate-specific antigen of 97 ng/ml (33-315). 367 (18%) patients received early docetaxel. 1082 (52%) participants nominated the daily radiotherapy schedule before randomisation and 979 (48%) the weekly schedule. 819 (40%) men had a low metastatic burden, 1120 (54%) had a high metastatic burden, and the metastatic burden was unknown for 122 (6%). radiotherapy improved failure-free survival (hr 0·76, 95% ci 0·68-0·84; p interpretation radiotherapy to the prostate did not improve overall survival for unselected patients with newly diagnosed metastatic prostate cancer. funding cancer research uk, uk medical research council, swiss group for clinical cancer research, astellas, clovis oncology, janssen, novartis, pfizer, and sanofi-aventis.",0
"metabolic syndrome, variously known also as syndrome x, insulin resistance, etc., is defined by who as a pathologic condition characterized by abdominal obesity, insulin resistance, hypertension, and hyperlipidemia. though there is some variation in the definition by other health care organization, the differences are minor. with the successful conquest of communicable infectious diseases in most of the world, this new non-communicable disease (ncd) has become the major health hazard of modern world. though it started in the western world, with the spread of the western lifestyle across the globe, it has become now a truly global problem. the prevalence of the metabolic syndrome is often more in the urban population of some developing countries than in its western counterparts. the two basic forces spreading this malady are the increase in consumption of high calorie-low fiber fast food and the decrease in physical activity due to mechanized transportations and sedentary form of leisure time activities. the syndrome feeds into the spread of the diseases like type 2 diabetes, coronary diseases, stroke, and other disabilities. the total cost of the malady including the cost of health care and loss of potential economic activity is in trillions. the present trend is not sustainable unless a magic cure is found (unlikely) or concerted global/governmental/societal efforts are made to change the lifestyle that is promoting it. there are certainly some elements in the causation of the metabolic syndrome that cannot be changed but many are amenable for corrections and curtailments. for example, better urban planning to encourage active lifestyle, subsidizing consumption of whole grains and possible taxing high calorie snacks, restricting media advertisement of unhealthy food, etc. revitalizing old fashion healthier lifestyle, promoting old-fashioned foods using healthy herbs rather than oil and sugar, and educating people about choosing healthy/wholesome food over junks are among the steps that can be considered.",0
"innate immunity provides the first line of defence against invading pathogens and provides important cues for the development of adaptive immunity. type-2 immunity-responsible for protective immune responses to helminth parasites and the underlying cause of the pathogenesis of allergic asthma-consists of responses dominated by the cardinal type-2 cytokines interleukin (il)4, il5 and il13 (ref. 5). t cells are an important source of these cytokines in adaptive immune responses, but the innate cell sources remain to be comprehensively determined. here, through the use of novel il13-egfp reporter mice, we present the identification and functional characterization of a new innate type-2 immune effector leukocyte that we have named the nuocyte. nuocytes expand in vivo in response to the type-2-inducing cytokines il25 and il33, and represent the predominant early source of il13 during helminth infection with nippostrongylus brasiliensis. in the combined absence of il25 and il33 signalling, nuocytes fail to expand, resulting in a severe defect in worm expulsion that is rescued by the adoptive transfer of in vitro cultured wild-type, but not il13-deficient, nuocytes. thus, nuocytes represent a critically important innate effector cell in type-2 immunity.",0
"background to evaluate binary classifications and their confusion matrices, scientific researchers can employ several statistical rates, accordingly to the goal of the experiment they are investigating. despite being a crucial issue in machine learning, no widespread consensus has been reached on a unified elective chosen measure yet. accuracy and f 1 score computed on confusion matrices have been (and still are) among the most popular adopted metrics in binary classification tasks. however, these statistical measures can dangerously show overoptimistic inflated results, especially on imbalanced datasets. results the matthews correlation coefficient (mcc), instead, is a more reliable statistical rate which produces a high score only if the prediction obtained good results in all of the four confusion matrix categories (true positives, false negatives, true negatives, and false positives), proportionally both to the size of positive elements and the size of negative elements in the dataset. conclusions in this article, we show how mcc produces a more informative and truthful score in evaluating binary classifications than accuracy and f 1 score, by first explaining the mathematical properties, and then the asset of mcc in six synthetic use cases and in a real genomics scenario. we believe that the matthews correlation coefficient should be preferred to accuracy and f 1 score in evaluating binary classification tasks by all scientific communities.",0
"tracking antibiotic consumption patterns over time and across countries could inform policies to optimize antibiotic prescribing and minimize antibiotic resistance, such as setting and enforcing per capita consumption targets or aiding investments in alternatives to antibiotics. in this study, we analyzed the trends and drivers of antibiotic consumption from 2000 to 2015 in 76 countries and projected total global antibiotic consumption through 2030. between 2000 and 2015, antibiotic consumption, expressed in defined daily doses (ddd), increased 65% (21.1-34.8 billion ddds), and the antibiotic consumption rate increased 39% (11.3-15.7 ddds per 1,000 inhabitants per day). the increase was driven by low- and middle-income countries (lmics), where rising consumption was correlated with gross domestic product per capita (gdppc) growth ( p = 0.004). in high-income countries (hics), although overall consumption increased modestly, ddds per 1,000 inhabitants per day fell 4%, and there was no correlation with gdppc. of particular concern was the rapid increase in the use of last-resort compounds, both in hics and lmics, such as glycylcyclines, oxazolidinones, carbapenems, and polymyxins. projections of global antibiotic consumption in 2030, assuming no policy changes, were up to 200% higher than the 42 billion ddds estimated in 2015. although antibiotic consumption rates in most lmics remain lower than in hics despite higher bacterial disease burden, consumption in lmics is rapidly converging to rates similar to hics. reducing global consumption is critical for reducing the threat of antibiotic resistance, but reduction efforts must balance access limitations in lmics and take account of local and global resistance patterns.",0
"background severe lower respiratory infections (lris) and atopic sensitization have been identified as independent risk factors for asthma. objective the nature of potential interactions between these risk factors was the subject of this study. methods a community-based cohort of 198 children at high atopic risk was followed from birth to 5 years. all episodes of acute respiratory illness in the first year were recorded and postnasal aspirates were collected for viral identification. history of wheeze and asthma was collected annually, and atopy was assessed at 6 months, 2 years, and 5 years. results a total of 815 episodes of acute respiratory illness were reported, and 33% were lris. viruses were detected in 69% of aspirates, most commonly rhinoviruses (48.3%) and respiratory syncytial virus (10.9%). at 5 years, 28.3% (n = 56) had current wheeze, and this was associated with wheezy and/or febrile lri , in particular those caused by respiratory syncytial virus or rhinoviruses . comparable findings were made for current asthma. strikingly these associations were restricted to children who displayed early sensitization ( conclusion these data suggest viral infections interact with atopy in infancy to promote later asthma. notably the occurrence of both of these events during this narrow developmental window is associated with maximal risk for subsequent asthma, which suggests a contribution from both classes of inflammatory insults to disease pathogenesis. clinical implications protection of ""high-risk"" children against the effects of severe respiratory infections during infancy may represent an effective strategy for primary asthma prevention. the potential benefits of these strategies merit more careful evaluation in this age group.",0
"neutrophil extracellular traps (nets) are extracellular structures composed of chromatin and granule proteins that bind and kill microorganisms. we show that upon stimulation, the nuclei of neutrophils lose their shape, and the eu- and heterochromatin homogenize. later, the nuclear envelope and the granule membranes disintegrate, allowing the mixing of net components. finally, the nets are released as the cell membrane breaks. this cell death process is distinct from apoptosis and necrosis and depends on the generation of reactive oxygen species (ros) by nadph oxidase. patients with chronic granulomatous disease carry mutations in nadph oxidase and cannot activate this cell-death pathway or make nets. this novel ros-dependent death allows neutrophils to fulfill their antimicrobial function, even beyond their lifespan.",0
"platelet/endothelial cell adhesion molecule 1 (pecam-1; cd31) is crucial to the process of leukocyte transmigration through intercellular junctions of vascular endothelial cells. a monoclonal antibody to pecam, or recombinant soluble pecam, blocks transendothelial migration of monocytes by 70-90%. pretreating either the monocytes or the endothelial junctions with antibody blocks transmigration. if the endothelium is first activated by cytokines, anti-pecam antibody or soluble recombinant pecam again block transmigration of both monocytes and neutrophils. anti-pecam does not block chemotaxis of either cell type. light and electron microscopy reveal that leukocytes blocked in transmigration remain tightly bound to the apical surface of the endothelial cell, precisely over the intercellular junction. thus, the process of leukocyte emigration can be dissected into three successive stages: rolling, mediated by the selectin class of adhesion molecules; tight adhesion, mediated by the leukocyte integrins and their endothelial cell counter-receptors; and now transmigration, which, based on these studies, requires pecam-1.",0
"elaboration of bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. it is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. including all relevant data into a single joint model is very challenging both conceptually and computationally. advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. beast 2 is one such computational software platform, and was first announced over 4 years ago. here we describe a series of major new developments in the beast 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.",0
"the avon longitudinal study of parents and children (alspac) is a transgenerational prospective observational study investigating influences on health and development across the life course. it considers multiple genetic, epigenetic, biological, psychological, social and other environmental exposures in relation to a similarly diverse range of health, social and developmental outcomes. recruitment sought to enroll pregnant women in the bristol area of the uk during 1990-92; this was extended to include additional children eligible using the original enrollment definition up to the age of 18 years. the children from 14541 pregnancies were recruited in 1990-92, increasing to 15247 pregnancies by the age of 18 years. this cohort profile describes the index children of these pregnancies. follow-up includes 59 questionnaires (4 weeks-18 years of age) and 9 clinical assessment visits (7-17 years of age). the resource comprises a wide range of phenotypic and environmental measures in addition to biological samples, genetic (dna on 11343 children, genome-wide data on 8365 children, complete genome sequencing on 2000 children) and epigenetic (methylation sampling on 1000 children) information and linkage to health and administrative records. data access is described in this article and is currently set up as a supported access resource. to date, over 700 peer-reviewed articles have been published using alspac data.",0
"a covid-19 epidemic has been spreading in china and other parts of the world since december 2019. the epidemic has brought not only the risk of death from infection but also unbearable psychological pressure. we sampled college students from changzhi medical college by using cluster sampling. they responded to a questionnaire packet that included the 7-item generalized anxiety disorder scale (gad-7) and those inquiring the participants' basic information. we received 7,143 responses. results indicated that 0.9% of the respondents were experiencing severe anxiety, 2.7% moderate anxiety, and 21.3% mild anxiety. moreover, living in urban areas (or = 0.810, 95% ci = 0.709 - 0.925), family income stability (or = 0.726, 95% ci = 0.645 - 0.817) and living with parents (or = 0.752, 95% ci = 0.596 - 0.950) were protective factors against anxiety. moreover, having relatives or acquaintances infected with covid-19 was a risk factor for increasing the anxiety of college students (or = 3.007, 95% ci = 2.377 - 3.804). results of correlation analysis indicated that economic effects, and effects on daily life, as well as delays in academic activities, were positively associated with anxiety symptoms (p < .001). however, social support was negatively correlated with the level of anxiety (p < .001). it is suggested that the mental health of college students should be monitored during epidemics.",0
"background previous attempts to characterise the burden of chronic respiratory diseases have focused only on specific disease conditions, such as chronic obstructive pulmonary disease (copd) or asthma. in this study, we aimed to characterise the burden of chronic respiratory diseases globally, providing a comprehensive and up-to-date analysis on geographical and time trends from 1990 to 2017. methods using data from the global burden of diseases, injuries, and risk factors study (gbd) 2017, we estimated the prevalence, morbidity, and mortality attributable to chronic respiratory diseases through an analysis of deaths, disability-adjusted life-years (dalys), and years of life lost (yll) by gbd super-region, from 1990 to 2017, stratified by age and sex. specific diseases analysed included asthma, copd, interstitial lung disease and pulmonary sarcoidosis, pneumoconiosis, and other chronic respiratory diseases. we also assessed the contribution of risk factors (smoking, second-hand smoke, ambient particulate matter and ozone pollution, household air pollution from solid fuels, and occupational risks) to chronic respiratory disease-attributable dalys. findings in 2017, 544·9 million people (95% uncertainty interval 506·9-584·8) worldwide had a chronic respiratory disease, representing an increase of 39·8% compared with 1990. chronic respiratory disease prevalence showed wide variability across gbd super-regions, with the highest prevalence among both males and females in high-income regions, and the lowest prevalence in sub-saharan africa and south asia. the age-sex-specific prevalence of each chronic respiratory disease in 2017 was also highly variable geographically. chronic respiratory diseases were the third leading cause of death in 2017 (7·0% of all deaths), behind cardiovascular diseases and neoplasms. deaths due to chronic respiratory diseases numbered 3 914 196 (95% ui 3 790 578-4 044 819) in 2017, an increase of 18·0% since 1990, while total dalys increased by 13·3%. however, when accounting for ageing and population growth, declines were observed in age-standardised prevalence (14·3% decrease), age-standardised death rates (42·6%), and age-standardised daly rates (38·2%). in males and females, most chronic respiratory disease-attributable deaths and dalys were due to copd. in regional analyses, mortality rates from chronic respiratory diseases were greatest in south asia and lowest in sub-saharan africa, also across both sexes. notably, although absolute prevalence was lower in south asia than in most other super-regions, ylls due to chronic respiratory diseases across the subcontinent were the highest in the world. death rates due to interstitial lung disease and pulmonary sarcoidosis were greater than those due to pneumoconiosis in all super-regions. smoking was the leading risk factor for chronic respiratory disease-related disability across all regions for men. among women, household air pollution from solid fuels was the predominant risk factor for chronic respiratory diseases in south asia and sub-saharan africa, while ambient particulate matter represented the leading risk factor in southeast asia, east asia, and oceania, and in the middle east and north africa super-region. interpretation our study shows that chronic respiratory diseases remain a leading cause of death and disability worldwide, with growth in absolute numbers but sharp declines in several age-standardised estimators since 1990. premature mortality from chronic respiratory diseases seems to be highest in regions with less-resourced health systems on a per-capita basis. funding bill & melinda gates foundation.",0
"transforming growth factor-beta (tgf-β)/bone morphogenic protein (bmp) signaling is involved in a vast majority of cellular processes and is fundamentally important throughout life. tgf-β/bmps have widely recognized roles in bone formation during mammalian development and exhibit versatile regulatory functions in the body. signaling transduction by tgf-β/bmps is specifically through both canonical smad-dependent pathways (tgf-β/bmp ligands, receptors and smads) and non-canonical smad-independent signaling pathway (e.g. p38 mitogen-activated protein kinase pathway, mapk). following tgf-β/bmp induction, both the smad and p38 mapk pathways converge at the runx2 gene to control mesenchymal precursor cell differentiation. the coordinated activity of runx2 and tgf-β/bmp-activated smads is critical for formation of the skeleton. recent advances in molecular and genetic studies using gene targeting in mice enable a better understanding of tgf-β/bmp signaling in bone and in the signaling networks underlying osteoblast differentiation and bone formation. this review summarizes the recent advances in our understanding of tgf-β/bmp signaling in bone from studies of genetic mouse models and human diseases caused by the disruption of tgf-β/bmp signaling. this review also highlights the different modes of cross-talk between tgf-β/bmp signaling and the signaling pathways of mapk, wnt, hedgehog, notch, and fgf in osteoblast differentiation and bone formation.",0
"the incidence and prevalence of diabetes mellitus have grown significantly throughout the world, due primarily to the increase in type 2 diabetes. this overall increase in the number of people with diabetes has had a major impact on development of diabetic kidney disease (dkd), one of the most frequent complications of both types of diabetes. dkd is the leading cause of end-stage renal disease (esrd), accounting for approximately 50% of cases in the developed world. although incidence rates for esrd attributable to dkd have recently stabilized, these rates continue to rise in high-risk groups such as middle-aged african americans, native americans, and hispanics. the costs of care for people with dkd are extraordinarily high. in the medicare population alone, dkd-related expenditures among this mostly older group were nearly $25 billion in 2011. due to the high human and societal costs, the consensus conference on chronic kidney disease and diabetes was convened by the american diabetes association in collaboration with the american society of nephrology and the national kidney foundation to appraise issues regarding patient management, highlighting current practices and new directions. major topic areas in dkd included 1) identification and monitoring, 2) cardiovascular disease and management of dyslipidemia, 3) hypertension and use of renin-angiotensin-aldosterone system blockade and mineralocorticoid receptor blockade, 4) glycemia measurement, hypoglycemia, and drug therapies, 5) nutrition and general care in advanced-stage chronic kidney disease, 6) children and adolescents, and 7) multidisciplinary approaches and medical home models for health care delivery. this current state summary and research recommendations are designed to guide advances in care and the generation of new knowledge that will meaningfully improve life for people with dkd.",0
"therapy options at the time of recurrence of glioblastoma multiforme are often limited. we investigated whether treatment with a new intratumoral thermotherapy procedure using magnetic nanoparticles improves survival outcome. in a single-arm study in two centers, 66 patients (59 with recurrent glioblastoma) received neuronavigationally controlled intratumoral instillation of an aqueous dispersion of iron-oxide (magnetite) nanoparticles and subsequent heating of the particles in an alternating magnetic field. treatment was combined with fractionated stereotactic radiotherapy. a median dose of 30 gy using a fractionation of 5 × 2 gy/week was applied. the primary study endpoint was overall survival following diagnosis of first tumor recurrence (os-2), while the secondary endpoint was overall survival after primary tumor diagnosis (os-1). survival times were calculated using the kaplan-meier method. analyses were by intention to treat. the median overall survival from diagnosis of the first tumor recurrence among the 59 patients with recurrent glioblastoma was 13.4 months (95% ci: 10.6-16.2 months). median os-1 was 23.2 months while the median time interval between primary diagnosis and first tumor recurrence was 8.0 months. only tumor volume at study entry was significantly correlated with ensuing survival (p < 0.01). no other variables predicting longer survival could be determined. the side effects of the new therapeutic approach were moderate, and no serious complications were observed. thermotherapy using magnetic nanoparticles in conjunction with a reduced radiation dose is safe and effective and leads to longer os-2 compared to conventional therapies in the treatment of recurrent glioblastoma.",0
"objective to systematically review all the prospective cohort studies that have analysed the relation between adherence to a mediterranean diet, mortality, and incidence of chronic diseases in a primary prevention setting. design meta-analysis of prospective cohort studies. data sources english and non-english publications in pubmed, embase, web of science, and the cochrane central register of controlled trials from 1966 to 30 june 2008. studies reviewed studies that analysed prospectively the association between adherence to a mediterranean diet, mortality, and incidence of diseases; 12 studies, with a total of 1 574,299 subjects followed for a time ranging from three to 18 years were included. results the cumulative analysis among eight cohorts (514,816 subjects and 33,576 deaths) evaluating overall mortality in relation to adherence to a mediterranean diet showed that a two point increase in the adherence score was significantly associated with a reduced risk of mortality (pooled relative risk 0.91, 95% confidence interval 0.89 to 0.94). likewise, the analyses showed a beneficial role for greater adherence to a mediterranean diet on cardiovascular mortality (pooled relative risk 0.91, 0.87 to 0.95), incidence of or mortality from cancer (0.94, 0.92 to 0.96), and incidence of parkinson's disease and alzheimer's disease (0.87, 0.80 to 0.96). conclusions greater adherence to a mediterranean diet is associated with a significant improvement in health status, as seen by a significant reduction in overall mortality (9%), mortality from cardiovascular diseases (9%), incidence of or mortality from cancer (6%), and incidence of parkinson's disease and alzheimer's disease (13%). these results seem to be clinically relevant for public health, in particular for encouraging a mediterranean-like dietary pattern for primary prevention of major chronic diseases.",0
"the signals controlling the checkpoints of dendritic cells (dc) maturation and the correlation between phenotypical and functional maturational stages were investigated in a defined model system of growth factor-dependent immature mouse dc. three sequential stages of dc maturation (immature, mature, and apoptotic) were defined and characterized. immature dc (stage 1) had low expression of costimulatory molecules, highly organized cytoskeleton, focal adhesion plaques, and slow motility; accordingly, they were very efficient in antigen uptake and processing of soluble proteins. further, at this stage most of major histocompatibility complex class ii molecules were within cytoplasmic compartments consistent with a poor allostimulatory capacity. bacteria or cytokines were very efficient in inducing progression from stage 1 towards stage 2 (mature). morphological changes were observed by confocal analysis including depolymerization of f-actin and loss of vinculin containing adhesive structures which correlates with acquisition of high motility. antigen uptake and presentation of native protein antigen was reduced. in contrast, presentation of immunogenic peptides and allostimulatory activity became very efficient and secretion of il-12 p75 was detectable after antigen presentation. this functional dc maturation ended by apoptotic cell death, and no reversion to the immature phenotype was observed.",0
"background in patients with suspected coronary heart disease, single-photon emission computed tomography (spect) is the most widely used test for the assessment of myocardial ischaemia, but its diagnostic accuracy is reported to be variable and it exposes patients to ionising radiation. the aim of this study was to establish the diagnostic accuracy of a multiparametric cardiovascular magnetic resonance (cmr) protocol with x-ray coronary angiography as the reference standard, and to compare cmr with spect, in patients with suspected coronary heart disease. methods in this prospective trial patients with suspected angina pectoris and at least one cardiovascular risk factor were scheduled for cmr, spect, and invasive x-ray coronary angiography. cmr consisted of rest and adenosine stress perfusion, cine imaging, late gadolinium enhancement, and mr coronary angiography. gated adenosine stress and rest spect used (99m)tc tetrofosmin. the primary outcome was diagnostic accuracy of cmr. this trial is registered at controlled-trials.com, number isrctn77246133. findings in the 752 recruited patients, 39% had significant chd as identified by x-ray angiography. for multiparametric cmr the sensitivity was 86·5% (95% ci 81·8-90·1), specificity 83·4% (79·5-86·7), positive predictive value 77·2%, (72·1-81·6) and negative predictive value 90·5% (87·1-93·0). the sensitivity of spect was 66·5% (95% ci 60·4-72·1), specificity 82·6% (78·5-86·1), positive predictive value 71·4% (65·3-76·9), and negative predictive value 79·1% (74·8-82·8). the sensitivity and negative predictive value of cmr and spect differed significantly (p interpretation ce-marc is the largest, prospective, real world evaluation of cmr and has established cmr's high diagnostic accuracy in coronary heart disease and cmr's superiority over spect. it should be adopted more widely than at present for the investigation of coronary heart disease. funding british heart foundation.",0
"the rapid spread of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has had a large impact on global health, travel, and economy. therefore, preventative and therapeutic measures are urgently needed. here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (covid-19) patients using a sars-cov-2 stabilized prefusion spike protein. these antibodies had low levels of somatic hypermutation and showed a strong enrichment in vh1-69, vh3-30-3, and vh1-24 gene usage. a subset of the antibodies was able to potently inhibit authentic sars-cov-2 infection at a concentration as low as 0.007 micrograms per milliliter. competition and electron microscopy studies illustrate that the sars-cov-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (rbd) epitopes as well as non-rbd epitopes. in addition to providing guidance for vaccine design, the antibodies described here are promising candidates for covid-19 treatment and prevention.",0
"the early induction of interleukin (il)-12 is a critical event in determining the development of both innate resistance and adaptive immunity to many intracellular pathogens. previous in vitro studies have suggested that the macrophage (mphi) is a major source of the initial il-12 produced upon microbial stimulation and that this response promotes the differentiation of protective t helper cell 1 (th1) cd4+ lymphocytes from precursors that are primed on antigen-bearing dendritic cells (dc). here, we demonstrate by immunolocalization experiments and flow cytometric analysis that, contrary to expectation, dc and not mphi are the initial cells to synthesize il-12 in the spleens of mice exposed in vivo to an extract of toxoplasma gondii or to lipopolysaccharide, two well characterized microbial stimulants of the cytokine. importantly, this production of il-12 occurs very rapidly and is independent of interferon gamma priming or of signals from t cells, such as cd40 ligand. il-12 production by splenic dc is accompanied by an increase in number of dcs, as well as a redistribution to the t cell areas and the acquisition of markers characteristic of interdigitating dendritic cells. the capacity of splenic dc but not mphi to synthesize de novo high levels of il-12 within hours of exposure to microbial products in vivo, as well as the ability of the same stimuli to induce migration of dc to the t cell areas, argues that dc function simultaneously as both antigen-presenting cells and il-12 producing accessory cells in the initiation of cell-mediated immunity to intracellular pathogens. this model avoids the need to invoke a three-cell interaction for th1 differentiation and points to the dc as both a sentinel for innate recognition and the dictator of class selection in the subsequent adaptive response.",0
"human natural killer (nk) cells express several killer cell immunoglobulin (ig)-like receptors (kirs) that inhibit their cytotoxicity upon recognition of human histocompatibility leukocyte antigen (hla) class i molecules on target cells. additional members of the kir family, including some that deliver activation signals, have unknown ligand specificity and function. one such kir, denoted kir2dl4, is structurally divergent from other kirs in the configuration of its two extracellular ig domains and of its transmembrane and cytoplasmic domains. here we show that recombinant soluble kir2dl4 binds to cells expressing hla-g but not to cells expressing other hla class i molecules. unlike other hla class i-specific kirs, which are clonally distributed on nk cells, kir2dl4 is expressed at the surface of all nk cells. furthermore, functional transfer of kir2dl4 into the cell line nk-92 resulted in inhibition of lysis of target cells that express hla-g, but not target cells that express other class i molecules including hla-e. therefore, given that hla-g expression is restricted to fetal trophoblast cells, kir2dl4 may provide important signals to maternal nk decidual cells that interact with trophoblast cells at the maternal-fetal interface during pregnancy.",0
"background world health organization expert groups recommended mortality trials of four repurposed antiviral drugs - remdesivir, hydroxychloroquine, lopinavir, and interferon beta-1a - in patients hospitalized with coronavirus disease 2019 (covid-19). methods we randomly assigned inpatients with covid-19 equally between one of the trial drug regimens that was locally available and open control (up to five options, four active and the local standard of care). the intention-to-treat primary analyses examined in-hospital mortality in the four pairwise comparisons of each trial drug and its control (drug available but patient assigned to the same care without that drug). rate ratios for death were calculated with stratification according to age and status regarding mechanical ventilation at trial entry. results at 405 hospitals in 30 countries, 11,330 adults underwent randomization; 2750 were assigned to receive remdesivir, 954 to hydroxychloroquine, 1411 to lopinavir (without interferon), 2063 to interferon (including 651 to interferon plus lopinavir), and 4088 to no trial drug. adherence was 94 to 96% midway through treatment, with 2 to 6% crossover. in total, 1253 deaths were reported (median day of death, day 8; interquartile range, 4 to 14). the kaplan-meier 28-day mortality was 11.8% (39.0% if the patient was already receiving ventilation at randomization and 9.5% otherwise). death occurred in 301 of 2743 patients receiving remdesivir and in 303 of 2708 receiving its control (rate ratio, 0.95; 95% confidence interval , 0.81 to 1.11; p = 0.50), in 104 of 947 patients receiving hydroxychloroquine and in 84 of 906 receiving its control (rate ratio, 1.19; 95% ci, 0.89 to 1.59; p = 0.23), in 148 of 1399 patients receiving lopinavir and in 146 of 1372 receiving its control (rate ratio, 1.00; 95% ci, 0.79 to 1.25; p = 0.97), and in 243 of 2050 patients receiving interferon and in 216 of 2050 receiving its control (rate ratio, 1.16; 95% ci, 0.96 to 1.39; p = 0.11). no drug definitely reduced mortality, overall or in any subgroup, or reduced initiation of ventilation or hospitalization duration. conclusions these remdesivir, hydroxychloroquine, lopinavir, and interferon regimens had little or no effect on hospitalized patients with covid-19, as indicated by overall mortality, initiation of ventilation, and duration of hospital stay. (funded by the world health organization; isrctn registry number, isrctn83971151; clinicaltrials.gov number, nct04315948.).",0
"the practice of social distancing and wearing masks has been popular worldwide in combating the contraction of covid-19. undeniably, although such practices help control the covid-19 pandemic to a greater extent, the complete control of virus-laden droplet and aerosol transmission by such practices is poorly understood. this review paper intends to outline the literature concerning the transmission of virus-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. the case studies that have come out in different countries have, with prima facie evidence, manifested that the airborne transmission plays a profound role in contracting susceptible hosts. the infection propensities in confined spaces (airplane, passenger car, and healthcare center) by the transmission of droplets and aerosols under varying ventilation conditions were discussed. interestingly, the nosocomial transmission by airborne sars-cov-2 virus-laden aerosols in healthcare facilities may be plausible. hence, clearly defined, science-based administrative, clinical, and physical measures are of paramount importance to eradicate the covid-19 pandemic from the world.",0
"temporary disruptions in routine and nonemergency medical care access and delivery have been observed during periods of considerable community transmission of sars-cov-2, the virus that causes coronavirus disease 2019 (covid-19) (1). however, medical care delay or avoidance might increase morbidity and mortality risk associated with treatable and preventable health conditions and might contribute to reported excess deaths directly or indirectly related to covid-19 (2). to assess delay or avoidance of urgent or emergency and routine medical care because of concerns about covid-19, a web-based survey was administered by qualtrics, llc, during june 24-30, 2020, to a nationwide representative sample of u.s. adults aged ≥18 years. overall, an estimated 40.9% of u.s. adults have avoided medical care during the pandemic because of concerns about covid-19, including 12.0% who avoided urgent or emergency care and 31.5% who avoided routine care. the estimated prevalence of urgent or emergency care avoidance was significantly higher among the following groups: unpaid caregivers for adults* versus noncaregivers (adjusted prevalence ratio = 2.9); persons with two or more selected underlying medical conditions † versus those without those conditions (apr = 1.9); persons with health insurance versus those without health insurance (apr = 1.8); non-hispanic black (black) adults (apr = 1.6) and hispanic or latino (hispanic) adults (apr = 1.5) versus non-hispanic white (white) adults; young adults aged 18-24 years versus adults aged 25-44 years (apr = 1.5); and persons with disabilities § versus those without disabilities (apr = 1.3). given this widespread reporting of medical care avoidance because of covid-19 concerns, especially among persons at increased risk for severe covid-19, urgent efforts are warranted to ensure delivery of services that, if deferred, could result in patient harm. even during the covid-19 pandemic, persons experiencing a medical emergency should seek and be provided care without delay (3).",0
"a model of arthritis was established by the injection of type ii collagen into mice. only mice bearing the h-2q haplotype were susceptible to the disease. susceptibility was further mapped by the use of recombinant strains on the iq locus. type ii collagen arthritis was observed in the (resistant x susceptible) f1 cross. mice strains were designated high, intermediate, or low responders with respect to the anti-type ii antibody levels measured by radioimmunoassay. arthritis-susceptible strains were all classified as high antibody responders. the clinical and histological appearance of type ii collagen arthritis in the mouse indicates that it may be a good animal model for the investigation of various immunogenetic traits in rheumatoid arthritis.",0
"autophagy is the primary cellular catabolic program activated in response to nutrient starvation. initiation of autophagy, particularly by amino-acid withdrawal, requires the ulk kinases. despite its pivotal role in autophagy initiation, little is known about the mechanisms by which ulk promotes autophagy. here we describe a molecular mechanism linking ulk to the pro-autophagic lipid kinase vps34. following amino-acid starvation or mtor inhibition, the activated ulk1 phosphorylates beclin-1 on ser 14, thereby enhancing the activity of the atg14l-containing vps34 complexes. the beclin-1 ser 14 phosphorylation by ulk is required for full autophagic induction in mammals and this requirement is conserved in caenorhabditis elegans. our study reveals a molecular link from ulk1 to activation of the autophagy-specific vps34 complex and autophagy induction.",0
"many species are experiencing sustained environmental change mainly due to human activities. the unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. to begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. we use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. two key parameters relating the environment to population biology have not yet received sufficient attention. phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. we use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.",0
"intact is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. two levels of curation are now available within the database, with both imex-level annotation and less detailed mimix-compatible entries currently supported. as from september 2011, intact contains approximately 275,000 curated binary interaction evidences from over 5000 publications. the intact website has been improved to enhance the search process and in particular the graphical display of the results. new data download formats are also available, which will facilitate the inclusion of intact's data in the semantic web. intact is an active contributor to the imex consortium ( intact source code and data are freely available at",0
"it has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. however, most of the focus in network studies has been on highly connected proteins (""hubs""). as a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many ""shortest paths"" going through them, analogous to major bridges and tunnels on a highway map). bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. in particular, they are more likely to be essential proteins. in fact, in regulatory and other directed networks, betweenness (i.e., ""bottleneck-ness"") is a much more significant indicator of essentiality than degree (i.e., ""hub-ness""). furthermore, bottlenecks correspond to the dynamic components of the interaction network-they are significantly less well coexpressed with their neighbors than non-bottlenecks, implying that expression dynamics is wired into the network topology.",0
"background stepped wedge randomised trial designs involve sequential roll-out of an intervention to participants (individuals or clusters) over a number of time periods. by the end of the study, all participants will have received the intervention, although the order in which participants receive the intervention is determined at random. the design is particularly relevant where it is predicted that the intervention will do more good than harm (making a parallel design, in which certain participants do not receive the intervention unethical) and/or where, for logistical, practical or financial reasons, it is impossible to deliver the intervention simultaneously to all participants. stepped wedge designs offer a number of opportunities for data analysis, particularly for modelling the effect of time on the effectiveness of an intervention. this paper presents a review of 12 studies (or protocols) that use (or plan to use) a stepped wedge design. one aim of the review is to highlight the potential for the stepped wedge design, given its infrequent use to date. methods comprehensive literature review of studies or protocols using a stepped wedge design. data were extracted from the studies in three categories for subsequent consideration: study information (epidemiology, intervention, number of participants), reasons for using a stepped wedge design and methods of data analysis. results the 12 studies included in this review describe evaluations of a wide range of interventions, across different diseases in different settings. however the stepped wedge design appears to have found a niche for evaluating interventions in developing countries, specifically those concerned with hiv. there were few consistent motivations for employing a stepped wedge design or methods of data analysis across studies. the methodological descriptions of stepped wedge studies, including methods of randomisation, sample size calculations and methods of analysis, are not always complete. conclusion while the stepped wedge design offers a number of opportunities for use in future evaluations, a more consistent approach to reporting and data analysis is required.",0
"background sequence similarity searching is a very important bioinformatics task. while basic local alignment search tool (blast) outperforms exact methods through its use of heuristics, the speed of the current blast software is suboptimal for very long queries or database sequences. there are also some shortcomings in the user-interface of the current command-line applications. results we describe features and improvements of rewritten blast software and introduce new command-line applications. long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. for long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing cpu time and memory usage for searches of short queries against databases of contigs or chromosomes. the program can now retrieve masking information for database sequences from the blast databases. a new modular software library can now access subject sequence data from arbitrary data sources. we introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. the strategy files can be uploaded to and downloaded from the ncbi blast web site. conclusion the new blast command-line applications, compared to the current blast tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. we have also improved the user interface of the command-line applications.",0
"the completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. peptideatlas ( addresses these needs by identifying peptides by tandem mass spectrometry (ms/ms), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. a meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. this uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. the raw data from many diverse proteomic experiments are made available in the associated peptideatlas repository in several formats. here we present a summary of our process and details about the human, drosophila and yeast peptideatlas builds.",0
"background negative attitudes towards vaccines and an uncertainty or unwillingness to receive vaccinations are major barriers to managing the covid-19 pandemic in the long-term. we estimate predictors of four domains of negative attitudes towards vaccines and identify groups most at risk of uncertainty and unwillingness to receive a covid-19 vaccine in a large sample of uk adults. methods data were cross-sectional and from 32,361 adults in the ucl covid-19 social study. ordinary least squares regression analyses examined the impact of socio-demographic and covid-19 related factors on four types of negative vaccine attitudes: mistrust of vaccine benefit, worries about unforeseen effects, concerns about commercial profiteering, and preference for natural immunity. multinomial regression examined the impact of socio-demographic and covid-19 related factors, negative vaccine attitudes, and prior vaccine behaviour on uncertainty and unwillingness to be vaccinated for covid-19. findings 16% of respondents displayed high levels of mistrust about vaccines across one or more domains. distrustful attitudes towards vaccination were higher amongst individuals from ethnic minority backgrounds, with lower levels of education, lower annual income, poor knowledge of covid-19, and poor compliance with government covid-19 guidelines. overall, 14% of respondents reported unwillingness to receive a vaccine for covid-19, whilst 23% were unsure. the largest predictors of both covid-19 vaccine uncertainty and refusal were low-income groups ( interpretation negative attitudes towards vaccines are a major public health concern in the uk. general mistrust in vaccines and concerns about future side effects in particular will be barriers to achieving population immunity to covid-19 through vaccination. public health messaging should be tailored to address these concerns and specifically to women, ethnic minorities, and people with lower levels of education and incomes. funding the nuffield foundation , the march mental health network funded by the cross-disciplinary mental health network plus initiative supported by uk research and innovation , and the wellcome trust .",0
"this report shows that cytotoxic t lymphocyte-associated antigen 4 (ctla-4) plays a key role in t cell-mediated dominant immunologic self-tolerance. in vivo blockade of ctla-4 for a limited period in normal mice leads to spontaneous development of chronic organ-specific autoimmune diseases, which are immunopathologically similar to human counterparts. in normal naive mice, ctla-4 is constitutively expressed on cd25(+)cd4(+) t cells, which constitute 5-10% of peripheral cd4(+) t cells. when the cd25(+)cd4(+) t cells are stimulated via the t cell receptor in vitro, they potently suppress antigen-specific and polyclonal activation and proliferation of other t cells, including ctla-4-deficient t cells, and blockade of ctla-4 abrogates the suppression. cd28-deficient cd25(+)cd4(+) t cells can also suppress normal t cells, indicating that cd28 is dispensable for activation of the regulatory t cells. thus, the cd25(+)cd4(+) regulatory t cell population engaged in dominant self-tolerance may require ctla-4 but not cd28 as a costimulatory molecule for its functional activation. furthermore, interference with this role of ctla-4 suffices to elicit autoimmune disease in otherwise normal animals, presumably through affecting cd25(+)cd4(+) t cell-mediated control of self-reactive t cells. this unique function of ctla-4 could be exploited to potentiate t cell-mediated immunoregulation, and thereby to induce immunologic tolerance or to control autoimmunity.",0
"breast cancer is a complex and heterogeneous disease. gene expression profiling has contributed significantly to our understanding of this heterogeneity at a molecular level, refining taxonomy based on simple measures such as histological type, tumour grade, lymph node status and the presence of predictive markers like oestrogen receptor and human epidermal growth factor receptor 2 (her2) to a more sophisticated classification comprising luminal a, luminal b, basal-like, her2-positive and normal subgroups. in the laboratory, breast cancer is often modelled using established cell lines. in the present review we discuss some of the issues surrounding the use of breast cancer cell lines as experimental models, in light of these revised clinical classifications, and put forward suggestions for improving their use in translational breast cancer research.",0
"targeted genetic engineering of human pluripotent cells is a prerequisite for exploiting their full potential. such genetic manipulations can be achieved using site-specific nucleases. here we engineered transcription activator-like effector nucleases (talens) for five distinct genomic loci. at all loci tested we obtained human embryonic stem cell (esc) and induced pluripotent stem cell (ipsc) clones carrying transgenic cassettes solely at the talen-specified location. our data suggest that talens employing the specific architectures described here mediate site-specific genome modification in human pluripotent cells with similar efficiency and precision as do zinc-finger nucleases (zfns).",0
"background statins reduce ldl cholesterol and prevent vascular events, but their net effects in people at low risk of vascular events remain uncertain. methods this meta-analysis included individual participant data from 22 trials of statin versus control (n=134,537; mean ldl cholesterol difference 1·08 mmol/l; median follow-up 4·8 years) and five trials of more versus less statin (n=39,612; difference 0·51 mmol/l; 5·1 years). major vascular events were major coronary events (ie, non-fatal myocardial infarction or coronary death), strokes, or coronary revascularisations. participants were separated into five categories of baseline 5-year major vascular event risk on control therapy (no statin or low-intensity statin) ( findings reduction of ldl cholesterol with a statin reduced the risk of major vascular events (rr 0·79, 95% ci 0·77-0·81, per 1·0 mmol/l reduction), largely irrespective of age, sex, baseline ldl cholesterol or previous vascular disease, and of vascular and all-cause mortality. the proportional reduction in major vascular events was at least as big in the two lowest risk categories as in the higher risk categories (rr per 1·0 mmol/l reduction from lowest to highest risk: 0·62 , 0·69 , 0·79 , 0·81 , and 0·79 ; trend p=0·04), which reflected significant reductions in these two lowest risk categories in major coronary events (rr 0·57, 99% ci 0·36-0·89, p=0·0012, and 0·61, 99% ci 0·50-0·74, p interpretation in individuals with 5-year risk of major vascular events lower than 10%, each 1 mmol/l reduction in ldl cholesterol produced an absolute reduction in major vascular events of about 11 per 1000 over 5 years. this benefit greatly exceeds any known hazards of statin therapy. under present guidelines, such individuals would not typically be regarded as suitable for ldl-lowering statin therapy. the present report suggests, therefore, that these guidelines might need to be reconsidered. funding british heart foundation; uk medical research council; cancer research uk; european community biomed programme; australian national health and medical research council; national heart foundation, australia.",0
"more than 25 million people in the world today are affected by dementia, most suffering from alzheimer's disease. in both developed and developing nations, alzheimer's disease has had tremendous impact on the affected individuals, caregivers, and society. the etiological factors, other than older age and genetic susceptibility, remain to be determined. nevertheless, increasing evidence strongly points to the potential risk roles of vascular risk factors and disorders (eg, cigarette smoking, midlife high blood pressure and obesity, diabetes, and cerebrovascular lesions) and the possible beneficial roles of psychosocial factors (eg, high education, active social engagement, physical exercise, and mentally stimulating activity) in the pathogenetic process and clinical manifestation of the dementing disorders. the long-term multidomain interventions toward the optimal control of multiple vascular risk factors and the maintenance of socially integrated lifestyles and mentally stimulating activities are expected to reduce the risk or postpone the clinical onset of dementia, including alzheimer's disease.",0
"as the third most common malignancy and the second most deadly cancer, colorectal cancer (crc) induces estimated 1.9 million incidence cases and 0.9 million deaths worldwide in 2020. the incidence of crc is higher in highly developed countries, and it is increasing in middle- and low-income countries due to westernization. moreover, a rising incidence of early-onset crc is also emerging. the large number of crc cases poses a growing global public health challenge. raising awareness of crc is important to promote healthy lifestyle choices, novel strategies for crc management, and implementation of global screening programs, which are critical to reducing crc morbidity and mortality in the future. crc is a heterogeneous disease, and its subtype affiliation influences prognosis and therapeutic response. an accurate crc subtype classification system is of great significance for basic research and clinical outcome. here, we present the global epidemiology of crc in 2020 and projections for 2040, review the major crc subtypes to better understand crc molecular basis, and summarize current risk factors, prevention, and screening strategies for crc.",0
"intraflagellar transport (ift) is a rapid movement of multi-subunit protein particles along flagellar microtubules and is required for assembly and maintenance of eukaryotic flagella. we cloned and sequenced a chlamydomonas cdna encoding the ift88 subunit of the ift particle and identified a chlamydomonas insertional mutant that is missing this gene. the phenotype of this mutant is normal except for the complete absence of flagella. ift88 is homologous to mouse and human genes called tg737. mice with defects in tg737 die shortly after birth from polycystic kidney disease. we show that the primary cilia in the kidney of tg737 mutant mice are shorter than normal. this indicates that ift is important for primary cilia assembly in mammals. it is likely that primary cilia have an important function in the kidney and that defects in their assembly can lead to polycystic kidney disease.",0
"an important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. here we introduce genomescope 2.0 ( which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. we describe and evaluate a practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity. we also present a method called smudgeplot ( to visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. we successfully apply the approach to systems of known variable ploidy levels in the meloidogyne genus and the extreme case of octoploid fragaria × ananassa.",0
"this paper describes a new program snpsift for filtering differential dna sequence variants between two or more experimental genomes after genotoxic chemical exposure. here, we illustrate how snpsift can be used to identify candidate phenotype-relevant variants including single nucleotide polymorphisms, multiple nucleotide polymorphisms, insertions, and deletions (indels) in mutant strains isolated from genome-wide chemical mutagenesis of drosophila melanogaster. first, the genomes of two independently isolated mutant fly strains that are allelic for a novel recessive male-sterile locus generated by genotoxic chemical exposure were sequenced using the illumina next-generation dna sequencer to obtain 20- to 29-fold coverage of the euchromatic sequences. the sequencing reads were processed and variants were called using standard bioinformatic tools. next, snpeff was used to annotate all sequence variants and their potential mutational effects on associated genes. then, snpsift was used to filter and select differential variants that potentially disrupt a common gene in the two allelic mutant strains. the potential causative dna lesions were partially validated by capillary sequencing of polymerase chain reaction-amplified dna in the genetic interval as defined by meiotic mapping and deletions that remove defined regions of the chromosome. of the five candidate genes located in the genetic interval, the pka-like gene cg12069 was found to carry a separate pre-mature stop codon mutation in each of the two allelic mutants whereas the other four candidate genes within the interval have wild-type sequences. the pka-like gene is therefore a strong candidate gene for the male-sterile locus. these results demonstrate that combining snpeff and snpsift can expedite the identification of candidate phenotype-causative mutations in chemically mutagenized drosophila strains. this technique can also be used to characterize the variety of mutations generated by genotoxic chemicals.",0
"rho-associated kinase (rho-kinase/rock/rok) is an effector of the small gtpase rho and belongs to the agc family of kinases. rho-kinase has pleiotropic functions including the regulation of cellular contraction, motility, morphology, polarity, cell division, and gene expression. pharmacological analyses have revealed that rho-kinase is involved in a wide range of diseases such as vasospasm, pulmonary hypertension, nerve injury, and glaucoma, and is therefore considered to be a potential therapeutic target. this review focuses on the structure, function, and modes of activation and action of rho-kinase.",0
"rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. extracting single nucleotide polymorphisms (snps) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. these tools are slow, memory inefficient and are installed through non-standard procedures. we present snp-sites which can rapidly extract snps from a multi-fasta alignment using modest resources and can output results in multiple formats for downstream analysis. snps can be extracted from a 8.3 gb alignment file (1842 taxa, 22 618 sites) in 267 seconds using 59 mb of ram and 1 cpu core, making it feasible to run on modest computers. it is easy to install through the debian and homebrew package managers, and has been successfully tested on more than 20 operating systems. snp-sites is implemented in c and is available under the open source license gnu gpl version 3.",0
"atherosclerosis, the major cause of cardiovascular disease (cvd), is a chronic inflammatory condition with immune competent cells in lesions producing mainly pro-inflammatory cytokines. dead cells and oxidized forms of low density lipoproteins (oxldl) are abundant. the major direct cause of cvd appears to be rupture of atherosclerotic plaques. oxldl has proinflammatory and immune-stimulatory properties, causes cell death at higher concentrations and contains inflammatory phospholipids with phosphorylcholine (pc) as an interesting epitope. antibodies against pc (anti-pc) may be atheroprotective, one mechanism being anti-inflammatory. bacteria and virus have been discussed, but it has been difficult to find direct evidence, and antibiotic trials have not been successful. heat shock proteins could be one major target for atherogenic immune reactions. more direct causes of plaque rupture include pro-inflammatory cytokines, chemokines, and lipid mediators. to prove that inflammation is a cause of atherosclerosis and cvd, clinical studies with anti-inflammatory and/or immune-modulatory treatment are needed. the potential causes of immune reactions and inflammation in atherosclerosis and how inflammation can be targeted therapeutically to provide novel treatments for cvd are reviewed.",0
"covid-19 can involve persistence, sequelae, and other medical complications that last weeks to months after initial recovery. this systematic review and meta-analysis aims to identify studies assessing the long-term effects of covid-19. litcovid and embase were searched to identify articles with original data published before the 1st of january 2021, with a minimum of 100 patients. for effects reported in two or more studies, meta-analyses using a random-effects model were performed using the metaxl software to estimate the pooled prevalence with 95% ci. prisma guidelines were followed. a total of 18,251 publications were identified, of which 15 met the inclusion criteria. the prevalence of 55 long-term effects was estimated, 21 meta-analyses were performed, and 47,910 patients were included (age 17-87 years). the included studies defined long-covid as ranging from 14 to 110 days post-viral infection. it was estimated that 80% of the infected patients with sars-cov-2 developed one or more long-term symptoms. the five most common symptoms were fatigue (58%), headache (44%), attention disorder (27%), hair loss (25%), and dyspnea (24%). multi-disciplinary teams are crucial to developing preventive measures, rehabilitation techniques, and clinical management strategies with whole-patient perspectives designed to address long covid-19 care.",0
"background reaching the therapeutic target of remission or low-disease activity has improved outcomes in patients with rheumatoid arthritis (ra) significantly. the treat-to-target recommendations, formulated in 2010, have provided a basis for implementation of a strategic approach towards this therapeutic goal in routine clinical practice, but these recommendations need to be re-evaluated for appropriateness and practicability in the light of new insights. objective to update the 2010 treat-to-target recommendations based on systematic literature reviews (slr) and expert opinion. methods a task force of rheumatologists, patients and a nurse specialist assessed the slr results and evaluated the individual items of the 2010 recommendations accordingly, reformulating many of the items. these were subsequently discussed, amended and voted upon by >40 experts, including 5 patients, from various regions of the world. levels of evidence, strengths of recommendations and levels of agreement were derived. results the update resulted in 4 overarching principles and 10 recommendations. the previous recommendations were partly adapted and their order changed as deemed appropriate in terms of importance in the view of the experts. the slr had now provided also data for the effectiveness of targeting low-disease activity or remission in established rather than only early disease. the role of comorbidities, including their potential to preclude treatment intensification, was highlighted more strongly than before. the treatment aim was again defined as remission with low-disease activity being an alternative goal especially in patients with long-standing disease. regular follow-up (every 1-3 months during active disease) with according therapeutic adaptations to reach the desired state was recommended. follow-up examinations ought to employ composite measures of disease activity that include joint counts. additional items provide further details for particular aspects of the disease, especially comorbidity and shared decision-making with the patient. levels of evidence had increased for many items compared with the 2010 recommendations, and levels of agreement were very high for most of the individual recommendations (≥9/10). conclusions the 4 overarching principles and 10 recommendations are based on stronger evidence than before and are supposed to inform patients, rheumatologists and other stakeholders about strategies to reach optimal outcomes of ra.",0
"ventral tegmental area (vta) dopamine neurons in the brain's reward circuit have a crucial role in mediating stress responses, including determining susceptibility versus resilience to social-stress-induced behavioural abnormalities. vta dopamine neurons show two in vivo patterns of firing: low frequency tonic firing and high frequency phasic firing. phasic firing of the neurons, which is well known to encode reward signals, is upregulated by repeated social-defeat stress, a highly validated mouse model of depression. surprisingly, this pathophysiological effect is seen in susceptible mice only, with no apparent change in firing rate in resilient individuals. however, direct evidence--in real time--linking dopamine neuron phasic firing in promoting the susceptible (depression-like) phenotype is lacking. here we took advantage of the temporal precision and cell-type and projection-pathway specificity of optogenetics to show that enhanced phasic firing of these neurons mediates susceptibility to social-defeat stress in freely behaving mice. we show that optogenetic induction of phasic, but not tonic, firing in vta dopamine neurons of mice undergoing a subthreshold social-defeat paradigm rapidly induced a susceptible phenotype as measured by social avoidance and decreased sucrose preference. optogenetic phasic stimulation of these neurons also quickly induced a susceptible phenotype in previously resilient mice that had been subjected to repeated social-defeat stress. furthermore, we show differences in projection-pathway specificity in promoting stress susceptibility: phasic activation of vta neurons projecting to the nucleus accumbens (nac), but not to the medial prefrontal cortex (mpfc), induced susceptibility to social-defeat stress. conversely, optogenetic inhibition of the vta-nac projection induced resilience, whereas inhibition of the vta-mpfc projection promoted susceptibility. overall, these studies reveal novel firing-pattern- and neural-circuit-specific mechanisms of depression.",0
"dendritic cells (dc) are the most efficient apc for t cells. the clinical use of dc as vectors for anti-tumor and infectious disease immunotherapy has been limited by their trace levels and accessibility in normal tissue and terminal state of differentiation. in the present study, daily injection of human flt3 ligand (flt3l) into mice results in a dramatic numerical increase in cells co-expressing the characteristic dc markers-class ii mhc, cd11c, dec205, and cd86. in contrast, in mice treated with either gm-csf, gm-csf plus il-4, c-kit ligand (c-kitl), or g-csf, class ii+ cd11c+ cells were not significantly increased. five distinct dc subpopulations were identified in the spleen of flt3l-treated mice using cd8 alpha and cd11b expression. these cells exhibited veiled and dendritic processes and were as efficient as rare, mature dc isolated from the spleens of untreated mice at presenting allo-ag or soluble ag to t cells, or in priming an ag-specific t cell response in vivo. dramatic numerical increases in dc were detected in the bone marrow, gastro-intestinal lymphoid tissue (galt), liver, lymph nodes, lung, peripheral blood, peritoneal cavity, spleen, and thymus. these results suggest that flt3l could be used to expand the numbers of functionally mature dc in vivo for use in clinical immunotherapy.",0
"background the swedish national inpatient register (ipr), also called the hospital discharge register, is a principal source of data for numerous research projects. the ipr is part of the national patient register. the swedish ipr was launched in 1964 (psychiatric diagnoses from 1973) but complete coverage did not begin until 1987. currently, more than 99% of all somatic (including surgery) and psychiatric hospital discharges are registered in the ipr. a previous validation of the ipr by the national board of health and welfare showed that 85-95% of all diagnoses in the ipr are valid. the current paper describes the history, structure, coverage and quality of the swedish ipr. methods and results in january 2010, we searched the medical databases, medline and highwire, using the search algorithm ""validat* (inpatient or hospital discharge) sweden"". we also contacted 218 members of the swedish society of epidemiology and an additional 201 medical researchers to identify papers that had validated the ipr. in total, 132 papers were reviewed. the positive predictive value (ppv) was found to differ between diagnoses in the ipr, but is generally 85-95%. conclusions in conclusion, the validity of the swedish ipr is high for many but not all diagnoses. the long follow-up makes the register particularly suitable for large-scale population-based research, but for certain research areas the use of other health registers, such as the swedish cancer register, may be more suitable.",0
"a procedure is described which permits the isolation from the prepuberal mouse testis of highly purified populations of primitive type a spermatogonia, type a spermatogonia, type b spermatogonia, preleptotene primary spermatocytes, leptotene and zygotene primary spermatocytes, pachytene primary spermatocytes and sertoli cells. the successful isolation of these prepuberal cell types was accomplished by: (a) defining distinctive morphological characteristics of the cells, (b) determining the temporal appearance of spermatogenic cells during prepuberal development, (c) isolating purified seminiferous cords, after dissociation of the testis with collagenase, (d) separating the trypsin-dispersed seminiferous cells by sedimentation velocity at unit gravity, and (e) assessing the identity and purity of the isolated cell types by microscopy. the seminiferous epithelium from day 6 animals contains only primitive type a spermatogonia and sertoli cells. type a and type b spermatogonia are present by day 8. at day 10, meiotic prophase is initiated, with the germ cells reaching the early and late pachytene stages by 14 and 18, respectively. secondary spermatocytes and haploid spermatids appear throughout this developmental period. the purity and optimum day for the recovery of specific cell types are as follows: day 6, sertoli cells (purity>99 percent) and primitive type a spermatogonia (90 percent); day 8, type a spermatogonia (91 percent) and type b spermatogonia (76 percent); day 18, preleptotene spermatocytes (93 percent), leptotene/zygotene spermatocytes (52 percent), and pachytene spermatocytes (89 percent), leptotene/zygotene spermatocytes (52 percent), and pachytene spermatocytes (89 percent).",0
"summary the biopython project is a mature open source international collaboration of volunteer developers, providing python libraries for a wide range of bioinformatics problems. biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3d macro molecular structures, interacting with common tools such as blast, clustalw and emboss, accessing key online databases, as well as providing numerical methods for statistical learning. availability biopython is freely available, with documentation and source code at ( under the biopython license.",0
"this paper describes an approach that we have evolved for developing successful digital interventions to help people manage their health or illness. we refer to this as the ""person-based"" approach to highlight the focus on understanding and accommodating the perspectives of the people who will use the intervention. while all intervention designers seek to elicit and incorporate the views of target users in a variety of ways, the person-based approach offers a distinctive and systematic means of addressing the user experience of intended behavior change techniques in particular and can enhance the use of theory-based and evidence-based approaches to intervention development. there are two key elements to the person-based approach. the first is a developmental process involving qualitative research with a wide range of people from the target user populations, carried out at every stage of intervention development, from planning to feasibility testing and implementation. this process goes beyond assessing acceptability, usability, and satisfaction, allowing the intervention designers to build a deep understanding of the psychosocial context of users and their views of the behavioral elements of the intervention. insights from this process can be used to anticipate and interpret intervention usage and outcomes, and most importantly to modify the intervention to make it more persuasive, feasible, and relevant to users. the second element of the person-based approach is to identify ""guiding principles"" that can inspire and inform the intervention development by highlighting the distinctive ways that the intervention will address key context-specific behavioral issues. this paper describes how to implement the person-based approach, illustrating the process with examples of the insights gained from our experience of carrying out over a thousand interviews with users, while developing public health and illness management interventions that have proven effective in trials involving tens of thousands of users.",0
"previous studies suggested that tetrodotoxin, a poison from the puffer fish, blocks conduction of nerve and muscle through its rather selective inhibition of the sodium-carrying mechanism. in order to verify this hypothesis, observations have been made of sodium and potassium currents in the lobster giant axons treated with tetrodotoxin by means of the sucrose-gap voltage-clamp technique. tetrodotoxin at concentrations of 1 x 10(-7) to 5 x 10(-9) gm/ml blocked the action potential but had no effect on the resting potential. partial or complete recovery might have occurred on washing with normal medium. the increase in sodium conductance normally occurring upon depolarization was very effectively suppressed when the action potential was blocked after tetrodotoxin, while the delayed increase in potassium conductance underwent no change. it is concluded that tetrodotoxin, at very low concentrations, blocks the action potential production through its selective inhibition of the sodium-carrying mechanism while keeping the potassium-carrying mechanism intact.",0
"background we recently showed that enzymes of the tet family convert 5-mc to 5-hydroxymethylcytosine (5-hmc) in dna. 5-hmc is present at high levels in embryonic stem cells and purkinje neurons. the methylation status of cytosines is typically assessed by reaction with sodium bisulfite followed by pcr amplification. reaction with sodium bisulfite promotes cytosine deamination, whereas 5-methylcytosine (5-mc) reacts poorly with bisulfite and is resistant to deamination. since 5-hmc reacts with bisulfite to yield cytosine 5-methylenesulfonate (cms), we asked how dna containing 5-hmc behaves in bisulfite sequencing. methodology/principal findings we used synthetic oligonucleotides with different distributions of cytosine as templates for generation of dnas containing c, 5-mc and 5-hmc. the resulting dnas were subjected in parallel to bisulfite treatment, followed by exposure to conditions promoting cytosine deamination. the extent of conversion of 5-hmc to cms was estimated to be 99.7%. sequencing of pcr products showed that neither 5-mc nor 5-hmc undergo c-to-t transitions after bisulfite treatment, confirming that these two modified cytosine species are indistinguishable by the bisulfite technique. dna in which cms constituted a large fraction of all bases (28/201) was much less efficiently amplified than dna in which those bases were 5-mc or uracil (the latter produced by cytosine deamination). using a series of primer extension experiments, we traced the inefficient amplification of cms-containing dna to stalling of taq polymerase at sites of cms modification, especially when two cms bases were either adjacent to one another or separated by 1-2 nucleotides. conclusions we have confirmed that the widely used bisulfite sequencing technique does not distinguish between 5-mc and 5-hmc. moreover, we show that cms, the product of bisulfite conversion of 5-hmc, tends to stall dna polymerases during pcr, suggesting that densely hydroxymethylated regions of dna may be underrepresented in quantitative methylation analyses.",0
"introduction e-cigarettes are largely unregulated and internet sales are substantial. this study examines how the online market for e-cigarettes has changed over time: in product design and in marketing messages appearing on websites. methods comprehensive internet searches of english-language websites from may-august 2012 and december 2013-january 2014 identified brands, models, flavours, nicotine strengths, ingredients and product claims. brands were divided into older and newer groups (by the two searches) for comparison. results by january 2014 there were 466 brands (each with its own website) and 7764 unique flavours. in the 17 months between the searches, there was a net increase of 10.5 brands and 242 new flavours per month. older brands were more likely than newer brands to offer cigalikes (86.9% vs. 52.1%, p conclusions the number of e-cigarette brands is large and has been increasing. older brands tend to highlight their advantages over conventional cigarettes while newer brands emphasise consumer choice in multiple flavours and product versatility. these results can serve as a benchmark for future research on the impact of upcoming regulations on product design and advertising messages of e-cigarettes.",0
"this first update of the asas/eular recommendations on the management of ankylosing spondylitis (as) is based on the original paper, a systematic review of existing recommendations and the literature since 2005 and the discussion and agreement among 21 international experts, 2 patients and 2 physiotherapists in a meeting in february 2010. each original bullet point was discussed in detail and reworded if necessary. decisions on new recommendations were made - if necessary after voting. the strength of the recommendations (sor) was scored on an 11-point numerical rating scale after the meeting by email. these recommendations apply to patients of all ages that fulfill the modified ny criteria for as, independent of extra-articular manifestations, and they take into account all drug and non-drug interventions related to as. four overarching principles were introduced, implying that one bullet has been moved to this section. there are now 11 bullet points including 2 new ones, one related to extra-articular manifestations and one to changes in the disease course. with a mean score of 9.1 (range 8-10) the sor was generally very good.",0
"we present a high-quality genome sequence of a neanderthal woman from siberia. we show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. we also sequenced the genome of a neanderthal from the caucasus to low coverage. an analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among neanderthals, denisovans and early modern humans, possibly including gene flow into denisovans from an unknown archaic group. thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the late pleistocene. in addition, the high-quality neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of neanderthals and denisovans.",0
"the initial genome-scale reconstruction of the metabolic network of escherichia coli k-12 mg1655 was assembled in 2000. it has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. an update has now been built, named ijo1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. ijo1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced e. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. like its predecessors, the ijo1366 reconstruction is expected to be widely deployed for studying the systems biology of e. coli and for metabolic engineering applications.",0
"the standard bootstrap (sbs), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. we recently proposed the ultrafast bootstrap approximation (ufboot) to reduce computing time while achieving more unbiased branch supports than sbs under mild model violations. ufboot has been steadily adopted as an efficient alternative to sbs and other bootstrap approaches. here, we present ufboot2, which substantially accelerates ufboot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. additionally, ufboot2 provides suitable bootstrap resampling strategies for phylogenomic data. ufboot2 is 778 times (median) faster than sbs and 8.4 times (median) faster than raxml rapid bootstrap on tested data sets. ufboot2 is implemented in the iq-tree software package version 1.6 and freely available at",0
"summary the avon longitudinal study of children and parents (alspac) was established to understand how genetic and environmental characteristics influence health and development in parents and children. all pregnant women resident in a defined area in the south west of england, with an expected date of delivery between 1st april 1991 and 31st december 1992, were eligible and 13761 women (contributing 13867 pregnancies) were recruited. these women have been followed over the last 19-22 years and have completed up to 20 questionnaires, have had detailed data abstracted from their medical records and have information on any cancer diagnoses and deaths through record linkage. a follow-up assessment was completed 17-18 years postnatal at which anthropometry, blood pressure, fat, lean and bone mass and carotid intima media thickness were assessed, and a fasting blood sample taken. the second follow-up clinic, which additionally measures cognitive function, physical capability, physical activity (with accelerometer) and wrist bone architecture, is underway and two further assessments with similar measurements will take place over the next 5 years. there is a detailed biobank that includes dna, with genome-wide data available on >10000, stored serum and plasma taken repeatedly since pregnancy and other samples; a wide range of data on completed biospecimen assays are available. details of how to access these data are provided in this cohort profile.",0
"we recently described a methodology that reliably predicted chemotherapeutic response in multiple independent clinical trials. the method worked by building statistical models from gene expression and drug sensitivity data in a very large panel of cancer cell lines, then applying these models to gene expression data from primary tumor biopsies. here, to facilitate the development and adoption of this methodology we have created an r package called prrophetic. this also extends the previously described pipeline, allowing prediction of clinical drug response for many cancer drugs in a user-friendly r environment. we have developed several other important use cases; as an example, we have shown that prediction of bortezomib sensitivity in multiple myeloma may be improved by training models on a large set of neoplastic hematological cell lines. we have also shown that the package facilitates model development and prediction using several different classes of data.",0
"background the evaluation of interventions and policies designed to promote resilience, and research to understand the determinants and associations, require reliable and valid measures to ensure data quality. this paper systematically reviews the psychometric rigour of resilience measurement scales developed for use in general and clinical populations. methods eight electronic abstract databases and the internet were searched and reference lists of all identified papers were hand searched. the focus was to identify peer reviewed journal articles where resilience was a key focus and/or is assessed. two authors independently extracted data and performed a quality assessment of the scale psychometric properties. results nineteen resilience measures were reviewed; four of these were refinements of the original measure. all the measures had some missing information regarding the psychometric properties. overall, the connor-davidson resilience scale, the resilience scale for adults and the brief resilience scale received the best psychometric ratings. the conceptual and theoretical adequacy of a number of the scales was questionable. conclusion we found no current 'gold standard' amongst 15 measures of resilience. a number of the scales are in the early stages of development, and all require further validation work. given increasing interest in resilience from major international funders, key policy makers and practice, researchers are urged to report relevant validation statistics when using the measures.",0
"background mutagenesis plays an essential role in molecular biology and biochemistry. it has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. the ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. results we have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the quikchange site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. this modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized dna to be used as the template in subsequent amplification cycles. these two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. conclusion our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard quikchange. furthermore the new protocol required significantly less parental dna which facilitated the dpni digestion after the pcr amplification and enhanced the overall efficiency and reliability. using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. the results demonstrated that this new protocol imposed no additional reagent costs (beyond basic quikchange) but increased the overall success rates.",0
"we did a case-control study in five hong kong hospitals, with 241 non-infected and 13 infected staff with documented exposures to 11 index patients with severe acute respiratory syndrome (sars) during patient care. all participants were surveyed about use of mask, gloves, gowns, and hand-washing, as recommended under droplets and contact precautions when caring for index patients with sars. 69 staff who reported use of all four measures were not infected, whereas all infected staff had omitted at least one measure (p=0.0224). fewer staff who wore masks (p=0.0001), gowns (p=0.006), and washed their hands (p=0.047) became infected compared with those who didn't, but stepwise logistic regression was significant only for masks (p=0.011). practice of droplets precaution and contact precaution is adequate in significantly reducing the risk of infection after exposures to patients with sars. the protective role of the mask suggests that in hospitals, infection is transmitted by droplets.",0
"background b-cell epitopes are the sites of molecules that are recognized by antibodies of the immune system. knowledge of b-cell epitopes may be used in the design of vaccines and diagnostics tests. it is therefore of interest to develop improved methods for predicting b-cell epitopes. in this paper, we describe an improved method for predicting linear b-cell epitopes. results in order to do this, three data sets of linear b-cell epitope annotated proteins were constructed. a data set was collected from the literature, another data set was extracted from the antijen database and a data sets of epitopes in the proteins of hiv was collected from the los alamos hiv database. an unbiased validation of the methods was made by testing on data sets on which they were neither trained nor optimized on. we have measured the performance in a non-parametric way by constructing roc-curves. conclusion the best single method for predicting linear b-cell epitopes is the hidden markov model. combining the hidden markov model with one of the best propensity scale methods, we obtained the bepipred method. when tested on the validation data set this method performs significantly better than any of the other methods tested. the server and data sets are publicly available at",0
"we previously demonstrated that the gap junction protein connexin43 is translated as a 42-kd protein (connexin43-np) that is efficiently phosphorylated to a 46,000-mr species (connexin43-p2) in gap junctional communication-competent, but not in communication-deficient, cells. in this study, we used a combination of metabolic radiolabeling and immunoprecipitation to investigate the assembly of connexin43 into gap junctions and the relationship of this event to phosphorylation of connexin43. examination of the detergent solubility of connexin43 in communication-competent nrk cells revealed that processing of connexin43 to the p2 form was accompanied by acquisition of resistance to solubilization in 1% triton x-100. immunohistochemical localization of connexin43 in triton-extracted nrk cells demonstrated that connexin43-p2 (triton-insoluble) was concentrated in gap junctional plaques, whereas connexin43-np (triton-soluble) was predominantly intracellular. using either a 20 degrees c intracellular transport block or cell-surface protein biotinylation, we determined that connexin43 was transported to the plasma membrane in the triton-soluble connexin43-np form. cell-surface biotinylated connexin43-np was processed to triton-insoluble connexin43-p2 at 37 degrees c. connexin43-np was also transported to the plasma membrane in communication defective, gap junction-deficient s180 and l929 cells but was not processed to triton-insoluble connexin43-p2. taken together, these results demonstrate that gap junction assembly is regulated after arrival of connexin43 at the plasma membrane and is temporally associated with acquisition of insolubility in triton x-100 and phosphorylation to the connexin43-p2 form.",0
"osteogenesis during bone modeling and remodeling is coupled with angiogenesis. a recent study showed that a specific vessel subtype, strongly positive for cd31 and endomucin (cd31(hi)emcn(hi)), couples angiogenesis and osteogenesis. here, we found that platelet-derived growth factor-bb (pdgf-bb) secreted by preosteoclasts induces cd31(hi)emcn(hi) vessel formation during bone modeling and remodeling. mice with depletion of pdgf-bb in the tartrate-resistant acid phosphatase-positive cell lineage show significantly lower trabecular and cortical bone mass, serum and bone marrow pdgf-bb concentrations, and fewer cd31(hi)emcn(hi) vessels compared to wild-type mice. in the ovariectomy (ovx)-induced osteoporotic mouse model, serum and bone marrow levels of pdgf-bb and numbers of cd31(hi)emcn(hi) vessels are significantly lower compared to sham-operated controls. treatment with exogenous pdgf-bb or inhibition of cathepsin k to increase the number of preosteoclasts, and thus the endogenous levels of pdgf-bb, increases cd31(hi)emcn(hi) vessel number and stimulates bone formation in ovx mice. thus, pharmacotherapies that increase pdgf-bb secretion from preosteoclasts offer a new therapeutic target for treating osteoporosis by promoting angiogenesis and thus bone formation.",0
"autophagy and the cvt pathway are examples of nonclassical vesicular transport from the cytoplasm to the vacuole via double-membrane vesicles. apg8/aut7, which plays an important role in the formation of such vesicles, tends to bind to membranes in spite of its hydrophilic nature. we show here that the nature of the association of apg8 with membranes changes depending on a series of modifications of the protein itself. first, the carboxy-terminal arg residue of newly synthesized apg8 is removed by apg4/aut2, a novel cysteine protease, and a gly residue becomes the carboxy-terminal residue of the protein that is now designated apg8fg. subsequently, apg8fg forms a conjugate with an unidentified molecule ""x"" and thereby binds tightly to membranes. this modification requires the carboxy-terminal gly residue of apg8fg and apg7, a ubiquitin e1-like enzyme. finally, the adduct apg8fg-x is reversed to soluble or loosely membrane-bound apg8fg by cleavage by apg4. the mode of action of apg4, which cleaves both newly synthesized apg8 and modified apg8fg, resembles that of deubiquitinating enzymes. a reaction similar to ubiquitination is probably involved in the second modification. the reversible modification of apg8 appears to be coupled to the membrane dynamics of autophagy and the cvt pathway.",0
"this article presents w-iq-tree, an intuitive and user-friendly web interface and server for iq-tree, an efficient phylogenetic software for maximum likelihood analysis. w-iq-tree supports multiple sequence types (dna, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. w-iq-tree performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. all computations are conducted on a dedicated computer cluster and the users receive the results via url or email. w-iq-tree is available at it is free and open to all users and there is no login requirement.",0
"hyperinflammatory responses can lead to a variety of diseases, including sepsis. we now report that extracellular histones released in response to inflammatory challenge contribute to endothelial dysfunction, organ failure and death during sepsis. they can be targeted pharmacologically by antibody to histone or by activated protein c (apc). antibody to histone reduced the mortality of mice in lipopolysaccharide (lps), tumor necrosis factor (tnf) or cecal ligation and puncture models of sepsis. extracellular histones are cytotoxic toward endothelium in vitro and are lethal in mice. in vivo, histone administration resulted in neutrophil margination, vacuolated endothelium, intra-alveolar hemorrhage and macro- and microvascular thrombosis. we detected histone in the circulation of baboons challenged with escherichia coli, and the increase in histone levels was accompanied by the onset of renal dysfunction. apc cleaves histones and reduces their cytotoxicity. co-infusion of apc with e. coli in baboons or histones in mice prevented lethality. blockade of protein c activation exacerbated sublethal lps challenge into lethality, which was reversed by treatment with antibody to histone. we conclude that extracellular histones are potential molecular targets for therapeutics for sepsis and other inflammatory diseases.",0
"in late 2019, cases of atypical pneumonia were detected in china. the etiological agent was quickly identified as a betacoronavirus (named sars-cov-2), which has since caused a pandemic. several methods allowing for the specific detection of viral nucleic acids have been established, but these only allow detection of the virus during a short period of time, generally during acute infection. serological assays are urgently needed to conduct serosurveys, to understand the antibody responses mounted in response to the virus, and to identify individuals who are potentially immune to re-infection. here we describe a detailed protocol for expression of antigens derived from the spike protein of sars-cov-2 that can serve as a substrate for immunological assays, as well as a two-stage serological enzyme-linked immunosorbent assay (elisa). these assays can be used for research studies and for testing in clinical laboratories. © 2020 the authors. basic protocol 1: mammalian cell transfection and protein purification basic protocol 2: a two-stage elisa for high-throughput screening of human serum samples for antibodies binding to the spike protein of sars-cov-2.",0
"for a number of years the biomart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the ensembl project. the launch of the ensembl genomes project in 2009 complemented the ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. the ensembl and ensembl genomes biomarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. this article aims to give a comprehensive overview of the ensembl and ensembl genomes biomarts as well as some useful examples and a description of current data content and future objectives. database urls:",0
"the american diabetes association and the european association for the study of diabetes have briefly updated their 2018 recommendations on management of hyperglycemia, based on important research findings from large cardiovascular outcomes trials published in 2019. important changes include: 1 ) the decision to treat high-risk individuals with a glucagon-like peptide 1 (glp-1) receptor agonist or sodium-glucose cotransporter 2 (sglt2) inhibitor to reduce major adverse cardiovascular events (mace), hospitalization for heart failure (hhf), cardiovascular death, or chronic kidney disease (ckd) progression should be considered independently of baseline hba 1c or individualized hba 1c target; 2 ) glp-1 receptor agonists can also be considered in patients with type 2 diabetes without established cardiovascular disease (cvd) but with the presence of specific indicators of high risk; and 3 ) sglt2 inhibitors are recommended in patients with type 2 diabetes and heart failure, particularly those with heart failure with reduced ejection fraction, to reduce hhf, mace, and cvd death, as well as in patients with type 2 diabetes with ckd (estimated glomerular filtration rate 30 to ≤60 ml min -1 -2 or urinary albumin-to-creatinine ratio >30 mg/g, particularly >300 mg/g) to prevent the progression of ckd, hhf, mace, and cardiovascular death.",0
"today's best perovskite solar cells use a mixture of formamidinium and methylammonium as the monovalent cations. with the addition of inorganic cesium, the resulting triple cation perovskite compositions are thermally more stable, contain less phase impurities and are less sensitive to processing conditions. this enables more reproducible device performances to reach a stabilized power output of 21.1% and ∼18% after 250 hours under operational conditions. these properties are key for the industrialization of perovskite photovoltaics.",0
"carbohydrate-active enzymes (cazymes) are very important to the biotech industry, particularly the emerging biofuel industry because cazymes are responsible for the synthesis, degradation and modification of all the carbohydrates on earth. we have developed a web resource, dbcan ( to provide a capability for automated cazyme signature domain-based annotation for any given protein data set (e.g. proteins from a newly sequenced genome) submitted to our server. to accomplish this, we have explicitly defined a signature domain for every cazyme family, derived based on the cdd (conserved domain database) search and literature curation. we have also constructed a hidden markov model to represent the signature domain of each cazyme family. these cazyme family-specific hmms are our key contribution and the foundation for the automated cazyme annotation.",0
"we introduce the mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images. to manually label the macroscopic anatomy in magnetic resonance images of 101 healthy participants, we created a new cortical labeling protocol that relies on robust anatomical landmarks and minimal manual edits after initialization with automated labels. the ""desikan-killiany-tourville"" (dkt) protocol is intended to improve the ease, consistency, and accuracy of labeling human cortical areas. given how difficult it is to label brains, the mindboggle-101 dataset is intended to serve as brain atlases for use in labeling other brains, as a normative dataset to establish morphometric variation in a healthy population for comparison against clinical populations, and contribute to the development, training, testing, and evaluation of automated registration and labeling algorithms. to this end, we also introduce benchmarks for the evaluation of such algorithms by comparing our manual labels with labels automatically generated by probabilistic and multi-atlas registration-based approaches. all data and related software and updated information are available on the website.",0
"it has been shown that the immune response of mice to infection with l. monocytogenes gives rise to a population of immunologically committed lymphoid cells which have the capacity to confer protection and a proportionate level of delayed-type hypersensitivity upon normal recipients. the cells were most numerous in the spleen on the 6th or 7th day of infection, but persisted for at least 20 days. further study revealed that the immune cells must be alive in order to confer protection, and free to multiply in the tissues of the recipient if they are to provide maximum resistance to a challenge infection. the antibacterial resistance conferred with immune lymphoid cells is not due to antibacterial antibody; it is mediated indirectly through the macrophages of the recipient. these become activated by a process which appears to depend upon some form of specific interaction between the immune lymphoid cells and the infecting organism. this was deduced from the finding that immune lymphoid cells from bcg-immunized donors, which were highly but nonspecifically resistant to listeria, failed to protect normal recipients against a listeria challenge unless the recipients were also injected with an eliciting dose of bcg. the peritoneal macrophages of animals so treated developed the morphology and microbicidal features of activated macrophages. it is inferred that acquired resistance depends upon the activation of host macrophages through a product resulting from specific interaction between sensitized lymphoid cells and the organism or or its antigenic products. discussion is also made of the possibility that activation of macrophages could be dependent upon antigenic stimulation of macrophages sensitized by a cytophilic antibody.",0
"background the international standard radiotherapy schedule for early breast cancer delivers 50 gy in 25 fractions of 2.0 gy over 5 weeks, but there is a long history of non-standard regimens delivering a lower total dose using fewer, larger fractions (hypofractionation). we aimed to test the benefits of radiotherapy schedules using fraction sizes larger than 2.0 gy in terms of local-regional tumour control, normal tissue responses, quality of life, and economic consequences in women prescribed post-operative radiotherapy. methods between 1999 and 2001, 2215 women with early breast cancer (pt1-3a pn0-1 m0) at 23 centres in the uk were randomly assigned after primary surgery to receive 50 gy in 25 fractions of 2.0 gy over 5 weeks or 40 gy in 15 fractions of 2.67 gy over 3 weeks. women were eligible for the trial if they were aged over 18 years, did not have an immediate reconstruction, and were available for follow-up. randomisation method was computer generated and was not blinded. the protocol-specified principal endpoints were local-regional tumour relapse, defined as reappearance of cancer at irradiated sites, late normal tissue effects, and quality of life. analysis was by intention to treat. this study is registered as an international standard randomised controlled trial, number isrctn59368779. findings 1105 women were assigned to the 50 gy group and 1110 to the 40 gy group. after a median follow up of 6.0 years (iqr 5.0-6.2) the rate of local-regional tumour relapse at 5 years was 2.2% (95% ci 1.3-3.1) in the 40 gy group and 3.3% (95% ci 2.2 to 4.5) in the 50 gy group, representing an absolute difference of -0.7% (95% ci -1.7% to 0.9%)--ie, the absolute difference in local-regional relapse could be up to 1.7% better and at most 1% worse after 40 gy than after 50 gy. photographic and patient self-assessments indicated lower rates of late adverse effects after 40 gy than after 50 gy. interpretation a radiation schedule delivering 40 gy in 15 fractions seems to offer rates of local-regional tumour relapse and late adverse effects at least as favourable as the standard schedule of 50 gy in 25 fractions.",0
"background implementing new practices requires changes in the behaviour of relevant actors, and this is facilitated by understanding of the determinants of current and desired behaviours. the theoretical domains framework (tdf) was developed by a collaboration of behavioural scientists and implementation researchers who identified theories relevant to implementation and grouped constructs from these theories into domains. the collaboration aimed to provide a comprehensive, theory-informed approach to identify determinants of behaviour. the first version was published in 2005, and a subsequent version following a validation exercise was published in 2012. this guide offers practical guidance for those who wish to apply the tdf to assess implementation problems and support intervention design. it presents a brief rationale for using a theoretical approach to investigate and address implementation problems, summarises the tdf and its development, and describes how to apply the tdf to achieve implementation objectives. examples from the implementation research literature are presented to illustrate relevant methods and practical considerations. methods researchers from canada, the uk and australia attended a 3-day meeting in december 2012 to build an international collaboration among researchers and decision-makers interested in the advancing use of the tdf. the participants were experienced in using the tdf to assess implementation problems, design interventions, and/or understand change processes. this guide is an output of the meeting and also draws on the authors' collective experience. examples from the implementation research literature judged by authors to be representative of specific applications of the tdf are included in this guide. results we explain and illustrate methods, with a focus on qualitative approaches, for selecting and specifying target behaviours key to implementation, selecting the study design, deciding the sampling strategy, developing study materials, collecting and analysing data, and reporting findings of tdf-based studies. areas for development include methods for triangulating data, e.g. from interviews, questionnaires and observation and methods for designing interventions based on tdf-based problem analysis. conclusions we offer this guide to the implementation community to assist in the application of the tdf to achieve implementation objectives. benefits of using the tdf include the provision of a theoretical basis for implementation studies, good coverage of potential reasons for slow diffusion of evidence into practice and a method for progressing from theory-based investigation to intervention.",0
"background the use of global health items permits an efficient way of gathering general perceptions of health. these items provide useful summary information about health and are predictive of health care utilization and subsequent mortality. methods analyses of 10 self-reported global health items obtained from an internet survey as part of the patient-reported outcome measurement information system (promis) project. we derived summary scores from the global health items. we estimated the associations of the summary scores with the eq-5d index score and the promis physical function, pain, fatigue, emotional distress, and social health domain scores. results exploratory and confirmatory factor analyses supported a two-factor model. global physical health (gph; 4 items on overall physical health, physical function, pain, and fatigue) and global mental health (gmh; 4 items on quality of life, mental health, satisfaction with social activities, and emotional problems) scales were created. the scales had internal consistency reliability coefficients of 0.81 and 0.86, respectively. gph correlated more strongly with the eq-5d than did gmh (r = 0.76 vs. 0.59). gph correlated most strongly with pain impact (r = -0.75) whereas gmh correlated most strongly with depressive symptoms (r = -0.71). conclusions two dimensions representing physical and mental health underlie the global health items in promis. these global health scales can be used to efficiently summarize physical and mental health in patient-reported outcome studies.",0
"the rate of acute kidney injury (aki) associated with patients hospitalized with covid-19, and associated outcomes are not well understood. this study describes the presentation, risk factors and outcomes of aki in patients hospitalized with covid-19. we reviewed the health records for all patients hospitalized with covid-19 between march 1, and april 5, 2020, at 13 academic and community hospitals in metropolitan new york. patients younger than 18 years of age, with end stage kidney disease or with a kidney transplant were excluded. aki was defined according to kdigo criteria. of 5,449 patients admitted with covid-19, aki developed in 1,993 (36.6%). the peak stages of aki were stage 1 in 46.5%, stage 2 in 22.4% and stage 3 in 31.1%. of these, 14.3% required renal replacement therapy (rrt). aki was primarily seen in covid-19 patients with respiratory failure, with 89.7% of patients on mechanical ventilation developing aki compared to 21.7% of non-ventilated patients. 276/285 (96.8%) of patients requiring rrt were on ventilators. of patients who required ventilation and developed aki, 52.2% had the onset of aki within 24 hours of intubation. risk factors for aki included older age, diabetes mellitus, cardiovascular disease, black race, hypertension and need for ventilation and vasopressor medications. among patients with aki, 694 died (35%), 519 (26%) were discharged and 780 (39%) were still hospitalized. aki occurs frequently among patients with covid-19 disease. it occurs early and in temporal association with respiratory failure and is associated with a poor prognosis.",0
"diverse membrane fusion reactions in biology involve close contact between two lipid bilayers, followed by the local distortion of the individual bilayers and reformation into a single, merged membrane. we consider the structures and energies of the fusion intermediates identified in experimental and theoretical work on protein-free lipid bilayers. on the basis of this analysis, we then discuss the conserved fusion-through-hemifusion pathway of merger between biological membranes and propose that the entire progression, from the close juxtaposition of membrane bilayers to the expansion of a fusion pore, is controlled by protein-generated membrane stresses.",0
"bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene transfer is or has been facilitated by genomic islands (geis). geis are discrete dna segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. a number of geis are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. geis play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. depending on the composition of gene modules, the same type of geis can promote survival of pathogenic as well as environmental bacteria.",0
"bipolar disorder is a highly heritable psychiatric disorder. we performed a genome-wide association study (gwas) including 20,352 cases and 31,358 controls of european descent, with follow-up analysis of 822 variants with p -4 in an additional 9,412 cases and 137,760 controls. eight of the 19 variants that were genome-wide significant (p -8 ) in the discovery gwas were not genome-wide significant in the combined analysis, consistent with small effect sizes and limited power but also with genetic heterogeneity. in the combined analysis, 30 loci were genome-wide significant, including 20 newly identified loci. the significant loci contain genes encoding ion channels, neurotransmitter transporters and synaptic components. pathway analysis revealed nine significantly enriched gene sets, including regulation of insulin secretion and endocannabinoid signaling. bipolar i disorder is strongly genetically correlated with schizophrenia, driven by psychosis, whereas bipolar ii disorder is more strongly correlated with major depressive disorder. these findings address key clinical questions and provide potential biological mechanisms for bipolar disorder.",0
"background improving the outcomes of hiv/aids treatment programs in resource-limited settings requires successful linkage of patients testing positive for hiv to pre-antiretroviral therapy (art) care and retention in pre-art care until art initiation. we conducted a systematic review of pre-art retention in care in africa. methods and findings we searched pubmed, isi web of knowledge, conference abstracts, and reference lists for reports on the proportion of adult patients retained between any two points between testing positive for hiv and initiating art in sub-saharan african hiv/aids care programs. results were categorized as stage 1 (from hiv testing to receipt of cd4 count results or clinical staging), stage 2 (from staging to art eligibility), or stage 3 (from art eligibility to art initiation). medians (ranges) were reported for the proportions of patients retained in each stage. we identified 28 eligible studies. the median proportion retained in stage 1 was 59% (35%-88%); stage 2, 46% (31%-95%); and stage 3, 68% (14%-84%). most studies reported on only one stage; none followed a cohort of patients through all three stages. enrollment criteria, terminology, end points, follow-up, and outcomes varied widely and were often poorly defined, making aggregation of results difficult. synthesis of findings from multiple studies suggests that fewer than one-third of patients testing positive for hiv and not yet eligible for art when diagnosed are retained continuously in care, though this estimate should be regarded with caution because of review limitations. conclusions studies of retention in pre-art care report substantial loss of patients at every step, starting with patients who do not return for their initial cd4 count results and ending with those who do not initiate art despite eligibility. better health information systems that allow patients to be tracked between service delivery points are needed to properly evaluate pre-art loss to care, and researchers should attempt to standardize the terminology, definitions, and time periods reported.",0
"the identification of mhc class ii restricted peptide epitopes is an important goal in immunological research. a number of computational tools have been developed for this purpose, but there is a lack of large-scale systematic evaluation of their performance. herein, we used a comprehensive dataset consisting of more than 10,000 previously unpublished mhc-peptide binding affinities, 29 peptide/mhc crystal structures, and 664 peptides experimentally tested for cd4+ t cell responses to systematically evaluate the performances of publicly available mhc class ii binding prediction tools. while in selected instances the best tools were associated with auc values up to 0.86, in general, class ii predictions did not perform as well as historically noted for class i predictions. it appears that the ability of mhc class ii molecules to bind variable length peptides, which requires the correct assignment of peptide binding cores, is a critical factor limiting the performance of existing prediction tools. to improve performance, we implemented a consensus prediction approach that combines methods with top performances. we show that this consensus approach achieved best overall performance. finally, we make the large datasets used publicly available as a benchmark to facilitate further development of mhc class ii binding peptide prediction methods.",0
"chronic traumatic encephalopathy (cte) is a neurodegeneration characterized by the abnormal accumulation of hyperphosphorylated tau protein within the brain. like many other neurodegenerative conditions, at present, cte can only be definitively diagnosed by post-mortem examination of brain tissue. as the first part of a series of consensus panels funded by the ninds/nibib to define the neuropathological criteria for cte, preliminary neuropathological criteria were used by 7 neuropathologists to blindly evaluate 25 cases of various tauopathies, including cte, alzheimer's disease, progressive supranuclear palsy, argyrophilic grain disease, corticobasal degeneration, primary age-related tauopathy, and parkinsonism dementia complex of guam. the results demonstrated that there was good agreement among the neuropathologists who reviewed the cases (cohen's kappa, 0.67) and even better agreement between reviewers and the diagnosis of cte (cohen's kappa, 0.78). based on these results, the panel defined the pathognomonic lesion of cte as an accumulation of abnormal hyperphosphorylated tau (p-tau) in neurons and astroglia distributed around small blood vessels at the depths of cortical sulci and in an irregular pattern. the group also defined supportive but non-specific p-tau-immunoreactive features of cte as: pretangles and nfts affecting superficial layers (layers ii-iii) of cerebral cortex; pretangles, nfts or extracellular tangles in ca2 and pretangles and proximal dendritic swellings in ca4 of the hippocampus; neuronal and astrocytic aggregates in subcortical nuclei; thorn-shaped astrocytes at the glial limitans of the subpial and periventricular regions; and large grain-like and dot-like structures. supportive non-p-tau pathologies include tdp-43 immunoreactive neuronal cytoplasmic inclusions and dot-like structures in the hippocampus, anteromedial temporal cortex and amygdala. the panel also recommended a minimum blocking and staining scheme for pathological evaluation and made recommendations for future study. this study provides the first step towards the development of validated neuropathological criteria for cte and will pave the way towards future clinical and mechanistic studies.",0
"background as the popularity of e-therapies grows, so too has the body of literature supporting their effectiveness. however, these interventions are often plagued by high attrition rates and varying levels of user adherence. understanding the role of adherence may be crucial to understanding how program usage influences the effectiveness of e-therapy interventions. objective the aim of this study was to systematically review the e-therapy literature to (1) describe the methods used to assess adherence and (2) evaluate the association of adherence with outcome of these interventions. methods a systematic review of e-therapy interventions was conducted across disease states and behavioral targets. data were collected on adherence measures, outcomes, and analyses exploring the relationship between adherence measures and outcomes. results of 69 studies that reported an adherence measure, only 33 (48%) examined the relationship between adherence and outcomes. the number of logins was the most commonly reported measure of adherence, followed by the number of modules completed. the heterogeneity of adherence and outcome measures limited analysis. however, logins appeared to be the measure of adherence most consistently related to outcomes in physical health interventions, while module completion was found to be most related to outcomes in psychological health interventions. conclusions there is large variation in the reporting of adherence and the association of adherence with outcomes. a lack of agreement about how best to measure adherence is likely to contribute to the variation in findings. physical and psychological outcomes seem influenced by different types of adherence. a composite measure encompassing time online, activity completion, and active engagements with the intervention may be the best measure of adherence. further research is required to establish a consensus for measuring adherence and to understand the role of adherence in influencing outcomes.",0
"dorsal root ganglion nerve cells undergoing axon elongation in vitro have been analyzed ultrastructurally. the growth cone at the axonal tip contains smooth endoplasmic reticulum, vesicles, neurofilaments, occasional microtubules, and a network of 50-a in diameter microfilaments. the filamentous network fills the periphery of the growth cone and is the only structure found in microspikes. elements of the network are oriented parallel to the axis of microspikes, but exhibit little orientation in the growth cone. cytochalasin b causes rounding up of growth cones, retraction of microspikes, and cessation of axon elongation. the latter biological effect correlates with an ultrastructural alteration in the filamentous network of growth cones and microspikes. no other organelle appears to be affected by the drug. removal of cytochalasin allows reinitiation of growth cone-microspike activity, and elongation begins anew. such recovery will occur in the presence of the protein synthesis inhibitor cycloheximide, and in the absence of exogenous nerve growth factor. the neurofilaments and microtubules of axons are regularly spaced. fine filaments indistinguishable from those in the growth cone interconnect neurofilaments, vesicles, microtubules, and plasma membrane. this filamentous network could provide the structural basis for the initiation of lateral microspikes and perhaps of collateral axons, besides playing a role in axonal transport.",0
"aeroallergy results from maladaptive immune responses to ubiquitous, otherwise innocuous environmental proteins. although the proteins targeted by aeroallergic responses represent a tiny fraction of the airborne proteins humans are exposed to, allergenicity is a quite public phenomenon-the same proteins typically behave as aeroallergens across the human population. why particular proteins tend to act as allergens in susceptible hosts is a fundamental mechanistic question that remains largely unanswered. the main house-dust-mite allergen, der p 2, has structural homology with md-2 (also known as ly96), the lipopolysaccharide (lps)-binding component of the toll-like receptor (tlr) 4 signalling complex. here we show that der p 2 also has functional homology, facilitating signalling through direct interactions with the tlr4 complex, and reconstituting lps-driven tlr4 signalling in the absence of md-2. mirroring this, airway sensitization and challenge with der p 2 led to experimental allergic asthma in wild type and md-2-deficient, but not tlr4-deficient, mice. our results indicate that der p 2 tends to be targeted by adaptive immune responses because of its auto-adjuvant properties. the fact that other members of the md-2-like lipid-binding family are allergens, and that most defined major allergens are thought to be lipid-binding proteins, suggests that intrinsic adjuvant activity by such proteins and their accompanying lipid cargo may have some generality as a mechanism underlying the phenomenon of allergenicity.",0
"many different theories have been advanced concerning the biological roles of the oligosaccharide units of individual classes of glycoconjugates. analysis of the evidence indicates that while all of these theories are correct, exceptions to each can also be found. the biological roles of oligosaccharides appear to span the spectrum from those that are trivial, to those that are crucial for the development, growth, function or survival of an organism. some general principles emerge. first, it is difficult to predict a priori the functions a given oligosaccharide on a given glycoconjugate might be mediating, or their relative importance to the organism. second, the same oligosaccharide sequence may mediate different functions at different locations within the same organism, or at different times in its ontogeny or life cycle. third, the more specific and crucial biological roles of oligosaccharides are often mediated by unusual oligosaccharide sequences, unusual presentations of common terminal sequences, or by further modifications of the sugars themselves. however, such oligosaccharide sequences are also more likely to be targets for recognition by pathogenic toxins and microorganisms. as such, they are subject to more intra- and inter-species variation because of ongoing host-pathogen interactions during evolution. in the final analysis, the only common features of the varied functions of oligosaccharides are that they either mediate 'specific recognition' events or that they provide 'modulation' of biological processes. in so doing, they generate much of the functional diversity required for the development and differentiation of complex organisms, and for their interactions with other organisms in the environment.",0
"24 di-, tri-, and tetrapeptides have been synthesized as a start of a systematic study of the structural requirements for chemotactic activity and lysosomal enzyme-releasing ability in rabbit neutrophils. all but two of them are n-formyl methionyl peptides. using the method of zigmond and hirsch (10), two representative peptides, f-met-leu-phe and f-met-met-met, were shown to stimulate directed, as well as, random locomotion; thus, they were truly chemotactic. the various peptides showed a wide spread in activity. f-met-leu-phe, the most active peptide studied, had an ed50 for induced migration of 7 x 10(-11) m and for lysozyme and beta-glucuronidase release of 2.4 x 10(-10) m and 2.6 x 10(-10) m, respectively; the least active, met-leu-glu was 26 million times less active in these respects. the relation of activity to structure is exceedingly specific, very small changes in structure making large changes in activity. moreover, this specificity exhibits a definite regularity and pattern; the activity of a given peptide depends not only on its constituent amino acids but on the position of the amino acid in the peptide chain. most striking in this last regards is the high activity conferred by phenylalanine when it is in the carboxyl terminal position of a tripeptide, whereas, as the second amino acid from the nh2 terminal end whether in a tripeptide or a dipeptide, it contributes no more to the activity than other amino acids with hydrophobic side chains such as leucine or methionine. the high activity and the specificity and nature of the structural requirements strongly suggest that the primary interaction of peptide and neutrophil leading to either chemotaxis or lysosomal enzyme release is a binding of the peptide with a stereospecific receptor on the neutrophil surface. whether all chemotactic factors act through the same receptor is not known. an essentially exact correlation exists between the concentrations of the various synthetic peptides required to induce migration and their ability to induce release of lysozyme or beta-glucuronidase. this implies that these two neutrophil functions are triggered by teh same primary interaction; possibly, the binding of the peptides to the same putative receptor. a higher concentration of a given peptide is required to stimulate lysosomal enzyme release than a corresponding migratory response. a slightly but significantly higher concentration of peptide is required to induce beta-glucuronidase secretion than lysozyme release.",0
"because undesirable pharmacokinetics and toxicity of candidate compounds are the main reasons for the failure of drug development, it has been widely recognized that absorption, distribution, metabolism, excretion and toxicity (admet) should be evaluated as early as possible. in silico admet evaluation models have been developed as an additional tool to assist medicinal chemists in the design and optimization of leads. here, we announced the release of admetlab 2.0, a completely redesigned version of the widely used amdetlab web server for the predictions of pharmacokinetics and toxicity properties of chemicals, of which the supported admet-related endpoints are approximately twice the number of the endpoints in the previous version, including 17 physicochemical properties, 13 medicinal chemistry properties, 23 adme properties, 27 toxicity endpoints and 8 toxicophore rules (751 substructures). a multi-task graph attention framework was employed to develop the robust and accurate models in admetlab 2.0. the batch computation module was provided in response to numerous requests from users, and the representation of the results was further optimized. the admetlab 2.0 server is freely available, without registration, at",0
"the programs shelxc, shelxd and shelxe are designed to provide simple, robust and efficient experimental phasing of macromolecules by the sad, mad, sir, siras and rip methods and are particularly suitable for use in automated structure-solution pipelines. this paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in shelxe by the inclusion of automated protein main-chain tracing. this gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. the autotracing algorithm starts with the location of possible seven-residue alpha-helices and common tripeptides. after extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-ala traces. noncrystallographic symmetry (ncs) is applied to the traced fragments, not to the density. further features are the use of a 'no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by ncs) that partly overlap.",0
"pediatric glioblastomas (gbm) including diffuse intrinsic pontine gliomas (dipg) are devastating brain tumors with no effective therapy. here, we investigated clinical and biological impacts of histone h3.3 mutations. forty-two dipgs were tested for h3.3 mutations. wild-type versus mutated (k27m-h3.3) subgroups were compared for hist1h3b, idh, atrx and tp53 mutations, copy number alterations and clinical outcome. k27m-h3.3 occurred in 71 %, tp53 mutations in 77 % and atrx mutations in 9 % of dipgs. atrx mutations were more frequent in older children (p < 0.0001). no g34v/r-h3.3, idh1/2 or h3.1 mutations were identified. k27m-h3.3 dipgs showed specific copy number changes, including all gains/amplifications of pdgfra and myc/pvt1 loci. notably, all long-term survivors were h3.3 wild type and this group of patients had better overall survival. k27m-h3.3 mutation defines clinically and biologically distinct subgroups and is prevalent in dipg, which will impact future therapeutic trial design. k27m- and g34v-h3.3 have location-based incidence (brainstem/cortex) and potentially play distinct roles in pediatric gbm pathogenesis. k27m-h3.3 is universally associated with short survival in dipg, while patients wild-type for h3.3 show improved survival. based on prognostic and therapeutic implications, our findings argue for h3.3-mutation testing at diagnosis, which should be rapidly integrated into the clinical decision-making algorithm, particularly in atypical dipg.",0
"no consensus on the indications for surgical resection of colorectal liver metastases exists. this systematic review has been undertaken to assess the published evidence for its efficacy and safety and to identify prognostic factors. studies were identified by computerised and hand searches of the literature, scanning references and contacting investigators. the outcome measures were overall survival, disease-free survival, postoperative morbidity and mortality, quality of life and cost effectiveness, and a qualitative summary of the trends across all studies was produced. only 30 of 529 independent studies met all the eligibility criteria for the review, and data on 30-day mortality and morbidity only were included from a further nine studies. the best available evidence came from prospective case series, but only two studies reported outcomes for all patients undergoing surgery. the remainder reported outcomes for selected groups of patients: those undergoing hepatic resection or those undergoing curative resection. postoperative mortality rates were generally low (median 2.8%). the majority of studies described only serious postoperative morbidity, the most common being bile leak and associated perihepatic abscess. approximately 30% of patients remained alive 5 years after resection and around two-thirds of these are disease free. the quality of the majority of published papers was poor and ascertaining the benefits of surgical resection of colorectal hepatic metastases is difficult in the absence of randomised trials. however, it is clear that there is group of patients with liver metastases who may become long-term disease-free survivors following hepatic resection. such survival is rare in apparently comparable patients who do not have surgical treatment. further work is needed to more accurately define this group of patients and to determine whether the addition of adjuvant treatments results in improved survival.",0
"although most meningiomas are encapsulated and benign tumors with limited numbers of genetic aberrations, their intracranial location often leads to serious and potentially lethal consequences. they are the most frequently diagnosed primary brain tumor accounting for 33.8% of all primary brain and central nervous system tumors reported in the united states between 2002 and 2006. inherited susceptibility to meningioma is suggested both by family history and candidate gene studies in dna repair genes. people with certain mutations in the neurofibromatosis gene (nf2) have a very substantial increased risk for meningioma. high dose ionizing radiation exposure is an established risk factor for meningioma, and lower doses may also increase risk, but which types and doses are controversial or understudied. because women are twice as likely as men to develop meningiomas and these tumors harbor hormone receptors, an etiologic role for hormones (both endogenous and exogenous) has been hypothesized. the extent to which immunologic factors influence meningioma etiology has been largely unexplored. growing emphasis on brain tumor research coupled with the advent of new genetic and molecular epidemiologic tools in genetic and molecular epidemiology promise hope for advancing knowledge about the causes of intra-cranial meningioma. in this review, we highlight current knowledge about meningioma epidemiology and etiology and suggest future research directions.",0
"the precise role of b cells in systemic autoimmunity is incompletely understood. although b cells are necessary for expression of disease (chan, o., and m.j. shlomchik. 1998. j. immunol. 160:51-59, and shlomchik, m.j., m.p. madaio, d. ni, m. trounstine, and d. huszar. 1994. j. exp. med. 180:1295-1306), it is unclear whether autoantibody production, antigen presentation, and/or other b cell functions are required for the complete pathologic phenotype. to address this issue, two experimental approaches were used. in the first, the individual contributions of circulating antibodies and b cells were analyzed using mrl/mpj-faslpr (mrl/lpr) mice that expressed a mutant transgene encoding surface immunoglobulin (ig), but which did not permit the secretion of circulating ig. these mice developed nephritis, characterized by cellular infiltration within the kidney, indicating that b cells themselves, without soluble autoantibody production, exert a pathogenic role. the results indicate that, independent of serum autoantibody, functional b cells expressing surface ig are essential for disease expression, either by serving as antigen-presenting cells for antigen-specific, autoreactive t cells, or by contributing directly to local inflammation.",0
"to estimate the global illness and deaths caused by rotavirus disease, we reviewed studies published from 1986 to 2000 on deaths caused by diarrhea and on rotavirus infections in children. we assessed rotavirus-associated illness in three clinical settings (mild cases requiring home care alone, moderate cases requiring a clinic visit, and severe cases requiring hospitalization) and death rates in countries in different world bank income groups. each year, rotavirus causes approximately 111 million episodes of gastroenteritis requiring only home care, 25 million clinic visits, 2 million hospitalizations, and 352,000-592,000 deaths (median, 440,000 deaths) in children <5 years of age. by age 5, nearly every child will have an episode of rotavirus gastroenteritis, 1 in 5 will visit a clinic, 1 in 65 will be hospitalized, and approximately 1 in 293 will die. children in the poorest countries account for 82% of rotavirus deaths. the tremendous incidence of rotavirus disease underscores the urgent need for interventions, such as vaccines, particularly to prevent childhood deaths in developing nations.",0
"automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. validation has since evolved into an easy-to-use checkcif/platon web-based iucr service. the result of a crystal structure determination has to be supplied as a cif-formatted computer-readable file. the checking software tests the data in the cif for completeness, quality and consistency. in addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. a validation report is generated in the form of a list of alerts on the issues to be corrected, checked or commented on. structure validation has largely eliminated obvious problems with structure reports published in iucr journals, such as refinement in a space group of too low symmetry. this paper reports on the current status of structure validation and possible future extensions.",0
"introduction and objective studies on telemedicine have shown success in reducing the geographical and time obstacles incurred in the receipt of care in traditional modalities with the same or greater effectiveness; however, there are several barriers that need to be addressed in order for telemedicine technology to spread. the aim of this review is to evaluate barriers to adopting telemedicine worldwide through the analysis of published work. methods the authors conducted a systematic literature review by extracting the data from the cumulative index of nursing and allied health literature (cinahl) and pubmed (medline) research databases. the reviewers in this study analysed 30 articles (nine from cinahl and 21 from medline) and identified barriers found in the literature. this review followed the checklist from preferred reporting items for systematic reviews and meta-analyses (prisma) 2009. the reviewers organized the results into one table and five figures that depict the data in different ways, organized by: barrier, country-specific barriers, organization-specific barriers, patient-specific barriers, and medical-staff and programmer-specific barriers. results the reviewers identified 33 barriers with a frequency of 100 occurrences through the 30 articles. the study identified the issues with technically challenged staff (11%), followed by resistance to change (8%), cost (8%), reimbursement (5%), age of patient (5%), and level of education of patient (5%). all other barriers occurred at or less than 4% of the time. discussion and conclusions telemedicine is not yet ubiquitous, and barriers vary widely. the top barriers are technology-specific and could be overcome through training, change-management techniques, and alternating delivery by telemedicine and personal patient-to-provider interaction. the results of this study identify several barriers that could be eliminated by focused policy. future work should evaluate policy to identify which one to lever to maximize the results.",0
"a major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. the prosa program (protein structure analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. the analysis of protein structures is generally a difficult and cumbersome exercise. the new service presented here is a straightforward and easy to use extension of the classic prosa program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. in particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3d molecule viewer. the service specifically addresses the needs encountered in the validation of protein structures obtained from x-ray analysis, nmr spectroscopy and theoretical calculations. prosa-web is accessible at",0
"homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. here, we present an update to the swiss-model server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. other major improvements include the implementation of a new modelling engine, promod3 and the introduction a new local model quality estimation method, qmeandisco. swiss-model is freely available at",0
"unlabelled a typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. we introduce roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. using a single cpu roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 gb of ram, with further speedups possible using multiple processors. availability and implementation roary is implemented in perl and is freely available under an open source gplv3 license from contact roary@sanger.ac.uk supplementary information supplementary data are available at bioinformatics online.",0
"background nationwide, unbiased, and unselected data of hospitalised patients with covid-19 are scarce. our aim was to provide a detailed account of case characteristics, resource use, and outcomes of hospitalised patients with covid-19 in germany, where the health-care system has not been overwhelmed by the pandemic. methods in this observational study, adult patients with a confirmed covid-19 diagnosis, who were admitted to hospital in germany between feb 26 and april 19, 2020, and for whom a complete hospital course was available (ie, the patient was discharged or died in hospital) were included in the study cohort. claims data from the german local health care funds were analysed. the data set included detailed information on patient characteristics, duration of hospital stay, type and duration of ventilation, and survival status. patients with adjacent completed hospital stays were grouped into one case. patients were grouped according to whether or not they had received any form of mechanical ventilation. to account for comorbidities, we used the charlson comorbidity index. findings of 10 021 hospitalised patients being treated in 920 different hospitals, 1727 (17%) received mechanical ventilation (of whom 422 were aged 18-59 years, 382 were aged 60-69 years, 535 were aged 70-79 years, and 388 were aged ≥80 years). the median age was 72 years (iqr 57-82). men and women were equally represented in the non-ventilated group, whereas twice as many men than women were in the ventilated group. the likelihood of being ventilated was 12% for women (580 of 4822) and 22% for men (1147 of 5199). the most common comorbidities were hypertension (5575 of 10 021), diabetes (2791 ), cardiac arrhythmia (2699 ), renal failure (2287 ), heart failure (1963 ), and chronic pulmonary disease (1358 ). dialysis was required in 599 (6%) of all patients and in 469 (27%) of 1727 ventilated patients. the charlson comorbidity index was 0 for 3237 (39%) of 8294 patients without ventilation, but only 374 (22%) of 1727 ventilated patients. the mean duration of ventilation was 13·5 days (sd 12·1). in-hospital mortality was 22% overall (2229 of 10 021), with wide variation between patients without ventilation (1323 of 8294) and with ventilation (906 of 1727; 65 of 145 for non-invasive ventilation only, 70 of 141 for non-invasive ventilation failure, and 696 of 1318 for invasive mechanical ventilation). in-hospital mortality in ventilated patients requiring dialysis was 73% (342 of 469). in-hospital mortality for patients with ventilation by age ranged from 28% (117 of 422) in patients aged 18-59 years to 72% (280 of 388) in patients aged 80 years or older. interpretation in the german health-care system, in which hospital capacities have not been overwhelmed by the covid-19 pandemic, mortality has been high for patients receiving mechanical ventilation, particularly for patients aged 80 years or older and those requiring dialysis, and has been considerably lower for patients younger than 60 years. funding none.",0
"three major modes of cancer therapy (surgery, radiation and chemotherapy) are the mainstay of modern oncologic therapy. to minimize the side effects of these therapies, molecular-targeted cancer therapies, including armed antibody therapy, have been developed with limited success. in this study, we have developed a new type of molecular-targeted cancer therapy, photoimmunotherapy (pit), that uses a target-specific photosensitizer based on a near-infrared (nir) phthalocyanine dye, ir700, conjugated to monoclonal antibodies (mabs) targeting epidermal growth factor receptors. cell death was induced immediately after irradiating mab-ir700-bound target cells with nir light. we observed in vivo tumor shrinkage after irradiation with nir light in target cells expressing the epidermal growth factor receptor. the mab-ir700 conjugates were most effective when bound to the cell membrane and produced no phototoxicity when not bound, suggesting a different mechanism for pit as compared to conventional photodynamic therapies. target-selective pit enables treatment of cancer based on mab binding to the cell membrane.",0
"background little is known about the nature and durability of the humoral immune response to infection with severe acute respiratory syndrome coronavirus 2 (sars-cov-2). methods we measured antibodies in serum samples from 30,576 persons in iceland, using six assays (including two pan-immunoglobulin assays), and we determined that the appropriate measure of seropositivity was a positive result with both pan-ig assays. we tested 2102 samples collected from 1237 persons up to 4 months after diagnosis by a quantitative polymerase-chain-reaction (qpcr) assay. we measured antibodies in 4222 quarantined persons who had been exposed to sars-cov-2 and in 23,452 persons not known to have been exposed. results of the 1797 persons who had recovered from sars-cov-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive; antiviral antibody titers assayed by two pan-ig assays increased during 2 months after diagnosis by qpcr and remained on a plateau for the remainder of the study. of quarantined persons, 2.3% were seropositive; of those with unknown exposure, 0.3% were positive. we estimate that 0.9% of icelanders were infected with sars-cov-2 and that the infection was fatal in 0.3%. we also estimate that 56% of all sars-cov-2 infections in iceland had been diagnosed with qpcr, 14% had occurred in quarantined persons who had not been tested with qpcr (or who had not received a positive result, if tested), and 30% had occurred in persons outside quarantine and not tested with qpcr. conclusions our results indicate that antiviral antibodies against sars-cov-2 did not decline within 4 months after diagnosis. we estimate that the risk of death from infection was 0.3% and that 44% of persons infected with sars-cov-2 in iceland were not diagnosed by qpcr.",0
"the pubmlst.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera. although the pubmlst website was conceived as part of the development of the first multi-locus sequence typing (mlst) scheme in 1998 the software it uses, the bacterial isolate genome sequence database (bigsdb, published in 2010), enables pubmlst to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes. here we describe developments in the bigsdb software made from publication to june 2018 and show how the platform realises microbial population genomics for a wide range of applications. the system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation. originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes. there are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question. in addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the bigsdb software includes a restful application programming interface (api) that enables access to all the underlying data for third-party applications and data analysis pipelines.",0
"cells in culture reveal high levels of protein tyrosine phosphorylation in their focal adhesions, the regions where cells adhere to the underlying substratum. we have examined the tyrosine phosphorylation of proteins in response to plating cells on extracellular matrix substrata. rat embryo fibroblasts, mouse balb/c 3t3, and nih 3t3 cells plated on fibronectin-coated surfaces revealed elevated phosphotyrosine levels in a cluster of proteins between 115 and 130 kd. this increase in tyrosine phosphorylation was also seen when rat embryo fibroblasts were plated on laminin or vitronectin, but not on polylysine or on uncoated plastic. integrin mediation of this effect was suggested by finding the same pattern of elevated tyrosine phosphorylation in cells plated on the cell-binding fragment of fibronectin and in cells plated on a synthetic polymer containing multiple rgd sequences. we have identified one of the proteins of the 115-130-kd cluster as pp125fak, a tyrosine kinase recently localized in focal adhesions (schaller, m. d., c. a. borgman, b. s. cobb, r. r. vines, a. b. reynolds, and j. t. parsons. 1992. proc. natl. acad. sci. usa. 89:5192). a second protein that becomes tyrosine phosphorylated in response to extracellular matrix adhesion is identified as paxillin, a 70-kd protein previously localized to focal adhesions. treatment of cells with the tyrosine kinase inhibitor herbimycin a diminished the adhesion-induced tyrosine phosphorylation of these proteins and inhibited the formation of focal adhesions and stress fibers. these results suggest a role for integrin-mediated tyrosine phosphorylation in the organization of the cytoskeleton as cells adhere to the extracellular matrix.",0
"unlabelled the country-specific risk of hip fracture and the 10-year probability of a major osteoporotic fracture were determined on a worldwide basis from a systematic review of literature. there was a greater than 10-fold variation in hip fracture risk and fracture probability between countries. introduction the present study aimed to update the available information base available on the heterogeneity in the risk of hip fracture on a worldwide basis. an additional aim was to document variations in major fracture probability as determined from the available frax models. methods studies on hip fracture risk were identified from 1950 to november 2011 by a medline ovid search. evaluable studies in each country were reviewed for quality and representativeness and a study (studies) chosen to represent that country. age-specific incidence rates were age-standardised to the world population in 2010 in men, women and both sexes combined. the 10-year probability of a major osteoporotic fracture for a specific clinical scenario was computed in those countries for which a frax model was available. results following quality evaluation, age-standardised rates of hip fracture were available for 63 countries and 45 frax models available in 40 countries to determine fracture probability. there was a greater than 10-fold variation in hip fracture risk and fracture probability between countries. conclusions worldwide, there are marked variations in hip fracture rates and in the 10-year probability of major osteoporotic fractures. the variation is sufficiently large that these cannot be explained by the often multiple sources of error in the ascertainment of cases or the catchment population. understanding the reasons for this heterogeneity may lead to global strategies for the prevention of fractures.",0
"randomized controlled trials often suffer from two major complications, i.e., noncompliance and missing outcomes. one potential solution to this problem is a statistical concept called intention-to-treat (itt) analysis. itt analysis includes every subject who is randomized according to randomized treatment assignment. it ignores noncompliance, protocol deviations, withdrawal, and anything that happens after randomization. itt analysis maintains prognostic balance generated from the original random treatment allocation. in itt analysis, estimate of treatment effect is generally conservative. a better application of the itt approach is possible if complete outcome data are available for all randomized subjects. per-protocol population is defined as a subset of the itt population who completed the study without any major protocol violations.",0
"online mendelian inheritance in man (omim) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. started by dr victor a. mckusick as the definitive reference mendelian inheritance in man, omim ( is now distributed electronically by the national center for biotechnology information, where it is integrated with the entrez suite of databases. derived from the biomedical literature, omim is written and edited at johns hopkins university with input from scientists and physicians around the world. each omim entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as dna and protein sequence, pubmed references, general and locus-specific mutation databases, hugo nomenclature, mapviewer, genetests, patient support groups and many others. omim is an easy and straightforward portal to the burgeoning information in human genetics.",0
"background positive association between obesity and survival after breast cancer was demonstrated in previous meta-analyses of published data, but only the results for the comparison of obese versus non-obese was summarised. methods we systematically searched in medline and embase for follow-up studies of breast cancer survivors with body mass index (bmi) before and after diagnosis, and total and cause-specific mortality until june 2013, as part of the world cancer research fund continuous update project. random-effects meta-analyses were conducted to explore the magnitude and the shape of the associations. results eighty-two studies, including 213 075 breast cancer survivors with 41 477 deaths (23 182 from breast cancer) were identified. for bmi before diagnosis, compared with normal weight women, the summary relative risks (rrs) of total mortality were 1.41 for obese (bmi >30.0), 1.07 (95 ci 1.02-1.12) for overweight (bmi 25.0- conclusions obesity is associated with poorer overall and breast cancer survival in pre- and post-menopausal breast cancer, regardless of when bmi is ascertained. being overweight is also related to a higher risk of mortality. randomised clinical trials are needed to test interventions for weight loss and maintenance on survival in women with breast cancer.",0
"our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. improvements in the throughput and accuracy of dna sequencing of the genomes of microbial communities that are associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes and by mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. however, many challenges remain. in this review, we focus on studies in humans to describe these challenges and propose strategies that leverage existing knowledge to move rapidly from correlation to causation and ultimately to translation into therapies.",0
"novel sequencing technologies permit the rapid production of large sequence data sets. these technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. we generated and analyzed two illumina 1g ultra-short read data sets, i.e. 2.8 million 27mer reads from a beta vulgaris genomic clone and 12.3 million 36mers from the helicobacter acinonychis genome. we found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. wrong base calls are frequently preceded by base g. base substitution error frequencies vary by 10- to 11-fold, with a > c transversion being among the most frequent and c > g transversions among the least frequent substitution errors. insertions and deletions of single bases occur at very low rates. when simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. the read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated gc content. high solexa quality scores are over-optimistic and low scores underestimate the data quality. our results show different types of biases and ways to detect them. such biases have implications on the use and interpretation of solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and dna methylation sites, as well as for transcriptome analysis.",0
"a disease with the characteristics of a leukemia has been found to be serially transmissible in adult swiss mice by means of cell-free filtrates. thus far, the disease has been transmitted through twenty-six serial passages with filtrates as well as cell suspensions. the agent readily passes through selas 03, berkefeld n, and gradocol membrane filters-these last having an average pore size of 220 mmicro. filtrates remain stable when stored for long periods at -70 degrees c. or when lyophilized. splenic tissue containing the agent, which was subjected to massive doses of x-ray (50,000 r),-far more than sufficient to kill the cells,-show undiminished infectivity. the agent is inactivated by heating to 56 degrees c. for 30 minutes and by exposure to ether or formalin. the disease can be transmitted to adult swiss mice or dba/2 mice, but not to adult pri, c(3)h, a, c(57)b1/6, or f(1)(c(58) x balb) mice. intraperitoneal, subcutaneous, intracerebral, and intramuscular injections are all effective.",0
"background cancer is a major cause of death in children worldwide, and the recorded incidence tends to increase with time. internationally comparable data on childhood cancer incidence in the past two decades are scarce. this study aimed to provide internationally comparable local data on the incidence of childhood cancer to promote research of causes and implementation of childhood cancer control. methods this population-based registry study, devised by the international agency for research on cancer in collaboration with the international association of cancer registries, collected data on all malignancies and non-malignant neoplasms of the cns diagnosed before age 20 years in populations covered by high-quality cancer registries with complete data for 2001-10. incidence rates per million person-years for the 0-14 years and 0-19 years age groups were age-adjusted using the world standard population to provide age-standardised incidence rates (wsrs), using the age-specific incidence rates (asr) for individual age groups (0-4 years, 5-9 years, 10-14 years, and 15-19 years). all rates were reported for 19 geographical areas or ethnicities by sex, age group, and cancer type. the regional wsrs for children aged 0-14 years were compared with comparable data obtained in the 1980s. findings of 532 invited cancer registries, 153 registries from 62 countries, departments, and territories met quality standards, and contributed data for the entire decade of 2001-10. 385 509 incident cases in children aged 0-19 years occurring in 2·64 billion person-years were included. the overall wsr was 140·6 per million person-years in children aged 0-14 years (based on 284 649 cases), and the most common cancers were leukaemia (wsr 46·4), followed by cns tumours (wsr 28·2), and lymphomas (wsr 15·2). in children aged 15-19 years (based on 100 860 cases), the asr was 185·3 per million person-years, the most common being lymphomas (asr 41·8) and the group of epithelial tumours and melanoma (asr 39·5). incidence varied considerably between and within the described regions, and by cancer type, sex, age, and racial and ethnic group. since the 1980s, the global wsr of registered cancers in children aged 0-14 years has increased from 124·0 (95% ci 123·3-124·7) to 140·6 (140·1-141·1) per million person-years. interpretation this unique global source of childhood cancer incidence will be used for aetiological research and to inform public health policy, potentially contributing towards attaining several targets of the sustainable development goals. the observed geographical, racial and ethnic, age, sex, and temporal variations require constant monitoring and research. funding international agency for research on cancer and the union for international cancer control.",0
"access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. biogrid is a freely accessible database of physical and genetic interactions available at biogrid release version 2.0 includes >116 000 interactions from saccharomyces cerevisiae, caenorhabditis elegans, drosophila melanogaster and homo sapiens. over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the saccharomyces cerevisiae primary literature. an internally hyper-linked web interface allows for rapid search and retrieval of interaction data. full or user-defined datasets are freely downloadable as tab-delimited text files and psi-mi xml. pre-computed graphical layouts of interactions are available in a variety of file formats. user-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called osprey that is dynamically linked to the biogrid.",0
"background plan-do-study-act (pdsa) cycles provide a structure for iterative testing of changes to improve quality of systems. the method is widely accepted in healthcare improvement; however there is little overarching evaluation of how the method is applied. this paper proposes a theoretical framework for assessing the quality of application of pdsa cycles and explores the consistency with which the method has been applied in peer-reviewed literature against this framework. methods nhs evidence and cochrane databases were searched by three independent reviewers. empirical studies were included that reported application of the pdsa method in healthcare. application of pdsa cycles was assessed against key features of the method, including documentation characteristics, use of iterative cycles, prediction-based testing of change, initial small-scale testing and use of data over time. results 73 of 409 individual articles identified met the inclusion criteria. of the 73 articles, 47 documented pdsa cycles in sufficient detail for full analysis against the whole framework. many of these studies reported application of the pdsa method that failed to accord with primary features of the method. less than 20% (14/73) fully documented the application of a sequence of iterative cycles. furthermore, a lack of adherence to the notion of small-scale change is apparent and only 15% (7/47) reported the use of quantitative data at monthly or more frequent data intervals to inform progression of cycles. discussion to progress the development of the science of improvement, a greater understanding of the use of improvement methods, including pdsa, is essential to draw reliable conclusions about their effectiveness. this would be supported by the development of systematic and rigorous standards for the application and reporting of pdsas.",0
"recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. here we present clonalframeml, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. clonalframeml can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. we find evidence for recombination hotspots associated with mobile elements in clostridium difficile st6 and a previously undescribed 310kb chromosomal replacement in staphylococcus aureus st582. clonalframeml is freely available at",0
"microprocessor-controlled changes of at the outer surface of the sarcoplasmic reticulum (sr) wrapped around individual myofibrils of a skinned canine cardiac purkinje cell and aequorin bioluminescence recording were used to study the mechanism of ca2+-induced release of ca2+ from the sr. this ca2+ release is triggered by a rapid increase of at the outer surface of the sr of a previously quiescent skinned cell. ca2+-induced release of ca2+ occurred under conditions that prevented any synthesis of atp from adp, was affected differentially by interventions that depressed the sr ca2+ pump about equally, and required ionic conditions incompatible with all known ca2+-releasing, uncoupled, partial reactions of the ca2+ pump. increasing the trigger up to an optimum increased the amount of ca2+ released. a supraoptimum increase of trigger inactivated ca2+-induced release of ca2+, but partial inactivation was also observed at below that necessary for its activation. the amplitude of the ca2+ release induced by a given increase of decreased when the rate of this increase was diminished. these results suggest that ca2+-induced release of ca2+ is through a channel across the sr membrane with time- and ca2+-dependent activation and inactivation. the inactivating binding site would have a higher affinity for ca2+ but a lower rate constant than the activating site. inactivation appeared to be a first-order kinetic reaction of ca2+ binding to a single site at the outer face of the sr with a q10 of 1.68. the removal of inactivation was the slowest step of the cycle, responsible for a highly temperature-dependent (q10 approximately 4.00) refractory period.",0
"the interpro database ( provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. here, we report recent developments with interpro (version 90.0) and its associated software, including updates to data content and to the website. these developments extend and enrich the information provided by interpro, and provide a more user friendly access to the data. additionally, we have worked on adding pfam website features to the interpro website, as the pfam website will be retired in late 2022. we also show that interpro's sequence coverage has kept pace with the growth of uniprotkb. moreover, we report the development of a card game as a method of engaging the non-scientific community. finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.",0
"previous estimates of drug development success rates rely on relatively small samples from databases curated by the pharmaceutical industry and are subject to potential selection biases. using a sample of 406 038 entries of clinical trial data for over 21 143 compounds from january 1, 2000 to october 31, 2015, we estimate aggregate clinical trial success rates and durations. we also compute disaggregated estimates across several trial features including disease type, clinical phase, industry or academic sponsor, biomarker presence, lead indication status, and time. in several cases, our results differ significantly in detail from widely cited statistics. for example, oncology has a 3.4% success rate in our sample vs. 5.1% in prior studies. however, after declining to 1.7% in 2012, this rate has improved to 2.5% and 8.3% in 2014 and 2015, respectively. in addition, trials that use biomarkers in patient-selection have higher overall success probabilities than trials without biomarkers.",0
"metastasis is the leading cause of cancer mortality. the metastatic cascade represents a multi-step process which includes local tumor cell invasion, entry into the vasculature followed by the exit of carcinoma cells from the circulation and colonization at the distal sites. at the earliest stage of successful cancer cell dissemination, the primary cancer adapts the secondary site of tumor colonization involving the tumor-stroma crosstalk. the migration and plasticity of cancer cells as well as the surrounding environment such as stromal and endothelial cells are mandatory. consequently, the mechanisms of cell movement are of utmost relevance for targeted intervention of which three different types have been reported. tumor cells can migrate either collectively, in a mesenchymal or in an amoeboid type of movement and intravasate the blood or lymph vasculature. intravasation by the interaction of tumor cells with the vascular endothelium is mechanistically poorly understood. changes in the epithelial plasticity enable carcinoma cells to switch between these types of motility. the types of migration may change depending on the intervention thereby increasing the velocity and aggressiveness of invading cancer cells. interference with collective or mesenchymal cell invasion by targeting integrin expression or metalloproteinase activity, respectively, resulted in an amoeboid cell phenotype as the ultimate exit strategy of cancer cells. there are little mechanistic details reported in vivo showing that the amoeboid behavior can be either reversed or efficiently inhibited. future concepts of metastasis intervention must simultaneously address the collective, mesenchymal and amoeboid mechanisms of cell invasion in order to advance in anti-metastatic strategies as these different types of movement can coexist and cooperate. beyond the targeting of cell movements, the adhesion of cancer cells to the stroma in heterotypic circulating tumor cell emboli is of paramount relevance for anti-metastatic therapy.",0
"dna methylation is highly dynamic during mammalian embryogenesis. it is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a minimum at the blastocyst stage. however, this model is based on limited data, and so far no base-resolution maps exist to support and refine it. here we generate genome-scale dna methylation maps in mouse gametes and from the zygote through post-implantation. we find that the oocyte already exhibits global hypomethylation, particularly at specific families of long interspersed element 1 and long terminal repeat retroelements, which are disparately methylated between gametes and have lower methylation values in the zygote than in sperm. surprisingly, the oocyte contributes a unique set of differentially methylated regions (dmrs)--including many cpg island promoters--that are maintained in the early embryo but are lost upon specification and absent from somatic cells. in contrast, sperm-contributed dmrs are largely intergenic and become hypermethylated after the blastocyst stage. our data provide a genome-scale, base-resolution timeline of dna methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern.",0
"all tools in the david bioinformatics resources aim to provide functional interpretation of large lists of genes derived from genomic studies. the newly updated david bioinformatics resources consists of the david knowledgebase and five integrated, web-based functional annotation tool suites: the david gene functional classification tool, the david functional annotation tool, the david gene id conversion tool, the david gene name viewer and the david niaid pathogen genome browser. the expanded david knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the david gene concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. for any uploaded gene list, the david resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. with david ( investigators gain more power to interpret the biological mechanisms associated with large gene lists.",0
"in vitro culture of human peripheral blood lymphocytes in il-2 results in the generation of cytotoxic cells that can lyse fresh and cultured solid tumor cells, as well as hematopoietic tumor cell lines, without deliberate immunization or mhc restriction. this has been referred to as the lymphokine activated killer (lak) phenomenon. here, we show that the majority of this activity is mediated by nk cells that express the leu-19 (nkh-1) antigen, but do not express cd3. the precursor of this effector population also expressed the phenotype cd3-, leu-19+. peripheral blood cd3+ t lymphocytes contributed little to the lak phenomenon, although low levels of non-mhc restricted cytotoxicity against hematopoietic tumor cell targets were mediated by a subset of cd3+ t lymphocytes that coexpressed the leu-19 antigen. these studies clearly indicated that the lak phenomenon is not mediated by a unique lak cell, but is mediated mainly by il-2-activated peripheral blood nk cells.",0
"objective to investigate the impact of advance care planning on end of life care in elderly patients. design prospective randomised controlled trial. setting single centre study in a university hospital in melbourne, australia. participants 309 legally competent medical inpatients aged 80 or more and followed for six months or until death. interventions participants were randomised to receive usual care or usual care plus facilitated advance care planning. advance care planning aimed to assist patients to reflect on their goals, values, and beliefs; to consider future medical treatment preferences; to appoint a surrogate; and to document their wishes. main outcome measures the primary outcome was whether a patient's end of life wishes were known and respected. other outcomes included patient and family satisfaction with hospital stay and levels of stress, anxiety, and depression in relatives of patients who died. results 154 of the 309 patients were randomised to advance care planning, 125 (81%) received advance care planning, and 108 (84%) expressed wishes or appointed a surrogate, or both. of the 56 patients who died by six months, end of life wishes were much more likely to be known and followed in the intervention group (25/29, 86%) compared with the control group (8/27, 30%; p conclusions advance care planning improves end of life care and patient and family satisfaction and reduces stress, anxiety, and depression in surviving relatives. trial registration australian new zealand clinical trials registry actrn12608000539336.",0
"background in 2009, damschroder et al. developed the consolidated framework for implementation research (cfir), which provides a comprehensive listing of constructs thought to influence implementation. this systematic review assesses the extent to which the cfir's use in implementation research fulfills goals set forth by damschroder et al. in terms of breadth of use, depth of application, and contribution to implementation research. methods we searched scopus and web of science for publications that cited the original cfir publication by damschroder et al. (implement sci 4:50, 2009) and downloaded each unique result for review. after applying exclusion criteria, the final articles were empirical studies published in peer-review journals that used the cfir in a meaningful way (i.e., used the cfir to guide data collection, measurement, coding, analysis, and/or reporting). a framework analysis approach was used to guide abstraction and synthesis of the included articles. results twenty-six of 429 unique articles (6 %) met inclusion criteria. we found great breadth in cfir application; the cfir was applied across a wide variety of study objectives, settings, and units of analysis. there was also variation in the method of included studies (mixed methods (n = 13); qualitative (n = 10); quantitative (n = 3)). depth of cfir application revealed some areas for improvement. few studies (n = 3) reported justification for selection of cfir constructs used; the majority of studies (n = 14) used the cfir to guide data analysis only; and few studies investigated any outcomes (n = 11). finally, reflections on the contribution of the cfir to implementation research were scarce. conclusions our results indicate that the cfir has been used across a wide range of studies, though more in-depth use of the cfir may help advance implementation science. to harness its potential, researchers should consider how to most meaningfully use the cfir. specific recommendations for applying the cfir include explicitly justifying selection of cfir constructs; integrating the cfir throughout the research process (in study design, data collection, and analysis); and appropriately using the cfir given the phase of implementation of the research (e.g., if the research is post-implementation, using the cfir to link determinants of implementation to outcomes).",0
"molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. however, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. membrane builder in the charmm-gui website ( helps users to build such a complex system using a web browser with a graphical user interface. through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. the efficacy of membrane builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (dmpc, dppc, and popc) and two types of system shapes (rectangular and hexagonal) are freely available on the charmm-gui website. one of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. therefore, membrane builder provides the intuitive and easy way to build and simulate the biologically important membrane system.",0
"the iuphar/bps guide to pharmacology (gtopdb, provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. developed by the international union of basic and clinical pharmacology (iuphar) and the british pharmacological society (bps), this resource, and its earlier incarnation as iuphar-db, is described in our 2014 publication. this update incorporates changes over the intervening seven database releases. the unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. most information comes from journal articles, but we now also index kinase cross-screening panels. targets are specified by uniprotkb ids. small molecules are defined by pubchem compound identifiers (cids); ligand capture also includes peptides and clinical antibodies. we have extended the capture of ligands and targets linked via published quantitative binding data (e.g. ki, ic50 or kd). the resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. the database also provides an expanded substrate for the biennially published compendium, the concise guide to pharmacology. this article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.",0
"the characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. however, comprehensive tools are not freely available to the research community. here, we present the protein-ligand interaction profiler (plip), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3d structures, freely available at projects.biotec.tu-dresden.de/plip-web. the input is either a protein data bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). in contrast to other tools, the rule-based plip algorithm does not require any structure preparation. it returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). plip stands out by offering publication-ready images, pymol session files to generate custom images and parsable result files to facilitate successive data processing. the full python source code is available for download on the website. plip's command-line mode allows for high-throughput interaction profiling.",0
"smart (simple modular architecture research tool) is a web resource ( for the identification and annotation of protein domains and the analysis of protein domain architectures. smart version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). all the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and xer like cellular recombinase. further updates include the synchronization of the underlying protein databases with uniprot (2), ensembl (3) and string (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. furthermore, smart's vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.",0
"single-cell analysis of bacteria and subcellular protein localization dynamics has shown that bacteria have elaborate life cycles, cytoskeletal protein networks and complex signal transduction pathways driven by localized proteins. the volume of multidimensional images generated in such experiments and the computation time required to detect, associate and track cells and subcellular features pose considerable challenges, especially for high-throughput experiments. there is therefore a need for a versatile, computationally efficient image analysis tool capable of extracting the desired relationships from images in a meaningful and unbiased way. here, we present microbej, a plug-in for the open-source platform imagej(1). microbej provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets. it performs the most common intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci and organelles, determines their subcellular localization with subpixel resolution, and tracks them over time. because a dynamic link is maintained between the images, measurements and all data representations derived from them, the editor and suite of advanced data presentation tools facilitates the image analysis process and provides a robust way to verify the accuracy and veracity of the data.",0
"covid-19 emerges as a pandemic disease with high mortality. development of effective prevention and treatment is an urgent need. we reviewed th17 responses in patients with sars-cov-2 and proposed an fda approved jak2 inhibitor fedratinib for reducing mortality of patients with th17 type immune profiles.",0
"the conserved domain database (cdd) is part of ncbi's entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in entrez. entrez's global query interface can be accessed at and will search cdd and many other databases. domain annotation for proteins in entrez has been pre-computed and is readily available in the form of 'conserved domain' links. novel protein sequences can be scanned against cdd using the cd-search service; this service searches databases of cdd-derived profile models with protein sequence queries using blast heuristics, at protein query sequences submitted to ncbi's protein blast search service are scanned for conserved domain signatures by default. the cdd collection contains models imported from pfam, smart and cog, as well as domain models curated at ncbi. ncbi curated models are organized into hierarchies of domains related by common descent. here we report on the status of the curation effort and present a novel helper application, cdtree, which enables users of the cdd resource to examine curated hierarchies. more importantly, cdd and cdtree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.",0
"background the contemporary associations of type 2 diabetes with a wide range of incident cardiovascular diseases have not been compared. we aimed to study associations between type 2 diabetes and 12 initial manifestations of cardiovascular disease. methods we used linked primary care, hospital admission, disease registry, and death certificate records from the caliber programme, which links data for people in england recorded in four electronic health data sources. we included people who were (or turned) 30 years or older between jan 1, 1998, to march 25, 2010, who were free from cardiovascular disease at baseline. the primary endpoint was the first record of one of 12 cardiovascular presentations in any of the data sources. we compared cumulative incidence curves for the initial presentation of cardiovascular disease and used cox models to estimate cause-specific hazard ratios (hrs). this study is registered at clinicaltrials.gov (nct01804439). findings our cohort consisted of 1 921 260 individuals, of whom 1 887 062 (98·2%) did not have diabetes and 34 198 (1·8%) had type 2 diabetes. we observed 113 638 first presentations of cardiovascular disease during a median follow-up of 5·5 years (iqr 2·1-10·1). of people with type 2 diabetes, 6137 (17·9%) had a first cardiovascular presentation, the most common of which were peripheral arterial disease (reported in 992 of 6137 patients) and heart failure (866 of 6137 patients). type 2 diabetes was positively associated with peripheral arterial disease (adjusted hr 2·98 ), ischaemic stroke (1·72 ), stable angina (1·62 ), heart failure (1·56 ), and non-fatal myocardial infarction (1·54 ), but was inversely associated with abdominal aortic aneurysm (0·46 ) and subarachnoid haemorrhage (0·48 ), and not associated with arrhythmia or sudden cardiac death (0·95 ). interpretation heart failure and peripheral arterial disease are the most common initial manifestations of cardiovascular disease in type 2 diabetes. the differences between relative risks of different cardiovascular diseases in patients with type 2 diabetes have implications for clinical risk assessment and trial design. funding wellcome trust, national institute for health research, and medical research council.",0
"angiogenesis is the generation of mature vascular networks from pre-existing vessels. angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. several murine experimental systems are well suited for studying developmental and pathological angiogenesis. they include the embryonic hindbrain, the post-natal retina and allantois explants. in these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. non-automated protocols are being used widely and they are, in general, time--and labour intensive, prone to human error and do not permit computation of complex spatial metrics. we have developed a light-weight, user friendly software, angiotool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. angiotool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. in addition, angiotool calculates the so-called ""branching index"" (branch points/unit area), providing a measurement of the sprouting activity of a specimen of interest. we have validated angiotool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. angiotool is open source and can be downloaded free of charge.",0
"background improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. the global burden of disease 2015 study (gbd 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. these results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures. methods we estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for gbd 2013 and gbd 2010. improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal gaussian process regression, and sibling history data processing. we also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. for gbd 2015, eight causes, including ebola virus disease, were added to the previous gbd cause list for mortality. we used six modelling approaches to assess cause-specific mortality, with the cause of death ensemble model (codem) generating estimates for most causes. we used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. first, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the socio-demographic index (sdi), a summary indicator derived from measures of income per capita, educational attainment, and fertility. second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. finally, we attributed changes in life expectancy to changes in cause of death. we documented each step of the gbd 2015 estimation processes, as well as data sources, in accordance with guidelines for accurate and transparent health estimates reporting (gather). findings globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. several countries in sub-saharan africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to hiv/aids. at the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. from 2005 to 2015, male life expectancy in syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. the result was similar for non-communicable diseases (ncds), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). globally, this mortality pattern emerged for several ncds, including several types of cancer, ischaemic heart disease, cirrhosis, and alzheimer's disease and other dementias. by contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to hiv/aids (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the middle east. in 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. our analyses on the expected associations between cause-specific mortality and sdi show the regular shifts in cause of death composition and population age structure with rising sdi. country patterns of premature mortality (measured as years of life lost ) and how they differ from the level expected on the basis of sdi alone revealed distinct but highly heterogeneous patterns by region and country or territory. ischaemic heart disease, stroke, and diabetes were among the leading causes of ylls in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected ylls based on sdi. communicable, maternal, neonatal, and nutritional diseases caused the most ylls throughout sub-saharan africa, with observed ylls far exceeding expected ylls for countries in which malaria or hiv/aids remained the leading causes of early death. interpretation at the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. progress has been faster in most countries than expected on the basis of development measured by the sdi. against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems. funding bill & melinda gates foundation.",0
"statistical machine learning methods are increasingly used for neuroimaging data analysis. their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional mri) or find sub-populations in large cohorts. by considering different functional neuroimaging applications, we illustrate how scikit-learn, a python machine learning library, can be used to perform some key analysis steps. scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain.",0
"background sleep-disordered breathing is a common condition associated with adverse health outcomes including hypertension and cardiovascular disease. the overall objective of this study was to determine whether sleep-disordered breathing and its sequelae of intermittent hypoxemia and recurrent arousals are associated with mortality in a community sample of adults aged 40 years or older. methods and findings we prospectively examined whether sleep-disordered breathing was associated with an increased risk of death from any cause in 6,441 men and women participating in the sleep heart health study. sleep-disordered breathing was assessed with the apnea-hypopnea index (ahi) based on an in-home polysomnogram. survival analysis and proportional hazards regression models were used to calculate hazard ratios for mortality after adjusting for age, sex, race, smoking status, body mass index, and prevalent medical conditions. the average follow-up period for the cohort was 8.2 y during which 1,047 participants (587 men and 460 women) died. compared to those without sleep-disordered breathing (ahi: or=30.0 events/h) sleep-disordered breathing were 0.93 (95% ci: 0.80-1.08), 1.17 (95% ci: 0.97-1.42), and 1.46 (95% ci: 1.14-1.86), respectively. stratified analyses by sex and age showed that the increased risk of death associated with severe sleep-disordered breathing was statistically significant in men aged 40-70 y (hazard ratio: 2.09; 95% ci: 1.31-3.33). measures of sleep-related intermittent hypoxemia, but not sleep fragmentation, were independently associated with all-cause mortality. coronary artery disease-related mortality associated with sleep-disordered breathing showed a pattern of association similar to all-cause mortality. conclusions sleep-disordered breathing is associated with all-cause mortality and specifically that due to coronary artery disease, particularly in men aged 40-70 y with severe sleep-disordered breathing. please see later in the article for the editors' summary.",0
"autophagy is a catabolic process in which lysosomes degrade intracytoplasmic contents transported in double-membraned autophagosomes. autophagosomes are formed by the elongation and fusion of phagophores, which derive from pre-autophagosomal structures. the membrane origins of autophagosomes are unclear and may involve multiple sources, including the endoplasmic reticulum and mitochondria. here we show in mammalian cells that the heavy chain of clathrin interacts with atg16l1 and is involved in the formation of atg16l1-positive early autophagosome precursors. atg16l1 associated with clathrin-coated structures, and inhibition of clathrin-mediated internalization decreased the formation of both atg16l1-positive precursors and mature autophagosomes. we tested and demonstrated that the plasma membrane contributes directly to the formation of early atg16l1-positive autophagosome precursors. this may be particularly important during periods of increased autophagosome formation, because the plasma membrane may serve as a large membrane reservoir that allows cells periods of autophagosome synthesis at levels many-fold higher than under basal conditions, without compromising other processes.",0
"programmed cell death protein 1 (pd-1) is an immune checkpoint receptor that is upregulated on activated t cells for the induction of immune tolerance. tumour cells frequently overexpress the ligand for pd-1, programmed cell death ligand 1 (pd-l1), facilitating their escape from the immune system. monoclonal antibodies that block the interaction between pd-1 and pd-l1, by binding to either the ligand or receptor, have shown notable clinical efficacy in patients with a variety of cancers, including melanoma, colorectal cancer, non-small-cell lung cancer and hodgkin's lymphoma. although it is well established that pd-1-pd-l1 blockade activates t cells, little is known about the role that this pathway may have in tumour-associated macrophages (tams). here we show that both mouse and human tams express pd-1. tam pd-1 expression increases over time in mouse models of cancer and with increasing disease stage in primary human cancers. tam pd-1 expression correlates negatively with phagocytic potency against tumour cells, and blockade of pd-1-pd-l1 in vivo increases macrophage phagocytosis, reduces tumour growth and lengthens the survival of mice in mouse models of cancer in a macrophage-dependent fashion. this suggests that pd-1-pd-l1 therapies may also function through a direct effect on macrophages, with substantial implications for the treatment of cancer with these agents.",0
"recirculation of fluid and cells through lymphatic vessels plays a key role in normal tissue homeostasis, inflammatory diseases, and cancer. despite recent advances in understanding lymphatic function (alitalo, k., t. tammela, and t.v. petrova. 2005. nature. 438:946-953), the cellular features responsible for entry of fluid and cells into lymphatics are incompletely understood. we report the presence of novel junctions between endothelial cells of initial lymphatics at likely sites of fluid entry. overlapping flaps at borders of oak leaf-shaped endothelial cells of initial lymphatics lacked junctions at the tip but were anchored on the sides by discontinuous button-like junctions (buttons) that differed from conventional, continuous, zipper-like junctions (zippers) in collecting lymphatics and blood vessels. however, both buttons and zippers were composed of vascular endothelial cadherin (ve-cadherin) and tight junction-associated proteins, including occludin, claudin-5, zonula occludens-1, junctional adhesion molecule-a, and endothelial cell-selective adhesion molecule. in c57bl/6 mice, ve-cadherin was required for maintenance of junctional integrity, but platelet/endothelial cell adhesion molecule-1 was not. growing tips of lymphatic sprouts had zippers, not buttons, suggesting that buttons are specialized junctions rather than immature ones. our findings suggest that fluid enters throughout initial lymphatics via openings between buttons, which open and close without disrupting junctional integrity, but most leukocytes enter the proximal half of initial lymphatics.",0
"objective to quantify the association of cancer treatment delay and mortality for each four week increase in delay to inform cancer treatment pathways. design systematic review and meta-analysis. data sources published studies in medline from 1 january 2000 to 10 april 2020. eligibility criteria for selecting studies curative, neoadjuvant, and adjuvant indications for surgery, systemic treatment, or radiotherapy for cancers of the bladder, breast, colon, rectum, lung, cervix, and head and neck were included. the main outcome measure was the hazard ratio for overall survival for each four week delay for each indication. delay was measured from diagnosis to first treatment, or from the completion of one treatment to the start of the next. the primary analysis only included high validity studies controlling for major prognostic factors. hazard ratios were assumed to be log linear in relation to overall survival and were converted to an effect for each four week delay. pooled effects were estimated using dersimonian and laird random effect models. results the review included 34 studies for 17 indications (n=1 272 681 patients). no high validity data were found for five of the radiotherapy indications or for cervical cancer surgery. the association between delay and increased mortality was significant (p conclusions cancer treatment delay is a problem in health systems worldwide. the impact of delay on mortality can now be quantified for prioritisation and modelling. even a four week delay of cancer treatment is associated with increased mortality across surgical, systemic treatment, and radiotherapy indications for seven cancers. policies focused on minimising system level delays to cancer treatment initiation could improve population level survival outcomes.",0
"since the publication of standards for quality improvement reporting excellence (squire 1.0) guidelines in 2008, the science of the field has advanced considerably. in this manuscript, we describe the development of squire 2.0 and its key components. we undertook the revision between 2012 and 2015 using (1) semistructured interviews and focus groups to evaluate squire 1.0 plus feedback from an international steering group, (2) two face-to-face consensus meetings to develop interim drafts and (3) pilot testing with authors and a public comment period. squire 2.0 emphasises the reporting of three key components of systematic efforts to improve the quality, value and safety of healthcare: the use of formal and informal theory in planning, implementing and evaluating improvement work; the context in which the work is done and the study of the intervention(s). squire 2.0 is intended for reporting the range of methods used to improve healthcare, recognising that they can be complex and multidimensional. it provides common ground to share these discoveries in the scholarly literature (",0
"objectives evaluating the variation in the strength of the effect across studies is a key feature of meta-analyses. this variability is reflected by measures like τ(2) or i(2), but their clinical interpretation is not straightforward. a prediction interval is less complicated: it presents the expected range of true effects in similar studies. we aimed to show the advantages of having the prediction interval routinely reported in meta-analyses. design we show how the prediction interval can help understand the uncertainty about whether an intervention works or not. to evaluate the implications of using this interval to interpret the results, we selected the first meta-analysis per intervention review of the cochrane database of systematic reviews issues 2009-2013 with a dichotomous (n=2009) or continuous (n=1254) outcome, and generated 95% prediction intervals for them. results in 72.4% of 479 statistically significant (random-effects p 0), the 95% prediction interval suggested that the intervention effect could be null or even be in the opposite direction. in 20.3% of those 479 meta-analyses, the prediction interval showed that the effect could be completely opposite to the point estimate of the meta-analysis. we demonstrate also how the prediction interval can be used to calculate the probability that a new trial will show a negative effect and to improve the calculations of the power of a new trial. conclusions the prediction interval reflects the variation in treatment effects over different settings, including what effect is to be expected in future patients, such as the patients that a clinician is interested to treat. prediction intervals should be routinely reported to allow more informative inferences in meta-analyses.",0
"cells comprising a tissue migrate as part of a collective. how collective processes are coordinated over large multi-cellular assemblies has remained unclear, however, because mechanical stresses exerted at cell-cell junctions have not been accessible experimentally. we report here maps of these stresses within and between cells comprising a monolayer. within the cell sheet there arise unanticipated fluctuations of mechanical stress that are severe, emerge spontaneously, and ripple across the monolayer. within that stress landscape, local cellular migrations follow local orientations of maximal principal stress. migrations of both endothelial and epithelial monolayers conform to this behaviour, as do breast cancer cell lines before but not after the epithelial-mesenchymal transition. collective migration in these diverse systems is seen to be governed by a simple but unifying physiological principle: neighbouring cells join forces to transmit appreciable normal stress across the cell-cell junction, but migrate along orientations of minimal intercellular shear stress.",0
"the novel coronavirus disease 2019 (covid-19) has become a pandemic affecting health and wellbeing globally. in addition to the physical health, economic, and social implications, the psychological impacts of this pandemic are increasingly being reported in the scientific literature. this narrative review reflected on scholarly articles on the epidemiology of mental health problems in covid-19. the current literature suggests that people affected by covid-19 may have a high burden of mental health problems, including depression, anxiety disorders, stress, panic attack, irrational anger, impulsivity, somatization disorder, sleep disorders, emotional disturbance, posttraumatic stress symptoms, and suicidal behavior. moreover, several factors associated with mental health problems in covid-19 are found, which include age, gender, marital status, education, occupation, income, place of living, close contact with people with covid-19, comorbid physical and mental health problems, exposure to covid-19 related news and social media, coping styles, stigma, psychosocial support, health communication, confidence in health services, personal protective measures, risk of contracting covid-19, and perceived likelihood of survival. furthermore, the epidemiological distribution of mental health problems and associated factors were heterogeneous among the general public, covid-19 patients, and healthcare providers. the current evidence suggests that a psychiatric epidemic is cooccurring with the covid-19 pandemic, which necessitates the attention of the global health community. future epidemiological studies should emphasize on psychopathological variations and temporality of mental health problems in different populations. nonetheless, multipronged interventions should be developed and adopted to address the existing psychosocial challenges and promote mental health amid the covid-19 pandemic.",0
"an in vitro technique is described for assessing the chemotactic activity of soluble substances on motile cells. antibody-antigen mixtures when incubated (37 degrees c) in medium containing fresh (i.e. non-inactivated) normal rabbit serum exert a strong chemotactic effect on rabbit polymorphonuclear leucocytes. results are described which indicate that, when antibody-antigen complexes are incubated (37 degrees c) in fresh serum, a heat-stable (56 degrees c) substance (or substances) is produced which acts directly as a chemotactic stimulus on the polymorphs. this heat-stable chemotactic substance is not produced when antibody-antigen complexes are incubated in serum which has been heated at 56 degrees c for 30 minutes.",0
"the prosite database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. the prosite database is now complemented by a series of rules that can give more precise information about specific residues. during the last 2 years, the documentation and the scanprosite web pages were redesigned to add more functionalities. the latest version of prosite (release 19.11 of september 27, 2005) contains 1329 patterns and 552 profile entries. over the past 2 years more than 200 domains have been added, and now 52% of uniprotkb/swiss-prot entries (release 48.1 of september 27, 2005) have a cross-reference to a prosite entry. the database is accessible at",0
"2-arachidonoylglycerol (2-ag) and anandamide are endocannabinoids that activate the cannabinoid receptors cb1 and cb2. endocannabinoid signaling is terminated by enzymatic hydrolysis, a process that for anandamide is mediated by fatty acid amide hydrolase (faah), and for 2-ag is thought to involve monoacylglycerol lipase (magl). faah inhibitors produce a select subset of the behavioral effects observed with cb1 agonists, which suggests a functional segregation of endocannabinoid signaling pathways in vivo. testing this hypothesis, however, requires specific tools to independently block anandamide and 2-ag metabolism. here, we report a potent and selective inhibitor of magl called jzl184 that, upon administration to mice, raises brain 2-ag by eight-fold without altering anandamide. jzl184-treated mice exhibited a broad array of cb1-dependent behavioral effects, including analgesia, hypothermia and hypomotility. these data indicate that 2-ag endogenously modulates several behavioral processes classically associated with the pharmacology of cannabinoids and point to overlapping and unique functions for 2-ag and anandamide in vivo.",0
"the neglected tropical diseases (ntds) are the most common conditions affecting the poorest 500 million people living in sub-saharan africa (ssa), and together produce a burden of disease that may be equivalent to up to one-half of ssa's malaria disease burden and more than double that caused by tuberculosis. approximately 85% of the ntd disease burden results from helminth infections. hookworm infection occurs in almost half of ssa's poorest people, including 40-50 million school-aged children and 7 million pregnant women in whom it is a leading cause of anemia. schistosomiasis is the second most prevalent ntd after hookworm (192 million cases), accounting for 93% of the world's number of cases and possibly associated with increased horizontal transmission of hiv/aids. lymphatic filariasis (46-51 million cases) and onchocerciasis (37 million cases) are also widespread in ssa, each disease representing a significant cause of disability and reduction in the region's agricultural productivity. there is a dearth of information on africa's non-helminth ntds. the protozoan infections, human african trypanosomiasis and visceral leishmaniasis, affect almost 100,000 people, primarily in areas of conflict in ssa where they cause high mortality, and where trachoma is the most prevalent bacterial ntd (30 million cases). however, there are little or no data on some very important protozoan infections, e.g., amebiasis and toxoplasmosis; bacterial infections, e.g., typhoid fever and non-typhoidal salmonellosis, the tick-borne bacterial zoonoses, and non-tuberculosis mycobaterial infections; and arboviral infections. thus, the overall burden of africa's ntds may be severely underestimated. a full assessment is an important step for disease control priorities, particularly in nigeria and the democratic republic of congo, where the greatest number of ntds may occur.",0
"objective to evaluate the impact of state supported overdose education and nasal naloxone distribution (oend) programs on rates of opioid related death from overdose and acute care utilization in massachusetts. design interrupted time series analysis of opioid related overdose death and acute care utilization rates from 2002 to 2009 comparing community-year strata with high and low rates of oend implementation to those with no implementation. setting 19 massachusetts communities (geographically distinct cities and towns) with at least five fatal opioid overdoses in each of the years 2004 to 2006. participants oend was implemented among opioid users at risk for overdose, social service agency staff, family, and friends of opioid users. intervention oend programs equipped people at risk for overdose and bystanders with nasal naloxone rescue kits and trained them how to prevent, recognize, and respond to an overdose by engaging emergency medical services, providing rescue breathing, and delivering naloxone. main outcome measures adjusted rate ratios for annual deaths related to opioid overdose and utilization of acute care hospitals. results among these communities, oend programs trained 2912 potential bystanders who reported 327 rescues. both community-year strata with 1-100 enrollments per 100,000 population (adjusted rate ratio 0.73, 95% confidence interval 0.57 to 0.91) and community-year strata with greater than 100 enrollments per 100,000 population (0.54, 0.39 to 0.76) had significantly reduced adjusted rate ratios compared with communities with no implementation. differences in rates of acute care hospital utilization were not significant. conclusions opioid overdose death rates were reduced in communities where oend was implemented. this study provides observational evidence that by training potential bystanders to prevent, recognize, and respond to opioid overdoses, oend is an effective intervention.",0
"background the covid-19 pandemic continues to adversely affect the u.s., which leads globally in total cases and deaths. as covid-19 vaccines are under development, public health officials and policymakers need to create strategic vaccine-acceptance messaging to effectively control the pandemic and prevent thousands of additional deaths. methods using an online platform, we surveyed the u.s. adult population in may 2020 to understand risk perceptions about the covid-19 pandemic, acceptance of a covid-19 vaccine, and trust in sources of information. these factors were compared across basic demographics. findings of the 672 participants surveyed, 450 (67%) said they would accept a covid-19 vaccine if it is recommended for them. males (72%) compared to females, older adults (≥55 years; 78%) compared to younger adults, asians (81%) compared to other racial and ethnic groups, and college and/or graduate degree holders (75%) compared to people with less than a college degree were more likely to accept the vaccine. when comparing reported influenza vaccine uptake to reported acceptance of the covid-19 vaccine: 1) participants who did not complete high school had a very low influenza vaccine uptake (10%), while 60% of the same group said they would accept the covid-19 vaccine; 2) unemployed participants reported lower influenza uptake and lower covid-19 vaccine acceptance when compared to those employed or retired; and, 3) black americans reported lower influenza vaccine uptake and lower covid-19 vaccine acceptance than all other racial groups reported in our study. lastly, we identified geographic differences with department of health and human services (dhhs) regions 2 (new york) and 5 (chicago) reporting less than 50 percent covid-19 vaccine acceptance. interpretation although our study found a 67% acceptance of a covid-19 vaccine, there were noticeable demographic and geographical disparities in vaccine acceptance. before a covid-19 vaccine is introduced to the u.s., public health officials and policymakers must prioritize effective covid-19 vaccine-acceptance messaging for all americans, especially those who are most vulnerable.",0
"this article describes the cms hierarchical condition categories (hcc) model implemented in 2004 to adjust medicare capitation payments to private health care plans for the health expenditure risk of their enrollees. we explain the model's principles, elements, organization, calibration, and performance. modifications to reduce plan data reporting burden and adaptations for disabled, institutionalized, newly enrolled, and secondary payer subpopulations are discussed.",0
"afilopodium protrudes by elongation of bundled actin filaments in its core. however, the mechanism of filopodia initiation remains unknown. using live-cell imaging with gfp-tagged proteins and correlative electron microscopy, we performed a kinetic-structural analysis of filopodial initiation in b16f1 melanoma cells. filopodial bundles arose not by a specific nucleation event, but by reorganization of the lamellipodial dendritic network analogous to fusion of established filopodia but occurring at the level of individual filaments. subsets of independently nucleated lamellipodial filaments elongated and gradually associated with each other at their barbed ends, leading to formation of cone-shaped structures that we term lambda-precursors. an early marker of initiation was the gradual coalescence of gfp-vasodilator-stimulated phosphoprotein (gfp-vasp) fluorescence at the leading edge into discrete foci. the gfp-vasp foci were associated with lambda-precursors, whereas arp2/3 was not. subsequent recruitment of fascin to the clustered barbed ends of lambda-precursors initiated filament bundling and completed formation of the nascent filopodium. we propose a convergent elongation model of filopodia initiation, stipulating that filaments within the lamellipodial dendritic network acquire privileged status by binding a set of molecules (including vasp) to their barbed ends, which protect them from capping and mediate association of barbed ends with each other.",0
"a recent manuscript (ferguson et al. in impact of non-pharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand, imperial college covid-19 response team, london, 2020. from imperial college modelers examining ways to mitigate and control the spread of covid-19 has attracted much attention. in this paper, we will discuss a coarse taxonomy of models and explore the context and significance of the imperial college and other models in contributing to the analysis of covid-19.",0
"although the respiratory and immune systems are the major targets of coronavirus disease 2019 (covid-19), acute kidney injury and proteinuria have also been observed. currently, detailed pathologic examination of kidney damage in critically ill patients with covid-19 has been lacking. to help define this we analyzed kidney abnormalities in 26 autopsies of patients with covid-19 by light microscopy, ultrastructural observation and immunostaining. patients were on average 69 years (19 male and 7 female) with respiratory failure associated with multiple organ dysfunction syndrome as the cause of death. nine of the 26 showed clinical signs of kidney injury that included increased serum creatinine and/or new-onset proteinuria. by light microscopy, diffuse proximal tubule injury with the loss of brush border, non-isometric vacuolar degeneration, and even frank necrosis was observed. occasional hemosiderin granules and pigmented casts were identified. there were prominent erythrocyte aggregates obstructing the lumen of capillaries without platelet or fibrinoid material. evidence of vasculitis, interstitial inflammation or hemorrhage was absent. electron microscopic examination showed clusters of coronavirus-like particles with distinctive spikes in the tubular epithelium and podocytes. furthermore, the receptor of sars-cov-2, ace2 was found to be upregulated in patients with covid-19, and immunostaining with sars-cov nucleoprotein antibody was positive in tubules. in addition to the direct virulence of sars-cov-2, factors contributing to acute kidney injury included systemic hypoxia, abnormal coagulation, and possible drug or hyperventilation-relevant rhabdomyolysis. thus, our studies provide direct evidence of the invasion of sarscov-2 into kidney tissue. these findings will greatly add to the current understanding of sars-cov-2 infection.",0
"motivation advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (tf) chip-seq experiments. while there are many existing tools for discovering tf binding site motifs in such datasets, most web-based tools cannot directly process such large datasets. results the meme-chip web service is designed to analyze chip-seq 'peak regions'--short genomic regions surrounding declared chip-seq 'peaks'. given a set of genomic regions, it performs (i) ab initio motif discovery, (ii) motif enrichment analysis, (iii) motif visualization, (iv) binding affinity analysis and (v) motif identification. it runs two complementary motif discovery algorithms on the input data--meme and dreme--and uses the motifs they discover in subsequent visualization, binding affinity and identification steps. meme-chip also performs motif enrichment analysis using the ame algorithm, which can detect very low levels of enrichment of binding sites for tfs with known dna-binding motifs. importantly, unlike with the meme web service, there is no restriction on the size or number of uploaded sequences, allowing very large chip-seq datasets to be analyzed. the analyses performed by meme-chip provide the user with a varied view of the binding and regulatory activity of the chip-ed tf, as well as the possible involvement of other dna-binding tfs. availability meme-chip is available as part of the meme suite at",0
"wolbachia are intracellular bacteria that manipulate the reproduction of their arthropod hosts in remarkable ways. they are predominantly transmitted vertically from mother to offspring but also occasionally horizontally between species. in doing so, they infect a huge range of arthropod species worldwide. recently, a statistical analysis estimated the infection frequency of wolbachia among arthropod hosts to be 66%. at the same time, the authors of this analysis highlighted some weaknesses of the underlying data and concluded that in order to improve the estimate, a larger number of individuals per species should be assayed and species be chosen more randomly. here we apply the statistical approach to a more appropriate data set from a recent survey that tested both a broad range of species and a sufficient number of individuals per species. indeed, we find a substantially different infection frequency: we now estimate the proportion of wolbachia-infected species to be around 40% which is lower than the previous estimate but still points to a surprisingly high number of arthropods harboring the bacteria. notwithstanding this difference, we confirm the previous result that, within a given species, typically most or only a few individuals are infected. moreover, we extend our analysis to include several reproductive parasites other than wolbachia that were also screened for in the aforementioned empirical survey. for these symbionts we find a large variation in estimated infection frequencies and corroborate the finding that wolbachia are the most abundant endosymbionts among arthropod species.",0
"human pluripotent stem cells (pscs) are a promising source of cells for applications in regenerative medicine. directed differentiation of pscs into specialized cells such as spinal motoneurons or midbrain dopamine (da) neurons has been achieved. however, the effective use of pscs for cell therapy has lagged behind. whereas mouse psc-derived da neurons have shown efficacy in models of parkinson's disease, da neurons from human pscs generally show poor in vivo performance. there are also considerable safety concerns for pscs related to their potential for teratoma formation or neural overgrowth. here we present a novel floor-plate-based strategy for the derivation of human da neurons that efficiently engraft in vivo, suggesting that past failures were due to incomplete specification rather than a specific vulnerability of the cells. midbrain floor-plate precursors are derived from pscs 11 days after exposure to small molecule activators of sonic hedgehog (shh) and canonical wnt signalling. engraftable midbrain da neurons are obtained by day 25 and can be maintained in vitro for several months. extensive molecular profiling, biochemical and electrophysiological data define developmental progression and confirm identity of psc-derived midbrain da neurons. in vivo survival and function is demonstrated in parkinson's disease models using three host species. long-term engraftment in 6-hydroxy-dopamine-lesioned mice and rats demonstrates robust survival of midbrain da neurons derived from human embryonic stem (es) cells, complete restoration of amphetamine-induced rotation behaviour and improvements in tests of forelimb use and akinesia. finally, scalability is demonstrated by transplantation into parkinsonian monkeys. excellent da neuron survival, function and lack of neural overgrowth in the three animal models indicate promise for the development of cell-based therapies in parkinson's disease.",0
"background xerostomia is the most common late side-effect of radiotherapy to the head and neck. compared with conventional radiotherapy, intensity-modulated radiotherapy (imrt) can reduce irradiation of the parotid glands. we assessed the hypothesis that parotid-sparing imrt reduces the incidence of severe xerostomia. methods we undertook a randomised controlled trial between jan 21, 2003, and dec 7, 2007, that compared conventional radiotherapy (control) with parotid-sparing imrt. we randomly assigned patients with histologically confirmed pharyngeal squamous-cell carcinoma (t1-4, n0-3, m0) at six uk radiotherapy centres between the two radiotherapy techniques (1:1 ratio). a dose of 60 or 65 gy was prescribed in 30 daily fractions given monday to friday. treatment was not masked. randomisation was by computer-generated permuted blocks and was stratified by centre and tumour site. our primary endpoint was the proportion of patients with grade 2 or worse xerostomia at 12 months, as assessed by the late effects of normal tissue (lent soma) scale. analyses were done on an intention-to-treat basis, with all patients who had assessments included. long-term follow-up of patients is ongoing. this study is registered with the international standard randomised controlled trial register, number isrctn48243537. findings 47 patients were assigned to each treatment arm. median follow-up was 44·0 months (iqr 30·0-59·7). six patients from each group died before 12 months and seven patients from the conventional radiotherapy and two from the imrt group were not assessed at 12 months. at 12 months xerostomia side-effects were reported in 73 of 82 alive patients; grade 2 or worse xerostomia at 12 months was significantly lower in the imrt group than in the conventional radiotherapy group (25 of 34 patients given conventional radiotherapy vs 15 of 39 given imrt, p=0·0027). the only recorded acute adverse event of grade 2 or worse that differed significantly between the treatment groups was fatigue, which was more prevalent in the imrt group (18 of 44 patients given conventional radiotherapy vs 35 of 47 given imrt, p=0·0015). at 24 months, grade 2 or worse xerostomia was significantly less common with imrt than with conventional radiotherapy (20 of 24 patients given conventional radiotherapy vs nine of 31 given imrt; p interpretation sparing the parotid glands with imrt significantly reduces the incidence of xerostomia and leads to recovery of saliva secretion and improvements in associated quality of life, and thus strongly supports a role for imrt in squamous-cell carcinoma of the head and neck. funding cancer research uk (cruk/03/005).",0
"background total hip or knee replacement is highly successful when judged by prosthesis-related outcomes. however, some people experience long-term pain. objectives to review published studies in representative populations with total hip or knee replacement for the treatment of osteoarthritis reporting proportions of people by pain intensity. data sources medline and embase databases searched to january 2011 with no language restrictions. citations of key articles in isi web of science and reference lists were checked. study eligibility criteria, participants and interventions prospective studies of consecutive, unselected osteoarthritis patients representative of the primary total hip or knee replacement population, with intensities of patient-centred pain measured after 3 months to 5-year follow-up. study appraisal and synthesis methods two authors screened titles and abstracts. data extracted by one author were checked independently against original articles by a second. for each study, the authors summarised the proportions of people with different severities of pain in the operated joint. results searches identified 1308 articles of which 115 reported patient-centred pain outcomes. fourteen articles describing 17 cohorts (6 with hip and 11 with knee replacement) presented appropriate data on pain intensity. the proportion of people with an unfavourable long-term pain outcome in studies ranged from about 7% to 23% after hip and 10% to 34% after knee replacement. in the best quality studies, an unfavourable pain outcome was reported in 9% or more of patients after hip and about 20% of patients after knee replacement. limitations other studies reported mean values of pain outcomes. these and routine clinical studies are potential sources of relevant data. conclusions and implications of key findings after hip and knee replacement, a significant proportion of people have painful joints. there is an urgent need to improve general awareness of this possibility and to address determinants of good and bad outcomes.",0
"the effectiveness of and adherence to ehealth interventions is enhanced by human support. however, human support has largely not been manualized and has usually not been guided by clear models. the objective of this paper is to develop a clear theoretical model, based on relevant empirical literature, that can guide research into human support components of ehealth interventions. a review of the literature revealed little relevant information from clinical sciences. applicable literature was drawn primarily from organizational psychology, motivation theory, and computer-mediated communication (cmc) research. we have developed a model, referred to as ""supportive accountability."" we argue that human support increases adherence through accountability to a coach who is seen as trustworthy, benevolent, and having expertise. accountability should involve clear, process-oriented expectations that the patient is involved in determining. reciprocity in the relationship, through which the patient derives clear benefits, should be explicit. the effect of accountability may be moderated by patient motivation. the more intrinsically motivated patients are, the less support they likely require. the process of support is also mediated by the communications medium (eg, telephone, instant messaging, email). different communications media each have their own potential benefits and disadvantages. we discuss the specific components of accountability, motivation, and cmc medium in detail. the proposed model is a first step toward understanding how human support enhances adherence to ehealth interventions. each component of the proposed model is a testable hypothesis. as we develop viable human support models, these should be manualized to facilitate dissemination.",0
"introduction type 2 diabetes (t2d) is a major health problem worldwide. this metabolic disease is indicated by high blood glucose levels due to insufficient insulin production by the pancreas. an inflammatory response occurs as a result of the immune response to high blood glucose levels as well as the presence of inflammatory mediators produced by adipocytes and macrophages in fat tissue. this low and chronic inflammation damages the pancreatic beta cells and leads to insufficient insulin production, which results in hyperglycemia. hyperglycemia in diabetes is thought to cause dysfunction of the immune response, which fails to control the spread of invading pathogens in diabetic subjects. therefore, diabetic subjects are known to more susceptible to infections. the increased prevalence of t2d will increase the incidence of infectious diseases and related comorbidities. objective this review provides an overview of the immunological aspect of t2d and the possible mechanisms that result in increased infections in diabetics. conclusion a better understanding of how immune dysfunctions occur during hyperglycemia can lead to novel treatments and preventions for infectious diseases and t2d comorbidities, thus improving the outcome of infectious disease treatment in t2d patients.",0
"antigen-presenting cells contain a specialized late endocytic compartment, miic (major histocompatibility complex class ii-enriched compartment), that harbors newly synthesized mhc class ii molecules in transit to the plasma membrane. miics have a limiting membrane enclosing characteristic internal membrane vesicles. both the limiting membrane and the internal vesicles contain mhc class ii. in this study on b lymphoblastoid cells, we demonstrate by immunoelectron microscopy that the limiting membrane of miics can fuse directly with the plasma membrane, resulting in release from the cells of internal mhc class ii-containing vesicles. these secreted vesicles, named exosomes, were isolated from the cell culture media by differential centrifugation followed by flotation on sucrose density gradients. the overall surface protein composition of exosomes differed significantly from that of the plasma membrane. exosome-bound mhc class ii was in a compact, peptide-bound conformation. metabolically labeled mhc class ii was released into the extracellular medium with relatively slow kinetics, 10 +/- 4% in 24 h, indicating that direct fusion of miics with the plasma membrane is not the major pathway by which mhc class ii reaches the plasma membrane. exosomes derived from both human and murine b lymphocytes induced antigen-specific mhc class ii-restricted t cell responses. these data suggest a role for exosomes in antigen presentation in vivo.",0
"background constraint-based reconstruction and analysis (cobra) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. due to the successes with metabolism, there is an increasing effort to apply cobra methods to reconstruct and analyze integrated models of cellular processes. the cobra toolbox for matlab is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. the opencobra project is a community effort to promote constraints-based research through the distribution of freely available software. results here, we describe cobra for python (cobrapy), a python package that provides support for basic cobra methods. cobrapy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. cobrapy does not require matlab to function; however, it includes an interface to the cobra toolbox for matlab to facilitate use of legacy codes. for improved performance, cobrapy includes parallel processing support for computationally intensive processes. conclusion cobrapy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. availability",0
"this article provides a review of the magnitude of mental disorders in children and adolescents from recent community surveys across the world. although there is substantial variation in the results depending upon the methodological characteristics of the studies, the findings converge in demonstrating that approximately one fourth of youth experience a mental disorder during the past year, and about one third across their lifetimes. anxiety disorders are the most frequent conditions in children, followed by behavior disorders, mood disorders, and substance use disorders. fewer than half of youth with current mental disorders receive mental health specialty treatment. however, those with the most severe disorders tend to receive mental health services. current issues that are now being identified in the field of child psychiatric epidemiology include: refinement of classification and assessment, inclusion of young children in epidemiologic surveys, integration of child and adult psychiatric epidemiology, and evaluation of both mental and physical disorders in children.",0
"high proportions of autistic children suffer from gastrointestinal (gi) disorders, implying a link between autism and abnormalities in gut microbial functions. increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. however, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related gi problems. we recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and gi symptoms. by pyrosequencing the v2/v3 regions in bacterial 16s rdna from fecal dna samples, we compared gut microbiomes of gi symptom-free neurotypical children with those of autistic children mostly presenting gi symptoms. unexpectedly, the presence of autistic symptoms, rather than the severity of gi symptoms, was associated with less diverse gut microbiomes. further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera prevotella, coprococcus, and unclassified veillonellaceae in autistic samples. these are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. however, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. taken together, autism and accompanying gi symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of prevotella, coprococcus, and unclassified veillonellaceae.",0
"clostridium difficile is the leading cause of infectious diarrhoea in hospitals worldwide, because of its virulence, spore-forming ability and persistence. c. difficile-associated diseases are induced by antibiotic treatment or disruption of the normal gastrointestinal flora. recently, morbidity and mortality resulting from c. difficile-associated diseases have increased significantly due to changes in the virulence of the causative strains and antibiotic usage patterns. since 2002, epidemic toxinotype iii nap1/027 strains, which produce high levels of the major virulence factors, toxin a and toxin b, have emerged. these toxins have 63% amino acid sequence similarity and are members of the large clostridial glucosylating toxin family, which are monoglucosyltransferases that are pro-inflammatory, cytotoxic and enterotoxic in the human colon. inside host cells, both toxins catalyse the transfer of glucose onto the rho family of gtpases, leading to cell death. however, the role of these toxins in the context of a c. difficile infection is unknown. here we describe the construction of isogenic tcda and tcdb (encoding toxin a and b, respectively) mutants of a virulent c. difficile strain and their use in the hamster disease model to show that toxin b is a key virulence determinant. previous studies showed that purified toxin a alone can induce most of the pathology observed after infection of hamsters with c. difficile and that toxin b is not toxic in animals unless it is co-administered with toxin a, suggesting that the toxins act synergistically. our work provides evidence that toxin b, not toxin a, is essential for virulence. furthermore, it is clear that the importance of these toxins in the context of infection cannot be predicted exclusively from studies using purified toxins, reinforcing the importance of using the natural infection process to dissect the role of toxins in disease.",0
"background physical activity has not been objectively measured in prospective cohorts with sufficiently large numbers to reliably detect associations with multiple health outcomes. technological advances now make this possible. we describe the methods used to collect and analyse accelerometer measured physical activity in over 100,000 participants of the uk biobank study, and report variation by age, sex, day, time of day, and season. methods participants were approached by email to wear a wrist-worn accelerometer for seven days that was posted to them. physical activity information was extracted from 100hz raw triaxial acceleration data after calibration, removal of gravity and sensor noise, and identification of wear / non-wear episodes. we report age- and sex-specific wear-time compliance and accelerometer measured physical activity, overall and by hour-of-day, week-weekend day and season. results 103,712 datasets were received (44.8% response), with a median wear-time of 6.9 days (iqr:6.5-7.0). 96,600 participants (93.3%) provided valid data for physical activity analyses. vector magnitude, a proxy for overall physical activity, was 7.5% (2.35mg) lower per decade of age (cohen's d = 0.9). women had a higher vector magnitude than men, apart from those aged 45-54yrs. there were major differences in vector magnitude by time of day (d = 0.66). vector magnitude differences between week and weekend days (d = 0.12 for men, d = 0.09 for women) and between seasons (d = 0.27 for men, d = 0.15 for women) were small. conclusions it is feasible to collect and analyse objective physical activity data in large studies. the summary measure of overall physical activity is lower in older participants and age-related differences in activity are most prominent in the afternoon and evening. this work lays the foundation for studies of physical activity and its health consequences. our summary variables are part of the uk biobank dataset and can be used by researchers as exposures, confounding factors or outcome variables in future analyses.",0
"macrophages mediate crucial innate immune responses via caspase-1-dependent processing and secretion of interleukin 1β (il-1β) and il-18. although infection with wild-type salmonella typhimurium is lethal to mice, we show here that a strain that persistently expresses flagellin was cleared by the cytosolic flagellin-detection pathway through the activation of caspase-1 by the nlrc4 inflammasome; however, this clearance was independent of il-1β and il-18. instead, caspase-1-induced pyroptotic cell death released bacteria from macrophages and exposed the bacteria to uptake and killing by reactive oxygen species in neutrophils. similarly, activation of caspase-1 cleared unmanipulated legionella pneumophila and burkholderia thailandensis by cytokine-independent mechanisms. this demonstrates that activation of caspase-1 clears intracellular bacteria in vivo independently of il-1β and il-18 and establishes pyroptosis as an efficient mechanism of bacterial clearance by the innate immune system.",0
"unlabelled : visualizing genes' structure and annotated features helps biologists to investigate their function and evolution intuitively. the gene structure display server (gsds) has been widely used by more than 60 000 users since its first publication in 2007. here, we reported the upgraded gsds 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis. the full source code is also available for downloading. availability and implementation web server and source code are freely available at contact gaog@mail.cbi.pku.edu.cn or gsds@mail.cbi.pku.edu.cn supplementary information supplementary data are available at bioinformatics online.",0
"a census of the biomass on earth is key for understanding the structure and dynamics of the biosphere. however, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (gt c) of biomass distributed among all of the kingdoms of life. we find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 gt c, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 gt c) are mainly marine, and bacteria (≈70 gt c) and archaea (≈7 gt c) are predominantly located in deep subsurface environments. we show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 gt c of marine biota, doubling the previous estimated quantity. our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.",0
"spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. the combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. here we describe methods for imaging the activity of neurons in the ca1 region of the hippocampus with subcellular resolution in behaving mice. neurons that expressed the genetically encoded calcium indicator gcamp3 were imaged through a chronic hippocampal window. head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. we optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. the combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.",0
"background identifying, developing, and testing implementation strategies are important goals of implementation science. however, these efforts have been complicated by the use of inconsistent language and inadequate descriptions of implementation strategies in the literature. the expert recommendations for implementing change (eric) study aimed to refine a published compilation of implementation strategy terms and definitions by systematically gathering input from a wide range of stakeholders with expertise in implementation science and clinical practice. methods purposive sampling was used to recruit a panel of experts in implementation and clinical practice who engaged in three rounds of a modified delphi process to generate consensus on implementation strategies and definitions. the first and second rounds involved web-based surveys soliciting comments on implementation strategy terms and definitions. after each round, iterative refinements were made based upon participant feedback. the third round involved a live polling and consensus process via a web-based platform and conference call. results participants identified substantial concerns with 31% of the terms and/or definitions and suggested five additional strategies. seventy-five percent of definitions from the originally published compilation of strategies were retained after voting. ultimately, the expert panel reached consensus on a final compilation of 73 implementation strategies. conclusions this research advances the field by improving the conceptual clarity, relevance, and comprehensiveness of implementation strategies that can be used in isolation or combination in implementation research and practice. future phases of eric will focus on developing conceptually distinct categories of strategies as well as ratings for each strategy's importance and feasibility. next, the expert panel will recommend multifaceted strategies for hypothetical yet real-world scenarios that vary by sites' endorsement of evidence-based programs and practices and the strength of contextual supports that surround the effort.",0
"wikipathways (wikipathways.org) captures the collective knowledge represented in biological pathways. by providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. wikipathways and other pathway databases are used to analyze experimental data by research groups in many fields. due to the open and collaborative nature of the wikipathways platform, our content keeps growing and is getting more accurate, making wikipathways a reliable and rich pathway database. previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in wikipathways. furthermore, we introduce an openapi documentation of our web services and the fair (findable, accessible, interoperable and reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. new search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.",0
"background content validity is the most important measurement property of a patient-reported outcome measure (prom) and the most challenging to assess. our aims were to: (1) develop standards for evaluating the quality of prom development; (2) update the original cosmin standards for assessing the quality of content validity studies of proms; (3) develop criteria for what constitutes good content validity of proms, and (4) develop a rating system for summarizing the evidence on a prom's content validity and grading the quality of the evidence in systematic reviews of proms. methods an online 4-round delphi study was performed among 159 experts from 21 countries. panelists rated the degree to which they (dis)agreed to proposed standards, criteria, and rating issues on 5-point rating scales ('strongly disagree' to 'strongly agree'), and provided arguments for their ratings. results discussion focused on sample size requirements, recording and field notes, transcribing cognitive interviews, and data coding. after four rounds, the required 67% consensus was reached on all standards, criteria, and rating issues. after pilot-testing, the steering committee made some final changes. ten criteria for good content validity were defined regarding item relevance, appropriateness of response options and recall period, comprehensiveness, and comprehensibility of the prom. discussion the consensus-based cosmin methodology for content validity is more detailed, standardized, and transparent than earlier published guidelines, including the previous cosmin standards. this methodology can contribute to the selection and use of high-quality proms in research and clinical practice.",0
"adult hippocampal neurogenesis is a unique form of neural circuit plasticity that results in the generation of new neurons in the dentate gyrus throughout life. neurons that arise in adults (adult-born neurons) show heightened synaptic plasticity during their maturation and can account for up to ten per cent of the entire granule cell population. moreover, levels of adult hippocampal neurogenesis are increased by interventions that are associated with beneficial effects on cognition and mood, such as learning, environmental enrichment, exercise and chronic treatment with antidepressants. together, these properties of adult neurogenesis indicate that this process could be harnessed to improve hippocampal functions. however, despite a substantial number of studies demonstrating that adult-born neurons are necessary for mediating specific cognitive functions, as well as some of the behavioural effects of antidepressants, it is unknown whether an increase in adult hippocampal neurogenesis is sufficient to improve cognition and mood. here we show that inducible genetic expansion of the population of adult-born neurons through enhancing their survival improves performance in a specific cognitive task in which two similar contexts need to be distinguished. mice with increased adult hippocampal neurogenesis show normal object recognition, spatial learning, contextual fear conditioning and extinction learning but are more efficient in differentiating between overlapping contextual representations, which is indicative of enhanced pattern separation. furthermore, stimulation of adult hippocampal neurogenesis, when combined with an intervention such as voluntary exercise, produces a robust increase in exploratory behaviour. however, increasing adult hippocampal neurogenesis alone does not produce a behavioural response like that induced by anxiolytic agents or antidepressants. together, our findings suggest that strategies that are designed to increase adult hippocampal neurogenesis specifically, by targeting the cell death of adult-born neurons or by other mechanisms, may have therapeutic potential for reversing impairments in pattern separation and dentate gyrus dysfunction such as those seen during normal ageing.",0
"the transient receptor potential (trp) multigene superfamily encodes integral membrane proteins that function as ion channels. members of this family are conserved in yeast, invertebrates and vertebrates. the trp family is subdivided into seven subfamilies: trpc (canonical), trpv (vanilloid), trpm (melastatin), trpp (polycystin), trpml (mucolipin), trpa (ankyrin) and trpn (nompc-like); the latter is found only in invertebrates and fish. trp ion channels are widely expressed in many different tissues and cell types, where they are involved in diverse physiological processes, such as sensation of different stimuli or ion homeostasis. most trps are non-selective cation channels, only few are highly ca2+ selective, some are even permeable for highly hydrated mg2+ ions. this channel family shows a variety of gating mechanisms, with modes of activation ranging from ligand binding, voltage and changes in temperature to covalent modifications of nucleophilic residues. activated trp channels cause depolarization of the cellular membrane, which in turn activates voltage-dependent ion channels, resulting in a change of intracellular ca2+ concentration; they serve as gatekeeper for transcellular transport of several cations (such as ca2+ and mg2+), and are required for the function of intracellular organelles (such as endosomes and lysosomes). because of their function as intracellular ca2+ release channels, they have an important regulatory role in cellular organelles. mutations in several trp genes have been implicated in diverse pathological states, including neurodegenerative disorders, skeletal dysplasia, kidney disorders and pain, and ongoing research may help find new therapies for treatments of related diseases.",0
"behavioral researchers are increasingly conducting their studies online, to gain access to large and diverse samples that would be difficult to get in a laboratory environment. however, there are technical access barriers to building experiments online, and web browsers can present problems for consistent timing-an important issue with reaction-time-sensitive measures. for example, to ensure accuracy and test-retest reliability in presentation and response recording, experimenters need a working knowledge of programming languages such as javascript. we review some of the previous and current tools for online behavioral research, as well as how well they address the issues of usability and timing. we then present the gorilla experiment builder (gorilla.sc), a fully tooled experiment authoring and deployment platform, designed to resolve many timing issues and make reliable online experimentation open and accessible to a wider range of technical abilities. to demonstrate the platform's aptitude for accessible, reliable, and scalable research, we administered a task with a range of participant groups (primary school children and adults), settings (without supervision, at home, and under supervision, in both schools and public engagement events), equipment (participant's own computer, computer supplied by the researcher), and connection types (personal internet connection, mobile phone 3g/4g). we used a simplified flanker task taken from the attentional network task (rueda, posner, & rothbart, 2004). we replicated the ""conflict network"" effect in all these populations, demonstrating the platform's capability to run reaction-time-sensitive experiments. unresolved limitations of running experiments online are then discussed, along with potential solutions and some future features of the platform.",0
"the national human genome research institute (nhgri) catalog of published genome-wide association studies (gwas) catalog provides a publicly available manually curated collection of published gwas assaying at least 100,000 single-nucleotide polymorphisms (snps) and all snp-trait associations with p <1 × 10(-5). the catalog includes 1751 curated publications of 11 912 snps. in addition to the snp-trait association data, the catalog also publishes a quarterly diagram of all snp-trait associations mapped to the snps' chromosomal locations. the catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an owl knowledge base. this article presents a number of recent improvements to the catalog, including novel ways for users to interact with the catalog and changes to the curation infrastructure.",0
"in the past three decades, total fat and saturated fat intake as a percentage of total calories has continuously decreased in western diets, while the intake of omega-6 fatty acid increased and the omega-3 fatty acid decreased, resulting in a large increase in the omega-6/omega-3 ratio from 1:1 during evolution to 20:1 today or even higher. this change in the composition of fatty acids parallels a significant increase in the prevalence of overweight and obesity. experimental studies have suggested that omega-6 and omega-3 fatty acids elicit divergent effects on body fat gain through mechanisms of adipogenesis, browning of adipose tissue, lipid homeostasis, brain-gut-adipose tissue axis, and most importantly systemic inflammation. prospective studies clearly show an increase in the risk of obesity as the level of omega-6 fatty acids and the omega-6/omega-3 ratio increase in red blood cell (rbc) membrane phospholipids, whereas high omega-3 rbc membrane phospholipids decrease the risk of obesity. recent studies in humans show that in addition to absolute amounts of omega-6 and omega-3 fatty acid intake, the omega-6/omega-3 ratio plays an important role in increasing the development of obesity via both aa eicosanoid metabolites and hyperactivity of the cannabinoid system, which can be reversed with increased intake of eicosapentaenoic acid (epa) and docosahexaenoic acid (dha). a balanced omega-6/omega-3 ratio is important for health and in the prevention and management of obesity.",0
"autophagy is a membrane trafficking to vacuole/lysosome induced by nutrient starvation. in saccharomyces cerevisiae, tor protein, a phosphatidylinositol kinase-related kinase, is involved in the repression of autophagy induction by a largely unknown mechanism. here, we show that the protein kinase activity of apg1 is enhanced by starvation or rapamycin treatment. in addition, we have also found that apg13, which binds to and activates apg1, is hyperphosphorylated in a tor-dependent manner, reducing its affinity to apg1. this apg1-apg13 association is required for autophagy, but not for the cytoplasm-to-vacuole targeting (cvt) pathway, another vesicular transport mechanism in which factors essential for autophagy (apg proteins) are also employed under vegetative growth conditions. finally, other apg1-associating proteins, such as apg17 and cvt9, are shown to function specifically in autophagy or the cvt pathway, respectively, suggesting that the apg1 complex plays an important role in switching between two distinct vesicular transport systems in a nutrient-dependent manner.",0
"previous work has shown that endogenous chemical mediators, of which histamine is the prototype, increase the permeability of blood vessels by causing gaps to appear between endothelial cells. in the present paper, morphologic and statistical evidence is presented, to suggest that endothelial cells contract under the influence of mediators, and that this contraction causes the formation of intercellular gaps. histamine, serotonin, and bradykinin were injected subcutaneously into the scrotum of the rat, and the vessels of the underlying cremaster muscle were examined by electron microscopy. to eliminate the vascular collapse induced by routine fixation, in one series of animals (including controls) the root of the cremaster was constricted for 2-4 min prior to sacrifice, and the tissues were fixed under conditions of mild venous congestion. electron micrographs were taken of 599 nuclei from the endothelium of small blood vessels representing the various experimental situations. nuclear deformations were classified into four types of increasing tightness (notches, foldsl closing folds, and pinches. in the latter the apposed surfaces of the nuclear membrane are in contact). it was found that: (1) venous congestion tends to straighten the nuclei in al groups; (2) mediators cause a highly significant increase in the number of pinches (p < 0.001), also if the vessels are distended by venous congestion; (3) fixation without venous congestion causes vascular collapse. the degree of endothelial recoil, as measured by nuclear pinches, is very different from that caused by mediators (p < 0.001). (4) pinched nuclei are more frequent in leaking vessels, and in cells adjacent to gaps (p < 0.001); (5) mediators also induce, in the endothelium, cytoplasmic changes suggestive of contraction, and similar to those of contracted smooth muscle; (6) there is no evidence of pericyte contraction under the conditions tested. occasional pericytes appeared to receive fine nerve endings. various hypotheses to explain nuclear pinching are discussed; the only satisfactory explanation is that which requires endothelial contraction.",0
"background chronic obstructive pulmonary disease (copd) is a complex condition with pulmonary and extra-pulmonary manifestations. this study describes the heterogeneity of copd in a large and well characterised and controlled copd cohort (eclipse). methods we studied 2164 clinically stable copd patients, 337 smokers with normal lung function and 245 never smokers. in these individuals, we measured clinical parameters, nutritional status, spirometry, exercise tolerance, and amount of emphysema by computed tomography. results copd patients were slightly older than controls and had more pack years of smoking than smokers with normal lung function. co-morbidities were more prevalent in copd patients than in controls, and occurred to the same extent irrespective of the gold stage. the severity of airflow limitation in copd patients was poorly related to the degree of breathlessness, health status, presence of co-morbidity, exercise capacity and number of exacerbations reported in the year before the study. the distribution of these variables within each gold stage was wide. even in subjects with severe airflow obstruction, a substantial proportion did not report symptoms, exacerbations or exercise limitation. the amount of emphysema increased with gold severity. the prevalence of bronchiectasis was low (4%) but also increased with gold stage. some gender differences were also identified. conclusions the clinical manifestations of copd are highly variable and the degree of airflow limitation does not capture the heterogeneity of the disease.",0
"parkin, an e3 ubiquitin ligase implicated in parkinson's disease, promotes degradation of dysfunctional mitochondria by autophagy. using proteomic and cellular approaches, we show that upon translocation to mitochondria, parkin activates the ubiquitin-proteasome system (ups) for widespread degradation of outer membrane proteins. this is evidenced by an increase in k48-linked polyubiquitin on mitochondria, recruitment of the 26s proteasome and rapid degradation of multiple outer membrane proteins. the degradation of proteins by the ups occurs independently of the autophagy pathway, and inhibition of the 26s proteasome completely abrogates parkin-mediated mitophagy in hela, sh-sy5y and mouse cells. although the mitofusins mfn1 and mfn2 are rapid degradation targets of parkin, we find that degradation of additional targets is essential for mitophagy. these results indicate that remodeling of the mitochondrial outer membrane proteome is important for mitophagy, and reveal a causal link between the ups and autophagy, the major pathways for degradation of intracellular substrates.",0
"background time series microarray experiments are widely used to study dynamical biological processes. due to the cost of microarray experiments, and also in some cases the limited availability of biological material, about 80% of microarray time series experiments are short (3-8 time points). previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data. results we introduce the short time-series expression miner (stem) the first software program specifically designed for the analysis of short time series microarray gene expression data. stem implements unique methods to cluster, compare, and visualize such data. stem also supports efficient and statistically rigorous biological interpretations of short time series data through its integration with the gene ontology. conclusion the unique algorithms stem implements to cluster and compare short time series gene expression data combined with its visualization capabilities and integration with the gene ontology should make stem useful in the analysis of data from a significant portion of all microarray studies. stem is available for download for free to academic and non-profit users at",0
"active suppression by t regulatory (tr) cells plays an important role in the downregulation of t cell responses to foreign and self-antigens. mouse cd4(+) tr cells that express cd25 possess remarkable suppressive activity in vitro and in autoimmune disease models in vivo. thus far, the existence of a similar subset of cd25(+)cd4(+) tr cells in humans has not been reported. here we show that human cd25(+)cd4(+) tr cells isolated from peripheral blood failed to proliferate and displayed reduced expression of cd40 ligand (cd40l), in response to t cell receptor-mediated polyclonal activation, but strongly upregulated cytotoxic t lymphocyte-associated antigen (ctla)-4. human cd25(+)cd4(+) tr cells also did not proliferate in response to allogeneic antigen-presenting cells, but they produced interleukin (il)-10, transforming growth factor (tgf)-beta, low levels of interferon (ifn)-gamma, and no il-4 or il-2. importantly, cd25(+)cd4(+) tr cells strongly inhibited the proliferative responses of both naive and memory cd4(+) t cells to alloantigens, but neither il-10, tgf-beta, nor ctla-4 seemed to be directly required for their suppressive effects. cd25(+)cd4(+) tr cells could be expanded in vitro in the presence of il-2 and allogeneic feeder cells and maintained their suppressive capacities. these findings that cd25(+)cd4(+) tr cells with immunosuppressive effects can be isolated from peripheral blood and expanded in vitro without loss of function represent a major advance towards the therapeutic use of these cells in t cell-mediated diseases.",0
"epithelia vary with respect to transepithelial permeability. in those that are considered ""leaky"", a large fraction of the passive transepithelial flux appears to follow the paracellular route, passing across the zonulae occludentes and moving down the intercellular clefts. in ""tight"" epithelia, the resistance of the paracellular pathway to passive flux is greatly increased. to see whether differences in the morphology of the zonula occludens could contribute to this variability in leakiness among epithelia, replicas of zonulae occludentes in freeze-fractured material from a variety of tight and leaky epithelia were examined. the junctions appear as a branching and anastomosing network of strands or grooves on the a and b membrane fracture faces, respectively. it was found that the zonula occludens from a ""very leaky"" epithelium, the proximal convoluted tubule of the mouse kidney, is extremely shallow in the apical-basal direction, consisting in most places of only one junctional strand. in contrast, the ""very tight"" frog urinary bladder exhibits a zonula occludens that is relatively deep (>0.5 microm) in the apical-basal direction, and consists of five or more interconnected junctional strands interposed between luminal and lateral membrane surfaces. epithelia of intermediate permeabilities exhibited junctions with intermediate or variable morphology. toad urinary bladder, mouse stomach, jejunum, and distal tubule, rabbit gallbladder, and necturus kidney and gallbladder were also examined, and the morphological data from these epithelia were compared to physiological data from the literature.",0
"background in systematic reviews and meta-analyses, time-to-event outcomes are most appropriately analysed using hazard ratios (hrs). in the absence of individual patient data (ipd), methods are available to obtain hrs and/or associated statistics by carefully manipulating published or other summary data. awareness and adoption of these methods is somewhat limited, perhaps because they are published in the statistical literature using statistical notation. methods this paper aims to 'translate' the methods for estimating a hr and associated statistics from published time-to-event-analyses into less statistical and more practical guidance and provide a corresponding, easy-to-use calculations spreadsheet, to facilitate the computational aspects. results a wider audience should be able to understand published time-to-event data in individual trial reports and use it more appropriately in meta-analysis. when faced with particular circumstances, readers can refer to the relevant sections of the paper. the spreadsheet can be used to assist them in carrying out the calculations. conclusion the methods cannot circumvent the potential biases associated with relying on published data for systematic reviews and meta-analysis. however, this practical guide should improve the quality of the analysis and subsequent interpretation of systematic reviews and meta-analyses that include time-to-event outcomes.",0
"background student mental health in higher education has been an increasing concern. the covid-19 pandemic situation has brought this vulnerable population into renewed focus. objective our study aims to conduct a timely assessment of the effects of the covid-19 pandemic on the mental health of college students. methods we conducted interview surveys with 195 students at a large public university in the united states to understand the effects of the pandemic on their mental health and well-being. the data were analyzed through quantitative and qualitative methods. results of the 195 students, 138 (71%) indicated increased stress and anxiety due to the covid-19 outbreak. multiple stressors were identified that contributed to the increased levels of stress, anxiety, and depressive thoughts among students. these included fear and worry about their own health and of their loved ones (177/195, 91% reported negative impacts of the pandemic), difficulty in concentrating (173/195, 89%), disruptions to sleeping patterns (168/195, 86%), decreased social interactions due to physical distancing (167/195, 86%), and increased concerns on academic performance (159/195, 82%). to cope with stress and anxiety, participants have sought support from others and helped themselves by adopting either negative or positive coping mechanisms. conclusions due to the long-lasting pandemic situation and onerous measures such as lockdown and stay-at-home orders, the covid-19 pandemic brings negative impacts on higher education. the findings of our study highlight the urgent need to develop interventions and preventive strategies to address the mental health of college students.",0
"the metacyc database (metacyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. metacyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. metacyc contains >2100 pathways derived from >37,000 publications, and is the largest curated collection of metabolic pathways currently available. biocyc (biocyc.org) is a collection of >3000 organism-specific pathway/genome databases (pgdbs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. additions to biocyc over the past 2 years include yeastcyc, a pgdb for saccharomyces cerevisiae, and 891 new genomes from the human microbiome project. the biocyc web site offers a variety of tools for querying and analysis of pgdbs, including omics viewers and tools for comparative analysis. new developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the web groups functionality, improvements to the omics viewers, a new representation of the enzyme commission system and, for the desktop version of the software, the ability to save display states.",0
"we describe a new method for subcellular fractionation of human neutrophils. neutrophils were disrupted by nitrogen cavitation and the nuclei removed by centrifugation. the postnuclear supernatant was applied on top of a discontinuous percoll density gradient. centrifugation for 15 min at 48,000 g resulted in complete separation of plasma membranes, azurophil granules, and specific granules. as determined by ultrastructure and the distribution of biochemical markers of these organelles, approximately 90% of the b-cytochrome in unstimulated cells was recovered from the band containing the specific granules and was shown to be in or tightly associated with the membrane. during stimulation of intact neutrophils with phorbol myristate acetate or the ionophore a23187, we observed translocation of 40-75% of the b-cytochrome to the plasma membrane. the extent of this translocation closely paralleled release of the specific granule marker, vitamin b12-binding protein. these data indicate that the b-cytochrome is in the membrane of the specific granules of unstimulated neutrophils and that stimulus-induced fusion of these granules with the plasma membrane results in a translocation of the cytochrome. our observations provide a basis for the assembly of the microbicidal oxidase of the human neutrophil.",0
"background laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. a major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. results we describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. data acquisition and control of laser scanning are achieved through standard data acquisition boards. the entire burden of signal integration and image processing is placed on the cpu of the computer. we quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. we implement our approach in an open source software package (scanimage) and describe its functionality. conclusions we present scanimage, software to run a flexible laser scanning microscope that allows easy custom design.",0
"a growing body of evidence indicates that resolution of acute inflammation is an active process. resolvins are a new family of lipid mediators enzymatically generated within resolution networks that possess unique and specific functions to orchestrate catabasis, the phase in which disease declines. resolvin d2 (rvd2) was originally identified in resolving exudates, yet its individual contribution in resolution remained to be elucidated. here, we establish rvd2's potent stereoselective actions in reducing excessive neutrophil trafficking to inflammatory loci. rvd2 decreased leukocyte-endothelial interactions in vivo by endothelial-dependent nitric oxide production, and by direct modulation of leukocyte adhesion receptor expression. in mice with microbial sepsis initiated by caecal ligation and puncture, rvd2 sharply decreased both local and systemic bacterial burden, excessive cytokine production and neutrophil recruitment, while increasing peritoneal mononuclear cells and macrophage phagocytosis. these multi-level pro-resolving actions of rvd2 translate to increased survival from sepsis induced by caecal ligation and puncture and surgery. together, these results identify rvd2 as a potent endogenous regulator of excessive inflammatory responses that acts via multiple cellular targets to stimulate resolution and preserve immune vigilance.",0
"two ets transcription factors of the pea3 subfamily are induced in subpopulations of dorsal root ganglion (drg) sensory and spinal motor neurons by target-derived factors. their expression controls late aspects of neuronal differentiation such as target invasion and branching. here, we show that the late onset of ets gene expression is an essential requirement for normal sensory neuron differentiation. we provide genetic evidence in the mouse that precocious ets expression in drg sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. together, our findings indicate that drg sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ets transcription factor signaling at sequential steps of neuronal maturation.",0
"quinolones are one of the most commonly prescribed classes of antibacterials in the world and are used to treat a variety of bacterial infections in humans. because of the wide use (and overuse) of these drugs, the number of quinolone-resistant bacterial strains has been growing steadily since the 1990s. as is the case with other antibacterial agents, the rise in quinolone resistance threatens the clinical utility of this important drug class. quinolones act by converting their targets, gyrase and topoisomerase iv, into toxic enzymes that fragment the bacterial chromosome. this review describes the development of the quinolones as antibacterials, the structure and function of gyrase and topoisomerase iv, and the mechanistic basis for quinolone action against their enzyme targets. it will then discuss the following three mechanisms that decrease the sensitivity of bacterial cells to quinolones. target-mediated resistance is the most common and clinically significant form of resistance. it is caused by specific mutations in gyrase and topoisomerase iv that weaken interactions between quinolones and these enzymes. plasmid-mediated resistance results from extrachromosomal elements that encode proteins that disrupt quinolone-enzyme interactions, alter drug metabolism, or increase quinolone efflux. chromosome-mediated resistance results from the underexpression of porins or the overexpression of cellular efflux pumps, both of which decrease cellular concentrations of quinolones. finally, this review will discuss recent advancements in our understanding of how quinolones interact with gyrase and topoisomerase iv and how mutations in these enzymes cause resistance. these last findings suggest approaches to designing new drugs that display improved activity against resistant strains.",0
"the human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. grch38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. we developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. for the first time, the reference assembly contains sequence-based representations for the centromeres. we also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. we demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. we additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. we assert that the collected updates in grch38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.",0
"apex is an engineered peroxidase that functions as an electron microscopy tag and a promiscuous labeling enzyme for live-cell proteomics. because limited sensitivity precludes applications requiring low apex expression, we used yeast-display evolution to improve its catalytic efficiency. apex2 is far more active in cells, enabling the use of electron microscopy to resolve the submitochondrial localization of calcium uptake regulatory protein micu1. apex2 also permits superior enrichment of endogenous mitochondrial and endoplasmic reticulum membrane proteins.",0
"the transporter classification database (tcdb) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. tcdb is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. the transporter classification (tc) system is an international union of biochemistry and molecular biology approved system of nomenclature for transport protein classification. tcdb is freely accessible at the web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or tc number and full-text searching. the functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. the tcdb website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. tcdb not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.",0
"in the cerebral cortex, local circuits consist of tens of thousands of neurons, each of which makes thousands of synaptic connections. perhaps the biggest impediment to understanding these networks is that we have no wiring diagrams of their interconnections. even if we had a partial or complete wiring diagram, however, understanding the network would also require information about each neuron's function. here we show that the relationship between structure and function can be studied in the cortex with a combination of in vivo physiology and network anatomy. we used two-photon calcium imaging to characterize a functional property--the preferred stimulus orientation--of a group of neurons in the mouse primary visual cortex. large-scale electron microscopy of serial thin sections was then used to trace a portion of these neurons' local network. consistent with a prediction from recent physiological experiments, inhibitory interneurons received convergent anatomical input from nearby excitatory neurons with a broad range of preferred orientations, although weak biases could not be rejected.",0
"importance people exposed to coronavirus disease 2019 (covid-19) and a series of imperative containment measures could be psychologically stressed, yet the burden of and factors associated with mental health symptoms remain unclear. objective to investigate the prevalence of and risk factors associated with mental health symptoms in the general population in china during the covid-19 pandemic. design, setting, and participants this large-sample, cross-sectional, population-based, online survey study was conducted from february 28, 2020, to march 11, 2020. it involved all 34 province-level regions in china and included participants aged 18 years and older. data analysis was performed from march to may 2020. main outcomes and measures the prevalence of symptoms of depression, anxiety, insomnia, and acute stress among the general population in china during the covid-19 pandemic was evaluated using the patient health questionnaire-9, generalized anxiety disorder-7, insomnia severity index, and acute stress disorder scale. logistic regression analyses were used to explore demographic and covid-19-related risk factors. results of 71 227 individuals who clicked on the survey link, 56 932 submitted the questionnaires, for a participation rate of 79.9%. after excluding the invalid questionnaires, 56 679 participants (mean age, 35.97 years; 27 149 men ) were included in the study; 39 468 respondents (69.6%) were aged 18 to 39 years. during the covid-19 pandemic, the rates of mental health symptoms among the survey respondents were 27.9% (95% ci, 27.5%-28.2%) for depression, 31.6% (95% ci, 31.2%-32.0%) for anxiety, 29.2% (95% ci, 28.8%-29.6%) for insomnia, and 24.4% (95% ci, 24.0%-24.7%) for acute stress. participants with confirmed or suspected covid-19 and their family members or friends had a high risk for symptoms of depression (adjusted odds ratios , 3.27 for patients; 1.53 for family or friends), anxiety (adjusted ors, 2.48 for patients; 1.53 for family or friends), insomnia (adjusted ors, 3.06 for patients; 1.62 for family or friends), and acute stress (adjusted ors, 3.50 for patients; 1.77 for family or friends). moreover, people with occupational exposure risks and residents in hubei province had increased odds of symptoms of depression (adjusted ors, 1.96 for occupational exposure; 1.42 for hubei residence), anxiety (adjusted ors, 1.93 for occupational exposure; 1.54 for hubei residence), insomnia (adjusted ors, 1.60 for occupational exposure; 1.20 for hubei residence), and acute stress (adjusted ors, 1.98 for occupational exposure; 1.49 for hubei residence). both centralized quarantine (adjusted ors, 1.33 for depression; 1.46 for anxiety; 1.63 for insomnia; 1.46 for acute stress) and home quarantine (adjusted ors, 1.30 for depression; 1.28 for anxiety; 1.24 for insomnia; 1.29 for acute stress) were associated with the 4 negative mental health outcomes. being at work was associated with lower risks of depression (adjusted or, 0.85 ), anxiety (adjusted or, 0.92 ), and insomnia (adjusted or, 0.87 ). conclusions and relevance the results of this survey indicate that mental health symptoms may have been common during the covid-19 outbreak among the general population in china, especially among infected individuals, people with suspected infection, and people who might have contact with patients with covid-19. some measures, such as quarantine and delays in returning to work, were also associated with mental health among the public. these findings identify populations at risk for mental health problems during the covid-19 pandemic and may help in implementing mental health intervention policies in other countries and regions.",0
"background the 30-item disabilities of the arm, shoulder and hand (dash) questionnaire is increasingly used in clinical research involving upper extremity musculoskeletal disorders. from the original dash a shorter version, the 11-item quickdash, has been developed. little is known about the discriminant ability of score changes for the quickdash compared to the dash. the aim of this study was to assess the performance of the quickdash and its cross-sectional and longitudinal validity and reliability. methods the study was based on extracting quickdash item responses from the responses to the full-length dash questionnaire completed by 105 patients with a variety of upper extremity disorders before surgery and at follow-up 6 to 21 months after surgery. the dash and quickdash scores were compared for the whole population and for different diagnostic groups. for longitudinal construct validity the effect size and standardized response mean were calculated. analyses with roc curves were performed to compare the ability of the dash and quickdash to discriminate among patients classified according to the magnitude of self-rated improvement. cross-sectional and test-retest reliability was assessed. results the mean dash score was 34 (sd 22) and the mean quickdash score was 39 (sd 24) at baseline. for the different diagnostic groups the mean and median quickdash scores were higher than the corresponding dash scores. for the whole population, the mean difference between the quickdash and dash baseline scores was 4.2 (95% ci 3.2-5.3), follow-up scores was 2.6 (1.7-3.4), and change scores was 1.7 (0.6-2.8). the overall effect size and standardized response mean measured with the dash and the quickdash were similar. in the roc analysis of change scores among patients who rated their arm status as somewhat or much better and those who rated it as unchanged the difference in the area under the roc curve for the dash and quickdash was 0.01 (95% ci -0.05-0.07) indicating similar discriminant ability.cross-sectional and test-retest reliability of the dash and quickdash were similar. conclusion the results indicate that the quickdash can be used instead of the dash with similar precision in upper extremity disorders.",0
"background low muscle mass and weakness are common and potentially disabling in older adults, but in order to become recognized as a clinical condition, criteria for diagnosis should be based on clinically relevant thresholds and independently validated. the foundation for the national institutes of health biomarkers consortium sarcopenia project used an evidence-based approach to develop these criteria. initial findings were presented at a conference in may 2012, which generated recommendations that guided additional analyses to determine final recommended criteria. details of the project and its findings are presented in four accompanying manuscripts. methods the foundation for the national institutes of health sarcopenia project used data from nine sources of community-dwelling older persons: age, gene/environment susceptibility-reykjavik study, boston puerto rican health study, a series of six clinical trials, framingham heart study, health, aging, and body composition, invecchiare in chianti, osteoporotic fractures in men study, rancho bernardo study, and study of osteoporotic fractures. feedback from conference attendees was obtained via surveys and breakout groups. results the pooled sample included 26,625 participants (57% women, mean age in men 75.2 and in women 78.6 years). conference attendees emphasized the importance of evaluating the influence of body mass on cutpoints. based on the analyses presented in this series, the final recommended cutpoints for weakness are grip strength conclusions these evidence-based cutpoints, based on a large and diverse population, may help identify participants for clinical trials and should be evaluated among populations with high rates of functional limitations.",0
"the mechanism, whereby histamine and serotonin increase the permeability of blood vessels, was studied in the rat by means of the electron microscope. the drugs were injected subcutaneously into the scrotum, whence they diffused into the underlying (striated) cremaster muscle. an intravenous injection of colloidal hgs was also given, in order to facilitate the identification of leaks by means of visible tracer particles. after intervals varying from 1 minute to 57 days the animals were killed; the cremaster was fixed, embedded in methacrylate, and examined with the electron microscope. one to 12 minutes after the injection, the blood vessels of the smallest caliber (3 to 5 micra as measured on electron micrographs) appeared intact. numerous endothelial openings were present in blood vessels with a diameter of 7 to 8 micra or more. these gaps were 0.1 to 0.8 micra in width; portions of intercellular junctions were often present in one or both of the margins. the underlying basement membrane was morphologically intact. an accumulation of tracer particles and chylomicra against the basement membrane indicated that the latter behaved as a filter, allowing fluid to escape but retaining and concentrating suspended particulate matter of the size used. uptake of tracer particles by endothelial vesicles was minimal. phagocytosis by endothelial cells became more prominent at 3 hours, but as a secondary occurrence; the pericytes were actively phagocytic at all stages. at the 3-hour stage no leaks were found. the changes induced by histamine and serotonin were indistinguishable, except that the latter was more potent on a mole-to-mole basis. in control animals only small accumulations of tracer particles were found in the wall of a number of blood vessels. with regard to the pathogenesis of the endothelial leaks, the electron microscopic findings suggested that the endothelial cells become partially disconnected along the intercellular junctions. supporting evidence was provided at the level of the light microscope, by demonstrating-in the same preparation-the leaks with appropriate tracer particles(1), and the intercellular junctions by the silver nitrate method. the lipid nature of the chylomicron deposits observed in electron micrographs was also confirmed at the level of the light microscope, using cremasters fixed in formalin and stained in toto with sudan red.",0
"scale development and validation are critical to much of the work in the health, social, and behavioral sciences. however, the constellation of techniques required for scale development and evaluation can be onerous, jargon-filled, unfamiliar, and resource-intensive. further, it is often not a part of graduate training. therefore, our goal was to concisely review the process of scale development in as straightforward a manner as possible, both to facilitate the development of new, valid, and reliable scales, and to help improve existing ones. to do this, we have created a primer for best practices for scale development in measuring complex phenomena. this is not a systematic review, but rather the amalgamation of technical literature and lessons learned from our experiences spent creating or adapting a number of scales over the past several decades. we identified three phases that span nine steps. in the first phase, items are generated and the validity of their content is assessed. in the second phase, the scale is constructed. steps in scale construction include pre-testing the questions, administering the survey, reducing the number of items, and understanding how many factors the scale captures. in the third phase, scale evaluation, the number of dimensions is tested, reliability is tested, and validity is assessed. we have also added examples of best practices to each step. in sum, this primer will equip both scientists and practitioners to understand the ontology and methodology of scale development and validation, thereby facilitating the advancement of our understanding of a range of health, social, and behavioral outcomes.",0
"the 11(th) st gallen (switzerland) expert consensus meeting on the primary treatment of early breast cancer in march 2009 maintained an emphasis on targeting adjuvant systemic therapies according to subgroups defined by predictive markers. any positive level of estrogen receptor (er) expression is considered sufficient to justify the use of endocrine adjuvant therapy in almost all patients. overexpression or amplification of her2 by standard criteria is an indication for anti-her2 therapy for all but the very lowest risk invasive tumours. the corollary is that er and her2 must be reliably and accurately measured. indications for cytotoxic adjuvant therapy were refined, acknowledging the role of risk factors with the caveat that risk per se is not a target. proliferation markers, including those identified in multigene array analyses, were recognised as important in this regard. the threshold for indication of each systemic treatment modality thus depends on different criteria which have been separately listed to clarify the therapeutic decision-making algorithm.",0
"background the coronavirus disease 2019 (covid-19) outbreak is evolving rapidly worldwide. objective to evaluate the risk of serious adverse outcomes in patients with covid-19 by stratifying the comorbidity status. methods we analysed data from 1590 laboratory confirmed hospitalised patients from 575 hospitals in 31 provinces/autonomous regions/provincial municipalities across mainland china between 11 december 2019 and 31 january 2020. we analysed the composite end-points, which consisted of admission to an intensive care unit, invasive ventilation or death. the risk of reaching the composite end-points was compared according to the presence and number of comorbidities. results the mean age was 48.9 years and 686 (42.7%) patients were female. severe cases accounted for 16.0% of the study population. 131 (8.2%) patients reached the composite end-points. 399 (25.1%) reported having at least one comorbidity. the most prevalent comorbidity was hypertension (16.9%), followed by diabetes (8.2%). 130 (8.2%) patients reported having two or more comorbidities. after adjusting for age and smoking status, copd (hr (95% ci) 2.681 (1.424-5.048)), diabetes (1.59 (1.03-2.45)), hypertension (1.58 (1.07-2.32)) and malignancy (3.50 (1.60-7.64)) were risk factors of reaching the composite end-points. the hazard ratio (95% ci) was 1.79 (1.16-2.77) among patients with at least one comorbidity and 2.59 (1.61-4.17) among patients with two or more comorbidities. conclusion among laboratory confirmed cases of covid-19, patients with any comorbidity yielded poorer clinical outcomes than those without. a greater number of comorbidities also correlated with poorer clinical outcomes.",0
"objective to assess the cancer risk in children and adolescents following exposure to low dose ionising radiation from diagnostic computed tomography (ct) scans. design population based, cohort, data linkage study in australia. cohort members: 10.9 million people identified from australian medicare records, aged 0-19 years on 1 january 1985 or born between 1 january 1985 and 31 december 2005; all exposures to ct scans funded by medicare during 1985-2005 were identified for this cohort. cancers diagnosed in cohort members up to 31 december 2007 were obtained through linkage to national cancer records. main outcome cancer incidence rates in individuals exposed to a ct scan more than one year before any cancer diagnosis, compared with cancer incidence rates in unexposed individuals. results 60,674 cancers were recorded, including 3150 in 680,211 people exposed to a ct scan at least one year before any cancer diagnosis. the mean duration of follow-up after exposure was 9.5 years. overall cancer incidence was 24% greater for exposed than for unexposed people, after accounting for age, sex, and year of birth (incidence rate ratio (irr) 1.24 (95% confidence interval 1.20 to 1.29); p conclusions the increased incidence of cancer after ct scan exposure in this cohort was mostly due to irradiation. because the cancer excess was still continuing at the end of follow-up, the eventual lifetime risk from ct scans cannot yet be determined. radiation doses from contemporary ct scans are likely to be lower than those in 1985-2005, but some increase in cancer risk is still likely from current scans. future ct scans should be limited to situations where there is a definite clinical indication, with every scan optimised to provide a diagnostic ct image at the lowest possible radiation dose.",0
"systemic lupus erythematosus (sle) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. previous genome-wide association studies (gwas) had modest sample sizes, reducing their scope and reliability. our study comprised 7,219 cases and 15,991 controls of european ancestry, constituting a new gwas, a meta-analysis with a published gwas and a replication study. we have mapped 43 susceptibility loci, including ten new associations. assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. other likely causal genes were established by examining associated alleles for cis-acting eqtl effects in a range of ex vivo immune cells. we found an over-representation (n = 16) of transcription factors among sle susceptibility genes. this finding supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing sle.",0
"to investigate the antigenic relationship between the macrophage and lymphocyte fc receptors (fcr), a monoclonal antibody capable of blocking mouse macrophage fc receptors was selected. hybrids were formed by fusing the p3u1 mouse myeloma and spleen cells from a rat immunized with the mouse macrophage-like cell lines j774 and p388d1. the fab fragment of the monoclonal igg secreted by clone 2.4g2, inhibited the trypsin-resistant fc receptor ii (fcrii), which is specific for immune aggregates of mouse igg1 and igg2b, but had no inhibitory effect on the trypsin-sensitive fc receptor i (fcri), which binds monomeric igg2a and erythrocytes coated with igg2a. thus, the monoclonal 2.4g2 igg appeared to be specific for macrophage fcrii. further evidence that the 2.4g2 igg was directed against fcrii came from binding studies of the monoclonal antibody to j774 cells and a series of independently isolated variants which do not express fcrii. these variants of j774 bound 5% as much of the monoclonal antibody as the parent line, which bound 600,000 molecules of 2.4g2 igg per cell. the antigenic relatedness of mouse lymphocyte fcr to mouse macrophage fcrii was demonstrated by the binding of 2.4g2 igg to fcr-bearing lymphoid cell lines and the inhibition of the lymphocyte fcr by the monoclonal antibody. preincubation of spleen cells and peritioneal cells with 2.3g2 igg likewise inhibited rosette formation with ox erythrocytes coated with rabbit igg. the ability of the hybridoma igg to inhibit mouse fcrii was independent of the major histocompatibility complex. the 2.4g2 igg antigenic determinant was not present on rat, guinea pig, rabbit, or human fcr-bearing cells.",0
"cd1d-restricted natural killer (nk)t cells are known to potently secrete t helper (th)1 and th2 cytokines and to mediate cytolysis, but it is unclear how these contrasting functional activities are regulated. using lipid antigen-loaded cd1d tetramers, we have distinguished two subsets of cd1d-restricted t cells in fresh peripheral blood that differ in cytokine production and cytotoxic activation. one subset, which was cd4(-), selectively produced the th1 cytokines interferon gamma and tumor necrosis factor alpha, and expressed nkg2d, a marker associated with cytolysis of microbially infected and neoplastic cells. this subset up-regulated perforin after exposure to interleukin (il)-2 or il-12. in contrast, cd4(+) cd1d-restricted nkt cells potently produced both th1 and th2 cytokines, up-regulated perforin in response to stimulation by phorbol myristate acetate and ionomycin but not il-2 or il-12, and could be induced to express cd95l. further, for both cd1d-restricted nkt cell subsets, we found that antigenic stimulation induced cytokine production but not perforin expression, whereas exposure to inflammatory factors enhanced perforin expression but did not stimulate cytokine production. these results show that the various activities of cd1d-restricted t cells in tumor rejection, autoimmune disease, and microbial infections could result from activation of functionally distinct subsets, and that inflammatory and antigenic stimuli may influence different effector functions.",0
"background estimating the burden of disease attributable to long-term exposure to fine particulate matter (pm2.5) in ambient air requires knowledge of both the shape and magnitude of the relative risk (rr) function. however, adequate direct evidence to identify the shape of the mortality rr functions at the high ambient concentrations observed in many places in the world is lacking. objective we developed rr functions over the entire global exposure range for causes of mortality in adults: ischemic heart disease (ihd), cerebrovascular disease (stroke), chronic obstructive pulmonary disease (copd), and lung cancer (lc). we also developed rr functions for the incidence of acute lower respiratory infection (alri) that can be used to estimate mortality and lost-years of healthy life in children methods we fit an integrated exposure-response (ier) model by integrating available rr information from studies of ambient air pollution (aap), second hand tobacco smoke, household solid cooking fuel, and active smoking (as). as exposures were converted to estimated annual pm2.5 exposure equivalents using inhaled doses of particle mass. we derived population attributable fractions (pafs) for every country based on estimated worldwide ambient pm2.5 concentrations. results the ier model was a superior predictor of rr compared with seven other forms previously used in burden assessments. the percent paf attributable to aap exposure varied among countries from 2 to 41 for ihd, 1 to 43 for stroke, conclusions we developed a fine particulate mass-based rr model that covered the global range of exposure by integrating rr information from different combustion types that generate emissions of particulate matter. the model can be updated as new rr information becomes available.",0
"background the vascular and gastrointestinal effects of non-steroidal anti-inflammatory drugs (nsaids), including selective cox-2 inhibitors (coxibs) and traditional non-steroidal anti-inflammatory drugs (tnsaids), are not well characterised, particularly in patients at increased risk of vascular disease. we aimed to provide such information through meta-analyses of randomised trials. methods we undertook meta-analyses of 280 trials of nsaids versus placebo (124,513 participants, 68,342 person-years) and 474 trials of one nsaid versus another nsaid (229,296 participants, 165,456 person-years). the main outcomes were major vascular events (non-fatal myocardial infarction, non-fatal stroke, or vascular death); major coronary events (non-fatal myocardial infarction or coronary death); stroke; mortality; heart failure; and upper gastrointestinal complications (perforation, obstruction, or bleed). findings major vascular events were increased by about a third by a coxib (rate ratio 1·37, 95% ci 1·14-1·66; p=0·0009) or diclofenac (1·41, 1·12-1·78; p=0·0036), chiefly due to an increase in major coronary events (coxibs 1·76, 1·31-2·37; p=0·0001; diclofenac 1·70, 1·19-2·41; p=0·0032). ibuprofen also significantly increased major coronary events (2·22, 1·10-4·48; p=0·0253), but not major vascular events (1·44, 0·89-2·33). compared with placebo, of 1000 patients allocated to a coxib or diclofenac for a year, three more had major vascular events, one of which was fatal. naproxen did not significantly increase major vascular events (0·93, 0·69-1·27). vascular death was increased significantly by coxibs (1·58, 99% ci 1·00-2·49; p=0·0103) and diclofenac (1·65, 0·95-2·85, p=0·0187), non-significantly by ibuprofen (1·90, 0·56-6·41; p=0·17), but not by naproxen (1·08, 0·48-2·47, p=0·80). the proportional effects on major vascular events were independent of baseline characteristics, including vascular risk. heart failure risk was roughly doubled by all nsaids. all nsaid regimens increased upper gastrointestinal complications (coxibs 1·81, 1·17-2·81, p=0·0070; diclofenac 1·89, 1·16-3·09, p=0·0106; ibuprofen 3·97, 2·22-7·10, p interpretation the vascular risks of high-dose diclofenac, and possibly ibuprofen, are comparable to coxibs, whereas high-dose naproxen is associated with less vascular risk than other nsaids. although nsaids increase vascular and gastrointestinal risks, the size of these risks can be predicted, which could help guide clinical decision making. funding uk medical research council and british heart foundation.",0
"the amyloid-beta(1-42) (abeta42) peptide rapidly aggregates to form oligomers, protofibils and fibrils en route to the deposition of amyloid plaques associated with alzheimer's disease. we show that low-temperature and low-salt conditions can stabilize disc-shaped oligomers (pentamers) that are substantially more toxic to mouse cortical neurons than protofibrils and fibrils. we find that these neurotoxic oligomers do not have the beta-sheet structure characteristic of fibrils. rather, the oligomers are composed of loosely aggregated strands whose c termini are protected from solvent exchange and which have a turn conformation, placing phe19 in contact with leu34. on the basis of nmr spectroscopy, we show that the structural conversion of abeta42 oligomers to fibrils involves the association of these loosely aggregated strands into beta-sheets whose individual beta-strands polymerize in a parallel, in-register orientation and are staggered at an intermonomer contact between gln15 and gly37.",0
"background coronavirus disease 2019 (covid-19) pneumonia is often associated with hyperinflammation. despite the disproportionate incidence of covid-19 among underserved and racial and ethnic minority populations, the safety and efficacy of the anti-interleukin-6 receptor antibody tocilizumab in patients from these populations who are hospitalized with covid-19 pneumonia are unclear. methods we randomly assigned (in a 2:1 ratio) patients hospitalized with covid-19 pneumonia who were not receiving mechanical ventilation to receive standard care plus one or two doses of either tocilizumab (8 mg per kilogram of body weight intravenously) or placebo. site selection was focused on the inclusion of sites enrolling high-risk and minority populations. the primary outcome was mechanical ventilation or death by day 28. results a total of 389 patients underwent randomization, and the modified intention-to-treat population included 249 patients in the tocilizumab group and 128 patients in the placebo group; 56.0% were hispanic or latino, 14.9% were black, 12.7% were american indian or alaska native, 12.7% were non-hispanic white, and 3.7% were of other or unknown race or ethnic group. the cumulative percentage of patients who had received mechanical ventilation or who had died by day 28 was 12.0% (95% confidence interval , 8.5 to 16.9) in the tocilizumab group and 19.3% (95% ci, 13.3 to 27.4) in the placebo group (hazard ratio for mechanical ventilation or death, 0.56; 95% ci, 0.33 to 0.97; p = 0.04 by the log-rank test). clinical failure as assessed in a time-to-event analysis favored tocilizumab over placebo (hazard ratio, 0.55; 95% ci, 0.33 to 0.93). death from any cause by day 28 occurred in 10.4% of the patients in the tocilizumab group and 8.6% of those in the placebo group (weighted difference, 2.0 percentage points; 95% ci, -5.2 to 7.8). in the safety population, serious adverse events occurred in 38 of 250 patients (15.2%) in the tocilizumab group and 25 of 127 patients (19.7%) in the placebo group. conclusions in hospitalized patients with covid-19 pneumonia who were not receiving mechanical ventilation, tocilizumab reduced the likelihood of progression to the composite outcome of mechanical ventilation or death, but it did not improve survival. no new safety signals were identified. (funded by genentech; empacta clinicaltrials.gov number, nct04372186.).",0
"background the regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. an initial regulatory map for s. cerevisiae was recently published using six motif discovery programs to analyze genome-wide chromatin immunoprecipitation data for 203 transcription factors. the programs were used to identify sequence motifs that were likely to correspond to the dna-binding specificity of the immunoprecipitated proteins. we report improved versions of two conservation-based motif discovery algorithms, phylocon and converge. using these programs, we create a refined regulatory map for s. cerevisiae by reanalyzing the same chromatin immunoprecipitation data. results applying the same conservative criteria that were applied in the original study, we find that phylocon and converge each separately discover more known specificities than the combination of all six programs in the previous study. combining the results of phylocon and converge, we discover significant sequence motifs for 36 transcription factors that were previously missed. the new set of motifs identifies 636 more regulatory interactions than the previous one. the new network contains 28% more regulatory interactions among transcription factors, evidence of greater cross-talk between regulators. conclusion combining two complementary computational strategies for conservation-based motif discovery improves the ability to identify the specificity of transcriptional regulators from genome-wide chromatin immunoprecipitation data. the increased sensitivity of these methods significantly expands the map of yeast regulatory sites without the need to alter any of the thresholds for statistical significance. the new map of regulatory sites reveals a more elaborate and complex view of the yeast genetic regulatory network than was observed previously.",0
"vitrification is the state-of-the-art specimen preparation technique for molecular electron microscopy (em) and therefore negative staining may appear to be an outdated approach. in this paper we illustrate the specific advantages of negative staining, ensuring that this technique will remain an important tool for the study of biological macromolecules. due to the higher image contrast, much smaller molecules can be visualized by negative staining. also, while molecules prepared by vitrification usually adopt random orientations in the amorphous ice layer, negative staining tends to induce preferred orientations of the molecules on the carbon support film. combining negative staining with image classification techniques makes it possible to work with very heterogeneous molecule populations, which are difficult or even impossible to analyze using vitrified specimens.",0
"drugbank is a richly annotated resource that combines detailed drug data with comprehensive drug target and drug action information. since its first release in 2006, drugbank has been widely used to facilitate in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. the latest version of drugbank (release 2.0) has been expanded significantly over the previous release. with approximately 4900 drug entries, it now contains 60% more fda-approved small molecule and biotech drugs including 10% more 'experimental' drugs. significantly, more protein target data has also been added to the database, with the latest version of drugbank containing three times as many non-redundant protein or drug target sequences as before (1565 versus 524). each drugcard entry now contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to pharmacological, pharmacogenomic and molecular biological data. a number of new data fields, including food-drug interactions, drug-drug interactions and experimental adme data have been added in response to numerous user requests. drugbank has also significantly improved the power and simplicity of its structure query and text query searches. drugbank is available at",0
"the newly identified 2019 novel coronavirus (2019-ncov) has caused more than 11,900 laboratory-confirmed human infections, including 259 deaths, posing a serious threat to human health. currently, however, there is no specific antiviral treatment or vaccine. considering the relatively high identity of receptor-binding domain (rbd) in 2019-ncov and sars-cov, it is urgent to assess the cross-reactivity of anti-sars cov antibodies with 2019-ncov spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-ncov. here, we report for the first time that a sars-cov-specific human monoclonal antibody, cr3022, could bind potently with 2019-ncov rbd (kd of 6.3 nm). the epitope of cr3022 does not overlap with the ace2 binding site within 2019-ncov rbd. these results suggest that cr3022 may have the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-ncov infections. interestingly, some of the most potent sars-cov-specific neutralizing antibodies (e.g. m396, cr3014) that target the ace2 binding site of sars-cov failed to bind 2019-ncov spike protein, implying that the difference in the rbd of sars-cov and 2019-ncov has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-ncov rbd.",0
"the immune response plays an important role in staving off cancer; however, mechanisms of immunosuppression hinder productive anti-tumor immunity. t cell dysfunction or exhaustion in tumor-bearing hosts is one such mechanism. pd-1 has been identified as a marker of exhausted t cells in chronic disease states, and blockade of pd-1-pd-1l interactions has been shown to partially restore t cell function. we have found that t cell immunoglobulin mucin (tim) 3 is expressed on cd8(+) tumor-infiltrating lymphocytes (tils) in mice bearing solid tumors. all tim-3(+) tils coexpress pd-1, and tim-3(+)pd-1(+) tils represent the predominant fraction of t cells infiltrating tumors. tim-3(+)pd-1(+) tils exhibit the most severe exhausted phenotype as defined by failure to proliferate and produce il-2, tnf, and ifn-γ. we further find that combined targeting of the tim-3 and pd-1 pathways is more effective in controlling tumor growth than targeting either pathway alone.",0
"two endosome populations involved in recycling of membranes and receptors to the plasma membrane have been described, the early and the recycling endosome. however, this distinction is mainly based on the flow of cargo molecules and the spatial distribution of these membranes within the cell. to get insights into the membrane organization of the recycling pathway, we have studied rab4, rab5, and rab11, three regulatory components of the transport machinery. following transferrin as cargo molecule and gfp-tagged rab proteins we could show that cargo moves through distinct domains on endosomes. these domains are occupied by different rab proteins, revealing compartmentalization within the same continuous membrane. endosomes are comprised of multiple combinations of rab4, rab5, and rab11 domains that are dynamic but do not significantly intermix over time. three major populations were observed: one that contains only rab5, a second with rab4 and rab5, and a third containing rab4 and rab11. these membrane domains display differential pharmacological sensitivity, reflecting their biochemical and functional diversity. we propose that endosomes are organized as a mosaic of different rab domains created through the recruitment of specific effector proteins, which cooperatively act to generate a restricted environment on the membrane.",0
"protein quantification without isotopic labels has been a long-standing interest in the proteomics field. however, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. we developed a new intensity determination and normalization procedure called maxlfq that is fully compatible with any peptide or protein separation prior to lc-ms analysis. protein abundance profiles are assembled using the maximum possible information from ms signals, given that the presence of quantifiable peptides varies from sample to sample. for a benchmark dataset with two proteomes mixed at known ratios, we accurately detected the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. the significance of individual label-free quantifications was obtained via a t test approach. for a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. maxlfq is a generic label-free quantification technology that is readily applicable to many biological questions; it is compatible with standard statistical analysis workflows, and it has been validated in many and diverse biological projects. our algorithms can handle very large experiments of 500+ samples in a manageable computing time. it is implemented in the freely available maxquant computational proteomics platform and works completely seamlessly at the click of a button.",0
"this study sought to identify factors associated with depression, anxiety, and ptsd symptomatology in u.s. young adults (18-30 years) during the covid-19 pandemic. this cross-sectional online study assessed 898 participants from april 13, 2020 to may 19, 2020, approximately one month after the u.s. declared a state of emergency due to covid-19 and prior to the initial lifting of restrictions across 50 u.s. states. respondents reported high levels of depression (43.3%, phq-8 scores ≥ 10), high anxiety scores (45.4%, gad-7 scores ≥ 10), and high levels of ptsd symptoms (31.8%, pcl-c scores ≥ 45). high levels of loneliness, high levels of covid-19-specific worry, and low distress tolerance were significantly associated with clinical levels of depression, anxiety, and ptsd symptoms. resilience was associated with low levels of depression and anxiety symptoms but not ptsd. most respondents had high levels of social support; social support from family, but not from partner or peers, was associated with low levels of depression and ptsd. compared to whites, asian americans were less likely to report high levels across mental health symptoms, and hispanic/latinos were less likely to report high levels of anxiety. these factors provide initial guidance regarding the clinical management for covid-19-related mental health problems.",0
"obesity is a chronic disease of multifactorial origin and can be defined as an increase in the accumulation of body fat. adipose tissue is not only a triglyceride storage organ, but studies have shown the role of white adipose tissue as a producer of certain bioactive substances called adipokines. among adipokines, we find some inflammatory functions, such as interleukin-6 (il-6); other adipokines entail the functions of regulating food intake, therefore exerting a direct effect on weight control. this is the case of leptin, which acts on the limbic system by stimulating dopamine uptake, creating a feeling of fullness. however, these adipokines induce the production of reactive oxygen species (ros), generating a process known as oxidative stress (os). because adipose tissue is the organ that secretes adipokines and these in turn generate ros, adipose tissue is considered an independent factor for the generation of systemic os. there are several mechanisms by which obesity produces os. the first of these is the mitochondrial and peroxisomal oxidation of fatty acids, which can produce ros in oxidation reactions, while another mechanism is over-consumption of oxygen, which generates free radicals in the mitochondrial respiratory chain that is found coupled with oxidative phosphorylation in mitochondria. lipid-rich diets are also capable of generating ros because they can alter oxygen metabolism. upon the increase of adipose tissue, the activity of antioxidant enzymes such as superoxide dismutase (sod), catalase (cat), and glutathione peroxidase (gpx), was found to be significantly diminished. finally, high ros production and the decrease in antioxidant capacity leads to various abnormalities, among which we find endothelial dysfunction, which is characterized by a reduction in the bioavailability of vasodilators, particularly nitric oxide (no), and an increase in endothelium-derived contractile factors, favoring atherosclerotic disease.",0
"since december 2019, china has been experiencing a large outbreak of a novel coronavirus (2019-ncov) which can cause respiratory disease and severe pneumonia. we estimated the basic reproduction number r0 of 2019-ncov to be around 2.2 (90% high density interval: 1.4-3.8), indicating the potential for sustained human-to-human transmission. transmission characteristics appear to be of similar magnitude to severe acute respiratory syndrome-related coronavirus (sars-cov) and pandemic influenza, indicating a risk of global spread.",0
"background rigorous analysis of levels and trends in exposure to leading risk factors and quantification of their effect on human health are important to identify where public health is making progress and in which cases current efforts are inadequate. the global burden of diseases, injuries, and risk factors study (gbd) 2019 provides a standardised and comprehensive assessment of the magnitude of risk factor exposure, relative risk, and attributable burden of disease. methods gbd 2019 estimated attributable mortality, years of life lost (ylls), years of life lived with disability (ylds), and disability-adjusted life-years (dalys) for 87 risk factors and combinations of risk factors, at the global level, regionally, and for 204 countries and territories. gbd uses a hierarchical list of risk factors so that specific risk factors (eg, sodium intake), and related aggregates (eg, diet quality), are both evaluated. this method has six analytical steps. (1) we included 560 risk-outcome pairs that met criteria for convincing or probable evidence on the basis of research studies. 12 risk-outcome pairs included in gbd 2017 no longer met inclusion criteria and 47 risk-outcome pairs for risks already included in gbd 2017 were added based on new evidence. (2) relative risks were estimated as a function of exposure based on published systematic reviews, 81 systematic reviews done for gbd 2019, and meta-regression. (3) levels of exposure in each age-sex-location-year included in the study were estimated based on all available data sources using spatiotemporal gaussian process regression, dismod-mr 2.1, a bayesian meta-regression method, or alternative methods. (4) we determined, from published trials or cohort studies, the level of exposure associated with minimum risk, called the theoretical minimum risk exposure level. (5) attributable deaths, ylls, ylds, and dalys were computed by multiplying population attributable fractions (pafs) by the relevant outcome quantity for each age-sex-location-year. (6) pafs and attributable burden for combinations of risk factors were estimated taking into account mediation of different risk factors through other risk factors. across all six analytical steps, 30 652 distinct data sources were used in the analysis. uncertainty in each step of the analysis was propagated into the final estimates of attributable burden. exposure levels for dichotomous, polytomous, and continuous risk factors were summarised with use of the summary exposure value to facilitate comparisons over time, across location, and across risks. because the entire time series from 1990 to 2019 has been re-estimated with use of consistent data and methods, these results supersede previously published gbd estimates of attributable burden. findings the largest declines in risk exposure from 2010 to 2019 were among a set of risks that are strongly linked to social and economic development, including household air pollution; unsafe water, sanitation, and handwashing; and child growth failure. global declines also occurred for tobacco smoking and lead exposure. the largest increases in risk exposure were for ambient particulate matter pollution, drug use, high fasting plasma glucose, and high body-mass index. in 2019, the leading level 2 risk factor globally for attributable deaths was high systolic blood pressure, which accounted for 10·8 million (95% uncertainty interval 9·51-12·1) deaths (19·2% of all deaths in 2019), followed by tobacco (smoked, second-hand, and chewing), which accounted for 8·71 million (8·12-9·31) deaths (15·4% of all deaths in 2019). the leading level 2 risk factor for attributable dalys globally in 2019 was child and maternal malnutrition, which largely affects health in the youngest age groups and accounted for 295 million (253-350) dalys (11·6% of all global dalys that year). the risk factor burden varied considerably in 2019 between age groups and locations. among children aged 0-9 years, the three leading detailed risk factors for attributable dalys were all related to malnutrition. iron deficiency was the leading risk factor for those aged 10-24 years, alcohol use for those aged 25-49 years, and high systolic blood pressure for those aged 50-74 years and 75 years and older. interpretation overall, the record for reducing exposure to harmful risks over the past three decades is poor. success with reducing smoking and lead exposure through regulatory policy might point the way for a stronger role for public policy on other risks in addition to continued efforts to provide information on risk factor harm to the general public. funding bill & melinda gates foundation.",0
"reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant dna. whether introduced during sample processing or through co-extraction alongside the target dna, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. we present blobtoolkit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. blobtoolkit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based viewer. blobtoolkit can be used during assembly to filter non-target dna, helping researchers produce assemblies with high biological credibility. we have been running an automated blobtoolkit pipeline on eukaryotic assemblies publicly available in the international nucleotide sequence data collaboration and are making the results available through a public instance of the viewer at we aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. we have worked to embed these views into the presentation of genome assemblies at the european nucleotide archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the viewer.",0
"background the global burden of disease attributable to respiratory syncytial virus (rsv) remains unknown. we aimed to estimate the global incidence of and mortality from episodes of acute lower respiratory infection (alri) due to rsv in children younger than 5 years in 2005. methods we estimated the incidence of rsv-associated alri in children younger than 5 years, stratified by age, using data from a systematic review of studies published between january, 1995, and june, 2009, and ten unpublished population-based studies. we estimated possible boundaries for rsv-associated alri mortality by combining case fatality ratios with incidence estimates from hospital-based reports from published and unpublished studies and identifying studies with population-based data for rsv seasonality and monthly alri mortality. findings in 2005, an estimated 33.8 (95% ci 19.3-46.2) million new episodes of rsv-associated alri occurred worldwide in children younger than 5 years (22% of alri episodes), with at least 3.4 (2.8-4.3) million episodes representing severe rsv-associated alri necessitating hospital admission. we estimated that 66 000-199 000 children younger than 5 years died from rsv-associated alri in 2005, with 99% of these deaths occurring in developing countries. incidence and mortality can vary substantially from year to year in any one setting. interpretation globally, rsv is the most common cause of childhood alri and a major cause of admission to hospital as a result of severe alri. mortality data suggest that rsv is an important cause of death in childhood from alri, after pneumococcal pneumonia and haemophilus influenzae type b. the development of novel prevention and treatment strategies should be accelerated as a priority. funding who; bill & melinda gates foundation.",0
"systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. selected reaction monitoring (srm)-also called multiple reaction monitoring-is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in complex mixtures. in an srm experiment, a predefined precursor ion and one of its fragments are selected by the two mass filters of a triple quadrupole instrument and monitored over time for precise quantification. a series of transitions (precursor/fragment ion pairs) in combination with the retention time of the targeted peptide can constitute a definitive assay. typically, a large number of peptides are quantified during a single lc-ms experiment. this tutorial explains the application of srm for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions. furthermore, normalization and various factors affecting sensitivity and accuracy are discussed.",0
"the 13th st gallen international breast cancer conference (2013) expert panel reviewed and endorsed substantial new evidence on aspects of the local and regional therapies for early breast cancer, supporting less extensive surgery to the axilla and shorter durations of radiation therapy. it refined its earlier approach to the classification and management of luminal disease in the absence of amplification or overexpression of the human epidermal growth factor receptor 2 (her2) oncogene, while retaining essentially unchanged recommendations for the systemic adjuvant therapy of her2-positive and 'triple-negative' disease. the panel again accepted that conventional clinico-pathological factors provided a surrogate subtype classification, while noting that in those areas of the world where multi-gene molecular assays are readily available many clinicians prefer to base chemotherapy decisions for patients with luminal disease on these genomic results rather than the surrogate subtype definitions. several multi-gene molecular assays were recognized as providing accurate and reproducible prognostic information, and in some cases prediction of response to chemotherapy. cost and availability preclude their application in many environments at the present time. broad treatment recommendations are presented. such recommendations do not imply that each panel member agrees: indeed, among more than 100 questions, only one (trastuzumab duration) commanded 100% agreement. the various recommendations in fact carried differing degrees of support, as reflected in the nuanced wording of the text below and in the votes recorded in supplementary appendix s1, available at annals of oncology online. detailed decisions on treatment will as always involve clinical consideration of disease extent, host factors, patient preferences and social and economic constraints.",0
"prognostic models are abundant in the medical literature yet their use in practice seems limited. in this article, the third in the progress series, the authors review how such models are developed and validated, and then address how prognostic models are assessed for their impact on practice and patient outcomes, illustrating these ideas with examples.",0
"traumatic spinal cord injury (sci) is a life changing neurological condition with substantial socioeconomic implications for patients and their care-givers. recent advances in medical management of sci has significantly improved diagnosis, stabilization, survival rate and well-being of sci patients. however, there has been small progress on treatment options for improving the neurological outcomes of sci patients. this incremental success mainly reflects the complexity of sci pathophysiology and the diverse biochemical and physiological changes that occur in the injured spinal cord. therefore, in the past few decades, considerable efforts have been made by sci researchers to elucidate the pathophysiology of sci and unravel the underlying cellular and molecular mechanisms of tissue degeneration and repair in the injured spinal cord. to this end, a number of preclinical animal and injury models have been developed to more closely recapitulate the primary and secondary injury processes of sci. in this review, we will provide a comprehensive overview of the recent advances in our understanding of the pathophysiology of sci. we will also discuss the neurological outcomes of human sci and the available experimental model systems that have been employed to identify sci mechanisms and develop therapeutic strategies for this condition.",0
"fluorescent calcium sensors are widely used to image neural activity. using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (gcamp6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo. in layer 2/3 pyramidal neurons of the mouse visual cortex, gcamp6 reliably detected single action potentials in neuronal somata and orientation-tuned synaptic calcium transients in individual dendritic spines. the orientation tuning of structurally persistent spines was largely stable over timescales of weeks. orientation tuning averaged across spine populations predicted the tuning of their parent cell. although the somata of gabaergic neurons showed little orientation tuning, their dendrites included highly tuned dendritic segments (5-40-µm long). gcamp6 sensors thus provide new windows into the organization and dynamics of neural circuits over multiple spatial and temporal scales.",0
"the author reviews research showing that repetitive thought (rt) can have constructive or unconstructive consequences. the main unconstructive consequences of rt are (a) depression, (b) anxiety, and (c) difficulties in physical health. the main constructive consequences of rt are (a) recovery from upsetting and traumatic events, (b) adaptive preparation and anticipatory planning, (c) recovery from depression, and (d) uptake of health-promoting behaviors. several potential principles accounting for these distinct consequences of rt are identified within this review: (a) the valence of thought content, (b) the intrapersonal and situational context in which rt occurs, and (c) the level of construal (abstract vs. concrete processing) adopted during rt. of the existing models of rt, it is proposed that an elaborated version of the control theory account provides the best theoretical framework to account for its distinct consequences.",0
"background cross-validation (cv) is an effective method for estimating the prediction error of a classifier. some recent articles have proposed methods for optimizing classifiers by choosing classifier parameter values that minimize the cv error estimate. we have evaluated the validity of using the cv error estimate of the optimized classifier as an estimate of the true error expected on independent data. results we used cv to optimize the classification parameters for two kinds of classifiers; shrunken centroids and support vector machines (svm). random training datasets were created, with no difference in the distribution of the features between the two classes. using these ""null"" datasets, we selected classifier parameter values that minimized the cv error estimate. 10-fold cv was used for shrunken centroids while leave-one-out-cv (loocv) was used for the svm. independent test data was created to estimate the true error. with ""null"" and ""non null"" (with differential expression between the classes) data, we also tested a nested cv procedure, where an inner cv loop is used to perform the tuning of the parameters while an outer cv is used to compute an estimate of the error. the cv error estimate for the classifier with the optimal parameters was found to be a substantially biased estimate of the true error that the classifier would incur on independent data. even though there is no real difference between the two classes for the ""null"" datasets, the cv error estimate for the shrunken centroid with the optimal parameters was less than 30% on 18.5% of simulated training data-sets. for svm with optimal parameters the estimated error rate was less than 30% on 38% of ""null"" data-sets. performance of the optimized classifiers on the independent test set was no better than chance. the nested cv procedure reduces the bias considerably and gives an estimate of the error that is very close to that obtained on the independent testing set for both shrunken centroids and svm classifiers for ""null"" and ""non-null"" data distributions. conclusion we show that using cv to compute an error estimate for a classifier that has itself been tuned using cv gives a significantly biased estimate of the true error. proper use of cv for estimating true error of a classifier developed using a well defined algorithm requires that all steps of the algorithm, including classifier parameter tuning, be repeated in each cv loop. a nested cv procedure provides an almost unbiased estimate of the true error.",0
"here we studied cell-free plasma dna (cfdna) collected from subjects with advanced lung cancer whose tumors had developed resistance to the epidermal growth factor receptor (egfr) tyrosine kinase inhibitor (tki) azd9291. we first performed next-generation sequencing of cfdna from seven subjects and detected an acquired egfr c797s mutation in one; expression of this mutant egfr construct in a cell line rendered it resistant to azd9291. we then performed droplet digital pcr on serial cfdna specimens collected from 15 azd9291-treated subjects. all were positive for the t790m mutation before treatment, but upon developing azd9291 resistance three molecular subtypes emerged: six cases acquired the c797s mutation, five cases maintained the t790m mutation but did not acquire the c797s mutation and four cases lost the t790m mutation despite the presence of the underlying egfr activating mutation. our findings provide insight into the diversity of mechanisms through which tumors acquire resistance to azd9291 and highlight the need for therapies that are able to overcome resistance mediated by the egfr c797s mutation.",0
"motivation robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. here, we describe a new java-based architecture for the widely used protein function prediction software package interproscan. developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. interproscan is freely available for download from the embl-ebi ftp site and the open source code is hosted at google code.",0
"we have developed gominer, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the gene ontology. gominer provides quantitative and statistical output files and two useful visualizations. the first is a tree-like structure analogous to that in the amigo browser and the second is a compact, dynamically interactive 'directed acyclic graph'. genes displayed in gominer are linked to major public bioinformatics resources.",0
"despite decades of unequivocal evidence that waist circumference provides both independent and additive information to bmi for predicting morbidity and risk of death, this measurement is not routinely obtained in clinical practice. this consensus statement proposes that measurements of waist circumference afford practitioners with an important opportunity to improve the management and health of patients. we argue that bmi alone is not sufficient to properly assess or manage the cardiometabolic risk associated with increased adiposity in adults and provide a thorough review of the evidence that will empower health practitioners and professional societies to routinely include waist circumference in the evaluation and management of patients with overweight or obesity. we recommend that decreases in waist circumference are a critically important treatment target for reducing adverse health risks for both men and women. moreover, we describe evidence that clinically relevant reductions in waist circumference can be achieved by routine, moderate-intensity exercise and/or dietary interventions. we identify gaps in the knowledge, including the refinement of waist circumference threshold values for a given bmi category, to optimize obesity risk stratification across age, sex and ethnicity. we recommend that health professionals are trained to properly perform this simple measurement and consider it as an important 'vital sign' in clinical practice.",0
"human ril-5 was found to selectively stimulate morphological changes and the function of human eosinophils. this molecule is thus a prime candidate for the selective eosinophilia and eosinophil activation seen in disease.",0
"macrophages and neutrophils play a decisive role in host responses to intracellular bacteria including the agent of tuberculosis (tb), mycobacterium tuberculosis as they represent the forefront of innate immune defense against bacterial invaders. at the same time, these phagocytes are also primary targets of intracellular bacteria to be abused as host cells. their efficacy to contain and eliminate intracellular m. tuberculosis decides whether a patient initially becomes infected or not. however, when the infection becomes chronic or even latent (as in the case of tb) despite development of specific immune activation, phagocytes have also important effector functions. macrophages have evolved a myriad of defense strategies to combat infection with intracellular bacteria such as m. tuberculosis. these include induction of toxic anti-microbial effectors such as nitric oxide and reactive oxygen intermediates, the stimulation of microbe intoxication mechanisms via acidification or metal accumulation in the phagolysosome, the restriction of the microbe's access to essential nutrients such as iron, fatty acids, or amino acids, the production of anti-microbial peptides and cytokines, along with induction of autophagy and efferocytosis to eliminate the pathogen. on the other hand, m. tuberculosis, as a prime example of a well-adapted facultative intracellular bacterium, has learned during evolution to counter-balance the host's immune defense strategies to secure survival or multiplication within this otherwise hostile environment. this review provides an overview of innate immune defense of macrophages directed against intracellular bacteria with a focus on m. tuberculosis. gaining more insights and knowledge into this complex network of host-pathogen interaction will identify novel target sites of intervention to successfully clear infection at a time of rapidly emerging multi-resistance of m. tuberculosis against conventional antibiotics.",0
"parkinson's disease (pd) is characterized pathologically by intraneuronal inclusions called lewy bodies, largely comprised of α-synuclein. multiplication of the α-synuclein gene locus increases α-synuclein expression and causes pd. thus, overexpression of wild-type α-synuclein is toxic. in this study, we demonstrate that α-synuclein overexpression impairs macroautophagy in mammalian cells and in transgenic mice. our data show that α-synuclein compromises autophagy via rab1a inhibition and rab1a overexpression rescues the autophagy defect caused by α-synuclein. inhibition of autophagy by α-synuclein overexpression or rab1a knockdown causes mislocalization of the autophagy protein, atg9, and decreases omegasome formation. rab1a, α-synuclein, and atg9 all regulate formation of the omegasome, which marks autophagosome precursors.",0
"there is currently a lack of pathologic data on the novel coronavirus (severe acute respiratory syndrome coronavirus 2) pneumonia, or coronavirus disease 2019 (covid-19), from autopsy or biopsy. two patients who recently underwent lung lobectomies for adenocarcinoma were retrospectively found to have had covid-19 at the time of the operation. these two cases thus provide important first opportunities to study the pathology of covid-19. pathologic examinations revealed that apart from the tumors, the lungs of both patients exhibited edema, proteinaceous exudate, focal reactive hyperplasia of pneumocytes with patchy inflammatory cellular infiltration, and multinucleated giant cells. hyaline membranes were not prominent. because both patients did not exhibit symptoms of pneumonia at the time of operation, these changes likely represent an early phase of the lung pathology of covid-19 pneumonia.",0
"since december 2019, more than 79,000 people have been diagnosed with infection of the corona virus disease 2019 (covid-19). a large number of medical staff was sent to wuhan city and hubei province to aid covid-19 control. psychological stress, especially vicarious traumatization caused by the covid-19 pandemic, should not be ignored. to address this concern, the study employed a total of 214 general public and 526 nurses (i.e., 234 front-line nurses and 292 non-front-line nurses) to evaluate vicarious traumatization scores via a mobile app-based questionnaire. front-line nurses are engaged in the process of providing care for patients with covid-19. the results showed that the vicarious traumatization scores for front-line nurses including scores for physiological and psychological responses, were significantly lower than those of non-front-line nurses (p 0.05). therefore, increased attention should be paid to the psychological problems of the medical staff, especially non-front-line nurses, and general public under the situation of the spread and control of covid-19. early strategies that aim to prevent and treat vicarious traumatization in medical staff and general public are extremely necessary.",0
"background the international physical activity questionnaire-short form (ipaq-sf) has been recommended as a cost-effective method to assess physical activity. several studies validating the ipaq-sf have been conducted with differing results, but no systematic review of these studies has been reported. methods the keywords ""ipaq"", ""validation"", and ""validity"" were searched in pubmed and scopus. studies published in english that validated the ipaq-sf against an objective physical activity measuring device, doubly labeled water, or an objective fitness measure were included. results twenty-three validation studies were included in this review. there was a great deal of variability in the methods used across studies, but the results were largely similar. correlations between the total physical activity level measured by the ipaq-sf and objective standards ranged from 0.09 to 0.39; none reached the minimal acceptable standard in the literature (0.50 for objective activity measuring devices, 0.40 for fitness measures). correlations between sections of the ipaq-sf for vigorous activity or moderate activity level/walking and an objective standard showed even greater variability (-0.18 to 0.76), yet several reached the minimal acceptable standard. only six studies provided comparisons between physical activity levels derived from the ipaq-sf and those obtained from objective criterion. in most studies the ipaq-sf overestimated physical activity level by 36 to 173 percent; one study underestimated by 28 percent. conclusions the correlation between the ipaq-sf and objective measures of activity or fitness in the large majority of studies was lower than the acceptable standard. furthermore, the ipaq-sf typically overestimated physical activity as measured by objective criterion by an average of 84 percent. hence, the evidence to support the use of the ipaq-sf as an indicator of relative or absolute physical activity is weak.",0
"objective consumption of sugar-sweetened beverages (ssbs), which include soft drinks, fruit drinks, iced tea, and energy and vitamin water drinks has risen across the globe. regular consumption of ssbs has been associated with weight gain and risk of overweight and obesity, but the role of ssbs in the development of related chronic metabolic diseases, such as metabolic syndrome and type 2 diabetes, has not been quantitatively reviewed. research design and methods we searched the medline database up to may 2010 for prospective cohort studies of ssb intake and risk of metabolic syndrome and type 2 diabetes. we identified 11 studies (three for metabolic syndrome and eight for type 2 diabetes) for inclusion in a random-effects meta-analysis comparing ssb intake in the highest to lowest quantiles in relation to risk of metabolic syndrome and type 2 diabetes. results based on data from these studies, including 310,819 participants and 15,043 cases of type 2 diabetes, individuals in the highest quantile of ssb intake (most often 1-2 servings/day) had a 26% greater risk of developing type 2 diabetes than those in the lowest quantile (none or conclusions in addition to weight gain, higher consumption of ssbs is associated with development of metabolic syndrome and type 2 diabetes. these data provide empirical evidence that intake of ssbs should be limited to reduce obesity-related risk of chronic metabolic diseases.",0
"plastics have outgrown most man-made materials and have long been under environmental scrutiny. however, robust global information, particularly about their end-of-life fate, is lacking. by identifying and synthesizing dispersed data on production, use, and end-of-life management of polymer resins, synthetic fibers, and additives, we present the first global analysis of all mass-produced plastics ever manufactured. we estimate that 8300 million metric tons (mt) as of virgin plastics have been produced to date. as of 2015, approximately 6300 mt of plastic waste had been generated, around 9% of which had been recycled, 12% was incinerated, and 79% was accumulated in landfills or the natural environment. if current production and waste management trends continue, roughly 12,000 mt of plastic waste will be in landfills or in the natural environment by 2050.",0
"aging is characterized by clonal expansion of myeloid-biased hematopoietic stem cells and by increased risk of myeloid malignancies. exome sequencing of three elderly females with clonal hematopoiesis, demonstrated by x-inactivation analysis, identified somatic tet2 mutations. recurrence testing identified tet2 mutations in 10 out of 182 individuals with x-inactivation skewing. tet2 mutations were specific to individuals with clonal hematopoiesis without hematological malignancies and were associated with alterations in dna methylation.",0
"background the global covid-19 pandemic has generated major mental and psychological health problems worldwide. we conducted a meta-analysis to assess the prevalence of depression, anxiety, distress, and insomnia during the covid-19 pandemic. methods we searched online biomedical databases (pubmed, embase, web of science, ovid, cnki, and wanfang data) and preprint databases (ssrn, biorxiv, and medrxiv) for observational studies from january 1, 2020 to march 16, 2020 investigating the prevalence of mental health problems during the covid-19 pandemic. results we retrieved 821 citations from the biomedical databases and 53 citations from the preprint databases: 66 studies with 221,970 participants were included in our meta-analysis. the overall pooled prevalence of depression, anxiety, distress, and insomnia was 31.4%, 31.9%, 41.1% and 37.9%, respectively. noninfectious chronic disease patients, quarantined persons, and covid-19 patients had a higher risk of depression (q=26.73, p limitations all included studies were from the early phase of the global pandemic. additional meta-analyses are needed to obtain more data in all phases of the pandemic. conclusions the covid-19 pandemic increases the mental health problems of the global population, particularly health care workers, noninfectious chronic disease patients, covid-19 patients, and quarantined persons. interventions for mental health are urgently needed for preventing mental health problems.",0
"stromal interacting molecule 1 (stim1), reported to be an endoplasmic reticulum (er) ca(2+) sensor controlling store-operated ca(2+) entry, redistributes from a diffuse er localization into puncta at the cell periphery after store depletion. stim1 redistribution is proposed to be necessary for ca(2+) release-activated ca(2+) (crac) channel activation, but it is unclear whether redistribution is rapid enough to play a causal role. furthermore, the location of stim1 puncta is uncertain, with recent reports supporting retention in the er as well as insertion into the plasma membrane (pm). using total internal reflection fluorescence (tirf) microscopy and patch-clamp recording from single jurkat cells, we show that stim1 puncta form several seconds before crac channels open, supporting a causal role in channel activation. fluorescence quenching and electron microscopy analysis reveal that puncta correspond to stim1 accumulation in discrete subregions of junctional er located 10-25 nm from the pm, without detectable insertion of stim1 into the pm. roughly one third of these er-pm contacts form in response to store depletion. these studies identify an er structure underlying store-operated ca(2+) entry, whose extreme proximity to the pm may enable stim1 to interact with crac channels or associated proteins.",0
"we tested some resin-based composites used in dentistry for their estrogenic activity. a sealant based on bisphenol-a diglycidylether methacrylate (bis-gma) increased cell yields, progesterone receptor expression, and ps2 secretion in human estrogen-target, serum-sensitive mcf7 breast cancer cells. estrogenicity was due to bisphenol-a and bisphenol-a dimethacrylate, monomers found in the base paste of the dental sealant and identified by mass spectrometry. samples of saliva from 18 subjects treated with 50 mg of a bis-gma-based sealant applied on their molars were collected 1 hr before and after treatment. bisphenol-a (range 90-931 micrograms) was identified only in saliva collected during a 1-hr period after treatment. the use of bis-gma-based resins in dentistry, and particularly the use of sealants in children, appears to contribute to human exposure to xenoestrogens.",0
"the rapid proliferation of many different engineered nanomaterials (defined as materials designed and produced to have structural features with at least one dimension of 100 nanometers or less) presents a dilemma to regulators regarding hazard identification. the international life sciences institute research foundation/risk science institute convened an expert working group to develop a screening strategy for the hazard identification of engineered nanomaterials. the working group report presents the elements of a screening strategy rather than a detailed testing protocol. based on an evaluation of the limited data currently available, the report presents a broad data gathering strategy applicable to this early stage in the development of a risk assessment process for nanomaterials. oral, dermal, inhalation, and injection routes of exposure are included recognizing that, depending on use patterns, exposure to nanomaterials may occur by any of these routes. the three key elements of the toxicity screening strategy are: physicochemical characteristics, in vitro assays (cellular and non-cellular), and in vivo assays. there is a strong likelihood that biological activity of nanoparticles will depend on physicochemical parameters not routinely considered in toxicity screening studies. physicochemical properties that may be important in understanding the toxic effects of test materials include particle size and size distribution, agglomeration state, shape, crystal structure, chemical composition, surface area, surface chemistry, surface charge, and porosity. in vitro techniques allow specific biological and mechanistic pathways to be isolated and tested under controlled conditions, in ways that are not feasible in in vivo tests. tests are suggested for portal-of-entry toxicity for lungs, skin, and the mucosal membranes, and target organ toxicity for endothelium, blood, spleen, liver, nervous system, heart, and kidney. non-cellular assessment of nanoparticle durability, protein interactions, complement activation, and pro-oxidant activity is also considered. tier 1 in vivo assays are proposed for pulmonary, oral, skin and injection exposures, and tier 2 evaluations for pulmonary exposures are also proposed. tier 1 evaluations include markers of inflammation, oxidant stress, and cell proliferation in portal-of-entry and selected remote organs and tissues. tier 2 evaluations for pulmonary exposures could include deposition, translocation, and toxicokinetics and biopersistence studies; effects of multiple exposures; potential effects on the reproductive system, placenta, and fetus; alternative animal models; and mechanistic studies.",0
"health risk factors such as body mass index (bmi) and serum cholesterol are associated with many common diseases. it often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. we develop and apply a method (called gsmr) that performs a multi-snp mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of bmi, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (eduyears) with common diseases (sample sizes of up to 405,072). we identify a number of causal associations including a protective effect of ldl-cholesterol against type-2 diabetes (t2d) that might explain the side effects of statins on t2d, a protective effect of eduyears against alzheimer's disease, and bidirectional associations with opposite effects (e.g., higher bmi increases the risk of t2d but the effect of t2d on bmi is negative).",0
"background understanding the prevalence of schizophrenia has important implications for both health service planning and risk factor epidemiology. the aims of this review are to systematically identify and collate studies describing the prevalence of schizophrenia, to summarize the findings of these studies, and to explore selected factors that may influence prevalence estimates. methods and findings studies with original data related to the prevalence of schizophrenia (published 1965-2002) were identified via searching electronic databases, reviewing citations, and writing to authors. these studies were divided into ""core"" studies, ""migrant"" studies, and studies based on ""other special groups."" between- and within-study filters were applied in order to identify discrete prevalence estimates. cumulative plots of prevalence estimates were made and the distributions described when the underlying estimates were sorted according to prevalence type (point, period, lifetime, and lifetime morbid risk). based on combined prevalence estimates, the influence of selected key variables was examined (sex, urbanicity, migrant status, country economic index, and study quality). a total of 1,721 prevalence estimates from 188 studies were identified. these estimates were drawn from 46 countries, and were based on an estimated 154,140 potentially overlapping prevalent cases. we identified 132 core studies, 15 migrant studies, and 41 studies based on other special groups. the median values per 1,000 persons (10%-90% quantiles) for the distributions for point, period, lifetime, and lifetime morbid risk were 4.6 (1.9-10.0), 3.3 (1.3-8.2), 4.0 (1.6-12.1), and 7.2 (3.1-27.1), respectively. based on combined prevalence estimates, we found no significant difference (a) between males and females, or (b) between urban, rural, and mixed sites. the prevalence of schizophrenia in migrants was higher compared to native-born individuals: the migrant-to-native-born ratio median (10%-90% quantile) was 1.8 (0.9-6.4). when sites were grouped by economic status, prevalence estimates from ""least developed"" countries were significantly lower than those from both ""emerging"" and ""developed"" sites (p = 0.04). studies that scored higher on a quality score had significantly higher prevalence estimates (p = 0.02). conclusions there is a wealth of data about the prevalence of schizophrenia. these gradients, and the variability found in prevalence estimate distributions, can provide direction for future hypothesis-driven research.",0
"optical coherence tomography angiography (octa) is a new, non-invasive imaging technique that generates volumetric angiography images in a matter of seconds. this is a nascent technology with a potential wide applicability for retinal vascular disease. at present, level 1 evidence of the technology's clinical applications doesn't exist. in this paper, we introduce the technology, review the available english language publications regarding octa, and compare it with the current angiographic gold standards, fluorescein angiography (fa) and indocyanine green angiography (icga). finally we summarize its potential application to retinal vascular diseases. octa is quick and non-invasive, and provides volumetric data with the clinical capability of specifically localizing and delineating pathology along with the ability to show both structural and blood flow information in tandem. its current limitations include a relatively small field of view, inability to show leakage, and proclivity for image artifact due to patient movement/blinking. published studies hint at octa's potential efficacy in the evaluation of common ophthalmologic diseases such age related macular degeneration (amd), diabetic retinopathy, artery and vein occlusions, and glaucoma. octa can detect changes in choroidal blood vessel flow and can elucidate the presence of choroidal neovascularization (cnv) in a variety of conditions but especially in amd. it provides a highly detailed view of the retinal vasculature, which allows for accurate delineation of the foveal avascular zone (faz) in diabetic eyes and detection of subtle microvascular abnormalities in diabetic and vascular occlusive eyes. optic disc perfusion in glaucomatous eyes is notable as well on octa. further studies are needed to more definitively determine octa's utility in the clinical setting and to establish if this technology may offer a non-invasive option of visualizing the retinal vasculature in detail.",0
"background analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. we develop deconstructsigs, which allows the identification of mutational signatures within a single tumor sample. results application of deconstructsigs identifies samples with dna repair deficiencies and reveals distinct and dynamic mutational processes molding the cancer genome in esophageal adenocarcinoma compared to squamous cell carcinomas. conclusions deconstructsigs confers the ability to define mutational processes driven by environmental exposures, dna repair abnormalities, and mutagenic processes in individual tumors with implications for precision cancer medicine.",0
"coronavirus disease 2019 (covid-19) has rapidly affected mortality worldwide 1 . there is unprecedented urgency to understand who is most at risk of severe outcomes, and this requires new approaches for the timely analysis of large datasets. working on behalf of nhs england, we created opensafely-a secure health analytics platform that covers 40% of all patients in england and holds patient data within the existing data centre of a major vendor of primary care electronic health records. here we used opensafely to examine factors associated with covid-19-related death. primary care records of 17,278,392 adults were pseudonymously linked to 10,926 covid-19-related deaths. covid-19-related death was associated with: being male (hazard ratio (hr) 1.59 (95% confidence interval 1.53-1.65)); greater age and deprivation (both with a strong gradient); diabetes; severe asthma; and various other medical conditions. compared with people of white ethnicity, black and south asian people were at higher risk, even after adjustment for other factors (hr 1.48 (1.29-1.69) and 1.45 (1.32-1.58), respectively). we have quantified a range of clinical factors associated with covid-19-related death in one of the largest cohort studies on this topic so far. more patient records are rapidly being added to opensafely, we will update and extend our results regularly.",0
"sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses g2/m nuclei to achieve 91% mean coverage breadth. we applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (er(+)) breast cancer and a triple-negative ductal carcinoma. in parallel, we performed single nuclei copy number profiling. our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. in contrast, point mutations evolved gradually, generating extensive clonal diversity. using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the er(+) tumour cells did not. these findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.",0
"one approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. essential to this technique is the choice of fluorescent probes; the properties of the probes, including photons per switching event, on-off duty cycle, photostability and number of switching cycles, largely dictate the quality of super-resolution images. although many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. here we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. this analysis provides guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low-cross-talk, four-color super-resolution imaging.",0
"a specific memory is thought to be encoded by a sparse population of neurons. these neurons can be tagged during learning for subsequent identification and manipulation. moreover, their ablation or inactivation results in reduced memory expression, suggesting their necessity in mnemonic processes. however, the question of sufficiency remains: it is unclear whether it is possible to elicit the behavioural output of a specific memory by directly activating a population of neurons that was active during learning. here we show in mice that optogenetic reactivation of hippocampal neurons activated during fear conditioning is sufficient to induce freezing behaviour. we labelled a population of hippocampal dentate gyrus neurons activated during fear learning with channelrhodopsin-2 (chr2) and later optically reactivated these neurons in a different context. the mice showed increased freezing only upon light stimulation, indicating light-induced fear memory recall. this freezing was not detected in non-fear-conditioned mice expressing chr2 in a similar proportion of cells, nor in fear-conditioned mice with cells labelled by enhanced yellow fluorescent protein instead of chr2. finally, activation of cells labelled in a context not associated with fear did not evoke freezing in mice that were previously fear conditioned in a different context, suggesting that light-induced fear memory recall is context specific. together, our findings indicate that activating a sparse but specific ensemble of hippocampal neurons that contribute to a memory engram is sufficient for the recall of that memory. moreover, our experimental approach offers a general method of mapping cellular populations bearing memory engrams.",0
"therapy for multiple myeloma (mm) has markedly changed in the past decade with the introduction of new drugs, but it is not clear whether the improvements have been sustained. we studied 1038 patients diagnosed between 2001 and 2010, grouping patients into two 5-year periods by diagnosis, 2001-2005 and 2006-2010. the median estimated follow-up for the cohort was 5.9 years with 47% alive at the last follow-up. the median overall survival (os) for the entire cohort was 5.2 years: 4.6 years for patients in the 2001-2005 group compared with 6.1 years for the 2006-2010 cohort (p=0.002). the improvement was primarily seen among patients over 65 years, the 6-year os improving from 31 to 56%, p<0.001. only 10% of patients died during the first year in the latter group, compared with 16% in the earlier cohort (p<0.01), suggesting improvement in early mortality. the improved outcomes were linked closely to the use of one or more new agents in initial therapy. the current results confirm continued survival improvement in mm and highlight the impact of initial therapy with novel agents. most importantly, we demonstrate that the improved survival is benefitting older patients and that early mortality in this disease has reduced considerably.",0
"estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved mad, sad and mir data sets. a simple bayesian approach to estimation of map quality from one or more measures is presented. it was found that a bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. a combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. the phenix autosol wizard carries out automated structure solution based on any combination of sad, mad, sir or mir data sets. the wizard is based on tools from the phenix package and uses the bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing.",0
"reprogramming of somatic cells to pluripotency, thereby creating induced pluripotent stem (ips) cells, promises to transform regenerative medicine. most instances of direct reprogramming have been achieved by forced expression of defined factors using multiple viral vectors. however, such ips cells contain a large number of viral vector integrations, any one of which could cause unpredictable genetic dysfunction. whereas c-myc is dispensable for reprogramming, complete elimination of the other exogenous factors is also desired because ectopic expression of either oct4 (also known as pou5f1) or klf4 can induce dysplasia. two transient transfection-reprogramming methods have been published to address this issue. however, the efficiency of both approaches is extremely low, and neither has been applied successfully to human cells so far. here we show that non-viral transfection of a single multiprotein expression vector, which comprises the coding sequences of c-myc, klf4, oct4 and sox2 linked with 2a peptides, can reprogram both mouse and human fibroblasts. moreover, the transgene can be removed once reprogramming has been achieved. ips cells produced with this non-viral vector show robust expression of pluripotency markers, indicating a reprogrammed state confirmed functionally by in vitro differentiation assays and formation of adult chimaeric mice. when the single-vector reprogramming system was combined with a piggybac transposon, we succeeded in establishing reprogrammed human cell lines from embryonic fibroblasts with robust expression of pluripotency markers. this system minimizes genome modification in ips cells and enables complete elimination of exogenous reprogramming factors, efficiently providing ips cells that are applicable to regenerative medicine, drug screening and the establishment of disease models.",0
"during inflammatory reactions, activated leukocytes are thought to produce a variety of small proteins (cytokines) that influence the behaviour of other cells (including other leukocytes). of these substances, which include the interleukins, interferons and tumour necrosis factors (tnfs), interleukin-1 (il-1) has been considered potentially a most important inflammatory mediator because of its wide range of effects. in vivo it is pyrogenic and promotes the acute phase response; in vitro it activates lymphocytes and stimulates resorption of cartilage and bone. cartilage resorption is a major feature of inflammatory diseases such as rheumatoid arthritis, and il-1 is the only cytokine hitherto known to promote it. tnfs are characterized by their effects on tumours and cytotoxicity to transformed cells, but share some actions with il-1. i report here that recombinant human tnf alpha stimulates resorption and inhibits synthesis of proteoglycan in explants of cartilage. its action is similar to and additive with il-1, and it is a second macrophage-derived cytokine whose production in rheumatoid arthritis, or inflammation generally, could contribute to tissue destruction.",0
"our web site ( runs the dali program for protein structure comparison. the web site consists of three parts: (i) the dali server compares newly solved structures against structures in the protein data bank (pdb), (ii) the dali database allows browsing precomputed structural neighbourhoods and (iii) the pairwise comparison generates suboptimal alignments for a pair of structures. each part has its own query form and a common format for the results page. the inputs are either pdb identifiers or novel structures uploaded by the user. the results pages are hyperlinked to aid interactive analysis. the web interface is simple and easy to use. the key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how conserved residues and ligands cluster together in multiple structure superimpositions. in favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis.",0
"chembl is an open data database containing binding, functional and admet information for a large number of drug-like bioactive compounds. these data are manually abstracted from the primary published literature on a regular basis, then further curated and standardized to maximize their quality and utility across a wide range of chemical biology and drug-discovery research problems. currently, the database contains 5.4 million bioactivity measurements for more than 1 million compounds and 5200 protein targets. access is available through a web-based interface, data downloads and web services at:",0
"summary kofamkoala is a web server to assign kegg orthologs (kos) to protein sequences by homology search against a database of profile hidden markov models (kofam) with pre-computed adaptive score thresholds. kofamkoala is faster than existing ko assignment tools with its accuracy being comparable to the best performing tools. function annotation by kofamkoala helps linking genes to kegg resources such as the kegg pathway maps and facilitates molecular network reconstruction. availability and implementation kofamkoala, kofamscan and kofam are freely available from genomenet ( supplementary information supplementary data are available at bioinformatics online.",0
"background through the global burden of diseases, injuries, and risk factors (gbd) studies, headache has emerged as a major global public health concern. we aimed to use data from the gbd 2016 study to provide new estimates for prevalence and years of life lived with disability (ylds) for migraine and tension-type headache and to present the methods and results in an accessible way for clinicians and researchers of headache disorders. methods data were derived from population-based cross-sectional surveys on migraine and tension-type headache. prevalence for each sex and 5-year age group interval (ie, age 5 years to ≥95 years) at different time points from 1990 and 2016 in all countries and gbd regions were estimated using a bayesian meta-regression model. disease burden measured in ylds was calculated from prevalence and average time spent with headache multiplied by disability weights (a measure of the relative severity of the disabling consequence of a disease). the burden stemming from medication overuse headache, which was included in earlier iterations of gbd as a separate cause, was subsumed as a sequela of either migraine or tension-type headache. because no deaths were assigned to headaches as the underlying cause, ylds equate to disability-adjusted life-years (dalys). we also analysed results on the basis of the socio-demographic index (sdi), a compound measure of income per capita, education, and fertility. findings almost three billion individuals were estimated to have a migraine or tension-type headache in 2016: 1·89 billion (95% uncertainty interval 1·71-2·10) with tension-type headache and 1·04 billion (95% ui 1·00-1·09) with migraine. however, because migraine had a much higher disability weight than tension-type headache, migraine caused 45·1 million (95% ui 29·0-62·8) and tension-type headache only 7·2 million (95% ui 4·6-10·5) ylds globally in 2016. the headaches were most burdensome in women between ages 15 and 49 years, with migraine causing 20·3 million (95% ui 12·9-28·5) and tension-type headache 2·9 million (95% ui 1·8-4·2) ylds in 2016, which was 11·2% of all ylds in this age group and sex. age-standardised dalys for each headache type showed a small increase as sdi increased. interpretation although current estimates are based on limited data, our study shows that headache disorders, and migraine in particular, are important causes of disability worldwide, and deserve greater attention in health policy debates and research resource allocation. future iterations of this study, based on sources from additional countries and with less methodological heterogeneity, should help to provide stronger evidence of the need for action. funding bill & melinda gates foundation.",0
"with more than 900 000 confirmed cases worldwide and nearly 50 000 deaths during the first 3 months of 2020, the coronavirus disease 2019 (covid-19) pandemic has emerged as an unprecedented health care crisis. the spread of covid-19 has been heterogeneous, resulting in some regions having sporadic transmission and relatively few hospitalized patients with covid-19 and others having community transmission that has led to overwhelming numbers of severe cases. for these regions, health care delivery has been disrupted and compromised by critical resource constraints in diagnostic testing, hospital beds, ventilators, and health care workers who have fallen ill to the virus exacerbated by shortages of personal protective equipment. although mild cases mimic common upper respiratory viral infections, respiratory dysfunction becomes the principal source of morbidity and mortality as the disease advances. thoracic imaging with chest radiography and ct are key tools for pulmonary disease diagnosis and management, but their role in the management of covid-19 has not been considered within the multivariable context of the severity of respiratory disease, pretest probability, risk factors for disease progression, and critical resource constraints. to address this deficit, a multidisciplinary panel comprised principally of radiologists and pulmonologists from 10 countries with experience managing patients with covid-19 across a spectrum of health care environments evaluated the utility of imaging within three scenarios representing varying risk factors, community conditions, and resource constraints. fourteen key questions, corresponding to 11 decision points within the three scenarios and three additional clinical situations, were rated by the panel based on the anticipated value of the information that thoracic imaging would be expected to provide. the results were aggregated, resulting in five main and three additional recommendations intended to guide medical practitioners in the use of chest radiography and ct in the management of covid-19.",0
"tumor vascularization occurs through several distinct biological processes, which not only vary between tumor type and anatomic location, but also occur simultaneously within the same cancer tissue. these processes are orchestrated by a range of secreted factors and signaling pathways and can involve participation of non-endothelial cells, such as progenitors or cancer stem cells. anti-angiogenic therapies using either antibodies or tyrosine kinase inhibitors have been approved to treat several types of cancer. however, the benefit of treatment has so far been modest, some patients not responding at all and others acquiring resistance. it is becoming increasingly clear that blocking tumors from accessing the circulation is not an easy task to accomplish. tumor vessel functionality and gene expression often differ vastly when comparing different cancer subtypes, and vessel phenotype can be markedly heterogeneous within a single tumor. here, we summarize the current understanding of cellular and molecular mechanisms involved in tumor angiogenesis and discuss challenges and opportunities associated with vascular targeting.",0
"three monoclonal antibodies (ae1, ae2, and ae3) were prepared against human epidermal keratins and used to study keratin expression during normal epidermal differentiation. immunofluorescence staining data suggested that the antibodies were specific for keratin-type intermediate filaments. the reactivity of these antibodies to individual human epidermal keratin polypeptides (65-67, 58, 56, and 50 kdaltons) was determined by the immunoblot technique. ae1 reacted with 56 and 50 kdalton keratins, ae2 with 65-67 and 56-kdalton keratins, and ae3 with 65-67 and 58 kdalton keratins. thus all major epidermal keratins were recognized by at least one of the monoclonal antibodies. moreover, common antigenic determinants were present in subsets of epidermal keratins. to correlate the expression of specific keratins with different stages of in vivo epidermal differentiation, the antibodies were used for immunohistochemical staining of frozen skin sections. ae1 reacted with epidermal basal cells, ae2 with cells above the basal layer, and ae3 with the entire epidermis. the observation that ae1 and ae2 antibodies (which recognized a common 56 kdalton keratin) stained mutually exclusive parts of the epidermis suggested that certain keratin antigens must be masked in situ. this was shown to be the case by direct analysis of keratins extracted from serial, horizontal skin sections using the immunoblot technique. the results from these immunohistochemical and biochemical approaches suggested that: (a) the 65- to 67-kdalton keratins were present only in cells above the basal layer, (b) the 58-kdalton keratin was detected throughout the entire epidermis including the basal layer, (c) the 56-kdalton keratin was absent in the basal layer and first appeared probably in the upper spinous layer, and (d) the 50-kdalton keratin was the only other major keratin detected in the basal layer and was normally eliminated during s. corneum formation. the 56 and 65-67-kdalton keratins, which are characteristic of epidermal cells undergoing terminal differentiation, may be regarded as molecular markers for keratinization.",0
"background the inflammatory response plays a critical role in coronavirus disease 2019 (covid-19), and inflammatory cytokine storm increases the severity of covid-19. objective to investigate the ability of interleukin-6 (il-6), c-reactive protein (crp), and procalcitonin (pct) to predict mild and severe cases of covid-19. study design this retrospective cohort study included 140 patients diagnosed with covid-19 from january 18, 2020, to march 12, 2020. the study population was divided into two groups according to disease severity: a mild group (mg) (n = 107) and a severe group (sg) (n = 33). data on demographic characteristics, baseline clinical characteristics, and the levels of il-6, crp, and pct on admission were collected. results among the 140 patients, the levels of il-6, crp, and pct increased in 95 (67.9 %), 91 (65.0 %), and 8 (5.7 %) patients on admission, respectively. the proportion of patients with increased il-6, crp, and pct levels was significantly higher in the sg than in the mg. cox proportional hazard model showed that il-6 and crp could be used as independent factors to predict the severity of covid-19. furthermore, patients with il-6 > 32.1 pg/ml or crp > 41.8 mg/l were more likely to have severe complications. conclusion the serum levels of il-6 and crp can effectively assess disease severity and predict outcome in patients with covid-19.",0
"interrupted time series (its) analysis is a valuable study design for evaluating the effectiveness of population-level health interventions that have been implemented at a clearly defined point in time. it is increasingly being used to evaluate the effectiveness of interventions ranging from clinical therapy to national public health legislation. whereas the design shares many properties of regression-based approaches in other epidemiological studies, there are a range of unique features of time series data that require additional methodological considerations. in this tutorial we use a worked example to demonstrate a robust approach to its analysis using segmented regression. we begin by describing the design and considering when its is an appropriate design choice. we then discuss the essential, yet often omitted, step of proposing the impact model a priori. subsequently, we demonstrate the approach to statistical analysis including the main segmented regression model. finally we describe the main methodological issues associated with its analysis: over-dispersion of time series data, autocorrelation, adjusting for seasonal trends and controlling for time-varying confounders, and we also outline some of the more complex design adaptations that can be used to strengthen the basic its design.",0
"background network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. we can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. results we introduce a novel cytoscape plugin cytohubba for ranking nodes in a network by their network features. cytohubba provides 11 topological analysis methods including degree, edge percolated component, maximum neighborhood component, density of maximum neighborhood component, maximal clique centrality and six centralities (bottleneck, eccentricity, closeness, radiality, betweenness, and stress) based on shortest paths. among the eleven methods, the new proposed method, mcc, has a better performance on the precision of predicting essential proteins from the yeast ppi network. conclusions cytohubba provide a user-friendly interface to explore important nodes in biological networks. it computes all eleven methods in one stop shopping way. besides, researchers are able to combine cytohubba with and other plugins into a novel analysis scheme. the network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. according to cytoscape plugin download statistics, the accumulated number of cytohubba is around 6,700 times since 2010.",0
"resistance to antimicrobial agents has become a major source of morbidity and mortality worldwide. when antibiotics were first introduced in the 1900's, it was thought that we had won the war against microorganisms. it was soon discovered however, that the microorganisms were capable of developing resistance to any of the drugs that were used. apparently most pathogenic microorganisms have the capability of developing resistance to at least some antimicrobial agents. the main mechanisms of resistance are: limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. these mechanisms may be native to the microorganisms, or acquired from other microorganisms. understanding more about these mechanisms should hopefully lead to better treatment options for infective diseases, and development of antimicrobial drugs that can withstand the microorganisms attempts to become resistant.",0
"background the dersimonian and laird approach (dl) is widely used for random effects meta-analysis, but this often results in inappropriate type i error rates. the method described by hartung, knapp, sidik and jonkman (hksj) is known to perform better when trials of similar size are combined. however evidence in realistic situations, where one trial might be much larger than the other trials, is lacking. we aimed to evaluate the relative performance of the dl and hksj methods when studies of different sizes are combined and to develop a simple method to convert dl results to hksj results. methods we evaluated the performance of the hksj versus dl approach in simulated meta-analyses of 2-20 trials with varying sample sizes and between-study heterogeneity, and allowing trials to have various sizes, e.g. 25% of the trials being 10-times larger than the smaller trials. we also compared the number of ""positive"" (statistically significant at p = 3 studies of interventions from the cochrane database of systematic reviews. results the simulations showed that the hksj method consistently resulted in more adequate error rates than the dl method. when the significance level was 5%, the hksj error rates at most doubled, whereas for dl they could be over 30%. dl, and, far less so, hksj had more inflated error rates when the combined studies had unequal sizes and between-study heterogeneity. the empirical data from 689 meta-analyses showed that 25.1% of the significant findings for the dl method were non-significant with the hksj method. dl results can be easily converted into hksj results. conclusions our simulations showed that the hksj method consistently results in more adequate error rates than the dl method, especially when the number of studies is small, and can easily be applied routinely in meta-analyses. even with the hksj method, extra caution is needed when there are = <5 studies of very unequal sizes.",0
"a key metric to assess molecular docking remains ligand enrichment against challenging decoys. whereas the directory of useful decoys (dud) has been widely used, clear areas for optimization have emerged. here we describe an improved benchmarking set that includes more diverse targets such as gpcrs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from chembl, each with 50 property-matched decoys drawn from zinc. to ensure chemotype diversity, we cluster each target's ligands by their bemis-murcko atomic frameworks. we add net charge to the matched physicochemical properties and include only the most dissimilar decoys, by topology, from the ligands. an online automated tool ( generates these improved matched decoys for user-supplied ligands. we test this data set by docking all 102 targets, using the results to improve the balance between ligand desolvation and electrostatics in dock 3.6. the complete dud-e benchmarking set is freely available at",0
"when the nerves of isolated frog sartorius muscles were stimulated at 10 hz, synaptic vesicles in the motor nerve terminals became transiently depleted. this depletion apparently resulted from a redistribution rather than disappearance of synaptic vesicle membrane, since the total amount of membrane comprising these nerve terminals remained constant during stimulation. at 1 min of stimulation, the 30% depletion in synaptic vesicle membrane was nearly balanced by an increase in plasma membrane, suggesting that vesicle membrane rapidly moved to the surface as it might if vesicles released their content of transmitter by exocytosis. after 15 min of stimulation, the 60% depletion of synaptic vesicle membrane was largely balanced by the appearance of numerous irregular membrane-walled cisternae inside the terminals, suggesting that vesicle membrane was retrieved from the surface as cisternae. when muscles were rested after 15 min of stimulation, cisternae disappeared and synaptic vesicles reappeared, suggesting that cisternae divided to form new synaptic vesicles so that the original vesicle membrane was now recycled into new synaptic vesicles. when muscles were soaked in horseradish peroxidase (hrp), this tracerfirst entered the cisternae which formed during stimulation and then entered a large proportion of the synaptic vesicles which reappeared during rest, strengthening the idea that synaptic vesicle membrane added to the surface was retrieved as cisternae which subsequently divided to form new vesicles. when muscles containing hrp in synaptic vesicles were washed to remove extracellular hrp and restimulated, hrp disappeared from vesicles without appearing in the new cisternae formed during the second stimulation, confirming that a one-way recycling of synaptic membrane, from the surface through cisternae to new vesicles, was occurring. coated vesicles apparently represented the actual mechanism for retrieval of synaptic vesicle membrane from the plasma membrane, because during nerve stimulation they proliferated at regions of the nerve terminals covered by schwann processes, took up peroxidase, and appeared in various stages of coalescence with cisternae. in contrast, synaptic vesicles did not appear to return directly from the surface to form cisternae, and cisternae themselves never appeared directly connected to the surface. thus, during stimulation the intracellular compartments of this synapse change shape and take up extracellular protein in a manner which indicates that synaptic vesicle membrane added to the surface during exocytosis is retrieved by coated vesicles and recycled into new synaptic vesicles by way of intermediate cisternae.",0
"background child sexual abuse is considered a modifiable risk factor for mental disorders across the life course. however the long-term consequences of other forms of child maltreatment have not yet been systematically examined. the aim of this study was to summarise the evidence relating to the possible relationship between child physical abuse, emotional abuse, and neglect, and subsequent mental and physical health outcomes. methods and findings a systematic review was conducted using the medline, embase, and psycinfo electronic databases up to 26 june 2012. published cohort, cross-sectional, and case-control studies that examined non-sexual child maltreatment as a risk factor for loss of health were included. all meta-analyses were based on quality-effects models. out of 285 articles assessed for eligibility, 124 studies satisfied the pre-determined inclusion criteria for meta-analysis. statistically significant associations were observed between physical abuse, emotional abuse, and neglect and depressive disorders (physical abuse , emotional abuse , and neglect ); drug use (physical abuse , emotional abuse , and neglect ); suicide attempts (physical abuse , emotional abuse , and neglect ); and sexually transmitted infections and risky sexual behaviour (physical abuse , emotional abuse , and neglect ). evidence for causality was assessed using bradford hill criteria. while suggestive evidence exists for a relationship between maltreatment and chronic diseases and lifestyle risk factors, more research is required to confirm these relationships. conclusions this overview of the evidence suggests a causal relationship between non-sexual child maltreatment and a range of mental disorders, drug use, suicide attempts, sexually transmitted infections, and risky sexual behaviour. all forms of child maltreatment should be considered important risks to health with a sizeable impact on major contributors to the burden of disease in all parts of the world. the awareness of the serious long-term consequences of child maltreatment should encourage better identification of those at risk and the development of effective interventions to protect children from violence.",0
"comprehensive discovery of structural variation (sv) from whole genome sequencing data requires multiple detection signals including read-pair, split-read, read-depth and prior knowledge. owing to technical challenges, extant sv discovery algorithms either use one signal in isolation, or at best use two sequentially. we present lumpy, a novel sv discovery framework that naturally integrates multiple sv signals jointly across multiple samples. we show that lumpy yields improved sensitivity, especially when sv signal is reduced owing to either low coverage data or low intra-sample variant allele frequency. we also report a set of 4,564 validated breakpoints from the na12878 human genome.",0
"the prevalence of rheumatoid arthritis (ra) is relatively constant in many populations, at 0.5-1.0%. however, a high prevalence of ra has been reported in the pima indians (5.3%) and in the chippewa indians (6.8%). in contrast, low occurrences have been reported in populations from china and japan. these data support a genetic role in disease risk. studies have so far shown that the familial recurrence risk in ra is small compared with other autoimmune diseases. the main genetic risk factor of ra is the hla drb1 alleles, and this has consistently been shown in many populations throughout the world. the strongest susceptibility factor so far has been the hla drb1*0404 allele. tumour necrosis factor alleles have also been linked with ra. however, it is estimated that these genes can explain only 50% of the genetic effect. a number of other non-mhc genes have thus been investigated and linked with ra (e.g. corticotrophin releasing hormone, oestrogen synthase, ifn-gamma and other cytokines). environmental factors have also been studied in relation to ra. female sex hormones may play a protective role in ra; for example, the use of the oral contraceptive pill and pregnancy are both associated with a decreased risk. however, the postpartum period has been highlighted as a risk period for the development of ra. furthermore, breastfeeding after a first pregnancy poses the greatest risk. exposure to infection may act as a trigger for ra, and a number of agents have been implicated (e.g. epstein-barr virus, parvovirus and some bacteria such as proteus and mycoplasma). however, the epidemiological data so far are inconclusive. there has recently been renewed interest in the link between cigarette smoking and ra, and the data presented so far are consistent with and suggestive of an increased risk.",0
"therapeutic efficacy of a tumor cell-based vaccine against experimental b16 melanoma requires the disruption of either of two immunoregulatory mechanisms that control autoreactive t cell responses: the cytotoxic t lymphocyte-associated antigen (ctla)-4 pathway or the cd25(+) regulatory t (treg) cells. combination of ctla-4 blockade and depletion of cd25(+) treg cells results in maximal tumor rejection. efficacy of the antitumor therapy correlates with the extent of autoimmune skin depigmentation as well as with the frequency of tyrosinase-related protein 2(180-188)-specific ctls detected in the periphery. furthermore, tumor rejection is dependent on the cd8(+) t cell subset. our data demonstrate that the ctl response against melanoma antigens is an important component of the therapeutic antitumor response and that the reactivity of these ctls can be augmented through interference with immunoregulatory mechanisms. the synergism in the effects of ctla-4 blockade and depletion of cd25(+) treg cells indicates that cd25(+) treg cells and ctla-4 signaling represent two alternative pathways for suppression of autoreactive t cell immunity. simultaneous intervention with both regulatory mechanisms is therefore a promising concept for the induction of therapeutic antitumor immunity.",0
"background multimorbidity and the associated use of multiple medicines (polypharmacy), is common in the older population. despite this, there is no consensus definition for polypharmacy. a systematic review was conducted to identify and summarise polypharmacy definitions in existing literature. methods the reporting of this systematic review conforms to the preferred reporting items for systematic reviews and meta-analyses (prisma) checklist. medline (ovid), embase and cochrane were systematically searched, as well as grey literature, to identify articles which defined the term polypharmacy (without any limits on the types of definitions) and were in english, published between 1st january 2000 and 30th may 2016. definitions were categorised as i. numerical only (using the number of medications to define polypharmacy), ii. numerical with an associated duration of therapy or healthcare setting (such as during hospital stay) or iii. descriptive (using a brief description to define polypharmacy). results a total of 1156 articles were identified and 110 articles met the inclusion criteria. articles not only defined polypharmacy but associated terms such as minor and major polypharmacy. as a result, a total of 138 definitions of polypharmacy and associated terms were obtained. there were 111 numerical only definitions (80.4% of all definitions), 15 numerical definitions which incorporated a duration of therapy or healthcare setting (10.9%) and 12 descriptive definitions (8.7%). the most commonly reported definition of polypharmacy was the numerical definition of five or more medications daily (n = 51, 46.4% of articles), with definitions ranging from two or more to 11 or more medicines. only 6.4% of articles classified the distinction between appropriate and inappropriate polypharmacy, using descriptive definitions to make this distinction. conclusions polypharmacy definitions were variable. numerical definitions of polypharmacy did not account for specific comorbidities present and make it difficult to assess safety and appropriateness of therapy in the clinical setting.",0
"cerebral small vessel disease (svd) is a common accompaniment of ageing. features seen on neuroimaging include recent small subcortical infarcts, lacunes, white matter hyperintensities, perivascular spaces, microbleeds, and brain atrophy. svd can present as a stroke or cognitive decline, or can have few or no symptoms. svd frequently coexists with neurodegenerative disease, and can exacerbate cognitive deficits, physical disabilities, and other symptoms of neurodegeneration. terminology and definitions for imaging the features of svd vary widely, which is also true for protocols for image acquisition and image analysis. this lack of consistency hampers progress in identifying the contribution of svd to the pathophysiology and clinical features of common neurodegenerative diseases. we are an international working group from the centres of excellence in neurodegeneration. we completed a structured process to develop definitions and imaging standards for markers and consequences of svd. we aimed to achieve the following: first, to provide a common advisory about terms and definitions for features visible on mri; second, to suggest minimum standards for image acquisition and analysis; third, to agree on standards for scientific reporting of changes related to svd on neuroimaging; and fourth, to review emerging imaging methods for detection and quantification of preclinical manifestations of svd. our findings and recommendations apply to research studies, and can be used in the clinical setting to standardise image interpretation, acquisition, and reporting. this position paper summarises the main outcomes of this international effort to provide the standards for reporting vascular changes on neuroimaging (strive).",0
"purpose the original consensus-based standards for the selection of health measurement instruments (cosmin) checklist was developed to assess the methodological quality of single studies on measurement properties of patient-reported outcome measures (proms). now it is our aim to adapt the cosmin checklist and its four-point rating system into a version exclusively for use in systematic reviews of proms, aiming to assess risk of bias of studies on measurement properties. methods for each standard (i.e., a design requirement or preferred statistical method), it was discussed within the cosmin steering committee if and how it should be adapted. the adapted checklist was pilot-tested to strengthen content validity in a systematic review on the quality of proms for patients with hand osteoarthritis. results most important changes were the reordering of the measurement properties to be assessed in a systematic review of proms; the deletion of standards that concerned reporting issues and standards that not necessarily lead to biased results; the integration of standards on general requirements for studies on item response theory with standards for specific measurement properties; the recommendation to the review team to specify hypotheses for construct validity and responsiveness in advance, and subsequently the removal of the standards about formulating hypotheses; and the change in the labels of the four-point rating system. conclusions the cosmin risk of bias checklist was developed exclusively for use in systematic reviews of proms to distinguish this application from other purposes of assessing the methodological quality of studies on measurement properties, such as guidance for designing or reporting a study on the measurement properties.",0
"background readers may question the interpretation of findings in clinical trials when multiple outcome measures are used without adjustment of the p-value. this question arises because of the increased risk of type i errors (findings of false ""significance"") when multiple simultaneous hypotheses are tested at set p-values. the primary aim of this study was to estimate the need to make appropriate p-value adjustments in clinical trials to compensate for a possible increased risk in committing type i errors when multiple outcome measures are used. discussion the classicists believe that the chance of finding at least one test statistically significant due to chance and incorrectly declaring a difference increases as the number of comparisons increases. the rationalists have the following objections to that theory: 1) p-value adjustments are calculated based on how many tests are to be considered, and that number has been defined arbitrarily and variably; 2) p-value adjustments reduce the chance of making type i errors, but they increase the chance of making type ii errors or needing to increase the sample size. summary readers should balance a study's statistical significance with the magnitude of effect, the quality of the study and with findings from other studies. researchers facing multiple outcome measures might want to either select a primary outcome measure or use a global assessment measure, rather than adjusting the p-value.",0
"sharing of research data in public repositories has become best practice in academia. with the accumulation of massive data, network bandwidth and storage requirements are rapidly increasing. the proteomexchange (px) consortium implements a mode of centralized metadata and distributed raw data management, which promotes effective data sharing. to facilitate open access of proteome data worldwide, we have developed the integrated proteome resource iprox ( as a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. the iprox repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. also, it deploys extensive controlled vocabularies and ontologies to annotate proteomics datasets. users can use a gui to provide and access data through a fast aspera-based transfer tool. iprox is a full member of the px consortium; all released datasets are freely accessible to the public. iprox is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of china, ensuring long-term and stable resource support. iprox will facilitate worldwide data analysis and sharing of proteomics experiments.",0
"the 2009 pandemic h1n1 influenza pandemic demonstrated the global health threat of reassortant influenza strains. herein, we report a detailed analysis of plasmablast and monoclonal antibody responses induced by pandemic h1n1 infection in humans. unlike antibodies elicited by annual influenza vaccinations, most neutralizing antibodies induced by pandemic h1n1 infection were broadly cross-reactive against epitopes in the hemagglutinin (ha) stalk and head domain of multiple influenza strains. the antibodies were from cells that had undergone extensive affinity maturation. based on these observations, we postulate that the plasmablasts producing these broadly neutralizing antibodies were predominantly derived from activated memory b cells specific for epitopes conserved in several influenza strains. consequently, most neutralizing antibodies were broadly reactive against divergent h1n1 and h5n1 influenza strains. this suggests that a pan-influenza vaccine may be possible, given the right immunogen. antibodies generated potently protected and rescued mice from lethal challenge with pandemic h1n1 or antigenically distinct influenza strains, making them excellent therapeutic candidates.",0
"numerous studies have tested the association between tp53 mutations in ovarian cancer and prognosis but these have been consistently confounded by limitations in study design, methodology, and/or heterogeneity in the sample cohort. high-grade serous (hgs) carcinoma is the most clinically important histological subtype of ovarian cancer. as these tumours may arise from the ovary, fallopian tube or peritoneum, they are collectively referred to as high-grade pelvic serous carcinoma (hgpsc). to identify the true prevalence of tp53 mutations in hgpsc, we sequenced exons 2-11 and intron-exon boundaries in tumour dna from 145 patients. hgpsc cases were defined as having histological grade 2 or 3 and figo stage iii or iv. surprisingly, pathogenic tp53 mutations were identified in 96.7% (n = 119/123) of hgpsc cases. molecular and pathological review of mutation-negative cases showed evidence of p53 dysfunction associated with copy number gain of mdm2 or mdm4, or indicated the exclusion of samples as being low-grade serous tumours or carcinoma of uncertain primary site. overall, p53 dysfunction rate approached 100% of confirmed hgpscs. no association between tp53 mutation and progression-free or overall survival was found. from this first comprehensive mapping of tp53 mutation rate in a homogeneous group of hgpsc patients, we conclude that mutant tp53 is a driver mutation in the pathogenesis of hgpsc cancers. because tp53 mutation is almost invariably present in hgpsc, it is not of substantial prognostic or predictive significance.",0
"the agrigo platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (go) enrichment analyses of plant and agricultural species. we continuously maintain and update the databases and accommodate the various requests of our global users. here, we present our updated agrigo that has a largely expanded number of supporting species (394) and datatypes (865). in addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. we further improved the computational efficiency, including the batch analysis and p-value distribution (pvd), and the user-friendliness of the web pages. more visualization features were added to the platform, including seacompare (cross comparison of singular enrichment analysis), direct acyclic graph (dag) and scatter plots, which can be merged by choosing any significant go term. the updated platform agrigo v2.0 is now publicly accessible at",0
"since the outbreak of coronavirus disease 2019 (covid-19) in wuhan, china, it has rapidly spread across many other countries. while the majority of patients were considered mild, critically ill patients involving respiratory failure and multiple organ dysfunction syndrome are not uncommon, which could result death. we hypothesized that cytokine storm is associated with severe outcome. we enrolled 102 covid-19 patients who were admitted to renmin hospital (wuhan, china). all patients were classified into moderate, severe and critical groups according to their symptoms. 45 control samples of healthy volunteers were also included. inflammatory cytokines and c-reactive protein (crp) profiles of serum samples were analyzed by specific immunoassays. results showed that covid-19 patients have higher serum level of cytokines (tnf-α, ifn-γ, il-2, il-4, il-6 and il-10) and crp than control individuals. within covid-19 patients, serum il-6 and il-10 levels are significantly higher in critical group ( n = 17) than in moderate ( n = 42) and severe ( n = 43) group. the levels of il-10 is positively correlated with crp amount ( r = 0.41, p < 0.01). using univariate logistic regression analysis, il-6 and il-10 are found to be predictive of disease severity and receiver operating curve analysis could further confirm this result (auc = 0.841, 0.822 respectively). our result indicated higher levels of cytokine storm is associated with more severe disease development. among them, il-6 and il-10 can be used as predictors for fast diagnosis of patients with higher risk of disease deterioration. given the high levels of cytokines induced by sars-cov-2, treatment to reduce inflammation-related lung damage is critical.",0
"in december 2019, an outbreak of severe acute respiratory syndrome coronavirus 2 infection occurred in wuhan, hubei province, china, and spread across china and beyond. on february 12, 2020, the world health organization officially named the disease caused by the novel coronavirus as coronavirus disease 2019 (covid-19). because most patients infected with covid-19 had pneumonia and characteristic ct imaging patterns, radiologic examinations have become vital in early diagnosis and the assessment of disease course. to date, ct findings have been recommended as major evidence for clinical diagnosis of covid-19 in hubei, china. this review focuses on the etiology, epidemiology, and clinical symptoms of covid-19 while highlighting the role of chest ct in prevention and disease control.",0
"injury or impaired clearance of apoptotic cells leads to the pathological accumulation of necrotic corpses, which induce an inflammatory response that initiates tissue repair. in addition, antigens present in necrotic cells can sometimes provoke a specific immune response and it has been argued that necrosis could explain adaptive immunity in seemingly infection-free situations, such as after allograft transplantation or in spontaneous and therapy-induced tumour rejection. in the mouse, the cd8alpha+ subset of dendritic cells phagocytoses dead cell remnants and cross-primes cd8+ t cells against cell-associated antigens. here we show that cd8alpha+ dendritic cells use clec9a (also known as dngr-1), a recently-characterized c-type lectin, to recognize a preformed signal that is exposed on necrotic cells. loss or blockade of clec9a does not impair the uptake of necrotic cell material by cd8+ dendritic cells, but specifically reduces cross-presentation of dead-cell-associated antigens in vitro and decreases the immunogenicity of necrotic cells in vivo. the function of clec9a requires a key tyrosine residue in its intracellular tail that allows the recruitment and activation of the tyrosine kinase syk, which is also essential for cross-presentation of dead-cell-associated antigens. thus, clec9a functions as a syk-coupled c-type lectin receptor to mediate sensing of necrosis by the principal dendritic-cell subset involved in regulating cross-priming to cell-associated antigens.",0
"bindingdb, is a publicly accessible database of experimental protein-small molecule interaction data. its collection of over a million data entries derives primarily from scientific articles and, increasingly, us patents. bindingdb provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. the pdb and pubmed provide links to data in bindingdb, and vice versa; and bindingdb provides links to pathway information, the zinc catalog of available compounds, and other resources. the bindingdb website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from bindingdb and organized for use in validating drug design methods. bindingdb offers several forms of programmatic access, and comes with extensive background material and documentation. here, we provide the first update of bindingdb since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.",0
"data saturation is the most commonly employed concept for estimating sample sizes in qualitative research. over the past 20 years, scholars using both empirical research and mathematical/statistical models have made significant contributions to the question: how many qualitative interviews are enough? this body of work has advanced the evidence base for sample size estimation in qualitative inquiry during the design phase of a study, prior to data collection, but it does not provide qualitative researchers with a simple and reliable way to determine the adequacy of sample sizes during and/or after data collection. using the principle of saturation as a foundation, we describe and validate a simple-to-apply method for assessing and reporting on saturation in the context of inductive thematic analyses. following a review of the empirical research on data saturation and sample size estimation in qualitative research, we propose an alternative way to evaluate saturation that overcomes the shortcomings and challenges associated with existing methods identified in our review. our approach includes three primary elements in its calculation and assessment: base size, run length, and new information threshold. we additionally propose a more flexible approach to reporting saturation. to validate our method, we use a bootstrapping technique on three existing thematically coded qualitative datasets generated from in-depth interviews. results from this analysis indicate the method we propose to assess and report on saturation is feasible and congruent with findings from earlier studies.",0
"kegg ( or is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. molecular functions of genes and proteins are associated with ortholog groups and stored in the kegg orthology (ko) database. the kegg pathway maps, brite hierarchies and kegg modules are developed as networks of ko nodes, representing high-level functions of the cell and the organism. currently, more than 4000 complete genomes are annotated with kos in the kegg genes database, which can be used as a reference data set for ko assignment and subsequent reconstruction of kegg pathways and other molecular networks. as an annotation resource, the following improvements have been made. first, each ko record is re-examined and associated with protein sequence data used in experiments of functional characterization. second, the genes database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes. third, new automatic annotation servers, blastkoala and ghostkoala, are made available utilizing the non-redundant pangenome data set generated from the genes database. as a resource for translational bioinformatics, various data sets are created for antimicrobial resistance and drug interaction networks.",0
"motivation the discovery of genomic structural variants (svs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of svs. results we have developed an sv discovery method, called delly, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. delly is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. delly, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. on simulated data, delly compares favorably to other sv prediction methods across a wide range of sequencing parameters. on real data, delly reliably uncovers svs from the 1000 genomes project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. availability delly is available at contact tobias.rausch@embl.de.",0
"the abcd study is a new and ongoing project of very substantial size and scale involving 21 data acquisition sites. it aims to recruit 11,500 children and follow them for ten years with extensive assessments at multiple timepoints. to deliver on its potential to adequately describe adolescent development, it is essential that it adopt recruitment procedures that are efficient and effective and will yield a sample that reflects the nation's diversity in an epidemiologically informed manner. here, we describe the sampling plans and recruitment procedures of this study. participants are largely recruited through the school systems with school selection informed by gender, race and ethnicity, socioeconomic status, and urbanicity. procedures for school selection designed to mitigate selection biases, dynamic monitoring of the accumulating sample to correct deviations from recruitment targets, and a description of the recruitment procedures designed to foster a collaborative attitude between the researchers, the schools and the local communities, are provided.",0
"the antimicrobial peptide database (apd, is an original database initially online in 2003. the apd2 (2009 version) has been regularly updated and further expanded into the apd3. this database currently focuses on natural antimicrobial peptides (amps) with defined sequence and activity. it includes a total of 2619 amps with 261 bacteriocins from bacteria, 4 amps from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. the apd3 contains 2169 antibacterial, 172 antiviral, 105 anti-hiv, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. newly annotated are amps with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. we also describe other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. amino acid profiles or signatures of natural amps are important for peptide classification, prediction and design. finally, we summarize various database applications in research and education.",0
"the ability of antigen receptors to engage self-ligands with varying affinity is crucial for lymphocyte development. to further explore this concept, we generated transgenic mice expressing gfp from the immediate early gene nr4a1 (nur77) locus. gfp was up-regulated in lymphocytes by antigen receptor stimulation but not by inflammatory stimuli. in t cells, gfp was induced during positive selection, required major histocompatibility complex for maintenance, and directly correlated with the strength of t cell receptor (tcr) stimulus. thus, our results define a novel tool for studying antigen receptor activation in vivo. using this model, we show that regulatory t cells (t(reg) cells) and invariant nkt cells (inkt cells) perceived stronger tcr signals than conventional t cells during development. however, although t(reg) cells continued to perceive strong tcr signals in the periphery, inkt cells did not. finally, we show that t(reg) cell progenitors compete for recognition of rare stimulatory tcr self-ligands.",0
"dopamine has a central role in motivation and reward. dopaminergic neurons in the ventral tegmental area (vta) signal the discrepancy between expected and actual rewards (that is, reward prediction error), but how they compute such signals is unknown. we recorded the activity of vta neurons while mice associated different odour cues with appetitive and aversive outcomes. we found three types of neuron based on responses to odours and outcomes: approximately half of the neurons (type i, 52%) showed phasic excitation after reward-predicting odours and rewards in a manner consistent with reward prediction error coding; the other half of neurons showed persistent activity during the delay between odour and outcome that was modulated positively (type ii, 31%) or negatively (type iii, 18%) by the value of outcomes. whereas the activity of type i neurons was sensitive to actual outcomes (that is, when the reward was delivered as expected compared to when it was unexpectedly omitted), the activity of type ii and type iii neurons was determined predominantly by reward-predicting odours. we 'tagged' dopaminergic and gabaergic neurons with the light-sensitive protein channelrhodopsin-2 and identified them based on their responses to optical stimulation while recording. all identified dopaminergic neurons were of type i and all gabaergic neurons were of type ii. these results show that vta gabaergic neurons signal expected reward, a key variable for dopaminergic neurons to calculate reward prediction error.",0
"background in an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. the global burden of diseases, injuries, and risk factors study (gbd) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. methods gbd estimates incidence, prevalence, mortality, years of life lost (ylls), years lived with disability (ylds), and disability-adjusted life-years (dalys) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. cause-specific death rates and cause fractions were calculated using the cause of death ensemble model and spatiotemporal gaussian process regression. cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the gbd population, fertility, and mortality estimates. deaths were multiplied by standard life expectancy at each age to calculate ylls. a bayesian meta-regression modelling tool, dismod-mr 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate ylds. we considered results in the context of the socio-demographic index (sdi), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. uncertainty intervals (uis) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. findings global health has steadily improved over the past 30 years as measured by age-standardised daly rates. after taking into account population growth and ageing, the absolute number of dalys has remained stable. since 2010, the pace of decline in global age-standardised daly rates has accelerated in age groups younger than 50 years compared with the 1990-2010 time period, with the greatest annualised rate of decline occurring in the 0-9-year age group. six infectious diseases were among the top ten causes of dalys in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). in adolescents aged 10-24 years, three injury causes were among the top causes of dalys: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). five of the causes that were in the top ten for ages 10-24 years were also in the top ten in the 25-49-year age group: road injuries (ranked first), hiv/aids (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). in 2019, ischaemic heart disease and stroke were the top-ranked causes of dalys in both the 50-74-year and 75-years-and-older age groups. since 1990, there has been a marked shift towards a greater proportion of burden due to ylds from non-communicable diseases and injuries. in 2019, there were 11 countries where non-communicable disease and injury ylds constituted more than half of all disease burden. decreases in age-standardised daly rates have accelerated over the past decade in countries at the lower end of the sdi range, while improvements have started to stagnate or even reverse in countries with higher sdi. interpretation as disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and development investment is needed to identify new, more effective intervention strategies. with a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. the mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. funding bill & melinda gates foundation.",0
"complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. carbohydrate active enzymes (cazymes) are the most important enzymes for complex carbohydrate metabolism. with an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of cazymes. we developed the dbcan web server in 2012 to provide a public service for automated cazyme annotation for newly sequenced genomes. here, dbcan2 ( is presented as an updated meta server, which integrates three state-of-the-art tools for cazome (all cazymes of a genome) annotation: (i) hmmer search against the dbcan hmm (hidden markov model) database; (ii) diamond search against the cazy pre-annotated cazyme sequence database and (iii) hotpep search against the conserved cazyme short peptide database. combining the three outputs and removing cazymes found by only one tool can significantly improve the cazome annotation accuracy. in addition, dbcan2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked cazyme gene clusters (cgcs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (puls) in microbial genomes or metagenomes.",0
"the proteomics identifications (pride) database is one of the world-leading data repositories of mass spectrometry (ms)-based proteomics data. since the beginning of 2014, pride archive ( is the new pride archival system, replacing the original pride database. here we summarize the developments in pride resources and related tools since the previous update manuscript in the database issue in 2013. pride archive constitutes a complete redevelopment of the original pride, comprising a new storage backend, data submission system and web interface, among other components. pride archive supports the most-widely used psi (proteomics standards initiative) data standard formats (mzml and mzidentml) and implements the data requirements and guidelines of the proteomexchange consortium. the wide adoption of proteomexchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). we outline some statistics on the current pride archive data contents. we also report on the status of the pride related stand-alone tools: pride inspector, pride converter 2 and the proteomexchange submission tool. finally, we will give a brief update on the resources under development 'pride cluster' and 'pride proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in pride archive.",0
"radiotherapy is one of the most successful cancer therapies. here the effect of irradiation on antigen presentation by mhc class i molecules was studied. cell surface expression of mhc class i molecules was increased for many days in a radiation dose-dependent manner as a consequence of three responses. initially, enhanced degradation of existing proteins occurred which resulted in an increased intracellular peptide pool. subsequently, enhanced translation due to activation of the mammalian target of rapamycin pathway resulted in increased peptide production, antigen presentation, as well as cytotoxic t lymphocyte recognition of irradiated cells. in addition, novel proteins were made in response to gamma-irradiation, resulting in new peptides presented by mhc class i molecules, which were recognized by cytotoxic t cells. we show that immunotherapy is successful in eradicating a murine colon adenocarcinoma only when preceded by radiotherapy of the tumor tissue. our findings indicate that directed radiotherapy can improve the efficacy of tumor immunotherapy.",0
"osmium tetroxide fixation of tissue blocks, as usually effected, is preceded by an acidification of the tissue. this acidification is probably responsible for morphological alterations which are notably disturbing in electron microscopy. the acidification and the resulting morphological alterations cannot be prevented by homogenizing the tissue directly in oso(4) solutions or by adding enzyme inhibitors (fluoride, iodoscetamide) to the fixative. fixation experiments with buffered oso(4) solutions have shown that the appearance of the fixed cells is conditioned by the ph of the fixative. the quality of fixation can be materially improved by buffering the oso(4) solutions at ph 7.3-7.5, the acetate-veronal buffer appeared to be the most favorable of the buffers tested, because of these findings, 1 per cent oso(4) buffered at ph 7.3-7.5 with acetate-veronal buffer is recommended as an appropriate fixative for electron microscopy.",0
"aims to appraise the clinical and genetic evidence that low-density lipoproteins (ldls) cause atherosclerotic cardiovascular disease (ascvd). methods and results we assessed whether the association between ldl and ascvd fulfils the criteria for causality by evaluating the totality of evidence from genetic studies, prospective epidemiologic cohort studies, mendelian randomization studies, and randomized trials of ldl-lowering therapies. in clinical studies, plasma ldl burden is usually estimated by determination of plasma ldl cholesterol level (ldl-c). rare genetic mutations that cause reduced ldl receptor function lead to markedly higher ldl-c and a dose-dependent increase in the risk of ascvd, whereas rare variants leading to lower ldl-c are associated with a correspondingly lower risk of ascvd. separate meta-analyses of over 200 prospective cohort studies, mendelian randomization studies, and randomized trials including more than 2 million participants with over 20 million person-years of follow-up and over 150 000 cardiovascular events demonstrate a remarkably consistent dose-dependent log-linear association between the absolute magnitude of exposure of the vasculature to ldl-c and the risk of ascvd; and this effect appears to increase with increasing duration of exposure to ldl-c. both the naturally randomized genetic studies and the randomized intervention trials consistently demonstrate that any mechanism of lowering plasma ldl particle concentration should reduce the risk of ascvd events proportional to the absolute reduction in ldl-c and the cumulative duration of exposure to lower ldl-c, provided that the achieved reduction in ldl-c is concordant with the reduction in ldl particle number and that there are no competing deleterious off-target effects. conclusion consistent evidence from numerous and multiple different types of clinical and genetic studies unequivocally establishes that ldl causes ascvd.",0
"the mouse was found to be natively susceptible to listeria monocytogenes. its susceptibility was attributed to the capacity of the organism to survive and multiplying in host macrophages. during the first 3 days of a primary infection the bacterial populations of spleen and liver were found to increase at a constant rate. on the 4th day of infection the host became hypersensitive to listeria antigens and at the same time bacterial growth ceased. a rapid inactivation of the organism ensued. convalescent mice were resistant to challenge, but no protective factor could be found in their serum. histological evidence suggested that acquired resistance was the result of a change occurring in the host's mononuclear phagocytes. when challenged in vitro, the macrophages of convalescent mice were found to resist infection with listeria monocytogenes. listeria-resistant cells appeared during the course of infection at a time which corresponded with the development of the antibacterial mechanism in the spleen. they persisted for as long as the antibacterial mechanism remained intact in this organ. this period of absolute resistance to listeria lasted about 3 weeks. thereafter, the host remained hypersensitive but unable to inactivate a challenge inoculum of listeria. however, it remained capable of producing an accelerated response to reinfection. this was thought to depend upon an ability to generate a new population of resistant cells from a residuum of specifically sensitized macrophages or macrophage precursors still surviving in the tissues as a result of the immunological activation which occurred during the primary infection.",0
"gastric cancer is the second most common cause of cancer-related deaths in the world, the epidemiology of which has changed within last decades. a trend of steady decline in gastric cancer incidence rates is the effect of the increased standards of hygiene, conscious nutrition, and helicobacter pylori eradication, which together constitute primary prevention. avoidance of gastric cancer remains a priority. however, patients with higher risk should be screened for early detection and chemoprevention. surgical resection enhanced by standardized lymphadenectomy remains the gold standard in gastric cancer therapy. this review briefly summarizes the most important aspects of gastric cancers, which include epidemiology, risk factors, classification, diagnosis, prevention, and treatment. the paper is mostly addressed to physicians who are interested in updating the state of art concerning gastric carcinoma from easily accessible and credible source.",0
"background the number of individuals living with dementia is increasing, negatively affecting families, communities, and health-care systems around the world. a successful response to these challenges requires an accurate understanding of the dementia disease burden. we aimed to present the first detailed analysis of the global prevalence, mortality, and overall burden of dementia as captured by the global burden of diseases, injuries, and risk factors (gbd) study 2016, and highlight the most important messages for clinicians and neurologists. methods gbd 2016 obtained data on dementia from vital registration systems, published scientific literature and surveys, and data from health-service encounters on deaths, excess mortality, prevalence, and incidence from 195 countries and territories from 1990 to 2016, through systematic review and additional data-seeking efforts. to correct for differences in cause of death coding across time and locations, we modelled mortality due to dementia using prevalence data and estimates of excess mortality derived from countries that were most likely to code deaths to dementia relative to prevalence. data were analysed by standardised methods to estimate deaths, prevalence, years of life lost (ylls), years of life lived with disability (ylds), and disability-adjusted life-years (dalys; computed as the sum of ylls and ylds), and the fractions of these metrics that were attributable to four risk factors that met gbd criteria for assessment (high body-mass index , high fasting plasma glucose, smoking, and a diet high in sugar-sweetened beverages). findings in 2016, the global number of individuals who lived with dementia was 43·8 million (95% uncertainty interval 37·8-51·0), increased from 20.2 million (17·4-23·5) in 1990. this increase of 117% (95% ui 114-121) contrasted with a minor increase in age-standardised prevalence of 1·7% (1·0-2·4), from 701 cases (95% ui 602-815) per 100 000 population in 1990 to 712 cases (614-828) per 100 000 population in 2016. more women than men had dementia in 2016 (27·0 million, 95% ui 23·3-31·4, vs 16.8 million, 14.4-19.6), and dementia was the fifth leading cause of death globally, accounting for 2·4 million (95% ui 2·1-2·8) deaths. overall, 28·8 million (95% ui 24·5-34·0) dalys were attributed to dementia; 6·4 million (95% ui 3·4-10·5) of these could be attributed to the modifiable gbd risk factors of high bmi, high fasting plasma glucose, smoking, and a high intake of sugar-sweetened beverages. interpretation the global number of people living with dementia more than doubled from 1990 to 2016, mainly due to increases in population ageing and growth. although differences in coding for causes of death and the heterogeneity in case-ascertainment methods constitute major challenges to the estimation of the burden of dementia, future analyses should improve on the methods for the correction of these biases. until breakthroughs are made in prevention or curative treatment, dementia will constitute an increasing challenge to health-care systems worldwide. funding bill & melinda gates foundation.",0
"molecular docking is an established in silico structure-based method widely used in drug discovery. docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineating structure-activity relationships (sar), without knowing a priori the chemical structure of other target modulators. although it was originally developed to help understanding the mechanisms of molecular recognition between small and large molecules, uses and applications of docking in drug discovery have heavily changed over the last years. in this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. then, we illustrate newer and emergent uses and applications of docking, including prediction of adverse effects, polypharmacology, drug repurposing, and target fishing and profiling, discussing also future applications and further potential of this technique when combined with emergent techniques, such as artificial intelligence.",0
"background hypertension can be detected at the primary health-care level and low-cost treatments can effectively control hypertension. we aimed to measure the prevalence of hypertension and progress in its detection, treatment, and control from 1990 to 2019 for 200 countries and territories. methods we used data from 1990 to 2019 on people aged 30-79 years from population-representative studies with measurement of blood pressure and data on blood pressure treatment. we defined hypertension as having systolic blood pressure 140 mm hg or greater, diastolic blood pressure 90 mm hg or greater, or taking medication for hypertension. we applied a bayesian hierarchical model to estimate the prevalence of hypertension and the proportion of people with hypertension who had a previous diagnosis (detection), who were taking medication for hypertension (treatment), and whose hypertension was controlled to below 140/90 mm hg (control). the model allowed for trends over time to be non-linear and to vary by age. findings the number of people aged 30-79 years with hypertension doubled from 1990 to 2019, from 331 (95% credible interval 306-359) million women and 317 (292-344) million men in 1990 to 626 (584-668) million women and 652 (604-698) million men in 2019, despite stable global age-standardised prevalence. in 2019, age-standardised hypertension prevalence was lowest in canada and peru for both men and women; in taiwan, south korea, japan, and some countries in western europe including switzerland, spain, and the uk for women; and in several low-income and middle-income countries such as eritrea, bangladesh, ethiopia, and solomon islands for men. hypertension prevalence surpassed 50% for women in two countries and men in nine countries, in central and eastern europe, central asia, oceania, and latin america. globally, 59% (55-62) of women and 49% (46-52) of men with hypertension reported a previous diagnosis of hypertension in 2019, and 47% (43-51) of women and 38% (35-41) of men were treated. control rates among people with hypertension in 2019 were 23% (20-27) for women and 18% (16-21) for men. in 2019, treatment and control rates were highest in south korea, canada, and iceland (treatment >70%; control >50%), followed by the usa, costa rica, germany, portugal, and taiwan. treatment rates were less than 25% for women and less than 20% for men in nepal, indonesia, and some countries in sub-saharan africa and oceania. control rates were below 10% for women and men in these countries and for men in some countries in north africa, central and south asia, and eastern europe. treatment and control rates have improved in most countries since 1990, but we found little change in most countries in sub-saharan africa and oceania. improvements were largest in high-income countries, central europe, and some upper-middle-income and recently high-income countries including costa rica, taiwan, kazakhstan, south africa, brazil, chile, turkey, and iran. interpretation improvements in the detection, treatment, and control of hypertension have varied substantially across countries, with some middle-income countries now outperforming most high-income nations. the dual approach of reducing hypertension prevalence through primary prevention and enhancing its treatment and control is achievable not only in high-income countries but also in low-income and middle-income settings. funding who.",0
"background a frequent problem in computational modeling is the interconversion of chemical structures between different formats. while standard interchange formats exist (for example, chemical markup language) and de facto standards have arisen (for example, smiles format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0d versus 3d, for example), and competition between software along with a lack of vendor-neutral formats. results we discuss, for the first time, open babel, an open-source chemical toolbox that speaks the many languages of chemical data. open babel version 2.3 interconverts over 110 formats. the need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. we detail the implementation of open babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. conclusions open babel presents a solution to the proliferation of multiple chemical file formats. in addition, it provides a variety of useful utilities from conformer searching and 2d depiction, to filtering, batch conversion, and substructure and similarity searching. for developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. it is freely available under an open-source license from",0
"background the efficacy of interleukin-6 receptor antagonists in critically ill patients with coronavirus disease 2019 (covid-19) is unclear. methods we evaluated tocilizumab and sarilumab in an ongoing international, multifactorial, adaptive platform trial. adult patients with covid-19, within 24 hours after starting organ support in the intensive care unit (icu), were randomly assigned to receive tocilizumab (8 mg per kilogram of body weight), sarilumab (400 mg), or standard care (control). the primary outcome was respiratory and cardiovascular organ support-free days, on an ordinal scale combining in-hospital death (assigned a value of -1) and days free of organ support to day 21. the trial uses a bayesian statistical model with predefined criteria for superiority, efficacy, equivalence, or futility. an odds ratio greater than 1 represented improved survival, more organ support-free days, or both. results both tocilizumab and sarilumab met the predefined criteria for efficacy. at that time, 353 patients had been assigned to tocilizumab, 48 to sarilumab, and 402 to control. the median number of organ support-free days was 10 (interquartile range, -1 to 16) in the tocilizumab group, 11 (interquartile range, 0 to 16) in the sarilumab group, and 0 (interquartile range, -1 to 15) in the control group. the median adjusted cumulative odds ratios were 1.64 (95% credible interval, 1.25 to 2.14) for tocilizumab and 1.76 (95% credible interval, 1.17 to 2.91) for sarilumab as compared with control, yielding posterior probabilities of superiority to control of more than 99.9% and of 99.5%, respectively. an analysis of 90-day survival showed improved survival in the pooled interleukin-6 receptor antagonist groups, yielding a hazard ratio for the comparison with the control group of 1.61 (95% credible interval, 1.25 to 2.08) and a posterior probability of superiority of more than 99.9%. all secondary analyses supported efficacy of these interleukin-6 receptor antagonists. conclusions in critically ill patients with covid-19 receiving organ support in icus, treatment with the interleukin-6 receptor antagonists tocilizumab and sarilumab improved outcomes, including survival. (remap-cap clinicaltrials.gov number, nct02735707.).",0
"motivation a sizeable fraction of eukaryotic proteins contain intrinsically disordered regions (idrs), which act in unfolded states or by undergoing transitions between structured and unstructured conformations. over time, sequence-based classifiers of idrs have become fairly accurate and currently a major challenge is linking idrs to their biological roles from the molecular to the systems level. results we describe disopred3, which extends its predecessor with new modules to predict idrs and protein-binding sites within them. based on recent casp evaluation results, disopred3 can be regarded as state of the art in the identification of idrs, and our self-assessment shows that it significantly improves over disopred2 because its predictions are more specific across the whole board and more sensitive to idrs longer than 20 amino acids. predicted idrs are annotated as protein binding through a novel svm based classifier, which uses profile data and additional sequence-derived features. based on benchmarking experiments with full cross-validation, we show that this predictor generates precise assignments of disordered protein binding regions and that it compares well with other publicly available tools.",0
"solid organ transplant recipients may be at a high risk for sars-cov-2 infection and poor associated outcomes. we herein report our initial experience with solid organ transplant recipients with sars-cov-2 infection at two centers during the first 3 weeks of the outbreak in new york city. baseline characteristics, clinical presentation, antiviral and immunosuppressive management were compared between patients with mild/moderate and severe disease (defined as icu admission, intubation or death). ninety patients were analyzed with a median age of 57 years. forty-six were kidney recipients, 17 lung, 13 liver, 9 heart, and 5 dual-organ transplants. the most common presenting symptoms were fever (70%), cough (59%), and dyspnea (43%). twenty-two (24%) had mild, 41 (46%) moderate, and 27 (30%) severe disease. among the 68 hospitalized patients, 12% required non-rebreather and 35% required intubation. 91% received hydroxychloroquine, 66% azithromycin, 3% remdesivir, 21% tocilizumab, and 24% bolus steroids. sixteen patients died (18% overall, 24% of hospitalized, 52% of icu) and 37 (54%) were discharged. in this initial cohort, transplant recipients with covid-19 appear to have more severe outcomes, although testing limitations likely led to undercounting of mild/asymptomatic cases. as this outbreak unfolds, covid-19 has the potential to severely impact solid organ transplant recipients.",0
"recent data indicate that the cell surface glycoprotein cd5 functions as a negative regulator of t cell receptor (tcr)-mediated signaling. in this study, we examined the regulation of cd5 surface expression during normal thymocyte ontogeny and in mice with developmental and/or signal transduction defects. the results demonstrate that low level expression of cd5 on cd4(-)cd8(-) (double negative, dn) thymocytes is independent of tcr gene rearrangement; however, induction of cd5 surface expression on dn thymocytes requires engagement of the pre-tcr and is dependent upon the activity of p56(lck). at the cd4(+)cd8(+) (double positive, dp) stage, intermediate cd5 levels are maintained by low affinity tcr-major histocompatibility complex (mhc) interactions, and cd5 surface expression is proportional to both the surface level and signaling capacity of the tcr. high-level expression of cd5 on dp and cd4(+) or cd8(+) (single positive, sp) thymocytes is induced by engagement of the alpha/beta-tcr by (positively or negatively) selecting ligands. significantly, cd5 surface expression on mature sp thymocytes and t cells was found to directly parallel the avidity or signaling intensity of the positively selecting tcr-mhc-ligand interaction. taken together, these observations suggest that the developmental regulation of cd5 in response to tcr signaling and tcr avidity represents a mechanism for fine tuning of the tcr signaling response.",0
"pbr28 binds the 18-kda translocator protein (tspo) and is used in positron emission tomography (pet) to detect microglial activation. however, quantitative interpretations of signal are confounded by large interindividual variability in binding affinity, which displays a trimodal distribution compatible with a codominant genetic trait. here, we tested directly for an underlying genetic mechanism to explain this. binding affinity of pbr28 was measured in platelets isolated from 41 human subjects and tested for association with polymorphisms in tspo and genes encoding other proteins in the tspo complex. complete agreement was observed between the tspo ala147thr genotype and pbr28 binding affinity phenotype (p value=3.1 × 10(-13)). the tspo ala147thr polymorphism predicts pbr28 binding affinity in human platelets. as all second-generation tspo pet radioligands tested hitherto display a trimodal distribution in binding affinity analogous to pbr28, testing for this polymorphism may allow quantitative interpretation of tspo pet studies with these radioligands.",0
"bone morphogenetic proteins (bmps) are a group of signaling molecules that belongs to the transforming growth factor-β (tgf-β) superfamily of proteins. initially discovered for their ability to induce bone formation, bmps are now known to play crucial roles in all organ systems. bmps are important in embryogenesis and development, and also in maintenance of adult tissue homeostasis. mouse knockout models of various components of the bmp signaling pathway result in embryonic lethality or marked defects, highlighting the essential functions of bmps. in this review, we first outline the basic aspects of bmp signaling and then focus on genetically manipulated mouse knockout models that have helped elucidate the role of bmps in development. a significant portion of this review is devoted to the prominent human pathologies associated with dysregulated bmp signaling.",0
"dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. knowledge of the contemporary distribution of their shared vectors, aedes aegypti and aedes albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. we show aedes distributions to be the widest ever recorded; now extensive in all continents, including north america and europe. these maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. it is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses.",0
"background to date, few data on paediatric covid-19 have been published, and most reports originate from china. this study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection across europe to inform physicians and health-care service planning during the ongoing pandemic. methods this multicentre cohort study involved 82 participating health-care institutions across 25 european countries, using a well established research network-the paediatric tuberculosis network european trials group (ptbnet)-that mainly comprises paediatric infectious diseases specialists and paediatric pulmonologists. we included all individuals aged 18 years or younger with confirmed sars-cov-2 infection, detected at any anatomical site by rt-pcr, between april 1 and april 24, 2020, during the initial peak of the european covid-19 pandemic. we explored factors associated with need for intensive care unit (icu) admission and initiation of drug treatment for covid-19 using univariable analysis, and applied multivariable logistic regression with backwards stepwise analysis to further explore those factors significantly associated with icu admission. findings 582 individuals with pcr-confirmed sars-cov-2 infection were included, with a median age of 5·0 years (iqr 0·5-12·0) and a sex ratio of 1·15 males per female. 145 (25%) had pre-existing medical conditions. 363 (62%) individuals were admitted to hospital. 48 (8%) individuals required icu admission, 25 (4%) mechanical ventilation (median duration 7 days, iqr 2-11, range 1-34), 19 (3%) inotropic support, and one ( interpretation covid-19 is generally a mild disease in children, including infants. however, a small proportion develop severe disease requiring icu admission and prolonged ventilation, although fatal outcome is overall rare. the data also reflect the current uncertainties regarding specific treatment options, highlighting that additional data on antiviral and immunomodulatory drugs are urgently needed. funding ptbnet is supported by deutsche gesellschaft für internationale zusammenarbeit.",0
"neuroinflammation is associated with neurodegenerative diseases, such as alzheimer's disease, parkinson's disease, and amyotrophic lateral sclerosis. microglia and astrocytes are key regulators of inflammatory responses in the central nervous system. the activation of microglia and astrocytes is heterogeneous and traditionally categorized as neurotoxic (m1-phenotype microglia and a1-phenotype astrocytes) or neuroprotective (m2-phenotype microglia and a2-phenotype astrocytes). however, this dichotomized classification may not reflect the various phenotypes of microglia and astrocytes. the relationship between these activated glial cells is also very complicated, and the phenotypic distribution can change, based on the progression of neurodegenerative diseases. a better understanding of the roles of microglia and astrocytes in neurodegenerative diseases is essential for developing effective therapies. in this review, we discuss the roles of inflammatory response in neurodegenerative diseases, focusing on the contributions of microglia and astrocytes and their relationship. in addition, we discuss biomarkers to measure neuroinflammation and studies on therapeutic drugs that can modulate neuroinflammation.",0
"free radicals and oxidants play a dual role as both toxic and beneficial compounds, since they can be either harmful or helpful to the body. they are produced either from normal cell metabolisms in situ or from external sources (pollution, cigarette smoke, radiation, medication). when an overload of free radicals cannot gradually be destroyed, their accumulation in the body generates a phenomenon called oxidative stress. this process plays a major part in the development of chronic and degenerative illness such as cancer, autoimmune disorders, aging, cataract, rheumatoid arthritis, cardiovascular and neurodegenerative diseases. the human body has several mechanisms to counteract oxidative stress by producing antioxidants, which are either naturally produced in situ, or externally supplied through foods and/or supplements. this mini-review deals with the taxonomy, the mechanisms of formation and catabolism of the free radicals, it examines their beneficial and deleterious effects on cellular activities, it highlights the potential role of the antioxidants in preventing and repairing damages caused by oxidative stress, and it discusses the antioxidant supplementation in health maintenance.",0
"background there is widespread interest in measuring healthcare provider attitudes about issues relevant to patient safety (often called safety climate or safety culture). here we report the psychometric properties, establish benchmarking data, and discuss emerging areas of research with the university of texas safety attitudes questionnaire. methods six cross-sectional surveys of health care providers (n = 10,843) in 203 clinical areas (including critical care units, operating rooms, inpatient settings, and ambulatory clinics) in three countries (usa, uk, new zealand). multilevel factor analyses yielded results at the clinical area level and the respondent nested within clinical area level. we report scale reliability, floor/ceiling effects, item factor loadings, inter-factor correlations, and percentage of respondents who agree with each item and scale. results a six factor model of provider attitudes fit to the data at both the clinical area and respondent nested within clinical area levels. the factors were: teamwork climate, safety climate, perceptions of management, job satisfaction, working conditions, and stress recognition. scale reliability was 0.9. provider attitudes varied greatly both within and among organizations. results are presented to allow benchmarking among organizations and emerging research is discussed. conclusion the safety attitudes questionnaire demonstrated good psychometric properties. healthcare organizations can use the survey to measure caregiver attitudes about six patient safety-related domains, to compare themselves with other organizations, to prompt interventions to improve safety attitudes and to measure the effectiveness of these interventions.",0
"the potential for genome-wide association studies to relate phenotypes to specific genetic variation is greatly increased when data can be combined or compared across multiple studies. to facilitate replication and validation across studies, rti international (research triangle park, north carolina) and the national human genome research institute (bethesda, maryland) are collaborating on the consensus measures for phenotypes and exposures (phenx) project. the goal of phenx is to identify 15 high-priority, well-established, and broadly applicable measures for each of 21 research domains. phenx measures are selected by working groups of domain experts using a consensus process that includes input from the scientific community. the selected measures are then made freely available to the scientific community via the phenx toolkit. thus, the phenx toolkit provides the research community with a core set of high-quality, well-established, low-burden measures intended for use in large-scale genomic studies. phenx measures will have the most impact when included at the experimental design stage. the phenx toolkit also includes links to standards and resources in an effort to facilitate data harmonization to legacy data. broad acceptance and use of phenx measures will promote cross-study comparisons to increase statistical power for identifying and replicating variants associated with complex diseases and with gene-gene and gene-environment interactions.",0
"background diverse datasets, including genomic, transcriptomic, proteomic and metabolomic data, are becoming readily available for specific organisms. there is currently a need to integrate these datasets within an in silico modeling framework. constraint-based models of escherichia coli k-12 mg1655 have been developed and used to study the bacterium's metabolism and phenotypic behavior. the most comprehensive e. coli model to date (e. coli ije660a gsm) accounts for 660 genes and includes 627 unique biochemical reactions. results an expanded genome-scale metabolic model of e. coli (ijr904 gsm/gpr) has been reconstructed which includes 904 genes and 931 unique biochemical reactions. the reactions in the expanded model are both elementally and charge balanced. network gap analysis led to putative assignments for 55 open reading frames (orfs). gene to protein to reaction associations (gpr) are now directly included in the model. comparisons between predictions made by ijr904 and ije660a models show that they are generally similar but differ under certain circumstances. analysis of genome-scale proton balancing shows how the flux of protons into and out of the medium is important for maximizing cellular growth. conclusions e. coli ijr904 has improved capabilities over ije660a. ijr904 is a more complete and chemically accurate description of e. coli metabolism than ije660a. perhaps most importantly, ijr904 can be used for analyzing and integrating the diverse datasets. ijr904 will help to outline the genotype-phenotype relationship for e. coli k-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously.",0
"environmental factors such as tobacco smoking may have long-lasting effects on dna methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. we conducted an epigenome-wide association study (ewas) comparing current, former and never smokers from 1793 participants of the population-based kora f4 panel, with replication in 479 participants from the kora f3 panel, carried out by the 450k beadchip with genomic dna obtained from whole blood. we observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31e-08 to 2.54e-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. in addition, methylation-specific protein binding patterns were observed for cg05575921 within ahrr, which had the highest level of detectable changes in dna methylation associated with tobacco smoking (-24.40% methylation; p = 2.54e-182), suggesting a regulatory role for gene expression. the results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the dna methylation state of never smokers.",0
"when integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. this is especially relevant to proteins for which lipids have both structural and regulatory roles. here we demonstrate the power of combining electron cryo-microscopy with lipid nanodisc technology to ascertain the structure of the rat trpv1 ion channel in a native bilayer environment. using this approach, we determined the locations of annular and regulatory lipids and showed that specific phospholipid interactions enhance binding of a spider toxin to trpv1 through formation of a tripartite complex. furthermore, phosphatidylinositol lipids occupy the binding site for capsaicin and other vanilloid ligands, suggesting a mechanism whereby chemical or thermal stimuli elicit channel activation by promoting the release of bioactive lipids from a critical allosteric regulatory site.",0
"background vegetables and fruit provide a significant part of human nutrition, as they are important sources of nutrients, dietary fibre, and phytochemicals. however, it is uncertain whether the risk of certain chronic diseases can be reduced by increased consumption of vegetables or fruit by the general public, and what strength of evidence has to be allocated to such an association. methods therefore, a comprehensive analysis of the studies available in the literature and the respective study results has been performed and evaluated regarding obesity, type 2 diabetes mellitus, hypertension, coronary heart disease (chd), stroke, cancer, chronic inflammatory bowel disease (ibd), rheumatoid arthritis (ra), chronic obstructive pulmonary disease (copd), asthma, osteoporosis, eye diseases, and dementia. for judgement, the strength of evidence for a risk association, the level of evidence, and the number of studies were considered, the quality of the studies and their estimated relevance based on study design and size. results for hypertension, chd, and stroke, there is convincing evidence that increasing the consumption of vegetables and fruit reduces the risk of disease. there is probable evidence that the risk of cancer in general is inversely associated with the consumption of vegetables and fruit. in addition, there is possible evidence that an increased consumption of vegetables and fruit may prevent body weight gain. as overweight is the most important risk factor for type 2 diabetes mellitus, an increased consumption of vegetables and fruit therefore might indirectly reduces the incidence of type 2 diabetes mellitus. independent of overweight, there is probable evidence that there is no influence of increased consumption on the risk of type 2 diabetes mellitus. there is possible evidence that increasing the consumption of vegetables and fruit lowers the risk of certain eye diseases, dementia and the risk of osteoporosis. likewise, current data on asthma, copd, and ra indicate that an increase in vegetable and fruit consumption may contribute to the prevention of these diseases. for ibd, glaucoma, and diabetic retinopathy, there was insufficient evidence regarding an association with the consumption of vegetables and fruit. conclusions this critical review on the associations between the intake of vegetables and fruit and the risk of several chronic diseases shows that a high daily intake of these foods promotes health. therefore, from a scientific point of view, national campaigns to increase vegetable and fruit consumption are justified. the promotion of vegetable and fruit consumption by nutrition and health policies is a preferable strategy to decrease the burden of several chronic diseases in western societies.",0
"the development of glomerulonephritis in nzb/w mice is closely related to the formation of antinuclear, particularly anti-dna, antibodies. the developing inflammatory glomerular lesions are characterized by the deposition of gammag- and beta(1c)-globulins plus dna and possibly other nuclear antigens, presumably as complexes, in a granular to lumpy pattern along the capillary walls and in the mesangia. elution studies revealed the gammag-globulin in the glomeruli to be largely gammag(2a)-type antibody to soluble nuclear antigens. enhancement of the antinuclear antibody response by active immunization of young nzb/w mice with dna-methylated bsa hastens the development and increases the severity of the glomerulonephritis. similarly, injections of soluble dna into nzb/w mice with circulating anti-dna antibodies but with as yet little nephritis causes rapid progression of nephritis.",0
"the emergence of immune checkpoint inhibitors (icis), mainly including anti-programmed cell death protein 1/programmed cell death ligand 1 (pd-1/pd-l1) and anti-cytotoxic t lymphocyte-associated antigen-4 (ctla-4) monoclonal antibodies (mabs), has shaped therapeutic landscape of some type of cancers. despite some icis have manifested compelling clinical effectiveness in certain tumor types, the majority of patients still showed de novo or adaptive resistance. at present, the overall efficiency of immune checkpoint therapy remains unsatisfactory. exploring additional immune checkpoint molecules is a hot research topic. recent studies have identified several new immune checkpoint targets, like lymphocyte activation gene-3 (lag-3), t cell immunoglobulin and mucin-domain containing-3 (tim-3), t cell immunoglobulin and itim domain (tigit), v-domain ig suppressor of t cell activation (vista), and so on. the investigations about these molecules have generated promising results in preclinical studies and/or clinical trials. in this review, we discussed the structure and expression of these newly-characterized immune checkpoints molecules, presented the current progress and understanding of them. moreover, we summarized the clinical data pertinent to these recent immune checkpoint molecules as well as their application prospects.",0
"formation of senile plaques containing the beta-amyloid peptide (a beta) derived from the amyloid precursor protein (app) is an invariant feature of alzheimer's disease (ad). app is cleaved either by beta-secretase or by alpha-secretase to initiate amyloidogenic (release of a beta) or nonamyloidogenic processing of app, respectively. a key to understanding ad is to unravel how access of these enzymes to app is regulated. here, we demonstrate that lipid rafts are critically involved in regulating a beta generation. reducing cholesterol levels in n2a cells decreased a beta production. app and the beta-site app cleavage enzyme (bace1) could be induced to copatch at the plasma membrane upon cross-linking with antibodies and to segregate away from nonraft markers. antibody cross-linking dramatically increased production of a beta in a cholesterol-dependent manner. a beta generation was dependent on endocytosis and was reduced after expression of the dynamin mutant k44a and the rab5 gtpase-activating protein, rn-tre. this inhibition could be overcome by antibody cross-linking. these observations suggest the existence of two app pools. although app inside raft clusters seems to be cleaved by beta-secretase, app outside rafts undergoes cleavage by alpha-secretase. thus, access of alpha- and beta-secretase to app, and therefore a beta generation, may be determined by dynamic interactions of app with lipid rafts.",0
"pancreatic cancer is the eighth major form of cancer-related death worldwide, causing 227 000 deaths annually. type-ii diabetes is widely considered to be associated with pancreatic cancer, but whether this represents a causal or consequential association is unclear. we conducted a meta-analysis to examine this association. a computer-based literature search from 1966 to 2005 yielded 17 case-control and 19 cohort or nested case-control studies with information on 9220 individuals with pancreatic cancer. the age and sex-adjusted odds ratio (or) for pancreatic cancer associated with type-ii diabetes was obtained from each study. the combined summary odds ratio was 1.82 (95% confidence interval (95% ci) 1.66-1.89), with evidence of heterogeneity across the studies (p=0.002 for case-control and p=0.05 for cohort studies) that was explained, in part, by higher risks being reported by smaller studies and studies that reported before 2000. individuals in whom diabetes had only recently been diagnosed ( or =5 years (or 2.1 vs 1.5; p=0.005). these results support a modest causal association between type-ii diabetes and pancreatic cancer.",0
"we have developed tm-align, a new algorithm to identify the best structural alignment between protein pairs that combines the tm-score rotation matrix and dynamic programming (dp). the algorithm is approximately 4 times faster than ce and 20 times faster than dali and sal. on average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. tm-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the protein data bank (pdb) with a sequence identity cutoff <95%: 1996 distinct folds are found when a tm-score threshold of 0.5 is used. we also use tm-align to match the models predicted by tasser for solved non-homologous proteins in pdb. for both folded and misfolded models, tm-align can almost always find close structural analogs, with an average root mean square deviation, rmsd, of 3 a and 87% alignment coverage. nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the pdb. this correlation could be used to assist in model selection in blind protein structure predictions. the tm-align program is freely downloadable at",0
"anxiety disorders, including panic disorder with or without agoraphobia, generalized anxiety disorder, social anxiety disorder, specific phobias, and separation anxiety disorder, are the most prevalent mental disorders and are associated with immense health care costs and a high burden of disease. according to large population-based surveys, up to 33.7% of the population are affected by an anxiety disorder during their lifetime. substantial underrecognition and undertreatment of these disorders have been demonstrated. there is no evidence that the prevalence rates of anxiety disorders have changed in the past years. in cross-cultural comparisons, prevalence rates are highly variable. it is more likely that this heterogeneity is due to differences in methodology than to cultural influences. anxiety disorders follow a chronic course; however, there is a natural decrease in prevalence rates with older age. anxiety disorders are highly comorbid with other anxiety disorders and other mental disorders.",0
"cell-matrix interactions have major effects upon phenotypic features such as gene regulation, cytoskeletal structure, differentiation, and aspects of cell growth control. programmed cell death (apoptosis) is crucial for maintaining appropriate cell number and tissue organization. it was therefore of interest to determine whether cell-matrix interactions affect apoptosis. the present report demonstrates that apoptosis was induced by disruption of the interactions between normal epithelial cells and extracellular matrix. we have termed this phenomenon ""anoikis."" overexpression of bcl-2 protected cells against anoikis. cellular sensitivity to anoikis was apparently regulated: (a) anoikis did not occur in normal fibroblasts; (b) it was abrogated in epithelial cells by transformation with v-ha-ras, v-src, or treatment with phorbol ester; (c) sensitivity to anoikis was conferred upon ht1080 cells or v-ha-ras-transformed mdck cells by reverse-transformation with adenovirus e1a; (d) anoikis in mdck cells was alleviated by the motility factor, scatter factor. the results suggest that the circumvention of anoikis accompanies the acquisition of anchorage independence or cell motility.",0
"a critical event during programmed cell death (pcd) appears to be the acquisition of plasma membrane (pm) changes that allows phagocytes to recognize and engulf these cells before they rupture. the majority of pcd seen in higher organisms exhibits strikingly similar morphological features, and this form of pcd has been termed apoptosis. the nature of the pm changes that occur on apoptotic cells remains poorly defined. in this study, we have used a phosphatidylserine (ps)-binding protein (annexin v) as a specific probe to detect redistribution of this phospholipid, which is normally confined to the inner pm leaflet, during apoptosis. here we show that ps externalization is an early and widespread event during apoptosis of a variety of murine and human cell types, regardless of the initiating stimulus, and precedes several other events normally associated with this mode of cell death. we also report that, under conditions in which the morphological features of apoptosis were prevented (macromolecular synthesis inhibition, overexpression of bcl-2 or abl), the appearance of ps on the external leaflet of the pm was similarly prevented. these data are compatible with the notion that activation of an inside-outside ps translocase is an early and widespread event during apoptosis.",0
"using myo-inositol labeled skeletal muscle, the effect of protein kinase c (pkc) activation on phosphoinositide turnover in high k~(+) stimulated and resting skeletal muscles of frogs was investigated. it is indicated that a negative feedback regulation of phosphoinositide hydrolysis is presnet in high k~(+) stimulated skeletal muscle, probably via activation of pkc. the differential effect suggests that some critical processe(s) in the activation of phosphoinositide turnover may be depressed by pkc.",0
"three-dimensional (3d) in vitro models have been used in cancer research as an intermediate model between in vitro cancer cell line cultures and in vivo tumor. spherical cancer models represent major 3d in vitro models that have been described over the past 4 decades. these models have gained popularity in cancer stem cell research using tumorospheres. thus, it is crucial to define and clarify the different spherical cancer models thus far described. here, we focus on in vitro multicellular spheres used in cancer research. all these spherelike structures are characterized by their well-rounded shape, the presence of cancer cells, and their capacity to be maintained as free-floating cultures. we propose a rational classification of the four most commonly used spherical cancer models in cancer research based on culture methods for obtaining them and on subsequent differences in sphere biology: the multicellular tumor spheroid model, first described in the early 70s and obtained by culture of cancer cell lines under nonadherent conditions; tumorospheres, a model of cancer stem cell expansion established in a serum-free medium supplemented with growth factors; tissue-derived tumor spheres and organotypic multicellular spheroids, obtained by tumor tissue mechanical dissociation and cutting. in addition, we describe their applications to and interest in cancer research; in particular, we describe their contribution to chemoresistance, radioresistance, tumorigenicity, and invasion and migration studies. although these models share a common 3d conformation, each displays its own intrinsic properties. therefore, the most relevant spherical cancer model must be carefully selected, as a function of the study aim and cancer type.",0
"metal halides perovskites, such as hybrid organic-inorganic ch3nh3pbi3, are newcomer optoelectronic materials that have attracted enormous attention as solution-deposited absorbing layers in solar cells with power conversion efficiencies reaching 20%. herein we demonstrate a new avenue for halide perovskites by designing highly luminescent perovskite-based colloidal quantum dot materials. we have synthesized monodisperse colloidal nanocubes (4-15 nm edge lengths) of fully inorganic cesium lead halide perovskites (cspbx3, x = cl, br, and i or mixed halide systems cl/br and br/i) using inexpensive commercial precursors. through compositional modulations and quantum size-effects, the bandgap energies and emission spectra are readily tunable over the entire visible spectral region of 410-700 nm. the photoluminescence of cspbx3 nanocrystals is characterized by narrow emission line-widths of 12-42 nm, wide color gamut covering up to 140% of the ntsc color standard, high quantum yields of up to 90%, and radiative lifetimes in the range of 1-29 ns. the compelling combination of enhanced optical properties and chemical robustness makes cspbx3 nanocrystals appealing for optoelectronic applications, particularly for blue and green spectral regions (410-530 nm), where typical metal chalcogenide-based quantum dots suffer from photodegradation.",0
"the field of synthetic biology promises to revolutionize biotechnology through the design of organisms with novel phenotypes useful for medicine, agriculture and industry. however, a limiting factor is the ability of current methods to assemble complex dna molecules encoding multiple genetic elements in various predefined arrangements. we present here a hierarchical modular cloning system that allows the creation at will and with high efficiency of any eukaryotic multigene construct, starting from libraries of defined and validated basic modules containing regulatory and coding sequences. this system is based on the ability of type iis restriction enzymes to assemble multiple dna fragments in a defined linear order. we constructed a 33 kb dna molecule containing 11 transcription units made from 44 individual basic modules in only three successive cloning steps. this modular cloning (moclo) system can be readily automated and will be extremely useful for applications such as gene stacking and metabolic engineering.",0
"loss of histotypic organization of epithelial cells is a common feature in normal development as well as in the invasion of carcinomas. here we show that the v-src oncogene is a potent effector of epithelial differentiation and invasiveness. mdck epithelial cells transformed with a temperature-sensitive mutant of v-src exhibit a strictly epithelial phenotype at the nonpermissive temperature for pp60v-src activity (40.5 degrees c) but rapidly loose cell-to-cell contacts and acquire a fibroblast-like morphology after culture at the permissive temperature (35 degrees c). furthermore, the invasiveness of the cells into collagen gels or into chick heart fragments was increased at the permissive temperature. the profound effects of v-src on intercellular adhesion were not linked to changes in the levels of expression of the epithelial cell adhesion molecule e-cadherin. rather, we observed an increase in tyrosine phosphorylation of e-cadherin and, in particular, of the associated protein beta-catenin. these results suggest a mechanism by which v-src counteracts junctional assembly and thereby promotes invasiveness and dedifferentiation of epithelial cells through phosphorylation of the e-cadherin/catenin complex.",0
"several major invasive bacterial pathogens are encapsulated. expression of a polysaccharide capsule is essential for survival in the blood, and thus for virulence, but also is a target for host antibodies and the basis for effective vaccines. encapsulated species typically exhibit antigenic variation and express one of a number of immunochemically distinct capsular polysaccharides that define serotypes. we provide the sequences of the capsular biosynthetic genes of all 90 serotypes of streptococcus pneumoniae and relate these to the known polysaccharide structures and patterns of immunological reactivity of typing sera, thereby providing the most complete understanding of the genetics and origins of bacterial polysaccharide diversity, laying the foundations for molecular serotyping. this is the first time, to our knowledge, that a complete repertoire of capsular biosynthetic genes has been available, enabling a holistic analysis of a bacterial polysaccharide biosynthesis system. remarkably, the total size of alternative coding dna at this one locus exceeds 1.8 mbp, almost equivalent to the entire s. pneumoniae chromosomal complement.",0
"ncbi's conserved domain database (cdd) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. an archive of pre-computed domain annotation is maintained for proteins tracked by ncbi's entrez database, and live search services are offered as well. cdd curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. cdd also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using sparcle: subfamily protein architecture labeling engine. cdd can be accessed at",0
"in recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-em) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. however, achieving this goal with smaller particles of lower symmetry remains challenging. using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (thon rings visible to ∼3 å). using this approach, we determined a 3.3-å-resolution structure of an ∼700-kda protein with d7 symmetry, the thermoplasma acidophilum 20s proteasome, showing clear side-chain density. our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-em to a broad range of protein samples.",0
"the use of nanotechnology in medicine and more specifically drug delivery is set to spread rapidly. currently many substances are under investigation for drug delivery and more specifically for cancer therapy. interestingly pharmaceutical sciences are using nanoparticles to reduce toxicity and side effects of drugs and up to recently did not realize that carrier systems themselves may impose risks to the patient. the kind of hazards that are introduced by using nanoparticles for drug delivery are beyond that posed by conventional hazards imposed by chemicals in classical delivery matrices. for nanoparticles the knowledge on particle toxicity as obtained in inhalation toxicity shows the way how to investigate the potential hazards of nanoparticles. the toxicology of particulate matter differs from toxicology of substances as the composing chemical(s) may or may not be soluble in biological matrices, thus influencing greatly the potential exposure of various internal organs. this may vary from a rather high local exposure in the lungs and a low or neglectable exposure for other organ systems after inhalation. however, absorbed species may also influence the potential toxicity of the inhaled particles. for nanoparticles the situation is different as their size opens the potential for crossing the various biological barriers within the body. from a positive viewpoint, especially the potential to cross the blood brain barrier may open new ways for drug delivery into the brain. in addition, the nanosize also allows for access into the cell and various cellular compartments including the nucleus. a multitude of substances are currently under investigation for the preparation of nanoparticles for drug delivery, varying from biological substances like albumin, gelatine and phospholipids for liposomes, and more substances of a chemical nature like various polymers and solid metal containing nanoparticles. it is obvious that the potential interaction with tissues and cells, and the potential toxicity, greatly depends on the actual composition of the nanoparticle formulation. this paper provides an overview on some of the currently used systems for drug delivery. besides the potential beneficial use also attention is drawn to the questions how we should proceed with the safety evaluation of the nanoparticle formulations for drug delivery. for such testing the lessons learned from particle toxicity as applied in inhalation toxicology may be of use. although for pharmaceutical use the current requirements seem to be adequate to detect most of the adverse effects of nanoparticle formulations, it can not be expected that all aspects of nanoparticle toxicology will be detected. so, probably additional more specific testing would be needed.",0
"genomic structural variants (svs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. despite progress in sv characterization, the nucleotide resolution architecture of most svs remains unknown. we constructed a map of unbalanced svs (that is, copy number variants) based on whole genome dna sequencing data from 185 human genomes, integrating evidence from complementary sv discovery approaches with extensive experimental validations. our map encompassed 22,025 deletions and 6,000 additional svs, including insertions and tandem duplications. most svs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. we examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. furthermore, we observed differences in the size spectra of svs originating from distinct formation mechanisms, and constructed a map of sv hotspots formed by common mechanisms. our analytical framework and sv map serves as a resource for sequencing-based association studies.",0
"interest in prebiotics and their potential application for human and animal health is flourishing. here, the effects of galacto-oligosaccharide (gos) on the performance and health of chickens, with the potential for human applications was evaluated. following a review of the poultry meat industry from economic and animal welfare standpoints, the outcomes of gos feedstuff on the gut health and immune function of broiler chickens were evaluated. first, the effects of in-feed inclusion of gos on broiler chicken performance and intestinal immune status were assessed in the absence of intestinal challenge. the gos diet was shown to modulate the juvenile gut microbiome and innate immunity to increase weight gain and reduce the cumulative feed conversion ratio. gos-associated activation of mucosal th17 immune response at a young age was accompanied with a shift in the microbiota composition promoting one member of autochthonous lactobacillus spp at the expense of another. the cecal abundance of immuno-modulatory l. johnsonii was shown to increase on the gos diet and positively correlate with bird growth weight at 35 days of age. the impact of gos was further assessed upon bacterial challenge with the foodborne pathogen ... (continues)",0
"after culture in interleukin (il)-2, natural killer (nk) cells acquire an increased capability of mediating non-major histocompatibility complex (mhc)-restricted tumor cell lysis. this may reflect, at least in part, the de novo expression by nk cells of triggering receptors involved in cytolysis. in this study we identified a novel 44-kd surface molecule (nkp44) that is absent in freshly isolated peripheral blood lymphocytes but is progressively expressed by all nk cells in vitro after culture in il-2. different from other markers of cell activation such as cd69 or vla.2, nkp44 is absent in activated t lymphocytes or t cell clones. since nkp44 was not detected in any of the other cell lineages analyzed, it appears as the first marker specific for activated human nk cells. monoclonal antibody (mab)-mediated cross-linking of nkp44 in cloned nk cells resulted in strong activation of target cell lysis in a redirected killing assay. this data indicated that nkp44 can mediate triggering of nk cell cytotoxicity. mab-mediated masking of nkp44 resulted in partial inhibition of cytolytic activity against certain (fcgammar-negative) nk-susceptible target cells. this inhibition was greatly increased by the simultaneous masking of p46, another recently identified nk-specific triggering surface molecule. these data strongly suggest that nkp44 functions as a triggering receptor selectively expressed by activated nk cells that, together with p46, may be involved in the process of non-mhc-restricted lysis. finally, we show that p46 and nkp44 are coupled to the intracytoplasmic transduction machinery via the association with cd3zeta or karap/dap12, respectively; these associated molecules are tyrosine phosphorylated upon nk cell stimulation.",0
"brain networks are increasingly understood as one of a large class of information processing systems that share important organizational principles in common, including the property of a modular community structure. a module is topologically defined as a subset of highly inter-connected nodes which are relatively sparsely connected to nodes in other modules. in brain networks, topological modules are often made up of anatomically neighboring and/or functionally related cortical regions, and inter-modular connections tend to be relatively long distance. moreover, brain networks and many other complex systems demonstrate the property of hierarchical modularity, or modularity on several topological scales: within each module there will be a set of sub-modules, and within each sub-module a set of sub-sub-modules, etc. there are several general advantages to modular and hierarchically modular network organization, including greater robustness, adaptivity, and evolvability of network function. in this context, we review some of the mathematical concepts available for quantitative analysis of (hierarchical) modularity in brain networks and we summarize some of the recent work investigating modularity of structural and functional brain networks derived from analysis of human neuroimaging data.",0
"objective to determine whether treatment with agonists of glucagon-like peptide-1 receptor (glp-1r) result in weight loss in overweight or obese patients with or without type 2 diabetes mellitus. design systematic review with meta-analyses. data sources electronic searches (cochrane library, medline, embase, and web of science) and manual searches (up to may 2011). review methods randomised controlled trials of adult participants with a body mass index of 25 or higher; with or without type 2 diabetes mellitus; and who received exenatide twice daily, exenatide once weekly, or liraglutide once daily at clinically relevant doses for at least 20 weeks. control interventions assessed were placebo, oral antidiabetic drugs, or insulin. data extraction three authors independently extracted data. we used random effects models for the primary meta-analyses. we also did subgroup, sensitivity, regression, and sequential analyses to evaluate sources of intertrial heterogeneity, bias, and the robustness of results after adjusting for multiple testing and random errors. results 25 trials were included in the analysis. glp-1r agonist groups achieved a greater weight loss than control groups (weighted mean difference -2.9 kg, 95% confidence interval -3.6 to -2.2; 21 trials, 6411 participants). we found evidence of intertrial heterogeneity, but no evidence of bias or small study effects in regression analyses. the results were confirmed in sequential analyses. we recorded weight loss in the glp-1r agonist groups for patients without diabetes (-3.2 kg, -4.3 to -2.1; three trials) as well as patients with diabetes (-2.8 kg, -3.4 to -2.3; 18 trials). in the overall analysis, glp-1r agonists had beneficial effects on systolic and diastolic blood pressure, plasma concentrations of cholesterol, and glycaemic control, but did not have a significant effect on plasma concentrations of liver enzymes. glp-1r agonists were associated with nausea, diarrhoea, and vomiting, but not with hypoglycaemia. conclusions the present review provides evidence that treatment with glp-1r agonists leads to weight loss in overweight or obese patients with or without type 2 diabetes mellitus.",0
"cigarette smoking is the leading cause of preventable disease and death in the united states (1). the prevalence of adult cigarette smoking has declined in recent years to 14.0% in 2017 (2). however, an array of new tobacco products, including e-cigarettes, has entered the u.s. market (3). to assess recent national estimates of tobacco product use among u.s. adults aged ≥18 years, cdc, the food and drug administration (fda), and the national cancer institute analyzed data from the 2018 national health interview survey (nhis). in 2018, an estimated 49.1 million u.s. adults (19.7%) reported currently using any tobacco product, including cigarettes (13.7%), cigars (3.9%), e-cigarettes (3.2%), smokeless tobacco (2.4%), and pipes* (1.0%). most tobacco product users (83.8%) reported using combustible products (cigarettes, cigars, or pipes), and 18.8% reported using two or more tobacco products. the prevalence of any current tobacco product use was higher in males; adults aged ≤65 years; non-hispanic american indian/alaska natives; those with a general educational development certificate (ged); those with an annual household income <$35,000; lesbian, gay, or bisexual adults; uninsured adults; those with a disability or limitation; and those with serious psychological distress. the prevalence of e-cigarette and smokeless tobacco use increased during 2017-2018. during 2009-2018, there were significant increases in all three cigarette cessation indicators (quit attempts, recent cessation, and quit ratio). implementing comprehensive population-based interventions in coordination with regulation of the manufacturing, marketing, and distribution of all tobacco products can reduce tobacco-related disease and death in the united states (1,4).",0
"advances in next generation technologies have driven the costs of dna sequencing down to the point that genotyping-by-sequencing (gbs) is now feasible for high diversity, large genome species. here, we report a procedure for constructing gbs libraries based on reducing genome complexity with restriction enzymes (res). this approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. by using methylation-sensitive res, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. this tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. the gbs procedure is demonstrated with maize (ibm) and barley (oregon wolfe barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. an advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. in such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. future application of gbs to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.",0
"we present an easy-to-use integrated software suite, dia-nn, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (dia) proteomics experiments. dia-nn improves the identification and quantification performance in conventional dia proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.",0
"the interaction between an electronically excited photocatalyst and an organic molecule can result in the genertion of a diverse array of reactive intermediates that can be manipulated in a variety of ways to result in synthetically useful bond constructions. this review summarizes dual-catalyst strategies that have been applied to synthetic photochemistry. mechanistically distinct modes of photocatalysis are discussed, including photoinduced electron transfer, hydrogen atom transfer, and energy transfer. we focus upon the cooperative interactions of photocatalysts with redox mediators, lewis and brønsted acids, organocatalysts, enzymes, and transition metal complexes.",0
"there is growing interest regarding the role of the right inferior frontal gyrus (rifg) during a particular form of executive control referred to as response inhibition. however, tasks used to examine neural activity at the point of response inhibition have rarely controlled for the potentially confounding effects of attentional demand. in particular, it is unclear whether the rifg is specifically involved in inhibitory control, or is involved more generally in the detection of salient or task relevant cues. the current fmri study sought to clarify the role of the rifg in executive control by holding the stimulus conditions of one of the most popular response inhibition tasks-the stop signal task-constant, whilst varying the response that was required on reception of the stop signal cue. our results reveal that the rifg is recruited when important cues are detected, regardless of whether that detection is followed by the inhibition of a motor response, the generation of a motor response, or no external response at all.",0
"background administration of convalescent plasma, serum, or hyperimmune immunoglobulin may be of clinical benefit for treatment of severe acute respiratory infections (saris) of viral etiology. we conducted a systematic review and exploratory meta-analysis to assess the overall evidence. methods healthcare databases and sources of grey literature were searched in july 2013. all records were screened against the protocol eligibility criteria, using a 3-stage process. data extraction and risk of bias assessments were undertaken. results we identified 32 studies of sars coronavirus infection and severe influenza. narrative analyses revealed consistent evidence for a reduction in mortality, especially when convalescent plasma is administered early after symptom onset. exploratory post hoc meta-analysis showed a statistically significant reduction in the pooled odds of mortality following treatment, compared with placebo or no therapy (odds ratio, 0.25; 95% confidence interval, .14-.45; i(2) = 0%). studies were commonly of low or very low quality, lacked control groups, and at moderate or high risk of bias. sources of clinical and methodological heterogeneity were identified. conclusions convalescent plasma may reduce mortality and appears safe. this therapy should be studied within the context of a well-designed clinical trial or other formal evaluation, including for treatment of middle east respiratory syndrome coronavirus cov infection.",0
"background the global burden of disease study 2010 (gbd 2010), estimated that a substantial proportion of the world's disease burden came from mental, neurological and substance use disorders. in this paper, we used gbd 2010 data to investigate time, year, region and age specific trends in burden due to mental, neurological and substance use disorders. method for each disorder, prevalence data were assembled from systematic literature reviews. dismod-mr, a bayesian meta-regression tool, was used to model prevalence by country, region, age, sex and year. prevalence data were combined with disability weights derived from survey data to estimate years lived with disability (ylds). years lost to premature mortality (ylls) were estimated by multiplying deaths occurring as a result of a given disorder by the reference standard life expectancy at the age death occurred. disability-adjusted life years (dalys) were computed as the sum of ylds and ylls. results in 2010, mental, neurological and substance use disorders accounted for 10.4% of global dalys, 2.3% of global ylls and, 28.5% of global ylds, making them the leading cause of ylds. mental disorders accounted for the largest proportion of dalys (56.7%), followed by neurological disorders (28.6%) and substance use disorders (14.7%). dalys peaked in early adulthood for mental and substance use disorders but were more consistent across age for neurological disorders. females accounted for more dalys in all mental and neurological disorders, except for mental disorders occurring in childhood, schizophrenia, substance use disorders, parkinson's disease and epilepsy where males accounted for more dalys. overall dalys were highest in eastern europe/central asia and lowest in east asia/the pacific. conclusion mental, neurological and substance use disorders contribute to a significant proportion of disease burden. health systems can respond by implementing established, cost effective interventions, or by supporting the research necessary to develop better prevention and treatment options.",0
"disruptions to brain development associated with shortened gestation place individuals at risk for the development of behavioral and psychological dysfunction throughout the lifespan. the purpose of the present study was to determine if the benefit for brain development conferred by increased gestational length exists on a continuum across the gestational age spectrum among healthy children with a stable neonatal course. neurodevelopment was evaluated with structural magnetic resonance imaging in 100 healthy right-handed 6- to 10-year-old children born between 28 and 41 gestational weeks with a stable neonatal course. data indicate that a longer gestational period confers an advantage for neurodevelopment. longer duration of gestation was associated with region-specific increases in gray matter density. further, the benefit of longer gestation for brain development was present even when only children born full term were considered. these findings demonstrate that even modest decreases in the duration of gestation can exert profound and lasting effects on neurodevelopment for both term and preterm infants and may contribute to long-term risk for health and disease.",0
"copy number variants (cnvs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. to address this we undertook a large, direct genome-wide study of association between cnvs and eight common human diseases. using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic cnvs, including an estimated approximately 50% of all common cnvs larger than 500 base pairs. we identified several biological artefacts that lead to false-positive associations, including systematic cnv differences between dnas derived from blood and cell lines. association testing and follow-up replication analyses confirmed three loci where cnvs were associated with disease-irgm for crohn's disease, hla for crohn's disease, rheumatoid arthritis and type 1 diabetes, and tspan8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (snp)-based studies, reflecting our observation that most common cnvs that are well-typed on our array are well tagged by snps and so have been indirectly explored through snp studies. we conclude that common cnvs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.",0
"the adipocyte-derived secretory factor adiponectin promotes insulin sensitivity, decreases inflammation and promotes cell survival. no unifying mechanism has yet explained how adiponectin can exert such a variety of beneficial systemic effects. here, we show that adiponectin potently stimulates a ceramidase activity associated with its two receptors, adipor1 and adipor2, and enhances ceramide catabolism and formation of its antiapoptotic metabolite--sphingosine-1-phosphate (s1p)--independently of amp-dependent kinase (ampk). using models of inducible apoptosis in pancreatic beta cells and cardiomyocytes, we show that transgenic overproduction of adiponectin decreases caspase-8-mediated death, whereas genetic ablation of adiponectin enhances apoptosis in vivo through a sphingolipid-mediated pathway. ceramidase activity is impaired in cells lacking both adiponectin receptor isoforms, leading to elevated ceramide levels and enhanced susceptibility to palmitate-induced cell death. combined, our observations suggest a unifying mechanism of action for the beneficial systemic effects exerted by adiponectin, with sphingolipid metabolism as its core upstream signaling component.",0
"metformin is a widely-used drug that results in clear benefits in relation to glucose metabolism and diabetes-related complications. the mechanisms underlying these benefits are complex and still not fully understood. physiologically, metformin has been shown to reduce hepatic glucose production, yet not all of its effects can be explained by this mechanism and there is increasing evidence of a key role for the gut. at the molecular level the findings vary depending on the doses of metformin used and duration of treatment, with clear differences between acute and chronic administration. metformin has been shown to act via both amp-activated protein kinase (ampk)-dependent and ampk-independent mechanisms; by inhibition of mitochondrial respiration but also perhaps by inhibition of mitochondrial glycerophosphate dehydrogenase, and a mechanism involving the lysosome. in the last 10 years, we have moved from a simple picture, that metformin improves glycaemia by acting on the liver via ampk activation, to a much more complex picture reflecting its multiple modes of action. more work is required to truly understand how this drug works in its target population: individuals with type 2 diabetes.",0
"the outbreak of coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome-coronavirus 2 (sars-cov-2) has now become a pandemic, but there is currently very little understanding of the antigenicity of the virus. we therefore determined the crystal structure of cr3022, a neutralizing antibody previously isolated from a convalescent sars patient, in complex with the receptor binding domain (rbd) of the sars-cov-2 spike (s) protein at 3.1-angstrom resolution. cr3022 targets a highly conserved epitope, distal from the receptor binding site, that enables cross-reactive binding between sars-cov-2 and sars-cov. structural modeling further demonstrates that the binding epitope can only be accessed by cr3022 when at least two rbds on the trimeric s protein are in the ""up"" conformation and slightly rotated. these results provide molecular insights into antibody recognition of sars-cov-2.",0
"localization of signaling complexes to specific microdomains coordinates signal transduction at the plasma membrane. using immunogold electron microscopy of plasma membrane sheets coupled with spatial point pattern analysis, we have visualized morphologically featureless microdomains, including lipid rafts, in situ and at high resolution. we find that an inner-plasma membrane lipid raft marker displays cholesterol-dependent clustering in microdomains with a mean diameter of 44 nm that occupy 35% of the cell surface. cross-linking an outer-leaflet raft protein results in the redistribution of inner leaflet rafts, but they retain their modular structure. analysis of ras microlocalization shows that inactive h-ras is distributed between lipid rafts and a cholesterol-independent microdomain. conversely, activated h-ras and k-ras reside predominantly in nonoverlapping, cholesterol-independent microdomains. galectin-1 stabilizes the association of activated h-ras with these nonraft microdomains, whereas k-ras clustering is supported by farnesylation, but not geranylgeranylation. these results illustrate that the inner plasma membrane comprises a complex mosaic of discrete microdomains. differential spatial localization within this framework can likely account for the distinct signal outputs from the highly homologous ras proteins.",0
"the novel coronavirus 2019 (covid-2019), which first appeared in wuhan city of china in december 2019, spread rapidly around the world and became a pandemic. it has caused a devastating effect on both daily lives, public health, and the global economy. it is critical to detect the positive cases as early as possible so as to prevent the further spread of this epidemic and to quickly treat affected patients. the need for auxiliary diagnostic tools has increased as there are no accurate automated toolkits available. recent findings obtained using radiology imaging techniques suggest that such images contain salient information about the covid-19 virus. application of advanced artificial intelligence (ai) techniques coupled with radiological imaging can be helpful for the accurate detection of this disease, and can also be assistive to overcome the problem of a lack of specialized physicians in remote villages. in this study, a new model for automatic covid-19 detection using raw chest x-ray images is presented. the proposed model is developed to provide accurate diagnostics for binary classification (covid vs. no-findings) and multi-class classification (covid vs. no-findings vs. pneumonia). our model produced a classification accuracy of 98.08% for binary classes and 87.02% for multi-class cases. the darknet model was used in our study as a classifier for the you only look once (yolo) real time object detection system. we implemented 17 convolutional layers and introduced different filtering on each layer. our model (available at ( can be employed to assist radiologists in validating their initial screening, and can also be employed via cloud to immediately screen patients.",0
"background to explore and describe the current literature surrounding bacterial/fungal coinfection in patients with coronavirus infection. methods medline, embase, and web of science were searched using broad-based search criteria relating to coronavirus and bacterial coinfection. articles presenting clinical data for patients with coronavirus infection (defined as sars-1, mers, sars-cov-2, and other coronavirus) and bacterial/fungal coinfection reported in english, mandarin, or italian were included. data describing bacterial/fungal coinfections, treatments, and outcomes were extracted. secondary analysis of studies reporting antimicrobial prescribing in sars-cov-2 even in absence of coinfection was performed. results 1007 abstracts were identified. eighteen full texts reporting bacterial/fungal coinfection were included. most studies did not identify or report bacterial/fungal coinfection (85/140; 61%). nine of 18 (50%) studies reported on covid-19, 5/18 (28%) on sars-1, 1/18 (6%) on mers, and 3/18 (17%) on other coronaviruses. for covid-19, 62/806 (8%) patients were reported as experiencing bacterial/fungal coinfection during hospital admission. secondary analysis demonstrated wide use of broad-spectrum antibacterials, despite a paucity of evidence for bacterial coinfection. on secondary analysis, 1450/2010 (72%) of patients reported received antimicrobial therapy. no antimicrobial stewardship interventions were described. for non-covid-19 cases, bacterial/fungal coinfection was reported in 89/815 (11%) of patients. broad-spectrum antibiotic use was reported. conclusions despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus-associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal coinfection. generation of prospective evidence to support development of antimicrobial policy and appropriate stewardship interventions specific for the covid-19 pandemic is urgently required.",0
"background access is central to the performance of health care systems around the world. however, access to health care remains a complex notion as exemplified in the variety of interpretations of the concept across authors. the aim of this paper is to suggest a conceptualisation of access to health care describing broad dimensions and determinants that integrate demand and supply-side-factors and enabling the operationalisation of access to health care all along the process of obtaining care and benefiting from the services. methods a synthesis of the published literature on the conceptualisation of access has been performed. the most cited frameworks served as a basis to develop a revised conceptual framework. results here, we view access as the opportunity to identify healthcare needs, to seek healthcare services, to reach, to obtain or use health care services, and to actually have a need for services fulfilled. we conceptualise five dimensions of accessibility: 1) approachability; 2) acceptability; 3) availability and accommodation; 4) affordability; 5) appropriateness. in this framework, five corresponding abilities of populations interact with the dimensions of accessibility to generate access. five corollary dimensions of abilities include: 1) ability to perceive; 2) ability to seek; 3) ability to reach; 4) ability to pay; and 5) ability to engage. conclusions this paper explains the comprehensiveness and dynamic nature of this conceptualisation of access to care and identifies relevant determinants that can have an impact on access from a multilevel perspective where factors related to health systems, institutions, organisations and providers are considered with factors at the individual, household, community, and population levels.",0
"background the coronavirus disease 2019 (covid-19) is spreading rapidly, bringing pressure and challenges to nursing staff. objective to explore the psychology of nurses caring for covid-19 patients. methods using a phenomenological approach, we enrolled 20 nurses who provided care for covid-19 patients in the first affiliated hospital of henan university of science and technology from january 20, to february 10, 2020. the interviews were conducted face-to-face or by telephone and were analysed by colaizzi's 7-step method. results the psychological experience of nurses caring for covid-19 patients can be summarized into 4 themes. first, negative emotions present in early stage consisting of fatigue, discomfort, and helplessness was caused by high-intensity work, fear and anxiety, and concern for patients and family members. second, self-coping styles included psychological and life adjustment, altruistic acts, team support, and rational cognition. third, we found growth under pressure, which included increased affection and gratefulness, development of professional responsibility, and self-reflection. finally, we showed that positive emotions occurred simultaneously with negative emotions. conclusions during an epidemic outbreak, positive and negative emotions of the front-line nurses interweaved and coexisted. in the early stage, negative emotions were dominant and positive emotions appeared gradually. self-coping styles and psychological growth played an important role in maintaining mental health of nurses.",0
"objective the purpose of this study was to perform a systematic review to assess the short-, middle- and long-term consequences of sarcopenia. methods prospective studies assessing the consequences of sarcopenia were searched across different electronic databases (medline, embase, ebm reviews, cochrane database of systematic reviews, ebm reviews acp journal club, ebm reviews dare and amed). only studies that used the definition of the european working group on sarcopenia in older people to diagnose sarcopenia were included. study selection and data extraction were performed by two independent reviewers. for outcomes reported by three or more studies, a meta-analysis was performed. the study results are expressed as odds ratios (or) with 95% ci. results of the 772 references identified through the database search, 17 were included in this systematic review. the number of participants in the included studies ranged from 99 to 6658, and the duration of follow-up varied from 3 months to 9.8 years. eleven out of 12 studies assessed the impact of sarcopenia on mortality. the results showed a higher rate of mortality among sarcopenic subjects (pooled or of 3.596 (95% ci 2.96-4.37)). the effect was higher in people aged 79 years or older compared with younger subjects (p = 0.02). sarcopenia is also associated with functional decline (pooled or of 6 studies 3.03 (95% ci 1.80-5.12)), a higher rate of falls (2/2 studies found a significant association) and a higher incidence of hospitalizations (1/1 study). the impact of sarcopenia on the incidence of fractures and the length of hospital stay was less clear (only 1/2 studies showed an association for both outcomes). conclusion sarcopenia is associated with several harmful outcomes, making this geriatric syndrome a real public health burden.",0
"because of its ability to efficiently inhibit in vitro cytokine production by activated macrophages, we hypothesized that interleukin (il) 10 might be of particular interest in preventing endotoxin-induced toxicity. we therefore examined the effects of il-10 administration before lipopolysaccharide (lps) challenge in mice. a marked reduction in the amounts of lps-induced tumor necrosis factor (tnf) release in the circulation was observed after il-10 pretreatment at doses at low as 10 u. il-10 also efficiently prevented the hypothermia generated by the injection of 100 micrograms lps. finally, pretreatment with a single injection of 1,000 u il-10 completely prevented the mortality consecutive to the challenge with 500 micrograms lps, a dose that was lethal in 50% of the control mice. we conclude that il-10 inhibits in vivo tnf secretion and protects against the lethality of endotoxin in a murine model of septic shock.",0
"to study the factors that determine whether cd4+ t cells produce interleukin 4 (il-4) or interferon gamma (ifn-gamma) upon stimulation we used a system allowing naive t cells to be primed in vitro by specific antigen. dense cd4+ t cells were purified from mice that expressed transgenes encoding a t cell receptor specific for pigeon cytochrome c peptide 88-104 in association with i-ek. these t cells produced very limited amounts of il-4 and ifn-gamma upon immediate challenge with 88-104 and antigen-presenting cells (apc). however, after an initial ""priming"" culture in which they were incubated for 4 d in the presence of 88-104, apc, and 1,000 u/ml il-4, the t cells acquired the capacity to produce substantial amounts of il-4 upon rechallenge but made very little ifn-gamma. cells primed in the absence of il-4 produced ifn-gamma upon rechallenge but virtually no il-4. the inhibitory effect of il-4 on ifn-gamma production did not appear to be mediated by the induction of il-10 production since il-10 addition to initial cultures did not suppress priming for ifn-gamma production, nor did anti-il-10 block the inhibitory effect of il-4. ifn-gamma itself did not increase priming for ifn-gamma production, nor did anti-ifn-gamma reduce such priming. ifn-gamma did, however, diminish priming for il-4 production when limiting amounts of il-4 (100 u/ml) were used in the initial culture. the dominant effect of il-4 in determining the lymphokine-producing phenotype of primed cells was observed with dendritic cells (dc), activated b cells, and i-ek-transfected fibroblasts as apc. however, the different apc did vary in their potency, with dc being superior to activated b cells, which were superior to transfected fibroblasts.",0
"background the isolation of symptomatic cases and tracing of contacts has been used as an early covid-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. to maintain control of infection while also reducing disruption to populations, there is a need to understand what combination of measures-including novel digital tracing approaches and less intensive physical distancing-might be required to reduce transmission. we aimed to estimate the reduction in transmission under different control measures across settings and how many contacts would be quarantined per day in different strategies for a given level of symptomatic case incidence. methods for this mathematical modelling study, we used a model of individual-level transmission stratified by setting (household, work, school, or other) based on bbc pandemic data from 40 162 uk participants. we simulated the effect of a range of different testing, isolation, tracing, and physical distancing scenarios. under optimistic but plausible assumptions, we estimated reduction in the effective reproduction number and the number of contacts that would be newly quarantined each day under different strategies. results we estimated that combined isolation and tracing strategies would reduce transmission more than mass testing or self-isolation alone: mean transmission reduction of 2% for mass random testing of 5% of the population each week, 29% for self-isolation alone of symptomatic cases within the household, 35% for self-isolation alone outside the household, 37% for self-isolation plus household quarantine, 64% for self-isolation and household quarantine with the addition of manual contact tracing of all contacts, 57% with the addition of manual tracing of acquaintances only, and 47% with the addition of app-based tracing only. if limits were placed on gatherings outside of home, school, or work, then manual contact tracing of acquaintances alone could have an effect on transmission reduction similar to that of detailed contact tracing. in a scenario where 1000 new symptomatic cases that met the definition to trigger contact tracing occurred per day, we estimated that, in most contact tracing strategies, 15 000-41 000 contacts would be newly quarantined each day. interpretation consistent with previous modelling studies and country-specific covid-19 responses to date, our analysis estimated that a high proportion of cases would need to self-isolate and a high proportion of their contacts to be successfully traced to ensure an effective reproduction number lower than 1 in the absence of other measures. if combined with moderate physical distancing measures, self-isolation and contact tracing would be more likely to achieve control of severe acute respiratory syndrome coronavirus 2 transmission. funding wellcome trust, uk engineering and physical sciences research council, european commission, royal society, medical research council.",0
"we present cisgenome, a software system for analyzing genome-wide chromatin immunoprecipitation (chip) data. cisgenome is designed to meet all basic needs of chip data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. in addition to implementing previously published chip-microarray (chip-chip) analysis methods, the software contains statistical methods designed specifically for chlp sequencing (chip-seq) data obtained by coupling chip with massively parallel sequencing. the modular design of cisgenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. a built-in browser allows visualization of array images, signals, gene structure, conservation, and dna sequence and motif information. we demonstrate the use of these tools by a comparative analysis of chip-chip and chip-seq data for the transcription factor nrsf/rest, a study of chip-seq analysis with or without a negative control sample, and an analysis of a new motif in nanog- and sox2-binding regions.",0
"background high-throughput dna sequencing technologies are generating vast amounts of data. fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. results we present a multithreaded program suite called angsd. this program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. conclusions the open source c/c++ program angsd is available at . the program is tested and validated on gnu/linux systems. the program facilitates multiple input formats including bam and imputed beagle genotype probability files. the program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.",0
"introduction the nominal group technique (ngt) and delphi technique are consensus methods used in research that is directed at problem-solving, idea-generation, or determining priorities. while consensus methods are commonly used in health services literature, few studies in pharmacy practice use these methods. this paper provides an overview of the ngt and delphi technique, including the steps involved and the types of research questions best suited to each method, with examples from the pharmacy literature. methodology the ngt entails face-to-face discussion in small groups, and provides a prompt result for researchers. the classic ngt involves four key stages: silent generation, round robin, clarification and voting (ranking). variations have occurred in relation to generating ideas, and how 'consensus' is obtained from participants. the delphi technique uses a multistage self-completed questionnaire with individual feedback, to determine consensus from a larger group of 'experts.' questionnaires have been mailed, or more recently, e-mailed to participants. when to use the ngt has been used to explore consumer and stakeholder views, while the delphi technique is commonly used to develop guidelines with health professionals. method choice is influenced by various factors, including the research question, the perception of consensus required, and associated practicalities such as time and geography. limitations the ngt requires participants to personally attend a meeting. this may prove difficult to organise and geography may limit attendance. the delphi technique can take weeks or months to conclude, especially if multiple rounds are required, and may be complex for lay people to complete.",0
"the purpose of this study was to use serial imaging to gain insight into the sequence of pathologic events in alzheimer's disease, and the clinical features associated with this sequence. we measured change in amyloid deposition over time using serial (11)c pittsburgh compound b (pib) positron emission tomography and progression of neurodegeneration using serial structural magnetic resonance imaging. we studied 21 healthy cognitively normal subjects, 32 with amnestic mild cognitive impairment and 8 with alzheimer's disease. subjects were drawn from two sources--ongoing longitudinal registries at mayo clinic, and the alzheimer's disease neuroimaging initiative (adni). all subjects underwent clinical assessments, mri and pib studies at two time points, approximately one year apart. pib retention was quantified in global cortical to cerebellar ratio units and brain atrophy in units of cm(3) by measuring ventricular expansion. the annual change in global pib retention did not differ by clinical group (p = 0.90), and although small (median 0.042 ratio units/year overall) was greater than zero among all subjects (p < 0.001). ventricular expansion rates differed by clinical group (p < 0.001) and increased in the following order: cognitively normal (1.3 cm(3)/year) < amnestic mild cognitive impairment (2.5 cm(3)/year) < alzheimer's disease (7.7 cm(3)/year). among all subjects there was no correlation between pib change and concurrent change on cdr-sb (r = -0.01, p = 0.97) but some evidence of a weak correlation with mmse (r =-0.22, p = 0.09). in contrast, greater rates of ventricular expansion were clearly correlated with worsening concurrent change on cdr-sb (r = 0.42, p < 0.01) and mmse (r =-0.52, p < 0.01). our data are consistent with a model of typical late onset alzheimer's disease that has two main features: (i) dissociation between the rate of amyloid deposition and the rate of neurodegeneration late in life, with amyloid deposition proceeding at a constant slow rate while neurodegeneration accelerates and (ii) clinical symptoms are coupled to neurodegeneration not amyloid deposition. significant plaque deposition occurs prior to clinical decline. the presence of brain amyloidosis alone is not sufficient to produce cognitive decline, rather, the neurodegenerative component of alzheimer's disease pathology is the direct substrate of cognitive impairment and the rate of cognitive decline is driven by the rate of neurodegeneration. neurodegeneration (atrophy on mri) both precedes and parallels cognitive decline. this model implies a complimentary role for mri and pib imaging in alzheimer's disease, with each reflecting one of the major pathologies, amyloid dysmetabolism and neurodegeneration.",0
"the rate at which nonsynonymous single nucleotide polymorphisms (nssnps) are being identified in the human genome is increasing dramatically owing to advances in whole-genome/whole-exome sequencing technologies. automated methods capable of accurately and reliably distinguishing between pathogenic and functionally neutral nssnps are therefore assuming ever-increasing importance. here, we describe the functional analysis through hidden markov models (fathmm) software and server: a species-independent method with optional species-specific weightings for the prediction of the functional effects of protein missense variants. using a model weighted for human mutations, we obtained performance accuracies that outperformed traditional prediction methods (i.e., sift, polyphen, and panther) on two separate benchmarks. furthermore, in one benchmark, we achieve performance accuracies that outperform current state-of-the-art prediction methods (i.e., snps&go and mutpred). we demonstrate that fathmm can be efficiently applied to high-throughput/large-scale human and nonhuman genome sequencing projects with the added benefit of phenotypic outcome associations. to illustrate this, we evaluated nssnps in wheat (triticum spp.) to identify some of the important genetic variants responsible for the phenotypic differences introduced by intense selection during domestication. a web-based implementation of fathmm, including a high-throughput batch facility and a downloadable standalone package, is available at",0
"a methodology designed to eliminate mitotic inhibitor action and involving use of pretested fetal calf serum and careful ph and temperature control has been described by which cells from normal human and animal tissue can be maintained in active growth for long periods in vitro without development of aneuploidy. by means of this procedure, it is possible reliably to establish cell cultures from minute skin biopsies which can be taken from any individual. clones of mammalian cells with chromosomal markers have been isolated by this means from x-irradiated non-irradiated cell cultures. application of these techniques to chromosome delineation in large numbers of human subjects; determination of chromosomal sex in patients; spontaneuos and induced genetic changes in somatic mammalian cells in vivo and in vitro; comparison of metabolic differences between normal and cancerous cells and other problems have been indicated.",0
"tumor cells harbor genetic alterations that promote a continuous and elevated production of reactive oxygen species. whereas such oxidative stress conditions would be harmful to normal cells, they facilitate tumor growth in multiple ways by causing dna damage and genomic instability, and ultimately, by reprogramming cancer cell metabolism. this review outlines the metabolic-dependent mechanisms that tumors engage in when faced with oxidative stress conditions that are critical for cancer progression by producing redox cofactors. in particular, we describe how the mitochondria has a key role in regulating the interplay between redox homeostasis and metabolism within tumor cells. last, we will discuss the potential therapeutic use of agents that directly or indirectly block metabolism.",0
"background knee osteoarthritis (oa) is a major cause of disability in the elderly, however, there are few studies to estimate the global prevalence, incidence, and risk factors of knee oa. methods for this study, we searched pubmed, embase and scopus from inception to april 4, 2020, without language restriction. we identified eligible studies with information on the prevalence or incidence of knee oa in population-based observational studies and extracted data from published reports. we did random-effects meta-analysis to generate estimates. this study was registered with prospero (crd42020181035). findings out of 9570 records identified, 88 studies with 10,081,952 participants were eligible for this study. the pooled global prevalence of knee oa was 16⋅0% (95% ci, 14⋅3%-17⋅8%) in individuals aged 15 and over and was 22⋅9% (95% ci, 19⋅8%-26⋅1%) in individuals aged 40 and over. correspondingly, there are around 654⋅1 (95% ci, 565⋅6-745⋅6) million individuals (40 years and older) with knee oa in 2020 worldwide. the pooled global incidence of knee oa was 203 per 10,000 person-years (95% ci, 106-331) in individuals aged 20 and over. correspondingly, there are around annual 86⋅7 (95% ci, 45⋅3-141⋅3) million individuals (20 years and older) with incident knee oa in 2020 worldwide. the prevalence and incidence varied substantially between individual countries and increased with age. the ratios of prevalence and incidence in females and males were 1⋅69 (95% ci, 1⋅59-1⋅80, p p interpretation our study provides the global prevalence (16⋅0% ) and incidence (203 per 10,000 person-years ) of knee oa. these findings can be used to better assess the global health burden of knee oa. further prospective cohort studies are warranted to identify modifiable risk factors for providing effectively preventive strategies in the early stages of the disease. funding this work was supported by grants from the national natural science foundation of china (nos. 81772384 and 81572174).",0
"wound healing is a complex, highly regulated process that is critical in maintaining the barrier function of skin. with numerous disease processes, the cascade of events involved in wound healing can be affected, resulting in chronic, non-healing wounds that subject the patient to significant discomfort and distress while draining the medical system of an enormous amount of resources. the healing of a superficial wound requires many factors to work in concert, and wound dressings and treatments have evolved considerably to address possible barriers to wound healing, ranging from infection to hypoxia. even optimally, wound tissue never reaches its pre-injured strength and multiple aberrant healing states can result in chronic non-healing wounds. this article will review wound healing physiology and discuss current approaches for treating a wound.",0
"breast cancer is the second leading cause of cancer deaths among women. the development of breast cancer is a multi-step process involving multiple cell types, and its prevention remains challenging in the world. early diagnosis of breast cancer is one of the best approaches to prevent this disease. in some developed countries, the 5-year relative survival rate of breast cancer patients is above 80% due to early prevention. in the recent decade, great progress has been made in the understanding of breast cancer as well as in the development of preventative methods. the pathogenesis and tumor drug-resistant mechanisms are revealed by discovering breast cancer stem cells, and many genes are found related to breast cancer. currently, people have more drug options for the chemoprevention of breast cancer, while biological prevention has been recently developed to improve patients' quality of life. in this review, we will summarize key studies of pathogenesis, related genes, risk factors and preventative methods on breast cancer over the past years. these findings represent a small step in the long fight against breast cancer.",0
"the spread of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks. a global response to prepare health systems worldwide is imperative. although containment measures in china have reduced new cases by more than 90%, this reduction is not the case elsewhere, and italy has been particularly affected. there is now grave concern regarding the italian national health system's capacity to effectively respond to the needs of patients who are infected and require intensive care for sars-cov-2 pneumonia. the percentage of patients in intensive care reported daily in italy between march 1 and march 11, 2020, has consistently been between 9% and 11% of patients who are actively infected. the number of patients infected since feb 21 in italy closely follows an exponential trend. if this trend continues for 1 more week, there will be 30 000 infected patients. intensive care units will then be at maximum capacity; up to 4000 hospital beds will be needed by mid-april, 2020. our analysis might help political leaders and health authorities to allocate enough resources, including personnel, beds, and intensive care facilities, to manage the situation in the next few days and weeks. if the italian outbreak follows a similar trend as in hubei province, china, the number of newly infected patients could start to decrease within 3-4 days, departing from the exponential trend. however, this cannot currently be predicted because of differences between social distancing measures and the capacity to quickly build dedicated facilities in china.",0
"digital pcr enables the absolute quantitation of nucleic acids in a sample. the lack of scalable and practical technologies for digital pcr implementation has hampered the widespread adoption of this inherently powerful technique. here we describe a high-throughput droplet digital pcr (ddpcr) system that enables processing of ~2 million pcr reactions using conventional taqman assays with a 96-well plate workflow. three applications demonstrate that the massive partitioning afforded by our ddpcr system provides orders of magnitude more precision and sensitivity than real-time pcr. first, we show the accurate measurement of germline copy number variation. second, for rare alleles, we show sensitive detection of mutant dna in a 100,000-fold excess of wildtype background. third, we demonstrate absolute quantitation of circulating fetal and maternal dna from cell-free plasma. we anticipate this ddpcr system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.",0
"background large-scale and contemporary population-based studies of heart failure incidence are needed to inform resource planning and research prioritisation but current evidence is scarce. we aimed to assess temporal trends in incidence and prevalence of heart failure in a large general population cohort from the uk, between 2002 and 2014. methods for this population-based study, we used linked primary and secondary electronic health records of 4 million individuals from the clinical practice research datalink (cprd), a cohort that is representative of the uk population in terms of age and sex. eligible patients were aged 16 years and older, had contributed data between jan 1, 2002, and dec 31, 2014, had an acceptable record according to cprd quality control, were approved for cprd and hospital episodes statistics linkage, and were registered with their general practice for at least 12 months. for patients with incident heart failure, we extracted the most recent measurement of baseline characteristics (within 2 years of diagnosis) from electronic health records, as well as information about comorbidities, socioeconomic status, ethnicity, and region. we calculated standardised rates by applying direct age and sex standardisation to the 2013 european standard population, and we inferred crude rates by applying year-specific, age-specific, and sex-specific incidence to uk census mid-year population estimates. we assumed no heart failure for patients aged 15 years or younger and report total incidence and prevalence for all ages (>0 years). findings from 2002 to 2014, heart failure incidence (standardised by age and sex) decreased, similarly for men and women, by 7% (from 358 to 332 per 100 000 person-years; adjusted incidence ratio 0·93, 95% ci 0·91-0·94). however, the estimated absolute number of individuals with newly diagnosed heart failure in the uk increased by 12% (from 170 727 in 2002 to 190 798 in 2014), largely due to an increase in population size and age. the estimated absolute number of prevalent heart failure cases in the uk increased even more, by 23% (from 750 127 to 920 616). over the study period, patient age and multi-morbidity at first presentation of heart failure increased (mean age 76·5 years to 77·0 years , adjusted difference 0·79 years, 95% ci 0·37-1·20; mean number of comorbidities 3·4 vs 5·4 ; adjusted difference 2·0, 95% ci 1·9-2·1). socioeconomically deprived individuals were more likely to develop heart failure than were affluent individuals (incidence rate ratio 1·61, 95% ci 1·58-1·64), and did so earlier in life than those from the most affluent group (adjusted difference -3·51 years, 95% ci -3·77 to -3·25). from 2002 to 2014, the socioeconomic gradient in age at first presentation with heart failure widened. socioeconomically deprived individuals also had more comorbidities, despite their younger age. interpretation despite a moderate decline in standardised incidence of heart failure, the burden of heart failure in the uk is increasing, and is now similar to the four most common causes of cancer combined. the observed socioeconomic disparities in disease incidence and age at onset within the same nation point to a potentially preventable nature of heart failure that still needs to be tackled. funding british heart foundation and national institute for health research.",0
"in 2011, the national institute on aging and alzheimer's association created separate diagnostic recommendations for the preclinical, mild cognitive impairment, and dementia stages of alzheimer's disease. scientific progress in the interim led to an initiative by the national institute on aging and alzheimer's association to update and unify the 2011 guidelines. this unifying update is labeled a ""research framework"" because its intended use is for observational and interventional research, not routine clinical care. in the national institute on aging and alzheimer's association research framework, alzheimer's disease (ad) is defined by its underlying pathologic processes that can be documented by postmortem examination or in vivo by biomarkers. the diagnosis is not based on the clinical consequences of the disease (i.e., symptoms/signs) in this research framework, which shifts the definition of ad in living people from a syndromal to a biological construct. the research framework focuses on the diagnosis of ad with biomarkers in living persons. biomarkers are grouped into those of β amyloid deposition, pathologic tau, and neurodegeneration . this atn classification system groups different biomarkers (imaging and biofluids) by the pathologic process each measures. the at(n) system is flexible in that new biomarkers can be added to the three existing at(n) groups, and new biomarker groups beyond at(n) can be added when they become available. we focus on ad as a continuum, and cognitive staging may be accomplished using continuous measures. however, we also outline two different categorical cognitive schemes for staging the severity of cognitive impairment: a scheme using three traditional syndromal categories and a six-stage numeric scheme. it is important to stress that this framework seeks to create a common language with which investigators can generate and test hypotheses about the interactions among different pathologic processes (denoted by biomarkers) and cognitive symptoms. we appreciate the concern that this biomarker-based research framework has the potential to be misused. therefore, we emphasize, first, it is premature and inappropriate to use this research framework in general medical practice. second, this research framework should not be used to restrict alternative approaches to hypothesis testing that do not use biomarkers. there will be situations where biomarkers are not available or requiring them would be counterproductive to the specific research goals (discussed in more detail later in the document). thus, biomarker-based research should not be considered a template for all research into age-related cognitive impairment and dementia; rather, it should be applied when it is fit for the purpose of the specific research goals of a study. importantly, this framework should be examined in diverse populations. although it is possible that β-amyloid plaques and neurofibrillary tau deposits are not causal in ad pathogenesis, it is these abnormal protein deposits that define ad as a unique neurodegenerative disease among different disorders that can lead to dementia. we envision that defining ad as a biological construct will enable a more accurate characterization and understanding of the sequence of events that lead to cognitive impairment that is associated with ad, as well as the multifactorial etiology of dementia. this approach also will enable a more precise approach to interventional trials where specific pathways can be targeted in the disease process and in the appropriate people.",0
"paralysis following spinal cord injury, brainstem stroke, amyotrophic lateral sclerosis and other disorders can disconnect the brain from the body, eliminating the ability to perform volitional movements. a neural interface system could restore mobility and independence for people with paralysis by translating neuronal activity directly into control signals for assistive devices. we have previously shown that people with long-standing tetraplegia can use a neural interface system to move and click a computer cursor and to control physical devices. able-bodied monkeys have used a neural interface system to control a robotic arm, but it is unknown whether people with profound upper extremity paralysis or limb loss could use cortical neuronal ensemble signals to direct useful arm actions. here we demonstrate the ability of two people with long-standing tetraplegia to use neural interface system-based control of a robotic arm to perform three-dimensional reach and grasp movements. participants controlled the arm and hand over a broad space without explicit training, using signals decoded from a small, local population of motor cortex (mi) neurons recorded from a 96-channel microelectrode array. one of the study participants, implanted with the sensor 5 years earlier, also used a robotic arm to drink coffee from a bottle. although robotic reach and grasp actions were not as fast or accurate as those of an able-bodied person, our results demonstrate the feasibility for people with tetraplegia, years after injury to the central nervous system, to recreate useful multidimensional control of complex devices directly from a small sample of neural signals.",0
"during embryogenesis, endothelial cells induce organogenesis before the development of circulation. these findings suggest that endothelial cells not only form passive conduits to deliver nutrients and oxygen, but also establish an instructive vascular niche, which through elaboration of paracrine trophogens stimulates organ regeneration, in a manner similar to endothelial-cell-derived angiocrine factors that support haematopoiesis. however, the precise mechanism by which tissue-specific subsets of endothelial cells promote organogenesis in adults is unknown. here we demonstrate that liver sinusoidal endothelial cells (lsecs) constitute a unique population of phenotypically and functionally defined vegfr3(+)cd34(-)vegfr2(+)ve-cadherin(+)factorviii(+)cd45(-) endothelial cells, which through the release of angiocrine trophogens initiate and sustain liver regeneration induced by 70% partial hepatectomy. after partial hepatectomy, residual liver vasculature remains intact without experiencing hypoxia or structural damage, which allows study of physiological liver regeneration. using this model, we show that inducible genetic ablation of vascular endothelial growth factor (vegf)-a receptor-2 (vegfr2) in the lsecs impairs the initial burst of hepatocyte proliferation (days 1-3 after partial hepatectomy) and subsequent reconstitution of the hepatovascular mass (days 4-8 after partial hepatectomy) by inhibiting upregulation of the endothelial-cell-specific transcription factor id1. accordingly, id1-deficient mice also manifest defects throughout liver regeneration, owing to diminished expression of lsec-derived angiocrine factors, including hepatocyte growth factor (hgf) and wnt2. notably, in in vitro co-cultures, vegfr2-id1 activation in lsecs stimulates hepatocyte proliferation. indeed, intrasplenic transplantation of id1(+/+) or id1(-/-) lsecs transduced with wnt2 and hgf (id1(-/-)wnt2(+)hgf(+) lsecs) re-establishes an inductive vascular niche in the liver sinusoids of the id1(-/-) mice, initiating and restoring hepatovascular regeneration. therefore, in the early phases of physiological liver regeneration, vegfr2-id1-mediated inductive angiogenesis in lsecs through release of angiocrine factors wnt2 and hgf provokes hepatic proliferation. subsequently, vegfr2-id1-dependent proliferative angiogenesis reconstitutes liver mass. therapeutic co-transplantation of inductive vegfr2(+)id1(+)wnt2(+)hgf(+) lsecs with hepatocytes provides an effective strategy to achieve durable liver regeneration.",0
"background suboptimal diet is an important preventable risk factor for non-communicable diseases (ncds); however, its impact on the burden of ncds has not been systematically evaluated. this study aimed to evaluate the consumption of major foods and nutrients across 195 countries and to quantify the impact of their suboptimal intake on ncd mortality and morbidity. methods by use of a comparative risk assessment approach, we estimated the proportion of disease-specific burden attributable to each dietary risk factor (also referred to as population attributable fraction) among adults aged 25 years or older. the main inputs to this analysis included the intake of each dietary factor, the effect size of the dietary factor on disease endpoint, and the level of intake associated with the lowest risk of mortality. then, by use of disease-specific population attributable fractions, mortality, and disability-adjusted life-years (dalys), we calculated the number of deaths and dalys attributable to diet for each disease outcome. findings in 2017, 11 million (95% uncertainty interval 10-12) deaths and 255 million (234-274) dalys were attributable to dietary risk factors. high intake of sodium (3 million deaths and 70 million dalys), low intake of whole grains (3 million deaths and 82 million dalys), and low intake of fruits (2 million deaths and 65 million dalys) were the leading dietary risk factors for deaths and dalys globally and in many countries. dietary data were from mixed sources and were not available for all countries, increasing the statistical uncertainty of our estimates. interpretation this study provides a comprehensive picture of the potential impact of suboptimal diet on ncd mortality and morbidity, highlighting the need for improving diet across nations. our findings will inform implementation of evidence-based dietary interventions and provide a platform for evaluation of their impact on human health annually. funding bill & melinda gates foundation.",0
"background the identification and characterisation of differentially methylated regions (dmrs) between phenotypes in the human genome is of prime interest in epigenetics. we present a novel method, dmrcate, that fits replicated methylation measurements from the illumina hm450k beadchip (or 450k array) spatially across the genome using a gaussian kernel. dmrcate identifies and ranks the most differentially methylated regions across the genome based on tunable kernel smoothing of the differential methylation (dm) signal. the method is agnostic to both genomic annotation and local change in the direction of the dm signal, removes the bias incurred from irregularly spaced methylation sites, and assigns significance to each dmr called via comparison to a null model. results we show that, for both simulated and real data, the predictive performance of dmrcate is superior to those of bumphunter and probe lasso, and commensurate with that of comb-p. for the real data, we validate all array-derived dmrs from the candidate methods on a suite of dmrs derived from whole-genome bisulfite sequencing called from the same dna samples, using two separate phenotype comparisons. conclusions the agglomeration of genomically localised individual methylation sites into discrete dmrs is currently best served by a combination of dm-signal smoothing and subsequent threshold specification. the findings also suggest the design of the 450k array shows preference for cpg sites that are more likely to be differentially methylated, but its overall coverage does not adequately reflect the depth and complexity of methylation signatures afforded by sequencing. for the convenience of the research community we have created a user-friendly r software package called dmrcate, downloadable from bioconductor and compatible with existing preprocessing packages, which allows others to apply the same dmr-finding method on 450k array data.",0
"case reports and case series are uncontrolled study designs known for increased risk of bias but have profoundly influenced the medical literature and continue to advance our knowledge. in this guide, we present a framework for appraisal, synthesis and application of evidence derived from case reports and case series. we propose a tool to evaluate the methodological quality of case reports and case series based on the domains of selection, ascertainment, causality and reporting and provide signalling questions to aid evidence-based practitioners and systematic reviewers in their assessment. we suggest using evidence derived from case reports and case series to inform decision-making when no other higher level of evidence is available.",0
"background chronic kidney disease (ckd) is becoming a major public health problem worldwide. this article reviews the published evidence of prevalence of ckd in population-based study samples that used the standardized definition from the kidney disease outcomes quality initiative of the national kidney foundation (k/doqi) practice guideline, and particularly focus on performance of serum-creatinine based equations for gfr estimation. we provide a summary of available data about the burden of ckd in various populations. methods we performed a systematic review of available published data in medline. a combination of various keywords relevant to ckd was used in this research. related data of included studies were extracted in a systematic way. results a total of 26 studies were included in this review. the studies were conducted in different populations, and the number of study participants ranged from 237 to 65181. the median prevalence of ckd was 7.2% in persons aged 30 years or older. in persons aged 64 years or older prevalence of ckd varied from 23.4% to 35.8%. importantly, the prevalence of ckd strongly depended on which estimating equations were used. the modification of diet in renal disease study (mdrd) equation was likely to be preferred in recent epidemiological studies compared to the adjusted cockcroft-gault (cg) equation. conclusion worldwide, ckd is becoming a common disease in the general population. accurately detecting ckd in special groups remains inadequate, particularly among elderly persons, females or other ethnic groups such as asians.",0
"the increasing incidence of obesity and the metabolic syndrome is disturbing. the activation of inflammatory pathways, used normally as host defence, reminds the seriousness of this condition. there is probably more than one cause for activation of inflammation. apparently, metabolic overload evokes stress reactions, such as oxidative, inflammatory, organelle and cell hypertrophy, generating vicious cycles. adipocyte hypertrophy, through physical reasons, facilitates cell rupture, what will evoke an inflammatory reaction. inability of adipose tissue development to engulf incoming fat leads to deposition in other organs, mainly in the liver, with consequences on insulin resistance. the oxidative stress which accompanies feeding, particularly when there is excessive ingestion of fat and/or other macronutrients without concomitant ingestion of antioxidant-rich foods/beverages, may contribute to inflammation attributed to obesity. moreover, data on the interaction of microbiota with food and obesity brought new hypothesis for the obesity/fat diet relationship with inflammation. beyond these, other phenomena, for instance psychological and/or circadian rhythm disturbances, may likewise contribute to oxidative/inflammatory status. the difficulty in the management of obesity/metabolic syndrome is linked to their multifactorial nature where environmental, genetic and psychosocial factors interact through complex networks.",0
"reactive oxygen species (ros) are essential components of the innate immune response against intracellular bacteria and it is thought that professional phagocytes generate ros primarily via the phagosomal nadph oxidase machinery. however, recent studies have suggested that mitochondrial ros (mros) also contribute to mouse macrophage bactericidal activity, although the mechanisms linking innate immune signalling to mitochondria for mros generation remain unclear. here we demonstrate that engagement of a subset of toll-like receptors (tlr1, tlr2 and tlr4) results in the recruitment of mitochondria to macrophage phagosomes and augments mros production. this response involves translocation of a tlr signalling adaptor, tumour necrosis factor receptor-associated factor 6 (traf6), to mitochondria, where it engages the protein ecsit (evolutionarily conserved signalling intermediate in toll pathways), which is implicated in mitochondrial respiratory chain assembly. interaction with traf6 leads to ecsit ubiquitination and enrichment at the mitochondrial periphery, resulting in increased mitochondrial and cellular ros generation. ecsit- and traf6-depleted macrophages have decreased levels of tlr-induced ros and are significantly impaired in their ability to kill intracellular bacteria. additionally, reducing macrophage mros levels by expressing catalase in mitochondria results in defective bacterial killing, confirming the role of mros in bactericidal activity. these results reveal a novel pathway linking innate immune signalling to mitochondria, implicate mros as an important component of antibacterial responses and further establish mitochondria as hubs for innate immune signalling.",0
"isfinder (www-is.biotoul.fr) is a dedicated database for bacterial insertion sequences (iss). it has superseded the stanford reference center. one of its functions is to assign is names and to provide a focal point for a coherent nomenclature. it is also the repository for iss. each new is is indexed together with information such as its dna sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. another objective is to continuously monitor iss to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. the site also contains extensive background information on iss and transposons in general. online tools are gradually being added. at present an online blast facility against the entire bank is available. but additional features will include alignment capability, psiblast and hmm profiles. isfinder also includes a section on bacterial genomes and is involved in annotating the is content of these genomes. finally, this database is currently recommended by several microbiology journals for registration of new is elements before their publication.",0
"the loss of chromosomal integrity from dna double-strand breaks introduced into mammalian cells by ionizing radiation results in the specific phosphorylation of histone h2ax on serine residue 139, yielding a specific modified form named gamma-h2ax. an antibody prepared to the unique region of human gamma-h2ax shows that h2ax homologues are phosphorylated not only in irradiated mammalian cells but also in irradiated cells from other species, including xenopus laevis, drosophila melanogaster, and saccharomyces cerevisiae. the antibody reveals that gamma-h2ax appears as discrete nuclear foci within 1 min after exposure of cells to ionizing radiation. the numbers of these foci are comparable to the numbers of induced dna double-strand breaks. when dna double-strand breaks are introduced into specific partial nuclear volumes of cells by means of a pulsed microbeam laser, gamma-h2ax foci form at these sites. in mitotic cells from cultures exposed to nonlethal amounts of ionizing radiation, gamma-h2ax foci form band-like structures on chromosome arms and on the end of broken arms. these results offer direct visual confirmation that gamma-h2ax forms en masse at chromosomal sites of dna double-strand breaks. the results further suggest the possible existence of units of higher order chromatin structure involved in monitoring dna integrity.",0
"background mitochondrial dysfunction and oxidative stress are pathophysiologic mechanisms implicated in experimental models and genetic forms of parkinson's disease (pd). certain pesticides may affect these mechanisms, but no pesticide has been definitively associated with pd in humans. objectives our goal was to determine whether pesticides that cause mitochondrial dysfunction or oxidative stress are associated with pd or clinical features of parkinsonism in humans. methods we assessed lifetime use of pesticides selected by mechanism in a case-control study nested in the agricultural health study (ahs). pd was diagnosed by movement disorders specialists. controls were a stratified random sample of all ahs participants frequency-matched to cases by age, sex, and state at approximately three controls:one case. results in 110 pd cases and 358 controls, pd was associated with use of a group of pesticides that inhibit mitochondrial complex i including rotenone (or=2.5; 95% ci, 1.3-4.7) and with use of a group of pesticides that cause oxidative stress (or = 2.0; 95% ci, 1.2-3.6), including paraquat (or=2.5; 95% ci, 1.4-4.7). conclusions pd was positively associated with two groups of pesticides defined by mechanisms implicated experimentally-those that impair mitochondrial function and those that increase oxidative stress-supporting a role for these mechanisms in pd pathophysiology.",0
"background the coronavirus disease 2019 (covid-19) outbreak originating in wuhan, hubei province, china, coincided with chunyun , the period of mass migration for the annual spring festival. to contain its spread, china adopted unprecedented nationwide interventions on january 23 2020. these policies included large-scale quarantine, strict controls on travel and extensive monitoring of suspected cases. however, it is unknown whether these policies have had an impact on the epidemic. we sought to show how these control measures impacted the containment of the epidemic. methods we integrated population migration data before and after january 23 and most updated covid-19 epidemiological data into the susceptible-exposed-infectious-removed (seir) model to derive the epidemic curve. we also used an artificial intelligence (ai) approach, trained on the 2003 sars data, to predict the epidemic. results we found that the epidemic of china should peak by late february, showing gradual decline by end of april. a five-day delay in implementation would have increased epidemic size in mainland china three-fold. lifting the hubei quarantine would lead to a second epidemic peak in hubei province in mid-march and extend the epidemic to late april, a result corroborated by the machine learning prediction. conclusions our dynamic seir model was effective in predicting the covid-19 epidemic peaks and sizes. the implementation of control measures on january 23 2020 was indispensable in reducing the eventual covid-19 epidemic size.",0
"the primary aim of this article is to provide an overview of perfluoroalkyl and polyfluoroalkyl substances (pfass) detected in the environment, wildlife, and humans, and recommend clear, specific, and descriptive terminology, names, and acronyms for pfass. the overarching objective is to unify and harmonize communication on pfass by offering terminology for use by the global scientific, regulatory, and industrial communities. a particular emphasis is placed on long-chain perfluoroalkyl acids, substances related to the long-chain perfluoroalkyl acids, and substances intended as alternatives to the use of the long-chain perfluoroalkyl acids or their precursors. first, we define pfass, classify them into various families, and recommend a pragmatic set of common names and acronyms for both the families and their individual members. terminology related to fluorinated polymers is an important aspect of our classification. second, we provide a brief description of the 2 main production processes, electrochemical fluorination and telomerization, used for introducing perfluoroalkyl moieties into organic compounds, and we specify the types of byproducts (isomers and homologues) likely to arise in these processes. third, we show how the principal families of pfass are interrelated as industrial, environmental, or metabolic precursors or transformation products of one another. we pay particular attention to those pfass that have the potential to be converted, by abiotic or biotic environmental processes or by human metabolism, into long-chain perfluoroalkyl carboxylic or sulfonic acids, which are currently the focus of regulatory action. the supplemental data lists 42 families and subfamilies of pfass and 268 selected individual compounds, providing recommended names and acronyms, and structural formulas, as well as chemical abstracts service registry numbers.",0
"to better quantify the impact of foodborne diseases on health in the united states, we compiled and analyzed information from multiple surveillance systems and other sources. we estimate that foodborne diseases cause approximately 76 million illnesses, 325,000 hospitalizations, and 5,000 deaths in the united states each year. known pathogens account for an estimated 14 million illnesses, 60, 000 hospitalizations, and 1,800 deaths. three pathogens, salmonella, listeria, and toxoplasma, are responsible for 1,500 deaths each year, more than 75% of those caused by known pathogens, while unknown agents account for the remaining 62 million illnesses, 265,000 hospitalizations, and 3,200 deaths. overall, foodborne diseases appear to cause more illnesses but fewer deaths than previously estimated.",0
"a fundamental challenge for systems neuroscience is to quantitatively relate its three major branches of research: brain-activity measurement, behavioral measurement, and computational modeling. using measured brain-activity patterns to evaluate computational network models is complicated by the need to define the correspondency between the units of the model and the channels of the brain-activity data, e.g., single-cell recordings or voxels from functional magnetic resonance imaging (fmri). similar correspondency problems complicate relating activity patterns between different modalities of brain-activity measurement (e.g., fmri and invasive or scalp electrophysiology), and between subjects and species. in order to bridge these divides, we suggest abstracting from the activity patterns themselves and computing representational dissimilarity matrices (rdms), which characterize the information carried by a given representation in a brain or model. building on a rich psychological and mathematical literature on similarity analysis, we propose a new experimental and data-analytical framework called representational similarity analysis (rsa), in which multi-channel measures of neural activity are quantitatively related to each other and to computational theory and behavior by comparing rdms. we demonstrate rsa by relating representations of visual objects as measured with fmri in early visual cortex and the fusiform face area to computational models spanning a wide range of complexities. the rdms are simultaneously related via second-level application of multidimensional scaling and tested using randomization and bootstrap techniques. we discuss the broad potential of rsa, including novel approaches to experimental design, and argue that these ideas, which have deep roots in psychology and neuroscience, will allow the integrated quantitative analysis of data from all three branches, thus contributing to a more unified systems neuroscience.",0
"cancers have the ability to develop resistance to traditional therapies, and the increasing prevalence of these drug resistant cancers necessitates further research and treatment development. this paper outlines the current knowledge of mechanisms that promote or enable drug resistance, such as drug inactivation, drug target alteration, drug efflux, dna damage repair, cell death inhibition, and the epithelial-mesenchymal transition, as well as how inherent tumor cell heterogeneity plays a role in drug resistance. it also describes the epigenetic modifications that can induce drug resistance and considers how such epigenetic factors may contribute to the development of cancer progenitor cells, which are not killed by conventional cancer therapies. lastly, this review concludes with a discussion on the best treatment options for existing drug resistant cancers, ways to prevent the formation of drug resistant cancers and cancer progenitor cells, and future directions of study.",0
"advances in high-resolution cryo-electron microscopy (cryo-em) require the development of validation metrics to independently assess map quality and model geometry. we report emringer, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. emringer ( will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-em.",0
"unlabelled for the analysis of microarray data, clustering techniques are frequently used. most of such methods are based on hard clustering of data wherein one gene (or sample) is assigned to exactly one cluster. hard clustering, however, suffers from several drawbacks such as sensitivity to noise and information loss. in contrast, soft clustering methods can assign a gene to several clusters. they can overcome shortcomings of conventional hard clustering techniques and offer further advantages. thus, we constructed an r package termed mfuzz implementing soft clustering tools for microarray data analysis. the additional package mfuzzgui provides a convenient tcltk based graphical user interface. availability the r package mfuzz and mfuzzgui are available at their distribution is subject to gpl version 2 license.",0
"background and aims diabetes mellitus (dm) is chronic conditions with devastating multi-systemic complication and may be associated with severe form of coronavirus disease 2019 (covid-19). we conducted a systematic review and meta-analysis in order to investigate the association between dm and poor outcome in patients with covid-19 pneumonia. methods systematic literature search was performed from several electronic databases on subjects that assess dm and outcome in covid-19 pneumonia. the outcome of interest was composite poor outcome, including mortality, severe covid-19, acute respiratory distress syndrome (ards), need for intensive care unit (icu) care, and disease progression. results there were a total of 6452 patients from 30 studies. meta-analysis showed that dm was associated with composite poor outcome (rr 2.38 , p 2 : 62%) and its subgroup which comprised of mortality (rr 2.12 , p 2 : 72%), severe covid-19 (rr 2.45 , p 2 : 45%), ards (rr 4.64 , p = 0.001; i 2 : 9%), and disease progression (rr 3.31 , p = 0.04; i 2 : 0%). meta-regression showed that the association with composite poor outcome was influenced by age (p = 0.003) and hypertension (p < 0.001). subgroup analysis showed that the association was weaker in studies with median age ≥55 years-old (rr 1.92) compared to <55 years-old (rr 3.48), and in prevalence of hypertension ≥25% (rr 1.93) compared to <25% (rr 3.06). subgroup analysis on median age <55 years-old and prevalence of hypertension <25% showed strong association (rr 3.33) conclusion: dm was associated with mortality, severe covid-19, ards, and disease progression in patients with covid-19.",0
"background: spirometry is the most common pulmonary function test. it is widely used in the assessment of lung function to provide objective information used in the diagnosis of lung diseases and monitoring lung health. in 2005, the american thoracic society and the european respiratory society jointly adopted technical standards for conducting spirometry. improvements in instrumentation and computational capabilities, together with new research studies and enhanced quality assurance approaches, have led to the need to update the 2005 technical standards for spirometry to take full advantage of current technical capabilities. methods: this spirometry technical standards document was developed by an international joint task force, appointed by the american thoracic society and the european respiratory society, with expertise in conducting and analyzing pulmonary function tests, laboratory quality assurance, and developing international standards. a comprehensive review of published evidence was performed. a patient survey was developed to capture patients' experiences. results: revisions to the 2005 technical standards for spirometry were made, including the addition of factors that were not previously considered. evidence to support the revisions was cited when applicable. the experience and expertise of task force members were used to develop recommended best practices. conclusions: standards and consensus recommendations are presented for manufacturers, clinicians, operators, and researchers with the aims of increasing the accuracy, precision, and quality of spirometric measurements and improving the patient experience. a comprehensive guide to aid in the implementation of these standards was developed as an online supplement.",0
"we have identified and purified a novel cytokine, nk cell stimulatory factor (nksf), from the cell-free supernatant fluid of the phorbol diester-induced ebv-transformed human b lymphoblastoid cell line rpmi 8866. nksf activity is mostly associated to a 70-kd anionic glycoprotein. the purified 70-kd protein, isolated from an sds-page gel, yields upon reduction two small species of molecular masses of 40 and 35 kd, suggesting that this cytokine is a heterodimer. when added to human pbl, purified nksf preparations induce ifn-gamma production and synergize with ril-2 in this activity, augment the nk cell-mediated cytotoxicity of pbl preparations against both nk-sensitive and nk-resistant target cell lines, and enhance the mitogenic response of t cells to mitogenic lectins and phorbol diesters. the three activities remain associated through different purification steps resulting in a 9,200-fold purification, and purified nksf mediates the three biological activities at concentrations in the range of 0.1-10 pm. these data strongly suggest that the same molecule mediates these three activities, although the presence of traces of contaminant peptides even in the most purified nksf preparations does not allow us to exclude the possibility that distinct biologically active molecules have been co-purified. the absence of other known cytokines in the purified nksf preparations, the unusual molecular conformation of nksf, the high specific activity of the purified protein, and the spectrum of biological activities distinguish nksf from other previously described cytokines.",0
"the geographic spread of 2019 novel coronavirus (covid-19) infections from the epicenter of wuhan, china, has provided an opportunity to study the natural history of the recently emerged virus. using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of covid-19 infections. our results show that the incubation period falls within the range of 2-14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. the mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3-4 days without truncation and at 5-9 days when right truncated. based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. the median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the covid-19 case fatality risk.",0
"a rapidly increasing number of chemicals, or their degradation products, are being recognized as possessing estrogenic activity, albeit usually weak. we have found that effluent from sewage treatment works contains a chemical, or mixture of chemicals, that induces vitellogenin synthesis in male fish maintained in the effluent, thus indicating that the effluent is estrogenic. the effect was extremely pronounced and occurred at all sewage treatment works tested. the nature of the chemical or chemicals causing the effect is presently not known. however, we have tested a number of chemicals known to be estrogenic to mammals and have shown that they are also estrogenic to fish; that is, no species specificity was apparent. many of these weakly estrogenic chemicals are known to be present in effluents. further, a mixture of different estrogenic chemicals was considerably more potent than each of the chemicals when tested individually, suggesting that enhanced effects could occur when fish are exposed simultaneously to various estrogenic chemicals (as is likely to occur in rivers receiving effluent). subsequent work should determine whether exposure to these chemicals at the concentrations present in the environment leads to any deleterious physiological effects.",0
"kegg ( or is an encyclopedia of genes and genomes. assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the kegg database project. molecular-level functions are stored in the ko (kegg orthology) database, where each ko is defined as a functional ortholog of genes and proteins. higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of kegg pathway maps, brite hierarchies and kegg modules. in the past the ko database was developed for the purpose of defining nodes of molecular networks, but now the content has been expanded and the quality improved irrespective of whether or not the kos appear in the three molecular network databases. the newly introduced addendum category of the genes database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of kos are defined. furthermore, the disease and drug databases have been improved by systematic analysis of drug labels for better integration of diseases and drugs with the kegg molecular networks. kegg is moving towards becoming a comprehensive knowledge base for both functional interpretation and practical application of genomic information.",0
"acute kidney injury (aki) is a common and serious problem affecting millions and causing death and disability for many. in 2012, kidney disease: improving global outcomes completed the first ever, international, multidisciplinary, clinical practice guideline for aki. the guideline is based on evidence review and appraisal, and covers aki definition, risk assessment, evaluation, prevention, and treatment. in this review we summarize key aspects of the guideline including definition and staging of aki, as well as evaluation and nondialytic management. contrast-induced aki and management of renal replacement therapy will be addressed in a separate review. treatment recommendations are based on systematic reviews of relevant trials. appraisal of the quality of the evidence and the strength of recommendations followed the grading of recommendations assessment, development and evaluation approach. limitations of the evidence are discussed and a detailed rationale for each recommendation is provided.",0
"background the covid-19 pandemic has had a significant impact on public mental health. therefore, monitoring and oversight of the population mental health during crises such as a panedmic is an immediate priority. the aim of this study is to analyze the existing research works and findings in relation to the prevalence of stress, anxiety and depression in the general population during the covid-19 pandemic. method in this systematic review and meta-analysis, articles that have focused on stress and anxiety prevalence among the general population during the covid-19 pandemic were searched in the science direct, embase, scopus, pubmed, web of science (isi) and google scholar databases, without a lower time limit and until may 2020. in order to perform a meta-analysis of the collected studies, the random effects model was used, and the heterogeneity of studies was investigated using the i 2 index. moreover. data analysis was conducted using the comprehensive meta-analysis (cma) software. results the prevalence of stress in 5 studies with a total sample size of 9074 is obtained as 29.6% (95% confidence limit: 24.3-35.4), the prevalence of anxiety in 17 studies with a sample size of 63,439 as 31.9% (95% confidence interval: 27.5-36.7), and the prevalence of depression in 14 studies with a sample size of 44,531 people as 33.7% (95% confidence interval: 27.5-40.6). conclusion covid-19 not only causes physical health concerns but also results in a number of psychological disorders. the spread of the new coronavirus can impact the mental health of people in different communities. thus, it is essential to preserve the mental health of individuals and to develop psychological interventions that can improve the mental health of vulnerable groups during the covid-19 pandemic.",0
"exposure to ambient fine particulate matter (pm 2.5 ) is a major global health concern. quantitative estimates of attributable mortality are based on disease-specific hazard ratio models that incorporate risk information from multiple pm 2.5 sources (outdoor and indoor air pollution from use of solid fuels and secondhand and active smoking), requiring assumptions about equivalent exposure and toxicity. we relax these contentious assumptions by constructing a pm 2.5 -mortality hazard ratio function based only on cohort studies of outdoor air pollution that covers the global exposure range. we modeled the shape of the association between pm 2.5 and nonaccidental mortality using data from 41 cohorts from 16 countries-the global exposure mortality model (gemm). we then constructed gemms for five specific causes of death examined by the global burden of disease (gbd). the gemm predicts 8.9 million deaths in 2015, a figure 30% larger than that predicted by the sum of deaths among the five specific causes (6.9; 95% ci: 4.9-8.5) and 120% larger than the risk function used in the gbd (4.0; 95% ci: 3.3-4.8). differences between the gemm and gbd risk functions are larger for a 20% reduction in concentrations, with the gemm predicting 220% higher excess deaths. these results suggest that pm 2.5 exposure may be related to additional causes of death than the five considered by the gbd and that incorporation of risk information from other, nonoutdoor, particle sources leads to underestimation of disease burden, especially at higher concentrations.",0
"background uncertainties persist about the magnitude of associations of diabetes mellitus and fasting glucose concentration with risk of coronary heart disease and major stroke subtypes. we aimed to quantify these associations for a wide range of circumstances. methods we undertook a meta-analysis of individual records of diabetes, fasting blood glucose concentration, and other risk factors in people without initial vascular disease from studies in the emerging risk factors collaboration. we combined within-study regressions that were adjusted for age, sex, smoking, systolic blood pressure, and body-mass index to calculate hazard ratios (hrs) for vascular disease. findings analyses included data for 698 782 people (52 765 non-fatal or fatal vascular outcomes; 8.49 million person-years at risk) from 102 prospective studies. adjusted hrs with diabetes were: 2.00 (95% ci 1.83-2.19) for coronary heart disease; 2.27 (1.95-2.65) for ischaemic stroke; 1.56 (1.19-2.05) for haemorrhagic stroke; 1.84 (1.59-2.13) for unclassified stroke; and 1.73 (1.51-1.98) for the aggregate of other vascular deaths. hrs did not change appreciably after further adjustment for lipid, inflammatory, or renal markers. hrs for coronary heart disease were higher in women than in men, at 40-59 years than at 70 years and older, and with fatal than with non-fatal disease. at an adult population-wide prevalence of 10%, diabetes was estimated to account for 11% (10-12%) of vascular deaths. fasting blood glucose concentration was non-linearly related to vascular risk, with no significant associations between 3.90 mmol/l and 5.59 mmol/l. compared with fasting blood glucose concentrations of 3.90-5.59 mmol/l, hrs for coronary heart disease were: 1.07 (0.97-1.18) for lower than 3.90 mmol/l; 1.11 (1.04-1.18) for 5.60-6.09 mmol/l; and 1.17 (1.08-1.26) for 6.10-6.99 mmol/l. in people without a history of diabetes, information about fasting blood glucose concentration or impaired fasting glucose status did not significantly improve metrics of vascular disease prediction when added to information about several conventional risk factors. interpretation diabetes confers about a two-fold excess risk for a wide range of vascular diseases, independently from other conventional risk factors. in people without diabetes, fasting blood glucose concentration is modestly and non-linearly associated with risk of vascular disease. funding british heart foundation, uk medical research council, and pfizer.",0
"the data and tools in panther-a comprehensive, curated database of protein families, trees, subfamilies and functions available at undergone continual, extensive improvement for over a decade. here, we describe the current panther process as a whole, as well as the website tools for analysis of user-uploaded data. the main goals of panther remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. yet the focus of panther has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. the trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. subfamilies are still curated and used to define hmms, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. finally, panther now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.",0
"here, we present a major advance of the orthofinder method. this extends orthofinder's high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, orthofinder is equivalent to or outperforms these methods. furthermore, orthofinder is the most accurate ortholog inference method on the quest for orthologs benchmark test. finally, orthofinder's comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. orthofinder is available at",0
"we sought to identify new susceptibility loci for alzheimer's disease through a staged association study (gerad+) and by testing suggestive loci reported by the alzheimer's disease genetic consortium (adgc) in a companion paper. we undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with p ≤ 1 × 10(-5). we tested these variants for association in an independent sample (stage 2). three snps at two loci replicated and showed evidence for association in a further sample (stage 3). meta-analyses of all data provided compelling evidence that abca7 (rs3764650, meta p = 4.5 × 10(-17); including adgc data, meta p = 5.0 × 10(-21)) and the ms4a gene cluster (rs610932, meta p = 1.8 × 10(-14); including adgc data, meta p = 1.2 × 10(-16)) are new alzheimer's disease susceptibility loci. we also found independent evidence for association for three loci reported by the adgc, which, when combined, showed genome-wide significance: cd2ap (gerad+, p = 8.0 × 10(-4); including adgc data, meta p = 8.6 × 10(-9)), cd33 (gerad+, p = 2.2 × 10(-4); including adgc data, meta p = 1.6 × 10(-9)) and epha1 (gerad+, p = 3.4 × 10(-4); including adgc data, meta p = 6.0 × 10(-10)).",0
"a historical tendency to use european ancestry samples hinders medical genetics research, including the use of polygenic scores, which are individual-level metrics of genetic risk. we analyze the first decade of polygenic scoring studies (2008-2017, inclusive), and find that 67% of studies included exclusively european ancestry participants and another 19% included only east asian ancestry participants. only 3.8% of studies were among cohorts of african, hispanic, or indigenous peoples. we find that predictive performance of european ancestry-derived polygenic scores is lower in non-european ancestry samples (e.g. african ancestry samples: t = -5.97, df = 24, p = 3.7 × 10 -6 ), and we demonstrate the effects of methodological choices in polygenic score distributions for worldwide populations. these findings highlight the need for improved treatment of linkage disequilibrium and variant frequencies when applying polygenic scoring to cohorts of non-european ancestry, and bolster the rationale for large-scale gwas in diverse human populations.",0
"decision-making requires the coordinated activity of diverse brain structures. for example, in maze-based tasks, the prefrontal cortex must integrate spatial information encoded in the hippocampus with mnemonic information concerning route and task rules in order to direct behavior appropriately. using simultaneous tetrode recordings from ca1 of the rat hippocampus and medial prefrontal cortex, we show that correlated firing in the two structures is selectively enhanced during behavior that recruits spatial working memory, allowing the integration of hippocampal spatial information into a broader, decision-making network. the increased correlations are paralleled by enhanced coupling of the two structures in the 4- to 12-hz theta-frequency range. thus the coordination of theta rhythms may constitute a general mechanism through which the relative timing of disparate neural activities can be controlled, allowing specialized brain structures to both encode information independently and to interact selectively according to current behavioral demands.",0
"multistep carcinogenesis involves more than six discrete events also important in normal development and cell behavior. of these, local invasion and metastasis cause most cancer deaths but are the least well understood molecularly. we employed a combined in vitro/in vivo carcinogenesis model, that is, polarized ha-ras-transformed mammary epithelial cells (epras), to dissect the role of ras downstream signaling pathways in epithelial cell plasticity, tumorigenesis, and metastasis. ha-ras cooperates with transforming growth factor beta (tgfbeta) to cause epithelial mesenchymal transition (emt) characterized by spindle-like cell morphology, loss of epithelial markers, and induction of mesenchymal markers. emt requires continuous tgfbeta receptor (tgfbeta-r) and oncogenic ras signaling and is stabilized by autocrine tgfbeta production. in contrast, fibroblast growth factors, hepatocyte growth factor/scatter factor, or tgfbeta alone induce scattering, a spindle-like cell phenotype fully reversible after factor withdrawal, which does not involve sustained marker changes. using specific inhibitors and effector-specific ras mutants, we show that a hyperactive raf/mitogen-activated protein kinase (mapk) is required for emt, whereas activation of phosphatidylinositol 3-kinase (pi3k) causes scattering and protects from tgfbeta-induced apoptosis. hyperactivation of the pi3k pathway or the raf/mapk pathway are sufficient for tumorigenesis, whereas emt in vivo and metastasis required a hyperactive raf/mapk pathway. thus, emt seems to be a close in vitro correlate of metastasis, both requiring synergism between tgfbeta-r and raf/mapk signaling.",0
"neutrophils release decondensed chromatin termed neutrophil extracellular traps (nets) to trap and kill pathogens extracellularly. reactive oxygen species are required to initiate net formation but the downstream molecular mechanism is unknown. we show that upon activation, neutrophil elastase (ne) escapes from azurophilic granules and translocates to the nucleus, where it partially degrades specific histones, promoting chromatin decondensation. subsequently, myeloperoxidase synergizes with ne in driving chromatin decondensation independent of its enzymatic activity. accordingly, ne knockout mice do not form nets in a pulmonary model of klebsiella pneumoniae infection, which suggests that this defect may contribute to the immune deficiency of these mice. this mechanism provides for a novel function for serine proteases and highly charged granular proteins in the regulation of chromatin density, and reveals that the oxidative burst induces a selective release of granular proteins into the cytoplasm through an unknown mechanism.",0
"background we aimed to accurately estimate the frequency of a hexanucleotide repeat expansion in c9orf72 that has been associated with a large proportion of cases of amyotrophic lateral sclerosis (als) and frontotemporal dementia (ftd). methods we screened 4448 patients diagnosed with als (el escorial criteria) and 1425 patients with ftd (lund-manchester criteria) from 17 regions worldwide for the ggggcc hexanucleotide expansion using a repeat-primed pcr assay. we assessed familial disease status on the basis of self-reported family history of similar neurodegenerative diseases at the time of sample collection. we compared haplotype data for 262 patients carrying the expansion with the known finnish founder risk haplotype across the chromosomal locus. we calculated age-related penetrance using the kaplan-meier method with data for 603 individuals with the expansion. findings in patients with sporadic als, we identified the repeat expansion in 236 (7·0%) of 3377 white individuals from the usa, europe, and australia, two (4·1%) of 49 black individuals from the usa, and six (8·3%) of 72 hispanic individuals from the usa. the mutation was present in 217 (39·3%) of 552 white individuals with familial als from europe and the usa. 59 (6·0%) of 981 white europeans with sporadic ftd had the mutation, as did 99 (24·8%) of 400 white europeans with familial ftd. data for other ethnic groups were sparse, but we identified one asian patient with familial als (from 20 assessed) and two with familial ftd (from three assessed) who carried the mutation. the mutation was not carried by the three native americans or 360 patients from asia or the pacific islands with sporadic als who were tested, or by 41 asian patients with sporadic ftd. all patients with the repeat expansion had (partly or fully) the founder haplotype, suggesting a one-off expansion occurring about 1500 years ago. the pathogenic expansion was non-penetrant in individuals younger than 35 years, 50% penetrant by 58 years, and almost fully penetrant by 80 years. interpretation a common mendelian genetic lesion in c9orf72 is implicated in many cases of sporadic and familial als and ftd. testing for this pathogenic expansion should be considered in the management and genetic counselling of patients with these fatal neurodegenerative diseases. funding full funding sources listed at end of paper (see acknowledgments).",0
"presented here is a genome sequence of an individual human. it was produced from approximately 32 million random dna fragments, sequenced by sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. we developed a modified version of the celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. comparison of this genome and the national center for biotechnology information human reference assembly revealed more than 4.1 million dna variants, encompassing 12.3 mb. these variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (snps), 53,823 block substitutions (2-206 bp), 292,102 heterozygous insertion/deletion events (indels)(1-571 bp), 559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. non-snp dna variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. this suggests an important role for non-snp genetic alterations in defining the diploid genome structure. moreover, 44% of genes were heterozygous for one or more variants. using a novel haplotype assembly strategy, we were able to span 1.5 gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. these data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.",0
"as next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. frameshifts and non-sense mutations are likely to cause a negative effect on protein function. existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. this alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for uniprot human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for uniprot non-human protein variations. in our approach, the area under the receiver operating characteristic curve (auc) for the human and non-human protein variation datasets is ∼0.85. we also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. in summary, we have developed a new algorithm, provean (protein variation effect analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. the provean tool is available online at",0
"background preoperative or postoperative radiotherapy reduces the risk of local recurrence in patients with operable rectal cancer. however, improvements in surgery and histopathological assessment mean that the role of radiotherapy needs to be reassessed. we compared short-course preoperative radiotherapy versus initial surgery with selective postoperative chemoradiotherapy. methods we undertook a randomised trial in 80 centres in four countries. 1350 patients with operable adenocarcinoma of the rectum were randomly assigned, by a minimisation procedure, to short-course preoperative radiotherapy (25 gy in five fractions; n=674) or to initial surgery with selective postoperative chemoradiotherapy (45 gy in 25 fractions with concurrent 5-fluorouracil) restricted to patients with involvement of the circumferential resection margin (n=676). the primary outcome measure was local recurrence. analysis was by intention to treat. this study is registered, number isrctn 28785842. findings at the time of analysis, which included all participants, 330 patients had died (157 preoperative radiotherapy group vs 173 selective postoperative chemoradiotherapy), and median follow-up of surviving patients was 4 years. 99 patients had developed local recurrence (27 preoperative radiotherapy vs 72 selective postoperative chemoradiotherapy). we noted a reduction of 61% in the relative risk of local recurrence for patients receiving preoperative radiotherapy (hazard ratio 0.39, 95% ci 0.27-0.58, p interpretation taken with results from other randomised trials, our findings provide convincing and consistent evidence that short-course preoperative radiotherapy is an effective treatment for patients with operable rectal cancer.",0
"motivation illumina dna sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. bioinformatic analysis pipelines are having trouble keeping pace. a common bottleneck in such pipelines is the requirement to read, write, sort and compress large bam files multiple times. results we present samblaster, a tool that reduces the number of times such costly operations are performed. samblaster is designed to mark duplicates in read-sorted sam files as a piped post-pass on dna aligner output before it is compressed to bam. in addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. as an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. as a stand-alone duplicate marking tool, it performs significantly better than picard or sambamba in terms of both speed and memory usage, while achieving nearly identical results. availability and implementation samblaster is open-source c+ + code and freely available for download from",0
"background the american cancer society (acs), the centers for disease control and prevention (cdc), the national cancer institute (nci), and the north american association of central cancer registries (naaccr) collaborate to provide annual updates on cancer occurrence and trends in the united states. methods incidence data were obtained from the cdc-funded and nci-funded population-based cancer registry programs and compiled by naaccr. data on cancer deaths were obtained from the national center for health statistics national vital statistics system. trends in age-standardized incidence and death rates for all cancers combined and for the leading cancer types by sex, race, and ethnicity were estimated by joinpoint analysis and expressed as the annual percent change. stage distribution and 5-year survival by stage at diagnosis were calculated for breast cancer, colon and rectum (colorectal) cancer, lung and bronchus cancer, and melanoma of the skin. results overall cancer incidence rates from 2008 to 2014 decreased by 2.2% per year among men but were stable among women. overall cancer death rates from 1999 to 2015 decreased by 1.8% per year among men and by 1.4% per year among women. among men, incidence rates during the most recent 5-year period (2010-2014) decreased for 7 of the 17 most common cancer types, and death rates (2011-2015) decreased for 11 of the 18 most common types. among women, incidence rates declined for 7 of the 18 most common cancers, and death rates declined for 14 of the 20 most common cancers. death rates decreased for cancer sites, including lung and bronchus (men and women), colorectal (men and women), female breast, and prostate. death rates increased for cancers of the liver (men and women); pancreas (men and women); brain and other nervous system (men and women); oral cavity and pharynx (men only); soft tissue, including heart (men only); nonmelanoma skin (men only); and uterus. incidence and death rates were higher among men than among women for all racial and ethnic groups. for all cancer sites combined, black men and white women had the highest incidence rates compared with other racial groups, and black men and black women had the highest death rates compared with other racial groups. non-hispanic men and women had higher incidence and mortality rates than those of hispanic ethnicity. five-year survival for cases diagnosed from 2007 through 2013 ranged from 100% (stage i) to 26.5% (stage iv) for female breast cancer, from 88.1% (stage i) to 12.6% (stage iv) for colorectal cancer, from 55.1% (stage i) to 4.2% (stage iv) for lung and bronchus cancer, and from 99.5% (stage i) to 16% (stage iv) for melanoma of the skin. among children, overall cancer incidence rates increased by 0.8% per year from 2010 to 2014, and overall cancer death rates decreased by 1.5% per year from 2011 to 2015. conclusions for all cancer sites combined, cancer incidence rates decreased among men but were stable among women. overall, there continue to be significant declines in cancer death rates among both men and women. differences in rates and trends by race and ethnic group remain. progress in reducing cancer mortality has not occurred for all sites. examining stage distribution and 5-year survival by stage highlights the potential benefits associated with early detection and treatment. cancer 2018;124:2785-2800. © 2018 american cancer society.",0
"background long-covid refers to a variety of symptoms affecting different organs reported by people following coronavirus disease 2019 (covid-19) infection. to date, there have been no robust estimates of the incidence and co-occurrence of long-covid features, their relationship to age, sex, or severity of infection, and the extent to which they are specific to covid-19. the aim of this study is to address these issues. methods and findings we conducted a retrospective cohort study based on linked electronic health records (ehrs) data from 81 million patients including 273,618 covid-19 survivors. the incidence and co-occurrence within 6 months and in the 3 to 6 months after covid-19 diagnosis were calculated for 9 core features of long-covid (breathing difficulties/breathlessness, fatigue/malaise, chest/throat pain, headache, abdominal symptoms, myalgia, other pain, cognitive symptoms, and anxiety/depression). their co-occurrence network was also analyzed. comparison with a propensity score-matched cohort of patients diagnosed with influenza during the same time period was achieved using kaplan-meier analysis and the cox proportional hazard model. the incidence of atopic dermatitis was used as a negative control. among covid-19 survivors (mean age: 46.3 , 55.6% female), 57.00% had one or more long-covid feature recorded during the whole 6-month period (i.e., including the acute phase), and 36.55% between 3 and 6 months. the incidence of each feature was: abnormal breathing (18.71% in the 1- to 180-day period; 7.94% in the 90- to180-day period), fatigue/malaise (12.82%; 5.87%), chest/throat pain (12.60%; 5.71%), headache (8.67%; 4.63%), other pain (11.60%; 7.19%), abdominal symptoms (15.58%; 8.29%), myalgia (3.24%; 1.54%), cognitive symptoms (7.88%; 3.95%), and anxiety/depression (22.82%; 15.49%). all 9 features were more frequently reported after covid-19 than after influenza (with an overall excess incidence of 16.60% and hazard ratios between 1.44 and 2.04, all p conclusions long-covid clinical features occurred and co-occurred frequently and showed some specificity to covid-19, though they were also observed after influenza. different long-covid clinical profiles were observed based on demographics and illness severity.",0
"background several studies have described the clinical characteristics of patients with novel coronavirus (sars-cov-2) infected pneumonia (covid-19), indicating severe patients tended to have higher neutrophil to lymphocyte ratio (nlr). whether baseline nlr could be an independent predictor of in-hospital death in chinese covid-19 patients remains to be investigated. methods a cohort of patients with covid-19 admitted to the zhongnan hospital of wuhan university from january 1 to february 29 was retrospectively analyzed. the baseline data of laboratory examinations, including nlr, were collected. univariate and multivariate logistic regression models were developed to assess the independent relationship between the baseline nlr and in-hospital all-cause death. a sensitivity analysis was performed by converting nlr from a continuous variable to a categorical variable according to tertile. interaction and stratified analyses were conducted as well. results 245 covid-19 patients were included in the final analyses, and the in-hospital mortality was 13.47%. multivariate analysis demonstrated that there was 8% higher risk of in-hospital mortality for each unit increase in nlr (odds ratio = 1.08; 95% confidence interval , 1.01 to 1.14; p = 0.0147). compared with patients in the lowest tertile, the nlr of patients in the highest tertile had a 15.04-fold higher risk of death (or = 16.04; 95% ci, 1.14 to 224.95; p = 0.0395) after adjustment for potential confounders. notably, the fully adjusted or for mortality was 1.10 in males for each unit increase of nlr (or = 1.10; 95% ci, 1.02 to 1.19; p = 0.016). conclusions nlr is an independent risk factor of the in-hospital mortality for covid-19 patients especially for male. assessment of nlr may help identify high risk individuals with covid-19.",0
"biofilm is a complex structure of microbiome having different bacterial colonies or single type of cells in a group; adhere to the surface. these cells are embedded in extracellular polymeric substances, a matrix which is generally composed of edna, proteins and polysaccharides, showed high resistance to antibiotics. it is one of the major causes of infection persistence especially in nosocomial settings through indwelling devices. quorum sensing plays an important role in regulating the biofilm formation. there are many approaches being used to control infections by suppressing its formation but crispr-cas (gene editing technique) and photo dynamic therapy (pdt) are proposed to be used as therapeutic approaches to subside bacterial biofim infections, especially caused by deadly drug resistant bad bugs.",0
"dna methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. here, we describe an r package, methylkit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylkit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of dna methylation. finally, we demonstrate methylkit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylkit is available at",0
"epoxy embedding methods of glauert and kushida have been modified so as to yield rapid, reproducible, and convenient embedding methods for electron microscopy. the sections are robust and tissue damage is less than with methacrylate embedding.",0
"the uk biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the united kingdom, aged between 40 and 69 at recruitment. the open resource is unique in its size and scope. a rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. follow-up information is provided by linking health and medical records. genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.",0
"genotyping by sequencing (gbs) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of snp markers. the relatively straightforward, robust, and cost-effective gbs protocol is currently being applied in numerous species by a large number of researchers. herein we describe a bioinformatics pipeline, tassel-gbs, designed for the efficient processing of raw gbs sequence data into snp genotypes. the tassel-gbs pipeline successfully fulfills the following key design criteria: (1) ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 gb of ram, (2) scalability from small to extremely large studies, where hundreds of thousands or even millions of snps can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. although a reference genome is required, the pipeline can also be run with an unfinished ""pseudo-reference"" consisting of numerous contigs. we describe the tassel-gbs pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based snp filters. overall, the gbs assay and the tassel-gbs pipeline provide robust tools for studying genomic diversity.",0
"background rapid spread of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) in wuhan, china, prompted heightened surveillance in shenzhen, china. the resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control measures. methods from jan 14 to feb 12, 2020, the shenzhen center for disease control and prevention identified 391 sars-cov-2 cases and 1286 close contacts. we compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. we estimated metrics of disease transmission and analysed factors influencing transmission risk. findings cases were older than the general population (mean age 45 years) and balanced between males (n=187) and females (n=204). 356 (91%) of 391 cases had mild or moderate clinical severity at initial assessment. as of feb 22, 2020, three cases had died and 225 had recovered (median time to recovery 21 days; 95% ci 20-22). cases were isolated on average 4·6 days (95% ci 4·1-5·0) after developing symptoms; contact tracing reduced this by 1·9 days (95% ci 1·1-2·7). household contacts and those travelling with a case were at higher risk of infection (odds ratio 6·27 for household contacts and 7·06 for those travelling with a case) than other close contacts. the household secondary attack rate was 11·2% (95% ci 9·1-13·8), and children were as likely to be infected as adults (infection rate 7·4% in children interpretation our data on cases as well as their infected and uninfected close contacts provide key insights into the epidemiology of sars-cov-2. this analysis shows that isolation and contact tracing reduce the time during which cases are infectious in the community, thereby reducing the r. the overall impact of isolation and contact tracing, however, is uncertain and highly dependent on the number of asymptomatic cases. moreover, children are at a similar risk of infection to the general population, although less likely to have severe symptoms; hence they should be considered in analyses of transmission and control. funding emergency response program of harbin institute of technology, emergency response program of peng cheng laboratory, us centers for disease control and prevention.",0
"seven monoclonal antibodies raised against tubulin from the axonemes of sea urchin sperm flagella recognize an acetylated form of alpha-tubulin present in the axoneme of a variety of organisms. the antigen was not detected among soluble, cytoplasmic alpha-tubulin isoforms from a variety of cells. the specificity of the antibodies was determined by in vitro acetylation of sea urchin and chlamydomonas cytoplasmic tubulins in crude extracts. of all the acetylated polypeptides in the extracts, only alpha-tubulin became antigenic. among chlamydomonas tubulin isoforms, the antibodies recognize only the axonemal alpha-tubulin isoform acetylated in vivo on the epsilon-amino group of lysine(s) (l'hernault, s.w., and j.l. rosenbaum, 1985, biochemistry, 24:473-478). the antibodies do not recognize unmodified axonemal alpha-tubulin, unassembled alpha-tubulin present in a flagellar matrix-plus-membrane fraction, or soluble, cytoplasmic alpha-tubulin from chlamydomonas cell bodies. the antigen was found in protein fractions that contained axonemal microtubules from a variety of sources, including cilia from sea urchin blastulae and tetrahymena, sperm and testis from drosophila, and human sperm. in contrast, the antigen was not detected in preparations of soluble, cytoplasmic tubulin, which would not have contained tubulin from stable microtubule arrays such as centrioles, from unfertilized sea urchin eggs, drosophila embryos, and hela cells. although the acetylated alpha-tubulin recognized by the antibodies is present in axonemes from a variety of sources and may be necessary for axoneme formation, it is not found exclusively in any one subset of morphologically distinct axonemal microtubules. the antigen was found in similar proportions in fractions from sea urchin sperm axonemes enriched for central pair or outer doublet b or outer doublet a microtubules. therefore the acetylation of alpha-tubulin does not provide the mechanism that specifies the structure of any one class of axonemal microtubules. preliminary evidence indicates that acetylated alpha-tubulin is not restricted to the axoneme. the antibodies described in this report may allow us to deduce the role of tubulin acetylation in the structure and function of microtubules in vivo.",0
"a small subpopulation of normal murine splenic b cells carrying all of the classic b cells markers (igm, igd, ia, and thb) also carries ly-1, one of the major t cell surface molecules. this ""ly-1 b"" subpopulation (identified and characterized by multiparameter facs analyses) consists of relatively large, high igm/low-igd/low-ly-1 lymphocytes that represent approximately 2% of the spleen cells in normal animals and, generally, 5-10% of spleen cells in nzb mice. ly-1 b are clearly detectable in all normal mouse strains tested as well as nzb, cba/n, other x-id mice and nude (nu/nu) mice. they are found primarily in the spleen; are either absent or very poorly represented in lymph node, bone marrow, and thymus; appear early during ontogeny, and comprise about a third of the small number of lymphocytes present in 5-d-old mice. nzb and (nzb x nzw)f1 mice have more ly-1 b than all other strains and, furthermore, have a unique ly-1 b population that secretes igm when cultured under usual conditions in the absence of added antigen. the igm secretion by these ly-1 b cells accounts for the previously reported ""spontaneous"" igm secretion by nzb spleen cells in culture. studies with facs-sorted cells show that the presence of ly-1 on these igm-secreting cells distinguishes them from the (ly-1 negative) igm-secreting ""direct"" plaque-forming cells generated in nzb mice after stimulation with sheep erythrocytes.",0
"background the prevalence of dementia is of interest worldwide. contemporary estimates are needed to plan for future care provision, but much evidence is decades old. we aimed to investigate whether the prevalence of dementia had changed in the past two decades by repeating the same approach and diagnostic methods as used in the medical research council cognitive function and ageing study (mrc cfas) in three of the original study areas in england. methods between 1989 and 1994, mrc cfas investigators did baseline interviews in populations aged 65 years and older in six geographically defined areas in england and wales. a two stage process, with screening followed by diagnostic assessment, was used to obtain data for algorithmic diagnoses (geriatric mental state-automated geriatric examination for computer assisted taxonomy), which were then used to estimate dementia prevalence. data from three of these areas--cambridgeshire, newcastle, and nottingham--were selected for cfas i. between 2008 and 2011, new fieldwork was done in the same three areas for the cfas ii study. for both cfas i and ii, each area needed to include 2500 individuals aged 65 years and older to provide power for geographical and generational comparison. sampling was stratified according to age group (65-74 years vs ≥75 years). cfas ii used identical sampling, approach, and diagnostic methods to cfas i, except that screening and assessement were combined into one stage. prevalence estimates were calculated using inverse probability weighting methods to adjust for sampling design and non-response. full likelihood bayesian models were used to investigate informative non-response. findings 7635 people aged 65 years or older were interviewed in cfas i (9602 approached, 80% response) in cambridgeshire, newcastle, and nottingham, with 1457 being diagnostically assessed. in the same geographical areas, the cfas ii investigators interviewed 7796 individuals (14,242 approached, 242 with limited frailty information, 56% response). using cfas i age and sex specific estimates of prevalence in individuals aged 65 years or older, standardised to the 2011 population, 8·3% (884,000) of this population would be expected to have dementia in 2011. however, cfas ii shows that the prevalence is lower (6·5%; 670,000), a decrease of 1·8% (odds ratio for cfas ii vs cfas i 0·7, 95% ci 0·6-0·9, p=0·003). sensitivity analyses suggest that these estimates are robust to the change in response. interpretation this study provides further evidence that a cohort effect exists in dementia prevalence. later-born populations have a lower risk of prevalent dementia than those born earlier in the past century. funding uk medical research council.",0
"in february 2020, cdc issued guidance advising persons and health care providers in areas affected by the coronavirus disease 2019 (covid-19) pandemic to adopt social distancing practices, specifically recommending that health care facilities and providers offer clinical services through virtual means such as telehealth.* telehealth is the use of two-way telecommunications technologies to provide clinical health care through a variety of remote methods. † to examine changes in the frequency of use of telehealth services during the early pandemic period, cdc analyzed deidentified encounter (i.e., visit) data from four of the largest u.s. telehealth providers that offer services in all states. § trends in telehealth encounters during january-march 2020 (surveillance weeks 1-13) were compared with encounters occurring during the same weeks in 2019. during the first quarter of 2020, the number of telehealth visits increased by 50%, compared with the same period in 2019, with a 154% increase in visits noted in surveillance week 13 in 2020, compared with the same period in 2019. during january-march 2020, most encounters were from patients seeking care for conditions other than covid-19. however, the proportion of covid-19-related encounters significantly increased (from 5.5% to 16.2%; p<0.05) during the last 3 weeks of march 2020 (surveillance weeks 11-13). this marked shift in practice patterns has implications for immediate response efforts and longer-term population health. continuing telehealth policy changes and regulatory waivers might provide increased access to acute, chronic, primary, and specialty care during and after the pandemic.",0
"background the number of mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. this is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. however, some genetic variants may not be valid instrumental variables, in particular due to them having more than one proximal phenotypic correlate (pleiotropy). methods we view mendelian randomization with multiple instruments as a meta-analysis, and show that bias caused by pleiotropy can be regarded as analogous to small study bias. causal estimates using each instrument can be displayed visually by a funnel plot to assess potential asymmetry. egger regression, a tool to detect small study bias in meta-analysis, can be adapted to test for bias from pleiotropy, and the slope coefficient from egger regression provides an estimate of the causal effect. under the assumption that the association of each genetic variant with the exposure is independent of the pleiotropic effect of the variant (not via the exposure), egger's test gives a valid test of the null causal hypothesis and a consistent causal effect estimate even when all the genetic variants are invalid instrumental variables. results we illustrate the use of this approach by re-analysing two published mendelian randomization studies of the causal effect of height on lung function, and the causal effect of blood pressure on coronary artery disease risk. the conservative nature of this approach is illustrated with these examples. conclusions an adaption of egger regression (which we call mr-egger) can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations. the approach provides a sensitivity analysis for the robustness of the findings from a mendelian randomization investigation.",0
"reactive oxygen species (ros) are produced by living organisms as a result of normal cellular metabolism and environmental factors, such as air pollutants or cigarette smoke. ros are highly reactive molecules and can damage cell structures such as carbohydrates, nucleic acids, lipids, and proteins and alter their functions. the shift in the balance between oxidants and antioxidants in favor of oxidants is termed ""oxidative stress."" regulation of reducing and oxidizing (redox) state is critical for cell viability, activation, proliferation, and organ function. aerobic organisms have integrated antioxidant systems, which include enzymatic and nonenzymatic antioxidants that are usually effective in blocking harmful effects of ros. however, in pathological conditions, the antioxidant systems can be overwhelmed. oxidative stress contributes to many pathological conditions and diseases, including cancer, neurological disorders, atherosclerosis, hypertension, ischemia/perfusion, diabetes, acute respiratory distress syndrome, idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, and asthma. in this review, we summarize the cellular oxidant and antioxidant systems and discuss the cellular effects and mechanisms of the oxidative stress.",0
"sirtuins are nad(+)-dependent protein deacetylases. they mediate adaptive responses to a variety of stresses, including calorie restriction and metabolic stress. sirtuin 3 (sirt3) is localized in the mitochondrial matrix, where it regulates the acetylation levels of metabolic enzymes, including acetyl coenzyme a synthetase 2 (refs 1, 2). mice lacking both sirt3 alleles appear phenotypically normal under basal conditions, but show marked hyperacetylation of several mitochondrial proteins. here we report that sirt3 expression is upregulated during fasting in liver and brown adipose tissues. during fasting, livers from mice lacking sirt3 had higher levels of fatty-acid oxidation intermediate products and triglycerides, associated with decreased levels of fatty-acid oxidation, compared to livers from wild-type mice. mass spectrometry of mitochondrial proteins shows that long-chain acyl coenzyme a dehydrogenase (lcad) is hyperacetylated at lysine 42 in the absence of sirt3. lcad is deacetylated in wild-type mice under fasted conditions and by sirt3 in vitro and in vivo; and hyperacetylation of lcad reduces its enzymatic activity. mice lacking sirt3 exhibit hallmarks of fatty-acid oxidation disorders during fasting, including reduced atp levels and intolerance to cold exposure. these findings identify acetylation as a novel regulatory mechanism for mitochondrial fatty-acid oxidation and demonstrate that sirt3 modulates mitochondrial intermediary metabolism and fatty-acid use during fasting.",0
"the aim of this guideline is to provide a minimum standard for the acquisition and interpretation of pet and pet/ct scans with -fluorodeoxyglucose (fdg). this guideline will therefore address general information about-fluorodeoxyglucose (fdg) positron emission tomography-computed tomography (pet/ct) and is provided to help the physician and physicist to assist to carrying out,interpret, and document quantitative fdg pet/ct examinations,but will concentrate on the optimisation of diagnostic quality and quantitative information.",0
"neurological disorders are now the leading source of disability globally, and the fastest growing neurological disorder in the world is parkinson disease. from 1990 to 2015, the number of people with parkinson disease doubled to over 6 million. driven principally by aging, this number is projected to double again to over 12 million by 2040. additional factors, including increasing longevity, declining smoking rates, and increasing industrialization, could raise the burden to over 17 million. for most of human history, parkinson has been a rare disorder. however, demography and the by-products of industrialization have now created a parkinson pandemic that will require heightened activism, focused planning, and novel approaches.",0
"background early diagnosis and immediate initiation of treatment are essential for an effective tuberculosis (tb) control program. delay in diagnosis is significant to both disease prognosis at the individual level and transmission within the community. most transmissions occur between the onset of cough and initiation of treatment. methods a systematic review of 58 studies addressing delay in diagnosis and treatment of tb was performed. we found different definitions of, for example, debut of symptoms, first appropriate health care provider, time to diagnosis, and start of treatment. rather than excluding studies that failed to meet strict scientific criteria (like in a meta-analysis), we tried to extract the ""solid findings"" from all of them to arrive on a more global understanding of diagnostic delay in tb. results the main factors associated with diagnostic delay included human immunodeficiency virus; coexistence of chronic cough and/or other lung diseases; negative sputum smear; extrapulmonary tb; rural residence; low access (geographical or sociopsychological barriers); initial visitation of a government low-level healthcare facility, private practitioner, or traditional healer; old age; poverty; female sex; alcoholism and substance abuse; history of immigration; low educational level; low awareness of tb; incomprehensive beliefs; self-treatment; and stigma. conclusion the core problem in delay of diagnosis and treatment seemed to be a vicious cycle of repeated visits at the same healthcare level, resulting in nonspecific antibiotic treatment and failure to access specialized tb services. once generation of a specific diagnosis was in reach, tb treatment was initiated within a reasonable period of time.",0
"human dendritic cells (dc) can now be generated in vitro in large numbers by culturing cd34+ hematopoietic progenitors in presence of gm-csf+tnf alpha for 12 d. the present study demonstrates that cord blood cd34+ hpc indeed differentiate along two independent dc pathways. at early time points (day 5-7) during the culture, two subsets of dc precursors identified by the exclusive expression of cd1a and cd14 emerge independently. both precursor subsets mature at day 12-14 into dc with typical morphology and phenotype (cd80, cd83, cd86, cd58, high hla class ii). cd1a+ precursors give rise to cells characterized by the expression of birbeck granules, the lag antigen and e-cadherin, three markers specifically expressed on langerhans cells in the epidermis. in contrast, the cd14+ progenitors mature into cd1a+ dc lacking birbeck granules, e-cadherin, and lag antigen but expressing cd2, cd9, cd68, and the coagulation factor xiiia described in dermal dendritic cells. the two mature dc were equally potent in stimulating allogeneic cd45ra+ naive t cells. interestingly, the cd14+ precursors, but not the cd1a+ precursors, represent bipotent cells that can be induced to differentiate, in response to m-csf, into macrophage-like cells, lacking accessory function for t cells. altogether, these results demonstrate that different pathways of dc development exist: the langerhans cells and the cd14(+)-derived dc related to dermal dc or circulating blood dc. the physiological relevance of these two pathways of dc development is discussed with regard to their potential in vivo counterparts.",0
"background supporting 21st century health care and the practice of evidence-based medicine (ebm) requires ubiquitous access to clinical information and to knowledge-based resources to answer clinical questions. many questions go unanswered, however, due to lack of skills in formulating questions, crafting effective search strategies, and accessing databases to identify best levels of evidence. methods this randomized trial was designed as a pilot study to measure the relevancy of search results using three different interfaces for the pubmed search system. two of the search interfaces utilized a specific framework called pico, which was designed to focus clinical questions and to prompt for publication type or type of question asked. the third interface was the standard pubmed interface readily available on the web. study subjects were recruited from interns and residents on an inpatient general medicine rotation at an academic medical center in the us. thirty-one subjects were randomized to one of the three interfaces, given 3 clinical questions, and asked to search pubmed for a set of relevant articles that would provide an answer for each question. the success of the search results was determined by a precision score, which compared the number of relevant or gold standard articles retrieved in a result set to the total number of articles retrieved in that set. results participants using the pico templates (protocol a or protocol b) had higher precision scores for each question than the participants who used protocol c, the standard pubmed web interface. (question 1: a = 35%, b = 28%, c = 20%; question 2: a = 5%, b = 6%, c = 4%; question 3: a = 1%, b = 0%, c = 0%) 95% confidence intervals were calculated for the precision for each question using a lower boundary of zero. however, the 95% confidence limits were overlapping, suggesting no statistical difference between the groups. conclusion due to the small number of searches for each arm, this pilot study could not demonstrate a statistically significant difference between the search protocols. however there was a trend towards higher precision that needs to be investigated in a larger study to determine if pico can improve the relevancy of search results.",0
"background long-term complications of critical illness include intensive care unit (icu)-acquired weakness and neuropsychiatric disease. immobilisation secondary to sedation might potentiate these problems. we assessed the efficacy of combining daily interruption of sedation with physical and occupational therapy on functional outcomes in patients receiving mechanical ventilation in intensive care. methods sedated adults (>/=18 years of age) in the icu who had been on mechanical ventilation for less than 72 h, were expected to continue for at least 24 h, and who met criteria for baseline functional independence were eligible for enrolment in this randomised controlled trial at two university hospitals. we randomly assigned 104 patients by computer-generated, permuted block randomisation to early exercise and mobilisation (physical and occupational therapy) during periods of daily interruption of sedation (intervention; n=49) or to daily interruption of sedation with therapy as ordered by the primary care team (control; n=55). the primary endpoint-the number of patients returning to independent functional status at hospital discharge-was defined as the ability to perform six activities of daily living and the ability to walk independently. therapists who undertook patient assessments were blinded to treatment assignment. secondary endpoints included duration of delirium and ventilator-free days during the first 28 days of hospital stay. analysis was by intention to treat. this trial is registered with clinicaltrials.gov, number nct00322010. findings all 104 patients were included in the analysis. return to independent functional status at hospital discharge occurred in 29 (59%) patients in the intervention group compared with 19 (35%) patients in the control group (p=0.02; odds ratio 2.7 ). patients in the intervention group had shorter duration of delirium (median 2.0 days, iqr 0.0-6.0 vs 4.0 days, 2.0-8.0; p=0.02), and more ventilator-free days (23.5 days, 7.4-25.6 vs 21.1 days, 0.0-23.8; p=0.05) during the 28-day follow-up period than did controls. there was one serious adverse event in 498 therapy sessions (desaturation less than 80%). discontinuation of therapy as a result of patient instability occurred in 19 (4%) of all sessions, most commonly for perceived patient-ventilator asynchrony. interpretation a strategy for whole-body rehabilitation-consisting of interruption of sedation and physical and occupational therapy in the earliest days of critical illness-was safe and well tolerated, and resulted in better functional outcomes at hospital discharge, a shorter duration of delirium, and more ventilator-free days compared with standard care. funding none.",0
"a score based on the combination of the systemic inflammatory response and albumin hazards ratio (hr) 1.70, 95% ci 1.23 - 2.35, p=0.001) was comparable in prognostic value to that based on stage and performance status (hr 1.48, 95% ci 1.12 - 1.95, p=0.006) in patients with inoperable non-small-cell lung cancer. the former is simple to measure and well standardised.",0
"the sodium current (i(na)) that develops after step depolarization of a voltage clamped squid axon is preceded by a transient outward current that is closely associated with the opening of the activation gates of the na pores. this ""gating current"" is best seen when permeant ions (na and k) are replaced by relatively impermeant ones, and when the linear portion of capacitative current is eliminated by adding current from positive steps to that from exactly equal negative ones. during opening of the na pores gating current is outward, and as the pores close there is an inward tail of current that decays with approximately the same time-course as i(na) recorded in na-containing medium. both outward and inward gating current are unaffected by tetrodotoxin (ttx). gating current is capacitative in origin, the result of relatively slow reorientation of charged or dipolar molecules in a suddenly altered membrane field. close association with the na activation process is clear from the time-course of gating current, and from the fact that three procedures that reversibly block i(na) also block gating current: internal perfusion with zn(2+), prolonged depolarization of the membrane, and inactivation of i(na) with a short positive prepulse.",0
"a rat monoclonal antibody specific for immunoglobulin (ig) heavy chain binding protein (bip) has allowed the examination of the association of bip with assembling ig precursors in mouse b lymphocyte-derived cell lines. the anti-bip monoclonal antibody immunoprecipitates bip along with noncovalently associated ig heavy chains. bip is a component of the endoplasmic reticulum and binds free intracellular heavy chains in nonsecreting pre-b (mu+, l-) cell lines or incompletely assembled ig precursors in (h+, l+) secreting hybridomas and myelomas. in the absence of light chain synthesis, heavy chains remain associated with bip and are not secreted. the association of bip with assembling ig molecules in secreting hybridomas is transient and is restricted to the incompletely assembled molecules which are found in the endoplasmic reticulum. bip loses affinity and disassociates with ig molecules when polymerization with light chain is complete. we propose that the association of bip with ig heavy chain precursors is a novel posttranslational processing event occurring in the endoplasmic reticulum. the ig heavy chains associated with bip are not efficiently transported from the endoplasmic reticulum to the golgi apparatus. therefore, bip may prevent the premature escape and eventual secretion of incompletely assembled ig molecules.",0
"background public health recommendations and governmental measures during the covid-19 pandemic have resulted in numerous restrictions on daily living including social distancing, isolation and home confinement. while these measures are imperative to abate the spreading of covid-19, the impact of these restrictions on health behaviours and lifestyles at home is undefined. therefore, an international online survey was launched in april 2020, in seven languages, to elucidate the behavioural and lifestyle consequences of covid-19 restrictions. this report presents the results from the first thousand responders on physical activity (pa) and nutrition behaviours. methods following a structured review of the literature, the ""effects of home confinement on multiple lifestyle behaviours during the covid-19 outbreak (eclb-covid19)"" electronic survey was designed by a steering group of multidisciplinary scientists and academics. the survey was uploaded and shared on the google online survey platform. thirty-five research organisations from europe, north-africa, western asia and the americas promoted the survey in english, german, french, arabic, spanish, portuguese and slovenian languages. questions were presented in a differential format, with questions related to responses ""before"" and ""during"" confinement conditions. results 1047 replies (54% women) from asia (36%), africa (40%), europe (21%) and other (3%) were included in the analysis. the covid-19 home confinement had a negative effect on all pa intensity levels (vigorous, moderate, walking and overall). additionally, daily sitting time increased from 5 to 8 h per day. food consumption and meal patterns (the type of food, eating out of control, snacks between meals, number of main meals) were more unhealthy during confinement, with only alcohol binge drinking decreasing significantly. conclusion while isolation is a necessary measure to protect public health, results indicate that it alters physical activity and eating behaviours in a health compromising direction. a more detailed analysis of survey data will allow for a segregation of these responses in different age groups, countries and other subgroups, which will help develop interventions to mitigate the negative lifestyle behaviours that have manifested during the covid-19 confinement.",0
"pink1 kinase activates the e3 ubiquitin ligase parkin to induce selective autophagy of damaged mitochondria. however, it has been unclear how pink1 activates and recruits parkin to mitochondria. although pink1 phosphorylates parkin, other pink1 substrates appear to activate parkin, as the mutation of all serine and threonine residues conserved between drosophila and human, including parkin s65, did not wholly impair parkin translocation to mitochondria. using mass spectrometry, we discovered that endogenous pink1 phosphorylated ubiquitin at serine 65, homologous to the site phosphorylated by pink1 in parkin's ubiquitin-like domain. recombinant tcpink1 directly phosphorylated ubiquitin and phospho-ubiquitin activated parkin e3 ubiquitin ligase activity in cell-free assays. in cells, the phosphomimetic ubiquitin mutant s65d bound and activated parkin. furthermore, expression of ubiquitin s65a, a mutant that cannot be phosphorylated by pink1, inhibited parkin translocation to damaged mitochondria. these results explain a feed-forward mechanism of pink1-mediated initiation of parkin e3 ligase activity.",0
"the speech, spatial and qualities of hearing scale (ssq) is designed to measure a range of hearing disabilities across several domains. particular attention is given to hearing speech in a variety of competing contexts, and to the directional, distance and movement components of spatial hearing. in addition, the abilities both to segregate sounds and to attend to simultaneous speech streams are assessed, reflecting the reality of hearing in the everyday world. qualities of hearing experience include ease of listening, and the naturalness, clarity and identifiability of different speakers, different musical pieces and instruments, and different everyday sounds. application of the ssq to 153 new clinic clients prior to hearing aid fitting showed that the greatest difficulty was experienced with simultaneous speech streams, ease of listening, listening in groups and in noise, and judging distance and movement. ssq ratings were compared with an independent measure of handicap. after differences in hearing level were controlled for, it was found that identification, attention and effort problems, as well as spatial hearing problems, feature prominently in the disability handicap relationship,. along with certain features of speech hearing. the results implicate aspects of temporal and spatial dynamics of hearing disability in the experience of handicap. the ssq shows promise as an instrument for evaluating interventions of various kinds, particularly (but not exclusively) those that implicate binaural function.",0
"deaths involving synthetic opioids other than methadone (synthetic opioids), which largely consist of illicitly manufactured fentanyl; psychostimulants with abuse potential (e.g., methamphetamine); and cocaine have increased in recent years, particularly since 2013 (1,2). in 2019, a total of 70,630 drug overdose deaths occurred, corresponding to an age-adjusted rate of 21.6 per 100,000 population and a 4.3% increase from the 2018 rate (20.7) (3). cdc analyzed trends in age-adjusted overdose death rates involving synthetic opioids, psychostimulants, cocaine, heroin, and prescription opioids during 2013-2019, as well as geographic patterns in synthetic opioid- and psychostimulant-involved deaths during 2018-2019. from 2013 to 2019, the synthetic opioid-involved death rate increased 1,040%, from 1.0 to 11.4 per 100,000 age-adjusted (3,105 to 36,359). the psychostimulant-involved death rate increased 317%, from 1.2 (3,627) in 2013 to 5.0 (16,167) in 2019. in the presence of synthetic opioid coinvolvement, death rates for prescription opioids, heroin, psychostimulants, and cocaine increased. in the absence of synthetic opioid coinvolvement, death rates increased only for psychostimulants and cocaine. from 2018 to 2019, the largest relative increase in the synthetic opioid-involved death rate occurred in the west (67.9%), and the largest relative increase in the psychostimulant-involved death rate occurred in the northeast (43.8%); these increases represent important changes in the geographic distribution of drug overdose deaths. evidence-based prevention and response strategies including substance use disorder treatment and overdose prevention and response efforts focused on polysubstance use must be adapted to address the evolving drug overdose epidemic.",0
"background alcohol is a risk factor for cancer of the oral cavity, pharynx, oesophagus, colorectum, liver, larynx and female breast, whereas its impact on other cancers remains controversial. methods we investigated the effect of alcohol on 23 cancer types through a meta-analytic approach. we used dose-response meta-regression models and investigated potential sources of heterogeneity. results a total of 572 studies, including 486 538 cancer cases, were identified. relative risks (rrs) for heavy drinkers compared with nondrinkers and occasional drinkers were 5.13 for oral and pharyngeal cancer, 4.95 for oesophageal squamous cell carcinoma, 1.44 for colorectal, 2.65 for laryngeal and 1.61 for breast cancer; for those neoplasms there was a clear dose-risk relationship. heavy drinkers also had a significantly higher risk of cancer of the stomach (rr 1.21), liver (2.07), gallbladder (2.64), pancreas (1.19) and lung (1.15). there was indication of a positive association between alcohol consumption and risk of melanoma and prostate cancer. alcohol consumption and risk of hodgkin's and non-hodgkin's lymphomas were inversely associated. conclusions alcohol increases risk of cancer of oral cavity and pharynx, oesophagus, colorectum, liver, larynx and female breast. there is accumulating evidence that alcohol drinking is associated with some other cancers such as pancreas and prostate cancer and melanoma.",0
"marlieke de kraker and colleagues reflect on the need for better global estimates for the burden of antimicrobial resistance.",0
"the organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. for example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. it is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. however, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. we used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. we describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. we demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. these live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. this methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics.",0
"zika virus (zikv) has recently caused a pandemic disease, and many cases of zikv infection in pregnant women resulted in abortion, stillbirth, deaths and congenital defects including microcephaly, which now has been proposed as zikv congenital syndrome. this study aimed to investigate the in situ immune response profile and mechanisms of neuronal cell damage in fatal zika microcephaly cases. brain tissue samples were collected from 15 cases, including 10 microcephalic zikv-positive neonates with fatal outcome and five neonatal control flavivirus-negative neonates that died due to other causes, but with preserved central nervous system (cns) architecture. in microcephaly cases, the histopathological features of the tissue samples were characterized in three cns areas (meninges, perivascular space, and parenchyma). the changes found were mainly calcification, necrosis, neuronophagy, gliosis, microglial nodules, and inflammatory infiltration of mononuclear cells. the in situ immune response against zikv in the cns of newborns is complex. despite the predominant expression of th2 cytokines, other cytokines such as th1, th17, treg, th9, and th22 are involved to a lesser extent, but are still likely to participate in the immunopathogenic mechanisms of neural disease in fatal cases of microcephaly caused by zikv.",0
"although much traditional sensory research has studied each sensory modality in isolation, there has been a recent explosion of interest in causal interplay between different senses. various techniques have now identified numerous multisensory convergence zones in the brain. some convergence may arise surprisingly close to low-level sensory-specific cortex, and some direct connections may exist even between primary sensory cortices. a variety of multisensory phenomena have now been reported in which sensory-specific brain responses and perceptual judgments concerning one sense can be affected by relations with other senses. we survey recent progress in this multisensory field, foregrounding human studies against the background of invasive animal work and highlighting possible underlying mechanisms. these include rapid feedforward integration, possible thalamic influences, and/or feedback from multisensory regions to sensory-specific brain areas. multisensory interplay is more prevalent than classic modular approaches assumed, and new methods are now available to determine the underlying circuits.",0
"measurement of glycated hemoglobin (hba 1c ) has been the traditional method for assessing glycemic control. however, it does not reflect intra- and interday glycemic excursions that may lead to acute events (such as hypoglycemia) or postprandial hyperglycemia, which have been linked to both microvascular and macrovascular complications. continuous glucose monitoring (cgm), either from real-time use (rtcgm) or intermittently viewed (icgm), addresses many of the limitations inherent in hba 1c testing and self-monitoring of blood glucose. although both provide the means to move beyond the hba 1c measurement as the sole marker of glycemic control, standardized metrics for analyzing cgm data are lacking. moreover, clear criteria for matching people with diabetes to the most appropriate glucose monitoring methodologies, as well as standardized advice about how best to use the new information they provide, have yet to be established. in february 2017, the advanced technologies & treatments for diabetes (attd) congress convened an international panel of physicians, researchers, and individuals with diabetes who are expert in cgm technologies to address these issues. this article summarizes the attd consensus recommendations and represents the current understanding of how cgm results can affect outcomes.",0
"loss-of-function mutations in park2, the gene coding for the ubiquitin ligase parkin, are a significant cause of early onset parkinson's disease. although the role of parkin in neuron maintenance is unknown, recent work has linked parkin to the regulation of mitochondria. its loss is associated with swollen mitochondria and muscle degeneration in drosophila melanogaster, as well as mitochondrial dysfunction and increased susceptibility to mitochondrial toxins in other species. here, we show that parkin is selectively recruited to dysfunctional mitochondria with low membrane potential in mammalian cells. after recruitment, parkin mediates the engulfment of mitochondria by autophagosomes and the selective elimination of impaired mitochondria. these results show that parkin promotes autophagy of damaged mitochondria and implicate a failure to eliminate dysfunctional mitochondria in the pathogenesis of parkinson's disease.",0
"the label 'chronic fatigue syndrome' (cfs) has persisted for many years because of the lack of knowledge of the aetiological agents and the disease process. in view of more recent research and clinical experience that strongly point to widespread inflammation and multisystemic neuropathology, it is more appropriate and correct to use the term 'myalgic encephalomyelitis' (me) because it indicates an underlying pathophysiology. it is also consistent with the neurological classification of me in the world health organization's international classification of diseases (icd g93.3). consequently, an international consensus panel consisting of clinicians, researchers, teaching faculty and an independent patient advocate was formed with the purpose of developing criteria based on current knowledge. thirteen countries and a wide range of specialties were represented. collectively, members have approximately 400 years of both clinical and teaching experience, authored hundreds of peer-reviewed publications, diagnosed or treated approximately 50 000 patients with me, and several members coauthored previous criteria. the expertise and experience of the panel members as well as pubmed and other medical sources were utilized in a progression of suggestions/drafts/reviews/revisions. the authors, free of any sponsoring organization, achieved 100% consensus through a delphi-type process. the scope of this paper is limited to criteria of me and their application. accordingly, the criteria reflect the complex symptomatology. operational notes enhance clarity and specificity by providing guidance in the expression and interpretation of symptoms. clinical and research application guidelines promote optimal recognition of me by primary physicians and other healthcare providers, improve the consistency of diagnoses in adult and paediatric patients internationally and facilitate clearer identification of patients for research studies.",0
"diversity and plasticity are two hallmarks of macrophages. m1 macrophages (classically activated macrophages) are pro-inflammatory and have a central role in host defense against infection, while m2 macrophages (alternatively activated macrophages) are associated with responses to anti-inflammatory reactions and tissue remodeling, and they represent two terminals of the full spectrum of macrophage activation. transformation of different phenotypes of macrophages regulates the initiation, development, and cessation of inflammatory diseases. here we reviewed the characters and functions of macrophage polarization in infection, atherosclerosis, obesity, tumor, asthma, and sepsis, and proposed that targeting macrophage polarization and skewing their phenotype to adapt to the microenvironment might hold great promise for the treatment of inflammatory diseases.",0
"motivation although many next-generation sequencing (ngs) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. we have developed trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. results the value of ngs read preprocessing is demonstrated for both reference-based and reference-free tasks. trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. availability and implementation trimmomatic is licensed under gpl v3. it is cross-platform (java 1.5+ required) and available at contact usadel@bio1.rwth-aachen.de supplementary information supplementary data are available at bioinformatics online.",0
"geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. computed atlas of surface topography of proteins (castp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. it has been widely used since its inception in 2003. in this article, we present the latest version of the web server, castp 3.0. castp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. in addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the protein data bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. the castp 3.0 web server is freely accessible at",0
"mutations in isocitrate dehydrogenases 1 and 2 (idh1 and idh2) have been shown to be present in most world health organization grade 2 and grade 3 gliomas in adults. these mutations are associated with the accumulation of 2-hydroxyglutarate (2hg) in the tumor. here we report the noninvasive detection of 2hg by proton magnetic resonance spectroscopy (mrs). we developed and optimized the pulse sequence with numerical and phantom analyses for 2hg detection, and we estimated the concentrations of 2hg using spectral fitting in the tumors of 30 subjects. detection of 2hg correlated with mutations in idh1 or idh2 and with increased levels of d-2hg by mass spectrometry of the resected tumors. noninvasive detection of 2hg may prove to be a valuable diagnostic and prognostic biomarker.",0
"instrumental variable analysis is an approach for obtaining causal inferences on the effect of an exposure (risk factor) on an outcome from observational data. it has gained in popularity over the past decade with the use of genetic variants as instrumental variables, known as mendelian randomization. an instrumental variable is associated with the exposure, but not associated with any confounder of the exposure-outcome association, nor is there any causal pathway from the instrumental variable to the outcome other than via the exposure. under the assumption that a single instrumental variable or a set of instrumental variables for the exposure is available, the causal effect of the exposure on the outcome can be estimated. there are several methods available for instrumental variable estimation; we consider the ratio method, two-stage methods, likelihood-based methods, and semi-parametric methods. techniques for obtaining statistical inferences and confidence intervals are presented. the statistical properties of estimates from these methods are compared, and practical advice is given about choosing a suitable analysis method. in particular, bias and coverage properties of estimators are considered, especially with weak instruments. settings particularly relevant to mendelian randomization are prioritized in the paper, notably the scenario of a continuous exposure and a continuous or binary outcome.",0
"objective to generate estimates of the global prevalence and incidence of urogenital infection with chlamydia, gonorrhoea, trichomoniasis and syphilis in women and men, aged 15-49 years, in 2016. methods for chlamydia, gonorrhoea and trichomoniasis, we systematically searched for studies conducted between 2009 and 2016 reporting prevalence. we also consulted regional experts. to generate estimates, we used bayesian meta-analysis. for syphilis, we aggregated the national estimates generated by using spectrum-sti. findings for chlamydia, gonorrhoea and/or trichomoniasis, 130 studies were eligible. for syphilis, the spectrum-sti database contained 978 data points for the same period. the 2016 global prevalence estimates in women were: chlamydia 3.8% (95% uncertainty interval, ui: 3.3-4.5); gonorrhoea 0.9% (95% ui: 0.7-1.1); trichomoniasis 5.3% (95% ui:4.0-7.2); and syphilis 0.5% (95% ui: 0.4-0.6). in men prevalence estimates were: chlamydia 2.7% (95% ui: 1.9-3.7); gonorrhoea 0.7% (95% ui: 0.5-1.1); trichomoniasis 0.6% (95% ui: 0.4-0.9); and syphilis 0.5% (95% ui: 0.4-0.6). total estimated incident cases were 376.4 million: 127.2 million (95% ui: 95.1-165.9 million) chlamydia cases; 86.9 million (95% ui: 58.6-123.4 million) gonorrhoea cases; 156.0 million (95% ui: 103.4-231.2 million) trichomoniasis cases; and 6.3 million (95% ui: 5.5-7.1 million) syphilis cases. conclusion global estimates of prevalence and incidence of these four curable sexually transmitted infections remain high. the study highlights the need to expand data collection efforts at country level and provides an initial baseline for monitoring progress of the world health organization global health sector strategy on sexually transmitted infections 2016-202 1.",0
"lipid-based drug delivery systems, or lipidic carriers, are being extensively employed to enhance the bioavailability of poorly-soluble drugs. they have the ability to incorporate both lipophilic and hydrophilic molecules and protecting them against degradation in vitro and in vivo. there is a number of physical attributes of lipid-based nanocarriers that determine their safety, stability, efficacy, as well as their in vitro and in vivo behaviour. these include average particle size/diameter and the polydispersity index (pdi), which is an indication of their quality with respect to the size distribution. the suitability of nanocarrier formulations for a particular route of drug administration depends on their average diameter, pdi and size stability, among other parameters. controlling and validating these parameters are of key importance for the effective clinical applications of nanocarrier formulations. this review highlights the significance of size and pdi in the successful design, formulation and development of nanosystems for pharmaceutical, nutraceutical and other applications. liposomes, nanoliposomes, vesicular phospholipid gels, solid lipid nanoparticles, transfersomes and tocosomes are presented as frequently-used lipidic drug carriers. the advantages and limitations of a range of available analytical techniques used to characterize lipidic nanocarrier formulations are also covered.",0
"cell migration through 3d tissue depends on a physicochemical balance between cell deformability and physical tissue constraints. migration rates are further governed by the capacity to degrade ecm by proteolytic enzymes, particularly matrix metalloproteinases (mmps), and integrin- and actomyosin-mediated mechanocoupling. yet, how these parameters cooperate when space is confined remains unclear. using mmp-degradable collagen lattices or nondegradable substrates of varying porosity, we quantitatively identify the limits of cell migration by physical arrest. mmp-independent migration declined as linear function of pore size and with deformation of the nucleus, with arrest reached at 10% of the nuclear cross section (tumor cells, 7 µm²; t cells, 4 µm²; neutrophils, 2 µm²). residual migration under space restriction strongly depended upon mmp-dependent ecm cleavage by enlarging matrix pore diameters, and integrin- and actomyosin-dependent force generation, which jointly propelled the nucleus. the limits of interstitial cell migration thus depend upon scaffold porosity and deformation of the nucleus, with pericellular collagenolysis and mechanocoupling as modulators.",0
"background next generation sequencing (ngs) technology has revolutionized genomic and genetic research. the pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: ion torrent's pgm, pacific biosciences' rs and the illumina miseq. here we compare the results obtained with those platforms to the performance of the illumina hiseq, the current market leader. in order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean gc content ranging from 19.3 to 67.7%. together, these represent a comprehensive range of genome content. here we report our analysis of that sequence data in terms of coverage distribution, bias, gc distribution, variant detection and accuracy. results sequence generated by ion torrent, miseq and pacific biosciences technologies displays near perfect coverage behaviour on gc-rich, neutral and moderately at-rich genomes, but a profound bias was observed upon sequencing the extremely at-rich genome of plasmodium falciparum on the pgm, resulting in no coverage for approximately 30% of the genome. we analysed the ability to call variants from each platform and found that we could call slightly more variants from ion torrent data compared to miseq data, but at the expense of a higher false positive rate. variant calling from pacific biosciences data was possible but higher coverage depth was required. context specific errors were observed in both pgm and miseq data, but not in that from the pacific biosciences platform. conclusions all three fast turnaround sequencers evaluated here were able to generate usable sequence. however there are key differences between the quality of that data and the applications it will support.",0
"purpose the immunomodulatory effect of lenvatinib (a multikinase inhibitor) on tumor microenvironments may contribute to antitumor activity when combined with programmed death receptor-1 (pd-1) signaling inhibitors in hepatocellular carcinoma (hcc). we report results from a phase ib study of lenvatinib plus pembrolizumab (an anti-pd-1 antibody) in unresectable hcc (uhcc). patients and methods in this open-label multicenter study, patients with uhcc received lenvatinib (bodyweight ≥ 60 kg, 12 mg; results a total of 104 patients were enrolled. no dlts were reported (n = 6) in the dlt phase; 100 patients (expansion phase; included n = 2 from dlt phase) had received no prior systemic therapy and had barcelona clinic liver cancer stage b (n = 29) or c disease (n = 71). at data cutoff, 37% of patients remained on treatment. median duration of follow-up was 10.6 months (95% ci, 9.2 to 11.5 months). confirmed orrs by iir were 46.0% (95% ci, 36.0% to 56.3%) per mrecist and 36.0% (95% ci, 26.6% to 46.2%) per recist v1.1. median dors by iir were 8.6 months (95% ci, 6.9 months to not estimable ) per mrecist and 12.6 months (95% ci, 6.9 months to ne) per recist v1.1. median progression-free survival by iir was 9.3 months per mrecist and 8.6 months per recist v1.1. median overall survival was 22 months. grade ≥ 3 treatment-related adverse events occurred in 67% (grade 5, 3%) of patients. no new safety signals were identified. conclusion lenvatinib plus pembrolizumab has promising antitumor activity in uhcc. toxicities were manageable, with no unexpected safety signals.",0
"cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. we describe cytoscape automation (ca), which marries cytoscape to highly productive workflow systems, for example, python/r in jupyter/rstudio. we expose over 270 cytoscape core functions and 34 cytoscape apps as rest-callable functions with standardized json interfaces backed by swagger documentation. independent projects to create and publish python/r native ca interface libraries have reached an advanced stage, and a number of automation workflows are already published.",0
"stroke is a leading cause of disability, but no pharmacological therapy is currently available for promoting recovery. the brain region adjacent to stroke damage-the peri-infarct zone-is critical for rehabilitation, as it shows heightened neuroplasticity, allowing sensorimotor functions to re-map from damaged areas. thus, understanding the neuronal properties constraining this plasticity is important for the development of new treatments. here we show that after a stroke in mice, tonic neuronal inhibition is increased in the peri-infarct zone. this increased tonic inhibition is mediated by extrasynaptic gaba(a) receptors and is caused by an impairment in gaba (γ-aminobutyric acid) transporter (gat-3/gat-4) function. to counteract the heightened inhibition, we administered in vivo a benzodiazepine inverse agonist specific for α5-subunit-containing extrasynaptic gaba(a) receptors at a delay after stroke. this treatment produced an early and sustained recovery of motor function. genetically lowering the number of α5- or δ-subunit-containing gaba(a) receptors responsible for tonic inhibition also proved beneficial for recovery after stroke, consistent with the therapeutic potential of diminishing extrasynaptic gaba(a) receptor function. together, our results identify new pharmacological targets and provide the rationale for a novel strategy to promote recovery after stroke and possibly other brain injuries.",0
"this paper describes the application of mixed method designs in implementation research in 22 mental health services research studies published in peer-reviewed journals over the last 5 years. our analyses revealed 7 different structural arrangements of qualitative and quantitative methods, 5 different functions of mixed methods, and 3 different ways of linking quantitative and qualitative data together. complexity of design was associated with number of aims or objectives, study context, and phase of implementation examined. the findings provide suggestions for the use of mixed method designs in implementation research.",0
"we present a global analysis of the spread of recently emerged sars-cov-2 variants and estimate changes in effective reproduction numbers at country-specific level using sequence data from gisaid. nearly all investigated countries demonstrated rapid replacement of previously circulating lineages by the world health organization-designated variants of concern, with estimated transmissibility increases of 29% (95% ci: 24-33), 25% (95% ci: 20-30), 38% (95% ci: 29-48) and 97% (95% ci: 76-117), respectively, for b.1.1.7, b.1.351, p.1 and b.1.617.2.",0
"recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. the amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. we present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) snp discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. we here discuss the application of these tools, instantiated in the genome analysis toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 genomes project datasets.",0
"this paper describes fieldtrip, an open source software package that we developed for the analysis of meg, eeg, and other electrophysiological data. the software is implemented as a matlab toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. it includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. the implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the matlab command line and batch scripting. furthermore, users and developers can easily extend the functionality and implement new algorithms. the modular design facilitates the reuse in other software packages.",0
"myd88, irak4 and irak2 are critical signalling mediators of the tlr/il1-r superfamily. here we report the crystal structure of the myd88-irak4-irak2 death domain (dd) complex, which surprisingly reveals a left-handed helical oligomer that consists of 6 myd88, 4 irak4 and 4 irak2 dds. assembly of this helical signalling tower is hierarchical, in which myd88 recruits irak4 and the myd88-irak4 complex recruits the irak4 substrates irak2 or the related irak1. formation of these myddosome complexes brings the kinase domains of iraks into proximity for phosphorylation and activation. composite binding sites are required for recruitment of the individual dds in the complex, which are confirmed by mutagenesis and previously identified signalling mutations. specificities in myddosome formation are dictated by both molecular complementarity and correspondence of surface electrostatics. the myd88-irak4-irak2 complex provides a template for toll signalling in drosophila and an elegant mechanism for versatile assembly and regulation of dd complexes in signal transduction.",0
"background in this study, we aimed to evaluate the effects of tocilizumab in adult patients admitted to hospital with covid-19 with both hypoxia and systemic inflammation. methods this randomised, controlled, open-label, platform trial (randomised evaluation of covid-19 therapy ), is assessing several possible treatments in patients hospitalised with covid-19 in the uk. those trial participants with hypoxia (oxygen saturation findings between april 23, 2020, and jan 24, 2021, 4116 adults of 21 550 patients enrolled into the recovery trial were included in the assessment of tocilizumab, including 3385 (82%) patients receiving systemic corticosteroids. overall, 621 (31%) of the 2022 patients allocated tocilizumab and 729 (35%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0·85; 95% ci 0·76-0·94; p=0·0028). consistent results were seen in all prespecified subgroups of patients, including those receiving systemic corticosteroids. patients allocated to tocilizumab were more likely to be discharged from hospital within 28 days (57% vs 50%; rate ratio 1·22; 1·12-1·33; p interpretation in hospitalised covid-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes. these benefits were seen regardless of the amount of respiratory support and were additional to the benefits of systemic corticosteroids. funding uk research and innovation (medical research council) and national institute of health research.",0
"the interpro database ( integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: gene3d, panther, pfam, pirsf, prints, prodom, prosite, smart, superfamily and tigrfams. integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an interpro entry. recently, we have started to also display the remaining un-integrated signatures via our web interface. other developments include the provision of non-signature data, such as structural data, in new xml files on our ftp site, as well as the inclusion of matchless uniprotkb proteins in the existing match xml files. the web interface has been extended and now links out to the adan predicted protein-protein interaction database and the spice and dasty viewers. the latest public release (v18.0) covers 79.8% of uniprotkb (v14.1) and consists of 16 549 entries. interpro data may be accessed either via the web address above, via web services, by downloading files by anonymous ftp or by using the interproscan search software (",0
"background in 2004, a review of pilot studies published in seven major medical journals during 2000-01 recommended that the statistical analysis of such studies should be either mainly descriptive or focus on sample size estimation, while results from hypothesis testing must be interpreted with caution. we revisited these journals to see whether the subsequent recommendations have changed the practice of reporting pilot studies. we also conducted a survey to identify the methodological components in registered research studies which are described as 'pilot' or 'feasibility' studies. we extended this survey to grant-awarding bodies and editors of medical journals to discover their policies regarding the function and reporting of pilot studies. methods papers from 2007-08 in seven medical journals were screened to retrieve published pilot studies. reports of registered and completed studies on the uk clinical research network (ukcrn) portfolio database were retrieved and scrutinized. guidance on the conduct and reporting of pilot studies was retrieved from the websites of three grant giving bodies and seven journal editors were canvassed. results 54 pilot or feasibility studies published in 2007-8 were found, of which 26 (48%) were pilot studies of interventions and the remainder feasibility studies. the majority incorporated hypothesis-testing (81%), a control arm (69%) and a randomization procedure (62%). most (81%) pointed towards the need for further research. only 8 out of 90 pilot studies identified by the earlier review led to subsequent main studies. twelve studies which were interventional pilot/feasibility studies and which included testing of some component of the research process were identified through the ukcrn portfolio database. there was no clear distinction in use of the terms 'pilot' and 'feasibility'. five journal editors replied to our entreaty. in general they were loathe to publish studies described as 'pilot'. conclusion pilot studies are still poorly reported, with inappropriate emphasis on hypothesis-testing. authors should be aware of the different requirements of pilot studies, feasibility studies and main studies and report them appropriately. authors should be explicit as to the purpose of a pilot study. the definitions of feasibility and pilot studies vary and we make proposals here to clarify terminology.",0
"background treatment with immune checkpoint blockade (icb) with agents such as anti-programmed cell death protein 1 (pd-1), anti-programmed death-ligand 1 (pd-l1), and/or anti-cytotoxic t-lymphocyte-associated protein 4 (ctla-4) can result in impressive response rates and durable disease remission but only in a subset of patients with cancer. expression of pd-l1 has demonstrated utility in selecting patients for response to icb and has proven to be an important biomarker for patient selection. tumor mutation burden (tmb) is emerging as a potential biomarker. however, refinement of interpretation and contextualization is required. materials and methods in this review, we outline the evolution of tmb as a biomarker in oncology, delineate how tmb can be applied in the clinic, discuss current limitations as a diagnostic test, and highlight mechanistic insights unveiled by the study of tmb. we review available data to date studying tmb as a biomarker for response to icb by tumor type, focusing on studies proposing a threshold for tmb as a predictive biomarker for icb activity. results high tmb consistently selects for benefit with icb therapy. in lung, bladder and head and neck cancers, the current predictive tmb thresholds proposed approximate 200 non-synonymous somatic mutations by whole exome sequencing (wes). pd-l1 expression influences response to icb in high tmb tumors with single agent pd-(l)1 antibodies; however, response may not be dependent on pd-l1 expression in the setting of anti-ctla4 or anti-pd-1/ctla-4 combination therapy. disease-specific tmb thresholds for effective prediction of response in various other malignancies are not well established. conclusions tmb, in concert with pd-l1 expression, has been demonstrated to be a useful biomarker for icb selection across some cancer types; however, further prospective validation studies are required. tmb determination by selected targeted panels has been correlated with wes. calibration and harmonization will be required for optimal utility and alignment across all platforms currently used internationally. key challenges will need to be addressed before broader use in different tumor types.",0
"background the increased use of meta-analysis in systematic reviews of healthcare interventions has highlighted several types of bias that can arise during the completion of a randomised controlled trial. study publication bias has been recognised as a potential threat to the validity of meta-analysis and can make the readily available evidence unreliable for decision making. until recently, outcome reporting bias has received less attention. methodology/principal findings we review and summarise the evidence from a series of cohort studies that have assessed study publication bias and outcome reporting bias in randomised controlled trials. sixteen studies were eligible of which only two followed the cohort all the way through from protocol approval to information regarding publication of outcomes. eleven of the studies investigated study publication bias and five investigated outcome reporting bias. three studies have found that statistically significant outcomes had a higher odds of being fully reported compared to non-significant outcomes (range of odds ratios: 2.2 to 4.7). in comparing trial publications to protocols, we found that 40-62% of studies had at least one primary outcome that was changed, introduced, or omitted. we decided not to undertake meta-analysis due to the differences between studies. conclusions recent work provides direct empirical evidence for the existence of study publication bias and outcome reporting bias. there is strong evidence of an association between significant results and publication; studies that report positive or significant results are more likely to be published and outcomes that are statistically significant have higher odds of being fully reported. publications have been found to be inconsistent with their protocols. researchers need to be aware of the problems of both types of bias and efforts should be concentrated on improving the reporting of trials.",0
"neonatal thymectomy (ntx), especially around day 3 after birth, causes various organ-specific autoimmune diseases in mice. this report shows that: (a) t cells expressing the interleukin 2 receptor alpha chains (cd25) ontogenically begin to appear in the normal periphery immediately after day 3, rapidly increasing within 2 wk to nearly adult levels (approximately 10% of cd3+ cells, especially of cd4+ cells); (b) ntx on day 3 eliminates cd25+ t cells from the periphery for several days; inoculation immediately after ntx of cd25+ splenic t cells from syngeneic non-tx adult mice prevents autoimmune development, whereas inoculation of cd25- t cells even at a larger dose does not; and furthermore, (c) similar autoimmune diseases can be produced in adult athymic nu/nu mice by inoculating either spleen cell suspensions from 3-d-old euthymic nu/+ mice or cd25+ cell-depleted spleen cell suspensions from older, even 1-yr-old, nu/+ mice. the cd25- populations from neonates or adults are also similar in the profile of cytokine formation. these results, taken together, indicate that one aspect of peripheral self-tolerance is maintained by cd25+ t cells that sustain potentially pathogenic self-reactive t cells in a cd25- dormant state; the thymic production of the former is developmentally programmed to begin on day 3 after birth in mice. thus, ntx on day 3 can, at least transiently, eliminate/reduce the autoimmune-preventive cd25+ t cells, thereby leading to activation of the self-reactive t cells that have been produced before ntx.",0
"transforming growth factor (tgf)-beta1 is a major pluripotential cytokine with a pronounced immunosuppressive effect and its deficiency results in lethal autoimmunity in mice. however, mechanisms of its immunosuppressive action are not completely understood. here, we report that tgf-beta1 supports the maintenance of foxp3 expression, regulatory function, and homeostasis in peripheral cd4(+)cd25(+) regulatory t (t reg) cells, but is not required for their thymic development. we found that in 8-10-d-old tgf-beta1-deficient mice, peripheral, but not thymic, t reg cells are significantly reduced in numbers. moreover, our experiments suggest that a defect in tgf-beta-mediated signaling in t reg cells is associated with a decrease in foxp3 expression and suppressor activity. thus, our results establish an essential link between tgf-beta1 signaling in peripheral t reg cells and t reg cell maintenance in vivo.",0
"background depression and suicide are responsible for a substantial burden of disease globally. evidence suggests that intimate partner violence (ipv) experience is associated with increased risk of depression, but also that people with mental disorders are at increased risk of violence. we aimed to investigate the extent to which ipv experience is associated with incident depression and suicide attempts, and vice versa, in both women and men. methods and findings we conducted a systematic review and meta-analysis of longitudinal studies published before february 1, 2013. more than 22,000 records from 20 databases were searched for studies examining physical and/or sexual intimate partner or dating violence and symptoms of depression, diagnosed major depressive disorder, dysthymia, mild depression, or suicide attempts. random effects meta-analyses were used to generate pooled odds ratios (ors). sixteen studies with 36,163 participants met our inclusion criteria. all studies included female participants; four studies also included male participants. few controlled for key potential confounders other than demographics. all but one depression study measured only depressive symptoms. for women, there was clear evidence of an association between ipv and incident depressive symptoms, with 12 of 13 studies showing a positive direction of association and 11 reaching statistical significance; pooled or from six studies = 1.97 (95% ci 1.56-2.48, i² = 50.4%, p(heterogeneity = 0.073). there was also evidence of an association in the reverse direction between depressive symptoms and incident ipv (pooled or from four studies = 1.93, 95% ci 1.51-2.48, i² = 0%, p = 0.481). ipv was also associated with incident suicide attempts. for men, evidence suggested that ipv was associated with incident depressive symptoms, but there was no clear evidence of an association between ipv and suicide attempts or depression and incident ipv. conclusions in women, ipv was associated with incident depressive symptoms, and depressive symptoms with incident ipv. ipv was associated with incident suicide attempts. in men, few studies were conducted, but evidence suggested ipv was associated with incident depressive symptoms. there was no clear evidence of association with suicide attempts.",0
"in the course of our supervisory work over the years, we have noticed that qualitative research tends to evoke a lot of questions and worries, so-called frequently asked questions (faqs). this series of four articles intends to provide novice researchers with practical guidance for conducting high-quality qualitative research in primary care. by 'novice' we mean master's students and junior researchers, as well as experienced quantitative researchers who are engaging in qualitative research for the first time. this series addresses their questions and provides researchers, readers, reviewers and editors with references to criteria and tools for judging the quality of qualitative research papers. the second article focused on context, research questions and designs, and referred to publications for further reading. this third article addresses faqs about sampling, data collection and analysis. the data collection plan needs to be broadly defined and open at first, and become flexible during data collection. sampling strategies should be chosen in such a way that they yield rich information and are consistent with the methodological approach used. data saturation determines sample size and will be different for each study. the most commonly used data collection methods are participant observation, face-to-face in-depth interviews and focus group discussions. analyses in ethnographic, phenomenological, grounded theory, and content analysis studies yield different narrative findings: a detailed description of a culture, the essence of the lived experience, a theory, and a descriptive summary, respectively. the fourth and final article will focus on trustworthiness and publishing qualitative research.",0
"in a recently developed human breast cancer model, treatment of tumor cells in a 3-dimensional culture with inhibitory beta1-integrin antibody or its fab fragments led to a striking morphological and functional reversion to a normal phenotype. a stimulatory beta1-integrin antibody proved to be ineffective. the newly formed reverted acini re-assembled a basement membrane and re-established e-cadherin-catenin complexes, and re-organized their cytoskeletons. at the same time they downregulated cyclin d1, upregulated p21(cip,wat-1), and stopped growing. tumor cells treated with the same antibody and injected into nude mice had significantly reduced number and size of tumors in nude mice. the tissue distribution of other integrins was also normalized, suggesting the existence of intimate interactions between the different integrin pathways as well as adherens junctions. on the other hand, nonmalignant cells when treated with either alpha6 or beta4 function altering antibodies continued to grow, and had disorganized colony morphologies resembling the untreated tumor colonies. this shows a significant role of the alpha6/beta4 heterodimer in directing polarity and tissue structure. the observed phenotypes were reversible when the cells were disassociated and the antibodies removed. our results illustrate that the extracellular matrix and its receptors dictate the phenotype of mammary epithelial cells, and thus in this model system the tissue phenotype is dominant over the cellular genotype.",0
"gastric cancer (gc) is one of the most common malignancies worldwide and it is the fourth leading cause of cancer-related death. gc is a multifactorial disease, where both environmental and genetic factors can have an impact on its occurrence and development. the incidence rate of gc rises progressively with age; the median age at diagnosis is 70 years. however, approximately 10% of gastric carcinomas are detected at the age of 45 or younger. early-onset gastric cancer is a good model to study genetic alterations related to the carcinogenesis process, as young patients are less exposed to environmental carcinogens. carcinogenesis is a multistage disease process specified by the progressive development of mutations and epigenetic alterations in the expression of various genes, which are responsible for the occurrence of the disease.",0
"nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. however, with the rapidly growing amount of data, this task remains a computational bottleneck. recently, approximation methods such as the raxml rapid bootstrap (rbs) and the shimodaira-hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. here, we suggest an ultrafast bootstrap approximation approach (ufboot) to compute the support of phylogenetic groups in maximum likelihood (ml) based trees. to achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. we also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. ufboot achieves a median speed up of 3.1 (range: 0.66-33.3) to 10.2 (range: 1.32-41.4) compared with raxml rbs for real dna and amino acid alignments, respectively. moreover, our extensive simulations show that ufboot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. this provides a more direct interpretation of the bootstrap support. we offer an efficient and easy-to-use software (available at to perform the ufboot analysis with ml tree inference.",0
"ulcerative colitis and crohn's disease are the principal forms of inflammatory bowel disease. both represent chronic inflammation of the gastrointestinal tract, which displays heterogeneity in inflammatory and symptomatic burden between patients and within individuals over time. optimal management relies on understanding and tailoring evidence-based interventions by clinicians in partnership with patients. this guideline for management of inflammatory bowel disease in adults over 16 years of age was developed by stakeholders representing uk physicians (british society of gastroenterology), surgeons (association of coloproctology of great britain and ireland), specialist nurses (royal college of nursing), paediatricians (british society of paediatric gastroenterology, hepatology and nutrition), dietitians (british dietetic association), radiologists (british society of gastrointestinal and abdominal radiology), general practitioners (primary care society for gastroenterology) and patients (crohn's and colitis uk). a systematic review of 88 247 publications and a delphi consensus process involving 81 multidisciplinary clinicians and patients was undertaken to develop 168 evidence- and expert opinion-based recommendations for pharmacological, non-pharmacological and surgical interventions, as well as optimal service delivery in the management of both ulcerative colitis and crohn's disease. comprehensive up-to-date guidance is provided regarding indications for, initiation and monitoring of immunosuppressive therapies, nutrition interventions, pre-, peri- and postoperative management, as well as structure and function of the multidisciplinary team and integration between primary and secondary care. twenty research priorities to inform future clinical management are presented, alongside objective measurement of priority importance, determined by 2379 electronic survey responses from individuals living with ulcerative colitis and crohn's disease, including patients, their families and friends.",0
"this paper describes a shift in medical education away from pedagogic approaches to stigma and inequalities that emphasize cross-cultural understandings of individual patients, toward attention to forces that influence health outcomes at levels above individual interactions. it reviews existing structural approaches to stigma and health inequalities developed outside of medicine, and proposes changes to u.s. medical education that will infuse clinical training with a structural focus. the approach, termed ""structural competency,"" consists of training in five core competencies: 1) recognizing the structures that shape clinical interactions; 2) developing an extra-clinical language of structure; 3) rearticulating ""cultural"" formulations in structural terms; 4) observing and imagining structural interventions; and 5) developing structural humility. examples are provided of structural health scholarship that should be adopted into medical didactic curricula, and of structural interventions that can provide participant-observation opportunities for clinical trainees. the paper ultimately argues that increasing recognition of the ways in which social and economic forces produce symptoms or methylate genes then needs to be better coupled with medical models for structural change.",0
"as a transmissible infectious disease, severe acute respiratory syndrome (sars) was successfully contained globally by instituting widespread quarantine measures. although these measures were successful in terminating the outbreak in all areas of the world, the adverse effects of quarantine have not previously been determined in a systematic manner. in this hypothesis-generating study supported by a convenience sample drawn in close temporal proximity to the period of quarantine, we examined the psychological effects of quarantine on persons in toronto, canada. the 129 quarantined persons who responded to a web-based survey exhibited a high prevalence of psychological distress. symptoms of posttraumatic stress disorder (ptsd) and depression were observed in 28.9% and 31.2% of respondents, respectively. longer durations of quarantine were associated with an increased prevalence of ptsd symptoms. acquaintance with or direct exposure to someone with a diagnosis of sars was also associated with ptsd and depressive symptoms.",0
"objective to conduct a comprehensive systematic review and meta-analysis of studies assessing the effect of alcohol consumption on multiple cardiovascular outcomes. design systematic review and meta-analysis. data sources a search of medline (1950 through september 2009) and embase (1980 through september 2009) supplemented by manual searches of bibliographies and conference proceedings. inclusion criteria prospective cohort studies on the association between alcohol consumption and overall mortality from cardiovascular disease, incidence of and mortality from coronary heart disease, and incidence of and mortality from stroke. studies reviewed of 4235 studies reviewed for eligibility, quality, and data extraction, 84 were included in the final analysis. results the pooled adjusted relative risks for alcohol drinkers relative to non-drinkers in random effects models for the outcomes of interest were 0.75 (95% confidence interval 0.70 to 0.80) for cardiovascular disease mortality (21 studies), 0.71 (0.66 to 0.77) for incident coronary heart disease (29 studies), 0.75 (0.68 to 0.81) for coronary heart disease mortality (31 studies), 0.98 (0.91 to 1.06) for incident stroke (17 studies), and 1.06 (0.91 to 1.23) for stroke mortality (10 studies). dose-response analysis revealed that the lowest risk of coronary heart disease mortality occurred with 1-2 drinks a day, but for stroke mortality it occurred with ≤1 drink per day. secondary analysis of mortality from all causes showed lower risk for drinkers compared with non-drinkers (relative risk 0.87 (0.83 to 0.92)). conclusions light to moderate alcohol consumption is associated with a reduced risk of multiple cardiovascular outcomes.",0
"lifestyle choices influence 20-40 % of adult peak bone mass. therefore, optimization of lifestyle factors known to influence peak bone mass and strength is an important strategy aimed at reducing risk of osteoporosis or low bone mass later in life. the national osteoporosis foundation has issued this scientific statement to provide evidence-based guidance and a national implementation strategy for the purpose of helping individuals achieve maximal peak bone mass early in life. in this scientific statement, we (1) report the results of an evidence-based review of the literature since 2000 on factors that influence achieving the full genetic potential for skeletal mass; (2) recommend lifestyle choices that promote maximal bone health throughout the lifespan; (3) outline a research agenda to address current gaps; and (4) identify implementation strategies. we conducted a systematic review of the role of individual nutrients, food patterns, special issues, contraceptives, and physical activity on bone mass and strength development in youth. an evidence grading system was applied to describe the strength of available evidence on these individual modifiable lifestyle factors that may (or may not) influence the development of peak bone mass (table 1). a summary of the grades for each of these factors is given below. we describe the underpinning biology of these relationships as well as other factors for which a systematic review approach was not possible. articles published since 2000, all of which followed the report by heaney et al. published in that year, were considered for this scientific statement. this current review is a systematic update of the previous review conducted by the national osteoporosis foundation . considering the evidence-based literature review, we recommend lifestyle choices that promote maximal bone health from childhood through young to late adolescence and outline a research agenda to address current gaps in knowledge. the best evidence (grade a) is available for positive effects of calcium intake and physical activity, especially during the late childhood and peripubertal years-a critical period for bone accretion. good evidence is also available for a role of vitamin d and dairy consumption and a detriment of dmpa injections. however, more rigorous trial data on many other lifestyle choices are needed and this need is outlined in our research agenda. implementation strategies for lifestyle modifications to promote development of peak bone mass and strength within one's genetic potential require a multisectored (i.e., family, schools, healthcare systems) approach.",0
"the human metabolome database or hmdb ( has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. over the past 15 years, the hmdb has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. this year's update, hmdb 5.0, brings a number of important improvements and upgrades to the database. these should make the hmdb more useful and more appealing to a larger cross-section of users. in particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted nmr spectra, more accurately predicted ms spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the hmdb's search functions to facilitate better compound identification. many other minor improvements and updates to the content, the interface, and general performance of the hmdb website have also been made. overall, we believe these upgrades and updates should greatly enhance the hmdb's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.",0
"α-synuclein is the major component of filamentous inclusions that constitute the defining characteristic of neurodegenerative α-synucleinopathies. however, the molecular mechanisms underlying α-synuclein accumulation and spread are unclear. here we show that intracerebral injections of sarkosyl-insoluble α-synuclein from brains of patients with dementia with lewy bodies induced hyperphosphorylated α-synuclein pathology in wild-type mice. furthermore, injection of fibrils of recombinant human and mouse α-synuclein efficiently induced similar α-synuclein pathologies in wild-type mice. c57bl/6j mice injected with α-synuclein fibrils developed abundant lewy body/lewy neurite-like pathology, whereas mice injected with soluble α-synuclein did not. immunoblot analysis demonstrated that endogenous mouse α-synuclein started to accumulate 3 months after inoculation, while injected human α-synuclein fibrils disappeared in about a week. these results indicate that α-synuclein fibrils have prion-like properties and inoculation into wild-type brain induces α-synuclein pathology in vivo. this is a new mouse model of sporadic α-synucleinopathy and should be useful for elucidating progression mechanisms and evaluating disease-modifying therapy.",0
"motivation the continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously. to get the best out of all these alternatives, we need to integrate their results in an unbiased manner. prioritized gene lists are a common result presentation method in genomic data analysis applications. thus, the rank aggregation methods can become a useful and general solution for the integration task. results standard rank aggregation methods are often ill-suited for biological settings where the gene lists are inherently noisy. as a remedy, we propose a novel robust rank aggregation (rra) method. our method detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene. the underlying probabilistic model makes the algorithm parameter free and robust to outliers, noise and errors. significance scores also provide a rigorous way to keep only the statistically relevant genes in the final list. these properties make our approach robust and compelling for many settings. availability all the methods are implemented as a gnu r package robustrankaggreg, freely available at the comprehensive r archive network",0
"the functions of, and interactions between, the innate and adaptive immune systems are vital for anticancer immunity. cytotoxic t cells expressing cell-surface cd8 are the most powerful effectors in the anticancer immune response and form the backbone of current successful cancer immunotherapies. immune-checkpoint inhibitors are designed to target immune-inhibitory receptors that function to regulate the immune response, whereas adoptive cell-transfer therapies use cd8 + t cells with genetically modified receptors-chimaeric antigen receptors-to specify and enhance cd8 + t-cell functionality. new generations of cytotoxic t cells with genetically modified or synthetic receptors are being developed and evaluated in clinical trials. furthermore, combinatory regimens might optimise treatment effects and reduce adverse events. this review summarises advances in research on the most prominent immune effectors in cancer and cancer immunotherapy, cytotoxic t cells, and discusses possible implications for future cancer treatment.",0
"the gastrointestinal tract is often considered as a key organ involved in the digestion of food and providing nutrients to the body for proper maintenance. however, this system is composed of organs that are extremely complex. among the different parts, the intestine is viewed as an incredible surface of contact with the environment and is colonised by hundreds of trillions of gut microbes. the role of the gut barrier has been studied for decades, but the exact mechanisms involved in the protection of the gut barrier are various and complementary. among them, the integrity of the mucus barrier is one of the first lines of protection of the gastrointestinal tract. in the past, this 'slimy' partner was mostly considered a simple lubricant for facilitating the progression of the food bolus and the stools in the gut. since then, different researchers have made important progress, and currently, the regulation of this mucus barrier is gaining increasing attention from the scientific community. among the factors influencing the mucus barrier, the microbiome plays a major role in driving mucus changes. additionally, our dietary habits (ie, high-fat diet, low-fibre/high-fibre diet, food additives, pre- probiotics) influence the mucus at different levels. given that the mucus layer has been linked with the appearance of diseases, proper knowledge is highly warranted. here, we debate different aspects of the mucus layer by focusing on its chemical composition, regulation of synthesis and degradation by the microbiota as well as some characteristics of the mucus layer in both physiological and pathological situations.",0
"synthetic oligodeoxynucleotides (odn) that contain unmethylated cpg motifs (cpg odn) induce macrophages to secrete il-12, which induces interferon (ifn)-gamma secretion by natural killer (nk) cells. since these cytokines can induce t helper 1 (th1) differentiation, we examined the effects of coadministered cpg odn on the differentiation of th responses to hen egg lysozyme (hel). in both balb/c (th2-biased) and b10.d2 (th1-biased) mice, immunization with hel in incomplete freund's adjuvant (ifa) resulted in th2-dominated immune responses characterized by hel-specific secretion of il-5 but not ifn-gamma. in contrast, immunization with ifa-hel plus cpg odn switched the immune response to a th1-dominated cytokine pattern, with high levels of hel-specific ifn-gamma secretion and decreased hel-specific il-5 production. ifa-hel plus cpg odn also induced anti-hel igg2a (a th1-associated isotype), which was not induced by ifa-hel alone. control non-cpg odn did not induce ifn-gamma or igg2a, excepting lesser increases in b10.d2 (th1-biased) mice. thus, cpg odn provide a signal to switch on th1-dominated responses to coadministered antigen and are potential adjuvants for human vaccines to elicit protective th1 immunity.",0
"t cell exhaustion often occurs during chronic infection and prevents optimal viral control. the molecular pathways involved in t cell exhaustion remain poorly understood. here we show that exhausted cd8+ t cells are subject to complex layers of negative regulation resulting from the coexpression of multiple inhibitory receptors. exhausted cd8+ t cells expressed up to seven inhibitory receptors. coexpression of multiple distinct inhibitory receptors was associated with greater t cell exhaustion and more severe infection. regulation of t cell exhaustion by various inhibitory pathways was nonredundant, as blockade of the t cell inhibitory receptors pd-1 and lag-3 simultaneously and synergistically improved t cell responses and diminished viral load in vivo. thus, cd8+ t cell responses during chronic viral infections are regulated by complex patterns of coexpressed inhibitory receptors.",0
"this study describes the construction of soluble major histocompatibility complexes consisting of the mouse class i molecule, h-2db, chemically biotinylated beta2 microglobulin and a peptide epitope derived from the glycoprotein (gp; amino acids 33-41) of lymphocytic choriomeningitis virus (lcmv). tetrameric class i complexes, which were produced by mixing the class i complexes with phycoerythrin-labeled neutravidin, permitted direct analysis of virus-specific cytotoxic t lymphocytes (ctls) by flow cytometry. this technique was validated by (a) staining cd8+ cells in the spleens of transgenic mice that express a t cell receptor (tcr) specific for h-2db in association with peptide gp33-41, and (b) by staining virus-specific ctls in the cerebrospinal fluid of c57bl/6 (b6) mice that had been infected intracranially with lcmv-docile. staining of spleen cells isolated from b6 mice revealed that up to 40% of cd8(+) t cells were gp33 tetramer+ during the initial phase of lcmv infection. in contrast, gp33 tetramers did not stain cd8+ t cells isolated from the spleens of b6 mice that had been infected 2 mo previously with lcmv above the background levels found in naive mice. the fate of virus-specific ctls was analyzed during the acute phase of infection in mice challenged both intracranially and intravenously with a high or low dose of lcmv-docile. the results of the study show that the outcome of infection by lcmv is determined by antigen load alone. furthermore, the data indicate that deletion of virus-specific ctls in the presence of excessive antigen is preceded by tcr downregulation and is dependent upon perforin.",0
"characterization of how the microenvironment, or niche, regulates stem cell activity is central to understanding stem cell biology and to developing strategies for the therapeutic manipulation of stem cells. low oxygen tension (hypoxia) is commonly thought to be a shared niche characteristic in maintaining quiescence in multiple stem cell types. however, support for the existence of a hypoxic niche has largely come from indirect evidence such as proteomic analysis, expression of hypoxia inducible factor-1α (hif-1α) and related genes, and staining with surrogate hypoxic markers (for example, pimonidazole). here we perform direct in vivo measurements of local oxygen tension (po2) in the bone marrow of live mice. using two-photon phosphorescence lifetime microscopy, we determined the absolute po2 of the bone marrow to be quite low (<32 mm hg) despite very high vascular density. we further uncovered heterogeneities in local po2, with the lowest po2 (∼9.9 mm hg, or 1.3%) found in deeper peri-sinusoidal regions. the endosteal region, by contrast, is less hypoxic as it is perfused with small arteries that are often positive for the marker nestin. these po2 values change markedly after radiation and chemotherapy, pointing to the role of stress in altering the stem cell metabolic microenvironment.",0
"the lipid maps structure database (lmsd) is a relational database encompassing structures and annotations of biologically relevant lipids. structures of lipids in the database come from four sources: (i) lipid maps consortium's core laboratories and partners; (ii) lipids identified by lipid maps experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from lipid bank, lipidat and other public sources. all the lipid structures in lmsd are drawn in a consistent fashion. in addition to a classification-based retrieval of lipids, users can search lmsd using either text-based or structure-based search options. the text-based search implementation supports data retrieval by any combination of these data fields: lipid maps id, systematic or common name, mass, formula, category, main class, and subclass data fields. the structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. search results, in addition to structure and annotations, also include relevant links to external databases. the lmsd is publicly available at",0
"prdos is a server that predicts the disordered regions of a protein from its amino acid sequence ( the server accepts a single protein amino acid sequence, in either plain text or fasta format. the prediction system is composed of two predictors: a predictor based on local amino acid sequence information and one based on template proteins. the server combines the results of the two predictors and returns a two-state prediction (order/disorder) and a disorder probability for each residue. the prediction results are sent by e-mail, and the server also provides a web-interface to check the results.",0
"background antimicrobial resistance (amr) poses a major threat to human health around the world. previous publications have estimated the effect of amr on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. to our knowledge, this study presents the most comprehensive estimates of amr burden to date. methods we estimated deaths and disability-adjusted life-years (dalys) attributable to and associated with bacterial amr for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. we obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. we used predictive statistical modelling to produce estimates of amr burden for all locations, including for locations with no data. our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. using these components, we estimated disease burden based on two counterfactuals: deaths attributable to amr (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with amr (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). we generated 95% uncertainty intervals (uis) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. we present final estimates aggregated to the global and regional level. findings on the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial amr in 2019, including 1·27 million (95% ui 0·911-1·71) deaths attributable to bacterial amr. at the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-saharan africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in australasia, at 6·5 deaths (4·3-9·4) per 100 000. lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. the six leading pathogens for deaths associated with resistance (escherichia coli, followed by staphylococcus aureus, klebsiella pneumoniae, streptococcus pneumoniae, acinetobacter baumannii, and pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to amr and 3·57 million (2·62-4·78) deaths associated with amr in 2019. one pathogen-drug combination, meticillin-resistant s aureus, caused more than 100 000 deaths attributable to amr in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant e coli, carbapenem-resistant a baumannii, fluoroquinolone-resistant e coli, carbapenem-resistant k pneumoniae, and third-generation cephalosporin-resistant k pneumoniae. interpretation to our knowledge, this study provides the first comprehensive assessment of the global burden of amr, as well as an evaluation of the availability of data. amr is a leading cause of death around the world, with the highest burdens in low-resource settings. understanding the burden of amr and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. there are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. funding bill & melinda gates foundation, wellcome trust, and department of health and social care using uk aid funding managed by the fleming fund.",0
"background the effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. the empa-kidney trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients. methods we enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (egfr) of at least 20 but less than 45 ml per minute per 1.73 m 2 of body-surface area, or who had an egfr of at least 45 but less than 90 ml per minute per 1.73 m 2 with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. the primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in egfr to 2 , a sustained decrease in egfr of ≥40% from baseline, or death from renal causes) or death from cardiovascular causes. results a total of 6609 patients underwent randomization. during a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval , 0.64 to 0.82; p conclusions among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (funded by boehringer ingelheim and others; empa-kidney clinicaltrials.gov number, nct03594110; eudract number, 2017-002971-24.).",0
"the increasing resistance of microorganisms to conventional chemicals and drugs is a serious and evident worldwide problem that has prompted research into the identification of new biocides with broad activity. plants and their derivatives, such as essential oils, are often used in folk medicine. in nature, essential oils play an important role in the protection of plants. essential oils contain a wide variety of secondary metabolites that are capable of inhibiting or slowing the growth of bacteria, yeasts and moulds. essential oils and their components have activity against a variety of targets, particularly the membrane and cytoplasm, and in some cases, they completely change the morphology of the cells. this brief review describes the activity of essential oils against pathogenic bacteria.",0
"we have used immunofluorescence staining to study the subcellular distribution of cyclin a and b1 during the somatic cell cycle. in both primary human fibroblasts and in epithelial tumor cells, we find that cyclin a is predominantly nuclear from s phase onwards. cyclin a may associated with condensing chromosomes in prophase, but is not associated with condensed chromosomes in metaphase. by contrast, cyclin b1 accumulates in the cytoplasm of interphase cells and only enters the nucleus at the beginning of mitosis, before nuclear lamina breakdown. in mitotic cells, cyclin b1 associates with condensed chromosomes in prophase and metaphase, and with the mitotic apparatus. cyclin a is degraded during metaphase and cyclin b1 is precipitously destroyed at the metaphase----anaphase transition. cell fractionation and immunoprecipitation studies showed that both cyclin a and cyclin b1 are associated with pstaire-containing proteins. the nuclear, but not the cytoplasmic form, of cyclin a is associated with a 33-kd pstaire-containing protein. cyclin b1 is associated with p34cdc2 in the cytoplasm. thus we propose that the different localization of cyclin a and cyclin b1 in the cell cycle could be the means by which the two types of mitotic cyclin confer substrate specificity upon their associated pstaire-containing protein kinase subunit.",0
"proper management of covid-19 mandates better understanding of disease pathogenesis. the sudden clinical deterioration 7-8 days after initial symptom onset suggests that severe respiratory failure (srf) in covid-19 is driven by a unique pattern of immune dysfunction. we studied immune responses of 54 covid-19 patients, 28 of whom had srf. all patients with srf displayed either macrophage activation syndrome (mas) or very low human leukocyte antigen d related (hla-dr) expression accompanied by profound depletion of cd4 lymphocytes, cd19 lymphocytes, and natural killer (nk) cells. tumor necrosis factor-α (tnf-α) and interleukin-6 (il-6) production by circulating monocytes was sustained, a pattern distinct from bacterial sepsis or influenza. sars-cov-2 patient plasma inhibited hla-dr expression, and this was partially restored by the il-6 blocker tocilizumab; off-label tocilizumab treatment of patients was accompanied by increase in circulating lymphocytes. thus, the unique pattern of immune dysregulation in severe covid-19 is characterized by il-6-mediated low hla-dr expression and lymphopenia, associated with sustained cytokine production and hyper-inflammation.",0
"nanomedicine and nano delivery systems are a relatively new but rapidly developing science where materials in the nanoscale range are employed to serve as means of diagnostic tools or to deliver therapeutic agents to specific targeted sites in a controlled manner. nanotechnology offers multiple benefits in treating chronic human diseases by site-specific, and target-oriented delivery of precise medicines. recently, there are a number of outstanding applications of the nanomedicine (chemotherapeutic agents, biological agents, immunotherapeutic agents etc.) in the treatment of various diseases. the current review, presents an updated summary of recent advances in the field of nanomedicines and nano based drug delivery systems through comprehensive scrutiny of the discovery and application of nanomaterials in improving both the efficacy of novel and old drugs (e.g., natural products) and selective diagnosis through disease marker molecules. the opportunities and challenges of nanomedicines in drug delivery from synthetic/natural sources to their clinical applications are also discussed. in addition, we have included information regarding the trends and perspectives in nanomedicine area.",0
"the meaning of language is represented in regions of the cerebral cortex collectively known as the 'semantic system'. however, little of the semantic system has been mapped comprehensively, and the semantic selectivity of most regions is unknown. here we systematically map semantic selectivity across the cortex using voxel-wise modelling of functional mri (fmri) data collected while subjects listened to hours of narrative stories. we show that the semantic system is organized into intricate patterns that seem to be consistent across individuals. we then use a novel generative model to create a detailed semantic atlas. our results suggest that most areas within the semantic system represent information about specific semantic domains, or groups of related concepts, and our atlas shows which domains are represented in each area. this study demonstrates that data-driven methods--commonplace in studies of human neuroanatomy and functional connectivity--provide a powerful and efficient means for mapping functional representations in the brain.",0
"metacyc (metacyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. it contains 2749 pathways derived from more than 60 000 publications, making it the largest curated collection of metabolic pathways. the data in metacyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. metacyc is also used as a knowledge base for generating thousands of organism-specific pathway/genome databases (pgdbs), which are available in biocyc.org and other genomic portals. this article provides an update on the developments in metacyc during september 2017 to august 2019, up to version 23.1. some of the topics that received intensive curation during this period include cobamides biosynthesis, sterol metabolism, fatty acid biosynthesis, lipid metabolism, carotenoid metabolism, protein glycosylation, antibiotics and cytotoxins biosynthesis, siderophore biosynthesis, bioluminescence, vitamin k metabolism, brominated compound metabolism, plant secondary metabolism and human metabolism. other additions include modifications to the glycanbuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, improvements in the pathologic component of pathway tools, and the optional addition of regulatory information to pathway diagrams.",0
"extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3c) analyses requires the elimination of systematic biases. we present a computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. we validate this ice (iterative correction and eigenvector decomposition) technique on published data obtained by the high-throughput 3c method hi-c, and we demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.",0
"increasing concerns about the rising rates of antibiotic therapy failure and advances in single-cell analyses have inspired a surge of research into antibiotic persistence. bacterial persister cells represent a subpopulation of cells that can survive intensive antibiotic treatment without being resistant. several approaches have emerged to define and measure persistence, and it is now time to agree on the basic definition of persistence and its relation to the other mechanisms by which bacteria survive exposure to bactericidal antibiotic treatments, such as antibiotic resistance, heteroresistance or tolerance. in this consensus statement, we provide definitions of persistence phenomena, distinguish between triggered and spontaneous persistence and provide a guide to measuring persistence. antibiotic persistence is not only an interesting example of non-genetic single-cell heterogeneity, it may also have a role in the failure of antibiotic treatments. therefore, it is our hope that the guidelines outlined in this article will pave the way for better characterization of antibiotic persistence and for understanding its relevance to clinical outcomes.",0
"background nirmatrelvir is an orally administered severe acute respiratory syndrome coronavirus 2 main protease (m pro ) inhibitor with potent pan-human-coronavirus activity in vitro. methods we conducted a phase 2-3 double-blind, randomized, controlled trial in which symptomatic, unvaccinated, nonhospitalized adults at high risk for progression to severe coronavirus disease 2019 (covid-19) were assigned in a 1:1 ratio to receive either 300 mg of nirmatrelvir plus 100 mg of ritonavir (a pharmacokinetic enhancer) or placebo every 12 hours for 5 days. covid-19-related hospitalization or death from any cause through day 28, viral load, and safety were evaluated. results a total of 2246 patients underwent randomization; 1120 patients received nirmatrelvir plus ritonavir (nirmatrelvir group) and 1126 received placebo (placebo group). in the planned interim analysis of patients treated within 3 days after symptom onset (modified intention-to treat population, comprising 774 of the 1361 patients in the full analysis population), the incidence of covid-19-related hospitalization or death by day 28 was lower in the nirmatrelvir group than in the placebo group by 6.32 percentage points (95% confidence interval , -9.04 to -3.59; p 10 copies per milliliter when treatment was initiated within 3 days after the onset of symptoms. the incidence of adverse events that emerged during the treatment period was similar in the two groups (any adverse event, 22.6% with nirmatrelvir plus ritonavir vs. 23.9% with placebo; serious adverse events, 1.6% vs. 6.6%; and adverse events leading to discontinuation of the drugs or placebo, 2.1% vs. 4.2%). dysgeusia (5.6% vs. 0.3%) and diarrhea (3.1% vs. 1.6%) occurred more frequently with nirmatrelvir plus ritonavir than with placebo. conclusions treatment of symptomatic covid-19 with nirmatrelvir plus ritonavir resulted in a risk of progression to severe covid-19 that was 89% lower than the risk with placebo, without evident safety concerns. (supported by pfizer; clinicaltrials.gov number, nct04960202.).",0
"older adults and special populations (living with disability and/or chronic illness that may limit mobility and/or physical endurance) can benefit from practicing a more physically active lifestyle, typically by increasing ambulatory activity. step counting devices (accelerometers and pedometers) offer an opportunity to monitor daily ambulatory activity; however, an appropriate translation of public health guidelines in terms of steps/day is unknown. therefore this review was conducted to translate public health recommendations in terms of steps/day. normative data indicates that 1) healthy older adults average 2,000-9,000 steps/day, and 2) special populations average 1,200-8,800 steps/day. pedometer-based interventions in older adults and special populations elicit a weighted increase of approximately 775 steps/day (or an effect size of 0.26) and 2,215 steps/day (or an effect size of 0.67), respectively. there is no evidence to inform a moderate intensity cadence (i.e., steps/minute) in older adults at this time. however, using the adult cadence of 100 steps/minute to demark the lower end of an absolutely-defined moderate intensity (i.e., 3 mets), and multiplying this by 30 minutes produces a reasonable heuristic (i.e., guiding) value of 3,000 steps. however, this cadence may be unattainable in some frail/diseased populations. regardless, to truly translate public health guidelines, these steps should be taken over and above activities performed in the course of daily living, be of at least moderate intensity accumulated in minimally 10 minute bouts, and add up to at least 150 minutes over the week. considering a daily background of 5,000 steps/day (which may actually be too high for some older adults and/or special populations), a computed translation approximates 8,000 steps on days that include a target of achieving 30 minutes of moderate-to-vigorous physical activity (mvpa), and approximately 7,100 steps/day if averaged over a week. measured directly and including these background activities, the evidence suggests that 30 minutes of daily mvpa accumulated in addition to habitual daily activities in healthy older adults is equivalent to taking approximately 7,000-10,000 steps/day. those living with disability and/or chronic illness (that limits mobility and or/physical endurance) display lower levels of background daily activity, and this will affect whole-day estimates of recommended physical activity.",0
"background meta-analyses of antidepressant medications have reported only modest benefits over placebo treatment, and when unpublished trial data are included, the benefit falls below accepted criteria for clinical significance. yet, the efficacy of the antidepressants may also depend on the severity of initial depression scores. the purpose of this analysis is to establish the relation of baseline severity and antidepressant efficacy using a relevant dataset of published and unpublished clinical trials. methods and findings we obtained data on all clinical trials submitted to the us food and drug administration (fda) for the licensing of the four new-generation antidepressants for which full datasets were available. we then used meta-analytic techniques to assess linear and quadratic effects of initial severity on improvement scores for drug and placebo groups and on drug-placebo difference scores. drug-placebo differences increased as a function of initial severity, rising from virtually no difference at moderate levels of initial depression to a relatively small difference for patients with very severe depression, reaching conventional criteria for clinical significance only for patients at the upper end of the very severely depressed category. meta-regression analyses indicated that the relation of baseline severity and improvement was curvilinear in drug groups and showed a strong, negative linear component in placebo groups. conclusions drug-placebo differences in antidepressant efficacy increase as a function of baseline severity, but are relatively small even for severely depressed patients. the relationship between initial severity and antidepressant efficacy is attributable to decreased responsiveness to placebo among very severely depressed patients, rather than to increased responsiveness to medication.",0
"we have developed video microscopy methods to visualize the assembly and disassembly of individual microtubules at 33-ms intervals. porcine brain tubulin, free of microtubule-associated proteins, was assembled onto axoneme fragments at 37 degrees c, and the dynamic behavior of the plus and minus ends of microtubules was analyzed for tubulin concentrations between 7 and 15.5 microm. elongation and rapid shortening were distinctly different phases. at each end, the elongation phase was characterized by a second order association and a substantial first order dissociation reaction. association rate constants were 8.9 and 4.3 microm-1 s-1 for the plus and minus ends, respectively; and the corresponding dissociation rate constants were 44 and 23 s-1. for both ends, the rate of tubulin dissociation equaled the rate of tubulin association at 5 microm. the rate of rapid shortening was similar at the two ends (plus = 733 s-1; minus = 915 s-1), and did not vary with tubulin concentration. transitions between phases were abrupt and stochastic. as the tubulin concentration was increased, catastrophe frequency decreased at both ends, and rescue frequency increased dramatically at the minus end. this resulted in fewer rapid shortening phases at higher tubulin concentrations for both ends and shorter rapid shortening phases at the minus end. at each concentration, the frequency of catastrophe was slightly greater at the plus end, and the frequency of rescue was greater at the minus end. our data demonstrate that microtubules assembled from pure tubulin undergo dynamic instability over a twofold range of tubulin concentrations, and that the dynamic instability of the plus and minus ends of microtubules can be significantly different. our analysis indicates that this difference could produce treadmilling, and establishes general limits on the effectiveness of length redistribution as a measure of dynamic instability. our results are consistent with the existence of a gtp cap during elongation, but are not consistent with existing gtp cap models.",0
"background samtools and bcftools are widely used programs for processing and analysing high-throughput sequencing data. they include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. findings the first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. the samtools and bcftools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. conclusion both samtools and bcftools are freely available on github under the permissive mit licence, free for both non-commercial and commercial use. both packages have been installed >1 million times via bioconda. the source code and documentation are available from",0
"the interactive tree of life ( is an online tool for the display, manipulation and annotation of phylogenetic and other trees. it is freely available and open to everyone. the current version introduces four new dataset types, together with numerous new features. annotation options have been expanded and new control options added for many display elements. an interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. font support has been rewritten with full support for utf-8 character encoding throughout the user interface. google web fonts are now fully supported in the tree text labels. itol v4 is the first tool which supports direct visualization of qiime 2 trees and associated annotations. the user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. full batch access has been implemented allowing programmatic upload and export of trees and annotations.",0
"the pattern of structural brain alterations associated with major depressive disorder (mdd) remains unresolved. this is in part due to small sample sizes of neuroimaging studies resulting in limited statistical power, disease heterogeneity and the complex interactions between clinical characteristics and brain morphology. to address this, we meta-analyzed three-dimensional brain magnetic resonance imaging data from 1728 mdd patients and 7199 controls from 15 research samples worldwide, to identify subcortical brain volumes that robustly discriminate mdd patients from healthy controls. relative to controls, patients had significantly lower hippocampal volumes (cohen's d=-0.14, % difference=-1.24). this effect was driven by patients with recurrent mdd (cohen's d=-0.17, % difference=-1.44), and we detected no differences between first episode patients and controls. age of onset ⩽21 was associated with a smaller hippocampus (cohen's d=-0.20, % difference=-1.85) and a trend toward smaller amygdala (cohen's d=-0.11, % difference=-1.23) and larger lateral ventricles (cohen's d=0.12, % difference=5.11). symptom severity at study inclusion was not associated with any regional brain volumes. sample characteristics such as mean age, proportion of antidepressant users and proportion of remitted patients, and methodological characteristics did not significantly moderate alterations in brain volumes in mdd. samples with a higher proportion of antipsychotic medication users showed larger caudate volumes in mdd patients compared with controls. this currently largest worldwide effort to identify subcortical brain alterations showed robust smaller hippocampal volumes in mdd patients, moderated by age of onset and first episode versus recurrent episode status.",0
"advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. there are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. genotyping-by-sequencing (gbs) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. gbs uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. here we present a gbs approach for species that currently lack a reference genome sequence. we developed a novel two-enzyme gbs protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified snps and tags. we were able to map over 34,000 snps and 240,000 tags onto the oregon wolfe barley reference map, and 20,000 snps and 367,000 tags on the synthetic w9784 × opata85 (synopdh) wheat reference map. to further evaluate gbs in wheat, we also constructed a de novo genetic map using only snp markers from the gbs data. the gbs approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. development of the sequenced reference genome(s) will in turn increase the utility of gbs data enabling physical mapping of genes and haplotype imputation of missing data. finally, as a result of low per-sample costs, gbs will have broad application in genomics-assisted plant breeding programs.",0
"in the last decade, optimized treatment for non-small cell lung cancer had lead to improved prognosis, but the overall survival is still very short. to further understand the molecular basis of the disease we have to identify biomarkers related to survival. here we present the development of an online tool suitable for the real-time meta-analysis of published lung cancer microarray datasets to identify biomarkers related to survival. we searched the cabig, geo and tcga repositories to identify samples with published gene expression data and survival information. univariate and multivariate cox regression analysis, kaplan-meier survival plot with hazard ratio and logrank p value are calculated and plotted in r. the complete analysis tool can be accessed online at: all together 1,715 samples of ten independent datasets were integrated into the system. as a demonstration, we used the tool to validate 21 previously published survival associated biomarkers. of these, survival was best predicted by cdk1 (p<1e-16), cd24 (p<1e-16) and cadm1 (p = 7e-12) in adenocarcinomas and by ccne1 (p = 2.3e-09) and vegf (p = 3.3e-10) in all nsclc patients. additional genes significantly correlated to survival include rad51, cdkn2a, opn, ezh2, anxa3, adam28 and ercc1. in summary, we established an integrated database and an online tool capable of uni- and multivariate analysis for in silico validation of new biomarker candidates in non-small cell lung cancer.",0
"congenital heart disease (chd) is the leading cause of mortality from birth defects. here, exome sequencing of a single cohort of 2,871 chd probands, including 2,645 parent-offspring trios, implicated rare inherited mutations in 1.8%, including a recessive founder mutation in gdf1 accounting for ∼5% of severe chd in ashkenazim, recessive genotypes in myh6 accounting for ∼11% of shone complex, and dominant flt4 mutations accounting for 2.3% of tetralogy of fallot. de novo mutations (dnms) accounted for 8% of cases, including ∼3% of isolated chd patients and ∼28% with both neurodevelopmental and extra-cardiac congenital anomalies. seven genes surpassed thresholds for genome-wide significance, and 12 genes not previously implicated in chd had >70% probability of being disease related. dnms in ∼440 genes were inferred to contribute to chd. striking overlap between genes with damaging dnms in probands with chd and autism was also found.",0
"fungal diseases kill more than 1.5 million and affect over a billion people. however, they are still a neglected topic by public health authorities even though most deaths from fungal diseases are avoidable. serious fungal infections occur as a consequence of other health problems including asthma, aids, cancer, organ transplantation and corticosteroid therapies. early accurate diagnosis allows prompt antifungal therapy; however this is often delayed or unavailable leading to death, serious chronic illness or blindness. recent global estimates have found 3,000,000 cases of chronic pulmonary aspergillosis, ~223,100 cases of cryptococcal meningitis complicating hiv/aids, ~700,000 cases of invasive candidiasis, ~500,000 cases of pneumocystis jirovecii pneumonia, ~250,000 cases of invasive aspergillosis, ~100,000 cases of disseminated histoplasmosis, over 10,000,000 cases of fungal asthma and ~1,000,000 cases of fungal keratitis occur annually. since 2013, the leading international fungal education (life) portal has facilitated the estimation of the burden of serious fungal infections country by country for over 5.7 billion people (>80% of the world's population). these studies have shown differences in the global burden between countries, within regions of the same country and between at risk populations. here we interrogate the accuracy of these fungal infection burden estimates in the 43 published papers within the life initiative.",0
"background studies have suggested that the symptoms of knee osteoarthritis (oa) are rather weakly associated with radiographic findings and vice versa. our objectives were to identify estimates of the prevalence of radiographic knee oa in adults with knee pain and of knee pain in adults with radiographic knee oa, and determine if the definitions of x ray osteoarthritis and symptoms, and variation in demographic factors influence these estimates. methods a systematic literature search identifying population studies which combined x rays, diagnosis, clinical signs and symptoms in knee oa. estimates of the prevalence of radiographic oa in people with knee pain were determined and vice versa. in addition the effects of influencing factors were scrutinised. results the proportion of those with knee pain found to have radiographic osteoarthritis ranged from 15-76%, and in those with radiographic knee oa the proportion with pain ranged from 15% - 81%. considerable variation occurred with x ray view, pain definition, oa grading and demographic factors conclusion knee pain is an imprecise marker of radiographic knee osteoarthritis but this depends on the extent of radiographic views used. radiographic knee osteoarthritis is likewise an imprecise guide to the likelihood that knee pain or disability will be present. both associations are affected by the definition of pain used and the nature of the study group. the results of knee x rays should not be used in isolation when assessing individual patients with knee pain.",0
"the chemokines (or chemotactic cytokines) are a large family of small, secreted proteins that signal through cell surface g protein-coupled heptahelical chemokine receptors. they are best known for their ability to stimulate the migration of cells, most notably white blood cells (leukocytes). consequently, chemokines play a central role in the development and homeostasis of the immune system, and are involved in all protective or destructive immune and inflammatory responses. classically viewed as inducers of directed chemotactic migration, it is now clear that chemokines can stimulate a variety of other types of directed and undirected migratory behavior, such as haptotaxis, chemokinesis, and haptokinesis, in addition to inducing cell arrest or adhesion. however, chemokine receptors on leukocytes can do more than just direct migration, and these molecules can also be expressed on, and regulate the biology of, many nonleukocytic cell types. chemokines are profoundly affected by post-translational modification, by interaction with the extracellular matrix (ecm), and by binding to heptahelical 'atypical' chemokine receptors that regulate chemokine localization and abundance. this guide gives a broad overview of the chemokine and chemokine receptor families; summarizes the complex physical interactions that occur in the chemokine network; and, using specific examples, discusses general principles of chemokine function, focusing particularly on their ability to direct leukocyte migration.",0
"the evolution in next-generation sequencing (ngs) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. these genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in genbank. producing organelle genome assembly from whole genome sequencing (wgs) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. we developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (wgs) data, starting from a related or distant single seed sequence. the algorithm has been tested on several new (gonioctena intermedia and avicennia marina) and public (arabidopsis thaliana and oryza sativa) whole genome illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. in our benchmark, novoplasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 gb and an accuracy over 99.99%. in conclusion, novoplasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from wgs data in one circular high quality contig. the software is open source and can be downloaded at",0
"we have resolved b220+ igm- b-lineage cells in mouse bone marrow into four fractions based on differential cell surface expression of determinants recognized by s7 (leukosialin, cd43), bp-1, and 30f1 (heat stable antigen). functional differences among these fractions can be correlated with ig gene rearrangement status. the largest fraction, lacking s7, consists of pre-b cells whereas the others, expressing s7, include b lineage cells before pre-b. these s7+ fractions, provisionally termed fr. a, fr. b, and fr. c, can differentiate in a stromal layer culture system. phenotypic alteration during such culture suggests an ordering of these stages from fr. a to fr. b to fr. c and thence to s7- pre-b cells. using polymerase chain reaction amplification with pairs of oligonucleotide primers for regions 5' of jh1, dfl16.1, and jk1, we find that the ig genes of fr. a are in germline configuration, whereas fr. b and c are pro-b cell stages with increasing d-j rearrangement, but no v-d-j. finally, functional analysis demonstrates that the proliferative response to il-7, an early b lineage growth factor, is restricted to s7+ stages and, furthermore, that an additional, cell contact-mediated signal is essential for survival of fr. a.",0
"as a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. the introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. here we introduce a bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. by implementing character mapping in a bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. standard markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. in addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. to visualize the spatial and temporal information, we summarize inferences using virtual globe software. we describe how bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza a h5n1 origin and h5n1 epidemiological linkage among sampling localities. analysis of rabies in west african dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. from these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.",0
"importance existing cerebrospinal fluid (csf) or imaging (tau positron emission tomography) biomarkers for alzheimer disease (ad) are invasive or expensive. biomarkers based on standard blood test results would be useful in research, drug development, and clinical practice. plasma neurofilament light (nfl) has recently been proposed as a blood-based biomarker for neurodegeneration in dementias. objective to test whether plasma nfl concentrations are increased in ad and associated with cognitive decline, other ad biomarkers, and imaging evidence of neurodegeneration. design, setting, and participants in this prospective case-control study, an ultrasensitive assay was used to measure plasma nfl concentration in 193 cognitively healthy controls, 197 patients with mild cognitive impairment (mci), and 180 patients with ad dementia from the alzheimer's disease neuroimaging initiative. the study dates were september 7, 2005, to february 13, 2012. the plasma nfl analysis was performed in september 2016. main outcomes and measures associations were tested between plasma nfl and diagnosis, aβ pathologic features, csf biomarkers of neuronal injury, cognition, brain structure, and metabolism. results among 193 cognitively healthy controls, 197 patients with mild cognitive impairment, and 180 patients with ad with dementia, plasma nfl correlated with csf nfl (spearman ρ = 0.59, p conclusions and relevance plasma nfl is associated with ad diagnosis and with cognitive, biochemical, and imaging hallmarks of the disease. this finding implies a potential usefulness for plasma nfl as a noninvasive biomarker in ad.",0
"in an attempt to account for antibody specificity and complementarity in terms of structure, human kappa-, human lambda-, and mouse kappa-bence jones proteins and light chains are considered as a single population and the variable and constant regions are compared using the sequence data available. statistical criteria are used in evaluating each position in the sequence as to whether it is essentially invariant or group-specific, subgroup-specific, species-specific, etc. examination of the invariant residues of the variable and constant regions confirms the existence of a large number of invariant glycines, no invariant valine, lysine, and histidine, and only one invariant leucine and alanine in the variable region, as compared with the absence of invariant glycines and presence of three each of invariant alanine, leucine, and valine and two each of invariant lysine and histidine in the constant region. the unique role of glycine in the variable region is emphasized. hydrophobicity of the invariant residues of the two regions is also evaluated. a parameter termed variability is defined and plotted against the position for the 107 residues of the variable region. three stretches of unusually high variability are noted at residues 24-34, 50-56, and 89-97; variations in length have been found in the first and third of these. it is hypothesized that positions 24-34 and 89-97 contain the complementarity-determining residues of the light chain-those which make contact with the antigenic determinant. the heavy chain also has been reported to have a similar region of very high variability which would also participate in forming the antibody-combining site. it is postulated that the information for site complementarity is contained in some extrachromosomal dna such as an episome and is incorporated by insertion into the dna of the structural genes for the variable region of short linear sequences of nucleotides. the advantages and disadvantages of this hypothesis are discussed.",0
"the relationship between vivid visual mental images and unexpected recall (incidental recall) was replicated, refined, and extended. in experiment 1, participants were asked to generate mental images from imagery-evoking verbal cues (controlled on several verbal properties) and then, on a trial-by-trial basis, rate the vividness of their images; 30 min later, participants were surprised with a task requiring free recall of the cues. higher vividness ratings predicted better incidental recall of the cues than individual differences (whose effect was modest). distributional analysis of image latencies through ex-gaussian modeling showed an inverse relation between vividness and latency. however, recall was unrelated to image latency. the follow-up experiment 2 showed that the processes underlying trial-by-trial vividness ratings are unrelated to the vividness of visual imagery questionnaire (vviq), as further supported by a meta-analysis of a randomly selected sample of relevant literature. the present findings suggest that vividness may act as an index of availability of long-term sensory traces, playing a non-epiphenomenal role in facilitating the access of those memories.",0
"polygenic risk scores (prs) have shown promise in predicting human complex traits and diseases. here, we present prs-cs, a polygenic prediction method that infers posterior effect sizes of single nucleotide polymorphisms (snps) using genome-wide association summary statistics and an external linkage disequilibrium (ld) reference panel. prs-cs utilizes a high-dimensional bayesian regression framework, and is distinct from previous work by placing a continuous shrinkage (cs) prior on snp effect sizes, which is robust to varying genetic architectures, provides substantial computational advantages, and enables multivariate modeling of local ld patterns. simulation studies using data from the uk biobank show that prs-cs outperforms existing methods across a wide range of genetic architectures, especially when the training sample size is large. we apply prs-cs to predict six common complex diseases and six quantitative traits in the partners healthcare biobank, and further demonstrate the improvement of prs-cs in prediction accuracy over alternative methods.",0
"in this article, we have discussed the basic knowledge to calculate sensitivity, specificity, positive predictive value and negative predictive value. we have discussed the advantage and limitations of these measures and have provided how we should use these measures in our day-to-day clinical practice. we also have illustrated how to calculate sensitivity and specificity while combining two tests and how to use these results for our patients in day-to-day practice.",0
"estimation of the prevalence and contagiousness of undocumented novel coronavirus infections is critical for understanding the overall prevalence and pandemic potential of this disease. here, we use observations of reported infection within china, in conjunction with mobility data, a networked dynamic metapopulation model, and bayesian inference, to infer critical epidemiological characteristics associated with sars-cov-2, including the fraction of undocumented infections and their contagiousness. we estimate that 86% of all infections were undocumented before the 23 january 2020 travel restrictions. the transmission rate of undocumented infections per person was 55% the transmission rate of documented infections (95% ci: 46-62%), yet, because of their greater numbers, undocumented infections were the source of 79% of the documented cases. these findings explain the rapid geographic spread of sars-cov-2 and indicate that containment of this virus will be particularly challenging.",0
"swisstargetprediction is a web tool, on-line since 2014, that aims to predict the most probable protein targets of small molecules. predictions are based on the similarity principle, through reverse screening. here, we describe the 2019 version, which represents a major update in terms of underlying data, backend and web interface. the bioactivity data were updated, the model retrained and similarity thresholds redefined. in the new version, the predictions are performed by searching for similar molecules, in 2d and 3d, within a larger collection of 376 342 compounds known to be experimentally active on an extended set of 3068 macromolecular targets. an efficient backend implementation allows to speed up the process that returns results for a druglike molecule on human proteins in 15-20 s. the refreshed web interface enhances user experience with new features for easy input and improved analysis. interoperability capacity enables straightforward submission of any input or output molecule to other on-line computer-aided drug design tools, developed by the sib swiss institute of bioinformatics. high levels of predictive performance were maintained despite more extended biological and chemical spaces to be explored, e.g. achieving at least one correct human target in the top 15 predictions for >70% of external compounds. the new swisstargetprediction is available free of charge (",0
"in the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. in the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. to this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. the resulting model contains information about biological properties in its representations. the representations are learned from sequence data alone. the learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.",0
"background before 2020, mental disorders were leading causes of the global health-related burden, with depressive and anxiety disorders being leading contributors to this burden. the emergence of the covid-19 pandemic has created an environment where many determinants of poor mental health are exacerbated. the need for up-to-date information on the mental health impacts of covid-19 in a way that informs health system responses is imperative. in this study, we aimed to quantify the impact of the covid-19 pandemic on the prevalence and burden of major depressive disorder and anxiety disorders globally in 2020. methods we conducted a systematic review of data reporting the prevalence of major depressive disorder and anxiety disorders during the covid-19 pandemic and published between jan 1, 2020, and jan 29, 2021. we searched pubmed, google scholar, preprint servers, grey literature sources, and consulted experts. eligible studies reported prevalence of depressive or anxiety disorders that were representative of the general population during the covid-19 pandemic and had a pre-pandemic baseline. we used the assembled data in a meta-regression to estimate change in the prevalence of major depressive disorder and anxiety disorders between pre-pandemic and mid-pandemic (using periods as defined by each study) via covid-19 impact indicators (human mobility, daily sars-cov-2 infection rate, and daily excess mortality rate). we then used this model to estimate the change from pre-pandemic prevalence (estimated using disease modelling meta-regression version 2.1 ) by age, sex, and location. we used final prevalence estimates and disability weights to estimate years lived with disability and disability-adjusted life-years (dalys) for major depressive disorder and anxiety disorders. findings we identified 5683 unique data sources, of which 48 met inclusion criteria (46 studies met criteria for major depressive disorder and 27 for anxiety disorders). two covid-19 impact indicators, specifically daily sars-cov-2 infection rates and reductions in human mobility, were associated with increased prevalence of major depressive disorder (regression coefficient 0·9 for human mobility, 18·1 for daily sars-cov-2 infection) and anxiety disorders (0·9 and 13·8 [10·7 to 17·0; p interpretation this pandemic has created an increased urgency to strengthen mental health systems in most countries. mitigation strategies could incorporate ways to promote mental wellbeing and target determinants of poor mental health and interventions to treat those with a mental disorder. taking no action to address the burden of major depressive disorder and anxiety disorders should not be an option. funding queensland health, national health and medical research council, and the bill and melinda gates foundation.",0
"visual working memory provides an essential link between perception and higher cognitive functions, allowing for the active maintenance of information about stimuli no longer in view. research suggests that sustained activity in higher-order prefrontal, parietal, inferotemporal and lateral occipital areas supports visual maintenance, and may account for the limited capacity of working memory to hold up to 3-4 items. because higher-order areas lack the visual selectivity of early sensory areas, it has remained unclear how observers can remember specific visual features, such as the precise orientation of a grating, with minimal decay in performance over delays of many seconds. one proposal is that sensory areas serve to maintain fine-tuned feature information, but early visual areas show little to no sustained activity over prolonged delays. here we show that orientations held in working memory can be decoded from activity patterns in the human visual cortex, even when overall levels of activity are low. using functional magnetic resonance imaging and pattern classification methods, we found that activity patterns in visual areas v1-v4 could predict which of two oriented gratings was held in memory with mean accuracy levels upwards of 80%, even in participants whose activity fell to baseline levels after a prolonged delay. these orientation-selective activity patterns were sustained throughout the delay period, evident in individual visual areas, and similar to the responses evoked by unattended, task-irrelevant gratings. our results demonstrate that early visual areas can retain specific information about visual features held in working memory, over periods of many seconds when no physical stimulus is present.",0
"objective to characterize patients with coronavirus disease 2019 (covid-19) in a large new york city medical center and describe their clinical course across the emergency department, hospital wards, and intensive care units. design retrospective manual medical record review. setting newyork-presbyterian/columbia university irving medical center, a quaternary care academic medical center in new york city. participants the first 1000 consecutive patients with a positive result on the reverse transcriptase polymerase chain reaction assay for severe acute respiratory syndrome coronavirus 2 (sars-cov-2) who presented to the emergency department or were admitted to hospital between 1 march and 5 april 2020. patient data were manually abstracted from electronic medical records. main outcome measures characterization of patients, including demographics, presenting symptoms, comorbidities on presentation, hospital course, time to intubation, complications, mortality, and disposition. results of the first 1000 patients, 150 presented to the emergency department, 614 were admitted to hospital (not intensive care units), and 236 were admitted or transferred to intensive care units. the most common presenting symptoms were cough (732/1000), fever (728/1000), and dyspnea (631/1000). patients in hospital, particularly those treated in intensive care units, often had baseline comorbidities including hypertension, diabetes, and obesity. patients admitted to intensive care units were older, predominantly male (158/236, 66.9%), and had long lengths of stay (median 23 days, interquartile range 12-32 days); 78.0% (184/236) developed acute kidney injury and 35.2% (83/236) needed dialysis. only 4.4% (6/136) of patients who required mechanical ventilation were first intubated more than 14 days after symptom onset. time to intubation from symptom onset had a bimodal distribution, with modes at three to four days, and at nine days. as of 30 april, 90 patients remained in hospital and 211 had died in hospital. conclusions patients admitted to hospital with covid-19 at this medical center faced major morbidity and mortality, with high rates of acute kidney injury and inpatient dialysis, prolonged intubations, and a bimodal distribution of time to intubation from symptom onset.",0
"background because chronic obstructive pulmonary disease (copd) is a heterogeneous condition, the identification of specific clinical phenotypes is key to developing more effective therapies. to explore if the persistence of systemic inflammation is associated with poor clinical outcomes in copd we assessed patients recruited to the well-characterized eclipse cohort (nct00292552). methods and findings six inflammatory biomarkers in peripheral blood (white blood cells (wbc) count and crp, il-6, il-8, fibrinogen and tnf-α levels) were quantified in 1,755 copd patients, 297 smokers with normal spirometry and 202 non-smoker controls that were followed-up for three years. we found that, at baseline, 30% of copd patients did not show evidence of systemic inflammation whereas 16% had persistent systemic inflammation. even though pulmonary abnormalities were similar in these two groups, persistently inflamed patients during follow-up had significantly increased all-cause mortality (13% vs. 2%, p conclusions overall, these results identify a novel systemic inflammatory copd phenotype that may be the target of specific research and treatment.",0
"eosinophils in visceral adipose tissue (vat) have been implicated in metabolic homeostasis and the maintenance of alternatively activated macrophages (aams). the absence of eosinophils can lead to adiposity and systemic insulin resistance in experimental animals, but what maintains eosinophils in adipose tissue is unknown. we show that interleukin-5 (il-5) deficiency profoundly impairs vat eosinophil accumulation and results in increased adiposity and insulin resistance when animals are placed on a high-fat diet. innate lymphoid type 2 cells (ilc2s) are resident in vat and are the major source of il-5 and il-13, which promote the accumulation of eosinophils and aam. deletion of ilc2s causes significant reductions in vat eosinophils and aams, and also impairs the expansion of vat eosinophils after infection with nippostrongylus brasiliensis, an intestinal parasite associated with increased adipose ilc2 cytokine production and enhanced insulin sensitivity. further, il-33, a cytokine previously shown to promote cytokine production by ilc2s, leads to rapid ilc2-dependent increases in vat eosinophils and aams. thus, ilc2s are resident in vat and promote eosinophils and aam implicated in metabolic homeostasis, and this axis is enhanced during th2-associated immune stimulation.",0
"human endothelial cells, obtained by collagenase treatment of term umbilical cord veins, were cultured using medium 199 supplemented with 20% fetal calf serum. small clusters of cells initially spread on plastic or glass, coalesced and grew to form confluent monolayers of polygonal cells by 7 days. cells in primary and subcultures were identified as endothelium by the presence of weibel-palade bodies by electron microscopy. a morphologically distinct subpopulation of cells contaminating some primary endothelial cultures was selectively subcultured, and identified by ultrastructural criteria as vascular smooth muscle. autoradiography of endothelial cells after exposure to thymidine showed progressive increases in labeling in growing cultures beginning at 24 h. in recently confluent cultures, labeling indices were 2.4% in central closely packed regions, and 53.2% in peripheral growing regions. 3 days after confluence, labeling was uniform, being 3.5 and 3.9% in central and peripheral areas, respectively. when small areas of confluent cultures were experimentally ""denuded,"" there were localized increases in thymidine labeling and eventual reconstitution of the monolayer. liquid scintillation measurements of thymidine incorporation in primary and secondary endothelial cultures in microwell trays showed a similar correlation of dna synthesis with cell density. these data indicate that endothelial cell cultures may provide a useful in vitro model for studying pathophysiologic factors in endothelial regeneration.",0
"polymerase chain reaction (pcr) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. reliable primer design is crucial for successful pcr, and for over a decade, the open-source primer3 software has been widely used for primer design, often in high-throughput genomics applications. it has also been incorporated into numerous publicly available software packages and web services. during this period, we have greatly expanded primer3's functionality. in this article, we describe primer3's current capabilities, emphasizing recent improvements. the most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. additional enhancements include more precise control of primer placement-a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. we also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. we have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. these improvements position primer3 for continued use with genome-scale data in the decade ahead.",0
"the number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. in the kegg database, genes in complete genomes are annotated with the kegg orthology (ko) identifiers, or the k numbers, based on the best hit information using smith-waterman scores as well as by the manual curation. each k number represents an ortholog group of genes, and it is directly linked to an object in the kegg pathway map or the brite functional hierarchy. here, we have developed a web-based server called kaas (kegg automatic annotation server: i.e. an implementation of a rapid method to automatically assign k numbers to genes in the genome, enabling reconstruction of kegg pathways and brite hierarchies. the method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated kegg genes database.",0
"the epithelia of a number of glands and cavitary organs of the rat and guinea pig have been surveyed, and in all cases investigated, a characteristic tripartite junctional complex has been found between adjacent cells. although the complex differs in precise arrangement from one organ to another, it has been regularly encountered in the mucosal epithelia of the stomach, intestine, gall bladder, uterus, and oviduct; in the glandular epithelia of the liver, pancreas, parotid, stomach, and thyroid; in the epithelia of pancreatic, hepatic, and salivary ducts; and finally, between the epithelial cells of the nephron (proximal and distal convolution, collecting ducts). the elements of the complex, identified as zonula occludens (tight junction), zonula adhaerens (intermediary junction), and macula adhaerens (desmosome), occupy a juxtaluminal position and succeed each other in the order given in an apical-basal direction. the zonula occludens (tight junction) is characterized by fusion of the adjacent cell membranes resulting in obliteration of the intercellular space over variable distances. within the obliterated zone, the dense outer leaflets of the adjoining cell membranes converge to form a single intermediate line. a diffuse band of dense cytoplasmic material is often associated with this junction, but its development varies from one epithelium to another. the zonula adhaerens (intermediate junction) is characterized by the presence of an intercellular space ( approximately 200 a) occupied by homogeneous, apparently amorphous material of low density; by strict parallelism of the adjoining cell membranes over distances of 0.2 to 0.5 micro; and by conspicuous bands of dense material located in the subjacent cytoplasmic matrix. the desmosome or macula adhaerens is also characterized by the presence of an intercellular space ( approximately 240 a) which, in this case, contains a central disc of dense material; by discrete cytoplasmic plaques disposed parallel to the inner leaflet of each cell membrane; and by the presence of bundles of cytoplasmic fibrils converging on the plaques. the zonula occludens appears to form a continuous belt-like attachment, whereas the desmosome is a discontinuous, button-like structure. the zomula adhaerens is continuous in most epithelia but discontinuous in some. observations made during experimental hemoglobinuria in rats showed that the hemoglobin, which undergoes enough concentration in the nephron lumina to act as an electron-opaque mass tracer, does not penetrate the intercellular spaces beyond the zonula occludens. similar observations were made in pancreatic acini and ducts where discharged zymogen served as a mass tracer. hence the tight junction is impervious to concentrated protein solutions and appears to function as a diffusion barrier or ""seal."" the desmosome and probably also the zonula adhaerens may represent intercellular attachment devices.",0
"permutation methods can provide exact control of false positives and allow the use of non-standard statistics, making only weak assumptions about the data. with the availability of fast and inexpensive computing, their main limitation would be some lack of flexibility to work with arbitrary experimental designs. in this paper we report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, and conduct detailed simulations to identify the best method for settings that are typical for imaging research scenarios. we present a generic framework for permutation inference for complex general linear models (glms) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful while providing excellent control of false positives in a wide range of common and relevant imaging research scenarios. we also demonstrate how the inference on glm parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. detailed examples of common neuroimaging applications are provided, as well as a complete algorithm - the ""randomise"" algorithm - for permutation inference with the glm.",0
"the gamma(1)a present in saliva and colostrum exists largely in the form of higher polymers, the major component of which has a sedimentation coefficient of 11s. the 11s gamma(1)a in these fluids differs from the polymers found in normal and myeloma sera both immunologically and by the fact that their sedimentation coefficients are unaffected by disulfide bond reduction in the absence of urea. however, like other gamma-globulins the 11s gamma(1)a molecules consist of multiple polypeptide chains linked by disulfide bonds. local synthesis of gamma(1)a in the salivary gland has been shown by fluorescent and autoradiographic studies, although the fraction of the total salivary gamma(1)a which is derived from local production is uncertain. no evidence of transport of intravenously administered i(131)-labeled 7s gamma(1)a from serum to saliva was obtained. immunological specificity has been demonstrated in the salivary and colostral gamma(1)a. whether that portion of the gamma(1)a which is immunologically specific is a piece incorporated during the local synthesis of gamma(1)a in the gland or is added by the epithelial cell in the process of transport remains to be determined. antibody activity (isohemagglutinins) have been demonstrated in saliva and colostrum and have been shown to be of the gamma(1)a-type. in both of these fluids activity is associated primarily with gamma(1)a-polymers of 11s and 18s sizes. there appears to be an immunological system which is characteristic of certain external secretions. its properties including the local production of a distinctive type of antibody separate it from the ""systemic"" system responsible for the production of circulating antibody. this system may play a significant role in the body's defense mechanisms against allergens and microorganisms.",0
"background the movement of evidence-based practices (ebps) into routine clinical usage is not spontaneous, but requires focused efforts. the field of implementation science has developed to facilitate the spread of ebps, including both psychosocial and medical interventions for mental and physical health concerns. discussion the authors aim to introduce implementation science principles to non-specialist investigators, administrators, and policymakers seeking to become familiar with this emerging field. this introduction is based on published literature and the authors' experience as researchers in the field, as well as extensive service as implementation science grant reviewers. implementation science is ""the scientific study of methods to promote the systematic uptake of research findings and other ebps into routine practice, and, hence, to improve the quality and effectiveness of health services."" implementation science is distinct from, but shares characteristics with, both quality improvement and dissemination methods. implementation studies can be either assess naturalistic variability or measure change in response to planned intervention. implementation studies typically employ mixed quantitative-qualitative designs, identifying factors that impact uptake across multiple levels, including patient, provider, clinic, facility, organization, and often the broader community and policy environment. accordingly, implementation science requires a solid grounding in theory and the involvement of trans-disciplinary research teams. the business case for implementation science is clear: as healthcare systems work under increasingly dynamic and resource-constrained conditions, evidence-based strategies are essential in order to ensure that research investments maximize healthcare value and improve public health. implementation science plays a critical role in supporting these efforts.",0
"background physical activity has many health benefits for young people. in 2018, who launched more active people for a healthier world, a new global action on physical activity, including new targets of a 15% relative reduction of global prevalence of insufficient physical activity by 2030 among adolescents and adults. we describe current prevalence and trends of insufficient physical activity among school-going adolescents aged 11-17 years by country, region, and globally. methods we did a pooled analysis of cross-sectional survey data that were collected through random sampling with a sample size of at least 100 individuals, were representative of a national or defined subnational population, and reported prevalence of of insufficient physical activity by sex in adolescents. prevalence had to be reported for at least three of the years of age within the 10-19-year age range. we estimated the prevalence of insufficient physical activity in school-going adolescents aged 11-17 years (combined and by sex) for individual countries, for four world bank income groups, nine regions, and globally for the years 2001-16. to derive a standard definition of insufficient physical activity and to adjust for urban-only survey coverage, we used regression models. we estimated time trends using multilevel mixed-effects modelling. findings we used data from 298 school-based surveys from 146 countries, territories, and areas including 1·6 million students aged 11-17 years. globally, in 2016, 81·0% (95% uncertainty interval 77·8-87·7) of students aged 11-17 years were insufficiently physically active (77·6% of boys and 84·7% of girls). although prevalence of insufficient physical activity significantly decreased between 2001 and 2016 for boys (from 80·1% in 2001), there was no significant change for girls (from 85·1% in 2001). there was no clear pattern according to country income group: insufficient activity prevalence in 2016 was 84·9% (82·6-88·2) in low-income countries, 79·3% (77·2-87·5) in lower-middle-income countries, 83·9% (79·5-89·2) in upper-middle-income countries, and 79·4% (74·0-86·2) in high-income countries. the region with the highest prevalence of insufficient activity in 2016 was high-income asia pacific for both boys (89·0%, 62·8-92·2) and girls (95·6%, 73·7-97·9). the regions with the lowest prevalence were high-income western countries for boys (72·1%, 71·1-73·6), and south asia for girls (77·5%, 72·8-89·3). in 2016, 27 countries had a prevalence of insufficient activity of 90% or more for girls, whereas this was the case for two countries for boys. interpretation the majority of adolescents do not meet current physical activity guidelines. urgent scaling up of implementation of known effective policies and programmes is needed to increase activity in adolescents. investment and leadership at all levels to intervene on the multiple causes and inequities that might perpetuate the low participation in physical activity and sex differences, as well as engagement of youth themselves, will be vital to strengthen the opportunities for physical activity in all communities. such action will improve the health of this and future young generations and support achieving the 2030 sustainable development goals. funding who.",0
"the adult cns contains an abundant population of oligodendrocyte precursor cells (ng2(+) cells) that generate oligodendrocytes and repair myelin, but how these ubiquitous progenitors maintain their density is unknown. we generated ng2-megfp mice and used in vivo two-photon imaging to study their dynamics in the adult brain. time-lapse imaging revealed that ng2(+) cells in the cortex were highly dynamic; they surveyed their local environment with motile filopodia, extended growth cones and continuously migrated. they maintained unique territories though self-avoidance, and ng2(+) cell loss though death, differentiation or ablation triggered rapid migration and proliferation of adjacent cells to restore their density. ng2(+) cells recruited to sites of focal cns injury were similarly replaced by a proliferative burst surrounding the injury site. thus, homeostatic control of ng2(+) cell density through a balance of active growth and self-repulsion ensures that these progenitors are available to replace oligodendrocytes and participate in tissue repair.",0
"deepmind presented notably accurate predictions at the recent 14th critical assessment of structure prediction (casp14) conference. we explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1d) sequence level, the 2d distance map level, and the 3d coordinate level is successively transformed and integrated. the three-track network produces structure predictions with accuracies approaching those of deepmind in casp14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. the network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. we make the method available to the scientific community to speed biological research.",0
"cumulative meta-analyses are used to evaluate the extent to which further studies are needed to confirm or refute a hypothesis. we used this approach to assess observational evidence on systemic inflammation in individuals with major depressive disorder. we identified 58 studies of four common inflammatory markers in a literature search of pubmed, embase and psychinfo databases in may 2014. pooled data from the earliest eight studies already showed an association between interleukin-6 concentrations and major depression; 23 more recent studies confirmed this finding (d=0.54, p<0.0001). a significant association between c-reactive protein levels and major depression was noted after 14 studies and this did not change after addition of six more studies (d=0.47, p<0.0001). for these two inflammatory markers, there was moderate heterogeneity in study-specific estimates, subgroup differences were small, and publication bias appeared to be an unlikely explanation for the findings. sensitivity analyses including only high-quality studies and subjects free of antidepressant medication further verified the associations. while there was a link between tumour necrosis factor-α levels and major depression (d=0.40, p=0.002), the cumulative effect remained uncertain due to the extensive heterogeneity in study-specific estimates and inconsistencies between subgroups. no evidence was found for the association between interleukin-1β levels and major depression (d=-0.05, p=0.86). in conclusion, this cumulative meta-analysis confirmed higher mean levels of interleukin-6 and c-reactive protein in patients with major depression compared to non-depressed controls. no consistent association between tumour necrosis factor-α, interleukin-1β and major depression was observed. future studies should clarify the specific immune mechanisms involved as well as continue testing anti-inflammatory therapies in patients suffering from major depression.",0
"recent advances in nanoscience and nanotechnology radically changed the way we diagnose, treat, and prevent various diseases in all aspects of human life. silver nanoparticles (agnps) are one of the most vital and fascinating nanomaterials among several metallic nanoparticles that are involved in biomedical applications. agnps play an important role in nanoscience and nanotechnology, particularly in nanomedicine. although several noble metals have been used for various purposes, agnps have been focused on potential applications in cancer diagnosis and therapy. in this review, we discuss the synthesis of agnps using physical, chemical, and biological methods. we also discuss the properties of agnps and methods for their characterization. more importantly, we extensively discuss the multifunctional bio-applications of agnps; for example, as antibacterial, antifungal, antiviral, anti-inflammatory, anti-angiogenic, and anti-cancer agents, and the mechanism of the anti-cancer activity of agnps. in addition, we discuss therapeutic approaches and challenges for cancer therapy using agnps. finally, we conclude by discussing the future perspective of agnps.",0
"background in many genomics projects, numerous lists containing biological identifiers are produced. often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. one of the most popular methods to visualize the overlap and differences between data sets is the venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. currently there are no programs available that can create area-proportional venn diagrams connected to a wide range of biological databases. results we designed a web application named biovenn to summarize the overlap between two or three lists of identifiers, using area-proportional venn diagrams. the user only needs to input these lists of identifiers in the textboxes and push the submit button. parameters like colors and text size can be adjusted easily through the web interface. the position of the text can be adjusted by 'drag-and-drop' principle. the output venn diagram can be shown as an svg or png image embedded in the web application, or as a standalone svg or png image. the latter option is useful for batch queries. besides the venn diagram, biovenn outputs lists of identifiers for each of the resulting subsets. if an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. finally, biovenn can map affymetrix and entrezgene identifiers to ensembl genes. conclusion biovenn is an easy-to-use web application to generate area-proportional venn diagrams from lists of biological identifiers. it supports a wide range of identifiers from the most used biological databases currently available. its implementation on the world wide web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. biovenn is freely accessible at",0
"bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. part i of this series outlined several advantages of bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. despite these and other practical advantages, bayesian hypothesis tests are still reported relatively rarely. an important impediment to the widespread adoption of bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, anova, correlation, regression, and contingency tables. in part ii of this series we introduce jasp ( ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out bayesian hypothesis tests for standard statistical problems. jasp is based in part on the bayesian analyses implemented in morey and rouder's bayesfactor package for r. armed with jasp, the practical advantages of bayesian hypothesis testing are only a mouse click away.",0
"much medical research is observational. the reporting of observational studies is often of insufficient quality. poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the strengthening the reporting of observational studies in epidemiology (strobe) recommendations to improve the quality of reporting of observational studies. the strobe statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. the strobe statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. this explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the strobe statement. the meaning and rationale for each checklist item are presented. for each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. examples of useful flow diagrams are also included. the strobe statement, this document, and the associated web site ( should be helpful resources to improve reporting of observational research.",0
"we provide a systematic review of epidemiological surveys of autistic disorder and pervasive developmental disorders (pdds) worldwide. a secondary aim was to consider the possible impact of geographic, cultural/ethnic, and socioeconomic factors on prevalence estimates and on clinical presentation of pdd. based on the evidence reviewed, the median of prevalence estimates of autism spectrum disorders was 62/10 000. while existing estimates are variable, the evidence reviewed does not support differences in pdd prevalence by geographic region nor of a strong impact of ethnic/cultural or socioeconomic factors. however, power to detect such effects is seriously limited in existing data sets, particularly in low-income countries. while it is clear that prevalence estimates have increased over time and these vary in different neighboring and distant regions, these findings most likely represent broadening of the diagnostic concets, diagnostic switching from other developmental disabilities to pdd, service availability, and awareness of autistic spectrum disorders in both the lay and professional public. the lack of evidence from the majority of the world's population suggests a critical need for further research and capacity building in low- and middle-income countries.",0
"optimum sample size is an essential component of any research. the main purpose of the sample size calculation is to determine the number of samples needed to detect significant changes in clinical parameters, treatment effects or associations after data gathering. it is not uncommon for studies to be underpowered and thereby fail to detect the existing treatment effects due to inadequate sample size. in this paper, we explain briefly the basic principles of sample size calculations in medical studies.",0
"background hydroxychloroquine and azithromycin have been used to treat patients with coronavirus disease 2019 (covid-19). however, evidence on the safety and efficacy of these therapies is limited. methods we conducted a multicenter, randomized, open-label, three-group, controlled trial involving hospitalized patients with suspected or confirmed covid-19 who were receiving either no supplemental oxygen or a maximum of 4 liters per minute of supplemental oxygen. patients were randomly assigned in a 1:1:1 ratio to receive standard care, standard care plus hydroxychloroquine at a dose of 400 mg twice daily, or standard care plus hydroxychloroquine at a dose of 400 mg twice daily plus azithromycin at a dose of 500 mg once daily for 7 days. the primary outcome was clinical status at 15 days as assessed with the use of a seven-level ordinal scale (with levels ranging from one to seven and higher scores indicating a worse condition) in the modified intention-to-treat population (patients with a confirmed diagnosis of covid-19). safety was also assessed. results a total of 667 patients underwent randomization; 504 patients had confirmed covid-19 and were included in the modified intention-to-treat analysis. as compared with standard care, the proportional odds of having a higher score on the seven-point ordinal scale at 15 days was not affected by either hydroxychloroquine alone (odds ratio, 1.21; 95% confidence interval , 0.69 to 2.11; p = 1.00) or hydroxychloroquine plus azithromycin (odds ratio, 0.99; 95% ci, 0.57 to 1.73; p = 1.00). prolongation of the corrected qt interval and elevation of liver-enzyme levels were more frequent in patients receiving hydroxychloroquine, alone or with azithromycin, than in those who were not receiving either agent. conclusions among patients hospitalized with mild-to-moderate covid-19, the use of hydroxychloroquine, alone or with azithromycin, did not improve clinical status at 15 days as compared with standard care. (funded by the coalition covid-19 brazil and ems pharma; clinicaltrials.gov number, nct04322123.).",0
"purpose the aim of this study was to assess the measurement properties of the 5-level classification system of the eq-5d (5l), in comparison with the 3-level eq-5d (3l). methods participants (n = 3,919) from six countries, including eight patient groups with chronic conditions (cardiovascular disease, respiratory disease, depression, diabetes, liver disease, personality disorders, arthritis, and stroke) and a student cohort, completed the 3l and 5l and, for most participants, also dimension-specific rating scales. the 3l and 5l were compared in terms of feasibility (missing values), redistribution properties, ceiling, discriminatory power, convergent validity, and known-groups validity. results missing values were on average 0.8% for 5l and 1.3% for 3l. in total, 2.9% of responses were inconsistent between 5l and 3l. redistribution from 3l to 5l using eq dimension-specific rating scales as reference was validated for all 35 3l-5l-level combinations. for 5l, 683 unique health states were observed versus 124 for 3l. the ceiling was reduced from 20.2% (3l) to 16.0% (5l). absolute discriminatory power (shannon index) improved considerably with 5l (mean 1.87 for 5l versus 1.24 for 3l), and relative discriminatory power (shannon evenness index) improved slightly (mean 0.81 for 5l versus 0.78 for 3l). convergent validity with who-5 was demonstrated and improved slightly with 5l. known-groups validity was confirmed for both 5l and 3l. conclusions the eq-5d-5l appears to be a valid extension of the 3-level system which improves upon the measurement properties, reducing the ceiling while improving discriminatory power and establishing convergent and known-groups validity.",0
"many aspects of the historical relationships between populations in a species are reflected in genetic data. inferring these relationships from genetic data, however, remains a challenging task. in this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. in our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. using genome-wide allele frequency data and a gaussian approximation to genetic drift, we infer the structure of this graph. we applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. in both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. while some of the migration events that we find have been detected previously, many have not. for example, in the human data, we infer that cambodians trace approximately 16% of their ancestry to a population ancestral to other extant east asian populations. in the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that east asian toy breeds (the shih tzu and the pekingese) result from admixture between modern toy breeds and ""ancient"" asian breeds. software implementing the model described here, called treemix, is available at",0
"matthew page and co-authors describe prisma 2020, an updated reporting guideline for systematic reviews and meta-analyses.",0
"background receiver operating characteristic (roc) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. however, conclusions are often reached through inconsistent use or insufficient statistical analysis. to support researchers in their roc curves analysis we developed proc, a package for r and s+ that contains a set of tools displaying, analyzing, smoothing and comparing roc curves in a user-friendly, object-oriented and flexible interface. results with data previously imported into the r or s+ environment, the proc package builds roc curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing roc curves. intermediary and final results are visualised in user-friendly interfaces. a case study based on published clinical and biomarker data shows how to perform a typical roc analysis with proc. conclusions proc is a package for r and s+ specifically dedicated to roc analysis. it proposes multiple statistical tests to compare roc curves, and in particular partial areas under the curve, allowing proper roc interpretation. proc is available in two versions: in the r programming language or with a graphical user interface in the s+ statistical software. it is accessible at under the gnu general public license. it is also distributed through the cran and csan public repositories, facilitating its installation.",0
"chronic pain, one of the most common reasons adults seek medical care (1), has been linked to restrictions in mobility and daily activities (2,3), dependence on opioids (4), anxiety and depression (2), and poor perceived health or reduced quality of life (2,3). population-based estimates of chronic pain among u.s. adults range from 11% to 40% (5), with considerable population subgroup variation. as a result, the 2016 national pain strategy called for more precise prevalence estimates of chronic pain and high-impact chronic pain (i.e., chronic pain that frequently limits life or work activities) to reliably establish the prevalence of chronic pain and aid in the development and implementation of population-wide pain interventions (5). national estimates of high-impact chronic pain can help differentiate persons with limitations in major life domains, including work, social, recreational, and self-care activities from those who maintain normal life activities despite chronic pain, providing a better understanding of the population in need of pain services. to estimate the prevalence of chronic pain and high-impact chronic pain in the united states, cdc analyzed 2016 national health interview survey (nhis) data. an estimated 20.4% (50.0 million) of u.s. adults had chronic pain and 8.0% of u.s. adults (19.6 million) had high-impact chronic pain, with higher prevalences of both chronic pain and high-impact chronic pain reported among women, older adults, previously but not currently employed adults, adults living in poverty, adults with public health insurance, and rural residents. these findings could be used to target pain management interventions.",0
"objective to review the evidence about the impact of hypoglycemia on patients with diabetes that has become available since the past reviews of this subject by the american diabetes association and the endocrine society and to provide guidance about how this new information should be incorporated into clinical practice. participants five members of the american diabetes association and five members of the endocrine society with expertise in different aspects of hypoglycemia were invited by the chair, who is a member of both, to participate in a planning conference call and a 2-day meeting that was also attended by staff from both organizations. subsequent communications took place via e-mail and phone calls. the writing group consisted of those invitees who participated in the writing of the manuscript. the workgroup meeting was supported by educational grants to the american diabetes association from lilly usa, llc and novo nordisk and sponsorship to the american diabetes association from sanofi. the sponsors had no input into the development of or content of the report. evidence the writing group considered data from recent clinical trials and other studies to update the prior workgroup report. unpublished data were not used. expert opinion was used to develop some conclusions. consensus process consensus was achieved by group discussion during conference calls and face-to-face meetings, as well as by iterative revisions of the written document. the document was reviewed and approved by the american diabetes association's professional practice committee in october 2012 and approved by the executive committee of the board of directors in november 2012 and was reviewed and approved by the endocrine society's clinical affairs core committee in october 2012 and by council in november 2012. conclusions the workgroup reconfirmed the previous definitions of hypoglycemia in diabetes, reviewed the implications of hypoglycemia on both short- and long-term outcomes, considered the implications of hypoglycemia on treatment outcomes, presented strategies to prevent hypoglycemia, and identified knowledge gaps that should be addressed by future research. in addition, tools for patients to report hypoglycemia at each visit and for clinicians to document counseling are provided.",0
"motivation venn and euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. a scalable alternative to venn and euler diagrams for visualizing intersecting sets and their properties is needed. results we developed upsetr, an open source r package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. availability and implementation upsetr is available at and released under the mit license. a shiny app is available at . contact nils@hms.harvard.edu. supplementary information supplementary data are available at bioinformatics online.",0
"objective the diabetes control and complications trial (dcct) was designed to test the glucose hypothesis and determine whether the complications of type 1 diabetes (t1dm) could be prevented or delayed. the epidemiology of diabetes interventions and complications (edic) observational follow-up determined the durability of the dcct effects on the more-advanced stages of diabetes complications including cardiovascular disease (cvd). research design and methods the dcct (1982-1993) was a controlled clinical trial in 1,441 subjects with t1dm comparing intensive therapy (int), aimed at achieving levels of glycemia as close to the nondiabetic range as safely possible, with conventional therapy (con), which aimed to maintain safe asymptomatic glucose control. int utilized three or more daily insulin injections or insulin pump therapy guided by self-monitored glucose. edic (1994-present) is an observational study of the dcct cohort. results the dcct followed >99% of the cohort for a mean of 6.5 years and demonstrated a 35-76% reduction in the early stages of microvascular disease with int, with a median hba1c of 7%, compared with conv, with a median hba1c of 9%. the major adverse effect of int was a threefold increased risk of hypoglycemia, which was not associated with a decline in cognitive function or quality of life. edic showed a durable effect of initial assigned therapies despite a loss of the glycemic separation (metabolic memory) and demonstrated that the reduction in early-stage complications during the dcct translated into substantial reductions in severe complications and cvd. conclusions dcct/edic has demonstrated the effectiveness of int in reducing the long-term complications of t1dm and improving the prospects for a healthy life span.",0
"this report of the european food safety authority and the european centre for disease prevention and control presents the results of zoonoses monitoring activities carried out in 2017 in 37 european countries (28 member states (ms) and nine non-ms). campylobacteriosis was the commonest reported zoonosis and its eu trend for confirmed human cases increasing since 2008 stabilised during 2013-2017. the decreasing eu trend for confirmed human salmonellosis cases since 2008 ended during 2013-2017, and the proportion of human salmonella enteritidis cases increased, mostly due to one ms starting to report serotype data. sixteen ms met all salmonella reduction targets for poultry, whereas 12 ms failed meeting at least one. the eu flock prevalence of target salmonella serovars in breeding hens, laying hens, broilers and fattening turkeys decreased or remained stable compared to 2016, and slightly increased in breeding turkeys. salmonella results on pig carcases and target salmonella serovar results for poultry from competent authorities tended to be generally higher compared to those from food business operators. the notification rate of human listeriosis further increased in 2017, despite listeria seldom exceeding the eu food safety limit in ready-to-eat food. the decreasing eu trend for confirmed yersiniosis cases since 2008 stabilised during 2013-2017. the number of confirmed shiga toxin-producing escherichia coli (stec) infections in humans was stable. a total of 5,079 food-borne (including waterborne) outbreaks were reported. salmonella was the commonest detected agent with s . enteritidis causing one out of seven outbreaks, followed by other bacteria, bacterial toxins and viruses. the agent was unknown in 37.6% of all outbreaks. salmonella in eggs and salmonella in meat and meat products were the highest risk agent/food pairs. the report further summarises trends and sources for bovine tuberculosis, brucella , trichinella , echinococcus , toxoplasma , rabies, coxiella burnetii (q fever), west nile virus and tularaemia.",0
"gephi is a network visualization software used in various disciplines (social network analysis, biology, genomics...). one of its key features is the ability to display the spatialization process, aiming at transforming the network into a map, and forceatlas2 is its default layout algorithm. the latter is developed by the gephi team as an all-around solution to gephi users' typical networks (scale-free, 10 to 10,000 nodes). we present here for the first time its functioning and settings. forceatlas2 is a force-directed layout close to other algorithms used for network spatialization. we do not claim a theoretical advance but an attempt to integrate different techniques such as the barnes hut simulation, degree-dependent repulsive force, and local and global adaptive temperatures. it is designed for the gephi user experience (it is a continuous algorithm), and we explain which constraints it implies. the algorithm benefits from much feedback and is developed in order to provide many possibilities through its settings. we lay out its complete functioning for the users who need a precise understanding of its behaviour, from the formulas to graphic illustration of the result. we propose a benchmark for our compromise between performance and quality. we also explain why we integrated its various features and discuss our design choices.",0
"several cancers are highly refractory to conventional chemotherapy. the survival of tumors in several cases is assisted by checkpoint immunomodulation to maintain the imbalance between immune surveillance and cancer cell proliferation. check point antibody inhibitors, such as anti-pd-1/pd-l1, are a novel class of inhibitors that function as a tumor suppressing factor via modulation of immune cell-tumor cell interaction. these checkpoint blockers are rapidly becoming a highly promising cancer therapeutic approach that yields remarkable antitumor responses with limited side effects. in recent times, more than four check point antibody inhibitors have been commercialized for targeting pd-1, pdl-1, and ctla-4. despite the huge success and efficacy of the anti-pd therapy response, it is limited to specific types of cancers, which attributes to the insufficient and heterogeneous expression of pd-1 in the tumor microenvironment. herein, we review the current landscape of the pd-1/pd-l1 mechanistic role in tumor immune evasion and therapeutic outcome for cancer treatment. we also review the current progress in clinical trials, combination of drug therapy with immunotherapy, safety, and future of check point inhibitors for multiple types of cancer.",0
"apart from efficacy and toxicity, many drug development failures are imputable to poor pharmacokinetics and bioavailability. gastrointestinal absorption and brain access are two pharmacokinetic behaviors crucial to estimate at various stages of the drug discovery processes. to this end, the brain or intestinal estimated permeation method (boiled-egg) is proposed as an accurate predictive model that works by computing the lipophilicity and polarity of small molecules. concomitant predictions for both brain and intestinal permeation are obtained from the same two physicochemical descriptors and straightforwardly translated into molecular design, owing to the speed, accuracy, conceptual simplicity and clear graphical output of the model. the boiled-egg can be applied in a variety of settings, from the filtering of chemical libraries at the early steps of drug discovery, to the evaluation of drug candidates for development.",0
"qupath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. in addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, qupath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. furthermore, qupath's flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.",0
"obtaining an electron-density map from x-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because mir and mad structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. a set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. these have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. the solve software has been used to solve mad data sets with as many as 52 selenium sites in the asymmetric unit. the automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.",0
"respiratory chain complexes assemble into functional quaternary structures called supercomplexes (rcs) within the folds of the inner mitochondrial membrane, or cristae. here, we investigate the relationship between respiratory function and mitochondrial ultrastructure and provide evidence that cristae shape determines the assembly and stability of rcs and hence mitochondrial respiratory efficiency. genetic and apoptotic manipulations of cristae structure affect assembly and activity of rcs in vitro and in vivo, independently of changes to mitochondrial protein synthesis or apoptotic outer mitochondrial membrane permeabilization. we demonstrate that, accordingly, the efficiency of mitochondria-dependent cell growth depends on cristae shape. thus, rcs assembly emerges as a link between membrane morphology and function.",0
"bone marrow-derived antigen-presenting cells (apcs) take up cell-associated antigens and present them in the context of major histocompatibility complex (mhc) class i molecules to cd8(+) t cells in a process referred to as cross-priming. cross-priming is essential for the induction of cd8(+) t cell responses directed towards antigens not expressed in professional apcs. although in vitro experiments have shown that dendritic cells (dcs) and macrophages are capable of presenting exogenous antigens in association with mhc class i, the cross-presenting cell in vivo has not been identified. we have isolated splenic dcs after in vivo priming with ovalbumin-loaded beta2-microglobulin-deficient splenocytes and show that they indeed present cell-associated antigens in the context of mhc class i molecules. this process is transporter associated with antigen presentation (tap) dependent, suggesting an endosome to cytosol transport. to determine whether a specific subset of splenic dcs is involved in this cross-presentation, we negatively and positively selected for cd8(-) and cd8(+) dcs. only the cd8(+), and not the cd8(-), dc subset demonstrates cross-priming ability. facs((r)) studies after injection of splenocytes loaded with fluorescent beads showed that 1 and 0.6% of the cd8(+) and the cd8(-) dc subsets, respectively, had one or more associated beads. these results indicate that cd8(+) dcs play an important role in the generation of cytotoxic t lymphocyte responses specific for cell-associated antigens.",0
"multiple processes may contribute to motor skill acquisition, but it is thought that many of these processes require sleep or the passage of long periods of time ranging from several hours to many days or weeks. here we demonstrate that within a timescale of minutes, two distinct fast-acting processes drive motor adaptation. one process responds weakly to error but retains information well, whereas the other responds strongly but has poor retention. this two-state learning system makes the surprising prediction of spontaneous recovery (or adaptation rebound) if error feedback is clamped at zero following an adaptation-extinction training episode. we used a novel paradigm to experimentally confirm this prediction in human motor learning of reaching, and we show that the interaction between the learning processes in this simple two-state system provides a unifying explanation for several different, apparently unrelated, phenomena in motor adaptation including savings, anterograde interference, spontaneous recovery, and rapid unlearning. our results suggest that motor adaptation depends on at least two distinct neural systems that have different sensitivity to error and retain information at different rates.",0
"diabetes mellitus is a leading cause of mortality and reduced life expectancy. we aim to estimate the burden of diabetes by type, year, regions, and socioeconomic status in 195 countries and territories over the past 28 years, which provide information to achieve the goal of world health organization global action plan for the prevention and control of noncommunicable diseases in 2025. data were obtained from the global burden of disease study 2017. overall, the global burden of diabetes had increased significantly since 1990. both the trend and magnitude of diabetes related diseases burden varied substantially across regions and countries. in 2017, global incidence, prevalence, death, and disability-adjusted life-years (dalys) associated with diabetes were 22.9 million, 476.0 million, 1.37 million, and 67.9 million, with a projection to 26.6 million, 570.9 million, 1.59 million, and 79.3 million in 2025, respectively. the trend of global type 2 diabetes burden was similar to that of total diabetes (including type 1 diabetes and type 2 diabetes), while global age-standardized rate of mortality and dalys for type 1 diabetes declined. globally, metabolic risks (high bmi) and behavioral factors (inappropriate diet, smoking, and low physical activity) contributed the most attributable death and dalys of diabetes. these estimations could be useful in policy-making, priority setting, and resource allocation in diabetes prevention and treatment.",0
"stem cells are cells specialized cell, capable of renewing themselves through cell division and can differentiate into multi-lineage cells. these cells are categorized as embryonic stem cells (escs), induced pluripotent stem cells (ipscs) and adult stem cells. mesenchymal stem cells (mscs) are adult stem cells which can be isolated from human and animal sources. human mscs (hmscs) are the non-haematopoietic, multipotent stem cells with the capacity to differentiate into mesodermal lineage such as osteocytes, adipocytes and chondrocytes as well ectodermal (neurocytes) and endodermal lineages (hepatocytes). mscs express cell surface markers like cluster of differentiation (cd)29, cd44, cd73, cd90, cd105 and lack the expression of cd14, cd34, cd45 and hla (human leucocyte antigen)-dr. hmscs for the first time were reported in the bone marrow and till now they have been isolated from various tissues, including adipose tissue, amniotic fluid, endometrium, dental tissues, umbilical cord and wharton's jelly which harbours potential mscs. hmscs have been cultured long-term in specific media without any severe abnormalities. furthermore, mscs have immunomodulatory features, secrete cytokines and immune-receptors which regulate the microenvironment in the host tissue. multilineage potential, immunomodulation and secretion of anti-inflammatory molecules makes mscs an effective tool in the treatment of chronic diseases. in the present review, we have highlighted recent research findings in the area of hmscs sources, expression of cell surface markers, long-term in vitro culturing, in vitro differentiation potential, immunomodulatory features, its homing capacity, banking and cryopreservation, its application in the treatment of chronic diseases and its use in clinical trials.",0
"the epidemic of coronavirus disease 2019 (covid-19), originating in wuhan, china, has become a major public health challenge for not only china but also countries around the world. the world health organization announced that the outbreaks of the novel coronavirus have constituted a public health emergency of international concern. as of february 26, 2020, covid-19 has been recognized in 34 countries, with a total of 80,239 laboratory-confirmed cases and 2,700 deaths. infection control measures are necessary to prevent the virus from further spreading and to help control the epidemic situation. due to the characteristics of dental settings, the risk of cross infection can be high between patients and dental practitioners. for dental practices and hospitals in areas that are (potentially) affected with covid-19, strict and effective infection control protocols are urgently needed. this article, based on our experience and relevant guidelines and research, introduces essential knowledge about covid-19 and nosocomial infection in dental settings and provides recommended management protocols for dental practitioners and students in (potentially) affected areas.",0
"cells from a variety of sources, principally differentiating fibroblasts and smooth muscle cells from neonatal chicken and mammalian tissues and from organ cultures of chicken duodenum, were used as materials for an electron microscopic study on the formation of rudimentary cilia. among the differentiating tissues many cells possessed a short, solitary cilium, which projected from one of the cell's pair of centrioles. many stages evidently intermediate in the fashioning of cilium from centriole were encountered and furnished the evidence from which a reconstruction of ciliogenesis was attempted. the whole process may be divided into three phases. at first a solitary vesicle appears at one end of a centriole. the ciliary bud grows out from the same end of the centriole and invaginates the sac, which then becomes the temporary ciliary sheath. during the second phase the bud lengthens into a shaft, while the sheath enlarges to contain it. enlargement of the sheath is effected by the repeated appearance of secondary vesicles nearby and their fusion with the sheath. shaft and sheath reach the surface of the cell, where the sheath fuses with the plasma membrane during the third phase. up to this point, formation of cilia follows the classical descriptions in outline. subsequently, internal development of the shaft makes the rudimentary cilia of the investigated material more like certain non-motile centriolar derivatives than motile cilia. the pertinent literature is examined, and the cilia are tentatively assigned a non-motile status and a sensory function.",0
"a key public health need is to identify individuals at high risk for a given disease to enable enhanced screening or preventive therapies. because most common diseases have a genetic component, one important approach is to stratify individuals based on inherited dna variation 1 . proposed clinical applications have largely focused on finding carriers of rare monogenic mutations at several-fold increased risk. although most disease risk is polygenic in nature 2-5 , it has not yet been possible to use polygenic predictors to identify individuals at risk comparable to monogenic mutations. here, we develop and validate genome-wide polygenic scores for five common diseases. the approach identifies 8.0, 6.1, 3.5, 3.2, and 1.5% of the population at greater than threefold increased risk for coronary artery disease, atrial fibrillation, type 2 diabetes, inflammatory bowel disease, and breast cancer, respectively. for coronary artery disease, this prevalence is 20-fold higher than the carrier frequency of rare monogenic mutations conferring comparable risk 6 . we propose that it is time to contemplate the inclusion of polygenic risk prediction in clinical care, and discuss relevant issues.",0
"the embl-ebi provides access to various mainstream sequence analysis applications. these include sequence similarity search services such as blast, fasta, interproscan and multiple sequence alignment tools such as clustalw, t-coffee and muscle. through the sequence similarity search services, the users can search mainstream sequence databases such as embl-bank and uniprot, and more than 2000 completed genomes and proteomes. we present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. these services are available over the web and via web services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. the framework features novel result visualizations and integration of domain and functional predictions for protein database searches. it is available at for sequence similarity searches and at for multiple sequence alignments.",0
"phenoscanner is a curated database of publicly available results from large-scale genetic association studies. this tool aims to facilitate 'phenome scans', the cross-referencing of genetic variants with many phenotypes, to help aid understanding of disease pathways and biology. the database currently contains over 350 million association results and over 10 million unique genetic variants, mostly single nucleotide polymorphisms. it is accompanied by a web-based tool that queries the database for associations with user-specified variants, providing results according to the same effect and non-effect alleles for each input variant. the tool provides the option of searching for trait associations with proxies of the input variants, calculated using the european samples from 1000 genomes and hapmap. availability and implementation phenoscanner is available at contact: jrs95@medschl.cam.ac.uksupplementary information: supplementary data are available at bioinformatics online.",0
"introduction pioneer (nct01185314) was a prospective, multinational, epidemiological study of epidermal growth factor receptor (egfr) mutations in patients from asia with newly diagnosed advanced lung adenocarcinoma. methods eligible patients (aged ≥20 years) had untreated stage iiib/iv adenocarcinoma. the egfr mutation status (primary end point: positive, negative, or undetermined) of tumor samples (biopsy, surgical specimen, or cytology) was determined (scorpion amplification refractory mutation system). egfr mutation frequency was calculated and compared between demographic and clinical subgroups. results of 1482 patients from seven asian regions, 43.4% of patients were female, median age was 60 years (range, 17-94), and 52.6% of patients were never-smokers. egfr mutation status was evaluable in tumors from 1450 patients (97.8%) (746 positive; 704 negative). country, sex, ethnicity, smoking status, pack-years (all p 0-10 pack-years, 57.9%; >50 pack-years, 31.4%) (similar trend by sex). ethnic group (p conclusion pioneer is the first prospective study to confirm high egfr mutation frequency (51.4% overall) in tumors from asian patients with adenocarcinoma. the observed high mutation frequency in demographic/clinical subgroups compared with white populations suggests that mutation testing should be considered for all patients with stage iiib/iv adenocarcinoma, even males and regular smokers, among asian populations.",0
"antibacterial activity of zinc oxide nanoparticles (zno-nps) has received significant interest worldwide particularly by the implementation of nanotechnology to synthesize particles in the nanometer region. many microorganisms exist in the range from hundreds of nanometers to tens of micrometers. zno-nps exhibit attractive antibacterial properties due to increased specific surface area as the reduced particle size leading to enhanced particle surface reactivity. zno is a bio-safe material that possesses photo-oxidizing and photocatalysis impacts on chemical and biological species. this review covered zno-nps antibacterial activity including testing methods, impact of uv illumination, zno particle properties (size, concentration, morphology, and defects), particle surface modification, and minimum inhibitory concentration. particular emphasize was given to bactericidal and bacteriostatic mechanisms with focus on generation of reactive oxygen species (ros) including hydrogen peroxide (h 2 o 2 ), oh - (hydroxyl radicals), and o 2 -2 (peroxide). ros has been a major factor for several mechanisms including cell wall damage due to zno-localized interaction, enhanced membrane permeability, internalization of nps due to loss of proton motive force and uptake of toxic dissolved zinc ions. these have led to mitochondria weakness, intracellular outflow, and release in gene expression of oxidative stress which caused eventual cell growth inhibition and cell death. in some cases, enhanced antibacterial activity can be attributed to surface defects on zno abrasive surface texture. one functional application of the zno antibacterial bioactivity was discussed in food packaging industry where zno-nps are used as an antibacterial agent toward foodborne diseases. proper incorporation of zno-nps into packaging materials can cause interaction with foodborne pathogens, thereby releasing nps onto food surface where they come in contact with bad bacteria and cause the bacterial death and/or inhibition.",0
"background the dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations in space and time. however, the size of the datasets generated also poses some daunting challenges. in particular, bayesian clustering algorithms based on pre-defined population genetics models such as the structure or baps software may not be able to cope with this unprecedented amount of data. thus, there is a need for less computer-intensive approaches. multivariate analyses seem particularly appealing as they are specifically devoted to extracting information from large datasets. unfortunately, currently available multivariate methods still lack some essential features needed to study the genetic structure of natural populations. results we introduce the discriminant analysis of principal components (dapc), a multivariate method designed to identify and describe clusters of genetically related individuals. when group priors are lacking, dapc uses sequential k-means and model selection to infer genetic clusters. our approach allows extracting rich information from genetic data, providing assignment of individuals to groups, a visual assessment of between-population differentiation, and contribution of individual alleles to population structuring. we evaluate the performance of our method using simulated data, which were also analyzed using structure as a benchmark. additionally, we illustrate the method by analyzing microsatellite polymorphism in worldwide human populations and hemagglutinin gene sequence variation in seasonal influenza. conclusions analysis of simulated data revealed that our approach performs generally better than structure at characterizing population subdivision. the tools implemented in dapc for the identification of clusters and graphical representation of between-group structures allow to unravel complex population structures. our approach is also faster than bayesian clustering algorithms by several orders of magnitude, and may be applicable to a wider range of datasets.",0
"background a range of public health measures have been implemented to suppress local transmission of coronavirus disease 2019 (covid-19) in hong kong. we examined the effect of these interventions and behavioural changes of the public on the incidence of covid-19, as well as on influenza virus infections, which might share some aspects of transmission dynamics with covid-19. methods we analysed data on laboratory-confirmed covid-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. we estimated the daily effective reproduction number (r t ) for covid-19 and influenza a h1n1 to estimate changes in transmissibility over time. attitudes towards covid-19 and changes in population behaviours were reviewed through three telephone surveys done on jan 20-23, feb 11-14, and march 10-13, 2020. findings covid-19 transmissibility measured by r t has remained at approximately 1 for 8 weeks in hong kong. influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late january, with a 44% (95% ci 34-53%) reduction in transmissibility in the community, from an estimated r t of 1·28 (95% ci 1·26-1·30) before the start of the school closures to 0·72 (0·70-0·74) during the closure weeks. similarly, a 33% (24-43%) reduction in transmissibility was seen based on paediatric hospitalisation rates, from an r t of 1·10 (1·06-1·12) before the start of the school closures to 0·73 (0·68-0·77) after school closures. among respondents to the surveys, 74·5%, 97·5%, and 98·8% reported wearing masks when going out, and 61·3%, 90·2%, and 85·1% reported avoiding crowded places in surveys 1 (n=1008), 2 (n=1000), and 3 (n=1005), respectively. interpretation our study shows that non-pharmaceutical interventions (including border restrictions, quarantine and isolation, distancing, and changes in population behaviour) were associated with reduced transmission of covid-19 in hong kong, and are also likely to have substantially reduced influenza transmission in early february, 2020. funding health and medical research fund, hong kong.",0
"the oft-repeated claim that earth's biota is entering a sixth ""mass extinction"" depends on clearly demonstrating that current extinction rates are far above the ""background"" rates prevailing between the five previous mass extinctions. earlier estimates of extinction rates have been criticized for using assumptions that might overestimate the severity of the extinction crisis. we assess, using extremely conservative assumptions, whether human activities are causing a mass extinction. first, we use a recent estimate of a background rate of 2 mammal extinctions per 10,000 species per 100 years (that is, 2 e/msy), which is twice as high as widely used previous estimates. we then compare this rate with the current rate of mammal and vertebrate extinctions. the latter is conservatively low because listing a species as extinct requires meeting stringent criteria. even under our assumptions, which would tend to minimize evidence of an incipient mass extinction, the average rate of vertebrate species loss over the last century is up to 100 times higher than the background rate. under the 2 e/msy background rate, the number of species that have gone extinct in the last century would have taken, depending on the vertebrate taxon, between 800 and 10,000 years to disappear. these estimates reveal an exceptionally rapid loss of biodiversity over the last few centuries, indicating that a sixth mass extinction is already under way. averting a dramatic decay of biodiversity and the subsequent loss of ecosystem services is still possible through intensified conservation efforts, but that window of opportunity is rapidly closing.",0
"we present an integrated stand-alone software package named kaks_calculator 2.0 as an updated version. it incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including gamma-ng, gamma-lwl, gamma-mlwl, gamma-lpb, gamma-mlpb, gamma-yn and gamma-myn, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. the package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5' to 3' direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. a toolbox, including c++ and java source code and executable files on both windows and linux platforms together with a user instruction, is downloadable from the website for academic purpose at",0
"background since a national lockdown was introduced across the uk in march, 2020, in response to the covid-19 pandemic, cancer screening has been suspended, routine diagnostic work deferred, and only urgent symptomatic cases prioritised for diagnostic intervention. in this study, we estimated the impact of delays in diagnosis on cancer survival outcomes in four major tumour types. methods in this national population-based modelling study, we used linked english national health service (nhs) cancer registration and hospital administrative datasets for patients aged 15-84 years, diagnosed with breast, colorectal, and oesophageal cancer between jan 1, 2010, and dec 31, 2010, with follow-up data until dec 31, 2014, and diagnosed with lung cancer between jan 1, 2012, and dec 31, 2012, with follow-up data until dec 31, 2015. we use a routes-to-diagnosis framework to estimate the impact of diagnostic delays over a 12-month period from the commencement of physical distancing measures, on march 16, 2020, up to 1, 3, and 5 years after diagnosis. to model the subsequent impact of diagnostic delays on survival, we reallocated patients who were on screening and routine referral pathways to urgent and emergency pathways that are associated with more advanced stage of disease at diagnosis. we considered three reallocation scenarios representing the best to worst case scenarios and reflect actual changes in the diagnostic pathway being seen in the nhs, as of march 16, 2020, and estimated the impact on net survival at 1, 3, and 5 years after diagnosis to calculate the additional deaths that can be attributed to cancer, and the total years of life lost (ylls) compared with pre-pandemic data. findings we collected data for 32 583 patients with breast cancer, 24 975 with colorectal cancer, 6744 with oesophageal cancer, and 29 305 with lung cancer. across the three different scenarios, compared with pre-pandemic figures, we estimate a 7·9-9·6% increase in the number of deaths due to breast cancer up to year 5 after diagnosis, corresponding to between 281 (95% ci 266-295) and 344 (329-358) additional deaths. for colorectal cancer, we estimate 1445 (1392-1591) to 1563 (1534-1592) additional deaths, a 15·3-16·6% increase; for lung cancer, 1235 (1220-1254) to 1372 (1343-1401) additional deaths, a 4·8-5·3% increase; and for oesophageal cancer, 330 (324-335) to 342 (336-348) additional deaths, 5·8-6·0% increase up to 5 years after diagnosis. for these four tumour types, these data correspond with 3291-3621 additional deaths across the scenarios within 5 years. the total additional ylls across these cancers is estimated to be 59 204-63 229 years. interpretation substantial increases in the number of avoidable cancer deaths in england are to be expected as a result of diagnostic delays due to the covid-19 pandemic in the uk. urgent policy interventions are necessary, particularly the need to manage the backlog within routine diagnostic services to mitigate the expected impact of the covid-19 pandemic on patients with cancer. funding uk research and innovation economic and social research council.",0
"background the just-in-time adaptive intervention (jitai) is an intervention design aiming to provide the right type/amount of support, at the right time, by adapting to an individual's changing internal and contextual state. the availability of increasingly powerful mobile and sensing technologies underpins the use of jitais to support health behavior, as in such a setting an individual's state can change rapidly, unexpectedly, and in his/her natural environment. purpose despite the increasing use and appeal of jitais, a major gap exists between the growing technological capabilities for delivering jitais and research on the development and evaluation of these interventions. many jitais have been developed with minimal use of empirical evidence, theory, or accepted treatment guidelines. here, we take an essential first step towards bridging this gap. methods building on health behavior theories and the extant literature on jitais, we clarify the scientific motivation for jitais, define their fundamental components, and highlight design principles related to these components. examples of jitais from various domains of health behavior research are used for illustration. conclusions as we enter a new era of technological capacity for delivering jitais, it is critical that researchers develop sophisticated and nuanced health behavior theories capable of guiding the construction of such interventions. particular attention has to be given to better understanding the implications of providing timely and ecologically sound support for intervention adherence and retention.",0
"brain enlargement has been observed in children with autism spectrum disorder (asd), but the timing of this phenomenon, and the relationship between asd and the appearance of behavioural symptoms, are unknown. retrospective head circumference and longitudinal brain volume studies of two-year olds followed up at four years of age have provided evidence that increased brain volume may emerge early in development. studies of infants at high familial risk of autism can provide insight into the early development of autism and have shown that characteristic social deficits in asd emerge during the latter part of the first and in the second year of life. these observations suggest that prospective brain-imaging studies of infants at high familial risk of asd might identify early postnatal changes in brain volume that occur before an asd diagnosis. in this prospective neuroimaging study of 106 infants at high familial risk of asd and 42 low-risk infants, we show that hyperexpansion of the cortical surface area between 6 and 12 months of age precedes brain volume overgrowth observed between 12 and 24 months in 15 high-risk infants who were diagnosed with autism at 24 months. brain volume overgrowth was linked to the emergence and severity of autistic social deficits. a deep-learning algorithm that primarily uses surface area information from magnetic resonance imaging of the brain of 6-12-month-old individuals predicted the diagnosis of autism in individual high-risk children at 24 months (with a positive predictive value of 81% and a sensitivity of 88%). these findings demonstrate that early brain changes occur during the period in which autistic behaviours are first emerging.",0
"the extracellular matrix (ecm) is a complex meshwork of cross-linked proteins providing both biophysical and biochemical cues that are important regulators of cell proliferation, survival, differentiation, and migration. we present here a proteomic strategy developed to characterize the in vivo ecm composition of normal tissues and tumors using enrichment of protein extracts for ecm components and subsequent analysis by mass spectrometry. in parallel, we have developed a bioinformatic approach to predict the in silico ""matrisome"" defined as the ensemble of ecm proteins and associated factors. we report the characterization of the extracellular matrices of murine lung and colon, each comprising more than 100 ecm proteins and each presenting a characteristic signature. moreover, using human tumor xenografts in mice, we show that both tumor cells and stromal cells contribute to the production of the tumor matrix and that tumors of differing metastatic potential differ in both the tumor- and the stroma-derived ecm components. the strategy we describe and illustrate here can be broadly applied and, to facilitate application of these methods by others, we provide resources including laboratory protocols, inventories of ecm domains and proteins, and instructions for bioinformatically deriving the human and mouse matrisome.",0
"reproducible science requires transparent reporting. the arrive guidelines (animal research: reporting of in vivo experiments) were originally developed in 2010 to improve the reporting of animal research. they consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. here, we introduce arrive 2.0. the guidelines have been updated and information reorganised to facilitate their use in practice. we used a delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the ""arrive essential 10,"" which constitutes the minimum requirement, and the ""recommended set,"" which describes the research context. this division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. this helps journal editors and reviewers verify that the most important items are being reported in manuscripts. we have also developed the accompanying explanation and elaboration document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. we aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.",0
"ease is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, sage and other high-throughput genomic data. the biological themes returned by ease recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. ease is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'.",0
"mammalian immune system development depends on instruction from resident commensal microorganisms. diseases associated with abnormal immune responses towards environmental and self antigens have been rapidly increasing over the last 50 years. these diseases include inflammatory bowel disease (ibd), multiple sclerosis (ms), type i diabetes (t1d), allergies and asthma. the observation that people with immune mediated diseases house a different microbial community when compared to healthy individuals suggests that pathogenesis arises from improper training of the immune system by the microbiota. however, with hundreds of different microorganisms on our bodies it is hard to know which of these contribute to health and more importantly how? microbiologists studying pathogenic organisms have long adhered to koch's postulates to directly relate a certain disease to a specific microbe, raising the question of whether this might be true of commensal-host relationships as well. emerging evidence supports that rather than one or two dominant organisms inducing host health, the composition of the entire community of microbial residents influences a balanced immune response. thus, perturbations to the structure of complex commensal communities (referred to as dysbiosis) can lead to deficient education of the host immune system and subsequent development of immune mediated diseases. here we will overview the literature that describes the causes of dysbiosis and the mechanisms evolved by the host to prevent these changes to community structure. building off these studies, we will categorize the different types of dysbiosis and define how collections of microorganisms can influence the host response. this research has broad implications for future therapies that go beyond the introduction of a single organism to induce health. we propose that identifying mechanisms to re-establish a healthy complex microbiota after dysbiosis has occurred, a process we will refer to as rebiosis, will be fundamental to treating complex immune diseases.",0
"dynamin is the mammalian homologue to the drosophila shibire gene product. mutations in this 100-kd gtpase cause a pleiotropic defect in endocytosis. to further investigate its role, we generated stable hela cell lines expressing either wild-type dynamin or a mutant defective in gtp binding and hydrolysis driven by a tightly controlled, tetracycline-inducible promoter. overexpression of wild-type dynamin had no effect. in contrast, coated pits failed to become constricted and coated vesicles failed to bud in cells overexpressing mutant dynamin so that endocytosis via both transferrin (tfn) and egf receptors was potently inhibited. coated pit assembly, invagination, and the recruitment of receptors into coated pits were unaffected. other vesicular transport pathways, including tfn receptor recycling, tfn receptor biosynthesis, and cathepsin d transport to lysosomes via golgi-derived coated vesicles, were unaffected. bulk fluid-phase uptake also continued at the same initial rates as wild type. em immunolocalization showed that membrane-bound dynamin was specifically associated with clathrin-coated pits on the plasma membrane. dynamin was also associated with isolated coated vesicles, suggesting that it plays a role in vesicle budding. like the drosophila shibire mutant, hela cells overexpressing mutant dynamin accumulated long tubules, many of which remained connected to the plasma membrane. we conclude that dynamin is specifically required for endocytic coated vesicle formation, and that its gtp binding and hydrolysis activities are required to form constricted coated pits and, subsequently, for coated vesicle budding.",0
"background in 2011, who member states signed up to the 25 × 25 initiative, a plan to cut mortality due to non-communicable diseases by 25% by 2025. however, socioeconomic factors influencing non-communicable diseases have not been included in the plan. in this study, we aimed to compare the contribution of socioeconomic status to mortality and years-of-life-lost with that of the 25 × 25 conventional risk factors. methods we did a multicohort study and meta-analysis with individual-level data from 48 independent prospective cohort studies with information about socioeconomic status, indexed by occupational position, 25 × 25 risk factors (high alcohol intake, physical inactivity, current smoking, hypertension, diabetes, and obesity), and mortality, for a total population of 1 751 479 (54% women) from seven high-income who member countries. we estimated the association of socioeconomic status and the 25 × 25 risk factors with all-cause mortality and cause-specific mortality by calculating minimally adjusted and mutually adjusted hazard ratios and 95% cis. we also estimated the population attributable fraction and the years of life lost due to suboptimal risk factors. findings during 26·6 million person-years at risk (mean follow-up 13·3 years ), 310 277 participants died. hr for the 25 × 25 risk factors and mortality varied between 1·04 (95% ci 0·98-1·11) for obesity in men and 2 ·17 (2·06-2·29) for current smoking in men. participants with low socioeconomic status had greater mortality compared with those with high socioeconomic status (hr 1·42, 95% ci 1·38-1·45 for men; 1·34, 1·28-1·39 for women); this association remained significant in mutually adjusted models that included the 25 × 25 factors (hr 1·26, 1·21-1·32, men and women combined). the population attributable fraction was highest for smoking, followed by physical inactivity then socioeconomic status. low socioeconomic status was associated with a 2·1-year reduction in life expectancy between ages 40 and 85 years, the corresponding years-of-life-lost were 0·5 years for high alcohol intake, 0·7 years for obesity, 3·9 years for diabetes, 1·6 years for hypertension, 2·4 years for physical inactivity, and 4·8 years for current smoking. interpretation socioeconomic circumstances, in addition to the 25 × 25 factors, should be targeted by local and global health strategies and health risk surveillance to reduce mortality. funding european commission, swiss state secretariat for education, swiss national science foundation, the medical research council, nordforsk, portuguese foundation for science and technology.",0
"microtubules are long, proteinaceous filaments that perform structural functions in eukaryotic cells by defining cellular shape and serving as tracks for intracellular motor proteins. we report the first accurate measurements of the flexural rigidity of microtubules. by analyzing the thermally driven fluctuations in their shape, we estimated the mean flexural rigidity of taxol-stabilized microtubules to be 2.2 x 10(-23) nm2 (with 6.4% uncertainty) for seven unlabeled microtubules and 2.1 x 10(-23) nm2 (with 4.7% uncertainty) for eight rhodamine-labeled microtubules. these values are similar to earlier, less precise estimates of microtubule bending stiffness obtained by modeling flagellar motion. a similar analysis on seven rhodamine-phalloidin-labeled actin filaments gave a flexural rigidity of 7.3 x 10(-26) nm2 (with 6% uncertainty), consistent with previously reported results. the flexural rigidity of these microtubules corresponds to a persistence length of 5,200 microns showing that a microtubule is rigid over cellular dimensions. by contrast, the persistence length of an actin filament is only approximately 17.7 microns, perhaps explaining why actin filaments within cells are usually cross-linked into bundles. the greater flexural rigidity of a microtubule compared to an actin filament mainly derives from the former's larger cross-section. if tubulin were homogeneous and isotropic, then the microtubule's young's modulus would be approximately 1.2 gpa, similar to plexiglas and rigid plastics. microtubules are expected to be almost inextensible: the compliance of cells is due primarily to filament bending or sliding between filaments rather than the stretching of the filaments themselves.",0
"spontaneously arising (de novo) mutations have an important role in medical genetics. for diseases with extensive locus heterogeneity, such as autism spectrum disorders (asds), the signal from de novo mutations is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. here we provide a statistical framework for the analysis of excesses in de novo mutation per gene and gene set by calibrating a model of de novo mutation. we applied this framework to de novo mutations collected from 1,078 asd family trios, and, whereas we affirmed a significant role for loss-of-function mutations, we found no excess of de novo loss-of-function mutations in cases with iq above 100, suggesting that the role of de novo mutations in asds might reside in fundamental neurodevelopmental processes. we also used our model to identify ∼1,000 genes that are significantly lacking in functional coding variation in non-asd samples and are enriched for de novo loss-of-function mutations identified in asd cases.",0
"the cells of a human epithelial cancer cultivated en masse have been shown to support the multiplication of all three types of poliomyelitis virus. these cells (strain hela of gey) have been maintained in vitro since their derivation from an epidermoid carcinoma of the cervix in february, 1951. as the virus multiplied it caused in from 12 to 96 hours degeneration and destruction of the cancer cells. the specific destructive effect of the virus was prevented by adding homotypic antibody to the cultures but not by adding heterotypic antibodies. methods for the preparation of large numbers of replicate cultures with suspensions of strain hela cells were described. the cells in suspension were readily quantitated by direct counts in a hemocytometer. a synthetic solution that maintains cellular viability was employed for viral propagation. the experimental results demonstrate the usefulness of strain hela cells for (a) the quantitation of poliomyelitis virus, (b) the measurement of poliomyelitis antibodies, and (c) the production of virus.",0
"background protein aggregation correlates with the development of several debilitating human disorders of growing incidence, such as alzheimer's and parkinson's diseases. on the biotechnological side, protein production is often hampered by the accumulation of recombinant proteins into aggregates. thus, the development of methods to anticipate the aggregation properties of polypeptides is receiving increasing attention. aggrescan is a web-based software for the prediction of aggregation-prone segments in protein sequences, the analysis of the effect of mutations on protein aggregation propensities and the comparison of the aggregation properties of different proteins or protein sets. results aggrescan is based on an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. the algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. it also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies. conclusion by identifying aggregation-prone segments in proteins, aggrescan shall facilitate (i) the identification of possible therapeutic targets for anti-depositional strategies in conformational diseases and (ii) the anticipation of aggregation phenomena during storage or recombinant production of bioactive polypeptides or polypeptide sets.",0
"this second paper in the born too soon supplement presents a review of the epidemiology of preterm birth, and its burden globally, including priorities for action to improve the data. worldwide an estimated 11.1% of all livebirths in 2010 were born preterm (14.9 million babies born before 37 weeks of gestation), with preterm birth rates increasing in most countries with reliable trend data. direct complications of preterm birth account for one million deaths each year, and preterm birth is a risk factor in over 50% of all neonatal deaths. in addition, preterm birth can result in a range of long-term complications in survivors, with the frequency and severity of adverse outcomes rising with decreasing gestational age and decreasing quality of care. the economic costs of preterm birth are large in terms of immediate neonatal intensive care, ongoing long-term complex health needs, as well as lost economic productivity. preterm birth is a syndrome with a variety of causes and underlying factors usually divided into spontaneous and provider-initiated preterm births. consistent recording of all pregnancy outcomes, including stillbirths, and standard application of preterm definitions is important in all settings to advance both the understanding and the monitoring of trends. context specific innovative solutions to prevent preterm birth and hence reduce preterm birth rates all around the world are urgently needed. strengthened data systems are required to adequately track trends in preterm birth rates and program effectiveness. these efforts must be coupled with action now to implement improved antenatal, obstetric and newborn care to increase survival and reduce disability amongst those born too soon.",0
"genome-wide association studies have shown unequivocally that common complex disorders have a polygenic genetic architecture and have enabled researchers to identify genetic variants associated with diseases. these variants can be combined into a polygenic risk score that captures part of an individual's susceptibility to diseases. polygenic risk scores have been widely applied in research studies, confirming the association between the scores and disease status, but their clinical utility has yet to be established. polygenic risk scores may be used to estimate an individual's lifetime genetic risk of disease, but the current discriminative ability is low in the general population. clinical implementation of polygenic risk score (prs) may be useful in cohorts where there is a higher prior probability of disease, for example, in early stages of diseases to assist in diagnosis or to inform treatment choices. important considerations are the weaker evidence base in application to non-european ancestry and the challenges in translating an individual's prs from a percentile of a normal distribution to a lifetime disease risk. in this review, we consider how prs may be informative at different points in the disease trajectory giving examples of progress in the field and discussing obstacles that need to be addressed before clinical implementation.",0
"the last 15 years have witnessed a steady increase in the number of resting-state functional neuroimaging studies. the connectivity patterns of multiple functional, distributed, large-scale networks of brain dynamics have been recognised for their potential as useful tools in the domain of systems and other neurosciences. the application of functional connectivity methods to areas such as cognitive psychology, clinical diagnosis and treatment progression has yielded promising preliminary results, but is yet to be fully realised. this is due, in part, to an array of methodological and interpretative issues that remain to be resolved. we here present a review of the methods most commonly applied in this rapidly advancing field, such as seed-based correlation analysis and independent component analysis, along with examples of their use at the individual subject and group analysis levels and a discussion of practical and theoretical issues arising from this data 'explosion'. we describe the similarities and differences across these varied statistical approaches to processing resting-state functional magnetic resonance imaging signals, and conclude that further technical optimisation and experimental refinement is required in order to fully delineate and characterise the gross complexity of the human neural functional architecture.",0
"crystalexplorer is a native cross-platform program supported on windows, macos and linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the gaussian and nwchem programs to calculate quantum-mechanical properties of molecules. the current version, crystalexplorer21 , incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.",0
"coronavirus disease 2019 (covid-19) is a novel, viral-induced respiratory disease that in ∼10-15% of patients progresses to acute respiratory distress syndrome (ards) triggered by a cytokine storm. in this perspective, autopsy results and literature are presented supporting the hypothesis that a little known yet powerful function of neutrophils-the ability to form neutrophil extracellular traps (nets)-may contribute to organ damage and mortality in covid-19. we show lung infiltration of neutrophils in an autopsy specimen from a patient who succumbed to covid-19. we discuss prior reports linking aberrant net formation to pulmonary diseases, thrombosis, mucous secretions in the airways, and cytokine production. if our hypothesis is correct, targeting nets directly and/or indirectly with existing drugs may reduce the clinical severity of covid-19.",0
"jaspar ( is an open-access database containing manually curated, non-redundant transcription factor (tf) binding profiles for tfs across six taxonomic groups. in this 9th release, we expanded the core collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. we added 298 new profiles to the unvalidated collection when no orthogonal evidence was found in the literature. all the profiles were clustered to provide familial binding profiles for each taxonomic group. moreover, we revised the structural classification of dna binding domains to consider plant-specific tfs. this release introduces word clouds to represent the scientific knowledge associated with each tf. we updated the genome tracks of tfbss predicted with jaspar profiles in eight organisms; the human and mouse tfbs predictions can be visualized as native tracks in the ucsc genome browser. finally, we provide a new tool to perform jaspar tfbs enrichment analysis in user-provided genomic regions. all the data is accessible through the jaspar website, its associated restful api, the r/bioconductor data package, and a new python package, pyjaspar, that facilitates serverless access to the data.",0
"objectives to describe the burden, epidemiology and outcomes of co-infections and superinfections occurring in hospitalized patients with coronavirus disease 2019 (covid-19). methods we performed an observational cohort study of all consecutive patients admitted for ≥48 hours to the hospital clinic of barcelona for covid-19 (28 february to 22 april 2020) who were discharged or dead. we describe demographic, epidemiologic, laboratory and microbiologic results, as well as outcome data retrieved from electronic health records. results of a total of 989 consecutive patients with covid-19, 72 (7.2%) had 88 other microbiologically confirmed infections: 74 were bacterial, seven fungal and seven viral. community-acquired co-infection at covid-19 diagnosis was uncommon (31/989, 3.1%) and mainly caused by streptococcus pneumoniae and staphylococcus aureus. a total of 51 hospital-acquired bacterial superinfections, mostly caused by pseudomonas aeruginosa and escherichia coli, were diagnosed in 43 patients (4.7%), with a mean (sd) time from hospital admission to superinfection diagnosis of 10.6 (6.6) days. overall mortality was 9.8% (97/989). patients with community-acquired co-infections and hospital-acquired superinfections had worse outcomes. conclusions co-infection at covid-19 diagnosis is uncommon. few patients developed superinfections during hospitalization. these findings are different compared to those of other viral pandemics. as it relates to hospitalized patients with covid-19, such findings could prove essential in defining the role of empiric antimicrobial therapy or stewardship strategies.",0
"programmed cell death (pcd) is a physiological process commonly defined by alterations in nuclear morphology (apoptosis) and/or characteristic stepwise degradation of chromosomal dna occurring before cytolysis. however, determined characteristics of pcd such as loss in mitochondrial reductase activity or cytolysis can be induced in enucleated cells, indicating cytoplasmic pcd control. here we report a sequential disregulation of mitochondrial function that precedes cell shrinkage and nuclear fragmentation. a first cyclosporin a-inhibitable step of ongoing pcd is characterized by a reduction of mitochondrial transmembrane potential, as determined by specific fluorochromes (5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolcarbocyanine++ + iodide; 3,3'dihexyloxacarbocyanine iodide). cytofluorometrically purified cells with reduced mitochondrial transmembrane potential are initially incapable of oxidizing hydroethidine (he) into ethidium. upon short-term in vitro culture, such cells acquire the capacity of he oxidation, thus revealing a second step of pcd marked by mitochondrial generation of reactive oxygen species (ros). this step can be selectively inhibited by rotenone and ruthenium red yet is not affected by cyclosporin a. finally, cells reduce their volume, a step that is delayed by radical scavengers, indicating the implication of ros in the apoptotic process. this sequence of alterations accompanying early pcd is found in very different models of apoptosis induction: glucocorticoid-induced death of lymphocytes, activation-induced pcd of t cell hybridomas, and tumor necrosis factor-induced death of u937 cells. transfection with the antiapoptotic protooncogene bcl-2 simultaneously inhibits mitochondrial alterations and apoptotic cell death triggered by steroids or ceramide. in vivo injection of fluorochromes such as 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolcarbocyanine iodide; 3,3'dihexyloxacarbocyanine iodide; or he allows for the detection of cells that are programmed for death but still lack nuclear dna fragmentation. in particular, assessment of mitochondrial ros generation provides an accurate picture of pcd-mediated lymphocyte depletion. in conclusion, alterations of mitochondrial function constitute an important feature of early pcd.",0
"background it is increasingly acknowledged that 'acceptability' should be considered when designing, evaluating and implementing healthcare interventions. however, the published literature offers little guidance on how to define or assess acceptability. the purpose of this study was to develop a multi-construct theoretical framework of acceptability of healthcare interventions that can be applied to assess prospective (i.e. anticipated) and retrospective (i.e. experienced) acceptability from the perspective of intervention delivers and recipients. methods two methods were used to select the component constructs of acceptability. 1) an overview of reviews was conducted to identify systematic reviews that claim to define, theorise or measure acceptability of healthcare interventions. 2) principles of inductive and deductive reasoning were applied to theorise the concept of acceptability and develop a theoretical framework. steps included (1) defining acceptability; (2) describing its properties and scope and (3) identifying component constructs and empirical indicators. results from the 43 reviews included in the overview, none explicitly theorised or defined acceptability. measures used to assess acceptability focused on behaviour (e.g. dropout rates) (23 reviews), affect (i.e. feelings) (5 reviews), cognition (i.e. perceptions) (7 reviews) or a combination of these (8 reviews). from the methods described above we propose a definition: acceptability is a multi-faceted construct that reflects the extent to which people delivering or receiving a healthcare intervention consider it to be appropriate, based on anticipated or experienced cognitive and emotional responses to the intervention. the theoretical framework of acceptability (tfa) consists of seven component constructs: affective attitude, burden, perceived effectiveness, ethicality, intervention coherence, opportunity costs, and self-efficacy. conclusion despite frequent claims that healthcare interventions have assessed acceptability, it is evident that acceptability research could be more robust. the proposed definition of acceptability and the tfa can inform assessment tools and evaluations of the acceptability of new or existing interventions.",0
"objective to investigate the occurrence of olfactory and gustatory dysfunctions in patients with laboratory-confirmed covid-19 infection. methods patients with laboratory-confirmed covid-19 infection were recruited from 12 european hospitals. the following epidemiological and clinical outcomes have been studied: age, sex, ethnicity, comorbidities, and general and otolaryngological symptoms. patients completed olfactory and gustatory questionnaires based on the smell and taste component of the national health and nutrition examination survey, and the short version of the questionnaire of olfactory disorders-negative statements (sqod-ns). results a total of 417 mild-to-moderate covid-19 patients completed the study (263 females). the most prevalent general symptoms consisted of cough, myalgia, and loss of appetite. face pain and nasal obstruction were the most disease-related otolaryngological symptoms. 85.6% and 88.0% of patients reported olfactory and gustatory dysfunctions, respectively. there was a significant association between both disorders (p conclusion olfactory and gustatory disorders are prevalent symptoms in european covid-19 patients, who may not have nasal symptoms. the sudden anosmia or ageusia need to be recognized by the international scientific community as important symptoms of the covid-19 infection.",0
"we have developed a protocol to assemble in one step and one tube at least nine separate dna fragments together into an acceptor vector, with 90% of recombinant clones obtained containing the desired construct. this protocol is based on the use of type iis restriction enzymes and is performed by simply subjecting a mix of 10 undigested input plasmids (nine insert plasmids and the acceptor vector) to a restriction-ligation and transforming the resulting mix in competent cells. the efficiency of this protocol allows generating libraries of recombinant genes by combining in one reaction several fragment sets prepared from different parental templates. as an example, we have applied this strategy for shuffling of trypsinogen from three parental templates (bovine cationic trypsinogen, bovine anionic trypsinogen and human cationic trypsinogen) each divided in 9 separate modules. we show that one round of shuffling using the 27 trypsinogen entry plasmids can easily produce the 19,683 different possible combinations in one single restriction-ligation and that expression screening of a subset of the library allows identification of variants that can lead to higher expression levels of trypsin activity. this protocol, that we call 'golden gate shuffling', is robust, simple and efficient, can be performed with templates that have no homology, and can be combined with other shuffling protocols in order to introduce any variation in any part of a given gene.",0
"it has been proposed that memories are encoded by modification of synaptic strengths through cellular mechanisms such as long-term potentiation (ltp) and long-term depression (ltd). however, the causal link between these synaptic processes and memory has been difficult to demonstrate. here we show that fear conditioning, a type of associative memory, can be inactivated and reactivated by ltd and ltp, respectively. we began by conditioning an animal to associate a foot shock with optogenetic stimulation of auditory inputs targeting the amygdala, a brain region known to be essential for fear conditioning. subsequent optogenetic delivery of ltd conditioning to the auditory input inactivates memory of the shock. then subsequent optogenetic delivery of ltp conditioning to the auditory input reactivates memory of the shock. thus, we have engineered inactivation and reactivation of a memory using ltd and ltp, supporting a causal link between these synaptic processes and memory.",0
"signal peptides (sps) are short amino acid sequences that control protein secretion and translocation in all living organisms. sps can be predicted from sequence data, but existing algorithms are unable to detect all known types of sps. we introduce signalp 6.0, a machine learning model that detects all five sp types and is applicable to metagenomic data.",0
"in this retrospective case series, chest ct scans of 21 symptomatic patients from china infected with the 2019 novel coronavirus (2019-ncov) were reviewed, with emphasis on identifying and characterizing the most common findings. typical ct findings included bilateral pulmonary parenchymal ground-glass and consolidative pulmonary opacities, sometimes with a rounded morphology and a peripheral lung distribution. notably, lung cavitation, discrete pulmonary nodules, pleural effusions, and lymphadenopathy were absent. follow-up imaging in a subset of patients during the study time window often demonstrated mild or moderate progression of disease, as manifested by increasing extent and density of lung opacities.",0
"background many reports on coronavirus disease 2019 (covid-19) have highlighted age- and sex-related differences in health outcomes. more information is needed about racial and ethnic differences in outcomes from covid-19. methods in this retrospective cohort study, we analyzed data from patients seen within an integrated-delivery health system (ochsner health) in louisiana between march 1 and april 11, 2020, who tested positive for severe acute respiratory syndrome coronavirus 2 (sars-cov-2, the virus that causes covid-19) on qualitative polymerase-chain-reaction assay. the ochsner health population is 31% black non-hispanic and 65% white non-hispanic. the primary outcomes were hospitalization and in-hospital death. results a total of 3626 patients tested positive, of whom 145 were excluded (84 had missing data on race or ethnic group, 9 were hispanic, and 52 were asian or of another race or ethnic group). of the 3481 covid-19-positive patients included in our analyses, 60.0% were female, 70.4% were black non-hispanic, and 29.6% were white non-hispanic. black patients had higher prevalences of obesity, diabetes, hypertension, and chronic kidney disease than white patients. a total of 39.7% of covid-19-positive patients (1382 patients) were hospitalized, 76.9% of whom were black. in multivariable analyses, black race, increasing age, a higher score on the charlson comorbidity index (indicating a greater burden of illness), public insurance (medicare or medicaid), residence in a low-income area, and obesity were associated with increased odds of hospital admission. among the 326 patients who died from covid-19, 70.6% were black. in adjusted time-to-event analyses, variables that were associated with higher in-hospital mortality were increasing age and presentation with an elevated respiratory rate; elevated levels of venous lactate, creatinine, or procalcitonin; or low platelet or lymphocyte counts. however, black race was not independently associated with higher mortality (hazard ratio for death vs. white race, 0.89; 95% confidence interval, 0.68 to 1.17). conclusions in a large cohort in louisiana, 76.9% of the patients who were hospitalized with covid-19 and 70.6% of those who died were black, whereas blacks comprise only 31% of the ochsner health population. black race was not associated with higher in-hospital mortality than white race, after adjustment for differences in sociodemographic and clinical characteristics on admission.",0
"stratification of women according to their risk of breast cancer based on polygenic risk scores (prss) could improve screening and prevention strategies. our aim was to develop prss, optimized for prediction of estrogen receptor (er)-specific disease, from the largest available genome-wide association dataset and to empirically validate the prss in prospective studies. the development dataset comprised 94,075 case subjects and 75,017 control subjects of european ancestry from 69 studies, divided into training and validation sets. samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (snps) were selected by stepwise regression or lasso penalized regression. the best performing prss were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from uk biobank (3,215 incident breast cancers). for the best prss (313 snps), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%ci: 1.57-1.65) with area under receiver-operator curve (auc) = 0.630 (95%ci: 0.628-0.651). the lifetime risk of overall breast cancer in the top centile of the prss was 32.6%. compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing er-positive and er-negative disease, respectively. goodness-of-fit tests indicated that this prs was well calibrated and predicts disease risk accurately in the tails of the distribution. this prs is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.",0
"background the knowledge and use of qualitative description as a qualitative research approach in health services research is limited.the aim of this article is to discuss the potential benefits of a qualitative descriptive approach, to identify its strengths and weaknesses and to provide examples of use. discussion qualitative description is a useful qualitative method in much medical research if you keep the limitations of the approach in mind. it is especially relevant in mixed method research, in questionnaire development and in research projects aiming to gain firsthand knowledge of patients', relatives' or professionals' experiences with a particular topic. another great advantage of the method is that it is suitable if time or resources are limited. summary as a consequence of the growth in qualitative research in the health sciences, researchers sometimes feel obliged to designate their work as phenomenology, grounded theory, ethnography or a narrative study when in fact it is not. qualitative description might be a useful alternative approach to consider.",0
"murine embryonal carcinoma cells can differentiate into a varied spectrum of cell types. we observed the abundant and precocious development of neuronlike cells when embryonal carcinoma cells of various pluripotent lines were aggregated and cultured in the presence of nontoxic concentrations of retinoic acid. neuronlike cells were also formed in retinoic acid-treated cultures of the embryonal carcinoma line, p19, which does not differentiate into neurons in the absence of the drug. the neuronal nature of these cells was confirmed by their staining with antiserum directed against neurofilament protein in indirect immunofluorescence experiments. retinoic acid-treated cultures also contained elevated acetylcholinesterase activity. glial cells, identified by immunofluorescence analysis of their intermediate filaments, and a population of fibroblastlike cells were also present in retinoic acid-treated cultures of p19 cells. we did not observe embryonal carcinoma, muscle, or epithelial cells in these cultures. neurons and glial cells appeared in cultures exposed to retinoic acid for as little as 48 h. we found no evidence for retinoic acid toxicity, suggesting that the effect of the drug was to induce the development of neurons and glia rather than to select against cells differentiating along other developmental pathways.",0
"context studies documenting racial/ethnic disparities in health care frequently implicate physicians' unconscious biases. no study to date has measured physicians' unconscious racial bias to test whether this predicts physicians' clinical decisions. objective to test whether physicians show implicit race bias and whether the magnitude of such bias predicts thrombolysis recommendations for black and white patients with acute coronary syndromes. design, setting, and participants an internet-based tool comprising a clinical vignette of a patient presenting to the emergency department with an acute coronary syndrome, followed by a questionnaire and three implicit association tests (iats). study invitations were e-mailed to all internal medicine and emergency medicine residents at four academic medical centers in atlanta and boston; 287 completed the study, met inclusion criteria, and were randomized to either a black or white vignette patient. main outcome measures iat scores (normal continuous variable) measuring physicians' implicit race preference and perceptions of cooperativeness. physicians' attribution of symptoms to coronary artery disease for vignette patients with randomly assigned race, and their decisions about thrombolysis. assessment of physicians' explicit racial biases by questionnaire. results physicians reported no explicit preference for white versus black patients or differences in perceived cooperativeness. in contrast, iats revealed implicit preference favoring white americans (mean iat score = 0.36, p conclusions this study represents the first evidence of unconscious (implicit) race bias among physicians, its dissociation from conscious (explicit) bias, and its predictive validity. results suggest that physicians' unconscious biases may contribute to racial/ethnic disparities in use of medical procedures such as thrombolysis for myocardial infarction.",0
"unlabelled the aim was to develop clinical guidelines for multi-parametric mri of the prostate by a group of prostate mri experts from the european society of urogenital radiology (esur), based on literature evidence and consensus expert opinion. true evidence-based guidelines could not be formulated, but a compromise, reflected by ""minimal"" and ""optimal"" requirements has been made. the scope of these esur guidelines is to promulgate high quality mri in acquisition and evaluation with the correct indications for prostate cancer across the whole of europe and eventually outside europe. the guidelines for the optimal technique and three protocols for ""detection"", ""staging"" and ""node and bone"" are presented. the use of endorectal coil vs. pelvic phased array coil and 1.5 vs. 3 t is discussed. clinical indications and a pi-rads classification for structured reporting are presented. key points this report provides guidelines for magnetic resonance imaging (mri) in prostate cancer. clinical indications, and minimal and optimal imaging acquisition protocols are provided. a structured reporting system (pi-rads) is described.",0
"the iuphar/bps guide to pharmacology (gtopdb, and its precursor iuphar-db, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. this resource continues to be developed in conjunction with the international union of basic and clinical pharmacology (iuphar) and the british pharmacological society (bps). as previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. this update describes content expansion, new features and interoperability improvements introduced in the 10 releases since august 2015. our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. as an important addition, we also introduce our newly funded project for the guide to immunopharmacology (gtoimmupdb, this has been 'forked' from the well-established gtopdb data model and expanded into new types of data related to the immune system and inflammatory processes. this includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new iuphar expert committees. designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.",0
"many of the major human infectious diseases, including some now confined to humans and absent from animals, are 'new' ones that arose only after the origins of agriculture. where did they come from? why are they overwhelmingly of old world origins? here we show that answers to these questions are different for tropical and temperate diseases; for instance, in the relative importance of domestic animals and wild primates as sources. we identify five intermediate stages through which a pathogen exclusively infecting animals may become transformed into a pathogen exclusively infecting humans. we propose an initiative to resolve disputed origins of major diseases, and a global early warning system to monitor pathogens infecting individuals exposed to wild animals.",0
"swedish health care and national health registers are dependent on the presence of a unique identifier. this paper describes the swedish personal identity number (pin) and explores ethical issues of its use in medical research. a ten-digit-pin is maintained by the national tax board for all individuals that have resided in sweden since 1947. until january 2008, an estimated 75,638 individuals have changed pin. the most common reasons for change of pin are incorrect recording of date of birth or sex among immigrants or newborns. although uncommon, change of sex always leads to change of pin since the pin is sex-specific. the most common reasons for re-use of pin (n = 15,887), is when immigrants are assigned a pin that has previously been assigned to someone else. this is sometimes necessary since there is a shortage of certain pin combinations referring to dates of birth in the 1950s and 1960s. several ethical issues can be raised pro and con the use of pin in medical research. the swedish pin is a useful tool for linkages between medical registers and allows for virtually 100% coverage of the swedish health care system. we suggest that matching of registers through pin and matching of national health registers without the explicit approval of the individual patient is to the benefit for both the individual patient and for society.",0
"the voltage-dependent anion channel (vdac) of the outer mitochondrial membrane mediates metabolic flow, ca(2+), and cell death signaling between the endoplasmic reticulum (er) and mitochondrial networks. we demonstrate that vdac1 is physically linked to the endoplasmic reticulum ca(2+)-release channel inositol 1,4,5-trisphosphate receptor (ip(3)r) through the molecular chaperone glucose-regulated protein 75 (grp75). functional interaction between the channels was shown by the recombinant expression of the ligand-binding domain of the ip(3)r on the er or mitochondrial surface, which directly enhanced ca(2+) accumulation in mitochondria. knockdown of grp75 abolished the stimulatory effect, highlighting chaperone-mediated conformational coupling between the ip(3)r and the mitochondrial ca(2+) uptake machinery. because organelle ca(2+) homeostasis influences fundamentally cellular functions and death signaling, the central location of grp75 may represent an important control point of cell fate and pathogenesis.",0
"immunity and inflammation are key elements of the pathobiology of stroke, a devastating illness second only to cardiac ischemia as a cause of death worldwide. the immune system participates in the brain damage produced by ischemia, and the damaged brain, in turn, exerts an immunosuppressive effect that promotes fatal infections that threaten the survival of people after stroke. inflammatory signaling is involved in all stages of the ischemic cascade, from the early damaging events triggered by arterial occlusion to the late regenerative processes underlying post-ischemic tissue repair. recent developments have revealed that stroke engages both innate and adaptive immunity. but adaptive immunity triggered by newly exposed brain antigens does not have an impact on the acute phase of the damage. nevertheless, modulation of adaptive immunity exerts a remarkable protective effect on the ischemic brain and offers the prospect of new stroke therapies. as immunomodulation is not devoid of deleterious side effects, a better understanding of the reciprocal interaction between the immune system and the ischemic brain is essential to harness the full therapeutic potential of the immunology of stroke.",0
"recently, two novel concepts have emerged in cancer biology: the role of so-called ""cancer stem cells"" in tumor initiation, and the involvement of an epithelial-mesenchymal transition (emt) in the metastatic dissemination of epithelial cancer cells. using a mammary tumor progression model, we show that cells possessing both stem and tumorigenic characteristics of ""cancer stem cells"" can be derived from human mammary epithelial cells following the activation of the ras-mapk pathway. the acquisition of these stem and tumorigenic characters is driven by emt induction.",0
"chromosomal instability (cin) is a hallmark of many tumours and correlates with the presence of extra centrosomes. however, a direct mechanistic link between extra centrosomes and cin has not been established. it has been proposed that extra centrosomes generate cin by promoting multipolar anaphase, a highly abnormal division that produces three or more aneuploid daughter cells. here we use long-term live-cell imaging to demonstrate that cells with multiple centrosomes rarely undergo multipolar cell divisions, and the progeny of these divisions are typically inviable. thus, multipolar divisions cannot explain observed rates of cin. in contrast, we observe that cin cells with extra centrosomes routinely undergo bipolar cell divisions, but display a significantly increased frequency of lagging chromosomes during anaphase. to define the mechanism underlying this mitotic defect, we generated cells that differ only in their centrosome number. we demonstrate that extra centrosomes alone are sufficient to promote chromosome missegregation during bipolar cell division. these segregation errors are a consequence of cells passing through a transient 'multipolar spindle intermediate' in which merotelic kinetochore-microtubule attachment errors accumulate before centrosome clustering and anaphase. these findings provide a direct mechanistic link between extra centrosomes and cin, two common characteristics of solid tumours. we propose that this mechanism may be a common underlying cause of cin in human cancer.",0
"scipy is an open-source scientific computing library for the python programming language. since its initial release in 2001, scipy has become a de facto standard for leveraging scientific algorithms in python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. in this work, we provide an overview of the capabilities and development practices of scipy 1.0 and highlight some recent technical developments.",0
"we have previously reported that the parkinson's disease-associated kinase pink1 (pten-induced putative kinase 1) is activated by mitochondrial depolarization and stimulates the parkin e3 ligase by phosphorylating ser65 within its ubl (ubiquitin-like) domain. using phosphoproteomic analysis, we identified a novel ubiquitin phosphopeptide phosphorylated at ser65 that was enriched 14-fold in hek (human embryonic kidney)-293 cells overexpressing wild-type pink1 stimulated with the mitochondrial uncoupling agent cccp (carbonyl cyanide m-chlorophenylhydrazone), to activate pink1, compared with cells expressing kinase-inactive pink1. ser65 in ubiquitin lies in a similar motif to ser65 in the ubl domain of parkin. remarkably, pink1 directly phosphorylates ser65 of ubiquitin in vitro. we undertook a series of experiments that provide striking evidence that ser65-phosphorylated ubiquitin (ubiquitinphospho-ser65) functions as a critical activator of parkin. first, we demonstrate that a fragment of parkin lacking the ubl domain encompassing ser65 (δubl-parkin) is robustly activated by ubiquitinphospho-ser65, but not by non-phosphorylated ubiquitin. secondly, we find that the isolated parkin ubl domain phosphorylated at ser65 (ublphospho-ser65) can also activate δubl-parkin similarly to ubiquitinphospho-ser65. thirdly, we establish that ubiquitinphospho-ser65, but not non-phosphorylated ubiquitin or ublphospho-ser65, activates full-length wild-type parkin as well as the non-phosphorylatable s65a parkin mutant. fourthly, we provide evidence that optimal activation of full-length parkin e3 ligase is dependent on pink1-mediated phosphorylation of both parkin at ser65 and ubiquitin at ser65, since only mutation of both proteins at ser65 completely abolishes parkin activation. in conclusion, the findings of the present study reveal that pink1 controls parkin e3 ligase activity not only by phosphorylating parkin at ser65, but also by phosphorylating ubiquitin at ser65. we propose that phosphorylation of parkin at ser65 serves to prime the e3 ligase enzyme for activation by ubiquitinphospho-ser65, suggesting that small molecules that mimic ubiquitinphospho-ser65 could hold promise as novel therapies for parkinson's disease.",0
"reactive oxygen species (ros), produced during various electron transfer reactions in vivo, are generally considered to be deleterious to cells. in the mammalian haematopoietic system, haematopoietic stem cells contain low levels of ros. however, unexpectedly, the common myeloid progenitors (cmps) produce significantly increased levels of ros(2). the functional significance of this difference in ros level in the two progenitor types remains unresolved. here we show that drosophila multipotent haematopoietic progenitors, which are largely akin to the mammalian myeloid progenitors, display increased levels of ros under in vivo physiological conditions, which are downregulated on differentiation. scavenging the ros from these haematopoietic progenitors by using in vivo genetic tools retards their differentiation into mature blood cells. conversely, increasing the haematopoietic progenitor ros beyond their basal level triggers precocious differentiation into all three mature blood cell types found in drosophila, through a signalling pathway that involves jnk and foxo activation as well as polycomb downregulation. we conclude that the developmentally regulated, moderately high ros level in the progenitor population sensitizes them to differentiation, and establishes a signalling role for ros in the regulation of haematopoietic cell fate. our results lead to a model that could be extended to reveal a probable signalling role for ros in the differentiation of cmps in mammalian haematopoietic development and oxidative stress response.",0
"as of april 2, 2020, the coronavirus disease 2019 (covid-19) pandemic has resulted in >890,000 cases and >45,000 deaths worldwide, including 239,279 cases and 5,443 deaths in the united states (1,2). in the united states, 22% of the population is made up of infants, children, and adolescents aged <18 years (children) (3). data from china suggest that pediatric covid-19 cases might be less severe than cases in adults and that children might experience different symptoms than do adults (4,5); however, disease characteristics among pediatric patients in the united states have not been described. data from 149,760 laboratory-confirmed covid-19 cases in the united states occurring during february 12-april 2, 2020 were analyzed. among 149,082 (99.6%) reported cases for which age was known, 2,572 (1.7%) were among children aged <18 years. data were available for a small proportion of patients on many important variables, including symptoms (9.4%), underlying conditions (13%), and hospitalization status (33%). among those with available information, 73% of pediatric patients had symptoms of fever, cough, or shortness of breath compared with 93% of adults aged 18-64 years during the same period; 5.7% of all pediatric patients, or 20% of those for whom hospitalization status was known, were hospitalized, lower than the percentages hospitalized among all adults aged 18-64 years (10%) or those with known hospitalization status (33%). three deaths were reported among the pediatric cases included in this analysis. these data support previous findings that children with covid-19 might not have reported fever or cough as often as do adults (4). whereas most covid-19 cases in children are not severe, serious covid-19 illness resulting in hospitalization still occurs in this age group. social distancing and everyday preventive behaviors remain important for all age groups as patients with less serious illness and those without symptoms likely play an important role in disease transmission (6,7).",0
"background over 40 000 patients with covid-19 have been hospitalised in new york city (ny, usa) as of april 28, 2020. data on the epidemiology, clinical course, and outcomes of critically ill patients with covid-19 in this setting are needed. methods this prospective observational cohort study took place at two newyork-presbyterian hospitals affiliated with columbia university irving medical center in northern manhattan. we prospectively identified adult patients (aged ≥18 years) admitted to both hospitals from march 2 to april 1, 2020, who were diagnosed with laboratory-confirmed covid-19 and were critically ill with acute hypoxaemic respiratory failure, and collected clinical, biomarker, and treatment data. the primary outcome was the rate of in-hospital death. secondary outcomes included frequency and duration of invasive mechanical ventilation, frequency of vasopressor use and renal replacement therapy, and time to in-hospital clinical deterioration following admission. the relation between clinical risk factors, biomarkers, and in-hospital mortality was modelled using cox proportional hazards regression. follow-up time was right-censored on april 28, 2020 so that each patient had at least 28 days of observation. findings between march 2 and april 1, 2020, 1150 adults were admitted to both hospitals with laboratory-confirmed covid-19, of which 257 (22%) were critically ill. the median age of patients was 62 years (iqr 51-72), 171 (67%) were men. 212 (82%) patients had at least one chronic illness, the most common of which were hypertension (162 ) and diabetes (92 ). 119 (46%) patients had obesity. as of april 28, 2020, 101 (39%) patients had died and 94 (37%) remained hospitalised. 203 (79%) patients received invasive mechanical ventilation for a median of 18 days (iqr 9-28), 170 (66%) of 257 patients received vasopressors and 79 (31%) received renal replacement therapy. the median time to in-hospital deterioration was 3 days (iqr 1-6). in the multivariable cox model, older age (adjusted hazard ratio 1·31 per 10-year increase), chronic cardiac disease (ahr 1·76 ), chronic pulmonary disease (ahr 2·94 ), higher concentrations of interleukin-6 (ahr 1·11 per decile increase), and higher concentrations of d-dimer (ahr 1·10 per decile increase) were independently associated with in-hospital mortality. interpretation critical illness among patients hospitalised with covid-19 in new york city is common and associated with a high frequency of invasive mechanical ventilation, extrapulmonary organ dysfunction, and substantial in-hospital mortality. funding national institute of allergy and infectious diseases and the national center for advancing translational sciences, national institutes of health, and the columbia university irving institute for clinical and translational research.",0
"india has been underrepresented in genome-wide surveys of human variation. we analyse 25 diverse groups in india to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most indians today. one, the 'ancestral north indians' (ani), is genetically close to middle easterners, central asians, and europeans, whereas the other, the 'ancestral south indians' (asi), is as distinct from ani and east asians as they are from each other. by introducing methods that can estimate ancestry without accurate ancestral populations, we show that ani ancestry ranges from 39-71% in most indian groups, and is higher in traditionally upper caste and indo-european speakers. groups with only asi ancestry may no longer exist in mainland india. however, the indigenous andaman islanders are unique in being asi-related groups without ani ancestry. allele frequency differences between groups in india are larger than in europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. we therefore predict that there will be an excess of recessive diseases in india, which should be possible to screen and map genetically.",0
"the quality of model structures generated by contemporary protein structure prediction methods strongly depends on the degree of similarity between the target and available template structures. therefore, the importance of improving template-based model structures beyond the accuracy available from template information has been emphasized in the structure prediction community. the galaxyrefine web server, freely available at is based on a refinement method that has been successfully tested in casp10. the method first rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. according to the casp10 assessment, this method showed the best performance in improving the local structure quality. the method can improve both global and local structure quality on average, when used for refining the models generated by state-of-the-art protein structure prediction servers.",0
"background epigenome-wide association studies of human disease and other quantitative traits are becoming increasingly common. a series of papers reporting age-related changes in dna methylation profiles in peripheral blood have already been published. however, blood is a heterogeneous collection of different cell types, each with a very different dna methylation profile. results using a statistical method that permits estimating the relative proportion of cell types from dna methylation profiles, we examine data from five previously published studies, and find strong evidence of cell composition change across age in blood. we also demonstrate that, in these studies, cellular composition explains much of the observed variability in dna methylation. furthermore, we find high levels of confounding between age-related variability and cellular composition at the cpg level. conclusions our findings underscore the importance of considering cell composition variability in epigenetic studies based on whole blood and other heterogeneous tissue sources. we also provide software for estimating and exploring this composition confounding for the illumina 450k microarray.",0
"background tuberculosis incidence in the uk has risen in the past decade. disease control depends on epidemiological data, which can be difficult to obtain. whole-genome sequencing can detect microevolution within mycobacterium tuberculosis strains. we aimed to estimate the genetic diversity of related m tuberculosis strains in the uk midlands and to investigate how this measurement might be used to investigate community outbreaks. methods in a retrospective observational study, we used illumina technology to sequence m tuberculosis genomes from an archive of frozen cultures. we characterised isolates into four groups: cross-sectional, longitudinal, household, and community. we measured pairwise nucleotide differences within hosts and between hosts in household outbreaks and estimated the rate of change in dna sequences. we used the findings to interpret network diagrams constructed from 11 community clusters derived from mycobacterial interspersed repetitive-unit-variable-number tandem-repeat data. findings we sequenced 390 separate isolates from 254 patients, including representatives from all five major lineages of m tuberculosis. the estimated rate of change in dna sequences was 0.5 single nucleotide polymorphisms (snps) per genome per year (95% ci 0.3-0.7) in longitudinal isolates from 30 individuals and 25 families. divergence is rarely higher than five snps in 3 years. 109 (96%) of 114 paired isolates from individuals and households differed by five or fewer snps. more than five snps separated isolates from none of 69 epidemiologically linked patients, two (15%) of 13 possibly linked patients, and 13 (17%) of 75 epidemiologically unlinked patients (three-way comparison exact p interpretation whole-genome sequencing can delineate outbreaks of tuberculosis and allows inference about direction of transmission between cases. the technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts. funding medical research council, wellcome trust, national institute for health research, and the health protection agency.",0
"background there is growing interest in realist synthesis as an alternative systematic review method. this approach offers the potential to expand the knowledge base in policy-relevant areas - for example, by explaining the success, failure or mixed fortunes of complex interventions. no previous publication standards exist for reporting realist syntheses. this standard was developed as part of the rameses (realist and meta-narrative evidence syntheses: evolving standards) project. the project's aim is to produce preliminary publication standards for realist systematic reviews. methods we (a) collated and summarized existing literature on the principles of good practice in realist syntheses; (b) considered the extent to which these principles had been followed by published syntheses, thereby identifying how rigor may be lost and how existing methods could be improved; (c) used a three-round online delphi method with an interdisciplinary panel of national and international experts in evidence synthesis, realist research, policy and/or publishing to produce and iteratively refine a draft set of methodological steps and publication standards; (d) provided real-time support to ongoing realist syntheses and the open-access rameses online discussion list so as to capture problems and questions as they arose; and (e) synthesized expert input, evidence syntheses and real-time problem analysis into a definitive set of standards. results we identified 35 published realist syntheses, provided real-time support to 9 on-going syntheses and captured questions raised in the rameses discussion list. through analysis and discussion within the project team, we summarized the published literature and common questions and challenges into briefing materials for the delphi panel, comprising 37 members. within three rounds this panel had reached consensus on 19 key publication standards, with an overall response rate of 91%. conclusion this project used multiple sources to develop and draw together evidence and expertise in realist synthesis. for each item we have included an explanation for why it is important and guidance on how it might be reported. realist synthesis is a relatively new method for evidence synthesis and as experience and methodological developments occur, we anticipate that these standards will evolve to reflect further methodological developments. we hope that these standards will act as a resource that will contribute to improving the reporting of realist syntheses.",0
"species distribution models predict a wholesale redistribution of trees in the next century, yet migratory responses necessary to spatially track climates far exceed maximum post-glacial rates. the extent to which populations will adapt will depend upon phenotypic variation, strength of selection, fecundity, interspecific competition, and biotic interactions. populations of temperate and boreal trees show moderate to strong clines in phenology and growth along temperature gradients, indicating substantial local adaptation. traits involved in local adaptation appear to be the product of small effects of many genes, and the resulting genotypic redundancy combined with high fecundity may facilitate rapid local adaptation despite high gene flow. gene flow with preadapted alleles from warmer climates may promote adaptation and migration at the leading edge, while populations at the rear will likely face extirpation. widespread species with large populations and high fecundity are likely to persist and adapt, but will likely suffer adaptational lag for a few generations. as all tree species will be suffering lags, interspecific competition may weaken, facilitating persistence under suboptimal conditions. species with small populations, fragmented ranges, low fecundity, or suffering declines due to introduced insects or diseases should be candidates for facilitated migration.",0
"""engagement"" with digital behaviour change interventions (dbcis) is considered important for their effectiveness. evaluating engagement is therefore a priority; however, a shared understanding of how to usefully conceptualise engagement is lacking. this review aimed to synthesise literature on engagement to identify key conceptualisations and to develop an integrative conceptual framework involving potential direct and indirect influences on engagement and relationships between engagement and intervention effectiveness. four electronic databases (ovid medline, psycinfo, isi web of knowledge, sciencedirect) were searched in november 2015. we identified 117 articles that met the inclusion criteria: studies employing experimental or non-experimental designs with adult participants explicitly or implicitly referring to engagement with dbcis, digital games or technology. data were synthesised using principles from critical interpretive synthesis. engagement with dbcis is conceptualised in terms of both experiential and behavioural aspects. a conceptual framework is proposed in which engagement with a dbci is influenced by the dbci itself (content and delivery), the context (the setting in which the dbci is used and the population using it) and the behaviour that the dbci is targeting. the context and ""mechanisms of action"" may moderate the influence of the dbci on engagement. engagement, in turn, moderates the influence of the dbci on those mechanisms of action. in the research literature, engagement with dbcis has been conceptualised in terms of both experience and behaviour and sits within a complex system involving the dbci, the context of use, the mechanisms of action of the dbci and the target behaviour.",0
"importance cancer and other noncommunicable diseases (ncds) are now widely recognized as a threat to global development. the latest united nations high-level meeting on ncds reaffirmed this observation and also highlighted the slow progress in meeting the 2011 political declaration on the prevention and control of noncommunicable diseases and the third sustainable development goal. lack of situational analyses, priority setting, and budgeting have been identified as major obstacles in achieving these goals. all of these have in common that they require information on the local cancer epidemiology. the global burden of disease (gbd) study is uniquely poised to provide these crucial data. objective to describe cancer burden for 29 cancer groups in 195 countries from 1990 through 2017 to provide data needed for cancer control planning. evidence review we used the gbd study estimation methods to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (dalys). results are presented at the national level as well as by socio-demographic index (sdi), a composite indicator of income, educational attainment, and total fertility rate. we also analyzed the influence of the epidemiological vs the demographic transition on cancer incidence. findings in 2017, there were 24.5 million incident cancer cases worldwide (16.8 million without nonmelanoma skin cancer ) and 9.6 million cancer deaths. the majority of cancer dalys came from years of life lost (97%), and only 3% came from years lived with disability. the odds of developing cancer were the lowest in the low sdi quintile (1 in 7) and the highest in the high sdi quintile (1 in 2) for both sexes. in 2017, the most common incident cancers in men were nmsc (4.3 million incident cases); tracheal, bronchus, and lung (tbl) cancer (1.5 million incident cases); and prostate cancer (1.3 million incident cases). the most common causes of cancer deaths and dalys for men were tbl cancer (1.3 million deaths and 28.4 million dalys), liver cancer (572 000 deaths and 15.2 million dalys), and stomach cancer (542 000 deaths and 12.2 million dalys). for women in 2017, the most common incident cancers were nmsc (3.3 million incident cases), breast cancer (1.9 million incident cases), and colorectal cancer (819 000 incident cases). the leading causes of cancer deaths and dalys for women were breast cancer (601 000 deaths and 17.4 million dalys), tbl cancer (596 000 deaths and 12.6 million dalys), and colorectal cancer (414 000 deaths and 8.3 million dalys). conclusions and relevance the national epidemiological profiles of cancer burden in the gbd study show large heterogeneities, which are a reflection of different exposures to risk factors, economic settings, lifestyles, and access to care and screening. the gbd study can be used by policy makers and other stakeholders to develop and improve national and local cancer control in order to achieve the global targets and improve equity in cancer care.",0
"body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. to increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. we identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (bmi), and an additional 19 loci newly associated with related waist and hip circumference measures (p < 5 × 10(-8)). in total, 20 of the 49 waist-to-hip ratio adjusted for bmi loci show significant sexual dimorphism, 19 of which display a stronger effect in women. the identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.",0
"as with other fields, medical sciences are subject to different sources of bias. while understanding sources of bias is a key element for drawing valid conclusions, bias in health research continues to be a very sensitive issue that can affect the focus and outcome of investigations. information bias, otherwise known as misclassification, is one of the most common sources of bias that affects the validity of health research. it originates from the approach that is utilized to obtain or confirm study measurements. this paper seeks to raise awareness of information bias in observational and experimental research study designs as well as to enrich discussions concerning bias problems. specifying the types of bias can be essential to limit its effects and, the use of adjustment methods might serve to improve clinical evaluation and health care practice.",0
"background analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. results we have developed treedyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. the main features of treedyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without html encapsulation and a new format called tgf, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of treedyn through cgi scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. conclusion treedyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.",0
"coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrhea outbreak on 4 swine breeding farms. diarrhea was reproduced in experimental pigs with one of the isolates, designated cv777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus.",0
"this study of the slow component of axonal transport was aimed at two problems: the specific identification of polypeptides transported into the axon from the cell body, and the identification of structural polypeptides of the axoplasm. the axonal transport paradigm was used to obtain radioactively labeled axonal polypeptides in the rat ventral motor neuron and the cat spinal ganglion sensory neuron. comparison of the slow component polypeptides from these two sources using sodium dodecyl sulfate (sds)-polyacrylamide electrophoresis revealed that they are identical. in both cases five polypeptides account for more than 75% of the total radioactivity present in the slow component. two of these polypeptides have been tentatively identified as tubulin, the microtubule protein, on the basis of their molecular weights. the three remaining polypeptides with molecular weights of 212,000, 160,000, and 68,000 daltons are constitutive, and as such appear to be associated with a single structure which has been tentatively identified as the 10-nm neurofilament. the 212,000-dalton polypeptide was found to comigrate in sds gels with the heavy chain of chick muscle myosin. the demonstration on sds gels that the slow component is composed of a small number of polypeptides which have identical molecular weights in neurons from different mammalian species suggests that these polypeptides comprise fundamental structures of vertebrate neurons.",0
"in addition to being a public physical health emergency, coronavirus disease 2019 (covid-19) affected global mental health, as evidenced by panic-buying worldwide as cases soared. little is known about changes in levels of psychological impact, stress, anxiety and depression during this pandemic. this longitudinal study surveyed the general population twice - during the initial outbreak, and the epidemic's peak four weeks later, surveying demographics, symptoms, knowledge, concerns, and precautionary measures against covid-19. there were 1738 respondents from 190 chinese cities (1210 first-survey respondents, 861 s-survey respondents; 333 respondents participated in both). psychological impact and mental health status were assessed by the impact of event scale-revised (ies-r) and the depression, anxiety and stress scale (dass-21), respectively. ies-r measures ptsd symptoms in survivorship after an event. dass -21 is based on tripartite model of psychopathology that comprise a general distress construct with distinct characteristics. this study found that there was a statistically significant longitudinal reduction in mean ies-r scores (from 32.98 to 30.76, p 24) for ptsd symptoms, suggesting that the reduction in scores was not clinically significant. during the initial evaluation, moderate-to-severe stress, anxiety and depression were noted in 8.1%, 28.8% and 16.5%, respectively and there were no significant longitudinal changes in stress, anxiety and depression levels (p > 0.05). protective factors included high level of confidence in doctors, perceived survival likelihood and low risk of contracting covid-19, satisfaction with health information, personal precautionary measures. as countries around the world brace for an escalation in cases, governments should focus on effective methods of disseminating unbiased covid-19 knowledge, teaching correct containment methods, ensuring availability of essential services/commodities, and providing sufficient financial support.",0
"activation of the μ-opioid receptor (μor) is responsible for the efficacy of the most effective analgesics. to shed light on the structural basis for μor activation, here we report a 2.1 å x-ray crystal structure of the murine μor bound to the morphinan agonist bu72 and a g protein mimetic camelid antibody fragment. the bu72-stabilized changes in the μor binding pocket are subtle and differ from those observed for agonist-bound structures of the β2-adrenergic receptor (β2ar) and the m2 muscarinic receptor. comparison with active β2ar reveals a common rearrangement in the packing of three conserved amino acids in the core of the μor, and molecular dynamics simulations illustrate how the ligand-binding pocket is conformationally linked to this conserved triad. additionally, an extensive polar network between the ligand-binding pocket and the cytoplasmic domains appears to play a similar role in signal propagation for all three g-protein-coupled receptors.",0
"background and aims nafld is a leading cause of liver-related morbidity and mortality. we assessed the global and regional prevalence, incidence, and mortality of nafld using an in-depth meta-analytic approach. approach and results pubmed and ovid medline were searched for nafld population-based studies from 1990 to 2019 survey year (last published 2022) per preferred reporting items for systematic reviews and meta-analyses (prisma). meta-analysis was conducted using random-effects models. bias risk assessment was per joanna briggs institute. of 2585 studies reviewed, 92 studies (n=9,361,716) met eligibility criteria. across the study period (1990-2019), meta-analytic pooling of nafld prevalence estimates and ultrasound-defined nafld yielded an overall global prevalence of 30.05% (95% ci: 27.88%-32.32%) and 30.69% (28.4-33.09), respectively. global nafld prevalence increased by +50.4% from 25.26% (21.59-29.33) in 1990-2006 to 38.00% (33.71-42.49) in 2016-2019 ( p conclusions nafld global prevalence is 30% and increasing which requires urgent and comprehensive strategies to raise awareness and address all aspects of nafld on local, regional, and global levels.",0
"competing risks occur frequently in the analysis of survival data. a competing risk is an event whose occurrence precludes the occurrence of the primary event of interest. in a study examining time to death attributable to cardiovascular causes, death attributable to noncardiovascular causes is a competing risk. when estimating the crude incidence of outcomes, analysts should use the cumulative incidence function, rather than the complement of the kaplan-meier survival function. the use of the kaplan-meier survival function results in estimates of incidence that are biased upward, regardless of whether the competing events are independent of one another. when fitting regression models in the presence of competing risks, researchers can choose from 2 different families of models: modeling the effect of covariates on the cause-specific hazard of the outcome or modeling the effect of covariates on the cumulative incidence function. the former allows one to estimate the effect of the covariates on the rate of occurrence of the outcome in those subjects who are currently event free. the latter allows one to estimate the effect of covariates on the absolute risk of the outcome over time. the former family of models may be better suited for addressing etiologic questions, whereas the latter model may be better suited for estimating a patient's clinical prognosis. we illustrate the application of these methods by examining cause-specific mortality in patients hospitalized with heart failure. statistical software code in both r and sas is provided.",0
"there is increasing concern that most current published research findings are false. the probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. in this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. in this essay, i discuss the implications of these problems for the conduct and interpretation of research.",0
"background the objective of most biomedical research is to determine an unbiased estimate of effect for an exposure on an outcome, i.e. to make causal inferences about the exposure. recent developments in epidemiology have shown that traditional methods of identifying confounding and adjusting for confounding may be inadequate. discussion the traditional methods of adjusting for ""potential confounders"" may introduce conditional associations and bias rather than minimize it. although previous published articles have discussed the role of the causal directed acyclic graph approach (dags) with respect to confounding, many clinical problems require complicated dags and therefore investigators may continue to use traditional practices because they do not have the tools necessary to properly use the dag approach. the purpose of this manuscript is to demonstrate a simple 6-step approach to the use of dags, and also to explain why the method works from a conceptual point of view. summary using the simple 6-step dag approach to confounding and selection bias discussed is likely to reduce the degree of bias for the effect estimate in the chosen statistical model.",0
"we have previously demonstrated that human peripheral blood low density mononuclear cells cultured in granulocyte/macrophage colony-stimulating factor (gm-csf) and interleukin (il)-4 develop into dendritic cells (dcs) that are extremely efficient in presenting soluble antigens to t cells. to identify the mechanisms responsible for efficient antigen capture, we studied the endocytic capacity of dcs using fluorescein isothiocyanate-dextran, horseradish peroxidase, and lucifer yellow. we found that dcs use two distinct mechanisms for antigen capture. the first is a high level of fluid phase uptake via macropinocytosis. in contrast to what has been found with other cell types, macropinocytosis in dcs is constitutive and allows continuous internalization of large volumes of fluid. the second mechanism of capture is mediated via the mannose receptor (mr), which is expressed at high levels on dcs. at low ligand concentrations, the mr can deliver a large number of ligands to the cell in successive rounds. thus, while macropinocytosis endows dcs with a high capacity, nonsaturable mechanism for capture of any soluble antigen, the mr gives an extra capacity for antigen capture with some degree of selectivity for non-self molecules. in addition to their high endocytic capacity, dcs from gm-csf + il-4-dependent cultures are characterized by the presence of a large intracellular compartment that contains high levels of class ii molecules, cathepsin d, and lysosomal-associated membrane protein-1, and is rapidly accessible to endocytic markers. we investigated whether the capacity of dcs to capture and process antigen could be modulated by exogenous stimuli. we found that dcs respond to tumor necrosis factor alpha, cd40 ligand, il-1, and lipopolysaccharide with a coordinate series of changes that include downregulation of macropinocytosis and fc receptors, disappearance of the class ii compartment, and upregulation of adhesion and costimulatory molecules. these changes occur within 1-2 d and are irreversible, since neither pinocytosis nor the class ii compartment are recovered when the maturation-inducing stimulus is removed. the specificity of the mr and the capacity to respond to inflammatory stimuli maximize the capacity of dcs to present infectious non-self antigens to t cells.",0
"multiple lung pathogens such as chemical agents, h5n1 avian flu, or sars cause high lethality due to acute respiratory distress syndrome. here we report that toll-like receptor 4 (tlr4) mutant mice display natural resistance to acid-induced acute lung injury (ali). we show that tlr4-trif-traf6 signaling is a key disease pathway that controls the severity of ali. the oxidized phospholipid (oxpl) oxpapc was identified to induce lung injury and cytokine production by lung macrophages via tlr4-trif. we observed oxpl production in the lungs of humans and animals infected with sars, anthrax, or h5n1. pulmonary challenge with an inactivated h5n1 avian influenza virus rapidly induces ali and oxpl formation in mice. loss of tlr4 or trif expression protects mice from h5n1-induced ali. moreover, deletion of ncf1, which controls ros production, improves the severity of h5n1-mediated ali. our data identify oxidative stress and innate immunity as key lung injury pathways that control the severity of ali.",0
"the hmmer webserver is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden markov model (hmm) libraries using the hmmer software suite ( the results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. for large scale usage, we provide an application programmatic interface (api) which has been expanded in scope, such that all result presentations are available via both html and api. furthermore, we have refactored our javascript visualization library to provide standalone components for different result representations. these consume the aforementioned api and can be integrated into third-party websites. the range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile hmm library (6 in total). to help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other embl-ebi databases.",0
"background a number of approaches have been used to grade levels of evidence and the strength of recommendations. the use of many different approaches detracts from one of the main reasons for having explicit approaches: to concisely characterise and communicate this information so that it can easily be understood and thereby help people make well-informed decisions. our objective was to critically appraise six prominent systems for grading levels of evidence and the strength of recommendations as a basis for agreeing on characteristics of a common, sensible approach to grading levels of evidence and the strength of recommendations. methods six prominent systems for grading levels of evidence and strength of recommendations were selected and someone familiar with each system prepared a description of each of these. twelve assessors independently evaluated each system based on twelve criteria to assess the sensibility of the different approaches. systems used by 51 organisations were compared with these six approaches. results there was poor agreement about the sensibility of the six systems. only one of the systems was suitable for all four types of questions we considered (effectiveness, harm, diagnosis and prognosis). none of the systems was considered usable for all of the target groups we considered (professionals, patients and policy makers). the raters found low reproducibility of judgements made using all six systems. systems used by 51 organisations that sponsor clinical practice guidelines included a number of minor variations of the six systems that we critically appraised. conclusions all of the currently used approaches to grading levels of evidence and the strength of recommendations have important shortcomings.",0
"three-dimensional (3d) structure determination by single particle electron cryomicroscopy (cryoem) involves the calculation of an initial 3d model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3d map. because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3d map, which can give a false impression of the resolution attained. the balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. there is a growing awareness in the cryoem community of how to avoid such over-fitting and over-estimation of resolution. equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. here we describe a simple test that is compatible with any image processing protocol. the test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3d map. we have applied the method to two different sets of cryoem images of the enzyme beta-galactosidase using several image processing packages. our procedure involves substituting the fourier components of the initial particle image stack beyond a chosen resolution by either the fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. this substituted noise thus has the same spectral power distribution as the original data. comparison of the fourier shell correlation (fsc) plots from the 3d map obtained using the experimental data with that from the same data with high-resolution noise (hr-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. a simple formula can be used to calculate an unbiased fsc from the two curves, even when a substantial amount of overfitting is present. the approach is software independent. the user is therefore completely free to use any established method or novel combination of methods, provided the hr-noise test is carried out in parallel. applying this procedure to cryoem images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 å. (382 words).",0
"rodents are commonly used to study the pathophysiological mechanisms of pain as studies in humans may be difficult to perform and ethically limited. as pain cannot be directly measured in rodents, many methods that quantify ""pain-like"" behaviors or nociception have been developed. these behavioral methods can be divided into stimulus-evoked or non-stimulus evoked (spontaneous) nociception, based on whether or not application of an external stimulus is used to elicit a withdrawal response. stimulus-evoked methods, which include manual and electronic von frey, randall-selitto and the hargreaves test, were the first to be developed and continue to be in widespread use. however, concerns over the clinical translatability of stimulus-evoked nociception in recent years has led to the development and increasing implementation of non-stimulus evoked methods, such as grimace scales, burrowing, weight bearing and gait analysis. this review article provides an overview, as well as discussion of the advantages and disadvantages of the most commonly used behavioral methods of stimulus-evoked and non-stimulus-evoked nociception used in rodents.",0
"targeting checkpoints of immune cell activation has been demonstrated to be the most effective approach for activation of anti-tumor immune responses. cytotoxic t-lymphocyte-associated protein 4 (ctla-4) and programmed cell death protein 1 (pd-1), both inhibitory checkpoints commonly seen on activated t-cells have been found to be the most reliable targets for the treatment of cancer. six drugs targeting pd-1 or its ligand pd-l1 and one drug targeting ctla-4 have been approved for treatment of different types of cancers and several others are in advanced stages of development. the drugs when administered as monotherapy had dramatic increase in durable response rates and had manageable safety profile, but more than 50% of patients failed to respond to treatment. combination of ctla-4 and pd-1 blockers was then evaluated to increase the response rates in patients, and ipilimumab (anti-ctla-4) plus nivolumab (anti-pd-1) combination was shown to significantly enhance efficacy in metastatic melanoma patients. subsequently, ipilimumab plus nivolumab was approved for treatment of metastatic melanoma, advanced renal cell carcinoma and metastatic colorectal cancer with mmr/msi-h aberrations. the success of combination encouraged multiple clinical studies in other cancer types. efficacy of the combination has been shown in a number of published studies and is under evaluation in multiple ongoing studies. this review aims to support future research in combination immunotherapy by discussing the basic details of ctla-4 and pd-1 pathways and the results from clinical studies that evaluated combination of ctla-4 and pd-1/pd-l1 blockers.",0
"treatment with monoclonal antibody specific for cytotoxic t lymphocyte-associated antigen 4 (ctla-4), an inhibitory receptor expressed by t lymphocytes, has emerged as an effective therapy for the treatment of metastatic melanoma. although subject to debate, current models favor a mechanism of activity involving blockade of the inhibitory activity of ctla-4 on both effector (t eff) and regulatory (t reg) t cells, resulting in enhanced antitumor effector t cell activity capable of inducing tumor regression. we demonstrate, however, that the activity of anti-ctla-4 antibody on the t reg cell compartment is mediated via selective depletion of t reg cells within tumor lesions. importantly, t reg cell depletion is dependent on the presence of fcγ receptor-expressing macrophages within the tumor microenvironment, indicating that t reg cells are depleted in trans in a context-dependent manner. our results reveal further mechanistic insight into the activity of anti-ctla-4-based cancer immunotherapy, and illustrate the importance of specific features of the local tumor environment on the final outcome of antibody-based immunomodulatory therapies.",0
"kegg (kyoto encyclopedia of genes and genomes; or is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. it is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of health information. kegg pathway maps, brite hierarchies and kegg modules have been developed as generic molecular networks with kegg orthology nodes of functional orthologs so that kegg pathway mapping and other procedures can be applied to any cellular organism. unfortunately, however, this generic approach was inadequate for knowledge representation in the health information category, where variations of human genomes, especially disease-related variations, had to be considered. thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call 'network variants' in the recently released kegg network database. this allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs. we expect that kegg network will become another reference knowledge base for the basic understanding of disease mechanisms and practical use in clinical sequencing and drug development.",0
"objectives to evaluate the individual risk factors composing the chads(2) (congestive heart failure, hypertension, age ≥ 75 years, diabetes, previous stroke) score and the cha(2)ds(2)-vasc (cha(2)ds(2)-vascular disease, age 65-74 years, sex category) score and to calculate the capability of the schemes to predict thromboembolism. design registry based cohort study. setting nationwide data on patients admitted to hospital with atrial fibrillation. population all patients with atrial fibrillation not treated with vitamin k antagonists in denmark in the period 1997-2006. main outcome measures stroke and thromboembolism. results of 121,280 patients with non-valvular atrial fibrillation, 73,538 (60.6%) fulfilled the study inclusion criteria. in patients at ""low risk"" (score = 0), the rate of thromboembolism per 100 person years was 1.67 (95% confidence interval 1.47 to 1.89) with chads(2) and 0.78 (0.58 to 1.04) with cha(2)ds(2)-vasc at one year's follow-up. in patients at ""intermediate risk"" (score = 1), this rate was 4.75 (4.45 to 5.07) with chads(2) and 2.01 (1.70 to 2.36) with cha(2)ds(2)-vasc. the rate of thromboembolism depended on the individual risk factors composing the scores, and both schemes underestimated the risk associated with previous thromboembolic events. when patients were categorised into low, intermediate, and high risk groups, c statistics at 10 years' follow-up were 0.812 (0.796 to 0.827) with chads(2) and 0.888 (0.875 to 0.900) with cha(2)ds(2)-vasc. conclusions the risk associated with a specific risk stratification score depended on the risk factors composing the score. cha(2)ds(2)-vasc performed better than chads(2) in predicting patients at high risk, and those categorised as low risk by cha(2)ds(2)-vasc were truly at low risk for thromboembolism.",0
"motivation transcription factor (tf) chip-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the chip-ed tf. results we present dreme, a motif discovery algorithm specifically designed to find the short, core dna-binding motifs of eukaryotic tfs, and optimized to analyze very large chip-seq datasets in minutes. using dreme, we discover the binding motifs of the the chip-ed tf and many cofactors in mouse es cell (mesc), mouse erythrocyte and human cell line chip-seq datasets. for example, in mesc chip-seq data for the tf esrrb, we discover the binding motifs for eight cofactor tfs important in the maintenance of pluripotency. several other commonly used algorithms find at most two cofactor motifs in this same dataset. dreme can also perform discriminative motif discovery, and we use this feature to provide evidence that sox2 and oct4 do not bind in mes cells as an obligate heterodimer. dreme is much faster than many commonly used algorithms, scales linearly in dataset size, finds multiple, non-redundant motifs and reports a reliable measure of statistical significance for each motif found. dreme is available as part of the meme suite of motif-based sequence analysis tools (",0
"this study provides data on the feasibility and impact of video-enabled telemedicine use among patients and providers and its impact on urgent and nonurgent healthcare delivery from one large health system (nyu langone health) at the epicenter of the coronavirus disease 2019 (covid-19) outbreak in the united states. between march 2nd and april 14th 2020, telemedicine visits increased from 102.4 daily to 801.6 daily. (683% increase) in urgent care after the system-wide expansion of virtual urgent care staff in response to covid-19. of all virtual visits post expansion, 56.2% and 17.6% urgent and nonurgent visits, respectively, were covid-19-related. telemedicine usage was highest by patients 20 to 44 years of age, particularly for urgent care. the covid-19 pandemic has driven rapid expansion of telemedicine use for urgent care and nonurgent care visits beyond baseline periods. this reflects an important change in telemedicine that other institutions facing the covid-19 pandemic should anticipate.",0
"macroautophagy is a key pathway for the clearance of aggregate-prone cytosolic proteins. currently, the only suitable pharmacologic strategy for up-regulating autophagy in mammalian cells is to use rapamycin, which inhibits the mammalian target of rapamycin (mtor), a negative regulator of autophagy. here we describe a novel mtor-independent pathway that regulates autophagy. we show that lithium induces autophagy, and thereby, enhances the clearance of autophagy substrates, like mutant huntingtin and alpha-synucleins. this effect is not mediated by glycogen synthase kinase 3beta inhibition. the autophagy-enhancing properties of lithium were mediated by inhibition of inositol monophosphatase and led to free inositol depletion. this, in turn, decreased myo-inositol-1,4,5-triphosphate (ip3) levels. our data suggest that the autophagy effect is mediated at the level of (or downstream of) lowered ip3, because it was abrogated by pharmacologic treatments that increased ip3. this novel pharmacologic strategy for autophagy induction is independent of mtor, and may help treatment of neurodegenerative diseases, like huntington's disease, where the toxic protein is an autophagy substrate.",0
"the spread of coronavirus disease 2019 (covid-19) in italy prompted drastic measures for transmission containment. we examine the effects of these interventions, based on modeling of the unfolding epidemic. we test modeling options of the spatially explicit type, suggested by the wave of infections spreading from the initial foci to the rest of italy. we estimate parameters of a metacommunity susceptible-exposed-infected-recovered (seir)-like transmission model that includes a network of 107 provinces connected by mobility at high resolution, and the critical contribution of presymptomatic and asymptomatic transmission. we estimate a generalized reproduction number ( = 3.60 ), the spectral radius of a suitable next-generation matrix that measures the potential spread in the absence of containment interventions. the model includes the implementation of progressive restrictions after the first case confirmed in italy (february 21, 2020) and runs until march 25, 2020. we account for uncertainty in epidemiological reporting, and time dependence of human mobility matrices and awareness-dependent exposure probabilities. we draw scenarios of different containment measures and their impact. results suggest that the sequence of restrictions posed to mobility and human-to-human interactions have reduced transmission by 45% (42 to 49%). averted hospitalizations are measured by running scenarios obtained by selectively relaxing the imposed restrictions and total about 200,000 individuals (as of march 25, 2020). although a number of assumptions need to be reexamined, like age structure in social mixing patterns and in the distribution of mobility, hospitalization, and fatality, we conclude that verifiable evidence exists to support the planning of emergency measures.",0
"cell movement is essential during embryogenesis to establish tissue patterns and to drive morphogenetic pathways and in the adult for tissue repair and to direct cells to sites of infection. animal cells move by crawling and the driving force is derived primarily from the coordinated assembly and disassembly of actin filaments. the small gtpases, rho, rac, and cdc42, regulate the organization of actin filaments and we have analyzed their contributions to the movement of primary embryo fibroblasts in an in vitro wound healing assay. rac is essential for the protrusion of lamellipodia and for forward movement. cdc42 is required to maintain cell polarity, which includes the localization of lamellipodial activity to the leading edge and the reorientation of the golgi apparatus in the direction of movement. rho is required to maintain cell adhesion during movement, but stress fibers and focal adhesions are not required. finally, ras regulates focal adhesion and stress fiber turnover and this is essential for cell movement. we conclude that the signal transduction pathways controlled by the four small gtpases, rho, rac, cdc42, and ras, cooperate to promote cell movement.",0
"motivation phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. finding the optimal tree under the popular maximum likelihood (ml) criterion is known to be np-hard. thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. results we present raxml-ng, a from-scratch re-implementation of the established greedy tree search algorithm of raxml/examl. raxml-ng offers improved accuracy, flexibility, speed, scalability, and usability compared with raxml/examl. on taxon-rich datasets, raxml-ng typically finds higher-scoring trees than iqtree, an increasingly popular recent tool for ml-based phylogenetic inference (although iq-tree shows better stability). finally, raxml-ng introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. availability and implementation the code is available under gnu gpl at raxml-ng web service (maintained by vital-it) is available at supplementary information supplementary data are available at bioinformatics online.",0
"interleukin 15 (il-15) is a novel cytokine that has recently been cloned and expressed. whereas it has no sequence homology with il-2, il-15 interacts with components of the il-2 receptor (il-2r). in the present study we performed a functional analysis of recombinant il-15 on phenotypically and functionally distinct populations of highly purified human natural killer (nk) cells. the cd56bright subset of human nk cells constitutively expresses the high affinity il-2r and exhibits a brisk proliferative response after the binding of picomolar amounts of il-2. using a proliferation assay, il-15 demonstrated a very steep dose-response curve that was distinct from the dose-response curve for il-2. the proliferative effects of il-15 could be abrogated by anti-il-2r beta (p75), but not by anti-il-2r alpha (p55). the proliferative effects of il-2 on cd56bright nk cells could be inhibited by both antibodies. cd56dim nk cells express the intermediate affinity il-2r in the absence of the high affinity il-2r. activation of cd56dim nk cells by il-15 was similar to that of il-2 as measured by enhanced nk cytotoxic activity, antibody-dependent cellular cytotoxicity, and nk cell production of interferon gamma, tumor necrosis factor alpha, and granulocyte/macrophage colony-stimulating factor. the il-15-enhanced nk cytotoxic activity could be completely blocked by anti-il-2r beta monoclonal antibody. the binding of radiolabeled il-2 and il-15 to cd56dim nk cells was inhibited in the presence of anti-il-2r beta. scatchard analysis of radiolabeled il-15 and il-2 binding to nk-enriched human lymphocytes revealed the presence of high and intermediate affinity receptors for both ligands. il-15 is a ligand that activates human nk cells through components of the il-2r in a pattern that is similar but not identical to that of il-2. unlike il-2, il-15 is produced by activated monocytes/macrophages. the discovery of il-15 may increase our understanding of how monocytes/macrophages participate in the regulation of nk cell function.",0
"summary a tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. in ensembl, a web-based tool (the snp effect predictor) and api interface can now functionally annotate variants in all ensembl and ensembl genomes supported species. availability the ensembl snp effect predictor can be accessed via the ensembl website at the ensembl api ( for installation instructions) is open source software.",0
"misfolded α-synuclein amyloid fibrils are the principal components of lewy bodies and neurites, hallmarks of parkinson's disease (pd). we present a high-resolution structure of an α-synuclein fibril, in a form that induces robust pathology in primary neuronal culture, determined by solid-state nmr spectroscopy and validated by em and x-ray fiber diffraction. over 200 unique long-range distance restraints define a consensus structure with common amyloid features including parallel, in-register β-sheets and hydrophobic-core residues, and with substantial complexity arising from diverse structural features including an intermolecular salt bridge, a glutamine ladder, close backbone interactions involving small residues, and several steric zippers stabilizing a new orthogonal greek-key topology. these characteristics contribute to the robust propagation of this fibril form, as supported by the structural similarity of early-onset-pd mutants. the structure provides a framework for understanding the interactions of α-synuclein with other proteins and small molecules, to aid in pd diagnosis and treatment.",0
"α-synuclein aggregation is implicated in a variety of diseases including parkinson's disease, dementia with lewy bodies, pure autonomic failure and multiple system atrophy. the association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. here we structurally and functionally characterize two polymorphs of α-synuclein. we present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies.",0
"the successful isolation and cultivation of lyme disease spirochetes traces its lineage to early attempts at cultivating relapsing fever borreliae. observations on the growth of lyme disease spirochetes under different in vitro conditions may yield important clues to both the metabolic characteristics of these newly discovered organisms and the pathogenesis of lyme disease.",0
"three-dimensional (3d) structure determination by single-particle analysis of cryo-electron microscopy (cryo-em) images requires many parameters to be determined from extremely noisy data. this makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. cryo-em structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. i describe a bayesian interpretation of cryo-em structure determination, where smoothness in the reconstructed density is imposed through a gaussian prior in the fourier domain. the statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3d linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures.",0
"cell interaction with adhesive proteins or growth factors in the extracellular matrix initiates ras/mitogen-activated protein (map) kinase signaling. evidence is provided that map kinase (erk1 and erk2) influences the cells' motility machinery by phosphorylating and, thereby, enhancing myosin light chain kinase (mlck) activity leading to phosphorylation of myosin light chains (mlc). inhibition of map kinase activity causes decreased mlck function, mlc phosphorylation, and cell migration on extracellular matrix proteins. in contrast, expression of mutationally active map kinase kinase causes activation of map kinase leading to phosphorylation of mlck and mlc and enhanced cell migration. in vitro results support these findings since erk-phosphorylated mlck has an increased capacity to phosphorylate mlc and shows increased sensitivity to calmodulin. thus, we define a signaling pathway directly downstream of map kinase, influencing cell migration on the extracellular matrix.",0
"a novel coronavirus (2019-ncov) is causing an outbreak of viral pneumonia that started in wuhan, china. using the travel history and symptom onset of 88 confirmed cases that were detected outside wuhan in the early outbreak phase, we estimate the mean incubation period to be 6.4 days (95% credible interval: 5.6-7.7), ranging from 2.1 to 11.1 days (2.5th to 97.5th percentile). these values should help inform 2019-ncov case definitions and appropriate quarantine durations.",0
"the availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. in this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology.",0
"network meta-analysis (multiple treatments meta-analysis, mixed treatment comparisons) attempts to make the best use of a set of studies comparing more than two treatments. however, it is important to assess whether a body of evidence is consistent or inconsistent. previous work on models for network meta-analysis that allow for heterogeneity between studies has either been restricted to two-arm trials or followed a bayesian framework. we propose two new frequentist ways to estimate consistency and inconsistency models by expressing them as multivariate random-effects meta-regressions, which can be implemented in some standard software packages. we illustrate the approach using the mvmeta package in stata. copyright © 2012 john wiley & sons, ltd.",0
"we investigated the capacity of a clonal osteogenic cell line mc3t3-e1, established from newborn mouse calvaria and selected on the basis of high alkaline phosphatase (alp) activity in the confluent state, to differentiate into osteoblasts and mineralize in vitro. the cells in the growing state showed a fibroblastic morphology and grew to form multiple layers. on day 21, clusters of cells exhibiting typical osteoblastic morphology were found in osmiophilic nodular regions. such nodules increased in number and size with incubation time and became easily identifiable with the naked eye by day 40-50. in the central part of well-developed nodules, osteocytes were embedded in heavily mineralized bone matrix. osteoblasts were arranged at the periphery of the bone spicules and were surrounded by lysosome-rich cells and a fibroblastic cell layer. numerous matrix vesicles were scattered around the osteoblasts and young osteocytes. matrix vesicles and plasma membranes of osteoblasts, young osteocytes, and lysosome-rich cells showed strong reaction to cytochemical stainings for alp activity and calcium ions. minerals were initially localized in the matrix vesicles and then deposited on well-banded collagen fibrils. deposited minerals consisted exclusively of calcium and phosphorus, and some of the crystals had matured into hydroxyapatite crystals. these results indicate that mc3t3-e1 cells have the capacity to differentiate into osteoblasts and osteocytes and to form calcified bone tissue in vitro.",0
"multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (mhc) exerts the greatest individual effect on risk. modestly powered genome-wide association studies (gwas) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. in a collaborative gwas involving 9,772 cases of european descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. within the mhc we have refined the identity of the hla-drb1 risk alleles and confirmed that variation in the hla-a gene underlies the independent protective effect attributable to the class i region. immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate t-helper-cell differentiation in the pathogenesis of multiple sclerosis.",0
"environmental stressors often show effects that are delayed in time, requiring the use of statistical models that are flexible enough to describe the additional time dimension of the exposure-response relationship. here we develop the family of distributed lag non-linear models (dlnm), a modelling framework that can simultaneously represent non-linear exposure-response dependencies and delayed effects. this methodology is based on the definition of a 'cross-basis', a bi-dimensional space of functions that describes simultaneously the shape of the relationship along both the space of the predictor and the lag dimension of its occurrence. in this way the approach provides a unified framework for a range of models that have previously been used in this setting, and new more flexible variants. this family of models is implemented in the package dlnm within the statistical environment r. to illustrate the methodology we use examples of dlnms to represent the relationship between temperature and mortality, using data from the national morbidity, mortality, and air pollution study (nmmaps) for new york during the period 1987-2000.",0
"background protoplasts isolated from leaves are useful materials in plant research. one application, the transient expression of recombinant genes using arabidopsis mesophyll protoplasts (teamp), is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein interactions. this method requires cutting leaves into very thin slivers to collect mesophyll cell protoplasts, a procedure that often causes cell damage, may yield only a few good protoplasts, and is time consuming. in addition, this protoplast isolation method normally requires a large number of leaves derived from plants grown specifically under low-light conditions, which may be a concern when material availability is limited such as with mutant plants, or in large scale experiments. results in this report, we present a new procedure that we call the tape-arabidopsis sandwich. this is a simple and fast mesophyll protoplast isolation method. two kinds of tape (time tape adhered to the upper epidermis and 3 m magic tape to the lower epidermis) are used to make a ""tape-arabidopsis sandwich"". the time tape supports the top side of the leaf during manipulation, while tearing off the 3 m magic tape allows easy removal of the lower epidermal layer and exposes mesophyll cells to cell wall digesting enzymes when the leaf is later incubated in an enzyme solution. the protoplasts released into solution are collected and washed for further use. for teamp, plasmids carrying a gene expression cassette for a fluorescent protein can be successfully delivered into protoplasts isolated from mature leaves grown under optimal conditions. alternatively, these protoplasts may be used for bimolecular fluorescence complementation (bifc) to investigate protein-protein interactions in vivo, or for western blot analysis. a significant advantage of this protocol over the current method is that it allows the generation of protoplasts in less than 1 hr, and allows teamp transfection to be carried out within 2 hr. conclusion the protoplasts generated by this new tape-arabidopsis sandwich method are suitable for the same range of research applications as those that use the current method, but require less operator skill, equipment and time.",0
"background the heterogeneity statistic i(2), interpreted as the percentage of variability due to heterogeneity between studies rather than sampling error, depends on precision, that is, the size of the studies included. methods based on a real meta-analysis, we simulate artificially 'inflating' the sample size under the random effects model. for a given inflation factor m = 1, 2, 3,... and for each trial i, we create a m-inflated trial by drawing a treatment effect estimate from the random effects model, using s(i)(2)/m as within-trial sampling variance. results as precision increases, while estimates of the heterogeneity variance tau(2) remain unchanged on average, estimates of i(2) increase rapidly to nearly 100%. a similar phenomenon is apparent in a sample of 157 meta-analyses. conclusion when deciding whether or not to pool treatment estimates in a meta-analysis, the yard-stick should be the clinical relevance of any heterogeneity present. tau(2), rather than i(2), is the appropriate measure for this purpose.",0
"background the surgical case report (scare) guidelines were first published in 2016 as a tool for surgeons to document and report their surgical cases in a standardised and comprehensive manner. however, with advances in technology and changes in the healthcare landscape, it is important to revise and update these guidelines to ensure they remain relevant and valuable for surgeons. materials and methods the updated guidelines were produced through a delphi consensus exercise. members of the scare 2020 guidelines delphi group, editorial board members, and peer reviewers were invited to participate. potential contributors were contacted by e-mail. an online survey was completed to indicate their agreement with the proposed changes to the guideline items. results a total of 54 participants were invited to participate and 44 (81.5%) completed the survey. there was a high degree of agreement among reviewers, with 36 items (83.7%) meeting the threshold for inclusion. conclusion through a completed delphi consensus exercise we present the scare 2023 guidelines. this will provide surgeons with a comprehensive and up-to-date tool for documenting and reporting their surgical cases while highlighting the importance of patient-centred care.",0
"bax is a pro-apoptotic protein of the bcl-2 family that is stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. anti-apoptotic proteins such as bcl-2 counteract bax-mediated cell death. although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for bax, rendering its explicit trigger mechanism unknown. we previously developed stabilized alpha-helix of bcl-2 domains (sahbs) that directly initiate bax-mediated mitochondrial apoptosis. here we demonstrate by nmr analysis that bim sahb binds bax at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. the specificity of the human bim-sahb-bax interaction is highlighted by point mutagenesis that disrupts functional activity, confirming that bax activation is initiated at this novel structural location. thus, we have now defined a bax interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis.",0
"motivation mutations play fundamental roles in evolution by introducing diversity into genomes. missense mutations in structural genes may become either selectively advantageous or disadvantageous to the organism by affecting protein stability and/or interfering with interactions between partners. thus, the ability to predict the impact of mutations on protein stability and interactions is of significant value, particularly in understanding the effects of mendelian and somatic mutations on the progression of disease. here, we propose a novel approach to the study of missense mutations, called mcsm, which relies on graph-based signatures. these encode distance patterns between atoms and are used to represent the protein residue environment and to train predictive models. to understand the roles of mutations in disease, we have evaluated their impacts not only on protein stability but also on protein-protein and protein-nucleic acid interactions. results we show that mcsm performs as well as or better than other methods that are used widely. the mcsm signatures were successfully used in different tasks demonstrating that the impact of a mutation can be correlated with the atomic-distance patterns surrounding an amino acid residue. we showed that mcsm can predict stability changes of a wide range of mutations occurring in the tumour suppressor protein p53, demonstrating the applicability of the proposed method in a challenging disease scenario. availability and implementation a web server is available at",0
"who reported that adherence among patients with chronic diseases averages only 50% in developed countries. this is recognized as a significant public health issue, since medication nonadherence leads to poor health outcomes and increased healthcare costs. improving medication adherence is, therefore, crucial and revealed on many studies, suggesting interventions can improve medication adherence. one significant aspect of the strategies to improve medication adherence is to understand its magnitude. however, there is a lack of general guidance for researchers and healthcare professionals to choose the appropriate tools that can explore the extent of medication adherence and the reasons behind this problem in order to orchestrate subsequent interventions. this paper reviews both subjective and objective medication adherence measures, including direct measures, those involving secondary database analysis, electronic medication packaging (emp) devices, pill count, and clinician assessments and self-report. subjective measures generally provide explanations for patient's nonadherence whereas objective measures contribute to a more precise record of patient's medication-taking behavior. while choosing a suitable approach, researchers and healthcare professionals should balance the reliability and practicality, especially cost effectiveness, for their purpose. meanwhile, because a perfect measure does not exist, a multimeasure approach seems to be the best solution currently.",0
"in the vertebrate visual system, all output of the retina is carried by retinal ganglion cells. each type encodes distinct visual features in parallel for transmission to the brain. how many such 'output channels' exist and what each encodes are areas of intense debate. in the mouse, anatomical estimates range from 15 to 20 channels, and only a handful are functionally understood. by combining two-photon calcium imaging to obtain dense retinal recordings and unsupervised clustering of the resulting sample of more than 11,000 cells, here we show that the mouse retina harbours substantially more than 30 functional output channels. these include all known and several new ganglion cell types, as verified by genetic and anatomical criteria. therefore, information channels from the mouse eye to the mouse brain are considerably more diverse than shown thus far by anatomical studies, suggesting an encoding strategy resembling that used in state-of-the-art artificial vision systems.",0
"the main route of transmission of sars cov infection is presumed to be respiratory droplets. however the virus is also detectable in other body fluids and excreta. the stability of the virus at different temperatures and relative humidity on smooth surfaces were studied. the dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22-25°c and relative humidity of 40-50%, that is, typical air-conditioned environments. however, virus viability was rapidly lost (>3 log(10)) at higher temperatures and higher relative humidity (e.g., 38°c, and relative humidity of >95%). the better stability of sars coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as hong kong) during the spring and in air-conditioned environments. it may also explain why some asian countries in tropical area (such as malaysia, indonesia or thailand) with high temperature and high relative humidity environment did not have major community outbreaks of sars.",0
"the leading edge (approximately 1 microgram) of lamellipodia in xenopus laevis keratocytes and fibroblasts was shown to have an extensively branched organization of actin filaments, which we term the dendritic brush. pointed ends of individual filaments were located at y-junctions, where the arp2/3 complex was also localized, suggesting a role of the arp2/3 complex in branch formation. differential depolymerization experiments suggested that the arp2/3 complex also provided protection of pointed ends from depolymerization. actin depolymerizing factor (adf)/cofilin was excluded from the distal 0.4 micrometer++ of the lamellipodial network of keratocytes and in fibroblasts it was located within the depolymerization-resistant zone. these results suggest that adf/cofilin, per se, is not sufficient for actin brush depolymerization and a regulatory step is required. our evidence supports a dendritic nucleation model (mullins, r.d., j.a. heuser, and t.d. pollard. 1998. proc. natl. acad. sci. usa. 95:6181-6186) for lamellipodial protrusion, which involves treadmilling of a branched actin array instead of treadmilling of individual filaments. in this model, arp2/3 complex and adf/cofilin have antagonistic activities. arp2/3 complex is responsible for integration of nascent actin filaments into the actin network at the cell front and stabilizing pointed ends from depolymerization, while adf/cofilin promotes filament disassembly at the rear of the brush, presumably by pointed end depolymerization after dissociation of the arp2/3 complex.",0
"the panther database (protein analysis through evolutionary relationships, contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. panther software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. in the past year, major improvements include a large expansion of classification information available in panther, as well as significant enhancements to the analysis tools. protein subfamily functional classifications have more than doubled due to progress of the gene ontology phylogenetic annotation project. for human genes (as well as a few other organisms), panther now also supports enrichment analysis using pathway classifications from the reactome resource. the gene list enrichment tools include a new 'hierarchical view' of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. the updated coding single-nucleotide polymorphisms (snp) scoring tool uses an improved algorithm. the hidden markov model (hmm) search tools now use hmmer3, dramatically reducing search times and improving accuracy of e-value statistics. finally, the panther tree-attribute viewer has been implemented in javascript, with new views for exploring protein sequence evolution.",0
"the outbreak of the novel coronavirus disease (covid-19) quickly spread all over china and to more than 20 other countries. although the virus (severe acute respiratory syndrome coronavirus ) nucleic acid real-time polymerase chain reaction (pcr) test has become the standard method for diagnosis of sars-cov-2 infection, these real-time pcr test kits have many limitations. in addition, high false-negative rates were reported. there is an urgent need for an accurate and rapid test method to quickly identify a large number of infected patients and asymptomatic carriers to prevent virus transmission and assure timely treatment of patients. we have developed a rapid and simple point-of-care lateral flow immunoassay that can detect immunoglobulin m (igm) and igg antibodies simultaneously against sars-cov-2 virus in human blood within 15 minutes which can detect patients at different infection stages. with this test kit, we carried out clinical studies to validate its clinical efficacy uses. the clinical detection sensitivity and specificity of this test were measured using blood samples collected from 397 pcr confirmed covid-19 patients and 128 negative patients at eight different clinical sites. the overall testing sensitivity was 88.66% and specificity was 90.63%. in addition, we evaluated clinical diagnosis results obtained from different types of venous and fingerstick blood samples. the results indicated great detection consistency among samples from fingerstick blood, serum and plasma of venous blood. the igm-igg combined assay has better utility and sensitivity compared with a single igm or igg test. it can be used for the rapid screening of sars-cov-2 carriers, symptomatic or asymptomatic, in hospitals, clinics, and test laboratories.",0
"a powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. here we present high-resolution analyses of somatic copy-number alterations (scnas) from 3,131 cancer specimens, belonging largely to 26 histological types. we identify 158 regions of focal scna that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. several gene families are enriched among these regions of focal scna, including the bcl2 family of apoptosis regulators and the nf-kappabeta pathway. we show that cancer cells containing amplifications surrounding the mcl1 and bcl2l1 anti-apoptotic genes depend on the expression of these genes for survival. finally, we demonstrate that a large majority of scnas identified in individual cancer types are present in several cancer types.",0
"background a significant number of patients with covid-19 experience prolonged symptoms, known as long covid. few systematic studies have investigated this population, particularly in outpatient settings. hence, relatively little is known about symptom makeup and severity, expected clinical course, impact on daily functioning, and return to baseline health. methods we conducted an online survey of people with suspected and confirmed covid-19, distributed via covid-19 support groups (e.g. body politic, long covid support group, long haul covid fighters) and social media (e.g. twitter, facebook). data were collected from september 6, 2020 to november 25, 2020. we analyzed responses from 3762 participants with confirmed (diagnostic/antibody positive; 1020) or suspected (diagnostic/antibody negative or untested; 2742) covid-19, from 56 countries, with illness lasting over 28 days and onset prior to june 2020. we estimated the prevalence of 203 symptoms in 10 organ systems and traced 66 symptoms over seven months. we measured the impact on life, work, and return to baseline health. findings for the majority of respondents (>91%), the time to recovery exceeded 35 weeks. during their illness, participants experienced an average of 55.9+/- 25.5 (mean+/-std) symptoms, across an average of 9.1 organ systems. the most frequent symptoms after month 6 were fatigue, post-exertional malaise, and cognitive dysfunction. symptoms varied in their prevalence over time, and we identified three symptom clusters, each with a characteristic temporal profile. 85.9% of participants (95% ci, 84.8% to 87.0%) experienced relapses, primarily triggered by exercise, physical or mental activity, and stress. 86.7% (85.6% to 92.5%) of unrecovered respondents were experiencing fatigue at the time of survey, compared to 44.7% (38.5% to 50.5%) of recovered respondents. 1700 respondents (45.2%) required a reduced work schedule compared to pre-illness, and an additional 839 (22.3%) were not working at the time of survey due to illness. cognitive dysfunction or memory issues were common across all age groups (~88%). except for loss of smell and taste, the prevalence and trajectory of all symptoms were similar between groups with confirmed and suspected covid-19. interpretation patients with long covid report prolonged, multisystem involvement and significant disability. by seven months, many patients have not yet recovered (mainly from systemic and neurological/cognitive symptoms), have not returned to previous levels of work, and continue to experience significant symptom burden. funding all authors contributed to this work in a voluntary capacity. the cost of survey hosting (on qualtrics) and publication fee was covered by aa's research grant (wellcome trust/gatsby charity via sainsbury wellcome center, ucl).",0
"background the presence of perfluorooctanesulfonate (pfos), perfluorohexanesulfonate (pfhs), and perfluorooctanoate (pfoa) has been reported in humans and wildlife. pharmacokinetic differences have been observed in laboratory animals. objective the purpose of this observational study was to estimate the elimination half-life of pfos, pfhs, and pfoa from human serum. methods twenty-six (24 male, 2 female) retired fluorochemical production workers, with no additional occupational exposure, had periodic blood samples collected over 5 years, with serum stored in plastic vials at -80 degrees c. at the end of the study, we used hplc-mass spectrometry to analyze the samples, with quantification based on the ion ratios for pfos and pfhs and the internal standard (18)o(2)-pfos. for pfoa, quantitation was based on the internal standard (13)c(2)-pfoa. results the arithmetic mean initial serum concentrations were as follows: pfos, 799 ng/ml (range, 145-3,490); pfhs, 290 ng/ml (range, 16-1,295); and pfoa, 691 ng/ml (range, 72-5,100). for each of the 26 subjects, the elimination appeared linear on a semi-log plot of concentration versus time; therefore, we used a first-order model for estimation. the arithmetic and geometric mean half-lives of serum elimination, respectively, were 5.4 years and 4.8 years (95% ci, 4.0-5.8) for pfos; 8.5 years (95% ci, 6.4-10.6) and 7.3 years (95% ci, 5.8-9.2) for pfhs; and 3.8 years (95% ci, 3.1-4.4) and 3.5 years (95% ci, 3.0-4.1) for pfoa. conclusions based on these data, humans appear to have a long half-life of serum elimination of pfos, pfhs, and pfoa. differences in species-specific pharmacokinetics may be due, in part, to a saturable renal resorption process.",0
"neutrophils are critical for antifungal defense, but the mechanisms that clear hyphae and other pathogens that are too large to be phagocytosed remain unknown. we found that neutrophils sensed microbe size and selectively released neutrophil extracellular traps (nets) in response to large pathogens, such as candida albicans hyphae and extracellular aggregates of mycobacterium bovis, but not in response to small yeast or single bacteria. nets were fundamental in countering large pathogens in vivo. phagocytosis via dectin-1 acted as a sensor of microbe size and prevented net release by downregulating the translocation of neutrophil elastase (ne) to the nucleus. dectin-1 deficiency led to aberrant net release and net-mediated tissue damage during infection. size-tailored neutrophil responses cleared large microbes and minimized pathology when microbes were small enough to be phagocytosed.",0
"curarized cutaneous pectoris nerve-muscle preparations from frogs were stimulated at 10/s or at 2/s for periods ranging from 20 min to 4 h. end plate potential were recorded intracellularly and used to estimate the quantity of transmitter secreted during the period of stimulation. at the ends of the periods of stimulation the preparations were either fixed for electron microscopy or treated with black widow spider venom to determine the quantities of transmitter remainind in the terminal. horseradish peroxidase or dextran was added to the bathing solution and used as a tracer to detect the formation of vesicles from the axolemma. during 4 h of stimulation at 2/s many new vesicles were formed from the axolemma and the quantity of transmitter secreted was several times greater than the quantity in the initial store. after this period of stimulation, the terminals were severely depleted of transmitter, but not of vesicles, and their general morphological organization was normal. during 20 min of stimulation at 10/s the nerve terminals swelled and were severely depleted both of vesicles and of transmitter. during a subsequent hour of rest the changes in morphology were largely reversed, many new vesicles were formed from the axolemma and the stores of transmitter were partially replenished. these results suggest (a) that synaptic vesicles fuse with, and re-form from, the membrane of the nerve terminal during and after stimulation and (b), that the re-formed vesicles can store and release transmitter.",0
"chembl is an open large-scale bioactivity database ( previously described in the 2012 and 2014 nucleic acids research database issues. since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. these include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. a number of improvements and new features have also been incorporated. these include the annotation of assays and targets using ontologies, the inclusion of targets and indications for clinical candidates, addition of metabolic pathways for drugs and calculation of structural alerts. the chembl data can be accessed via a web-interface, rdf distribution, data downloads and restful web-services.",0
"modeltest-ng is a reimplementation from scratch of jmodeltest and prottest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. modeltest-ng is one to two orders of magnitude faster than jmodeltest and prottest but equally accurate and introduces several new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions. modeltest-ng is available under a gnu gpl3 license at , last accessed september 2, 2019.",0
"immune checkpoint blockade therapy has become a major weapon in fighting cancer. antibody drugs, such as anti-pd-1 and anti-pd-l1, demonstrate obvious advantages such as broad applicability across cancer types and durable clinical response when treatment is effective. however, the overall response rates are still unsatisfying, especially for cancers with low mutational burden. moreover, adverse effects, such as autoimmune symptoms and tumor hyperprogression, present a significant downside in some clinical applications. these challenges reflect the urgent need to fully understand the basic biology of immune checkpoints. in this review, we discuss regulation of immune checkpoint signaling at multiple levels to provide an overview of our current understanding of checkpoint biology. topics include the regulation of surface expression levels for known immune checkpoint proteins via surface delivery, internalization, recycling, and degradation. upon reaching the surface, checkpoints engage in both conventional trans and also cis interactions with ligands to induce signaling and regulate immune responses. novel therapeutic strategies targeting these pathways in addition to classical checkpoint blockade have recently emerged and been tested in preclinical models, providing new avenues for developing next-generation immunotherapies.",0
"getorganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. it recruits organelle-associated reads using a modified ""baiting and iterative mapping"" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. for 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using getorganelle. getorganelle assemblies are more accurate than published and/or novoplasty-reassembled plastomes as assessed by mapping. we also assemble complete mitochondrial genomes using getorganelle. getorganelle is freely released under a gpl-3 license ( ).",0
"phosphatidylinositol 4,5-bisphosphate (ptdinsp2) pools that bind pleckstrin homology (ph) domains were visualized by cellular expression of a phospholipase c (plc)delta ph domain-green fluorescent protein fusion construct and analysis of confocal images in living cells. plasma membrane localization of the fluorescent probe required the presence of three basic residues within the plcdelta ph domain known to form critical contacts with ptdins(4, 5)p2. activation of endogenous plcs by ionophores or by receptor stimulation produced rapid redistribution of the fluorescent signal from the membrane to cytosol, which was reversed after ca2+ chelation. in both ionomycin- and agonist-stimulated cells, fluorescent probe distribution closely correlated with changes in absolute mass of ptdins(4,5)p2. inhibition of ptdins(4,5)p2 synthesis by quercetin or phenylarsine oxide prevented the relocalization of the fluorescent probe to the membranes after ca2+ chelation in ionomycin-treated cells or during agonist stimulation. in contrast, the synthesis of the ptdins(4,5)p2 imaged by the ph domain was not sensitive to concentrations of wortmannin that had been found inhibitory of the synthesis of myo-inositol- labeled ptdins(4,5)p2. identification and dynamic imaging of phosphoinositides that interact with ph domains will further our understanding of the regulation of such proteins by inositol phospholipids.",0
"pd-1 blockade is a cancer immunotherapy effective in various types of cancer. in a fraction of treated patients, however, it causes rapid cancer progression called hyperprogressive disease (hpd). with our observation of hpd in ∼10% of anti-pd-1 monoclonal antibody (mab)-treated advanced gastric cancer (gc) patients, we explored how anti-pd-1 mab caused hpd in these patients and how hpd could be treated and prevented. in the majority of gc patients, tumor-infiltrating foxp3 high cd45ra - cd4 + t cells , which were abundant and highly suppressive in tumors, expressed pd-1 at equivalent levels as tumor-infiltrating cd4 + or cd8 + effector/memory t cells and at much higher levels than circulating etreg cells. comparison of gc tissue samples before and after anti-pd-1 mab therapy revealed that the treatment markedly increased tumor-infiltrating proliferative (ki67 + ) etreg cells in hpd patients, contrasting with their reduction in non-hpd patients. functionally, circulating and tumor-infiltrating pd-1 + etreg cells were highly activated, showing higher expression of ctla-4 than pd-1 - etreg cells. pd-1 blockade significantly enhanced in vitro treg cell suppressive activity. similarly, in mice, genetic ablation or antibody-mediated blockade of pd-1 in treg cells increased their proliferation and suppression of antitumor immune responses. taken together, pd-1 blockade may facilitate the proliferation of highly suppressive pd-1 + etreg cells in hpds, resulting in inhibition of antitumor immunity. the presence of actively proliferating pd-1 + etreg cells in tumors is therefore a reliable marker for hpd. depletion of etreg cells in tumor tissues would be effective in treating and preventing hpd in pd-1 blockade cancer immunotherapy.",0
"the data-independent acquisition (dia) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. here, we evaluate, whether swath-ms type dia effectively translates into a better protein profiling as compared with the established shotgun proteomics. we implemented a novel dia method on the widely used orbitrap platform and used retention-time-normalized (irt) spectral libraries for targeted data extraction using spectronaut. we call this combination hyper reaction monitoring (hrm). using a controlled sample set, we show that hrm outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. the reproducibility of hrm in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. utilizing hrm, we profiled acetaminophen (apap)(1)-treated three-dimensional human liver microtissues. an early onset of relevant proteome changes was revealed at subtoxic doses of apap. further, we detected and quantified for the first time human napqi-protein adducts that might be relevant for the toxicity of apap. the adducts were identified on four mitochondrial oxidative stress related proteins (gatm, park7, prdx6, and vdac2) and two other proteins (anxa2 and ftcd). our findings imply that dia should be the preferred method for quantitative protein profiling.",0
"researchers worldwide with information about the kirsten ras (ki-ras) tumour genotype and outcome of patients with colorectal cancer were invited to provide that data in a schematized format for inclusion in a collaborative database called rascal (the kirsten ras in-colorectal-cancer collaborative group). our results from 2721 such patients have been presented previously and for the first time in any common cancer, showed conclusively that different gene mutations have different impacts on outcome, even when the mutations occur at the same site on the genome. to explore the effect of ki-ras mutations at different stages of colorectal cancer, more patients were recruited to the database, which was reanalysed when information on 4268 patients from 42 centres in 21 countries had been entered. after predetermined exclusion criteria were applied, data on 3439 patients were entered into a multivariate analysis. this found that of the 12 possible mutations on codons 12 and 13 of kirsten ras, only one mutation on codon 12, glycine to valine, found in 8.6% of all patients, had a statistically significant impact on failure-free survival (p = 0.004, hr 1.3) and overall survival (p = 0.008, hr 1.29). this mutation appeared to have a greater impact on outcome in dukes' c cancers (failure-free survival, p = 0.008, hr 1.5; overall survival p = 0.02, hr 1.45) than in dukes' b tumours (failure-free survival, p = 0.46, hr 1.12; overall survival p = 0.36, hr 1.15). ki-ras mutations may occur early in the development of pre-cancerous adenomas in the colon and rectum. however, this collaborative study suggests that not only is the presence of a codon 12 glycine to valine mutation important for cancer progression but also that it may predispose to more aggressive biological behaviour in patients with advanced colorectal cancer.",0
"the coronavirus disease 2019 (covid-19) pandemic has been associated with mental health challenges related to the morbidity and mortality caused by the disease and to mitigation activities, including the impact of physical distancing and stay-at-home orders.* symptoms of anxiety disorder and depressive disorder increased considerably in the united states during april-june of 2020, compared with the same period in 2019 (1,2). to assess mental health, substance use, and suicidal ideation during the pandemic, representative panel surveys were conducted among adults aged ≥18 years across the united states during june 24-30, 2020. overall, 40.9% of respondents reported at least one adverse mental or behavioral health condition, including symptoms of anxiety disorder or depressive disorder (30.9%), symptoms of a trauma- and stressor-related disorder (tsrd) related to the pandemic † (26.3%), and having started or increased substance use to cope with stress or emotions related to covid-19 (13.3%). the percentage of respondents who reported having seriously considered suicide in the 30 days before completing the survey (10.7%) was significantly higher among respondents aged 18-24 years (25.5%), minority racial/ethnic groups (hispanic respondents , non-hispanic black respondents ), self-reported unpaid caregivers for adults § (30.7%), and essential workers ¶ (21.7%). community-level intervention and prevention efforts, including health communication strategies, designed to reach these groups could help address various mental health conditions associated with the covid-19 pandemic.",0
"oxidative stress plays an essential role in the pathogenesis of chronic diseases such as cardiovascular diseases, diabetes, neurodegenerative diseases, and cancer. long term exposure to increased levels of pro-oxidant factors can cause structural defects at a mitochondrial dna level, as well as functional alteration of several enzymes and cellular structures leading to aberrations in gene expression. the modern lifestyle associated with processed food, exposure to a wide range of chemicals and lack of exercise plays an important role in oxidative stress induction. however, the use of medicinal plants with antioxidant properties has been exploited for their ability to treat or prevent several human pathologies in which oxidative stress seems to be one of the causes. in this review we discuss the diseases in which oxidative stress is one of the triggers and the plant-derived antioxidant compounds with their mechanisms of antioxidant defenses that can help in the prevention of these diseases. finally, both the beneficial and detrimental effects of antioxidant molecules that are used to reduce oxidative stress in several human conditions are discussed.",0
"the positron emission tomography (pet) radiotracer pittsburgh compound-b (pib) binds with high affinity to beta-pleated sheet aggregates of the amyloid-beta (abeta) peptide in vitro. the in vivo retention of pib in brains of people with alzheimer's disease shows a regional distribution that is very similar to distribution of abeta deposits observed post-mortem. however, the basis for regional variations in pib binding in vivo, and the extent to which it binds to different types of abeta-containing plaques and tau-containing neurofibrillary tangles (nft), has not been thoroughly investigated. the present study examined 28 clinically diagnosed and autopsy-confirmed alzheimer's disease subjects, including one alzheimer's disease subject who had undergone pib-pet imaging 10 months prior to death, to evaluate region- and substrate-specific binding of the highly fluorescent pib derivative 6-cn-pib. these data were then correlated with region-matched abeta plaque load and peptide levels, pib binding in vitro, and in vivo pet retention levels. we found that in alzheimer's disease brain tissue sections, the preponderance of 6-cn-pib binding is in plaques immunoreactive to either abeta42 or abeta40, and to vascular abeta deposits. 6-cn-pib labelling was most robust in compact/cored plaques in the prefrontal and temporal cortices. while diffuse plaques, including those in caudate nucleus and presubiculum, were less prominently labelled, amorphous abeta plaques in the cerebellum were not detectable with 6-cn-pib. only a small subset of nft were 6-cn-pib positive; these resembled extracellular 'ghost' nft. in alzheimer's disease brain tissue homogenates, there was a direct correlation between pib binding and insoluble abeta peptide levels. in the alzheimer's disease subject who underwent pib-pet prior to death, in vivo pib retention levels correlated directly with region-matched post-mortem measures of pib binding, insoluble abeta peptide levels, 6-cn-pib- and abeta plaque load, but not with measures of nft. these results demonstrate, in a typical alzheimer's disease brain, that pib binding is highly selective for insoluble (fibrillar) abeta deposits, and not for neurofibrillary pathology. the strong direct correlation of in vivo pib retention with region-matched quantitative analyses of abeta plaques in the same subject supports the validity of pib-pet imaging as a method for in vivo evaluation of abeta plaque burden.",0
"the assembly of long reads from pacific biosciences and oxford nanopore technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. we show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a simd-accelerated, partial-order alignment-based, stand-alone consensus module called racon. based on tests with pacbio and oxford nanopore data sets, we show that racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.",0
"phyml online is a web interface to phyml, a software that implements a fast and accurate heuristic for estimating maximum likelihood phylogenies from dna and protein sequences. this tool provides the user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters, in order to perform comprehensive phylogenetic analyses on large datasets in reasonable computing time. the server and its documentation are available at",0
"objective depression is common in patients with diabetes and is associated with worse treatment outcomes. its relationship to treatment adherence, however, has not been systematically reviewed. we used meta-analysis to examine the relationship between depression and treatment nonadherence in patients with type 1 and type 2 diabetes. research design and methods we searched medline and psycinfo databases for all studies published by june 2007 and reviewed references of published articles. meta-analytic procedures were used to estimate the effect size r in a random effects model. significance values, weighted effect sizes, 95% cis, and tests of homogeneity of variance were calculated. results results from 47 independent samples showed that depression was significantly associated with nonadherence to the diabetes treatment regimen (z = 9.97, p conclusions these findings demonstrate a significant association between depression and treatment nonadherence in patients with diabetes. studies that used stronger methodologies had larger effects. treatment nonadherence may represent an important pathway between depression and worse diabetes clinical outcomes.",0
"nanoparticle (np) drug delivery systems (5-250 nm) have the potential to improve current disease therapies because of their ability to overcome multiple biological barriers and releasing a therapeutic load in the optimal dosage range. rapid clearance of circulating nanoparticles during systemic delivery is a critical issue for these systems and has made it necessary to understand the factors affecting particle biodistribution and blood circulation half-life. in this review, we discuss the factors which can influence nanoparticle blood residence time and organ specific accumulation. these factors include interactions with biological barriers and tunable nanoparticle parameters, such as composition, size, core properties, surface modifications (pegylation and surface charge), and finally, targeting ligand functionalization. all these factors have been shown to substantially affect the biodistribution and blood circulation half-life of circulating nanoparticles by reducing the level of nonspecific uptake, delaying opsonization, and increasing the extent of tissue specific accumulation.",0
"smart (simple modular architecture research tool) is a web resource ( providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. in the current version, smart contains manually curated models for more than 1200 protein domains, with ∼ 200 new models since our last update article. the underlying protein databases were synchronized with uniprot, ensembl and string, bringing the total number of annotated domains and other protein features above 100 million. smart's 'genomic' mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. smart analysis results pages have been completely redesigned and include links to several new information sources. a new, vector-based display engine has been developed for protein schematics in smart, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. taxonomic tree displays in smart have been significantly improved, and can be easily navigated using the integrated search engine.",0
"glutathione (gsh) is a tripeptide, which has many biological roles including protection against reactive oxygen and nitrogen species. the primary goal of this paper is to characterize the principal mechanisms of the protective role of gsh against reactive species and electrophiles. the ancillary goals are to provide up-to-date knowledge of gsh biosynthesis, hydrolysis, and utilization; intracellular compartmentalization and interorgan transfer; elimination of endogenously produced toxicants; involvement in metal homeostasis; glutathione-related enzymes and their regulation; glutathionylation of sulfhydryls. individual sections are devoted to the relationships between gsh homeostasis and pathologies as well as to developed research tools and pharmacological approaches to manipulating gsh levels. special attention is paid to compounds mainly of a natural origin (phytochemicals) which affect gsh-related processes. the paper provides starting points for development of novel tools and provides a hypothesis for investigation of the physiology and biochemistry of glutathione with a focus on human and animal health.",0
"objective delphi technique is a structured process commonly used to developed healthcare quality indicators, but there is a little recommendation for researchers who wish to use it. this study aimed 1) to describe reporting of the delphi method to develop quality indicators, 2) to discuss specific methodological skills for quality indicators selection 3) to give guidance about this practice. methodology and main finding three electronic data bases were searched over a 30 years period (1978-2009). all articles that used the delphi method to select quality indicators were identified. a standardized data extraction form was developed. four domains (questionnaire preparation, expert panel, progress of the survey and delphi results) were assessed. of 80 included studies, quality of reporting varied significantly between items (9% for year's number of experience of the experts to 98% for the type of delphi used). reporting of methodological aspects needed to evaluate the reliability of the survey was insufficient: only 39% (31/80) of studies reported response rates for all rounds, 60% (48/80) that feedback was given between rounds, 77% (62/80) the method used to achieve consensus and 57% (48/80) listed quality indicators selected at the end of the survey. a modified delphi procedure was used in 49/78 (63%) with a physical meeting of the panel members, usually between delphi rounds. median number of panel members was 17(q1:11; q3:31). in 40/70 (57%) studies, the panel included multiple stakeholders, who were healthcare professionals in 95% (38/40) of cases. among 75 studies describing criteria to select quality indicators, 28 (37%) used validity and 17(23%) feasibility. conclusion the use and reporting of the delphi method for quality indicators selection need to be improved. we provide some guidance to the investigators to improve the using and reporting of the method in future surveys.",0
"background diabetes has been associated with increased covid-19-related mortality, but the association between modifiable risk factors, including hyperglycaemia and obesity, and covid-19-related mortality among people with diabetes is unclear. we assessed associations between risk factors and covid-19-related mortality in people with type 1 and type 2 diabetes. methods we did a population-based cohort study of people with diagnosed diabetes who were registered with a general practice in england. national population data on people with type 1 and type 2 diabetes collated by the national diabetes audit were linked to mortality records collated by the office for national statistics from jan 2, 2017, to may 11, 2020. we identified the weekly number of deaths in people with type 1 and type 2 diabetes during the first 19 weeks of 2020 and calculated the percentage change from the mean number of deaths for the corresponding weeks in 2017, 2018, and 2019. the associations between risk factors (including sex, age, ethnicity, socioeconomic deprivation, hba 1c , renal impairment , bmi, tobacco smoking status, and cardiovascular comorbidities) and covid-19-related mortality (defined as international classification of diseases, version 10, code u07.1 or u07.2 as a primary or secondary cause of death) between feb 16 and may 11, 2020, were investigated by use of cox proportional hazards models. findings weekly death registrations in the first 19 weeks of 2020 exceeded the corresponding 3-year weekly averages for 2017-19 by 672 (50·9%) in people with type 1 diabetes and 16 071 (64·3%) in people with type 2 diabetes. between feb 16 and may 11, 2020, among 264 390 people with type 1 diabetes and 2 874 020 people with type 2 diabetes, 1604 people with type 1 diabetes and 36 291 people with type 2 diabetes died from all causes. of these total deaths, 464 in people with type 1 diabetes and 10 525 in people with type 2 diabetes were defined as covid-19 related, of which 289 (62·3%) and 5833 (55·4%), respectively, occurred in people with a history of cardiovascular disease or with renal impairment (egfr 2 ). male sex, older age, renal impairment, non-white ethnicity, socioeconomic deprivation, and previous stroke and heart failure were associated with increased covid-19-related mortality in both type 1 and type 2 diabetes. compared with people with an hba 1c of 48-53 mmol/mol (6·5-7·0%), people with an hba 1c of 86 mmol/mol (10·0%) or higher had increased covid-19-related mortality (hazard ratio 2·23 [95% ci 1·50-3·30, p 1c of 59 mmol/mol (7·6%) or higher than in those with an hba 1c of 48-53 mmol/mol (hr 1·22 [95% ci 1·15-1·30, p 2 , a bmi of less than 20·0 kg/m 2 had an hr of 2·45 (95% ci 1·60-3·75, p 2 or higher had an hr of 2·33 (1·53-3·56, p interpretation deaths in people with type 1 and type 2 diabetes rose sharply during the initial covid-19 pandemic in england. increased covid-19-related mortality was associated not only with cardiovascular and renal complications of diabetes but, independently, also with glycaemic control and bmi. funding none.",0
"background one of the most consistent findings from clinical and health services research is the failure to translate research into practice and policy. as a result of these evidence-practice and policy gaps, patients fail to benefit optimally from advances in healthcare and are exposed to unnecessary risks of iatrogenic harms, and healthcare systems are exposed to unnecessary expenditure resulting in significant opportunity costs. over the last decade, there has been increasing international policy and research attention on how to reduce the evidence-practice and policy gap. in this paper, we summarise the current concepts and evidence to guide knowledge translation activities, defined as t2 research (the translation of new clinical knowledge into improved health). we structure the article around five key questions: what should be transferred; to whom should research knowledge be transferred; by whom should research knowledge be transferred; how should research knowledge be transferred; and, with what effect should research knowledge be transferred? discussion we suggest that the basic unit of knowledge translation should usually be up-to-date systematic reviews or other syntheses of research findings. knowledge translators need to identify the key messages for different target audiences and to fashion these in language and knowledge translation products that are easily assimilated by different audiences. the relative importance of knowledge translation to different target audiences will vary by the type of research and appropriate endpoints of knowledge translation may vary across different stakeholder groups. there are a large number of planned knowledge translation models, derived from different disciplinary, contextual (i.e., setting), and target audience viewpoints. most of these suggest that planned knowledge translation for healthcare professionals and consumers is more likely to be successful if the choice of knowledge translation strategy is informed by an assessment of the likely barriers and facilitators. although our evidence on the likely effectiveness of different strategies to overcome specific barriers remains incomplete, there is a range of informative systematic reviews of interventions aimed at healthcare professionals and consumers (i.e., patients, family members, and informal carers) and of factors important to research use by policy makers. summary there is a substantial (if incomplete) evidence base to guide choice of knowledge translation activities targeting healthcare professionals and consumers. the evidence base on the effects of different knowledge translation approaches targeting healthcare policy makers and senior managers is much weaker but there are a profusion of innovative approaches that warrant further evaluation.",0
"the human gene mutation database (hgmd((r))) is a comprehensive core collection of germline mutations in nuclear genes that underlie or are associated with human inherited disease. here, we summarize the history of the database and its current resources. by december 2008, the database contained over 85,000 different lesions detected in 3,253 different genes, with new entries currently accumulating at a rate exceeding 9,000 per annum. although originally established for the scientific study of mutational mechanisms in human genes, hgmd has since acquired a much broader utility for researchers, physicians, clinicians and genetic counselors as well as for companies specializing in biopharmaceuticals, bioinformatics and personalized genomics. hgmd was first made publicly available in april 1996, and a collaboration was initiated in 2006 between hgmd and biobase gmbh. this cooperative agreement covers the exclusive worldwide marketing of the most up-to-date (subscription) version of hgmd, hgmd professional, to academic, clinical and commercial users.",0
"pubchem ( is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the molecular libraries roadmap initiatives of the us national institutes of health (nih). for the past 11 years, pubchem has grown to a sizable system, serving as a chemical information resource for the scientific research community. pubchem consists of three inter-linked databases, substance, compound and bioassay. the substance database contains chemical information deposited by individual data contributors to pubchem, and the compound database stores unique chemical structures extracted from the substance database. biological activity data of chemical substances tested in assay experiments are contained in the bioassay database. this paper provides an overview of the pubchem substance and compound databases, including data sources and contents, data organization, data submission using pubchem upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. it also gives a brief description of pubchem3d, a resource derived from theoretical three-dimensional structures of compounds in pubchem, as well as pubchemrdf, resource description framework (rdf)-formatted pubchem data for data sharing, analysis and integration with information contained in other databases.",0
"three integral membrane proteins, clau- din-1, -2, and occludin, are known to be components of tight junction (tj) strands. to examine their ability to form tj strands, their cdnas were introduced into mouse l fibroblasts lacking tjs. immunofluorescence microscopy revealed that both flag-tagged claudin-1 and -2 were highly concentrated at cell contact sites as planes through a homophilic interaction. in freeze-fracture replicas of these contact sites, well-developed networks of strands were identified that were similar to tj strand networks in situ and were specifically labeled with anti-flag mab. in glutaraldehyde-fixed samples, claudin-1-induced strands were largely associated with the protoplasmic (p) face as mostly continuous structures, whereas claudin-2-induced strands were discontinuous at the p face with complementary grooves at the extracellular (e) face which were occupied by chains of particles. although occludin was also concentrated at cell contact sites as dots through its homophilic interaction, freeze-fracture replicas identified only a small number of short strands that were labeled with anti-occludin mab. however, when occludin was cotransfected with claudin-1, it was concentrated at cell contact sites as planes to be incorporated into well- developed claudin-1-based strands. these findings suggested that claudin-1 and -2 are mainly responsible for tj strand formation, and that occludin is an accessory protein in some function of tj strands.",0
"francisella tularensis, the causative agent of tularemia, infects host macrophages, which triggers production of the proinflammatory cytokines interleukin 1beta (il-1beta) and il-18. we elucidate here how host macrophages recognize f. tularensis and elicit this proinflammatory response. using mice deficient in the dna-sensing inflammasome component aim2, we demonstrate here that aim2 is required for sensing f. tularensis. aim2-deficient mice were extremely susceptible to f. tularensis infection, with greater mortality and bacterial burden than that of wild-type mice. caspase-1 activation, il-1beta secretion and cell death were absent in aim2(-/-) macrophages in response to f. tularensis infection or the presence of cytoplasmic dna. our study identifies aim2 as a crucial sensor of f. tularensis infection and provides genetic proof of its critical role in host innate immunity to intracellular pathogens.",0
"the aberrant wnt/β-catenin signaling pathway facilitates cancer stem cell renewal, cell proliferation and differentiation, thus exerting crucial roles in tumorigenesis and therapy response. accumulated investigations highlight the therapeutic potential of agents targeting wnt/β-catenin signaling in cancer. wnt ligand/ receptor interface, β-catenin destruction complex and tcf/β-catenin transcription complex are key components of the cascade and have been targeted with interventions in preclinical and clinical evaluations. this scoping review aims at outlining the latest progress on the current approaches and perspectives of wnt/β-catenin signaling pathway targeted therapy in various cancer types. better understanding of the updates on the inhibitors, antagonists and activators of wnt/β-catenin pathway rationalizes innovative strategies for personalized cancer treatment. further investigations are warranted to confirm precise and secure targeted agents and achieve optimal use with clinical benefits in malignant diseases.",0
"objective pancreatic ductal adenocarcinoma (pda) is characterised by stromal desmoplasia and vascular dysfunction, which critically impair drug delivery. this study examines the role of an abundant extracellular matrix component, the megadalton glycosaminoglycan hyaluronan (ha), as a novel therapeutic target in pda. methods using a genetically engineered mouse model of pda, the authors enzymatically depleted ha by a clinically formulated pegylated human recombinant ph20 hyaluronidase (pegph20) and examined tumour perfusion, vascular permeability and drug delivery. the preclinical utility of pegph20 in combination with gemcitabine was assessed by short-term and survival studies. results pegph20 rapidly and sustainably depleted ha, inducing the re-expansion of pda blood vessels and increasing the intratumoral delivery of two chemotherapeutic agents, doxorubicin and gemcitabine. moreover, pegph20 triggered fenestrations and interendothelial junctional gaps in pda tumour endothelia and promoted a tumour-specific increase in macromolecular permeability. finally, combination therapy with pegph20 and gemcitabine led to inhibition of pda tumour growth and prolonged survival over gemcitabine monotherapy, suggesting immediate clinical utility. conclusions the authors demonstrate that ha impedes the intratumoral vasculature in pda and propose that its enzymatic depletion be explored as a means to improve drug delivery and response in patients with pancreatic cancer.",0
"background the objective of this study was to develop and psychometrically evaluate a general measure of patients' satisfaction with medication, the treatment satisfaction questionnaire for medication (tsqm). methods the content and format of 55 initial questions were based on a formal conceptual framework, an extensive literature review, and the input from three patient focus groups. patient interviews were used to select the most relevant questions for further evaluation (n = 31). the psychometric performance of items and resulting tsqm scales were examined using eight diverse patient groups (arthritis, asthma, major depression, type i diabetes, high cholesterol, hypertension, migraine, and psoriasis) recruited from a national longitudinal panel study of chronic illness (n = 567). participants were then randomized to complete the test items using one of two alternate scaling methods (visual analogue vs. likert-type). results a factor analysis (principal component extraction with varimax rotation) of specific items revealed three factors (eigenvalues > 1.7) explaining 75.6% of the total variance; namely side effects (4 items, 28.4%, cronbach's alpha =.87), effectiveness (3 items, 24.1%, cronbach's alpha =.85), and convenience (3 items, 23.1%, cronbach's alpha =.87). a second factor analysis of more generally worded items yielded a global satisfaction scale (3 items, eigenvalue = 2.3, 79.1%, cronbach's alpha =.85). the final four scales possessed good psychometric properties, with the likert-type scaling method performing better than the vas approach. significant differences were found on the tsqm by the route of medication administration (oral, injectable, topical, inhalable), level of illness severity, and length of time on medication. regression analyses using the tsqm scales accounted for 40-60% of variation in patients' ratings of their likelihood to persist with their current medication. conclusion the tsqm is a psychometrically sound and valid measure of the major dimensions of patients' satisfaction with medication. preliminary evidence suggests that the tsqm may also be a good predictor of patients' medication adherence across different types of medication and patient populations.",0
"the reproductive development of alligators from a contaminated and a control lake in central florida was examined. lake apopka is adjacent to an epa superfund site, listed due to an extensive spill of dicofol and ddt or its metabolites. these compounds can act as estrogens. contaminants in the lake also have been derived from extensive agricultural activities around the lake that continue today and a sewage treatment facility associated with the city of winter garden, florida. we examined the hypothesis that an estrogenic contaminant has caused the current failure in recruitment of alligators on lake apopka. supporting data include the following: at 6 months of age, female alligators from lake apopka had plasma estradiol-17 beta concentrations almost two times greater than normal females from the control lake, lake woodruff. the apopka females exhibited abnormal ovarian morphology with large numbers of polyovular follicles and polynuclear oocytes. male juvenile alligators had significantly depressed plasma testosterone concentrations comparable to levels observed in normal lake woodruff females but more than three times lower than normal lake woodruff males. additionally, males from lake apopka had poorly organized testes and abnormally small phalli. the differences between lakes and sexes in plasma hormone concentrations of juvenile alligators remain even after stimulation with luteinizing hormone. our data suggest that the gonads of juveniles from lake apopka have been permanently modified in ovo, so that normal steroidogenesis is not possible, and thus normal sexual maturation is unlikely.",0
"background questions remain about the strength and shape of the dose-response relationship between fruit and vegetable intake and risk of cardiovascular disease, cancer and mortality, and the effects of specific types of fruit and vegetables. we conducted a systematic review and meta-analysis to clarify these associations. methods pubmed and embase were searched up to 29 september 2016. prospective studies of fruit and vegetable intake and cardiovascular disease, total cancer and all-cause mortality were included. summary relative risks (rrs) were calculated using a random effects model, and the mortality burden globally was estimated; 95 studies (142 publications) were included. results for fruits and vegetables combined, the summary rr per 200 g/day was 0.92 for coronary heart disease, 0.84 (95% ci: 0.76-0.92, i 2 = 73%, n = 10) for stroke, 0.92 (95% ci: 0.90-0.95, i 2 = 31%, n = 13) for cardiovascular disease, 0.97 (95% ci: 0.95-0.99, i 2 = 49%, n = 12) for total cancer and 0.90 (95% ci: 0.87-0.93, i 2 = 83%, n = 15) for all-cause mortality. similar associations were observed for fruits and vegetables separately. reductions in risk were observed up to 800 g/day for all outcomes except cancer (600 g/day). inverse associations were observed between the intake of apples and pears, citrus fruits, green leafy vegetables, cruciferous vegetables, and salads and cardiovascular disease and all-cause mortality, and between the intake of green-yellow vegetables and cruciferous vegetables and total cancer risk. an estimated 5.6 and 7.8 million premature deaths worldwide in 2013 may be attributable to a fruit and vegetable intake below 500 and 800 g/day, respectively, if the observed associations are causal. conclusions fruit and vegetable intakes were associated with reduced risk of cardiovascular disease, cancer and all-cause mortality. these results support public health recommendations to increase fruit and vegetable intake for the prevention of cardiovascular disease, cancer, and premature mortality.",0
"zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. using diverse assays for antibodies recognizing sars-cov-2 proteins, we detected preexisting humoral immunity. sars-cov-2 spike glycoprotein (s)-reactive antibodies were detectable using a flow cytometry-based method in sars-cov-2-uninfected individuals and were particularly prevalent in children and adolescents. they were predominantly of the immunoglobulin g (igg) class and targeted the s2 subunit. by contrast, sars-cov-2 infection induced higher titers of sars-cov-2 s-reactive igg antibodies targeting both the s1 and s2 subunits, and concomitant igm and iga antibodies, lasting throughout the observation period. sars-cov-2-uninfected donor sera exhibited specific neutralizing activity against sars-cov-2 and sars-cov-2 s pseudotypes. distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of sars-cov-2 infection.",0
"metastasis, the dissemination and growth of neoplastic cells in an organ distinct from that in which they originated, is the most common cause of death in cancer patients. this is particularly true for pancreatic cancers, where most patients are diagnosed with metastatic disease and few show a sustained response to chemotherapy or radiation therapy. whether the dismal prognosis of patients with pancreatic cancer compared to patients with other types of cancer is a result of late diagnosis or early dissemination of disease to distant organs is not known. here we rely on data generated by sequencing the genomes of seven pancreatic cancer metastases to evaluate the clonal relationships among primary and metastatic cancers. we find that clonal populations that give rise to distant metastases are represented within the primary carcinoma, but these clones are genetically evolved from the original parental, non-metastatic clone. thus, genetic heterogeneity of metastases reflects that within the primary carcinoma. a quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell. at least five more years are required for the acquisition of metastatic ability and patients die an average of two years thereafter. these data provide novel insights into the genetic features underlying pancreatic cancer progression and define a broad time window of opportunity for early detection to prevent deaths from metastatic disease.",0
"two-dimensional crystals are emerging materials for nanoelectronics. development of the field requires candidate systems with both a high carrier mobility and, in contrast to graphene, a sufficiently large electronic bandgap. here we present a detailed theoretical investigation of the atomic and electronic structure of few-layer black phosphorus (bp) to predict its electrical and optical properties. this system has a direct bandgap, tunable from 1.51 ev for a monolayer to 0.59 ev for a five-layer sample. we predict that the mobilities are hole-dominated, rather high and highly anisotropic. the monolayer is exceptional in having an extremely high hole mobility (of order 10,000 cm(2) v(-1) s(-1)) and anomalous elastic properties which reverse the anisotropy. light absorption spectra indicate linear dichroism between perpendicular in-plane directions, which allows optical determination of the crystalline orientation and optical activation of the anisotropic transport properties. these results make few-layer bp a promising candidate for future electronics.",0
"a study was carried out on the seasonal change in content as well as relationships between organic nutrients such as protein, fat, cellulose, and nitrogen-free extract, and inorganic nutrients including ca, p, and ash in the aboveground edible spray of the strong xerophils zygophyllum xanthoxylum and reaumuria soorgorica in the alashan desert area. in the early stage of growth, the cellulose content was relatively low, and the content of other nutrients all showed increasing trends. in entering the last growth stage, the differ-ent nutrient contents showed decreasing trends, but the cellulose content reached its highest value. for the entire growth and development period, there were significant negative correlations between crude protein and crude fibre, and between crude fibre and crude ash, and significant positive correlations between crude protein and crude ash, crude protein and p, and ca and crude ash.",0
"the outbreak of sars warrants the search for antiviral compounds to treat the disease. at present, no specific treatment has been identified for sars-associated coronavirus infection. we assessed the antiviral potential of ribavirin, 6-azauridine, pyrazofurin, mycophenolic acid, and glycyrrhizin against two clinical isolates of coronavirus (ffm-1 and ffm-2) from patients with sars admitted to the clinical centre of frankfurt university, germany. of all the compounds, glycyrrhizin was the most active in inhibiting replication of the sars-associated virus. our findings suggest that glycyrrhizin should be assessed for treatment of sars.",0
"we introduce a new empirical bayes approach for large-scale hypothesis testing, including estimating false discovery rates (fdrs), and effect sizes. this approach has two key differences from existing approaches to fdr analysis. first, it assumes that the distribution of the actual (unobserved) effects is unimodal, with a mode at 0. this ""unimodal assumption"" (ua), although natural in many contexts, is not usually incorporated into standard fdr analysis, and we demonstrate how incorporating it brings many benefits. specifically, the ua facilitates efficient and robust computation-estimating the unimodal distribution involves solving a simple convex optimization problem-and enables more accurate inferences provided that it holds. second, the method takes as its input two numbers for each test (an effect size estimate and corresponding standard error), rather than the one number usually used ($p$ value or $z$ score). when available, using two numbers instead of one helps account for variation in measurement precision across tests. it also facilitates estimation of effects, and unlike standard fdr methods, our approach provides interval estimates (credible regions) for each effect in addition to measures of significance. to provide a bridge between interval estimates and significance measures, we introduce the term ""local false sign rate"" to refer to the probability of getting the sign of an effect wrong and argue that it is a superior measure of significance than the local fdr because it is both more generally applicable and can be more robustly estimated. our methods are implemented in an r package ashr available from",0
"mimic-iii ('medical information mart for intensive care') is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. the database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework.",0
"the merops database ( is an integrated source of information about peptidases, their substrates and inhibitors. the hierarchical classification is: protein-species, family, clan, with an identifier at each level. the merops website moved to the embl-ebi in 2017, requiring refactoring of the code-base and services provided. the interface to sequence searching has changed and the merops protein sequence libraries can be searched at the embl-ebi with hmmer, fasta and blastp. cross-references have been established between merops and the panther database at both the family and protein-species level, which will help to improve curation and coverage between the resources. because of the increasing size of the merops sequence collection, in future only sequences of characterized proteins, and from completely sequenced genomes of organisms of evolutionary, medical or commercial significance will be added. as an example, peptidase homologues in four proteomes from the asgard superphylum of archaea have been identified and compared to other archaean, bacterial and eukaryote proteomes. this has given insights into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in asgard archaeotes and as organisms increase in complexity. novel structures for proteasome complexes in archaea are postulated.",0
"gallbladder cancer, though generally considered rare, is the most common malignancy of the biliary tract, accounting for 80%-95% of biliary tract cancers. an early diagnosis is essential as this malignancy progresses silently with a late diagnosis, often proving fatal. its carcinogenesis follows a progression through a metaplasia-dysplasia-carcinoma sequence. this comprehensive review focuses on and explores the risks, management, and outcomes for primary gallbladder carcinoma. epidemiological studies have identified striking geographic and ethnic disparities - inordinately high occurrence in american indians, elevated in southeast asia, yet quite low elsewhere in the americas and the world. age, female sex, congenital biliary tract anomalies, and a genetic predisposition represent important risk factors that are immutable. environmental triggers play a critical role in eliciting cancer developing in the gallbladder, best exemplified by cholelithiasis and chronic inflammation from biliary tract and parasitic infections. mortality rates closely follow incidence; those countries with the highest prevalence of gallstones experience the greatest mortality from gallbladder cancer. vague symptoms often delay the diagnosis of gallbladder cancer, contributing to its overall progression and poor outcome. surgery represents the only potential for cure. some individuals are fortunate to be incidentally found to have gallbladder cancer at the time of cholecystectomy being performed for cholelithiasis. such an early diagnosis is imperative as a late presentation connotes advanced staging, nodal involvement, and possible recurrence following attempted resection. overall mean survival is a mere 6 months, while 5-year survival rate is only 5%. the dismal prognosis, in part, relates to the gallbladder lacking a serosal layer adjacent to the liver, enabling hepatic invasion and metastatic progression. improved imaging modalities are helping to diagnose patients at an earlier stage. the last decade has witnessed improved outcomes as aggressive surgical management and preoperative adjuvant therapy has helped prolong survival in patients with gallbladder cancer. in the future, the development of potential diagnostic markers for disease will yield screening opportunities for those at risk either with ethnic susceptibility or known anatomic anomalies of the biliary tract. meanwhile, clarification of the value of prophylactic cholecystectomy should provide an opportunity for secondary prevention. primary prevention will arrive once the predictive biomarkers and environmental risk factors are more clearly identified.",0
"background understanding potential trajectories in health and drivers of health is crucial to guiding long-term investments and policy implementation. past work on forecasting has provided an incomplete landscape of future health scenarios, highlighting a need for a more robust modelling platform from which policy options and potential health trajectories can be assessed. this study provides a novel approach to modelling life expectancy, all-cause mortality and cause of death forecasts -and alternative future scenarios-for 250 causes of death from 2016 to 2040 in 195 countries and territories. methods we modelled 250 causes and cause groups organised by the global burden of diseases, injuries, and risk factors study (gbd) hierarchical cause structure, using gbd 2016 estimates from 1990-2016, to generate predictions for 2017-40. our modelling framework used data from the gbd 2016 study to systematically account for the relationships between risk factors and health outcomes for 79 independent drivers of health. we developed a three-component model of cause-specific mortality: a component due to changes in risk factors and select interventions; the underlying mortality rate for each cause that is a function of income per capita, educational attainment, and total fertility rate under 25 years and time; and an autoregressive integrated moving average model for unexplained changes correlated with time. we assessed the performance by fitting models with data from 1990-2006 and using these to forecast for 2007-16. our final model used for generating forecasts and alternative scenarios was fitted to data from 1990-2016. we used this model for 195 countries and territories to generate a reference scenario or forecast through 2040 for each measure by location. additionally, we generated better health and worse health scenarios based on the 85th and 15th percentiles, respectively, of annualised rates of change across location-years for all the gbd risk factors, income per person, educational attainment, select intervention coverage, and total fertility rate under 25 years in the past. we used the model to generate all-cause age-sex specific mortality, life expectancy, and years of life lost (ylls) for 250 causes. scenarios for fertility were also generated and used in a cohort component model to generate population scenarios. for each reference forecast, better health, and worse health scenarios, we generated estimates of mortality and ylls attributable to each risk factor in the future. findings globally, most independent drivers of health were forecast to improve by 2040, but 36 were forecast to worsen. as shown by the better health scenarios, greater progress might be possible, yet for some drivers such as high body-mass index (bmi), their toll will rise in the absence of intervention. we forecasted global life expectancy to increase by 4·4 years (95% ui 2·2 to 6·4) for men and 4·4 years (2·1 to 6·4) for women by 2040, but based on better and worse health scenarios, trajectories could range from a gain of 7·8 years (5·9 to 9·8) to a non-significant loss of 0·4 years (-2·8 to 2·2) for men, and an increase of 7·2 years (5·3 to 9·1) to essentially no change (0·1 years ) for women. in 2040, japan, singapore, spain, and switzerland had a forecasted life expectancy exceeding 85 years for both sexes, and 59 countries including china were projected to surpass a life expectancy of 80 years by 2040. at the same time, central african republic, lesotho, somalia, and zimbabwe had projected life expectancies below 65 years in 2040, indicating global disparities in survival are likely to persist if current trends hold. forecasted ylls showed a rising toll from several non-communicable diseases (ncds), partly driven by population growth and ageing. differences between the reference forecast and alternative scenarios were most striking for hiv/aids, for which a potential increase of 120·2% (95% ui 67·2-190·3) in ylls (nearly 118 million) was projected globally from 2016-40 under the worse health scenario. compared with 2016, ncds were forecast to account for a greater proportion of ylls in all gbd regions by 2040 (67·3% of ylls globally); nonetheless, in many lower-income countries, communicable, maternal, neonatal, and nutritional (cmnn) diseases still accounted for a large share of ylls in 2040 (eg, 53·5% of ylls in sub-saharan africa). there were large gaps for many health risks between the reference forecast and better health scenario for attributable ylls. in most countries, metabolic risks amenable to health care (eg, high blood pressure and high plasma fasting glucose) and risks best targeted by population-level or intersectoral interventions (eg, tobacco, high bmi, and ambient particulate matter pollution) had some of the largest differences between reference and better health scenarios. the main exception was sub-saharan africa, where many risks associated with poverty and lower levels of development (eg, unsafe water and sanitation, household air pollution, and child malnutrition) were projected to still account for substantive disparities between reference and better health scenarios in 2040. interpretation with the present study, we provide a robust, flexible forecasting platform from which reference forecasts and alternative health scenarios can be explored in relation to a wide range of independent drivers of health. our reference forecast points to overall improvements through 2040 in most countries, yet the range found across better and worse health scenarios renders a precarious vision of the future-a world with accelerating progress from technical innovation but with the potential for worsening health outcomes in the absence of deliberate policy action. for some causes of ylls, large differences between the reference forecast and alternative scenarios reflect the opportunity to accelerate gains if countries move their trajectories toward better health scenarios-or alarming challenges if countries fall behind their reference forecasts. generally, decision makers should plan for the likely continued shift toward ncds and target resources toward the modifiable risks that drive substantial premature mortality. if such modifiable risks are prioritised today, there is opportunity to reduce avoidable mortality in the future. however, cmnn causes and related risks will remain the predominant health priority among lower-income countries. based on our 2040 worse health scenario, there is a real risk of hiv mortality rebounding if countries lose momentum against the hiv epidemic, jeopardising decades of progress against the disease. continued technical innovation and increased health spending, including development assistance for health targeted to the world's poorest people, are likely to remain vital components to charting a future where all populations can live full, healthy lives. funding bill & melinda gates foundation.",0
"long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. however, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. we address these issues with canu, a successor of celera assembler that is specifically designed for noisy single-molecule sequences. canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus celera assembler 8.2. these advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based on tf-idf weighted minhash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. we demonstrate that canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either pacific biosciences (pacbio) or oxford nanopore technologies and achieves a contig ng50 of >21 mbp on both human and drosophila melanogaster pacbio data sets. for assembly structures that cannot be linearly represented, canu provides graph-based assembly outputs in graphical fragment assembly (gfa) format for analysis or integration with complementary phasing and scaffolding techniques. the combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.",0
"summary we present yahs, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from hi-c data. it can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity. availability and implementation yahs is implemented in c and licensed under the mit license. the source code, documentation and tutorial are available at supplementary information supplementary data are available at bioinformatics online.",0
"for many years, cardiovascular disease (cvd) has been the leading cause of death around the world. often associated with cvd are comorbidities such as obesity, abnormal lipid profiles and insulin resistance. insulin is a key hormone that functions as a regulator of cellular metabolism in many tissues in the human body. insulin resistance is defined as a decrease in tissue response to insulin stimulation thus insulin resistance is characterized by defects in uptake and oxidation of glucose, a decrease in glycogen synthesis, and, to a lesser extent, the ability to suppress lipid oxidation. literature widely suggests that free fatty acids are the predominant substrate used in the adult myocardium for atp production, however, the cardiac metabolic network is highly flexible and can use other substrates, such as glucose, lactate or amino acids. during insulin resistance, several metabolic alterations induce the development of cardiovascular disease. for instance, insulin resistance can induce an imbalance in glucose metabolism that generates chronic hyperglycemia, which in turn triggers oxidative stress and causes an inflammatory response that leads to cell damage. insulin resistance can also alter systemic lipid metabolism which then leads to the development of dyslipidemia and the well-known lipid triad: (1) high levels of plasma triglycerides, (2) low levels of high-density lipoprotein, and (3) the appearance of small dense low-density lipoproteins. this triad, along with endothelial dysfunction, which can also be induced by aberrant insulin signaling, contribute to atherosclerotic plaque formation. regarding the systemic consequences associated with insulin resistance and the metabolic cardiac alterations, it can be concluded that insulin resistance in the myocardium generates damage by at least three different mechanisms: (1) signal transduction alteration, (2) impaired regulation of substrate metabolism, and (3) altered delivery of substrates to the myocardium. the aim of this review is to discuss the mechanisms associated with insulin resistance and the development of cvd. new therapies focused on decreasing insulin resistance may contribute to a decrease in both cvd and atherosclerotic plaque generation.",0
"the authors review research showing that when recalling autobiographical events, many emotionally disturbed patients summarize categories of events rather than retrieving a single episode. the mechanisms underlying such overgeneral memory are examined, with a focus on m. a. conway and c. w. pleydell-pearce's (2000) hierarchical search model of personal event retrieval. an elaboration of this model is proposed to account for overgeneral memory, focusing on how memory search can be affected by (a) capture and rumination processes, when mnemonic information used in retrieval activates ruminative thinking; (b) functional avoidance, when episodic material threatens to cause affective disturbance; and (c) impairment in executive capacity and control that limits an individual's ability to remain focused on retrieval in the face of distraction.",0
"the rapidly emerging field of nanotechnology has offered innovative discoveries in the medical, industrial, and consumer sectors. the unique physicochemical and electrical properties of engineered nanoparticles (np) make them highly desirable in a variety of applications. however, these novel properties of np are fraught with concerns for environmental and occupational exposure. changes in structural and physicochemical properties of np can lead to changes in biological activities including ros generation, one of the most frequently reported np-associated toxicities. oxidative stress induced by engineered np is due to acellular factors such as particle surface, size, composition, and presence of metals, while cellular responses such as mitochondrial respiration, np-cell interaction, and immune cell activation are responsible for ros-mediated damage. np-induced oxidative stress responses are torch bearers for further pathophysiological effects including genotoxicity, inflammation, and fibrosis as demonstrated by activation of associated cell signaling pathways. since oxidative stress is a key determinant of np-induced injury, it is necessary to characterize the ros response resulting from np. through physicochemical characterization and understanding of the multiple signaling cascades activated by np-induced ros, a systemic toxicity screen with oxidative stress as a predictive model for np-induced injury can be developed.",0
"the mucosal tissues of the gastrointestinal, respiratory, reproductive, and urinary tracts, and the surface of the eye present an enormous surface area to the exterior environment. all of these tissues are covered with resident microbial flora, which vary considerably in composition and complexity. mucosal tissues represent the site of infection or route of access for the majority of viruses, bacteria, yeast, protozoa, and multicellular parasites that cause human disease. mucin glycoproteins are secreted in large quantities by mucosal epithelia, and cell surface mucins are a prominent feature of the apical glycocalyx of all mucosal epithelia. in this review, we highlight the central role played by mucins in accommodating the resident commensal flora and limiting infectious disease, interplay between underlying innate and adaptive immunity and mucins, and the strategies used by successful mucosal pathogens to subvert or avoid the mucin barrier, with a particular focus on bacteria.",0
"the transendothelial passage of horseradish peroxidase, injected intravenously into mice, was studied at the ultrastructural level in capillaries of cardiac and skeletal muscle. peroxidase appeared to permeate endothelial intercellular clefts and cell junctions. abnormal peroxidase-induced vascular leakage was excluded. neutral lanthanum tracer gave similar results. the endothelial cell junctions were considered to be maculae occludentes, with gaps of about 40 a in width between the maculae, rather than zonulae occludentes. some observations in favor of concurrent vesicular transport of peroxidase were also made. it is concluded that the endothelial cell junctions are most likely to be the morphological equivalent of the small pore system proposed by physiologists for the passage of small, lipid-insoluble molecules across the endothelium.",0
"pleiotropy, the phenomenon of a single genetic variant influencing multiple traits, is likely widespread in the human genome. if pleiotropy arises because the single nucleotide polymorphism (snp) influences one trait, which in turn influences another ('vertical pleiotropy'), then mendelian randomization (mr) can be used to estimate the causal influence between the traits. of prime focus among the many limitations to mr is the unprovable assumption that apparent pleiotropic associations are mediated by the exposure (i.e. reflect vertical pleiotropy), and do not arise due to snps influencing the two traits through independent pathways ('horizontal pleiotropy'). the burgeoning treasure trove of genetic associations yielded through genome wide association studies makes for a tantalizing prospect of phenome-wide causal inference. recent years have seen substantial attention devoted to the problem of horizontal pleiotropy, and in this review we outline how newly developed methods can be used together to improve the reliability of mr.",0
"crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (ibd), affect over 2.5 million people of european ancestry, with rising prevalence in other populations. genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some ibd loci are shared with other inflammatory diseases. here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. we identify 71 new associations, for a total of 163 ibd loci, that meet genome-wide significance thresholds. most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. many ibd loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. we also observe considerable overlap between susceptibility loci for ibd and mycobacterial infection. gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to ibd.",0
"with the goal of providing a comprehensive, high-quality resource for both plant transcription factors (tfs) and their regulatory interactions with target genes, we upgraded plant tf database planttfdb to version 4.0 ( in the new version, we identified 320 370 tfs from 165 species, presenting a more comprehensive genomic tf repertoires of green plants. besides updating the pre-existing abundant functional and evolutionary annotation for identified tfs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant tf binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining tf binding motifs and regulatory elements. in addition, we upgraded previous tf prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. finally, we set up a novel companion portal plantregmap ( for users to access the regulation resource and analysis tools conveniently.",0
"prosite ( consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. it is complemented by prorule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. prosite signatures, together with prorule, are used for the annotation of domains and features of uniprotkb/swiss-prot entries. here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. the latest version of prosite (release 20.85, of 30 august 2012) contains 1308 patterns, 1039 profiles and 1041 prorules.",0
"therapy-related acute myeloid leukaemia (t-aml) and therapy-related myelodysplastic syndrome (t-mds) are well-recognized complications of cytotoxic chemotherapy and/or radiotherapy. there are several features that distinguish t-aml from de novo aml, including a higher incidence of tp53 mutations, abnormalities of chromosomes 5 or 7, complex cytogenetics and a reduced response to chemotherapy. however, it is not clear how prior exposure to cytotoxic therapy influences leukaemogenesis. in particular, the mechanism by which tp53 mutations are selectively enriched in t-aml/t-mds is unknown. here, by sequencing the genomes of 22 patients with t-aml, we show that the total number of somatic single-nucleotide variants and the percentage of chemotherapy-related transversions are similar in t-aml and de novo aml, indicating that previous chemotherapy does not induce genome-wide dna damage. we identified four cases of t-aml/t-mds in which the exact tp53 mutation found at diagnosis was also present at low frequencies (0.003-0.7%) in mobilized blood leukocytes or bone marrow 3-6 years before the development of t-aml/t-mds, including two cases in which the relevant tp53 mutation was detected before any chemotherapy. moreover, functional tp53 mutations were identified in small populations of peripheral blood cells of healthy chemotherapy-naive elderly individuals. finally, in mouse bone marrow chimaeras containing both wild-type and tp53(+/-) haematopoietic stem/progenitor cells (hspcs), the tp53(+/-) hspcs preferentially expanded after exposure to chemotherapy. these data suggest that cytotoxic therapy does not directly induce tp53 mutations. rather, they support a model in which rare hspcs carrying age-related tp53 mutations are resistant to chemotherapy and expand preferentially after treatment. the early acquisition of tp53 mutations in the founding hspc clone probably contributes to the frequent cytogenetic abnormalities and poor responses to chemotherapy that are typical of patients with t-aml/t-mds.",0
"background the severe inflammatory state secondary to covid-19 leads to a severe derangement of hemostasis that has been recently described as a state of disseminated intravascular coagulation (dic) and consumption coagulopathy, defined as decreased platelet count, increased fibrin(ogen) degradation products such as d-dimer, as well as low fibrinogen. aims whole blood from 24 patients admitted at the intensive care unit because of covid-19 was collected and evaluated with thromboelastography by the teg point-of-care device on a single occasion and six underwent repeated measurements on two consecutive days for a total of 30 observations. plasma was evaluated for the other parameters of hemostasis. results teg parameters are consistent with a state of hypercoagulability as shown by decreased values, and increased values of k angle and ma. platelet count was normal or increased, prothrombin time and activated partial thromboplastin time were near(normal). fibrinogen was increased and d-dimer was dramatically increased. c-reactive protein was increased. factor viii and von willebrand factor (n = 11) were increased. antithrombin (n = 11) was marginally decreased and protein c (n = 11) was increased. conclusion the results of this cohort of patients with covid-19 are not consistent with acute dic, rather they support hypercoagulability together with a severe inflammatory state. these findings may explain the events of venous thromboembolism observed in some of these patients and support antithrombotic prophylaxis/treatment. clinical trials are urgently needed to establish the type of drug, dosage, and optimal duration of prophylaxis.",0
"background human aging is associated with dna methylation changes at specific sites in the genome. these epigenetic modifications may be used to track donor age for forensic analysis or to estimate biological age. results we perform a comprehensive analysis of methylation profiles to narrow down 102 age-related cpg sites in blood. we demonstrate that most of these age-associated methylation changes are reversed in induced pluripotent stem cells (ipscs). methylation levels at three age-related cpgs--located in the genes itga2b, aspa and pde4c--were subsequently analyzed by bisulfite pyrosequencing of 151 blood samples. this epigenetic aging signature facilitates age predictions with a mean absolute deviation from chronological age of less than 5 years. this precision is higher than age predictions based on telomere length. variation of age predictions correlates moderately with clinical and lifestyle parameters supporting the notion that age-associated methylation changes are associated more with biological age than with chronological age. furthermore, patients with acquired aplastic anemia or dyskeratosis congenita--two diseases associated with progressive bone marrow failure and severe telomere attrition--are predicted to be prematurely aged. conclusions our epigenetic aging signature provides a simple biomarker to estimate the state of aging in blood. age-associated dna methylation changes are counteracted in ipscs. on the other hand, over-estimation of chronological age in bone marrow failure syndromes is indicative for exhaustion of the hematopoietic cell pool. thus, epigenetic changes upon aging seem to reflect biological aging of blood.",0
"objective the significant roles of brown adipose tissue (bat) in the regulation of energy expenditure and adiposity are established in small rodents but have been controversial in humans. the objective is to examine the prevalence of metabolically active bat in healthy adult humans and to clarify the effects of cold exposure and adiposity. research design and methods in vivo 2-fluoro-2-deoxyglucose (fdg) uptake into adipose tissue was measured in 56 healthy volunteers (31 male and 25 female subjects) aged 23-65 years by positron emission tomography (pet) combined with x-ray computed tomography (ct). results when exposed to cold (19 degrees c) for 2 h, 17 of 32 younger subjects (aged 23-35 years) and 2 of 24 elderly subjects (aged 38-65 years) showed a substantial fdg uptake into adipose tissue of the supraclavicular and paraspinal regions, whereas they showed no detectable uptake when kept warm (27 degrees c). histological examinations confirmed the presence of brown adipocytes in these regions. the cold-activated fdg uptake was increased in winter compared with summer (p conclusions our findings, being against the conventional view, indicate the high incidence of metabolically active bat in adult humans and suggest a role in the control of body temperature and adiposity.",0
"treatment of rat liver mitochondria with digitonin followed by differential centrifugation was used to resolve the intramitochondrial localization of both soluble and particulate enzymes. rat liver mitochondria were separated into three fractions: inner membrane plus matrix, outer membrane, and a soluble fraction containing enzymes localized between the membranes plus some solublized outer membrane. monoamine oxidase, kynurenine hydroxylase, and rotenone-insensitive nadh-cytochrome c reductase were found primarily in the outer membrane fraction. succinate-cytochrome c reductase, succinate dehydrogenase, cytochrome oxidase, beta-hydroxybutyrate dehydrogenase, alpha-ketoglutarate dehydrogenase, lipoamide dehydrogenase, nad- and nadh-isocitrate dehydrogenase, glutamate dehydrogenase, aspartate aminotransferase, and ornithine transcarbamoylase were found in the inner membrane-matrix fraction. nucleoside diphosphokinase was found in both the outer membrane and soluble fractions; this suggests a dual localization. adenylate kinase was found entirely in the soluble fraction and was released at a lower digitonin concentration than was the outer membrane; this suggests that this enzyme is localized between the two membranes. the inner membrane-matrix fraction was separated into inner membrane and matrix by treatment with the nonionic detergent lubrol, and this separation was used as a basis for calculating the relative protein content of the mitochondrial components. the inner membrane-matrix fraction retained a high degree of morphological and biochemical integrity and exhibited a high respiratory rate and respiratory control when assayed in a sucrose-mannitol medium containing edta.",0
"online mendelian inheritance in man, omim(®), is a comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. the new official website for omim, omim.org ( was launched in january 2011. omim is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (mim numbers). omim entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner. omim also has a derivative table of genes and genetic phenotypes, the morbid map. omim.org has enhanced search capabilities such as genome coordinate searching and thesaurus-enhanced search term options. phenotypic series have been created to facilitate viewing genetic heterogeneity of phenotypes. clinical synopsis features are enhanced with umls, human phenotype ontology and elements of morphology terms and image links. all omim data are available for ftp download and through an api. mimmatch is a novel outreach feature to disseminate updates and encourage collaboration.",0
"background surveys are popular methods to measure public perceptions in emergencies but can be costly and time consuming. we suggest and evaluate a complementary ""infoveillance"" approach using twitter during the 2009 h1n1 pandemic. our study aimed to: 1) monitor the use of the terms ""h1n1"" versus ""swine flu"" over time; 2) conduct a content analysis of ""tweets""; and 3) validate twitter as a real-time content, sentiment, and public attention trend-tracking tool. methodology/principal findings between may 1 and december 31, 2009, we archived over 2 million twitter posts containing keywords ""swine flu,"" ""swineflu,"" and/or ""h1n1."" using infovigil, an infoveillance system. tweets using ""h1n1"" increased from 8.8% to 40.5% (r(2) = .788; p conclusions this study illustrates the potential of using social media to conduct ""infodemiology"" studies for public health. 2009 h1n1-related tweets were primarily used to disseminate information from credible sources, but were also a source of opinions and experiences. tweets can be used for real-time content analysis and knowledge translation research, allowing health authorities to respond to public concerns.",0
"apoptosis and necrosis are considered conceptually and morphologically distinct forms of cell death. here, we report that demise of human t cells caused by two classic apoptotic triggers (staurosporin and cd95 stimulation) changed from apoptosis to necrosis, when cells were preemptied of adenosine triphosphate (atp). nuclear condensation and dna fragmentation did not occur in cells predepleted of atp and treated with either of the two inducers, although the kinetics of cell death were unchanged. selective and graded repletion of the extramitochondrial atp/pool with glucose prevented necrosis and restored the ability of the cells to undergo apoptosis. pulsed atp/depletion/repletion experiments also showed that atp generation either by glycolysis or by mitochondria was required for the active execution of the final phase of apoptosis, which involves nuclear condensation and dna degradation.",0
"background liquid chromatography coupled to mass spectrometry (lc/ms) is an important analytical technology for e.g. metabolomics experiments. determining the boundaries, centres and intensities of the two-dimensional signals in the lc/ms raw data is called feature detection. for the subsequent analysis of complex samples such as plant extracts, which may contain hundreds of compounds, corresponding to thousands of features -- a reliable feature detection is mandatory. results we developed a new feature detection algorithm centwave for high-resolution lc/ms data sets, which collects regions of interest (partial mass traces) in the raw-data, and applies continuous wavelet transformation and optionally gauss-fitting in the chromatographic domain. we evaluated our feature detection algorithm on dilution series and mixtures of seed and leaf extracts, and estimated recall, precision and f-score of seed and leaf specific features in two experiments of different complexity. conclusion the new feature detection algorithm meets the requirements of current metabolomics experiments. centwave can detect close-by and partially overlapping features and has the highest overall recall and precision values compared to the other algorithms, matchedfilter (the original algorithm of xcms) and the centroidpicker from mzmine. the centwave algorithm was integrated into the bioconductor r-package xcms and is available from (",0
"mendelianrandomization is a software package for the r open-source software environment that performs mendelian randomization analyses using summarized data. the core functionality is to implement the inverse-variance weighted, mr-egger and weighted median methods for multiple genetic variants. several options are available to the user, such as the use of robust regression, fixed- or random-effects models and the penalization of weights for genetic variants with heterogeneous causal estimates. extensions to these methods, such as allowing for variants to be correlated, can be chosen if appropriate. graphical commands allow summarized data to be displayed in an interactive graph, or the plotting of causal estimates from multiple methods, for comparison. although the main method of data entry is directly by the user, there is also an option for allowing summarized data to be incorporated from the phenoscanner database of genotype-phenotype associations. we hope to develop this feature in future versions of the package. the r software environment is available for download from . the mendelianrandomization package can be downloaded from the comprehensive r archive network (cran) within r, or directly from . both r and the mendelianrandomization package are released under gnu general public licenses (gpl-2|gpl-3).",0
"background a categorical ct assessment scheme for suspicion of pulmonary involvement of coronavirus disease 2019 (covid-19 provides a basis for gathering scientific evidence and improved communication with referring physicians. purpose to introduce the covid-19 reporting and data system (co-rads) for use in the standardized assessment of pulmonary involvement of covid-19 on unenhanced chest ct images and to report its initial interobserver agreement and performance. materials and methods the dutch radiological society developed co-rads based on other efforts for standardization, such as the lung imaging reporting and data system or breast imaging reporting and data system. co-rads assesses the suspicion for pulmonary involvement of covid-19 on a scale from 1 (very low) to 5 (very high). the system is meant to be used in patients with moderate to severe symptoms of covid-19. the system was evaluated by using 105 chest ct scans of patients admitted to the hospital with clinical suspicion of covid-19 and in whom reverse transcription-polymerase chain reaction (rt-pcr) was performed (mean, 62 years ± 16 ; 61 men, 53 with positive rt-pcr results). eight observers used co-rads to assess the scans. fleiss κ value was calculated, and scores of individual observers were compared with the median of the remaining seven observers. the resulting area under the receiver operating characteristics curve (auc) was compared with results from rt-pcr and clinical diagnosis of covid-19. results there was absolute agreement among observers in 573 (68.2%) of 840 observations. fleiss κ value was 0.47 (95% confidence interval : 0.45, 0.47), with the highest κ value for co-rads categories 1 (0.58, 95% ci: 0.54, 0.62) and 5 (0.68, 95% ci: 0.65, 0.72). the average auc was 0.91 (95% ci: 0.85, 0.97) for predicting rt-pcr outcome and 0.95 (95% ci: 0.91, 0.99) for clinical diagnosis. the false-negative rate for co-rads 1 was nine of 161 cases (5.6%; 95% ci: 1.0%, 10%), and the false-positive rate for co-rads category 5 was one of 286 (0.3%; 95% ci: 0%, 1.0%). conclusion the coronavirus disease 2019 (covid-19) reporting and data system (co-rads) is a categorical assessment scheme for pulmonary involvement of covid-19 at unenhanced chest ct that performs very well in predicting covid-19 in patients with moderate to severe symptoms and has substantial interobserver agreement, especially for categories 1 and 5. © rsna, 2020 online supplemental material is available for this article.",0
"background due to the general susceptibility of new coronaviruses, the clinical characteristics and outcomes of elderly and young patients may be different. objective to analyze the clinical characteristics of elderly patients with 2019 new-type coronavirus pneumonia (covid-19). methods this is a retrospective study of patients with new coronavirus pneumonia (covid-19) who were hospitalized in hainan provincial people's hospital from january 15, 2020 to february 18, 2020. compare the clinical characteristics of elderly with young and middle-aged patients. results a total of 56 patients were enrolled 18 elderly patients (32.14%), and 38 young and middle-aged patients (67.86%). the most common symptoms in both groups were fever, followed by cough and sputum. four patients in the elderly group received negative pressure icu for mechanical ventilation, and five patients in the young and middle-aged group. one patient died in the elderly group (5.56%), and two patients died in the young and middle-aged group (5.26%). the psi score of the elderly group was higher than that of the young and middle-aged group (p interpretation the mortality of elderly patients with covid-19 is higher than that of young and middle-aged patients, and the proportion of patients with psi grade iv and v is significantly higher than that of young and middle-aged patients. elderly patients with covid-19 are more likely to progress to severe disease.",0
"quality-space theory (qst) explains the nature of the mental qualities distinctive of perceptual states by appeal to their role in perceiving. qst is typically described in terms of the mental qualities that pertain to color. here we apply qst to the olfactory modalities. olfaction is in various respects more complex than vision, and so provides a useful test case for qst. to determine whether qst can deal with the challenges olfaction presents, we show how a quality space (qs) could be constructed relying on olfactory perceptible properties and the olfactory mental qualities then defined by appeal to that qs of olfactory perceptible properties. we also consider how to delimit the olfactory qs from other modalities. we further apply qst to the role that experience plays in refining our olfactory discriminative abilities and the occurrence of olfactory mental qualities in non-conscious olfactory states. qst is shown to be fully applicable to and useful for understanding the complex domain of olfaction.",0
"the past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. these methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. numerous cases of molecular adaptation are being identified in various systems from viruses to humans. although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.",0
"resequencing is an emerging tool for identification of rare disease-associated mutations. rare mutations are difficult to tag with snp genotyping, as genotyping studies are designed to detect common variants. however, studies have shown that genetic heterogeneity is a probable scenario for common diseases, in which multiple rare mutations together explain a large proportion of the genetic basis for the disease. thus, we propose a weighted-sum method to jointly analyse a group of mutations in order to test for groupwise association with disease status. for example, such a group of mutations may result from resequencing a gene. we compare the proposed weighted-sum method to alternative methods and show that it is powerful for identifying disease-associated genes, both on simulated and encode data. using the weighted-sum method, a resequencing study can identify a disease-associated gene with an overall population attributable risk (par) of 2%, even when each individual mutation has much lower par, using 1,000 to 7,000 affected and unaffected individuals, depending on the underlying genetic model. this study thus demonstrates that resequencing studies can identify important genetic associations, provided that specialised analysis methods, such as the weighted-sum method, are used.",0
"interferon-gamma (ifn-γ) is a pleiotropic molecule with associated antiproliferative, pro-apoptotic and antitumor mechanisms. this effector cytokine, often considered as a major effector of immunity, has been used in the treatment of several diseases, despite its adverse effects. although broad evidence implicating ifn-γ in tumor immune surveillance, ifn-γ-based therapies undergoing clinical trials have been of limited success. in fact, recent reports suggested that it may also play a protumorigenic role, namely, through ifn-γ signaling insensitivity, downregulation of major histocompatibility complexes, and upregulation of indoleamine 2,3-dioxygenase and of checkpoint inhibitors, as programmed cell-death ligand 1. however, the ifn-γ-mediated responses are still positively associated with patient's survival in several cancers. consequently, major research efforts are required to understand the immune contexture in which ifn-γ induces its intricate and highly regulated effects in the tumor microenvironment. this review discusses the current knowledge on the pro- and antitumorigenic effects of ifn-γ as part of the complex immune response to cancer, highlighting the relevance to identify ifn-γ responsive patients for the improvement of therapies that exploit associated signaling pathways.",0
"in macroautophagy, cytoplasmic components are delivered to lysosomes for degradation via autophagosomes that are formed by closure of cup-shaped isolation membranes. however, how the isolation membranes are formed is poorly understood. we recently found in yeast that a novel ubiquitin-like system, the apg12-apg5 conjugation system, is essential for autophagy. here we show that mouse apg12-apg5 conjugate localizes to the isolation membranes in mouse embryonic stem cells. using green fluorescent protein-tagged apg5, we revealed that the cup-shaped isolation membrane is developed from a small crescent-shaped compartment. apg5 localizes on the isolation membrane throughout its elongation process. to examine the role of apg5, we generated apg5-deficient embryonic stem cells, which showed defects in autophagosome formation. the covalent modification of apg5 with apg12 is not required for its membrane targeting, but is essential for involvement of apg5 in elongation of the isolation membranes. we also show that apg12-apg5 is required for targeting of a mammalian aut7/apg8 homologue, lc3, to the isolation membranes. these results suggest that the apg12-apg5 conjugate plays essential roles in isolation membrane development.",0
"unlabelled understanding the cause of failure and type of revision total knee arthroplasty (tka) procedures performed in the united states is essential in guiding research, implant design, and clinical decision making in tka. we assessed the causes of failure and specific types of revision tka procedures performed in the united states using newly implemented icd-9-cm diagnosis and procedure codes related to revision tka data from the nationwide inpatient sample (nis) database. clinical, demographic, and economic data were reviewed and analyzed from 60,355 revision tka procedures performed in the united states between october 1, 2005 and december 31, 2006. the most common causes of revision tka were infection (25.2%) and implant loosening (16.1%), and the most common type of revision tka procedure reported was all component revision (35.2%). revision tka procedures were most commonly performed in large, urban, nonteaching hospitals in medicare patients ages 65 to 74. the average length of hospital stay (los) for all revision tka procedures was 5.1 days, and the average total charges were $49,360. however, average los, average charges, and procedure frequencies varied considerably by census region, hospital type, and procedure performed. level of evidence level ii, economic and decision analysis. see guidelines for authors for a complete description of levels of evidence.",0
"aims the first aim was to critically evaluate the extent to which familial hypercholesterolaemia (fh) is underdiagnosed and undertreated. the second aim was to provide guidance for screening and treatment of fh, in order to prevent coronary heart disease (chd). methods and results of the theoretical estimated prevalence of 1/500 for heterozygous fh, conclusion owing to severe underdiagnosis and undertreatment of fh, there is an urgent worldwide need for diagnostic screening together with early and aggressive treatment of this extremely high-risk condition.",0
"the last few years have witnessed significant changes in pfam ( the number of families has grown substantially to a total of 17,929 in release 32.0. new additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into pfam clans, as well as their functional annotation. we recently began to collaborate with the repeatsdb resource to improve the definition of tandem repeat families within pfam. we carried out a significant comparison to the structural classification database, namely the evolutionary classification of protein domains (ecod) that led to the creation of 825 new families based on their set of uncharacterized families (eufs). furthermore, we also connected pfam entries to the sequence ontology (so) through mapping of the pfam type definitions to so terms. since pfam has many community contributors, we recently enabled the linking between authorship of all pfam entries with the corresponding authors' orcid identifiers. this effectively permits authors to claim credit for their pfam curation and link them to their orcid record.",0
"background scoping reviews are a relatively new approach to evidence synthesis and currently there exists little guidance regarding the decision to choose between a systematic review or scoping review approach when synthesising evidence. the purpose of this article is to clearly describe the differences in indications between scoping reviews and systematic reviews and to provide guidance for when a scoping review is (and is not) appropriate. results researchers may conduct scoping reviews instead of systematic reviews where the purpose of the review is to identify knowledge gaps, scope a body of literature, clarify concepts or to investigate research conduct. while useful in their own right, scoping reviews may also be helpful precursors to systematic reviews and can be used to confirm the relevance of inclusion criteria and potential questions. conclusions scoping reviews are a useful tool in the ever increasing arsenal of evidence synthesis approaches. although conducted for different purposes compared to systematic reviews, scoping reviews still require rigorous and transparent methods in their conduct to ensure that the results are trustworthy. our hope is that with clear guidance available regarding whether to conduct a scoping review or a systematic review, there will be less scoping reviews being performed for inappropriate indications better served by a systematic review, and vice-versa.",0
"the simple modular architecture research tool (smart) is an online resource ( used for protein domain identification and the analysis of protein domain architectures. many new features were implemented to make smart more accessible to scientists from different fields. the new 'genomic' mode in smart makes it easy to analyze domain architectures in completely sequenced genomes. domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 smart domains is now available, based on the presence of essential amino acids. furthermore, intrinsically disordered protein regions can be identified and displayed. the network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions.",0
"objective observational studies show breaking up prolonged sitting has beneficial associations with cardiometabolic risk markers, but intervention studies are required to investigate causality. we examined the acute effects on postprandial glucose and insulin levels of uninterrupted sitting compared with sitting interrupted by brief bouts of light- or moderate-intensity walking. research design and methods overweight/obese adults (n = 19), aged 45-65 years, were recruited for a randomized three-period, three-treatment acute crossover trial: 1) uninterrupted sitting; 2) seated with 2-min bouts of light-intensity walking every 20 min; and 3) seated with 2-min bouts of moderate-intensity walking every 20 min. a standardized test drink was provided after an initial 2-h period of uninterrupted sitting. the positive incremental area under curves (iauc) for glucose and insulin (mean ) for the 5 h after the test drink (75 g glucose, 50 g fat) were calculated for the respective treatments. results the glucose iauc (mmol/l) · h after both activity-break conditions was reduced (light: 5.2 ; moderate: 4.9 ; both p conclusions interrupting sitting time with short bouts of light- or moderate-intensity walking lowers postprandial glucose and insulin levels in overweight/obese adults. this may improve glucose metabolism and potentially be an important public health and clinical intervention strategy for reducing cardiovascular risk.",0
"background there is dogma that higher training load causes higher injury rates. however, there is also evidence that training has a protective effect against injury. for example, team sport athletes who performed more than 18 weeks of training before sustaining their initial injuries were at reduced risk of sustaining a subsequent injury, while high chronic workloads have been shown to decrease the risk of injury. second, across a wide range of sports, well-developed physical qualities are associated with a reduced risk of injury. clearly, for athletes to develop the physical capacities required to provide a protective effect against injury, they must be prepared to train hard. finally, there is also evidence that under-training may increase injury risk. collectively, these results emphasise that reductions in workloads may not always be the best approach to protect against injury. main thesis this paper describes the 'training-injury prevention paradox' model; a phenomenon whereby athletes accustomed to high training loads have fewer injuries than athletes training at lower workloads. the model is based on evidence that non-contact injuries are not caused by training per se, but more likely by an inappropriate training programme. excessive and rapid increases in training loads are likely responsible for a large proportion of non-contact, soft-tissue injuries. if training load is an important determinant of injury, it must be accurately measured up to twice daily and over periods of weeks and months (a season). this paper outlines ways of monitoring training load ('internal' and 'external' loads) and suggests capturing both recent ('acute') training loads and more medium-term ('chronic') training loads to best capture the player's training burden. i describe the critical variable-acute:chronic workload ratio-as a best practice predictor of training-related injuries. this provides the foundation for interventions to reduce players risk, and thus, time-loss injuries. summary the appropriately graded prescription of high training loads should improve players' fitness, which in turn may protect against injury, ultimately leading to (1) greater physical outputs and resilience in competition, and (2) a greater proportion of the squad available for selection each week.",0
"innate immune responses to pathogens critically impact the development of adaptive immune responses. however, it is not completely understood how innate immunity controls the initiation of adaptive immunities or how it determines which type of adaptive immunity will be induced to eliminate a given pathogen. here we show that viral stimulation not only triggers natural interferon (ifn)-alpha/beta-producing cells (ipcs) to produce vast amounts of antiviral ifn-alpha/beta but also induces these cells to differentiate into dendritic cells (dcs). ifn-alpha/beta and tumor necrosis factor alpha produced by virus-activated ipcs act as autocrine survival and dc differentiation factors, respectively. the virus-induced dcs stimulate naive cd4(+) t cells to produce ifn-gamma and interleukin (il)-10, in contrast to il-3-induced dcs, which stimulate naive cd4(+) t cells to produce t helper type 2 cytokines il-4, il-5, and il-10. thus, ipcs may play two master roles in antiviral immune responses: directly inhibiting viral replication by producing large amounts of ifn-alpha/beta, and subsequently triggering adaptive t cell-mediated immunity by differentiating into dcs. ipcs constitute a critical link between innate and adaptive immunity.",0
"unlabelled cytoscape is a popular bioinformatics package for biological network visualization and data integration. version 2.8 introduces two powerful new features--custom node graphics and attribute equations--which can be used jointly to greatly enhance cytoscape's data integration and visualization capabilities. custom node graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. attribute equations provide cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. availability and implementation cytoscape is a desktop java application released under the library gnu public license (lgpl). binary install bundles and source code for cytoscape 2.8 are available for download from",0
"background since its inception, the carbohydrate-active enzymes database (cazy; has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (gh), the polysaccharide lyases (pl), the carbohydrate esterases (ce), the glycosyltransferases (gt) and their appended non-catalytic carbohydrate-binding modules (cbm). the recent discovery that members of families cbm33 and family gh61 are in fact lytic polysaccharide monooxygenases (lpmo), demands a reclassification of these families into a suitable category. results because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (lpmo), we have decided to join the families of lignin degradation enzymes to the lpmo families and launch a new cazy class that we name ""auxiliary activities"" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). conclusions the new class introduced in the cazy database extends the traditional cazy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.",0
"the human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. altered gut microbial ecosystems have been associated with increased metabolic and immune disorders in animals and humans. molecular interactions linking the gut microbiota with host energy metabolism, lipid accumulation, and immunity have also been identified. however, the exact mechanisms that link specific variations in the composition of the gut microbiota with the development of obesity and metabolic diseases in humans remain obscure owing to the complex etiology of these pathologies. in this review, we discuss current knowledge about the mechanistic interactions between the gut microbiota, host energy metabolism, and the host immune system in the context of obesity and metabolic disease, with a focus on the importance of the axis that links gut microbes and host metabolic inflammation. finally, we discuss therapeutic approaches aimed at reshaping the gut microbial ecosystem to regulate obesity and related pathologies, as well as the challenges that remain in this area.",0
"calculation of exact sample size is an important part of research design. it is very important to understand that different study design need different method of sample size calculation and one formula cannot be used in all designs. in this short review we tried to educate researcher regarding various method of sample size calculation available for different study designs. in this review sample size calculation for most frequently used study designs are mentioned. for genetic and microbiological studies readers are requested to read other sources.",0
"recent high-throughput techniques have generated a flood of biological data in all aspects. the transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. in this work, we developed an easy-to-use tool named hemi (heat map illustrator), which can visualize either gene or protein expression data in heatmaps. additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. in addition, hemi provides multiple clustering strategies for analyzing the data. publication-quality figures can be exported directly. we propose that hemi can be a useful toolkit for conveniently visualizing and manipulating heatmaps. the stand-alone packages of hemi were implemented in java and can be accessed at",0
"a saccharomyces cerevisiae mutant in cell division cycle gene cdc48 shows typical markers of apoptosis: membrane staining with annexin v, indicating an exposure of phosphatidylserine at the outer layer of the cytoplasmic membrane; intense staining, using the terminal deoxynucleotidyl transferase-mediated dutp nick end labeling method, indicating dna fragmentation; and chromatin condensation and fragmentation. the coordinate occurrence of these events at different locations in the cell, which have no obvious connection except their relation to apoptosis, implies the presence of the molecular machinery performing the basic steps of apoptosis already in yeast. saccharomyces cerevisiae may prove a suitable model to trace the roots of apoptosis.",0
"motivation the illumina infinium 450 k dna methylation beadchip is a prime candidate technology for epigenome-wide association studies (ewas). however, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different dna methylation distributions and dynamic range, which may bias downstream analyses. a key statistical issue is therefore how best to adjust for the two different probe designs. results here we propose a novel model-based intra-array normalization strategy for 450 k data, called bmiq (beta mixture quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. the strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. we validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that bmiq compares favourably with two competing methods. specifically, we show that bmiq improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. bmiq will be useful as a preprocessing step for any study using the illumina infinium 450 k platform. availability bmiq is freely available from contact a.teschendorff@ucl.ac.uk supplementary information supplementary data are available at bioinformatics online.",0
"background rabies is a notoriously underreported and neglected disease of low-income countries. this study aims to estimate the public health and economic burden of rabies circulating in domestic dog populations, globally and on a country-by-country basis, allowing an objective assessment of how much this preventable disease costs endemic countries. methodology/principal findings we established relationships between rabies mortality and rabies prevention and control measures, which we incorporated into a model framework. we used data derived from extensive literature searches and questionnaires on disease incidence, control interventions and preventative measures within this framework to estimate the disease burden. the burden of rabies impacts on public health sector budgets, local communities and livestock economies, with the highest risk of rabies in the poorest regions of the world. this study estimates that globally canine rabies causes approximately 59,000 (95% confidence intervals: 25-159,000) human deaths, over 3.7 million (95% cis: 1.6-10.4 million) disability-adjusted life years (dalys) and 8.6 billion usd (95% cis: 2.9-21.5 billion) economic losses annually. the largest component of the economic burden is due to premature death (55%), followed by direct costs of post-exposure prophylaxis (pep, 20%) and lost income whilst seeking pep (15.5%), with only limited costs to the veterinary sector due to dog vaccination (1.5%), and additional costs to communities from livestock losses (6%). conclusions/significance this study demonstrates that investment in dog vaccination, the single most effective way of reducing the disease burden, has been inadequate and that the availability and affordability of pep needs improving. collaborative investments by medical and veterinary sectors could dramatically reduce the current large, and unnecessary, burden of rabies on affected communities. improved surveillance is needed to reduce uncertainty in burden estimates and to monitor the impacts of control efforts.",0
"real-world observable physical and chemical characteristics are increasingly being calculated from the 3d structures of biomolecules. methods for calculating pk(a) values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of pdb structures into formats ready for use with biomolecular simulation software. the continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. as described previously, the pdb2pqr web server addresses this need for electrostatic field calculations (dolinsky et al., nucleic acids research, 32, w665-w667, 2004). here we report the significantly expanded pdb2pqr that includes the following features: robust standalone command line support, improved pk(a) estimation via the propka framework, ligand parameterization via peoe_pb charge methodology, expanded set of force fields and easily incorporated user-defined parameters via xml input files, and improvement of atom addition and optimization code. these features are available through a new web interface ( which offers users a wide range of options for pdb file conversion, modification and parameterization.",0
"current t-cell engineering approaches redirect patient t cells to tumors by transducing them with antigen-specific t-cell receptors (tcrs) or chimeric antigen receptors (cars) that target a single antigen. however, few truly tumor-specific antigens have been identified, and healthy tissues that express the targeted antigen may undergo t cell-mediated damage. here we present a strategy to render t cells specific for a tumor in the absence of a truly tumor-restricted antigen. t cells are transduced with both a car that provides suboptimal activation upon binding of one antigen and a chimeric costimulatory receptor (ccr) that recognizes a second antigen. using the prostate tumor antigens psma and psca, we show that co-transduced t cells destroy tumors that express both antigens but do not affect tumors expressing either antigen alone. this 'tumor-sensing' strategy may help broaden the applicability and avoid some of the side effects of targeted t-cell therapies.",0
"the prognostic value of foxp3(+) regulatory t cells (tregs) in cancer remains controversial. we did a meta-analysis to assess the prognostic effect of foxp3(+) treg across different types of cancer and to investigate factors associated with variations in this effect. pubmed, embase, cochrane central, and scopus were searched to identify eligible studies. in total, we analyzed 76 articles encompassing 17 types of cancer, and including 15,512 cancer cases. the overall pooled analysis including all types of cancer suggested foxp3(+)tregs had a significant negative effect on overall survival (os) (or 1.46, p < 0.001), but the prognostic effect varied greatly according to tumor site. high foxp3(+) tregs infiltration was significantly associated with shorter os in the majority of solid tumors studied, including cervical, renal, melanomas, and breast cancers, et al; whereas, foxp3(+) tregs were associated with improved survival in colorectal, head and neck, and oesophageal cancers. the stratified analysis suggested the molecular subtype and tumor stage significantly influenced the prognostic value of foxp3(+) tregs in certain types of cancer. in conclusion, our meta-analysis suggests that the prognostic role of foxp3(+) tregs was highly influenced by tumor site, and was also correlated with the molecular subtype and tumor stage.",0
"the basic local alignment search tool (blast) website at the national center for biotechnology (ncbi) is an important resource for searching and aligning sequences. a new blast report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. here, we describe these improvements to the blast report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. the ncbi blast url is",0
"several modifications that have been made to the nddo core-core interaction term and to the method of parameter optimization are described. these changes have resulted in a more complete parameter optimization, called pm6, which has, in turn, allowed 70 elements to be parameterized. the average unsigned error (aue) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol(-1). for the subset of 1,373 compounds involving only the elements h, c, n, o, f, p, s, cl, and br, the pm6 aue was 4.4 kcal mol(-1). the equivalent aue for other methods were: rm1: 5.0, b3lyp 6-31g*: 5.2, pm5: 5.7, pm3: 6.3, hf 6-31g*: 7.4, and am1: 10.0 kcal mol(-1). several long-standing faults in am1 and pm3 have been corrected and significant improvements have been made in the prediction of geometries.",0
"background despite remarkable progress in the improvement of child survival between 1990 and 2015, the millennium development goal (mdg) 4 target of a two-thirds reduction of under-5 mortality rate (u5mr) was not achieved globally. in this paper, we updated our annual estimates of child mortality by cause to 2000-15 to reflect on progress toward the mdg 4 and consider implications for the sustainable development goals (sdg) target for child survival. methods we increased the estimation input data for causes of deaths by 43% among neonates and 23% among 1-59-month-olds, respectively. we used adequate vital registration (vr) data where available, and modelled cause-specific mortality fractions applying multinomial logistic regressions using adequate vr for low u5mr countries and verbal autopsy data for high u5mr countries. we updated the estimation to use plasmodium falciparum parasite rate in place of malaria index in the modelling of malaria deaths; to use adjusted empirical estimates instead of modelled estimates for china; and to consider the effects of pneumococcal conjugate vaccine and rotavirus vaccine in the estimation. findings in 2015, among the 5·9 million under-5 deaths, 2·7 million occurred in the neonatal period. the leading under-5 causes were preterm birth complications (1·055 million ), pneumonia (0·921 million ), and intrapartum-related events (0·691 million ). in the two mdg regions with the most under-5 deaths, the leading cause was pneumonia in sub-saharan africa and preterm birth complications in southern asia. reductions in mortality rates for pneumonia, diarrhoea, neonatal intrapartum-related events, malaria, and measles were responsible for 61% of the total reduction of 35 per 1000 livebirths in u5mr in 2000-15. stratified by u5mr, pneumonia was the leading cause in countries with very high u5mr. preterm birth complications and pneumonia were both important in high, medium high, and medium child mortality countries; whereas congenital abnormalities was the most important cause in countries with low and very low u5mr. interpretation in the sdg era, countries are advised to prioritise child survival policy and programmes based on their child cause-of-death composition. continued and enhanced efforts to scale up proven life-saving interventions are needed to achieve the sdg child survival target. funding bill & melinda gates foundation, who.",0
"public health measures have successfully identified and contained outbreaks of the severe acute respiratory syndrome (sars) coronavirus (sars-cov), but concerns remain over the possibility of future recurrences. finding a vaccine for this virus therefore remains a high priority. here, we show that a dna vaccine encoding the spike (s) glycoprotein of the sars-cov induces t cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. alternative forms of s were analysed by dna immunization. these expression vectors induced robust immune responses mediated by cd4 and cd8 cells, as well as significant antibody titres, measured by enzyme-linked immunosorbent assay. moreover, antibody responses in mice vaccinated with an expression vector encoding a form of s that includes its transmembrane domain elicited neutralizing antibodies. viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these s plasmid dna expression vectors, and protection was mediated by a humoral but not a t-cell-dependent immune mechanism. gene-based vaccination for the sars-cov elicits effective immune responses that generate protective immunity in an animal model.",0
"background recent declines in honey bees for crop pollination threaten fruit, nut, vegetable and seed production in the united states. a broad survey of pesticide residues was conducted on samples from migratory and other beekeepers across 23 states, one canadian province and several agricultural cropping systems during the 2007-08 growing seasons. methodology/principal findings we have used lc/ms-ms and gc/ms to analyze bees and hive matrices for pesticide residues utilizing a modified quechers method. we have found 121 different pesticides and metabolites within 887 wax, pollen, bee and associated hive samples. almost 60% of the 259 wax and 350 pollen samples contained at least one systemic pesticide, and over 47% had both in-hive acaricides fluvalinate and coumaphos, and chlorothalonil, a widely-used fungicide. in bee pollen were found chlorothalonil at levels up to 99 ppm and the insecticides aldicarb, carbaryl, chlorpyrifos and imidacloprid, fungicides boscalid, captan and myclobutanil, and herbicide pendimethalin at 1 ppm levels. almost all comb and foundation wax samples (98%) were contaminated with up to 204 and 94 ppm, respectively, of fluvalinate and coumaphos, and lower amounts of amitraz degradates and chlorothalonil, with an average of 6 pesticide detections per sample and a high of 39. there were fewer pesticides found in adults and brood except for those linked with bee kills by permethrin (20 ppm) and fipronil (3.1 ppm). conclusions/significance the 98 pesticides and metabolites detected in mixtures up to 214 ppm in bee pollen alone represents a remarkably high level for toxicants in the brood and adult food of this primary pollinator. this represents over half of the maximum individual pesticide incidences ever reported for apiaries. while exposure to many of these neurotoxicants elicits acute and sublethal reductions in honey bee fitness, the effects of these materials in combinations and their direct association with ccd or declining bee health remains to be determined.",0
"infections caused by community-acquired (ca)-methicillin--resistant staphylococcus aureus (mrsa) have been reported worldwide. we assessed whether any common genetic markers existed among 117 ca-mrsa isolates from the united states, france, switzerland, australia, new zealand, and western samoa by performing polymerase chain reaction for 24 virulence factors and the methicillin-resistance determinant. the genetic background of the strain was analyzed by pulsed-field gel electrophoresis (pfge) and multi-locus sequence typing (mlst). the ca-mrsa strains shared a type iv sccmec cassette and the panton-valentine leukocidin locus, whereas the distribution of the other toxin genes was quite specific to the strains from each continent. pfge and mlst analysis indicated distinct genetic backgrounds associated with each geographic origin, although predominantly restricted to the agr3 background. within each continent, the genetic background of ca-mrsa strains did not correspond to that of the hospital-acquired mrsa.",0
"the transplantation of cultured myoblasts into mature skeletal muscle is the basis for a new therapeutic approach to muscle and non-muscle diseases: myoblast-mediated gene therapy. the success of myoblast transplantation for correction of intrinsic muscle defects depends on the fusion of implanted cells with host myofibers. previous studies in mice have been problematic because they have involved transplantation of established myogenic cell lines or primary muscle cultures. both of these cell populations have disadvantages: myogenic cell lines are tumorigenic, and primary cultures contain a substantial percentage of non-myogenic cells which will not fuse to host fibers. furthermore, for both cell populations, immune suppression of the host has been necessary for long-term retention of transplanted cells. to overcome these difficulties, we developed novel culture conditions that permit the purification of mouse myoblasts from primary cultures. both enriched and clonal populations of primary myoblasts were characterized in assays of cell proliferation and differentiation. primary myoblasts were dependent on added bfgf for growth and retained the ability to differentiate even after 30 population doublings. the fate of the pure myoblast populations after transplantation was monitored by labeling the cells with the marker enzyme beta-galactosidase (beta-gal) using retroviral mediated gene transfer. within five days of transplantation into muscle of mature mice, primary myoblasts had fused with host muscle cells to form hybrid myofibers. to examine the immunobiology of primary myoblasts, we compared transplanted cells in syngeneic and allogeneic hosts. even without immune suppression, the hybrid fibers persisted with continued beta-gal expression up to six months after myoblast transplantation in syngeneic hosts. in allogeneic hosts, the implanted cells were completely eliminated within three weeks. to assess tumorigenicity, primary myoblasts and myoblasts from the c2 myogenic cell line were transplanted into immunodeficient mice. only c2 myoblasts formed tumors. the ease of isolation, growth, and transfection of primary mouse myoblasts under the conditions described here expand the opportunities to study muscle cell growth and differentiation using myoblasts from normal as well as mutant strains of mice. the properties of these cells after transplantation--the stability of resulting hybrid myofibers without immune suppression, the persistence of transgene expression, and the lack of tumorigenicity--suggest that studies of cell-mediated gene therapy using primary myoblasts can now be broadly applied to mouse models of human muscle and non-muscle diseases.",0
"elastography-based imaging techniques have received substantial attention in recent years for non-invasive assessment of tissue mechanical properties. these techniques take advantage of changed soft tissue elasticity in various pathologies to yield qualitative and quantitative information that can be used for diagnostic purposes. measurements are acquired in specialized imaging modes that can detect tissue stiffness in response to an applied mechanical force (compression or shear wave). ultrasound-based methods are of particular interest due to its many inherent advantages, such as wide availability including at the bedside and relatively low cost. several ultrasound elastography techniques using different excitation methods have been developed. in general, these can be classified into strain imaging methods that use internal or external compression stimuli, and shear wave imaging that use ultrasound-generated traveling shear wave stimuli. while ultrasound elastography has shown promising results for non-invasive assessment of liver fibrosis, new applications in breast, thyroid, prostate, kidney and lymph node imaging are emerging. here, we review the basic principles, foundation physics, and limitations of ultrasound elastography and summarize its current clinical use and ongoing developments in various clinical applications.",0
"background artemisinin-resistant falciparum malaria has arisen in western cambodia. a concerted international effort is underway to contain artemisinin-resistant plasmodium falciparum, but containment strategies are dependent on whether resistance has emerged elsewhere. we aimed to establish whether artemisinin resistance has spread or emerged on the thailand-myanmar (burma) border. methods in malaria clinics located along the northwestern border of thailand, we measured six hourly parasite counts in patients with uncomplicated hyperparasitaemic falciparum malaria (≥4% infected red blood cells) who had been given various oral artesunate-containing regimens since 2001. parasite clearance half-lives were estimated and parasites were genotyped for 93 single nucleotide polymorphisms. findings 3202 patients were studied between 2001 and 2010. parasite clearance half-lives lengthened from a geometric mean of 2·6 h (95% ci 2·5-2·7) in 2001, to 3·7 h (3·6-3·8) in 2010, compared with a mean of 5·5 h (5·2-5·9) in 119 patients in western cambodia measured between 2007 and 2010. the proportion of slow-clearing infections (half-life ≥6·2 h) increased from 0·6% in 2001, to 20% in 2010, compared with 42% in western cambodia between 2007 and 2010. of 1583 infections genotyped, 148 multilocus parasite genotypes were identified, each of which infected between two and 13 patients. the proportion of variation in parasite clearance attributable to parasite genetics increased from 30% between 2001 and 2004, to 66% between 2007 and 2010. interpretation genetically determined artemisinin resistance in p falciparum emerged along the thailand-myanmar border at least 8 years ago and has since increased substantially. at this rate of increase, resistance will reach rates reported in western cambodia in 2-6 years. funding the wellcome trust and national institutes of health.",0
"pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. the integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. this approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. the purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.",0
"here, we present the new ucl bioinformatics group's psipred protein analysis workbench. the workbench unites all of our previously available analysis methods into a single web-based framework. the new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. we offer a number of additional services to enable computationally scalable execution of our prediction methods; these include soap and xml-rpc web server access and new hadoop packages. all software and services are available via the ucl bioinformatics group website at",0
"the inparanoid eukaryotic ortholog database ( is a collection of pairwise ortholog groups between 17 whole genomes; anopheles gambiae, caenorhabditis briggsae, caenorhabditis elegans, drosophila melanogaster, danio rerio, takifugu rubripes, gallus gallus, homo sapiens, mus musculus, pan troglodytes, rattus norvegicus, oryza sativa, plasmodium falciparum, arabidopsis thaliana, escherichia coli, saccharomyces cerevisiae and schizosaccharomyces pombe. complete proteomes for these genomes were derived from ensembl and uniprot and compared pairwise using blast, followed by a clustering step using the inparanoid program. an inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. the ortholog clusters can be searched on the website using ensembl gene/protein or uniprot identifiers, annotation text or by blast alignment against our protein datasets. the entire dataset can be downloaded, as can the inparanoid program itself.",0
"background plink 1 is a widely used open-source c/c++ toolset for genome-wide association studies (gwas) and research in population genetics. however, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. in addition, gwas and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by plink 1's primary data format. findings to address these issues, we are developing a second-generation codebase for plink. the first major release from this codebase, plink 1.9, introduces extensive use of bit-level parallelism, -time/constant-space hardy-weinberg equilibrium and fisher's exact tests, and many other algorithmic improvements. in combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in ram. we have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (plink 2.0). conclusions the second-generation versions of plink will offer dramatic improvements in performance and compatibility. for the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.",0
"the objectives of this study were to determine whether differences in the size and composition of coarse (2.5-10 micro m), fine (< 2.5 microm), and ultrafine (< 0.1 microm) particulate matter (pm) are related to their uptake in macrophages and epithelial cells and their ability to induce oxidative stress. the premise for this study is the increasing awareness that various pm components induce pulmonary inflammation through the generation of oxidative stress. coarse, fine, and ultrafine particles (ufps) were collected by ambient particle concentrators in the los angeles basin in california and used to study their chemical composition in parallel with assays for generation of reactive oxygen species (ros) and ability to induce oxidative stress in macrophages and epithelial cells. ufps were most potent toward inducing cellular heme oxygenase-1 (ho-1) expression and depleting intracellular glutathione. ho-1 expression, a sensitive marker for oxidative stress, is directly correlated with the high organic carbon and polycyclic aromatic hydrocarbon (pah) content of ufps. the dithiothreitol (dtt) assay, a quantitative measure of in vitro ros formation, was correlated with pah content and ho-1 expression. ufps also had the highest ros activity in the dtt assay. because the small size of ufps allows better tissue penetration, we used electron microscopy to study subcellular localization. ufps and, to a lesser extent, fine particles, localize in mitochondria, where they induce major structural damage. this may contribute to oxidative stress. our studies demonstrate that the increased biological potency of ufps is related to the content of redox cycling organic chemicals and their ability to damage mitochondria.",0
"to further understanding of the genetic basis of type 2 diabetes (t2d) susceptibility, we aggregated published meta-analyses of genome-wide association studies (gwas), including 26,488 cases and 83,964 controls of european, east asian, south asian and mexican and mexican american ancestry. we observed a significant excess in the directional consistency of t2d risk alleles across ancestry groups, even at snps demonstrating only weak evidence of association. by following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of european ancestry, we identified seven new t2d susceptibility loci. furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several t2d susceptibility loci. these observations highlight the benefits of trans-ethnic gwas for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.",0
"a typical diffraction experiment will generate many images and data sets from different crystals in a very short time. this creates a challenge for the high-throughput operation of modern synchrotron beamlines as well as for the subsequent data processing. novice users in particular may feel overwhelmed by the tables, plots and numbers that the different data-processing programs and software packages present to them. here, some of the more common problems that a user has to deal with when processing a set of images that will finally make up a processed data set are shown, concentrating on difficulties that may often show up during the first steps along the path of turning the experiment (i.e. data collection) into a model (i.e. interpreted electron density). difficulties such as unexpected crystal forms, issues in crystal handling and suboptimal choices of data-collection strategies can often be dealt with, or at least diagnosed, by analysing specific data characteristics during processing. in the end, one wants to distinguish problems over which one has no immediate control once the experiment is finished from problems that can be remedied a posteriori. a new software package, autoproc, is also presented that combines third-party processing programs with new tools and an automated workflow script that is intended to provide users with both guidance and insight into the offline processing of data affected by the difficulties mentioned above, with particular emphasis on the automated treatment of multi-sweep data sets collected on multi-axis goniostats.",0
"objective to investigate the association between intake of dietary fibre and whole grains and risk of colorectal cancer. design systematic review and meta-analysis of prospective observational studies. data sources pubmed and several other databases up to december 2010 and the reference lists of studies included in the analysis as well as those listed in published meta-analyses. study selection prospective cohort and nested case-control studies of dietary fibre or whole grain intake and incidence of colorectal cancer. results 25 prospective studies were included in the analysis. the summary relative risk of developing colorectal cancer for 10 g daily of total dietary fibre (16 studies) was 0.90 (95% confidence interval 0.86 to 0.94, i(2) = 0%), for fruit fibre (n = 9) was 0.93 (0.82 to 1.05, i(2) = 23%), for vegetable fibre (n = 9) was 0.98 (0.91 to 1.06, i(2) = 0%), for legume fibre (n = 4) was 0.62 (0.27 to 1.42, i(2) = 58%), and for cereal fibre (n = 8) was 0.90 (0.83 to 0.97, i(2) = 0%). the summary relative risk for an increment of three servings daily of whole grains (n = 6) was 0.83 (0.78 to 0.89, i(2) = 18%). conclusion a high intake of dietary fibre, in particular cereal fibre and whole grains, was associated with a reduced risk of colorectal cancer. further studies should report more detailed results, including those for subtypes of fibre and be stratified by other risk factors to rule out residual confounding. further assessment of the impact of measurement errors on the risk estimates is also warranted.",0
"hydrogen peroxide emerged as major redox metabolite operative in redox sensing, signaling and redox regulation. generation, transport and capture of h 2 o 2 in biological settings as well as their biological consequences can now be addressed. the present overview focuses on recent progress on metabolic sources and sinks of h 2 o 2 and on the role of h 2 o 2 in redox signaling under physiological conditions (1-10nm), denoted as oxidative eustress. higher concentrations lead to adaptive stress responses via master switches such as nrf2/keap1 or nf-κb. supraphysiological concentrations of h 2 o 2 (>100nm) lead to damage of biomolecules, denoted as oxidative distress. three questions are addressed: how can h 2 o 2 be assayed in the biological setting? what are the metabolic sources and sinks of h 2 o 2 ? what is the role of h 2 o 2 in redox signaling and oxidative stress?",0
"background missing data may seriously compromise inferences from randomised clinical trials, especially if missing data are not handled appropriately. the potential bias due to missing data depends on the mechanism causing the data to be missing, and the analytical methods applied to amend the missingness. therefore, the analysis of trial data with missing values requires careful planning and attention. methods the authors had several meetings and discussions considering optimal ways of handling missing data to minimise the bias potential. we also searched pubmed (key words: missing data; randomi*; statistical analysis) and reference lists of known studies for papers (theoretical papers; empirical studies; simulation studies; etc.) on how to deal with missing data when analysing randomised clinical trials. results handling missing data is an important, yet difficult and complex task when analysing results of randomised clinical trials. we consider how to optimise the handling of missing data during the planning stage of a randomised clinical trial and recommend analytical approaches which may prevent bias caused by unavoidable missing data. we consider the strengths and limitations of using of best-worst and worst-best sensitivity analyses, multiple imputation, and full information maximum likelihood. we also present practical flowcharts on how to deal with missing data and an overview of the steps that always need to be considered during the analysis stage of a trial. conclusions we present a practical guide and flowcharts describing when and how multiple imputation should be used to handle missing data in randomised clinical.",0
"these are exciting times for cancer immunotherapy. after many years of disappointing results, the tide has finally changed and immunotherapy has become a clinically validated treatment for many cancers. immunotherapeutic strategies include cancer vaccines, oncolytic viruses, adoptive transfer of ex vivo activated t and natural killer cells, and administration of antibodies or recombinant proteins that either costimulate cells or block the so-called immune checkpoint pathways. the recent success of several immunotherapeutic regimes, such as monoclonal antibody blocking of cytotoxic t lymphocyte-associated protein 4 (ctla-4) and programmed cell death protein 1 (pd1), has boosted the development of this treatment modality, with the consequence that new therapeutic targets and schemes which combine various immunological agents are now being described at a breathtaking pace. in this review, we outline some of the main strategies in cancer immunotherapy (cancer vaccines, adoptive cellular immunotherapy, immune checkpoint blockade, and oncolytic viruses) and discuss the progress in the synergistic design of immune-targeting combination therapies.",0
"t-cell exhaustion was originally identified during chronic infection in mice, and was subsequently observed in humans with cancer. the exhausted t cells in the tumor microenvironment show overexpressed inhibitory receptors, decreased effector cytokine production and cytolytic activity, leading to the failure of cancer elimination. restoring exhausted t cells represents an inspiring strategy for cancer treatment, which has yielded promising results and become a significant breakthrough in the cancer immunotherapy. in this review, we overview the updated understanding on the exhausted t cells in cancer and their potential regulatory mechanisms and discuss current therapeutic interventions targeting exhausted t cells in clinical trials.",0
"the university of california santa cruz (ucsc) genome browser ( offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. the browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. as of september 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. in the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. among these are an updated ucsc genes track for human and mouse assemblies. we have also introduced several features to improve usability, including new navigation menus. this article provides an update to the ucsc genome browser database, which has been previously featured in the database issue of this journal.",0
"heart rate variability (hrv), the change in the time intervals between adjacent heartbeats, is an emergent property of interdependent regulatory systems that operate on different time scales to adapt to challenges and achieve optimal performance. this article briefly reviews neural regulation of the heart, and its basic anatomy, the cardiac cycle, and the sinoatrial and atrioventricular pacemakers. the cardiovascular regulation center in the medulla integrates sensory information and input from higher brain centers, and afferent cardiovascular system inputs to adjust heart rate and blood pressure via sympathetic and parasympathetic efferent pathways. this article reviews sympathetic and parasympathetic influences on the heart, and examines the interpretation of hrv and the association between reduced hrv, risk of disease and mortality, and the loss of regulatory capacity. this article also discusses the intrinsic cardiac nervous system and the heart-brain connection, through which afferent information can influence activity in the subcortical and frontocortical areas, and motor cortex. it also considers new perspectives on the putative underlying physiological mechanisms and properties of the ultra-low-frequency (ulf), very-low-frequency (vlf), low-frequency (lf), and high-frequency (hf) bands. additionally, it reviews the most common time and frequency domain measurements as well as standardized data collection protocols. in its final section, this article integrates porges' polyvagal theory, thayer and colleagues' neurovisceral integration model, lehrer et al.'s resonance frequency model, and the institute of heartmath's coherence model. the authors conclude that a coherent heart is not a metronome because its rhythms are characterized by both complexity and stability over longer time scales. future research should expand understanding of how the heart and its intrinsic nervous system influence the brain.",0
"linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. however, existing methods are computationally intractable in large cohorts and may not optimize power. all existing methods require time cost o(mn(2)) (where n is the number of samples and m is the number of snps) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power. here we present a far more efficient mixed-model association method, bolt-lmm, which requires only a small number of o(mn) time iterations and increases power by modeling more realistic, non-infinitesimal genetic architectures via a bayesian mixture prior on marker effect sizes. we applied bolt-lmm to 9 quantitative traits in 23,294 samples from the women's genome health study (wghs) and observed significant increases in power, consistent with simulations. theory and simulations show that the boost in power increases with cohort size, making bolt-lmm appealing for genome-wide association studies in large cohorts.",0
"the universal protein resource (uniprot) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. the uniprot consortium is a collaboration between the european bioinformatics institute (ebi), the protein information resource (pir) and the swiss institute of bioinformatics (sib). the core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly uniprot website, and the provision of additional value-added information through cross-references to other databases. uniprot is comprised of four major components, each optimized for different uses: the uniprot knowledgebase, the uniprot reference clusters, the uniprot archive and the uniprot metagenomic and environmental sequences database. uniprot is updated and distributed every three weeks, and can be accessed online for searches or download at",0
"background polygenic risk score (prs) analyses have become an integral part of biomedical research, exploited to gain insights into shared aetiology among traits, to control for genomic profile in experimental studies, and to strengthen causal inference, among a range of applications. substantial efforts are now devoted to biobank projects to collect large genetic and phenotypic data, providing unprecedented opportunity for genetic discovery and applications. to process the large-scale data provided by such biobank resources, highly efficient and scalable methods and software are required. results here we introduce prsice-2, an efficient and scalable software program for automating and simplifying prs analyses on large-scale data. prsice-2 handles both genotyped and imputed data, provides empirical association p-values free from inflation due to overfitting, supports different inheritance models, and can evaluate multiple continuous and binary target traits simultaneously. we demonstrate that prsice-2 is dramatically faster and more memory-efficient than prsice-1 and alternative prs software, ldpred and lassosum, while having comparable predictive power. conclusion prsice-2's combination of efficiency and power will be increasingly important as data sizes grow and as the applications of prs become more sophisticated, e.g., when incorporated into high-dimensional or gene set-based analyses. prsice-2 is written in c++, with an r script for plotting, and is freely available for download from",0
"the remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (hiv-1) envelope (env), including substantial rearrangement of the gp120 glycoprotein upon binding the cd4 receptor, allow it to evade antibody-mediated neutralization. despite this complexity, the hiv-1 env must retain conserved determinants that mediate cd4 binding. to evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the cd4-bound state, assessed binding of cd4 and of receptor-binding-site antibodies, and determined the structure at 2.3 a resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the cd4-binding site. this surface is involved in the metastable attachment of cd4, before the gp120 rearrangement required for stable engagement. a site of vulnerability, related to a functional requirement for efficient association with cd4, can therefore be targeted by antibody to neutralize hiv-1.",0
"the european hernia society (ehs) is proud to present the ehs guidelines for the treatment of inguinal hernia in adult patients. the guidelines contain recommendations for the treatment of inguinal hernia from diagnosis till aftercare. they have been developed by a working group consisting of expert surgeons with representatives of 14 country members of the ehs. they are evidence-based and, when necessary, a consensus was reached among all members. the guidelines have been reviewed by a steering committee. before finalisation, feedback from different national hernia societies was obtained. the appraisal of guidelines for research and evaluation (agree) instrument was used by the cochrane association to validate the guidelines. the guidelines can be used to adjust local protocols, for training purposes and quality control. they will be revised in 2012 in order to keep them updated. in between revisions, it is the intention of the working group to provide every year, during the ehs annual congress, a short update of new high-level evidence (randomised controlled trials and meta-analyses). developing guidelines leads to questions that remain to be answered by specific research. therefore, we provide recommendations for further research that can be performed to raise the level of evidence concerning certain aspects of inguinal hernia treatment. in addition, a short summary, specifically for the general practitioner, is given. in order to increase the practical use of the guidelines by consultants and residents, more details on the most important surgical techniques, local infiltration anaesthesia and a patient information sheet is provided. the most important challenge now will be the implementation of the guidelines in daily surgical practice. this remains an important task for the ehs. the establishment of an ehs school for teaching inguinal hernia repair surgical techniques, including tips and tricks from experts to overcome the learning curve (especially in endoscopic repair), will be the next step. working together on this project was a great learning experience, and it was worthwhile and fun. cultural differences between members were easily overcome by educating each other, respecting different views and always coming back to the principles of evidence-based medicine. the members of the working group would like to thank the ehs board for their support and especially ethicon for sponsoring the many meetings that were needed to finalise such an ambitious project.",0
"background in the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (covid-19) have been produced that differ substantially in magnitude. we aimed to provide robust estimates, accounting for censoring and ascertainment biases. methods we collected individual-case data for patients who died from covid-19 in hubei, mainland china (reported by national and provincial health commissions to feb 8, 2020), and for cases outside of mainland china (from government or ministry of health websites and media reports for 37 countries, as well as hong kong and macau, until feb 25, 2020). these individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). we next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in china, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. we also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland china. using data on the prevalence of pcr-confirmed cases in international residents repatriated from china, we obtained age-stratified estimates of the infection fatality ratio. furthermore, data on age-stratified severity in a subset of 3665 cases from china were used to estimate the proportion of infected individuals who are likely to require hospitalisation. findings using data on 24 deaths that occurred in mainland china and 165 recoveries outside of china, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). in all laboratory confirmed and clinically diagnosed cases from mainland china (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% cri 3·56-3·80). however, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in china of 1·38% (1·23-1·53), with substantially higher ratios in older age groups (0·32% in those aged interpretation these early estimates give an indication of the fatality ratio across the spectrum of covid-19 disease and show a strong age gradient in risk of death. funding uk medical research council.",0
"the gene expression omnibus (geo) at the national center for biotechnology information (ncbi) is the largest public repository for high-throughput gene expression data. additionally, geo hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. these data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. the database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'minimum information about a microarray experiment' (miame). in addition to serving as a centralized data storage hub, geo offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. this article summarizes the geo repository structure, content and operating procedures, as well as recently introduced data mining features. geo is freely accessible at",0
"a wide variety of agents activate ampk, but in many cases the mechanisms remain unclear. we generated isogenic cell lines stably expressing ampk complexes containing amp-sensitive (wild-type, wt) or amp-insensitive (r531g) gamma2 variants. mitochondrial poisons such as oligomycin and dinitrophenol only activated ampk in wt cells, as did aicar, 2-deoxyglucose, hydrogen peroxide, metformin, phenformin, galegine, troglitazone, phenobarbital, resveratrol, and berberine. excluding aicar, all of these also inhibited cellular energy metabolism, shown by increases in adp:atp ratio and/or by decreases in cellular oxygen uptake measured using an extracellular flux analyzer. by contrast, a769662, the ca(2+) ionophore, a23187, osmotic stress, and quercetin activated both variants to varying extents. a23187 and osmotic stress also increased cytoplasmic ca(2+), and their effects were inhibited by sto609, a camkk inhibitor. our approaches distinguish at least six different mechanisms for ampk activation and confirm that the widely used antidiabetic drug metformin activates ampk by inhibiting mitochondrial respiration.",0
"we present new global maps of the köppen-geiger climate classification at an unprecedented 1-km resolution for the present-day (1980-2016) and for projected future conditions (2071-2100) under climate change. the present-day map is derived from an ensemble of four high-resolution, topographically-corrected climatic maps. the future map is derived from an ensemble of 32 climate model projections (scenario rcp8.5), by superimposing the projected climate change anomaly on the baseline high-resolution climatic maps. for both time periods we calculate confidence levels from the ensemble spread, providing valuable indications of the reliability of the classifications. the new maps exhibit a higher classification accuracy and substantially more detail than previous maps, particularly in regions with sharp spatial or elevation gradients. we anticipate the new maps will be useful for numerous applications, including species and vegetation distribution modeling. the new maps including the associated confidence maps are freely available via",0
"motivation artemis and artemis comparison tool (act) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. since its first release, artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. therefore, a new version of artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. results artemis and act have now been extended to read and write directly to the generic model organism database (gmod, chado relational database schema. in addition, a gene builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. availability artemis and act are freely available (under a gpl licence) for download (for macosx, unix and windows) at the wellcome trust sanger institute web sites:",0
"background recombinant tissue plasminogen activator (rt-pa, alteplase) improved functional outcome in patients treated soon after acute ischaemic stroke in randomised trials, but licensing is restrictive and use varies widely. the ist-3 trial adds substantial new data. we therefore assessed all the evidence from randomised trials for rt-pa in acute ischaemic stroke in an updated systematic review and meta-analysis. methods we searched for randomised trials of intravenous rt-pa versus control given within 6 h of onset of acute ischaemic stroke up to march 30, 2012. we estimated summary odds ratios (ors) and 95% ci in the primary analysis for prespecified outcomes within 7 days and at the final follow-up of all patients treated up to 6 h after stroke. findings in up to 12 trials (7012 patients), rt-pa given within 6 h of stroke significantly increased the odds of being alive and independent (modified rankin scale, mrs 0-2) at final follow-up (1611/3483 vs 1434/3404 , or 1·17, 95% ci 1·06-1·29; p=0·001), absolute increase of 42 (19-66) per 1000 people treated, and favourable outcome (mrs 0-1) absolute increase of 55 (95% ci 33-77) per 1000. the benefit of rt-pa was greatest in patients treated within 3 h (mrs 0-2, 365/896 vs 280/883 , 1·53, 1·26-1·86, p interpretation the evidence indicates that intravenous rt-pa increased the proportion of patients who were alive with favourable outcome and alive and independent at final follow-up. the data strengthen previous evidence to treat patients as early as possible after acute ischaemic stroke, although some patients might benefit up to 6 h after stroke. funding uk medical research council, stroke association, university of edinburgh, national health service health technology assessment programme, swedish heart-lung fund, afa insurances stockholm (arbetsmarknadens partners forsakringsbolag), karolinska institute, marianne and marcus wallenberg foundation, research council of norway, oslo university hospital.",0
"hhpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden markov models (hmms). it allows to search a wide choice of databases, such as the pdb, scop, pfam, smart, cogs and cdd. it accepts a single query sequence or a multiple alignment as input. within only a few minutes it returns the search results in a user-friendly format similar to that of psi-blast. search options include local or global alignment and scoring secondary structure similarity. hhpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3d structural models that are calculated by the modeller software from these alignments. a detailed help facility is available. as a demonstration, we analyze the sequence of spovt, a transcriptional regulator from bacillus subtilis. hhpred can be accessed at",0
"cytotoxic effector t cells of f1 (balb/c x balb.b) (h-2d/b) mice immunized against the minor histocompatibility differences of c57bl/10 (h-2b) can lyse targets from c57bl/10, but cannot lyse b10.d2 (h-2d) targets. despite this lack of cross-reaction in the cytotoxic assay, c57bl/10 cells do prime f1 (balb/c x balb.b) mice for a secondary cytotoxic response to b10.d2. c57bl/10-primed, b10.d2-boosted cytotoxic cells lyse b10.d2 targets but not c57bl/10 targets. dba/2 (h-2d) spleen cells or thymocytes prime f1 mice for a secondary response to dba/2, b10.d2, and c57bl/10 cells, but dba/2 mastocytes, p815, do not prime for a response to c57bl/10. whether h-2 congenic lymphoid cells express minor histocompatibility determinants which cross-react at the cytotoxic t-cell level or the helper t-cell level is discussed.",0
"several cell types have been proposed to create niches for haematopoietic stem cells (hscs). however, the expression patterns of hsc maintenance factors have not been systematically studied and no such factor has been conditionally deleted from any candidate niche cell. thus, the cellular sources of these factors are undetermined. stem cell factor (scf; also known as kitl) is a key niche component that maintains hscs. here, using scf(gfp) knock-in mice, we found that scf was primarily expressed by perivascular cells throughout the bone marrow. hsc frequency and function were not affected when scf was conditionally deleted from haematopoietic cells, osteoblasts, nestin-cre- or nestin-creer-expressing cells. however, hscs were depleted from bone marrow when scf was deleted from endothelial cells or leptin receptor (lepr)-expressing perivascular stromal cells. most hscs were lost when scf was deleted from both endothelial and lepr-expressing perivascular cells. thus, hscs reside in a perivascular niche in which multiple cell types express factors that promote hsc maintenance.",0
"the primary mission of uniprot is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. uniprot is produced by the uniprot consortium which consists of groups from the european bioinformatics institute (ebi), the swiss institute of bioinformatics (sib) and the protein information resource (pir). uniprot is comprised of four major components, each optimized for different uses: the uniprot archive, the uniprot knowledgebase, the uniprot reference clusters and the uniprot metagenomic and environmental sequence database. uniprot is updated and distributed every 3 weeks and can be accessed online for searches or download at",0
"objective to quantify the dose-response associations between total physical activity and risk of breast cancer, colon cancer, diabetes, ischemic heart disease, and ischemic stroke events. design systematic review and bayesian dose-response meta-analysis. data sources pubmed and embase from 1980 to 27 february 2016, and references from relevant systematic reviews. data from the study on global ageing and adult health conducted in china, ghana, india, mexico, russia, and south africa from 2007 to 2010 and the us national health and nutrition examination surveys from 1999 to 2011 were used to map domain specific physical activity (reported in included studies) to total activity. eligibility criteria for selecting studies prospective cohort studies examining the associations between physical activity (any domain) and at least one of the five diseases studied. results 174 articles were identified: 35 for breast cancer, 19 for colon cancer, 55 for diabetes, 43 for ischemic heart disease, and 26 for ischemic stroke (some articles included multiple outcomes). although higher levels of total physical activity were significantly associated with lower risk for all outcomes, major gains occurred at lower levels of activity (up to 3000-4000 metabolic equivalent (met) minutes/week). for example, individuals with a total activity level of 600 met minutes/week (the minimum recommended level) had a 2% lower risk of diabetes compared with those reporting no physical activity. an increase from 600 to 3600 met minutes/week reduced the risk by an additional 19%. the same amount of increase yielded much smaller returns at higher levels of activity: an increase of total activity from 9000 to 12 000 met minutes/week reduced the risk of diabetes by only 0.6%. compared with insufficiently active individuals (total activity conclusions people who achieve total physical activity levels several times higher than the current recommended minimum level have a significant reduction in the risk of the five diseases studied. more studies with detailed quantification of total physical activity will help to find more precise relative risk estimates for different levels of activity.",0
"human papillomavirus (hpv) causes cervical, vulvar, and vaginal cancers, precancerous dysplasia, and genital warts. we report data for the longest efficacy evaluation to date of a prophylactic hpv vaccine. in total, 552 women (16-23 years) were enrolled in a randomised, placebo-controlled study of a quadrivalent hpv 6/11/16/18 l1 virus-like-particle vaccine with vaccination at months 0, 2, and 6. at regular intervals through 3 years, subjects underwent gynaecologic examination, cervicovaginal sampling for hpv dna, serum anti-hpv testing, and pap testing, with follow-up biopsy as indicated. a subset of 241 subjects underwent two further years of follow-up. at 5 years post enrollment, the combined incidence of hpv 6/11/16/18-related persistent infection or disease was reduced in vaccine-recipients by 96% (two cases vaccine versus 46 placebo). there were no cases of hpv 6/11/16/18-related precancerous cervical dysplasia or genital warts in vaccine recipients, and six cases in placebo recipients (efficacy = 100%; 95% ci:12-100%). through 5 years, vaccine-induced anti-hpv geometric mean titres remained at or above those following natural infection. in conclusion, a prophylactic quadrivalent hpv vaccine was effective through 5 years for prevention of persistent infection and disease caused by hpv 6/11/16/18. this duration supports vaccination of adolescents and young adults, which is expected to greatly reduce the burden of cervical and genital cancers, precancerous dysplasia, and genital warts.",0
"determine age-specific infection fatality rates for covid-19 to inform public health policies and communications that help protect vulnerable age groups. studies of covid-19 prevalence were collected by conducting an online search of published articles, preprints, and government reports that were publicly disseminated prior to 18 september 2020. the systematic review encompassed 113 studies, of which 27 studies (covering 34 geographical locations) satisfied the inclusion criteria and were included in the meta-analysis. age-specific ifrs were computed using the prevalence data in conjunction with reported fatalities 4 weeks after the midpoint date of the study, reflecting typical lags in fatalities and reporting. meta-regression procedures in stata were used to analyze the infection fatality rate (ifr) by age. our analysis finds a exponential relationship between age and ifr for covid-19. the estimated age-specific ifr is very low for children and younger adults (e.g., 0.002% at age 10 and 0.01% at age 25) but increases progressively to 0.4% at age 55, 1.4% at age 65, 4.6% at age 75, and 15% at age 85. moreover, our results indicate that about 90% of the variation in population ifr across geographical locations reflects differences in the age composition of the population and the extent to which relatively vulnerable age groups were exposed to the virus. these results indicate that covid-19 is hazardous not only for the elderly but also for middle-aged adults, for whom the infection fatality rate is two orders of magnitude greater than the annualized risk of a fatal automobile accident and far more dangerous than seasonal influenza. moreover, the overall ifr for covid-19 should not be viewed as a fixed parameter but as intrinsically linked to the age-specific pattern of infections. consequently, public health measures to mitigate infections in older adults could substantially decrease total deaths.",0
"h. bart van der worp and colleagues discuss the controversies and possibilities of translating the results of animal experiments into human clinical trials.",0
"objectives to examine the prospective associations between consumption of sugar sweetened beverages, artificially sweetened beverages, and fruit juice with type 2 diabetes before and after adjustment for adiposity, and to estimate the population attributable fraction for type 2 diabetes from consumption of sugar sweetened beverages in the united states and united kingdom. design systematic review and meta-analysis. data sources and eligibility pubmed, embase, ovid, and web of knowledge for prospective studies of adults without diabetes, published until february 2014. the population attributable fraction was estimated in national surveys in the usa, 2009-10 (n = 4729 representing 189.1 million adults without diabetes) and the uk, 2008-12 (n = 1932 representing 44.7 million). synthesis methods random effects meta-analysis and survey analysis for population attributable fraction associated with consumption of sugar sweetened beverages. results prespecified information was extracted from 17 cohorts (38,253 cases/10,126,754 person years). higher consumption of sugar sweetened beverages was associated with a greater incidence of type 2 diabetes, by 18% per one serving/day (95% confidence interval 9% to 28%, i(2) for heterogeneity = 89%) and 13% (6% to 21%, i(2) = 79%) before and after adjustment for adiposity; for artificially sweetened beverages, 25% (18% to 33%, i(2) = 70%) and 8% (2% to 15%, i(2) = 64%); and for fruit juice, 5% (-1% to 11%, i(2) = 58%) and 7% (1% to 14%, i(2) = 51%). potential sources of heterogeneity or bias were not evident for sugar sweetened beverages. for artificially sweetened beverages, publication bias and residual confounding were indicated. for fruit juice the finding was non-significant in studies ascertaining type 2 diabetes objectively (p for heterogeneity = 0.008). under specified assumptions for population attributable fraction, of 20.9 million events of type 2 diabetes predicted to occur over 10 years in the usa (absolute event rate 11.0%), 1.8 million would be attributable to consumption of sugar sweetened beverages (population attributable fraction 8.7%, 95% confidence interval 3.9% to 12.9%); and of 2.6 million events in the uk (absolute event rate 5.8%), 79,000 would be attributable to consumption of sugar sweetened beverages (population attributable fraction 3.6%, 1.7% to 5.6%). conclusions habitual consumption of sugar sweetened beverages was associated with a greater incidence of type 2 diabetes, independently of adiposity. although artificially sweetened beverages and fruit juice also showed positive associations with incidence of type 2 diabetes, the findings were likely to involve bias. none the less, both artificially sweetened beverages and fruit juice were unlikely to be healthy alternatives to sugar sweetened beverages for the prevention of type 2 diabetes. under assumption of causality, consumption of sugar sweetened beverages over years may be related to a substantial number of cases of new onset diabetes.",0
"objectives wgs-based antimicrobial susceptibility testing (ast) is as reliable as phenotypic ast for several antimicrobial/bacterial species combinations. however, routine use of wgs-based ast is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (amr) determinants to operate the vast majority of tools developed to date. by leveraging on resfinder and pointfinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. methods the resfinder code was re-written to process raw reads and use kmer-based alignment. the existing resfinder and pointfinder databases were revised and expanded. additional databases were developed including a genotype-to-phenotype key associating each amr determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. resfinder 4.0 was validated using escherichia coli (n = 584), salmonella spp. (n = 1081), campylobacter jejuni (n = 239), enterococcus faecium (n = 106), enterococcus faecalis (n = 50) and staphylococcus aureus (n = 163) exhibiting different ast profiles, and from different human and animal sources and geographical origins. results genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for gram-negative and gram-positive bacteria, respectively. when genotype-phenotype concordance was conclusions wgs-based ast using resfinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic ast at least for the bacterial species/antimicrobial agents of major public health relevance considered.",0
"the ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. to date, high capacity, low cost genotyping has been largely achieved via ""snp chip"" microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. this method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as rad-tag or radseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current snp chip technology, while requiring similar hands-on time investment, comparable amounts of input dna, and downstream analysis times on the order of hours. finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. because of its flexibility, this modified radseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.",0
"since the 1st world symposium on pulmonary hypertension (wsph) in 1973, pulmonary hypertension (ph) has been arbitrarily defined as mean pulmonary arterial pressure (mpap) ≥25 mmhg at rest, measured by right heart catheterisation. recent data from normal subjects has shown that normal mpap was 14.0±3.3 mmhg. two standard deviations above this mean value would suggest mpap >20 mmhg as above the upper limit of normal (above the 97.5th percentile). this definition is no longer arbitrary, but based on a scientific approach. however, this abnormal elevation of mpap is not sufficient to define pulmonary vascular disease as it can be due to an increase in cardiac output or pulmonary arterial wedge pressure. thus, this 6th wsph task force proposes to include pulmonary vascular resistance ≥3 wood units in the definition of all forms of pre-capillary ph associated with mpap >20 mmhg. prospective trials are required to determine whether this ph population might benefit from specific management.regarding clinical classification, the main task force changes were the inclusion in group 1 of a subgroup ""pulmonary arterial hypertension (pah) long-term responders to calcium channel blockers"", due to the specific prognostic and management of these patients, and a subgroup ""pah with overt features of venous/capillaries (pulmonary veno-occlusive disease/pulmonary capillary haemangiomatosis) involvement"", due to evidence suggesting a continuum between arterial, capillary and vein involvement in pah.",0
"large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ml) phylogenies. fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. thus, there is need for additional approaches that employ different search strategies to find ml trees and that are at the same time as fast as currently available ml programs. we show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. if we allow the same cpu time as raxml and phyml, then our software iq-tree found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. if we use the iq-tree stopping rule, raxml and phyml are faster in 75.7% and 47.1% of the dna alignments and 42.2% and 100% of the protein alignments, respectively. however, the range of obtaining higher likelihoods with iq-tree improves to 73.3-97.1%. iq-tree is freely available at",0
"the endoplasmic reticulum (er) is the main site of protein and lipid synthesis, membrane biogenesis, xenobiotic detoxification and cellular calcium storage, and perturbation of er homeostasis leads to stress and the activation of the unfolded protein response. chronic activation of er stress has been shown to have an important role in the development of insulin resistance and diabetes in obesity. however, the mechanisms that lead to chronic er stress in a metabolic context in general, and in obesity in particular, are not understood. here we comparatively examined the proteomic and lipidomic landscape of hepatic er purified from lean and obese mice to explore the mechanisms of chronic er stress in obesity. we found suppression of protein but stimulation of lipid synthesis in the obese er without significant alterations in chaperone content. alterations in er fatty acid and lipid composition result in the inhibition of sarco/endoplasmic reticulum calcium atpase (serca) activity and er stress. correcting the obesity-induced alteration of er phospholipid composition or hepatic serca overexpression in vivo both reduced chronic er stress and improved glucose homeostasis. hence, we established that abnormal lipid and calcium metabolism are important contributors to hepatic er stress in obesity.",0
"psychopy is a software library written in python, using opengl to generate very precise visual stimuli on standard personal computers. it is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. by writing scripts in standard python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fmri, eeg, meg etc.). the structure of scripts is simple and intuitive. as a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. psychopy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. this paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.",0
"tumours with mutant braf are dependent on the raf-mek-erk signalling pathway for their growth. we found that atp-competitive raf inhibitors inhibit erk signalling in cells with mutant braf, but unexpectedly enhance signalling in cells with wild-type braf. here we demonstrate the mechanistic basis for these findings. we used chemical genetic methods to show that drug-mediated transactivation of raf dimers is responsible for paradoxical activation of the enzyme by inhibitors. induction of erk signalling requires direct binding of the drug to the atp-binding site of one kinase of the dimer and is dependent on ras activity. drug binding to one member of raf homodimers (craf-craf) or heterodimers (craf-braf) inhibits one protomer, but results in transactivation of the drug-free protomer. in braf(v600e) tumours, ras is not activated, thus transactivation is minimal and erk signalling is inhibited in cells exposed to raf inhibitors. these results indicate that raf inhibitors will be effective in tumours in which braf is mutated. furthermore, because raf inhibitors do not inhibit erk signalling in other cells, the model predicts that they would have a higher therapeutic index and greater antitumour activity than mitogen-activated protein kinase (mek) inhibitors, but could also cause toxicity due to mek/erk activation. these predictions have been borne out in a recent clinical trial of the raf inhibitor plx4032 (refs 4, 5). the model indicates that promotion of raf dimerization by elevation of wild-type raf expression or ras activity could lead to drug resistance in mutant braf tumours. in agreement with this prediction, raf inhibitors do not inhibit erk signalling in cells that coexpress braf(v600e) and mutant ras.",0
"infodemiology can be defined as the science of distribution and determinants of information in an electronic medium, specifically the internet, or in a population, with the ultimate aim to inform public health and public policy. infodemiology data can be collected and analyzed in near real time. examples for infodemiology applications include the analysis of queries from internet search engines to predict disease outbreaks (eg. influenza), monitoring peoples' status updates on microblogs such as twitter for syndromic surveillance, detecting and quantifying disparities in health information availability, identifying and monitoring of public health relevant publications on the internet (eg. anti-vaccination sites, but also news articles or expert-curated outbreak reports), automated tools to measure information diffusion and knowledge translation, and tracking the effectiveness of health marketing campaigns. moreover, analyzing how people search and navigate the internet for health-related information, as well as how they communicate and share this information, can provide valuable insights into health-related behavior of populations. seven years after the infodemiology concept was first introduced, this paper revisits the emerging fields of infodemiology and infoveillance and proposes an expanded framework, introducing some basic metrics such as information prevalence, concept occurrence ratios, and information incidence. the framework distinguishes supply-based applications (analyzing what is being published on the internet, eg. on web sites, newsgroups, blogs, microblogs and social media) from demand-based methods (search and navigation behavior), and further distinguishes passive from active infoveillance methods. infodemiology metrics follow population health relevant events or predict them. thus, these metrics and methods are potentially useful for public health practice and research, and should be further developed and standardized.",0
"the ability to detect single protein molecules in blood could accelerate the discovery and use of more sensitive diagnostic biomarkers. to detect low-abundance proteins in blood, we captured them on microscopic beads decorated with specific antibodies and then labeled the immunocomplexes (one or zero labeled target protein molecules per bead) with an enzymatic reporter capable of generating a fluorescent product. after isolating the beads in 50-fl reaction chambers designed to hold only a single bead, we used fluorescence imaging to detect single protein molecules. our single-molecule enzyme-linked immunosorbent assay (digital elisa) approach detected as few as approximately 10-20 enzyme-labeled complexes in 100 microl of sample (approximately 10(-19) m) and routinely allowed detection of clinically relevant proteins in serum at concentrations (<10(-15) m) much lower than conventional elisa. digital elisa detected prostate-specific antigen (psa) in sera from patients who had undergone radical prostatectomy at concentrations as low as 14 fg/ml (0.4 fm).",0
"purpose the efficacy of neoadjuvant chemoradiotherapy (ncrt) plus surgery for locally advanced esophageal squamous cell carcinoma (escc) remains controversial. in this trial, we compared the survival and safety of ncrt plus surgery with surgery alone in patients with locally advanced escc. patients and methods from june 2007 to december 2014, 451 patients with potentially resectable thoracic escc, clinically staged as t1-4n1m0/t4n0m0, were randomly allocated to ncrt plus surgery (group crt; n = 224) and surgery alone (group s; n = 227). in group crt, patients received vinorelbine 25 mg/m 2 intravenously (iv) on days 1 and 8 and cisplatin 75 mg/m 2 iv day 1, or 25 mg/m 2 iv on days 1 to 4 every 3 weeks for two cycles, with a total concurrent radiation dose of 40.0 gy administered in 20 fractions of 2.0 gy on 5 days per week. in both groups, patients underwent mckeown or ivor lewis esophagectomy. the primary end point was overall survival. results the pathologic complete response rate was 43.2% in group crt. compared with group s, group crt had a higher r0 resection rate (98.4% v 91.2%; p = .002), a better median overall survival (100.1 months v 66.5 months; hazard ratio, 0.71; 95% ci, 0.53 to 0.96; p = .025), and a prolonged disease-free survival (100.1 months v 41.7 months; hazard ratio, 0.58; 95% ci, 0.43 to 0.78; p < .001). leukopenia (48.9%) and neutropenia (45.7%) were the most common grade 3 or 4 adverse events during chemoradiotherapy. incidences of postoperative complications were similar between groups, with the exception of arrhythmia (group crt: 13% v group s: 4.0%; p = .001). peritreatment mortality was 2.2% in group crt versus 0.4% in group s ( p = .212). conclusion this trial shows that ncrt plus surgery improves survival over surgery alone among patients with locally advanced escc, with acceptable and manageable adverse events.",0
"objective to characterise the clinical features of patients admitted to hospital with coronavirus disease 2019 (covid-19) in the united kingdom during the growth phase of the first wave of this outbreak who were enrolled in the international severe acute respiratory and emerging infections consortium (isaric) world health organization (who) clinical characterisation protocol uk (ccp-uk) study, and to explore risk factors associated with mortality in hospital. design prospective observational cohort study with rapid data gathering and near real time analysis. setting 208 acute care hospitals in england, wales, and scotland between 6 february and 19 april 2020. a case report form developed by isaric and who was used to collect clinical data. a minimal follow-up time of two weeks (to 3 may 2020) allowed most patients to complete their hospital admission. participants 20 133 hospital inpatients with covid-19. main outcome measures admission to critical care (high dependency unit or intensive care unit) and mortality in hospital. results the median age of patients admitted to hospital with covid-19, or with a diagnosis of covid-19 made in hospital, was 73 years (interquartile range 58-82, range 0-104). more men were admitted than women (men 60%, n=12 068; women 40%, n=8065). the median duration of symptoms before admission was 4 days (interquartile range 1-8). the commonest comorbidities were chronic cardiac disease (31%, 5469/17 702), uncomplicated diabetes (21%, 3650/17 599), non-asthmatic chronic pulmonary disease (18%, 3128/17 634), and chronic kidney disease (16%, 2830/17 506); 23% (4161/18 525) had no reported major comorbidity. overall, 41% (8199/20 133) of patients were discharged alive, 26% (5165/20 133) died, and 34% (6769/20 133) continued to receive care at the reporting date. 17% (3001/18 183) required admission to high dependency or intensive care units; of these, 28% (826/3001) were discharged alive, 32% (958/3001) died, and 41% (1217/3001) continued to receive care at the reporting date. of those receiving mechanical ventilation, 17% (276/1658) were discharged alive, 37% (618/1658) died, and 46% (764/1658) remained in hospital. increasing age, male sex, and comorbidities including chronic cardiac disease, non-asthmatic chronic pulmonary disease, chronic kidney disease, liver disease and obesity were associated with higher mortality in hospital. conclusions isaric who ccp-uk is a large prospective cohort study of patients in hospital with covid-19. the study continues to enrol at the time of this report. in study participants, mortality was high, independent risk factors were increasing age, male sex, and chronic comorbidity, including obesity. this study has shown the importance of pandemic preparedness and the need to maintain readiness to launch research studies in response to outbreaks. study registration isrctn66726260.",0
"background severe coronavirus disease 2019 (covid-19) is associated with dysregulated inflammation. the effects of combination treatment with baricitinib, a janus kinase inhibitor, plus remdesivir are not known. methods we conducted a double-blind, randomized, placebo-controlled trial evaluating baricitinib plus remdesivir in hospitalized adults with covid-19. all the patients received remdesivir (≤10 days) and either baricitinib (≤14 days) or placebo (control). the primary outcome was the time to recovery. the key secondary outcome was clinical status at day 15. results a total of 1033 patients underwent randomization (with 515 assigned to combination treatment and 518 to control). patients receiving baricitinib had a median time to recovery of 7 days (95% confidence interval , 6 to 8), as compared with 8 days (95% ci, 7 to 9) with control (rate ratio for recovery, 1.16; 95% ci, 1.01 to 1.32; p = 0.03), and a 30% higher odds of improvement in clinical status at day 15 (odds ratio, 1.3; 95% ci, 1.0 to 1.6). patients receiving high-flow oxygen or noninvasive ventilation at enrollment had a time to recovery of 10 days with combination treatment and 18 days with control (rate ratio for recovery, 1.51; 95% ci, 1.10 to 2.08). the 28-day mortality was 5.1% in the combination group and 7.8% in the control group (hazard ratio for death, 0.65; 95% ci, 0.39 to 1.09). serious adverse events were less frequent in the combination group than in the control group (16.0% vs. 21.0%; difference, -5.0 percentage points; 95% ci, -9.8 to -0.3; p = 0.03), as were new infections (5.9% vs. 11.2%; difference, -5.3 percentage points; 95% ci, -8.7 to -1.9; p = 0.003). conclusions baricitinib plus remdesivir was superior to remdesivir alone in reducing recovery time and accelerating improvement in clinical status among patients with covid-19, notably among those receiving high-flow oxygen or noninvasive ventilation. the combination was associated with fewer serious adverse events. (funded by the national institute of allergy and infectious diseases; clinicaltrials.gov number, nct04401579.).",0
"background prescription opioid-related overdose deaths increased sharply during 1999-2010 in the united states in parallel with increased opioid prescribing. cdc assessed changes in national-level and county-level opioid prescribing during 2006-2015. methods cdc analyzed retail prescription data from quintilesims to assess opioid prescribing in the united states from 2006 to 2015, including rates, amounts, dosages, and durations prescribed. cdc examined county-level prescribing patterns in 2010 and 2015. results the amount of opioids prescribed in the united states peaked at 782 morphine milligram equivalents (mme) per capita in 2010 and then decreased to 640 mme per capita in 2015. despite significant decreases, the amount of opioids prescribed in 2015 remained approximately three times as high as in 1999 and varied substantially across the country. county-level factors associated with higher amounts of prescribed opioids include a larger percentage of non-hispanic whites; a higher prevalence of diabetes and arthritis; micropolitan status (i.e., town/city; nonmetro); and higher unemployment and medicaid enrollment. conclusions and implications for public health practice despite reductions in opioid prescribing in some parts of the country, the amount of opioids prescribed remains high relative to 1999 levels and varies substantially at the county-level. given associations between opioid prescribing, opioid use disorder, and overdose rates, health care providers should carefully weigh the benefits and risks when prescribing opioids outside of end-of-life care, follow evidence-based guidelines, such as cdc's guideline for prescribing opioids for chronic pain, and consider nonopioid therapy for chronic pain treatment. state and local jurisdictions can use these findings combined with prescription drug monitoring program data to identify areas with prescribing patterns that place patients at risk for opioid use disorder and overdose and to target interventions with prescribers based on opioid prescribing guidelines.",0
"background the global burden of diseases, injuries, and risk factors study (gbd) 2017 comparative risk assessment (cra) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. with each annual gbd study, we update the gbd cra to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk-outcome associations. methods we used the cra framework developed for previous iterations of gbd to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (dalys), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. this study included 476 risk-outcome pairs that met the gbd study criteria for convincing or probable evidence of causation. we extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. we used statistical models to pool data, adjust for bias, and incorporate covariates. using the counterfactual scenario of theoretical minimum risk exposure level (tmrel), we estimated the portion of deaths and dalys that could be attributed to a given risk. we explored the relationship between development and risk exposure by modelling the relationship between the socio-demographic index (sdi) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by sdi. finally, we explored temporal changes in risk-attributable dalys by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and daly rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the tmrel for all risk factors included in gbd 2017. findings in 2017, 34·1 million (95% uncertainty interval 33·3-35·0) deaths and 1·21 billion (1·14-1·28) dalys were attributable to gbd risk factors. globally, 61·0% (59·6-62·4) of deaths and 48·3% (46·3-50·2) of dalys were attributed to the gbd 2017 risk factors. when ranked by risk-attributable dalys, high systolic blood pressure (sbp) was the leading risk factor, accounting for 10·4 million (9·39-11·5) deaths and 218 million (198-237) dalys, followed by smoking (7·10 million deaths and 182 million dalys), high fasting plasma glucose (6·53 million deaths and 171 million dalys), high body-mass index (bmi; 4·72 million deaths and 148 million dalys), and short gestation for birthweight (1·43 million deaths and 139 million dalys). in total, risk-attributable dalys declined by 4·9% (3·3-6·5) between 2007 and 2017. in the absence of demographic changes (ie, population growth and ageing), changes in risk exposure and risk-deleted dalys would have led to a 23·5% decline in dalys during that period. conversely, in the absence of changes in risk exposure and risk-deleted dalys, demographic changes would have led to an 18·6% increase in dalys during that period. the ratios of observed risk exposure levels to exposure levels expected based on sdi (o/e ratios) increased globally for unsafe drinking water and household air pollution between 1990 and 2017. this result suggests that development is occurring more rapidly than are changes in the underlying risk structure in a population. conversely, nearly universal declines in o/e ratios for smoking and alcohol use indicate that, for a given sdi, exposure to these risks is declining. in 2017, the leading level 4 risk factor for age-standardised daly rates was high sbp in four super-regions: central europe, eastern europe, and central asia; north africa and middle east; south asia; and southeast asia, east asia, and oceania. the leading risk factor in the high-income super-region was smoking, in latin america and caribbean was high bmi, and in sub-saharan africa was unsafe sex. o/e ratios for unsafe sex in sub-saharan africa were notably high, and those for alcohol use in north africa and the middle east were notably low. interpretation by quantifying levels and trends in exposures to risk factors and the resulting disease burden, this assessment offers insight into where past policy and programme efforts might have been successful and highlights current priorities for public health action. decreases in behavioural, environmental, and occupational risks have largely offset the effects of population growth and ageing, in relation to trends in absolute burden. conversely, the combination of increasing metabolic risks and population ageing will probably continue to drive the increasing trends in non-communicable diseases at the global level, which presents both a public health challenge and opportunity. we see considerable spatiotemporal heterogeneity in levels of risk exposure and risk-attributable burden. although levels of development underlie some of this heterogeneity, o/e ratios show risks for which countries are overperforming or underperforming relative to their level of development. as such, these ratios provide a benchmarking tool to help to focus local decision making. our findings reinforce the importance of both risk exposure monitoring and epidemiological research to assess causal connections between risks and health outcomes, and they highlight the usefulness of the gbd study in synthesising data to draw comprehensive and robust conclusions that help to inform good policy and strategic health planning. funding bill & melinda gates foundation.",0
"background since early december 2019, the 2019 novel coronavirus disease (covid-19) has caused pneumonia epidemic in wuhan, hubei province of china. this study aimed to investigate the factors affecting the progression of pneumonia in covid-19 patients. associated results will be used to evaluate the prognosis and to find the optimal treatment regimens for covid-19 pneumonia. methods patients tested positive for the covid-19 based on nucleic acid detection were included in this study. patients were admitted to 3 tertiary hospitals in wuhan between december 30, 2019, and january 15, 2020. individual data, laboratory indices, imaging characteristics, and clinical data were collected, and statistical analysis was performed. based on clinical typing results, the patients were divided into a progression group or an improvement/stabilization group. continuous variables were analyzed using independent samples t-test or mann-whitney u test. categorical variables were analyzed using chi-squared test or fisher's exact test. logistic regression analysis was performed to explore the risk factors for disease progression. results seventy-eight patients with covid-19-induced pneumonia met the inclusion criteria and were included in this study. efficacy evaluation at 2 weeks after hospitalization indicated that 11 patients (14.1%) had deteriorated, and 67 patients (85.9%) had improved/stabilized. the patients in the progression group were significantly older than those in the disease improvement/stabilization group (66 vs. 37 years, u = 4.932, p = 0.001). the progression group had a significantly higher proportion of patients with a history of smoking than the improvement/stabilization group (27.3% vs. 3.0%, χ = 9.291, p = 0.018). for all the 78 patients, fever was the most common initial symptom, and the maximum body temperature at admission was significantly higher in the progression group than in the improvement/stabilization group (38.2 vs. 37.5 °c, u = 2.057, p = 0.027). moreover, the proportion of patients with respiratory failure (54.5% vs. 20.9%, χ = 5.611, p = 0.028) and respiratory rate (34 vs. 24 breaths/min, u = 4.030, p = 0.004) were significantly higher in the progression group than in the improvement/stabilization group. c-reactive protein was significantly elevated in the progression group compared to the improvement/stabilization group (38.9 vs. 10.6 mg/l, u = 1.315, p = 0.024). albumin was significantly lower in the progression group than in the improvement/stabilization group (36.62 ± 6.60 vs. 41.27 ± 4.55 g/l, u = 2.843, p = 0.006). patients in the progression group were more likely to receive high-level respiratory support than in the improvement/stabilization group (χ = 16.01, p = 0.001). multivariate logistic analysis indicated that age (odds ratio , 8.546; 95% confidence interval : 1.628-44.864; p = 0.011), history of smoking (or, 14.285; 95% ci: 1.577-25.000; p = 0.018), maximum body temperature at admission (or, 8.999; 95% ci: 1.036-78.147, p = 0.046), respiratory failure (or, 8.772, 95% ci: 1.942-40.000; p = 0.016), albumin (or, 7.353, 95% ci: 1.098-50.000; p = 0.003), and c-reactive protein (or, 10.530; 95% ci: 1.224-34.701, p = 0.028) were risk factors for disease progression. conclusions several factors that led to the progression of covid-19 pneumonia were identified, including age, history of smoking, maximum body temperature at admission, respiratory failure, albumin, and c-reactive protein. these results can be used to further enhance the ability of management of covid-19 pneumonia.",0
"we report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. this model allows us to generate new molecules for efficient exploration and optimization through open-ended spaces of chemical compounds. a deep neural network was trained on hundreds of thousands of existing chemical structures to construct three coupled functions: an encoder, a decoder, and a predictor. the encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to discrete molecular representations. the predictor estimates chemical properties from the latent continuous vector representation of the molecule. continuous representations of molecules allow us to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. continuous representations also allow the use of powerful gradient-based optimization to efficiently guide the search for optimized functional compounds. we demonstrate our method in the domain of drug-like molecules and also in a set of molecules with fewer that nine heavy atoms.",0
"background patients with critical illness due to infection with the 2019 coronavirus disease (covid-19) show rapid disease progression to acute respiratory failure. the study aimed to screen the most useful predictive factor for critical illness caused by covid-19. methods the study prospectively involved 61 patients with covid-19 infection as a derivation cohort, and 54 patients as a validation cohort. the predictive factor for critical illness was selected using lasso regression analysis. a nomogram based on non-specific laboratory indicators was built to predict the probability of critical illness. results the neutrophil-to-lymphocyte ratio (nlr) was identified as an independent risk factor for critical illness in patients with covid-19 infection. the nlr had an area under receiver operating characteristic of 0.849 (95% confidence interval , 0.707 to 0.991) in the derivation cohort and 0.867 (95% ci 0.747 to 0.944) in the validation cohort, the calibration curves fitted well, and the decision and clinical impact curves showed that the nlr had high standardized net benefit. in addition, the incidence of critical illness was 9.1% (1/11) for patients aged ≥ 50 and having an nlr conclusions we found that nlr is a predictive factor for early-stage prediction of patients infected with covid-19 who are likely to develop critical illness. patients aged ≥ 50 and having an nlr ≥ 3.13 are predicted to develop critical illness, and they should thus have rapid access to an intensive care unit if necessary.",0
"oestrogen receptor-α (er) is the defining and driving transcription factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic understanding of er function has been restricted to model systems. here we map genome-wide er-binding events, by chromatin immunoprecipitation followed by high-throughput sequencing (chip-seq), in primary breast cancers from patients with different clinical outcomes and in distant er-positive metastases. we find that drug-resistant cancers still recruit er to the chromatin, but that er binding is a dynamic process, with the acquisition of unique er-binding regions in tumours from patients that are likely to relapse. the acquired er regulatory regions associated with poor clinical outcome observed in primary tumours reveal gene signatures that predict clinical outcome in er-positive disease exclusively. we find that the differential er-binding programme observed in tumours from patients with poor outcome is not due to the selection of a rare subpopulation of cells, but is due to the foxa1-mediated reprogramming of er binding on a rapid timescale. the parallel redistribution of er and foxa1 binding events in drug-resistant cellular contexts is supported by histological co-expression of er and foxa1 in metastatic samples. by establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in er-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes.",0
"illness and death from diseases caused by contaminated food are a constant threat to public health and a significant impediment to socio-economic development worldwide. to measure the global and regional burden of foodborne disease (fbd), the world health organization (who) established the foodborne disease burden epidemiology reference group (ferg), which here reports their first estimates of the incidence, mortality, and disease burden due to 31 foodborne hazards. we find that the global burden of fbd is comparable to those of the major infectious diseases, hiv/aids, malaria and tuberculosis. the most frequent causes of foodborne illness were diarrheal disease agents, particularly norovirus and campylobacter spp. diarrheal disease agents, especially non-typhoidal salmonella enterica, were also responsible for the majority of deaths due to fbd. other major causes of fbd deaths were salmonella typhi, taenia solium and hepatitis a virus. the global burden of fbd caused by the 31 hazards in 2010 was 33 million disability adjusted life years (dalys); children under five years old bore 40% of this burden. the 14 subregions, defined on the basis of child and adult mortality, had considerably different burdens of fbd, with the greatest falling on the subregions in africa, followed by the subregions in south-east asia and the eastern mediterranean d subregion. some hazards, such as non-typhoidal s. enterica, were important causes of fbd in all regions of the world, whereas others, such as certain parasitic helminths, were highly localised. thus, the burden of fbd is borne particularly by children under five years old-although they represent only 9% of the global population-and people living in low-income regions of the world. these estimates are conservative, i.e., underestimates rather than overestimates; further studies are needed to address the data gaps and limitations of the study. nevertheless, all stakeholders can contribute to improvements in food safety throughout the food chain by incorporating these estimates into policy development at national and international levels.",0
"objectives to develop and validate updated qrisk3 prediction algorithms to estimate the 10 year risk of cardiovascular disease in women and men accounting for potential new risk factors. design prospective open cohort study. setting general practices in england providing data for the qresearch database. participants 1309 qresearch general practices in england: 981 practices were used to develop the scores and a separate set of 328 practices were used to validate the scores. 7.89 million patients aged 25-84 years were in the derivation cohort and 2.67 million patients in the validation cohort. patients were free of cardiovascular disease and not prescribed statins at baseline. methods cox proportional hazards models in the derivation cohort to derive separate risk equations in men and women for evaluation at 10 years. risk factors considered included those already in qrisk2 (age, ethnicity, deprivation, systolic blood pressure, body mass index, total cholesterol: high density lipoprotein cholesterol ratio, smoking, family history of coronary heart disease in a first degree relative aged less than 60 years, type 1 diabetes, type 2 diabetes, treated hypertension, rheumatoid arthritis, atrial fibrillation, chronic kidney disease (stage 4 or 5)) and new risk factors (chronic kidney disease (stage 3, 4, or 5), a measure of systolic blood pressure variability (standard deviation of repeated measures), migraine, corticosteroids, systemic lupus erythematosus (sle), atypical antipsychotics, severe mental illness, and hiv/aids). we also considered erectile dysfunction diagnosis or treatment in men. measures of calibration and discrimination were determined in the validation cohort for men and women separately and for individual subgroups by age group, ethnicity, and baseline disease status. main outcome measures incident cardiovascular disease recorded on any of the following three linked data sources: general practice, mortality, or hospital admission records. results 363 565 incident cases of cardiovascular disease were identified in the derivation cohort during follow-up arising from 50.8 million person years of observation. all new risk factors considered met the model inclusion criteria except for hiv/aids, which was not statistically significant. the models had good calibration and high levels of explained variation and discrimination. in women, the algorithm explained 59.6% of the variation in time to diagnosis of cardiovascular disease (r 2 , with higher values indicating more variation), and the d statistic was 2.48 and harrell's c statistic was 0.88 (both measures of discrimination, with higher values indicating better discrimination). the corresponding values for men were 54.8%, 2.26, and 0.86. overall performance of the updated qrisk3 algorithms was similar to the qrisk2 algorithms. conclusion updated qrisk3 risk prediction models were developed and validated. the inclusion of additional clinical variables in qrisk3 (chronic kidney disease, a measure of systolic blood pressure variability (standard deviation of repeated measures), migraine, corticosteroids, sle, atypical antipsychotics, severe mental illness, and erectile dysfunction) can help enable doctors to identify those at most risk of heart disease and stroke.",0
"background the impact of coronavirus disease (covid-19) and the governmental restrictions on mental health have been reported for different countries. this study evaluated mental health during covid-19 lockdown in austria and the effect of age, gender, income, work, and physical activity. methods an online survey was performed through qualtrics® after four weeks of lockdown in austria to recruit a representative sample regarding gender, age, education, and region. indicators of mental health were quality of life (who-qol bref), well-being (who-5), depression (phq-9), anxiety (gad-7), stress (pss-10), and sleep quality (isi). results in total, n = 1005 individuals were included (53% women). 21% scored above the cut off ≥10 points (phq-9) for moderate depressive symptoms, 119% scored above the cut-off ≥10 points (gad-7) for moderate anxiety symptoms, and 16% above the cut-off ≥15 points (isi) for clinical insomnia. anovas, bonferroni-corrected post-hoc tests, and t-tests showed highest mental health problems in adults under 35 years, women, people with no work, and low income (all p-values conclusions depressive symptoms (21%) and anxiety symptoms (19%) are higher during covid-19 compared to previous epidemiological data. 16% rated over the cut-off for moderate or severe clinical insomnia. the covid-19 pandemic and lockdown seems particularly stressful for younger adults (<35 years), women, people without work, and low income.",0
"the human metabolome database (hmdb, is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. since its first release in 2007, the hmdb has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. the most recent release of hmdb (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). in particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). similarly, the number of purified compounds with reference to nmr, lc-ms and gc-ms spectra has more than doubled (from 380 to more than 790 compounds). in addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. these include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. these improvements should make the hmdb much more useful to a much wider community of users.",0
"background faced with the coronavirus disease 2019 (covid-19) pandemic, the development of covid-19 vaccines has been progressing at an unprecedented rate. this study aimed to evaluate the acceptance of covid-19 vaccination in china and give suggestions for vaccination strategies and immunization programs accordingly. methods in march 2020, an anonymous cross-sectional survey was conducted online among chinese adults. the questionnaire collected socio-demographic characteristics, risk perception, the impact of covid-19, attitudes, acceptance and attribute preferences of vaccines against covid-19 during the pandemic. multivariate logistic regression was performed to identify the influencing factors of vaccination acceptance. results of the 2058 participants surveyed, 1879 (91.3%) stated that they would accept covid-19 vaccination after the vaccine becomes available, among whom 980 (52.2%) wanted to get vaccinated as soon as possible, while others (47.8%) would delay the vaccination until the vaccine's safety was confirmed. participants preferred a routine immunization schedule (49.4%) to emergency vaccination (9.0%) or either of them (41.6%). logistic regression showed that being male, being married, perceiving a high risk of infection, being vaccinated against influenza in the past season, believing in the efficacy of covid-19 vaccination or valuing doctor's recommendations could increase the probability of accepting covid-19 vaccination as soon as possible, while having confirmed or suspected cases in local areas, valuing vaccination convenience or vaccine price in decision-making could hinder participants from immediate vaccination. conclusion during the pandemic period, a strong demand for and high acceptance of covid-19 vaccination has been shown among the chinese population, while concerns about vaccine safety may hinder the promotion of vaccine uptake. to expand vaccination coverage, immunization programs should be designed to remove barriers in terms of vaccine price and vaccination convenience, and health education and communication from authoritative sources are important ways to alleviate public concerns about vaccine safety.",0
"rat small intestinal epithelial cell lines have been established in vitro and subcultured serially for periods up to 6 mo. these cells have an epithelioid morphology, grow as monolayers of closely opposed polygonal cells, and during the logarithmic phase of growth have a population doubling time of 19--22 h. ultrastructural studies revealed the presence of microvilli, tight junctions, an extensive golgi complex, and the presence of extracellular amorphous material similar in appearance to isolated basement membrane. these cells exhibit a number of features characteristic of normal cells in culture; namely, a normal rat diploid karyotype, strong density inhibition of growth, lack of growth in soft agar, and a low plating efficiency when seeded at low density. they did not produce tumors when injected in syngeneic animals. immunochemical studies were performed to determine their origin using antisera prepared against rat small intestinal crypt cell plasma membrane, brush border membrane of villus cells and isolated sucrase-isomaltase complex. antigenic determinants specific for small intestinal epithelial (crypt and villus) cells were demonstrated on the surface of the epithelioid cells, but they lacked immunological determinants specific for differentiated villus cells. an antiserum specifically staining extracellular material surrounding the cells cultured in vitro demonstrated cross-reactivity to basement membrane in rat intestinal frozen sections. it is concluded that the cultured epithelioid cells have features of undifferentiated small intestinal crypt cells.",0
"background anxiety and depression symptoms in pregnancy typically affect between 10 and 25% of pregnant individuals. elevated symptoms of depression and anxiety are associated with increased risk of preterm birth, postpartum depression, and behavioural difficulties in children. the current covid-19 pandemic is a unique stressor with potentially wide-ranging consequences for pregnancy and beyond. methods we assessed symptoms of anxiety and depression among pregnant individuals during the current covid-19 pandemic and determined factors that were associated with psychological distress. 1987 pregnant participants in canada were surveyed in april 2020. the assessment included questions about covid-19-related stress and standardized measures of depression, anxiety, pregnancy-related anxiety, and social support. results we found substantially elevated anxiety and depression symptoms compared to similar pre-pandemic pregnancy cohorts, with 37% reporting clinically relevant symptoms of depression and 57% reporting clinically relevant symptoms of anxiety. higher symptoms of depression and anxiety were associated with more concern about threats of covid-19 to the life of the mother and baby, as well as concerns about not getting the necessary prenatal care, relationship strain, and social isolation due to the covid-19 pandemic. higher levels of perceived social support and support effectiveness, as well as more physical activity, were associated with lower psychological symptoms. conclusion this study shows concerningly elevated symptoms of anxiety and depression among pregnant individuals during the covid-19 pandemic, that may have long-term impacts on their children. potential protective factors include increased social support and exercise, as these were associated with lower symptoms and thus may help mitigate long-term negative outcomes.",0
"severe acute respiratory syndrome coronavirus 2 is the causative agent of the ongoing coronavirus disease pandemic. initial estimates of the early dynamics of the outbreak in wuhan, china, suggested a doubling time of the number of infected persons of 6-7 days and a basic reproductive number (r 0 ) of 2.2-2.7. we collected extensive individual case reports across china and estimated key epidemiologic parameters, including the incubation period (4.2 days). we then designed 2 mathematical modeling approaches to infer the outbreak dynamics in wuhan by using high-resolution domestic travel and infection data. results show that the doubling time early in the epidemic in wuhan was 2.3-3.3 days. assuming a serial interval of 6-9 days, we calculated a median r 0 value of 5.7 (95% ci 3.8-8.9). we further show that active surveillance, contact tracing, quarantine, and early strong social distancing efforts are needed to stop transmission of the virus.",0
"numerous studies over several decades suggest that following the mediterranean diet (meddiet) can reduce the risk of cardiovascular disease and cancer, and improve cognitive health. however, there are inconsistencies among methods used for evaluating and defining the meddiet. through a review of the literature, we aimed to quantitatively define the meddiet by food groups and nutrients. databases pubmed, medline, science direct, academic search premier and the university of south australia library catalogue were searched. articles were included if they defined the meddiet in at least two of the following ways: (1) general descriptive definitions; (2) diet pyramids/numbers of servings of key foods; (3) grams of key foods/food groups; and (4) nutrient and flavonoid content. quantity of key foods and nutrient content was recorded and the mean was calculated. the meddiet contained three to nine serves of vegetables, half to two serves of fruit, one to 13 serves of cereals and up to eight serves of olive oil daily. it contained approximately 9300 kj, 37% as total fat, 18% as monounsaturated and 9% as saturated, and 33 g of fibre per day. our results provide a defined nutrient content and range of servings for the meddiet based on past and current literature. more detailed reporting amongst studies could refine the definition further.",0
"background existing who estimates of the prevalence of mental disorders in emergency settings are more than a decade old and do not reflect modern methods to gather existing data and derive estimates. we sought to update who estimates for the prevalence of mental disorders in conflict-affected settings and calculate the burden per 1000 population. methods in this systematic review and meta-analysis, we updated a previous systematic review by searching medline (pubmed), psycinfo, and embase for studies published between jan 1, 2000, and aug 9, 2017, on the prevalence of depression, anxiety disorder, post-traumatic stress disorder, bipolar disorder, and schizophrenia. we also searched the grey literature, such as government reports, conference proceedings, and dissertations, to source additional data, and we searched datasets from existing literature reviews of the global prevalence of depression and anxiety and reference lists from the studies that were identified. we applied the guidelines for accurate and transparent health estimates reporting and used bayesian meta-regression techniques that adjust for predictors of mental disorders to calculate new point prevalence estimates with 95% uncertainty intervals (uis) in settings that had experienced conflict less than 10 years previously. findings we estimated that the prevalence of mental disorders (depression, anxiety, post-traumatic stress disorder, bipolar disorder, and schizophrenia) was 22·1% (95% ui 18·8-25·7) at any point in time in the conflict-affected populations assessed. the mean comorbidity-adjusted, age-standardised point prevalence was 13·0% (95% ui 10·3-16·2) for mild forms of depression, anxiety, and post-traumatic stress disorder and 4·0% (95% ui 2·9-5·5) for moderate forms. the mean comorbidity-adjusted, age-standardised point prevalence for severe disorders (schizophrenia, bipolar disorder, severe depression, severe anxiety, and severe post-traumatic stress disorder) was 5·1% (95% ui 4·0-6·5). as only two studies provided epidemiological data for psychosis in conflict-affected populations, existing global burden of disease study estimates for schizophrenia and bipolar disorder were applied in these estimates for conflict-affected populations. interpretation the burden of mental disorders is high in conflict-affected populations. given the large numbers of people in need and the humanitarian imperative to reduce suffering, there is an urgent need to implement scalable mental health interventions to address this burden. funding who; queensland department of health, australia; and bill & melinda gates foundation.",0
"preceding the joint meeting of the 19th annual diabetic neuropathy study group of the european association for the study of diabetes (neurodiab) and the 8th international symposium on diabetic neuropathy in toronto, canada, 13-18 october 2009, expert panels were convened to provide updates on classification, definitions, diagnostic criteria, and treatments of diabetic peripheral neuropathies (dpns), autonomic neuropathy, painful dpns, and structural alterations in dpns.",0
"background low haemoglobin concentrations and anaemia are important risk factors for the health and development of women and children. we estimated trends in the distributions of haemoglobin concentration and in the prevalence of anaemia and severe anaemia in young children and pregnant and non-pregnant women between 1995 and 2011. methods we obtained data about haemoglobin and anaemia for children aged 6-59 months and women of childbearing age (15-49 years) from 257 population-representative data sources from 107 countries worldwide. we used health, nutrition, and household surveys; summary statistics from who's vitamin and mineral nutrition information system; and summary statistics reported by other national and international agencies. we used a bayesian hierarchical mixture model to estimate haemoglobin distributions and systematically addressed missing data, non-linear time trends, and representativeness of data sources. we quantified the uncertainty of our estimates. findings global mean haemoglobin improved slightly between 1995 and 2011, from 125 g/l (95% credibility interval 123-126) to 126 g/l (124-128) in non-pregnant women, from 112 g/l (111-113) to 114 g/l (112-116) in pregnant women, and from 109 g/l (107-111) to 111 g/l (110-113) in children. anaemia prevalence decreased from 33% (29-37) to 29% (24-35) in non-pregnant women, from 43% (39-47) to 38% (34-43) in pregnant women, and from 47% (43-51) to 43% (38-47) in children. these prevalences translated to 496 million (409-595 million) non-pregnant women, 32 million (28-36 million) pregnant women, and 273 million (242-304 million) children with anaemia in 2011. in 2011, concentrations of mean haemoglobin were lowest and anaemia prevalence was highest in south asia and central and west africa. interpretation children's and women's haemoglobin statuses improved in some regions where concentrations had been low in the 1990s, leading to a modest global increase in mean haemoglobin and a reduction in anaemia prevalence. further improvements are needed in some regions, particularly south asia and central and west africa, to improve the health of women and children and achieve global targets for reducing anaemia. funding bill & melinda gates foundation, grand challenges canada, and the uk medical research council.",0
"purpose positron emission tomography (pet) with choline tracers has found widespread use for the diagnosis of prostate cancer (pc). however, choline metabolism is not increased in a considerable number of cases, whereas prostate-specific membrane antigen (psma) is overexpressed in most pcs. therefore, a (68)ga-labelled psma ligand could be superior to choline tracers by obtaining a high contrast. the aim of this study was to compare such a novel tracer with standard choline-based pet/ct. methods thirty-seven patients with biochemical relapse of pc were retrospectively analysed after (18)f-fluoromethylcholine and (68)ga-psma pet/ct within a time window of 30 days. radiotracer uptake that was visually considered as pc was semi-quantitatively analysed by measuring the maximum standardized uptake values (suvmax) of the scans acquired 1 h after injection of (68)ga-psma complex solution (median 132 mbq, range 59-263 mbq) and (18)f-fluoromethylcholine (median 237 mbq, range 114-374 mbq), respectively. in addition, tumour to background ratios were calculated. results a total of 78 lesions characteristic for pc were detected in 32 patients using (68)ga-psma pet/ct and 56 lesions were detected in 26 patients using choline pet/ct. the higher detection rate in (68)ga-psma pet/ct was statistically significant (p=0.04). in five patients no lesion was found with both methods. all lesions detected by (18)f-fluoromethylcholine pet/ct were also seen by (68)ga-psma pet/ct. in (68)ga-psma pet/ct suvmax was clearly (>10 %) higher in 62 of 78 lesions (79.1 %) and the tumour to background ratio was clearly (>10 %) higher in 74 of 78 lesions (94.9 %) when compared to (18)f-fluoromethylcholine pet/ct. conclusion (68)ga-psma pet/ct can detect lesions characteristic for pc with improved contrast when compared to standard (18)f-fluoromethylcholine pet/ct, especially at low psa levels.",0
"the evolution of sars-cov-2 could impair recognition of the virus by human antibody-mediated immunity. to facilitate prospective surveillance for such evolution, we map how convalescent plasma antibodies are impacted by all mutations to the spike's receptor-binding domain (rbd), the main target of plasma neutralizing activity. binding by polyclonal plasma antibodies is affected by mutations in three main epitopes in the rbd, but longitudinal samples reveal that the impact of these mutations on antibody binding varies substantially both among individuals and within the same individual over time. despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the rbd's receptor-binding motif. the most important site is e484, where neutralization by some plasma is reduced >10-fold by several mutations, including one in the emerging 20h/501y.v2 and 20j/501y.v3 sars-cov-2 lineages. going forward, these plasma escape maps can inform surveillance of sars-cov-2 evolution.",0
"here, we present the algorithm and validation for omega, a systematic, knowledge-based conformer generator. the algorithm consists of three phases: assembly of an initial 3d structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by geometric and energy criteria. validation of conformer generators like omega has often been undertaken by comparing computed conformer sets to experimental molecular conformations from crystallography, usually from the protein databank (pdb). such an approach is fraught with difficulty due to the systematic problems with small molecule structures in the pdb. methods are presented to identify a diverse set of small molecule structures from cocomplexes in the pdb that has maximal reliability. a challenging set of 197 high quality, carefully selected ligand structures from well-solved models was obtained using these methods. this set will provide a sound basis for comparison and validation of conformer generators in the future. validation results from this set are compared to the results using structures of a set of druglike molecules extracted from the cambridge structural database (csd). omega is found to perform very well in reproducing the crystallographic conformations from both these data sets using two complementary metrics of success.",0
"to adhere and migrate, cells must be capable of applying cytoskeletal force to the extracellular matrix (ecm) through integrin receptors. however, it is unclear if connections between integrins and the ecm are immediately capable of transducing cytoskeletal contraction into migration force, or whether engagement of force transmission requires maturation of the adhesion. here, we show that initial integrin-ecm adhesions become capable of exerting migration force with the recruitment of vinculin, a marker for focal complexes, which are precursors of focal adhesions. we are able to induce the development of focal complexes by the application of mechanical force to fibronectin receptors from inside or outside the cell, and we are able to extend focal complex formation to vitronectin receptors by the removal of c-src. these results indicate that cells use mechanical force as a signal to strengthen initial integrin-ecm adhesions into focal complexes and regulate the amount of migration force applied to individual adhesions at localized regions of the advancing lamella.",0
"bone mineral density (bmd) is a heritable complex trait used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. we performed meta-analysis of five genome-wide association studies of femoral neck and lumbar spine bmd in 19,195 subjects of northern european descent. we identified 20 bmd loci that reached genome-wide significance (gws; p < 5 x 10(-8)), of which 13 map to regions not previously associated with this trait: 1p31.3 (gpr177), 2p21 (sptbn1), 3p22 (ctnnb1), 4q21.1 (mepe), 5q14 (mef2c), 7p14 (stard3nl), 7q21.3 (flj42280), 11p11.2 (lrp4, arhgap1, f2), 11p14.1 (dcdc5), 11p15 (sox6), 16q24 (foxl1), 17q21 (hdac5) and 17q12 (crhr1). the meta-analysis also confirmed at gws level seven known bmd loci on 1p36 (zbtb40), 6q25 (esr1), 8q24 (tnfrsf11b), 11q13.4 (lrp5), 12q13 (sp7), 13q14 (tnfsf11) and 18q21 (tnfrsf11a). the many snps associated with bmd map to genes in signaling pathways with relevance to bone metabolism and highlight the complex genetic architecture that underlies osteoporosis and variation in bmd.",0
"ferroptosis is a new type of cell death that was discovered in recent years and is usually accompanied by a large amount of iron accumulation and lipid peroxidation during the cell death process; the occurrence of ferroptosis is iron-dependent. ferroptosis-inducing factors can directly or indirectly affect glutathione peroxidase through different pathways, resulting in a decrease in antioxidant capacity and accumulation of lipid reactive oxygen species (ros) in cells, ultimately leading to oxidative cell death. recent studies have shown that ferroptosis is closely related to the pathophysiological processes of many diseases, such as tumors, nervous system diseases, ischemia-reperfusion injury, kidney injury, and blood diseases. how to intervene in the occurrence and development of related diseases by regulating cell ferroptosis has become a hotspot and focus of etiological research and treatment, but the functional changes and specific molecular mechanisms of ferroptosis still need to be further explored. this paper systematically summarizes the latest progress in ferroptosis research, with a focus on providing references for further understanding of its pathogenesis and for proposing new targets for the treatment of related diseases.",0
"we performed a scan for genetic variants associated with multiple phenotypes by comparing large genome-wide association studies (gwas) of 42 traits or diseases. we identified 341 loci (at a false discovery rate of 10%) associated with multiple traits. several loci are associated with multiple phenotypes; for example, a nonsynonymous variant in the zinc transporter slc39a8 influences seven of the traits, including risk of schizophrenia (rs13107325: log-transformed odds ratio (log or) = 0.15, p = 2 × 10(-12)) and parkinson disease (log or = -0.15, p = 1.6 × 10(-7)), among others. second, we used these loci to identify traits that have multiple genetic causes in common. for example, variants associated with increased risk of schizophrenia also tended to be associated with increased risk of inflammatory bowel disease. finally, we developed a method to identify pairs of traits that show evidence of a causal relationship. for example, we show evidence that increased body mass index causally increases triglyceride levels.",0
"background a comprehensive self-administered diet history questionnaire (dhq: 150-item semi-quantitative questionnaire) and a brief self-administered dhq (bdhq: 58-item fixed-portion-type questionnaire) were developed for assessing japanese diets. we compared the relative validity of nutrient intake derived from dhq with that from the bdhq, using semi-weighed 16-day dietary records (drs) as reference. methods ninety-two japanese women aged 31 to 69 years and 92 japanese men aged 32 to 76 years completed a 4-nonconsecutive-day dr, a dhq, and a bdhq 4 times each (once per season) in 3 areas of japan (osaka, nagano, and tottori). results no significant differences were seen in estimates of energy-adjusted intakes of 42 selected nutrients (based on the residual method) between the 16-day drs and the first dhq (dhq1) or between the dr and the first bdhq (bdhq1) for 18 (43%) and 14 (33%) nutrients, respectively, among women and for 4 (10%) and 21 (50%) nutrients among men. the median (interquartile range) pearson correlation coefficients with the dr for energy-adjusted intakes of the 42 nutrients were 0.57 (0.50 to 0.64) for the dhq1 and 0.54 (0.45 to 0.61) for the bdhq1 in women; in men, the respective values were 0.50 (0.42 to 0.59) and 0.56 (0.41 to 0.63). similar results were observed for the means of the 4 dhqs and bdhqs. conclusions the dhq and bdhq had satisfactory ranking ability for the energy-adjusted intakes of many nutrients among the present japanese population, although these instruments were satisfactory in estimating mean values for only a small number of nutrients.",0
"problem/condition autism spectrum disorder (asd). period covered 2016. description of system the autism and developmental disabilities monitoring (addm) network is an active surveillance program that provides estimates of the prevalence of asd among children aged 8 years whose parents or guardians live in 11 addm network sites in the united states (arizona, arkansas, colorado, georgia, maryland, minnesota, missouri, new jersey, north carolina, tennessee, and wisconsin). surveillance is conducted in two phases. the first phase involves review and abstraction of comprehensive evaluations that were completed by medical and educational service providers in the community. in the second phase, experienced clinicians who systematically review all abstracted information determine asd case status. the case definition is based on asd criteria described in the diagnostic and statistical manual of mental disorders, fifth edition. results for 2016, across all 11 sites, asd prevalence was 18.5 per 1,000 (one in 54) children aged 8 years, and asd was 4.3 times as prevalent among boys as among girls. asd prevalence varied by site, ranging from 13.1 (colorado) to 31.4 (new jersey). prevalence estimates were approximately identical for non-hispanic white (white), non-hispanic black (black), and asian/pacific islander children (18.5, 18.3, and 17.9, respectively) but lower for hispanic children (15.4). among children with asd for whom data on intellectual or cognitive functioning were available, 33% were classified as having intellectual disability (intelligence quotient ≤70); this percentage was higher among girls than boys (39% versus 32%) and among black and hispanic than white children (47%, 36%, and 27%, respectively) . black children with asd were less likely to have a first evaluation by age 36 months than were white children with asd (40% versus 45%). the overall median age at earliest known asd diagnosis (51 months) was similar by sex and racial and ethnic groups; however, black children with iq ≤70 had a later median age at asd diagnosis than white children with iq ≤70 (48 months versus 42 months). interpretation the prevalence of asd varied considerably across sites and was higher than previous estimates since 2014. although no overall difference in asd prevalence between black and white children aged 8 years was observed, the disparities for black children persisted in early evaluation and diagnosis of asd. hispanic children also continue to be identified as having asd less frequently than white or black children. public health action these findings highlight the variability in the evaluation and detection of asd across communities and between sociodemographic groups. continued efforts are needed for early and equitable identification of asd and timely enrollment in services.",0
"implementation science is a quickly growing discipline. lessons learned from business and medical settings are being applied but it is unclear how well they translate to settings with different historical origins and customs (e.g., public mental health, social service, alcohol/drug sectors). the purpose of this paper is to propose a multi-level, four phase model of the implementation process (i.e., exploration, adoption/preparation, implementation, sustainment), derived from extant literature, and apply it to public sector services. we highlight features of the model likely to be particularly important in each phase, while considering the outer and inner contexts (i.e., levels) of public sector service systems.",0
"brainstorm is a collaborative open-source application dedicated to magnetoencephalography (meg) and electroencephalography (eeg) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (mri) data. the primary objective of the software is to connect meg/eeg neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (gui).",0
"quantitative mass spectrometry-based proteomics is highly versatile but not easily multiplexed. isobaric labeling strategies allow mass spectrometry-based multiplexed proteome quantification; however, ratio distortion owing to protein quantification interference is a common effect. we present a two-proteome model (mixture of human and yeast proteins) in a sixplex isobaric labeling system to fully document the interference effect, and we report that applying triple-stage mass spectrometry (ms3) almost completely eliminates interference.",0
"chebi is a database and ontology containing information about chemical entities of biological interest. it currently includes over 46,000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. all content is freely available and can be accessed online at in this update paper, we describe recent improvements and additions to the chebi offering. we have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, escherichia coli and yeast. our front-end has also been reworked and updated, improving the user experience, removing our dependency on java applets in favour of embedded javascript components and moving from a monthly release update to a 'live' website. programmatic access has been improved by the introduction of a library, libchebi, in java, python and matlab. furthermore, we have added two new tools, namely an analysis tool, binche, and a query tool for the ontology, ontoquery.",0
"background the effects of coronavirus disease 2019 (covid-19) on the population's mental health and well-being are likely to be profound and long lasting. aims to investigate the trajectory of mental health and well-being during the first 6 weeks of lockdown in adults in the uk. method a quota survey design and a sampling frame that permitted recruitment of a national sample was employed. findings for waves 1 (31 march to 9 april 2020), 2 (10 april to 27 april 2020) and 3 (28 april to 11 may 2020) are reported here. a range of mental health factors was assessed: pre-existing mental health problems, suicide attempts and self-harm, suicidal ideation, depression, anxiety, defeat, entrapment, mental well-being and loneliness. results a total of 3077 adults in the uk completed the survey at wave 1. suicidal ideation increased over time. symptoms of anxiety, and levels of defeat and entrapment decreased across waves whereas levels of depressive symptoms did not change significantly. positive well-being also increased. levels of loneliness did not change significantly over waves. subgroup analyses showed that women, young people (18-29 years), those from more socially disadvantaged backgrounds and those with pre-existing mental health problems have worse mental health outcomes during the pandemic across most factors. conclusions the mental health and well-being of the uk adult population appears to have been affected in the initial phase of the covid-19 pandemic. the increasing rates of suicidal thoughts across waves, especially among young adults, are concerning.",0
"background as a major virus outbreak in the 21st century, the coronavirus disease 2019 (covid-19) pandemic has led to unprecedented hazards to mental health globally. while psychological support is being provided to patients and healthcare workers, the general public's mental health requires significant attention as well. this systematic review aims to synthesize extant literature that reports on the effects of covid-19 on psychological outcomes of the general population and its associated risk factors. methods a systematic search was conducted on pubmed, embase, medline, web of science, and scopus from inception to 17 may 2020 following the prisma guidelines. a manual search on google scholar was performed to identify additional relevant studies. articles were selected based on the predetermined eligibility criteria. results relatively high rates of symptoms of anxiety (6.33% to 50.9%), depression (14.6% to 48.3%), post-traumatic stress disorder (7% to 53.8%), psychological distress (34.43% to 38%), and stress (8.1% to 81.9%) are reported in the general population during the covid-19 pandemic in china, spain, italy, iran, the us, turkey, nepal, and denmark. risk factors associated with distress measures include female gender, younger age group (≤40 years), presence of chronic/psychiatric illnesses, unemployment, student status, and frequent exposure to social media/news concerning covid-19. limitations a significant degree of heterogeneity was noted across studies. conclusions the covid-19 pandemic is associated with highly significant levels of psychological distress that, in many cases, would meet the threshold for clinical relevance. mitigating the hazardous effects of covid-19 on mental health is an international public health priority.",0
"the dementia with lewy bodies (dlb) consortium has refined its recommendations about the clinical and pathologic diagnosis of dlb, updating the previous report, which has been in widespread use for the last decade. the revised dlb consensus criteria now distinguish clearly between clinical features and diagnostic biomarkers, and give guidance about optimal methods to establish and interpret these. substantial new information has been incorporated about previously reported aspects of dlb, with increased diagnostic weighting given to rem sleep behavior disorder and 123 iodine-metaiodobenzylguanidine (mibg) myocardial scintigraphy. the diagnostic role of other neuroimaging, electrophysiologic, and laboratory investigations is also described. minor modifications to pathologic methods and criteria are recommended to take account of alzheimer disease neuropathologic change, to add previously omitted lewy-related pathology categories, and to include assessments for substantia nigra neuronal loss. recommendations about clinical management are largely based upon expert opinion since randomized controlled trials in dlb are few. substantial progress has been made since the previous report in the detection and recognition of dlb as a common and important clinical disorder. during that period it has been incorporated into dsm-5, as major neurocognitive disorder with lewy bodies. there remains a pressing need to understand the underlying neurobiology and pathophysiology of dlb, to develop and deliver clinical trials with both symptomatic and disease-modifying agents, and to help patients and carers worldwide to inform themselves about the disease, its prognosis, best available treatments, ongoing research, and how to get adequate support.",0
"the proteomics identifications (pride, database at the european bioinformatics institute is one of the most prominent data repositories of mass spectrometry (ms)-based proteomics data. here, we summarize recent developments in the pride database and related tools. first, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. we then describe the tools that are part of the pride submission pipeline, especially the recently developed pride converter 2 (new submission tool) and pride inspector (visualization and analysis tool). we also give an update about the integration of pride with other ms proteomics resources in the context of the proteomexchange consortium. finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.",0
"objectives in 2019, a new coronavirus has been identified and many efforts have been directed toward the development of effective vaccines. however, the willingness for vaccination is deeply influenced by several factors. so the aim of our review was to analyze the theme of vaccine hesitancy during covid-19 pandemic, with a particular focus on vaccine hesitancy toward covid-19 vaccine. study design narrative review. methods in november 2020, we performed a search for original peer-reviewed articles in the electronic database pubmed (medline). the key search terms were ""vaccine hesitancy and covid-19"". we searched for studies published during covid-19 pandemic and reporting information about the phenomenon of vaccine hesitancy. results fifteen studies were included in the review. the percentage of covid-19 vaccine acceptance was not so high (up to 86.1% students or 77.6% general population); for influenza vaccine, the maximum percentage was 69%. several factors influenced the acceptance or refusal (ethnicity, working status, religiosity, politics, gender, age, education, income, etc.). the most given reasons to refuse vaccine were as follows: being against vaccines in general, concerns about safety/thinking that a vaccine produced in a rush is too dangerous, considering the vaccine useless because of the harmless nature of covid-19, general lack of trust, doubts about the efficiency of the vaccine, belief to be already immunized, doubt about the provenience of vaccine. conclusions the high vaccine hesitancy, also during covid-19 pandemic, represents an important problem, and further efforts should be done to support people and give them correct information about vaccines.",0
"most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: nigeria-cameroon/western and central/eastern populations. we find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. we discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. this comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.",0
"the cytotoxic t-lymphocyte-associated antigen 4 (ctla-4) and programmed death 1 (pd-1) immune checkpoints are negative regulators of t-cell immune function. inhibition of these targets, resulting in increased activation of the immune system, has led to new immunotherapies for melanoma, non-small cell lung cancer, and other cancers. ipilimumab, an inhibitor of ctla-4, is approved for the treatment of advanced or unresectable melanoma. nivolumab and pembrolizumab, both pd-1 inhibitors, are approved to treat patients with advanced or metastatic melanoma and patients with metastatic, refractory non-small cell lung cancer. in addition the combination of ipilimumab and nivolumab has been approved in patients with braf wt metastatic or unresectable melanoma. the roles of ctla-4 and pd-1 in inhibiting immune responses, including antitumor responses, are largely distinct. ctla-4 is thought to regulate t-cell proliferation early in an immune response, primarily in lymph nodes, whereas pd-1 suppresses t cells later in an immune response, primarily in peripheral tissues. the clinical profiles of immuno-oncology agents inhibiting these 2 checkpoints may vary based on their mechanistic differences. this article provides an overview of the ctla-4 and pd-1 pathways and implications of their inhibition in cancer therapy.",0
"model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. we present modelfinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.",0
"summary metal provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. metal provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. availability and implementation metal, including source code, documentation, examples, and executables, is available at",0
"cancers emerge from an ongoing darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. this evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. however, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and interclonal cooperation between multiple subclones. here we sought definitive evidence for the existence of polyclonal seeding in human malignancy and to establish the clonal relationship among different metastases in the context of androgen-deprived metastatic prostate cancer. using whole-genome sequencing, we characterized multiple metastases arising from prostate tumours in ten patients. integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen-deprivation therapy in prostate cancer.",0
"background mutations in lrrk2, the gene that encodes leucine-rich repeat kinase 2, are a cause of parkinson's disease (pd). the international lrrk2 consortium was established to answer three key clinical questions: can lrrk2-associated pd be distinguished from idiopathic pd; which mutations in lrrk2 are pathogenic; and what is the age-specific cumulative risk of pd for individuals who inherit or are at risk of inheriting a deleterious mutation in lrrk2? methods researchers from 21 centres across the world collaborated on this study. the frequency of the common lrrk2 gly2019ser mutation was estimated on the basis of data from 24 populations worldwide, and the penetrance of the mutation was defined in 1045 people with mutations in lrrk2 from 133 families. the lrrk2 phenotype was defined on the basis of 59 motor and non-motor symptoms in 356 patients with lrrk2-associated pd and compared with the symptoms of 543 patients with pathologically proven idiopathic pd. findings six mutations met the consortium's criteria for being proven pathogenic. the frequency of the common lrrk2 gly2019ser mutation was 1% of patients with sporadic pd and 4% of patients with hereditary pd; the frequency was highest in the middle east and higher in southern europe than in northern europe. the risk of pd for a person who inherits the lrrk2 gly2019ser mutation was 28% at age 59 years, 51% at 69 years, and 74% at 79 years. the motor symptoms (eg, disease severity, rate of progression, occurrence of falls, and dyskinesia) and non-motor symptoms (eg, cognition and olfaction) of lrrk2-associated pd were more benign than those of idiopathic pd. interpretation mutations in lrrk2 are a clinically relevant cause of pd that merit testing in patients with hereditary pd and in subgroups of patients with pd. however, this knowledge should be applied with caution in the diagnosis and counselling of patients. funding uk medical research council; uk parkinson's disease society; uk brain research trust; internationaal parkinson fonds; volkswagen foundation; national institutes of health: national institute of neurological disorders and stroke and national institute of aging; udall parkinson's disease centre of excellence; pacific alzheimer research foundation centre; italian telethon foundation; fondazione grigioni per il morbo di parkinson; michael j fox foundation for parkinson's research; safra global genetics consortium; us department of veterans affairs; french agence nationale de la recherche.",0
"background the risk of severe covid-19 if an individual becomes infected is known to be higher in older individuals and those with underlying health conditions. understanding the number of individuals at increased risk of severe covid-19 and how this varies between countries should inform the design of possible strategies to shield or vaccinate those at highest risk. methods we estimated the number of individuals at increased risk of severe disease (defined as those with at least one condition listed as ""at increased risk of severe covid-19"" in current guidelines) by age (5-year age groups), sex, and country for 188 countries using prevalence data from the global burden of diseases, injuries, and risk factors study (gbd) 2017 and un population estimates for 2020. the list of underlying conditions relevant to covid-19 was determined by mapping the conditions listed in gbd 2017 to those listed in guidelines published by who and public health agencies in the uk and the usa. we analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. to help interpretation of the degree of risk among those at increased risk, we also estimated the number of individuals at high risk (defined as those that would require hospital admission if infected) using age-specific infection-hospitalisation ratios for covid-19 estimated for mainland china and making adjustments to reflect country-specific differences in the prevalence of underlying conditions and frailty. we assumed males were twice at likely as females to be at high risk. we also calculated the number of individuals without an underlying condition that could be considered at increased risk because of their age, using minimum ages from 50 to 70 years. we generated uncertainty intervals (uis) for our estimates by running low and high scenarios using the lower and upper 95% confidence limits for country population size, disease prevalences, multimorbidity fractions, and infection-hospitalisation ratios, and plausible low and high estimates for the degree of clustering, informed by multimorbidity studies. findings we estimated that 1·7 billion (ui 1·0-2·4) people, comprising 22% (ui 15-28) of the global population, have at least one underlying condition that puts them at increased risk of severe covid-19 if infected (ranging from 66% of those aged 70 years or older). we estimated that 349 million (186-787) people (4% of the global population) are at high risk of severe covid-19 and would require hospital admission if infected (ranging from interpretation about one in five individuals worldwide could be at increased risk of severe covid-19, should they become infected, due to underlying health conditions, but this risk varies considerably by age. our estimates are uncertain, and focus on underlying conditions rather than other risk factors such as ethnicity, socioeconomic deprivation, and obesity, but provide a starting point for considering the number of individuals that might need to be shielded or vaccinated as the global pandemic unfolds. funding uk department for international development, wellcome trust, health data research uk, medical research council, and national institute for health research.",0
"unite ( is a web-based database and sequence management environment for the molecular identification of fungi. it targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (its) region-and offers all ∼1 000 000 public fungal its sequences for reference. these are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (dois) to promote unambiguous reference across studies. in-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. unite serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the global biodiversity information facility, and support for an unlimited number of parallel taxonomic classification systems.",0
"objective since the declaration of the coronavirus 2019 (covid-19) outbreak as pandemic, there are reports on the increased prevalence of physical symptoms observed in the general population. we investigated the association between psychological outcomes and physical symptoms among healthcare workers. methods healthcare workers from 5 major hospitals, involved in the care for covid-19 patients, in singapore and india were invited to participate in a study by performing a self-administered questionnaire within the period of february 19 to april 17, 2020. healthcare workers included doctors, nurses, allied healthcare workers, administrators, clerical staff and maintenance workers. this questionnaire collected information on demographics, medical history, symptom prevalence in the past month, depression anxiety stress scales (dass-21) and the impact of events scale-revised (ies-r) instrument. the prevalence of physical symptoms displayed by healthcare workers and the associations between physical symptoms and psychological outcomes of depression, anxiety, stress, and post-traumatic stress disorder (ptsd) were evaluated. results out of the 906 healthcare workers who participated in the survey, 48 (5.3%) screened positive for moderate to very-severe depression, 79 (8.7%) for moderate to extremely-severe anxiety, 20 (2.2%) for moderate to extremely-severe stress, and 34 (3.8%) for moderate to severe levels of psychological distress. the commonest reported symptom was headache (32.3%), with a large number of participants (33.4%) reporting more than four symptoms. participants who had experienced symptoms in the preceding month were more likely to be older, have pre-existing comorbidities and a positive screen for depression, anxiety, stress, and ptsd. after adjusting for age, gender and comorbidities, it was found that depression (or 2.79, 95% ci 1.54-5.07, p = 0.001), anxiety (or 2.18, 95% ci 1.36-3.48, p = 0.001), stress (or 3.06, 95% ci 1.27-7.41, p = 0.13), and ptsd (or 2.20, 95% ci 1.12-4.35, p = 0.023) remained significantly associated with the presence of physical symptoms experienced in the preceding month. linear regression revealed that the presence of physical symptoms was associated with higher mean scores in the ies-r, dass anxiety, stress and depression subscales. conclusions our study demonstrates a significant association between the prevalence of physical symptoms and psychological outcomes among healthcare workers during the covid-19 outbreak. we postulate that this association may be bi-directional, and that timely psychological interventions for healthcare workers with physical symptoms should be considered once an infection has been excluded.",0
"background underweight, overweight, and obesity in childhood and adolescence are associated with adverse health consequences throughout the life-course. our aim was to estimate worldwide trends in mean body-mass index (bmi) and a comprehensive set of bmi categories that cover underweight to obesity in children and adolescents, and to compare trends with those of adults. methods we pooled 2416 population-based studies with measurements of height and weight on 128·9 million participants aged 5 years and older, including 31·5 million aged 5-19 years. we used a bayesian hierarchical model to estimate trends from 1975 to 2016 in 200 countries for mean bmi and for prevalence of bmi in the following categories for children and adolescents aged 5-19 years: more than 2 sd below the median of the who growth reference for children and adolescents (referred to as moderate and severe underweight hereafter), 2 sd to more than 1 sd below the median (mild underweight), 1 sd below the median to 1 sd above the median (healthy weight), more than 1 sd to 2 sd above the median (overweight but not obese), and more than 2 sd above the median (obesity). findings regional change in age-standardised mean bmi in girls from 1975 to 2016 ranged from virtually no change (-0·01 kg/m 2 per decade; 95% credible interval -0·42 to 0·39, posterior probability of the observed decrease being a true decrease=0·5098) in eastern europe to an increase of 1·00 kg/m 2 per decade (0·69-1·35, pp>0·9999) in central latin america and an increase of 0·95 kg/m 2 per decade (0·64-1·25, pp>0·9999) in polynesia and micronesia. the range for boys was from a non-significant increase of 0·09 kg/m 2 per decade (-0·33 to 0·49, pp=0·6926) in eastern europe to an increase of 0·77 kg/m 2 per decade (0·50-1·06, pp>0·9999) in polynesia and micronesia. trends in mean bmi have recently flattened in northwestern europe and the high-income english-speaking and asia-pacific regions for both sexes, southwestern europe for boys, and central and andean latin america for girls. by contrast, the rise in bmi has accelerated in east and south asia for both sexes, and southeast asia for boys. global age-standardised prevalence of obesity increased from 0·7% (0·4-1·2) in 1975 to 5·6% (4·8-6·5) in 2016 in girls, and from 0·9% (0·5-1·3) in 1975 to 7·8% (6·7-9·1) in 2016 in boys; the prevalence of moderate and severe underweight decreased from 9·2% (6·0-12·9) in 1975 to 8·4% (6·8-10·1) in 2016 in girls and from 14·8% (10·4-19·5) in 1975 to 12·4% (10·3-14·5) in 2016 in boys. prevalence of moderate and severe underweight was highest in india, at 22·7% (16·7-29·6) among girls and 30·7% (23·5-38·0) among boys. prevalence of obesity was more than 30% in girls in nauru, the cook islands, and palau; and boys in the cook islands, nauru, palau, niue, and american samoa in 2016. prevalence of obesity was about 20% or more in several countries in polynesia and micronesia, the middle east and north africa, the caribbean, and the usa. in 2016, 75 (44-117) million girls and 117 (70-178) million boys worldwide were moderately or severely underweight. in the same year, 50 (24-89) million girls and 74 (39-125) million boys worldwide were obese. interpretation the rising trends in children's and adolescents' bmi have plateaued in many high-income countries, albeit at high levels, but have accelerated in parts of asia, with trends no longer correlated with those of adults. funding wellcome trust, astrazeneca young health programme.",0
"background two bayesian methods, bayescπ and bayesdπ, were developed for genomic prediction to address the drawback of bayesa and bayesb regarding the impact of prior hyperparameters and treat the prior probability π that a snp has zero effect as unknown. the methods were compared in terms of inference of the number of qtl and accuracy of genomic estimated breeding values (gebvs), using simulated scenarios and real data from north american holstein bulls. results estimates of π from bayescπ, in contrast to bayesdπ, were sensitive to the number of simulated qtl and training data size, and provide information about genetic architecture. milk yield and fat yield have qtl with larger effects than protein yield and somatic cell score. the drawback of bayesa and bayesb did not impair the accuracy of gebvs. accuracies of alternative bayesian methods were similar. bayesa was a good choice for gebv with the real data. computing time was shorter for bayescπ than for bayesdπ, and longest for our implementation of bayesa. conclusions collectively, accounting for computing effort, uncertainty as to the number of qtl (which affects the gebv accuracy of alternative methods), and fundamental interest in the number of qtl underlying quantitative traits, we believe that bayescπ has merit for routine applications.",0
"nonalcoholic fatty liver disease (nafld) and resulting nonalcoholic steatohepatitis (nash) are highly prevalent in the united states, where they are a growing cause of cirrhosis and hepatocellular carcinoma (hcc) and increasingly an indicator for liver transplantation. a markov model was used to forecast nafld disease progression. incidence of nafld was based on historical and projected changes in adult prevalence of obesity and type 2 diabetes mellitus (dm). assumptions were derived from published literature where available and validated using national surveillance data for incidence of nafld-related hcc. projected changes in nafld-related cirrhosis, advanced liver disease, and liver-related mortality were quantified through 2030. prevalent nafld cases are forecasted to increase 21%, from 83.1 million (2015) to 100.9 million (2030), while prevalent nash cases will increase 63% from 16.52 million to 27.00 million cases. overall nafld prevalence among the adult population (aged ≥15 years) is projected at 33.5% in 2030, and the median age of the nafld population will increase from 50 to 55 years during 2015-2030. in 2015, approximately 20% of nafld cases were classified as nash, increasing to 27% by 2030, a reflection of both disease progression and an aging population. incidence of decompensated cirrhosis will increase 168% to 105,430 cases by 2030, while incidence of hcc will increase by 137% to 12,240 cases. liver deaths will increase 178% to an estimated 78,300 deaths in 2030. during 2015-2030, there are projected to be nearly 800,000 excess liver deaths. conclusion with continued high rates of adult obesity and dm along with an aging population, nafld-related liver disease and mortality will increase in the united states. strategies to slow the growth of nafld cases and therapeutic options are necessary to mitigate disease burden. (hepatology 2018;67:123-133).",0
"cancer patients often develop chronic, clinically significant symptoms of depression and anxiety. previous studies suggest that psilocybin may decrease depression and anxiety in cancer patients. the effects of psilocybin were studied in 51 cancer patients with life-threatening diagnoses and symptoms of depression and/or anxiety. this randomized, double-blind, cross-over trial investigated the effects of a very low (placebo-like) dose (1 or 3 mg/70 kg) vs. a high dose (22 or 30 mg/70 kg) of psilocybin administered in counterbalanced sequence with 5 weeks between sessions and a 6-month follow-up. instructions to participants and staff minimized expectancy effects. participants, staff, and community observers rated participant moods, attitudes, and behaviors throughout the study. high-dose psilocybin produced large decreases in clinician- and self-rated measures of depressed mood and anxiety, along with increases in quality of life, life meaning, and optimism, and decreases in death anxiety. at 6-month follow-up, these changes were sustained, with about 80% of participants continuing to show clinically significant decreases in depressed mood and anxiety. participants attributed improvements in attitudes about life/self, mood, relationships, and spirituality to the high-dose experience, with >80% endorsing moderately or greater increased well-being/life satisfaction. community observer ratings showed corresponding changes. mystical-type psilocybin experience on session day mediated the effect of psilocybin dose on therapeutic outcomes. trial registration clinicaltrials.gov identifier: nct00465595.",0
"background theories are important tools in the social and natural sciences. the methods by which they are derived are rarely described and discussed. normalization process theory explains how new technologies, ways of acting, and ways of working become routinely embedded in everyday practice, and has applications in the study of implementation processes. this paper describes the process by which it was built. methods between 1998 and 2008, we developed a theory. we derived a set of empirical generalizations from analysis of data collected in qualitative studies of healthcare work and organization. we developed an applied theoretical model through analysis of empirical generalizations. finally, we built a formal theory through a process of extension and implication analysis of the applied theoretical model. results each phase of theory development showed that the constructs of the theory did not conflict with each other, had explanatory power, and possessed sufficient robustness for formal testing. as the theory developed, its scope expanded from a set of observed regularities in data with procedural explanations, to an applied theoretical model, to a formal middle-range theory. conclusion normalization process theory has been developed through procedures that were properly sceptical and critical, and which were opened to review at each stage of development. the theory has been shown to merit formal testing.",0
"taiwan's national health insurance research database (nhird) exemplifies a population-level data source for generating real-world evidence to support clinical decisions and health care policy-making. like with all claims databases, there have been some validity concerns of studies using the nhird, such as the accuracy of diagnosis codes and issues around unmeasured confounders. endeavors to validate diagnosed codes or to develop methodologic approaches to address unmeasured confounders have largely increased the reliability of nhird studies. recently, taiwan's ministry of health and welfare (mohw) established a health and welfare data center (hwdc), a data repository site that centralizes the nhird and about 70 other health-related databases for data management and analyses. to strengthen the protection of data privacy, investigators are required to conduct on-site analysis at an hwdc through remote connection to mohw servers. although the tight regulation of this on-site analysis has led to inconvenience for analysts and has increased time and costs required for research, the hwdc has created opportunities for enriched dimensions of study by linking across the nhird and other databases. in the near future, researchers will have greater opportunity to distill knowledge from the nhird linked to hospital-based electronic medical records databases containing unstructured patient-level information by using artificial intelligence techniques, including machine learning and natural language processes. we believe that nhird with multiple data sources could represent a powerful research engine with enriched dimensions and could serve as a guiding light for real-world evidence-based medicine in taiwan.",0
"despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. this paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions. to fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice . these data are available through the vista enhancer browser ( this growing database currently contains over 250 experimentally tested dna fragments, of which more than 100 have been validated as tissue-specific enhancers. for each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern. users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth. these experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function.",0
"autophagy is an evolutionarily conserved process by which cytoplasmic proteins and organelles are catabolized. during starvation, the protein tor (target of rapamycin), a nutrient-responsive kinase, is inhibited, and this induces autophagy. in autophagy, double-membrane autophagosomes envelop and sequester intracellular components and then fuse with lysosomes to form autolysosomes, which degrade their contents to regenerate nutrients. current models of autophagy terminate with the degradation of the autophagosome cargo in autolysosomes, but the regulation of autophagy in response to nutrients and the subsequent fate of the autolysosome are poorly understood. here we show that mtor signalling in rat kidney cells is inhibited during initiation of autophagy, but reactivated by prolonged starvation. reactivation of mtor is autophagy-dependent and requires the degradation of autolysosomal products. increased mtor activity attenuates autophagy and generates proto-lysosomal tubules and vesicles that extrude from autolysosomes and ultimately mature into functional lysosomes, thereby restoring the full complement of lysosomes in the cell-a process we identify in multiple animal species. thus, an evolutionarily conserved cycle in autophagy governs nutrient sensing and lysosome homeostasis during starvation.",0
"estimates of biological age based on dna methylation patterns, often referred to as ""epigenetic age"", ""dnam age"", have been shown to be robust biomarkers of age in humans. we previously demonstrated that independent of chronological age, epigenetic age assessed in blood predicted all-cause mortality in four human cohorts. here, we expanded our original observation to 13 different cohorts for a total sample size of 13,089 individuals, including three racial/ethnic groups. in addition, we examined whether incorporating information on blood cell composition into the epigenetic age metrics improves their predictive power for mortality. all considered measures of epigenetic age acceleration were predictive of mortality (p≤8.2x10 -9 ) , independent of chronological age, even after adjusting for additional risk factors (p -4 ) , and within the racial/ethnic groups that we examined (non-hispanic whites, hispanics, african americans). epigenetic age estimates that incorporated information on blood cell composition led to the smallest p-values for time to death (p=7.5x10 -43 ). overall, this study a) strengthens the evidence that epigenetic age predicts all-cause mortality above and beyond chronological age and traditional risk factors, and b) demonstrates that epigenetic age estimates that incorporate information on blood cell counts lead to highly significant associations with all-cause mortality.",0
"mutations generate sequence diversity and provide a substrate for selection. the rate of de novo mutations is therefore of major importance to evolution. here we conduct a study of genome-wide mutation rates by sequencing the entire genomes of 78 icelandic parent-offspring trios at high coverage. we show that in our samples, with an average father's age of 29.7, the average de novo mutation rate is 1.20 × 10(-8) per nucleotide per generation. most notably, the diversity in mutation rate of single nucleotide polymorphisms is dominated by the age of the father at conception of the child. the effect is an increase of about two mutations per year. an exponential model estimates paternal mutations doubling every 16.5 years. after accounting for random poisson variation, father's age is estimated to explain nearly all of the remaining variation in the de novo mutation counts. these observations shed light on the importance of the father's age on the risk of diseases such as schizophrenia and autism.",0
"background healthy childhood development is fostered through sufficient physical activity (pa; including time outdoors), limiting sedentary behaviours (sb), and adequate sleep; collectively known as movement behaviours. though the covid-19 virus outbreak has changed the daily lives of children and youth, it is unknown to what extent related restrictions may compromise the ability to play and meet movement behaviour recommendations. this secondary data analysis examined the immediate impacts of covid-19 restrictions on movement and play behaviours in children and youth. methods a national sample of canadian parents (n = 1472) of children (5-11 years) or youth (12-17 years) (54% girls) completed an online survey that assessed immediate changes in child movement and play behaviours during the covid-19 outbreak. behaviours included pa and play, sb, and sleep. family demographics and parental factors that may influence movement behaviours were assessed. correlations between behaviours and demographic and parental factors were determined. for open-ended questions, word frequency distributions were reported. results only 4.8% (2.8% girls, 6.5% boys) of children and 0.6% (0.8% girls, 0.5% boys) of youth were meeting combined movement behaviour guidelines during covid-19 restrictions. children and youth had lower pa levels, less outside time, higher sb (including leisure screen time), and more sleep during the outbreak. parental encouragement and support, parental engagement in pa, and family dog ownership were positively associated with healthy movement behaviours. although families spent less time in pa and more time in sb, several parents reported adopting new hobbies or accessing new resources. conclusions this study provides evidence of immediate collateral consequences of the covid-19 outbreak, demonstrating an adverse impact on the movement and play behaviours of canadian children and youth. these findings can guide efforts to preserve and promote child health during the covid-19 outbreak and crisis recovery period, and to inform strategies to mitigate potential harm during future pandemics.",0
"a hitherto unknown rod-shaped cytoplasmic component which consists of a bundle of fine tubules, enveloped by a tightly fitted membrane, was regularly found in endothelial cells of small arteries in various organs in rat and man. it is about 0.1 micro thick, measures up to 3 micro in length, and contains several small tubules, approximately 150 a thick, embedded in a dense matrix, and disposed parallel to the long axis of the rod. in some of these cells, the cisternae of the endoplasmic reticulum are greatly distended by the accumulation of a dense, finely granular material. the nature and significance of these cytoplasmic components are yet unknown.",0
"the newest version of mummer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. two new graphical viewing tools provide alternative ways to analyze genome alignments. the new system is the first version of mummer to be released as open-source software. this allows other developers to contribute to the code base and freely redistribute the code. the mummer sources are available at",0
"unlabelled dendextend is an r package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objects (their color, shape and content) as well as several advanced methods for comparing trees to one another (both statistically and visually). as such, dendextend offers a flexible framework for enhancing r's rich ecosystem of packages for performing hierarchical clustering of items. availability and implementation the dendextend r package (including detailed introductory vignettes) is available under the gpl-2 open source license and is freely available to download from cran at: ( contact tal.galili@math.tau.ac.il.",0
"childhood obesity has reached epidemic levels in developed as well as in developing countries. overweight and obesity in childhood are known to have significant impact on both physical and psychological health. overweight and obese children are likely to stay obese into adulthood and more likely to develop non-communicable diseases like diabetes and cardiovascular diseases at a younger age. the mechanism of obesity development is not fully understood and it is believed to be a disorder with multiple causes. environmental factors, lifestyle preferences, and cultural environment play pivotal roles in the rising prevalence of obesity worldwide. in general, overweight and obesity are assumed to be the results of an increase in caloric and fat intake. on the other hand, there are supporting evidence that excessive sugar intake by soft drink, increased portion size, and steady decline in physical activity have been playing major roles in the rising rates of obesity all around the world. childhood obesity can profoundly affect children's physical health, social, and emotional well-being, and self esteem. it is also associated with poor academic performance and a lower quality of life experienced by the child. many co-morbid conditions like metabolic, cardiovascular, orthopedic, neurological, hepatic, pulmonary, and renal disorders are also seen in association with childhood obesity.",0
"background pneumococcal conjugate vaccine (pcv) and haemophilus influenzae type b (hib) vaccine are now used in most countries. to monitor global and regional progress towards improving child health and to inform national policies for disease prevention and treatment, we prepared global, regional, and national disease burden estimates for these pathogens in children from 2000 to 2015. methods using who and maternal and child epidemiology estimation collaboration country-specific estimates of pneumonia and meningitis mortality and pneumonia morbidity from 2000 to 2015, we applied pneumococcal and hib cause-specific proportions to estimate pathogen-specific deaths and cases. summary estimates of the proportion of pneumonia deaths and cases attributable to these pathogens were derived from four hib vaccine and six pcv efficacy and effectiveness study values. the proportion of meningitis deaths due to each pathogen was derived from bacterial meningitis aetiology and adjusted pathogen-specific meningitis case-fatality data. pneumococcal and hib meningitis cases were inferred from modelled pathogen-specific meningitis deaths and literature-derived case-fatality estimates. cases of pneumococcal and hib syndromes other than pneumonia and meningitis were estimated using the ratio of pathogen-specific non-pneumonia, non-meningitis cases to pathogen-specific meningitis cases from the literature. we accounted for annual hiv infection prevalence, access to care, and vaccine use. findings we estimated that there were 294 000 pneumococcal deaths (uncertainty range 192 000-366 000) and 29 500 hib deaths (18 400-40 700) in hiv-uninfected children aged 1-59 months in 2015. an additional 23 300 deaths (15 300-28 700) associated with pneumococcus and fewer than 1000 deaths associated hib were estimated to have occurred in children infected with hiv. we estimate that pneumococcal deaths declined by 51% (7-74) and hib deaths by 90% (78-96) from 2000 to 2015. most children who died of pneumococcus (81%) and hib (76%) presented with pneumonia. less conservative assumptions result in pneumococcccal death estimates that could be as high as 515 000 deaths (302 000-609 000) in 2015. approximately 50% of all pneumococcal deaths in 2015 occurred in four countries in africa and asia: india (68 700 deaths, ur 44 600-86 100), nigeria (49 000 deaths, 32 400-59 000), the democratic republic of the congo (14 500 deaths, 9300-18 700), and pakistan (14 400 deaths, 9700-17 000]). india (15 600 deaths, 9800-21 500), nigeria (3600 deaths, 2200-5100), china (3400 deaths, 2300-4600), and south sudan (1000 deaths, 600-1400) had the greatest number of hib deaths in 2015. we estimated 3·7 million episodes (ur 2·7 million-4·3 million) of severe pneumococcus and 340 000 episodes (196 000-669 000) of severe hib globally in children in 2015. interpretation the widespread use of hib vaccine and the recent introduction of pcv in countries with high child mortality is associated with reductions in hib and pneumococcal cases and deaths. uncertainties in the burden of pneumococcal disease are largely driven by the fraction of pneumonia deaths attributable to pneumococcus. progress towards further reducing the global burden of hib and pneumococcal disease burden will depend on the efforts of a few large countries in africa and asia. funding bill & melinda gates foundation.",0
"objective overweight and obese individuals are encouraged to lose 5-10% of their body weight to improve cardiovascular disease (cvd) risk, but data supporting this recommendation are limited, particularly for individuals with type 2 diabetes. research design and methods we conducted an observational analysis of participants in the look ahead (action for health in diabetes) study (n=5,145, 40.5% male, 37% from ethnic/racial minorities) and examined the association between the magnitude of weight loss and changes in cvd risk factors at 1 year and the odds of meeting predefined criteria for clinically significant improvements in risk factors in individuals with type 2 diabetes. results the magnitude of weight loss at 1 year was strongly (p conclusions modest weight losses of 5 to <10% were associated with significant improvements in cvd risk factors at 1 year, but larger weight losses had greater benefits.",0
"study question what is the recommended assessment and management of women with polycystic ovary syndrome (pcos), based on the best available evidence, clinical expertise and consumer preference? summary answer international evidence-based guidelines, including 166 recommendations and practice points, addressed prioritized questions to promote consistent, evidence-based care and improve the experience and health outcomes of women with pcos. what is known already previous guidelines either lacked rigorous evidence-based processes, did not engage consumer and international multidisciplinary perspectives, or were outdated. diagnosis of pcos remains controversial, and assessment and management are inconsistent. the needs of women with pcos are not being adequately met and evidence practice gaps persist. study design, size, duration international evidence-based guideline development engaged professional societies and consumer organizations with multidisciplinary experts and women with pcos directly involved at all stages. appraisal of guidelines for research and evaluation (agree) ii-compliant processes were followed, with extensive evidence synthesis. the grading of recommendations, assessment, development and evaluation (grade) framework was applied across evidence quality, feasibility, acceptability, cost, implementation and ultimately recommendation strength. participants/materials, setting, methods governance included a six continent international advisory and a project board, five guideline development groups, and consumer and translation committees. extensive health professional and consumer engagement informed guideline scope and priorities. engaged international society-nominated panels included pediatrics, endocrinology, gynecology, primary care, reproductive endocrinology, obstetrics, psychiatry, psychology, dietetics, exercise physiology, public health and other experts, alongside consumers, project management, evidence synthesis and translation experts. in total, 37 societies and organizations covering 71 countries engaged in the process. twenty face-to-face meetings over 15 months addressed 60 prioritized clinical questions involving 40 systematic and 20 narrative reviews. evidence-based recommendations were developed and approved via consensus voting within the five guideline panels, modified based on international feedback and peer review, with final recommendations approved across all panels. main results and the role of chance the evidence in the assessment and management of pcos is generally of low to moderate quality. the guideline provides 31 evidence based recommendations, 59 clinical consensus recommendations and 76 clinical practice points all related to assessment and management of pcos. key changes in this guideline include: (i) considerable refinement of individual diagnostic criteria with a focus on improving accuracy of diagnosis; (ii) reducing unnecessary testing; (iii) increasing focus on education, lifestyle modification, emotional wellbeing and quality of life; and (iv) emphasizing evidence based medical therapy and cheaper and safer fertility management. limitations, reasons for caution overall evidence is generally low to moderate quality, requiring significantly greater research in this neglected, yet common condition, especially around refining specific diagnostic features in pcos. regional health system variation is acknowledged and a process for guideline and translation resource adaptation is provided. wider implications of the findings the international guideline for the assessment and management of pcos provides clinicians with clear advice on best practice based on the best available evidence, expert multidisciplinary input and consumer preferences. research recommendations have been generated and a comprehensive multifaceted dissemination and translation program supports the guideline with an integrated evaluation program. study funding/competing interest(s) the guideline was primarily funded by the australian national health and medical research council of australia (nhmrc) supported by a partnership with eshre and the american society for reproductive medicine. guideline development group members did not receive payment. travel expenses were covered by the sponsoring organizations. disclosures of conflicts of interest were declared at the outset and updated throughout the guideline process, aligned with nhmrc guideline processes. full details of conflicts declared across the guideline development groups are available at in the register of disclosures of interest. of named authors, dr costello has declared shares in virtus health and past sponsorship from merck serono for conference presentations. prof. laven declared grants from ferring, euroscreen and personal fees from ferring, euroscreen, danone and titus healthcare. prof. norman has declared a minor shareholder interest in an ivf unit. the remaining authors have no conflicts of interest to declare. the guideline was peer reviewed by special interest groups across our partner and collaborating societies and consumer organizations, was independently assessed against agree-ii criteria, and underwent methodological review. this guideline was approved by all members of the guideline development groups and was submitted for final approval by the nhmrc.",0
"background the exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. for the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. methodology/principal findings in order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic fluorescent pictograph - or efp - browser, available at for exploring microarray and other data for hypothesis generation. this efp browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. we give examples of using the tool to present arabidopsis gene expression data from the atgenexpress consortium (arabidopsis efp browser), data for subcellular localization of arabidopsis proteins (cell efp browser), and mouse tissue atlas microarray data (mouse efp browser). conclusions/significance the efp browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.",0
"background mathematical modelling of infectious diseases transmitted by the respiratory or close-contact route (e.g., pandemic influenza) is increasingly being used to determine the impact of possible interventions. although mixing patterns are known to be crucial determinants for model outcome, researchers often rely on a priori contact assumptions with little or no empirical basis. we conducted a population-based prospective survey of mixing patterns in eight european countries using a common paper-diary methodology. methods and findings 7,290 participants recorded characteristics of 97,904 contacts with different individuals during one day, including age, sex, location, duration, frequency, and occurrence of physical contact. we found that mixing patterns and contact characteristics were remarkably similar across different european countries. contact patterns were highly assortative with age: schoolchildren and young adults in particular tended to mix with people of the same age. contacts lasting at least one hour or occurring on a daily basis mostly involved physical contact, while short duration and infrequent contacts tended to be nonphysical. contacts at home, school, or leisure were more likely to be physical than contacts at the workplace or while travelling. preliminary modelling indicates that 5- to 19-year-olds are expected to suffer the highest incidence during the initial epidemic phase of an emerging infection transmitted through social contacts measured here when the population is completely susceptible. conclusions to our knowledge, our study provides the first large-scale quantitative approach to contact patterns relevant for infections transmitted by the respiratory or close-contact route, and the results should lead to improved parameterisation of mathematical models used to design control strategies.",0
"despite the ever-increasing output of illumina sequencing data, loci with extreme base compositions are often under-represented or absent. to evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% gc through the process by quantitative pcr. we identified pcr during library preparation as a principal source of bias and optimized the conditions. our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of pcr instrument and temperature ramp rate.",0
"the american diabetes association and the european association for the study of diabetes convened a panel to update the prior position statements, published in 2012 and 2015, on the management of type 2 diabetes in adults. a systematic evaluation of the literature since 2014 informed new recommendations. these include additional focus on lifestyle management and diabetes self-management education and support. for those with obesity, efforts targeting weight loss, including lifestyle, medication, and surgical interventions, are recommended. with regards to medication management, for patients with clinical cardiovascular disease, a sodium-glucose cotransporter 2 (sglt2) inhibitor or a glucagon-like peptide 1 (glp-1) receptor agonist with proven cardiovascular benefit is recommended. for patients with chronic kidney disease or clinical heart failure and atherosclerotic cardiovascular disease, an sglt2 inhibitor with proven benefit is recommended. glp-1 receptor agonists are generally recommended as the first injectable medication.",0
"pilot studies for phase iii trials - which are comparative randomized trials designed to provide preliminary evidence on the clinical efficacy of a drug or intervention - are routinely performed in many clinical areas. also commonly know as ""feasibility"" or ""vanguard"" studies, they are designed to assess the safety of treatment or interventions; to assess recruitment potential; to assess the feasibility of international collaboration or coordination for multicentre trials; to increase clinical experience with the study medication or intervention for the phase iii trials. they are the best way to assess feasibility of a large, expensive full-scale study, and in fact are an almost essential pre-requisite. conducting a pilot prior to the main study can enhance the likelihood of success of the main study and potentially help to avoid doomed main studies. the objective of this paper is to provide a detailed examination of the key aspects of pilot studies for phase iii trials including: 1) the general reasons for conducting a pilot study; 2) the relationships between pilot studies, proof-of-concept studies, and adaptive designs; 3) the challenges of and misconceptions about pilot studies; 4) the criteria for evaluating the success of a pilot study; 5) frequently asked questions about pilot studies; 7) some ethical aspects related to pilot studies; and 8) some suggestions on how to report the results of pilot investigations using the consort format.",0
"background: there is a continued need to develop more effective cancer immunotherapy strategies. exosomes, cell-derived lipid vesicles that express high levels of a narrow spectrum of cell proteins represent a novel platform for delivering high levels of antigen in conjunction with costimulatory molecules. we performed this study to test the safety, feasibility and efficacy of autologous dendritic cell (dc)-derived exosomes (dex) loaded with the mage tumor antigens in patients with non-small cell lung cancer (nsclc). methods: this phase i study enrolled hla a2+ patients with pre-treated stage iiib (n = 4) and iv (n = 9) nsclc with tumor expression of mage-a3 or a4. patients underwent leukapheresis to generate dc from which dex were produced and loaded with mage-a3, -a4, -a10, and mage-3dpo4 peptides. patients received 4 doses of dex at weekly intervals. results: thirteen patients were enrolled and 9 completed therapy. three formulations of dex were evaluated; all were well tolerated with only grade 1-2 adverse events related to the use of dex (injection site reactions (n = 8), flu like illness (n = 1), and peripheral arm pain (n = 1)). the time from the first dose of dex until disease progression was 30 to 429+ days. three patients had disease progression before the first dex dose. survival of patients after the first dex dose was 52-665+ days. dth reactivity against mage peptides was detected in 3/9 patients. immune responses were detected in patients as follows: mage-specific t cell responses in 1/3, increased nk lytic activity in 2/4. conclusion: production of the dex vaccine was feasible and dex therapy was well tolerated in patients with advanced nsclc. some patients experienced long term stability of disease and activation of immune effectors.",0
"the human phenotype ontology (hpo, was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. the hpo is now a worldwide standard for phenotype exchange. the hpo has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. here, we present recent major extensions of the hpo for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. for example, the seizure subontology now reflects the international league against epilepsy (ilae) guidelines and these enhancements have already shown clinical validity. we present new efforts to harmonize computational definitions of phenotypic abnormalities across the hpo and multiple phenotype ontologies used for animal models of disease. these efforts will benefit software such as exomiser by improving the accuracy and scope of cross-species phenotype matching. the computational modeling strategy used by the hpo to define disease entities and phenotypic features and distinguish between them is explained in detail.we also report on recent efforts to translate the hpo into indigenous languages. finally, we summarize recent advances in the use of hpo in electronic health record systems.",0
"problem/condition autism spectrum disorder (asd). period covered 2018. description of system the autism and developmental disabilities monitoring (addm) network conducts active surveillance of asd. this report focuses on the prevalence and characteristics of asd among children aged 8 years in 2018 whose parents or guardians lived in 11 addm network sites in the united states (arizona, arkansas, california, georgia, maryland, minnesota, missouri, new jersey, tennessee, utah, and wisconsin). to ascertain asd among children aged 8 years, addm network staff review and abstract developmental evaluations and records from community medical and educational service providers. in 2018, children met the case definition if their records documented 1) an asd diagnostic statement in an evaluation (diagnosis), 2) a special education classification of asd (eligibility), or 3) an asd international classification of diseases (icd) code. results for 2018, across all 11 addm sites, asd prevalence per 1,000 children aged 8 years ranged from 16.5 in missouri to 38.9 in california. the overall asd prevalence was 23.0 per 1,000 (one in 44) children aged 8 years, and asd was 4.2 times as prevalent among boys as among girls. overall asd prevalence was similar across racial and ethnic groups, except american indian/alaska native children had higher asd prevalence than non-hispanic white (white) children (29.0 versus 21.2 per 1,000 children aged 8 years). at multiple sites, hispanic children had lower asd prevalence than white children (arizona, arkansas, georgia, and utah), and non-hispanic black (black) children (georgia and minnesota). the associations between asd prevalence and neighborhood-level median household income varied by site. among the 5,058 children who met the asd case definition, 75.8% had a diagnostic statement of asd in an evaluation, 18.8% had an asd special education classification or eligibility and no asd diagnostic statement, and 5.4% had an asd icd code only. asd prevalence per 1,000 children aged 8 years that was based exclusively on documented asd diagnostic statements was 17.4 overall (range: 11.2 in maryland to 29.9 in california). the median age of earliest known asd diagnosis ranged from 36 months in california to 63 months in minnesota. among the 3,007 children with asd and data on cognitive ability, 35.2% were classified as having an intelligence quotient (iq) score ≤70. the percentages of children with asd with iq scores ≤70 were 49.8%, 33.1%, and 29.7% among black, hispanic, and white children, respectively. overall, children with asd and iq scores ≤70 had earlier median ages of asd diagnosis than children with asd and iq scores >70 (44 versus 53 months). interpretation in 2018, one in 44 children aged 8 years was estimated to have asd, and prevalence and median age of identification varied widely across sites. whereas overall asd prevalence was similar by race and ethnicity, at certain sites hispanic children were less likely to be identified as having asd than white or black children. the higher proportion of black children compared with white and hispanic children classified as having intellectual disability was consistent with previous findings. public health action the variability in asd prevalence and community asd identification practices among children with different racial, ethnic, and geographical characteristics highlights the importance of research into the causes of that variability and strategies to provide equitable access to developmental evaluations and services. these findings also underscore the need for enhanced infrastructure for diagnostic, treatment, and support services to meet the needs of all children.",0
"background: the 2019 coronavirus disease (covid-19) epidemic is a public health emergency of international concern and poses a challenge to psychological resilience. research data are needed to develop evidence-driven strategies to reduce adverse psychological impacts and psychiatric symptoms during the epidemic. the aim of this study was to survey the general public in china to better understand their levels of psychological impact, anxiety, depression, and stress during the initial stage of the covid-19 outbreak. the data will be used for future reference. methods: from 31 january to 2 february 2020, we conducted an online survey using snowball sampling techniques. the online survey collected information on demographic data, physical symptoms in the past 14 days, contact history with covid-19, knowledge and concerns about covid-19, precautionary measures against covid-19, and additional information required with respect to covid-19. psychological impact was assessed by the impact of event scale-revised (ies-r), and mental health status was assessed by the depression, anxiety and stress scale (dass-21). results: this study included 1210 respondents from 194 cities in china. in total, 53.8% of respondents rated the psychological impact of the outbreak as moderate or severe; 16.5% reported moderate to severe depressive symptoms; 28.8% reported moderate to severe anxiety symptoms; and 8.1% reported moderate to severe stress levels. most respondents spent 20-24 h per day at home (84.7%); were worried about their family members contracting covid-19 (75.2%); and were satisfied with the amount of health information available (75.1%). female gender, student status, specific physical symptoms (e.g., myalgia, dizziness, coryza), and poor self-rated health status were significantly associated with a greater psychological impact of the outbreak and higher levels of stress, anxiety, and depression ( p p conclusions: during the initial phase of the covid-19 outbreak in china, more than half of the respondents rated the psychological impact as moderate-to-severe, and about one-third reported moderate-to-severe anxiety. our findings identify factors associated with a lower level of psychological impact and better mental health status that can be used to formulate psychological interventions to improve the mental health of vulnerable groups during the covid-19 epidemic.",0
"the mechanisms underlying cd4(+) t cell depletion in human immunodeficiency virus (hiv) infection are not well understood. comparative studies of lymphoid tissues, where the vast majority of t cells reside, and peripheral blood can potentially illuminate the pathogenesis of hiv-associated disease. here, we studied the effect of hiv infection on the activation and depletion of defined subsets of cd4(+) and cd8(+) t cells in the blood, gastrointestinal (gi) tract, and lymph node (ln). we also measured hiv-specific t cell frequencies in lns and blood, and ln collagen deposition to define architectural changes associated with chronic inflammation. the major findings to emerge are the following: the gi tract has the most substantial cd4(+) t cell depletion at all stages of hiv disease; this depletion occurs preferentially within ccr5(+) cd4(+) t cells; hiv-associated immune activation results in abnormal accumulation of effector-type t cells within lns; hiv-specific t cells in lns do not account for all effector t cells; and t cell activation in lns is associated with abnormal collagen deposition. taken together, these findings define the nature and extent of cd4(+) t cell depletion in lymphoid tissue and point to mechanisms of profound depletion of specific t cell subsets related to elimination of ccr5(+) cd4(+) t cell targets and disruption of t cell homeostasis that accompanies chronic immune activation.",0
"background in 2010, the european working group on sarcopenia in older people (ewgsop) published a sarcopenia definition that aimed to foster advances in identifying and caring for people with sarcopenia. in early 2018, the working group met again (ewgsop2) to update the original definition in order to reflect scientific and clinical evidence that has built over the last decade. this paper presents our updated findings. objectives to increase consistency of research design, clinical diagnoses and ultimately, care for people with sarcopenia. recommendations sarcopenia is a muscle disease (muscle failure) rooted in adverse muscle changes that accrue across a lifetime; sarcopenia is common among adults of older age but can also occur earlier in life. in this updated consensus paper on sarcopenia, ewgsop2: (1) focuses on low muscle strength as a key characteristic of sarcopenia, uses detection of low muscle quantity and quality to confirm the sarcopenia diagnosis, and identifies poor physical performance as indicative of severe sarcopenia; (2) updates the clinical algorithm that can be used for sarcopenia case-finding, diagnosis and confirmation, and severity determination and (3) provides clear cut-off points for measurements of variables that identify and characterise sarcopenia. conclusions ewgsop2's updated recommendations aim to increase awareness of sarcopenia and its risk. with these new recommendations, ewgsop2 calls for healthcare professionals who treat patients at risk for sarcopenia to take actions that will promote early detection and treatment. we also encourage more research in the field of sarcopenia in order to prevent or delay adverse health outcomes that incur a heavy burden for patients and healthcare systems.",0
"current genome-wide association studies (gwas) use commercial genotyping microarrays that can assay over a million single nucleotide polymorphisms (snps). the number of snps is further boosted by advanced statistical genotype-imputation algorithms and large snp databases for reference human populations. the testing of a huge number of snps needs to be taken into account in the interpretation of statistical significance in such genome-wide studies, but this is complicated by the non-independence of snps because of linkage disequilibrium (ld). several previous groups have proposed the use of the effective number of independent markers (m(e)) for the adjustment of multiple testing, but current methods of calculation for m(e) are limited in accuracy or computational speed. here, we report a more robust and fast method to calculate m(e). applying this efficient method , we systematically examined the m(e), and the corresponding p-value thresholds required to control the genome-wide type 1 error rate at 0.05, for 13 illumina or affymetrix genotyping arrays, as well as for hapmap project and 1000 genomes project datasets which are widely used in genotype imputation as reference panels. our results suggested the use of a p-value threshold of ~10(-7) as the criterion for genome-wide significance for early commercial genotyping arrays, but slightly more stringent p-value thresholds ~5 × 10(-8) for current or merged commercial genotyping arrays, ~10(-8) for all common snps in the 1000 genomes project dataset and ~5 × 10(-8) for the common snps only within genes.",0
"background frailty can be measured in relation to the accumulation of deficits using a frailty index. a frailty index can be developed from most ageing databases. our objective is to systematically describe a standard procedure for constructing a frailty index. methods this is a secondary analysis of the yale precipitating events project cohort study, based in new haven ct. non-disabled people aged 70 years or older (n = 754) were enrolled and re-contacted every 18 months. the database includes variables on function, cognition, co-morbidity, health attitudes and practices and physical performance measures. data came from the baseline cohort and those available at the first 18-month follow-up assessment. results procedures for selecting health variables as candidate deficits were applied to yield 40 deficits. recoding procedures were applied for categorical, ordinal and interval variables such that they could be mapped to the interval 0-1, where 0 = absence of a deficit, and 1= full expression of the deficit. these individual deficit scores were combined in an index, where 0= no deficit present, and 1= all 40 deficits present. the values of the index were well fit by a gamma distribution. between the baseline and follow-up cohorts, the age-related slope of deficit accumulation increased from 0.020 (95% confidence interval, 0.014-0.026) to 0.026 (0.020-0.032). the 99% limit to deficit accumulation was 0.6 in the baseline cohort and 0.7 in the follow-up cohort. multivariate cox analysis showed the frailty index, age and sex to be significant predictors of mortality. conclusion a systematic process for creating a frailty index, which relates deficit accumulation to the individual risk of death, showed reproducible properties in the yale precipitating events project cohort study. this method of quantifying frailty can aid our understanding of frailty-related health characteristics in older adults.",0
"the propensity score is defined as a subject's probability of treatment selection, conditional on observed baseline covariates. weighting subjects by the inverse probability of treatment received creates a synthetic sample in which treatment assignment is independent of measured baseline covariates. inverse probability of treatment weighting (iptw) using the propensity score allows one to obtain unbiased estimates of average treatment effects. however, these estimates are only valid if there are no residual systematic differences in observed baseline characteristics between treated and control subjects in the sample weighted by the estimated inverse probability of treatment. we report on a systematic literature review, in which we found that the use of iptw has increased rapidly in recent years, but that in the most recent year, a majority of studies did not formally examine whether weighting balanced measured covariates between treatment groups. we then proceed to describe a suite of quantitative and qualitative methods that allow one to assess whether measured baseline covariates are balanced between treatment groups in the weighted sample. the quantitative methods use the weighted standardized difference to compare means, prevalences, higher-order moments, and interactions. the qualitative methods employ graphical methods to compare the distribution of continuous baseline covariates between treated and control subjects in the weighted sample. finally, we illustrate the application of these methods in an empirical case study. we propose a formal set of balance diagnostics that contribute towards an evolving concept of 'best practice' when using iptw to estimate causal treatment effects using observational data.",0
"expasy ( has worldwide reputation as one of the main bioinformatics resources for proteomics. it has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. the individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the sib swiss institute of bioinformatics and partner institutions. specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different sib groups and external institutions. the portal features a search function across 'selected' resources. additionally, the availability and usage of resources are monitored. the portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. the new web interface provides, in particular, visual guidance for newcomers to expasy.",0
"background there is increasing interest in the potential role of the natural environment in human health and well-being. however, the evidence-base for specific and direct health or well-being benefits of activity within natural compared to more synthetic environments has not been systematically assessed. methods we conducted a systematic review to collate and synthesise the findings of studies that compare measurements of health or well-being in natural and synthetic environments. effect sizes of the differences between environments were calculated and meta-analysis used to synthesise data from studies measuring similar outcomes. results twenty-five studies met the review inclusion criteria. most of these studies were crossover or controlled trials that investigated the effects of short-term exposure to each environment during a walk or run. this included 'natural' environments, such as public parks and green university campuses, and synthetic environments, such as indoor and outdoor built environments. the most common outcome measures were scores of different self-reported emotions. based on these data, a meta-analysis provided some evidence of a positive benefit of a walk or run in a natural environment in comparison to a synthetic environment. there was also some support for greater attention after exposure to a natural environment but not after adjusting effect sizes for pretest differences. meta-analysis of data on blood pressure and cortisol concentrations found less evidence of a consistent difference between environments across studies. conclusions overall, the studies are suggestive that natural environments may have direct and positive impacts on well-being, but support the need for investment in further research on this question to understand the general significance for public health.",0
"antigen activation of dna synthesis in immune thymus-derived lymphocytes of guinea pigs requires the cooperation of macrophages and lymphocytes. we have investigated the role of histocompatibility determinants in this macrophage-lymphocyte interaction using cells from inbred strain 2 and 13 guinea pigs. the data demonstrate that efficient presentation of macrophage-associated antigen to the lymphocyte requires identity between macrophage and lymphocyte at some portion of the major histocompatibility complex. the failure of allogeneic macrophages to effectively initiate immune lymphocyte proliferation was not the result of the presence of an inhibitor of blastogenesis released in mixtures of allogeneic cells, peculiarities of the antigen or lymphoid cells employed, nor differing kinetics of activation by allogeneic macrophages. in addition, data were presented that demonstrated that alloantisera inhibit lymphocyte dna synthesis by functional interference with macrophage-lymphocyte interaction.",0
"long terminal repeat retrotransposons (ltr elements) are ubiquitous eukaryotic transposable elements. they play important roles in the evolution of genes and genomes. ever-growing amount of genomic sequences of many organisms present a great challenge to fast identifying them. that is the first and indispensable step to study their structure, distribution, functions and other biological impacts. however, until today, tools for efficient ltr retrotransposon discovery are very limited. thus, we developed ltr_finder web server. given dna sequences, it predicts locations and structure of full-length ltr retrotransposons accurately by considering common structural features. ltr_finder is a system capable of scanning large-scale sequences rapidly and the first web server for ab initio ltr retrotransposon finding. we illustrate its usage and performance on the genome of saccharomyces cerevisiae. the web server is freely accessible at",0
"we investigated the antigen specificity and presentation requirements for inactivation of t lymphocytes in vitro and in vivo. in vitro studies revealed that splenocytes treated with the crosslinker 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (ecdi) and soluble antigen fragments failed to stimulate significant proliferation by normal pigeon cytochrome c-specific t cell clones, suggesting that the chemical treatment inactivated full antigen presentation function. however, t cell clones exposed to ecdi-treated splenocytes and antigen in vitro were rendered unresponsive for at least 8 d to subsequent antigen stimulation with normal presenting cells. as predicted by the in vitro results, specific t cell unresponsiveness was also induced in vivo in b10.a mice injected intravenously with b10.a, but not b10.a(4r), splenocytes coupled with pigeon cytochrome c via ecdi. the antigen and mhc specificity of the induction of this t cell unresponsiveness in vitro and in vivo was identical to that required for t cell activation. these results suggest that nonmitogenic t cell recognition of antigen/mhc on ecdi-modified apcs results in the functional inactivation of t cell clones.",0
"background frailty is an especially problematic expression of population ageing. international guidelines recommend routine identification of frailty to provide evidence-based treatment, but currently available tools require additional resource. objectives to develop and validate an electronic frailty index (efi) using routinely available primary care electronic health record data. study design and setting retrospective cohort study. development and internal validation cohorts were established using a randomly split sample of the researchone primary care database. external validation cohort established using thin database. participants patients aged 65-95, registered with a researchone or thin practice on 14 october 2008. predictors we constructed the efi using the cumulative deficit frailty model as our theoretical framework. the efi score is calculated by the presence or absence of individual deficits as a proportion of the total possible. categories of fit, mild, moderate and severe frailty were defined using population quartiles. outcomes outcomes were 1-, 3- and 5-year mortality, hospitalisation and nursing home admission. statistical analysis hazard ratios (hrs) were estimated using bivariate and multivariate cox regression analyses. discrimination was assessed using receiver operating characteristic (roc) curves. calibration was assessed using pseudo-r(2) estimates. results we include data from a total of 931,541 patients. the efi incorporates 36 deficits constructed using 2,171 ctv3 codes. one-year adjusted hr for mortality was 1.92 (95% ci 1.81-2.04) for mild frailty, 3.10 (95% ci 2.91-3.31) for moderate frailty and 4.52 (95% ci 4.16-4.91) for severe frailty. corresponding estimates for hospitalisation were 1.93 (95% ci 1.86-2.01), 3.04 (95% ci 2.90-3.19) and 4.73 (95% ci 4.43-5.06) and for nursing home admission were 1.89 (95% ci 1.63-2.15), 3.19 (95% ci 2.73-3.73) and 4.76 (95% ci 3.92-5.77), with good to moderate discrimination but low calibration estimates. conclusions the efi uses routine data to identify older people with mild, moderate and severe frailty, with robust predictive validity for outcomes of mortality, hospitalisation and nursing home admission. routine implementation of the efi could enable delivery of evidence-based interventions to improve outcomes for this vulnerable group.",0
"diffuse large b-cell lymphoma (dlbcl) is the most common form of human lymphoma. although a number of structural alterations have been associated with the pathogenesis of this malignancy, the full spectrum of genetic lesions that are present in the dlbcl genome, and therefore the identity of dysregulated cellular pathways, remains unknown. by combining next-generation sequencing and copy number analysis, we show that the dlbcl coding genome contains, on average, more than 30 clonally represented gene alterations per case. this analysis also revealed mutations in genes not previously implicated in dlbcl pathogenesis, including those regulating chromatin methylation (mll2; 24% of samples) and immune recognition by t cells. these results provide initial data on the complexity of the dlbcl coding genome and identify novel dysregulated pathways underlying its pathogenesis.",0
"background underweight and severe and morbid obesity are associated with highly elevated risks of adverse health outcomes. we estimated trends in mean body-mass index (bmi), which characterises its population distribution, and in the prevalences of a complete set of bmi categories for adults in all countries. methods we analysed, with use of a consistent protocol, population-based studies that had measured height and weight in adults aged 18 years and older. we applied a bayesian hierarchical model to these data to estimate trends from 1975 to 2014 in mean bmi and in the prevalences of bmi categories ( findings we used 1698 population-based data sources, with more than 19·2 million adult participants (9·9 million men and 9·3 million women) in 186 of 200 countries for which estimates were made. global age-standardised mean bmi increased from 21·7 kg/m(2) (95% credible interval 21·3-22·1) in 1975 to 24·2 kg/m(2) (24·0-24·4) in 2014 in men, and from 22·1 kg/m(2) (21·7-22·5) in 1975 to 24·4 kg/m(2) (24·2-24·6) in 2014 in women. regional mean bmis in 2014 for men ranged from 21·4 kg/m(2) in central africa and south asia to 29·2 kg/m(2) (28·6-29·8) in polynesia and micronesia; for women the range was from 21·8 kg/m(2) (21·4-22·3) in south asia to 32·2 kg/m(2) (31·5-32·8) in polynesia and micronesia. over these four decades, age-standardised global prevalence of underweight decreased from 13·8% (10·5-17·4) to 8·8% (7·4-10·3) in men and from 14·6% (11·6-17·9) to 9·7% (8·3-11·1) in women. south asia had the highest prevalence of underweight in 2014, 23·4% (17·8-29·2) in men and 24·0% (18·9-29·3) in women. age-standardised prevalence of obesity increased from 3·2% (2·4-4·1) in 1975 to 10·8% (9·7-12·0) in 2014 in men, and from 6·4% (5·1-7·8) to 14·9% (13·6-16·1) in women. 2·3% (2·0-2·7) of the world's men and 5·0% (4·4-5·6) of women were severely obese (ie, have bmi ≥35 kg/m(2)). globally, prevalence of morbid obesity was 0·64% (0·46-0·86) in men and 1·6% (1·3-1·9) in women. interpretation if post-2000 trends continue, the probability of meeting the global obesity target is virtually zero. rather, if these trends continue, by 2025, global obesity prevalence will reach 18% in men and surpass 21% in women; severe obesity will surpass 6% in men and 9% in women. nonetheless, underweight remains prevalent in the world's poorest regions, especially in south asia. funding wellcome trust, grand challenges canada.",0
"background reduced saturated fat (sfa) consumption is recommended to reduce coronary heart disease (chd), but there is an absence of strong supporting evidence from randomized controlled trials (rcts) of clinical chd events and few guidelines focus on any specific replacement nutrient. additionally, some public health groups recommend lowering or limiting polyunsaturated fat (pufa) consumption, a major potential replacement for sfa. methods and findings we systematically investigated and quantified the effects of increased pufa consumption, as a replacement for sfa, on chd endpoints in rcts. rcts were identified by systematic searches of multiple online databases through june 2009, grey literature sources, hand-searching related articles and citations, and direct contacts with experts to identify potentially unpublished trials. studies were included if they randomized participants to increased pufa for at least 1 year without major concomitant interventions, had an appropriate control group, and reported incidence of chd (myocardial infarction and/or cardiac death). inclusions/exclusions were adjudicated and data were extracted independently and in duplicate by two investigators and included population characteristics, control and intervention diets, follow-up duration, types of events, risk ratios, and ses. pooled effects were calculated using inverse-variance-weighted random effects meta-analysis. from 346 identified abstracts, eight trials met inclusion criteria, totaling 13,614 participants with 1,042 chd events. average weighted pufa consumption was 14.9% energy (range 8.0%-20.7%) in intervention groups versus 5.0% energy (range 4.0%-6.4%) in controls. the overall pooled risk reduction was 19% (rr = 0.81, 95% confidence interval 0.70-0.95, p = 0.008), corresponding to 10% reduced chd risk (rr = 0.90, 95% ci = 0.83-0.97) for each 5% energy of increased pufa, without evidence for statistical heterogeneity (q-statistic p = 0.13; i(2) = 37%). meta-regression identified study duration as an independent determinant of risk reduction (p = 0.017), with studies of longer duration showing greater benefits. conclusions these findings provide evidence that consuming pufa in place of sfa reduces chd events in rcts. this suggests that rather than trying to lower pufa consumption, a shift toward greater population pufa consumption in place of sfa would significantly reduce rates of chd. please see later in the article for the editors' summary.",0
"objective to test the efficacy of supplemental vitamin d and active forms of vitamin d with or without calcium in preventing falls among older individuals. data sources we searched medline, the cochrane central register of controlled trials, biosis, and embase up to august 2008 for relevant articles. further studies were identified by consulting clinical experts, bibliographies, and abstracts. we contacted authors for additional data when necessary. review methods only double blind randomised controlled trials of older individuals (mean age 65 years or older) receiving a defined oral dose of supplemental vitamin d (vitamin d(3) (cholecalciferol) or vitamin d(2) (ergocalciferol)) or an active form of vitamin d (1alpha-hydroxyvitamin d(3) (1alpha-hydroxycalciferol) or 1,25-dihydroxyvitamin d(3) (1,25-dihydroxycholecalciferol)) and with sufficiently specified fall assessment were considered for inclusion. results eight randomised controlled trials (n=2426) of supplemental vitamin d met our inclusion criteria. heterogeneity among trials was observed for dose of vitamin d (700-1000 iu/day v 200-600 iu/day; p=0.02) and achieved 25-hydroxyvitamin d(3) concentration (25(oh)d concentration: or=60 nmol/l; p=0.005). high dose supplemental vitamin d reduced fall risk by 19% (pooled relative risk (rr) 0.81, 95% ci 0.71 to 0.92; n=1921 from seven trials), whereas achieved serum 25(oh)d concentrations of 60 nmol/l or more resulted in a 23% fall reduction (pooled rr 0.77, 95% ci 0.65 to 0.90). falls were not notably reduced by low dose supplemental vitamin d (pooled rr 1.10, 95% ci 0.89 to 1.35; n=505 from two trials) or by achieved serum 25-hydroxyvitamin d concentrations of less than 60 nmol/l (pooled rr 1.35, 95% ci 0.98 to 1.84). two randomised controlled trials (n=624) of active forms of vitamin d met our inclusion criteria. active forms of vitamin d reduced fall risk by 22% (pooled rr 0.78, 95% ci 0.64 to 0.94). conclusions supplemental vitamin d in a dose of 700-1000 iu a day reduced the risk of falling among older individuals by 19% and to a similar degree as active forms of vitamin d. doses of supplemental vitamin d of less than 700 iu or serum 25-hydroxyvitamin d concentrations of less than 60 nmol/l may not reduce the risk of falling among older individuals.",0
"the clinical practice research datalink (cprd) is an ongoing primary care database of anonymised medical records from general practitioners, with coverage of over 11.3 million patients from 674 practices in the uk. with 4.4 million active (alive, currently registered) patients meeting quality criteria, approximately 6.9% of the uk population are included and patients are broadly representative of the uk general population in terms of age, sex and ethnicity. general practitioners are the gatekeepers of primary care and specialist referrals in the uk. the cprd primary care database is therefore a rich source of health data for research, including data on demographics, symptoms, tests, diagnoses, therapies, health-related behaviours and referrals to secondary care. for over half of patients, linkage with datasets from secondary care, disease-specific cohorts and mortality records enhance the range of data available for research. the cprd is very widely used internationally for epidemiological research and has been used to produce over 1000 research studies, published in peer-reviewed journals across a broad range of health outcomes. however, researchers must be aware of the complexity of routinely collected electronic health records, including ways to manage variable completeness, misclassification and development of disease definitions for research.",0
"brain regions in the mammalian cerebral cortex are linked by a complex network of fiber bundles. these inter-regional networks have previously been analyzed in terms of their node degree, structural motif, path length and clustering coefficient distributions. in this paper we focus on the identification and classification of hub regions, which are thought to play pivotal roles in the coordination of information flow. we identify hubs and characterize their network contributions by examining motif fingerprints and centrality indices for all regions within the cerebral cortices of both the cat and the macaque. motif fingerprints capture the statistics of local connection patterns, while measures of centrality identify regions that lie on many of the shortest paths between parts of the network. within both cat and macaque networks, we find that a combination of degree, motif participation, betweenness centrality and closeness centrality allows for reliable identification of hub regions, many of which have previously been functionally classified as polysensory or multimodal. we then classify hubs as either provincial (intra-cluster) hubs or connector (inter-cluster) hubs, and proceed to show that lesioning hubs of each type from the network produces opposite effects on the small-world index. our study presents an approach to the identification and classification of putative hub regions in brain networks on the basis of multiple network attributes and charts potential links between the structural embedding of such regions and their functional roles.",0
"objective to determine associations of gestational diabetes mellitus (gdm) and obesity with adverse pregnancy outcomes in the hyperglycemia and adverse pregnancy outcome (hapo) study. research design and methods participants underwent a 75-g oral glucose tolerance test (ogtt) between 24 and 32 weeks. gdm was diagnosed post hoc using international association of diabetes and pregnancy study groups criteria. neonatal anthropometrics and cord serum c-peptide were measured. adverse pregnancy outcomes included birth weight, newborn percent body fat, and cord c-peptide >90th percentiles, primary cesarean delivery, preeclampsia, and shoulder dystocia/birth injury. bmi was determined at the ogtt. multiple logistic regression was used to examine associations of gdm and obesity with outcomes. results mean maternal bmi was 27.7, 13.7% were obese (bmi ≥33.0 kg/m(2)), and gdm was diagnosed in 16.1%. relative to non-gdm and nonobese women, odds ratio for birth weight >90th percentile for gdm alone was 2.19 (1.93-2.47), for obesity alone 1.73 (1.50-2.00), and for both gdm and obesity 3.62 (3.04-4.32). results for primary cesarean delivery and preeclampsia and for cord c-peptide and newborn percent body fat >90th percentiles were similar. odds for birth weight >90th percentile were progressively greater with both higher ogtt glucose and higher maternal bmi. there was a 339-g difference in birth weight for babies of obese gdm women, compared with babies of normal/underweight women (64.2% of all women) with normal glucose based on a composite ogtt measure of fasting plasma glucose and 1- and 2-h plasma glucose values (61.8% of all women). conclusions both maternal gdm and obesity are independently associated with adverse pregnancy outcomes. their combination has a greater impact than either one alone.",0
"genome sequence assemblies provide the basis for our understanding of biology. generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near error-free genome assemblies for eukaryotes. whilst working towards improved datasets and fully automated pipelines, assembly evaluation and curation is actively used to bridge this shortcoming and significantly reduce the number of assembly errors. in addition to this increase in product value, the insights gained from assembly curation are fed back into the automated assembly strategy and contribute to notable improvements in genome assembly quality. we describe our tried and tested approach for assembly curation using geval, the genome evaluation browser. we outline the procedures applied to genome curation using geval and also our recommendations for assembly curation in a geval-independent context to facilitate the uptake of genome curation in the wider community.",0
"here we present singularity, software developed to bring containers and reproducibility to scientific computing. using singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. as its primary use case, singularity brings mobility of computing to both users and hpc centers, providing a secure means to capture and distribute software and compute environments. this ability to create and deploy reproducible environments across these centers, a previously unmet need, makes singularity a game changing development for computational science.",0
"whole genome sequencing (wgs) shows great potential for real-time monitoring and identification of infectious disease outbreaks. however, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. so far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. we developed two different procedures for identifying variable sites and inferring phylogenies in wgs data across multiple platforms. the methods were evaluated on three bacterial data sets and sequenced on three different platforms (illumina, 454, ion torrent). we show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. it is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. the procedures are available as web tools.",0
"kyoto encyclopedia of genes and genomes (kegg, or is a database resource that integrates genomic, chemical and systemic functional information. in particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of kegg pathway maps, brite functional hierarchies and kegg modules. continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the kegg orthology system. here we report kegg mapper, a collection of tools for kegg pathway, brite and module mapping, enabling integration and interpretation of large-scale data sets. we also report a variant of the kegg mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease genes and drug targets, are integrated as part of the kegg molecular networks. finally, we describe recent enhancements to the kegg content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.",0
"brb-arraytools is an integrated software system for the comprehensive analysis of dna microarray experiments. it was developed by professional biostatisticians experienced in the design and analysis of dna microarray studies and incorporates methods developed by leading statistical laboratories. the software is designed for use by biomedical scientists who wish to have access to state-of-the-art statistical methods for the analysis of gene expression data and to receive training in the statistical analysis of high dimensional data. the software provides the most extensive set of tools available for predictive classifier development and complete cross-validation. it offers extensive links to genomic websites for gene annotation and analysis tools for pathway analysis. an archive of over 100 datasets of published microarray data with associated clinical data is provided and brb-arraytools automatically imports data from the gene expression omnibus public archive at the national center for biotechnology information.",0
"cell-derived nanoparticles have been garnering increased attention due to their ability to mimic many of the natural properties displayed by their source cells. this top-down engineering approach can be applied toward the development of novel therapeutic strategies owing to the unique interactions enabled through the retention of complex antigenic information. herein, we report on the biological functionalization of polymeric nanoparticles with a layer of membrane coating derived from cancer cells. the resulting core-shell nanostructures, which carry the full array of cancer cell membrane antigens, offer a robust platform with applicability toward multiple modes of anticancer therapy. we demonstrate that by coupling the particles with an immunological adjuvant, the resulting formulation can be used to promote a tumor-specific immune response for use in vaccine applications. moreover, we show that by taking advantage of the inherent homotypic binding phenomenon frequently observed among tumor cells the membrane functionalization allows for a unique cancer targeting strategy that can be utilized for drug delivery applications.",0
"inflammasomes activate caspase-1 for processing and secretion of the cytokines interleukin-1beta (il-1beta) and il-18. cryopyrin/nalp3/nlrp3 is an essential component of inflammasomes triggered by microbial ligands, danger-associated molecular patterns (damps), and crystals. inappropriate cryopyrin activity has been incriminated in the pathogenesis of gouty arthritis, alzheimer's, and silicosis. therefore, inhibitors of the nalp3 inflammasome offer considerable therapeutic promise. in this study, we show that the type 2 diabetes drug glyburide prevented activation of the cryopyrin inflammasome. glyburide's cyclohexylurea group, which binds to adenosine triphosphatase (atp)-sensitive k(+) (k(atp)) channels for insulin secretion, is dispensable for inflammasome inhibition. macrophages lacking k(atp) subunits or atp-binding cassette transporters also activate the cryopyrin inflammasome normally. glyburide analogues inhibit atp- but not hypothermia-induced il-1beta secretion from human monocytes expressing familial cold-associated autoinflammatory syndrome-associated cryopyrin mutations, thus suggesting that inhibition occurs upstream of cryopyrin. concurrent with the role of cryopyrin in endotoxemia, glyburide significantly delays lipopolysaccharide-induced lethality in mice. therefore, glyburide is the first identified compound to prevent cryopyrin activation and microbial ligand-, damp-, and crystal-induced il-1beta secretion.",0
"background the xpert mtb/rif test (cepheid, sunnyvale, ca, usa) can detect tuberculosis and its multidrug-resistant form with very high sensitivity and specificity in controlled studies, but no performance data exist from district and subdistrict health facilities in tuberculosis-endemic countries. we aimed to assess operational feasibility, accuracy, and effectiveness of implementation in such settings. methods we assessed adults (≥18 years) with suspected tuberculosis or multidrug-resistant tuberculosis consecutively presenting with cough lasting at least 2 weeks to urban health centres in south africa, peru, and india, drug-resistance screening facilities in azerbaijan and the philippines, and an emergency room in uganda. patients were excluded from the main analyses if their second sputum sample was collected more than 1 week after the first sample, or if no valid reference standard or mtb/rif test was available. we compared one-off direct mtb/rif testing in nine microscopy laboratories adjacent to study sites with 2-3 sputum smears and 1-3 cultures, dependent on site, and drug-susceptibility testing. we assessed indicators of robustness including indeterminate rate and between-site performance, and compared time to detection, reporting, and treatment, and patient dropouts for the techniques used. findings we enrolled 6648 participants between aug 11, 2009, and june 26, 2010. one-off mtb/rif testing detected 933 (90·3%) of 1033 culture-confirmed cases of tuberculosis, compared with 699 (67·1%) of 1041 for microscopy. mtb/rif test sensitivity was 76·9% in smear-negative, culture-positive patients (296 of 385 samples), and 99·0% specific (2846 of 2876 non-tuberculosis samples). mtb/rif test sensitivity for rifampicin resistance was 94·4% (236 of 250) and specificity was 98·3% (796 of 810). unlike microscopy, mtb/rif test sensitivity was not significantly lower in patients with hiv co-infection. median time to detection of tuberculosis for the mtb/rif test was 0 days (iqr 0-1), compared with 1 day (0-1) for microscopy, 30 days (23-43) for solid culture, and 16 days (13-21) for liquid culture. median time to detection of resistance was 20 days (10-26) for line-probe assay and 106 days (30-124) for conventional drug-susceptibility testing. use of the mtb/rif test reduced median time to treatment for smear-negative tuberculosis from 56 days (39-81) to 5 days (2-8). the indeterminate rate of mtb/rif testing was 2·4% (126 of 5321 samples) compared with 4·6% (441 of 9690) for cultures. interpretation the mtb/rif test can effectively be used in low-resource settings to simplify patients' access to early and accurate diagnosis, thereby potentially decreasing morbidity associated with diagnostic delay, dropout and mistreatment. funding foundation for innovative new diagnostics, bill & melinda gates foundation, european and developing countries clinical trials partnership (ta2007.40200.009), wellcome trust (085251/b/08/z), and uk department for international development.",0
"reaching and grasping in primates depend on the coordination of neural activity in large frontoparietal ensembles. here we demonstrate that primates can learn to reach and grasp virtual objects by controlling a robot arm through a closed-loop brain-machine interface (bmic) that uses multiple mathematical models to extract several motor parameters (i.e., hand position, velocity, gripping force, and the emgs of multiple arm muscles) from the electrical activity of frontoparietal neuronal ensembles. as single neurons typically contribute to the encoding of several motor parameters, we observed that high bmic accuracy required recording from large neuronal ensembles. continuous bmic operation by monkeys led to significant improvements in both model predictions and behavioral performance. using visual feedback, monkeys succeeded in producing robot reach-and-grasp movements even when their arms did not move. learning to operate the bmic was paralleled by functional reorganization in multiple cortical areas, suggesting that the dynamic properties of the bmic were incorporated into motor and sensory cortical representations.",0
"the consort statement is used worldwide to improve the reporting of randomised controlled trials. kenneth schulz and colleagues describe the latest version, consort 2010, which updates the reporting guideline based on new methodological evidence and accumulating experience.to encourage dissemination of the consort 2010 statement, this article is freely accessible on bmj.com and will also be published in the lancet, obstetrics and gynecology, plos medicine, annals of internal medicine, open medicine, journal of clinical epidemiology, bmc medicine, and trials.",0
"background acpype (or antechamber python parser interface) is a wrapper script around the antechamber software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like gromacs, charmm and cns. it is written in the python programming language and was developed as a tool for interfacing with other python based applications such as the ccpn software suite (for nmr data analysis) and aria (for structure calculations from nmr data). acpype is open source code, under gnu gpl v3, and is available as a stand-alone application at and as a web portal application at findings we verified the topologies generated by acpype in three ways: by comparing with default amber topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the pdb; and by recalculating the structures for 5 protein-ligand complexes from the pdb. conclusions acpype is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.",0
"background: the outbreak of coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has posed great threat to human health. t cells play a critical role in antiviral immunity but their numbers and functional state in covid-19 patients remain largely unclear. methods: we retrospectively reviewed the counts of t cells and serum cytokine concentration from data of 522 patients with laboratory-confirmed covid-19 and 40 healthy controls. in addition, the expression of t cell exhaustion markers were measured in 14 covid-19 cases. results: the number of total t cells, cd4 + and cd8 + t cells were dramatically reduced in covid-19 patients, especially in patients requiring intensive care unit (icu) care. counts of total t cells, cd8 + t cells or cd4 + t cells lower than 800, 300, or 400/μl, respectively, were negatively correlated with patient survival. t cell numbers were negatively correlated to serum il-6, il-10, and tnf-α concentration, with patients in the disease resolution period showing reduced il-6, il-10, and tnf-α concentrations and restored t cell counts. t cells from covid-19 patients had significantly higher levels of the exhausted marker pd-1. increasing pd-1 and tim-3 expression on t cells was seen as patients progressed from prodromal to overtly symptomatic stages. conclusions: t cell counts are reduced significantly in covid-19 patients, and the surviving t cells appear functionally exhausted. non-icu patients with total t cells counts lower than 800/μl may still require urgent intervention, even in the immediate absence of more severe symptoms due to a high risk for further deterioration in condition.",0
"an observational study is a type of epidemiological study design, which can take the form of a cohort, a case-control, or a cross-sectional study. when presenting observational studies in manuscripts, an author needs to ascertain a clear presentation of the work and provide the reader with appropriate information to enable critical appraisal of the research. the strengthening the reporting of observational studies in epidemiology (strobe) guidelines were created to aid the author in ensuring high-quality presentation of the conducted observational study. the original articles publishing the strobe guidelines together with their bibliographies were identified and thoroughly reviewed. these guidelines consist of 22 checklist items that the author needs to fulfil before submitting the manuscript to a journal. the strobe guidelines were created to aid the authors in presenting their work and not to act as a validation tool for the conducted study or as a framework to conduct an observational study on. the authors complying with these guidelines are more likely to succeed in publishing their observational study work in a journal.",0
"voltage-gated sodium (na(v)) channels initiate electrical signalling in excitable cells and are the molecular targets for drugs and disease mutations, but the structural basis for their voltage-dependent activation, ion selectivity and drug block is unknown. here we report the crystal structure of a voltage-gated na(+) channel from arcobacter butzleri (navab) captured in a closed-pore conformation with four activated voltage sensors at 2.7 å resolution. the arginine gating charges make multiple hydrophilic interactions within the voltage sensor, including unanticipated hydrogen bonds to the protein backbone. comparisons to previous open-pore potassium channel structures indicate that the voltage-sensor domains and the s4-s5 linkers dilate the central pore by pivoting together around a hinge at the base of the pore module. the navab selectivity filter is short, ∼4.6 å wide, and water filled, with four acidic side chains surrounding the narrowest part of the ion conduction pathway. this unique structure presents a high-field-strength anionic coordination site, which confers na(+) selectivity through partial dehydration via direct interaction with glutamate side chains. fenestrations in the sides of the pore module are unexpectedly penetrated by fatty acyl chains that extend into the central cavity, and these portals are large enough for the entry of small, hydrophobic pore-blocking drugs. this structure provides the template for understanding electrical signalling in excitable cells and the actions of drugs used for pain, epilepsy and cardiac arrhythmia at the atomic level.",0
"with the accomplishment of human genome sequencing, the number of sequence-known proteins has increased explosively. in contrast, the pace is much slower in determining their biological attributes. as a consequence, the gap between sequence-known proteins and attribute-known proteins has become increasingly large. the unbalanced situation, which has critically limited our ability to timely utilize the newly discovered proteins for basic research and drug development, has called for developing computational methods or high-throughput automated tools for fast and reliably identifying various attributes of uncharacterized proteins based on their sequence information alone. actually, during the last two decades or so, many methods in this regard have been established in hope to bridge such a gap. in the course of developing these methods, the following things were often needed to consider: (1) benchmark dataset construction, (2) protein sample formulation, (3) operating algorithm (or engine), (4) anticipated accuracy, and (5) web-server establishment. in this review, we are to discuss each of the five procedures, with a special focus on the introduction of pseudo amino acid composition (pseaac), its different modes and applications as well as its recent development, particularly in how to use the general formulation of pseaac to reflect the core and essential features that are deeply hidden in complicated protein sequences.",0
"although genome-wide association studies (gwas) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. using a web site we developed to serve results of expression quantitative trait locus (eqtl) studies in lymphoblastoid cell lines from hapmap samples ( we show that single nucleotide polymorphisms (snps) associated with complex traits (from are significantly more likely to be eqtls than minor-allele-frequency-matched snps chosen from high-throughput gwas platforms. these findings are robust across a range of thresholds for establishing eqtls (p-values from 10(-4)-10(-8)), and a broad spectrum of human complex traits. analyses of gwas data from the wellcome trust studies confirm that annotating snps with a score reflecting the strength of the evidence that the snp is an eqtl can improve the ability to discover true associations and clarify the nature of the mechanism driving the associations. our results showing that trait-associated snps are more likely to be eqtls and that application of this information can enhance discovery of trait-associated snps for complex phenotypes raise the possibility that we can utilize this information both to increase the heritability explained by identifiable genetic factors and to gain a better understanding of the biology underlying complex traits.",0
"adenosine receptors and β-adrenoceptors are g-protein-coupled receptors (gpcrs) that activate intracellular g proteins on binding the agonists adenosine or noradrenaline, respectively. gpcrs have similar structures consisting of seven transmembrane helices that contain well-conserved sequence motifs, indicating that they are probably activated by a common mechanism. recent structures of β-adrenoceptors highlight residues in transmembrane region 5 that initially bind specifically to agonists rather than to antagonists, indicating that these residues have an important role in agonist-induced activation of receptors. here we present two crystal structures of the thermostabilized human adenosine a(2a) receptor (a(2a)r-gl31) bound to its endogenous agonist adenosine and the synthetic agonist neca. the structures represent an intermediate conformation between the inactive and active states, because they share all the features of gpcrs that are thought to be in a fully activated state, except that the cytoplasmic end of transmembrane helix 6 partially occludes the g-protein-binding site. the adenine substituent of the agonists binds in a similar fashion to the chemically related region of the inverse agonist zm241385 (ref. 8). both agonists contain a ribose group, not found in zm241385, which extends deep into the ligand-binding pocket where it makes polar interactions with conserved residues in h7 (ser 277(7.42) and his 278(7.43); superscripts refer to ballesteros-weinstein numbering) and non-polar interactions with residues in h3. in contrast, the inverse agonist zm241385 does not interact with any of these residues and comparison with the agonist-bound structures indicates that zm241385 sterically prevents the conformational change in h5 and therefore it acts as an inverse agonist. comparison of the agonist-bound structures of a(2a)r with the agonist-bound structures of β-adrenoceptors indicates that the contraction of the ligand-binding pocket caused by the inward motion of helices 3, 5 and 7 may be a common feature in the activation of all gpcrs.",0
"objective to develop a model to assess severity of illness and predict vital status at hospital discharge based on icu admission data. design prospective multicentre, multinational cohort study. patients and setting a total of 16,784 patients consecutively admitted to 303 intensive care units from 14 october to 15 december 2002. measurements and results icu admission data (recorded within +/-1 h) were used, describing: prior chronic conditions and diseases; circumstances related to and physiologic derangement at icu admission. selection of variables for inclusion into the model used different complementary strategies. for cross-validation, the model-building procedure was run five times, using randomly selected four fifths of the sample as a development- and the remaining fifth as validation-set. logistic regression methods were then used to reduce complexity of the model. final estimates of regression coefficients were determined by use of multilevel logistic regression. variables selection and weighting were further checked by bootstraping (at patient level and at icu level). twenty variables were selected for the final model, which exhibited good discrimination (aroc curve 0.848), without major differences across patient typologies. calibration was also satisfactory (hosmer-lemeshow goodness-of-fit test h=10.56, p=0.39, c=14.29, p=0.16). customized equations for major areas of the world were computed and demonstrate a good overall goodness-of-fit. conclusions the saps 3 admission score is able to predict vital status at hospital discharge with use of data recorded at icu admission. furthermore, saps 3 conceptually dissociates evaluation of the individual patient from evaluation of the icu and thus allows them to be assessed at their respective reference levels.",0
"systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. we describe the development of a reporting guideline, the preferred reporting items for systematic reviews and meta-analyses for protocols 2015 (prisma-p 2015). prisma-p consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium.",0
"resting naive cd8(+) t cells have an astounding capacity to react to pathogens by massive expansion and differentiation into cytotoxic effector cells that migrate to all corners of the body to clear the infection. the initial interaction with antigen-presenting cells in the central lymphoid organs drives an orchestrated program of differentiation aimed at producing sufficient numbers of effectors to get the job done without resulting in clonal exhaustion. interactions with antigen-presenting cells and other immune cells continue at the site of infection to regulate further on-site expansion and differentiation, all with the goal of protecting the host with minimal bystander tissue damage. here we review recent advances in cd8(+) t cell recognition of antigen in lymphoid as well as in nonlymphoid tissues in the periphery, and how cd8(+) t cell expansion and differentiation are controlled in these contexts.",0
"quantitative computational models play an increasingly important role in modern biology. such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. we also showed that the model had a ""sloppy"" spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. we also test several consequences of this sloppiness for building predictive models. in particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. tests over our model collection are consistent with this suggestion. this difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. we confirm this implication in our growth-factor-signaling model. our results suggest that sloppy sensitivity spectra are universal in systems biology models. the prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.",0
"the gene ontology resource (go; provides structured, computable knowledge regarding the functions of genes and gene products. founded in 1998, go has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. here, we report the major developments of the go resource during the past two years. each monthly release of the go resource is now packaged and given a unique identifier (doi), enabling go-based analyses on a specific release to be reproduced in the future. the molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. new evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. go-cam, a new framework for representing gene function that is more expressive than standard go annotations, has been released, and users can now explore the growing repository of these models. we also provide the 'go ribbon' widget for visualizing go annotations to a gene; the widget can be easily embedded in any web page.",0
"objective to determine whether hospitals with a good organisation of care (such as improved nurse staffing and work environments) can affect patient care and nurse workforce stability in european countries. design cross sectional surveys of patients and nurses. setting nurses were surveyed in general acute care hospitals (488 in 12 european countries; 617 in the united states); patients were surveyed in 210 european hospitals and 430 us hospitals. participants 33 659 nurses and 11 318 patients in europe; 27 509 nurses and more than 120 000 patients in the us. main outcome measures nurse outcomes (hospital staffing, work environments, burnout, dissatisfaction, intention to leave job in the next year, patient safety, quality of care), patient outcomes (satisfaction overall and with nursing care, willingness to recommend hospitals). results the percentage of nurses reporting poor or fair quality of patient care varied substantially by country (from 11% (ireland) to 47% (greece)), as did rates for nurses who gave their hospital a poor or failing safety grade (4% (switzerland) to 18% (poland)). we found high rates of nurse burnout (10% (netherlands) to 78% (greece)), job dissatisfaction (11% (netherlands) to 56% (greece)), and intention to leave (14% (us) to 49% (finland, greece)). patients' high ratings of their hospitals also varied considerably (35% (spain) to 61% (finland, ireland)), as did rates of patients willing to recommend their hospital (53% (greece) to 78% (switzerland)). improved work environments and reduced ratios of patients to nurses were associated with increased care quality and patient satisfaction. in european hospitals, after adjusting for hospital and nurse characteristics, nurses with better work environments were half as likely to report poor or fair care quality (adjusted odds ratio 0.56, 95% confidence interval 0.51 to 0.61) and give their hospitals poor or failing grades on patient safety (0.50, 0.44 to 0.56). each additional patient per nurse increased the odds of nurses reporting poor or fair quality care (1.11, 1.07 to 1.15) and poor or failing safety grades (1.10, 1.05 to 1.16). patients in hospitals with better work environments were more likely to rate their hospital highly (1.16, 1.03 to 1.32) and recommend their hospitals (1.20, 1.05 to 1.37), whereas those with higher ratios of patients to nurses were less likely to rate them highly (0.94, 0.91 to 0.97) or recommend them (0.95, 0.91 to 0.98). results were similar in the us. nurses and patients agreed on which hospitals provided good care and could be recommended. conclusions deficits in hospital care quality were common in all countries. improvement of hospital work environments might be a relatively low cost strategy to improve safety and quality in hospital care and to increase patient satisfaction.",0
"population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but they do not always account for loci of larger effect. here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate. we apply our method to human and arabidopsis thaliana data, identifying new associations and evidence for allelic heterogeneity. we also show how a priori knowledge from an a. thaliana linkage mapping study can be integrated into our method using a bayesian approach. our implementation is computationally efficient, making the analysis of large data sets (n > 10,000) practicable.",0
"background there is considerable international interest in exploiting the potential of digital solutions to enhance the quality and safety of health care. implementations of transformative ehealth technologies are underway globally, often at very considerable cost. in order to assess the impact of ehealth solutions on the quality and safety of health care, and to inform policy decisions on ehealth deployments, we undertook a systematic review of systematic reviews assessing the effectiveness and consequences of various ehealth technologies on the quality and safety of care. methods and findings we developed novel search strategies, conceptual maps of health care quality, safety, and ehealth interventions, and then systematically identified, scrutinised, and synthesised the systematic review literature. major biomedical databases were searched to identify systematic reviews published between 1997 and 2010. related theoretical, methodological, and technical material was also reviewed. we identified 53 systematic reviews that focused on assessing the impact of ehealth interventions on the quality and/or safety of health care and 55 supplementary systematic reviews providing relevant supportive information. this systematic review literature was found to be generally of substandard quality with regards to methodology, reporting, and utility. we thematically categorised ehealth technologies into three main areas: (1) storing, managing, and transmission of data; (2) clinical decision support; and (3) facilitating care from a distance. we found that despite support from policymakers, there was relatively little empirical evidence to substantiate many of the claims made in relation to these technologies. whether the success of those relatively few solutions identified to improve quality and safety would continue if these were deployed beyond the contexts in which they were originally developed, has yet to be established. importantly, best practice guidelines in effective development and deployment strategies are lacking. conclusions there is a large gap between the postulated and empirically demonstrated benefits of ehealth technologies. in addition, there is a lack of robust research on the risks of implementing these technologies and their cost-effectiveness has yet to be demonstrated, despite being frequently promoted by policymakers and ""techno-enthusiasts"" as if this was a given. in the light of the paucity of evidence in relation to improvements in patient outcomes, as well as the lack of evidence on their cost-effectiveness, it is vital that future ehealth technologies are evaluated against a comprehensive set of measures, ideally throughout all stages of the technology's life cycle. such evaluation should be characterised by careful attention to socio-technical factors to maximise the likelihood of successful implementation and adoption.",0
"the pandemic outbreak of coronavirus disease 2019 (covid-19) is rapidly spreading all over the world. reports from china showed that about 20% of patients developed severe disease, resulting in a fatality of 4%. in the past two months, we clinical immunologists participated in multi-rounds of mdt (multidiscipline team) discussion on the anti-inflammation management of critical covid-19 patients, with our colleagues dispatched from chinese leading pumc hospital to wuhan to admit and treat the most severe patients. here, from the perspective of clinical immunologists, we will discuss the clinical and immunological characteristics of severe patients, and summarize the current evidence and share our experience in anti-inflammation treatment, including glucocorticoids, il-6 antagonist, jak inhibitors and choloroquine/hydrocholoroquine, of patients with severe covid-19 that may have an impaired immune system.",0
"cell-free dna in the blood provides a non-invasive diagnostic avenue for patients with cancer 1 . however, characteristics of the origins and molecular features of cell-free dna are poorly understood. here we developed an approach to evaluate fragmentation patterns of cell-free dna across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. we used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. a machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. combining our approach with mutation-based cell-free dna analyses detected 91% of patients with cancer. the results of these analyses highlight important properties of cell-free dna and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer.",0
"mutational activation of braf is the earliest and most common genetic alteration in human melanoma. to build a model of human melanoma, we generated mice with conditional melanocyte-specific expression of braf(v600e). upon induction of braf(v600e) expression, mice developed benign melanocytic hyperplasias that failed to progress to melanoma over 15-20 months. by contrast, expression of braf(v600e) combined with pten tumor suppressor gene silencing elicited development of melanoma with 100% penetrance, short latency and with metastases observed in lymph nodes and lungs. melanoma was prevented by inhibitors of mtorc1 (rapamycin) or mek1/2 (pd325901) but, upon cessation of drug administration, mice developed melanoma, indicating the presence of long-lived melanoma-initiating cells in this system. notably, combined treatment with rapamycin and pd325901 led to shrinkage of established melanomas. these mice, engineered with a common genetic profile to human melanoma, provide a system to study melanoma's cardinal feature of metastasis and for preclinical evaluation of agents designed to prevent or treat metastatic disease.",0
"introduction there is no consensus definition of acute renal failure (arf) in critically ill patients. more than 30 different definitions have been used in the literature, creating much confusion and making comparisons difficult. similarly, strong debate exists on the validity and clinical relevance of animal models of arf; on choices of fluid management and of end-points for trials of new interventions in this field; and on how information technology can be used to assist this process. accordingly, we sought to review the available evidence, make recommendations and delineate key questions for future studies. methods we undertook a systematic review of the literature using medline and pubmed searches. we determined a list of key questions and convened a 2-day consensus conference to develop summary statements via a series of alternating breakout and plenary sessions. in these sessions, we identified supporting evidence and generated recommendations and/or directions for future research. results we found sufficient consensus on 47 questions to allow the development of recommendations. importantly, we were able to develop a consensus definition for arf. in some cases it was also possible to issue useful consensus recommendations for future investigations. we present a summary of the findings. (full versions of the six workgroups' findings are available on the internet at conclusion despite limited data, broad areas of consensus exist for the physiological and clinical principles needed to guide the development of consensus recommendations for defining arf, selection of animal models, methods of monitoring fluid therapy, choice of physiological and clinical end-points for trials, and the possible role of information technology.",0
"online gene annotation resources are indispensable for analysis of genomics data. however, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. here, we introduce biogps a centralized gene portal for aggregating distributed gene annotation resources. moreover, biogps embraces the principle of community intelligence, enabling any user to easily and directly contribute to the biogps platform.",0
"background the danish national patient registry (dnpr) is one of the world's oldest nationwide hospital registries and is used extensively for research. many studies have validated algorithms for identifying health events in the dnpr, but the reports are fragmented and no overview exists. objectives to review the content, data quality, and research potential of the dnpr. methods we examined the setting, history, aims, content, and classification systems of the dnpr. we searched pubmed and the danish medical journal to create a bibliography of validation studies. we included also studies that were referenced in retrieved papers or known to us beforehand. methodological considerations related to dnpr data were reviewed. results during 1977-2012, the dnpr registered 8,085,603 persons, accounting for 7,268,857 inpatient, 5,953,405 outpatient, and 5,097,300 emergency department contacts. the dnpr provides nationwide longitudinal registration of detailed administrative and clinical data. it has recorded information on all patients discharged from danish nonpsychiatric hospitals since 1977 and on psychiatric inpatients and emergency department and outpatient specialty clinic contacts since 1995. for each patient contact, one primary and optional secondary diagnoses are recorded according to the international classification of diseases. the dnpr provides a data source to identify diseases, examinations, certain in-hospital medical treatments, and surgical procedures. long-term temporal trends in hospitalization and treatment rates can be studied. the positive predictive values of diseases and treatments vary widely ( conclusion the dnpr is a valuable tool for epidemiological research. however, both its strengths and limitations must be considered when interpreting research results, and continuous validation of its clinical data is essential.",0
"objective to present results of the kyoto global consensus meeting, which was convened to develop global consensus on (1) classification of chronic gastritis and duodenitis, (2) clinical distinction of dyspepsia caused by helicobacter pylori from functional dyspepsia, (3) appropriate diagnostic assessment of gastritis and (4) when, whom and how to treat h. pylori gastritis. design twenty-three clinical questions addressing the above-mentioned four domains were drafted for which expert panels were asked to formulate relevant statements. a delphi method using an anonymous electronic system was adopted to develop the consensus, the level of which was predefined as ≥80%. final modifications of clinical questions and consensus were achieved at the face-to-face meeting in kyoto. results all 24 statements for 22 clinical questions after extensive modifications and omission of one clinical question were achieved with a consensus level of >80%. to better organise classification of gastritis and duodenitis based on aetiology, a new classification of gastritis and duodenitis is recommended for the 11th international classification. a new category of h. pylori-associated dyspepsia together with a diagnostic algorithm was proposed. the adoption of grading systems for gastric cancer risk stratification, and modern image-enhancing endoscopy for the diagnosis of gastritis, were recommended. treatment to eradicate h. pylori infection before preneoplastic changes develop, if feasible, was recommended to minimise the risk of more serious complications of the infection. conclusions a global consensus for gastritis was developed for the first time, which will be the basis for an international classification system and for further research on the subject.",0
"introduction multiple gene expression based prognostic biomarkers have been repeatedly identified in gastric carcinoma. however, without confirmation in an independent validation study, their clinical utility is limited. our goal was to establish a robust database enabling the swift validation of previous and future gastric cancer survival biomarker candidates. results the entire database incorporates 1,065 gastric carcinoma samples, gene expression data. out of 29 established markers, higher expression of becn1 (hr = 0.68, p = 1.5e-05), casp3 (hr = 0.5, p = 6e-14), cox2 (hr = 0.72, p = 0.0013), ctgf (hr = 0.72, p = 0.00051), ctnnb1 (hr = 0.47, p = 4.3e-15), met (hr = 0.63, p = 1.3e-05), and sirt1 (hr = 0.64, p = 2.2e-07) correlated to longer os. higher expression of birc5 (hr = 1.45, p = 1e-04), cntn1 (hr = 1.44, p = 3.5e- 05), egfr (hr = 1.86, p = 8.5e-11), ercc1 (hr = 1.36, p = 0.0012), her2 (hr = 1.41, p = 0.00011), mmp2 (hr = 1.78, p = 2.6e-09), pfkb4 (hr = 1.56, p = 3.2e-07), sphk1 (hr = 1.61, p = 3.1e-06), sp1 (hr = 1.45, p = 1.6e-05), timp1 (hr = 1.92, p = 2.2e- 10) and vegf (hr = 1.53, p = 5.7e-06) were predictive for poor os. materials and methods we integrated samples of three major cancer research centers (berlin, bethesda and melbourne datasets) and publicly available datasets with available follow-up data to form a single integrated database. subsequently, we performed a literature search for prognostic markers in gastric carcinomas (pubmed, 2012-2015) and re-validated their findings predicting first progression (fp) and overall survival (os) using uni- and multivariate cox proportional hazards regression analysis. conclusions the major advantage of our analysis is that we evaluated all genes in the same set of patients thereby making direct comparison of the markers feasible. the best performing genes include birc5, casp3, ctnnb1, timp-1, mmp-2, sirt, and vegf.",0
"as of april 9, 2020, the coronavirus disease 2019 (covid-19) pandemic had resulted in 1,521,252 cases and 92,798 deaths worldwide, including 459,165 cases and 16,570 deaths in the united states (1,2). health care personnel (hcp) are essential workers defined as paid and unpaid persons serving in health care settings who have the potential for direct or indirect exposure to patients or infectious materials (3). during february 12-april 9, among 315,531 covid-19 cases reported to cdc using a standardized form, 49,370 (16%) included data on whether the patient was a health care worker in the united states; including 9,282 (19%) who were identified as hcp. among hcp patients with data available, the median age was 42 years (interquartile range = 32-54 years), 6,603 (73%) were female, and 1,779 (38%) reported at least one underlying health condition. among hcp patients with data on health care, household, and community exposures, 780 (55%) reported contact with a covid-19 patient only in health care settings. although 4,336 (92%) hcp patients reported having at least one symptom among fever, cough, or shortness of breath, the remaining 8% did not report any of these symptoms. most hcp with covid-19 (6,760, 90%) were not hospitalized; however, severe outcomes, including 27 deaths, occurred across all age groups; deaths most frequently occurred in hcp aged ≥65 years. these preliminary findings highlight that whether hcp acquire infection at work or in the community, it is necessary to protect the health and safety of this essential national workforce.",0
"background non-fatal outcomes of disease and injury increasingly detract from the ability of the world's population to live in full health, a trend largely attributable to an epidemiological transition in many countries from causes affecting children, to non-communicable diseases (ncds) more common in adults. for the global burden of diseases, injuries, and risk factors study 2015 (gbd 2015), we estimated the incidence, prevalence, and years lived with disability for diseases and injuries at the global, regional, and national scale over the period of 1990 to 2015. methods we estimated incidence and prevalence by age, sex, cause, year, and geography with a wide range of updated and standardised analytical procedures. improvements from gbd 2013 included the addition of new data sources, updates to literature reviews for 85 causes, and the identification and inclusion of additional studies published up to november, 2015, to expand the database used for estimation of non-fatal outcomes to 60 900 unique data sources. prevalence and incidence by cause and sequelae were determined with dismod-mr 2.1, an improved version of the dismod-mr bayesian meta-regression tool first developed for gbd 2010 and gbd 2013. for some causes, we used alternative modelling strategies where the complexity of the disease was not suited to dismod-mr 2.1 or where incidence and prevalence needed to be determined from other data. for gbd 2015 we created a summary indicator that combines measures of income per capita, educational attainment, and fertility (the socio-demographic index ) and used it to compare observed patterns of health loss to the expected pattern for countries or locations with similar sdi scores. findings we generated 9·3 billion estimates from the various combinations of prevalence, incidence, and ylds for causes, sequelae, and impairments by age, sex, geography, and year. in 2015, two causes had acute incidences in excess of 1 billion: upper respiratory infections (17·2 billion, 95% uncertainty interval 15·4-19·2 billion) and diarrhoeal diseases (2·39 billion, 2·30-2·50 billion). eight causes of chronic disease and injury each affected more than 10% of the world's population in 2015: permanent caries, tension-type headache, iron-deficiency anaemia, age-related and other hearing loss, migraine, genital herpes, refraction and accommodation disorders, and ascariasis. the impairment that affected the greatest number of people in 2015 was anaemia, with 2·36 billion (2·35-2·37 billion) individuals affected. the second and third leading impairments by number of individuals affected were hearing loss and vision loss, respectively. between 2005 and 2015, there was little change in the leading causes of years lived with disability (ylds) on a global basis. ncds accounted for 18 of the leading 20 causes of age-standardised ylds on a global scale. where rates were decreasing, the rate of decrease for ylds was slower than that of years of life lost (ylls) for nearly every cause included in our analysis. for low sdi geographies, group 1 causes typically accounted for 20-30% of total disability, largely attributable to nutritional deficiencies, malaria, neglected tropical diseases, hiv/aids, and tuberculosis. lower back and neck pain was the leading global cause of disability in 2015 in most countries. the leading cause was sense organ disorders in 22 countries in asia and africa and one in central latin america; diabetes in four countries in oceania; hiv/aids in three southern sub-saharan african countries; collective violence and legal intervention in two north african and middle eastern countries; iron-deficiency anaemia in somalia and venezuela; depression in uganda; onchoceriasis in liberia; and other neglected tropical diseases in the democratic republic of the congo. interpretation ageing of the world's population is increasing the number of people living with sequelae of diseases and injuries. shifts in the epidemiological profile driven by socioeconomic change also contribute to the continued increase in years lived with disability (ylds) as well as the rate of increase in ylds. despite limitations imposed by gaps in data availability and the variable quality of the data available, the standardised and comprehensive approach of the gbd study provides opportunities to examine broad trends, compare those trends between countries or subnational geographies, benchmark against locations at similar stages of development, and gauge the strength or weakness of the estimates available. funding bill & melinda gates foundation.",0
"human cytomegalovirus (hcmv) infections of immunocompetent hosts are characterized by a dynamic, life-long interaction in which host immune responses, particularly of t cells, restrain viral replication and prevent disease but do not eliminate the virus or preclude transmission. because hcmv is among the largest and most complex of known viruses, the t cell resources committed to maintaining this balance have never been characterized completely. here, using cytokine flow cytometry and 13,687 overlapping 15mer peptides comprising 213 hcmv open reading frames (orfs), we found that 151 hcmv orfs were immunogenic for cd4(+) and/or cd8(+) t cells, and that orf immunogenicity was influenced only modestly by orf expression kinetics and function. we further documented that total hcmv-specific t cell responses in seropositive subjects were enormous, comprising on average approximately 10% of both the cd4(+) and cd8(+) memory compartments in blood, whereas cross-reactive recognition of hcmv proteins in seronegative individuals was limited to cd8(+) t cells and was rare. these data provide the first glimpse of the total human t cell response to a complex infectious agent and will provide insight into the rules governing immunodominance and cross-reactivity in complex viral infections of humans.",0
"background recent ehealth developments have elevated the importance of assessing the extent to which technology has empowered patients and improved health, particularly among the most vulnerable populations. with noted disparities across racial and social groups in chronic health outcomes, such as cancer, obesity, and diabetes, it is essential that researchers examine any differences in the implementation, uptake, and impact of ehealth strategies across groups that bear a disproportionate burden of disease. objective the goal was to examine ehealth use by sociodemographic factors, such as race/ethnicity, socioeconomic status (ses), age, and sex. methods we drew data from national cancer institute's 2012 health information national trends survey (hints) (n=3959) which is publicly available online. we estimated multivariable logistic regression models to assess sociodemographic predictors of ehealth use among adult internet users (n=2358) across 3 health communication domains (health care, health information-seeking, and user-generated content/sharing). results among online adults, we saw no evidence of a digital use divide by race/ethnicity. however, there were significant differences in use by ses, particularly for health care and health information-seeking items. patients with lower levels of education had significantly lower odds of going online to look for a health care provider (high school or less: or 0.50, 95% ci 0.33-0.76) using email or the internet to communicate with a doctor (high school or less: or 0.46, 95% ci 0.29-0.72), tracking their personal health information online (high school or less: or 0.53, 95% ci 0.32-0.84), using a website to help track diet, weight, and physical activity (high school or less: or 0.64, 95% ci 0.42-0.98; some college: or 0.67, 95% ci 0.49-0.93), or downloading health information to a mobile device (some college: or 0.54, 95% ci 0.33-0.89). being female was a consistent predictor of ehealth use across health care and user-generated content/sharing domains, whereas age was primarily influential for health information-seeking. conclusions this study illustrates that lower ses, older, and male online us adults were less likely to engage in a number of ehealth activities compared to their counterparts. future studies should assess issues of health literacy and ehealth literacy and their influence on ehealth engagement across social groups. clinical care and public health communication efforts attempting to leverage web 2.0 and 3.0 platforms should acknowledge differential ehealth usage to better address communication inequalities and persistent disparities in health.",0
"background the global burden of diseases, injuries, and risk factors study 2017 (gbd 2017) includes a comprehensive assessment of incidence, prevalence, and years lived with disability (ylds) for 354 causes in 195 countries and territories from 1990 to 2017. previous gbd studies have shown how the decline of mortality rates from 1990 to 2016 has led to an increase in life expectancy, an ageing global population, and an expansion of the non-fatal burden of disease and injury. these studies have also shown how a substantial portion of the world's population experiences non-fatal health loss with considerable heterogeneity among different causes, locations, ages, and sexes. ongoing objectives of the gbd study include increasing the level of estimation detail, improving analytical strategies, and increasing the amount of high-quality data. methods we estimated incidence and prevalence for 354 diseases and injuries and 3484 sequelae. we used an updated and extensive body of literature studies, survey data, surveillance data, inpatient admission records, outpatient visit records, and health insurance claims, and additionally used results from cause of death models to inform estimates using a total of 68 781 data sources. newly available clinical data from india, iran, japan, jordan, nepal, china, brazil, norway, and italy were incorporated, as well as updated claims data from the usa and new claims data from taiwan (province of china) and singapore. we used dismod-mr 2.1, a bayesian meta-regression tool, as the main method of estimation, ensuring consistency between rates of incidence, prevalence, remission, and cause of death for each condition. ylds were estimated as the product of a prevalence estimate and a disability weight for health states of each mutually exclusive sequela, adjusted for comorbidity. we updated the socio-demographic index (sdi), a summary development indicator of income per capita, years of schooling, and total fertility rate. additionally, we calculated differences between male and female ylds to identify divergent trends across sexes. gbd 2017 complies with the guidelines for accurate and transparent health estimates reporting. findings globally, for females, the causes with the greatest age-standardised prevalence were oral disorders, headache disorders, and haemoglobinopathies and haemolytic anaemias in both 1990 and 2017. for males, the causes with the greatest age-standardised prevalence were oral disorders, headache disorders, and tuberculosis including latent tuberculosis infection in both 1990 and 2017. in terms of ylds, low back pain, headache disorders, and dietary iron deficiency were the leading level 3 causes of yld counts in 1990, whereas low back pain, headache disorders, and depressive disorders were the leading causes in 2017 for both sexes combined. all-cause age-standardised yld rates decreased by 3·9% (95% uncertainty interval 3·1-4·6) from 1990 to 2017; however, the all-age yld rate increased by 7·2% (6·0-8·4) while the total sum of global ylds increased from 562 million (421-723) to 853 million (642-1100). the increases for males and females were similar, with increases in all-age yld rates of 7·9% (6·6-9·2) for males and 6·5% (5·4-7·7) for females. we found significant differences between males and females in terms of age-standardised prevalence estimates for multiple causes. the causes with the greatest relative differences between sexes in 2017 included substance use disorders (3018 cases per 100 000 in males vs s1400 per 100 000 in females), transport injuries (3322 vs 2336 ), and self-harm and interpersonal violence (3265 vs 5643 ). interpretation global all-cause age-standardised yld rates have improved only slightly over a period spanning nearly three decades. however, the magnitude of the non-fatal disease burden has expanded globally, with increasing numbers of people who have a wide spectrum of conditions. a subset of conditions has remained globally pervasive since 1990, whereas other conditions have displayed more dynamic trends, with different ages, sexes, and geographies across the globe experiencing varying burdens and trends of health loss. this study emphasises how global improvements in premature mortality for select conditions have led to older populations with complex and potentially expensive diseases, yet also highlights global achievements in certain domains of disease and injury. funding bill & melinda gates foundation.",0
"background consciousness poses two main problems. the first is understanding the conditions that determine to what extent a system has conscious experience. for instance, why is our consciousness generated by certain parts of our brain, such as the thalamocortical system, and not by other parts, such as the cerebellum? and why are we conscious during wakefulness and much less so during dreamless sleep? the second problem is understanding the conditions that determine what kind of consciousness a system has. for example, why do specific parts of the brain contribute specific qualities to our conscious experience, such as vision and audition? presentation of the hypothesis this paper presents a theory about what consciousness is and how it can be measured. according to the theory, consciousness corresponds to the capacity of a system to integrate information. this claim is motivated by two key phenomenological properties of consciousness: differentiation - the availability of a very large number of conscious experiences; and integration - the unity of each such experience. the theory states that the quantity of consciousness available to a system can be measured as the phi value of a complex of elements. phi is the amount of causally effective information that can be integrated across the informational weakest link of a subset of elements. a complex is a subset of elements with phi>0 that is not part of a subset of higher phi. the theory also claims that the quality of consciousness is determined by the informational relationships among the elements of a complex, which are specified by the values of effective information among them. finally, each particular conscious experience is specified by the value, at any given time, of the variables mediating informational interactions among the elements of a complex. testing the hypothesis the information integration theory accounts, in a principled manner, for several neurobiological observations concerning consciousness. as shown here, these include the association of consciousness with certain neural systems rather than with others; the fact that neural processes underlying consciousness can influence or be influenced by neural processes that remain unconscious; the reduction of consciousness during dreamless sleep and generalized seizures; and the time requirements on neural interactions that support consciousness. implications of the hypothesis the theory entails that consciousness is a fundamental quantity, that it is graded, that it is present in infants and animals, and that it should be possible to build conscious artifacts.",0
"most consensus leukemia & lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. here we present the validated euroflow 8-color antibody panels for immunophenotyping of hematological malignancies. the single-tube screening panels and multi-tube classification panels fit into the euroflow diagnostic algorithm with entries defined by clinical and laboratory parameters. the panels were constructed in 2-7 sequential design-evaluation-redesign rounds, using novel infinicyt software tools for multivariate data analysis. two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. in multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). the characterization markers were positioned according to the diagnostic utility of the combined markers. each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and who-based disease entities, respectively. the euroflow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies.",0
"although there are many commercially available statistical software packages, only a few implement a competing risk analysis or a proportional hazards regression model with time-dependent covariates, which are necessary in studies on hematopoietic sct. in addition, most packages are not clinician friendly, as they require that commands be written based on statistical languages. this report describes the statistical software 'ezr' (easy r), which is based on r and r commander. ezr enables the application of statistical functions that are frequently used in clinical studies, such as survival analyses, including competing risk analyses and the use of time-dependent covariates, receiver operating characteristics analyses, meta-analyses, sample size calculation and so on, by point-and-click access. ezr is freely available on our website ( and runs on both windows (microsoft corporation, usa) and mac os x (apple, usa). this report provides instructions for the installation and operation of ezr.",0
"a metabolic pathway of activated macrophages (m phi) involving oxidation of the guanido nitrogens of l-arginine is required for inhibition of growth and respiration of some target cells. the goal of this study was to identify the m phi metabolite(s) that induce these injuries. the stable products of the l-arginine pathway, no2- and no3-, were incapable of causing cytostasis under coculture conditions. however, no2- became cytostatic upon mild acidification, which favors its transformation into nitrogen oxides of greater reactivity. this suggested that no. (and/or no2), recently identified as an m phi metabolite of l-arginine, could be a mediator. authentic no. caused cytostasis and respiratory inhibition in l1210 cells in a dose-dependent manner. the mitochondrial lesions caused by no. were confined to complex 1 and 2, a pattern of injury identical to that seen after coculture with activated m phi. inclusion of no. scavenger systems prevented cytostasis from developing in m phi-l1210 cocultures. thus, m phi-generated no. can account for l-arginine-dependent cytostasis and respiratory inhibition.",0
"purpose to evaluate the diagnostic value of computed tomography (ct) and real-time reverse-transcriptase-polymerase chain reaction (rrt-pcr) for covid-19 pneumonia. methods this retrospective study included all patients with covid-19 pneumonia suspicion, who were examined by both ct and rrt-pcr at initial presentation. the sensitivities of both tests were then compared. for patients with a final confirmed diagnosis, clinical and laboratory data, in addition to ct imaging findings were evaluated. results a total of 36 patients were finally diagnosed with covid-19 pneumonia. thirty-five patients had abnormal ct findings at presentation, whereas one patient had a normal ct. using rrt-pcr, 30 patients were tested positive, with 6 cases initially missed. amongst these 6 patients, 3 became positive in the second rrt-pcr assay(after 2 days, 2 days and 3 days respectively), and the other 3 became positive only in the third round of rrt-pcr tests(after 5 days, 6 days and 8 days respectively). at presentation, ct sensitivity was therefore 97.2%, whereas the sensitivity of initial rrt-pcr was only 83.3%. conclusion rrt-pcr may produce initial false negative results. we suggest that patients with typical ct findings but negative rrt-pcr results should be isolated, and rrt-pcr should be repeated to avoid misdiagnosis.",0
"the worldwide increases in both environmental damage and human population pressure have the unfortunate consequence that global food production may soon become insufficient to feed all of the world's people. it is therefore essential that agricultural productivity be significantly increased within the next few decades. to this end, agricultural practice is moving toward a more sustainable and environmentally friendly approach. this includes both the increasing use of transgenic plants and plant growth-promoting bacteria as a part of mainstream agricultural practice. here, a number of the mechanisms utilized by plant growth-promoting bacteria are discussed and considered. it is envisioned that in the not too distant future, plant growth-promoting bacteria (pgpb) will begin to replace the use of chemicals in agriculture, horticulture, silviculture, and environmental cleanup strategies. while there may not be one simple strategy that can effectively promote the growth of all plants under all conditions, some of the strategies that are discussed already show great promise.",0
"background endometriosis is a risk factor for epithelial ovarian cancer; however, whether this risk extends to all invasive histological subtypes or borderline tumours is not clear. we undertook an international collaborative study to assess the association between endometriosis and histological subtypes of ovarian cancer. methods data from 13 ovarian cancer case-control studies, which were part of the ovarian cancer association consortium, were pooled and logistic regression analyses were undertaken to assess the association between self-reported endometriosis and risk of ovarian cancer. analyses of invasive cases were done with respect to histological subtypes, grade, and stage, and analyses of borderline tumours by histological subtype. age, ethnic origin, study site, parity, and duration of oral contraceptive use were included in all analytical models. findings 13 226 controls and 7911 women with invasive ovarian cancer were included in this analysis. 818 and 738, respectively, reported a history of endometriosis. 1907 women with borderline ovarian cancer were also included in the analysis, and 168 of these reported a history of endometriosis. self-reported endometriosis was associated with a significantly increased risk of clear-cell (136 of 674 cases vs 818 of 13 226 controls, odds ratio 3·05, 95% ci 2·43-3·84, p interpretation clinicians should be aware of the increased risk of specific subtypes of ovarian cancer in women with endometriosis. future efforts should focus on understanding the mechanisms that might lead to malignant transformation of endometriosis so as to help identify subsets of women at increased risk of ovarian cancer. funding ovarian cancer research fund, national institutes of health, california cancer research program, california department of health services, lon v smith foundation, european community's seventh framework programme, german federal ministry of education and research of germany, programme of clinical biomedical research, german cancer research centre, eve appeal, oak foundation, uk national institute of health research, national health and medical research council of australia, us army medical research and materiel command, cancer council tasmania, cancer foundation of western australia, mermaid 1, danish cancer society, and roswell park alliance foundation.",0
"integrin receptors play important roles in organizing the actin-containing cytoskeleton and in signal transduction from the extracellular matrix. the initial steps in integrin function can be analyzed experimentally using beads coated with ligands or anti-integrin antibodies to trigger rapid focal transmembrane responses. a hierarchy of transmembrane actions was identified in this study. simple integrin aggregation triggered localized transmembrane accumulation of 20 signal transduction molecules, including rhoa, rac1, ras, raf, mek, erk, and jnk. in contrast, out of eight cytoskeletal molecules tested, only tensin coaccumulated. integrin aggregation alone was also sufficient to induce rapid activation of the jnk pathway, with kinetics of activation different from those of erk. the tyrosine kinase inhibitors herbimycin a or genistein blocked both the accumulation of 19 out of 20 signal transduction molecules and jnk- and erk-mediated signaling. cytochalasin d had identical effects, whereas three other tyrosine kinase inhibitors did not. the sole exception among signaling molecules was the kinase pp125fak which continued to coaggregate with alpha 5 beta 1 integrins even in the presence of these inhibitors. tyrosine kinase inhibition also failed to block the ability of ligand occupancy plus integrin aggregation to trigger transmembrane accumulation of the three cytoskeletal molecules talin, alpha-actinin, and vinculin; these molecules accumulated even in the presence of cytochalasin d. however, it was necessary to fulfill all four conditions, i.e., integrin aggregation, integrin occupancy, tyrosine kinase activity, and actin cytoskeletal integrity, to achieve integrin-mediated focal accumulation of other cytoskeletal molecules including f-actin and paxillin. integrins therefore mediate a transmembrane hierarchy of molecular responses.",0
"background the amp-activated protein kinase (ampk) cascade is a sensor of cellular energy charge that acts as a 'metabolic master switch' and inhibits cell proliferation. activation requires phosphorylation of thr172 of ampk within the activation loop by upstream kinases (ampkks) that have not been identified. recently, we identified three related protein kinases acting upstream of the yeast homolog of ampk. although they do not have obvious mammalian homologs, they are related to lkb1, a tumor suppressor that is mutated in the human peutz-jeghers cancer syndrome. we recently showed that lkb1 exists as a complex with two accessory subunits, strad alpha/beta and mo25 alpha/beta. results we report the following observations. first, two ampkk activities purified from rat liver contain lkb1, strad alpha and mo25 alpha, and can be immunoprecipitated using anti-lkb1 antibodies. second, both endogenous and recombinant complexes of lkb1, strad alpha/beta and mo25 alpha/beta activate ampk via phosphorylation of thr172. third, catalytically active lkb1, strad alpha or strad beta and mo25 alpha or mo25 beta are required for full activity. fourth, the ampk-activating drugs aica riboside and phenformin do not activate ampk in hela cells (which lack lkb1), but activation can be restored by stably expressing wild-type, but not catalytically inactive, lkb1. fifth, aica riboside and phenformin fail to activate ampk in immortalized fibroblasts from lkb1-knockout mouse embryos. conclusions these results provide the first description of a physiological substrate for the lkb1 tumor suppressor and suggest that it functions as an upstream regulator of ampk. our findings indicate that the tumors in peutz-jeghers syndrome could result from deficient activation of ampk as a consequence of lkb1 inactivation.",0
"we present a new open source, extensible and flexible software platform for bayesian evolutionary analysis called beast 2. this software platform is a re-design of the popular beast 1 platform to correct structural deficiencies that became evident as the beast 1 software evolved. key among those deficiencies was the lack of post-deployment extensibility. beast 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the beast 2 analysis platform via a package manager without requiring a new software release of the platform. this package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. a second major improvement is the ability to read/write the entire state of the mcmc chain to/from disk allowing it to be easily shared between multiple instances of the beast software. this facilitates checkpointing and better support for multi-processor and high-end computing extensions. finally, the functionality in new packages can be easily added to the user interface (beauti 2) by a simple xml template-based mechanism because beast 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example beast and beauti use exactly the same xml file format.",0
"many public health responses and modeled scenarios for covid-19 outbreaks caused by sars-cov-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. the presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. here, we review the scientific literature on antibody immunity to coronaviruses, including sars-cov-2 as well as the related sars-cov, mers-cov and endemic human coronaviruses (hcovs). we reviewed 2,452 abstracts and identified 491 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. while further studies of sars-cov-2 are necessary to determine immune responses, evidence from other coronaviruses can provide clues and guide future research.",0
"polyphenols are the biggest group of phytochemicals, and many of them have been found in plant-based foods. polyphenol-rich diets have been linked to many health benefits. this paper is intended to review the chemistry and biochemistry of polyphenols as related to classification, extraction, separation and analytical methods, their occurrence and biosynthesis in plants, and the biological activities and implications in human health. the discussions are focused on important and most recent advances in the above aspects, and challenges are identified for future research.",0
"the extent to which a doctor or health professional can make a valid assessment of a patient's quality of life, anxiety and depression was investigated in a series of cancer patients. doctors and patients filled out the same forms, viz. the karnofsky, spitzer, linear analogue self assessment scales and a series of simple scales designed for this study, at the same time. correlations between the two sets of scores were poor, suggesting that the doctors could not accurately determine what the patients felt. a further study examining the reproducibility of these scales demonstrated considerable variability in results between different doctors. it is concluded that if a reliable and consistent method of measuring quality of life in cancer patients is required, it must come from the patients themselves and not from their doctors and nurses.",0
"the global population at risk from mosquito-borne diseases-including dengue, yellow fever, chikungunya and zika-is expanding in concert with changes in the distribution of two key vectors: aedes aegypti and aedes albopictus. the distribution of these species is largely driven by both human movement and the presence of suitable climate. using statistical mapping techniques, we show that human movement patterns explain the spread of both species in europe and the united states following their introduction. we find that the spread of ae. aegypti is characterized by long distance importations, while ae. albopictus has expanded more along the fringes of its distribution. we describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and zika viruses must consider the so far unabated spread of these mosquitos. our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally.",0
"the cytological response to the ingestion of tubercle bacilli by cultured mouse peritoneal macrophages has been studied by electron microscopy. methods included a quantitative assessment based on systematic surveying of cell profiles, and of phagosomes and their contained bacteria, encountered in thin sections; classification of the sectioned bacteria into visibly damaged and apparently intact categories; prelabeling of dense granules (secondary lysosomes) with ferritin as an aid to identifying the occurrence and frequency of phagosome-lysosome fusion; and monitoring of bacterial growth and viability by light microscopy and cultural counts. the situations studied were as follows: progressive infection with the multiplying virulent strain h37rv; ingestion of the same strain previously inactivated by gamma radiation; infection with an attenuated strain (bcg); and a stabilized virulent infection induced by the surfactant macrocyclon. in the bacterial suspensions used routinely for inoculation, about half the bacilli were viable, matching closely the proportions of intact and damaged organisms identified with the electron microscope. in the inoculated macrophages, some phagosomes containing intact bacilli and others containing damaged bacilli were always to be found; but the proportion of organisms scored as damaged increased, and that of intact organisms decreased, in situations where the population as a whole had been rendered nonviable before inoculation, or where they became so intracellularly as in the late stages of a bcg infection. evidence of fusion of ferritin-marked lysosomes with some bacterium-containing phagosomes was obtained in all experiments, but a significant difference was regularly observed according to whether the bacilli were damaged or intact. virtually all phagosomes containing damaged bacilli showed signs of fusion; but when many phagosomes were present containing apparently intact organisms (as with actively multiplying strain h37rv or with this strain held at a steady level of viability by macrocyclon, and also with strain bcg at an early stage of that infection), signs of fusion of lysosomes with these phagosomes were infrequent. from these findings it is inferred that intracellular survival of m. tuberculosis in cultured macrophages is associated with a tendency to nonfusion of dense granules with the phagosome, thus avoiding direct exposure of the bacilli to the contents of these organelles. it is suggested, further, that fusion of dense granules with the phagosome, leading to digestion, is determined by recognition of the bacillus as nonviable. the possibility is discussed that the cytological response to different mycobacterial infections may reflect differences of a basic nature between facultative and obligate intracellular parasitism.",0
"the human gene mutation database (hgmd®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. by june 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. hgmd was originally established in 1996 for the scientific study of mutational mechanisms in human genes. however, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. the public version of hgmd ( is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (hgmd professional) is available to academic, clinical and commercial users under license via biobase gmbh.",0
"the evolutionary importance of hybridization and introgression has long been debated. hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. here we use genomic tools to investigate introgression in heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. we sequenced the genome of heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in lepidoptera and gene flow among multiple heliconius species and races. among 12,669 predicted genes, biologically important expansions of families of chemosensory and hox genes are particularly noteworthy. chromosomal organization has remained broadly conserved since the cretaceous period, when butterflies split from the bombyx (silkmoth) lineage. using genomic resequencing, we show hybrid exchange of genes between three co-mimics, heliconius melpomene, heliconius timareta and heliconius elevatus, especially at two genomic regions that control mimicry pattern. we infer that closely related heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.",0
"problem/condition traumatic brain injury (tbi) has short- and long-term adverse clinical outcomes, including death and disability. tbi can be caused by a number of principal mechanisms, including motor-vehicle crashes, falls, and assaults. this report describes the estimated incidence of tbi-related emergency department (ed) visits, hospitalizations, and deaths during 2013 and makes comparisons to similar estimates from 2007. reporting period 2007 and 2013. description of system state-based administrative health care data were used to calculate estimates of tbi-related ed visits and hospitalizations by principal mechanism of injury, age group, sex, and injury intent. categories of injury intent included unintentional (motor-vehicle crashes, falls, being struck by or against an object, mechanism unspecified), intentional (self-harm and assault/homicide), and undetermined intent. these health records come from the healthcare cost and utilization project's national emergency department sample and national inpatient sample. tbi-related death analyses used cdc multiple-cause-of-death public-use data files, which contain death certificate data from all 50 states and the district of columbia. results in 2013, a total of approximately 2.8 million tbi-related ed visits, hospitalizations, and deaths (tbi-edhds) occurred in the united states. this consisted of approximately 2.5 million tbi-related ed visits, approximately 282,000 tbi-related hospitalizations, and approximately 56,000 tbi-related deaths. tbis were diagnosed in nearly 2.8 million (1.9%) of the approximately 149 million total injury- and noninjury-related edhds that occurred in the united states during 2013. rates of tbi-edhds varied by age, with the highest rates observed among persons aged ≥75 years (2,232.2 per 100,000 population), 0-4 years (1,591.5), and 15-24 years (1,080.7). overall, males had higher age-adjusted rates of tbi-edhds (959.0) compared with females (810.8) and the most common principal mechanisms of injury for all age groups included falls (413.2, age-adjusted), being struck by or against an object (142.1, age-adjusted), and motor-vehicle crashes (121.7, age-adjusted). the age-adjusted rate of ed visits was higher in 2013 (787.1) versus 2007 (534.4), with fall-related tbis among persons aged ≥75 years accounting for 17.9% of the increase in the number of tbi-related ed visits. the number and rate of tbi-related hospitalizations also increased among persons aged ≥75 years (from 356.9 in 2007 to 454.4 in 2013), primarily because of falls. whereas motor-vehicle crashes were the leading cause of tbi-related deaths in 2007 in both number and rate, in 2013, intentional self-harm was the leading cause in number and rate. the overall age-adjusted rate of tbi-related deaths for all ages decreased from 17.9 in 2007 to 17.0 in 2013; however, age-adjusted tbi-related death rates attributable to falls increased from 3.8 in 2007 to 4.5 in 2013, primarily among older adults. although the age-adjusted rate of tbi-related deaths attributable to motor-vehicle crashes decreased from 5.0 in 2007 to 3.4 in 2013, the age-adjusted rate of tbi-related ed visits attributable to motor-vehicle crashes increased from 83.8 in 2007 to 99.5 in 2013. the age-adjusted rate of tbi-related hospitalizations attributable to motor-vehicle crashes decreased from 23.5 in 2007 to 18.8 in 2013. interpretation progress has been made to prevent motor-vehicle crashes, resulting in a decrease in the number of tbi-related hospitalizations and deaths from 2007 to 2013. however, during the same time, the number and rate of older adult fall-related tbis have increased substantially. although considerable public interest has focused on sports-related concussion in youth, the findings in this report suggest that tbis attributable to older adult falls, many of which result in hospitalization and death, should receive public health attention. public health actions the increase in the number of fall-related tbis in older adults suggests an urgent need to enhance fall-prevention efforts in that population. multiple effective interventions have been identified, and cdc has developed the steadi initiative (stopping elderly accidents deaths and injuries) as a comprehensive strategy that incorporates empirically supported clinical guidelines and scientifically tested interventions to help primary care providers address their patients' fall risk through the identification of modifiable risk factors and implementation of effective interventions (e.g., exercise, medication management, and vitamin d supplementation).",0
"krabbe disease (kd) is a neurodegenerative disorder caused by the lack of β- galactosylceramidase enzymatic activity and by widespread accumulation of the cytotoxic galactosyl-sphingosine in neuronal, myelinating and endothelial cells. despite the wide use of twitcher mice as experimental model for kd, the ultrastructure of this model is partial and mainly addressing peripheral nerves. more details are requested to elucidate the basis of the motor defects, which are the first to appear during kd onset. here we use transmission electron microscopy (tem) to focus on the alterations produced by kd in the lower motor system at postnatal day 15 (p15), a nearly asymptomatic stage, and in the juvenile p30 mouse. we find mild effects on motorneuron soma, severe ones on sciatic nerves and very severe effects on nerve terminals and neuromuscular junctions at p30, with peripheral damage being already detectable at p15. finally, we find that the gastrocnemius muscle undergoes atrophy and structural changes that are independent of denervation at p15. our data further characterize the ultrastructural analysis of the kd mouse model, and support recent theories of a dying-back mechanism for neuronal degeneration, which is independent of demyelination.",0
"problem/condition autism spectrum disorder (asd). period covered 2014. description of system the autism and developmental disabilities monitoring (addm) network is an active surveillance system that provides estimates of the prevalence of autism spectrum disorder (asd) among children aged 8 years whose parents or guardians reside within 11 addm sites in the united states (arizona, arkansas, colorado, georgia, maryland, minnesota, missouri, new jersey, north carolina, tennessee, and wisconsin). addm surveillance is conducted in two phases. the first phase involves review and abstraction of comprehensive evaluations that were completed by professional service providers in the community. staff completing record review and abstraction receive extensive training and supervision and are evaluated according to strict reliability standards to certify effective initial training, identify ongoing training needs, and ensure adherence to the prescribed methodology. record review and abstraction occurs in a variety of data sources ranging from general pediatric health clinics to specialized programs serving children with developmental disabilities. in addition, most of the addm sites also review records for children who have received special education services in public schools. in the second phase of the study, all abstracted information is reviewed systematically by experienced clinicians to determine asd case status. a child is considered to meet the surveillance case definition for asd if he or she displays behaviors, as described on one or more comprehensive evaluations completed by community-based professional providers, consistent with the diagnostic and statistical manual of mental disorders, fourth edition, text revision (dsm-iv-tr) diagnostic criteria for autistic disorder; pervasive developmental disorder-not otherwise specified (pdd-nos, including atypical autism); or asperger disorder. this report provides updated asd prevalence estimates for children aged 8 years during the 2014 surveillance year, on the basis of dsm-iv-tr criteria, and describes characteristics of the population of children with asd. in 2013, the american psychiatric association published the diagnostic and statistical manual of mental disorders, fifth edition (dsm-5), which made considerable changes to asd diagnostic criteria. the change in asd diagnostic criteria might influence addm asd prevalence estimates; therefore, most (85%) of the records used to determine prevalence estimates based on dsm-iv-tr criteria underwent additional review under a newly operationalized surveillance case definition for asd consistent with the dsm-5 diagnostic criteria. children meeting this new surveillance case definition could qualify on the basis of one or both of the following criteria, as documented in abstracted comprehensive evaluations: 1) behaviors consistent with the dsm-5 diagnostic features; and/or 2) an asd diagnosis, whether based on dsm-iv-tr or dsm-5 diagnostic criteria. stratified comparisons of the number of children meeting either of these two case definitions also are reported. results for 2014, the overall prevalence of asd among the 11 addm sites was 16.8 per 1,000 (one in 59) children aged 8 years. overall asd prevalence estimates varied among sites, from 13.1-29.3 per 1,000 children aged 8 years. asd prevalence estimates also varied by sex and race/ethnicity. males were four times more likely than females to be identified with asd. prevalence estimates were higher for non-hispanic white (henceforth, white) children compared with non-hispanic black (henceforth, black) children, and both groups were more likely to be identified with asd compared with hispanic children. among the nine sites with sufficient data on intellectual ability, 31% of children with asd were classified in the range of intellectual disability (intelligence quotient 85). the distribution of intellectual ability varied by sex and race/ethnicity. although mention of developmental concerns by age 36 months was documented for 85% of children with asd, only 42% had a comprehensive evaluation on record by age 36 months. the median age of earliest known asd diagnosis was 52 months and did not differ significantly by sex or race/ethnicity. for the targeted comparison of dsm-iv-tr and dsm-5 results, the number and characteristics of children meeting the newly operationalized dsm-5 case definition for asd were similar to those meeting the dsm-iv-tr case definition, with dsm-iv-tr case counts exceeding dsm-5 counts by less than 5% and approximately 86% overlap between the two case definitions (kappa = 0.85). interpretation findings from the addm network, on the basis of 2014 data reported from 11 sites, provide updated population-based estimates of the prevalence of asd among children aged 8 years in multiple communities in the united states. the overall asd prevalence estimate of 16.8 per 1,000 children aged 8 years in 2014 is higher than previously reported estimates from the addm network. because the addm sites do not provide a representative sample of the entire united states, the combined prevalence estimates presented in this report cannot be generalized to all children aged 8 years in the united states. consistent with reports from previous addm surveillance years, findings from 2014 were marked by variation in asd prevalence when stratified by geographic area, sex, and level of intellectual ability. differences in prevalence estimates between black and white children have diminished in most sites, but remained notable for hispanic children. for 2014, results from application of the dsm-iv-tr and dsm-5 case definitions were similar, overall and when stratified by sex, race/ethnicity, dsm-iv-tr diagnostic subtype, or level of intellectual ability. public health action beginning with surveillance year 2016, the dsm-5 case definition will serve as the basis for addm estimates of asd prevalence in future surveillance reports. although the dsm-iv-tr case definition will eventually be phased out, it will be applied in a limited geographic area to offer additional data for comparison. future analyses will examine trends in the continued use of dsm-iv-tr diagnoses, such as autistic disorder, pdd-nos, and asperger disorder in health and education records, documentation of symptoms consistent with dsm-5 terminology, and how these trends might influence estimates of asd prevalence over time. the latest findings from the addm network provide evidence that the prevalence of asd is higher than previously reported estimates and continues to vary among certain racial/ethnic groups and communities. with prevalence of asd ranging from 13.1 to 29.3 per 1,000 children aged 8 years in different communities throughout the united states, the need for behavioral, educational, residential, and occupational services remains high, as does the need for increased research on both genetic and nongenetic risk factors for asd.",0
"background older people are increasing users of health care globally. we aimed to establish whether older people with characteristics of frailty and who are at risk of adverse health-care outcomes could be identified using routinely collected data. methods a three-step approach was used to develop and validate a hospital frailty risk score from international statistical classification of diseases and related health problems, tenth revision (icd-10) diagnostic codes. first, we carried out a cluster analysis to identify a group of older people (≥75 years) admitted to hospital who had high resource use and diagnoses associated with frailty. second, we created a hospital frailty risk score based on icd-10 codes that characterised this group. third, in separate cohorts, we tested how well the score predicted adverse outcomes and whether it identified similar groups as other frailty tools. findings in the development cohort (n=22 139), older people with frailty diagnoses formed a distinct group and had higher non-elective hospital use (33·6 bed-days over 2 years compared with 23·0 bed-days for the group with the next highest number of bed-days). in the national validation cohort (n=1 013 590), compared with the 429 762 (42·4%) patients with the lowest risk scores, the 202 718 (20·0%) patients with the highest hospital frailty risk scores had increased odds of 30-day mortality (odds ratio 1·71, 95% ci 1·68-1·75), long hospital stay (6·03, 5·92-6·10), and 30-day readmission (1·48, 1·46-1·50). the c statistics (ie, model discrimination) between individuals for these three outcomes were 0·60, 0·68, and 0·56, respectively. the hospital frailty risk score showed fair overlap with dichotomised fried and rockwood scales (kappa scores 0·22, 95% ci 0·15-0·30 and 0·30, 0·22-0·38, respectively) and moderate agreement with the rockwood frailty index (pearson's correlation coefficient 0·41, 95% ci 0·38-0·47). interpretation the hospital frailty risk score provides hospitals and health systems with a low-cost, systematic way to screen for frailty and identify a group of patients who are at greater risk of adverse outcomes and for whom a frailty-attuned approach might be useful. funding national institute for health research.",0
"the rapid growth of the literature on neuroimaging in humans has led to major advances in our understanding of human brain function but has also made it increasingly difficult to aggregate and synthesize neuroimaging findings. here we describe and validate an automated brain-mapping framework that uses text-mining, meta-analysis and machine-learning techniques to generate a large database of mappings between neural and cognitive states. we show that our approach can be used to automatically conduct large-scale, high-quality neuroimaging meta-analyses, address long-standing inferential problems in the neuroimaging literature and support accurate 'decoding' of broad cognitive states from brain activity in both entire studies and individual human subjects. collectively, our results have validated a powerful and generative framework for synthesizing human neuroimaging data on an unprecedented scale.",0
"background malignant cells of classical hodgkin's lymphoma are characterised by genetic alterations at the 9p24.1 locus, leading to overexpression of pd-1 ligands and evasion of immune surveillance. in a phase 1b study, nivolumab, a pd-1-blocking antibody, produced a high response in patients with relapsed and refractory classical hodgkin's lymphoma, with an acceptable safety profile. we aimed to assess the clinical benefit and safety of nivolumab monotherapy in patients with classical hodgkin's lymphoma after failure of both autologous stem-cell transplantation and brentuximab vedotin. methods in this ongoing, single-arm phase 2 study, adult patients (aged ≥18 years) with recurrent classical hodgkin's lymphoma who had failed to respond to autologous stem-cell transplantation and had either relapsed after or failed to respond to brentuximab vedotin, and with an eastern cooperative oncology group performance status score of 0 or 1, were enrolled from 34 hospitals and academic centres across europe and north america. patients were given nivolumab intravenously over 60 min at 3 mg/kg every 2 weeks until progression, death, unacceptable toxicity, or withdrawal from study. the primary endpoint was objective response following a prespecified minimum follow-up period of 6 months, assessed by an independent radiological review committee (irrc). all patients who received at least one dose of nivolumab were included in the primary and safety analyses. this trial is registered with clinicaltrials.gov, number nct02181738. findings among 80 treated patients recruited between aug 26, 2014, and feb 20, 2015, the median number of previous therapies was four (iqr 4-7). at a median follow-up of 8·9 months (iqr 7·8-9·9), 53 (66·3%, 95% ci 54·8-76·4) of 80 patients achieved an irrc-assessed objective response. the most common drug-related adverse events (those that occurred in ≥15% of patients) included fatigue (20 patients), infusion-related reaction (16 ), and rash (13 ). the most common drug-related grade 3 or 4 adverse events were neutropenia (four patients) and increased lipase concentrations (four ). the most common serious adverse event (any grade) was pyrexia (three patients). three patients died during the study; none of these deaths were judged to be treatment related. interpretation nivolumab resulted in frequent responses with an acceptable safety profile in patients with classical hodgkin's lymphoma who progressed after autologous stem-cell transplantation and brentuximab vedotin. therefore, nivolumab might be a new treatment option for a patient population with a high unmet need. ongoing follow-up will help to assess the durability of response. funding bristol-myers squibb.",0
"in an ongoing effort of this journal to develop and further the theories, models, and best practices around ehealth research, this paper argues for the need for a ""science of attrition"", that is, a need to develop models for discontinuation of ehealth applications and the related phenomenon of participants dropping out of ehealth trials. what i call ""law of attrition"" here is the observation that in any ehealth trial a substantial proportion of users drop out before completion or stop using the application. this feature of ehealth trials is a distinct characteristic compared to, for example, drug trials. the traditional clinical trial and evidence-based medicine paradigm stipulates that high dropout rates make trials less believable. consequently ehealth researchers tend to gloss over high dropout rates, or not to publish their study results at all, as they see their studies as failures. however, for many ehealth trials, in particular those conducted on the internet and in particular with self-help applications, high dropout rates may be a natural and typical feature. usage metrics and determinants of attrition should be highlighted, measured, analyzed, and discussed. this also includes analyzing and reporting the characteristics of the subpopulation for which the application eventually ""works"", ie, those who stay in the trial and use it. for the question of what works and what does not, such attrition measures are as important to report as pure efficacy measures from intention-to-treat (itt) analyses. in cases of high dropout rates efficacy measures underestimate the impact of an application on a population which continues to use it. methods of analyzing attrition curves can be drawn from survival analysis methods, eg, the kaplan-meier analysis and proportional hazards regression analysis (cox model). measures to be reported include the relative risk of dropping out or of stopping the use of an application, as well as a ""usage half-life"", and prediction models reporting demographic usage discontinuation in a population. differential dropout or usage rates between two interventions could be a standard metric for the ""usability efficacy"" of a system. a ""run-in and withdrawal"" trial design is suggested as a methodological innovation for internet-based trials with a high number of initial dropouts/nonusers and a stable group of hardcore users.",0
"an unresolved issue in the field of implementation research is how to conceptualize and evaluate successful implementation. this paper advances the concept of ""implementation outcomes"" distinct from service system and clinical treatment outcomes. this paper proposes a heuristic, working ""taxonomy"" of eight conceptually distinct implementation outcomes-acceptability, adoption, appropriateness, feasibility, fidelity, implementation cost, penetration, and sustainability-along with their nominal definitions. we propose a two-pronged agenda for research on implementation outcomes. conceptualizing and measuring implementation outcomes will advance understanding of implementation processes, enhance efficiency in implementation research, and pave the way for studies of the comparative effectiveness of implementation strategies.",0
"background aim of the cosmin study (consensus-based standards for the selection of health status measurement instruments) was to develop a consensus-based checklist to evaluate the methodological quality of studies on measurement properties. we present the cosmin checklist and the agreement of the panel on the items of the checklist. methods a four-round delphi study was performed with international experts (psychologists, epidemiologists, statisticians and clinicians). of the 91 invited experts, 57 agreed to participate (63%). panel members were asked to rate their (dis)agreement with each proposal on a five-point scale. consensus was considered to be reached when at least 67% of the panel members indicated 'agree' or 'strongly agree'. results consensus was reached on the inclusion of the following measurement properties: internal consistency, reliability, measurement error, content validity (including face validity), construct validity (including structural validity, hypotheses testing and cross-cultural validity), criterion validity, responsiveness, and interpretability. the latter was not considered a measurement property. the panel also reached consensus on how these properties should be assessed. conclusions the resulting cosmin checklist could be useful when selecting a measurement instrument, peer-reviewing a manuscript, designing or reporting a study on measurement properties, or for educational purposes.",0
"monocyte chemoattractant protein 1 (mcp-1) is a cc chemokine that attracts monocytes, memory t lymphocytes, and natural killer cells. because other chemokines have similar target cell specificities and because ccr2, a cloned mcp-1 receptor, binds other ligands, it has been uncertain whether mcp-1 plays a unique role in recruiting mononuclear cells in vivo. to address this question, we disrupted scya2 (the gene encoding mcp-1) and tested mcp-1-deficient mice in models of inflammation. despite normal numbers of circulating leukocytes and resident macrophages, mcp-1(-/-) mice were specifically unable to recruit monocytes 72 h after intraperitoneal thioglycollate administration. similarly, accumulation of f4/80+ monocytes in delayed-type hypersensitivity lesions was impaired, although the swelling response was normal. development of secondary pulmonary granulomata in response to schistosoma mansoni eggs was blunted in mcp-1(-/-) mice, as was expression of il-4, il-5, and interferon gamma in splenocytes. in contrast, mcp-1(-/-) mice were indistinguishable from wild-type mice in their ability to clear mycobacterium tuberculosis. our data indicate that mcp-1 is uniquely essential for monocyte recruitment in several inflammatory models in vivo and influences expression of cytokines related to t helper responses.",0
"imgt/v-quest is the highly customized and integrated system for the standardized analysis of the immunoglobulin (ig) and t cell receptor (tr) rearranged nucleotide sequences. imgt/v-quest identifies the variable (v), diversity (d) and joining (j) genes and alleles by alignment with the germline ig and tr gene and allele sequences of the imgt reference directory. new functionalities were added through a complete rewrite in java. imgt/v-quest analyses batches of sequences (up to 50) in a single run. imgt/v-quest describes the v-region mutations and identifies the hot spot positions in the closest germline v gene. imgt/v-quest can detect insertions and deletions in the submitted sequences by reference to the imgt unique numbering. imgt/v-quest integrates imgt/junctionanalysis for a detailed analysis of the v-j and v-d-j junctions, and imgt/automat for a full v-j- and v-d-j-region annotation. imgt/v-quest displays, in 'detailed view', the results and alignments for each submitted sequence individually and, in 'synthesis view', the alignments of the sequences that, in a given run, express the same v gene and allele. the 'advanced parameters' allow to modify default parameters used by imgt/v-quest and imgt/junctionanalysis according to the users' interest. imgt/v-quest is freely available for academic research at",0
"background sepsis is life-threatening organ dysfunction due to a dysregulated host response to infection. it is considered a major cause of health loss, but data for the global burden of sepsis are limited. as a syndrome caused by underlying infection, sepsis is not part of standard global burden of diseases, injuries, and risk factors study (gbd) estimates. accurate estimates are important to inform and monitor health policy interventions, allocation of resources, and clinical treatment initiatives. we estimated the global, regional, and national incidence of sepsis and mortality from this disorder using data from gbd 2017. methods we used multiple cause-of-death data from 109 million individual death records to calculate mortality related to sepsis among each of the 282 underlying causes of death in gbd 2017. the percentage of sepsis-related deaths by underlying gbd cause in each location worldwide was modelled using mixed-effects linear regression. sepsis-related mortality for each age group, sex, location, gbd cause, and year (1990-2017) was estimated by applying modelled cause-specific fractions to gbd 2017 cause-of-death estimates. we used data for 8·7 million individual hospital records to calculate in-hospital sepsis-associated case-fatality, stratified by underlying gbd cause. in-hospital sepsis-associated case-fatality was modelled for each location using linear regression, and sepsis incidence was estimated by applying modelled case-fatality to sepsis-related mortality estimates. findings in 2017, an estimated 48·9 million (95% uncertainty interval 38·9-62·9) incident cases of sepsis were recorded worldwide and 11·0 million (10·1-12·0) sepsis-related deaths were reported, representing 19·7% (18·2-21·4) of all global deaths. age-standardised sepsis incidence fell by 37·0% (95% ui 11·8-54·5) and mortality decreased by 52·8% (47·7-57·5) from 1990 to 2017. sepsis incidence and mortality varied substantially across regions, with the highest burden in sub-saharan africa, oceania, south asia, east asia, and southeast asia. interpretation despite declining age-standardised incidence and mortality, sepsis remains a major cause of health loss worldwide and has an especially high health-related burden in sub-saharan africa. funding the bill & melinda gates foundation, the national institutes of health, the university of pittsburgh, the british columbia children's hospital foundation, the wellcome trust, and the fleming fund.",0
"background recent methods have been developed to perform high-throughput sequencing of dna by single molecule sequencing (sms). while next-generation sequencing methods may produce reads up to several hundred bases long, sms sequencing produces reads up to tens of kilobases long. existing alignment methods are either too inefficient for high-throughput datasets, or not sensitive enough to align sms reads, which have a higher error rate than next-generation sequencing. results we describe the method blasr (basic local alignment with successive refinement) for mapping single molecule sequencing (sms) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error. the method is benchmarked using both simulated reads and reads from a bacterial sequencing project. we also present a combinatorial model of sequencing error that motivates why our approach is effective. conclusions the results indicate that it is possible to map sms reads with high accuracy and speed. furthermore, the inferences made on the mapability of sms reads using our combinatorial model of sequencing error are in agreement with the mapping accuracy demonstrated on simulated reads.",0
"acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. this organism was susceptible to most antibiotics in the 1970s. it has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant a. baumannii strain aye, which is epidemic in france, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible a. baumannii strain sdf, which is associated with human body lice. the assembly of the whole shotgun genome sequences of the strains aye and sdf gave an estimated size of 3.9 and 3.2 mb, respectively. a. baumannii strain aye exhibits an 86-kb genomic region termed a resistance island--the largest identified to date--in which 45 resistance genes are clustered. at the homologous location, the sdf strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the a. baumannii strain aye have been recently acquired from bacteria of the genera pseudomonas, salmonella, or escherichia. this study also resulted in the discovery of 19 new putative resistance genes. whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.",0
"the colon is inhabited by a dense population of microorganisms, the so-called ""gut microbiota,"" able to ferment carbohydrates and proteins that escape absorption in the small intestine during digestion. this microbiota produces a wide range of metabolites, including short chain fatty acids (scfa). these compounds are absorbed in the large bowel and are defined as 1-6 carbon volatile fatty acids which can present straight or branched-chain conformation. their production is influenced by the pattern of food intake and diet-mediated changes in the gut microbiota. scfa have distinct physiological effects: they contribute to shaping the gut environment, influence the physiology of the colon, they can be used as energy sources by host cells and the intestinal microbiota and they also participate in different host-signaling mechanisms. we summarize the current knowledge about the production of scfa, including bacterial cross-feedings interactions, and the biological properties of these metabolites with impact on the human health.",0
"artificial intelligence (ai) aims to mimic human cognitive functions. it is bringing a paradigm shift to healthcare, powered by increasing availability of healthcare data and rapid progress of analytics techniques. we survey the current status of ai applications in healthcare and discuss its future. ai can be applied to various types of healthcare data (structured and unstructured). popular ai techniques include machine learning methods for structured data, such as the classical support vector machine and neural network, and the modern deep learning, as well as natural language processing for unstructured data. major disease areas that use ai tools include cancer, neurology and cardiology. we then review in more details the ai applications in stroke, in the three major areas of early detection and diagnosis, treatment, as well as outcome prediction and prognosis evaluation. we conclude with discussion about pioneer ai systems, such as ibm watson, and hurdles for real-life deployment of ai.",0
"the world health organization has declared sars-cov-2 virus outbreak a worldwide pandemic. however, there is very limited understanding on the immune responses, especially adaptive immune responses to sars-cov-2 infection. here, we collected blood from covid-19 patients who have recently become virus-free, and therefore were discharged, and detected sars-cov-2-specific humoral and cellular immunity in eight newly discharged patients. follow-up analysis on another cohort of six patients 2 weeks post discharge also revealed high titers of immunoglobulin g (igg) antibodies. in all 14 patients tested, 13 displayed serum-neutralizing activities in a pseudotype entry assay. notably, there was a strong correlation between neutralization antibody titers and the numbers of virus-specific t cells. our work provides a basis for further analysis of protective immunity to sars-cov-2, and understanding the pathogenesis of covid-19, especially in the severe cases. it also has implications in developing an effective vaccine to sars-cov-2 infection.",0
"deficits in eye contact have been a hallmark of autism since the condition's initial description. they are cited widely as a diagnostic feature and figure prominently in clinical instruments; however, the early onset of these deficits has not been known. here we show in a prospective longitudinal study that infants later diagnosed with autism spectrum disorders (asds) exhibit mean decline in eye fixation from 2 to 6 months of age, a pattern not observed in infants who do not develop asd. these observations mark the earliest known indicators of social disability in infancy, but also falsify a prior hypothesis: in the first months of life, this basic mechanism of social adaptive action--eye looking--is not immediately diminished in infants later diagnosed with asd; instead, eye looking appears to begin at normative levels prior to decline. the timing of decline highlights a narrow developmental window and reveals the early derailment of processes that would otherwise have a key role in canalizing typical social development. finally, the observation of this decline in eye fixation--rather than outright absence--offers a promising opportunity for early intervention that could build on the apparent preservation of mechanisms subserving reflexive initial orientation towards the eyes.",0
"background after breast-conserving surgery, radiotherapy reduces recurrence and breast cancer death, but it may do so more for some groups of women than for others. we describe the absolute magnitude of these reductions according to various prognostic and other patient characteristics, and relate the absolute reduction in 15-year risk of breast cancer death to the absolute reduction in 10-year recurrence risk. methods we undertook a meta-analysis of individual patient data for 10,801 women in 17 randomised trials of radiotherapy versus no radiotherapy after breast-conserving surgery, 8337 of whom had pathologically confirmed node-negative (pn0) or node-positive (pn+) disease. findings overall, radiotherapy reduced the 10-year risk of any (ie, locoregional or distant) first recurrence from 35·0% to 19·3% (absolute reduction 15·7%, 95% ci 13·7-17·7, 2p interpretation after breast-conserving surgery, radiotherapy to the conserved breast halves the rate at which the disease recurs and reduces the breast cancer death rate by about a sixth. these proportional benefits vary little between different groups of women. by contrast, the absolute benefits from radiotherapy vary substantially according to the characteristics of the patient and they can be predicted at the time when treatment decisions need to be made. funding cancer research uk, british heart foundation, and uk medical research council.",0
"background concerns for arsenic exposure are not limited to toxic waste sites and massive poisoning events. chronic exposure continues to be a major public health problem worldwide, affecting hundreds of millions of persons. objectives we reviewed recent information on worldwide concerns for arsenic exposures and public health to heighten awareness of the current scope of arsenic exposure and health outcomes and the importance of reducing exposure, particularly during pregnancy and early life. methods we synthesized the large body of current research pertaining to arsenic exposure and health outcomes with an emphasis on recent publications. discussion locations of high arsenic exposure via drinking water span from bangladesh, chile, and taiwan to the united states. the u.s. environmental protection agency maximum contaminant level (mcl) in drinking water is 10 µg/l; however, concentrations of > 3,000 µg/l have been found in wells in the united states. in addition, exposure through diet is of growing concern. knowledge of the scope of arsenic-associated health effects has broadened; arsenic leaves essentially no bodily system untouched. arsenic is a known carcinogen associated with skin, lung, bladder, kidney, and liver cancer. dermatological, developmental, neurological, respiratory, cardiovascular, immunological, and endocrine effects are also evident. most remarkably, early-life exposure may be related to increased risks for several types of cancer and other diseases during adulthood. conclusions these data call for heightened awareness of arsenic-related pathologies in broader contexts than previously perceived. testing foods and drinking water for arsenic, including individual private wells, should be a top priority to reduce exposure, particularly for pregnant women and children, given the potential for life-long effects of developmental exposure.",0
"background aiming at therapeutic targets has reduced the risk of organ failure in many diseases such as diabetes or hypertension. such targets have not been defined for rheumatoid arthritis (ra). objective /st> to develop recommendations for achieving optimal therapeutic outcomes in ra. methods a task force of rheumatologists and a patient developed a set of recommendations on the basis of evidence derived from a systematic literature review and expert opinion; these were subsequently discussed, amended and voted upon by >60 experts from various regions of the world in a delphi-like procedure. levels of evidence, strength of recommendations and levels of agreement were derived. results the treat-to-target activity resulted in 10 recommendations. the treatment aim was defined as remission with low disease activity being an alternative goal in patients with long-standing disease. regular follow-up (every 1-3 months during active disease) with appropriate therapeutic adaptation to reach the desired state within 3 to a maximum of 6 months was recommended. follow-up examinations ought to employ composite measures of disease activity which include joint counts. additional items provide further details for particular aspects of the disease. levels of agreement were very high for many of these recommendations (> or =9/10). conclusion the 10 recommendations are supposed to inform patients, rheumatologists and other stakeholders about strategies to reach optimal outcomes of ra based on evidence and expert opinion.",0
"we describe the design and operation of a machine that freezes biological tissues by contact with a cold metal block, which incorporates a timing circuit that stimulates frog neuromuscular junctions in the last few milliseconds before thay are frozen. we show freeze-fracture replicas of nerve terminals frozen during transmitter discharge, which display synpatic vesicles caught in the act of exocytosis. we use 4-aminopyridine (4-ap) to increase the number of transmitter quanta discharged with each nerve impulse, and show that the number of exocytotic vesicles caught by quick-freezing increases commensurately, indicating that one vesicle undergoes exocytosis for each quantum that is discharged. we perform statistical analyses on the spatial distribution of synaptic vesicle discharge sites along the ""active zones"" that mark the secretory regions of these nerves, and show that individual vesicles fuse with the plasma membrane independent of one another, as expected from physiological demonstrations that quanta are discharged independently. thus, the utility of quick-freezing as a technique to capture biological processes as evanescent as synaptic transmission has been established. an appendix describes a new capacitance method to measure freezing rates, which shows that the ""temporal resolution"" of our quick-freezing technique is 2 ms or better.",0
"antibodies to the n-methyl-d-aspartate subtype of glutamate receptor have been associated with a newly-described encephalopathy that has been mainly identified in young females with ovarian tumours. however, the full clinical spectrum and treatment responses are not yet clear. we established a sensitive cell-based assay for detection of n-methyl-d-aspartate receptor antibodies in serum or cerebrospinal fluid, and a quantitative fluorescent immunoprecipitation assay for serial studies. although there was marked intrathecal synthesis of n-methyl-d-aspartate receptor antibodies, the absolute levels of n-methyl-d-aspartate receptor antibodies were higher in serum than in cerebrospinal fluid. n-methyl-d-aspartate receptor antibodies were of the immunoglobulin g1 subclass and were able to activate complement on n-methyl d-aspartate receptor-expressing human embryonic kidney cells. from questionnaires returned on 44 n-methyl-d-aspartate receptor antibody-positive patients, we identified a high proportion without a detected tumour (35/44, 80%: follow-up 3.6-121 months, median 16 months). among the latter were 15 adult females (43%), 10 adult males (29%) and 10 children (29%), with four in the first decade of life. overall, there was a high proportion (29%) of non-caucasians. good clinical outcomes, as defined by reductions in modified rankin scores, correlated with decreased n-methyl-d-aspartate receptor antibody levels and were associated with early (<40 days) administration of immunotherapies in non-paraneoplastic patients (p < 0.0001) and earlier tumour removal in paraneoplastic patients (p = 0.02). ten patients (23%) who were first diagnosed during relapses had no evidence of tumours but had received minimal or no immunotherapy during earlier episodes. temporal analysis of the onset of the neurological features suggested progression through two main stages. the time of onset of the early features, characterized by neuropsychiatric symptoms and seizures preceded by a median of 10-20 days, the onset of movement disorders, reduction in consciousness and dysautonomia. this temporal dichotomy was also seen in the timing of cerebrospinal fluid, electroencephalographic and in the rather infrequent cerebral imaging changes. overall, our data support a model in which the early features are associated with cerebrospinal fluid lymphocytosis, and the later features with appearance of oligoclonal bands. the immunological events and neuronal mechanisms underlying these observations need to be explored further, but one possibility is that the early stage represents diffusion of serum antibodies into the cortical grey matter, whereas the later stage results from secondary expansion of the immunological repertoire within the intrathecal compartment acting on subcortical neurons. four patients, who only had temporal lobe epilepsy without oligoclonal bands, may represent restriction to the first stage.",0
"background visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. few tools exist to automate the generation of extensively-customizable, high-resolution venn and euler diagrams in the r statistical environment. to fill this gap we introduce venndiagram, an r package that enables the automated generation of highly-customizable, high-resolution venn diagrams with up to four sets and euler diagrams with up to three sets. results the venndiagram package offers the user the ability to customize essentially all aspects of the generated diagrams, including font sizes, label styles and locations, and the overall rotation of the diagram. we have implemented scaled venn and euler diagrams, which increase graphical accuracy and visual appeal. diagrams are generated as high-definition tiff files, simplifying the process of creating publication-quality figures and easing integration with established analysis pipelines. conclusions the venndiagram package allows the creation of high quality venn and euler diagrams in the r statistical environment.",0
"background the ad26.cov2.s vaccine is a recombinant, replication-incompetent human adenovirus type 26 vector encoding full-length severe acute respiratory syndrome coronavirus 2 (sars-cov-2) spike protein in a prefusion-stabilized conformation. methods in an international, randomized, double-blind, placebo-controlled, phase 3 trial, we randomly assigned adult participants in a 1:1 ratio to receive a single dose of ad26.cov2.s (5×10 10 viral particles) or placebo. the primary end points were vaccine efficacy against moderate to severe-critical coronavirus disease 2019 (covid-19) with an onset at least 14 days and at least 28 days after administration among participants in the per-protocol population who had tested negative for sars-cov-2. safety was also assessed. results the per-protocol population included 19,630 sars-cov-2-negative participants who received ad26.cov2.s and 19,691 who received placebo. ad26.cov2.s protected against moderate to severe-critical covid-19 with onset at least 14 days after administration (116 cases in the vaccine group vs. 348 in the placebo group; efficacy, 66.9%; adjusted 95% confidence interval , 59.0 to 73.4) and at least 28 days after administration (66 vs. 193 cases; efficacy, 66.1%; adjusted 95% ci, 55.0 to 74.8). vaccine efficacy was higher against severe-critical covid-19 (76.7% for onset at ≥14 days and 85.4% for onset at ≥28 days). despite 86 of 91 cases (94.5%) in south africa with sequenced virus having the 20h/501y.v2 variant, vaccine efficacy was 52.0% and 64.0% against moderate to severe-critical covid-19 with onset at least 14 days and at least 28 days after administration, respectively, and efficacy against severe-critical covid-19 was 73.1% and 81.7%, respectively. reactogenicity was higher with ad26.cov2.s than with placebo but was generally mild to moderate and transient. the incidence of serious adverse events was balanced between the two groups. three deaths occurred in the vaccine group (none were covid-19-related), and 16 in the placebo group (5 were covid-19-related). conclusions a single dose of ad26.cov2.s protected against symptomatic covid-19 and asymptomatic sars-cov-2 infection and was effective against severe-critical disease, including hospitalization and death. safety appeared to be similar to that in other phase 3 trials of covid-19 vaccines. (funded by janssen research and development and others; ensemble clinicaltrials.gov number, nct04505722.).",0
"horseradish peroxidase was administered to mice by intravenous injection, and its distribution in cerebral cortex studied with a recently available technique for localizing peroxidase with the electron microscope. brains were fixed by either immersion or vascular perfusion 10-60 min after administration of various doses of peroxidase. exogenous peroxidase was localized in the lumina of blood vessels and in some micropinocytotic vesicles within endothelial cells; none was found beyond the vascular endothelium. micropinocytotic vesicles were few in number and did not appear to transport peroxidase while tight junctions between endothelial cells were probably responsible for preventing its intercellular passage. our findings therefore localize, at a fine structural level, a ""barrier"" to the passage of peroxidase at the endothelium of vessels in the cerebral cortex. the significance of these findings is discussed, particularly with reference to a recent study in which similar techniques were applied to capillaries in heart and skeletal muscle.",0
"immunostimulatory properties of dendritic cells (dcs) are linked to their maturation state. injection of mature dcs rapidly enhances antigen-specific cd4+ and cd8+ t cell immunity in humans. here we describe the immune response to a single injection of immature dcs pulsed with influenza matrix peptide (mp) and keyhole limpet hemocyanin (klh) in two healthy subjects. in contrast to prior findings using mature dcs, injection of immature dcs in both subjects led to the specific inhibition of mp-specific cd8+ t cell effector function in freshly isolated t cells and the appearance of mp-specific interleukin 10-producing cells. when pre- and postimmunization t cells were boosted in culture, there were greater numbers of mp-specific major histocompatibility complex tetramer-binding cells after immunization, but these had reduced interferon production and lacked killer activity. these data demonstrate the feasibility of antigen-specific inhibition of effector t cell function in vivo in humans and urge caution with the use of immature dcs when trying to enhance tumor or microbial immunity.",0
"melanoma, a skin cancer associated with high mortality rates, is highly radio- and chemotherapy resistant but can also be very immunogenic. these circumstances have led to a recent surge in research into therapies aiming to boost anti-tumor immune responses in cancer patients. among these immunotherapies, neutralizing antibodies targeting the immune checkpoints t-lymphocyte-associated protein 4 (ctla-4) and programmed cell death protein 1 (pd-1) are being hailed as particularly successful. these antibodies have resulted in dramatic improvements in disease outcome and are now clinically approved in many countries. however, the majority of advanced stage melanoma patients do not respond or will relapse, and the hunt for the ""magic bullet"" to treat the disease continues. this review examines the mechanisms of action and the limitations of anti-pd-1/pd-l1 and anti-ctla-4 antibodies which are the two types of checkpoint inhibitors currently available to patients and further explores the future avenues of their use in melanoma and other cancers.",0
"prevalence estimates of autism are essential for informing public policy, raising awareness, and developing research priorities. using a systematic review, we synthesized estimates of the prevalence of autism worldwide. we examined factors accounting for variability in estimates and critically reviewed evidence relevant for hypotheses about biological or social determinants (viz., biological sex, sociodemographic status, ethnicity/race, and nativity) potentially modifying prevalence estimates of autism. we performed the search in november 2021 within medline for studies estimating autism prevalence, published since our last systematic review in 2012. data were extracted by two independent researchers. since 2012, 99 estimates from 71 studies were published indicating a global autism prevalence that ranges within and across regions, with a median prevalence of 100/10,000 (range: 1.09/10,000 to 436.0/10,000). the median male-to-female ratio was 4.2. the median percentage of autism cases with co-occurring intellectual disability was 33.0%. estimates varied, likely reflecting complex and dynamic interactions between patterns of community awareness, service capacity, help seeking, and sociodemographic factors. a limitation of this review is that synthesizing methodological features precludes a quality appraisal of studies. our findings reveal an increase in measured autism prevalence globally, reflecting the combined effects of multiple factors including the increase in community awareness and public health response globally, progress in case identification and definition, and an increase in community capacity. hypotheses linking factors that increase the likelihood of developing autism with variations in prevalence will require research with large, representative samples and comparable autism diagnostic criteria and case-finding methods in diverse world regions over time. lay summary: we reviewed studies of the prevalence of autism worldwide, considering the impact of geographic, ethnic, and socioeconomic factors on prevalence estimates. approximately 1/100 children are diagnosed with autism spectrum disorder around the world. prevalence estimates increased over time and varied greatly within and across sociodemographic groups. these findings reflect changes in the definition of autism and differences in the methodology and contexts of prevalence studies.",0
"background sex and gender differences are often overlooked in research design, study implementation and scientific reporting, as well as in general science communication. this oversight limits the generalizability of research findings and their applicability to clinical practice, in particular for women but also for men. this article describes the rationale for an international set of guidelines to encourage a more systematic approach to the reporting of sex and gender in research across disciplines. methods a panel of 13 experts representing nine countries developed the guidelines through a series of teleconferences, conference presentations and a 2-day workshop. an internet survey of 716 journal editors, scientists and other members of the international publishing community was conducted as well as a literature search on sex and gender policies in scientific publishing. results the sex and gender equity in research (sager) guidelines are a comprehensive procedure for reporting of sex and gender information in study design, data analyses, results and interpretation of findings. conclusions the sager guidelines are designed primarily to guide authors in preparing their manuscripts, but they are also useful for editors, as gatekeepers of science, to integrate assessment of sex and gender into all manuscripts as an integral part of the editorial process.",0
"there is an epidemic of diabetes in asia. type 2 diabetes develops in east asian patients at a lower mean body mass index (bmi) compared with those of european descent. at any given bmi, east asians have a greater amount of body fat and a tendency to visceral adiposity. in asian patients, diabetes develops at a younger age and is characterized by early β cell dysfunction in the setting of insulin resistance, with many requiring early insulin treatment. the increasing proportion of young-onset and childhood type 2 diabetes is posing a particular threat, with these patients being at increased risk of developing diabetic complications. east asian patients with type 2 diabetes have a higher risk of developing renal complications than europeans and, with regard to cardiovascular complications, a predisposition for developing strokes. in addition to cardiovascular-renal disease, cancer is emerging as the other main cause of mortality. while more research is needed to explain these interethnic differences, urgent and concerted actions are needed to raise awareness, facilitate early diagnosis, and encourage preventive strategies to combat these growing disease burdens.",0
"long-term potentiation (ltp) of synaptic transmission provides an experimental model for studying mechanisms of memory. the classical form of ltp relies on n-methyl-d-aspartate receptors (nmdars), and it has been shown that astroglia can regulate their activation through ca(2+)-dependent release of the nmdar co-agonist d-serine. release of d-serine from glia enables ltp in cultures and explains a correlation between glial coverage of synapses and ltp in the supraoptic nucleus. however, increases in ca(2+) concentration in astroglia can also release other signalling molecules, most prominently glutamate, atp and tumour necrosis factor-alpha, whereas neurons themselves can synthesize and supply d-serine. furthermore, loading an astrocyte with exogenous ca(2+) buffers does not suppress ltp in hippocampal area ca1 (refs 14-16), and the physiological relevance of experiments in cultures or strong exogenous stimuli applied to astrocytes has been questioned. the involvement of glia in ltp induction therefore remains controversial. here we show that clamping internal ca(2+) in individual ca1 astrocytes blocks ltp induction at nearby excitatory synapses by decreasing the occupancy of the nmdar co-agonist sites. this ltp blockade can be reversed by exogenous d-serine or glycine, whereas depletion of d-serine or disruption of exocytosis in an individual astrocyte blocks local ltp. we therefore demonstrate that ca(2+)-dependent release of d-serine from an astrocyte controls nmdar-dependent plasticity in many thousands of excitatory synapses nearby.",0
"important steps in the processing of rotation data are described that are common to most software packages. these programs differ in the details and in the methods implemented to carry out the tasks. here, the working principles underlying the data-reduction package xds are explained, including the new features of automatic determination of spot size and reflecting range, recognition and assignment of crystal symmetry and a highly efficient algorithm for the determination of correction/scaling factors.",0
"selecting an appropriate set of confounders for which to control is critical for reliable causal inference. recent theoretical and methodological developments have helped clarify a number of principles of confounder selection. when complete knowledge of a causal diagram relating all covariates to each other is available, graphical rules can be used to make decisions about covariate control. unfortunately, such complete knowledge is often unavailable. this paper puts forward a practical approach to confounder selection decisions when the somewhat less stringent assumption is made that knowledge is available for each covariate whether it is a cause of the exposure, and whether it is a cause of the outcome. based on recent theoretically justified developments in the causal inference literature, the following proposal is made for covariate control decisions: control for each covariate that is a cause of the exposure, or of the outcome, or of both; exclude from this set any variable known to be an instrumental variable; and include as a covariate any proxy for an unmeasured variable that is a common cause of both the exposure and the outcome. various principles of confounder selection are then further related to statistical covariate selection methods.",0
"when using conventional transmembrane topology and signal peptide predictors, such as tmhmm and signalp, there is a substantial overlap between these two types of predictions. applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all predicted transmembrane topologies overlap. this impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. to address this problem, we previously designed a hidden markov model, phobius, that combines transmembrane topology and signal peptide predictions. the method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. we here present a web interface ( and to access phobius.",0
"introduction microvascular alterations may play an important role in the development of organ failure in critically ill patients and especially in sepsis. recent advances in technology have allowed visualization of the microcirculation, but several scoring systems have been used so it is sometimes difficult to compare studies. this paper reports the results of a round table conference that was organized in amsterdam in november 2006 in order to achieve consensus on image acquisition and analysis. methods the participants convened to discuss the various aspects of image acquisition and the different scores, and a consensus statement was drafted using the delphi methodology. results the participants identified the following five key points for optimal image acquisition: five sites per organ, avoidance of pressure artifacts, elimination of secretions, adequate focus and contrast adjustment, and recording quality. the scores that can be used to describe numerically the microcirculatory images consist of the following: a measure of vessel density (total and perfused vessel density; two indices of perfusion of the vessels (proportion of perfused vessels and microcirculatory flow index); and a heterogeneity index. in addition, this information should be provided for all vessels and for small vessels (mostly capillaries) identified as smaller than 20 microm. venular perfusion should be reported as a quality control index, because venules should always be perfused in the absence of pressure artifact. it is anticipated that although this information is currently obtained manually, it is likely that image analysis software will ease analysis in the future. conclusion we proposed that scoring of the microcirculation should include an index of vascular density, assessment of capillary perfusion and a heterogeneity index.",0
"the parkin ubiquitin ligase (also known as park2) and its regulatory kinase pink1 (also known as park6), often mutated in familial early-onset parkinson's disease, have central roles in mitochondrial homeostasis and mitophagy. whereas parkin is recruited to the mitochondrial outer membrane (mom) upon depolarization via pink1 action and can ubiquitylate porin, mitofusin and miro proteins on the mom, the full repertoire of parkin substrates--the parkin-dependent ubiquitylome--remains poorly defined. here we use quantitative digly capture proteomics (digly) to elucidate the ubiquitylation site specificity and topology of parkin-dependent target modification in response to mitochondrial depolarization. hundreds of dynamically regulated ubiquitylation sites in dozens of proteins were identified, with strong enrichment for mom proteins, indicating that parkin dramatically alters the ubiquitylation status of the mitochondrial proteome. using complementary interaction proteomics, we found depolarization-dependent parkin association with numerous mom targets, autophagy receptors, and the proteasome. mutation of the parkin active site residue c431, which has been found mutated in parkinson's disease patients, largely disrupts these associations. structural and topological analysis revealed extensive conservation of parkin-dependent ubiquitylation sites on cytoplasmic domains in vertebrate and drosophila melanogaster mom proteins. these studies provide a resource for understanding how the pink1-parkin pathway re-sculpts the proteome to support mitochondrial homeostasis.",0
"background. in the last decades, thyroid cancer incidence has continuously and sharply increased all over the world. this review analyzes the possible reasons of this increase. summary. many experts believe that the increased incidence of thyroid cancer is apparent, because of the increased detection of small cancers in the preclinical stage. however, a true increase is also possible, as suggested by the observation that large tumors have also increased and gender differences and birth cohort effects are present. moreover, thyroid cancer mortality, in spite of earlier diagnosis and better treatment, has not decreased but is rather increasing. therefore, some environmental carcinogens in the industrialized lifestyle may have specifically affected the thyroid. among potential carcinogens, the increased exposure to medical radiations is the most likely risk factor. other factors specific for the thyroid like increased iodine intake and increased prevalence of chronic autoimmune thyroiditis cannot be excluded, while other factors like the increasing prevalence of obesity are not specific for the thyroid. conclusions. the increased incidence of thyroid cancer is most likely due to a combination of an apparent increase due to more sensitive diagnostic procedures and of a true increase, a possible consequence of increased population exposure to radiation and to other still unrecognized carcinogens.",0
"psychopy is an application for the creation of experiments in behavioral science (psychology, neuroscience, linguistics, etc.) with precise spatial control and timing of stimuli. it now provides a choice of interface; users can write scripts in python if they choose, while those who prefer to construct experiments graphically can use the new builder interface. here we describe the features that have been added over the last 10 years of its development. the most notable addition has been that builder interface, allowing users to create studies with minimal or no programming, while also allowing the insertion of python code for maximal flexibility. we also present some of the other new features, including further stimulus options, asynchronous time-stamped hardware polling, and better support for open science and reproducibility. tens of thousands of users now launch psychopy every month, and more than 90 people have contributed to the code. we discuss the current state of the project, as well as plans for the future.",0
"cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (acd). in most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'regulated cell death' (rcd) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. the biochemical phenomena that accompany rcd may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. nonetheless, efficiently inhibiting the processes that are commonly thought to cause rcd, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. thus, the mechanisms that truly execute rcd may be less understood, less inhibitable and perhaps more homogeneous than previously thought. here, the nomenclature committee on cell death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.",0
"the interpro database ( is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. central to the interpro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. interpro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. here, we report on the status of interpro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated web interfaces and software. in particular, the new domain architecture search tool is described and the process of mapping of gene ontology terms to interpro is outlined. we also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. interpro (version 48.0) contains 36,766 member database signatures integrated into 26,238 interpro entries, an increase of over 3993 entries (5081 signatures), since 2012.",0
"the 1000 genomes project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. we characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (snps), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. this resource includes >99% of snp variants with a frequency of >1% for a variety of ancestries. we describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.",0
"acute graft-versus-host disease (agvhd) is still a major obstacle in clinical allogeneic bone marrow (bm) transplantation. cd4(+)cd25(+) regulatory t (t(reg)) cells have recently been shown to suppress proliferative responses of cd4(+)cd25(-) t cells to alloantigenic stimulation in vitro and are required for ex vivo tolerization of donor t cells, which results in their reduced potential to induce agvhd. here we show that cd4(+)cd25(+) t cells isolated from the spleen or bm of donor c57bl/6 (h-2(b)) mice that have not been tolerized are still potent inhibitors of the alloresponse in vitro and of lethal agvhd induced by c57bl/6 cd4(+)cd25(-) t cells in irradiated balb/c (h-2(d)) hosts in vivo. the addition of the cd4(+)cd25(+) t(reg) cells at a 1:1 ratio with responder/inducer cd4(+)cd25(-) t cells resulted in a >90% inhibition of the mixed leukocyte reaction and marked protection from lethal gvhd. this protective effect depended in part on the ability of the transferred cd4(+)cd25(+) t cells to secrete interleukin 10 and occurred if the t(reg) cells were of donor, but not host, origin. our results demonstrate that the balance of donor-type cd4(+)cd25(+) t(reg) and conventional cd4(+)cd25(-) t cells can determine the outcome of agvhd.",0
"background although diabetes has been associated with covid-19-related mortality, the absolute and relative risks for type 1 and type 2 diabetes are unknown. we assessed the independent effects of diabetes status, by type, on in-hospital death in england in patients with covid-19 during the period from march 1 to may 11, 2020. methods we did a whole-population study assessing risks of in-hospital death with covid-19 between march 1 and may 11, 2020. we included all individuals registered with a general practice in england who were alive on feb 16, 2020. we used multivariable logistic regression to examine the effect of diabetes status, by type, on in-hospital death with covid-19, adjusting for demographic factors and cardiovascular comorbidities. because of the absence of data on total numbers of people infected with covid-19 during the observation period, we calculated mortality rates for the population as a whole, rather than the population who were infected. findings of the 61 414 470 individuals who were alive and registered with a general practice on feb 16, 2020, 263 830 (0·4%) had a recorded diagnosis of type 1 diabetes, 2 864 670 (4·7%) had a diagnosis of type 2 diabetes, 41 750 (0·1%) had other types of diabetes, and 58 244 220 (94·8%) had no diabetes. 23 698 in-hospital covid-19-related deaths occurred during the study period. a third occurred in people with diabetes: 7434 (31·4%) in people with type 2 diabetes, 364 (1·5%) in those with type 1 diabetes, and 69 (0·3%) in people with other types of diabetes. unadjusted mortality rates per 100 000 people over the 72-day period were 27 (95% ci 27-28) for those without diabetes, 138 (124-153) for those with type 1 diabetes, and 260 (254-265) for those with type 2 diabetes. adjusted for age, sex, deprivation, ethnicity, and geographical region, compared with people without diabetes, the odds ratios (ors) for in-hospital covid-19-related death were 3·51 (95% ci 3·16-3·90) in people with type 1 diabetes and 2·03 (1·97-2·09) in people with type 2 diabetes. these effects were attenuated to ors of 2·86 (2·58-3·18) for type 1 diabetes and 1·80 (1·75-1·86) for type 2 diabetes when also adjusted for previous hospital admissions with coronary heart disease, cerebrovascular disease, or heart failure. interpretation the results of this nationwide analysis in england show that type 1 and type 2 diabetes were both independently associated with a significant increased odds of in-hospital death with covid-19. funding none.",0
"background due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in the 6th experiment on critical assessment of techniques for protein structure prediction (casp6). since the initial work by romero et al. (identifying disordered regions in proteins from amino acid sequences, ieee int. conf. neural netw., 1997), our group has developed several predictors optimized for long disordered regions (>30 residues) with prediction accuracy exceeding 85%. however, these predictors are less successful on short disordered regions ( results we proposed two new predictor models, vsl2-m1 and vsl2-m2, to address this length-dependency problem in prediction of intrinsic protein disorder. these two predictors are similar to the original vsl1 predictor used in the casp6 experiment. in both models, two specialized predictors were first built and optimized for short ( 30 residues), respectively. a meta predictor was then trained to integrate the specialized predictors into the final predictor model. as the 10-fold cross-validation results showed, the vsl2 predictors achieved well-balanced prediction accuracies of 81% on both short and long disordered regions. comparisons over the vsl2 training dataset via 10-fold cross-validation and a blind-test set of unrelated recent pdb chains indicated that vsl2 predictors were significantly more accurate than several existing predictors of intrinsic protein disorder. conclusion the vsl2 predictors are applicable to disordered regions of any length and can accurately identify the short disordered regions that are often misclassified by our previous disorder predictors. the success of the vsl2 predictors further confirmed the previously observed differences in amino acid compositions and sequence properties between short and long disordered regions, and justified our approaches for modelling short and long disordered regions separately. the vsl2 predictors are freely accessible for non-commercial use at",0
"dose-response analysis can be carried out using multi-purpose commercial statistical software, but except for a few special cases the analysis easily becomes cumbersome as relevant, non-standard output requires manual programming. the extension package drc for the statistical environment r provides a flexible and versatile infrastructure for dose-response analyses in general. the present version of the package, reflecting extensions and modifications over the last decade, provides a user-friendly interface to specify the model assumptions about the dose-response relationship and comes with a number of extractors for summarizing fitted models and carrying out inference on derived parameters. the aim of the present paper is to provide an overview of state-of-the-art dose-response analysis, both in terms of general concepts that have evolved and matured over the years and by means of concrete examples.",0
"improvements in sensor accuracy, greater convenience and ease of use, and expanding reimbursement have led to growing adoption of continuous glucose monitoring (cgm). however, successful utilization of cgm technology in routine clinical practice remains relatively low. this may be due in part to the lack of clear and agreed-upon glycemic targets that both diabetes teams and people with diabetes can work toward. although unified recommendations for use of key cgm metrics have been established in three separate peer-reviewed articles, formal adoption by diabetes professional organizations and guidance in the practical application of these metrics in clinical practice have been lacking. in february 2019, the advanced technologies & treatments for diabetes (attd) congress convened an international panel of physicians, researchers, and individuals with diabetes who are expert in cgm technologies to address this issue. this article summarizes the attd consensus recommendations for relevant aspects of cgm data utilization and reporting among the various diabetes populations.",0
"disaggregated mouse embryo cells, grown in monolayers, underwent a progressive decline in growth rate upon successive transfer, the rapidity of the decline depending, among other things, on the inoculation density. nevertheless, nearly all cultures developed into established lines within 3 months of culture. the first sign of the emergence of an established line was the ability of the cells to maintain a constant or rising potential growth rate. this occurred while the cultures were morphologically unchanged. the growth rate continued to increase until it equaled or exceeded that of the original culture. the early established cells showed an increasing metabolic autonomy, as indicated by decreasing dependence on cell-to-cell feeding. it is suggested that the process of establishment involves an alteration in cell permeability properties. chromosome studies indicated that the cells responsible for the upturn in growth rate were diploid, but later the population shifted to the tetraploid range, often very rapidly. still later, marker chromosomes appeared. different lines acquired different properties, depending on the culture conditions employed; one line developed which is extremely sensitive to contact inhibition.",0
"background tumor spatial heterogeneity is an important prognostic factor, which may be reflected in medical images methods image texture analysis is an approach of quantifying heterogeneity that may not be appreciated by the naked eye. different methods can be applied including statistical-, model-, and transform-based methods. results early evidence suggests that texture analysis has the potential to augment diagnosis and characterization as well as improve tumor staging and therapy response assessment in oncological practice. conclusion this review provides an overview of the application of texture analysis with different imaging modalities, ct, mri, and pet, to date and describes the technical challenges that have limited its widespread clinical implementation so far. with further efforts to refine its application, image texture analysis has the potential to develop into a valuable clinical tool for oncologic imaging. teaching points : • tumor spatial heterogeneity is an important prognostic factor. • image texture analysis is an approach of quantifying heterogeneity. • different methods can be applied, including statistical-, model-, and transform-based methods. • texture analysis could improve the diagnosis, tumor staging, and therapy response assessment.",0
"insights from prospective, longitudinal studies of individuals at risk for developing type 1 diabetes have demonstrated that the disease is a continuum that progresses sequentially at variable but predictable rates through distinct identifiable stages prior to the onset of symptoms. stage 1 is defined as the presence of β-cell autoimmunity as evidenced by the presence of two or more islet autoantibodies with normoglycemia and is presymptomatic, stage 2 as the presence of β-cell autoimmunity with dysglycemia and is presymptomatic, and stage 3 as onset of symptomatic disease. adoption of this staging classification provides a standardized taxonomy for type 1 diabetes and will aid the development of therapies and the design of clinical trials to prevent symptomatic disease, promote precision medicine, and provide a framework for an optimized benefit/risk ratio that will impact regulatory approval, reimbursement, and adoption of interventions in the early stages of type 1 diabetes to prevent symptomatic disease.",0
"with the aging of the population, the burden of alzheimer's disease (ad) is rapidly expanding. more than 5 million people in the us alone are affected with ad and this number is expected to triple by 2050. while men may have a higher risk of mild cognitive impairment (mci), an intermediate stage between normal aging and dementia, women are disproportionally affected with ad. one explanation is that men may die of competing causes of death earlier in life, so that only the most resilient men may survive to older ages. however, many other factors should also be considered to explain the sex differences. in this review, we discuss the differences observed in men versus women in the incidence and prevalence of mci and ad, in the structure and function of the brain, and in the sex-specific and gender-specific risk and protective factors for ad. in medical research, sex refers to biological differences such as chromosomal differences (eg, xx versus xy chromosomes), gonadal differences, or hormonal differences. in contrast, gender refers to psychosocial and cultural differences between men and women (eg, access to education and occupation). both factors play an important role in the development and progression of diseases, including ad. understanding both sex- and gender-specific risk and protective factors for ad is critical for developing individualized interventions for the prevention and treatment of ad.",0
"in a number of experimental systems in which lymphocyte depletion was induced by apoptosis-inducing manipulations, no apoptotic morphology and ladder-type dna fragmentation were detected among freshly isolated peripheral lymphocytes ex vivo. here we report that one alteration that can be detected among splenocytes stimulated with lymphocyte-depleting doses of dexamethasone (dex) in vivo is a reduced uptake of 3,3'dihexyloxacarbocyanine iodide (dioc6), a fluorochrome which incorporates into cells dependent upon their mitochondrial transmembrane potential (delta psi m). in contrast, ex vivo isolated splenocytes still lacked established signs of programmed cell death (pcd):dna degradation into high or low molecular weight fragments, ultrastructural changes of chromatin arrangement and endoplasmatic reticulum, loss in viability, or accumulation of intracellular peroxides. moreover, no changes in cell membrane potential could be detected. a reduced delta psi m has been observed in response to different agents inducing lymphoid cell depletion in vivo (superantigen and glucocorticoids ), in mature t and b lymphocytes, as well as their precursors. dex treatment in vivo, followed by cytofluorometric purification of viable delta psi mlow splenic t cells ex vivo, revealed that this fraction of cells is irreversibly committed to undergoing dna fragmentation. immediately after purification neither delta psi mlow, nor delta psi mhigh cells, exhibit detectable dna fragmentation. however, after short-term culture (37 degrees c, 1 h) delta psi mlow cells show endonucleolysis, followed by cytolysis several hours later. incubation of delta psi mlow cells in the presence of excess amount of the gc receptor antagonist ru38486 (which displaces dex from the gc receptor), cytokines that inhibit dex-induced cell death, or cycloheximide fails to prevent cytolysis. the antioxidant, n-acetylcysteine, as well as linomide, an agent that effectively inhibits dex or superantigen-induced lymphocyte depletion in vivo, also stabilize the dioc6(3) uptake. in contrast, the endonuclease inhibitor, aurintricarboxylic acid acts at later stages of apoptosis and only retards the transition from the viable delta psi mlow to the nonviable fraction. altogether, these data suggest a sequence of pcd-associated events in which a reduction in delta psi m constitutes an obligate irreversible step of ongoing lymphocyte death, preceding other alterations of cellular physiology, and thus allowing for the ex vivo assessment of pcd.",0
"we have studied the leukocyte-dependent mechanism of histamine release (ldhr) from rabbit platelets, a complement-independent mechanism which has been implicated in the deposition of immune complexes in acute serum sickness of rabbits. it was found by chromatography and passive transfer of serum from immunized rabbits that the antibody responsible for the ldhr was of ige type. by electron microscope study of the reaction, the leukocyte involved in agglutination of platelets and release of their histamine content was identified as the basophil. upon addition of antigen, basophils sensitized with ige degranulated, released their histamine content and a platelet-activating factor (paf) that caused aggregation of platelets and release of their histamine. conditions of preparing and preserving paf activity and some properties of this factor have been elucidated. ldhr must, therefore, be considered as an immediate hypersensitivity-type mechanism which may link allergic reactions with immunologic disease associated with severe structural injury.",0
"the fourth edition of the world health organization (who) classification of tumours of the central nervous system, published in 2007, lists several new entities, including angiocentric glioma, papillary glioneuronal tumour, rosette-forming glioneuronal tumour of the fourth ventricle, papillary tumour of the pineal region, pituicytoma and spindle cell oncocytoma of the adenohypophysis. histological variants were added if there was evidence of a different age distribution, location, genetic profile or clinical behaviour; these included pilomyxoid astrocytoma, anaplastic medulloblastoma and medulloblastoma with extensive nodularity. the who grading scheme and the sections on genetic profiles were updated and the rhabdoid tumour predisposition syndrome was added to the list of familial tumour syndromes typically involving the nervous system. as in the previous, 2000 edition of the who 'blue book', the classification is accompanied by a concise commentary on clinico-pathological characteristics of each tumour type. the 2007 who classification is based on the consensus of an international working group of 25 pathologists and geneticists, as well as contributions from more than 70 international experts overall, and is presented as the standard for the definition of brain tumours to the clinical oncology and cancer research communities world-wide.",0
"anucleate cells can be induced to undergo programmed cell death (pcd), indicating the existence of a cytoplasmic pcd pathway that functions independently from the nucleus. cytoplasmic structures including mitochondria have been shown to participate in the control of apoptotic nuclear disintegration. before cells exhibit common signs of nuclear apoptosis (chromatin condensation and endonuclease-mediated dna fragmentation), they undergo a reduction of the mitochondrial transmembrane potential (delta psi m) that may be due to the opening of mitochondrial permeability transition (pt) pores. here, we present direct evidence indicating that mitochondrial pt constitutes a critical early event of the apoptotic process. in a cell-free system combining purified mitochondria and nuclei, mitochondria undergoing pt suffice to induce chromatin condensation and dna fragmentation. induction of pt by pharmacological agents augments the apoptosis-inducing potential of mitochondria. in contrast, prevention of pt by pharmacological agents impedes nuclear apoptosis, both in vitro and in vivo. mitochondria from hepatocytes or lymphoid cells undergoing apoptosis, but not those from normal cells, induce disintegration of isolated hela nuclei. a specific ligand of the mitochondrial adenine nucleotide translocator (ant), bongkreik acid, inhibits pt and reduces apoptosis induction by mitochondria in a cell-free system. moreover, it inhibits the induction of apoptosis in intact cells. several pieces of evidence suggest that the proto-oncogene product bcl-2 inhibits apoptosis by preventing mitochondrial pt. first, to inhibit nuclear apoptosis, bcl-2 must be localized in mitochondrial but not nuclear membranes. second, transfection-enforced hyperexpression of bcl-2 directly abolishes the induction of mitochondrial pt in response to a protonophore, a pro-oxidant, as well as to the ant ligand atractyloside, correlating with its apoptosis-inhibitory effect. in conclusion, mitochondrial pt appears to be a critical step of the apoptotic cascade.",0
"the conserved domain database (cdd) is the protein classification component of ncbi's entrez query and retrieval system. cdd is linked to other entrez databases such as proteins, taxonomy and pubmed, and can be accessed at cd-search, which is available at is a fast, interactive tool to identify conserved domains in new protein sequences. cd-search results for protein sequences in entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. protein-protein queries submitted to ncbi's blast search service at are scanned for the presence of conserved domains by default. while cdd started out as essentially a mirror of publicly available domain alignment collections, such as smart, pfam and cog, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the ncbi. here, we report on the progress of the curation effort and associated improvements in the functionality of the cdd information retrieval system.",0
"acetylation within the globular core domain of histone h3 on lysine 56 (h3k56) has recently been shown to have a critical role in packaging dna into chromatin following dna replication and repair in budding yeast. however, the function or occurrence of this specific histone mark has not been studied in multicellular eukaryotes, mainly because the rtt109 enzyme that is known to mediate acetylation of h3k56 (h3k56ac) is fungal-specific. here we demonstrate that the histone acetyl transferase cbp (also known as nejire) in flies and cbp and p300 (ep300) in humans acetylate h3k56, whereas drosophila sir2 and human sirt1 and sirt2 deacetylate h3k56ac. the histone chaperones asf1a in humans and asf1 in drosophila are required for acetylation of h3k56 in vivo, whereas the histone chaperone caf-1 (chromatin assembly factor 1) in humans and caf1 in drosophila are required for the incorporation of histones bearing this mark into chromatin. we show that, in response to dna damage, histones bearing acetylated k56 are assembled into chromatin in drosophila and human cells, forming foci that colocalize with sites of dna repair. furthermore, acetylation of h3k56 is increased in multiple types of cancer, correlating with increased levels of asf1a in these tumours. our identification of multiple proteins regulating the levels of h3k56 acetylation in metazoans will allow future studies of this critical and unique histone modification that couples chromatin assembly to dna synthesis, cell proliferation and cancer.",0
"the cell surface expression and function of the lfa-1 ligand, intercellular adhesion molecule 1 (icam-1), on epidermal keratinocytes (ek) was studied. icam-1 expression on the surface of cultured ek was either absent or weak, but was induced by treating ek with rifn-gamma or tnf for 4-48 h. ifn-gamma and tnf were synergistic. ifn-gamma treatment increased t lymphoblast adhesion from less than 2% to 20-40%, with a concentration dependence similar to that seen for icam-1 induction. all of the adhesion to ek was inhibited by lfa-1 and icam-1 mabs, but not by hla-dr, cd2, or lfa-3 mabs. there was no difference in the level of t lymphoblast adhesion to ifn-gamma-treated allogeneic or autologous ek. icam-1 purified from the hela epithelioid cell line and reconstituted into planar membranes also supported efficient adhesion of t lymphoblasts that was blocked by lfa-1 mab bound to the t lymphoblasts or icam-1 mab bound to the planar membranes. t lymphoblasts adherent to ek or icam-1 planar membranes were isolated by panning, and surface markers were analyzed by immunofluorescence flow cytometry. the adherent t cells were a phenotypically skewed subpopulation. they were enriched for cd8+ cells and expressed 1.5-2.5-fold higher lfa-1 and cd2 compared with the unseparated population.",0
"the covid-19 pandemic has resulted in over 4.3 million confirmed cases and over 290,000 deaths globally. it has also sparked fears of an impending economic crisis and recession. social distancing, self-isolation and travel restrictions have lead to a reduced workforce across all economic sectors and caused many jobs to be lost. schools have closed down, and the need for commodities and manufactured products has decreased. in contrast, the need for medical supplies has significantly increased. the food sector is also facing increased demand due to panic-buying and stockpiling of food products. in response to this global outbreak, we summarise the socio-economic effects of covid-19 on individual aspects of the world economy.",0
"swiss-model repository (smr) is a database of annotated 3d protein structure models generated by the automated swiss-model homology modeling pipeline. it currently holds >400 000 high quality models covering almost 20% of swiss-prot/uniprotkb entries. in this manuscript, we provide an update of features and functionalities which have been implemented recently. we address improvements in target coverage, model quality estimates, functional annotations and improved in-page visualization. we also introduce a new update concept which includes regular updates of an expanded set of core organism models and uniprotkb-based targets, complemented by user-driven on-demand update of individual models. with the new release of the modeling pipeline, smr has implemented a rest-api and adopted an open licencing model for accessing model coordinates, thus enabling bulk download for groups of targets fostering re-use of models in other contexts. smr can be accessed at",0
"motivation there is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging. results we present pindel, a pattern growth approach, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads. we use both simulated reads and real data to demonstrate the efficiency of the computer program and accuracy of the results. availability the binary code and a short user manual can be freely downloaded from approximately kye/pindel/. contact k.ye@lumc.nl; zn1@sanger.ac.uk.",0
"turmeric, a spice that has long been recognized for its medicinal properties, has received interest from both the medical/scientific world and from culinary enthusiasts, as it is the major source of the polyphenol curcumin. it aids in the management of oxidative and inflammatory conditions, metabolic syndrome, arthritis, anxiety, and hyperlipidemia. it may also help in the management of exercise-induced inflammation and muscle soreness, thus enhancing recovery and performance in active people. in addition, a relatively low dose of the complex can provide health benefits for people that do not have diagnosed health conditions. most of these benefits can be attributed to its antioxidant and anti-inflammatory effects. ingesting curcumin by itself does not lead to the associated health benefits due to its poor bioavailability, which appears to be primarily due to poor absorption, rapid metabolism, and rapid elimination. there are several components that can increase bioavailability. for example, piperine is the major active component of black pepper and, when combined in a complex with curcumin, has been shown to increase bioavailability by 2000%. curcumin combined with enhancing agents provides multiple health benefits. the purpose of this review is to provide a brief overview of the plethora of research regarding the health benefits of curcumin.",0
"unlabelled thunderstorm is an open-source, interactive and modular plug-in for imagej designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. thunderstorm offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. thunderstorm also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using monte carlo simulations. availability and implementation thunderstorm and the online documentation are both freely accessible at",0
"persons with multiple chronic conditions are a large and growing segment of the us population. however, little is known about how chronic conditions cluster, and the ramifications of having specific combinations of chronic conditions. clinical guidelines and disease management programs focus on single conditions, and clinical research often excludes persons with multiple chronic conditions. understanding how conditions in combination impact the burden of disease and the costs and quality of care received is critical to improving care for the 1 in 5 americans with multiple chronic conditions. this medline review of publications examining somatic chronic conditions co-occurring with 1 or more additional specific chronic illness between january 2000 and march 2007 summarizes the state of our understanding of the prevalence and health challenges of multiple chronic conditions and the implications for quality, care management, and costs.",0
"background synthesis of multiple randomized controlled trials (rcts) in a systematic review can summarize the effects of individual outcomes and provide numerical answers about the effectiveness of interventions. filtering of searches is time consuming, and no single method fulfills the principal requirements of speed with accuracy. automation of systematic reviews is driven by a necessity to expedite the availability of current best evidence for policy and clinical decision-making. we developed rayyan ( ), a free web and mobile app, that helps expedite the initial screening of abstracts and titles using a process of semi-automation while incorporating a high level of usability. for the beta testing phase, we used two published cochrane reviews in which included studies had been selected manually. their searches, with 1030 records and 273 records, were uploaded to rayyan. different features of rayyan were tested using these two reviews. we also conducted a survey of rayyan's users and collected feedback through a built-in feature. results pilot testing of rayyan focused on usability, accuracy against manual methods, and the added value of the prediction feature. the ""taster"" review (273 records) allowed a quick overview of rayyan for early comments on usability. the second review (1030 records) required several iterations to identify the previously identified 11 trials. the ""suggestions"" and ""hints,"" based on the ""prediction model,"" appeared as testing progressed beyond five included studies. post rollout user experiences and a reflexive response by the developers enabled real-time modifications and improvements. the survey respondents reported 40% average time savings when using rayyan compared to others tools, with 34% of the respondents reporting more than 50% time savings. in addition, around 75% of the respondents mentioned that screening and labeling studies as well as collaborating on reviews to be the two most important features of rayyan. as of november 2016, rayyan users exceed 2000 from over 60 countries conducting hundreds of reviews totaling more than 1.6m citations. feedback from users, obtained mostly through the app web site and a recent survey, has highlighted the ease in exploration of searches, the time saved, and simplicity in sharing and comparing include-exclude decisions. the strongest features of the app, identified and reported in user feedback, were its ability to help in screening and collaboration as well as the time savings it affords to users. conclusions rayyan is responsive and intuitive in use with significant potential to lighten the load of reviewers.",0
"objectives this study aimed to assess the immediate stress and psychological impact experienced by quarantined patients undergoing hemodialysis and university hospital workers who treated patients middle east respiratory syndrome (mers) during its outbreak. design the group of subjects consisted of 1800 hospital practitioners and 73 quarantined patients undergoing hemodialysis. the impact of events scale-revised (ies-r) was administered to the practitioners twice, once during the hospital shutdown and again one month after the shutdown. the mini international neuropsychiatric interview and hospital anxiety and depression scale were administered to patients undergoing hemodialysis. results during the initial stages of the mers outbreak, healthcare workers who performed mers-related tasks scored significantly higher on the total ies-r and its subscales. in the second assessment of the high-risk group, the sleep and numbness subscale scores from the ies-r differed depending on the implementation of home quarantine, and the intrusion subscale scores differed depending on the performance of mers-related tasks. conclusion medical staff that performed mers-related tasks showed the highest risk for post-traumatic stress disorder symptoms even after time had elapsed. the risk increased even after home quarantine. prompt and continuous psychiatric intervention is needed in high mortality infectious disease outbreaks.",0
"background the global burden of diseases (gbd), injuries, and risk factors study used the disability-adjusted life year (daly) to quantify the burden of diseases, injuries, and risk factors. this paper provides an overview of injury estimates from the 2013 update of gbd, with detailed information on incidence, mortality, dalys and rates of change from 1990 to 2013 for 26 causes of injury, globally, by region and by country. methods injury mortality was estimated using the extensive gbd mortality database, corrections for ill-defined cause of death and the cause of death ensemble modelling tool. morbidity estimation was based on inpatient and outpatient data sets, 26 cause-of-injury and 47 nature-of-injury categories, and seven follow-up studies with patient-reported long-term outcome measures. results in 2013, 973 million (uncertainty interval (ui) 942 to 993) people sustained injuries that warranted some type of healthcare and 4.8 million (ui 4.5 to 5.1) people died from injuries. between 1990 and 2013 the global age-standardised injury daly rate decreased by 31% (ui 26% to 35%). the rate of decline in daly rates was significant for 22 cause-of-injury categories, including all the major injuries. conclusions injuries continue to be an important cause of morbidity and mortality in the developed and developing world. the decline in rates for almost all injuries is so prominent that it warrants a general statement that the world is becoming a safer place to live in. however, the patterns vary widely by cause, age, sex, region and time and there are still large improvements that need to be made.",0
"growth, repair, and regeneration of adult skeletal muscle depends on the persistence of satellite cells: muscle stem cells resident beneath the basal lamina that surrounds each myofiber. however, how the satellite cell compartment is maintained is unclear. here, we use cultured myofibers to model muscle regeneration and show that satellite cells adopt divergent fates. quiescent satellite cells are synchronously activated to coexpress the transcription factors pax7 and myod. most then proliferate, down-regulate pax7, and differentiate. in contrast, other proliferating cells maintain pax7 but lose myod and withdraw from immediate differentiation. these cells are typically located in clusters, together with pax7-ve progeny destined for differentiation. some of the pax7+ve/myod-ve cells then leave the cell cycle, thus regaining the quiescent satellite cell phenotype. significantly, noncycling cells contained within a cluster can be stimulated to proliferate again. these observations suggest that satellite cells either differentiate or switch from terminal myogenesis to maintain the satellite cell pool.",0
"optical coherence tomography (oct) was one of the biggest advances in ophthalmic imaging. building on that platform, oct angiography (octa) provides depth resolved images of blood flow in the retina and choroid with levels of detail far exceeding that obtained with older forms of imaging. this new modality is challenging because of the need for new equipment and processing techniques, current limitations of imaging capability, and rapid advancements in both imaging and in our understanding of the imaging and applicable pathophysiology of the retina and choroid. these factors lead to a steep learning curve, even for those with a working understanding dye-based ocular angiography. all for a method of imaging that is a little more than 10 years old. this review begins with a historical account of the development of octa, and the methods used in octa, including signal processing, image generation, and display techniques. this forms the basis to understand what octa images show as well as how image artifacts arise. the anatomy and imaging of specific vascular layers of the eye are reviewed. the integration of octa in multimodal imaging in the evaluation of retinal vascular occlusive diseases, diabetic retinopathy, uveitis, inherited diseases, age-related macular degeneration, and disorders of the optic nerve is presented. octa is an exciting, disruptive technology. its use is rapidly expanding in clinical practice as well as for research into the pathophysiology of diseases of the posterior pole.",0
"background nowadays more and more clinical guidelines for health care professionals are being developed. however, this does not automatically mean that these guidelines are actually implemented. the aim of this meta-review is twofold: firstly, to gain a better understanding of which factors affect the implementation of guidelines, and secondly, to provide insight into the ""state-of-the-art"" regarding research within this field. methods a search of five literature databases and one website was performed to find relevant existing systematic reviews or meta-reviews. subsequently, a two-step inclusion process was conducted: (1) screening on the basis of references and abstracts and (2) screening based on full-text papers. after that, relevant data from the included reviews were extracted and the methodological quality of the reviews was assessed by using the quality assessment checklist for reviews. results twelve systematic reviews met our inclusion criteria. no previous systematic meta-reviews meeting all our inclusion criteria were found. two of the twelve reviews scored high on the checklist used, indicating only ""minimal"" or ""minor flaws"". the other ten reviews scored in the lowest of middle ranges, indicating ""extensive"" or ""major"" flaws. a substantial proportion (although not all) of the reviews indicates that effective strategies often have multiple components and that the use of one single strategy, such as reminders only or an educational intervention, is less effective. besides, characteristics of the guidelines themselves affect actual use. for instance, guidelines that are easy to understand, can easily be tried out, and do not require specific resources, have a greater chance of implementation. in addition, characteristics of professionals - e.g., awareness of the existence of the guideline and familiarity with its content - likewise affect implementation. furthermore, patient characteristics appear to exert influence: for instance, co-morbidity reduces the chance that guidelines are followed. finally, environmental characteristics may influence guideline implementation. for example, a lack of support from peers or superiors, as well as insufficient staff and time, appear to be the main impediments. conclusion existing reviews describe various factors that influence whether guidelines are actually used. however, the evidence base is still thin, and future sound research - for instance comparing combinations of implementation strategies versus single strategies - is needed.",0
"despite a growing body of epidemiological evidence in recent years documenting the health impacts of racism, the cumulative evidence base has yet to be synthesized in a comprehensive meta-analysis focused specifically on racism as a determinant of health. this meta-analysis reviewed the literature focusing on the relationship between reported racism and mental and physical health outcomes. data from 293 studies reported in 333 articles published between 1983 and 2013, and conducted predominately in the u.s., were analysed using random effects models and mean weighted effect sizes. racism was associated with poorer mental health (negative mental health: r = -.23, 95% ci , k = 227; positive mental health: r = -.13, 95% ci , k = 113), including depression, anxiety, psychological stress and various other outcomes. racism was also associated with poorer general health (r = -.13 (95% ci , k = 30), and poorer physical health (r = -.09, 95% ci , k = 50). moderation effects were found for some outcomes with regard to study and exposure characteristics. effect sizes of racism on mental health were stronger in cross-sectional compared with longitudinal data and in non-representative samples compared with representative samples. age, sex, birthplace and education level did not moderate the effects of racism on health. ethnicity significantly moderated the effect of racism on negative mental health and physical health: the association between racism and negative mental health was significantly stronger for asian american and latino(a) american participants compared with african american participants, and the association between racism and physical health was significantly stronger for latino(a) american participants compared with african american participants. protocol prospero registration number: crd42013005464.",0
"accumulating evidence implicates metabolites produced by gut microbes as crucial mediators of diet-induced host-microbial cross-talk. here, we review emerging data suggesting that microbial tryptophan catabolites resulting from proteolysis are influencing host health. these metabolites are suggested to activate the immune system through binding to the aryl hydrocarbon receptor (ahr), enhance the intestinal epithelial barrier, stimulate gastrointestinal motility, as well as secretion of gut hormones, exert anti-inflammatory, anti-oxidative or toxic effects in systemic circulation, and putatively modulate gut microbial composition. tryptophan catabolites thus affect various physiological processes and may contribute to intestinal and systemic homeostasis in health and disease.",0
"neutrophil extracellular traps (nets) are released as neutrophils die in vitro in a process requiring hours, leaving a temporal gap that invasive microbes may exploit. neutrophils capable of migration and phagocytosis while undergoing netosis have not been documented. during gram-positive skin infections, we directly visualized live polymorphonuclear cells (pmns) in vivo rapidly releasing nets, which prevented systemic bacterial dissemination. netosis occurred during crawling, thereby casting large areas of nets. net-releasing pmns developed diffuse decondensed nuclei, ultimately becoming devoid of dna. cells with abnormal nuclei showed unusual crawling behavior highlighted by erratic pseudopods and hyperpolarization consistent with the nucleus being a fulcrum for crawling. a requirement for both toll-like receptor 2 and complement-mediated opsonization tightly regulated net release. additionally, live human pmns injected into mouse skin developed decondensed nuclei and formed nets in vivo, and intact anuclear neutrophils were abundant in gram-positive human abscesses. therefore early in infection netosis involves neutrophils that do not undergo lysis and retain the ability to multitask.",0
"absolute metabolite concentrations are critical to a quantitative understanding of cellular metabolism, as concentrations impact both the free energies and rates of metabolic reactions. here we use lc-ms/ms to quantify more than 100 metabolite concentrations in aerobic, exponentially growing escherichia coli with glucose, glycerol or acetate as the carbon source. the total observed intracellular metabolite pool was approximately 300 mm. a small number of metabolites dominate the metabolome on a molar basis, with glutamate being the most abundant. metabolite concentration exceeds k(m) for most substrate-enzyme pairs. an exception is lower glycolysis, where concentrations of intermediates are near the k(m) of their consuming enzymes and all reactions are near equilibrium. this may facilitate efficient flux reversibility given thermodynamic and osmotic constraints. the data and analyses presented here highlight the ability to identify organizing metabolic principles from systems-level absolute metabolite concentration data.",0
"background exposure to chemicals during fetal development can increase the risk of adverse health effects, and while biomonitoring studies suggest pregnant women are exposed to chemicals, little is known about the extent of multiple chemicals exposures among pregnant women in the united states. objective we analyzed biomonitoring data from the national health and nutritional examination survey (nhanes) to characterize both individual and multiple chemical exposures in u.s. pregnant women. methods we analyzed data for 163 chemical analytes in 12 chemical classes for subsamples of 268 pregnant women from nhanes 2003-2004, a nationally representative sample of the u.s. population. for each chemical analyte, we calculated descriptive statistics. we calculated the number of chemicals detected within the following chemical classes: polybrominated diphenyl ethers (pbdes), perfluorinated compounds (pfcs), organochlorine pesticides, and phthalates and across multiple chemical classes. we compared chemical analyte concentrations for pregnant and nonpregnant women using least-squares geometric means, adjusting for demographic and physiological covariates. results the percentage of pregnant women with detectable levels of an individual chemical ranged from 0 to 100%. certain polychlorinated biphenyls, organochlorine pesticides, pfcs, phenols, pbdes, phthalates, polycyclic aromatic hydrocarbons, and perchlorate were detected in 99-100% of pregnant women. the median number of detected chemicals by chemical class ranged from 4 of 12 pfcs to 9 of 13 phthalates. across chemical classes, median number ranged from 8 of 17 chemical analytes to 50 of 71 chemical analytes. we found, generally, that levels in pregnant women were similar to or lower than levels in nonpregnant women; adjustment for covariates tended to increase levels in pregnant women compared with nonpregnant women. conclusions pregnant women in the u.s. are exposed to multiple chemicals. further efforts are warranted to understand sources of exposure and implications for policy making.",0
"metabolomics is a newly emerging field of 'omics' research that is concerned with characterizing large numbers of metabolites using nmr, chromatography and mass spectrometry. it is frequently used in biomarker identification and the metabolic profiling of cells, tissues or organisms. the data processing challenges in metabolomics are quite unique and often require specialized (or expensive) data analysis software and a detailed knowledge of cheminformatics, bioinformatics and statistics. in an effort to simplify metabolomic data analysis while at the same time improving user accessibility, we have developed a freely accessible, easy-to-use web server for metabolomic data analysis called metaboanalyst. fundamentally, metaboanalyst is a web-based metabolomic data processing tool not unlike many of today's web-based microarray analysis packages. it accepts a variety of input data (nmr peak lists, binned spectra, ms peak lists, compound/concentration data) in a wide variety of formats. it also offers a number of options for metabolomic data processing, data normalization, multivariate statistical analysis, graphing, metabolite identification and pathway mapping. in particular, metaboanalyst supports such techniques as: fold change analysis, t-tests, pca, pls-da, hierarchical clustering and a number of more sophisticated statistical or machine learning methods. it also employs a large library of reference spectra to facilitate compound identification from most kinds of input spectra. metaboanalyst guides users through a step-by-step analysis pipeline using a variety of menus, information hyperlinks and check boxes. upon completion, the server generates a detailed report describing each method used, embedded with graphical and tabular outputs. metaboanalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. metaboanalyst is accessible at",0
"background coronavirus disease 2019 (covid-19) can lead to systemic coagulation activation and thrombotic complications. objectives to investigate the incidence of objectively confirmed venous thromboembolism (vte) in hospitalized patients with covid-19. methods single-center cohort study of 198 hospitalized patients with covid-19. results seventy-five patients (38%) were admitted to the intensive care unit (icu). at time of data collection, 16 (8%) were still hospitalized and 19% had died. during a median follow-up of 7 days (iqr, 3-13), 39 patients (20%) were diagnosed with vte of whom 25 (13%) had symptomatic vte, despite routine thrombosis prophylaxis. the cumulative incidences of vte at 7, 14 and 21 days were 16% (95% ci, 10-22), 33% (95% ci, 23-43) and 42% (95% ci 30-54) respectively. for symptomatic vte, these were 10% (95% ci, 5.8-16), 21% (95% ci, 14-30) and 25% (95% ci 16-36). vte appeared to be associated with death (adjusted hr, 2.4; 95% ci, 1.02-5.5). the cumulative incidence of vte was higher in the icu (26% (95% ci, 17-37), 47% (95% ci, 34-58), and 59% (95% ci, 42-72) at 7, 14 and 21 days) than on the wards (any vte and symptomatic vte 5.8% (95% ci, 1.4-15), 9.2% (95% ci, 2.6-21), and 9.2% (2.6-21) at 7, 14, and 21 days). conclusions the observed risk for vte in covid-19 is high, particularly in icu patients, which should lead to a high level of clinical suspicion and low threshold for diagnostic imaging for dvt or pe. future research should focus on optimal diagnostic and prophylactic strategies to prevent vte and potentially improve survival.",0
"background systematic reviews (srs) of experimental animal studies are not yet common practice, but awareness of the merits of conducting such srs is steadily increasing. as animal intervention studies differ from randomized clinical trials (rct) in many aspects, the methodology for srs of clinical trials needs to be adapted and optimized for animal intervention studies. the cochrane collaboration developed a risk of bias (rob) tool to establish consistency and avoid discrepancies in assessing the methodological quality of rcts. a similar initiative is warranted in the field of animal experimentation. methods we provide an rob tool for animal intervention studies (syrcle's rob tool). this tool is based on the cochrane rob tool and has been adjusted for aspects of bias that play a specific role in animal intervention studies. to enhance transparency and applicability, we formulated signalling questions to facilitate judgment. results the resulting rob tool for animal studies contains 10 entries. these entries are related to selection bias, performance bias, detection bias, attrition bias, reporting bias and other biases. half these items are in agreement with the items in the cochrane rob tool. most of the variations between the two tools are due to differences in design between rcts and animal studies. shortcomings in, or unfamiliarity with, specific aspects of experimental design of animal studies compared to clinical studies also play a role. conclusions syrcle's rob tool is an adapted version of the cochrane rob tool. widespread adoption and implementation of this tool will facilitate and improve critical appraisal of evidence from animal studies. this may subsequently enhance the efficiency of translating animal research into clinical practice and increase awareness of the necessity of improving the methodological quality of animal studies.",0
"cancer is associated with higher morbidity and mortality and is the second leading cause of death in the us. further, in some nations, cancer has overtaken heart disease as the leading cause of mortality. identification of molecular mechanisms by which cancerous cells evade t cell-mediated cytotoxic damage has led to the modern era of immunotherapy in cancer treatment. agents that release these immune brakes have shown activity to recover dysfunctional t cells and regress various cancer. both cytotoxic t-lymphocyte-associated protein 4 (ctla-4) and programmed death-1 (pd-1) play their role as physiologic brakes on unrestrained cytotoxic t effector function. ctla-4 (cd 152) is a b7/cd28 family; it mediates immunosuppression by indirectly diminishing signaling through the co-stimulatory receptor cd28. ipilimumab is the first and only fda-approved ctla-4 inhibitor; pd-1 is an inhibitory transmembrane protein expressed on t cells, b cells, natural killer cells (nks), and myeloid-derived suppressor cells (mdscs). programmed death-ligand 1 (pd-l1) is expressed on the surface of multiple tissue types, including many tumor cells and hematopoietic cells. pd-l2 is more restricted to hematopoietic cells. blockade of the pd-1 /pdl-1 pathway can enhance anti-tumor t cell reactivity and promotes immune control over the cancerous cells. since the fda approval of ipilimumab (human igg1 k anti-ctla-4 monoclonal antibody) in 2011, six more immune checkpoint inhibitors (icis) have been approved for cancer therapy. pd-1 inhibitors nivolumab, pembrolizumab, cemiplimab and pd-l1 inhibitors atezolizumab, avelumab, and durvalumab are in the current list of the approved agents in addition to ipilimumab. in this review paper, we discuss the role of each immune checkpoint inhibitor (ici), the landmark trials which led to their fda approval, and the strength of the evidence per national comprehensive cancer network (nccn), which is broadly utilized by medical oncologists and hematologists in their daily practice.",0
"the newly emergent human virus sars-cov-2 (severe acute respiratory syndrome-coronavirus 2) is resulting in high fatality rates and incapacitated health systems. preventing further transmission is a priority. we analyzed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact tracing needed to stop the epidemic. although sars-cov-2 is spreading too fast to be contained by manual contact tracing, it could be controlled if this process were faster, more efficient, and happened at scale. a contact-tracing app that builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. by targeting recommendations to only those at risk, epidemics could be contained without resorting to mass quarantines (""lockdowns"") that are harmful to society. we discuss the ethical requirements for an intervention of this kind.",0
"polycystic ovary syndrome (pcos) is of clinical and public health importance as it is very common, affecting up to one in five women of reproductive age. it has significant and diverse clinical implications including reproductive (infertility, hyperandrogenism, hirsutism), metabolic (insulin resistance, impaired glucose tolerance, type 2 diabetes mellitus, adverse cardiovascular risk profiles) and psychological features (increased anxiety, depression and worsened quality of life). polycystic ovary syndrome is a heterogeneous condition and, as such, clinical and research agendas are broad and involve many disciplines. the phenotype varies widely depending on life stage, genotype, ethnicity and environmental factors including lifestyle and bodyweight. importantly, pcos has unique interactions with the ever increasing obesity prevalence worldwide as obesity-induced insulin resistance significantly exacerbates all the features of pcos. furthermore, it has clinical implications across the lifespan and is relevant to related family members with an increased risk for metabolic conditions reported in first-degree relatives. therapy should focus on both the short and long-term reproductive, metabolic and psychological features. given the aetiological role of insulin resistance and the impact of obesity on both hyperinsulinaemia and hyperandrogenism, multidisciplinary lifestyle improvement aimed at normalising insulin resistance, improving androgen status and aiding weight management is recognised as a crucial initial treatment strategy. modest weight loss of 5% to 10% of initial body weight has been demonstrated to improve many of the features of pcos. management should focus on support, education, addressing psychological factors and strongly emphasising healthy lifestyle with targeted medical therapy as required. monitoring and management of long-term metabolic complications is also an important part of routine clinical care. comprehensive evidence-based guidelines are needed to aid early diagnosis, appropriate investigation, regular screening and treatment of this common condition. whilst reproductive features of pcos are well recognised and are covered here, this review focuses primarily on the less appreciated cardiometabolic and psychological features of pcos.",0
"since the outbreak of coronavirus disease 2019 (covid-19) in late december 2019, it has brought significant harm and challenges to over 200 countries and regions around the world. however, there is increasing evidence that many patients with covid-19 are asymptomatic or have only mild symptoms, but they are able to transmit the virus to others. there are difficulties in screening for asymptomatic infections, which makes it more difficult for national prevention and control of this epidemic. this article reviews the characteristics, treatment, and outcomes of asymptomatic infections with covid-19, hoping it would be helpful for early prevention and control of this severe public health threat worldwide.",0
"unlabelled jspecies web server (jspeciesws) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. the service measures the average nucleotide identity (ani) based on blast+ (anib) and mummer (anim), as well as correlation indexes of tetra-nucleotide signatures (tetra). in addition, it provides a tetra correlation search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. for comparison, own genomes can be uploaded and references can be selected from the jspeciesws reference database. the service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. availability and implementation jspeciesws is available at supplementary information supplementary data are available at bioinformatics online. contact mrichter@ribocon.com.",0
"continuous turnover of intracellular components by autophagy is necessary to preserve cellular homeostasis in all tissues. alterations in macroautophagy, the main process responsible for bulk autophagic degradation, have been proposed to contribute to pathogenesis in huntington's disease (hd), a genetic neurodegenerative disorder caused by an expanded polyglutamine tract in the huntingtin protein. however, the precise mechanism behind macroautophagy malfunction in hd is poorly understood. in this work, using cellular and mouse models of hd and cells from humans with hd, we have identified a primary defect in the ability of autophagic vacuoles to recognize cytosolic cargo in hd cells. autophagic vacuoles form at normal or even enhanced rates in hd cells and are adequately eliminated by lysosomes, but they fail to efficiently trap cytosolic cargo in their lumen. we propose that inefficient engulfment of cytosolic components by autophagosomes is responsible for their slower turnover, functional decay and accumulation inside hd cells.",0
"background set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. venn diagrams are frequently employed for such analysis but current tools are limited. results we have developed interactivenn, a more flexible tool for interacting with venn diagrams including up to six sets. it offers a clean interface for venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. the tool also allows obtaining subsets' elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. interactivenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains. conclusions interactivenn allows set unions in venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. interactivenn is freely available online at: .",0
"objectives isolation due to the management of infectious diseases is thought to affect mental health, but the effects are still unknown. we examined the prevalence of anxiety symptoms and anger in persons isolated during the middle east respiratory syndrome (mers) epidemic both at isolation period and at four to six months after release from isolation. we also determined risk factors associated with these symptoms at four to six months. methods of 14,992 individuals isolated for 2-week due to having contact with mers patients in 2015, when mers was introduced to korea, 1,692 individuals were included in this study. anxiety symptoms were evaluated with the generalized anxiety disorder 7-item scale and anger was assessed with the state-trait anger expression inventory at four to six months after release from isolation for mers. results of 1,692 who came in contact with mers patients, 1,656 were not diagnosed with mers. among 1,656, anxiety symptoms showed 7.6% (95% confidence interval , 6.3 to 8.9%) and feelings of anger were present in 16.6% (95% ci, 14.8 to 18.4%) during the isolation period. at four to six months after release from isolation, anxiety symptoms were observed in 3.0% (95%ci, 2.2 to 3.9%). feelings of anger were present in 6.4% (95% ci, 5.2 to 7.6%). risk factors for experiencing anxiety symptoms and anger at four to six months after release included symptoms related to mers during isolation, inadequate supplies (food, clothes, accommodation), social networking activities (email, text, internet), history of psychiatric illnesses, and financial loss. conclusions mental health problems at four to six month after release from isolation might be prevented by providing mental health support to individuals with vulnerable mental health, and providing accurate information as well as appropriate supplies, including food, clothes, and accommodation.",0
"using granulocyte/macrophage colony-stimulating factor (gm-csf) and interleukin 4 we have established dendritic cell (dc) lines from blood mononuclear cells that maintain the antigen capturing and processing capacity characteristic of immature dendritic cells in vivo. these cells have typical dendritic morphology, express high levels of major histocompatibility complex (mhc) class i and class ii molecules, cd1, fc gamma rii, cd40, b7, cd44, and icam-1, and lack cd14. cultured dcs are highly stimulatory in mixed leukocyte reaction (mlr) and are also capable of triggering cord blood naive t cells. most strikingly, these dcs are as efficient as antigen-specific b cells in presenting tetanus toxoid (tt) to specific t cell clones. their efficiency of antigen presentation can be further enhanced by specific antibodies via fcr-mediated antigen uptake. incubation of these cultured dcs with tumor necrosis factor alpha (tnf-alpha) or soluble cd40 ligand (cd40l) for 24 h results in an increased surface expression of mhc class i and class ii molecules, b7, and icam-1 and in the appearance of the cd44 exon 9 splice variant (cd44-v9); by contrast, fc gamma rii is markedly and sometimes completely downregulated. the functional consequences of the short contact with tnf-alpha are in increased t cell stimulatory capacity in mlr, but a 10-fold decrease in presentation of soluble tt and a 100-fold decrease in presentation of tt-immunoglobulin g complexes.",0
"purpose little evidence of increased thrombotic risk is available in covid-19 patients. our purpose was to assess thrombotic risk in severe forms of sars-cov-2 infection. methods all patients referred to 4 intensive care units (icus) from two centers of a french tertiary hospital for acute respiratory distress syndrome (ards) due to covid-19 between march 3rd and 31st 2020 were included. medical history, symptoms, biological data and imaging were prospectively collected. propensity score matching was performed to analyze the occurrence of thromboembolic events between non-covid-19 ards and covid-19 ards patients. results 150 covid-19 patients were included (122 men, median age 63 years, sapsii 49 points). sixty-four clinically relevant thrombotic complications were diagnosed in 150 patients, mainly pulmonary embolisms (16.7%). 28/29 patients (96.6%) receiving continuous renal replacement therapy experienced circuit clotting. three thrombotic occlusions (in 2 patients) of centrifugal pump occurred in 12 patients (8%) supported by ecmo. most patients (> 95%) had elevated d-dimer and fibrinogen. no patient developed disseminated intravascular coagulation. von willebrand (vwf) activity, vwf antigen and fviii were considerably increased, and 50/57 tested patients (87.7%) had positive lupus anticoagulant. comparison with non-covid-19 ards patients (n = 145) confirmed that covid-19 ards patients (n = 77) developed significantly more thrombotic complications, mainly pulmonary embolisms (11.7 vs. 2.1%, p conclusion despite anticoagulation, a high number of patients with ards secondary to covid-19 developed life-threatening thrombotic complications. higher anticoagulation targets than in usual critically ill patients should therefore probably be suggested.",0
"differentiated macrophages are the resident tissue phagocytes and sentinel cells of the innate immune response. the phenotype of mature tissue macrophages represents the composite of environmental and differentiation-dependent imprinting. phorbol-12-myristate-13-acetate (pma) and 1,25-dihydroxyvitamin d3 (vd(3)) are stimuli commonly used to induce macrophage differentiation in monocytic cell lines but the extent of differentiation in comparison to primary tissue macrophages is unclear. we have compared the phenotype of the promonocytic thp-1 cell line after various protocols of differentiation utilising vd(3) and pma in comparison to primary human monocytes or monocyte-derived macrophages (mdm). both stimuli induced changes in cell morphology indicative of differentiation but neither showed differentiation comparable to mdm. in contrast, pma treatment followed by 5 days resting in culture without pma (pmar) increased cytoplasmic to nuclear ratio, increased mitochondrial and lysosomal numbers and altered differentiation-dependent cell surface markers in a pattern similar to mdm. moreover, pmar cells showed relative resistance to apoptotic stimuli and maintained levels of the differentiation-dependent anti-apoptotic protein mcl-1 similar to mdm. pmar cells retained a high phagocytic capacity for latex beads, and expressed a cytokine profile that resembled mdm in response to tlr ligands, in particular with marked tlr2 responses. moreover, both mdm and pmar retained marked plasticity to stimulus-directed polarization. these findings suggest a modified pma differentiation protocol can enhance macrophage differentiation of thp-1 cells and identify increased numbers of mitochondria and lysosomes, resistance to apoptosis and the potency of tlr2 responses as important discriminators of the level of macrophage differentiation for transformed cells.",0
"developments in genome-wide association studies and the increasing availability of summary genetic association data have made application of mendelian randomization relatively straightforward. however, obtaining reliable results from a mendelian randomization investigation remains problematic, as the conventional inverse-variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. we present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. this estimator is consistent even when up to 50% of the information comes from invalid instrumental variables. in a simulation analysis, it is shown to have better finite-sample type 1 error rates than the inverse-variance weighted method, and is complementary to the recently proposed mr-egger (mendelian randomization-egger) regression method. in analyses of the causal effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol on coronary artery disease risk, the inverse-variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and mr-egger regression methods suggest a null effect of high-density lipoprotein cholesterol that corresponds with the experimental evidence. both median-based and mr-egger regression methods should be considered as sensitivity analyses for mendelian randomization investigations with multiple genetic variants.",0
"objective to assess the association between leucocyte telomere length and risk of cardiovascular disease. design systematic review and meta-analysis. data sources studies published up to march 2014 identified through searches of medline, web of science, and embase. eligibility criteria prospective and retrospective studies that reported on associations between leucocyte telomere length and coronary heart disease (defined as non-fatal myocardial infarction, coronary heart disease death, or coronary revascularisation) or cerebrovascular disease (defined as non-fatal stroke or death from cerebrovascular disease) and were broadly representative of general populations--that is, they did not select cohort or control participants on the basis of pre-existing cardiovascular disease or diabetes. results twenty four studies involving 43,725 participants and 8400 patients with cardiovascular disease (5566 with coronary heart disease and 2834 with cerebrovascular disease) were found to be eligible. in a comparison of the shortest versus longest third of leucocyte telomere length, the pooled relative risk for coronary heart disease was 1.54 (95% confidence interval 1.30 to 1.83) in all studies, 1.40 (1.15 to 1.70) in prospective studies, and 1.80 (1.32 to 2.44) in retrospective studies. heterogeneity between studies was moderate (i(2) = 64%, 41% to 77%, phet conclusion available observational data show an inverse association between leucocyte telomere length and risk of coronary heart disease independent of conventional vascular risk factors. the association with cerebrovascular disease is less certain.",0
"objective this study updates previous estimates of the economic burden of diagnosed diabetes and quantifies the increased health resource use and lost productivity associated with diabetes in 2017. research design and methods we use a prevalence-based approach that combines the demographics of the u.s. population in 2017 with diabetes prevalence, epidemiological data, health care cost, and economic data into a cost of diabetes model. health resource use and associated medical costs are analyzed by age, sex, race/ethnicity, insurance coverage, medical condition, and health service category. data sources include national surveys, medicare standard analytical files, and one of the largest claims databases for the commercially insured population in the u.s. results the total estimated cost of diagnosed diabetes in 2017 is $327 billion, including $237 billion in direct medical costs and $90 billion in reduced productivity. for the cost categories analyzed, care for people with diagnosed diabetes accounts for 1 in 4 health care dollars in the u.s., and more than half of that expenditure is directly attributable to diabetes. people with diagnosed diabetes incur average medical expenditures of ∼$16,750 per year, of which ∼$9,600 is attributed to diabetes. people with diagnosed diabetes, on average, have medical expenditures ∼2.3 times higher than what expenditures would be in the absence of diabetes. indirect costs include increased absenteeism ($3.3 billion) and reduced productivity while at work ($26.9 billion) for the employed population, reduced productivity for those not in the labor force ($2.3 billion), inability to work because of disease-related disability ($37.5 billion), and lost productivity due to 277,000 premature deaths attributed to diabetes ($19.9 billion). conclusions after adjusting for inflation, economic costs of diabetes increased by 26% from 2012 to 2017 due to the increased prevalence of diabetes and the increased cost per person with diabetes. the growth in diabetes prevalence and medical costs is primarily among the population aged 65 years and older, contributing to a growing economic cost to the medicare program. the estimates in this article highlight the substantial financial burden that diabetes imposes on society, in addition to intangible costs from pain and suffering, resources from care provided by nonpaid caregivers, and costs associated with undiagnosed diabetes.",0
"vaccine hesitancy remains a barrier to full population inoculation against highly infectious diseases. coincident with the rapid developments of covid-19 vaccines globally, concerns about the safety of such a vaccine could contribute to vaccine hesitancy. we analyzed 1941 anonymous questionnaires completed by healthcare workers and members of the general israeli population, regarding acceptance of a potential covid-19 vaccine. our results indicate that healthcare staff involved in the care of covid-19 positive patients, and individuals considering themselves at risk of disease, were more likely to self-report acquiescence to covid-19 vaccination if and when available. in contrast, parents, nurses, and medical workers not caring for sars-cov-2 positive patients expressed higher levels of vaccine hesitancy. interventional educational campaigns targeted towards populations at risk of vaccine hesitancy are therefore urgently needed to combat misinformation and avoid low inoculation rates.",0
"after analyzing the immune characteristics of patients with severe coronavirus disease 2019 (covid-19), we have identified that pathogenic t cells and inflammatory monocytes with large amount of interleukin 6 secreting may incite the inflammatory storm, which may potentially be curbed through monoclonal antibody that targets the il-6 pathways. here, we aimed to assess the efficacy of tocilizumab in severe patients with covid-19 and seek a therapeutic strategy. the patients diagnosed as severe or critical covid-19 in the first affiliated hospital of university of science and technology of china (anhui provincial hospital) and anhui fuyang second people's hospital were given tocilizumab in addition to routine therapy between 5 and 14 february 2020. the changes of clinical manifestations, computerized tomography (ct) scan image, and laboratory examinations were retrospectively analyzed. fever returned to normal on the first day, and other symptoms improved remarkably within a few days. within 5 d after tocilizumab, 15 of the 20 patients (75.0%) had lowered their oxygen intake, and 1 patient needed no oxygen therapy. ct scans manifested that the lung lesion opacity absorbed in 19 patients (90.5%). the percentage of lymphocytes in peripheral blood, which decreased in 85.0% of patients (17/20) before treatment (mean, 15.52 ± 8.89%), returned to normal in 52.6% of patients (10/19) on the fifth day after treatment. abnormally elevated c-reactive protein decreased significantly in 84.2% of patients (16/19). no obvious adverse reactions were observed. all patients have been discharged on average 15.1 d after giving tocilizumab. preliminary data show that tocilizumab, which improved the clinical outcome immediately in severe and critical covid-19 patients, is an effective treatment to reduce mortality.",0
"background gene set analysis (gsa) is a widely used strategy for gene expression data analysis based on pathway knowledge. gsa focuses on sets of related genes and has established major advantages over individual gene analyses, including greater robustness, sensitivity and biological relevance. however, previous gsa methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs. results to address these limitations, we present a new gsa method called generally applicable gene-set enrichment (gage). we successfully apply gage to multiple microarray datasets with different sample sizes, experimental designs and profiling techniques. gage shows significantly better results when compared to two other commonly used gsa methods of gsea and page. we demonstrate this improvement in the following three aspects: (1) consistency across repeated studies/experiments; (2) sensitivity and specificity; (3) biological relevance of the regulatory mechanisms inferred.gage reveals novel and relevant regulatory mechanisms from both published and previously unpublished microarray studies. from two published lung cancer data sets, gage derived a more cohesive and predictive mechanistic scheme underlying lung cancer progress and metastasis. for a previously unpublished bmp6 study, gage predicted novel regulatory mechanisms for bmp6 induced osteoblast differentiation, including the canonical bmp-tgf beta signaling, jak-stat signaling, wnt signaling, and estrogen signaling pathways-all of which are supported by the experimental literature. conclusion gage is generally applicable to gene expression datasets with different sample sizes and experimental designs. gage consistently outperformed two most frequently used gsa methods and inferred statistically and biologically more relevant regulatory pathways. the gage method is implemented in r in the ""gage"" package, available under the gnu gpl from",0
"guidance is provided in a european setting on the assessment and treatment of postmenopausal women at risk from fractures due to osteoporosis. introduction the international osteoporosis foundation and european society for clinical and economic aspects of osteoporosis and osteoarthritis published guidance for the diagnosis and management of osteoporosis in 2013. this manuscript updates these in a european setting. methods systematic reviews were updated. results the following areas are reviewed: the role of bone mineral density measurement for the diagnosis of osteoporosis and assessment of fracture risk; general and pharmacological management of osteoporosis; monitoring of treatment; assessment of fracture risk; case-finding strategies; investigation of patients; health economics of treatment. the update includes new information on the evaluation of bone microstructure evaluation in facture risk assessment, the role of frax® and fracture liaison services in secondary fracture prevention, long-term effects on fracture risk of dietary intakes, and increased fracture risk on stopping drug treatment. conclusions a platform is provided on which specific guidelines can be developed for national use.",0
"eggnog is a public database of orthology relationships, gene evolutionary histories and functional annotations. here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. in total, 4.4m orthologous groups (ogs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, hmm models and functional descriptors. precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each og. our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. finally, we improved eggnog online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. all precomputed data are publicly available for downloading or via api queries at",0
"over the years, the mitochondrial fatty acid β-oxidation (fao) pathway has been characterised at the biochemical level as well as the molecular biological level. fao plays a pivotal role in energy homoeostasis, but it competes with glucose as the primary oxidative substrate. the mechanisms behind this so-called glucose-fatty acid cycle operate at the hormonal, transcriptional and biochemical levels. inherited defects for most of the fao enzymes have been identified and characterised and are currently included in neonatal screening programmes. symptoms range from hypoketotic hypoglycaemia to skeletal and cardiac myopathies. the pathophysiology of these diseases is still not completely understood, hampering optimal treatment. studies of patients and mouse models will contribute to our understanding of the pathogenesis and will ultimately lead to better treatment.",0
"cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. the absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. we also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.",0
"a 15-year-old patient with cystic fibrosis with a disseminated mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. effective lytic phage derivatives that efficiently kill the infectious m. abscessus strain were developed by genome engineering and forward genetics. intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.",0
"according to globocan 2018 data, colorectal cancer (crc) is the third most deadly and fourth most commonly diagnosed cancer in the world. nearly 2 million new cases and about 1 million deaths are expected in 2018. crc incidence has been steadily rising worldwide, especially in developing countries that are adopting the ""western"" way of life. obesity, sedentary lifestyle, red meat consumption, alcohol, and tobacco are considered the driving factors behind the growth of crc. however, recent advances in early detection screenings and treatment options have reduced crc mortality in developed nations, even in the face of growing incidence. genetic testing and better family history documentation can enable those with a hereditary predisposition for the neoplasm to take preventive measures. meanwhile, the general population can reduce their risk by lowering their red meat, alcohol, and tobacco consumption and raising their consumption of fibre, wholesome foods, and certain vitamins and minerals.",0
"whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. here we present the harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. harvest includes parsnp, a fast core-genome multi-aligner, and gingr, a dynamic visual platform. together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. the harvest suite is open-source and freely available from:",0
"background low-risk limits recommended for alcohol consumption vary substantially across different national guidelines. to define thresholds associated with lowest risk for all-cause mortality and cardiovascular disease, we studied individual-participant data from 599 912 current drinkers without previous cardiovascular disease. methods we did a combined analysis of individual-participant data from three large-scale data sources in 19 high-income countries (the emerging risk factors collaboration, epic-cvd, and the uk biobank). we characterised dose-response associations and calculated hazard ratios (hrs) per 100 g per week of alcohol (12·5 units per week) across 83 prospective studies, adjusting at least for study or centre, age, sex, smoking, and diabetes. to be eligible for the analysis, participants had to have information recorded about their alcohol consumption amount and status (ie, non-drinker vs current drinker), plus age, sex, history of diabetes and smoking status, at least 1 year of follow-up after baseline, and no baseline history of cardiovascular disease. the main analyses focused on current drinkers, whose baseline alcohol consumption was categorised into eight predefined groups according to the amount in grams consumed per week. we assessed alcohol consumption in relation to all-cause mortality, total cardiovascular disease, and several cardiovascular disease subtypes. we corrected hrs for estimated long-term variability in alcohol consumption using 152 640 serial alcohol assessments obtained some years apart (median interval 5·6 years ) from 71 011 participants from 37 studies. findings in the 599 912 current drinkers included in the analysis, we recorded 40 310 deaths and 39 018 incident cardiovascular disease events during 5·4 million person-years of follow-up. for all-cause mortality, we recorded a positive and curvilinear association with the level of alcohol consumption, with the minimum mortality risk around or below 100 g per week. alcohol consumption was roughly linearly associated with a higher risk of stroke (hr per 100 g per week higher consumption 1·14, 95% ci, 1·10-1·17), coronary disease excluding myocardial infarction (1·06, 1·00-1·11), heart failure (1·09, 1·03-1·15), fatal hypertensive disease (1·24, 1·15-1·33); and fatal aortic aneurysm (1·15, 1·03-1·28). by contrast, increased alcohol consumption was log-linearly associated with a lower risk of myocardial infarction (hr 0·94, 0·91-0·97). in comparison to those who reported drinking >0-≤100 g per week, those who reported drinking >100-≤200 g per week, >200-≤350 g per week, or >350 g per week had lower life expectancy at age 40 years of approximately 6 months, 1-2 years, or 4-5 years, respectively. interpretation in current drinkers of alcohol in high-income countries, the threshold for lowest risk of all-cause mortality was about 100 g/week. for cardiovascular disease subtypes other than myocardial infarction, there were no clear risk thresholds below which lower alcohol consumption stopped being associated with lower disease risk. these data support limits for alcohol consumption that are lower than those recommended in most current guidelines. funding uk medical research council, british heart foundation, national institute for health research, european union framework 7, and european research council.",0
"background millennium development goal 5 calls for a 75% reduction in the maternal mortality ratio (mmr) between 1990 and 2015. we estimated levels and trends in maternal mortality for 183 countries to assess progress made. based on mmr estimates for 2015, we constructed projections to show the requirements for the sustainable development goal (sdg) of less than 70 maternal deaths per 100,000 livebirths globally by 2030. methods we updated the un maternal mortality estimation inter-agency group (mmeig) database with more than 200 additional records (vital statistics from civil registration systems, surveys, studies, or reports). we generated estimates of maternal mortality and related indicators with 80% uncertainty intervals (uis) using a bayesian model. the model combines the rate of change implied by a multilevel regression model with a time-series model to capture data-driven changes in country-specific mmrs, and includes a data model to adjust for systematic and random errors associated with different data sources. results we had data for 171 of 183 countries. the global mmr fell from 385 deaths per 100,000 livebirths (80% ui 359-427) in 1990, to 216 (207-249) in 2015, corresponding to a relative decline of 43·9% (34·0-48·7), with 303,000 (291,000-349,000) maternal deaths worldwide in 2015. regional progress in reducing the mmr since 1990 ranged from an annual rate of reduction of 1·8% (0·0-3·1) in the caribbean to 5·0% (4·0-6·0) in eastern asia. regional mmrs for 2015 ranged from 12 deaths per 100,000 livebirths (11-14) for high-income regions to 546 (511-652) for sub-saharan africa. accelerated progress will be needed to achieve the sdg goal; countries will need to reduce their mmrs at an annual rate of reduction of at least 7·5%. interpretation despite global progress in reducing maternal mortality, immediate action is needed to meet the ambitious sdg 2030 target, and ultimately eliminate preventable maternal mortality. although the rates of reduction that are needed to achieve country-specific sdg targets are ambitious for most high mortality countries, countries that made a concerted effort to reduce maternal mortality between 2000 and 2010 provide inspiration and guidance on how to accomplish the acceleration necessary to substantially reduce preventable maternal deaths. funding national university of singapore, national institute of child health and human development, usaid, and the undp/unfpa/unicef/who/world bank special programme of research, development and research training in human reproduction.",0
"objective brain-computer interfaces (bcis) could potentially be used to interact with pathological brain signals to intervene and ameliorate their effects in disease states. here, we provide proof-of-principle of this approach by using a bci to interpret pathological brain activity in patients with advanced parkinson disease (pd) and to use this feedback to control when therapeutic deep brain stimulation (dbs) is delivered. our goal was to demonstrate that by personalizing and optimizing stimulation in real time, we could improve on both the efficacy and efficiency of conventional continuous dbs. methods we tested bci-controlled adaptive dbs (adbs) of the subthalamic nucleus in 8 pd patients. feedback was provided by processing of the local field potentials recorded directly from the stimulation electrodes. the results were compared to no stimulation, conventional continuous stimulation (cdbs), and random intermittent stimulation. both unblinded and blinded clinical assessments of motor effect were performed using the unified parkinson's disease rating scale. results motor scores improved by 66% (unblinded) and 50% (blinded) during adbs, which were 29% (p = 0.03) and 27% (p = 0.005) better than cdbs, respectively. these improvements were achieved with a 56% reduction in stimulation time compared to cdbs, and a corresponding reduction in energy requirements (p interpretation bci-controlled dbs is tractable and can be more efficient and efficacious than conventional continuous neuromodulation for pd.",0
"background the potential impact of the covid-19 pandemic on population mental health is of increasing global concern. we examine changes in adult mental health in the uk population before and during the lockdown. methods in this secondary analysis of a national, longitudinal cohort study, households that took part in waves 8 or 9 of the uk household longitudinal study (ukhls) panel, including all members aged 16 or older in april, 2020, were invited to complete the covid-19 web survey on april 23-30, 2020. participants who were unable to make an informed decision as a result of incapacity, or who had unknown postal addresses or addresses abroad were excluded. mental health was assessed using the 12-item general health questionnaire (ghq-12). repeated cross-sectional analyses were done to examine temporal trends. fixed-effects regression models were fitted to identify within-person change compared with preceding trends. findings waves 6-9 of the ukhls had 53 351 participants. eligible participants for the covid-19 web survey were from households that took part in waves 8 or 9, and 17 452 (41·2%) of 42 330 eligible people participated in the web survey. population prevalence of clinically significant levels of mental distress rose from 18·9% (95% ci 17·8-20·0) in 2018-19 to 27·3% (26·3-28·2) in april, 2020, one month into uk lockdown. mean ghq-12 score also increased over this time, from 11·5 (95% ci 11·3-11·6) in 2018-19, to 12·6 (12·5-12·8) in april, 2020. this was 0·48 (95% ci 0·07-0·90) points higher than expected when accounting for previous upward trends between 2014 and 2018. comparing ghq-12 scores within individuals, adjusting for time trends and significant predictors of change, increases were greatest in 18-24-year-olds (2·69 points, 95% ci 1·89-3·48), 25-34-year-olds (1·57, 0·96-2·18), women (0·92, 0·50-1·35), and people living with young children (1·45, 0·79-2·12). people employed before the pandemic also averaged a notable increase in ghq-12 score (0·63, 95% ci 0·20-1·06). interpretation by late april, 2020, mental health in the uk had deteriorated compared with pre-covid-19 trends. policies emphasising the needs of women, young people, and those with preschool aged children are likely to play an important part in preventing future mental illness. funding none.",0
"background in cancer research, the association between a gene and clinical outcome suggests the underlying etiology of the disease and consequently can motivate further studies. the recent availability of published cancer microarray datasets with clinical annotation provides the opportunity for linking gene expression to prognosis. however, the data are not easy to access and analyze without an effective analysis platform. description to take advantage of public resources in full, a database named ""prognoscan"" has been developed. this is 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between gene expression and prognosis. prognoscan employs the minimum p-value approach for grouping patients for survival analysis that finds the optimal cutpoint in continuous gene expression measurement without prior biological knowledge or assumption and, as a result, enables systematic meta-analysis of multiple datasets. conclusion prognoscan provides a powerful platform for evaluating potential tumor markers and therapeutic targets and would accelerate cancer research. the database is publicly accessible at",0
"summary the minfi package is widely used for analyzing illumina dna methylation array data. here we describe modifications to the minfi package required to support the humanmethylationepic ('epic') array from illumina. we discuss methods for the joint analysis and normalization of data from the humanmethylation450 ('450k') and epic platforms. we introduce the single-sample noob ( ssnoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of infinium methylation arrays. we show how to use reference 450k datasets to estimate cell type composition of samples on epic arrays. the cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming illumina methylation array data. availability and implementation the minfi package version 1.19.12 or higher is available for all platforms from the bioconductor project. contact khansen@jhsph.edu. supplementary information supplementary data are available at bioinformatics online.",0
"given the results from early trials, covid-19 vaccines will be available by 2021. however, little is known about what americans think of getting immunized with a covid-19 vaccine. thus, the purpose of this study was to conduct a comprehensive and systematic national assessment of covid-19 vaccine hesitancy in a community-based sample of the american adult population. a multi-item valid and reliable questionnaire was deployed online via mturk and social media sites to recruit u.s. adults from the general population. a total of 1878 individuals participated in the study where the majority were: females (52%), whites (74%), non-hispanic (81%), married (56%), employed full time (68%), and with a bachelor's degree or higher (77%). the likelihood of getting a covid-19 immunization in the study population was: very likely (52%), somewhat likely (27%), not likely (15%), definitely not (7%), with individuals who had lower education, income, or perceived threat of getting infected being more likely to report that they were not likely/definitely not going to get covid-19 vaccine (i.e., vaccine hesitancy). in unadjusted group comparisons, compared to their counterparts, vaccine hesitancy was higher among african-americans (34%), hispanics (29%), those who had children at home (25%), rural dwellers (29%), people in the northeastern u.s. (25%), and those who identified as republicans (29%). in multiple regression analyses, vaccine hesitancy was predicted significantly by sex, education, employment, income, having children at home, political affiliation, and the perceived threat of getting infected with covid-19 in the next 1 year. given the high prevalence of covid-19 vaccine hesitancy, evidence-based communication, mass media strategies, and policy measures will have to be implemented across the u.s. to convert vaccines into vaccinations and mass immunization with special attention to the groups identified in this study.",0
"background traumatic brain injury (tbi) and spinal cord injury (sci) are increasingly recognised as global health priorities in view of the preventability of most injuries and the complex and expensive medical care they necessitate. we aimed to measure the incidence, prevalence, and years of life lived with disability (ylds) for tbi and sci from all causes of injury in every country, to describe how these measures have changed between 1990 and 2016, and to estimate the proportion of tbi and sci cases caused by different types of injury. methods we used results from the global burden of diseases, injuries, and risk factors (gbd) study 2016 to measure the global, regional, and national burden of tbi and sci by age and sex. we measured the incidence and prevalence of all causes of injury requiring medical care in inpatient and outpatient records, literature studies, and survey data. by use of clinical record data, we estimated the proportion of each cause of injury that required medical care that would result in tbi or sci being considered as the nature of injury. we used literature studies to establish standardised mortality ratios and applied differential equations to convert incidence to prevalence of long-term disability. finally, we applied gbd disability weights to calculate ylds. we used a bayesian meta-regression tool for epidemiological modelling, used cause-specific mortality rates for non-fatal estimation, and adjusted our results for disability experienced with comorbid conditions. we also analysed results on the basis of the socio-demographic index, a compound measure of income per capita, education, and fertility. findings in 2016, there were 27·08 million (95% uncertainty interval 24·30-30·30 million) new cases of tbi and 0·93 million (0·78-1·16 million) new cases of sci, with age-standardised incidence rates of 369 (331-412) per 100 000 population for tbi and 13 (11-16) per 100 000 for sci. in 2016, the number of prevalent cases of tbi was 55·50 million (53·40-57·62 million) and of sci was 27·04 million (24·98-30·15 million). from 1990 to 2016, the age-standardised prevalence of tbi increased by 8·4% (95% ui 7·7 to 9·2), whereas that of sci did not change significantly (-0·2% ). age-standardised incidence rates increased by 3·6% (1·8 to 5·5) for tbi, but did not change significantly for sci (-3·6% ). tbi caused 8·1 million (95% ui 6·0-10·4 million) ylds and sci caused 9·5 million (6·7-12·4 million) ylds in 2016, corresponding to age-standardised rates of 111 (82-141) per 100 000 for tbi and 130 (90-170) per 100 000 for sci. falls and road injuries were the leading causes of new cases of tbi and sci in most regions. interpretation tbi and sci constitute a considerable portion of the global injury burden and are caused primarily by falls and road injuries. the increase in incidence of tbi over time might continue in view of increases in population density, population ageing, and increasing use of motor vehicles, motorcycles, and bicycles. the number of individuals living with sci is expected to increase in view of population growth, which is concerning because of the specialised care that people with sci can require. our study was limited by data sparsity in some regions, and it will be important to invest greater resources in collection of data for tbi and sci to improve the accuracy of future assessments. funding bill & melinda gates foundation.",0
"transient receptor potential (trp) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. elucidating how these channels integrate and convert physiological signals into channel opening is essential to understanding how they regulate cell excitability under normal and pathophysiological conditions. here we exploit pharmacological probes (a peptide toxin and small vanilloid agonists) to determine structures of two activated states of the capsaicin receptor, trpv1. a domain (consisting of transmembrane segments 1-4) that moves during activation of voltage-gated channels remains stationary in trpv1, highlighting differences in gating mechanisms for these structurally related channel superfamilies. trpv1 opening is associated with major structural rearrangements in the outer pore, including the pore helix and selectivity filter, as well as pronounced dilation of a hydrophobic constriction at the lower gate, suggesting a dual gating mechanism. allosteric coupling between upper and lower gates may account for rich physiological modulation exhibited by trpv1 and other trp channels.",0
"in the institute for genomic research rice genome annotation project ( we have continued to update the rice genome sequence with new data and improve the quality of the annotation. in our current release of annotation (release 4.0; january 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. we have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. all structural and functional annotation is viewable through our rice genome browser which currently supports 59 tracks. enhanced data access is available through web interfaces, ftp downloads and a data extractor tool developed in order to support discrete dataset downloads.",0
"studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell differentiation. however, the extent and cell-type-specificity of three-dimensional (3d) chromosome arrangements has remained controversial. in order to overcome technical limitations of previous studies, we have developed tools that allow the quantitative 3d positional mapping of all chromosomes simultaneously. we present unequivocal evidence for a probabilistic 3d order of prometaphase chromosomes, as well as of chromosome territories (cts) in nuclei of quiescent (g0) and cycling (early s-phase) human diploid fibroblasts (46, xy). radial distance measurements showed a probabilistic, highly nonrandom correlation with chromosome size: small chromosomes-independently of their gene density-were distributed significantly closer to the center of the nucleus or prometaphase rosette, while large chromosomes were located closer to the nuclear or rosette rim. this arrangement was independently confirmed in both human fibroblast and amniotic fluid cell nuclei. notably, these cell types exhibit flat-ellipsoidal cell nuclei, in contrast to the spherical nuclei of lymphocytes and several other human cell types, for which we and others previously demonstrated gene-density-correlated radial 3d ct arrangements. modeling of 3d ct arrangements suggests that cell-type-specific differences in radial ct arrangements are not solely due to geometrical constraints that result from nuclear shape differences. we also found gene-density-correlated arrangements of higher-order chromatin shared by all human cell types studied so far. chromatin domains, which are gene-poor, form a layer beneath the nuclear envelope, while gene-dense chromatin is enriched in the nuclear interior. we discuss the possible functional implications of this finding.",0
"background cirrhosis and other chronic liver diseases (collectively referred to as cirrhosis in this paper) are a major cause of morbidity and mortality globally, although the burden and underlying causes differ across locations and demographic groups. we report on results from the global burden of diseases, injuries, and risk factors study (gbd) 2017 on the burden of cirrhosis and its trends since 1990, by cause, sex, and age, for 195 countries and territories. methods we used data from vital registrations, vital registration samples, and verbal autopsies to estimate mortality. we modelled prevalence of total, compensated, and decompensated cirrhosis on the basis of hospital and claims data. disability-adjusted life-years (dalys) were calculated as the sum of years of life lost due to premature death and years lived with disability. estimates are presented as numbers and age-standardised or age-specific rates per 100 000 population, with 95% uncertainty intervals (uis). all estimates are presented for five causes of cirrhosis: hepatitis b, hepatitis c, alcohol-related liver disease, non-alcoholic steatohepatitis (nash), and other causes. we compared mortality, prevalence, and daly estimates with those expected according to the socio-demographic index (sdi) as a proxy for the development status of regions and countries. findings in 2017, cirrhosis caused more than 1·32 million (95% ui 1·27-1·45) deaths (440 000 in females and 883 000 in males) globally, compared with less than 899 000 (829 000-948 000) deaths in 1990. deaths due to cirrhosis constituted 2·4% (2·3-2·6) of total deaths globally in 2017 compared with 1·9% (1·8-2·0) in 1990. despite an increase in the number of deaths, the age-standardised death rate decreased from 21·0 (19·2-22·3) per 100 000 population in 1990 to 16·5 (15·8-18·1) per 100 000 population in 2017. sub-saharan africa had the highest age-standardised death rate among gbd super-regions for all years of the study period (32·2 deaths per 100 000 population in 2017), and the high-income super-region had the lowest (10·1 deaths per 100 000 population in 2017). the age-standardised death rate decreased or remained constant from 1990 to 2017 in all gbd regions except eastern europe and central asia, where the age-standardised death rate increased, primarily due to increases in alcohol-related liver disease prevalence. at the national level, the age-standardised death rate of cirrhosis was lowest in singapore in 2017 (3·7 per 100 000 in 2017) and highest in egypt in all years since 1990 (103·3 per 100 000 in 2017). there were 10·6 million (10·3-10·9) prevalent cases of decompensated cirrhosis and 112 million (107-119) prevalent cases of compensated cirrhosis globally in 2017. there was a significant increase in age-standardised prevalence rate of decompensated cirrhosis between 1990 and 2017. cirrhosis caused by nash had a steady age-standardised death rate throughout the study period, whereas the other four causes showed declines in age-standardised death rate. the age-standardised prevalence of compensated and decompensated cirrhosis due to nash increased more than for any other cause of cirrhosis (by 33·2% for compensated cirrhosis and 54·8% for decompensated cirrhosis) over the study period. from 1990 to 2017, the number of prevalent cases more than doubled for compensated cirrhosis due to nash and more than tripled for decompensated cirrhosis due to nash. in 2017, age-standardised death and daly rates were lower among countries and territories with higher sdi. interpretation cirrhosis imposes a substantial health burden on many countries and this burden has increased at the global level since 1990, partly due to population growth and ageing. although the age-standardised death and daly rates of cirrhosis decreased from 1990 to 2017, numbers of deaths and dalys and the proportion of all global deaths due to cirrhosis increased. despite the availability of effective interventions for the prevention and treatment of hepatitis b and c, they were still the main causes of cirrhosis burden worldwide, particularly in low-income countries. the impact of hepatitis b and c is expected to be attenuated and overtaken by that of nash in the near future. cost-effective interventions are required to continue the prevention and treatment of viral hepatitis, and to achieve early diagnosis and prevention of cirrhosis due to alcohol-related liver disease and nash. funding bill & melinda gates foundation.",0
"by means of a new ""quick-sampling"" method, micropellets of mouse liver mitochondria were rapidly prepared for electron microscopy during the recording of steady state metabolism. reversible ultrastructural changes were found to accompany change in metabolic steady states. the most dramatic reversible ultrastructural change occurs when adp is added to systems in which only phosphate acceptor is deficient, i.e., during the state iv to state iii transition as defined by chance and williams. after 15 min in state iv, mitochondria display an ""orthodox"" ultrastructural appearance as is usually observed after fixation within intact tissue. on transition to state iii, a dramatic change in the manner of folding of the inner membrane takes place. in addition, the electron opacity of the matrix increases as the volume of the matrix decreases, but total mitochondrial volume does not appear to change during this transition. this conformation is called ""condensed."" isolated mitochondria were found to oscillate between the orthodox and condensed conformations during reversible transitions between state iii and state iv. various significant ultrastructural changes in mitochondria also occur during transitions in other functional states, e.g., when substrate or substrate and acceptor is made limiting. internal structural flexibility is discussed with respect to structural and functional integrity of isolated mitochondria. reversible changes in the manner of folding of the inner membrane and in the manner of packing of small granules in the matrix as respiration is activated by adp represent an ultrastructural basis for metabolically linked mechanical activity in tightly coupled mitochondria.",0
"cadherins are calcium-dependent cell-cell adhesion molecules that require the interaction of the cytoplasmic tail with the actin cytoskeleton for adhesive activity. because of the functional relationship between cadherin receptors and actin filament organization, we investigated whether members of the rho family of small gtpases are necessary for cadherin adhesion. in fibroblasts, the rho family members rho and rac regulate actin polymerization to produce stress fibers and lamellipodia, respectively. in epithelial cells, we demonstrate that rho and rac are required for the establishment of cadherin-mediated cell-cell adhesion and the actin reorganization necessary to stabilize the receptors at sites of intercellular junctions. blocking endogenous rho or rac selectively removed cadherin complexes from junctions induced for up to 3 h, while desmosomes were not perturbed. in addition, withdrawal of cadherins from intercellular junctions temporally precedes the removal of cd44 and integrins, other microfilament-associated receptors. our data showed that the concerted action of rho and rac modulate the establishment of cadherin adhesion: a constitutively active form of rac was not sufficient to stabilize cadherindependent cell-cell contacts when endogenous rho was inhibited. upon induction of calcium-dependent intercellular adhesion, there was a rapid accumulation of actin at sites of cell-cell contacts, which was prevented by blocking cadherin function, rho or rac activity. however, if cadherin complexes are clustered by specific antibodies attached to beads, actin recruitment to the receptors was perturbed by inhibiting rac but not rho. our results provide new insights into the role of the small gtpases in the cadherin-dependent cell- cell contact formation and the remodelling of actin filaments in epithelial cells.",0
"the human cytokine interferon-inducible protein 10 (ip-10) is a small glycoprotein secreted by activated t cells, monocytes, endothelial cells, and keratinocytes, and is structurally related to a family of chemotactic cytokines called chemokines. although this protein is present in sites of delayed-type hypersensitivity reactions and lepromatous leprosy lesions, the biological activity of ip-10 remains unknown. we report here that recombinant human ip-10 stimulated significant in vitro chemotaxis of human peripheral blood monocytes but not neutrophils. recombinant human ip-10 also stimulated chemotaxis of stimulated, but not unstimulated, human peripheral blood t lymphocytes. phenotypic analysis of the stimulated t cell population responsive to ip-10 demonstrated that stimulated cd4+ and cd29+ t cells migrated in response to ip-10. this resembles the biological activity of the previously described t cell chemoattractant rantes. using an endothelial cell adhesion assay, we demonstrated that stimulated t cells pretreated with optimal doses of ip-10 exhibited a greatly enhanced ability to bind to an interleukin 1-treated endothelial cell monolayer. these results demonstrate that the ip-10 gene encodes for an inflammatory mediator that specifically stimulates the directional migration of t cells and monocytes as well as potentiates t cell adhesion to endothelium.",0
"over the last 10 years, high-density snp arrays and dna re-sequencing have illuminated the majority of the genotypic space for a number of organisms, including humans, maize, rice and arabidopsis. for any researcher willing to define and score a phenotype across many individuals, genome wide association studies (gwas) present a powerful tool to reconnect this trait back to its underlying genetics. in this review we discuss the biological and statistical considerations that underpin a successful analysis or otherwise. the relevance of biological factors including effect size, sample size, genetic heterogeneity, genomic confounding, linkage disequilibrium and spurious association, and statistical tools to account for these are presented. gwas can offer a valuable first insight into trait architecture or candidate loci for subsequent validation.",0
"the coronavirus disease 2019 (covid-19) pandemic resulted in 5,817,385 reported cases and 362,705 deaths worldwide through may, 30, 2020, † including 1,761,503 aggregated reported cases and 103,700 deaths in the united states. § previous analyses during february-early april 2020 indicated that age ≥65 years and underlying health conditions were associated with a higher risk for severe outcomes, which were less common among children aged ¶ was similar among males (401.1) and females (406.0) and highest among persons aged ≥80 years (902.0). among 599,636 (45%) cases with known information, 33% of persons were hispanic or latino of any race (hispanic), 22% were non-hispanic black (black), and 1.3% were non-hispanic american indian or alaska native (ai/an). among 287,320 (22%) cases with sufficient data on underlying health conditions, the most common were cardiovascular disease (32%), diabetes (30%), and chronic lung disease (18%). overall, 184,673 (14%) patients were hospitalized, 29,837 (2%) were admitted to an intensive care unit (icu), and 71,116 (5%) died. hospitalizations were six times higher among patients with a reported underlying condition (45.4%) than those without reported underlying conditions (7.6%). deaths were 12 times higher among patients with reported underlying conditions (19.5%) compared with those without reported underlying conditions (1.6%). the covid-19 pandemic continues to be severe, particularly in certain population groups. these preliminary findings underscore the need to build on current efforts to collect and analyze case data, especially among those with underlying health conditions. these data are used to monitor trends in covid-19 illness, identify and respond to localized incidence increase, and inform policies and practices designed to reduce transmission in the united states.",0
"covid-19 disease, caused by infection with sars-cov-2, is related to a series of physiopathological mechanisms that mobilize a wide variety of biomolecules, mainly immunological in nature. in the most severe cases, the prognosis can be markedly worsened by the hyperproduction of mainly proinflammatory cytokines, such as il-1, il-6, il-12, ifn-γ, and tnf-α, preferentially targeting lung tissue. this study reviews published data on alterations in the expression of different cytokines in patients with covid-19 who require admission to an intensive care unit. data on the implication of cytokines in this disease and their effect on outcomes will support the design of more effective approaches to the management of covid-19.",0
"background body-mass index (bmi) and diabetes have increased worldwide, whereas global average blood pressure and cholesterol have decreased or remained unchanged in the past three decades. we quantified how much of the effects of bmi on coronary heart disease and stroke are mediated through blood pressure, cholesterol, and glucose, and how much is independent of these factors. methods we pooled data from 97 prospective cohort studies that collectively enrolled 1·8 million participants between 1948 and 2005, and that included 57,161 coronary heart disease and 31,093 stroke events. for each cohort we excluded participants who were younger than 18 years, had a bmi of lower than 20 kg/m(2), or who had a history of coronary heart disease or stroke. we estimated the hazard ratio (hr) of bmi on coronary heart disease and stroke with and without adjustment for all possible combinations of blood pressure, cholesterol, and glucose. we pooled hrs with a random-effects model and calculated the attenuation of excess risk after adjustment for mediators. findings the hr for each 5 kg/m(2) higher bmi was 1·27 (95% ci 1·23-1·31) for coronary heart disease and 1·18 (1·14-1·22) for stroke after adjustment for confounders. additional adjustment for the three metabolic risk factors reduced the hrs to 1·15 (1·12-1·18) for coronary heart disease and 1·04 (1·01-1·08) for stroke, suggesting that 46% (95% ci 42-50) of the excess risk of bmi for coronary heart disease and 76% (65-91) for stroke is mediated by these factors. blood pressure was the most important mediator, accounting for 31% (28-35) of the excess risk for coronary heart disease and 65% (56-75) for stroke. the percentage excess risks mediated by these three mediators did not differ significantly between asian and western cohorts (north america, western europe, australia, and new zealand). both overweight (bmi ≥25 to interpretation interventions that reduce high blood pressure, cholesterol, and glucose might address about half of excess risk of coronary heart disease and three-quarters of excess risk of stroke associated with high bmi. maintenance of optimum bodyweight is needed for the full benefits. funding us national institute of health, uk medical research council, national institute for health research comprehensive biomedical research centre at imperial college healthcare nhs trust, lown scholars in residence program on cardiovascular disease prevention, and harvard global health institute doctoral research grant.",0
"periodontitis, a major inflammatory disease of the oral mucosa, is epidemiologically associated with other chronic inflammation-driven disorders, including cardio-metabolic, neurodegenerative and autoimmune diseases and cancer. emerging evidence from interventional studies indicates that local treatment of periodontitis ameliorates surrogate markers of comorbid conditions. the potential causal link between periodontitis and its comorbidities is further strengthened by recent experimental animal studies establishing biologically plausible and clinically consistent mechanisms whereby periodontitis could initiate or aggravate a comorbid condition. this multi-faceted 'mechanistic causality' aspect of the link between periodontitis and comorbidities is the focus of this review. understanding how certain extra-oral pathologies are affected by disseminated periodontal pathogens and periodontitis-associated systemic inflammation, including adaptation of bone marrow haematopoietic progenitors, may provide new therapeutic options to reduce the risk of periodontitis-associated comorbidities.",0
"rock (rho-kinase), an effector molecule of rhoa, phosphorylates the myosin binding subunit (mbs) of myosin phosphatase and inhibits the phosphatase activity. this inhibition increases phosphorylation of myosin light chain (mlc) of myosin ii, which is suggested to induce rhoa-mediated assembly of stress fibers and focal adhesions. rock is also known to directly phosphorylate mlc in vitro; however, the physiological significance of this mlc kinase activity is unknown. it is also not clear whether mlc phosphorylation alone is sufficient for the assembly of stress fibers and focal adhesions. we have developed two reagents with opposing effects on myosin phosphatase. one is an antibody against mbs that is able to inhibit myosin phosphatase activity. the other is a truncation mutant of mbs that constitutively activates myosin phosphatase. through microinjection of these two reagents followed by immunofluorescence with a specific antibody against phosphorylated mlc, we have found that mlc phosphorylation is both necessary and sufficient for the assembly of stress fibers and focal adhesions in 3t3 fibroblasts. the assembly of stress fibers in the center of cells requires rock activity in addition to the inhibition of myosin phosphatase, suggesting that rock not only inhibits myosin phosphatase but also phosphorylates mlc directly in the center of cells. at the cell periphery, on the other hand, mlck but not rock appears to be the kinase responsible for phosphorylating mlc. these results suggest that rock and mlck play distinct roles in spatial regulation of mlc phosphorylation.",0
"summary understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. the visualization integrates sequence data with other data types such as geographic information, serology, or host species. nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. availability and implementation all code (predominantly javascript and python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.",0
"unlabelled rdp3 is a new version of the rdp program for characterizing recombination events in dna-sequence alignments. among other novelties, this version includes four new recombination analysis methods (3seq, visrd, phylro and ldhat), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. complementary to a high degree of analysis flow automation, rdp3 also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. the new rdp3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000 × 10 kilobase sequences to 20 × 2 megabase sequences within 48 h on a desktop pc. availability rdp3 is available for free from its web site",0
"background patients' beliefs about treatment influence treatment engagement and adherence. the necessity-concerns framework postulates that adherence is influenced by implicit judgements of personal need for the treatment (necessity beliefs) and concerns about the potential adverse consequences of taking it. objective to assess the utility of the ncf in explaining nonadherence to prescribed medicines. data sources we searched embase, medline, psycinfo, cdsr/dare/cct and cinahl from january 1999 to april 2013 and handsearched reference sections from relevant articles. study eligibility criteria studies using the beliefs about medicines questionnaire (bmq) to examine perceptions of personal necessity for medication and concerns about potential adverse effects, in relation to a measure of adherence to medication. participants patients with long-term conditions. study appraisal and synthesis methods systematic review and meta-analysis of methodological quality was assessed by two independent reviewers. we pooled odds ratios for adherence using random effects models. results we identified 3777 studies, of which 94 (n = 25,072) fulfilled the inclusion criteria. across studies, higher adherence was associated with stronger perceptions of necessity of treatment, or = 1.742, 95% ci , p limitations few prospective longitudinal studies using objective adherence measures were identified. conclusions the necessity-concerns framework is a useful conceptual model for understanding patients' perspectives on prescribed medicines. taking account of patients' necessity beliefs and concerns could enhance the quality of prescribing by helping clinicians to engage patients in treatment decisions and support optimal adherence to appropriate prescriptions.",0
"objective to determine the accuracy of the patient health questionnaire-9 (phq-9) for screening to detect major depression. design individual participant data meta-analysis. data sources medline, medline in-process and other non-indexed citations, psycinfo, and web of science (january 2000-february 2015). inclusion criteria eligible studies compared phq-9 scores with major depression diagnoses from validated diagnostic interviews. primary study data and study level data extracted from primary reports were synthesized. for phq-9 cut-off scores 5-15, bivariate random effects meta-analysis was used to estimate pooled sensitivity and specificity, separately, among studies that used semistructured diagnostic interviews, which are designed for administration by clinicians; fully structured interviews, which are designed for lay administration; and the mini international neuropsychiatric (mini) diagnostic interviews, a brief fully structured interview. sensitivity and specificity were examined among participant subgroups and, separately, using meta-regression, considering all subgroup variables in a single model. results data were obtained for 58 of 72 eligible studies (total n=17 357; major depression cases n=2312). combined sensitivity and specificity was maximized at a cut-off score of 10 or above among studies using a semistructured interview (29 studies, 6725 participants; sensitivity 0.88, 95% confidence interval 0.83 to 0.92; specificity 0.85, 0.82 to 0.88). across cut-off scores 5-15, sensitivity with semistructured interviews was 5-22% higher than for fully structured interviews (mini excluded; 14 studies, 7680 participants) and 2-15% higher than for the mini (15 studies, 2952 participants). specificity was similar across diagnostic interviews. the phq-9 seems to be similarly sensitive but may be less specific for younger patients than for older patients; a cut-off score of 10 or above can be used regardless of age.. conclusions phq-9 sensitivity compared with semistructured diagnostic interviews was greater than in previous conventional meta-analyses that combined reference standards. a cut-off score of 10 or above maximized combined sensitivity and specificity overall and for subgroups. registration prospero crd42014010673.",0
"aims/hypothesis the aim of the study was to compare the efficacy and safety of liraglutide in type 2 diabetes mellitus vs placebo and insulin glargine (a21gly,b31arg,b32arg human insulin), all in combination with metformin and glimepiride. methods this randomised (using a telephone or web-based randomisation system), parallel-group, controlled 26 week trial of 581 patients with type 2 diabetes mellitus on prior monotherapy (hba(1c) 7.5-10%) and combination therapy (7.0-10%) was conducted in 107 centres in 17 countries. the primary endpoint was hba(1c). patients were randomised (2:1:2) to liraglutide 1.8 mg once daily (n = 232), liraglutide placebo (n = 115) and open-label insulin glargine (n = 234), all in combination with metformin (1 g twice daily) and glimepiride (4 mg once daily). investigators, participants and study monitors were blinded to the treatment status of the liraglutide and placebo groups at all times. results the number of patients analysed as intention to treat were: liraglutide n = 230, placebo n = 114, insulin glargine n = 232. liraglutide reduced hba(1c) significantly vs glargine (1.33% vs 1.09%; -0.24% difference, 95% ci 0.08, 0.39; p = 0.0015) and placebo (-1.09% difference, 95% ci 0.90, 1.28; p conclusions/interpretation liraglutide added to metformin and sulfonylurea produced significant improvement in glycaemic control and bodyweight compared with placebo and insulin glargine. the difference vs insulin glargine in hba(1c) was within the predefined non-inferiority margin. trial registration clinicaltrials.gov nct00331851. funding the study was funded by novo nordisk a/s.",0
"accumulating evidence suggests that, independent of physical activity levels, sedentary behaviours are associated with increased risk of cardio-metabolic disease, all-cause mortality, and a variety of physiological and psychological problems. therefore, the purpose of this systematic review is to determine the relationship between sedentary behaviour and health indicators in school-aged children and youth aged 5-17 years. online databases (medline, embase and psycinfo), personal libraries and government documents were searched for relevant studies examining time spent engaging in sedentary behaviours and six specific health indicators (body composition, fitness, metabolic syndrome and cardiovascular disease, self-esteem, pro-social behaviour and academic achievement). 232 studies including 983,840 participants met inclusion criteria and were included in the review. television (tv) watching was the most common measure of sedentary behaviour and body composition was the most common outcome measure. qualitative analysis of all studies revealed a dose-response relation between increased sedentary behaviour and unfavourable health outcomes. watching tv for more than 2 hours per day was associated with unfavourable body composition, decreased fitness, lowered scores for self-esteem and pro-social behaviour and decreased academic achievement. meta-analysis was completed for randomized controlled studies that aimed to reduce sedentary time and reported change in body mass index (bmi) as their primary outcome. in this regard, a meta-analysis revealed an overall significant effect of -0.81 (95% ci of -1.44 to -0.17, p = 0.01) indicating an overall decrease in mean bmi associated with the interventions. there is a large body of evidence from all study designs which suggests that decreasing any type of sedentary time is associated with lower health risk in youth aged 5-17 years. in particular, the evidence suggests that daily tv viewing in excess of 2 hours is associated with reduced physical and psychosocial health, and that lowering sedentary time leads to reductions in bmi.",0
"microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. in 2011, we introduced antismash, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at here, we present version 3.0 of antismash, which has undergone major improvements. a full integration of the recently published clusterfinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. also, a new dereplication variant of the clusterblast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. at the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and enzyme commission numbers are assigned to functionally classify all enzyme-coding genes. additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. finally, in order for users to be able to organize and analyze multiple antismash outputs in a private setting, a new xml output module allows offline editing of antismash annotations within the geneious software.",0
"smooth muscle derived from the inner media and intima of immature guinea pig aorta were grown for up to 8 wk in cell culture. the cells maintained the morphology of smooth muscle at all phases of their growth in culture. after growing to confluency, they grew in multiple overlapping layers. by 4 wk in culture, microfibrils (110 a) appeared within the spaces between the layers of cells. basement membrane-like material also appeared adjacent to the cells. analysis of the microfibrils showed that they have an amino acid composition similar to that of the microfibrillar protein of the intact elastic fiber. these investigations coupled with the radioautographic observations of the ability of aortic smooth muscle to synthesize and secrete extracellular proteins demonstrate that this cell is a connective tissue synthetic cell.",0
"background observational studies report reduced colorectal cancer in regular aspirin consumers. randomised controlled trials have shown reduced risk of adenomas but none have employed prevention of colorectal cancer as a primary endpoint. the capp2 trial aimed to investigate the antineoplastic effects of aspirin and a resistant starch in carriers of lynch syndrome, the major form of hereditary colorectal cancer; we now report long-term follow-up of participants randomly assigned to aspirin or placebo. methods in the capp2 randomised trial, carriers of lynch syndrome were randomly assigned in a two-by-two factorial design to 600 mg aspirin or aspirin placebo or 30 g resistant starch or starch placebo, for up to 4 years. randomisation was in blocks of 16 with provision for optional single-agent randomisation and extended postintervention double-blind follow-up; participants and investigators were masked to treatment allocation. the primary endpoint was development of colorectal cancer. analysis was by intention to treat and per protocol. this trial is registered, isrctn59521990. results 861 participants were randomly assigned to aspirin or aspirin placebo. at a mean follow-up of 55·7 months, 48 participants had developed 53 primary colorectal cancers (18 of 427 randomly assigned to aspirin, 30 of 434 to aspirin placebo). intention-to-treat analysis of time to first colorectal cancer showed a hazard ratio (hr) of 0·63 (95% ci 0·35-1·13, p=0·12). poisson regression taking account of multiple primary events gave an incidence rate ratio (irr) of 0·56 (95% ci 0·32-0·99, p=0·05). for participants completing 2 years of intervention (258 aspirin, 250 aspirin placebo), per-protocol analysis yielded an hr of 0·41 (0·19-0·86, p=0·02) and an irr of 0·37 (0·18-0·78, p=0·008). no data for adverse events were available postintervention; during the intervention, adverse events did not differ between aspirin and placebo groups. interpretation 600 mg aspirin per day for a mean of 25 months substantially reduced cancer incidence after 55·7 months in carriers of hereditary colorectal cancer. further studies are needed to establish the optimum dose and duration of aspirin treatment. funding european union; cancer research uk; bayer corporation; national starch and chemical co; uk medical research council; newcastle hospitals trustees; cancer council of victoria australia; thripp south africa; the finnish cancer foundation; siak switzerland; bayer pharma.",0
"since 1991, a nationwide histopathology and cytopathology network and archive is in operation in the netherlands under the name palga, encompassing all sixty-four pathology laboratories in the netherlands. the overall system comprises decentralized systems at the participating laboratories, a central databank, and a dedicated communication and information exchange tool. excerpts of all histopathology and cytopathology reports are generated automatically at the participating laboratories and transferred to the central databank. both the decentralized systems and the central system perform checks on the quality and completeness of excerpts. currently, about 42 million records on almost 10 million patients are stored in the central databank. each excerpt contains patient identifiers, including demographic data and the so-called palga diagnosis. the latter is structured along five classification axes: topography, morphology, function, procedure, and diseases. all data transfer and communication occurs electronically with encryption of patient and laboratory identifiers. all excerpts are continuously available to all participating pathology laboratories, thus contributing to the quality of daily patient care. in addition, external parties may obtain permission to use data from the palga system, either on an ongoing basis or on the basis of a specific permission. annually, 40 to 60 applications for permission to use palga data are submitted. among external users are the dutch cancer registry, population-based screening programs for cancer of the uterine cervix and breast cancer in the netherlands, and individual investigators addressing a range of research questions. many scientific papers and theses incorporating palga data have been published already. in conclusion, the palga system is a unique system that requires a minimal effort on the part of the participating laboratories, while providing them a powerful tool in their daily practices.",0
"background adherence to highly active antiretroviral therapy (haart) medication is the greatest patient-enabled predictor of treatment success and mortality for those who have access to drugs. we systematically reviewed the literature to determine patient-reported barriers and facilitators to adhering to antiretroviral therapy. methods and findings we examined both developed and developing nations. we searched the following databases: amed (inception to june 2005), campbell collaboration (inception to june 2005), cinahl (inception to june 2005), cochrane library (inception to june 2005), embase (inception to june 2005), eric (inception to june 2005), medline (inception to june 2005), and nhs eed (inception to june 2005). we retrieved studies conducted in both developed and developing nation settings that examined barriers and facilitators addressing adherence. both qualitative and quantitative studies were included. we independently, in duplicate, extracted data reported in qualitative studies addressing adherence. we then examined all quantitative studies addressing barriers and facilitators noted from the qualitative studies. in order to place the findings of the qualitative studies in a generalizable context, we meta-analyzed the surveys to determine a best estimate of the overall prevalence of issues. we included 37 qualitative studies and 47 studies using a quantitative methodology (surveys). seventy-two studies (35 qualitative) were conducted in developed nations, while the remaining 12 (two qualitative) were conducted in developing nations. important barriers reported in both economic settings included fear of disclosure, concomitant substance abuse, forgetfulness, suspicions of treatment, regimens that are too complicated, number of pills required, decreased quality of life, work and family responsibilities, falling asleep, and access to medication. important facilitators reported by patients in developed nation settings included having a sense of self-worth, seeing positive effects of antiretrovirals, accepting their seropositivity, understanding the need for strict adherence, making use of reminder tools, and having a simple regimen. among 37 separate meta-analyses examining the generalizability of these findings, we found large heterogeneity. conclusions we found that important barriers to adherence are consistent across multiple settings and countries. research is urgently needed to determine patient-important factors for adherence in developing world settings. clinicians should use this information to engage in open discussion with patients to promote adherence and identify barriers and facilitators within their own populations.",0
"molecular machine learning has been maturing rapidly over the last few years. improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. however, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. this work introduces moleculenet, a large scale benchmark for molecular machine learning. moleculenet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the deepchem open source library). moleculenet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. however, this result comes with caveats. learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. for quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.",0
"the human metabolome database (hmdb) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. it contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. in addition to its comprehensive literature-derived data, the hmdb also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (ms) and nuclear magnetic resonance (nmr) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. this is further supplemented with thousands of nmr and ms spectra collected on purified, reference metabolites. each metabolite entry in the hmdb contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference nmr and ms spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, snp and mutation data as well as extensive links to images, references and other public databases. extensive searching, relational querying and data browsing tools are also provided. the hmdb is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. the hmdb is available at:",0
"the question of whether tumorigenic cancer stem cells exist in human melanomas has arisen in the last few years. here we show that in melanomas, tumour stem cells (mtscs, for melanoma tumour stem cells) can be isolated prospectively as a highly enriched cd271(+) mtsc population using a process that maximizes viable cell transplantation. the tumours sampled in this study were taken from a broad spectrum of sites and stages. high-viability cells isolated by fluorescence-activated cell sorting and re-suspended in a matrigel vehicle were implanted into t-, b- and natural-killer-deficient rag2(-/-)gammac(-/-) mice. the cd271(+) subset of cells was the tumour-initiating population in 90% (nine out of ten) of melanomas tested. transplantation of isolated cd271(+) melanoma cells into engrafted human skin or bone in rag2(-/-)gammac(-/-) mice resulted in melanoma; however, melanoma did not develop after transplantation of isolated cd271(-) cells. we also show that in mice, tumours derived from transplanted human cd271(+) melanoma cells were capable of metastatsis in vivo. cd271(+) melanoma cells lacked expression of tyr, mart1 and mage in 86%, 69% and 68% of melanoma patients, respectively, which helps to explain why t-cell therapies directed at these antigens usually result in only temporary tumour shrinkage.",0
"the mechanisms of localization and retention of membrane proteins in the inner nuclear membrane and the fate of this membrane system during mitosis were studied in living cells using the inner nuclear membrane protein, lamin b receptor, fused to green fluorescent protein (lbr-gfp). photobleaching techniques revealed the majority of lbr-gfp to be completely immobilized in the nuclear envelope (ne) of interphase cells, suggesting a tight binding to heterochromatin and/or lamins. a subpopulation of lbr-gfp within er membranes, by contrast, was entirely mobile and diffused rapidly and freely (d = 0. 41 +/- 0.1 microm2/s). high resolution confocal time-lapse imaging in mitotic cells revealed lbr-gfp redistributing into the interconnected er membrane system in prometaphase, exhibiting the same high mobility and diffusion constant as observed in interphase er membranes. lbr-gfp rapidly diffused across the cell within the membrane network defined by the er, suggesting the integrity of the er was maintained in mitosis, with little or no fragmentation and vesiculation. at the end of mitosis, nuclear membrane reformation coincided with immobilization of lbr-gfp in er elements at contact sites with chromatin. lbr-gfp-containing er membranes then wrapped around chromatin over the course of 2-3 min, quickly and efficiently compartmentalizing nuclear material. expansion of the ne followed over the course of 30-80 min. thus, selective changes in lateral mobility of lbr-gfp within the er/ne membrane system form the basis for its localization to the inner nuclear membrane during interphase. such changes, rather than vesiculation mechanisms, also underlie the redistribution of this molecule during ne disassembly and reformation in mitosis.",0
"the heterotrimeric amp-activated protein kinase (ampk) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular atp levels it activates energy-producing pathways and inhibits energy-consuming processes. ampk has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. ampk is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain: amp binding to the γ-regulatory domain promotes phosphorylation by the upstream kinase, protects the enzyme against dephosphorylation, as well as causing allosteric activation. here we show that adp binding to just one of the two exchangeable axp (amp/adp/atp) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. our studies show that active mammalian ampk displays significantly tighter binding to adp than to mg-atp, explaining how the enzyme is regulated under physiological conditions where the concentration of mg-atp is higher than that of adp and much higher than that of amp. we have determined the crystal structure of an active ampk complex. the structure shows how the activation loop of the kinase domain is stabilized by the regulatory domain and how the kinase linker region interacts with the regulatory nucleotide-binding site that mediates protection against dephosphorylation. from our biochemical and structural data we develop a model for how the energy status of a cell regulates ampk activity.",0
"background and aims alcohol use is a major contributor to injuries, mortality and the burden of disease. this review updates knowledge on risk relations between dimensions of alcohol use and health outcomes to be used in global and national comparative risk assessments (cras). methods systematic review of reviews and meta-analyses on alcohol consumption and health outcomes attributable to alcohol use. for dimensions of exposure: volume of alcohol use, blood alcohol concentration and patterns of drinking, in particular heavy drinking occasions were studied. for liver cirrhosis, quality of alcohol was additionally considered. for all outcomes (mortality and/or morbidity): cause of death and disease/injury categories based on international classification of diseases (icd) codes used in global cras; harm to others. results in total, 255 reviews and meta-analyses were identified. alcohol use was found to be linked causally to many disease and injury categories, with more than 40 icd-10 three-digit categories being fully attributable to alcohol. most partially attributable disease categories showed monotonic relationships with volume of alcohol use: the more alcohol consumed, the higher the risk of disease or death. exceptions were ischaemic diseases and diabetes, with curvilinear relationships, and with beneficial effects of light to moderate drinking in people without heavy irregular drinking occasions. biological pathways suggest an impact of heavy drinking occasions on additional diseases; however, the lack of medical epidemiological studies measuring this dimension of alcohol use precluded an in-depth analysis. for injuries, except suicide, blood alcohol concentration was the most important dimension of alcohol use. alcohol use caused marked harm to others, which has not yet been researched sufficiently. conclusions research since 2010 confirms the importance of alcohol use as a risk factor for disease and injuries; for some health outcomes, more than one dimension of use needs to be considered. epidemiological studies should include measurement of heavy drinking occasions in line with biological knowledge.",0
"obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. to identify genetic loci for obesity susceptibility, we examined associations between body mass index and ∼ 2.8 million snps in up to 123,865 individuals with targeted follow up of 42 snps in up to 125,931 additional individuals. we confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (p < 5 × 10⁻⁸), one of which includes a copy number variant near gprc5b. some loci (at mc4r, pomc, sh2b1 and bdnf) map near key hypothalamic regulators of energy balance, and one of these loci is near gipr, an incretin receptor. furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.",0
"background in recent years, a growing number of methods for synthesising qualitative research have emerged, particularly in relation to health-related research. there is a need for both researchers and commissioners to be able to distinguish between these methods and to select which method is the most appropriate to their situation. discussion a number of methodological and conceptual links between these methods were identified and explored, while contrasting epistemological positions explained differences in approaches to issues such as quality assessment and extent of iteration. methods broadly fall into 'realist' or 'idealist' epistemologies, which partly accounts for these differences. summary methods for qualitative synthesis vary across a range of dimensions. commissioners of qualitative syntheses might wish to consider the kind of product they want and select their method - or type of method - accordingly.",0
"purpose systematic reviews of patient-reported outcome measures (proms) differ from reviews of interventions and diagnostic test accuracy studies and are complex. in fact, conducting a review of one or more proms comprises of multiple reviews (i.e., one review for each measurement property of each prom). in the absence of guidance specifically designed for reviews on measurement properties, our aim was to develop a guideline for conducting systematic reviews of proms. methods based on literature reviews and expert opinions, and in concordance with existing guidelines, the consensus-based standards for the selection of health measurement instruments (cosmin) steering committee developed a guideline for systematic reviews of proms. results a consecutive ten-step procedure for conducting a systematic review of proms is proposed. steps 1-4 concern preparing and performing the literature search, and selecting relevant studies. steps 5-8 concern the evaluation of the quality of the eligible studies, the measurement properties, and the interpretability and feasibility aspects. steps 9 and 10 concern formulating recommendations and reporting the systematic review. conclusions the cosmin guideline for systematic reviews of proms includes methodology to combine the methodological quality of studies on measurement properties with the quality of the prom itself (i.e., its measurement properties). this enables reviewers to draw transparent conclusions and making evidence-based recommendations on the quality of proms, and supports the evidence-based selection of proms for use in research and in clinical practice.",0
"background intimate partner violence (ipv) against women is a global public health and human rights concern. despite a growing body of research into risk factors for ipv, methodological differences limit the extent to which comparisons can be made between studies. we used data from ten countries included in the who multi-country study on women's health and domestic violence to identify factors that are consistently associated with abuse across sites, in order to inform the design of ipv prevention programs. methods standardised population-based household surveys were done between 2000 and 2003. one woman aged 15-49 years was randomly selected from each sampled household. those who had ever had a male partner were asked about their experiences of physically and sexually violent acts. we performed multivariate logistic regression to identify predictors of physical and/or sexual partner violence within the past 12 months. results despite wide variations in the prevalence of ipv, many factors affected ipv risk similarly across sites. secondary education, high ses, and formal marriage offered protection, while alcohol abuse, cohabitation, young age, attitudes supportive of wife beating, having outside sexual partners, experiencing childhood abuse, growing up with domestic violence, and experiencing or perpetrating other forms of violence in adulthood, increased the risk of ipv. the strength of the association was greatest when both the woman and her partner had the risk factor. conclusions ipv prevention programs should increase focus on transforming gender norms and attitudes, addressing childhood abuse, and reducing harmful drinking. development initiatives to improve access to education for girls and boys may also have an important role in violence prevention.",0
"the heart failure syndrome has first been described as an emerging epidemic about 25 years ago. today, because of a growing and ageing population, the total number of heart failure patients still continues to rise. however, the case mix of heart failure seems to be evolving. incidence has stabilized and may even be decreasing in some populations, but alarming opposite trends have been observed in the relatively young, possibly related to an increase in obesity. in addition, a clear transition towards heart failure with a preserved ejection fraction has occurred. although this transition is partially artificial, due to improved recognition of heart failure as a disorder affecting the entire left ventricular ejection fraction spectrum, links can be made with the growing burden of obesity-related diseases and with the ageing of the population. similarly, evidence suggests that the number of patients with heart failure may be on the rise in low-income countries struggling under the double burden of communicable diseases and conditions associated with a western-type lifestyle. these findings, together with the observation that the mortality rate of heart failure is declining less rapidly than previously, indicate we have not reached the end of the epidemic yet. in this review, the evolving epidemiology of heart failure is put into perspective, to discern major trends and project future directions.",0
"in this study, a dataset of x-ray images from patients with common bacterial pneumonia, confirmed covid-19 disease, and normal incidents, was utilized for the automatic detection of the coronavirus disease. the aim of the study is to evaluate the performance of state-of-the-art convolutional neural network architectures proposed over the recent years for medical image classification. specifically, the procedure called transfer learning was adopted. with transfer learning, the detection of various abnormalities in small medical image datasets is an achievable target, often yielding remarkable results. the datasets utilized in this experiment are two. firstly, a collection of 1427 x-ray images including 224 images with confirmed covid-19 disease, 700 images with confirmed common bacterial pneumonia, and 504 images of normal conditions. secondly, a dataset including 224 images with confirmed covid-19 disease, 714 images with confirmed bacterial and viral pneumonia, and 504 images of normal conditions. the data was collected from the available x-ray images on public medical repositories. the results suggest that deep learning with x-ray imaging may extract significant biomarkers related to the covid-19 disease, while the best accuracy, sensitivity, and specificity obtained is 96.78%, 98.66%, and 96.46% respectively. since by now, all diagnostic tests show failure rates such as to raise concerns, the probability of incorporating x-rays into the diagnosis of the disease could be assessed by the medical community, based on the findings, while more research to evaluate the x-ray approach from different aspects may be conducted.",0
"we report that the actin assembly inhibitor latrunculin-a (lat-a) causes complete disruption of the yeast actin cytoskeleton within 2-5 min, suggesting that although yeast are nonmotile, their actin filaments undergo rapid cycles of assembly and disassembly in vivo. differences in the lat-a sensitivities of strains carrying mutations in components of the actin cytoskeleton suggest that tropomyosin, fimbrin, capping protein, sla2p, and srv2p act to increase actin cytoskeleton stability, while end3p and sla1p act to decrease stability. identification of three lat-a resistant actin mutants demonstrated that in vivo effects of lat-a are due specifically to impairment of actin function and implicated a region on the three-dimensional actin structure as the lat-a binding site. lat-a was used to determine which of 19 different proteins implicated in cell polarity development require actin to achieve polarized localization. results show that at least two molecular pathways, one actin-dependent and the other actin-independent, underlie polarity development. the actin-dependent pathway localizes secretory vesicles and a putative vesicle docking complex to sites of cell surface growth, providing an explanation for the dependence of polarized cell surface growth on actin function. unexpectedly, several proteins that function with actin during cell polarity development, including an unconventional myosin (myo2p), calmodulin, and an actin-interacting protein (bud6/aip3p), achieved polarized localization by an actin-independent pathway, revealing interdependence among cell polarity pathways. finally, transient actin depolymerization caused many cells to abandon one bud site or mating projection and to initiate growth at a second site. thus, actin filaments are also required for maintenance of an axis of cell polarity.",0
"acute respiratory failure and a systemic coagulopathy are critical aspects of the morbidity and mortality characterizing infection with severe acute respiratory distress syndrome-associated coronavirus-2, the etiologic agent of coronavirus disease 2019 (covid-19). we examined skin and lung tissues from 5 patients with severe covid-19 characterized by respiratory failure (n= 5) and purpuric skin rash (n = 3). covid-19 pneumonitis was predominantly a pauci-inflammatory septal capillary injury with significant septal capillary mural and luminal fibrin deposition and permeation of the interalveolar septa by neutrophils. no viral cytopathic changes were observed and the diffuse alveolar damage (dad) with hyaline membranes, inflammation, and type ii pneumocyte hyperplasia, hallmarks of classic acute respiratory distress syndrome, were not prominent. these pulmonary findings were accompanied by significant deposits of terminal complement components c5b-9 (membrane attack complex), c4d, and mannose binding lectin (mbl)-associated serine protease (masp)2, in the microvasculature, consistent with sustained, systemic activation of the complement pathways. the purpuric skin lesions similarly showed a pauci-inflammatory thrombogenic vasculopathy, with deposition of c5b-9 and c4d in both grossly involved and normally-appearing skin. in addition, there was co-localization of covid-19 spike glycoproteins with c4d and c5b-9 in the interalveolar septa and the cutaneous microvasculature of 2 cases examined. in conclusion, at least a subset of sustained, severe covid-19 may define a type of catastrophic microvascular injury syndrome mediated by activation of complement pathways and an associated procoagulant state. it provides a foundation for further exploration of the pathophysiologic importance of complement in covid-19, and could suggest targets for specific intervention.",0
"the dna sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. we report the optimization of circular consensus sequencing (ccs) to improve the accuracy of single-molecule real-time (smrt) sequencing (pacbio) and generate highly accurate (99.8%) long high-fidelity (hifi) reads with an average length of 13.5 kilobases (kb). we applied our approach to sequence the well-characterized human hg002/na24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (snvs), 95.98% for insertions and deletions 15 megabases (mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.",0
"meta-analyses are typically used to estimate the overall/mean of an outcome of interest. however, inference about between-study variability, which is typically modelled using a between-study variance parameter, is usually an additional aim. the dersimonian and laird method, currently widely used by default to estimate the between-study variance, has been long challenged. our aim is to identify known methods for estimation of the between-study variance and its corresponding uncertainty, and to summarise the simulation and empirical evidence that compares them. we identified 16 estimators for the between-study variance, seven methods to calculate confidence intervals, and several comparative studies. simulation studies suggest that for both dichotomous and continuous data the estimator proposed by paule and mandel and for continuous data the restricted maximum likelihood estimator are better alternatives to estimate the between-study variance. based on the scenarios and results presented in the published studies, we recommend the q-profile method and the alternative approach based on a 'generalised cochran between-study variance statistic' to compute corresponding confidence intervals around the resulting estimates. our recommendations are based on a qualitative evaluation of the existing literature and expert consensus. evidence-based recommendations require an extensive simulation study where all methods would be compared under the same scenarios.",0
"in the central nervous system, ageing results in a precipitous decline in adult neural stem/progenitor cells and neurogenesis, with concomitant impairments in cognitive functions. interestingly, such impairments can be ameliorated through systemic perturbations such as exercise. here, using heterochronic parabiosis we show that blood-borne factors present in the systemic milieu can inhibit or promote adult neurogenesis in an age-dependent fashion in mice. accordingly, exposing a young mouse to an old systemic environment or to plasma from old mice decreased synaptic plasticity, and impaired contextual fear conditioning and spatial learning and memory. we identify chemokines--including ccl11 (also known as eotaxin)--the plasma levels of which correlate with reduced neurogenesis in heterochronic parabionts and aged mice, and the levels of which are increased in the plasma and cerebrospinal fluid of healthy ageing humans. lastly, increasing peripheral ccl11 chemokine levels in vivo in young mice decreased adult neurogenesis and impaired learning and memory. together our data indicate that the decline in neurogenesis and cognitive impairments observed during ageing can be in part attributed to changes in blood-borne factors.",0
"a clear-cut serological differentiation between akr lymphocytes of thymic and non-thymic origin is reported: these two cell types are antigenically distinct. in newborn mice, the akr thymic antigen was found at a high concentration only in thymus. in adult mice, the antigen was present at a high level in thymus, all nervous tissues tested, and some leukemias. it was present at much lower levels in lymph node lymphocytes, splenic lymphocytes, appendix, lung, and certain other leukemias, which appeared to be of non-thymic origin. the akr thymic antigen was present at a high level in thymus and nervous tissues of rf mice, but was absent from thymocytes of sixteen other mouse strains. these sixteen strains possessed the c3heb/fe thymic antigen. the distribution of this antigen in neonatal and adult tissues of the strains tested was similar to that of the akr thymic antigen in akr mice. no exceptions were found. these results were obtained by use of immune cytolysis, and of a new method for the quantitative treatment of data from absorption experiments.",0
"background covid-19 has the potential to cause substantial disruptions to health services, due to cases overburdening the health system or response measures limiting usual programmatic activities. we aimed to quantify the extent to which disruptions to services for hiv, tuberculosis, and malaria in low-income and middle-income countries with high burdens of these diseases could lead to additional loss of life over the next 5 years. methods assuming a basic reproduction number of 3·0, we constructed four scenarios for possible responses to the covid-19 pandemic: no action, mitigation for 6 months, suppression for 2 months, or suppression for 1 year. we used established transmission models of hiv, tuberculosis, and malaria to estimate the additional impact on health that could be caused in selected settings, either due to covid-19 interventions limiting activities, or due to the high demand on the health system due to the covid-19 pandemic. findings in high-burden settings, deaths due to hiv, tuberculosis, and malaria over 5 years could increase by up to 10%, 20%, and 36%, respectively, compared with if there was no covid-19 pandemic. the greatest impact on hiv was estimated to be from interruption to antiretroviral therapy, which could occur during a period of high health system demand. for tuberculosis, the greatest impact would be from reductions in timely diagnosis and treatment of new cases, which could result from any prolonged period of covid-19 suppression interventions. the greatest impact on malaria burden could be as a result of interruption of planned net campaigns. these disruptions could lead to a loss of life-years over 5 years that is of the same order of magnitude as the direct impact from covid-19 in places with a high burden of malaria and large hiv and tuberculosis epidemics. interpretation maintaining the most critical prevention activities and health-care services for hiv, tuberculosis, and malaria could substantially reduce the overall impact of the covid-19 pandemic. funding bill & melinda gates foundation, wellcome trust, uk department for international development, and medical research council.",0
"prenatal phthalate exposure impairs testicular function and shortens anogenital distance (agd) in male rodents. we present data from the first study to examine agd and other genital measurements in relation to prenatal phthalate exposure in humans. a standardized measure of agd was obtained in 134 boys 2-36 months of age. agd was significantly correlated with penile volume (r = 0.27, p = 0.001) and the proportion of boys with incomplete testicular descent (r = 0.20, p = 0.02). we defined the anogenital index (agi) as agd divided by weight at examination and calculated the age-adjusted agi by regression analysis. we examined nine phthalate monoester metabolites, measured in prenatal urine samples, as predictors of age-adjusted agi in regression and categorical analyses that included all participants with prenatal urine samples (n = 85). urinary concentrations of four phthalate metabolites were inversely related to agi. after adjusting for age at examination, p-values for regression coefficients ranged from 0.007 to 0.097. comparing boys with prenatal mbp concentration in the highest quartile with those in the lowest quartile, the odds ratio for a shorter than expected agi was 10.2 (95% confidence interval, 2.5 to 42.2). the corresponding odds ratios for mep, mbzp, and mibp were 4.7, 3.8, and 9.1, respectively (all p-values < 0.05). we defined a summary phthalate score to quantify joint exposure to these four phthalate metabolites. the age-adjusted agi decreased significantly with increasing phthalate score (p-value for slope = 0.009). the associations between male genital development and phthalate exposure seen here are consistent with the phthalate-related syndrome of incomplete virilization that has been reported in prenatally exposed rodents. the median concentrations of phthalate metabolites that are associated with short agi and incomplete testicular descent are below those found in one-quarter of the female population of the united states, based on a nationwide sample. these data support the hypothesis that prenatal phthalate exposure at environmental levels can adversely affect male reproductive development in humans.",0
"natural extracellular matrices (ecms) are viscoelastic and exhibit stress relaxation. however, hydrogels used as synthetic ecms for three-dimensional (3d) culture are typically elastic. here, we report a materials approach to tune the rate of stress relaxation of hydrogels for 3d culture, independently of the hydrogel's initial elastic modulus, degradation, and cell-adhesion-ligand density. we find that cell spreading, proliferation, and osteogenic differentiation of mesenchymal stem cells (mscs) are all enhanced in cells cultured in gels with faster relaxation. strikingly, mscs form a mineralized, collagen-1-rich matrix similar to bone in rapidly relaxing hydrogels with an initial elastic modulus of 17 kpa. we also show that the effects of stress relaxation are mediated by adhesion-ligand binding, actomyosin contractility and mechanical clustering of adhesion ligands. our findings highlight stress relaxation as a key characteristic of cell-ecm interactions and as an important design parameter of biomaterials for cell culture.",0
"to maintain immune homeostasis, the intestinal immune system has evolved redundant regulatory strategies. in this regard, the gut is home to a large number of regulatory t (t reg) cells, including the foxp3(+) t reg cell. therefore, we hypothesized that the gut environment preferentially supports extrathymic t reg cell development. we show that peripheral conversion of cd4(+) t cells to t reg cells occurs primarily in gut-associated lymphoid tissue (galt) after oral exposure to antigen and in a lymphopenic environment. dendritic cells (dcs) purified from the lamina propria (lp; lpdcs) of the small intestine were found to promote a high level of t reg cell conversion relative to lymphoid organ-derived dcs. this enhanced conversion by lpdcs was dependent on tgf-beta and retinoic acid (ra), which is a vitamin a metabolite highly expressed in galt. together, these data demonstrate that the intestinal immune system has evolved a self-contained strategy to promote t reg cell neoconversion.",0
"genetic association studies have identified 215 risk loci for inflammatory bowel disease, thereby uncovering fundamental aspects of its molecular biology. we performed a genome-wide association study of 25,305 individuals and conducted a meta-analysis with published summary statistics, yielding a total sample size of 59,957 subjects. we identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease. the associated variants are correlated with expression changes in response to immune stimulus at two of these genes (itga4 and itgb8) and at previously implicated loci (itgal and icam1). in all four cases, the expression-increasing allele also increases disease risk. we also identified likely causal missense variants in a gene implicated in primary immune deficiency, plcg2, and a negative regulator of inflammation, slamf8. our results demonstrate that new associations at common variants continue to identify genes relevant to therapeutic target identification and prioritization.",0
"background network meta-analysis is used to compare three or more treatments for the same condition. within a bayesian framework, for each treatment the probability of being best, or, more general, the probability that it has a certain rank can be derived from the posterior distributions of all treatments. the treatments can then be ranked by the surface under the cumulative ranking curve (sucra). for comparing treatments in a network meta-analysis, we propose a frequentist analogue to sucra which we call p-score that works without resampling. methods p-scores are based solely on the point estimates and standard errors of the frequentist network meta-analysis estimates under normality assumption and can easily be calculated as means of one-sided p-values. they measure the mean extent of certainty that a treatment is better than the competing treatments. results using case studies of network meta-analysis in diabetes and depression, we demonstrate that the numerical values of sucra and p-score are nearly identical. conclusions ranking treatments in frequentist network meta-analysis works without resampling. like the sucra values, p-scores induce a ranking of all treatments that mostly follows that of the point estimates, but takes precision into account. however, neither sucra nor p-score offer a major advantage compared to looking at credible or confidence intervals.",0
"hku1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic sars and mers betacoronaviruses, which have high fatality rates and pandemic potential. cell tropism and host range is determined in part by the coronavirus spike (s) protein, which binds cellular receptors and mediates membrane fusion. as the largest known class i fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. here we present the 4.0 å resolution structure of the trimeric hku1 s protein determined using single-particle cryo-electron microscopy. in the pre-fusion conformation, the receptor-binding subunits, s1, rest above the fusion-mediating subunits, s2, preventing their conformational rearrangement. surprisingly, the s1 c-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. these features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive s protein destabilization through receptor binding and proteolytic cleavage. these studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens.",0
"background multiple major health organisations recommend the use of extracorporeal membrane oxygenation (ecmo) support for covid-19-related acute hypoxaemic respiratory failure. however, initial reports of ecmo use in patients with covid-19 described very high mortality and there have been no large, international cohort studies of ecmo for covid-19 reported to date. methods we used data from the extracorporeal life support organization (elso) registry to characterise the epidemiology, hospital course, and outcomes of patients aged 16 years or older with confirmed covid-19 who had ecmo support initiated between jan 16 and may 1, 2020, at 213 hospitals in 36 countries. the primary outcome was in-hospital death in a time-to-event analysis assessed at 90 days after ecmo initiation. we applied a multivariable cox model to examine whether patient and hospital factors were associated with in-hospital mortality. findings data for 1035 patients with covid-19 who received ecmo support were included in this study. of these, 67 (6%) remained hospitalised, 311 (30%) were discharged home or to an acute rehabilitation centre, 101 (10%) were discharged to a long-term acute care centre or unspecified location, 176 (17%) were discharged to another hospital, and 380 (37%) died. the estimated cumulative incidence of in-hospital mortality 90 days after the initiation of ecmo was 37·4% (95% ci 34·4-40·4). mortality was 39% (380 of 968) in patients with a final disposition of death or hospital discharge. the use of ecmo for circulatory support was independently associated with higher in-hospital mortality (hazard ratio 1·89, 95% ci 1·20-2·97). in the subset of patients with covid-19 receiving respiratory (venovenous) ecmo and characterised as having acute respiratory distress syndrome, the estimated cumulative incidence of in-hospital mortality 90 days after the initiation of ecmo was 38·0% (95% ci 34·6-41·5). interpretation in patients with covid-19 who received ecmo, both estimated mortality 90 days after ecmo and mortality in those with a final disposition of death or discharge were less than 40%. these data from 213 hospitals worldwide provide a generalisable estimate of ecmo mortality in the setting of covid-19. funding none.",0
"drug development has a high attrition rate, with poor pharmacokinetic and safety properties a significant hurdle. computational approaches may help minimize these risks. we have developed a novel approach (pkcsm) which uses graph-based signatures to develop predictive models of central admet properties for drug development. pkcsm performs as well or better than current methods. a freely accessible web server ( which retains no information submitted to it, provides an integrated platform to rapidly evaluate pharmacokinetic and toxicity properties.",0
"alpha-band oscillations are the dominant oscillations in the human brain and recent evidence suggests that they have an inhibitory function. nonetheless, there is little doubt that alpha-band oscillations also play an active role in information processing. in this article, i suggest that alpha-band oscillations have two roles (inhibition and timing) that are closely linked to two fundamental functions of attention (suppression and selection), which enable controlled knowledge access and semantic orientation (the ability to be consciously oriented in time, space, and context). as such, alpha-band oscillations reflect one of the most basic cognitive processes and can also be shown to play a key role in the coalescence of brain activity in different frequencies.",0
"bindingdb ( is a publicly accessible database currently containing approximately 20,000 experimentally determined binding affinities of protein-ligand complexes, for 110 protein targets including isoforms and mutational variants, and approximately 11,000 small molecule ligands. the data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the protein data bank. the bindingdb website supports a range of query types, including searches by chemical structure, substructure and similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. data sets generated by bindingdb queries can be downloaded in the form of annotated sdfiles for further analysis, or used as the basis for virtual screening of a compound database uploaded by the user. the data in bindingdb are linked both to structural data in the pdb via pdb ids and chemical and sequence searches, and to the literature in pubmed via pubmed ids.",0
"diffusion mri tractography has emerged as a useful and popular tool for mapping connections between brain regions. in this study, we examined the performance of quantitative anisotropy (qa) in facilitating deterministic fiber tracking. two phantom studies were conducted. the first phantom study examined the susceptibility of fractional anisotropy (fa), generalized factional anisotropy (gfa), and qa to various partial volume effects. the second phantom study examined the spatial resolution of the fa-aided, gfa-aided, and qa-aided tractographies. an in vivo study was conducted to track the arcuate fasciculus, and two neurosurgeons blind to the acquisition and analysis settings were invited to identify false tracks. the performance of qa in assisting fiber tracking was compared with fa, gfa, and anatomical information from t1-weighted images. our first phantom study showed that qa is less sensitive to the partial volume effects of crossing fibers and free water, suggesting that it is a robust index. the second phantom study showed that the qa-aided tractography has better resolution than the fa-aided and gfa-aided tractography. our in vivo study further showed that the qa-aided tractography outperforms the fa-aided, gfa-aided, and anatomy-aided tractographies. in the shell scheme (hardi), the fa-aided, gfa-aided, and anatomy-aided tractographies have 30.7%, 32.6%, and 24.45% of the false tracks, respectively, while the qa-aided tractography has 16.2%. in the grid scheme (dsi), the fa-aided, gfa-aided, and anatomy-aided tractographies have 12.3%, 9.0%, and 10.93% of the false tracks, respectively, while the qa-aided tractography has 4.43%. the qa-aided deterministic fiber tracking may assist fiber tracking studies and facilitate the advancement of human connectomics.",0
"hepatitis b virus (hbv) is a noncytopathic virus, and the recognition of infected hepatocytes by hbv-specific cd8 cells has been assumed to be the central mechanism causing both liver damage and virus control. to understand the role of cytotoxic t cells in the pathogenesis of hbv infection, we used functional assays that require t cell expansion in vitro and human histocompatibility leukocyte antigen (hla)-peptide tetramers that allow direct ex vivo quantification of circulating and liver-infiltrating hbv-specific cd8 cells. two groups of patients with persistent hbv infection were studied: one without liver inflammation and hbv replication, the other with liver inflammation and a high level of hbv replication. contrary to expectation, a high frequency of intrahepatic hbv-specific cd8 cells was found in the absence of hepatic immunopathology. in contrast, virus-specific t cells were more diluted among liver infiltrates in viremic patients, but their absolute number was similar because of the massive cellular infiltration. furthermore, inhibition of hbv replication was associated with the presence of a circulating reservoir of cd8(+) cells able to expand after specific virus recognition that was not detectable in highly viremic patients with liver inflammation. these results show that in the presence of an effective hbv-specific cd8 response, inhibition of virus replication can be independent of liver damage. when the hbv-specific cd8 response is unable to control virus replication, it may contribute to liver pathology not only directly but by causing the recruitment of nonvirus-specific t cells.",0
"during the last three decades, the impact of chemical pollution has focused almost exclusively on the conventional ""priority"" pollutants, especially those acutely toxic/carcinogenic pesticides and industrial intermediates displaying persistence in the environment. this spectrum of chemicals, however, is only one piece of the larger puzzle in ""holistic"" risk assessment. another diverse group of bioactive chemicals receiving comparatively little attention as potential environmental pollutants includes the pharmaceuticals and active ingredients in personal care products (in this review collectively termed ppcps), both human and veterinary, including not just prescription drugs and biologics, but also diagnostic agents, ""nutraceuticals,"" fragrances, sun-screen agents, and numerous others. these compounds and their bioactive metabolites can be continually introduced to the aquatic environment as complex mixtures via a number of routes but primarily by both untreated and treated sewage. aquatic pollution is particularly troublesome because aquatic organisms are captive to continual life-cycle, multigenerational exposure. the possibility for continual but undetectable or unnoticed effects on aquatic organisms is particularly worrisome because effects could accumulate so slowly that major change goes undetected until the cumulative level of these effects finally cascades to irreversible change--change that would otherwise be attributed to natural adaptation or ecologic succession. as opposed to the conventional, persistent priority pollutants, ppcps need not be persistent if they are continually introduced to surface waters, even at low parts-per-trillion/parts-per-billion concentrations (ng-microg/l). even though some ppcps are extremely persistent and introduced to the environment in very high quantities and perhaps have already gained ubiquity worldwide, others could act as if they were persistent, simply because their continual infusion into the aquatic environment serves to sustain perpetual life-cycle exposures for aquatic organisms. this review attempts to synthesize the literature on environmental origin, distribution/occurrence, and effects and to catalyze a more focused discussion in the environmental science community.",0
"systemic anticancer chemotherapy is immunosuppressive and mostly induces nonimmunogenic tumor cell death. here, we show that even in the absence of any adjuvant, tumor cells dying in response to anthracyclins can elicit an effective antitumor immune response that suppresses the growth of inoculated tumors or leads to the regression of established neoplasia. although both antracyclins and mitomycin c induced apoptosis with caspase activation, only anthracyclin-induced immunogenic cell death was immunogenic. caspase inhibition by z-vad-fmk or transfection with the baculovirus inhibitor p35 did not inhibit doxorubicin (dx)-induced cell death, yet suppressed the immunogenicity of dying tumor cells in several rodent models of neoplasia. depletion of dendritic cells (dcs) or cd8+t cells abolished the immune response against dx-treated apoptotic tumor cells in vivo. caspase inhibition suppressed the capacity of dx-killed cells to be phagocytosed by dcs, yet had no effect on their capacity to elicit dc maturation. freshly excised tumors became immunogenic upon dx treatment in vitro, and intratumoral inoculation of dx could trigger the regression of established tumors in immunocompetent mice. these results delineate a procedure for the generation of cancer vaccines and the stimulation of anti-neoplastic immune responses in vivo.",0
"malignant transformation, driven by gain-of-function mutations in oncogenes and loss-of-function mutations in tumour suppressor genes, results in cell deregulation that is frequently associated with enhanced cellular stress (for example, oxidative, replicative, metabolic and proteotoxic stress, and dna damage). adaptation to this stress phenotype is required for cancer cells to survive, and consequently cancer cells may become dependent upon non-oncogenes that do not ordinarily perform such a vital function in normal cells. thus, targeting these non-oncogene dependencies in the context of a transformed genotype may result in a synthetic lethal interaction and the selective death of cancer cells. here we used a cell-based small-molecule screening and quantitative proteomics approach that resulted in the unbiased identification of a small molecule that selectively kills cancer cells but not normal cells. piperlongumine increases the level of reactive oxygen species (ros) and apoptotic cell death in both cancer cells and normal cells engineered to have a cancer genotype, irrespective of p53 status, but it has little effect on either rapidly or slowly dividing primary normal cells. significant antitumour effects are observed in piperlongumine-treated mouse xenograft tumour models, with no apparent toxicity in normal mice. moreover, piperlongumine potently inhibits the growth of spontaneously formed malignant breast tumours and their associated metastases in mice. our results demonstrate the ability of a small molecule to induce apoptosis selectively in cells that have a cancer genotype, by targeting a non-oncogene co-dependency acquired through the expression of the cancer genotype in response to transformation-induced oxidative stress.",0
"background there is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (ngs) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. soapdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. findings to overcome these challenges, we have developed its successor, soapdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. conclusions benchmark using the assemblathon1 and gage datasets showed that soapdenovo2 greatly surpasses its predecessor soapdenovo and is competitive to other assemblers on both assembly length and accuracy. we also provide an updated assembly version of the 2008 asian (yh) genome using soapdenovo2. here, the contig and scaffold n50 of the yh genome were ~20.9 kbp and ~22 mbp, respectively, which is 3-fold and 50-fold longer than the first published version. the genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.",0
"the alphafold protein structure database (alphafold db, is an openly accessible, extensive database of high-accuracy protein-structure predictions. powered by alphafold v2.0 of deepmind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. alphafold db provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. the initial release of alphafold db contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the uniref90 data set.",0
"background the associations of blood pressure with the different manifestations of incident cardiovascular disease in a contemporary population have not been compared. in this study, we aimed to analyse the associations of blood pressure with 12 different presentations of cardiovascular disease. methods we used linked electronic health records from 1997 to 2010 in the caliber (cardiovascular research using linked bespoke studies and electronic health records) programme to assemble a cohort of 1·25 million patients, 30 years of age or older and initially free from cardiovascular disease, a fifth of whom received blood pressure-lowering treatments. we studied the heterogeneity in the age-specific associations of clinically measured blood pressure with 12 acute and chronic cardiovascular diseases, and estimated the lifetime risks (up to 95 years of age) and cardiovascular disease-free life-years lost adjusted for other risk factors at index ages 30, 60, and 80 years. this study is registered at clinicaltrials.gov, number nct01164371. findings during 5·2 years median follow-up, we recorded 83,098 initial cardiovascular disease presentations. in each age group, the lowest risk for cardiovascular disease was in people with systolic blood pressure of 90-114 mm hg and diastolic blood pressure of 60-74 mm hg, with no evidence of a j-shaped increased risk at lower blood pressures. the effect of high blood pressure varied by cardiovascular disease endpoint, from strongly positive to no effect. associations with high systolic blood pressure were strongest for intracerebral haemorrhage (hazard ratio 1·44 ), subarachnoid haemorrhage (1·43 ), and stable angina (1·41 ), and weakest for abdominal aortic aneurysm (1·08 ). compared with diastolic blood pressure, raised systolic blood pressure had a greater effect on angina, myocardial infarction, and peripheral arterial disease, whereas raised diastolic blood pressure had a greater effect on abdominal aortic aneurysm than did raised systolic pressure. pulse pressure associations were inverse for abdominal aortic aneurysm (hr per 10 mm hg 0·91 ) and strongest for peripheral arterial disease (1·23 ). people with hypertension (blood pressure ≥140/90 mm hg or those receiving blood pressure-lowering drugs) had a lifetime risk of overall cardiovascular disease at 30 years of age of 63·3% (95% ci 62·9-63·8) compared with 46·1% (45·5-46·8) for those with normal blood pressure, and developed cardiovascular disease 5·0 years earlier (95% ci 4·8-5·2). stable and unstable angina accounted for most (43%) of the cardiovascular disease-free years of life lost associated with hypertension from index age 30 years, whereas heart failure and stable angina accounted for the largest proportion (19% each) of years of life lost from index age 80 years. interpretation the widely held assumptions that blood pressure has strong associations with the occurrence of all cardiovascular diseases across a wide age range, and that diastolic and systolic associations are concordant, are not supported by the findings of this high-resolution study. despite modern treatments, the lifetime burden of hypertension is substantial. these findings emphasise the need for new blood pressure-lowering strategies, and will help to inform the design of randomised trials to assess them. funding medical research council, national institute for health research, and wellcome trust.",0
"tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. caver is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. herein we present a new version of caver enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. caver 3.0 implements new algorithms for the calculation and clustering of pathways. a trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. to illustrate the capabilities of caver 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase dhaa. caver 3.0 safely identified and reliably estimated the importance of all previously published dhaa tunnels, including the tunnels closed in dhaa crystal structures. obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. caver 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. the software is freely available as a multiplatform command-line application at",0
"unlabelled the two main functions of bioinformatics are the organization and analysis of biological data using computational resources. geneious basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. it integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. one key contribution to researchers in the life sciences is the geneious public application programming interface (api) that affords the ability to leverage the existing framework of the geneious basic software platform for virtually unlimited extension and customization. the result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public api. geneious basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. availability and implementation binaries and public api freely available for download at implemented in java and supported on linux, apple osx and ms windows. the software is also available from the bio-linux package repository at",0
"objective to examine and quantify the potential dose-response relation between fruit and vegetable consumption and risk of all cause, cardiovascular, and cancer mortality. data sources medline, embase, and the cochrane library searched up to 30 august 2013 without language restrictions. reference lists of retrieved articles. study selection prospective cohort studies that reported risk estimates for all cause, cardiovascular, and cancer mortality by levels of fruit and vegetable consumption. data synthesis random effects models were used to calculate pooled hazard ratios and 95% confidence intervals and to incorporate variation between studies. the linear and non-linear dose-response relations were evaluated with data from categories of fruit and vegetable consumption in each study. results sixteen prospective cohort studies were eligible in this meta-analysis. during follow-up periods ranging from 4.6 to 26 years there were 56,423 deaths (11,512 from cardiovascular disease and 16,817 from cancer) among 833,234 participants. higher consumption of fruit and vegetables was significantly associated with a lower risk of all cause mortality. pooled hazard ratios of all cause mortality were 0.95 (95% confidence interval 0.92 to 0.98) for an increment of one serving a day of fruit and vegetables (p=0.001), 0.94 (0.90 to 0.98) for fruit (p=0.002), and 0.95 (0.92 to 0.99) for vegetables (p=0.006). there was a threshold around five servings of fruit and vegetables a day, after which the risk of all cause mortality did not reduce further. a significant inverse association was observed for cardiovascular mortality (hazard ratio for each additional serving a day of fruit and vegetables 0.96, 95% confidence interval 0.92 to 0.99), while higher consumption of fruit and vegetables was not appreciably associated with risk of cancer mortality. conclusions this meta-analysis provides further evidence that a higher consumption of fruit and vegetables is associated with a lower risk of all cause mortality, particularly cardiovascular mortality.",0
"dna methylation, an important type of epigenetic modification in humans, participates in crucial cellular processes, such as embryonic development, x-inactivation, genomic imprinting and chromosome stability. several platforms have been developed to study genome-wide dna methylation. many investigators in the field have chosen the illumina infinium humanmethylation microarray for its ability to reliably assess dna methylation following sodium bisulfite conversion. here, we analyzed methylation profiles of 489 adult males and 357 adult females generated by the infinium humanmethylation450 microarray. among the autosomal cpg sites that displayed significant methylation differences between the two sexes, we observed a significant enrichment of cross-reactive probes co-hybridizing to the sex chromosomes with more than 94% sequence identity. this could lead investigators to mistakenly infer the existence of significant autosomal sex-associated methylation. using sequence identity cutoffs derived from the sex methylation analysis, we concluded that 6% of the array probes can potentially generate spurious signals because of co-hybridization to alternate genomic sequences highly homologous to the intended targets. additionally, we discovered probes targeting polymorphic cpgs that overlapped snps. the methylation levels detected by these probes are simply the reflection of underlying genetic polymorphisms but could be misinterpreted as true signals. the existence of probes that are cross-reactive or of target polymorphic cpgs in the illumina humanmethylation microarrays can confound data obtained from such microarrays. therefore, investigators should exercise caution when significant biological associations are found using these array platforms. a list of all cross-reactive probes and polymorphic cpgs identified by us are annotated in this paper.",0
"the difficulty in delineating brain tumor margins is a major obstacle in the path toward better outcomes for patients with brain tumors. current imaging methods are often limited by inadequate sensitivity, specificity and spatial resolution. here we show that a unique triple-modality magnetic resonance imaging-photoacoustic imaging-raman imaging nanoparticle (termed here mpr nanoparticle) can accurately help delineate the margins of brain tumors in living mice both preoperatively and intraoperatively. the mprs were detected by all three modalities with at least a picomolar sensitivity both in vitro and in living mice. intravenous injection of mprs into glioblastoma-bearing mice led to mpr accumulation and retention by the tumors, with no mpr accumulation in the surrounding healthy tissue, allowing for a noninvasive tumor delineation using all three modalities through the intact skull. raman imaging allowed for guidance of intraoperative tumor resection, and a histological correlation validated that raman imaging was accurately delineating the brain tumor margins. this new triple-modality-nanoparticle approach has promise for enabling more accurate brain tumor imaging and resection.",0
"recent studies have suggested that the brain's structural and functional networks (i.e., connectomics) can be constructed by various imaging technologies (e.g., eeg/meg; structural, diffusion and functional mri) and further characterized by graph theory. given the huge complexity of network construction, analysis and statistics, toolboxes incorporating these functions are largely lacking. here, we developed the graph theoretical network analysis (gretna) toolbox for imaging connectomics. the gretna contains several key features as follows: (i) an open-source, matlab-based, cross-platform (windows and unix os) package with a graphical user interface (gui); (ii) allowing topological analyses of global and local network properties with parallel computing ability, independent of imaging modality and species; (iii) providing flexible manipulations in several key steps during network construction and analysis, which include network node definition, network connectivity processing, network type selection and choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics and assessments of relationship between these network metrics and clinical or behavioral variables of interest; and (v) including functionality in image preprocessing and network construction based on resting-state functional mri (r-fmri) data. after applying the gretna to a publicly released r-fmri dataset of 54 healthy young adults, we demonstrated that human brain functional networks exhibit efficient small-world, assortative, hierarchical and modular organizations and possess highly connected hubs and that these findings are robust against different analytical strategies. with these efforts, we anticipate that gretna will accelerate imaging connectomics in an easy, quick and flexible manner. gretna is freely available on the nitrc website.",0
"bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. to find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. however, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. here, we present antismash (antibiotics & secondary metabolite analysis shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). it aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antismash is available at",0
"this article summarizes the new 2011 report on dietary requirements for calcium and vitamin d from the institute of medicine (iom). an iom committee charged with determining the population needs for these nutrients in north america conducted a comprehensive review of the evidence for both skeletal and extraskeletal outcomes. the committee concluded that available scientific evidence supports a key role of calcium and vitamin d in skeletal health, consistent with a cause-and-effect relationship and providing a sound basis for determination of intake requirements. for extraskeletal outcomes, including cancer, cardiovascular disease, diabetes, and autoimmune disorders, the evidence was inconsistent, inconclusive as to causality, and insufficient to inform nutritional requirements. randomized clinical trial evidence for extraskeletal outcomes was limited and generally uninformative. based on bone health, recommended dietary allowances (rdas; covering requirements of ≥97.5% of the population) for calcium range from 700 to 1300 mg/d for life-stage groups at least 1 yr of age. for vitamin d, rdas of 600 iu/d for ages 1-70 yr and 800 iu/d for ages 71 yr and older, corresponding to a serum 25-hydroxyvitamin d level of at least 20 ng/ml (50 nmol/liter), meet the requirements of at least 97.5% of the population. rdas for vitamin d were derived based on conditions of minimal sun exposure due to wide variability in vitamin d synthesis from ultraviolet light and the risks of skin cancer. higher values were not consistently associated with greater benefit, and for some outcomes u-shaped associations were observed, with risks at both low and high levels. the committee concluded that the prevalence of vitamin d inadequacy in north america has been overestimated. urgent research and clinical priorities were identified, including reassessment of laboratory ranges for 25-hydroxyvitamin d, to avoid problems of both undertreatment and overtreatment.",0
"background the consort statement is intended to improve reporting of randomised controlled trials and focuses on minimising the risk of bias (internal validity). the applicability of a trial's results (generalisability or external validity) is also important, particularly for pragmatic trials. a pragmatic trial (a term first used in 1967 by schwartz and lellouch) can be broadly defined as a randomised controlled trial whose purpose is to inform decisions about practice. this extension of the consort statement is intended to improve the reporting of such trials and focuses on applicability. methods at two, two-day meetings held in toronto in 2005 and 2008, we reviewed the consort statement and its extensions, the literature on pragmatic trials and applicability, and our experiences in conducting pragmatic trials. recommendations we recommend extending eight consort checklist items for reporting of pragmatic trials: the background, participants, interventions, outcomes, sample size, blinding, participant flow, and generalisability of the findings. these extensions are presented, along with illustrative examples of reporting, and an explanation of each extension. adherence to these reporting criteria will make it easier for decision makers to judge how applicable the results of randomised controlled trials are to their own conditions. empirical studies are needed to ascertain the usefulness and comprehensiveness of these consort checklist item extensions. in the meantime we recommend that those who support, conduct, and report pragmatic trials should use this extension of the consort statement to facilitate the use of trial results in decisions about health care.",0
"the new computer program shelxt employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group p1. missing data are taken into account and the resolution extended if necessary. all space groups in the specified laue group are tested to find which are consistent with the p1 phases. after applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. an isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a flack parameter and, if appropriate, inversion of the structure. the structure is assembled to maximize its connectivity and centred optimally in the unit cell. shelxt has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. it is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.",0
"background back pain remains a challenge for primary care internationally. one model that has not been tested is stratification of the management according to the patient's prognosis (low, medium, or high risk). we compared the clinical effectiveness and cost-effectiveness of stratified primary care (intervention) with non-stratified current best practice (control). methods 1573 adults (aged ≥18 years) with back pain (with or without radiculopathy) consultations at ten general practices in england responded to invitations to attend an assessment clinic. eligible participants were randomly assigned by use of computer-generated stratified blocks with a 2:1 ratio to intervention or control group. primary outcome was the effect of treatment on the roland morris disability questionnaire (rmdq) score at 12 months. in the economic evaluation, we focused on estimating incremental quality-adjusted life years (qalys) and health-care costs related to back pain. analysis was by intention to treat. this study is registered, number isrctn37113406. findings 851 patients were assigned to the intervention (n=568) and control groups (n=283). overall, adjusted mean changes in rmdq scores were significantly higher in the intervention group than in the control group at 4 months (4·7 vs 3·0 , between-group difference 1·81 ) and at 12 months (4·3 vs 3·3 , 1·06 ), equating to effect sizes of 0·32 (0·19-0·45) and 0·19 (0·04-0·33), respectively. at 12 months, stratified care was associated with a mean increase in generic health benefit (0·039 additional qalys) and cost savings (£240·01 vs £274·40) compared with the control group. interpretation the results show that a stratified approach, by use of prognostic screening with matched pathways, will have important implications for the future management of back pain in primary care. funding arthritis research uk.",0
"we studied the effect of microtubule-associated tau protein on trafficking of vesicles and organelles in primary cortical neurons, retinal ganglion cells, and neuroblastoma cells. tau inhibits kinesin-dependent transport of peroxisomes, neurofilaments, and golgi-derived vesicles into neurites. loss of peroxisomes makes cells vulnerable to oxidative stress and leads to degeneration. in particular, tau inhibits transport of amyloid precursor protein (app) into axons and dendrites, causing its accumulation in the cell body. app tagged with yellow fluorescent protein and transfected by adenovirus associates with vesicles moving rapidly forward in the axon (approximately 80%) and slowly back (approximately 20%). both movements are strongly inhibited by cotransfection with fluorescently tagged tau (cyan fluorescent protein-tau) as seen by two-color confocal microscopy. the data suggests a linkage between tau and app trafficking, which may be significant in alzheimer's disease.",0
"background adherence to chronic disease management is critical to achieving improved health outcomes, quality of life, and cost-effective health care. as the burden of chronic diseases continues to grow globally, so does the impact of non-adherence. mobile technologies are increasingly being used in health care and public health practice (mhealth) for patient communication, monitoring, and education, and to facilitate adherence to chronic diseases management. objective we conducted a systematic review of the literature to evaluate the effectiveness of mhealth in supporting the adherence of patients to chronic diseases management (""madherence""), and the usability, feasibility, and acceptability of madherence tools and platforms in chronic disease management among patients and health care providers. methods we searched pubmed, embase, and ebsco databases for studies that assessed the role of madherence in chronic disease management of diabetes mellitus, cardiovascular disease, and chronic lung diseases from 1980 through may 2014. outcomes of interest included effect of mhealth on patient adherence to chronic diseases management, disease-specific clinical outcomes after intervention, and the usability, feasibility, and acceptability of madherence tools and platforms in chronic disease management among target end-users. results in all, 107 articles met all inclusion criteria. short message service was the most commonly used madherence tool in 40.2% (43/107) of studies. usability, feasibility, and acceptability or patient preferences for madherence interventions were assessed in 57.9% (62/107) of studies and found to be generally high. a total of 27 studies employed randomized controlled trial (rct) methods to assess impact on adherence behaviors, and significant improvements were observed in 15 of those studies (56%). of the 41 rcts that measured effects on disease-specific clinical outcomes, significant improvements between groups were reported in 16 studies (39%). conclusions there is potential for mhealth tools to better facilitate adherence to chronic disease management, but the evidence supporting its current effectiveness is mixed. further research should focus on understanding and improving how mhealth tools can overcome specific barriers to adherence.",0
"in the course of our supervisory work over the years we have noticed that qualitative research tends to evoke a lot of questions and worries, so-called frequently asked questions (faqs). this series of four articles intends to provide novice researchers with practical guidance for conducting high-quality qualitative research in primary care. by 'novice' we mean master's students and junior researchers, as well as experienced quantitative researchers who are engaging in qualitative research for the first time. this series addresses their questions and provides researchers, readers, reviewers and editors with references to criteria and tools for judging the quality of qualitative research papers. the first article provides an introduction to this series. the second article focused on context, research questions and designs. the third article focused on sampling, data collection and analysis. this fourth article addresses faqs about trustworthiness and publishing. quality criteria for all qualitative research are credibility, transferability, dependability, and confirmability. reflexivity is an integral part of ensuring the transparency and quality of qualitative research. writing a qualitative research article reflects the iterative nature of the qualitative research process: data analysis continues while writing. a qualitative research article is mostly narrative and tends to be longer than a quantitative paper, and sometimes requires a different structure. editors essentially use the criteria: is it new, is it true, is it relevant? an effective cover letter enhances confidence in the newness, trueness and relevance, and explains why your study required a qualitative design. it provides information about the way you applied quality criteria or a checklist, and you can attach the checklist to the manuscript.",0
"these experiments indicate that, in dogs at least, ischemia localized to the kidneys is a sufficient condition for the production of persistently elevated systolic blood pressure. when the constriction of both main renal arteries is made only moderately severe in the beginning, the elevation of systolic blood pressure is unaccompanied by signs of materially decreased renal function. in this respect the hypertension in these animals resembles the hypertension which is associated with so called benign nephrosclerosis in man. subsequent increase of the constriction of the main renal arteries does not materially damage renal function, probably because of adequate development of accessory circulation. more delicate methods for detecting a change may yet prove that some damage does occur. almost complete constriction of both main renal arteries, from the beginning, results in great elevation of systolic blood pressure which is accompanied by severe disturbance of renal function and uremia. this resembles the type of hypertension which is associated with so called malignant nephrosclerosis, in the sense of fahr (17). in several of the animals with persistent elevation of systolic blood pressure, anatomical changes were observed in the glomeruli, vessels and parenchyma of the kidneys which are most probably directly referable to the ischemia. it is hoped that these investigations will afford a means of studying the pathogenesis of hypertension that is associated with renal vascular disease.",0
"neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (rbd) of the trimeric spike. here, we characterized polyclonal immunoglobulin gs (iggs) and fabs from covid-19 convalescent individuals for recognition of coronavirus spikes. plasma iggs differed in their focus on rbd epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of iggs over fabs. using electron microscopy, we examined specificities of polyclonal plasma fabs, revealing recognition of both s1 a and rbd epitopes on sars-cov-2 spike. moreover, a 3.4 å cryo-electron microscopy (cryo-em) structure of a neutralizing monoclonal fab-spike complex revealed an epitope that blocks ace2 receptor binding. modeling based on these structures suggested different potentials for inter-spike crosslinking by iggs on viruses, and characterized iggs would not be affected by identified sars-cov-2 spike mutations. overall, our studies structurally define a recurrent anti-sars-cov-2 antibody class derived from vh3-53/vh3-66 and similarity to a sars-cov vh3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.",0
"context participatory research (pr) is the co-construction of research through partnerships between researchers and people affected by and/or responsible for action on the issues under study. evaluating the benefits of pr is challenging for a number of reasons: the research topics, methods, and study designs are heterogeneous; the extent of collaborative involvement may vary over the duration of a project and from one project to the next; and partnership activities may generate a complex array of both short- and long-term outcomes. methods our review team consisted of a collaboration among researchers and decision makers in public health, research funding, ethics review, and community-engaged scholarship. we identified, selected, and appraised a large-variety sample of primary studies describing pr partnerships, and in each stage, two team members independently reviewed and coded the literature. we used key realist review concepts (middle-range theory, demi-regularity, and context-mechanism-outcome configurations ) to analyze and synthesize the data, using the pr partnership as the main unit of analysis. findings from 7,167 abstracts and 591 full-text papers, we distilled for synthesis a final sample of twenty-three pr partnerships described in 276 publications. the link between process and outcome in these partnerships was best explained using the middle-range theory of partnership synergy, which demonstrates how pr can (1) ensure culturally and logistically appropriate research, (2) enhance recruitment capacity, (3) generate professional capacity and competence in stakeholder groups, (4) result in productive conflicts followed by useful negotiation, (5) increase the quality of outputs and outcomes over time, (6) increase the sustainability of project goals beyond funded time frames and during gaps in external funding, and (7) create system changes and new unanticipated projects and activities. negative examples illustrated why these outcomes were not a guaranteed product of pr partnerships but were contingent on key aspects of context. conclusions we used a realist approach to embrace the heterogeneity and complexity of the pr literature. this theory-driven synthesis identified mechanisms by which pr may add value to the research process. using the middle-range theory of partnership synergy, our review confirmed findings from previous pr reviews, documented and explained some negative outcomes, and generated new insights into the benefits of pr regarding conflicts and negotiation between stakeholders, program sustainability and advancement, unanticipated project activity, and the generation of systemic change.",0
"rationale coronary artery disease (cad) is a complex phenotype driven by genetic and environmental factors. ninety-seven genetic risk loci have been identified to date, but the identification of additional susceptibility loci might be important to enhance our understanding of the genetic architecture of cad. objective to expand the number of genome-wide significant loci, catalog functional insights, and enhance our understanding of the genetic architecture of cad. methods and results we performed a genome-wide association study in 34 541 cad cases and 261 984 controls of uk biobank resource followed by replication in 88 192 cases and 162 544 controls from cardiogramplusc4d. we identified 75 loci that replicated and were genome-wide significant ( p -8 ) in meta-analysis, 13 of which had not been reported previously. next, to further identify novel loci, we identified all promising ( p p -8 ) in meta-analysis. finally, we performed a genome-wide meta-analysis of all available data revealing 30 additional novel loci ( p -8 ) without further replication. the increase in sample size by uk biobank raised the number of reconstituted gene sets from 4.2% to 13.9% of all gene sets to be involved in cad. for the 64 novel loci, 155 candidate causal genes were prioritized, many without an obvious connection to cad. fine mapping of the 161 cad loci generated lists of credible sets of single causal variants and genes for functional follow-up. genetic risk variants of cad were linked to development of atrial fibrillation, heart failure, and death. conclusions we identified 64 novel genetic risk loci for cad and performed fine mapping of all 161 risk loci to obtain a credible set of causal variants. the large expansion of reconstituted gene sets argues in favor of an expanded omnigenic model view on the genetic architecture of cad.",0
"background national cancer center (ncc) of china annually reports the nationwide statistics for cancer incidence and mortality using population-based cancer registry data from all available cancer registries in china. methods there were a total of 487 registries which reported high quality data of cancer incidence and mortality across china in 2016. the nationwide numbers of new cancer cases and deaths were estimated using the pooled cancer registry data, which were stratified by area (urban/rural), sex, age group (0, 1-4, 5-9, 10-14…85+) and cancer site for incidence and mortality, and then multiplied by corresponding national population. the world segi's population was applied for the calculation of age-standardized rates. results about 4,064,000 new cancer cases and 2,413,500 new cancer deaths occurred in china in 2016. cancers of the lung, colon-rectum, stomach, liver and female breast were the top five common cancers, accounting for 57.4% of total cancer new cases. cancers of the lung, liver, stomach, colon-rectum and esophagus were the five leading causes of cancer deaths, accounting for 69.3% of total cancer deaths. the crude and age-standardized incidence rates (asir) were 293.91 and 186.46 per 100,000 population, respectively. the crude mortality rate was 174.55/100,000 and the age-standardized mortality rate (asmr) was 105.19/100,000. the asir was higher but the asmr was lower in urban areas than that in rural areas. in past decades, the asir was relatively stable in males, but significantly increased by about 2.3% per year in females for overall cancers combined. in contrast, the asmr significantly decreased by about 1.2% per year for both sexes during 2000-2016. notably, the cancer-specific asir and asmr of esophageal, stomach, and liver cancers decreased significantly, whereas both rates for cancers of the colon-rectum, prostate, female breast, cervix, and thyroid increased significantly. conclusions cancer remains a major public health problem in china, which demands long-term collaborative efforts of a broad community. with the national guideline on cancer prevention and control, tailored cancer prevention and control programs are needed in different regions to help reduce the burden of these highly fatal diseases in china.",0
"the human metabolome database (hmdb) ( is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. since its first release in 2007, the hmdb has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. the most recent release of hmdb (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). in particular, the number of annotated metabolite entries has grown from 6500 to more than 40,000 (a 600% increase). this enormous expansion is a result of the inclusion of both 'detected' metabolites (those with measured concentrations or experimental confirmation of their existence) and 'expected' metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). the latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. in addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. these include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. this article describes these enhancements to the hmdb, which was previously featured in the 2009 nar database issue. (note to referees, hmdb 3.0 will go live on 18 september 2012.).",0
"chembl is a large, open-access bioactivity database ( previously described in the 2012, 2014 and 2017 nucleic acids research database issues. in the last two years, several important improvements have been made to the database and are described here. these include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.",0
"global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships 1,2 . here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'huri'. with approximately 53,000 protein-protein interactions, huri has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. the integration of huri with genome 3 , transcriptome 4 and proteome 5 data enables cellular function to be studied within most physiological or pathological cellular contexts. we demonstrate the utility of huri in identifying the specific subcellular roles of protein-protein interactions. inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of mendelian diseases. huri is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.",0
"background mass spectrometry (ms) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. an ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. here we introduce a new generation of a popular open-source data processing toolbox, mzmine 2. results a key concept of the mzmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. newly introduced functionality includes the identification of peaks using online databases, msn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (ransac) algorithm. the performance of the ransac alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. conclusions mzmine 2 is freely available under a gnu gpl license and can be obtained from the project website at: the current version of mzmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.",0
"background long-term hormone therapy has been the standard of care for advanced prostate cancer since the 1940s. stampede is a randomised controlled trial using a multiarm, multistage platform design. it recruits men with high-risk, locally advanced, metastatic or recurrent prostate cancer who are starting first-line long-term hormone therapy. we report primary survival results for three research comparisons testing the addition of zoledronic acid, docetaxel, or their combination to standard of care versus standard of care alone. methods standard of care was hormone therapy for at least 2 years; radiotherapy was encouraged for men with n0m0 disease to november, 2011, then mandated; radiotherapy was optional for men with node-positive non-metastatic (n+m0) disease. stratified randomisation (via minimisation) allocated men 2:1:1:1 to standard of care only (soc-only; control), standard of care plus zoledronic acid (soc + za), standard of care plus docetaxel (soc + doc), or standard of care with both zoledronic acid and docetaxel (soc + za + doc). zoledronic acid (4 mg) was given for six 3-weekly cycles, then 4-weekly until 2 years, and docetaxel (75 mg/m(2)) for six 3-weekly cycles with prednisolone 10 mg daily. there was no blinding to treatment allocation. the primary outcome measure was overall survival. pairwise comparisons of research versus control had 90% power at 2·5% one-sided α for hazard ratio (hr) 0·75, requiring roughly 400 control arm deaths. statistical analyses were undertaken with standard log-rank-type methods for time-to-event data, with hazard ratios (hrs) and 95% cis derived from adjusted cox models. this trial is registered at clinicaltrials.gov (nct00268476) and controlledtrials.com (isrctn78818544). findings 2962 men were randomly assigned to four groups between oct 5, 2005, and march 31, 2013. median age was 65 years (iqr 60-71). 1817 (61%) men had m+ disease, 448 (15%) had n+/x m0, and 697 (24%) had n0m0. 165 (6%) men were previously treated with local therapy, and median prostate-specific antigen was 65 ng/ml (iqr 23-184). median follow-up was 43 months (iqr 30-60). there were 415 deaths in the control group (347 prostate cancer). median overall survival was 71 months (iqr 32 to not reached) for soc-only, not reached (32 to not reached) for soc + za (hr 0·94, 95% ci 0·79-1·11; p=0·450), 81 months (41 to not reached) for soc + doc (0·78, 0·66-0·93; p=0·006), and 76 months (39 to not reached) for soc + za + doc (0·82, 0·69-0·97; p=0·022). there was no evidence of heterogeneity in treatment effect (for any of the treatments) across prespecified subsets. grade 3-5 adverse events were reported for 399 (32%) patients receiving soc, 197 (32%) receiving soc + za, 288 (52%) receiving soc + doc, and 269 (52%) receiving soc + za + doc. interpretation zoledronic acid showed no evidence of survival improvement and should not be part of standard of care for this population. docetaxel chemotherapy, given at the time of long-term hormone therapy initiation, showed evidence of improved survival accompanied by an increase in adverse events. docetaxel treatment should become part of standard of care for adequately fit men commencing long-term hormone therapy. funding cancer research uk, medical research council, novartis, sanofi-aventis, pfizer, janssen, astellas, nihr clinical research network, swiss group for clinical cancer research.",0
"background the host immune reaction is represented by immune/inflammatory cell infiltrates. here we systematically analysed tumour-infiltrating immune/inflammatory cells in pancreatic ductal carcinoma (pdc) and evaluated their clinicopathological impact. methods using immunohistochemistry, we examined tumour-infiltrating cd68(+) pan-macrophages, hla-dr(+)cd68(+) m1 macrophages (m1), cd163(+) or cd204(+) m2 macrophages (m2), cd66b(+) neutrophils (neu), cd4(+) t cells (cd4(+)t), cd8(+) t cells (cd8(+)t), and foxp3(+)cd4(+) regulatory t cells (treg) in 212 cases of pdc, and conducted correlation and survival analyses using the kaplan-meier method and cox proportional hazards model. results higher levels of tumour-infiltrating pan-macrophages, m2, neu, or the ratio of tregs to cd4(+)t (%treg) were significantly associated with shorter survival, whereas higher levels of tumour-infiltrating cd4(+)t, cd8(+)t, or the ratio of m1 to pan-macrophages (%m1) were significantly associated with longer survival. survival analysis of pairs of these variables revealed that some of the resulting patient groups had exclusively longer survival. we then connected the apparently related factors, and two significant variables emerged: tumour-infiltrating cd4(+)t(high)/cd8(+)t(high)/%treg(low) and tumour-infiltrating %m1(high)/m2(low). multivariate survival analysis revealed that these variables were significantly correlated with longer survival and had a higher hazard ratio. conclusion tumour-infiltrating cd4(+)t(high)/cd8(+)t(high)/%treg(low) and %m1(high)/m2(low) are independent prognosticators useful for evaluating the immune microenvironment of pdc.",0
"the combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the sequence read archive (sra). the preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the sra. the sra was established as a public repository for the next-generation sequence data and is operated by the international nucleotide sequence database collaboration (insdc). insdc partners include the national center for biotechnology information (ncbi), the european bioinformatics institute (ebi) and the dna data bank of japan (ddbj). the sra is accessible at from ncbi, at from ebi and at from ddbj. in this article, we present the content and structure of the sra, detail our support for sequencing platforms and provide recommended data submission levels and formats. we also briefly outline our response to the challenge of data growth.",0
"background stroke is a leading cause of mortality and disability worldwide and the economic costs of treatment and post-stroke care are substantial. the global burden of diseases, injuries, and risk factors study (gbd) provides a systematic, comparable method of quantifying health loss by disease, age, sex, year, and location to provide information to health systems and policy makers on more than 300 causes of disease and injury, including stroke. the results presented here are the estimates of burden due to overall stroke and ischaemic and haemorrhagic stroke from gbd 2016. methods we report estimates and corresponding uncertainty intervals (uis), from 1990 to 2016, for incidence, prevalence, deaths, years of life lost (ylls), years lived with disability (ylds), and disability-adjusted life-years (dalys). dalys were generated by summing ylls and ylds. cause-specific mortality was estimated using an ensemble modelling process with vital registration and verbal autopsy data as inputs. non-fatal estimates were generated using bayesian meta-regression incorporating data from registries, scientific literature, administrative records, and surveys. the socio-demographic index (sdi), a summary indicator generated using educational attainment, lagged distributed income, and total fertility rate, was used to group countries into quintiles. findings in 2016, there were 5·5 million (95% ui 5·3 to 5·7) deaths and 116·4 million (111·4 to 121·4) dalys due to stroke. the global age-standardised mortality rate decreased by 36·2% (-39·3 to -33·6) from 1990 to 2016, with decreases in all sdi quintiles. over the same period, the global age-standardised daly rate declined by 34·2% (-37·2 to -31·5), also with decreases in all sdi quintiles. there were 13·7 million (12·7 to 14·7) new stroke cases in 2016. global age-standardised incidence declined by 8·1% (-10·7 to -5·5) from 1990 to 2016 and decreased in all sdi quintiles except the middle sdi group. there were 80·1 million (74·1 to 86·3) prevalent cases of stroke globally in 2016; 41·1 million (38·0 to 44·3) in women and 39·0 million (36·1 to 42·1) in men. interpretation although age-standardised mortality rates have decreased sharply from 1990 to 2016, the decrease in age-standardised incidence has been less steep, indicating that the burden of stroke is likely to remain high. planned updates to future gbd iterations include generating separate estimates for subarachnoid haemorrhage and intracerebral haemorrhage, generating estimates of transient ischaemic attack, and including atrial fibrillation as a risk factor. funding bill & melinda gates foundation.",0
"to be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. drug development involves assessment of absorption, distribution, metabolism and excretion (adme) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. in that context, computer models constitute valid alternatives to experiments. here, we present the new swissadme web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the boiled-egg, ilogp and bioavailability radar. easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours.",0
"evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. the dn/ds ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. nevertheless, the dn/ds measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. here, we study the expected dn/ds ratio for samples drawn from a single population under selection, and we find that in this context, dn/ds is relatively insensitive to the selection coefficient. moreover, the hallmark signature of positive selection over divergent lineages, dn/ds>1, is violated within a population. for population samples, the relationship between selection and dn/ds does not follow a monotonic function, and so it may be impossible to infer selection pressures from dn/ds. these results have significant implications for the interpretation of dn/ds measurements among population-genetic samples.",0
"epidemiologic evidence suggests that cancer incidence is associated with diabetes as well as certain diabetes risk factors and diabetes treatments. this consensus statement of experts assembled jointly by the american diabetes association and the american cancer society reviews the state of science concerning 1) the association between diabetes and cancer incidence or prognosis, 2) risk factors common to both diabetes and cancer, 3) possible biologic links between diabetes and cancer risk, and 4) whether diabetes treatments influence risk of cancer or cancer prognosis. in addition, key unanswered questions for future research are posed.",0
"background lung adenocarcinomas from patients who respond to the tyrosine kinase inhibitors gefitinib (iressa) or erlotinib (tarceva) usually harbor somatic gain-of-function mutations in exons encoding the kinase domain of the epidermal growth factor receptor (egfr). despite initial responses, patients eventually progress by unknown mechanisms of ""acquired"" resistance. methods and findings we show that in two of five patients with acquired resistance to gefitinib or erlotinib, progressing tumors contain, in addition to a primary drug-sensitive mutation in egfr, a secondary mutation in exon 20, which leads to substitution of methionine for threonine at position 790 (t790m) in the kinase domain. tumor cells from a sixth patient with a drug-sensitive egfr mutation whose tumor progressed on adjuvant gefitinib after complete resection also contained the t790m mutation. this mutation was not detected in untreated tumor samples. moreover, no tumors with acquired resistance had kras mutations, which have been associated with primary resistance to these drugs. biochemical analyses of transfected cells and growth inhibition studies with lung cancer cell lines demonstrate that the t790m mutation confers resistance to egfr mutants usually sensitive to either gefitinib or erlotinib. interestingly, a mutation analogous to t790m has been observed in other kinases with acquired resistance to another kinase inhibitor, imatinib (gleevec). conclusion in patients with tumors bearing gefitinib- or erlotinib-sensitive egfr mutations, resistant subclones containing an additional egfr mutation emerge in the presence of drug. this observation should help guide the search for more effective therapy against a specific subset of lung cancers.",0
"summary the proteowizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. the tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and lcms dataset computations. the library contains readers and writers of the mzml data format, which has been written using modern c++ techniques and design principles and supports a variety of platforms with native compilers. the software has been specifically released under the apache v2 license to ensure it can be used in both academic and commercial projects. in addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the proteowizard library. availability cross-platform software that compiles using native compilers (i.e. gcc on linux, msvc on windows and xcode on osx) is available for download free of charge, at this website also provides code examples, and documentation. it is our hope the proteowizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.",0
"during cognitive tasks electrical activity in the brain shows changes in power in specific frequency ranges, such as the alpha (8-12 hz) or gamma (30-80 hz) bands, as well as in a broad range above ∼80 hz, called the high-gamma band. the role or significance of this broadband high-gamma activity is unclear. one hypothesis states that high-gamma oscillations serve just like gamma oscillations, operating at a higher frequency and consequently at a faster timescale. another hypothesis states that high-gamma power is related to spiking activity. because gamma power and spiking activity tend to co-vary during most stimulus manipulations (such as contrast modulations) or cognitive tasks (such as attentional modulation), it is difficult to dissociate these two hypotheses. we studied the relationship between high-gamma power, gamma rhythm, and spiking activity in the primary visual cortex (v1) of awake monkeys while varying the stimulus size, which increased the gamma power but decreased the firing rate, permitting a dissociation. we found that gamma power became anti-correlated with the high-gamma power, suggesting that the two phenomena are distinct and have different origins. on the other hand, high-gamma power remained tightly correlated with spiking activity under a wide range of stimulus manipulations. we studied this relationship using a signal processing technique called matching pursuit and found that action potentials are associated with sharp transients in the lfp with broadband power, which is visible at frequencies as low as ∼50 hz. these results distinguish broadband high-gamma activity from gamma rhythms as an easily obtained and reliable electrophysiological index of neuronal firing near the microelectrode. further, they highlight the importance of making a careful dissociation between gamma rhythms and spike-related transients that could be incorrectly decomposed as rhythms using traditional signal processing methods.",0
"ncbi's conserved domain database (cdd) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. the collection can be accessed at and is also part of ncbi's entrez query and retrieval system, cross-linked to numerous other resources. cdd provides annotation of domain footprints and conserved functional sites on protein sequences. precalculated domain annotation can be retrieved for protein sequences tracked in ncbi's entrez system, and cdd's collection of models can be queried with novel protein sequences via the cd-search service at starting with the latest version of cdd, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either 'specific' (identifying molecular function with high confidence) or as 'non-specific' (identifying superfamily membership only).",0
"background the plant working group of the consortium for the barcode of life recommended the two-locus combination of rbcl+matk as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. the group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. methodology/principal findings here, we compared seven candidate dna barcodes (psba-trnh, matk, rbcl, rpoc1, ycf5, its2, and its) from medicinal plant species. our ranking criteria included pcr amplification efficiency, differential intra- and inter-specific divergences, and the dna barcoding gap. our data suggest that the second internal transcribed spacer (its2) of nuclear ribosomal dna represents the most suitable region for dna barcoding applications. furthermore, we tested the discrimination ability of its2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the its2 was 92.7% at the species level. conclusions the its2 region can be potentially used as a standard dna barcode to identify medicinal plants and their closely related species. we also propose that its2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.",0
"improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. here we argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. there is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. we discuss the goals of these measures, and how they can be implemented, in the hope that this will facilitate action toward improving the transparency, reproducibility and efficiency of scientific research.",0
"major histocompatibility complex (mhc) molecules are expressed on the cell surface, where they present peptides to t cells, which gives them a key role in the development of t-cell immune responses. mhc molecules come in two main variants: mhc class i (mhc-i) and mhc class ii (mhc-ii). mhc-i predominantly present peptides derived from intracellular proteins, whereas mhc-ii predominantly presents peptides from extracellular proteins. in both cases, the binding between mhc and antigenic peptides is the most selective step in the antigen presentation pathway. therefore, the prediction of peptide binding to mhc is a powerful utility to predict the possible specificity of a t-cell immune response. commonly mhc binding prediction tools are trained on binding affinity or mass spectrometry-eluted ligands. recent studies have however demonstrated how the integration of both data types can boost predictive performances. inspired by this, we here present netmhcpan-4.1 and netmhciipan-4.0, two web servers created to predict binding between peptides and mhc-i and mhc-ii, respectively. both methods exploit tailored machine learning strategies to integrate different training data types, resulting in state-of-the-art performance and outperforming their competitors. the servers are available at and",0
"the origin and turnover of efferent populations of mouse mononuclear phagocytes has been described. mononuclear phagocytes were defined as mononuclear cells which are able to adhere to glass and phagocytize. in vitro labeling studies with thymidine-(3)h showed that monocytes in the peripheral blood and peritoneal macrophages do not multiply and can be considered end cells in a normal, steady state situation. however, the mononuclear phagocytes of the bone marrow appear to be rapidly dividing cells. this conclusion was supported by in vivo labeling experiments. a peak of labeled mononuclear phagocytes of the bone marrow was found 24 hr after a pulse of thymidine-(3)h. this was followed, 24 hr later, by a peak of labeled monocytes in the peripheral blood. from these experiments it was concluded that the rapidly dividing mononuclear phagocytes of the bone marrow, called promonocytes, are the progenitor cells of the monocytes. labeling studies after splenectomy and after x-irradiation excluded other organs as a major source of the monocytes. peak labeling of both the blood monocyte and peritoneal macrophages occurred at the same time. a rapid entry of monocytes from the blood into the peritoneal cavity was observed, after a sterile inflammation was evoked by an injection of newborn calf serum. these data have led to the conclusion that monocytes give rise to peritoneal macrophages. no indications have been obtained that mononuclear phagocytes originate from lymphocytes. in the normal steady state the monocytes leave the circulation by a random process, with a half-time of 22 hr. the average blood transit time of the monocytes has been calculated to be 32 hr. the turnover rate of peritoneal macrophages was low and estimated at about 0.1% per hour. on the basis of these studies the life history of mouse mononuclear phagocytes was formulated to be: promonocytes in the bone marrow, --> monocytes in the peripheral blood, --> macrophages in the tissue.",0
"background the scoping review has become an increasingly popular approach for synthesizing research evidence. it is a relatively new approach for which a universal study definition or definitive procedure has not been established. the purpose of this scoping review was to provide an overview of scoping reviews in the literature. methods a scoping review was conducted using the arksey and o'malley framework. a search was conducted in four bibliographic databases and the gray literature to identify scoping review studies. review selection and characterization were performed by two independent reviewers using pretested forms. results the search identified 344 scoping reviews published from 1999 to october 2012. the reviews varied in terms of purpose, methodology, and detail of reporting. nearly three-quarter of reviews (74.1%) addressed a health topic. study completion times varied from 2 weeks to 20 months, and 51% utilized a published methodological framework. quality assessment of included studies was infrequently performed (22.38%). conclusions scoping reviews are a relatively new but increasingly common approach for mapping broad topics. because of variability in their conduct, there is a need for their methodological standardization to ensure the utility and strength of evidence.",0
"a conventional mendelian randomization analysis assesses the causal effect of a risk factor on an outcome by using genetic variants that are solely associated with the risk factor of interest as instrumental variables. however, in some cases, such as the case of triglyceride level as a risk factor for cardiovascular disease, it may be difficult to find a relevant genetic variant that is not also associated with related risk factors, such as other lipid fractions. such a variant is known as pleiotropic. in this paper, we propose an extension of mendelian randomization that uses multiple genetic variants associated with several measured risk factors to simultaneously estimate the causal effect of each of the risk factors on the outcome. this ""multivariable mendelian randomization"" approach is similar to the simultaneous assessment of several treatments in a factorial randomized trial. in this paper, methods for estimating the causal effects are presented and compared using real and simulated data, and the assumptions necessary for a valid multivariable mendelian randomization analysis are discussed. subject to these assumptions, we demonstrate that triglyceride-related pathways have a causal effect on the risk of coronary heart disease independent of the effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol.",0
"flybase ( is a database of drosophila genetic and genomic information. gene ontology (go) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. this article describes recent changes to the flybase go annotation strategy that are improving the quality of the go annotation data. many of these changes stem from our participation in the go reference genome annotation project--a multi-database collaboration producing comprehensive go annotation sets for 12 diverse species.",0
"background in the medical research council (mrc) coin trial, the epidermal growth factor receptor (egfr)-targeted antibody cetuximab was added to standard chemotherapy in first-line treatment of advanced colorectal cancer with the aim of assessing effect on overall survival. methods in this randomised controlled trial, patients who were fit for but had not received previous chemotherapy for advanced colorectal cancer were randomly assigned to oxaliplatin and fluoropyrimidine chemotherapy (arm a), the same combination plus cetuximab (arm b), or intermittent chemotherapy (arm c). the choice of fluoropyrimidine therapy (capecitabine or infused fluouroracil plus leucovorin) was decided before randomisation. randomisation was done centrally (via telephone) by the mrc clinical trials unit using minimisation. treatment allocation was not masked. the comparison of arms a and c is described in a companion paper. here, we present the comparison of arm a and b, for which the primary outcome was overall survival in patients with kras wild-type tumours. analysis was by intention to treat. further analyses with respect to nras, braf, and egfr status were done. the trial is registered, isrctn27286448. findings 1630 patients were randomly assigned to treatment groups (815 to standard therapy and 815 to addition of cetuximab). tumour samples from 1316 (81%) patients were used for somatic molecular analyses; 565 (43%) had kras mutations. in patients with kras wild-type tumours (arm a, n=367; arm b, n=362), overall survival did not differ between treatment groups (median survival 17·9 months in the control group vs 17·0 months in the cetuximab group; hr 1·04, 95% ci 0·87-1·23, p=0·67). similarly, there was no effect on progression-free survival (8·6 months in the control group vs 8·6 months in the cetuximab group; hr 0·96, 0·82-1·12, p=0·60). overall response rate increased from 57% (n=209) with chemotherapy alone to 64% (n=232) with addition of cetuximab (p=0·049). grade 3 and higher skin and gastrointestinal toxic effects were increased with cetuximab (14 vs 114 and 67 vs 97 patients in the control group vs the cetuximab group with kras wild-type tumours, respectively). overall survival differs by somatic mutation status irrespective of treatment received: braf mutant, 8·8 months (iqr 4·5-27·4); kras mutant, 14·4 months (8·5-24·0); all wild-type, 20·1 months (11·5-31·7). interpretation this trial has not confirmed a benefit of addition of cetuximab to oxaliplatin-based chemotherapy in first-line treatment of patients with advanced colorectal cancer. cetuximab increases response rate, with no evidence of benefit in progression-free or overall survival in kras wild-type patients or even in patients selected by additional mutational analysis of their tumours. the use of cetuximab in combination with oxaliplatin and capecitabine in first-line chemotherapy in patients with widespread metastases cannot be recommended. funding cancer research uk, cancer research wales, uk medical research council, merck kgga.",0
"rationale: the global death toll from coronavirus disease (covid-19) virus as of may 12, 2020, exceeds 286,000. the risk factors for death were attributed to advanced age and comorbidities but have not been accurately defined. objectives: to report the clinical features of 85 fatal cases of covid-19 in two hospitals in wuhan. methods: medical records were collected of 85 fatal cases of covid-19 between january 9, 2020, and february 15, 2020. information recorded included medical history, exposure history, comorbidities, symptoms, signs, laboratory findings, computed tomographic scans, and clinical management. measurements and main results: the median age of the patients was 65.8 years, and 72.9% were male. common symptoms were fever (78 ), shortness of breath (50 ), fatigue (50 ), and dyspnea (60 ). hypertension, diabetes, and coronary heart disease were the most common comorbidities. notably, 81.2% of patients had very low eosinophil counts on admission. complications included respiratory failure (80 ), shock (69 ), acute respiratory distress syndrome (63 ), and arrhythmia (51 ), among others. most patients received antibiotic (77 ), antiviral (78 ), and glucocorticoid (65 ) treatments. a total of 38 (44.7%) and 33 (38.8%) patients received intravenous immunoglobulin and ifn-α2b, respectively. conclusions: in this depictive study of 85 fatal cases of covid-19, most cases were males aged over 50 years with noncommunicable chronic diseases. the majority of the patients died of multiple organ failure. early onset of shortness of breath may be used as an observational symptom for covid-19 exacerbations. eosinophilopenia may indicate a poor prognosis. a combination of antimicrobial drugs did not offer considerable benefit to the outcome of this group of patients.",0
"in contrast to mouse epidermal cells, human skin keratinocytes are rather resistant to transformation in vitro. immortalization has been achieved by sv40 but has resulted in cell lines with altered differentiation. we have established a spontaneously transformed human epithelial cell line from adult skin, which maintains full epidermal differentiation capacity. this hacat cell line is obviously immortal (greater than 140 passages), has a transformed phenotype in vitro (clonogenic on plastic and in agar) but remains nontumorigenic. despite the altered and unlimited growth potential, hacat cells, similar to normal keratinocytes, reform an orderly structured and differentiated epidermal tissue when transplanted onto nude mice. differentiation-specific keratins (nos. 1 and 10) and other markers (involucrin and filaggrin) are expressed and regularly located. thus, hacat is the first permanent epithelial cell line from adult human skin that exhibits normal differentiation and provides a promising tool for studying regulation of keratinization in human cells. on karyotyping this line is aneuploid (initially hypodiploid) with unique stable marker chromosomes indicating monoclonal origin. the identity of the hacat line with the tissue of origin was proven by dna fingerprinting using hypervariable minisatellite probes. this is the first demonstration that the dna fingerprint pattern is unaffected by long-term cultivation, transformation, and multiple chromosomal alterations, thereby offering a unique possibility for unequivocal identification of human cell lines. the characteristics of the hacat cell line clearly document that spontaneous transformation of human adult keratinocytes can occur in vitro and is associated with sequential chromosomal alterations, though not obligatorily linked to major defects in differentiation.",0
"as a growing applied science, nanotechnology has considerable global socioeconomic value, and the benefits afforded by nanoscale materials and processes are expected to have significant impacts on almost all industries and all areas of society. a diverse array of engineered nanoscale products and processes have emerged , with widespread applications in fields such as medicine, plastics, energy, electronics, and aerospace. with the nanotechnology economy estimated to be valued at dollar 1 trillion by 2012, the prevalence of these materials in society will be increasing, as will the likelihood of exposures. importantly, the vastness and novelty of the nanotechnology frontier leave many areas unexplored, or underexplored, such as the potential adverse human health effects resulting from exposure to novel nanomaterials. it is within this context that the need for understanding the potentially harmful side effects of these materials becomes clear. the reviewed literature suggests several key points: not all qds are alike; engineered qds cannot be considered a uniform group of substances. qd absorption, distribution, metabolism, excretion, and toxicity depend on multiple factors derived from both inherent physicochemical properties and environmental conditions; qd size, charge, concentration, outer coating bioactivity (capping material and functional groups), and oxidative, photolytic, and mechanical stability have each been implicated as determining factors in qd toxicity. although they offer potentially invaluable societal benefits such as drug targeting and in vivo biomedical imaging, qds may also pose risks to human health and the environment under certain conditions. key words: environment, human health, nanomaterials, nanosized particles, nanotechnology, nanotoxicology, quantum dots, toxicology.",0
"objective to assess the relationship between habitual sleep disturbances and the incidence of type 2 diabetes and to obtain an estimate of the risk. research design and methods we conducted a systematic search of publications using medline (1955-april 2009), embase, and the cochrane library and manual searches without language restrictions. we included studies if they were prospective with follow-up >3 years and had an assessment of sleep disturbances at baseline and incidence of type 2 diabetes. we recorded several characteristics for each study. we extracted quantity and quality of sleep, how they were assessed, and incident cases defined with different validated methods. we extracted relative risks (rrs) and 95% ci and pooled them using random-effects models. we performed sensitivity analysis and assessed heterogeneity and publication bias. results we included 10 studies (13 independent cohort samples; 107,756 male and female participants, follow-up range 4.2-32 years, and 3,586 incident cases of type 2 diabetes). in pooled analyses, quantity and quality of sleep predicted the risk of development of type 2 diabetes. for short duration of sleep ( 8-9 h/night), the rr was 1.48 (1.13-1.96, p = 0.005); for difficulty in initiating sleep, the rr was 1.57 (1.25-1.97, p conclusions quantity and quality of sleep consistently and significantly predict the risk of the development of type 2 diabetes. the mechanisms underlying this relation may differ between short and long sleepers.",0
"autism spectrum disorders (asd) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. to identify further genetic risk factors, here we assess the role of de novo mutations in asd by sequencing the exomes of asd cases and their parents (n = 175 trios). fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant, and the overall rate of mutation is only modestly higher than the expected rate. in contrast, the proteins encoded by genes that harboured de novo missense or nonsense mutations showed a higher degree of connectivity among themselves and to previous asd genes as indexed by protein-protein interaction screens. the small increase in the rate of de novo events, when taken together with the protein interaction results, are consistent with an important but limited role for de novo point mutations in asd, similar to that documented for de novo copy number variants. genetic models incorporating these data indicate that most of the observed de novo events are unconnected to asd; those that do confer risk are distributed across many genes and are incompletely penetrant (that is, not necessarily sufficient for disease). our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favour of chd8 and katnal2 as genuine autism risk factors.",0
"intense nonpharmaceutical interventions were put in place in china to stop transmission of the novel coronavirus disease 2019 (covid-19). as transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection, and covid-19 dynamics remains unclear. to answer these questions, we analyze contact survey data for wuhan and shanghai before and during the outbreak and contact-tracing information from hunan province. daily contacts were reduced seven- to eightfold during the covid-19 social distancing period, with most interactions restricted to the household. we find that children 0 to 14 years of age are less susceptible to severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection than adults 15 to 64 years of age (odds ratio 0.34, 95% confidence interval 0.24 to 0.49), whereas individuals more than 65 years of age are more susceptible to infection (odds ratio 1.47, 95% confidence interval 1.12 to 1.92). based on these data, we built a transmission model to study the impact of social distancing and school closure on transmission. we find that social distancing alone, as implemented in china during the outbreak, is sufficient to control covid-19. although proactive school closures cannot interrupt transmission on their own, they can reduce peak incidence by 40 to 60% and delay the epidemic.",0
"tumor-associated macrophages (tams) represent one of the main tumor-infiltrating immune cell types and are generally categorized into either of two functionally contrasting subtypes, namely classical activated m1 macrophages and alternatively activated m2 macrophages. the former typically exerts anti-tumor functions, including directly mediate cytotoxicity and antibody-dependent cell-mediated cytotoxicity (adcc) to kill tumor cells; the latter can promote the occurrence and metastasis of tumor cells, inhibit t cell-mediated anti-tumor immune response, promote tumor angiogenesis, and lead to tumor progression. both m1 and m2 macrophages have high degree of plasticity and thus can be converted into each other upon tumor microenvironment changes or therapeutic interventions. as the relationship between tams and malignant tumors becoming clearer, tams have become a promising target for developing new cancer treatment. in this review, we summarize the origin and types of tams, tams interaction with tumors and tumor microenvironment, and up-to-date treatment strategies targeting tams.",0
"objective this study was undertaken to evaluate the pregnancy and perinatal outcomes of pregnant women with severe acute respiratory syndrome (sars). study design all pregnant women (12) who presented with sars in hong kong between february 1 and july 31, 2003, were included. the pregnancy and perinatal outcomes were collected. evidence of perinatal transmission of virus was assessed with the sars-associated coronavirus reverse-transcriptase polymerase chain reaction on cord blood, placenta tissue, and subsequent follow-up of the neonate on serology. results three deaths occurred among the 12 patients, giving a case fatality rate of 25%. four of the 7 patients (57%) who presented in the first trimester had spontaneous miscarriage. four of the 5 patients who presented after 24 weeks were delivered preterm. two mothers recovered without delivery, but their ongoing pregnancies were complicated by intrauterine growth restriction. no newborn infant had clinical sars and all investigations were negative for sars. conclusion sars during pregnancy is associated with high incidences of spontaneous miscarriage, preterm delivery, and intrauterine growth restriction. there is no evidence of perinatal sars infection among infants born to these mothers.",0
"mendelian randomization (mr) uses genetic data to probe questions of causality in epidemiological research, by invoking the instrumental variable (iv) assumptions. in recent years, it has become commonplace to attempt mr analyses by synthesising summary data estimates of genetic association gleaned from large and independent study populations. this is referred to as two-sample summary data mr. unfortunately, due to the sheer number of variants that can be easily included into summary data mr analyses, it is increasingly likely that some do not meet the iv assumptions due to pleiotropy. there is a pressing need to develop methods that can both detect and correct for pleiotropy, in order to preserve the validity of the mr approach in this context. in this paper, we aim to clarify how established methods of meta-regression and random effects modelling from mainstream meta-analysis are being adapted to perform this task. specifically, we focus on two contrastin g approaches: the inverse variance weighted (ivw) method which assumes in its simplest form that all genetic variants are valid ivs, and the method of mr-egger regression that allows all variants to violate the iv assumptions, albeit in a specific way. we investigate the ability of two popular random effects models to provide robustness to pleiotropy under the ivw approach, and propose statistics to quantify the relative goodness-of-fit of the ivw approach over mr-egger regression. © 2017 the authors. statistics in medicine published by johnwiley & sons ltd.",0
"globally, approximately 170,000 confirmed cases of coronavirus disease 2019 (covid-19) caused by the 2019 novel coronavirus (sars-cov-2) have been reported, including an estimated 7,000 deaths in approximately 150 countries (1). on march 11, 2020, the world health organization declared the covid-19 outbreak a pandemic (2). data from china have indicated that older adults, particularly those with serious underlying health conditions, are at higher risk for severe covid-19-associated illness and death than are younger persons (3). although the majority of reported covid-19 cases in china were mild (81%), approximately 80% of deaths occurred among adults aged ≥60 years; only one (0.1%) death occurred in a person aged ≤19 years (3). in this report, covid-19 cases in the united states that occurred during february 12-march 16, 2020 and severity of disease (hospitalization, admission to intensive care unit , and death) were analyzed by age group. as of march 16, a total of 4,226 covid-19 cases in the united states had been reported to cdc, with multiple cases reported among older adults living in long-term care facilities (4). overall, 31% of cases, 45% of hospitalizations, 53% of icu admissions, and 80% of deaths associated with covid-19 were among adults aged ≥65 years with the highest percentage of severe outcomes among persons aged ≥85 years. in contrast, no icu admissions or deaths were reported among persons aged ≤19 years. similar to reports from other countries, this finding suggests that the risk for serious disease and death from covid-19 is higher in older age groups.",0
"the availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. so far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. here we present a new method that overcomes these shortcomings. the multiple sequentially markovian coalescent (msmc) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. results from applying msmc to genome sequences from nine populations across the world suggest that the genetic separation of non-african ancestors from african yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the americas and separations within africa, east asia and europe.",0
"objective to provide an update to the ""surviving sepsis campaign guidelines for management of severe sepsis and septic shock,"" last published in 2008. design a consensus committee of 68 international experts representing 30 international organizations was convened. nominal groups were assembled at key international meetings (for those committee members attending the conference). a formal conflict of interest policy was developed at the onset of the process and enforced throughout. the entire guidelines process was conducted independent of any industry funding. a stand-alone meeting was held for all subgroup heads, co- and vice-chairs, and selected individuals. teleconferences and electronic-based discussion among subgroups and among the entire committee served as an integral part of the development. methods the authors were advised to follow the principles of the grading of recommendations assessment, development and evaluation (grade) system to guide assessment of quality of evidence from high (a) to very low (d) and to determine the strength of recommendations as strong (1) or weak (2). the potential drawbacks of making strong recommendations in the presence of low-quality evidence were emphasized. recommendations were classified into three groups: (1) those directly targeting severe sepsis; (2) those targeting general care of the critically ill patient and considered high priority in severe sepsis; and (3) pediatric considerations. results key recommendations and suggestions, listed by category, include: early quantitative resuscitation of the septic patient during the first 6 h after recognition (1c); blood cultures before antibiotic therapy (1c); imaging studies performed promptly to confirm a potential source of infection (ug); administration of broad-spectrum antimicrobials therapy within 1 h of the recognition of septic shock (1b) and severe sepsis without septic shock (1c) as the goal of therapy; reassessment of antimicrobial therapy daily for de-escalation, when appropriate (1b); infection source control with attention to the balance of risks and benefits of the chosen method within 12 h of diagnosis (1c); initial fluid resuscitation with crystalloid (1b) and consideration of the addition of albumin in patients who continue to require substantial amounts of crystalloid to maintain adequate mean arterial pressure (2c) and the avoidance of hetastarch formulations (1b); initial fluid challenge in patients with sepsis-induced tissue hypoperfusion and suspicion of hypovolemia to achieve a minimum of 30 ml/kg of crystalloids (more rapid administration and greater amounts of fluid may be needed in some patients (1c); fluid challenge technique continued as long as hemodynamic improvement is based on either dynamic or static variables (ug); norepinephrine as the first-choice vasopressor to maintain mean arterial pressure ≥65 mmhg (1b); epinephrine when an additional agent is needed to maintain adequate blood pressure (2b); vasopressin (0.03 u/min) can be added to norepinephrine to either raise mean arterial pressure to target or to decrease norepinephrine dose but should not be used as the initial vasopressor (ug); dopamine is not recommended except in highly selected circumstances (2c); dobutamine infusion administered or added to vasopressor in the presence of (a) myocardial dysfunction as suggested by elevated cardiac filling pressures and low cardiac output, or (b) ongoing signs of hypoperfusion despite achieving adequate intravascular volume and adequate mean arterial pressure (1c); avoiding use of intravenous hydrocortisone in adult septic shock patients if adequate fluid resuscitation and vasopressor therapy are able to restore hemodynamic stability (2c); hemoglobin target of 7-9 g/dl in the absence of tissue hypoperfusion, ischemic coronary artery disease, or acute hemorrhage (1b); low tidal volume (1a) and limitation of inspiratory plateau pressure (1b) for acute respiratory distress syndrome (ards); application of at least a minimal amount of positive end-expiratory pressure (peep) in ards (1b); higher rather than lower level of peep for patients with sepsis-induced moderate or severe ards (2c); recruitment maneuvers in sepsis patients with severe refractory hypoxemia due to ards (2c); prone positioning in sepsis-induced ards patients with a pao (2)/fio (2) ratio of ≤100 mm hg in facilities that have experience with such practices (2c); head-of-bed elevation in mechanically ventilated patients unless contraindicated (1b); a conservative fluid strategy for patients with established ards who do not have evidence of tissue hypoperfusion (1c); protocols for weaning and sedation (1a); minimizing use of either intermittent bolus sedation or continuous infusion sedation targeting specific titration endpoints (1b); avoidance of neuromuscular blockers if possible in the septic patient without ards (1c); a short course of neuromuscular blocker (no longer than 48 h) for patients with early ards and a pao (2)/fi o (2) 180 mg/dl, targeting an upper blood glucose ≤180 mg/dl (1a); equivalency of continuous veno-venous hemofiltration or intermittent hemodialysis (2b); prophylaxis for deep vein thrombosis (1b); use of stress ulcer prophylaxis to prevent upper gastrointestinal bleeding in patients with bleeding risk factors (1b); oral or enteral (if necessary) feedings, as tolerated, rather than either complete fasting or provision of only intravenous glucose within the first 48 h after a diagnosis of severe sepsis/septic shock (2c); and addressing goals of care, including treatment plans and end-of-life planning (as appropriate) (1b), as early as feasible, but within 72 h of intensive care unit admission (2c). recommendations specific to pediatric severe sepsis include: therapy with face mask oxygen, high flow nasal cannula oxygen, or nasopharyngeal continuous peep in the presence of respiratory distress and hypoxemia (2c), use of physical examination therapeutic endpoints such as capillary refill (2c); for septic shock associated with hypovolemia, the use of crystalloids or albumin to deliver a bolus of 20 ml/kg of crystalloids (or albumin equivalent) over 5-10 min (2c); more common use of inotropes and vasodilators for low cardiac output septic shock associated with elevated systemic vascular resistance (2c); and use of hydrocortisone only in children with suspected or proven ""absolute""' adrenal insufficiency (2c). conclusions strong agreement existed among a large cohort of international experts regarding many level 1 recommendations for the best care of patients with severe sepsis. although a significant number of aspects of care have relatively weak support, evidence-based recommendations regarding the acute management of sepsis and septic shock are the foundation of improved outcomes for this important group of critically ill patients.",0
"magnetoencephalography and electroencephalography (m/eeg) measure the weak electromagnetic signals generated by neuronal activity in the brain. using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. as part of the mne software suite, mne-python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. all algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create m/eeg data analysis pipelines by writing python scripts. moreover, mne-python is tightly integrated with the core python libraries for scientific comptutation (numpy, scipy) and visualization (matplotlib and mayavi), as well as the greater neuroimaging ecosystem in python via the nibabel package. the code is provided under the new bsd license allowing code reuse, even in commercial products. although mne-python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. mne-python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. full documentation, including dozens of examples, is available at",0
"background lesbian, gay and bisexual (lgb) people may be at higher risk of mental disorders than heterosexual people. method we conducted a systematic review and meta-analysis of the prevalence of mental disorder, substance misuse, suicide, suicidal ideation and deliberate self harm in lgb people. we searched medline, embase, psycinfo, cinahl, the cochrane library database, the web of knowledge, the applied social sciences index and abstracts, the international bibliography of the social sciences, sociological abstracts, the campbell collaboration and grey literature databases for articles published january 1966 to april 2005. we also used google and google scholar and contacted authors where necessary. we searched all terms related to homosexual, lesbian and bisexual people and all terms related to mental disorders, suicide, and deliberate self harm. we included papers on population based studies which contained concurrent heterosexual comparison groups and valid definition of sexual orientation and mental health outcomes. results of 13706 papers identified, 476 were initially selected and 28 (25 studies) met inclusion criteria. only one study met all our four quality criteria and seven met three of these criteria. data was extracted on 214,344 heterosexual and 11,971 non heterosexual people. meta-analyses revealed a two fold excess in suicide attempts in lesbian, gay and bisexual people . the risk for depression and anxiety disorders (over a period of 12 months or a lifetime) on meta-analyses were at least 1.5 times higher in lesbian, gay and bisexual people (rr range 1.54-2.58) and alcohol and other substance dependence over 12 months was also 1.5 times higher (rr range 1.51-4.00). results were similar in both sexes but meta analyses revealed that lesbian and bisexual women were particularly at risk of substance dependence (alcohol 12 months: rr 4.00, ci 2.85, 5.61; drug dependence: rr 3.50, ci 1.87, 6.53; any substance use disorder rr 3.42, ci 1.97-5.92), while lifetime prevalence of suicide attempt was especially high in gay and bisexual men (rr 4.28, ci 2.32, 7.88). conclusion lgb people are at higher risk of mental disorder, suicidal ideation, substance misuse, and deliberate self harm than heterosexual people.",0
"enterobase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. here, we provide an overview of how enterobase works, what it can do, and its future prospects. enterobase has currently assembled more than 300,000 genomes from illumina short reads from salmonella , escherichia , yersinia , clostridioides , helicobacter , vibrio , and moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgmlst). hierarchical clustering of cgmlst sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. case study 1 illustrates this process for local transmissions of salmonella enterica serovar agama between neighboring social groups of badgers and humans. enterobase also supports single nucleotide polymorphism (snp) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of yersinia pestis over the last 5000 years of pandemic plague. enterobase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within escherichia .",0
"coronavirus disease 2019 (covid-19) exhibits variable symptom severity ranging from asymptomatic to life-threatening, yet the relationship between severity and the humoral immune response is poorly understood. we examined antibody responses in 113 covid-19 patients and found that severe cases resulting in intubation or death exhibited increased inflammatory markers, lymphopenia, pro-inflammatory cytokines, and high anti-receptor binding domain (rbd) antibody levels. although anti-rbd immunoglobulin g (igg) levels generally correlated with neutralization titer, quantitation of neutralization potency revealed that high potency was a predictor of survival. in addition to neutralization of wild-type sars-cov-2, patient sera were also able to neutralize the recently emerged sars-cov-2 mutant d614g, suggesting cross-protection from reinfection by either strain. however, sars-cov-2 sera generally lacked cross-neutralization to a highly homologous pre-emergent bat coronavirus, wiv1-cov, which has not yet crossed the species barrier. these results highlight the importance of neutralizing humoral immunity on disease progression and the need to develop broadly protective interventions to prevent future coronavirus pandemics.",0
"complications of acute respiratory distress syndrome (ards) are common among critically ill patients infected with highly pathogenic influenza viruses. macrophages and neutrophils constitute the majority of cells recruited into infected lungs, and are associated with immunopathology in influenza pneumonia. we examined pathological manifestations in models of macrophage- or neutrophil-depleted mice challenged with sublethal doses of influenza a virus h1n1 strain pr8. infected mice depleted of macrophages displayed excessive neutrophilic infiltration, alveolar damage, and increased viral load, later progressing into ards-like pathological signs with diffuse alveolar damage, pulmonary edema, hemorrhage, and hypoxemia. in contrast, neutrophil-depleted animals showed mild pathology in lungs. the brochoalveolar lavage fluid of infected macrophage-depleted mice exhibited elevated protein content, t1-α, thrombomodulin, matrix metalloproteinase-9, and myeloperoxidase activities indicating augmented alveolar-capillary damage, compared to neutrophil-depleted animals. we provide evidence for the formation of neutrophil extracellular traps (nets), entangled with alveoli in areas of tissue injury, suggesting their potential link with lung damage. when co-incubated with infected alveolar epithelial cells in vitro, neutrophils from infected lungs strongly induced nets generation, and augmented endothelial damage. nets induction was abrogated by anti-myeloperoxidase antibody and an inhibitor of superoxide dismutase, thus implying that nets generation is induced by redox enzymes in influenza pneumonia. these findings support the pathogenic effects of excessive neutrophils in acute lung injury of influenza pneumonia by instigating alveolar-capillary damage.",0
"background & aims the burden of liver cancer varies across the world. herein, we present updated estimates of the current global burden of liver cancer (incidence and mortality) and provide predictions of the number of cases/deaths to 2040. methods we extracted data on primary liver cancer cases and deaths from the globocan 2020 database, which includes 185 countries. age-standardised incidence and mortality rates (asrs) per 100,000 person-years were calculated. cases and deaths up to the year 2040 were predicted based on incidence and mortality rates for 2020 and global demographic projections to 2040. results in 2020, an estimated 905,700 people were diagnosed with, and 830,200 people died from, liver cancer globally. global asrs for liver cancer were 9.5 and 8.7 for new cases and deaths, respectively, per 100,000 people and were highest in eastern asia (17.8 new cases, 16.1 deaths), northern africa (15.2 new cases, 14.5 deaths), and south-eastern asia (13.7 new cases, 13.2 deaths). liver cancer was among the top three causes of cancer death in 46 countries and was among the top five causes of cancer death in 90 countries. asrs of both incidence and mortality were higher among males than females in all world regions (male:female asr ratio ranged between 1.2-3.6). the number of new cases of liver cancer per year is predicted to increase by 55.0% between 2020 and 2040, with a possible 1.4 million people diagnosed in 2040. a predicted 1.3 million people could die from liver cancer in 2040 (56.4% more than in 2020). conclusions liver cancer is a major cause of death in many countries, and the number of people diagnosed with liver cancer is predicted to rise. efforts to reduce the incidence of preventable liver cancer should be prioritised. lay summary the burden of liver cancer varies across the world. liver cancer was among the top three causes of cancer death in 46 countries and was among the top five causes of cancer death in 90 countries worldwide. we predict the number of cases and deaths will rise over the next 20 years as the world population grows. primary liver cancer due to some causes is preventable if control efforts are prioritised and the predicted rise in cases may increase the need for resources to manage care of patients with liver cancer.",0
"many factors are involved in determining the latitudinal and altitudinal spread of the important tick vector ixodes ricinus (acari: ixodidae) in europe, as well as in changes in the distribution within its prior endemic zones. this paper builds on published literature and unpublished expert opinion from the vbornet network with the aim of reviewing the evidence for these changes in europe and discusses the many climatic, ecological, landscape and anthropogenic drivers. these can be divided into those directly related to climatic change, contributing to an expansion in the tick's geographic range at extremes of altitude in central europe, and at extremes of latitude in scandinavia; those related to changes in the distribution of tick hosts, particularly roe deer and other cervids; other ecological changes such as habitat connectivity and changes in land management; and finally, anthropogenically induced changes. these factors are strongly interlinked and often not well quantified. although a change in climate plays an important role in certain geographic regions, for much of europe it is non-climatic factors that are becoming increasingly important. how we manage habitats on a landscape scale, and the changes in the distribution and abundance of tick hosts are important considerations during our assessment and management of the public health risks associated with ticks and tick-borne disease issues in 21(st) century europe. better understanding and mapping of the spread of i. ricinus (and changes in its abundance) is, however, essential to assess the risk of the spread of infections transmitted by this vector species. enhanced tick surveillance with harmonized approaches for comparison of data enabling the follow-up of trends at eu level will improve the messages on risk related to tick-borne diseases to policy makers, other stake holders and to the general public.",0
"genotype imputation methods are now being widely used in the analysis of genome-wide association studies. most imputation analyses to date have used the hapmap as a reference dataset, but new reference panels (such as controls genotyped on multiple snp chips and densely typed samples from the 1,000 genomes project) will soon allow a broader range of snps to be imputed with higher accuracy, thereby increasing power. we describe a genotype imputation method (impute version 2) that is designed to address the challenges presented by these new datasets. the main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. we find that impute v2 attains higher accuracy than other methods when the hapmap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. we also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that impute v2 outperforms other methods in this setting at both rare and common snps, with overall error rates that are 15%-20% lower than those of the closest competing method. one particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of snps; we show that our approach to this problem has practical advantages over other suggested solutions.",0
"understanding immune memory to severe acute respiratory syndrome coronavirus 2 (sars-cov-2) is critical for improving diagnostics and vaccines and for assessing the likely future course of the covid-19 pandemic. we analyzed multiple compartments of circulating immune memory to sars-cov-2 in 254 samples from 188 covid-19 cases, including 43 samples at ≥6 months after infection. immunoglobulin g (igg) to the spike protein was relatively stable over 6+ months. spike-specific memory b cells were more abundant at 6 months than at 1 month after symptom onset. sars-cov-2-specific cd4 + t cells and cd8 + t cells declined with a half-life of 3 to 5 months. by studying antibody, memory b cell, cd4 + t cell, and cd8 + t cell memory to sars-cov-2 in an integrated manner, we observed that each component of sars-cov-2 immune memory exhibited distinct kinetics.",0
"there is strong evidence of brain-related abnormalities in covid-19 1-13 . however, it remains unknown whether the impact of sars-cov-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. here we investigated brain changes in 785 participants of uk biobank (aged 51-81 years) who were imaged twice using magnetic resonance imaging, including 401 cases who tested positive for infection with sars-cov-2 between their two scans-with 141 days on average separating their diagnosis and the second scan-as well as 384 controls. the availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. we identified significant longitudinal effects when comparing the two groups, including (1) a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; (2) greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and (3) a greater reduction in global brain size in the sars-cov-2 cases. the participants who were infected with sars-cov-2 also showed on average a greater cognitive decline between the two time points. importantly, these imaging and cognitive longitudinal effects were still observed after excluding the 15 patients who had been hospitalised. these mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease through olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. whether this deleterious effect can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow-up.",0
"motivation rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. however, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. several tools have been developed to resolve this problem. however, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. results here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. in comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines. availability and implementation the source code is written in c and is available at supplementary information supplementary data are available at bioinformatics online.",0
"background the cosmin checklist is a standardized tool for assessing the methodological quality of studies on measurement properties. it contains 9 boxes, each dealing with one measurement property, with 5-18 items per box about design aspects and statistical methods. our aim was to develop a scoring system for the cosmin checklist to calculate quality scores per measurement property when using the checklist in systematic reviews of measurement properties. methods the scoring system was developed based on discussions among experts and testing of the scoring system on 46 articles from a systematic review. four response options were defined for each cosmin item (excellent, good, fair, and poor). a quality score per measurement property is obtained by taking the lowest rating of any item in a box (""worst score counts""). results specific criteria for excellent, good, fair, and poor quality for each cosmin item are described. in defining the criteria, the ""worst score counts"" algorithm was taken into consideration. this means that only fatal flaws were defined as poor quality. the scores of the 46 articles show how the scoring system can be used to provide an overview of the methodological quality of studies included in a systematic review of measurement properties. conclusions based on experience in testing this scoring system on 46 articles, the cosmin checklist with the proposed scoring system seems to be a useful tool for assessing the methodological quality of studies included in systematic reviews of measurement properties.",0
"the coronavirus disease 2019 (covid-19) epidemic emerged in wuhan, china, spread nationwide and then onto half a dozen other countries between december 2019 and early 2020. the implementation of unprecedented strict quarantine measures in china has kept a large number of people in isolation and affected many aspects of people's lives. it has also triggered a wide variety of psychological problems, such as panic disorder, anxiety and depression. this study is the first nationwide large-scale survey of psychological distress in the general population of china during the covid-19 epidemic.",0
"heavy meromyosin (hmm) forms characteristic arrowhead complexes with actin filaments in situ. these complexes are readily visualized in sectioned muscle. following hmm treatment similar complexes appear in sectioned fibroblasts, chondrogenic cells, nerve cells, and several types of epithelial cells. thin filaments freshly isolated from chondrogenic cells also bind hmm and form arrowhead structures in negatively stained preparations. hmm-filament complexes are prominent in the cortex of a variety of normal metaphase and colcemid-arrested metaphase cells. there is no detectable binding of hmm with other cellular components such as microtubules, 100-a filaments, tonofilaments, membranes, nuclei, or collagen fibrils. the significance of hmm-filament binding is discussed in view of the finding that arrowhead complexes form in types of cells not usually thought to contain actin filaments.",0
"background the psychological impact of the coronavirus disease 2019 (covid-19) outbreak and lockdown measures on the italian population are unknown. the current study assesses rates of mental health outcomes in the italian general population three to 4 weeks into lockdown measures and explores the impact of covid-19 related potential risk factors. methods a web-based survey spread throughout the internet between march 27 th and april 6 th 2020. eighteen thousand one hundred forty-seven individuals completed the questionnaire, 79.6% women. selected outcomes were post-traumatic stress symptoms (ptss), depression, anxiety, insomnia, perceived stress, and adjustment disorder symptoms (ads). seemingly unrelated logistic regression analysis was performed to identify covid-19 related risk factors. results endorsement rates for ptss were 6,604 (37%), 3,084 (17.3%) for depression, 3,700 (20.8%) for anxiety, 1,301 (7.3%) for insomnia, 3,895 (21.8%) for high perceived stress and 4,092 (22.9%) for adjustment disorder. being woman and younger age were associated with all of the selected outcomes. quarantine was associated with ptss, anxiety and ads. any recent covid-related stressful life event was associated with all the selected outcomes. discontinued working activity due to the covid-19 was associated with all the selected outcomes, except for ads; working more than usual was associated with ptss, perceived stress and ads. having a loved one deceased by covid-19 was associated with ptss, depression, perceived stress, and insomnia. conclusion we found high rates of negative mental health outcomes in the italian general population 3 weeks into the covid-19 lockdown measures and different covid-19 related risk factors. these findings warrant further monitoring on the italian population's mental health.",0
"the novel coronavirus disease-19 (covid-19) pandemic has altered our economy, society, and healthcare system. while this crisis has presented the u.s. healthcare delivery system with unprecedented challenges, the pandemic has catalyzed rapid adoption of telehealth, or the entire spectrum of activities used to deliver care at a distance. using examples reported by u.s. healthcare organizations, including ours, we describe the role that telehealth has played in transforming healthcare delivery during the 3 phases of the u.s. covid-19 pandemic: (1) stay-at-home outpatient care, (2) initial covid-19 hospital surge, and (3) postpandemic recovery. within each of these 3 phases, we examine how people, process, and technology work together to support a successful telehealth transformation. whether healthcare enterprises are ready or not, the new reality is that virtual care has arrived.",0
"schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. however, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. we subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. in particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. group differences are weak or absent during other connectivity states. dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. while important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences.",0
"the physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease. here we present bioplex 2.0 (biophysical interactions of orfeome-derived complexes), which uses robust affinity purification-mass spectrometry methodology to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome, and constitutes, to our knowledge, the largest such network so far. with more than 56,000 candidate interactions, bioplex 2.0 contains more than 29,000 previously unknown co-associations and provides functional insights into hundreds of poorly characterized proteins while enhancing network-based analyses of domain associations, subcellular localization, and co-complex formation. unsupervised markov clustering of interacting proteins identified more than 1,300 protein communities representing diverse cellular activities. genes essential for cell fitness are enriched within 53 communities representing central cellular functions. moreover, we identified 442 communities associated with more than 2,000 disease annotations, placing numerous candidate disease genes into a cellular framework. bioplex 2.0 exceeds previous experimentally derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biology of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.",0
"cancer immunoediting is the process whereby the immune system suppresses neoplastic growth and shapes tumor immunogenicity. we previously reported that type i interferon (ifn-α/β) plays a central role in this process and that hematopoietic cells represent critical targets of type i ifn's actions. however, the specific cells affected by ifn-α/β and the functional processes that type i ifn induces remain undefined. herein, we show that type i ifn is required to initiate the antitumor response and that its actions are temporally distinct from ifn-γ during cancer immunoediting. using mixed bone marrow chimeric mice, we demonstrate that type i ifn sensitivity selectively within the innate immune compartment is essential for tumor-specific t cell priming and tumor elimination. we further show that mice lacking ifnar1 (ifn-α/β receptor 1) in dendritic cells (dcs; itgax-cre(+)ifnar1(f/f) mice) cannot reject highly immunogenic tumor cells and that cd8α(+) dcs from these mice display defects in antigen cross-presentation to cd8(+) t cells. in contrast, mice depleted of nk cells or mice that lack ifnar1 in granulocytes and macrophage populations reject these tumors normally. thus, dcs and specifically cd8α(+) dcs are functionally relevant targets of endogenous type i ifn during lymphocyte-mediated tumor rejection.",0
"objective to quantify the overall effects of bariatric surgery compared with non-surgical treatment for obesity. design systematic review and meta-analysis based on a random effects model. data sources searches of medline, embase, and the cochrane library from their inception to december 2012 regardless of language or publication status. eligibility criteria eligible studies were randomised controlled trials with ≥ 6 months of follow-up that included individuals with a body mass index ≥ 30, compared current bariatric surgery techniques with non-surgical treatment, and reported on body weight, cardiovascular risk factors, quality of life, or adverse events. results the meta-analysis included 11 studies with 796 individuals (range of mean body mass index at baseline 30-52). individuals allocated to bariatric surgery lost more body weight (mean difference -26 kg (95% confidence interval -31 to -21)) compared with non-surgical treatment, had a higher remission rate of type 2 diabetes (relative risk 22.1 (3.2 to 154.3) in a complete case analysis; 5.3 (1.8 to 15.8) in a conservative analysis assuming diabetes remission in all non-surgically treated individuals with missing data) and metabolic syndrome (relative risk 2.4 (1.6 to 3.6) in complete case analysis; 1.5 (0.9 to 2.3) in conservative analysis), greater improvements in quality of life and reductions in medicine use (no pooled data). plasma triglyceride concentrations decreased more (mean difference -0.7 mmol/l (-1.0 to -0.4) and high density lipoprotein cholesterol concentrations increased more (mean difference 0.21 mmol/l (0.1 to 0.3)). changes in blood pressure and total or low density lipoprotein cholesterol concentrations were not significantly different. there were no cardiovascular events or deaths reported after bariatric surgery. the most common adverse events after bariatric surgery were iron deficiency anaemia (15% of individuals undergoing malabsorptive bariatric surgery) and reoperations (8%). conclusions compared with non-surgical treatment of obesity, bariatric surgery leads to greater body weight loss and higher remission rates of type 2 diabetes and metabolic syndrome. however, results are limited to two years of follow-up and based on a small number of studies and individuals. systematic review registration prospero crd42012003317 (",0
"previous studies have demonstrated the presence of myocardial depression in clinical and experimental septic shock. this depression is associated with the presence of a circulating myocardial depressant substance with physical characteristics consistent with cytokines. the present study utilized an in vitro myocardial cell assay to examine the role of various human recombinant cytokines, including tumor necrosis factor (tnf)alpha and interleukin (il)1beta, in depression of cardiac myocyte contractile function induced by serum from humans with septic shock. the extent and velocity of electrically paced rat cardiac myocytes in tissue culture was quantified by a closed loop video tracking system. individually, tnf-alpha and il-1beta each caused significant concentration-dependent depression of maximum extent and peak velocity of myocyte shortening in vitro. in combination, tnf-alpha and il-1beta induced depression of myocardial cell contractility at substantially lower concentrations consistent with a synergistic effect. using immunoabsorption, removal of both tnf-alpha and il-1beta (but not either alone) from the serum of five patients with acute septic shock and marked reversible myocardial depression resulted in elimination of serum myocardial depressant activity. il-2, -4, -6, -8, -10, and interferon gamma failed to cause significant cardiac myocyte depression over a wide range of concentrations. these data demonstrate that tnf-alpha and il-1beta cause depression of myocardial cell contraction in vitro and suggest that these two cytokines act synergistically to cause sepsis-associated myocardial depression in humans.",0
"background this study explored the feasibility of using an internet survey of people with fibromyalgia (fm), with a view to providing information on demographics, sources of information, symptoms, functionality, perceived aggravating factors, perceived triggering events, health care utilization, management strategies, and medication use. methods a survey questionnaire was developed by the national fibromyalgia association (nfa) in conjunction with a task force of ""experts in the field"". the questionnaire underwent several rounds of testing to improve its face validity, content validity, clarity and readability before it was mounted on the internet. the questionnaire consisted of 121 items and is available online at the website of the national fibromyalgia association. results the questionnaire was completed by 2,569 people. most were from the united states, with at least one respondent from each of the 50 states. respondents were predominantly middle-aged caucasian females, most of whom had fm symptoms for > or = 4 years. the most common problems were morning stiffness, fatigue, nonrestorative sleep, pain, concentration, and memory. aggravating factors included: emotional distress, weather changes, insomnia, and strenuous activity. respondents rated the most effective management modalities as rest, heat, pain medications, antidepressants, and hypnotics. the most commonly used medications were: acetaminophen, ibuprofen, naproxen, cyclobenzaprine, amitriptyline, and aspirin. the medications perceived to be the most effective were: hydrocodone preparations, aprazolam, oxycodone preparations, zolpidem, cyclobenzaprine, and clonazepam. conclusion this survey provides a snap-shot of fm at the end of 2005, as reported by a self-selected population of people. this descriptive data has a heuristic function, in that it identifies several issues for further research, such as the prescribing habits of fm health care providers, the role of emotional precipitants, the impact of obesity, the significance of low back pain and the nature of fm related stiffness.",0
"objective the aim was to formulate practice guidelines for the diagnosis and treatment of polycystic ovary syndrome (pcos). participants an endocrine society-appointed task force of experts, a methodologist, and a medical writer developed the guideline. evidence this evidence-based guideline was developed using the grading of recommendations, assessment, development, and evaluation (grade) system to describe both the strength of recommendations and the quality of evidence. consensus process one group meeting, several conference calls, and e-mail communications enabled consensus. committees and members of the endocrine society and the european society of endocrinology reviewed and commented on preliminary drafts of these guidelines. two systematic reviews were conducted to summarize supporting evidence. conclusions we suggest using the rotterdam criteria for diagnosing pcos (presence of two of the following criteria: androgen excess, ovulatory dysfunction, or polycystic ovaries). establishing a diagnosis of pcos is problematic in adolescents and menopausal women. hyperandrogenism is central to the presentation in adolescents, whereas there is no consistent phenotype in postmenopausal women. evaluation of women with pcos should exclude alternate androgen-excess disorders and risk factors for endometrial cancer, mood disorders, obstructive sleep apnea, diabetes, and cardiovascular disease. hormonal contraceptives are the first-line management for menstrual abnormalities and hirsutism/acne in pcos. clomiphene is currently the first-line therapy for infertility; metformin is beneficial for metabolic/glycemic abnormalities and for improving menstrual irregularities, but it has limited or no benefit in treating hirsutism, acne, or infertility. hormonal contraceptives and metformin are the treatment options in adolescents with pcos. the role of weight loss in improving pcos status per se is uncertain, but lifestyle intervention is beneficial in overweight/obese patients for other health benefits. thiazolidinediones have an unfavorable risk-benefit ratio overall, and statins require further study.",0
"the immune epitope database (iedb, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available and easily searchable to the public. the scope of the iedb extends across immune epitope data related to all species studied and includes antibody, t cell, and mhc binding contexts associated with infectious, allergic, autoimmune, and transplant related diseases. having been publicly accessible for >10 years, the recent focus of the iedb has been improved query and reporting functionality to meet the needs of our users to access and summarize data that continues to grow in quantity and complexity. here we present an update on our current efforts and future goals.",0
"vitamin c is an essential micronutrient for humans, with pleiotropic functions related to its ability to donate electrons. it is a potent antioxidant and a cofactor for a family of biosynthetic and gene regulatory enzymes. vitamin c contributes to immune defense by supporting various cellular functions of both the innate and adaptive immune system. vitamin c supports epithelial barrier function against pathogens and promotes the oxidant scavenging activity of the skin, thereby potentially protecting against environmental oxidative stress. vitamin c accumulates in phagocytic cells, such as neutrophils, and can enhance chemotaxis, phagocytosis, generation of reactive oxygen species, and ultimately microbial killing. it is also needed for apoptosis and clearance of the spent neutrophils from sites of infection by macrophages, thereby decreasing necrosis/netosis and potential tissue damage. the role of vitamin c in lymphocytes is less clear, but it has been shown to enhance differentiation and proliferation of b- and t-cells, likely due to its gene regulating effects. vitamin c deficiency results in impaired immunity and higher susceptibility to infections. in turn, infections significantly impact on vitamin c levels due to enhanced inflammation and metabolic requirements. furthermore, supplementation with vitamin c appears to be able to both prevent and treat respiratory and systemic infections. prophylactic prevention of infection requires dietary vitamin c intakes that provide at least adequate, if not saturating plasma levels (i.e., 100-200 mg/day), which optimize cell and tissue levels. in contrast, treatment of established infections requires significantly higher (gram) doses of the vitamin to compensate for the increased inflammatory response and metabolic demand.",0
"background although studies have provided estimates of premature deaths attributable to either heat or cold in selected countries, none has so far offered a systematic assessment across the whole temperature range in populations exposed to different climates. we aimed to quantify the total mortality burden attributable to non-optimum ambient temperature, and the relative contributions from heat and cold and from moderate and extreme temperatures. methods we collected data for 384 locations in australia, brazil, canada, china, italy, japan, south korea, spain, sweden, taiwan, thailand, uk, and usa. we fitted a standard time-series poisson model for each location, controlling for trends and day of the week. we estimated temperature-mortality associations with a distributed lag non-linear model with 21 days of lag, and then pooled them in a multivariate metaregression that included country indicators and temperature average and range. we calculated attributable deaths for heat and cold, defined as temperatures above and below the optimum temperature, which corresponded to the point of minimum mortality, and for moderate and extreme temperatures, defined using cutoffs at the 2·5th and 97·5th temperature percentiles. findings we analysed 74,225,200 deaths in various periods between 1985 and 2012. in total, 7·71% (95% empirical ci 7·43-7·91) of mortality was attributable to non-optimum temperature in the selected countries within the study period, with substantial differences between countries, ranging from 3·37% (3·06 to 3·63) in thailand to 11·00% (9·29 to 12·47) in china. the temperature percentile of minimum mortality varied from roughly the 60th percentile in tropical areas to about the 80-90th percentile in temperate regions. more temperature-attributable deaths were caused by cold (7·29%, 7·02-7·49) than by heat (0·42%, 0·39-0·44). extreme cold and hot temperatures were responsible for 0·86% (0·84-0·87) of total mortality. interpretation most of the temperature-related mortality burden was attributable to the contribution of cold. the effect of days of extreme temperature was substantially less than that attributable to milder but non-optimum weather. this evidence has important implications for the planning of public-health interventions to minimise the health consequences of adverse temperatures, and for predictions of future effect in climate-change scenarios. funding uk medical research council.",0
"colorectal tumours that are wild type for kras are often sensitive to egfr blockade, but almost always develop resistance within several months of initiating therapy. the mechanisms underlying this acquired resistance to anti-egfr antibodies are largely unknown. this situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of abl, egfr, braf and mek, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. the simplest hypothesis to account for the development of resistance to egfr blockade is that rare cells with kras mutations pre-exist at low levels in tumours with ostensibly wild-type kras genes. although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. to test this hypothesis, we determined whether mutant kras dna could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-egfr antibody. we found that 9 out of 24 (38%) patients whose tumours were initially kras wild type developed detectable mutations in kras in their sera, three of which developed multiple different kras mutations. the appearance of these mutations was very consistent, generally occurring between 5 and 6 months following treatment. mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. these results suggest that the emergence of kras mutations is a mediator of acquired resistance to egfr blockade and that these mutations can be detected in a non-invasive manner. they explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.",0
"phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. the phylogeny.fr platform transparently chains programs to automatically perform these tasks. it is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. phylogeny.fr offers three main modes. the 'one click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: muscle for multiple alignment, phyml for tree building, and treedyn for tree rendering. all parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. the 'advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. the 'a la carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running blast on general or specialized databases. a guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. phylogeny.fr is available at:",0
"many questions about the biological activity and availability of small molecules remain inaccessible to investigators who could most benefit from their answers. to narrow the gap between chemoinformatics and biology, we have developed a suite of ligand annotation, purchasability, target, and biology association tools, incorporated into zinc and meant for investigators who are not computer specialists. the new version contains over 120 million purchasable ""drug-like"" compounds--effectively all organic molecules that are for sale--a quarter of which are available for immediate delivery. zinc connects purchasable compounds to high-value ones such as metabolites, drugs, natural products, and annotated compounds from the literature. compounds may be accessed by the genes for which they are annotated as well as the major and minor target classes to which those genes belong. it offers new analysis tools that are easy for nonspecialists yet with few limitations for experts. zinc retains its original 3d roots--all molecules are available in biologically relevant, ready-to-dock formats. zinc is freely available at",0
"the specific tissue changes which follow the deprivation of fat-soluble vitamin a in albino white rats and in the human concerns epithelial tissues. this effect is the substitution of stratified keratinizing epithelium for normal epithelium in various parts of the respiratory tract, alimentary tract, eyes, and paraocular glands and the genitourinary tract. we have described the morphological sequences which clearly show that the replacement of epithelium arises from focal proliferation of cells arising from the original epithelium and not by differentiation or change of preexisting cells. young rats respond to the deficiency more promptly than adults. growth activity of epithelium is not diminished. on the contrary, there is convincing evidence that it is greatly augmented. in a few of our animals the behavior of the replacing epithelium in respect to numbers of mitotic figures and response on the part of connective tissue and blood vessels suggests the acquisition of neoplastic properties. while the epitheliums which are the seats of these changes are largely of covering types, glandular epithelium is involved, specifically in the paraocular glands and salivary glands. it is highly probable also that the epithelium of gland ducts, respiratory mucosa, and genitourinary tract have secretory functions so that we conclude that the deficiency results in loss of specific (chemical) functions of the epitheliums concerned, while the power of growth becomes augmented. explanation for the substitution of a chemically inactive (nonsecretory) epithelium, common in type for all locations, remains a matter of speculation. we can only speculate also in regard to the absence of change in the epithelium of such organ as the liver, parenchyma of the kidney, stomach, and intestines. the significance of the order or sequence in which different organs exhibit this change has not been determined. in general the respiratory mucosa in nares, trachea, and bronchi respond first, then the salivary glands, eye, genitourinary tract, then paraocular glands and pancreas, although as has been noted there are exceptions to this order. our studies show that the mitochondrial apparatus is not primarily affected. study of individual cells indicates that the first morphological evidence of avitaminosis will be found in the nucleus. we have not devoted sufficient study to be certain, but an increase of chromatin and in some instances in size of nucleoli are early morphological manifestations. other important effects of fat-soluble a deficiency are atrophy of glandular organs, emaciation, localized edema of testes, submaxillary gland, and connective tissue structures of the lungs and focal myocardial lesions. from our own limited experience with rats fed on a water-soluble b deficient diet and from work by cramer, drew, and mottram, the loss of fat in water-soluble b deficiency is as great, if not greater than in vitamin a deuciency, so that tor tne present we assume that this is not a specific manifestation of any one avitaminosis. the same applies to glandular atrophy. both of these effects probably concern the nutrition as a whole and may be ascribed to inanition. the occurrence of transient edema in testes and salivary gland coinciding with a period of maximum atrophic change, suggests the hypothesis that this edema is the result of failure of epithelium to utilize transported material, which leads further to the hypothesis that the capillaries of these organs are differentiated in regard to permeability to the respective materials utilized by the cells. it would seem that in the case of the testis we have a unique instance of complete atrophy producible at will without impairment of circulation and supporting tissues. this phenomenon may possibly be followed with advantage in the study of the mechanism of edema. vascularization of the cornea, as we have shown it to be independent of infection, must be a physiological response to the increased demands of the rapidly growing epithelium which has replaced the corneal epithelium. we have assumed throughout this work that the diet on which we kept our animals was deficient in respect to a single substance or group of substances having similar physiological properties, designated by the term fat-soluble vitamin a. whether or not more than one so called vitamin or accessory substance was missing in the diet we employed does not affect the theoretical importance of the morphological results. work by evans and bishop would indicate that other factors affecting fertility in addition to the so called antixerophthalmic or vitamin a factor may have been missing. our own experience leads us to believe the specific effects we have described upon epithelial tissues were in all probability due to withdrawal of a single factor. we have shown how these effects, that is the replacement of uterine epithelium by keratinizing epithelium can account for sterility in the female. whether or not the atrophy of the testis is due to the same factor remains to be proved, but presumptive evidence is strong that this is the case. the study of the reverse changes that follow in the rapid amelioration when the rats are restored to an adequate diet has been begun and will be reported later. we have shown that the substitution of keratinizing epithelium in all locations is not secondary to infections, and presumably is a primary effect of the withdrawal of factors essential for the chemical activities or maintenance of differentiation of the epitheliums concerned. it is, of course, possible that the phenomenon is produced in a roundabout way in that it may be secondary to the effects of the avitaminosis upon the metabolism of tissue-sustaining substances. this possibility is supported by the cessation of growth of the skeleton and teeth, although we know that other avitaminoses produce retardation of growth.",0
"the adams (a disintegrin and metalloproteinase) are a fascinating family of transmembrane and secreted proteins with important roles in regulating cell phenotype via their effects on cell adhesion, migration, proteolysis and signalling. though all adams contain metalloproteinase domains, in humans only 13 of the 21 genes in the family encode functional proteases, indicating that at least for the other eight members, protein-protein interactions are critical aspects of their biological functions. the functional adam metalloproteinases are involved in ""ectodomain shedding"" of diverse growth factors, cytokines, receptors and adhesion molecules. the archetypal activity is shown by adam-17 (tumour necrosis factor-alpha convertase, tace), which is the principal protease involved in the activation of pro-tnf-alpha, but whose sheddase functions cover a broad range of cell surface molecules. in particular, adam-17 is required for generation of the active forms of epidermal growth factor receptor (egfr) ligands, and its function is essential for the development of epithelial tissues. several other adams have important sheddase functions in particular tissue contexts. another major family member, adam-10, is a principal player in signalling via the notch and eph/ephrin pathways. for a growing number of substrates, foremost among them being notch, cleavage by adam sheddases is essential for their subsequent ""regulated intramembrane proteolysis"" (rip), which generates cleaved intracellular domains that translocate to the nucleus and regulate gene transcription. several adams play roles in spermatogenesis and sperm function, potentially by effecting maturation of sperm and their adhesion and migration in the uterus. other non-catalytic adams function in the cns via effects on guidance mechanisms. the adam family are thus fundamental to many control processes in development and homeostasis, and unsurprisingly they are also linked to pathological states when their functions are dysregulated, including cancer, cardiovascular disease, asthma, alzheimer's disease. this review will provide an overview of current knowledge of the human adams, discussing their structure, function, regulation and disease involvement.",0
"glucose production by the liver is essential for providing a substrate for the brain during fasting. the inability of insulin to suppress hepatic glucose output is a major aetiological factor in the hyperglycaemia of type-2 diabetes mellitus and other diseases of insulin resistance. for fifty years, one of the few classes of therapeutics effective in reducing glucose production has been the biguanides, which include phenformin and metformin, the latter the most frequently prescribed drug for type-2 diabetes. nonetheless, the mechanism of action of biguanides remains imperfectly understood. the suggestion a decade ago that metformin reduces glucose synthesis through activation of the enzyme amp-activated protein kinase (ampk) has recently been challenged by genetic loss-of-function experiments. here we provide a novel mechanism by which metformin antagonizes the action of glucagon, thus reducing fasting glucose levels. in mouse hepatocytes, metformin leads to the accumulation of amp and related nucleotides, which inhibit adenylate cyclase, reduce levels of cyclic amp and protein kinase a (pka) activity, abrogate phosphorylation of critical protein targets of pka, and block glucagon-dependent glucose output from hepatocytes. these data support a mechanism of action for metformin involving antagonism of glucagon, and suggest an approach for the development of antidiabetic drugs.",0
"in the current context of the global pandemic of coronavirus disease-2019 (covid-19), health professionals are working with social scientists to inform government policy on how to slow the spread of the virus. an increasing amount of social scientific research has looked at the role of public message framing, for instance, but few studies have thus far examined the role of individual differences in emotional and personality-based variables in predicting virus-mitigating behaviors. in this study, we recruited a large international community sample ( n = 324) to complete measures of self-perceived risk of contracting covid-19, fear of the virus, moral foundations, political orientation, and behavior change in response to the pandemic. consistently, the only predictor of positive behavior change (e.g., social distancing, improved hand hygiene) was fear of covid-19, with no effect of politically relevant variables. we discuss these data in relation to the potentially functional nature of fear in global health crises.",0
"identifying homology relationships between sequences is fundamental to biological research. here we provide a novel orthogroup inference algorithm called orthofinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. using real benchmark datasets we demonstrate that orthofinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. furthermore, we demonstrate the utility of orthofinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships.",0
"background data on patients with covid-19 who have cancer are lacking. here we characterise the outcomes of a cohort of patients with cancer and covid-19 and identify potential prognostic factors for mortality and severe illness. methods in this cohort study, we collected de-identified data on patients with active or previous malignancy, aged 18 years and older, with confirmed severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection from the usa, canada, and spain from the covid-19 and cancer consortium (ccc19) database for whom baseline data were added between march 17 and april 16, 2020. we collected data on baseline clinical conditions, medications, cancer diagnosis and treatment, and covid-19 disease course. the primary endpoint was all-cause mortality within 30 days of diagnosis of covid-19. we assessed the association between the outcome and potential prognostic variables using logistic regression analyses, partially adjusted for age, sex, smoking status, and obesity. this study is registered with clinicaltrials.gov, nct04354701, and is ongoing. findings of 1035 records entered into the ccc19 database during the study period, 928 patients met inclusion criteria for our analysis. median age was 66 years (iqr 57-76), 279 (30%) were aged 75 years or older, and 468 (50%) patients were male. the most prevalent malignancies were breast (191 ) and prostate (152 ). 366 (39%) patients were on active anticancer treatment, and 396 (43%) had active (measurable) cancer. at analysis (may 7, 2020), 121 (13%) patients had died. in logistic regression analysis, independent factors associated with increased 30-day mortality, after partial adjustment, were: increased age (per 10 years; partially adjusted odds ratio 1·84, 95% ci 1·53-2·21), male sex (1·63, 1·07-2·48), smoking status (former smoker vs never smoked: 1·60, 1·03-2·47), number of comorbidities (two vs none: 4·50, 1·33-15·28), eastern cooperative oncology group performance status of 2 or higher (status of 2 vs 0 or 1: 3·89, 2·11-7·18), active cancer (progressing vs remission: 5·20, 2·77-9·77), and receipt of azithromycin plus hydroxychloroquine (vs treatment with neither: 2·93, 1·79-4·79; confounding by indication cannot be excluded). compared with residence in the us-northeast, residence in canada (0·24, 0·07-0·84) or the us-midwest (0·50, 0·28-0·90) were associated with decreased 30-day all-cause mortality. race and ethnicity, obesity status, cancer type, type of anticancer therapy, and recent surgery were not associated with mortality. interpretation among patients with cancer and covid-19, 30-day all-cause mortality was high and associated with general risk factors and risk factors unique to patients with cancer. longer follow-up is needed to better understand the effect of covid-19 on outcomes in patients with cancer, including the ability to continue specific cancer treatments. funding american cancer society, national institutes of health, and hope foundation for cancer research.",0
"background coronavirus disease 2019 (covid-19) may disproportionately affect people with cardiovascular disease. concern has been aroused regarding a potential harmful effect of angiotensin-converting-enzyme (ace) inhibitors and angiotensin-receptor blockers (arbs) in this clinical context. methods using an observational database from 169 hospitals in asia, europe, and north america, we evaluated the relationship of cardiovascular disease and drug therapy with in-hospital death among hospitalized patients with covid-19 who were admitted between december 20, 2019, and march 15, 2020, and were recorded in the surgical outcomes collaborative registry as having either died in the hospital or survived to discharge as of march 28, 2020. results of the 8910 patients with covid-19 for whom discharge status was available at the time of the analysis, a total of 515 died in the hospital (5.8%) and 8395 survived to discharge. the factors we found to be independently associated with an increased risk of in-hospital death were an age greater than 65 years (mortality of 10.0%, vs. 4.9% among those ≤65 years of age; odds ratio, 1.93; 95% confidence interval , 1.60 to 2.41), coronary artery disease (10.2%, vs. 5.2% among those without disease; odds ratio, 2.70; 95% ci, 2.08 to 3.51), heart failure (15.3%, vs. 5.6% among those without heart failure; odds ratio, 2.48; 95% ci, 1.62 to 3.79), cardiac arrhythmia (11.5%, vs. 5.6% among those without arrhythmia; odds ratio, 1.95; 95% ci, 1.33 to 2.86), chronic obstructive pulmonary disease (14.2%, vs. 5.6% among those without disease; odds ratio, 2.96; 95% ci, 2.00 to 4.40), and current smoking (9.4%, vs. 5.6% among former smokers or nonsmokers; odds ratio, 1.79; 95% ci, 1.29 to 2.47). no increased risk of in-hospital death was found to be associated with the use of ace inhibitors (2.1% vs. 6.1%; odds ratio, 0.33; 95% ci, 0.20 to 0.54) or the use of arbs (6.8% vs. 5.7%; odds ratio, 1.23; 95% ci, 0.87 to 1.74). conclusions our study confirmed previous observations suggesting that underlying cardiovascular disease is associated with an increased risk of in-hospital death among patients hospitalized with covid-19. our results did not confirm previous concerns regarding a potential harmful association of ace inhibitors or arbs with in-hospital death in this clinical context. (funded by the william harvey distinguished chair in advanced cardiovascular medicine at brigham and women's hospital.).",0
"patients with chronic kidney disease (ckd) exhibit an elevated cardiovascular risk manifesting as coronary artery disease, heart failure, arrhythmias, and sudden cardiac death. although the incidence and prevalence of cardiovascular events is already significantly higher in patients with early ckd stages (ckd stages 1-3) compared with the general population, patients with advanced ckd stages (ckd stages 4-5) exhibit a markedly elevated risk. cardiovascular rather than end-stage kidney disease (ckd stage 5) is the leading cause of death in this high-risk population. ckd causes a systemic, chronic proinflammatory state contributing to vascular and myocardial remodeling processes resulting in atherosclerotic lesions, vascular calcification, and vascular senescence as well as myocardial fibrosis and calcification of cardiac valves. in this respect, ckd mimics an accelerated aging of the cardiovascular system. this overview article summarizes the current understanding and clinical consequences of cardiovascular disease in ckd.",0
"p53 binding protein 1 (53bp1), a protein proposed to function as a transcriptional coactivator of the p53 tumor suppressor, has brct domains with high homology to the saccharomyces cerevisiae rad9p dna damage checkpoint protein. to examine whether 53bp1 has a role in the cellular response to dna damage, we probed its intracellular localization by immunofluorescence. in untreated primary cells and u2os osteosarcoma cells, 53bp1 exhibited diffuse nuclear staining; whereas, within 5-15 min after exposure to ionizing radiation (ir), 53bp1 localized at discreet nuclear foci. we propose that these foci represent sites of processing of dna double-strand breaks (dsbs), because they were induced by ir and chemicals that cause dsbs, but not by ultraviolet light; their peak number approximated the number of dsbs induced by ir and decreased over time with kinetics that parallel the rate of dna repair; and they colocalized with ir-induced mre11/nbs and gamma-h2ax foci, which have been previously shown to localize at sites of dsbs. formation of 53bp1 foci after irradiation was not dependent on ataxia-telangiectasia mutated (atm), nijmegen breakage syndrome (nbs1), or wild-type p53. thus, the fast kinetics of 53bp1 focus formation after irradiation and the lack of dependency on atm and nbs1 suggest that 53bp1 functions early in the cellular response to dna dsbs.",0
"current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. several sophisticated software packages (e.g., afni, brainvoyager, fsl, freesurfer, nipy, r, spm) are used to process and analyze large and often diverse (highly multi-dimensional) data. however, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) no uniform access to neuroimaging analysis software and usage information; (2) no framework for comparative algorithm development and dissemination; (3) personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) neuroimaging software packages do not address computational efficiency; and (5) methods sections in journal articles are inadequate for reproducing results. to address these issues, we present nipype (neuroimaging in python: pipelines and interfaces; an open-source, community-developed, software package, and scriptable library. nipype solves the issues by providing interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using workflows. nipype provides an environment that encourages interactive exploration of algorithms, eases the design of workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. nipype is berkeley software distribution licensed, allowing anyone unrestricted usage. an open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.",0
"this study aimed to assess and compare the immediate stress and psychological impact experienced by people with and without psychiatric illnesses during the peak of 2019 coronavirus disease (covid-19) epidemic with strict lockdown measures. seventy-six psychiatric patients and 109 healthy control subjects were recruited from chongqing, china and completed a survey on demographic data, physical symptoms during the past 14 days and a range of psychiatric symptoms using the impact of event scale-revised (ies-r), depression, anxiety and stress scale (dass-21) and insomnia severity index (isi). ies-r measures ptsd symptoms in survivorship after an event. dass-21 is based on tripartite model of psychopathology that comprise a general distress construct with distinct characteristics. the mean ies-r, dass-21 anxiety, depression and stress subscale and isi scores were higher in psychiatric patients than healthy controls (p < 0.001). serious worries about their physical health, anger and impulsivity and intense suicidal ideation were significantly higher in psychiatric patients than healthy controls (p < 0.05). more than one-third of psychiatric patients might fulfil the diagnostic criteria post-traumatic stress disorder (ptsd). more than one-quarter of psychiatric patients suffered from moderately severe to severe insomnia. respondents who reported no change, poor or worse physical health status and had a psychiatric illness were significantly more likely to have higher mean ies-r, dass depression, anxiety and stress subscale scores and isi scores (p < 0.05). this study confirms the severity of negative psychological impact on psychiatric patients during the covid-19 epidemic with strict lockdown measures. understanding the psychological impact on psychiatric patients during the covid-19 pandemic has the potential to provide insight into how to develop a new immunopsychiatry service. further research is required to compare pro-inflammatory cytokines between psychiatric patients and healthy controls during the pandemic.",0
"in the present article, we introduce opensesame, a graphical experiment builder for the social sciences. opensesame is free, open-source, and cross-platform. it features a comprehensive and intuitive graphical user interface and supports python scripting for complex tasks. additional functionality, such as support for eyetrackers, input devices, and video playback, is available through plug-ins. opensesame can be used in combination with existing software for creating experiments.",0
"background electronic health resources are helpful only when people are able to use them, yet there remain few tools available to assess consumers' capacity for engaging in ehealth. over 40% of us and canadian adults have low basic literacy levels, suggesting that ehealth resources are likely to be inaccessible to large segments of the population. using information technology for health requires ehealth literacy-the ability to read, use computers, search for information, understand health information, and put it into context. the ehealth literacy scale (eheals) was designed (1) to assess consumers' perceived skills at using information technology for health and (2) to aid in determining the fit between ehealth programs and consumers. objectives the eheals is an 8-item measure of ehealth literacy developed to measure consumers' combined knowledge, comfort, and perceived skills at finding, evaluating, and applying electronic health information to health problems. the objective of the study was to psychometrically evaluate the properties of the eheals within a population context. a youth population was chosen as the focus for the initial development primarily because they have high levels of ehealth use and familiarity with information technology tools. methods data were collected at baseline, post-intervention, and 3- and 6-month follow-up using control group data as part of a single session, randomized intervention trial evaluating web-based ehealth programs. scale reliability was tested using item analysis for internal consistency (coefficient alpha) and test-retest reliability estimates. principal components factor analysis was used to determine the theoretical fit of the measures with the data. results a total of 664 participants (370 boys; 294 girls) aged 13 to 21 (mean = 14.95; sd = 1.24) completed the eheals at four time points over 6 months. item analysis was performed on the 8-item scale at baseline, producing a tight fitting scale with alpha = .88. item-scale correlations ranged from r = .51 to .76. test-retest reliability showed modest stability over time from baseline to 6-month follow-up (r = .68 to .40). principal components analysis produced a single factor solution (56% of variance). factor loadings ranged from .60 to .84 among the 8 items. conclusions the eheals reliably and consistently captures the ehealth literacy concept in repeated administrations, showing promise as tool for assessing consumer comfort and skill in using information technology for health. within a clinical environment, the eheals has the potential to serve as a means of identifying those who may or may not benefit from referrals to an ehealth intervention or resource. further research needs to examine the applicability of the eheals to other populations and settings while exploring the relationship between ehealth literacy and health care outcomes.",0
"dna amplification is essential to most nucleic acid testing strategies, but established techniques require sophisticated equipment or complex experimental procedures, and their uptake outside specialised laboratories has been limited. our novel approach, recombinase polymerase amplification (rpa), couples isothermal recombinase-driven primer targeting of template material with strand-displacement dna synthesis. it achieves exponential amplification with no need for pretreatment of sample dna. reactions are sensitive, specific, and rapid and operate at constant low temperature. we have also developed a probe-based detection system. key aspects of the combined rpa amplification/detection process are illustrated by a test for the pathogen methicillin-resistant staphylococcus aureus. the technology proves to be sensitive to fewer than ten copies of genomic dna. furthermore, products can be detected in a simple sandwich assay, thereby establishing an instrument-free dna testing system. this unique combination of properties is a significant advance in the development of portable and widely accessible nucleic acid-based tests.",0
"adoptive t-cell therapy with gene-modified t cells expressing a tumor-reactive t-cell receptor or chimeric antigen receptor (car) is a rapidly growing field of translational medicine and has shown success in the treatment of b-cell malignancies and solid tumors. in all reported trials, patients have received t-cell products comprising random compositions of cd4(+) and cd8(+) naive and memory t cells, meaning that each patient received a different therapeutic agent. this variation may have influenced the efficacy of t-cell therapy, and complicates comparison of outcomes between different patients and across trials. we analyzed cd19 car-expressing effector t cells derived from different subsets (cd4(+)/cd8(+) naive, central memory, effector memory). t cells derived from each of the subsets were efficiently transduced and expanded, but showed clear differences in effector function and proliferation in vitro and in vivo. combining the most potent cd4(+) and cd8(+) car-expressing subsets, resulted in synergistic antitumor effects in vivo. we show that car-t-cell products generated from defined t-cell subsets can provide uniform potency compared with products derived from unselected t cells that vary in phenotypic composition. these findings have important implications for the formulation of t-cell products for adoptive therapies.",0
"background meta-analyses have become an essential tool in synthesizing evidence on clinical and epidemiological questions derived from a multitude of similar studies assessing the particular issue. appropriate and accessible statistical software is needed to produce the summary statistic of interest. methods metaprop is a statistical program implemented to perform meta-analyses of proportions in stata. it builds further on the existing stata procedure metan which is typically used to pool effects (risk ratios, odds ratios, differences of risks or means) but which is also used to pool proportions. metaprop implements procedures which are specific to binomial data and allows computation of exact binomial and score test-based confidence intervals. it provides appropriate methods for dealing with proportions close to or at the margins where the normal approximation procedures often break down, by use of the binomial distribution to model the within-study variability or by allowing freeman-tukey double arcsine transformation to stabilize the variances. metaprop was applied on two published meta-analyses: 1) prevalence of hpv-infection in women with a pap smear showing asc-us; 2) cure rate after treatment for cervical precancer using cold coagulation. results the first meta-analysis showed a pooled hpv-prevalence of 43% (95% ci: 38%-48%). in the second meta-analysis, the pooled percentage of cured women was 94% (95% ci: 86%-97%). conclusion by using metaprop, no studies with 0% or 100% proportions were excluded from the meta-analysis. furthermore, study specific and pooled confidence intervals always were within admissible values, contrary to the original publication, where metan was used.",0
"b-raf is the most frequently mutated protein kinase in human cancers. the finding that oncogenic mutations in braf are common in melanoma, followed by the demonstration that these tumours are dependent on the raf/mek/erk pathway, offered hope that inhibition of b-raf kinase activity could benefit melanoma patients. herein, we describe the structure-guided discovery of plx4032 (rg7204), a potent inhibitor of oncogenic b-raf kinase activity. preclinical experiments demonstrated that plx4032 selectively blocked the raf/mek/erk pathway in braf mutant cells and caused regression of braf mutant xenografts. toxicology studies confirmed a wide safety margin consistent with the high degree of selectivity, enabling phase 1 clinical trials using a crystalline formulation of plx4032 (ref. 5). in a subset of melanoma patients, pathway inhibition was monitored in paired biopsy specimens collected before treatment initiation and following two weeks of treatment. this analysis revealed substantial inhibition of erk phosphorylation, yet clinical evaluation did not show tumour regressions. at higher drug exposures afforded by a new amorphous drug formulation, greater than 80% inhibition of erk phosphorylation in the tumours of patients correlated with clinical response. indeed, the phase 1 clinical data revealed a remarkably high 81% response rate in metastatic melanoma patients treated at an oral dose of 960 mg twice daily. these data demonstrate that braf-mutant melanomas are highly dependent on b-raf kinase activity.",0
"statistical errors are common in scientific literature and about 50% of the published articles have at least one error. the assumption of normality needs to be checked for many statistical procedures, namely parametric tests, because their validity depends on it. the aim of this commentary is to overview checking for normality in statistical analysis using spss.",0
"the dystrophin-glycoprotein complex was tested for interaction with several components of the extracellular matrix as well as actin. the 156-kd dystrophin-associated glycoprotein (156-kd dystroglycan) specifically bound laminin in a calcium-dependent manner and was inhibited by nacl (ic50 = 250 mm) but was not affected by 1,000-fold (wt/wt) excesses of lactose, ikvav, or yigsr peptides. laminin binding was inhibited by heparin (ic50 = 100 micrograms/ml), suggesting that one of the heparin-binding domains of laminin is involved in binding dystroglycan while negatively charged oligosaccharide moieties on dystroglycan were found to be necessary for its laminin-binding activity. no interaction between any component of the dystrophin-glycoprotein complex and fibronectin, collagen i, collagen iv, entactin, or heparan sulfate proteoglycan was detected by 125i-protein overlay and/or extracellular matrix protein-sepharose precipitation. in addition, laminin-sepharose quantitatively precipitated purified dystrophin-glycoprotein complex, demonstrating that the laminin-binding site is accessible when dystroglycan is associated with the complex. dystroglycan of nonmuscle tissues also bound laminin. however, the other proteins of the striated muscle dystrophin-glycoprotein complex appear to be absent, antigenically dissimilar or less tightly associated with dystroglycan in nonmuscle tissues. finally, we show that the dystrophin-glycoprotein complex cosediments with f-actin but does not bind calcium or calmodulin. our results support a role for the striated muscle dystrophin-glycoprotein complex in linking the actin-based cytoskeleton with the extracellular matrix. furthermore, our results suggest that dystrophin and dystroglycan may play substantially different functional roles in nonmuscle tissues.",0
"drugbank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. the database contains >4100 drug entries including >800 fda approved small molecule and biotech drugs as well as >3200 experimental drugs. additionally, >14,000 protein or drug target sequences are linked to these drug entries. each drugcard entry contains >80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. many data fields are hyperlinked to other databases (kegg, pubchem, chebi, pdb, swiss-prot and genbank) and a variety of structure viewing applets. the database is fully searchable supporting extensive text, sequence, chemical structure and relational query searches. potential applications of drugbank include in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. drugbank is available at",0
"motivation the enormous amount of short reads generated by the new dna sequencing technologies call for the development of fast and accurate read alignment programs. a first generation of hash table-based methods has been developed, including maq, which is accurate, feature rich and fast enough to align short reads from a single individual. however, maq does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. the speed of maq is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. results we implemented burrows-wheeler alignment tool (bwa), a new read alignment package that is based on backward search with burrows-wheeler transform (bwt), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. bwa supports both base space reads, e.g. from illumina sequencing machines, and color space reads from ab solid machines. evaluations on both simulated and real data suggest that bwa is approximately 10-20x faster than maq, while achieving similar accuracy. in addition, bwa outputs alignment in the new standard sam (sequence alignment/map) format. variant calling and other downstream analyses after the alignment can be achieved with the open source samtools software package. availability",0
"antibodies that immunoprecipitate (125)i-alpha-dendrotoxin-labelled voltage-gated potassium channels extracted from mammalian brain tissue have been identified in patients with neuromyotonia, morvan's syndrome, limbic encephalitis and a few cases of adult-onset epilepsy. these conditions often improve following immunomodulatory therapies. however, the proportions of the different syndromes, the numbers with associated tumours and the relationships with potassium channel subunit antibody specificities have been unclear. we documented the clinical phenotype and tumour associations in 96 potassium channel antibody positive patients (titres >400 pm). five had thymomas and one had an endometrial adenocarcinoma. to define the antibody specificities, we looked for binding of serum antibodies and their effects on potassium channel currents using human embryonic kidney cells expressing the potassium channel subunits. surprisingly, only three of the patients had antibodies directed against the potassium channel subunits. by contrast, we found antibodies to three proteins that are complexed with (125)i-alpha-dendrotoxin-labelled potassium channels in brain extracts: (i) contactin-associated protein-2 that is localized at the juxtaparanodes in myelinated axons; (ii) leucine-rich, glioma inactivated 1 protein that is most strongly expressed in the hippocampus; and (iii) tag-1/contactin-2 that associates with contactin-associated protein-2. antibodies to kv1 subunits were found in three sera, to contactin-associated protein-2 in 19 sera, to leucine-rich, glioma inactivated 1 protein in 55 sera and to contactin-2 in five sera, four of which were also positive for the other antibodies. the remaining 18 sera were negative for potassium channel subunits and associated proteins by the methods employed. of the 19 patients with contactin-associated protein-antibody-2, 10 had neuromyotonia or morvan's syndrome, compared with only 3 of the 55 leucine-rich, glioma inactivated 1 protein-antibody positive patients (p < 0.0001), who predominantly had limbic encephalitis. the responses to immunomodulatory therapies, defined by changes in modified rankin scores, were good except in the patients with tumours, who all had contactin-associated-2 protein antibodies. this study confirms that the majority of patients with high potassium channel antibodies have limbic encephalitis without tumours. the identification of leucine-rich, glioma inactivated 1 protein and contactin-associated protein-2 as the major targets of potassium channel antibodies, and their associations with different clinical features, begins to explain the diversity of these syndromes; furthermore, detection of contactin-associated protein-2 antibodies should help identify the risk of an underlying tumour and a poor prognosis in future patients.",0
"introduction the phenotypic and functional differences between cells that initiate human breast tumors (cancer stem cells) and those that comprise the tumor bulk are difficult to study using only primary tumor tissue. we embarked on this study hypothesizing that breast cancer cell lines would contain analogous hierarchical differentiation programs to those found in primary breast tumors. methods eight human breast cell lines (human mammary epithelial cells, and mcf10a, mcf7, sum149, sum159, sum1315 and mda.mb.231 cells) were analyzed using flow cytometry for cd44, cd24, and epithelial-specific antigen (esa) expression. limiting dilution orthotopic injections were used to evaluate tumor initiation, while serial colony-forming unit, reconstitution and tumorsphere assays were performed to assess self-renewal and differentiation. pulse-chase bromodeoxyuridine (5-bromo-2-deoxyuridine ) labeling was used to examine cell cycle and label-retention of cancer stem cells. cells were treated with paclitaxel and 5-fluorouracil to test selective resistance to chemotherapy, and gene expression profile after chemotherapy were examined. results the percentage of cd44+/cd24- cells within cell lines does not correlate with tumorigenicity, but as few as 100 cells can form tumors when sorted for cd44+/cd24-/low/esa+. furthermore, cd44+/cd24-/esa+ cells can self-renew, reconstitute the parental cell line, retain brdu label, and preferentially survive chemotherapy. conclusion these data validate the use of cancer cell lines as models for the development and testing of novel therapeutics aimed at eradicating cancer stem cells.",0
"the human metabolome database or hmdb ( is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. first described in 2007, the hmdb is now considered the standard metabolomic resource for human metabolic studies. over the past decade the hmdb has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. this year's update, hmdb 4.0, represents the most significant upgrade to the database in its history. for instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. significant improvements have also been made to the hmdb's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. a great deal of brand new data has also been added to hmdb 4.0. this includes large quantities of predicted ms/ms and gc-ms reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. additional information on metabolite-snp interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. many other important improvements in the content, the interface, and the performance of the hmdb website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.",0
"diarrhoea and pneumonia are the leading infectious causes of childhood morbidity and mortality. we comprehensively reviewed the epidemiology of childhood diarrhoea and pneumonia in 2010-11 to inform the planning of integrated control programmes for both illnesses. we estimated that, in 2010, there were 1·731 billion episodes of diarrhoea (36 million of which progressed to severe episodes) and 120 million episodes of pneumonia (14 million of which progressed to severe episodes) in children younger than 5 years. we estimated that, in 2011, 700,000 episodes of diarrhoea and 1·3 million of pneumonia led to death. a high proportion of deaths occurs in the first 2 years of life in both diseases--72% for diarrhoea and 81% for pneumonia. the epidemiology of childhood diarrhoea and that of pneumonia overlap, which might be partly because of shared risk factors, such as undernutrition, suboptimum breastfeeding, and zinc deficiency. rotavirus is the most common cause of vaccine-preventable severe diarrhoea (associated with 28% of cases), and streptococcus pneumoniae (18·3%) of vaccine-preventable severe pneumonia. morbidity and mortality from childhood pneumonia and diarrhoea are falling, but action is needed globally and at country level to accelerate the reduction.",0
"a study has been made of the general properties of crystalline soybean trypsin inhibitor. the soy inhibitor is a stable protein of the globulin type of a molecular weight of about 24,000. its isoelectric point is at ph 4.5. it inhibits the proteolytic action approximately of an equal weight of crystalline trypsin by combining with trypsin to form a stable compound. chymotrypsin is only slightly inhibited by soy inhibitor. the reaction between chymotrypsin and the soy inhibitor consists in the formation of a reversibly dissociable compound. the inhibitor has no effect on pepsin. the inhibiting action of the soybean inhibitor is associated with the native state of the protein molecule. denaturation of the soy protein by heat or acid or alkali brings about a proportional decrease in its inhibiting action on trypsin. reversal of denaturation results in a proportional gain in the inhibiting activity. crystalline soy protein when denatured is readily digestible by pepsin, and less readily by chymotrypsin and by trypsin. methods are given for measuring trypsin and inhibitor activity and also protein concentration with the aid of spectrophotometric density measurements at 280 mmicro.",0
"background china has undergone rapid demographic and epidemiological changes in the past few decades, including striking declines in fertility and child mortality and increases in life expectancy at birth. popular discontent with the health system has led to major reforms. to help inform these reforms, we did a comprehensive assessment of disease burden in china, how it changed between 1990 and 2010, and how china's health burden compares with other nations. methods we used results of the global burden of diseases, injuries, and risk factors study 2010 (gbd 2010) for 1990 and 2010 for china and 18 other countries in the g20 to assess rates and trends in mortality, causes of death, years of life lost (ylls), years lived with disability (ylds), disability-adjusted life-years (dalys), and healthy life expectancy (hale). we present results for 231 diseases and injuries and for 67 risk factors or clusters of risk factors relevant to china. we assessed relative performance of china against g20 countries (significantly better, worse, or indistinguishable from the g20 mean) with age-standardised rates and 95% uncertainty intervals. findings the leading causes of death in china in 2010 were stroke (1·7 million deaths, 95% ui 1·5-1·8 million), ischaemic heart disease (948,700 deaths, 774,500-1,024,600), and chronic obstructive pulmonary disease (934,000 deaths, 846,600-1,032,300). age-standardised ylls in china were lower in 2010 than all emerging economies in the g20, and only slightly higher than noted in the usa. china had the lowest age-standardised yld rate in the g20 in 2010. china also ranked tenth (95% ui eighth to tenth) for hale and 12th (11th to 13th) for life expectancy. ylls from neonatal causes, infectious diseases, and injuries in children declined substantially between 1990 and 2010. mental and behavioural disorders, substance use disorders, and musculoskeletal disorders were responsible for almost half of all ylds. the fraction of dalys from ylds rose from 28·1% (95% ui 24·2-32·5) in 1990 to 39·4% (34·9-43·8) in 2010. leading causes of dalys in 2010 were cardiovascular diseases (stroke and ischaemic heart disease), cancers (lung and liver cancer), low back pain, and depression. dietary risk factors, high blood pressure, and tobacco exposure are the risk factors that constituted the largest number of attributable dalys in china. ambient air pollution ranked fourth (third to fifth; the second highest in the g20) and household air pollution ranked fifth (fourth to sixth; the third highest in the g20) in terms of the age-standardised daly rate in 2010. interpretation the rapid rise of non-communicable diseases driven by urbanisation, rising incomes, and ageing poses major challenges for china's health system, as does a shift to chronic disability. reduction of population exposures from poor diet, high blood pressure, tobacco use, cholesterol, and fasting blood glucose are public policy priorities for china, as are the control of ambient and household air pollution. these changes will require an integrated government response to improve primary care and undertake required multisectoral action to tackle key risks. analyses of disease burden provide a useful framework to guide policy responses to the changing disease spectrum in china. funding bill & melinda gates foundation.",0
"invasive strains of non-typhoidal salmonellae have emerged as a prominent cause of bloodstream infection in african adults and children, with an associated case fatality of 20-25%. the clinical presentation of invasive non-typhoidal salmonella disease in africa is diverse: fever, hepatosplenomegaly, and respiratory symptoms are common, and features of enterocolitis are often absent. the most important risk factors are hiv infection in adults, and malaria, hiv, and malnutrition in children. a distinct genotype of salmonella enterica var typhimurium, st313, has emerged as a new pathogenic clade in sub-saharan africa, and might have adapted to cause invasive disease in human beings. multidrug-resistant st313 has caused epidemics in several african countries, and has driven the use of expensive antimicrobial drugs in the poorest health services in the world. studies of systemic cellular and humoral immune responses in adults infected with hiv have revealed key host immune defects contributing to invasive non-typhoidal salmonella disease. this emerging pathogen might therefore have adapted to occupy an ecological and immunological niche provided by hiv, malaria, and malnutrition in africa. a good understanding of the epidemiology of this neglected disease will open new avenues for development and implementation of vaccine and public health strategies to prevent infections and interrupt transmission.",0
"lead is a confirmed neurotoxin, but questions remain about lead-associated intellectual deficits at blood lead levels or = 7.5 microg/dl (p = 0.015). we conclude that environmental lead exposure in children who have maximal blood lead levels < 7.5 microg/dl is associated with intellectual deficits.",0
"the severity and outcome of coronavirus disease 2019 (covid-19) largely depends on a patient's age. adults over 65 years of age represent 80% of hospitalizations and have a 23-fold greater risk of death than those under 65. in the clinic, covid-19 patients most commonly present with fever, cough and dyspnea, and from there the disease can progress to acute respiratory distress syndrome, lung consolidation, cytokine release syndrome, endotheliitis, coagulopathy, multiple organ failure and death. comorbidities such as cardiovascular disease, diabetes and obesity increase the chances of fatal disease, but they alone do not explain why age is an independent risk factor. here, we present the molecular differences between young, middle-aged and older people that may explain why covid-19 is a mild illness in some but life-threatening in others. we also discuss several biological age clocks that could be used in conjunction with genetic tests to identify both the mechanisms of the disease and individuals most at risk. finally, based on these mechanisms, we discuss treatments that could increase the survival of older people, not simply by inhibiting the virus, but by restoring patients' ability to clear the infection and effectively regulate immune responses.",0
"a simple technique is described for the preparation of collagen substrata containing 0 1% of collagen by weight, in the form of native bundles with a 640 a period, the substrata are similar in these respects to soft-tissue matrices these substrate are hydrated collagen lattices (hcls) in which the watery milieu is held within a fibrous collagen net mainly by capillary forces. hcls have been characterized in terms of the course of collagen precipitation and aggregation, ultrastructure, and their stability under various conditions. the ways in which hcls can be employed as both two- and three-dimensional substrata in cell behavioral studies are illustrated with some preliminary observations on the form, motility, adhesion, and growth of human diploid cells and two lines of malignant cells.",0
"foldx is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. the core functionality of foldx, namely the calculation of the free energy of a macromolecule based on its high-resolution 3d structure, is now publicly available through a web server at the current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. alanine scanning, the systematic truncation of side chains to alanine, is also included. in addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. this core functionality will be further extended as more foldx applications are developed.",0
"background we have previously estimated that respiratory syncytial virus (rsv) was associated with 22% of all episodes of (severe) acute lower respiratory infection (alri) resulting in 55 000 to 199 000 deaths in children younger than 5 years in 2005. in the past 5 years, major research activity on rsv has yielded substantial new data from developing countries. with a considerably expanded dataset from a large international collaboration, we aimed to estimate the global incidence, hospital admission rate, and mortality from rsv-alri episodes in young children in 2015. methods we estimated the incidence and hospital admission rate of rsv-associated alri (rsv-alri) in children younger than 5 years stratified by age and world bank income regions from a systematic review of studies published between jan 1, 1995, and dec 31, 2016, and unpublished data from 76 high quality population-based studies. we estimated the rsv-alri incidence for 132 developing countries using a risk factor-based model and 2015 population estimates. we estimated the in-hospital rsv-alri mortality by combining in-hospital case fatality ratios with hospital admission estimates from hospital-based (published and unpublished) studies. we also estimated overall rsv-alri mortality by identifying studies reporting monthly data for alri mortality in the community and rsv activity. findings we estimated that globally in 2015, 33·1 million (uncertainty range 21·6-50·3) episodes of rsv-alri, resulted in about 3·2 million (2·7-3·8) hospital admissions, and 59 600 (48 000-74 500) in-hospital deaths in children younger than 5 years. in children younger than 6 months, 1·4 million (ur 1·2-1·7) hospital admissions, and 27 300 (ur 20 700-36 200) in-hospital deaths were due to rsv-alri. we also estimated that the overall rsv-alri mortality could be as high as 118 200 (ur 94 600-149 400). incidence and mortality varied substantially from year to year in any given population. interpretation globally, rsv is a common cause of childhood alri and a major cause of hospital admissions in young children, resulting in a substantial burden on health-care services. about 45% of hospital admissions and in-hospital deaths due to rsv-alri occur in children younger than 6 months. an effective maternal rsv vaccine or monoclonal antibody could have a substantial effect on disease burden in this age group. funding the bill & melinda gates foundation.",0
"an important pathway for immune tolerance is provided by thymic-derived cd25+ cd4+ t cells that suppress other cd25- autoimmune disease-inducing t cells. the antigen-presenting cell (apc) requirements for the control of cd25+ cd4+ suppressor t cells remain to be identified, hampering their study in experimental and clinical situations. cd25+ cd4+ t cells are classically anergic, unable to proliferate in response to mitogenic antibodies to the t cell receptor complex. we now find that cd25+ cd4+ t cells can proliferate in the absence of added cytokines in culture and in vivo when stimulated by antigen-loaded dendritic cells (dcs), especially mature dcs. with high doses of dcs in culture, cd25+ cd4+ and cd25- cd4+ populations initially proliferate to a comparable extent. with current methods, one third of the antigen-reactive t cell receptor transgenic t cells enter into cycle for an average of three divisions in 3 d. the expansion of cd25+ cd4+ t cells stops by day 5, in the absence or presence of exogenous interleukin (il)-2, whereas cd25- cd4+ t cells continue to grow. cd25+ cd4+ t cell growth requires dc-t cell contact and is partially dependent upon the production of small amounts of il-2 by the t cells and b7 costimulation by the dcs. after antigen-specific expansion, the cd25+ cd4+ t cells retain their known surface features and actively suppress cd25- cd4+ t cell proliferation to splenic apcs. dcs also can expand cd25+ cd4+ t cells in the absence of specific antigen but in the presence of exogenous il-2. in vivo, both steady state and mature antigen-processing dcs induce proliferation of adoptively transferred cd25+ cd4+ t cells. the capacity to expand cd25+ cd4+ t cells provides dcs with an additional mechanism to regulate autoimmunity and other immune responses.",0
"background high plasma hdl cholesterol is associated with reduced risk of myocardial infarction, but whether this association is causal is unclear. exploiting the fact that genotypes are randomly assigned at meiosis, are independent of non-genetic confounding, and are unmodified by disease processes, mendelian randomisation can be used to test the hypothesis that the association of a plasma biomarker with disease is causal. methods we performed two mendelian randomisation analyses. first, we used as an instrument a single nucleotide polymorphism (snp) in the endothelial lipase gene (lipg asn396ser) and tested this snp in 20 studies (20,913 myocardial infarction cases, 95,407 controls). second, we used as an instrument a genetic score consisting of 14 common snps that exclusively associate with hdl cholesterol and tested this score in up to 12,482 cases of myocardial infarction and 41,331 controls. as a positive control, we also tested a genetic score of 13 common snps exclusively associated with ldl cholesterol. findings carriers of the lipg 396ser allele (2·6% frequency) had higher hdl cholesterol (0·14 mmol/l higher, p=8×10(-13)) but similar levels of other lipid and non-lipid risk factors for myocardial infarction compared with non-carriers. this difference in hdl cholesterol is expected to decrease risk of myocardial infarction by 13% (odds ratio 0·87, 95% ci 0·84-0·91). however, we noted that the 396ser allele was not associated with risk of myocardial infarction (or 0·99, 95% ci 0·88-1·11, p=0·85). from observational epidemiology, an increase of 1 sd in hdl cholesterol was associated with reduced risk of myocardial infarction (or 0·62, 95% ci 0·58-0·66). however, a 1 sd increase in hdl cholesterol due to genetic score was not associated with risk of myocardial infarction (or 0·93, 95% ci 0·68-1·26, p=0·63). for ldl cholesterol, the estimate from observational epidemiology (a 1 sd increase in ldl cholesterol associated with or 1·54, 95% ci 1·45-1·63) was concordant with that from genetic score (or 2·13, 95% ci 1·69-2·69, p=2×10(-10)). interpretation some genetic mechanisms that raise plasma hdl cholesterol do not seem to lower risk of myocardial infarction. these data challenge the concept that raising of plasma hdl cholesterol will uniformly translate into reductions in risk of myocardial infarction. funding us national institutes of health, the wellcome trust, european union, british heart foundation, and the german federal ministry of education and research.",0
"array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. numpy is the primary array programming library for the python language. it has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. for example, in astronomy, numpy was an important part of the software stack used in the discovery of gravitational waves 1 and in the first imaging of a black hole 2 . here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. numpy is the foundation upon which the scientific python ecosystem is constructed. it is so pervasive that several projects, targeting audiences with specialized needs, have developed their own numpy-like interfaces and array objects. owing to its central position in the ecosystem, numpy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (api), provides a flexible framework to support the next decade of scientific and industrial analysis.",0
"the role of the epithelial adhesion molecule uvomorulin in the formation of the epithelial junctional complex in the madin-darby canine kidney (mdck) cell line was investigated. experiments were carried out to determine whether specific inhibition of uvomorulin function would interfere selectively with the formation, stability, or function of the apical zonula adherens (za) and zonula occludens (zo), or whether it would interfere with all forms of intercellular contact including the desmosomes. the effects of blocking antibodies and fab fragments to uvomorulin on the formation of the junctional complex was examined with a ca2+ switch assay for de novo junction assembly. the formation of the zo, the za, and the desmosomes was assayed by fluorescence staining with an antibody to the tight junction-specific protein zo-1, with rhodamine-phalloidin for za-associated actin filaments, and with an anti-desmoplakin antibody, respectively. under different conditions and times of antibody treatment the extent of inhibition of the formation of each of the junctional elements was very similar. the ability of the cells to eventually overcome the inhibitory effect of the antibodies and form junctions correlated with the reappearance of uvomorulin at the regions of cell-cell contact. therefore uvomorulin seems to mediate an early adhesion event between epithelial cells that is a prerequisite for the assembly of all elements of the junctional complex. in contrast, the transepithelial electrical resistance of confluent, well-established monolayers of mdck cells grown on filters was not greatly affected by treatment with the various antibodies or fab fragments. a small transient decrease in resistance observed with the polyclonal alpha-uvomorulin igg may be due to a more subtle modulation of the junctional complex.",0
"as the field of nanomedicine emerges, there is a lag in research surrounding the topic of nanoparticle (np) toxicity, particularly concerned with mechanisms of action. the continuous emergence of bacterial resistance has challenged the research community to develop novel antibiotic agents. metal nps are among the most promising of these because show strong antibacterial activity. this review summarizes and discusses proposed mechanisms of antibacterial action of different metal nps. these mechanisms of bacterial killing include the production of reactive oxygen species, cation release, biomolecule damages, atp depletion, and membrane interaction. finally, a comprehensive analysis of the effects of nps on the regulation of genes and proteins (transcriptomic and proteomic) profiles is discussed.",0
"natural language processing (nlp) is one of the most captivating applications of deep learning. in this survey, we consider how the data augmentation training strategy can aid in its development. we begin with the major motifs of data augmentation summarized into strengthening local decision boundaries, brute force training, causality and counterfactual examples, and the distinction between meaning and form. we follow these motifs with a concrete list of augmentation frameworks that have been developed for text data. deep learning generally struggles with the measurement of generalization and characterization of overfitting. we highlight studies that cover how augmentations can construct test sets for generalization. nlp is at an early stage in applying data augmentation compared to computer vision. we highlight the key differences and promising ideas that have yet to be tested in nlp. for the sake of practical implementation, we describe tools that facilitate data augmentation such as the use of consistency regularization, controllers, and offline and online augmentation pipelines, to preview a few. finally, we discuss interesting topics around data augmentation in nlp such as task-specific augmentations, the use of prior knowledge in self-supervised learning versus data augmentation, intersections with transfer and multi-task learning, and ideas for ai-gas (ai-generating algorithms). we hope this paper inspires further research interest in text data augmentation.",0
"background neoadjuvant chemotherapy (nact) for early breast cancer can make breast-conserving surgery more feasible and might be more likely to eradicate micrometastatic disease than might the same chemotherapy given after surgery. we investigated the long-term benefits and risks of nact and the influence of tumour characteristics on outcome with a collaborative meta-analysis of individual patient data from relevant randomised trials. methods we obtained information about prerandomisation tumour characteristics, clinical tumour response, surgery, recurrence, and mortality for 4756 women in ten randomised trials in early breast cancer that began before 2005 and compared nact with the same chemotherapy given postoperatively. primary outcomes were tumour response, extent of local therapy, local and distant recurrence, breast cancer death, and overall mortality. analyses by intention-to-treat used standard regression (for response and frequency of breast-conserving therapy) and log-rank methods (for recurrence and mortality). findings patients entered the trials from 1983 to 2002 and median follow-up was 9 years (iqr 5-14), with the last follow-up in 2013. most chemotherapy was anthracycline based (3838 of 4756 women). more than two thirds (1349 of 1947) of women allocated nact had a complete or partial clinical response. patients allocated nact had an increased frequency of breast-conserving therapy (1504 of 2320 treated with nact vs 1135 of 2318 treated with adjuvant chemotherapy). nact was associated with more frequent local recurrence than was adjuvant chemotherapy: the 15 year local recurrence was 21·4% for nact versus 15·9% for adjuvant chemotherapy (5·5% increase ; rate ratio 1·37 ; p=0·0001). no significant difference between nact and adjuvant chemotherapy was noted for distant recurrence (15 year risk 38·2% for nact vs 38·0% for adjuvant chemotherapy; rate ratio 1·02 ; p=0·66), breast cancer mortality (34·4% vs 33·7%; 1·06 ; p=0·31), or death from any cause (40·9% vs 41·2%; 1·04 ; p=0·45). interpretation tumours downsized by nact might have higher local recurrence after breast-conserving therapy than might tumours of the same dimensions in women who have not received nact. strategies to mitigate the increased local recurrence after breast-conserving therapy in tumours downsized by nact should be considered-eg, careful tumour localisation, detailed pathological assessment, and appropriate radiotherapy. funding cancer research uk, british heart foundation, uk medical research council, and uk department of health.",0
"diseases of the gallbladder are common and costly. the best epidemiological screening method to accurately determine point prevalence of gallstone disease is ultrasonography. many risk factors for cholesterol gallstone formation are not modifiable such as ethnic background, increasing age, female gender and family history or genetics. conversely, the modifiable risks for cholesterol gallstones are obesity, rapid weight loss and a sedentary lifestyle. the rising epidemic of obesity and the metabolic syndrome predicts an escalation of cholesterol gallstone frequency. risk factors for biliary sludge include pregnancy, drugs like ceftiaxone, octreotide and thiazide diuretics, and total parenteral nutrition or fasting. diseases like cirrhosis, chronic hemolysis and ileal crohn's disease are risk factors for black pigment stones. gallstone disease in childhood, once considered rare, has become increasingly recognized with similar risk factors as those in adults, particularly obesity. gallbladder cancer is uncommon in developed countries. in the u.s., it accounts for only ~ 5,000 cases per year. elsewhere, high incidence rates occur in north and south american indians. other than ethnicity and female gender, additional risk factors for gallbladder cancer include cholelithiasis, advancing age, chronic inflammatory conditions affecting the gallbladder, congenital biliary abnormalities, and diagnostic confusion over gallbladder polyps.",0
"about 200 million cases of viral community-acquired pneumonia occur every year-100 million in children and 100 million in adults. molecular diagnostic tests have greatly increased our understanding of the role of viruses in pneumonia, and findings indicate that the incidence of viral pneumonia has been underestimated. in children, respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses are the agents identified most frequently in both developed and developing countries. dual viral infections are common, and a third of children have evidence of viral-bacterial co-infection. in adults, viruses are the putative causative agents in a third of cases of community-acquired pneumonia, in particular influenza viruses, rhinoviruses, and coronaviruses. bacteria continue to have a predominant role in adults with pneumonia. presence of viral epidemics in the community, patient's age, speed of onset of illness, symptoms, biomarkers, radiographic changes, and response to treatment can help differentiate viral from bacterial pneumonia. however, no clinical algorithm exists that will distinguish clearly the cause of pneumonia. no clear consensus has been reached about whether patients with obvious viral community-acquired pneumonia need to be treated with antibiotics. apart from neuraminidase inhibitors for pneumonia caused by influenza viruses, there is no clear role for use of specific antivirals to treat viral community-acquired pneumonia. influenza vaccines are the only available specific preventive measures. further studies are needed to better understand the cause and pathogenesis of community-acquired pneumonia. furthermore, regional differences in cause of pneumonia should be investigated, in particular to obtain more data from developing countries.",0
"functional enrichment analysis is an essential task for the interpretation of gene lists derived from large-scale genetic, transcriptomic and proteomic studies. webgestalt (web-based gene set analysis toolkit) has become one of the popular software tools in this field since its publication in 2005. for the last 7 years, webgestalt data holdings have grown substantially to satisfy the requirements of users from different research areas. the current version of webgestalt supports 8 organisms and 201 gene identifiers from various databases and different technology platforms, making it directly available to the fast growing omics community. meanwhile, by integrating functional categories derived from centrally and publicly curated databases as well as computational analyses, webgestalt has significantly increased the coverage of functional categories in various biological contexts including gene ontology, pathway, network module, gene-phenotype association, gene-disease association, gene-drug association and chromosomal location, leading to a total of 78 612 functional categories. finally, new interactive features, such as pathway map, hierarchical network visualization and phenotype ontology visualization have been added to webgestalt to help users better understand the enrichment results. webgestalt can be freely accessed through or",0
"background data for front-line health-care workers and risk of covid-19 are limited. we sought to assess risk of covid-19 among front-line health-care workers compared with the general community and the effect of personal protective equipment (ppe) on risk. methods we did a prospective, observational cohort study in the uk and the usa of the general community, including front-line health-care workers, using self-reported data from the covid symptom study smartphone application (app) from march 24 (uk) and march 29 (usa) to april 23, 2020. participants were voluntary users of the app and at first use provided information on demographic factors (including age, sex, race or ethnic background, height and weight, and occupation) and medical history, and subsequently reported any covid-19 symptoms. we used cox proportional hazards modelling to estimate multivariate-adjusted hazard ratios (hrs) of our primary outcome, which was a positive covid-19 test. the covid symptom study app is registered with clinicaltrials.gov, nct04331509. findings among 2 035 395 community individuals and 99 795 front-line health-care workers, we recorded 5545 incident reports of a positive covid-19 test over 34 435 272 person-days. compared with the general community, front-line health-care workers were at increased risk for reporting a positive covid-19 test (adjusted hr 11·61, 95% ci 10·93-12·33). to account for differences in testing frequency between front-line health-care workers and the general community and possible selection bias, an inverse probability-weighted model was used to adjust for the likelihood of receiving a covid-19 test (adjusted hr 3·40, 95% ci 3·37-3·43). secondary and post-hoc analyses suggested adequacy of ppe, clinical setting, and ethnic background were also important factors. interpretation in the uk and the usa, risk of reporting a positive test for covid-19 was increased among front-line health-care workers. health-care systems should ensure adequate availability of ppe and develop additional strategies to protect health-care workers from covid-19, particularly those from black, asian, and minority ethnic backgrounds. additional follow-up of these observational findings is needed. funding zoe global, wellcome trust, engineering and physical sciences research council, national institutes of health research, uk research and innovation, alzheimer's society, national institutes of health, national institute for occupational safety and health, and massachusetts consortium on pathogen readiness.",0
"meme (multiple em for motif elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. applications include the discovery of new transcription factor binding sites and protein domains. meme works by searching for repeated, ungapped sequence patterns that occur in the dna or protein sequences provided by the user. users can perform meme searches via the web server hosted by the national biomedical computation resource ( and several mirror sites. through the same web server, users can also access the motif alignment and search tool to search sequence databases for matches to motifs encoded in several popular formats. by clicking on buttons in the meme output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. this article describes the freely accessible web server and its architecture, and discusses ways to use meme effectively to find new sequence patterns in biological sequences and analyze their significance.",0
"background alteplase is effective for treatment of acute ischaemic stroke but debate continues about its use after longer times since stroke onset, in older patients, and among patients who have had the least or most severe strokes. we assessed the role of these factors in affecting good stroke outcome in patients given alteplase. methods we did a pre-specified meta-analysis of individual patient data from 6756 patients in nine randomised trials comparing alteplase with placebo or open control. we included all completed randomised phase 3 trials of intravenous alteplase for treatment of acute ischaemic stroke for which data were available. retrospective checks confirmed that no eligible trials had been omitted. we defined a good stroke outcome as no significant disability at 3-6 months, defined by a modified rankin score of 0 or 1. additional outcomes included symptomatic intracranial haemorrhage (defined by type 2 parenchymal haemorrhage within 7 days and, separately, by the sits-most definition of parenchymal type 2 haemorrhage within 36 h), fatal intracranial haemorrhage within 7 days, and 90-day mortality. findings alteplase increased the odds of a good stroke outcome, with earlier treatment associated with bigger proportional benefit. treatment within 3·0 h resulted in a good outcome for 259 (32·9%) of 787 patients who received alteplase versus 176 (23·1%) of 762 who received control (or 1·75, 95% ci 1·35-2·27); delay of greater than 3·0 h, up to 4·5 h, resulted in good outcome for 485 (35·3%) of 1375 versus 432 (30·1%) of 1437 (or 1·26, 95% ci 1·05-1·51); and delay of more than 4·5 h resulted in good outcome for 401 (32·6%) of 1229 versus 357 (30·6%) of 1166 (or 1·15, 95% ci 0·95-1·40). proportional treatment benefits were similar irrespective of age or stroke severity. alteplase significantly increased the odds of symptomatic intracranial haemorrhage (type 2 parenchymal haemorrhage definition 231 of 3391 vs 44 of 3365, or 5·55, 95% ci 4·01-7·70, p interpretation irrespective of age or stroke severity, and despite an increased risk of fatal intracranial haemorrhage during the first few days after treatment, alteplase significantly improves the overall odds of a good stroke outcome when delivered within 4·5 h of stroke onset, with earlier treatment associated with bigger proportional benefits. funding uk medical research council, british heart foundation, university of glasgow, university of edinburgh.",0
"an epithelial cell line (mdck) was used to prepare monolayers which, in vitro, develop properties of transporting epithelia. monolayers were formed by plating cells at high densities (10(6) cells/cm2) on collagen-coated nylon cloth disks to saturate the area available for attachment, thus avoiding the need for cell division. an electrical resistance developed within 4-6 h after plating and achieved a steady-state value of 104 +/- 1.8 omega-cm2 after 24 h. mature monolayers were morphologically and functionally polarized. they contained junctional complexes composed of desmosomes and tight junctions with properties similar to those of ""leaky"" epithelia. monolayers were capable of maintaining a spontaneous electrical potential sensitive to amiloride, produced a net water flux from the apical to basal side, and discriminated between na+ and cl- ions. the mdck permeability barrier behaves as a ""thin"" membrane with negatively charged sites. it has: (a) a linear conductance/concentration relationship; (b) an asymmetric instantaneous current/voltage relationship; (c) a reduced ability to discriminate between na+ and cl- caused by lowering the ph; and (d) a characteristic pattern of ionic selectivity which suggests that the negatively charged sites are highly hydrates and of medium field strength. measurements of na+ permeability of electrical and tracer methods ruled out exchange diffusion as a mechanism for ion permeation and the lack of current saturation in the i/deltapsi curves does not support the involvement of carriers. the discrimination between na+ and cl- was severely but reversibly decreased at low ph, suggesting that na+-specific channels which exclude cl- contain acidic groups dissociated at neutral ph. bound ca++ ions are involved in maintaining the integrity of the junctions in mdck monolayers as was shown by a reversible drop of resistance and opening of the junctions in ca++-free medium containing egta. several other epithelial cell lines are capable of developing a significant resistance under the conditions used to obtain mdck monolayers.",0
"objective the objective of the predict-hd study is to use genetic, neurobiological and refined clinical markers to understand the early progression of huntington's disease (hd), prior to the point of traditional diagnosis, in persons with a known gene mutation. here we estimate the approximate onset and initial course of various measurable aspects of hd relative to the time of eventual diagnosis. methods we studied 438 participants who were positive for the hd gene mutation, but did not yet meet the diagnostic criteria for hd and had no functional decline. predictability of baseline cognitive, motor, psychiatric and imaging measures was modelled non-linearly using estimated time until diagnosis (based on cag repeat length and current age) as the predictor. results estimated time to diagnosis was related to most clinical and neuroimaging markers. the patterns of association suggested the commencement of detectable changes one to two decades prior to the predicted time of clinical diagnosis. the patterns were highly robust and consistent, despite the varied types of markers and diverse measurement methodologies. conclusions these findings from the predict-hd study suggest the approximate time scale of measurable disease development, and suggest candidate disease markers for use in preventive hd trials.",0
"background the parihs framework (promoting action on research implementation in health services) has proved to be a useful practical and conceptual heuristic for many researchers and practitioners in framing their research or knowledge translation endeavours. however, as a conceptual framework it still remains untested and therefore its contribution to the overall development and testing of theory in the field of implementation science is largely unquantified. discussion this being the case, the paper provides an integrated summary of our conceptual and theoretical thinking so far and introduces a typology (derived from social policy analysis) used to distinguish between the terms conceptual framework, theory and model - important definitional and conceptual issues in trying to refine theoretical and methodological approaches to knowledge translation. secondly, the paper describes the next phase of our work, in particular concentrating on the conceptual thinking and mapping that has led to the generation of the hypothesis that the parihs framework is best utilised as a two-stage process: as a preliminary (diagnostic and evaluative) measure of the elements and sub-elements of evidence (e) and context (c), and then using the aggregated data from these measures to determine the most appropriate facilitation method. the exact nature of the intervention is thus determined by the specific actors in the specific context at a specific time and place. in the process of refining this next phase of our work, we have had to consider the wider issues around the use of theories to inform and shape our research activity; the ongoing challenges of developing robust and sensitive measures; facilitation as an intervention for getting research into practice; and finally to note how the current debates around evidence into practice are adopting wider notions that fit innovations more generally. summary the paper concludes by suggesting that the future direction of the work on the parihs framework is to develop a two-stage diagnostic and evaluative approach, where the intervention is shaped and moulded by the information gathered about the specific situation and from participating stakeholders. in order to expedite the generation of new evidence and testing of emerging theories, we suggest the formation of an international research implementation science collaborative that can systematically collect and analyse experiences of using and testing the parihs framework and similar conceptual and theoretical approaches. we also recommend further refinement of the definitions around conceptual framework, theory, and model, suggesting a wider discussion that embraces multiple epistemological and ontological perspectives.",0
"the vast majority of studies into visual processing are conducted using computer display technology. the current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. psychopy is a platform-independent experimental control system written in the python interpreted language using entirely free libraries. psychopy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. most importantly, psychopy is highly extensible and the whole system can evolve via user contributions. if a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits.",0
"the current coronavirus (covid-19) pandemic is again reminding us of the importance of using telehealth to deliver care, especially as means of reducing the risk of cross-contamination caused by close contact. for telehealth to be effective as part of an emergency response it first needs to become a routinely used part of our health system. hence, it is time to step back and ask why telehealth is not mainstreamed. in this article, we highlight key requirements for this to occur. strategies to ensure that telehealth is used regularly in acute, post-acute and emergency situations, alongside conventional service delivery methods, include flexible funding arrangements, training and accrediting our health workforce. telehealth uptake also requires a significant change in management effort and the redesign of existing models of care. implementing telehealth proactively rather than reactively is more likely to generate greater benefits in the long-term, and help with the everyday (and emergency) challenges in healthcare.",0
"recent evidence, has demonstrated an association between a subpopulation of peripheral blood mononuclear cells, morphologically identified as large granular lymphocytes (lgl), and natural killer (nk) activity. we have now evaluated more directly the role of lgl in both nk activity and antibody- dependent cellular cytotoxicity (adcc), by using highly enriched populations of lgl, obtained by centrifugation of peripheral blood mononuclear cells on percoll discontinuous density gradients. both spontaneous and interferon- augmented nk and adcc activities were exclusively associated with the lgl- enriched, low density fractions. the majority of lgl formed conjugates with nk-susceptible and antibody-coated target cells. approximately 20 percent of small conventional lymphocytes also formed conjugates with the target cells for nk, but this was not associated with cytotoxic activity. virtually all lgl were found to have receptors for the fc portion of igg (fcgammar). the frequency of lgl among blood leukocytes was 2-6 percent. lgl could be enriched to an average purity of 95 percent by combining discontinuous density gradient centrifugation with subsequent adsorptions of the low density fractions on monolayers of immobilized immune complexes. about 50 percent of lgl were found to be fcgammar-bearing t cells (t(g)), forming low affinity rosettes with sheep erythrocytes at 4 degrees c. only 10-20 percent of lgl formed high affinity rosettes with sheep erythrocytes at 29 degrees c. lgl could be enriched to a purity of more than 90 percent by depleting high affinity rosette-forming cells from low density percoll fractions. lgl were only a subpopulation of t(g) cells, because some lymphocytes with conventional morphology also adhered to the immobilized immune complex monolayers and formed high affinity rosettes with sheep erythrocytes. separation of these cells from lgl by discontinuous density gradient centrifugation indicated that they are not cytotoxic, suggesting a morphological and functional subdivision of t(g) cells. the verification in this study that virtually all human nk and k cells have a characteristic morphology adds a useful parameter to the monitoring of human lymphocytes, and the ability to purify these cells by simple physical procedures should be invaluable in their further characterization.",0
"objective physical or mental imbalance caused by harmful stimuli can induce stress to maintain homeostasis. during chronic stress, the sympathetic nervous system is hyperactivated, causing physical, psychological, and behavioral abnormalities. at present, there is no accepted standard for stress evaluation. this review aimed to survey studies providing a rationale for selecting heart rate variability (hrv) as a psychological stress indicator. methods term searches in the web of science ® , national library of medicine (pubmed), and google scholar databases yielded 37 publications meeting our criteria. the inclusion criteria were involvement of human participants, hrv as an objective psychological stress measure, and measured hrv reactivity. results in most studies, hrv variables changed in response to stress induced by various methods. the most frequently reported factor associated with variation in hrv variables was low parasympathetic activity, which is characterized by a decrease in the high-frequency band and an increase in the low-frequency band. neuroimaging studies suggested that hrv may be linked to cortical regions (e.g., the ventromedial prefrontal cortex) that are involved in stressful situation appraisal. conclusion in conclusion, the current neurobiological evidence suggests that hrv is impacted by stress and supports its use for the objective assessment of psychological health and stress.",0
"we have previously characterized a monoclonal antibody, s12, that binds only to activated platelets (mcever, r.p., and m.n. martin, 1984, j. biol. chem., 259:9799-9804). it identifies a platelet membrane protein of mr 140,000, which we have designated as gmp-140. using immunocytochemical techniques we have now localized this protein in unstimulated and thrombin-stimulated platelets. polyclonal antibodies to purified gmp-140 were used to enhance the sensitivity of detection. nonpermeabilized, unstimulated platelets, incubated with anti-gmp-140 antibodies, and then with igg-gold probes, showed very little label for gmp-140 along their plasma membranes. in contrast, thrombin-stimulated platelets exhibited at least a 50-fold increase in the amount of label along the plasma membrane. on frozen thin sections of unstimulated platelets we observed immunogold label along the alpha-granule membranes. we also employed the more sensitive technique of permeabilizing with saponin unstimulated platelets in suspension, and then incubating the cells with polyclonal anti-gmp-140 antibodies and fab-peroxidase conjugate. alpha-granule membranes showed heavy reaction product, but no other intracellular organelles were specifically labeled. these results demonstrate that gmp-140 is an alpha-granule membrane protein that is expressed on the platelet plasma membrane during degranulation.",0
"p2x receptors are cation-selective ion channels gated by extracellular atp, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. because p2x receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. here we present crystal structures of the zebrafish p2x(4) receptor in its closed, resting state. the chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. in the transmembrane pore, the 'gate' is defined by an approximately 8 a slab of protein. we define the location of three non-canonical, intersubunit atp-binding sites, and suggest that atp binding promotes subunit rearrangement and ion channel opening.",0
"background hh-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. it is based on pairwise alignment of profile hidden markov models (hmms), which represent multiple sequence alignments of homologous proteins. results we developed a single-instruction multiple-data (simd) vectorized implementation of the viterbi algorithm for profile hmm alignment and introduced various other speed-ups. these accelerated the search methods hhsearch by a factor 4 and hhblits by a factor 2 over the previous version 2.0.16. hhblits3 is ∼10× faster than psi-blast and ∼20× faster than hmmer3. jobs to perform hhsearch and hhblits searches with many query profile hmms can be parallelized over cores and over cluster servers using openmp and message passing interface (mpi). the free, open-source, gplv3-licensed software is available at . conclusion the added functionalities and increased speed of hhsearch and hhblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.",0
"in humans, the monocyte pool comprises three subsets (classical, intermediate, and nonclassical) that circulate in dynamic equilibrium. the kinetics underlying their generation, differentiation, and disappearance are critical to understanding both steady-state homeostasis and inflammatory responses. here, using human in vivo deuterium labeling, we demonstrate that classical monocytes emerge first from marrow, after a postmitotic interval of 1.6 d, and circulate for a day. subsequent labeling of intermediate and nonclassical monocytes is consistent with a model of sequential transition. intermediate and nonclassical monocytes have longer circulating lifespans (∼4 and ∼7 d, respectively). in a human experimental endotoxemia model, a transient but profound monocytopenia was observed; restoration of circulating monocytes was achieved by the early release of classical monocytes from bone marrow. the sequence of repopulation recapitulated the order of maturation in healthy homeostasis. this developmental relationship between monocyte subsets was verified by fate mapping grafted human classical monocytes into humanized mice, which were able to differentiate sequentially into intermediate and nonclassical cells.",0
"in this retrospective study, chest cts of 121 symptomatic patients infected with coronavirus disease-19 (covid-19) from four centers in china from january 18, 2020 to february 2, 2020 were reviewed for common ct findings in relationship to the time between symptom onset and the initial ct scan (i.e. early, 0-2 days (36 patients), intermediate 3-5 days (33 patients), late 6-12 days (25 patients)). the hallmarks of covid-19 infection on imaging were bilateral and peripheral ground-glass and consolidative pulmonary opacities. notably, 20/36 (56%) of early patients had a normal ct. with a longer time after the onset of symptoms, ct findings were more frequent, including consolidation, bilateral and peripheral disease, greater total lung involvement, linear opacities, ""crazy-paving"" pattern and the ""reverse halo"" sign. bilateral lung involvement was observed in 10/36 early patients (28%), 25/33 intermediate patients (76%), and 22/25 late patients (88%).",0
"we measured the urinary monoester metabolites of seven commonly used phthalates in approximately 2,540 samples collected from participants of the national health and nutrition examination survey (nhanes), 1999-2000, who were greater than or equal to 6 years of age. we found detectable levels of metabolites monoethyl phthalate (mep), monobutyl phthalate (mbp), monobenzyl phthalate (mbzp), and mono-(2-ethylhexyl) phthalate (mehp) in > 75% of the samples, suggesting widespread exposure in the united states to diethyl phthalate, dibutyl phthalate or diisobutylphthalate, benzylbutyl phthalate, and di-(2-ethylhexyl) phthalate, respectively. we infrequently detected monoisononyl phthalate, mono-cyclohexyl phthalate, and mono-n-octyl phthalate, suggesting that human exposures to di-isononyl phthalate, dioctylphthalate, and dicyclohexyl phthalate, respectively, are lower than those listed above, or the pathways, routes of exposure, or pharmacokinetic factors such as absorption, distribution, metabolism, and elimination are different. non-hispanic blacks had significantly higher concentrations of mep than did mexican americans and non-hispanic whites. compared with adolescents and adults, children had significantly higher levels of mbp, mbzp, and mehp but had significantly lower concentrations of mep. females had significantly higher concentrations of mep and mbzp than did males, but similar mehp levels. of particular interest, females of all ages had significantly higher concentrations of the reproductive toxicant mbp than did males of all ages; however, women of reproductive age (i.e., 20-39 years of age) had concentrations similar to adolescent girls and women 40 years of age. these population data on exposure to phthalates will serve an important role in public health by helping to set research priorities and by establishing a nationally representative baseline of exposure with which population levels can be compared.",0
"interpro ( is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via web-based interfaces and services. central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. interpro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and web and programmatic interfaces.",0
"we suggested recently that attention can be understood as inferring the level of uncertainty or precision during hierarchical perception. in this paper, we try to substantiate this claim using neuronal simulations of directed spatial attention and biased competition. these simulations assume that neuronal activity encodes a probabilistic representation of the world that optimizes free-energy in a bayesian fashion. because free-energy bounds surprise or the (negative) log-evidence for internal models of the world, this optimization can be regarded as evidence accumulation or (generalized) predictive coding. crucially, both predictions about the state of the world generating sensory data and the precision of those data have to be optimized. here, we show that if the precision depends on the states, one can explain many aspects of attention. we illustrate this in the context of the posner paradigm, using the simulations to generate both psychophysical and electrophysiological responses. these simulated responses are consistent with attentional bias or gating, competition for attentional resources, attentional capture and associated speed-accuracy trade-offs. furthermore, if we present both attended and non-attended stimuli simultaneously, biased competition for neuronal representation emerges as a principled and straightforward property of bayes-optimal perception.",0
"the present study demonstrates that fibroblasts associated with carcinomas stimulate tumor progression of initiated nontumorigenic epithelial cells both in an in vivo tissue recombination system and in an in vitro coculture system. human prostatic carcinoma-associated fibroblasts grown with initiated human prostatic epithelial cells dramatically stimulated growth and altered histology of the epithelial population. this effect was not detected when normal prostatic fibroblasts were grown with the initiated epithelial cells under the same experimental conditions. in contrast, carcinoma-associated fibroblasts did not affect growth of normal human prostatic epithelial cells under identical conditions. from these data, we conclude that in this human prostate cancer model, carcinoma-associated fibroblasts stimulate progression of tumorigenesis. thus, carcinoma-associated fibroblasts can direct tumor progression of an initiated prostate epithelial cell.",0
"motivation modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3d). confocal microscopy produces high-resolution 3d images, but is limited by a relatively small field of view compared with the size of large biological specimens. therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. the physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (stitching) of the whole image from individual image stacks. results to optimally stitch a large collection of 3d confocal images, we developed a method that, based on the fourier shift theorem, computes all possible translations between pairs of 3d images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3d images. this method avoids the propagation of errors by consecutive registration steps. additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. our stitching approach is fast, works on 2d and 3d images, and for small image sets does not require prior knowledge about the tile configuration. availability the implementation of this method is available as an imagej plugin distributed as a part of the fiji project (fiji is just imagej:",0
"we have used a lipophilic styryl dye, n-(3-triethylammoniumpropyl)-4- (p-diethylaminophenyl-hexatrienyl) pyridinium dibromide (fm 4-64), as a vital stain to follow bulk membrane-internalization and transport to the vacuole in yeast. after treatment for 60 min at 30 degrees c, fm 4-64 stained the vacuole membrane (ring staining pattern). fm 4-64 did not appear to reach the vacuole by passive diffusion because at 0 degree c it exclusively stained the plasma membrane (pm). the pm staining decreased after warming cells to 25 degrees c and small punctate structures became apparent in the cytoplasm within 5-10 min. after an additional 20-40 min, the pm and cytoplasmic punctate staining disappeared concomitant with staining of the vacuolar membrane. under steady state conditions, fm 4-64 staining was specific for vacuolar membranes; other membrane structures were not stained. the dye served as a sensitive reporter of vacuolar dynamics, detecting such events as segregation structure formation during mitosis, vacuole fission/fusion events, and vacuolar morphology in different classes of vacuolar protein sorting (vps) mutants. a particularly striking pattern was observed in class e mutants (e.g., vps27) where 500-700 nm organelles (presumptive prevacuolar compartments) were intensely stained with fm 4-64 while the vacuole membrane was weakly fluorescent. internalization of fm 4-64 at 15 degrees c delayed vacuolar labeling and trapped fm 4-64 in cytoplasmic intermediates between the pm and the vacuole. the intermediate structures in the cytoplasm are likely to be endosomes as their staining was temperature, time, and energy dependent. interestingly, unlike lucifer yellow uptake, vacuolar labeling by fm 4-64 was not blocked in sec18, sec14, end3, and end4 mutants, but was blocked in sec1 mutant cells. finally, using permeabilized yeast spheroplasts to reconstitute fm 4-64 transport, we found that delivery of fm 4-64 from the endosome-like intermediate compartment (labeled at 15 degrees c) to the vacuole was atp and cytosol dependent. thus, we show that fm 4-64 is a new vital stain for the vacuolar membrane, a marker for endocytic intermediates, and a fluor for detecting endosome to vacuole membrane transport in vitro.",0
"early preclinical evidence provided the rationale for programmed cell death 1 (pd-1) and programmed death ligand 1 (pd-l1) blockade as a potential form of cancer immunotherapy given that activation of the pd-1/pd-l1 axis putatively served as a mechanism for tumor evasion of host tumor antigen-specific t-cell immunity. early-phase studies investigating several humanized monoclonal igg4 antibodies targeting pd-1 and pd-l1 in advanced solid tumors paved way for the development of the first pd-1 inhibitors, nivolumab and pembrolizumab, approved by the food and drug administration (fda) in 2014. the number of fda-approved agents of this class is rapidly enlarging with indications for treatment spanning across a spectrum of malignancies. the purpose of this review is to highlight the clinical development of pd-1 and pd-l1 inhibitors in cancer therapy to date. in particular, we focus on detailing the registration trials that have led to fda-approved indications of anti-pd-1 and anti-pd-l1 therapies in cancer. as the number of pd-1/pd-l1 inhibitors continues to grow, predictive biomarkers, mechanisms of resistance, hyperprogressors, treatment duration and treatment beyond progression, immune-related toxicities, and clinical trial design are key concepts in need of further consideration to optimize the anticancer potential of this class of immunotherapy.",0
"this study investigates students' social networks and mental health before and at the time of the covid-19 pandemic in april 2020, using longitudinal data collected since 2018. we analyze change on multiple dimensions of social networks (interaction, friendship, social support, co-studying) and mental health indicators (depression, anxiety, stress, loneliness) within two cohorts of swiss undergraduate students experiencing the crisis (n = 212), and make additional comparisons to an earlier cohort which did not experience the crisis (n = 54). in within-person comparisons we find that interaction and co-studying networks had become sparser, and more students were studying alone. furthermore, students' levels of stress, anxiety, loneliness, and depressive symptoms got worse, compared to measures before the crisis. stressors shifted from fears of missing out on social life to worries about health, family, friends, and their future. exploratory analyses suggest that covid-19 specific worries, isolation in social networks, lack of interaction and emotional support, and physical isolation were associated with negative mental health trajectories. female students appeared to have worse mental health trajectories when controlling for different levels of social integration and covid-19 related stressors. as universities and researchers discuss future strategies on how to combine on-site teaching with online courses, our results indicate the importance of considering social contacts in students' mental health and offer starting points to identify and support students at higher risk of social isolation and negative psychological effects during the covid-19 pandemic.",0
"next generation sequencing (ngs) technologies provide a high-throughput means to generate large amount of sequence data. however, quality control (qc) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. further, highly efficient and fast processing tools are required to handle the large volume of datasets. here, we have developed an application, ngs qc toolkit, for quality check and filtering of high-quality data. this toolkit is a standalone and open source application freely available at all the tools in the application have been implemented in perl programming language. the toolkit is comprised of user-friendly tools for qc of sequencing data generated using roche 454 and illumina platforms, and additional tools to aid qc (sequence format converter and trimming tools) and analysis (statistics tools). a variety of options have been provided to facilitate the qc at user-defined parameters. the toolkit is expected to be very useful for the qc of ngs data to facilitate better downstream analysis.",0
"aaindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. we have added a collection of protein contact potentials to the aaindex as a new section. accordingly aaindex consists of three sections now: aaindex1 for the amino acid index of 20 numerical values, aaindex2 for the amino acid substitution matrix and aaindex3 for the statistical protein contact potentials. all data are derived from published literature. the database can be accessed through the dbget/linkdb system at genomenet ( or downloaded by anonymous ftp (ftp://ftp.genome.jp/pub/db/community/aaindex/).",0
"bacterial persistence is a state in which a sub-population of dormant cells, or 'persisters', tolerates antibiotic treatment. bacterial persisters have been implicated in biofilms and in chronic and recurrent infections. despite this clinical relevance, there are currently no viable means for eradicating persisters. here we show that specific metabolic stimuli enable the killing of both gram-negative (escherichia coli) and gram-positive (staphylococcus aureus) persisters with aminoglycosides. this potentiation is aminoglycoside-specific, it does not rely on growth resumption and it is effective in both aerobic and anaerobic conditions. it proceeds by the generation of a proton-motive force which facilitates aminoglycoside uptake. our results demonstrate that persisters, although dormant, are primed for metabolite uptake, central metabolism and respiration. we show that aminoglycosides can be used in combination with specific metabolites to treat e. coli and s. aureus biofilms. furthermore, we demonstrate that this approach can improve the treatment of chronic infections in a mouse urinary tract infection model. this work establishes a strategy for eradicating bacterial persisters that is based on metabolism, and highlights the importance of the metabolic environment to antibiotic treatment.",0
"population-level analyses often use average quantities to describe heterogeneous systems, particularly when variation does not arise from identifiable groups. a prominent example, central to our current understanding of epidemic spread, is the basic reproductive number, r(0), which is defined as the mean number of infections caused by an infected individual in a susceptible population. population estimates of r(0) can obscure considerable individual variation in infectiousness, as highlighted during the global emergence of severe acute respiratory syndrome (sars) by numerous 'superspreading events' in which certain individuals infected unusually large numbers of secondary cases. for diseases transmitted by non-sexual direct contacts, such as sars or smallpox, individual variation is difficult to measure empirically, and thus its importance for outbreak dynamics has been unclear. here we present an integrated theoretical and statistical analysis of the influence of individual variation in infectiousness on disease emergence. using contact tracing data from eight directly transmitted diseases, we show that the distribution of individual infectiousness around r(0) is often highly skewed. model predictions accounting for this variation differ sharply from average-based approaches, with disease extinction more likely and outbreaks rarer but more explosive. using these models, we explore implications for outbreak control, showing that individual-specific control measures outperform population-wide measures. moreover, the dramatic improvements achieved through targeted control policies emphasize the need to identify predictive correlates of higher infectiousness. our findings indicate that superspreading is a normal feature of disease spread, and to frame ongoing discussion we propose a rigorous definition for superspreading events and a method to predict their frequency.",0
"the outbreak of coronavirus disease (covid-19) in late december 2019 in china, which later developed into a pandemic, has forced different countries to implement strict sanitary regimes and social distancing measures. globally, at least four billion people were under lockdown, working remotely, homeschooling children, and facing challenges coping with quarantine and the stressful events. the present cross-sectional online survey of adult poles ( n = 1097), conducted during a nationwide quarantine, aimed to assess whether nutritional and consumer habits have been affected under these conditions. over 43.0% and nearly 52% reported eating and snacking more, respectively, and these tendencies were more frequent in overweight and obese individuals. almost 30% and over 18% experienced weight gain (mean ± sd 3.0 ± 1.6 kg) and loss (-2.9 ± 1.5 kg), respectively. overweight, obese, and older subjects (aged 36-45 and >45) tended to gain weight more frequently, whereas those with underweight tended to lose it further. increased bmi was associated with less frequent consumption of vegetables, fruit, and legumes during quarantine, and higher adherence to meat, dairy, and fast-foods. an increase in alcohol consumption was seen in 14.6%, with a higher tendency to drink more found among alcohol addicts. over 45% of smokers experienced a rise in smoking frequency during the quarantine. the study highlights that lockdown imposed to contain an infectious agent may affect eating behaviors and dietary habits, and advocates for organized nutritional support during future epidemic-related quarantines, particularly for the most vulnerable groups, including overweight and obese subjects.",0
"we investigated the possibility that t helper cells might enhance the stimulatory function of dendritic cells (dcs). we found that ligation of cd40 by cd40l triggers the production of extremely high levels of bioactive il-12. other stimuli such as microbial agents, tnf-alpha or lps are much less effective or not at all. in addition, cd40l is the most potent stimulus in upregulating the expression of icam-1, cd80, and cd86 molecules on dcs. these effects of cd40 ligation result in an increased capacity of dcs to trigger proliferative responses and ifn-gamma production by t cells. these findings reveal a new role for cd40-cd40l interaction in regulating dc function and are relevant to design therapeutic strategies using cultured dcs.",0
"polyphenols are secondary metabolites of plants and are generally involved in defense against ultraviolet radiation or aggression by pathogens. in the last decade, there has been much interest in the potential health benefits of dietary plant polyphenols as antioxidant. epidemiological studies and associated meta-analyses strongly suggest that long term consumption of diets rich in plant polyphenols offer protection against development of cancers, cardiovascular diseases, diabetes, osteoporosis and neurodegenerative diseases. here we present knowledge about the biological effects of plant polyphenols in the context of relevance to human health.",0
"background there is growing evidence of vaccine delays or refusals due to a lack of trust in the importance, safety, or effectiveness of vaccines, alongside persisting access issues. although immunisation coverage is reported administratively across the world, no similarly robust monitoring system exists for vaccine confidence. in this study, vaccine confidence was mapped across 149 countries between 2015 and 2019. methods in this large-scale retrospective data-driven analysis, we examined global trends in vaccine confidence using data from 290 surveys done between september, 2015, and december, 2019, across 149 countries, and including 284 381 individuals. we used a bayesian multinomial logit gaussian process model to produce estimates of public perceptions towards the safety, importance, and effectiveness of vaccines. associations between vaccine uptake and a large range of putative drivers of uptake, including vaccine confidence, socioeconomic status, and sources of trust, were determined using univariate bayesian logistic regressions. gibbs sampling was used for bayesian model inference, with 95% bayesian highest posterior density intervals used to capture uncertainty. findings between november, 2015, and december, 2019, we estimate that confidence in the importance, safety, and effectiveness of vaccines fell in afghanistan, indonesia, pakistan, the philippines, and south korea. we found significant increases in respondents strongly disagreeing that vaccines are safe between 2015 and 2019 in six countries: afghanistan, azerbaijan, indonesia, nigeria, pakistan, and serbia. we find signs that confidence has improved between 2018 and 2019 in some eu member states, including finland, france, ireland, and italy, with recent losses detected in poland. confidence in the importance of vaccines (rather than in their safety or effectiveness) had the strongest univariate association with vaccine uptake compared with other determinants considered. when a link was found between individuals' religious beliefs and uptake, findings indicated that minority religious groups tended to have lower probabilities of uptake. interpretation to our knowledge, this is the largest study of global vaccine confidence to date, allowing for cross-country comparisons and changes over time. our findings highlight the importance of regular monitoring to detect emerging trends to prompt interventions to build and sustain vaccine confidence. funding european commission, wellcome, and engineering and physical sciences research council.",0
"widespread acceptance of covid-19 vaccines is crucial for achieving sufficient immunization coverage to end the global pandemic, yet few studies have investigated covid-19 vaccination attitudes in lower-income countries, where large-scale vaccination is just beginning. we analyze covid-19 vaccine acceptance across 15 survey samples covering 10 low- and middle-income countries (lmics) in asia, africa and south america, russia (an upper-middle-income country) and the united states, including a total of 44,260 individuals. we find considerably higher willingness to take a covid-19 vaccine in our lmic samples (mean 80.3%; median 78%; range 30.1 percentage points) compared with the united states (mean 64.6%) and russia (mean 30.4%). vaccine acceptance in lmics is primarily explained by an interest in personal protection against covid-19, while concern about side effects is the most common reason for hesitancy. health workers are the most trusted sources of guidance about covid-19 vaccines. evidence from this sample of lmics suggests that prioritizing vaccine distribution to the global south should yield high returns in advancing global immunization coverage. vaccination campaigns should focus on translating the high levels of stated acceptance into actual uptake. messages highlighting vaccine efficacy and safety, delivered by healthcare workers, could be effective for addressing any remaining hesitancy in the analyzed lmics.",0
"convolutional neural network (cnn), a class of artificial neural networks that has become dominant in various computer vision tasks, is attracting interest across a variety of domains, including radiology. cnn is designed to automatically and adaptively learn spatial hierarchies of features through backpropagation by using multiple building blocks, such as convolution layers, pooling layers, and fully connected layers. this review article offers a perspective on the basic concepts of cnn and its application to various radiological tasks, and discusses its challenges and future directions in the field of radiology. two challenges in applying cnn to radiological tasks, small dataset and overfitting, will also be covered in this article, as well as techniques to minimize them. being familiar with the concepts and advantages, as well as limitations, of cnn is essential to leverage its potential in diagnostic radiology, with the goal of augmenting the performance of radiologists and improving patient care. key points: • convolutional neural network is a class of deep learning methods which has become dominant in various computer vision tasks and is attracting interest across a variety of domains, including radiology. • convolutional neural network is composed of multiple building blocks, such as convolution layers, pooling layers, and fully connected layers, and is designed to automatically and adaptively learn spatial hierarchies of features through a backpropagation algorithm. • familiarity with the concepts and advantages, as well as limitations, of convolutional neural network is essential to leverage its potential to improve radiologist performance and, eventually, patient care.",0
"background metastatic melanoma is an untreatable cancer lacking reliable and non-invasive markers of disease progression. exosomes are small vesicles secreted by normal as well as tumor cells. human tumor-derived exosomes are involved in malignant progression and we evaluated the presence of exosomes in plasma of melanoma patients as a potential tool for cancer screening and follow-up. methodology/principal findings we designed an in-house sandwich elisa (exotest) to capture and quantify exosomes in plasma based on expression of housekeeping proteins (cd63 and rab-5b) and a tumor-associated marker (caveolin-1). western blot and flow cytometry analysis of exosomes were used to confirm the exotest-based findings. the exotest allowed sensitive detection and quantification of exosomes purified from human tumor cell culture supernatants and plasma from scid mice engrafted with human melanoma. plasma levels of exosomes in melanoma-engrafted scid mice correlated to tumor size. we evaluated the levels of plasma exosomes expressing cd63 and caveolin-1 in melanoma patients (n = 90) and healthy donors (n = 58). consistently, plasma exosomes expressing cd63 (504+/-315) or caveolin-1 (619+/-310) were significantly increased in melanoma patients as compared to healthy donors (223+/-125 and 228+/-102, respectively). while the exotest for cd63+ plasma exosomes had limited sensitivity (43%) the exotest for detection of caveolin-1+ plasma exosomes showed a higher sensitivity (68%). moreover, caveolin-1+ plasma exosomes were significantly increased with respect to cd63+ exosomes in the patients group. conclusions/significance we describe a new non-invasive assay allowing detection and quantification of human exosomes in plasma of melanoma patients. our results suggest that the exotest for detection of plasma exosomes carrying tumor-associated antigens may represent a novel tool for clinical management of cancer patients.",0
"a central challenge in interpreting personal genomes is determining which mutations most likely influence disease. although progress has been made in scoring the functional impact of individual mutations, the characteristics of the genes in which those mutations are found remain largely unexplored. for example, genes known to carry few common functional variants in healthy individuals may be judged more likely to cause certain kinds of disease than genes known to carry many such variants. until now, however, it has not been possible to develop a quantitative assessment of how well genes tolerate functional genetic variation on a genome-wide scale. here we describe an effort that uses sequence data from 6503 whole exome sequences made available by the nhlbi exome sequencing project (esp). specifically, we develop an intolerance scoring system that assesses whether genes have relatively more or less functional genetic variation than expected based on the apparently neutral variation found in the gene. to illustrate the utility of this intolerance score, we show that genes responsible for mendelian diseases are significantly more intolerant to functional genetic variation than genes that do not cause any known disease, but with striking variation in intolerance among genes causing different classes of genetic disease. we conclude by showing that use of an intolerance ranking system can aid in interpreting personal genomes and identifying pathogenic mutations.",0
"summary phenoscanner is a curated database of publicly available results from large-scale genetic association studies in humans. this online tool facilitates 'phenome scans', where genetic variants are cross-referenced for association with many phenotypes of different types. here we present a major update of phenoscanner ('phenoscanner v2'), including over 150 million genetic variants and more than 65 billion associations (compared to 350 million associations in phenoscanner v1) with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers. the query options have been extended to include searches by genes, genomic regions and phenotypes, as well as for genetic variants. all variants are positionally annotated using the variant effect predictor and the phenotypes are mapped to experimental factor ontology terms. linkage disequilibrium statistics from the 1000 genomes project can be used to search for phenotype associations with proxy variants. availability and implementation phenoscanner v2 is available at",0
"the covid-19 pandemic is a major health crisis affecting several nations, with over 720,000 cases and 33,000 confirmed deaths reported to date. such widespread outbreaks are associated with adverse mental health consequences. keeping this in mind, existing literature on the covid-19 outbreak pertinent to mental health was retrieved via a literature search of the pubmed database. published articles were classified according to their overall themes and summarized. preliminary evidence suggests that symptoms of anxiety and depression (16-28%) and self-reported stress (8%) are common psychological reactions to the covid-19 pandemic, and may be associated with disturbed sleep. a number of individual and structural variables moderate this risk. in planning services for such populations, both the needs of the concerned people and the necessary preventive guidelines must be taken into account. the available literature has emerged from only a few of the affected countries, and may not reflect the experience of persons living in other parts of the world. in conclusion, subsyndromal mental health problems are a common response to the covid-19 pandemic. there is a need for more representative research from other affected countries, particularly in vulnerable populations.",0
"the orientations of proteins in membranes (opm) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. opm currently contains more than 1200 transmembrane and peripheral proteins and peptides from approximately 350 organisms that represent approximately 3800 protein data bank entries. proteins are classified into classes, superfamilies and families and assigned to 21 distinct membrane types. spatial positions of proteins with respect to the lipid bilayer are optimized by the ppm 2.0 method that accounts for the hydrophobic, hydrogen bonding and electrostatic interactions of the proteins with the anisotropic water-lipid environment described by the dielectric constant and hydrogen-bonding profiles. the opm database is freely accessible at data can be sorted, searched or retrieved using the hierarchical classification, source organism, localization in different types of membranes. the database offers downloadable coordinates of proteins and peptides with membrane boundaries. a gallery of protein images and several visualization tools are provided. the database is supplemented by the ppm server ( which can be used for calculating spatial positions in membranes of newly determined proteins structures or theoretical models.",0
"background cancer survival is a key measure of the effectiveness of health-care systems. persistent regional and international differences in survival represent many avoidable deaths. differences in survival have prompted or guided cancer control strategies. this is the first study in a programme to investigate international survival disparities, with the aim of informing health policy to raise standards and reduce inequalities in survival. methods data from population-based cancer registries in 12 jurisdictions in six countries were provided for 2·4 million adults diagnosed with primary colorectal, lung, breast (women), or ovarian cancer during 1995-2007, with follow-up to dec 31, 2007. data quality control and analyses were done centrally with a common protocol, overseen by external experts. we estimated 1-year and 5-year relative survival, constructing 252 complete life tables to control for background mortality by age, sex, and calendar year. we report age-specific and age-standardised relative survival at 1 and 5 years, and 5-year survival conditional on survival to the first anniversary of diagnosis. we also examined incidence and mortality trends during 1985-2005. findings relative survival improved during 1995-2007 for all four cancers in all jurisdictions. survival was persistently higher in australia, canada, and sweden, intermediate in norway, and lower in denmark, england, northern ireland, and wales, particularly in the first year after diagnosis and for patients aged 65 years and older. international differences narrowed at all ages for breast cancer, from about 9% to 5% at 1 year and from about 14% to 8% at 5 years, but less or not at all for the other cancers. for colorectal cancer, the international range narrowed only for patients aged 65 years and older, by 2-6% at 1 year and by 2-3% at 5 years. interpretation up-to-date survival trends show increases but persistent differences between countries. trends in cancer incidence and mortality are broadly consistent with these trends in survival. data quality and changes in classification are not likely explanations. the patterns are consistent with later diagnosis or differences in treatment, particularly in denmark and the uk, and in patients aged 65 years and older. funding department of health, england; and cancer research uk.",0
"the re-aim planning and evaluation framework was conceptualized two decades ago. as one of the most frequently applied implementation frameworks, re-aim has now been cited in over 2,800 publications. this paper describes the application and evolution of re-aim as well as lessons learned from its use. re-aim has been applied most often in public health and health behavior change research, but increasingly in more diverse content areas and within clinical, community, and corporate settings. we discuss challenges of using re-aim while encouraging a more pragmatic use of key dimensions rather than comprehensive applications of all elements. current foci of re-aim include increasing the emphasis on cost and adaptations to programs and expanding the use of qualitative methods to understand ""how"" and ""why"" results came about. the framework will continue to evolve to focus on contextual and explanatory factors related to re-aim outcomes, package re-aim for use by non-researchers, and integrate re-aim with other pragmatic and reporting frameworks.",0
"community detection is often used to understand the structure of large and complex networks. one of the most popular algorithms for uncovering community structure is the so-called louvain algorithm. we show that this algorithm has a major defect that largely went unnoticed until now: the louvain algorithm may yield arbitrarily badly connected communities. in the worst case, communities may even be disconnected, especially when running the algorithm iteratively. in our experimental analysis, we observe that up to 25% of the communities are badly connected and up to 16% are disconnected. to address this problem, we introduce the leiden algorithm. we prove that the leiden algorithm yields communities that are guaranteed to be connected. in addition, we prove that, when the leiden algorithm is applied iteratively, it converges to a partition in which all subsets of all communities are locally optimally assigned. furthermore, by relying on a fast local move approach, the leiden algorithm runs faster than the louvain algorithm. we demonstrate the performance of the leiden algorithm for several benchmark and real-world networks. we find that the leiden algorithm is faster than the louvain algorithm and uncovers better partitions, in addition to providing explicit guarantees.",0
"background given the projected trends in population ageing and population growth, the number of people with dementia is expected to increase. in addition, strong evidence has emerged supporting the importance of potentially modifiable risk factors for dementia. characterising the distribution and magnitude of anticipated growth is crucial for public health planning and resource prioritisation. this study aimed to improve on previous forecasts of dementia prevalence by producing country-level estimates and incorporating information on selected risk factors. methods we forecasted the prevalence of dementia attributable to the three dementia risk factors included in the global burden of diseases, injuries, and risk factors study (gbd) 2019 (high body-mass index, high fasting plasma glucose, and smoking) from 2019 to 2050, using relative risks and forecasted risk factor prevalence to predict gbd risk-attributable prevalence in 2050 globally and by world region and country. using linear regression models with education included as an additional predictor, we then forecasted the prevalence of dementia not attributable to gbd risks. to assess the relative contribution of future trends in gbd risk factors, education, population growth, and population ageing, we did a decomposition analysis. findings we estimated that the number of people with dementia would increase from 57·4 (95% uncertainty interval 50·4-65·1) million cases globally in 2019 to 152·8 (130·8-175·9) million cases in 2050. despite large increases in the projected number of people living with dementia, age-standardised both-sex prevalence remained stable between 2019 and 2050 (global percentage change of 0·1% ). we estimated that there were more women with dementia than men with dementia globally in 2019 (female-to-male ratio of 1·69 ), and we expect this pattern to continue to 2050 (female-to-male ratio of 1·67 ). there was geographical heterogeneity in the projected increases across countries and regions, with the smallest percentage changes in the number of projected dementia cases in high-income asia pacific (53% ) and western europe (74% ), and the largest in north africa and the middle east (367% ) and eastern sub-saharan africa (357% ). projected increases in cases could largely be attributed to population growth and population ageing, although their relative importance varied by world region, with population growth contributing most to the increases in sub-saharan africa and population ageing contributing most to the increases in east asia. interpretation growth in the number of individuals living with dementia underscores the need for public health planning efforts and policy to address the needs of this group. country-level estimates can be used to inform national planning efforts and decisions. multifaceted approaches, including scaling up interventions to address modifiable risk factors and investing in research on biological mechanisms, will be key in addressing the expected increases in the number of individuals affected by dementia. funding bill & melinda gates foundation and gates ventures.",0
"cd4+cd25+ regulatory t cells contribute to the maintenance of peripheral tolerance by active suppression because their deletion causes spontaneous autoimmune diseases in mice. human cd4+ regulatory t cells expressing high levels of cd25 are suppressive in vitro and mimic the activity of murine cd4+cd25+ regulatory t cells. multiple sclerosis (ms) is an inflammatory disease thought to be mediated by t cells recognizing myelin protein peptides. we hypothesized that altered functions of cd4+cd25hi regulatory t cells play a role in the breakdown of immunologic self-tolerance in patients with ms. here, we report a significant decrease in the effector function of cd4+cd25hi regulatory t cells from peripheral blood of patients with ms as compared with healthy donors. differences were also apparent in single cell cloning experiments in which the cloning frequency of cd4+cd25hi t cells was significantly reduced in patients as compared with normal controls. these data are the first to demonstrate alterations of cd4+cd25hi regulatory t cell function in patients with ms.",0
"occludin is an integral membrane protein localizing at tight junctions (tj) with four transmembrane domains and a long cooh-terminal cytoplasmic domain (domain e) consisting of 255 amino acids. immunofluorescence and laser scan microscopy revealed that chick full-length occludin introduced into human and bovine epithelial cells was correctly delivered to and incorporated into preexisting tj. further transfection studies with various deletion mutants showed that the domain e, especially its cooh-terminal approximately 150 amino acids (domain e358/504), was necessary for the localization of occludin at tj. secondly, domain e was expressed in escherichia coli as a fusion protein with glutathione-s-transferase, and this fusion protein was shown to be specifically bound to a complex of zo-1 (220 kd) and zo-2 (160 kd) among various membrane peripheral proteins. in vitro binding analyses using glutathione-s-transferase fusion proteins of various deletion mutants of domain e narrowed down the sequence necessary for the zo-1/zo-2 association into the domain e358/504. furthermore, this region directly associated with the recombinant zo-1 produced in e. coli. we concluded that occludin itself can localize at tj and directly associate with zo-1. the coincidence of the sequence necessary for the zo-1 association with that for the tj localization suggests that the association with underlying cytoskeletons through zo-1 is required for occludin to be localized at tj.",0
"the drug-gene interaction database (dgidb, consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. dgidb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (api) and public cloud-based server image. dgidb v3.0 represents a major update of the database. nine of the previously included 24 sources were updated. six new resources were added, bringing the total number of sources to 30. these updates and additions of sources have cumulatively resulted in 56 309 interaction claims. this has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the dgidb. along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. in addition, the expanded api features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of pubmed ids, interaction type and other interaction metadata.",0
"previous studies have showed clinical characteristics of patients with the 2019 novel coronavirus disease (covid-19) and the evidence of person-to-person transmission. limited data are available for asymptomatic infections. this study aims to present the clinical characteristics of 24 cases with asymptomatic infection screened from close contacts and to show the transmission potential of asymptomatic covid-19 virus carriers. epidemiological investigations were conducted among all close contacts of covid-19 patients (or suspected patients) in nanjing, jiangsu province, china, from jan 28 to feb 9, 2020, both in clinic and in community. asymptomatic carriers were laboratory-confirmed positive for the covid-19 virus by testing the nucleic acid of the pharyngeal swab samples. their clinical records, laboratory assessments, and chest ct scans were reviewed. as a result, none of the 24 asymptomatic cases presented any obvious symptoms while nucleic acid screening. five cases (20.8%) developed symptoms (fever, cough, fatigue, etc.) during hospitalization. twelve (50.0%) cases showed typical ct images of ground-glass chest and 5 (20.8%) presented stripe shadowing in the lungs. the remaining 7 (29.2%) cases showed normal ct image and had no symptoms during hospitalization. these 7 cases were younger (median age: 14.0 years; p=0.012) than the rest. none of the 24 cases developed severe covid-19 pneumonia or died. the median communicable period, defined as the interval from the first day of positive nucleic acid tests to the first day of continuous negative tests, was 9.5 days (up to 21 days among the 24 asymptomatic cases). through epidemiological investigation, we observed a typical asymptomatic transmission to the cohabiting family members, which even caused severe covid-19 pneumonia. overall, the asymptomatic carriers identified from close contacts were prone to be mildly ill during hospitalization. however, the communicable period could be up to three weeks and the communicated patients could develop severe illness. these results highlighted the importance of close contact tracing and longitudinally surveillance via virus nucleic acid tests. further isolation recommendation and continuous nucleic acid tests may also be recommended to the patients discharged.",0
"natural tumor surveillance capabilities of the host were investigated in six different mouse tumor models where endogenous interleukin (il)-12 does or does not dictate the efficiency of the innate immune response. gene-targeted and lymphocyte subset-depleted mice were used to establish the relative importance of natural killer (nk) and nk1.1(+) t (nkt) cells in protection from tumor initiation and metastasis. in the models examined, cd3(-) nk cells were responsible for tumor rejection and protection from metastasis in models where control of major histocompatibility complex class i-deficient tumors was independent of il-12. a protective role for nkt cells was only observed when tumor rejection required endogenous il-12 activity. in particular, t cell receptor jalpha281 gene-targeted mice confirmed a critical function for nkt cells in protection from spontaneous tumors initiated by the chemical carcinogen, methylcholanthrene. this is the first description of an antitumor function for nkt cells in the absence of exogenously administered potent stimulators such as il-12 or alpha-galactosylceramide.",0
"over the past decade, the database of genomic variants (dgv; has provided a publicly accessible, comprehensive curated catalogue of structural variation (sv) found in the genomes of control individuals from worldwide populations. here, we describe updates and new features, which have expanded the utility of dgv for both the basic research and clinical diagnostic communities. the current version of dgv consists of 55 published studies, comprising >2.5 million entries identified in >22,300 genomes. studies included in dgv are selected from the accessioned data sets in the archival sv databases dbvar (ncbi) and dgva (ebi), and then further curated for accuracy and validity. the core visualization tool (gbrowse) has been upgraded with additional functions to facilitate data analysis and comparison, and a new query tool has been developed to provide flexible and interactive access to the data. the content from dgv is regularly incorporated into other large-scale genome reference databases and represents a standard data resource for new product and database development, in particular for copy number variation testing in clinical labs. the accurate cataloguing of variants in dgv will continue to enable medical genetics and genome sequencing research.",0
"background the estimated number of new hiv infections in the united states reflects the leading edge of the epidemic. previously, cdc estimated hiv incidence in the united states in 2006 as 56,300 (95% ci: 48,200-64,500). we updated the 2006 estimate and calculated incidence for 2007-2009 using improved methodology. methodology we estimated incidence using incidence surveillance data from 16 states and 2 cities and a modification of our previously described stratified extrapolation method based on a sample survey approach with multiple imputation, stratification, and extrapolation to account for missing data and heterogeneity of hiv testing behavior among population groups. principal findings estimated hiv incidence among persons aged 13 years and older was 48,600 (95% ci: 42,400-54,700) in 2006, 56,000 (95% ci: 49,100-62,900) in 2007, 47,800 (95% ci: 41,800-53,800) in 2008 and 48,100 (95% ci: 42,200-54,000) in 2009. from 2006 to 2009 incidence did not change significantly overall or among specific race/ethnicity or risk groups. however, there was a 21% (95% ci:1.9%-39.8%; p = 0.017) increase in incidence for people aged 13-29 years, driven by a 34% (95% ci: 8.4%-60.4%) increase in young men who have sex with men (msm). there was a 48% increase among young black/african american msm (12.3%-83.0%; p conclusions/significance overall, hiv incidence in the united states was relatively stable 2006-2009; however, among young msm, particularly black/african american msm, incidence increased. hiv continues to be a major public health burden, disproportionately affecting several populations in the united states, especially msm and racial and ethnic minorities. expanded, improved, and targeted prevention is necessary to reduce hiv incidence.",0
"the lipid maps consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (ms) data. a simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. the structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. the structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion ms experimental data. the ms prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. the lipid maps online tools are publicly available at",0
"caspase-8 has two opposing biological functions--it promotes cell death by triggering the extrinsic pathway of apoptosis, but also has a survival activity, as it is required for embryonic development, t-lymphocyte activation, and resistance to necrosis induced by tumour necrosis factor-α (tnf-α) and related family ligands. here we show that development of caspase-8-deficient mice is completely rescued by ablation of receptor interacting protein kinase-3 (ripk3). adult animals lacking both caspase-8 and ripk3 display a progressive lymphoaccumulative disease resembling that seen with defects in cd95 or cd95-ligand (also known as fas and faslg, respectively), and resist the lethal effects of cd95 ligation in vivo. we have found that caspase-8 prevents ripk3-dependent necrosis without inducing apoptosis by functioning in a proteolytically active complex with flice-like inhibitory protein long (flip(l), also known as cflar), and this complex is required for the protective function.",0
"the restrictions put in place to contain the covid-19 virus have led to widespread social isolation, impacting mental health worldwide. these restrictions may be particularly difficult for adolescents, who rely heavily on their peer connections for emotional support. however, there has been no longitudinal research examining the psychological impact of the covid-19 pandemic among adolescents. this study addresses this gap by investigating the impact of the covid-19 pandemic on adolescents' mental health, and moderators of change, as well as assessing the factors perceived as causing the most distress. two hundred and forty eight adolescents (m age = 14.4; 51% girls; 81.8% caucasian) were surveyed over two time points; in the 12 months leading up to the covid-19 outbreak (t1), and again two months following the implementation of government restrictions and online learning (t2). online surveys assessed depressive symptoms, anxiety, and life satisfaction at t1 and t2, and participants' schooling, peer and family relationships, social connection, media exposure, covid-19 related stress, and adherence to government stay-at-home directives at t2 only. in line with predictions, adolescents experienced significant increases in depressive symptoms and anxiety, and a significant decrease in life satisfaction from t1 to t2, which was particularly pronounced among girls. moderation analyses revealed that covid-19 related worries, online learning difficulties, and increased conflict with parents predicted increases in mental health problems from t1 to t2, whereas adherence to stay-at-home orders and feeling socially connected during the covid-19 lockdown protected against poor mental health. this study provides initial longitudinal evidence for the decline of adolescent's mental health during the covid-19 pandemic. the results suggest that adolescents are more concerned about the government restrictions designed to contain the spread of the virus, than the virus itself, and that those concerns are associated with increased anxiety and depressive symptoms, and decreased life satisfaction.",0
"dominant markers such as amplified fragment length polymorphisms (aflps) provide an economical way of surveying variation at many loci. however, the uncertainty about the underlying genotypes presents a problem for statistical analysis. similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to aflp data from whitefish. the approach is implemented in the program structure version 2.2, which is available from",0
"background the amyloid beta-protein (abeta) is believed to be the key mediator of alzheimer's disease (ad) pathology. abeta is most often characterized as an incidental catabolic byproduct that lacks a normal physiological role. however, abeta has been shown to be a specific ligand for a number of different receptors and other molecules, transported by complex trafficking pathways, modulated in response to a variety of environmental stressors, and able to induce pro-inflammatory activities. methodology/principal findings here, we provide data supporting an in vivo function for abeta as an antimicrobial peptide (amp). experiments used established in vitro assays to compare antimicrobial activities of abeta and ll-37, an archetypical human amp. findings reveal that abeta exerts antimicrobial activity against eight common and clinically relevant microorganisms with a potency equivalent to, and in some cases greater than, ll-37. furthermore, we show that ad whole brain homogenates have significantly higher antimicrobial activity than aged matched non-ad samples and that amp action correlates with tissue abeta levels. consistent with abeta-mediated activity, the increased antimicrobial action was ablated by immunodepletion of ad brain homogenates with anti-abeta antibodies. conclusions/significance our findings suggest abeta is a hitherto unrecognized amp that may normally function in the innate immune system. this finding stands in stark contrast to current models of abeta-mediated pathology and has important implications for ongoing and future ad treatment strategies.",0
"elastic net type regression methods have become very popular for prediction of certain outcomes in epigenome-wide association studies (ewas). the methods considered accept biased coefficient estimates in return for lower variance thus obtaining improved prediction accuracy. we provide guidelines on how to obtain parsimonious models with low mean squared error and include easy to follow walk-through examples for each step in r.",0
"objective to assess the prevalence of diabetes and its risk factors. design population based, cross sectional study. setting 31 provinces in mainland china with nationally representative cross sectional data from 2015 to 2017. participants 75 880 participants aged 18 and older-a nationally representative sample of the mainland chinese population. main outcome measures prevalence of diabetes among adults living in china, and the prevalence by sex, regions, and ethnic groups, estimated by the 2018 american diabetes association (ada) and the world health organization diagnostic criteria. demographic characteristics, lifestyle, and history of disease were recorded by participants on a questionnaire. anthropometric and clinical assessments were made of serum concentrations of fasting plasma glucose (one measurement), two hour plasma glucose, and glycated haemoglobin (hba 1c ). results the weighted prevalence of total diabetes (n=9772), self-reported diabetes (n=4464), newly diagnosed diabetes (n=5308), and prediabetes (n=27 230) diagnosed by the ada criteria were 12.8% (95% confidence interval 12.0% to 13.6%), 6.0% (5.4% to 6.7%), 6.8% (6.1% to 7.4%), and 35.2% (33.5% to 37.0%), respectively, among adults living in china. the weighted prevalence of total diabetes was higher among adults aged 50 and older and among men. the prevalence of total diabetes in 31 provinces ranged from 6.2% in guizhou to 19.9% in inner mongolia. han ethnicity had the highest prevalence of diabetes (12.8%) and hui ethnicity had the lowest (6.3%) among five investigated ethnicities. the weighted prevalence of total diabetes (n=8385) using the who criteria was 11.2% (95% confidence interval 10.5% to 11.9%). conclusion the prevalence of diabetes has increased slightly from 2007 to 2017 among adults living in china. the findings indicate that diabetes is an important public health problem in china.",0
"the program mercury , developed at the cambridge crystallographic data centre, was originally designed primarily as a crystal structure visualization tool. over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.",0
"docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. for a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and interactions are mandatory. here we present an interface between the popular molecular graphics system pymol and the molecular docking suites autodock and vina and demonstrate how the combination of docking and visualization can aid structure-based drug design efforts.",0
"azoles are the mainstay of oral therapy for aspergillosis. azole resistance in aspergillus has been reported infrequently. the first resistant isolate was detected in 1999 in manchester, uk. in a clinical collection of 519 a. fumigatus isolates, the frequency of itraconazole resistance was 5%, a significant increase since 2004 (p<0.001). of the 34 itraconazole-resistant isolates we studied, 65% (22) were cross-resistant to voriconazole and 74% (25) were cross-resistant to posaconazole. thirteen of 14 evaluable patients in our study had prior azole exposure; 8 infections failed therapy (progressed), and 5 failed to improve (remained stable). eighteen amino acid alterations were found in the target enzyme, cyp51a, 4 of which were novel. a population genetic analysis of microsatellites showed the existence of resistant mutants that evolved from originally susceptible strains, different cyp51a mutations in the same strain, and microalterations in microsatellite repeat number. azole resistance in a. fumigatus is an emerging problem and may develop during azole therapy.",0
"cancer is the leading cause of death in china and depicting the cancer pattern of china would provide basic knowhows on how to tackle it more effectively. in this study we have reviewed several reports of cancer burden, including the global cancer statistics 2018 and cancer statistics in china, 2015, along with the globcan 2018 online database, to investigate the differences of cancer patterns between china, the united states (usa) and the united kingdom (uk). an estimated 4.3 million new cancer cases and 2.9 million new cancer deaths occurred in china in 2018. compared to the usa and uk, china has lower cancer incidence but a 30% and 40% higher cancer mortality than the uk and usa, among which 36.4% of the cancer-related deaths were from the digestive tract cancers (stomach, liver, and esophagus cancer) and have relatively poorer prognoses. in comparison, the digestive cancer deaths only took up ≤ 5% of the total cancer deaths in either usa or uk. other reasons for the higher mortality in china may be the low rate of early-stage cancers at diagnosis and non-uniformed clinical cancer treatment strategies performed by different regions. china is undergoing the cancer transition stage where the cancer spectrum is changing from developing country to developed country, with a rapidly increase cancer burden of colorectal, prostate, female breast cancers in addition to a high occurrence of infection-related and digestive cancers. the incidence of westernized lifestyle-related cancers in china (i.e. colorectal cancer, prostate, bladder cancer) has risen but the incidence of the digestive cancers has decreased from 2000 to 2011. an estimated 40% of the risk factors can be attributed to environmental and lifestyle factors either in china or other developed countries. tobacco smoking is the single most important carcinogenic risk factor in china, contributing to ~ 24.5% of cancers in males. chronic infection is another important preventable cancer contributor which is responsible for ~ 17% of cancers. comprehensive prevention and control strategies in china should include effective tobacco-control policy, recommendations for healthier lifestyles, along with enlarging the coverage of effective screening, educating, and vaccination programs to better sensitize greater awareness control to the general public.",0
"the uk biobank cohort is a population-based cohort of 500,000 participants recruited in the united kingdom (uk) between 2006 and 2010. approximately 9.2 million individuals aged 40-69 years who lived within 25 miles (40 km) of one of 22 assessment centers in england, wales, and scotland were invited to enter the cohort, and 5.5% participated in the baseline assessment. the representativeness of the uk biobank cohort was investigated by comparing demographic characteristics between nonresponders and responders. sociodemographic, physical, lifestyle, and health-related characteristics of the cohort were compared with nationally representative data sources. uk biobank participants were more likely to be older, to be female, and to live in less socioeconomically deprived areas than nonparticipants. compared with the general population, participants were less likely to be obese, to smoke, and to drink alcohol on a daily basis and had fewer self-reported health conditions. at age 70-74 years, rates of all-cause mortality and total cancer incidence were 46.2% and 11.8% lower, respectively, in men and 55.5% and 18.1% lower, respectively, in women than in the general population of the same age. uk biobank is not representative of the sampling population; there is evidence of a ""healthy volunteer"" selection bias. nonetheless, valid assessment of exposure-disease relationships may be widely generalizable and does not require participants to be representative of the population at large.",0
"background lowering of ldl cholesterol with standard statin regimens reduces the risk of occlusive vascular events in a wide range of individuals. we aimed to assess the safety and efficacy of more intensive lowering of ldl cholesterol with statin therapy. methods we undertook meta-analyses of individual participant data from randomised trials involving at least 1000 participants and at least 2 years' treatment duration of more versus less intensive statin regimens (five trials; 39 612 individuals; median follow-up 5·1 years) and of statin versus control (21 trials; 129 526 individuals; median follow-up 4·8 years). for each type of trial, we calculated not only the average risk reduction, but also the average risk reduction per 1·0 mmol/l ldl cholesterol reduction at 1 year after randomisation. findings in the trials of more versus less intensive statin therapy, the weighted mean further reduction in ldl cholesterol at 1 year was 0·51 mmol/l. compared with less intensive regimens, more intensive regimens produced a highly significant 15% (95% ci 11-18; p interpretation further reductions in ldl cholesterol safely produce definite further reductions in the incidence of heart attack, of revascularisation, and of ischaemic stroke, with each 1·0 mmol/l reduction reducing the annual rate of these major vascular events by just over a fifth. there was no evidence of any threshold within the cholesterol range studied, suggesting that reduction of ldl cholesterol by 2-3 mmol/l would reduce risk by about 40-50%. funding uk medical research council, british heart foundation, european community biomed programme, australian national health and medical research council, and national heart foundation.",0
"summary a polygenic risk score (prs) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study. the application of prs has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; prs can also be used to establish the presence of a genetic signal in underpowered studies, to infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. here we present the first dedicated prs software, prsice ('precise'), for calculating, applying, evaluating and plotting the results of prs. prsice can calculate prs at a large number of thresholds (""high resolution"") to provide the best-fit prs, as well as provide results calculated at broad p-value thresholds, can thin single nucleotide polymorphisms (snps) according to linkage disequilibrium and p-value or use all snps, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply prs across multiple traits in a single run. we exemplify the use of prsice via application to data on schizophrenia, major depressive disorder and smoking, illustrate the importance of identifying the best-fit prs and estimate a p-value significance threshold for high-resolution prs studies. availability and implementation prsice is written in r, including wrappers for bash data management scripts and plink-1.9 to minimize computational time. prsice runs as a command-line program with a variety of user-options, and is freely available for download from contact jack.euesden@kcl.ac.uk or paul.oreilly@kcl.ac.uk supplementary information supplementary data are available at bioinformatics online.",0
"background & aims hepatocellular carcinoma (hcc) is the second most common cause of cancer deaths worldwide. the global hcc bridge study was a multiregional, large-scale, longitudinal cohort study undertaken to improve understanding of real-life management of patients with hcc, from diagnosis to death. methods data were collected retrospectively from january 2005 to september 2012 by chart reviews of eligible patients newly diagnosed with hcc at participating institutions. results forty-two sites in 14 countries contributed final data for 18 031 patients. asia accounted for 67% of patients, europe for 20% and north america for 13%. as expected, the most common risk factor was hepatitis c virus in north america, europe and japan, and hepatitis b virus in china, south korea and taiwan. the most common barcelona clinic liver cancer stage at diagnosis was c in north america, europe, china and south korea, and a in taiwan and japan. across all stages, first hcc treatment was most frequently transarterial chemoembolization in north america, europe, china and south korea, percutaneous ethanol injection or radiofrequency ablation in japan and resection in taiwan. survival from first hcc treatment varied significantly by region, with median overall survival not reached for taiwan and 60, 33, 31, 24 and 23 months for japan, north america, south korea, europe and china respectively (p conclusions initial results from the bridge study confirm previously reported regional trends in patient demographic characteristics and hcc risk factors, document the heterogeneity of treatment approaches across regions/countries and underscore the need for earlier hcc diagnosis worldwide.",0
"the biological general repository for interaction datasets (biogrid: is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. as of september 2016 (build 3.4.140), the biogrid contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. this dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 biogrid update. biogrid curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. to facilitate network-based approaches to drug discovery, biogrid now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the drugbank database. a new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. biogrid data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.",0
"background health authorities worldwide, especially in the asia pacific region, are seeking effective public-health interventions in the continuing epidemic of severe acute respiratory syndrome (sars). we assessed the epidemiology of sars in hong kong. methods we included 1425 cases reported up to april 28, 2003. an integrated database was constructed from several sources containing information on epidemiological, demographic, and clinical variables. we estimated the key epidemiological distributions: infection to onset, onset to admission, admission to death, and admission to discharge. we measured associations between the estimated case fatality rate and patients' age and the time from onset to admission. findings after the initial phase of exponential growth, the rate of confirmed cases fell to less than 20 per day by april 28. public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. the mean incubation period of the disease is estimated to be 6.4 days (95% ci 5.2-7.7). the mean time from onset of clinical symptoms to admission to hospital varied between 3 and 5 days, with longer times earlier in the epidemic. the estimated case fatality rate was 13.2% (9.8-16.8) for patients younger than 60 years and 43.3% (35.2-52.4) for patients aged 60 years or older assuming a parametric gamma distribution. a non-parametric method yielded estimates of 6.8% (4.0-9.6) and 55.0% (45.3-64.7), respectively. case clusters have played an important part in the course of the epidemic. interpretation patients' age was strongly associated with outcome. the time between onset of symptoms and admission to hospital did not alter outcome, but shorter intervals will be important to the wider population by restricting the infectious period before patients are placed in quarantine.",0
"genome-wide association scans with high-throughput metabolic profiling provide unprecedented insights into how genetic variation influences metabolism and complex disease. here we report the most comprehensive exploration of genetic loci influencing human metabolism thus far, comprising 7,824 adult individuals from 2 european population studies. we report genome-wide significant associations at 145 metabolic loci and their biochemical connectivity with more than 400 metabolites in human blood. we extensively characterize the resulting in vivo blueprint of metabolism in human blood by integrating it with information on gene expression, heritability and overlap with known loci for complex disorders, inborn errors of metabolism and pharmacological targets. we further developed a database and web-based resources for data mining and results visualization. our findings provide new insights into the role of inherited variation in blood metabolic diversity and identify potential new opportunities for drug development and for understanding disease.",0
"hyperphosphorylated tau makes up the filamentous intracellular inclusions of several neurodegenerative diseases, including alzheimer's disease. in the disease process, neuronal tau inclusions first appear in the transentorhinal cortex from where they seem to spread to the hippocampal formation and neocortex. cognitive impairment becomes manifest when inclusions reach the hippocampus, with abundant neocortical tau inclusions and extracellular beta-amyloid deposits being the defining pathological hallmarks of alzheimer's disease. an abundance of tau inclusions, in the absence of beta-amyloid deposits, defines pick's disease, progressive supranuclear palsy, corticobasal degeneration and other diseases. tau mutations cause familial forms of frontotemporal dementia, establishing that tau protein dysfunction is sufficient to cause neurodegeneration and dementia. thus, transgenic mice expressing mutant (for example, p301s) human tau in nerve cells show the essential features of tauopathies, including neurodegeneration and abundant filaments made of hyperphosphorylated tau protein. by contrast, mouse lines expressing single isoforms of wild-type human tau do not produce tau filaments or show neurodegeneration. here we have used tau-expressing lines to investigate whether experimental tauopathy can be transmitted. we show that injection of brain extract from mutant p301s tau-expressing mice into the brain of transgenic wild-type tau-expressing animals induces assembly of wild-type human tau into filaments and spreading of pathology from the site of injection to neighbouring brain regions.",0
"swiss-model repository ( is a database of 3d protein structure models generated by the swiss-model homology-modelling pipeline. the aim of the swiss-model repository is to provide access to an up-to-date collection of annotated 3d protein models generated by automated homology modelling for all sequences in swiss-prot and for relevant models organisms. regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. as of september 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the uniprot database. swiss-model repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via swiss-model workspace ( annotation of models with functional information and cross-linking with other databases such as the protein model portal ( of the psi structural genomics knowledge base facilitates the navigation between protein sequence and structure resources.",0
"one of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sits. actually, such multiplex proteins might have special biological functions worthy of particular notice. the present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. a new predictor called ""plant-mploc"" is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. it can be used to identify plant proteins among the following 12 location sites: (1) cell membrane, (2) cell wall, (3) chloroplast, (4) cytoplasm, (5) endoplasmic reticulum, (6) extracellular, (7) golgi apparatus, (8) mitochondrion, (9) nucleus, (10) peroxisome, (11) plastid, and (12) vacuole. compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. as a user-friendly web-server, plant-mploc is freely accessible at moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. it is anticipated that the plant-mploc predictor as presented in this paper will become a very useful tool in plant science as well as all the relevant areas.",0
"to determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in wuhan, china, we tested air and surface samples. contamination was greater in intensive care units than general wards. virus was widely distributed on floors, computer mice, trash cans, and sickbed handrails and was detected in air ≈4 m from patients.",0
"metabolic syndrome (mets) is a complex disorder defined by a cluster of interconnected factors that increase the risk of cardiovascular atherosclerotic diseases and diabetes mellitus type 2. currently, several different definitions of mets exist, causing substantial confusion as to whether they identify the same individuals or represent a surrogate of risk factors. recently, a number of other factors besides those traditionally used to define mets that are also linked to the syndrome have been identified. in this review, we critically consider existing definitions and evolving information, and conclude that there is still a need to develop uniform criteria to define mets, so as to enable comparisons between different studies and to better identify patients at risk. as the application of the mets model has not been fully validated in children and adolescents as yet, and because of its alarmingly increasing prevalence in this population, we suggest that diagnosis, prevention and treatment in this age group should better focus on established risk factors rather than the diagnosis of mets.",0
"background the balance of risk and benefit from early neurosurgical intervention for conscious patients with superficial lobar intracerebral haemorrhage of 10-100 ml and no intraventricular haemorrhage admitted within 48 h of ictus is unclear. we therefore tested the hypothesis that early surgery compared with initial conservative treatment could improve outcome in these patients. methods in this international, parallel-group trial undertaken in 78 centres in 27 countries, we compared early surgical haematoma evacuation within 12 h of randomisation plus medical treatment with initial medical treatment alone (later evacuation was allowed if judged necessary). an automatic telephone and internet-based randomisation service was used to assign patients to surgery and initial conservative treatment in a 1:1 ratio. the trial was not masked. the primary outcome was a prognosis-based dichotomised (favourable or unfavourable) outcome of the 8 point extended glasgow outcome scale (gose) obtained by questionnaires posted to patients at 6 months. analysis was by intention to treat. this trial is registered, number isrctn22153967. findings 307 of 601 patients were randomly assigned to early surgery and 294 to initial conservative treatment; 298 and 291 were followed up at 6 months, respectively; and 297 and 286 were included in the analysis, respectively. 174 (59%) of 297 patients in the early surgery group had an unfavourable outcome versus 178 (62%) of 286 patients in the initial conservative treatment group (absolute difference 3·7% , odds ratio 0·86 ; p=0·367). interpretation the stich ii results confirm that early surgery does not increase the rate of death or disability at 6 months and might have a small but clinically relevant survival advantage for patients with spontaneous superficial intracerebral haemorrhage without intraventricular haemorrhage. funding uk medical research council.",0
"meta-analyses that simultaneously compare multiple treatments (usually referred to as network meta-analyses or mixed treatment comparisons) are becoming increasingly common. an important component of a network meta-analysis is an assessment of the extent to which different sources of evidence are compatible, both substantively and statistically. a simple indirect comparison may be confounded if the studies involving one of the treatments of interest are fundamentally different from the studies involving the other treatment of interest. here, we discuss methods for addressing inconsistency of evidence from comparative studies of different treatments. we define and review basic concepts of heterogeneity and inconsistency, and attempt to introduce a distinction between 'loop inconsistency' and 'design inconsistency'. we then propose that the notion of design-by-treatment interaction provides a useful general framework for investigating inconsistency. in particular, using design-by-treatment interactions successfully addresses complications that arise from the presence of multi-arm trials in an evidence network. we show how the inconsistency model proposed by lu and ades is a restricted version of our full design-by-treatment interaction model and that there may be several distinct lu-ades models for any particular data set. we introduce novel graphical methods for depicting networks of evidence, clearly depicting multi-arm trials and illustrating where there is potential for inconsistency to arise. we apply various inconsistency models to data from trials of different comparisons among four smoking cessation interventions and show that models seeking to address loop inconsistency alone can run into problems. copyright © 2012 john wiley & sons, ltd.",0
"complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. the complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. the subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. here, we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. this article will review the mechanisms of activation of alternative, classical, and lectin pathways, the formation of c3 and c5 convertases, the action of anaphylatoxins, and the membrane-attack-complex. we will also discuss the importance of structure-function relationships using the example of atypical hemolytic uremic syndrome. lastly, we will discuss the development and benefits of therapies using complement inhibitors.",0
"oxidative stress has been implicated in many chronic diseases. however, antioxidant trials are so far largely unsuccessful as a preventive or curative measure. chronic low-grade inflammatory process, on the other hand, plays a central role in the pathogenesis of a number of chronic diseases. oxidative stress and inflammation are closely related pathophysiological processes, one of which can be easily induced by another. thus, both processes are simultaneously found in many pathological conditions. therefore, the failure of antioxidant trials might result from failure to select appropriate agents that specifically target both inflammation and oxidative stress or failure to use both antioxidants and anti-inflammatory agents simultaneously or use of nonselective agents that block some of the oxidative and/or inflammatory pathways but exaggerate the others. to examine whether the interdependence between oxidative stress and inflammation can explain the antioxidant paradox we discussed in the present review the basic aspects of oxidative stress and inflammation and their relationship and dependence.",0
"over the period 1987-1991 an inter-disciplinary five-country group developed the euroqol instrument, a five-dimensional three-level generic measure subsequently termed the 'eq-5d'. it was designed to measure and value health status. the salient features of its development and its consolidation and expansion are discussed. initial expansion came, in particular, in the form of new language versions. their development raised translation and semantic issues, experience with which helped feed into the design of two further instruments, the eq-5d-5l and the youth version eq-5d-y. the expanded usage across clinical programmes, disease and condition areas, population surveys, patient-reported outcomes, and value sets is outlined. valuation has been of continued relevance for the group as this has allowed its instruments to be utilised as part of the economic appraisal of health programmes and their incorporation into health technology assessments. the future of the group is considered in the context of: (1) its scientific strategy, (2) changes in the external environment affecting the demand for eq-5d, and (3) a variety of issues it is facing in the context of the design of the instrument, its use in health technology assessment, and potential new uses for eq-5d outside of clinical trials and technology appraisal.",0
"implementation studies are often poorly reported and indexed, reducing their potential to inform initiatives to improve healthcare services. the standards for reporting implementation studies (stari) initiative aimed to develop guidelines for transparent and accurate reporting of implementation studies. informed by the findings of a systematic review and a consensus-building e-delphi exercise, an international working group of implementation science experts discussed and agreed the stari checklist comprising 27 items. it prompts researchers to describe both the implementation strategy (techniques used to promote implementation of an underused evidence-based intervention) and the effectiveness of the intervention that was being implemented. an accompanying explanation and elaboration document (published in bmj open , doi:10.1136/bmjopen-2016-013318) details each of the items, explains the rationale, and provides examples of good reporting practice. adoption of stari will improve the reporting of implementation studies, potentially facilitating translation of research into practice and improving the health of individuals and populations.",0
"background the pediatric complex chronic conditions (ccc) classification system, developed in 2000, requires revision to accommodate the international classification of disease 10th revision (icd-10). to update the ccc classification system, we incorporated icd-9 diagnostic codes that had been either omitted or incorrectly specified in the original system, and then translated between icd-9 and icd-10 using general equivalence mappings (gems). we further reviewed all codes in the icd-9 and icd-10 systems to include both diagnostic and procedural codes indicative of technology dependence or organ transplantation. we applied the provisional ccc version 2 (v2) system to death certificate information and 2 databases of health utilization, reviewed the resulting ccc classifications, and corrected any misclassifications. finally, we evaluated performance of the ccc v2 system by assessing: 1) the stability of the system between icd-9 and icd-10 codes using data which included both icd-9 codes and icd-10 codes; 2) the year-to-year stability before and after icd-10 implementation; and 3) the proportions of patients classified as having a ccc in both the v1 and v2 systems. results the ccc v2 classification system consists of diagnostic and procedural codes that incorporate a new neonatal ccc category as well as domains of complexity arising from technology dependence or organ transplantation. ccc v2 demonstrated close comparability between icd-9 and icd-10 and did not detect significant discontinuity in temporal trends of death in the united states. compared to the original system, ccc v2 resulted in a 1.0% absolute (10% relative) increase in the number of patients identified as having a ccc in national hospitalization dataset, and a 0.4% absolute (24% relative) increase in a national emergency department dataset. conclusions the updated ccc v2 system is comprehensive and multidimensional, and provides a necessary update to accommodate widespread implementation of icd-10.",0
"smart (simple modular architecture research tool) is a web resource ( for the identification and annotation of protein domains and the analysis of protein domain architectures. smart version 8 contains manually curated models for more than 1300 protein domains, with approximately 100 new models added since our last update article (1). the underlying protein databases were synchronized with uniprot (2), ensembl (3) and string (4), doubling the total number of annotated domains and other protein features to more than 200 million. in its 20th year, the smart analysis results pages have been streamlined again and its information sources have been updated. smart's vector based display engine has been extended to all protein schematics in smart and rewritten to use the latest web technologies. the internal full text search engine has been redesigned and updated, resulting in greatly increased search speed.",0
"this is a review of the health utilities index (hui) multi-attribute health-status classification systems, and single- and multi-attribute utility scoring systems. hui refers to both hui mark 2 (hui2) and hui mark 3 (hui3) instruments. the classification systems provide compact but comprehensive frameworks within which to describe health status. the multi-attribute utility functions provide all the information required to calculate single-summary scores of health-related quality of life (hrql) for each health state defined by the classification systems. the use of hui in clinical studies for a wide variety of conditions in a large number of countries is illustrated. hui provides comprehensive, reliable, responsive and valid measures of health status and hrql for subjects in clinical studies. utility scores of overall hrql for patients are also used in cost-utility and cost-effectiveness analyses. population norm data are available from numerous large general population surveys. the widespread use of hui facilitates the interpretation of results and permits comparisons of disease and treatment outcomes, and comparisons of long-term sequelae at the local, national and international levels.",0
"over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. however, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight 1 . here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of mri data ( ). with the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of mri studies relative to the diversity of the global population, we aggregated 123,984 mri scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. mri metrics were quantified by centile scores, relative to non-linear trajectories 2 of brain structural changes, and rates of change, over the lifespan. brain charts identified previously unreported neurodevelopmental milestones 3 , showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. centile scores showed increased heritability compared with non-centiled mri phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. in summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.",0
"education, income, and occupation are factors known to affect health and disease. in this review we describe the swedish longitudinal integrated database for health insurance and labour market studies (lisa, longitudinell integrationsdatabas för sjukförsäkrings- och arbetsmarknadsstudier). lisa covers the adult swedish population aged ≥ 16 years registered on december 31 each year since 1990 (since 2010 individuals aged ≥ 15 years). the database was launched in response to rising levels of sick leave in the country. participation in swedish government-administered registers such as lisa is compulsory, and hence selection bias is minimized. the lisa database allows researchers to identify individuals who do not work because of injury, disease, or rehabilitation. it contains data on sick leave and disability pension based on calendar year. lisa also includes information on unemployment benefits, disposable income, social welfare payments, civil status, and migration. during 2000-2017, an average of 97,000 individuals immigrated to sweden each year. this corresponds to about 1% of the swedish population (10 million people in 2017). data on occupation have a completeness of 95%. income data consist primarily of income from employment, capital, and allowances, including parental allowance. in sweden, work force participation is around 80% (2017: overall: 79.1%; men 80.3% and women 77.9%). education data are available in > 98% of all individuals aged 25-64 years, with an estimated accuracy for highest attained level of education of 85%. some information on civil status, income, education, and employment before 1990 can be obtained through the population and housing census data (fob, folk- och bostadsräkningen).",0
"a randomized, multicentre, open-label, phase ii study compared temozolomide (tmz), an oral second-generation alkylating agent, and procarbazine (pcb) in 225 patients with glioblastoma multiforme at first relapse. primary objectives were to determine progression-free survival (pfs) at 6 months and safety for tmz and pcb in adult patients who failed conventional treatment. secondary objectives were to assess overall survival and health-related quality of life (hrql). tmz was given orally at 200 mg/m(2)/day or 150 mg/m(2)/day (prior chemotherapy) for 5 days, repeated every 28 days. pcb was given orally at 150 mg/m(2)/day or 125 mg/m(2)/day (prior chemotherapy) for 28 days, repeated every 56 days. hrql was assessed using the european organization for research and treatment of cancer quality of life questionnaire (eortc qlq-c30 ) and the brain cancer module 20 (bcm20). the 6-month pfs rate for patients who received tmz was 21%, which met the protocol objective. the 6-month pfs rate for those who received pcb was 8% (p = 0.008, for the comparison). overall pfs significantly improved with tmz, with a median pfs of 12.4 weeks in the tmz group and 8.32 weeks in the pcb group (p = 0.0063). the 6-month overall survival rate for tmz patients was 60% vs. 44% for pcb patients (p = 0.019). freedom from disease progression was associated with maintenance of hrql, regardless of treatment received. tmz had an acceptable safety profile; most adverse events were mild or moderate in severity.",0
"the purpose of these guidelines is to assist physicians in recommending, performing, interpreting and reporting the results of fdg pet/ct for oncological imaging of adult patients. pet is a quantitative imaging technique and therefore requires a common quality control (qc)/quality assurance (qa) procedure to maintain the accuracy and precision of quantitation. repeatability and reproducibility are two essential requirements for any quantitative measurement and/or imaging biomarker. repeatability relates to the uncertainty in obtaining the same result in the same patient when he or she is examined more than once on the same system. however, imaging biomarkers should also have adequate reproducibility, i.e. the ability to yield the same result in the same patient when that patient is examined on different systems and at different imaging sites. adequate repeatability and reproducibility are essential for the clinical management of patients and the use of fdg pet/ct within multicentre trials. a common standardised imaging procedure will help promote the appropriate use of fdg pet/ct imaging and increase the value of publications and, therefore, their contribution to evidence-based medicine. moreover, consistency in numerical values between platforms and institutes that acquire the data will potentially enhance the role of semiquantitative and quantitative image interpretation. precision and accuracy are additionally important as fdg pet/ct is used to evaluate tumour response as well as for diagnosis, prognosis and staging. therefore both the previous and these new guidelines specifically aim to achieve standardised uptake value harmonisation in multicentre settings.",0
"the quantification of transmissibility during epidemics is essential to designing and adjusting public health responses. transmissibility can be measured by the reproduction number r, the average number of secondary cases caused by an infected individual. several methods have been proposed to estimate r over the course of an epidemic; however, they are usually difficult to implement for people without a strong background in statistical modeling. here, we present a ready-to-use tool for estimating r from incidence time series, which is implemented in popular software including microsoft excel (microsoft corporation, redmond, washington). this tool produces novel, statistically robust analytical estimates of r and incorporates uncertainty in the distribution of the serial interval (the time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases). we applied the method to 5 historical outbreaks; the resulting estimates of r are consistent with those presented in the literature. this tool should help epidemiologists quantify temporal changes in the transmission intensity of future epidemics by using surveillance data.",0
"critical care has evolved from treatment of poliomyelitis victims with respiratory failure in an intensive care unit to treatment of severely ill patients irrespective of location or specific technology. population-based studies in the developed world suggest that the burden of critical illness is higher than generally appreciated and will increase as the population ages. critical care capacity has long been needed in the developing world, and efforts to improve the care of the critically ill in these settings are starting to occur. expansion of critical care to handle the consequences of an ageing population, natural disasters, conflict, inadequate primary care, and higher-risk medical therapies will be challenged by high costs at a time of economic constraint. to meet this challenge, investigators in this discipline will need to measure the global burden of critical illness and available critical-care resources, and develop both preventive and therapeutic interventions that are generalisable across countries.",0
"background the cosmin checklist (consensus-based standards for the selection of health status measurement instruments) was developed in an international delphi study to evaluate the methodological quality of studies on measurement properties of health-related patient reported outcomes (hr-pros). in this paper, we explain our choices for the design requirements and preferred statistical methods for which no evidence is available in the literature or on which the delphi panel members had substantial discussion. methods the issues described in this paper are a reflection of the delphi process in which 43 panel members participated. results the topics discussed are internal consistency (relevance for reflective and formative models, and distinction with unidimensionality), content validity (judging relevance and comprehensiveness), hypotheses testing as an aspect of construct validity (specificity of hypotheses), criterion validity (relevance for pros), and responsiveness (concept and relation to validity, and (in) appropriate measures). conclusions we expect that this paper will contribute to a better understanding of the rationale behind the items, thereby enhancing the acceptance and use of the cosmin checklist.",0
"allergic asthma is an inflammatory lung disease initiated and directed by t helper cells type 2 (th2). the mechanism involved in generation of th2 responses to inert inhaled antigens, however, is unknown. epidemiological evidence suggests that exposure to lipopolysaccharide (lps) or other microbial products can influence the development and severity of asthma. however, the mechanism by which lps influences asthma pathogenesis remains undefined. although it is known that signaling through toll-like receptors (tlr) is required for adaptive t helper cell type 1 (th1) responses, it is unclear if tlrs are needed for th2 priming. here, we report that low level inhaled lps signaling through tlr4 is necessary to induce th2 responses to inhaled antigens in a mouse model of allergic sensitization. the mechanism by which lps signaling results in th2 sensitization involves the activation of antigen-containing dendritic cells. in contrast to low levels, inhalation of high levels of lps with antigen results in th1 responses. these studies suggest that the level of lps exposure can determine the type of inflammatory response generated and provide a potential mechanistic explanation of epidemiological data on endotoxin exposure and asthma prevalence.",0
"ferrostatin-1 (fer-1) inhibits ferroptosis, a form of regulated, oxidative, nonapoptotic cell death. we found that fer-1 inhibited cell death in cellular models of huntington's disease (hd), periventricular leukomalacia (pvl), and kidney dysfunction; fer-1 inhibited lipid peroxidation, but not mitochondrial reactive oxygen species formation or lysosomal membrane permeability. we developed a mechanistic model to explain the activity of fer-1, which guided the development of ferrostatins with improved properties. these studies suggest numerous therapeutic uses for ferrostatins, and that lipid peroxidation mediates diverse disease phenotypes.",0
"major depressive disorder (mdd), one of the most frequently encountered forms of mental illness and a leading cause of disability worldwide, poses a major challenge to genetic analysis. to date, no robustly replicated genetic loci have been identified, despite analysis of more than 9,000 cases. here, using low-coverage whole-genome sequencing of 5,303 chinese women with recurrent mdd selected to reduce phenotypic heterogeneity, and 5,337 controls screened to exclude mdd, we identified, and subsequently replicated in an independent sample, two loci contributing to risk of mdd on chromosome 10: one near the sirt1 gene (p = 2.53 × 10(-10)), the other in an intron of the lhpp gene (p = 6.45 × 10(-12)). analysis of 4,509 cases with a severe subtype of mdd, melancholia, yielded an increased genetic signal at the sirt1 locus. we attribute our success to the recruitment of relatively homogeneous cases with severe illness.",0
"the primary circulating form of vitamin d, 25-hydroxy-vitamin d , is associated with multiple medical outcomes, including rickets, osteoporosis, multiple sclerosis and cancer. in a genome-wide association study (gwas) of 4501 persons of european ancestry drawn from five cohorts, we identified single-nucleotide polymorphisms (snps) in the gene encoding group-specific component (vitamin d binding) protein, gc, on chromosome 4q12-13 that were associated with 25(oh)d concentrations: rs2282679 (p=2.0x10(-30)), in linkage disequilibrium (ld) with rs7041, a non-synonymous snp (d432e; p=4.1x10(-22)) and rs1155563 (p=3.8x10(-25)). suggestive signals for association with 25(oh)d were also observed for snps in or near three other genes involved in vitamin d synthesis or activation: rs3829251 on chromosome 11q13.4 in nadsyn1 , which was in high ld with rs1790349, located in dhcr7, the gene encoding 7-dehydrocholesterol reductase that synthesizes cholesterol from 7-dehydrocholesterol; rs6599638 in the region harboring the open-reading frame 88 (c10orf88) on chromosome 10q26.13 in the vicinity of acadsb (acyl-coenzyme a dehydrogenase), involved in cholesterol and vitamin d synthesis (p=3.3x10(-7)); and rs2060793 on chromosome 11p15.2 in cyp2r1 (cytochrome p450, family 2, subfamily r, polypeptide 1, encoding a key c-25 hydroxylase that converts vitamin d3 to an active vitamin d receptor ligand; p=1.4x10(-5)). we genotyped snps in these four regions in 2221 additional samples and confirmed strong genome-wide significant associations with 25(oh)d through meta-analysis with the gwas data for gc (p=1.8x10(-49)), nadsyn1/dhcr7 (p=3.4x10(-9)) and cyp2r1 (p=2.9x10(-17)), but not c10orf88 (p=2.4x10(-5)).",0
"zika virus (zikv) was discovered in 1947 and was thought to lead to relatively mild disease. the recent explosive outbreak of zikv in south america has led to widespread concern, with reports of neurological sequelae ranging from guillain barré syndrome to microcephaly. zikv infection has occurred in areas previously exposed to dengue virus (denv), a flavivirus closely related to zikv. here we investigated the serological cross-reaction between the two viruses. plasma immune to denv showed substantial cross-reaction to zikv and was able to drive antibody-dependent enhancement (ade) of zikv infection. using a panel of human monoclonal antibodies (mabs) to denv, we showed that most antibodies that reacted to denv envelope protein also reacted to zikv. antibodies to linear epitopes, including the immunodominant fusion-loop epitope, were able to bind zikv but were unable to neutralize the virus and instead promoted ade. our data indicate that immunity to denv might drive greater zikv replication and have clear implications for disease pathogenesis and future vaccine programs for zikv and denv.",0
"the conjunctive presence of mechanical stress and active transforming growth factor beta1 (tgf-beta1) is essential to convert fibroblasts into contractile myofibroblasts, which cause tissue contractures in fibrotic diseases. using cultured myofibroblasts and conditions that permit tension modulation on the extracellular matrix (ecm), we establish that myofibroblast contraction functions as a mechanism to directly activate tgf-beta1 from self-generated stores in the ecm. contraction of myofibroblasts and myofibroblast cytoskeletons prepared with triton x-100 releases active tgf-beta1 from the ecm. this process is inhibited either by antagonizing integrins or reducing ecm compliance and is independent from protease activity. stretching myofibroblast-derived ecm in the presence of mechanically apposing stress fibers immediately activates latent tgf-beta1. in myofibroblast-populated wounds, activation of the downstream targets of tgf-beta1 signaling smad2/3 is higher in stressed compared to relaxed tissues despite similar levels of total tgf-beta1 and its receptor. we propose activation of tgf-beta1 via integrin-mediated myofibroblast contraction as a potential checkpoint in the progression of fibrosis, restricting autocrine generation of myofibroblasts to a stiffened ecm.",0
"the ensembl ( project provides a comprehensive and integrated source of annotation of chordate genome sequences. over the past year the number of genomes available from ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (ciona savignyi) and the mosquito (aedes aegypti). some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.",0
"g protein coupled receptors (gpcrs) exhibit a spectrum of functional behaviours in response to natural and synthetic ligands. recent crystal structures provide insights into inactive states of several gpcrs. efforts to obtain an agonist-bound active-state gpcr structure have proven difficult due to the inherent instability of this state in the absence of a g protein. we generated a camelid antibody fragment (nanobody) to the human β(2) adrenergic receptor (β(2)ar) that exhibits g protein-like behaviour, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. comparison with the inactive β(2)ar structure reveals subtle changes in the binding pocket; however, these small changes are associated with an 11 å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those observed in opsin, an active form of rhodopsin. this structure provides insights into the process of agonist binding and activation.",0
"motivation psortb has remained the most precise bacterial protein subcellular localization (scl) predictor since it was first made available in 2003. however, the recall needs to be improved and no accurate scl predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. results we developed psortb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. it is the first scl predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. it features an improved standalone program, with a new batch results delivery system complementing its web interface. we evaluated the most accurate scl predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that psortb 3.0 is the most accurate but can benefit from being complemented by proteome analyst predictions. availability (download open source software or use the web interface). contact psort-mail@sfu.ca supplementary information supplementary data are available at bioinformatics online.",0
"background the novel coronavirus disease 2019 (covid-19) epidemic has spread from china to 25 countries. local cycles of transmission have already occurred in 12 countries after case importation. in africa, egypt has so far confirmed one case. the management and control of covid-19 importations heavily rely on a country's health capacity. here we evaluate the preparedness and vulnerability of african countries against their risk of importation of covid-19. methods we used data on the volume of air travel departing from airports in the infected provinces in china and directed to africa to estimate the risk of importation per country. we determined the country's capacity to detect and respond to cases with two indicators: preparedness, using the who international health regulations monitoring and evaluation framework; and vulnerability, using the infectious disease vulnerability index. countries were clustered according to the chinese regions contributing most to their risk. findings countries with the highest importation risk (ie, egypt, algeria, and south africa) have moderate to high capacity to respond to outbreaks. countries at moderate risk (ie, nigeria, ethiopia, sudan, angola, tanzania, ghana, and kenya) have variable capacity and high vulnerability. we identified three clusters of countries that share the same exposure to the risk originating from the provinces of guangdong, fujian, and the city of beijing, respectively. interpretation many countries in africa are stepping up their preparedness to detect and cope with covid-19 importations. resources, intensified surveillance, and capacity building should be urgently prioritised in countries with moderate risk that might be ill-prepared to detect imported cases and to limit onward transmission. funding eu framework programme for research and innovation horizon 2020, agence nationale de la recherche.",0
"unlabelled quickgo is a web-based tool that allows easy browsing of the gene ontology (go) and all associated electronic and manual go annotations provided by the go consortium annotation groups quickgo has been a popular go browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of go annotation data which can be extensively filtered by a range of different parameters and go slim set generation. availability and implementation quickgo has implemented in javascript, ajax and html, with all major browsers supported. it can be queried online at the software for quickgo is freely available under the apache 2 licence and can be downloaded from",0
"the 14th st gallen international breast cancer conference (2015) reviewed substantial new evidence on locoregional and systemic therapies for early breast cancer. further experience has supported the adequacy of tumor margins defined as 'no ink on invasive tumor or dcis' and the safety of omitting axillary dissection in specific cohorts. radiotherapy trials support irradiation of regional nodes in node-positive disease. considering subdivisions within luminal disease, the panel was more concerned with indications for the use of specific therapies, rather than surrogate identification of intrinsic subtypes as measured by multiparameter molecular tests. for the treatment of her2-positive disease in patients with node-negative cancers up to 1 cm, the panel endorsed a simplified regimen comprising paclitaxel and trastuzumab without anthracycline as adjuvant therapy. for premenopausal patients with endocrine responsive disease, the panel endorsed the role of ovarian function suppression with either tamoxifen or exemestane for patients at higher risk. the panel noted the value of an lhrh agonist given during chemotherapy for premenopausal women with er-negative disease in protecting against premature ovarian failure and preserving fertility. the panel noted increasing evidence for the prognostic value of commonly used multiparameter molecular markers, some of which also carried prognostic information for late relapse. the panel noted that the results of such tests, where available, were frequently used to assist decisions about the inclusion of cytotoxic chemotherapy in the treatment of patients with luminal disease, but noted that threshold values had not been established for this purpose for any of these tests. multiparameter molecular assays are expensive and therefore unavailable in much of the world. the majority of new breast cancer cases and breast cancer deaths now occur in less developed regions of the world. in these areas, less expensive pathology tests may provide valuable information. the panel recommendations on treatment are not intended to apply to all patients, but rather to establish norms appropriate for the majority. again, economic considerations may require that less expensive and only marginally less effective therapies may be necessary in less resourced areas. panel recommendations do not imply unanimous agreement among panel members. indeed, very few of the 200 questions received 100% agreement from the panel. in the text below, wording is intended to convey the strength of panel support for each recommendation, while details of panel voting on each question are available in supplementary appendix s2, available at annals of oncology online.",0
"objective obesity alters gut microbiota ecology and associates with low-grade inflammation in humans. roux-en-y gastric bypass (rygb) surgery is one of the most efficient procedures for the treatment of morbid obesity resulting in drastic weight loss and improvement of metabolic and inflammatory status. we analyzed the impact of rygb on the modifications of gut microbiota and examined links with adaptations associated with this procedure. research design and methods gut microbiota was profiled from fecal samples by real-time quantitative pcr in 13 lean control subjects and in 30 obese individuals (with seven type 2 diabetics) explored before (m0), 3 months (m3), and 6 months (m6) after rygb. results four major findings are highlighted: 1) bacteroides/prevotella group was lower in obese subjects than in control subjects at m0 and increased at m3. it was negatively correlated with corpulence, but the correlation depended highly on caloric intake; 2) escherichia coli species increased at m3 and inversely correlated with fat mass and leptin levels independently of changes in food intake; 3) lactic acid bacteria including lactobacillus/leuconostoc/pediococcus group and bifidobacterium genus decreased at m3; and 4) faecalibacterium prausnitzii species was lower in subjects with diabetes and associated negatively with inflammatory markers at m0 and throughout the follow-up after surgery independently of changes in food intake. conclusions these results suggest that components of the dominant gut microbiota rapidly adapt in a starvation-like situation induced by rygb while the f. prausnitzii species is directly linked to the reduction in low-grade inflammation state in obesity and diabetes independently of calorie intake.",0
"plastic pollution is ubiquitous throughout the marine environment, yet estimates of the global abundance and weight of floating plastics have lacked data, particularly from the southern hemisphere and remote regions. here we report an estimate of the total number of plastic particles and their weight floating in the world's oceans from 24 expeditions (2007-2013) across all five sub-tropical gyres, costal australia, bay of bengal and the mediterranean sea conducting surface net tows (n = 680) and visual survey transects of large plastic debris (n = 891). using an oceanographic model of floating debris dispersal calibrated by our data, and correcting for wind-driven vertical mixing, we estimate a minimum of 5.25 trillion particles weighing 268,940 tons. when comparing between four size classes, two microplastic 4.75 mm, a tremendous loss of microplastics is observed from the sea surface compared to expected rates of fragmentation, suggesting there are mechanisms at play that remove <4.75 mm plastic particles from the ocean surface.",0
"autophagy defends the mammalian cytosol against bacterial infection. efficient pathogen engulfment is mediated by cargo-selecting autophagy adaptors that rely on unidentified pattern-recognition or danger receptors to label invading pathogens as autophagy cargo, typically by polyubiquitin coating. here we show in human cells that galectin 8 (also known as lgals8), a cytosolic lectin, is a danger receptor that restricts salmonella proliferation. galectin 8 monitors endosomal and lysosomal integrity and detects bacterial invasion by binding host glycans exposed on damaged salmonella-containing vacuoles. by recruiting ndp52 (also known as calcoco2), galectin 8 activates antibacterial autophagy. galectin-8-dependent recruitment of ndp52 to salmonella-containing vesicles is transient and followed by ubiquitin-dependent ndp52 recruitment. because galectin 8 also detects sterile damage to endosomes or lysosomes, as well as invasion by listeria or shigella, we suggest that galectin 8 serves as a versatile receptor for vesicle-damaging pathogens. our results illustrate how cells deploy the danger receptor galectin 8 to combat infection by monitoring endosomal and lysosomal integrity on the basis of the specific lack of complex carbohydrates in the cytosol.",0
"identifying and understanding covid-19 vaccine hesitancy within distinct populations may aid future public health messaging. using nationally representative data from the general adult populations of ireland (n = 1041) and the united kingdom (uk; n = 2025), we found that vaccine hesitancy/resistance was evident for 35% and 31% of these populations respectively. vaccine hesitant/resistant respondents in ireland and the uk differed on a number of sociodemographic and health-related variables but were similar across a broad array of psychological constructs. in both populations, those resistant to a covid-19 vaccine were less likely to obtain information about the pandemic from traditional and authoritative sources and had similar levels of mistrust in these sources compared to vaccine accepting respondents. given the geographical proximity and socio-economic similarity of the populations studied, it is not possible to generalize findings to other populations, however, the methodology employed here may be useful to those wishing to understand covid-19 vaccine hesitancy elsewhere.",0
"background risk-reducing salpingo-oophorectomy (rrso) is widely used by carriers of brca1 or brca2 (brca1/2) mutations to reduce their risks of breast and ovarian cancer. to guide women and their clinicians in optimizing cancer prevention strategies, we summarized the magnitude of the risk reductions in women with brca1/2 mutations who have undergone rrso compared with those who have not. methods all reports of rrso and breast and/or ovarian or fallopian tube cancer in brca1/2 mutation carriers published between 1999 and 2007 were obtained from a pubmed search. hazard ratio (hr) estimates were identified directly from the original articles. pooled results were computed from nonoverlapping studies by fixed-effects meta-analysis. results ten studies investigated breast or gynecologic cancer outcomes in brca1/2 mutation carriers who had undergone rrso. breast cancer outcomes were investigated in three nonoverlapping studies of brca1/2 mutation carriers, four of brca1 mutation carriers, and three of brca2 mutation carriers. gynecologic cancer outcomes were investigated in three nonoverlapping studies of brca1/2 mutation carriers and one of brca1 mutation carriers. rrso was associated with a statistically significant reduction in risk of breast cancer in brca1/2 mutation carriers (hr = 0.49; 95% confidence interval = 0.37 to 0.65). similar risk reductions were observed in brca1 mutation carriers (hr = 0.47; 95% ci = 0.35 to 0.64) and in brca2 mutation carriers (hr = 0.47; 95% ci = 0.26 to 0.84). rrso was also associated with a statistically significant reduction in the risk of brca1/2-associated ovarian or fallopian tube cancer (hr = 0.21; 95% ci = 0.12 to 0.39). data were insufficient to obtain separate estimates for ovarian or fallopian tube cancer risk reduction with rrso in brca1 or brca2 mutation carriers. conclusion the summary estimates presented here indicate that rrso is strongly associated with reductions in the risk of breast, ovarian, and fallopian tube cancers and should provide guidance to women in planning cancer risk reduction strategies.",0
"the emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. it is becoming increasingly recognized that not only antibiotic resistance genes (args) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria-and also mobile genetic elements and bacteriophages-form a reservoir of args (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (hgt). hgt has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important args. of the three canonical mechanisms of hgt, conjugation is thought to have the greatest influence on the dissemination of args. while transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. here, we will discuss the concept of the resistome, provide examples of hgt of clinically relevant args and present an overview of the current knowledge of the contributions the various hgt mechanisms make to the spread of antibiotic resistance.",0
"the human gut microbiome is a critical component of digestion, breaking down complex carbohydrates, proteins, and to a lesser extent fats that reach the lower gastrointestinal tract. this process results in a multitude of microbial metabolites that can act both locally and systemically (after being absorbed into the bloodstream). the impact of these biochemicals on human health is complex, as both potentially beneficial and potentially toxic metabolites can be yielded from such microbial pathways, and in some cases, these effects are dependent upon the metabolite concentration or organ locality. the aim of this review is to summarize our current knowledge of how macronutrient metabolism by the gut microbiome influences human health. metabolites to be discussed include short-chain fatty acids and alcohols (mainly yielded from monosaccharides); ammonia, branched-chain fatty acids, amines, sulfur compounds, phenols, and indoles (derived from amino acids); glycerol and choline derivatives (obtained from the breakdown of lipids); and tertiary cycling of carbon dioxide and hydrogen. key microbial taxa and related disease states will be referred to in each case, and knowledge gaps that could contribute to our understanding of overall human wellness will be identified.",0
"functional annotation of proteins is a fundamental problem in the post-genomic era. the recent availability of protein interaction networks for many model species has spurred on the development of computational methods for interpreting such data in order to elucidate protein function. in this review, we describe the current computational approaches for the task, including direct methods, which propagate functional information through the network, and module-assisted methods, which infer functional modules within the network and use those for the annotation task. although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community.",0
"many genomes have been sequenced to high-quality draft status using sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. however, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. traditionally, draft genomes were upgraded to ""phase 3 finished"" status using time-consuming and expensive sanger-based manual finishing processes. for more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the pacific biosciences rs (pacbio) platform. our algorithm and associated software tool, pbjelly, (publicly available at automates the finishing process using long sequence reads in a reference-guided assembly process. pbjelly also provides ""lift-over"" co-ordinate tables to easily port existing annotations to the upgraded assembly. using pbjelly and long pacbio reads, we upgraded the draft genome sequences of a simulated drosophila melanogaster, the version 2 draft drosophila pseudoobscura, an assembly of the assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the sooty mangabey. with 24× mapped coverage of pacbio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in d. pseudoobscura. with 4× mapped coverage of pacbio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. with 6.8× mapped coverage of mangabey pacbio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. the accuracy of gap closure was validated by comparison to sanger sequencing on gaps from the original d. pseudoobscura draft assembly and shown to be dependent on initial reference quality.",0
"for dengue viruses 1 to 4 (denv1-4), a specific range of antibody titer has been shown to enhance viral replication in vitro and severe disease in animal models. although suspected, such antibody-dependent enhancement of severe disease has not been shown to occur in humans. using multiple statistical approaches to study a long-term pediatric cohort in nicaragua, we show that risk of severe dengue disease is highest within a narrow range of preexisting anti-denv antibody titers. by contrast, we observe protection from all symptomatic dengue disease at high antibody titers. thus, immune correlates of severe dengue must be evaluated separately from correlates of protection against symptomatic disease. these results have implications for studies of dengue pathogenesis and for vaccine development, because enhancement, not just lack of protection, is of concern.",0
"the formation of scfa is the result of a complex interplay between diet and the gut microbiota within the gut lumen environment. the discovery of receptors, across a range of cell and tissue types for which short chain fatty acids scfa appear to be the natural ligands, has led to increased interest in scfa as signaling molecules between the gut microbiota and the host. scfa represent the major carbon flux from the diet through the gut microbiota to the host and evidence is emerging for a regulatory role of scfa in local, intermediary and peripheral metabolism. however, a lack of well-designed and controlled human studies has hampered our understanding of the significance of scfa in human metabolic health. this review aims to pull together recent findings on the role of scfa in human metabolism to highlight the multi-faceted role of scfa on different metabolic systems.",0
"increasing the hydrogen ion concentration of the bathing medium reversibly depresses the sodium permeability of voltage-clamped frog nerves. the depression depends on membrane voltage: changing from ph 7 to ph 5 causes a 60% reduction in sodium permeability at +20 mv, but only a 20% reduction at +180 mv. this voltage-dependent block of sodium channels by hydrogen ions is explained by assuming that hydrogen ions enter the open sodium channel and bind there, preventing sodium ion passage. the voltage dependence arises because the binding site is assumed to lie far enough across the membrane for bound ions to be affected by part of the potential difference across the membrane. equations are derived for the general case where the blocking ion enters the channel from either side of the membrane. for h(+) ion blockage, a simpler model, in which h(+) enters the channel only from the bathing medium, is found to be sufficient. the dissociation constant of h(+) ions from the channel site, 3.9 x 10(-6) m (pk(a) 5.4), is like that of a carboxylic acid. from the voltage dependence of the block, this acid site is about one-quarter of the way across the membrane potential from the outside. in addition to blocking as described by the model, hydrogen ions also shift the responses of sodium channel ""gates"" to voltage, probably by altering the surface potential of the nerve. evidence for voltage-dependent blockage by calcium ions is also presented.",0
"background how long one lives, how many years of life are spent in good and poor health, and how the population's state of health and leading causes of disability change over time all have implications for policy, planning, and provision of services. we comparatively assessed the patterns and trends of healthy life expectancy (hale), which quantifies the number of years of life expected to be lived in good health, and the complementary measure of disability-adjusted life-years (dalys), a composite measure of disease burden capturing both premature mortality and prevalence and severity of ill health, for 359 diseases and injuries for 195 countries and territories over the past 28 years. methods we used data for age-specific mortality rates, years of life lost (ylls) due to premature mortality, and years lived with disability (ylds) from the global burden of diseases, injuries, and risk factors study (gbd) 2017 to calculate hale and dalys from 1990 to 2017. we calculated hale using age-specific mortality rates and ylds per capita for each location, age, sex, and year. we calculated dalys for 359 causes as the sum of ylls and ylds. we assessed how observed hale and dalys differed by country and sex from expected trends based on socio-demographic index (sdi). we also analysed hale by decomposing years of life gained into years spent in good health and in poor health, between 1990 and 2017, and extra years lived by females compared with males. findings globally, from 1990 to 2017, life expectancy at birth increased by 7·4 years (95% uncertainty interval 7·1-7·8), from 65·6 years (65·3-65·8) in 1990 to 73·0 years (72·7-73·3) in 2017. the increase in years of life varied from 5·1 years (5·0-5·3) in high sdi countries to 12·0 years (11·3-12·8) in low sdi countries. of the additional years of life expected at birth, 26·3% (20·1-33·1) were expected to be spent in poor health in high sdi countries compared with 11·7% (8·8-15·1) in low-middle sdi countries. hale at birth increased by 6·3 years (5·9-6·7), from 57·0 years (54·6-59·1) in 1990 to 63·3 years (60·5-65·7) in 2017. the increase varied from 3·8 years (3·4-4·1) in high sdi countries to 10·5 years (9·8-11·2) in low sdi countries. even larger variations in hale than these were observed between countries, ranging from 1·0 year (0·4-1·7) in saint vincent and the grenadines (62·4 years in 1990 to 63·5 years in 2017) to 23·7 years (21·9-25·6) in eritrea (30·7 years in 1990 to 54·4 years in 2017). in most countries, the increase in hale was smaller than the increase in overall life expectancy, indicating more years lived in poor health. in 180 of 195 countries and territories, females were expected to live longer than males in 2017, with extra years lived varying from 1·4 years (0·6-2·3) in algeria to 11·9 years (10·9-12·9) in ukraine. of the extra years gained, the proportion spent in poor health varied largely across countries, with less than 20% of additional years spent in poor health in bosnia and herzegovina, burundi, and slovakia, whereas in bahrain all the extra years were spent in poor health. in 2017, the highest estimate of hale at birth was in singapore for both females (75·8 years ) and males (72·6 years ) and the lowest estimates were in central african republic (47·0 years for females and 42·8 years for males). globally, in 2017, the five leading causes of dalys were neonatal disorders, ischaemic heart disease, stroke, lower respiratory infections, and chronic obstructive pulmonary disease. between 1990 and 2017, age-standardised daly rates decreased by 41·3% (38·8-43·5) for communicable diseases and by 49·8% (47·9-51·6) for neonatal disorders. for non-communicable diseases, global dalys increased by 40·1% (36·8-43·0), although age-standardised daly rates decreased by 18·1% (16·0-20·2). interpretation with increasing life expectancy in most countries, the question of whether the additional years of life gained are spent in good health or poor health has been increasingly relevant because of the potential policy implications, such as health-care provisions and extending retirement ages. in some locations, a large proportion of those additional years are spent in poor health. large inequalities in hale and disease burden exist across countries in different sdi quintiles and between sexes. the burden of disabling conditions has serious implications for health system planning and health-related expenditures. despite the progress made in reducing the burden of communicable diseases and neonatal disorders in low sdi countries, the speed of this progress could be increased by scaling up proven interventions. the global trends among non-communicable diseases indicate that more effort is needed to maximise hale, such as risk prevention and attention to upstream determinants of health. funding bill & melinda gates foundation.",0
"kaplan-meier estimate is one of the best options to be used to measure the fraction of subjects living for a certain amount of time after treatment. in clinical trials or community trials, the effect of an intervention is assessed by measuring the number of subjects survived or saved after that intervention over a period of time. the time starting from a defined point to the occurrence of a given event, for example death is called as survival time and the analysis of group data as survival analysis. this can be affected by subjects under study that are uncooperative and refused to be remained in the study or when some of the subjects may not experience the event or death before the end of the study, although they would have experienced or died if observation continued, or we lose touch with them midway in the study. we label these situations as censored observations. the kaplan-meier estimate is the simplest way of computing the survival over time in spite of all these difficulties associated with subjects or situations. the survival curve can be created assuming various situations. it involves computing of probabilities of occurrence of event at a certain point of time and multiplying these successive probabilities by any earlier computed probabilities to get the final estimate. this can be calculated for two groups of subjects and also their statistical difference in the survivals. this can be used in ayurveda research when they are comparing two drugs and looking for survival of subjects.",0
"the ability to analyze multiple single-cell parameters is critical for understanding cellular heterogeneity. despite recent advances in measurement technology, methods for analyzing high-dimensional single-cell data are often subjective, labor intensive and require prior knowledge of the biological system. to objectively uncover cellular heterogeneity from single-cell measurements, we present a versatile computational approach, spanning-tree progression analysis of density-normalized events (spade). we applied spade to flow cytometry data of mouse bone marrow and to mass cytometry data of human bone marrow. in both cases, spade organized cells in a hierarchy of related phenotypes that partially recapitulated well-described patterns of hematopoiesis. we demonstrate that spade is robust to measurement noise and to the choice of cellular markers. spade facilitates the analysis of cellular heterogeneity, the identification of cell types and comparison of functional markers in response to perturbations.",0
"glioblastoma multiforme is the most common primary malignant brain tumour, with a median survival of about one year. this poor prognosis is due to therapeutic resistance and tumour recurrence after surgical removal. precisely how recurrence occurs is unknown. using a genetically engineered mouse model of glioma, here we identify a subset of endogenous tumour cells that are the source of new tumour cells after the drug temozolomide (tmz) is administered to transiently arrest tumour growth. a nestin-δtk-ires-gfp (nes-δtk-gfp) transgene that labels quiescent subventricular zone adult neural stem cells also labels a subset of endogenous glioma tumour cells. on arrest of tumour cell proliferation with tmz, pulse-chase experiments demonstrate a tumour re-growth cell hierarchy originating with the nes-δtk-gfp transgene subpopulation. ablation of the gfp+ cells with chronic ganciclovir administration significantly arrested tumour growth, and combined tmz and ganciclovir treatment impeded tumour development. thus, a relatively quiescent subset of endogenous glioma cells, with properties similar to those proposed for cancer stem cells, is responsible for sustaining long-term tumour growth through the production of transient populations of highly proliferative cells.",0
"objective to investigate whether calcium supplements increase the risk of cardiovascular events. design patient level and trial level meta-analyses. data sources medline, embase, and cochrane central register of controlled trials (1966-march 2010), reference lists of meta-analyses of calcium supplements, and two clinical trial registries. initial searches were carried out in november 2007, with electronic database searches repeated in march 2010. study selection eligible studies were randomised, placebo controlled trials of calcium supplements (>or=500 mg/day), with 100 or more participants of mean age more than 40 years and study duration more than one year. the lead authors of eligible trials supplied data. cardiovascular outcomes were obtained from self reports, hospital admissions, and death certificates. results 15 trials were eligible for inclusion, five with patient level data (8151 participants, median follow-up 3.6 years, interquartile range 2.7-4.3 years) and 11 with trial level data (11 921 participants, mean duration 4.0 years). in the five studies contributing patient level data, 143 people allocated to calcium had a myocardial infarction compared with 111 allocated to placebo (hazard ratio 1.31, 95% confidence interval 1.02 to 1.67, p=0.035). non-significant increases occurred in the incidence of stroke (1.20, 0.96 to 1.50, p=0.11), the composite end point of myocardial infarction, stroke, or sudden death (1.18, 1.00 to 1.39, p=0.057), and death (1.09, 0.96 to 1.23, p=0.18). the meta-analysis of trial level data showed similar results: 296 people had a myocardial infarction (166 allocated to calcium, 130 to placebo), with an increased incidence of myocardial infarction in those allocated to calcium (pooled relative risk 1.27, 95% confidence interval 1.01 to 1.59, p=0.038). conclusions calcium supplements (without coadministered vitamin d) are associated with an increased risk of myocardial infarction. as calcium supplements are widely used these modest increases in risk of cardiovascular disease might translate into a large burden of disease in the population. a reassessment of the role of calcium supplements in the management of osteoporosis is warranted.",0
"unprecedented measures have been adopted to control the rapid spread of the ongoing covid-19 epidemic in china. people's adherence to control measures is affected by their knowledge, attitudes, and practices (kap) towards covid-19. in this study, we investigated chinese residents' kap towards covid-19 during the rapid rise period of the outbreak. an online sample of chinese residents was successfully recruited via the authors' networks with residents and popular media in hubei, china. a self-developed online kap questionnaire was completed by the participants. the knowledge questionnaire consisted of 12 questions regarding the clinical characteristics and prevention of covid-19. assessments on residents' attitudes and practices towards covid-19 included questions on confidence in winning the battle against covid-19 and wearing masks when going out in recent days. among the survey completers (n=6910), 65.7% were women, 63.5% held a bachelor degree or above, and 56.2% engaged in mental labor. the overall correct rate of the knowledge questionnaire was 90%. the majority of the respondents (97.1%) had confidence that china can win the battle against covid-19. nearly all of the participants (98.0%) wore masks when going out in recent days. in multiple logistic regression analyses, the covid-19 knowledge score (or: 0.75-0.90, p<0.001) was significantly associated with a lower likelihood of negative attitudes and preventive practices towards covid-2019. most chinese residents of a relatively high socioeconomic status, in particular women, are knowledgeable about covid-19, hold optimistic attitudes, and have appropriate practices towards covid-19. health education programs aimed at improving covid-19 knowledge are helpful for chinese residents to hold optimistic attitudes and maintain appropriate practices. due to the limited sample representativeness, we must be cautious when generalizing these findings to populations of a low socioeconomic status.",0
"background fully understanding the determinants and sequelae of fetal growth requires a continuous measure of birth weight adjusted for gestational age. published united states reference data, however, provide estimates only of the median and lowest and highest 5th and 10th percentiles for birth weight at each gestational age. the purpose of our analysis was to create more continuous reference measures of birth weight for gestational age for use in epidemiologic analyses. methods we used data from the most recent nationwide united states natality datasets to generate multiple reference percentiles of birth weight at each completed week of gestation from 22 through 44 weeks. gestational age was determined from last menstrual period. we analyzed data from 6,690,717 singleton infants with recorded birth weight and sex born to united states resident mothers in 1999 and 2000. results birth weight rose with greater gestational age, with increasing slopes during the third trimester and a leveling off beyond 40 weeks. boys had higher birth weights than girls, later born children higher weights than firstborns, and infants born to non-hispanic white mothers higher birth weights than those born to non-hispanic black mothers. these results correspond well with previously published estimates reporting limited percentiles. conclusions our method provides comprehensive reference values of birth weight at 22 through 44 completed weeks of gestation, derived from broadly based nationwide data. other approaches require assumptions of normality or of a functional relationship between gestational age and birth weight, which may not be appropriate. these data should prove useful for researchers investigating the predictors and outcomes of altered fetal growth.",0
"this discussion paper argues that both the use of cronbach's alpha as a reliability estimate and as a measure of internal consistency suffer from major problems. first, alpha always has a value, which cannot be equal to the test score's reliability given the interitem covariance matrix and the usual assumptions about measurement error. second, in practice, alpha is used more often as a measure of the test's internal consistency than as an estimate of reliability. however, it can be shown easily that alpha is unrelated to the internal structure of the test. it is further discussed that statistics based on a single test administration do not convey much information about the accuracy of individuals' test performance. the paper ends with a list of conclusions about the usefulness of alpha.",0
"background bisphenol a (bpa) is one of the highest-volume chemicals produced worldwide, and human exposure to bpa is thought to be ubiquitous. thus, there are concerns that the amount of bpa to which humans are exposed may cause adverse health effects. importantly, results from a large number of biomonitoring studies are at odds with the results from two toxicokinetic studies. objective we examined several possibilities for why biomonitoring and toxicokinetic studies could come to seemingly conflicting conclusions. data sources we examined > 80 published human biomonitoring studies that measured bpa concentrations in human tissues, urine, blood, and other fluids, along with two toxicokinetic studies of human bpa metabolism. data extraction and synthesis the > 80 biomonitoring studies examined included measurements in thousands of individuals from several different countries, and these studies overwhelmingly detected bpa in individual adults, adolescents, and children. unconjugated bpa was routinely detected in blood (in the nanograms per milliliter range), and conjugated bpa was routinely detected in the vast majority of urine samples (also in the nanograms per milliliter range). in stark contrast, toxicokinetic studies proposed that humans are not internally exposed to bpa. some regulatory agencies have relied solely on these toxicokinetic models in their risk assessments. conclusions available data from biomonitoring studies clearly indicate that the general population is exposed to bpa and is at risk from internal exposure to unconjugated bpa. the two toxicokinetic studies that suggested human bpa exposure is negligible have significant deficiencies, are directly contradicted by hypothesis-driven studies, and are therefore not reliable for risk assessment purposes.",0
"background to develop more efficient programmes for promoting dietary and/or physical activity change (in order to prevent type 2 diabetes) it is critical to ensure that the intervention components and characteristics most strongly associated with effectiveness are included. the aim of this systematic review of reviews was to identify intervention components that are associated with increased change in diet and/or physical activity in individuals at risk of type 2 diabetes. methods medline, embase, cinahl, psycinfo, and the cochrane library were searched for systematic reviews of interventions targeting diet and/or physical activity in adults at risk of developing type 2 diabetes from 1998 to 2008. two reviewers independently selected reviews and rated methodological quality. individual analyses from reviews relating effectiveness to intervention components were extracted, graded for evidence quality and summarised. results of 3856 identified articles, 30 met the inclusion criteria and 129 analyses related intervention components to effectiveness. these included causal analyses (based on randomisation of participants to different intervention conditions) and associative analyses (e.g. meta-regression). overall, interventions produced clinically meaningful weight loss (3-5 kg at 12 months; 2-3 kg at 36 months) and increased physical activity (30-60 mins/week of moderate activity at 12-18 months). based on causal analyses, intervention effectiveness was increased by engaging social support, targeting both diet and physical activity, and using well-defined/established behaviour change techniques. increased effectiveness was also associated with increased contact frequency and using a specific cluster of ""self-regulatory"" behaviour change techniques (e.g. goal-setting, self-monitoring). no clear relationships were found between effectiveness and intervention setting, delivery mode, study population or delivery provider. evidence on long-term effectiveness suggested the need for greater consideration of behaviour maintenance strategies. conclusions this comprehensive review of reviews identifies specific components which are associated with increased effectiveness in interventions to promote change in diet and/or physical activity. to maximise the efficiency of programmes for diabetes prevention, practitioners and commissioning organisations should consider including these components.",0
"coronavirus disease 2019 (covid-19) or severe acute respiratory syndrome coronavirus 2 (sars-cov-2), a novel coronavirus strain disease, has recently emerged in china and rapidly spread worldwide. this novel strain is highly transmittable and severe disease has been reported in up to 16% of hospitalized cases. more than 600,000 cases have been confirmed and the number of deaths is constantly increasing. covid-19 hospitalized patients, especially those suffering from severe respiratory or systemic manifestations, fall under the spectrum of the acutely ill medical population, which is at increased venous thromboembolism risk. thrombotic complications seem to emerge as an important issue in patients infected with covid-19. preliminary reports on covid-19 patients' clinical and laboratory findings include thrombocytopenia, elevated d-dimer, prolonged prothrombin time, and disseminated intravascular coagulation. as the pandemic is spreading and the whole picture is yet unknown, we highlight the importance of coagulation disorders in covid-19 infected patients and review relevant data of previous coronavirus epidemics caused by the severe acute respiratory syndrome coronavirus 1 (sars-cov-1) and the middle east respiratory syndrome coronavirus (mers-cov).",0
"functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. the gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. the comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.",0
"three worldwide (pandemic) outbreaks of influenza occurred in the 20th century: in 1918, 1957, and 1968. the latter 2 were in the era of modern virology and most thoroughly characterized. all 3 have been informally identified by their presumed sites of origin as spanish, asian, and hong kong influenza, respectively. they are now known to represent 3 different antigenic subtypes of influenza a virus: h1n1, h2n2, and h3n2, respectively. not classified as true pandemics are 3 notable epidemics: a pseudopandemic in 1947 with low death rates, an epidemic in 1977 that was a pandemic in children, and an abortive epidemic of swine influenza in 1976 that was feared to have pandemic potential. major influenza epidemics show no predictable periodicity or pattern, and all differ from one another. evidence suggests that true pandemics with changes in hemagglutinin subtypes arise from genetic reassortment with animal influenza a viruses.",0
"objective to compare the risk for all cause and overdose mortality in people with opioid dependence during and after substitution treatment with methadone or buprenorphine and to characterise trends in risk of mortality after initiation and cessation of treatment. design systematic review and meta-analysis. data sources medline, embase, psycinfo, and lilacs to september 2016. study selection prospective or retrospective cohort studies in people with opioid dependence that reported deaths from all causes or overdose during follow-up periods in and out of opioid substitution treatment with methadone or buprenorphine. data extraction and synthesis two independent reviewers performed data extraction and assessed study quality. mortality rates in and out of treatment were jointly combined across methadone or buprenorphine cohorts by using multivariate random effects meta-analysis. results there were 19 eligible cohorts, following 122 885 people treated with methadone over 1.3-13.9 years and 15 831 people treated with buprenorphine over 1.1-4.5 years. pooled all cause mortality rates were 11.3 and 36.1 per 1000 person years in and out of methadone treatment (unadjusted out-to-in rate ratio 3.20, 95% confidence interval 2.65 to 3.86) and reduced to 4.3 and 9.5 in and out of buprenorphine treatment (2.20, 1.34 to 3.61). in pooled trend analysis, all cause mortality dropped sharply over the first four weeks of methadone treatment and decreased gradually two weeks after leaving treatment. all cause mortality remained stable during induction and remaining time on buprenorphine treatment. overdose mortality evolved similarly, with pooled overdose mortality rates of 2.6 and 12.7 per 1000 person years in and out of methadone treatment (unadjusted out-to-in rate ratio 4.80, 2.90 to 7.96) and 1.4 and 4.6 in and out of buprenorphine treatment. conclusions retention in methadone and buprenorphine treatment is associated with substantial reductions in the risk for all cause and overdose mortality in people dependent on opioids. the induction phase onto methadone treatment and the time immediately after leaving treatment with both drugs are periods of particularly increased mortality risk, which should be dealt with by both public health and clinical strategies to mitigate such risk. these findings are potentially important, but further research must be conducted to properly account for potential confounding and selection bias in comparisons of mortality risk between opioid substitution treatments, as well as throughout periods in and out of each treatment.",0
"research and clinical observations suggest that during times of pandemic many people exhibit stress- or anxiety-related responses that include fear of becoming infected, fear of coming into contact with possibly contaminated objects or surfaces, fear of foreigners who might be carrying infection (i.e., disease-related xenophobia), fear of the socio-economic consequences of the pandemic, compulsive checking and reassurance-seeking regarding possible pandemic-related threats, and traumatic stress symptoms about the pandemic (e.g., nightmares, intrusive thoughts). we developed the 36-item covid stress scales (css) to measure these features, as they pertain to covid-19. the css were developed to better understand and assess covid-19-related distress. the scales were intentionally designed so they could be readily adapted for future pandemics. the css were developed and initially validated in population-representative samples from canada (n = 3479) and the united states (n = 3375). a stable 5-factor solution was identified, corresponding to scales assessing covid-related stress and anxiety symptoms: (1) danger and contamination fears, (2) fears about economic consequences, (3) xenophobia, (4) compulsive checking and reassurance seeking, and (5) traumatic stress symptoms about covid-19. the scales performed well on various indices of reliability and validity. the scales were intercorrelated, providing evidence of a covid stress syndrome. the scales offer promise as tools for better understanding the distress associated with covid-19 and for identifying people in need of mental health services.",0
"background optimal drug treatment for patients with resistant hypertension is undefined. we aimed to test the hypotheses that resistant hypertension is most often caused by excessive sodium retention, and that spironolactone would therefore be superior to non-diuretic add-on drugs at lowering blood pressure. methods in this double-blind, placebo-controlled, crossover trial, we enrolled patients aged 18-79 years with seated clinic systolic blood pressure 140 mm hg or greater (or ≥135 mm hg for patients with diabetes) and home systolic blood pressure (18 readings over 4 days) 130 mm hg or greater, despite treatment for at least 3 months with maximally tolerated doses of three drugs, from 12 secondary and two primary care sites in the uk. patients rotated, in a preassigned, randomised order, through 12 weeks of once daily treatment with each of spironolactone (25-50 mg), bisoprolol (5-10 mg), doxazosin modified release (4-8 mg), and placebo, in addition to their baseline blood pressure drugs. random assignment was done via a central computer system. investigators and patients were masked to the identity of drugs, and to their sequence allocation. the dose was doubled after 6 weeks of each cycle. the hierarchical primary endpoints were the difference in averaged home systolic blood pressure between spironolactone and placebo, followed (if significant) by the difference in home systolic blood pressure between spironolactone and the average of the other two active drugs, followed by the difference in home systolic blood pressure between spironolactone and each of the other two drugs. analysis was by intention to treat. the trial is registered with eudract number 2008-007149-30, and clinicaltrials.gov number, nct02369081. findings between may 15, 2009, and july 8, 2014, we screened 436 patients, of whom 335 were randomly assigned. after 21 were excluded, 285 patients received spironolactone, 282 doxazosin, 285 bisoprolol, and 274 placebo; 230 patients completed all treatment cycles. the average reduction in home systolic blood pressure by spironolactone was superior to placebo (-8·70 mm hg ; p interpretation spironolactone was the most effective add-on drug for the treatment of resistant hypertension. the superiority of spironolactone supports a primary role of sodium retention in this condition. funding the british heart foundation and national institute for health research.",0
"background caesarean section (cs) rates continue to evoke worldwide concern because of their steady increase, lack of consensus on the appropriate cs rate and the associated additional short- and long-term risks and costs. we present the latest cs rates and trends over the last 24 years. methods we collected nationally-representative data on cs rates between 1990 to 2014 and calculated regional and subregional weighted averages. we conducted a longitudinal analysis calculating differences in cs rates as absolute change and as the average annual rate of increase (aari). results according to the latest data from 150 countries, currently 18.6% of all births occur by cs, ranging from 6% to 27.2% in the least and most developed regions, respectively. latin america and the caribbean region has the highest cs rates (40.5%), followed by northern america (32.3%), oceania (31.1%), europe (25%), asia (19.2%) and africa (7.3%). based on the data from 121 countries, the trend analysis showed that between 1990 and 2014, the global average cs rate increased 12.4% (from 6.7% to 19.1%) with an average annual rate of increase of 4.4%. the largest absolute increases occurred in latin america and the caribbean (19.4%, from 22.8% to 42.2%), followed by asia (15.1%, from 4.4% to 19.5%), oceania (14.1%, from 18.5% to 32.6%), europe (13.8%, from 11.2% to 25%), northern america (10%, from 22.3% to 32.3%) and africa (4.5%, from 2.9% to 7.4%). asia and northern america were the regions with the highest and lowest average annual rate of increase (6.4% and 1.6%, respectively). conclusion the use of cs worldwide has increased to unprecedented levels although the gap between higher- and lower-resource settings remains. the information presented is essential to inform policy and global and regional strategies aimed at optimizing the use of cs.",0
"the central nervous system (cns) is considered an organ devoid of lymphatic vasculature. yet, part of the cerebrospinal fluid (csf) drains into the cervical lymph nodes (lns). the mechanism of csf entry into the lns has been unclear. here we report the surprising finding of a lymphatic vessel network in the dura mater of the mouse brain. we show that dural lymphatic vessels absorb csf from the adjacent subarachnoid space and brain interstitial fluid (isf) via the glymphatic system. dural lymphatic vessels transport fluid into deep cervical lns (dclns) via foramina at the base of the skull. in a transgenic mouse model expressing a vegf-c/d trap and displaying complete aplasia of the dural lymphatic vessels, macromolecule clearance from the brain was attenuated and transport from the subarachnoid space into dclns was abrogated. surprisingly, brain isf pressure and water content were unaffected. overall, these findings indicate that the mechanism of csf flow into the dclns is directly via an adjacent dural lymphatic network, which may be important for the clearance of macromolecules from the brain. importantly, these results call for a reexamination of the role of the lymphatic system in cns physiology and disease.",0
"adeno-associated viruses (aavs) are commonly used for in vivo gene transfer. nevertheless, aavs that provide efficient transduction across specific organs or cell populations are needed. here, we describe aav-php.eb and aav-php.s, capsids that efficiently transduce the central and peripheral nervous systems, respectively. in the adult mouse, intravenous administration of 1 × 10 11 vector genomes (vg) of aav-php.eb transduced 69% of cortical and 55% of striatal neurons, while 1 × 10 12 vg of aav-php.s transduced 82% of dorsal root ganglion neurons, as well as cardiac and enteric neurons. the efficiency of these vectors facilitates robust cotransduction and stochastic, multicolor labeling for individual cell morphology studies. to support such efforts, we provide methods for labeling a tunable fraction of cells without compromising color diversity. furthermore, when used with cell-type-specific promoters and enhancers, these aavs enable efficient and targetable genetic modification of cells throughout the nervous system of transgenic and non-transgenic animals.",0
"during resting conditions the brain remains functionally and metabolically active. one manifestation of this activity that has become an important research tool is spontaneous fluctuations in the blood oxygen level-dependent (bold) signal of functional magnetic resonance imaging (fmri). the identification of correlation patterns in these spontaneous fluctuations has been termed resting state functional connectivity (fcmri) and has the potential to greatly increase the translation of fmri into clinical care. in this article we review the advantages of the resting state signal for clinical applications including detailed discussion of signal to noise considerations. we include guidelines for performing resting state research on clinical populations, outline the different areas for clinical application, and identify important barriers to be addressed to facilitate the translation of resting state fcmri into the clinical realm.",0
"background and aims the impact of coronavirus disease 2019 (covid-19) on patients with inflammatory bowel disease (ibd) is unknown. we sought to characterize the clinical course of covid-19 among patients with ibd and evaluate the association among demographics, clinical characteristics, and immunosuppressant treatments on covid-19 outcomes. methods surveillance epidemiology of coronavirus under research exclusion for inflammatory bowel disease (secure-ibd) is a large, international registry created to monitor outcomes of patients with ibd with confirmed covid-19. we calculated age-standardized mortality ratios and used multivariable logistic regression to identify factors associated with severe covid-19, defined as intensive care unit admission, ventilator use, and/or death. results 525 cases from 33 countries were reported (median age 43 years, 53% men). thirty-seven patients (7%) had severe covid-19, 161 (31%) were hospitalized, and 16 patients died (3% case fatality rate). standardized mortality ratios for patients with ibd were 1.8 (95% confidence interval , 0.9-2.6), 1.5 (95% ci, 0.7-2.2), and 1.7 (95% ci, 0.9-2.5) relative to data from china, italy, and the united states, respectively. risk factors for severe covid-19 among patients with ibd included increasing age (adjusted odds ratio , 1.04; 95% ci, 1.01-1.02), ≥2 comorbidities (aor, 2.9; 95% ci, 1.1-7.8), systemic corticosteroids (aor, 6.9; 95% ci, 2.3-20.5), and sulfasalazine or 5-aminosalicylate use (aor, 3.1; 95% ci, 1.3-7.7). tumor necrosis factor antagonist treatment was not associated with severe covid-19 (aor, 0.9; 95% ci, 0.4-2.2). conclusions increasing age, comorbidities, and corticosteroids are associated with severe covid-19 among patients with ibd, although a causal relationship cannot be definitively established. notably, tumor necrosis factor antagonists do not appear to be associated with severe covid-19.",0
"we identified the neurons comprising the drosophila mushroom body (mb), an associative center in invertebrate brains, and provide a comprehensive map describing their potential connections. each of the 21 mb output neuron (mbon) types elaborates segregated dendritic arbors along the parallel axons of ∼2000 kenyon cells, forming 15 compartments that collectively tile the mb lobes. mbon axons project to five discrete neuropils outside of the mb and three mbon types form a feedforward network in the lobes. each of the 20 dopaminergic neuron (dan) types projects axons to one, or at most two, of the mbon compartments. convergence of dan axons on compartmentalized kenyon cell-mbon synapses creates a highly ordered unit that can support learning to impose valence on sensory representations. the elucidation of the complement of neurons of the mb provides a comprehensive anatomical substrate from which one can infer a functional logic of associative olfactory learning and memory.",0
"the pandemic coronavirus sars-cov-2 threatens public health worldwide. the viral spike protein mediates sars-cov-2 entry into host cells and harbors a s1/s2 cleavage site containing multiple arginine residues (multibasic) not found in closely related animal coronaviruses. however, the role of this multibasic cleavage site in sars-cov-2 infection is unknown. here, we report that the cellular protease furin cleaves the spike protein at the s1/s2 site and that cleavage is essential for s-protein-mediated cell-cell fusion and entry into human lung cells. moreover, optimizing the s1/s2 site increased cell-cell, but not virus-cell, fusion, suggesting that the corresponding viral variants might exhibit increased cell-cell spread and potentially altered virulence. our results suggest that acquisition of a s1/s2 multibasic cleavage site was essential for sars-cov-2 infection of humans and identify furin as a potential target for therapeutic intervention.",0
"we developed a method for production of antigen-specific, h-2-restricted t cell hybrids. the tumor cell partner in the fusions was itself a t cell hybrid, fs6-14.13.ag2 (or its derivatives), which could be induced to produce the growth factor, interleukin-2 (il-2), in response to a challenge with concanavalin a, but had no known antigen specificity. the normal t cell partner in the fusions was a population of lymph node t cell blasts that had been highly enriched in antigen-specific, h-2-restricted t cells by in vivo immunization, followed by in vitro challenge with antigen and clonal expansion in il-2-containing medium. these fusions produced hybrids that grew constitutively in culture. a sizable proportion of the hybrids demonstrated the ability to produce il-2 in response to a challenge with specific antigen presented by irradiated spleen cells of the appropriate h-2 type. four cloned antigen/h-2-specific hybrid lines were produced. ao-40.10 responded to chicken ovalbumin (ova) when presented by i-a(k)-bearing cells. dc1.18.3 responded to the apo form of beef cytochrome c when presented with i-a(d). aodk-10.4 responded to keyhole limpet hemocyanin (klh) presented with i-a (d). aodk-1.16 also responded to klh presented by a product of the i region of h-2(d), but the data were consistent with either a product of the i-j-i-e(d) region or a combinatorial molecule with elements from both i-a(d) and i-e(d)/i-c(d). coincidentally, ao-40.10 was shown to have an unexpected alloreactivity with a product of h-2(b) mapping to the k-i-a region. these hybrids should prove invaluable as sources of monoclonal material for the study of the receptor(s) on t cells with h-2-restricted antigen specificities. we also generated t cell hybrids with two antigen/h-2 specificities by fusing an azaguanine-resistant clone of ao-40.10 to normal t cells with a different antigen/h-2 specificity. many of the hybrids retained reactivity to ova plus h-2(a) and to the second antigen/h-2 combination. none reacted to either ova plus the second h-2 type or to the second antigen plus h-2(a). one of these hybrids was successfully cloned to produce the line aofk- 11.11.1. it retained the ability to recognize ova plus i-a(k) inherited from one parent, and klh plus ia(f) inherited from the other. it did not recognize ova plus ia(f) or klh plus i-a(k). these results have some bearing on models describing the nature of t cell receptors for antigen recognized in association with h-2 products. they do not support models in which antigen and h-2 are recognized separately by two independent t cell receptors.",0
"despite the essential role of the corticospinal tract (cst) in controlling voluntary movements, successful regeneration of large numbers of injured cst axons beyond a spinal cord lesion has never been achieved. we found that pten/mtor are critical for controlling the regenerative capacity of mouse corticospinal neurons. after development, the regrowth potential of cst axons was lost and this was accompanied by a downregulation of mtor activity in corticospinal neurons. axonal injury further diminished neuronal mtor activity in these neurons. forced upregulation of mtor activity in corticospinal neurons by conditional deletion of pten, a negative regulator of mtor, enhanced compensatory sprouting of uninjured cst axons and enabled successful regeneration of a cohort of injured cst axons past a spinal cord lesion. furthermore, these regenerating cst axons possessed the ability to reform synapses in spinal segments distal to the injury. thus, modulating neuronal intrinsic pten/mtor activity represents a potential therapeutic strategy for promoting axon regeneration and functional repair after adult spinal cord injury.",0
"background polyfluoroalkyl chemicals (pfcs) have been used since the 1950s in numerous commercial applications. exposure of the general u.s. population to pfcs is widespread. since 2002, the manufacturing practices for pfcs in the united states have changed considerably. objectives we aimed to assess exposure to perfluorooctane sulfonic acid (pfos), perfluorooctanoic acid (pfoa), perfluorohexane sulfonic acid (pfhxs), perfluorononanoic acid (pfna), and eight other pfcs in a representative 2003-2004 sample of the general u.s. population >or= 12 years of age and to determine whether serum concentrations have changed since the 1999-2000 national health and nutrition examination survey (nhanes). methods by using automated solid-phase extraction coupled to isotope dilution-high-performance liquid chromatography-tandem mass spectrometry, we analyzed 2,094 serum samples collected from nhanes 2003-2004 participants. results we detected pfos, pfoa, pfhxs, and pfna in > 98% of the samples. concentrations differed by race/ethnicity and sex. geometric mean concentrations were significantly lower (approximately 32% for pfos, 25% for pfoa, 10% for pfhxs) and higher (100%, pfna) than the concentrations reported in nhanes 1999-2000 (p conclusions in the general u.s. population in 2003-2004, pfos, pfoa, pfhxs, and pfna serum concentrations were measurable in each demographic population group studied. geometric mean concentrations of pfos, pfoa, and pfhxs in 2003-2004 were lower than in 1999-2000. the apparent reductions in concentrations of pfos, pfoa, and pfhxs most likely are related to discontinuation in 2002 of industrial production by electrochemical fluorination of pfos and related perfluorooctanesulfonyl fluoride compounds.",0
"estrogens are defined by their ability to induce the proliferation of cells of the female genital tract. the wide chemical diversity of estrogenic compounds precludes an accurate prediction of estrogenic activity on the basis of chemical structure. rodent bioassays are not suited for the large-scale screening of chemicals before their release into the environment because of their cost, complexity, and ethical concerns. the e-screen assay was developed to assess the estrogenicity of environmental chemicals using the proliferative effect of estrogens on their target cells as an end point. this quantitative assay compares the cell number achieved by similar inocula of mcf-7 cells in the absence of estrogens (negative control) and in the presence of 17 beta-estradiol (positive control) and a range of concentrations of chemicals suspected to be estrogenic. among the compounds tested, several ""new"" estrogens were found; alkylphenols, phthalates, some pcb congeners and hydroxylated pcbs, and the insecticides dieldrin, endosulfan, and toxaphene were estrogenic by the e-screen assay. in addition, these compounds competed with estradiol for binding to the estrogen receptor and increased the levels of progesterone receptor and ps2 in mcf-7 cells, as expected from estrogen mimics. recombinant human growth factors (bfgf, egf, igf-1) and insulin did not increase in cell yields. the aims of the work summarized in this paper were a) to validate the e-screen assay; b) to screen a variety of chemicals present in the environment to identify those that may be causing reproductive effects in wildlife and humans; c) to assess whether environmental estrogens may act cumulatively; and finally d) to discuss the reliability of this and other assays to screen chemicals for their estrogenicity before they are released into the environment.",0
"the usage of psychological networks that conceptualize behavior as a complex interplay of psychological and other components has gained increasing popularity in various research fields. while prior publications have tackled the topics of estimating and interpreting such networks, little work has been conducted to check how accurate (i.e., prone to sampling variation) networks are estimated, and how stable (i.e., interpretation remains similar with less observations) inferences from the network structure (such as centrality indices) are. in this tutorial paper, we aim to introduce the reader to this field and tackle the problem of accuracy under sampling variation. we first introduce the current state-of-the-art of network estimation. second, we provide a rationale why researchers should investigate the accuracy of psychological networks. third, we describe how bootstrap routines can be used to (a) assess the accuracy of estimated network connections, (b) investigate the stability of centrality indices, and (c) test whether network connections and centrality estimates for different variables differ from each other. we introduce two novel statistical methods: for (b) the correlation stability coefficient, and for (c) the bootstrapped difference test for edge-weights and centrality indices. we conducted and present simulation studies to assess the performance of both methods. finally, we developed the free r-package bootnet that allows for estimating psychological networks in a generalized framework in addition to the proposed bootstrap methods. we showcase bootnet in a tutorial, accompanied by r syntax, in which we analyze a dataset of 359 women with posttraumatic stress disorder available online.",0
"systematic reviews that collate data about the relative effects of multiple interventions via network meta-analysis are highly informative for decision-making purposes. a network meta-analysis provides two types of findings for a specific outcome: the relative treatment effect for all pairwise comparisons, and a ranking of the treatments. it is important to consider the confidence with which these two types of results can enable clinicians, policy makers and patients to make informed decisions. we propose an approach to determining confidence in the output of a network meta-analysis. our proposed approach is based on methodology developed by the grading of recommendations assessment, development and evaluation (grade) working group for pairwise meta-analyses. the suggested framework for evaluating a network meta-analysis acknowledges (i) the key role of indirect comparisons (ii) the contributions of each piece of direct evidence to the network meta-analysis estimates of effect size; (iii) the importance of the transitivity assumption to the validity of network meta-analysis; and (iv) the possibility of disagreement between direct evidence and indirect evidence. we apply our proposed strategy to a systematic review comparing topical antibiotics without steroids for chronically discharging ears with underlying eardrum perforations. the proposed framework can be used to determine confidence in the results from a network meta-analysis. judgements about evidence from a network meta-analysis can be different from those made about evidence from pairwise meta-analyses.",0
"since its first release over a decade ago, the metaboanalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. here we introduce metaboanalyst version 5.0, aiming to narrow the gap from raw data to functional insights for global metabolomics based on high-resolution mass spectrometry (hrms). three modules have been developed to help achieve this goal, including: (i) a lc-ms spectra processing module which offers an easy-to-use pipeline that can perform automated parameter optimization and resumable analysis to significantly lower the barriers to lc-ms1 spectra processing; (ii) a functional analysis module which expands the previous ms peaks to pathways module to allow users to intuitively select any peak groups of interest and evaluate their enrichment of potential functions as defined by metabolic pathways and metabolite sets; (iii) a functional meta-analysis module to combine multiple global metabolomics datasets obtained under complementary conditions or from similar studies to arrive at comprehensive functional insights. there are many other new functions including weighted joint-pathway analysis, data-driven network analysis, batch effect correction, merging technical replicates, improved compound name matching, etc. the web interface, graphics and underlying codebase have also been refactored to improve performance and user experience. at the end of an analysis session, users can now easily switch to other compatible modules for a more streamlined data analysis. metaboanalyst 5.0 is freely available at",0
"the roots and rhizomes of licorice (glycyrrhiza) species have long been used worldwide as a herbal medicine and natural sweetener. licorice root is a traditional medicine used mainly for the treatment of peptic ulcer, hepatitis c, and pulmonary and skin diseases, although clinical and experimental studies suggest that it has several other useful pharmacological properties such as antiinflammatory, antiviral, antimicrobial, antioxidative, anticancer activities, immunomodulatory, hepatoprotective and cardioprotective effects. a large number of components have been isolated from licorice, including triterpene saponins, flavonoids, isoflavonoids and chalcones, with glycyrrhizic acid normally being considered to be the main biologically active component. this review summarizes the phytochemical, pharmacological and pharmacokinetics data, together with the clinical and adverse effects of licorice and its bioactive components.",0
"predictive modeling with electronic health record (ehr) data is anticipated to drive personalized medicine and improve healthcare quality. constructing predictive statistical models typically requires extraction of curated predictor variables from normalized ehr data, a labor-intensive process that discards the vast majority of information in each patient's record. we propose a representation of patients' entire raw ehr records based on the fast healthcare interoperability resources (fhir) format. we demonstrate that deep learning methods using this representation are capable of accurately predicting multiple medical events from multiple centers without site-specific data harmonization. we validated our approach using de-identified ehr data from two us academic medical centers with 216,221 adult patients hospitalized for at least 24 h. in the sequential format we propose, this volume of ehr data unrolled into a total of 46,864,534,945 data points, including clinical notes. deep learning models achieved high accuracy for tasks such as predicting: in-hospital mortality (area under the receiver operator curve across sites 0.93-0.94), 30-day unplanned readmission (auroc 0.75-0.76), prolonged length of stay (auroc 0.85-0.86), and all of a patient's final discharge diagnoses (frequency-weighted auroc 0.90). these models outperformed traditional, clinically-used predictive models in all cases. we believe that this approach can be used to create accurate and scalable predictions for a variety of clinical scenarios. in a case study of a particular prediction, we demonstrate that neural networks can be used to identify relevant information from the patient's chart.",0
"background the last decade has evidenced a dramatic increase in the development and utilization of pediatric health-related quality of life (hrqol) measures in an effort to improve pediatric patient health and well-being and determine the value of healthcare services. the emerging paradigm shift toward patient-reported outcomes (pros) in clinical trials has provided the opportunity to further emphasize the value and essential need for pediatric patient self-reported outcomes measurement. data from the pedsql databasesm were utilized to test the hypothesis that children as young as 5 years of age can reliably and validly report their hrqol. methods the sample analyzed represented child self-report age data on 8,591 children ages 5 to 16 years from the pedsql 4.0 generic core scales databasesm. participants were recruited from general pediatric clinics, subspecialty clinics, and hospitals in which children were being seen for well-child checks, mild acute illness, or chronic illness care (n = 2,603, 30.3%), and from a state children's health insurance program (schip) in california (n = 5,988, 69.7%). results items on the pedsql 4.0 generic core scales had minimal missing responses for children as young as 5 years old, supporting feasibility. the majority of the child self-report scales across the age subgroups, including for children as young as 5 years, exceeded the minimum internal consistency reliability standard of 0.70 required for group comparisons, while the total scale scores across the age subgroups approached or exceeded the reliability criterion of 0.90 recommended for analyzing individual patient scale scores. construct validity was demonstrated utilizing the known groups approach. for each pedsql scale and summary score, across age subgroups, including children as young as 5 years, healthy children demonstrated a statistically significant difference in hrqol (better hrqol) than children with a known chronic health condition, with most effect sizes in the medium to large effect size range. conclusion the results demonstrate that children as young as the 5 year old age subgroup can reliably and validly self-report their hrqol when given the opportunity to do so with an age-appropriate instrument. these analyses are consistent with recent fda guidelines which require instrument development and validation testing for children and adolescents within fairly narrow age groupings and which determine the lower age limit at which children can provide reliable and valid responses across age categories.",0
"summary the illumina infinium humanmethylationepic beadchip is the new platform for high-throughput dna methylation analysis, effectively doubling the coverage compared to the older 450 k array. here we present a significantly updated and improved version of the bioconductor package champ, which can be used to analyze epic and 450k data. many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. availability and implementation champ is a bioc package available from contact a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. supplementary information supplementary data are available at bioinformatics online.",0
"background one of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age-standardised adult prevalence of diabetes at its 2010 levels. we aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are affecting the number of adults with diabetes. methods we pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. we used a bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/l or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. we also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue. findings we used data from 751 studies including 4,372,000 adults from 146 of the 200 countries we make estimates for. global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-7.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. the number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). age-standardised adult diabetes prevalence in 2014 was lowest in northwestern europe, and highest in polynesia and micronesia, at nearly 25%, followed by melanesia and the middle east and north africa. between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western europe, although crude prevalence rose because of ageing of the population. by contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in polynesia and micronesia. in 2014, american samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in polynesia and micronesia. if post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. only nine countries for men and 29 countries for women, mostly in western europe, have a 50% or higher probability of meeting the global target. interpretation since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. the burden of diabetes, both in terms of prevalence and number of adults affected, has increased faster in low-income and middle-income countries than in high-income countries. funding wellcome trust.",0
"objective to examine the dose-response associations between accelerometer assessed total physical activity, different intensities of physical activity, and sedentary time and all cause mortality. design systematic review and harmonised meta-analysis. data sources pubmed, psycinfo, embase, web of science, sport discus from inception to 31 july 2018. eligibility criteria prospective cohort studies assessing physical activity and sedentary time by accelerometry and associations with all cause mortality and reported effect estimates as hazard ratios, odds ratios, or relative risks with 95% confidence intervals. data extraction and analysis guidelines for meta-analyses and systematic reviews for observational studies and prisma guidelines were followed. two authors independently screened the titles and abstracts. one author performed a full text review and another extracted the data. two authors independently assessed the risk of bias. individual level participant data were harmonised and analysed at study level. data on physical activity were categorised by quarters at study level, and study specific associations with all cause mortality were analysed using cox proportional hazards regression analyses. study specific results were summarised using random effects meta-analysis. main outcome measure all cause mortality. results 39 studies were retrieved for full text review; 10 were eligible for inclusion, three were excluded owing to harmonisation challenges (eg, wrist placement of the accelerometer), and one study did not participate. two additional studies with unpublished mortality data were also included. thus, individual level data from eight studies (n=36 383; mean age 62.6 years; 72.8% women), with median follow-up of 5.8 years (range 3.0-14.5 years) and 2149 (5.9%) deaths were analysed. any physical activity, regardless of intensity, was associated with lower risk of mortality, with a non-linear dose-response. hazards ratios for mortality were 1.00 (referent) in the first quarter (least active), 0.48 (95% confidence interval 0.43 to 0.54) in the second quarter, 0.34 (0.26 to 0.45) in the third quarter, and 0.27 (0.23 to 0.32) in the fourth quarter (most active). corresponding hazards ratios for light physical activity were 1.00, 0.60 (0.54 to 0.68), 0.44 (0.38 to 0.51), and 0.38 (0.28 to 0.51), and for moderate-to-vigorous physical activity were 1.00, 0.64 (0.55 to 0.74), 0.55 (0.40 to 0.74), and 0.52 (0.43 to 0.61). for sedentary time, hazards ratios were 1.00 (referent; least sedentary), 1.28 (1.09 to 1.51), 1.71 (1.36 to 2.15), and 2.63 (1.94 to 3.56). conclusion higher levels of total physical activity, at any intensity, and less time spent sedentary, are associated with substantially reduced risk for premature mortality, with evidence of a non-linear dose-response pattern in middle aged and older adults. systematic review registration prospero crd42018091808.",0
"denmark has a large network of population-based medical databases, which routinely collect high-quality data as a by-product of health care provision. the danish medical databases include administrative, health, and clinical quality databases. understanding the full research potential of these data sources requires insight into the underlying health care system. this review describes key elements of the danish health care system from planning and delivery to record generation. first, it presents the history of the health care system, its overall organization and financing. second, it details delivery of primary, hospital, psychiatric, and elderly care. third, the path from a health care contact to a database record is followed. finally, an overview of the available data sources is presented. this review discusses the data quality of each type of medical database and describes the relative technical ease and cost-effectiveness of exact individual-level linkage among them. it is shown, from an epidemiological point of view, how denmark's population represents an open dynamic cohort with complete long-term follow-up, censored only at emigration or death. it is concluded that denmark's constellation of universal health care, long-standing routine registration of most health and life events, and the possibility of exact individual-level data linkage provides unlimited possibilities for epidemiological research.",0
"motivation many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. however, some sequencing platforms already produce longer reads and others are expected to become available soon. for longer reads, hashing-based software such as blat and ssaha2 remain the only choices. nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. results we designed and implemented a new algorithm, burrows-wheeler aligner's smith-waterman alignment (bwa-sw), to align long sequences up to 1 mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. the algorithm is as accurate as ssaha2, more accurate than blat, and is several to tens of times faster than both. availability",0
"recently, a requirement for beta-arrestin-mediated endocytosis in the activation of extracellular signal-regulated kinases 1 and 2 (erk1/2) by several g protein-coupled receptors (gpcrs) has been proposed. however, the importance of this requirement for function of erk1/2 is unknown. we report that agonists of galphaq-coupled proteinase-activated receptor 2 (par2) stimulate formation of a multiprotein signaling complex, as detected by gel filtration, immunoprecipitation and immunofluorescence. the complex, which contains internalized receptor, beta-arrestin, raf-1, and activated erk, is required for erk1/2 activation. however, erk1/2 activity is retained in the cytosol and neither translocates to the nucleus nor causes proliferation. in contrast, a mutant par2 (par2deltast363/6a), which is unable to interact with beta-arrestin and, thus, does not desensitize or internalize, activates erk1/2 by a distinct pathway, and fails to promote both complex formation and cytosolic retention of the activated erk1/2. whereas wild-type par2 activates erk1/2 by a pkc-dependent and probably a ras-independent pathway, par2(deltast363/6a) appears to activate erk1/2 by a ras-dependent pathway, resulting in increased cell proliferation. thus, formation of a signaling complex comprising par2, beta-arrestin, raf-1, and activated erk1/2 might ensure appropriate subcellular localization of par2-mediated erk activity, and thereby determine the mitogenic potential of receptor agonists.",0
"electronic health tools provide little value if the intended users lack the skills to effectively engage them. with nearly half the adult population in the united states and canada having literacy levels below what is needed to fully engage in an information-rich society, the implications for using information technology to promote health and aid in health care, or for ehealth, are considerable. engaging with ehealth requires a skill set, or literacy, of its own. the concept of ehealth literacy is introduced and defined as the ability to seek, find, understand, and appraise health information from electronic sources and apply the knowledge gained to addressing or solving a health problem. in this paper, a model of ehealth literacy is introduced, comprised of multiple literacy types, including an outline of a set of fundamental skills consumers require to derive direct benefits from ehealth. a profile of each literacy type with examples of the problems patient-clients might present is provided along with a resource list to aid health practitioners in supporting literacy improvement with their patient-clients across each domain. facets of the model are illustrated through a set of clinical cases to demonstrate how health practitioners can address ehealth literacy issues in clinical or public health practice. potential future applications of the model are discussed.",0
"the genomic landscape of breast cancer is complex, and inter- and intra-tumour heterogeneity are important challenges in treating the disease. in this study, we sequence 173 genes in 2,433 primary breast tumours that have copy number aberration (cna), gene expression and long-term clinical follow-up data. we identify 40 mutation-driver (mut-driver) genes, and determine associations between mutations, driver cna profiles, clinical-pathological parameters and survival. we assess the clonal states of mut-driver mutations, and estimate levels of intra-tumour heterogeneity using mutant-allele fractions. associations between pik3ca mutations and reduced survival are identified in three subgroups of er-positive cancer (defined by amplification of 17q23, 11q13-14 or 8q24). high levels of intra-tumour heterogeneity are in general associated with a worse outcome, but highly aggressive tumours with 11q13-14 amplification have low levels of intra-tumour heterogeneity. these results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies.",0
"the ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. the gene archaerhodopsin-3 (arch) from halorubrum sodomense enables near-100% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light. arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 pa at light powers easily achievable in vivo. furthermore, arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. these properties of arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally relevant timescales. arch function in neurons is well tolerated because ph excursions created by arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins or natural spike firing. to highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue-green light-drivable proton pump from the fungus leptosphaeria maculans (mac) can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue versus red light. light-driven proton pumps thus represent a high-performance and extremely versatile class of 'optogenetic' voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.",0
"advances in understanding the role of vascular endothelial growth factor (vegf) in normal physiology are giving insight into the basis of adverse effects attributed to the use of vegf inhibitors in clinical oncology. these effects are typically downstream consequences of suppression of cellular signalling pathways important in the regulation and maintenance of the microvasculature. downregulation of these pathways in normal organs can lead to vascular disturbances and even regression of blood vessels, which could be intensified by concurrent pathological conditions. these changes are generally manageable and pose less risk than the tumours being treated, but they highlight the properties shared by tumour vessels and the vasculature of normal organs.",0
"the sorting intolerant from tolerant (sift) algorithm predicts the effect of coding variants on protein function. it was first introduced in 2001, with a corresponding website that provides users with predictions on their variants. since its release, sift has become one of the standard tools for characterizing missense variation. we have updated sift's genome-wide prediction tool since our last publication in 2009, and added new features to the insertion/deletion (indel) tool. we also show accuracy metrics on independent data sets. the original developers have hosted the sift web server at fhcrc, jcvi and the web server is currently located at bii. the url is (24 may 2012, date last accessed).",0
"the gene expression omnibus (geo) repository at the national center for biotechnology information (ncbi) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. the database has a minimum information about a microarray experiment (miame)-compliant infrastructure that captures fully annotated raw and processed data. several data deposit options and formats are supported, including web forms, spreadsheets, xml and simple omnibus format in text (soft). in addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in geo. this paper provides a summary of the geo database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. geo is accessible at",0
"it has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. in addition to the measured variable(s) of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. we show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. this phenomenon is true even for well-designed, randomized studies. we introduce ""surrogate variable analysis"" (sva) to overcome the problems caused by heterogeneity in expression studies. sva can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. we apply sva to disease class, time course, and genetics of gene expression studies. we show that sva increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.",0
"background scoping reviews are used to identify knowledge gaps, set research agendas, and identify implications for decision-making. the conduct and reporting of scoping reviews is inconsistent in the literature. we conducted a scoping review to identify: papers that utilized and/or described scoping review methods; guidelines for reporting scoping reviews; and studies that assessed the quality of reporting of scoping reviews. methods we searched nine electronic databases for published and unpublished literature scoping review papers, scoping review methodology, and reporting guidance for scoping reviews. two independent reviewers screened citations for inclusion. data abstraction was performed by one reviewer and verified by a second reviewer. quantitative (e.g. frequencies of methods) and qualitative (i.e. content analysis of the methods) syntheses were conducted. results after searching 1525 citations and 874 full-text papers, 516 articles were included, of which 494 were scoping reviews. the 494 scoping reviews were disseminated between 1999 and 2014, with 45% published after 2012. most of the scoping reviews were conducted in north america (53%) or europe (38%), and reported a public source of funding (64%). the number of studies included in the scoping reviews ranged from 1 to 2600 (mean of 118). using the joanna briggs institute methodology guidance for scoping reviews, only 13% of the scoping reviews reported the use of a protocol, 36% used two reviewers for selecting citations for inclusion, 29% used two reviewers for full-text screening, 30% used two reviewers for data charting, and 43% used a pre-defined charting form. in most cases, the results of the scoping review were used to identify evidence gaps (85%), provide recommendations for future research (84%), or identify strengths and limitations (69%). we did not identify any guidelines for reporting scoping reviews or studies that assessed the quality of scoping review reporting. conclusion the number of scoping reviews conducted per year has steadily increased since 2012. scoping reviews are used to inform research agendas and identify implications for policy or practice. as such, improvements in reporting and conduct are imperative. further research on scoping review methodology is warranted, and in particular, there is need for a guideline to standardize reporting.",0
"objective to investigate the characteristics and prognostic factors in the elderly patients with covid-19. methods consecutive cases over 60 years old with covid-19 in renmin hospital of wuhan university from jan 1 to feb 6, 2020 were included. the primary outcomes were death and survival till march 5. data of demographics, clinical features, comorbidities, laboratory tests and complications were collected and compared for different outcomes. cox regression was performed for prognostic factors. results 339 patients with covid-19 (aged 71±8 years,173 females (51%)) were enrolled, including 80 (23.6%) critical, 159 severe (46.9%) and 100 moderate (29.5%) cases. common comorbidities were hypertension (40.8%), diabetes (16.0%) and cardiovascular disease (15.7%). common symptoms included fever (92.0%), cough (53.0%), dyspnea (40.8%) and fatigue (39.9%). lymphocytopenia was a common laboratory finding (63.2%). common complications included bacterial infection (42.8%), liver enzyme abnormalities (28.7%) and acute respiratory distress syndrome (21.0%). till mar 5, 2020, 91 cases were discharged (26.8%), 183 cases stayed in hospital (54.0%) and 65 cases (19.2%) were dead. shorter length of stay was found for the dead compared with the survivors (5 (3-8) vs. 28 (26-29), p conclusions high proportion of severe to critical cases and high fatality rate were observed in the elderly covid-19 patients. rapid disease progress was noted in the dead with a median survival time of 5 days after admission. dyspnea, lymphocytopenia, comorbidities including cardiovascular disease and chronic obstructive pulmonary disease, and acute respiratory distress syndrome were predictive of poor outcome. close monitoring and timely treatment should be performed for the elderly patients at high risk.",0
"interactive tree of life ( is a web-based tool for the display, manipulation and annotation of phylogenetic trees. it is freely available and open to everyone. in addition to classical tree viewer functions, itol offers many novel ways of annotating trees with various additional data. current version introduces numerous new features and greatly expands the number of supported data set types. trees can be interactively manipulated and edited. a free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. export to various bitmap and vector graphics formats is supported. batch access interface is available for programmatic access or inclusion of interactive trees into other web services.",0
"detection of somatic point substitutions is a key step in characterizing the cancer genome. however, existing methods typically miss low-allelic-fraction mutations that occur in only a subset of the sequenced cells owing to either tumor heterogeneity or contamination by normal cells. here we present mutect, a method that applies a bayesian classifier to detect somatic mutations with very low allele fractions, requiring only a few supporting reads, followed by carefully tuned filters that ensure high specificity. we also describe benchmarking approaches that use real, rather than simulated, sequencing data to evaluate the sensitivity and specificity as a function of sequencing depth, base quality and allelic fraction. compared with other methods, mutect has higher sensitivity with similar specificity, especially for mutations with allelic fractions as low as 0.1 and below, making mutect particularly useful for studying cancer subclones and their evolution in standard exome and genome sequencing data.",0
"background despite growth in implementation research, limited scientific attention has focused on understanding and improving sustainability of health interventions. models of sustainability have been evolving to reflect challenges in the fit between intervention and context. discussion we examine the development of concepts of sustainability, and respond to two frequent assumptions -'voltage drop,' whereby interventions are expected to yield lower benefits as they move from efficacy to effectiveness to implementation and sustainability, and 'program drift,' whereby deviation from manualized protocols is assumed to decrease benefit. we posit that these assumptions limit opportunities to improve care, and instead argue for understanding the changing context of healthcare to continuously refine and improve interventions as they are sustained. sustainability has evolved from being considered as the endgame of a translational research process to a suggested 'adaptation phase' that integrates and institutionalizes interventions within local organizational and cultural contexts. these recent approaches locate sustainability in the implementation phase of knowledge transfer, but still do not address intervention improvement as a central theme. we propose a dynamic sustainability framework that involves: continued learning and problem solving, ongoing adaptation of interventions with a primary focus on fit between interventions and multi-level contexts, and expectations for ongoing improvement as opposed to diminishing outcomes over time. summary a dynamic sustainability framework provides a foundation for research, policy and practice that supports development and testing of falsifiable hypotheses and continued learning to advance the implementation, transportability and impact of health services research.",0
"imosflm is a graphical user interface to the diffraction data-integration program mosflm. it is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user. suitable values for integration parameters are set automatically, but additional menus provide a detailed level of control for experienced users. the image display and the interfaces to the different tasks (indexing, strategy calculation, cell refinement, integration and history) are described. the most important parameters for each step and the best way of assessing success or failure are discussed.",0
"defensins, antimicrobial peptides of the innate immune system, protect human mucosal epithelia and skin against microbial infections and are produced in large amounts by neutrophils. the bacterial pathogen staphylococcus aureus is insensitive to defensins by virtue of an unknown resistance mechanism. we describe a novel staphylococcal gene, mprf, which determines resistance to several host defense peptides such as defensins and protegrins. an mprf mutant strain was killed considerably faster by human neutrophils and exhibited attenuated virulence in mice, indicating a key role for defensin resistance in the pathogenicity of s. aureus. analysis of membrane lipids demonstrated that the mprf mutant no longer modifies phosphatidylglycerol with l-lysine. as this unusual modification leads to a reduced negative charge of the membrane surface, mprf-mediated peptide resistance is most likely based on repulsion of the cationic peptides. accordingly, inactivation of mprf led to increased binding of antimicrobial peptides by the bacteria. mprf has no similarity with genes of known function, but related genes were identified in the genomes of several pathogens including mycobacterium tuberculosis, pseudomonas aeruginosa, and enterococcus faecalis. mprf thus constitutes a novel virulence factor, which may be of general relevance for bacterial pathogens and represents a new target for attacking multidrug resistant bacteria.",0
"haematopoietic stem cells (hscs) are the founder cells of the adult haematopoietic system, and thus knowledge of the molecular program directing their generation during development is important for regenerative haematopoietic strategies. runx1 is a pivotal transcription factor required for hsc generation in the vascular regions of the mouse conceptus-the aorta, vitelline and umbilical arteries, yolk sac and placenta. it is thought that hscs emerge from vascular endothelial cells through the formation of intra-arterial clusters and that runx1 functions during the transition from 'haemogenic endothelium' to hscs. here we show by conditional deletion that runx1 activity in vascular-endothelial-cadherin-positive endothelial cells is indeed essential for intra-arterial cluster, haematopoietic progenitor and hsc formation in mice. in contrast, runx1 is not required in cells expressing vav1, one of the first pan-haematopoietic genes expressed in hscs. collectively these data show that runx1 function is essential in endothelial cells for haematopoietic progenitor and hsc formation from the vasculature, but its requirement ends once or before vav is expressed.",0
"vitamin d testing and the use of vitamin d supplements have increased substantially in recent years. currently, the role of vitamin d supplementation, and the optimal vitamin d dose and status, is a subject of debate, because large interventional studies have been unable to show a clear benefit (in mostly vitamin d replete populations). this may be attributed to limitations in trial design, as most studies did not meet the basic requirements of a nutrient intervention study, including vitamin d-replete populations, too small sample sizes, and inconsistent intervention methods regarding dose and metabolites. vitamin d deficiency (serum 25-hydroxyvitamin d 50 nmol/l or 20 ng/ml is, therefore, the primary treatment goal, although some data suggest a benefit for a higher threshold. severe vitamin d deficiency with a 25(oh)d concentration below <30 nmol/l (or 12 ng/ml) dramatically increases the risk of excess mortality, infections, and many other diseases, and should be avoided whenever possible. the data on a benefit for mortality and prevention of infections, at least in severely deficient individuals, appear convincing. vitamin d is clearly not a panacea, and is most likely efficient only in deficiency. given its rare side effects and its relatively wide safety margin, it may be an important, inexpensive, and safe adjuvant therapy for many diseases, but future large and well-designed studies should evaluate this further. a worldwide public health intervention that includes vitamin d supplementation in certain risk groups, and systematic vitamin d food fortification to avoid severe vitamin d deficiency, would appear to be important. in this narrative review, the current international literature on vitamin d deficiency, its relevance, and therapeutic options is discussed.",0
"asthma is a common disease with a complex risk architecture including both genetic and environmental factors. we performed a meta-analysis of north american genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of european american, african american or african caribbean, and latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. we identified five susceptibility loci. four were at previously reported loci on 17q21, near il1rl1, tslp and il33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. in addition, we identified a new asthma susceptibility locus at pyhin1, with the association being specific to individuals of african descent (p = 3.9 × 10(-9)). these results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma.",0
"background global and regional projections of mortality and burden of disease by cause for the years 2000, 2010, and 2030 were published by murray and lopez in 1996 as part of the global burden of disease project. these projections, which are based on 1990 data, continue to be widely quoted, although they are substantially outdated; in particular, they substantially underestimated the spread of hiv/aids. to address the widespread demand for information on likely future trends in global health, and thereby to support international health policy and priority setting, we have prepared new projections of mortality and burden of disease to 2030 starting from world health organization estimates of mortality and burden of disease for 2002. this paper describes the methods, assumptions, input data, and results. methods and findings relatively simple models were used to project future health trends under three scenarios-baseline, optimistic, and pessimistic-based largely on projections of economic and social development, and using the historically observed relationships of these with cause-specific mortality rates. data inputs have been updated to take account of the greater availability of death registration data and the latest available projections for hiv/aids, income, human capital, tobacco smoking, body mass index, and other inputs. in all three scenarios there is a dramatic shift in the distribution of deaths from younger to older ages and from communicable, maternal, perinatal, and nutritional causes to noncommunicable disease causes. the risk of death for children younger than 5 y is projected to fall by nearly 50% in the baseline scenario between 2002 and 2030. the proportion of deaths due to noncommunicable disease is projected to rise from 59% in 2002 to 69% in 2030. global hiv/aids deaths are projected to rise from 2.8 million in 2002 to 6.5 million in 2030 under the baseline scenario, which assumes coverage with antiretroviral drugs reaches 80% by 2012. under the optimistic scenario, which also assumes increased prevention activity, hiv/aids deaths are projected to drop to 3.7 million in 2030. total tobacco-attributable deaths are projected to rise from 5.4 million in 2005 to 6.4 million in 2015 and 8.3 million in 2030 under our baseline scenario. tobacco is projected to kill 50% more people in 2015 than hiv/aids, and to be responsible for 10% of all deaths globally. the three leading causes of burden of disease in 2030 are projected to include hiv/aids, unipolar depressive disorders, and ischaemic heart disease in the baseline and pessimistic scenarios. road traffic accidents are the fourth leading cause in the baseline scenario, and the third leading cause ahead of ischaemic heart disease in the optimistic scenario. under the baseline scenario, hiv/aids becomes the leading cause of burden of disease in middle- and low-income countries by 2015. conclusions these projections represent a set of three visions of the future for population health, based on certain explicit assumptions. despite the wide uncertainty ranges around future projections, they enable us to appreciate better the implications for health and health policy of currently observed trends, and the likely impact of fairly certain future trends, such as the ageing of the population, the continued spread of hiv/aids in many regions, and the continuation of the epidemiological transition in developing countries. the results depend strongly on the assumption that future mortality trends in poor countries will have a relationship to economic and social development similar to those that have occurred in the higher-income countries.",0
"summary we developed a python package, prody, for structure-based analysis of protein dynamics. prody allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. prody application programming interface (api) has been designed so that users can easily extend the software and implement new methods. availability prody is open source and freely available under gnu general public license from",0
"importance coping with the current and future burden of cancer requires an in-depth understanding of trends in cancer incidences and deaths. estimated projections of cancer incidences and deaths will be important to guide future research funding allocations, health care planning, and health policy efforts. objective to estimate cancer incidences and deaths in the united states to the year 2040. design and setting this cross-sectional study's estimated projection analysis used population growth projections and current population-based cancer incidence and death rates to calculate the changes in incidences and deaths to the year 2040. cancer-specific incidences and deaths in the us were estimated for the most common cancer types. demographic cancer-specific delay-adjusted incidence rates from the surveillance, epidemiology, and end results program were combined with us census bureau population growth projections (2016) and average annual percentage changes in incidence and death rates. statistical analyses were performed from july 2020 to february 2021. main outcomes and measures total cancer incidences and deaths to the year 2040. results this study estimated that the most common cancers in 2040 will be breast (364 000 cases) with melanoma (219 000 cases) becoming the second most common cancer; lung, third (208 000 cases); colorectal remaining fourth (147 000 cases); and prostate cancer dropping to the fourteenth most common cancer (66 000 cases). lung cancer (63 000 deaths) was estimated to continue as the leading cause of cancer-related death in 2040, with pancreatic cancer (46 000 deaths) and liver and intrahepatic bile duct cancer (41 000 deaths) surpassing colorectal cancer (34 000 deaths) to become the second and third most common causes of cancer-related death, respectively. breast cancer (30 000 deaths) was estimated to decrease to the fifth most common cause of cancer death. conclusions and relevance these findings suggest that there will be marked changes in the landscape of cancer incidence and deaths by 2040.",0
"the agr quorum-sensing system of staphylococcus aureus modulates the expression of virulence factors in response to autoinducing peptides (aips). recent studies have suggested a role for the agr system in s. aureus biofilm development, as agr mutants exhibit a high propensity to form biofilms, and cells dispersing from a biofilm have been observed displaying an active agr system. here, we report that repression of agr is necessary to form a biofilm and that reactivation of agr in established biofilms through aip addition or glucose depletion triggers detachment. inhibitory aip molecules did not induce detachment and an agr mutant was non-responsive, indicating a dependence on a functional, active agr system for dispersal. biofilm detachment occurred in multiple s. aureus strains possessing divergent agr systems, suggesting it is a general s. aureus phenomenon. importantly, detachment also restored sensitivity of the dispersed cells to the antibiotic rifampicin. proteinase k inhibited biofilm formation and dispersed established biofilms, suggesting agr-mediated detachment occurred in an ica-independent manner. consistent with a protease-mediated mechanism, increased levels of serine proteases were detected in detaching biofilm effluents, and the serine protease inhibitor pmsf reduced the degree of agr-mediated detachment. through genetic analysis, a double mutant in the agr-regulated aur metalloprotease and the splabcdef serine proteases displayed minimal extracellular protease activity, improved biofilm formation, and a strongly attenuated detachment phenotype. these findings indicate that induction of the agr system in established s. aureus biofilms detaches cells and demonstrate that the dispersal mechanism requires extracellular protease activity.",0
"objective to describe outcomes of people admitted to hospital with coronavirus disease 2019 (covid-19) in the united states, and the clinical and laboratory characteristics associated with severity of illness. design prospective cohort study. setting single academic medical center in new york city and long island. participants 5279 patients with laboratory confirmed severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection between 1 march 2020 and 8 april 2020. the final date of follow up was 5 may 2020. main outcome measures outcomes were admission to hospital, critical illness (intensive care, mechanical ventilation, discharge to hospice care, or death), and discharge to hospice care or death. predictors included patient characteristics, medical history, vital signs, and laboratory results. multivariable logistic regression was conducted to identify risk factors for adverse outcomes, and competing risk survival analysis for mortality. results of 11 544 people tested for sars-cov-2, 5566 (48.2%) were positive. after exclusions, 5279 were included. 2741 of these 5279 (51.9%) were admitted to hospital, of whom 1904 (69.5%) were discharged alive without hospice care and 665 (24.3%) were discharged to hospice care or died. of 647 (23.6%) patients requiring mechanical ventilation, 391 (60.4%) died and 170 (26.2%) were extubated or discharged. the strongest risk for hospital admission was associated with age, with an odds ratio of >2 for all age groups older than 44 years and 37.9 (95% confidence interval 26.1 to 56.0) for ages 75 years and older. other risks were heart failure (4.4, 2.6 to 8.0), male sex (2.8, 2.4 to 3.2), chronic kidney disease (2.6, 1.9 to 3.6), and any increase in body mass index (bmi) (eg, for bmi >40: 2.5, 1.8 to 3.4). the strongest risks for critical illness besides age were associated with heart failure (1.9, 1.4 to 2.5), bmi >40 (1.5, 1.0 to 2.2), and male sex (1.5, 1.3 to 1.8). admission oxygen saturation of 1 (4.8, 2.1 to 10.9), c reactive protein level >200 (5.1, 2.8 to 9.2), and d-dimer level >2500 (3.9, 2.6 to 6.0) were, however, more strongly associated with critical illness than age or comorbidities. risk of critical illness decreased significantly over the study period. similar associations were found for mortality alone. conclusions age and comorbidities were found to be strong predictors of hospital admission and to a lesser extent of critical illness and mortality in people with covid-19; however, impairment of oxygen on admission and markers of inflammation were most strongly associated with critical illness and mortality. outcomes seem to be improving over time, potentially suggesting improvements in care.",0
"the medical research council has for some years encouraged collaborative clinical trials in leukaemia and other cancers, reporting the results in the medical literature. one unreported result which deserves such publication is the development of the expertise to design and analyse such trials. this report was prepared by a group of british and american statisticians, but it is intended for people without any statistical expertise. part i, which appears in this issue, discusses the design of such trials; part ii, which will appear separately in the january 1977 issue of the journal, gives full instructions for the statistical analysis of such trials by means of life tables and the logrank test, including a worked example, and discusses the interpretation of trial results, including brief reports of 2 particular trials. both parts of this report are relevant to all clinical trials which study time to death, and wound be equally relevant to clinical trials which study time to other particular classes of untoward event: first stroke, perhaps, or first relapse, metastasis, disease recurrence, thrombosis, transplant rejection, or death from a particular cause. part i, in this issue, collects together ideas that have mostly already appeared in the medical literature, but part ii, next month, is the first simple account yet published for non-statistical physicians of how to analyse efficiently data from clinical trials of survival duration. such trials include the majority of all clinical trials of cancer therapy; in cancer trials,however, it may be preferable to use these statistical methods to study time to local recurrence of tumour, or to study time to detectable metastatic spread, in addition to studying total survival. solid tumours can be staged at diagnosis; if this, or any other available information in some other disease is an important determinant of outcome, it can be used to make the overall logrank test for the whole heterogeneous trial population more sensitive, and more intuitively satisfactory, for it will then only be necessary to compare like with like, and not, by chance, stage i with stage iii.",0
"more than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. this has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. to address this challenge, we developed haploreg ( to aid the functional dissection of genome-wide association study (gwas) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. since first launching the website in 2011, we have greatly expanded haploreg, increasing the number of chromatin state maps to 127 reference epigenomes from encode 2012 and roadmap epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eqtl) variants and their tissue-specific target genes from gtex, geuvadis, and other recent studies. we present these updates as haploreg v4, and illustrate a use case of haploreg for attention deficit hyperactivity disorder (adhd)-associated snps with putative brain regulatory mechanisms.",0
"ncbi's conserved domain database (cdd) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. cdd includes manually curated domain models that make use of protein 3d structure to refine domain models and provide insights into sequence/structure/function relationships. manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. as cdd also imports domain family models from a variety of external sources, it is a partially redundant collection. to simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. by default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. pre-computed domain annotation is available for proteins in the entrez/protein dataset, and a novel interface, batch cd-search, allows the computation and download of annotation for large sets of protein queries. cdd can be accessed via",0
"background stress and compromised parenting often place children at risk of abuse and neglect. child maltreatment has generally been viewed as a highly individualistic problem by focusing on stressors and parenting behaviors that impact individual families. however, because of the global coronavirus disease 2019 (covid-19), families across the world are experiencing a new range of stressors that threaten their health, safety, and economic well-being. objective this study examined the impacts of the covid-19 pandemic in relation to parental perceived stress and child abuse potential. participants and setting participants included parents (n = 183) with a child under the age of 18 years in the western united states. method tests of group differences and hierarchical multiple regression analyses were employed to assess the relationships among demographic characteristics, covid-19 risk factors, mental health risk factors, protective factors, parental perceived stress, and child abuse potential. results greater covid-19 related stressors and high anxiety and depressive symptoms are associated with higher parental perceived stress. receipt of financial assistance and high anxiety and depressive symptoms are associated with higher child abuse potential. conversely, greater parental support and perceived control during the pandemic are associated with lower perceived stress and child abuse potential. results also indicate racial and ethnic differences in covid-19 related stressors, but not in mental health risk, protective factors, perceived stress, or child abuse potential. conclusion findings suggest that although families experience elevated stressors from covid-19, providing parental support and increasing perceived control may be promising intervention targets.",0
"we have studied various factors involved in the optimal use of a tetrazolium (mtt) based colorimetric assay for cell growth and chemosensitivity. the assay is dependent on the ability of viable cells to metabolise a water-soluble tetrazolium salt into a water-insoluble formazan product. we have found that dmso is the best solvent for dissolving the formazan product, especially where a significant amount of residual medium is left in the wells of the microtitre tray used for the assay. a reaction occurs between medium and a solution of mtt formazan in dmso which changes the shape of the absorbance spectrum of the solution. the resulting optical density is not however greatly dependent upon the volume of added medium in the range 1-10 microliters. between 10 and 40 microliters of added medium results in a gradually lower optical density than that produced by the smaller volumes. above 40 microliters, the optical density increases again due to turbidity as protein precipitation occurs. when cells are incubated with mtt, the resulting optical density of the formazan product is dependent upon both the concentration of mtt and the incubation time. the optical density is stable for several hours after solution of the formazan in dmso. a linear relationship is seen between optical density and cell number for incubation times of 2, 4, 6 or 24 h with 20 microliters of mtt (5 mg ml-1) added to 200 microliters medium. we have adopted 4 h as the standard incubation time for the assay. only a small amount of mtt formazan product can be detected in the growth medium of wells in which cells have been exposed to mtt. comparative chemosensitivity data for emt6 mouse tumour cells show good agreement between results obtained using the mtt assay and results based on total cell count after a fixed period of growth.",0
"unlabelled unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. the consensus clustering (cc) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. consensusclusterplus implements the cc method in r and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. these new features provide users with detailed information that enable more specific decisions in unsupervised class discovery. availability consensusclusterplus is open source software, written in r, under gpl-2, and available through the bioconductor project ( supplementary information supplementary data are available at bioinformatics online.",0
"background stromal-epithelial interactions are of particular significance in breast tissue as misregulation of these interactions can promote tumorigenesis and invasion. moreover, collagen-dense breast tissue increases the risk of breast carcinoma, although the relationship between collagen density and tumorigenesis is not well understood. as little is known about epithelial-stromal interactions in vivo, it is necessary to visualize the stroma surrounding normal epithelium and mammary tumors in intact tissues to better understand how matrix organization, density, and composition affect tumor formation and progression. methods epithelial-stromal interactions in normal mammary glands, mammary tumors, and tumor explants in three-dimensional culture were studied with histology, electron microscopy, and nonlinear optical imaging methodologies. imaging of the tumor-stromal interface in live tumor tissue ex vivo was performed with multiphoton laser-scanning microscopy (mplsm) to generate multiphoton excitation (mpe) of endogenous fluorophores and second harmonic generation (shg) to image stromal collagen. results we used both laser-scanning multiphoton and second harmonic generation microscopy to determine the organization of specific collagen structures around ducts and tumors in intact, unfixed and unsectioned mammary glands. local alterations in collagen density were clearly seen, allowing us to obtain three-dimensional information regarding the organization of the mammary stroma, such as radiating collagen fibers that could not have been obtained using classical histological techniques. moreover, we observed and defined three tumor-associated collagen signatures (tacs) that provide novel markers to locate and characterize tumors. in particular, local cell invasion was found predominantly to be oriented along certain aligned collagen fibers, suggesting that radial alignment of collagen fibers relative to tumors facilitates invasion. consistent with this observation, primary tumor explants cultured in a randomly organized collagen matrix realigned the collagen fibers, allowing individual tumor cells to migrate out along radially aligned fibers. conclusion the presentation of these tumor-associated collagen signatures allowed us to identify pre-palpable tumors and see cells at the tumor-stromal boundary invading into the stroma along radially aligned collagen fibers. as such, tacs should provide indications that a tumor is, or could become, invasive, and may serve as part of a strategy to help identify and characterize breast tumors in animal and human tissues.",0
"linear mixed models have attracted considerable attention recently as a powerful and effective tool for accounting for population stratification and relatedness in genetic association tests. however, existing methods for exact computation of standard test statistics are computationally impractical for even moderate-sized genome-wide association studies. to address this issue, several approximate methods have been proposed. here, we present an efficient exact method, which we refer to as genome-wide efficient mixed-model association (gemma), that makes approximations unnecessary in many contexts. this method is approximately n times faster than the widely used exact method known as efficient mixed-model association (emma), where n is the sample size, making exact genome-wide association analysis computationally practical for large numbers of individuals.",0
"the many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. however, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. the string database ( aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. the new version 10.0 of string covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. for this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an api interface for the r computing environment and improved statistical analysis for enrichment tests in user-provided networks.",0
"the virulence factor database (vfdb, is dedicated to providing up-to-date knowledge of virulence factors (vfs) of various bacterial pathogens. since its inception the vfdb has served as a comprehensive repository of bacterial vfs for over a decade. the exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. we recently improved two aspects of the infrastructural dataset of vfdb: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets--one core dataset of experimentally verified vfs only and another full dataset including all known and predicted vfs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. our efforts enhanced the data quality of the vfdb and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial vfs.",0
"background as trials of 5 years of tamoxifen in early breast cancer mature, the relevance of hormone receptor measurements (and other patient characteristics) to long-term outcome can be assessed increasingly reliably. we report updated meta-analyses of the trials of 5 years of adjuvant tamoxifen. methods we undertook a collaborative meta-analysis of individual patient data from 20 trials (n=21,457) in early breast cancer of about 5 years of tamoxifen versus no adjuvant tamoxifen, with about 80% compliance. recurrence and death rate ratios (rrs) were from log-rank analyses by allocated treatment. findings in oestrogen receptor (er)-positive disease (n=10,645), allocation to about 5 years of tamoxifen substantially reduced recurrence rates throughout the first 10 years (rr 0·53 during years 0-4 and rr 0·68 during years 5-9 [both 2p interpretation 5 years of adjuvant tamoxifen safely reduces 15-year risks of breast cancer recurrence and death. er status was the only recorded factor importantly predictive of the proportional reductions. hence, the absolute risk reductions produced by tamoxifen depend on the absolute breast cancer risks (after any chemotherapy) without tamoxifen. funding cancer research uk, british heart foundation, and medical research council.",0
"background the charlson comorbidity index is often used to control for confounding in research based on medical databases. there are few studies of the accuracy of the codes obtained from these databases. we examined the positive predictive value (ppv) of the icd-10 diagnostic coding in the danish national registry of patients (nrp) for the 19 charlson conditions. methods among all hospitalizations in northern denmark between 1 january 1998 and 31 december 2007 with a first-listed diagnosis of a charlson condition in the nrp, we selected 50 hospital contacts for each condition. we reviewed discharge summaries and medical records to verify the nrp diagnoses, and computed the ppv as the proportion of confirmed diagnoses. results a total of 950 records were reviewed. the overall ppv for the 19 charlson conditions was 98.0% (95% ci; 96.9, 98.8). the ppvs ranged from 82.0% (95% ci; 68.6%, 91.4%) for diabetes with diabetic complications to 100% (one-sided 97.5% ci; 92.9%, 100%) for congestive heart failure, peripheral vascular disease, chronic pulmonary disease, mild and severe liver disease, hemiplegia, renal disease, leukaemia, lymphoma, metastatic tumour, and aids. conclusion the ppv of nrp coding of the charlson conditions was consistently high.",0
"the coronavirus disease 2019 (covid-19) pandemic has caused enormous psychological impact worldwide. we conducted a systematic review and meta-analysis on the psychological and mental impact of covid-19 among healthcare workers, the general population, and patients with higher covid-19 risk published between 1 nov 2019 to 25 may 2020. we conducted literature research using embase, pubmed, google scholar and who covid-19 databases. among the initial search of 9207 studies, 62 studies with 162,639 participants from 17 countries were included in the review. the pooled prevalence of anxiety and depression was 33% (95% confidence interval: 28%-38%) and 28% (23%-32%), respectively. the prevalence of anxiety and depression was the highest among patients with pre-existing conditions and covid-19 infection (56% and 55% ), and it was similar between healthcare workers and the general public. studies from china, italy, turkey, spain and iran reported higher-than-pooled prevalence among healthcare workers and the general public. common risk factors included being women, being nurses, having lower socioeconomic status, having high risks of contracting covid-19, and social isolation. protective factors included having sufficient medical resources, up-to-date and accurate information, and taking precautionary measures. in conclusion, psychological interventions targeting high-risk populations with heavy psychological distress are in urgent need.",0
"background nonnegative matrix factorization (nmf) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. recent applications of nmf in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. developments in nmf theory and applications have resulted in a variety of algorithms and methods. however, most nmf implementations have been on commercial platforms, while those that are freely available typically require programming skills. this limits their use by the wider research community. results our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard nmf algorithms, as well as with a simple framework to help implement and test new nmf methods. for that purpose, we have developed a package for the r/bioconductor platform. the package ports public code to r, and is structured to enable users to easily modify and/or add algorithms. it includes a number of published nmf algorithms and initialization methods and facilitates the combination of these to produce new nmf strategies. commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results. conclusions the nmf package helps realize the potential of nonnegative matrix factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications. documentation, source code and sample data are available from cran.",0
"the widespread use of antibiotics is selecting for a variety of resistance mechanisms that seriously challenge our ability to treat bacterial infections. resistant bacteria can be selected at the high concentrations of antibiotics used therapeutically, but what role the much lower antibiotic concentrations present in many environments plays in selection remains largely unclear. here we show using highly sensitive competition experiments that selection of resistant bacteria occurs at extremely low antibiotic concentrations. thus, for three clinically important antibiotics, drug concentrations up to several hundred-fold below the minimal inhibitory concentration of susceptible bacteria could enrich for resistant bacteria, even when present at a very low initial fraction. we also show that de novo mutants can be selected at sub-mic concentrations of antibiotics, and we provide a mathematical model predicting how rapidly such mutants would take over in a susceptible population. these results add another dimension to the evolution of resistance and suggest that the low antibiotic concentrations found in many natural environments are important for enrichment and maintenance of resistance in bacterial populations.",0
"the ezrin/radixin/moesin (erm) proteins are involved in actin filament/plasma membrane interaction that is regulated by rho. we examined whether erm proteins are directly phosphorylated by rho-associated kinase (rho-kinase), a direct target of rho. recombinant full-length and cooh-terminal half radixin were incubated with constitutively active catalytic domain of rho-kinase, and approximately 30 and approximately 100% of these molecules, respectively, were phosphorylated mainly at the cooh-terminal threonine (t564). next, to detect rho-kinase-dependent phosphorylation of erm proteins in vivo, we raised a mab that recognized the t564-phosphorylated radixin as well as ezrin and moesin phosphorylated at the corresponding threonine residue (t567 and t558, respectively). immunoblotting of serum-starved swiss 3t3 cells with this mab revealed that after lpa stimulation erm proteins were rapidly phosphorylated at t567 (ezrin), t564 (radixin), and t558 (moesin) in a rho-dependent manner and then dephosphorylated within 2 min. furthermore, the t564 phosphorylation of recombinant cooh-terminal half radixin did not affect its ability to bind to actin filaments in vitro but significantly suppressed its direct interaction with the nh2-terminal half of radixin. these observations indicate that the rho-kinase-dependent phosphorylation interferes with the intramolecular and/ or intermolecular head-to-tail association of erm proteins, which is an important mechanism of regulation of their activity as actin filament/plasma membrane cross-linkers.",0
"understanding the pathophysiogenesis of temporal lobe epilepsy (tle) largely rests on the use of models of status epilepticus (se), as in the case of the pilocarpine model. the main features of tle are: (i) epileptic foci in the limbic system; (ii) an ""initial precipitating injury""; (iii) the so-called ""latent period""; and (iv) the presence of hippocampal sclerosis leading to reorganization of neuronal networks. many of these characteristics can be reproduced in rodents by systemic injection of pilocarpine; in this animal model, se is followed by a latent period and later by the appearance of spontaneous recurrent seizures (srss). these processes are, however, influenced by experimental conditions such as rodent species, strain, gender, age, doses and routes of pilocarpine administration, as well as combinations with other drugs administered before and/or after se. in the attempt to limit these sources of variability, we evaluated the methodological procedures used by several investigators in the pilocarpine model; in particular, we have focused on the behavioural, electrophysiological and histopathological findings obtained with different protocols. we addressed the various experimental approaches published to date, by comparing mortality rates, onset of srss, neuronal damage, and network reorganization. based on the evidence reviewed here, we propose that the pilocarpine model can be a valuable tool to investigate the mechanisms involved in tle, and even more so when standardized to reduce mortality at the time of pilocarpine injection, differences in latent period duration, variability in the lesion extent, and srs frequency.",0
"cancer cells engage in a metabolic program to enhance biosynthesis and support cell proliferation. the regulatory properties of pyruvate kinase m2 (pkm2) influence altered glucose metabolism in cancer. the interaction of pkm2 with phosphotyrosine-containing proteins inhibits enzyme activity and increases the availability of glycolytic metabolites to support cell proliferation. this suggests that high pyruvate kinase activity may suppress tumor growth. we show that expression of pkm1, the pyruvate kinase isoform with high constitutive activity, or exposure to published small-molecule pkm2 activators inhibits the growth of xenograft tumors. structural studies reveal that small-molecule activators bind pkm2 at the subunit interaction interface, a site that is distinct from that of the endogenous activator fructose-1,6-bisphosphate (fbp). however, unlike fbp, binding of activators to pkm2 promotes a constitutively active enzyme state that is resistant to inhibition by tyrosine-phosphorylated proteins. these data support the notion that small-molecule activation of pkm2 can interfere with anabolic metabolism.",0
"myosin was isolated from 14 different muscles (mammals, lower vertebrates, and invertebrates) of known maximal speed of shortening. these myosin preparations were homogeneous in the analytical ultracentrifuge or, in a few cases, showed, in addition to the main myosin peak, part of the myosin in aggregated form. actin- and ca(++)-activated atpase activities of the myosins were generally proportional to the speed of shortening of their respective muscles; i.e. the greater the intrinsic speed, the higher the atpase activity. this relation was found when the speed of shortening ranged from 0.1 to 24 muscle lengths/sec. the temperature coefficient of the ca(++)-activated myosin atpase was the same as that of the speed of shortening, q(10) about 2. higher q(10) values were found for the actin-activated myosin atpase, especially below 10 degrees c. by using myofibrils instead of reconstituted actomyosin, q(10) values close to 2 could be obtained for the mg(++)-activated myofibrillar atpase at ionic strength of 0.014. in another series of experiments, myosin was isolated from 11 different muscles of known isometric twitch contraction time. the atpase activity of these myosins was inversely proportional to the contraction time of the muscles. these results suggest a role for the atpase activity of myosin in determining the speed of muscle contraction. in contrast to the atpase activity of myosin, which varied according to the speed of contraction, the f-actin-binding ability of myosin from various muscles was rather constant.",0
"objective independently of total caloric intake, a better quality of the diet (for example, conformity to the mediterranean diet) is associated with lower obesity risk. it is unclear whether a brief dietary assessment tool, instead of full-length comprehensive methods, can also capture this association. in addition to reduced costs, a brief tool has the interesting advantage of allowing immediate feedback to participants in interventional studies. another relevant question is which individual items of such a brief tool are responsible for this association. we examined these associations using a 14-item tool of adherence to the mediterranean diet as exposure and body mass index, waist circumference and waist-to-height ratio (whtr) as outcomes. design cross-sectional assessment of all participants in the ""prevención con dieta mediterránea"" (predimed) trial. subjects 7,447 participants (55-80 years, 57% women) free of cardiovascular disease, but with either type 2 diabetes or ≥ 3 cardiovascular risk factors. trained dietitians used both a validated 14-item questionnaire and a full-length validated 137-item food frequency questionnaire to assess dietary habits. trained nurses measured weight, height and waist circumference. results strong inverse linear associations between the 14-item tool and all adiposity indexes were found. for a two-point increment in the 14-item score, the multivariable-adjusted differences in whtr were -0.0066 (95% confidence interval, -0.0088 to -0.0049) for women and -0.0059 (-0.0079 to -0.0038) for men. the multivariable-adjusted odds ratio for a whtr>0.6 in participants scoring ≥ 10 points versus ≤ 7 points was 0.68 (0.57 to 0.80) for women and 0.66 (0.54 to 0.80) for men. high consumption of nuts and low consumption of sweetened/carbonated beverages presented the strongest inverse associations with abdominal obesity. conclusions a brief 14-item tool was able to capture a strong monotonic inverse association between adherence to a good quality dietary pattern (mediterranean diet) and obesity indexes in a population of adults at high cardiovascular risk.",0
"regulatory t (treg) cells suppress abnormal/excessive immune responses to self- and nonself-antigens to maintain immune homeostasis. in tumor immunity, treg cells are involved in tumor development and progression by inhibiting antitumor immunity. there are several treg cell immune suppressive mechanisms: inhibition of costimulatory signals by cd80 and cd86 expressed by dendritic cells through cytotoxic t-lymphocyte antigen-4, interleukin (il)-2 consumption by high-affinity il-2 receptors with high cd25 (il-2 receptor α-chain) expression, secretion of inhibitory cytokines, metabolic modulation of tryptophan and adenosine, and direct killing of effector t cells. infiltration of treg cells into the tumor microenvironment (tme) occurs in multiple murine and human tumors. regulatory t cells are chemoattracted to the tme by chemokine gradients such as ccr4-ccl17/22, ccr8-ccl1, ccr10-ccl28, and cxcr3-ccl9/10/11. regulatory t cells are then activated and inhibit antitumor immune responses. a high infiltration by treg cells is associated with poor survival in various types of cancer. therefore, strategies to deplete treg cells and control of treg cell functions to increase antitumor immune responses are urgently required in the cancer immunotherapy field. various molecules that are highly expressed by treg cells, such as immune checkpoint molecules, chemokine receptors, and metabolites, have been targeted by abs or small molecules, but additional strategies are needed to fine-tune and optimize for augmenting antitumor effects restricted in the tme while avoiding systemic autoimmunity. here, we provide a brief synopsis of these cells in cancer and how they can be controlled to achieve therapeutic outcomes.",0
"background a hot new topic in medical treatment is the use of mesenchymal stem cells (msc) in therapy. the low frequency of this subpopulation of stem cells in bone marrow (bm) necessitates their in vitro expansion prior to clinical use. we evaluated the effect of long term culture on the senescence of these cells. results the mean long term culture was 118 days and the mean passage number was 9. the average number of pd decreased from 7.7 to 1.2 in the 10th passage. the mean telomere length decreased from 9.19 kbp to 8.7 kbp in the 9th passage. differentiation potential dropped from the 6th passage on. the culture's morphological abnormalities were typical of the hayflick model of cellular aging. conclusion we believe that msc enter senescence almost undetectably from the moment of in vitro culturing. simultaneously these cells are losing their stem cell characteristics. therefore, it is much better to consider them for cell and gene therapy early on.",0
"background somatic mutations in the gene for the epidermal growth factor receptor (egfr) are found in adenocarcinomas of the lung and are associated with sensitivity to the kinase inhibitors gefitinib (iressa) and erlotinib (tarceva). lung adenocarcinomas also harbor activating mutations in the downstream gtpase, kras, and mutations in egfr and kras appear to be mutually exclusive. methods and findings we sought to determine whether mutations in kras could be used to further enhance prediction of response to gefitinib or erlotinib. we screened 60 lung adenocarcinomas defined as sensitive or refractory to gefitinib or erlotinib for mutations in egfr and kras. we show that mutations in kras are associated with a lack of sensitivity to either drug. conclusion our results suggest that treatment decisions regarding use of these kinase inhibitors might be improved by determining the mutational status of both egfr and kras.",0
"objectives there is little consensus regarding the burden of pain in the uk. the purpose of this review was to synthesise existing data on the prevalence of various chronic pain phenotypes in order to produce accurate and contemporary national estimates. design major electronic databases were searched for articles published after 1990, reporting population-based prevalence estimates of chronic pain (pain lasting >3 months), chronic widespread pain, fibromyalgia and chronic neuropathic pain. pooled prevalence estimates were calculated for chronic pain and chronic widespread pain. results of the 1737 articles generated through our searches, 19 studies matched our inclusion criteria, presenting data from 139 933 adult residents of the uk. the prevalence of chronic pain, derived from 7 studies, ranged from 35.0% to 51.3% (pooled estimate 43.5%, 95% cis 38.4% to 48.6%). the prevalence of moderate-severely disabling chronic pain (von korff grades iii/iv), based on 4 studies, ranged from 10.4% to 14.3%. 12 studies stratified chronic pain prevalence by age group, demonstrating a trend towards increasing prevalence with increasing age from 14.3% in 18-25 years old, to 62% in the over 75 age group, although the prevalence of chronic pain in young people (18-39 years old) may be as high as 30%. reported prevalence estimates were summarised for chronic widespread pain (pooled estimate 14.2%, 95% ci 12.3% to 16.1%; 5 studies), chronic neuropathic pain (8.2% to 8.9%; 2 studies) and fibromyalgia (5.4%; 1 study). chronic pain was more common in female than male participants, across all measured phenotypes. conclusions chronic pain affects between one-third and one-half of the population of the uk, corresponding to just under 28 million adults, based on data from the best available published studies. this figure is likely to increase further in line with an ageing population.",0
"peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. the merops database ( aims to fulfil the need for an integrated source of information about these. the database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. the database has been expanded to include proteolytic enzymes other than peptidases. special identifiers for peptidases from a variety of model organisms have been established so that orthologues can be detected in other species. a table of predicted active-site residue and metal ligand positions and the residue ranges of the peptidase domains in orthologues has been added to each peptidase summary. new displays of tertiary structures, which can be rotated or have the surfaces displayed, have been added to the structure pages. new indexes for gene names and peptidase substrates have been made available. among the enhancements to existing features are the inclusion of small-molecule inhibitors in the tables of peptidase-inhibitor interactions, a table of known cleavage sites for each protein substrate, and tables showing the substrate-binding preferences of peptidases derived from combinatorial peptide substrate libraries.",0
"by screening specific populations of rat brain cells, we found that ameboid microglia secrete an 18 kd peptide with il-1 biological activity. the il-1 activity released by microglia was found to be identical to rat macrophage il-1 on fractionation by gel filtration and high pressure liquid anion-exchange chromatography, and it was neutralized by an antiserum specific for murine il-1. when added to astroglia grown in culture, microglial il-1 increased the cell number of five- to sevenfold, and increased astroglial incorporation of thymidine by three- to fivefold. we propose that the proliferation of astroglia in specific brain regions may be regulated by the signaled release of il-1 from activated microglial cells.",0
"an antibody-secreting b cell hybridoma, kj1-26.1, has been prepared from mice immunized with the t cell hybridoma do-11.10, which recognizes chicken ovalbumin in association with i-ad (cova/i-ad). kj1-26.1 blocks i-restricted antigen recognition by do-11.10 and a subclone of this t cell hybridoma, do-11.10.24, which has the same specificity for cova/i-ad as its parent. kj1-26.1 does not block i-restricted antigen recognition by any other t cell hybridoma tested, including a number of t cell hybridomas closely related to do-11.10, with similar, but not identical, specificities for antigen/i. moreover, kj1-26.1 binds to do-11.10 and do-11.10.24, but not to any other t cell hybridomas tested, including three subclones of do-11.10 that have lost the ability to recognize cova/i-ad. thus, in every regard kj1-26.1 appears to be binding to all or part of the receptors for antigen/i on the t cell hybridoma do-11.10. kj1-26.1 appears to bind to approximately 15,000 molecules/cell on the surface of do-11.10. the antibody precipitates an 80,000 dimer from the cells, which on reduction migrates as 40-44,000 monomers. the receptor(s) for antigen/i on do-11.10 therefore includes molecules with these properties.",0
"background physical therapy (pt) is one of the key disciplines in interdisciplinary stroke rehabilitation. the aim of this systematic review was to provide an update of the evidence for stroke rehabilitation interventions in the domain of pt. methods and findings randomized controlled trials (rcts) regarding pt in stroke rehabilitation were retrieved through a systematic search. outcomes were classified according to the icf. rcts with a low risk of bias were quantitatively analyzed. differences between phases poststroke were explored in subgroup analyses. a best evidence synthesis was performed for neurological treatment approaches. the search yielded 467 rcts (n = 25373; median pedro score 6 ), identifying 53 interventions. no adverse events were reported. strong evidence was found for significant positive effects of 13 interventions related to gait, 11 interventions related to arm-hand activities, 1 intervention for adl, and 3 interventions for physical fitness. summary effect sizes (sess) ranged from 0.17 (95%ci 0.03-0.70; i(2) = 0%) for therapeutic positioning of the paretic arm to 2.47 (95%ci 0.84-4.11; i(2) = 77%) for training of sitting balance. there is strong evidence that a higher dose of practice is better, with sess ranging from 0.21 (95%ci 0.02-0.39; i(2) = 6%) for motor function of the paretic arm to 0.61 (95%ci 0.41-0.82; i(2) = 41%) for muscle strength of the paretic leg. subgroup analyses yielded significant differences with respect to timing poststroke for 10 interventions. neurological treatment approaches to training of body functions and activities showed equal or unfavorable effects when compared to other training interventions. main limitations of the present review are not using individual patient data for meta-analyses and absence of correction for multiple testing. conclusions there is strong evidence for pt interventions favoring intensive high repetitive task-oriented and task-specific training in all phases poststroke. effects are mostly restricted to the actually trained functions and activities. suggestions for prioritizing pt stroke research are given.",0
"introduction the molecular mechanics energies combined with the poisson-boltzmann or generalized born and surface area continuum solvation (mm/pbsa and mm/gbsa) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. they are typically based on molecular dynamics simulations of the receptor-ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. they have been applied to a large number of systems with varying success. areas covered the authors review the use of mm/pbsa and mm/gbsa methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. expert opinion mm/pbsa and mm/gbsa are attractive approaches owing to their modular nature and that they do not require calculations on a training set. they have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. however, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. moreover, there are many variants of the method and their performance varies strongly with the tested system. likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results.",0
"the microbiota of the human gut is gaining broad attention owing to its association with a wide range of diseases, ranging from metabolic disorders (e.g. obesity and type 2 diabetes) to autoimmune diseases (such as inflammatory bowel disease and type 1 diabetes), cancer and even neurodevelopmental disorders (e.g. autism). having been increasingly used in biomedical research, mice have become the model of choice for most studies in this emerging field. mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. however, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. in this special article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.",0
"the genetic association of the major histocompatibility complex (mhc) to rheumatoid arthritis risk has commonly been attributed to alleles in hla-drb1. however, debate persists about the identity of the causal variants in hla-drb1 and the presence of independent effects elsewhere in the mhc. using existing genome-wide snp data in 5,018 individuals with seropositive rheumatoid arthritis (cases) and 14,974 unaffected controls, we imputed and tested classical alleles and amino acid polymorphisms in hla-a, hla-b, hla-c, hla-dpa1, hla-dpb1, hla-dqa1, hla-dqb1 and hla-drb1, as well as 3,117 snps across the mhc. conditional and haplotype analyses identified that three amino acid positions (11, 71 and 74) in hla-drβ1 and single-amino-acid polymorphisms in hla-b (at position 9) and hla-dpβ1 (at position 9), which are all located in peptide-binding grooves, almost completely explain the mhc association to rheumatoid arthritis risk. this study shows how imputation of functional variation from large reference panels can help fine map association signals in the mhc.",0
"summary today's graphics processing units (gpus) compose the scene from individual triangles. as about 320 triangles are needed to approximate a single sphere-an atom-in a convincing way, visualizing larger proteins with atomic details requires tens of millions of triangles, far too many for smooth interactive frame rates. we describe a new approach to solve this 'molecular graphics problem', which shares the work between gpu and multiple cpu cores, generates high-quality results with perfectly round spheres, shadows and ambient lighting and requires only opengl 1.0 functionality, without any pixel shader z-buffer access (a feature which is missing in most mobile devices). availability and implementation yasara view, a molecular modeling program built around the visualization algorithm described here, is freely available (including commercial use) for linux, macos, windows and android (intel) from contact elmar@yasara.org supplementary information supplementary data are available at bioinformatics online.",0
"in this study we have shown that activation of arthritogenic splenocytes with antigen and agonistic anti-cd40 gives raise to a b cell population that produce high levels of interleukin (il)-10 and low levels of interferon (ifn)-gamma. transfer of these b cells into dba/1-tcr-beta-tg mice, immunized with bovine collagen (cii) emulsified in complete freund's adjuvant inhibited t helper type 1 differentiation, prevented arthritis development, and was also effective in ameliorating established disease. il-10 is essential for the regulatory function of this subset of b cells, as the b cells population isolated from il-10 knockout mice failed to mediate this protective function. furthermore, b cells isolated from arthritogenic splenocytes treated in vitro with anti-il-10/anti-il-10r were unable to protect recipient mice from developing arthritis. our results suggest a new role of a subset of b cells in controlling t cell differentiation and autoimmune disorders.",0
"background the cancer burden in the united states of america (usa) has decreased gradually. however, china is experiencing a transition in its cancer profiles, with greater incidence of cancers that were previously more common in the usa. this study compared the latest cancer profiles, trends, and determinants between china and usa. methods this was a comparative study using open-source data. cancer cases and deaths in 2022 were calculated using cancer estimates from globocan 2020 and population estimates from the united nations. trends in cancer incidence and mortality rates in the usa used data from the surveillance, epidemiology, and end results program and national center for health statistics. chinese data were obtained from cancer registry reports. data from the global burden of disease 2019 and a decomposition method were used to express cancer deaths as the product of four determinant factors. results in 2022, there will be approximately 4,820,000 and 2,370,000 new cancer cases, and 3,210,000 and 640,000 cancer deaths in china and the usa, respectively. the most common cancers are lung cancer in china and breast cancer in the usa, and lung cancer is the leading cause of cancer death in both. age-standardized incidence and mortality rates for lung cancer and colorectal cancer in the usa have decreased significantly recently, but rates of liver cancer have increased slightly. rates of stomach, liver, and esophageal cancer decreased gradually in china, but rates have increased for colorectal cancer in the whole population, prostate cancer in men, and other seven cancer types in women. increases in adult population size and population aging were major determinants for incremental cancer deaths, and case-fatality rates contributed to reduced cancer deaths in both countries. conclusions the decreasing cancer burden in liver, stomach, and esophagus, and increasing burden in lung, colorectum, breast, and prostate, mean that cancer profiles in china and the usa are converging. population aging is a growing determinant of incremental cancer burden. progress in cancer prevention and care in the usa, and measures to actively respond to population aging, may help china to reduce the cancer burden.",0
"netmhc-3.0 is trained on a large number of quantitative peptide data using both affinity data from the immune epitope database and analysis resource (iedb) and elution data from syfpeithi. the method generates high-accuracy predictions of major histocompatibility complex (mhc): peptide binding. the predictions are based on artificial neural networks trained on data from 55 mhc alleles (43 human and 12 non-human), and position-specific scoring matrices (pssms) for additional 67 hla alleles. as only the mhc class i prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles. artificial neural network predictions are given as actual ic(50) values whereas pssm predictions are given as a log-odds likelihood scores. the output is optionally available as download for easy post-processing. the training method underlying the server is the best available, and has been used to predict possible mhc-binding peptides in a series of pathogen viral proteomes including sars, influenza and hiv, resulting in an average of 75-80% confirmed mhc binders. here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. the server is free of use and available at:",0
"the selection of appropriate outcomes or domains is crucial when designing clinical trials in order to compare directly the effects of different interventions in ways that minimize bias. if the findings are to influence policy and practice then the chosen outcomes need to be relevant and important to key stakeholders including patients and the public, health care professionals and others making decisions about health care. there is a growing recognition that insufficient attention has been paid to the outcomes measured in clinical trials. these issues could be addressed through the development and use of an agreed standardized collection of outcomes, known as a core outcome set, which should be measured and reported, as a minimum, in all trials for a specific clinical area. accumulating work in this area has identified the need for general guidance on the development of core outcome sets. key issues to consider in the development of a core outcome set include its scope, the stakeholder groups to involve, choice of consensus method and the achievement of a consensus.",0
"numerous observational studies have attempted to identify risk factors for infection with sars-cov-2 and covid-19 disease outcomes. studies have used datasets sampled from patients admitted to hospital, people tested for active infection, or people who volunteered to participate. here, we highlight the challenge of interpreting observational evidence from such non-representative samples. collider bias can induce associations between two or more variables which affect the likelihood of an individual being sampled, distorting associations between these variables in the sample. analysing uk biobank data, compared to the wider cohort the participants tested for covid-19 were highly selected for a range of genetic, behavioural, cardiovascular, demographic, and anthropometric traits. we discuss the mechanisms inducing these problems, and approaches that could help mitigate them. while collider bias should be explored in existing studies, the optimal way to mitigate the problem is to use appropriate sampling strategies at the study design stage.",0
"pathogenic escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic e. coli constitute part of the normal intestinal flora of healthy mammals and birds. the evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. specific pathogen types have arisen independently and repeatedly in several lineages, whereas other lineages contain only few pathogens. rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex. this long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response.",0
"phaster (phage search tool - enhanced release) is a significant upgrade to the popular phast web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. although the steps in the phage identification pipeline in phaster remain largely the same as in the original phast, numerous software improvements and significant hardware enhancements have now made phaster faster, more efficient, more visually appealing and much more user friendly. in particular, phaster is now 4.3× faster than phast when analyzing a typical bacterial genome. more specifically, software optimizations have made the backend of phaster 2.7x faster than phast, while the addition of 80 cpus to the phaster compute cluster are responsible for the remaining speed-up. phaster can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated genbank file. a number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of phaster's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously phast/phaster annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). phaster's web interface has also been entirely rewritten. a new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. phaster is available online at",0
"the rate of detection of thyroid nodules and carcinomas has increased with the widespread use of ultrasonography (us), which is the mainstay for the detection and risk stratification of thyroid nodules as well as for providing guidance for their biopsy and nonsurgical treatment. the korean society of thyroid radiology (ksthr) published their first recommendations for the us-based diagnosis and management of thyroid nodules in 2011. these recommendations have been used as the standard guidelines for the past several years in korea. lately, the application of us has been further emphasized for the personalized management of patients with thyroid nodules. the task force on thyroid nodules of the ksthr has revised the recommendations for the ultrasound diagnosis and imaging-based management of thyroid nodules. the review and recommendations in this report have been based on a comprehensive analysis of the current literature and the consensus of experts.",0
"free radical damage is linked to formation of many degenerative diseases, including cancer, cardiovascular disease, cataracts, and aging. excessive reactive oxygen species (ros) formation can induce oxidative stress, leading to cell damage that can culminate in cell death. therefore, cells have antioxidant networks to scavenge excessively produced ros. the balance between the production and scavenging of ros leads to homeostasis in general; however, the balance is somehow shifted towards the formation of free radicals, which results in accumulated cell damage in time. antioxidants can attenuate the damaging effects of ros in vitro and delay many events that contribute to cellular aging. the use of multivitamin/mineral supplements (mvms) has grown rapidly over the past decades. some recent studies demonstrated no effect of antioxidant therapy; sometimes the intake of antioxidants even increased mortality. oxidative stress is damaging and beneficial for the organism, as some ros are signaling molecules in cellular signaling pathways. lowering the levels of oxidative stress by antioxidant supplements is not beneficial in such cases. the balance between ros and antioxidants is optimal, as both extremes, oxidative and antioxidative stress, are damaging. therefore, there is a need for accurate determination of individual's oxidative stress levels before prescribing the supplement antioxidants.",0
"cd34+ cells in human cord blood and marrow are known to give rise to dendritic cells (dc), as well as to other myeloid lineages. cd34+ cells are rare in adult blood, however, making it difficult to use cd34+ cells to ascertain if dc progenitors are present in the circulation and if blood can be a starting point to obtain large numbers of these immunostimulatory antigen-presenting cells for clinical studies. a systematic search for dc progenitors was therefore carried out in several contexts. in each case, we looked initially for the distinctive proliferating aggregates that were described previously in mice. in cord blood, it was only necessary to deplete erythroid progenitors, and add granulocyte/macrophage colony-stimulating factor (gm-csf) together with tumor necrosis factor (tnf), to observe many aggregates and the production of typical dc progeny. in adult blood from patients receiving csfs after chemotherapy for malignancy, gm-csf and tnf likewise generated characteristic dcs from hla-dr negative precursors. however, in adult blood from healthy donors, the above approaches only generated small dc aggregates which then seemed to become monocytes. when interleukin 4 was used to suppress monocyte development (jansen, j. h., g.-j. h. m. wientjens, w. e. fibbe, r. willemze, and h. c. kluin-nelemans. 1989. j. exp. med. 170:577.), the addition of gm-csf led to the formation of large proliferating dc aggregates and within 5-7 d, many nonproliferating progeny, about 3-8 million cells per 40 ml of blood. the progeny had a characteristic morphology and surface composition (e.g., abundant hla-dr and accessory molecules for cell-mediated immunity) and were potent stimulators of quiescent t cells. therefore, large numbers of dcs can be mobilized by specific cytokines from progenitors in the blood stream. these relatively large numbers of dc progeny should facilitate future studies of their fc epsilon ri and cd4 receptors, and their use in stimulating t cell-mediated resistance to viruses and tumors.",0
"background evidence from retrospective studies suggests that disease progression after first-line chemotherapy for metastatic non-small-cell lung cancer (nsclc) occurs most often at sites of disease known to exist at baseline. however, the potential effect of aggressive local consolidative therapy for patients with oligometastatic nsclc is unknown. we aimed to assess the effect of local consolidative therapy on progression-free survival. methods in this multicentre, randomised, controlled, phase 2 study, eligible patients from three hospitals had histological confirmation of stage iv nsclc, three or fewer metastatic disease lesions after first-line systemic therapy, an eastern cooperative oncology group performance status score of 2 or less, had received standard first-line systemic therapy, and had no disease progression before randomisation. first-line therapy was four or more cycles of platinum doublet therapy or 3 or more months of egfr or alk inhibitors for patients with egfr mutations or alk rearrangements, respectively. patients were randomly assigned (1:1) to either local consolidative therapy (radiotherapy or resection of all lesions) with or without subsequent maintenance treatment or to maintenance treatment alone, which could be observation only. maintenance treatment was recommended based on a list of approved regimens, and observation was defined as close surveillance without cytotoxic treatment. randomisation was not masked and was balanced dynamically on five factors: number of metastases, response to initial therapy, cns metastases, intrathoracic nodal status, and egfr and alk status. the primary endpoint was progression-free survival analysed in all patients who were treated and had at least one post-baseline imaging assessment. the study is ongoing but not recruiting participants. this study is registered with clinicaltrials.gov, number nct01725165. findings between nov 28, 2012, and jan 19, 2016, 74 patients were enrolled either during or at the completion of first-line systemic therapy. the study was terminated early after randomisation of 49 patients (25 in the local consolidative therapy group and 24 in the maintenance treatment group) as part of the annual analyses done by the data safety monitoring committee of all randomised trials at md anderson cancer center, and before a planned interim analysis of 44 events. at a median follow-up time for all randomised patients of 12·39 months (iqr 5·52-20·30), the median progression-free survival in the local consolidative therapy group was 11·9 months (90% ci 5·7-20·9) versus 3·9 months (2·3-6·6) in the maintenance treatment group (hazard ratio 0·35 , log-rank p=0·0054). adverse events were similar between groups, with no grade 4 adverse events or deaths due to treatment. grade 3 adverse events in the maintenance therapy group were fatigue (n=1) and anaemia (n=1) and in the local consolidative therapy group were oesophagitis (n=2), anaemia (n=1), pneumothorax (n=1), and abdominal pain (n=1, unlikely related). interpretation local consolidative therapy with or without maintenance therapy for patients with three or fewer metastases from nsclc that did not progress after initial systemic therapy improved progression-free survival compared with maintenance therapy alone. these findings suggest that aggressive local therapy should be further explored in phase 3 trials as a standard treatment option in this clinical scenario. funding md anderson lung cancer priority fund, md anderson cancer center moon shot initiative, and cancer center support (core), national cancer institute, national institutes of health.",0
"inhibition of the tor signalling pathway by genetic or pharmacological intervention extends lifespan in invertebrates, including yeast, nematodes and fruitflies; however, whether inhibition of mtor signalling can extend lifespan in a mammalian species was unknown. here we report that rapamycin, an inhibitor of the mtor pathway, extends median and maximal lifespan of both male and female mice when fed beginning at 600 days of age. on the basis of age at 90% mortality, rapamycin led to an increase of 14% for females and 9% for males. the effect was seen at three independent test sites in genetically heterogeneous mice, chosen to avoid genotype-specific effects on disease susceptibility. disease patterns of rapamycin-treated mice did not differ from those of control mice. in a separate study, rapamycin fed to mice beginning at 270 days of age also increased survival in both males and females, based on an interim analysis conducted near the median survival point. rapamycin may extend lifespan by postponing death from cancer, by retarding mechanisms of ageing, or both. to our knowledge, these are the first results to demonstrate a role for mtor signalling in the regulation of mammalian lifespan, as well as pharmacological extension of lifespan in both genders. these findings have implications for further development of interventions targeting mtor for the treatment and prevention of age-related diseases.",0
"monkeypox, a zoonotic disease caused by an orthopoxvirus, results in a smallpox-like disease in humans. since monkeypox in humans was initially diagnosed in 1970 in the democratic republic of the congo (drc), it has spread to other regions of africa (primarily west and central), and cases outside africa have emerged in recent years. we conducted a systematic review of peer-reviewed and grey literature on how monkeypox epidemiology has evolved, with particular emphasis on the number of confirmed, probable, and/or possible cases, age at presentation, mortality, and geographical spread. the review is registered with prospero (crd42020208269). we identified 48 peer-reviewed articles and 18 grey literature sources for data extraction. the number of human monkeypox cases has been on the rise since the 1970s, with the most dramatic increases occurring in the drc. the median age at presentation has increased from 4 (1970s) to 21 years (2010-2019). there was an overall case fatality rate of 8.7%, with a significant difference between clades-central african 10.6% (95% ci: 8.4%- 13.3%) vs. west african 3.6% (95% ci: 1.7%- 6.8%). since 2003, import- and travel-related spread outside of africa has occasionally resulted in outbreaks. interactions/activities with infected animals or individuals are risk behaviors associated with acquiring monkeypox. our review shows an escalation of monkeypox cases, especially in the highly endemic drc, a spread to other countries, and a growing median age from young children to young adults. these findings may be related to the cessation of smallpox vaccination, which provided some cross-protection against monkeypox, leading to increased human-to-human transmission. the appearance of outbreaks beyond africa highlights the global relevance of the disease. increased surveillance and detection of monkeypox cases are essential tools for understanding the continuously changing epidemiology of this resurging disease.",0
"although serum from patients with parkinson's disease contains elevated levels of numerous pro-inflammatory cytokines including il-6, tnf, il-1β, and ifnγ, whether inflammation contributes to or is a consequence of neuronal loss remains unknown 1 . mutations in parkin, an e3 ubiquitin ligase, and pink1, a ubiquitin kinase, cause early onset parkinson's disease 2,3 . both pink1 and parkin function within the same biochemical pathway and remove damaged mitochondria from cells in culture and in animal models via mitophagy, a selective form of autophagy 4 . the in vivo role of mitophagy, however, is unclear, partly because mice that lack either pink1 or parkin have no substantial parkinson's-disease-relevant phenotypes 5-7 . mitochondrial stress can lead to the release of damage-associated molecular patterns (damps) that can activate innate immunity 8-12 , suggesting that mitophagy may mitigate inflammation. here we report a strong inflammatory phenotype in both prkn -/- and pink1 -/- mice following exhaustive exercise and in prkn -/- ;mutator mice, which accumulate mutations in mitochondrial dna (mtdna) 13,14 . inflammation resulting from either exhaustive exercise or mtdna mutation is completely rescued by concurrent loss of sting, a central regulator of the type i interferon response to cytosolic dna 15,16 . the loss of dopaminergic neurons from the substantia nigra pars compacta and the motor defect observed in aged prkn -/- ;mutator mice are also rescued by loss of sting, suggesting that inflammation facilitates this phenotype. humans with mono- and biallelic prkn mutations also display elevated cytokines. these results support a role for pink1- and parkin-mediated mitophagy in restraining innate immunity.",0
"scientists should be able to provide support for the absence of a meaningful effect. currently, researchers often incorrectly conclude an effect is absent based a nonsignificant result. a widely recommended approach within a frequentist framework is to test for equivalence . in equivalence tests, such as the two one-sided tests (tost) procedure discussed in this article, an upper and lower equivalence bound is specified based on the smallest effect size of interest. the tost procedure can be used to statistically reject the presence of effects large enough to be considered worthwhile. this practical primer with accompanying spreadsheet and r package enables psychologists to easily perform equivalence tests (and power analyses) by setting equivalence bounds based on standardized effect sizes and provides recommendations to prespecify equivalence bounds. extending your statistical tool kit with equivalence tests is an easy way to improve your statistical and theoretical inferences.",0
"improved, largely automated methods are described for the purification and analysis o peroxisomes, lysosomes, and mitochondria from the livers of rats injected with triton wr-1339. with these new methods, it has become possible to obtain, in less than 6 hr and with reliable reproducibility, mitochondria practically free of contaminants, as well as the rarer cytoplasmic particles in amounts (about 100 mg of protein) and in a state of purity (95%) that make them suitable for detailed biochemical studies. the results obtained so far on these preparations have made more conclusive and precise previous estimates of the biochemical and morphological properties of the three groups of cytoplasmic particles. in addition, peroxisomes were found to contain essentially all the l-alpha-hydroxy acid oxidase of the liver, as well as a small, but significant fraction of its nadp-linked isocitrate dehydrogenase activity. another small fraction of the latter enzyme is present in the mitochondria, the remainder being associated with the cell sap. the mitochondrial localization of the metabolically active cytoplasmic dna could be verified. the relative content of the fractions in mitochondria, whole peroxisomes, peroxisome cores, lysosomes, and endoplasmic reticulum was estimated independently by direct measurements on electron micrographs, and by linear programming (based on the assumption that the particles are biochemically homogeneous) of the results of enzyme assays. the two types of estimates agreed very well, except for one fraction in which low cytochrome oxidase activity was associated with mitochondrial damage.",0
"objective to compare the effects of treatments for coronavirus disease 2019 (covid-19). design living systematic review and network meta-analysis. data sources who covid-19 database, a comprehensive multilingual source of global covid-19 literature, up to 3 december 2021 and six additional chinese databases up to 20 february 2021. studies identified as of 1 december 2021 were included in the analysis. study selection randomised clinical trials in which people with suspected, probable, or confirmed covid-19 were randomised to drug treatment or to standard care or placebo. pairs of reviewers independently screened potentially eligible articles. methods after duplicate data abstraction, a bayesian network meta-analysis was conducted. risk of bias of the included studies was assessed using a modification of the cochrane risk of bias 2.0 tool, and the certainty of the evidence using the grading of recommendations assessment, development, and evaluation (grade) approach. for each outcome, interventions were classified in groups from the most to the least beneficial or harmful following grade guidance. results 463 trials enrolling 166 581 patients were included; 267 (57.7%) trials and 89 814 (53.9%) patients are new from the previous iteration; 265 (57.2%) trials evaluating treatments with at least 100 patients or 20 events met the threshold for inclusion in the analyses. compared with standard care, three drugs reduced mortality in patients with mostly severe disease with at least moderate certainty: systemic corticosteroids (risk difference 23 fewer per 1000 patients, 95% credible interval 40 fewer to 7 fewer, moderate certainty), interleukin-6 receptor antagonists when given with corticosteroids (23 fewer per 1000, 36 fewer to 7 fewer, moderate certainty), and janus kinase inhibitors (44 fewer per 1000, 64 fewer to 20 fewer, high certainty). compared with standard care, two drugs probably reduce hospital admission in patients with non-severe disease: nirmatrelvir/ritonavir (36 fewer per 1000, 41 fewer to 26 fewer, moderate certainty) and molnupiravir (19 fewer per 1000, 29 fewer to 5 fewer, moderate certainty). remdesivir may reduce hospital admission (29 fewer per 1000, 40 fewer to 6 fewer, low certainty). only molnupiravir had at least moderate quality evidence of a reduction in time to symptom resolution (3.3 days fewer, 4.8 fewer to 1.6 fewer, moderate certainty); several others showed a possible benefit. several drugs may increase the risk of adverse effects leading to drug discontinuation; hydroxychloroquine probably increases the risk of mechanical ventilation (moderate certainty). conclusion corticosteroids, interleukin-6 receptor antagonists, and janus kinase inhibitors probably reduce mortality and confer other important benefits in patients with severe covid-19. molnupiravir and nirmatrelvir/ritonavir probably reduce admission to hospital in patients with non-severe covid-19. systematic review registration this review was not registered. the protocol is publicly available in the supplementary material. readers' note this article is a living systematic review that will be updated to reflect emerging evidence. updates may occur for up to two years from the date of original publication. this is the fifth version of the original article published on 30 july 2020 (bmj 2020;370:m2980), and previous versions can be found as data supplements. when citing this paper please consider adding the version number and date of access for clarity.",0
"background comparative, functional, and developmental studies of animal morphology require accurate visualization of three-dimensional structures, but few widely applicable methods exist for non-destructive whole-volume imaging of animal tissues. quantitative studies in particular require accurately aligned and calibrated volume images of animal structures. x-ray microtomography (microct) has the potential to produce quantitative 3d images of small biological samples, but its widespread use for non-mineralized tissues has been limited by the low x-ray contrast of soft tissues. although osmium staining and a few other techniques have been used for contrast enhancement, generally useful methods for microct imaging for comparative morphology are still lacking. results several very simple and versatile staining methods are presented for microct imaging of animal soft tissues, along with advice on tissue fixation and sample preparation. the stains, based on inorganic iodine and phosphotungstic acid, are easier to handle and much less toxic than osmium, and they produce high-contrast x-ray images of a wide variety of soft tissues. the breadth of possible applications is illustrated with a few microct images of model and non-model animals, including volume and section images of vertebrates, embryos, insects, and other invertebrates. each image dataset contains x-ray absorbance values for every point in the imaged volume, and objects as small as individual muscle fibers and single blood cells can be resolved in their original locations and orientations within the sample. conclusion with very simple contrast staining, microct imaging can produce quantitative, high-resolution, high-contrast volume images of animal soft tissues, without destroying the specimens and with possibilities of combining with other preparation and imaging methods. such images are expected to be useful in comparative, developmental, functional, and quantitative studies of morphology.",0
"a new hypervirulent (hypermucoviscous) variant of klebsiella pneumoniae has emerged. first described in the asian pacific rim, it now increasingly recognized in western countries. defining clinical features are the ability to cause serious, life-threatening community-acquired infection in younger healthy hosts, including liver abscess, pneumonia, meningitis and endophthalmitis and the ability to metastatically spread, an unusual feature for enteric gram-negative bacilli in the non-immunocompromised. despite infecting a healthier population, significant morbidity and mortality occurs. although epidemiologic features are still being defined, colonization, particularly intestinal colonization, appears to be a critical step leading to infection. however the route of entry remains unclear. the majority of cases described to date are in asians, raising the issue of a genetic predisposition vs. geospecific strain acquisition. the traits that enhance its virulence when compared with ""classical"" k. pneumoniae are the ability to more efficiently acquire iron and perhaps an increase in capsule production, which confers the hypermucoviscous phenotype. an objective diagnostic test suitable for routine use in the clinical microbiology laboratory is needed. if/when these strains become increasingly resistant to antimicrobials, we will be faced with a frightening clinical scenario.",0
"the pharmmapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. the original version of pharmmapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. in this article, we present a new version of the pharmmapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. the expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. in addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. it also features an improved user interface. the proposed web server is freely available at",0
"motivation ancient dna (adna) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. however, the analysis of adna generally faces two major issues. firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem dna damage. such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. we recently developed the user-friendly mapdamage package that identifies such patterns from next-generation sequencing (ngs) sequence datasets. the absence of formal statistical modeling of the dna damage process, however, precluded rigorous quantitative comparisons across samples. results here, we describe mapdamage 2.0 that extends the original features of mapdamage by incorporating a statistical model of dna damage. assuming that damage events depend only on sequencing position and post-mortem deamination, our bayesian statistical framework provides estimates of four key features of adna molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions ( ) and overhangs ( ). our model enables rescaling base quality scores according to their probability of being damaged. mapdamage 2.0 handles ngs datasets with ease and is compatible with a wide range of dna library protocols. availability mapdamage 2.0 is available at ginolhac.github.io/mapdamage/ as a python package and documentation is maintained at the centre for geogenetics web site (geogenetics.ku.dk/publications/mapdamage2.0/). supplementary information supplementary data are available at bioinformatics online.",0
"objective to do a quantitative systematic review, including published and unpublished data, examining the associations between individual objective measures of physical capability (grip strength, walking speed, chair rising, and standing balance times) and mortality in community dwelling populations. design systematic review and meta-analysis. data sources relevant studies published by may 2009 identified through literature searches using embase (from 1980) and medline (from 1950) and manual searching of reference lists; unpublished results were obtained from study investigators. study selection eligible observational studies were those done in community dwelling people of any age that examined the association of at least one of the specified measures of physical capability (grip strength, walking speed, chair rises, or standing balance) with mortality. data synthesis effect estimates obtained were pooled by using random effects meta-analysis models with heterogeneity between studies investigated. results although heterogeneity was detected, consistent evidence was found of associations between all four measures of physical capability and mortality; those people who performed less well in these tests were found to be at higher risk of all cause mortality. for example, the summary hazard ratio for mortality comparing the weakest with the strongest quarter of grip strength (14 studies, 53 476 participants) was 1.67 (95% confidence interval 1.45 to 1.93) after adjustment for age, sex, and body size (i(2)=84.0%, 95% confidence interval 74% to 90%; p from q statistic conclusions objective measures of physical capability are predictors of all cause mortality in older community dwelling populations. such measures may therefore provide useful tools for identifying older people at higher risk of death.",0
"ensembl ( is unique in its flexible infrastructure for access to genomic data and annotation. it has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. genomes representing a greater diversity of species are increasingly being sequenced. in response, we have focussed our recent efforts on expediting the annotation of new assemblies. here, we report the release of the greatest annual number of newly annotated genomes in the history of ensembl via our dedicated ensembl rapid release platform ( we have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. we have a range of specific software tools for specific tasks, such as the ensembl variant effect predictor (vep) and the newly developed interface for the variant recoder. all ensembl data, software and tools are freely available for download and are accessible programmatically.",0
"germline copy number variants (cnvs) and somatic copy number alterations (scnas) are of significant importance in syndromic conditions and cancer. massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. however, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. we present a method for copy number detection, implemented in the software package cnvkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. this combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. in particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. after normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: gc content, target footprint size and spacing, and repetitive sequences. we compared the performance of cnvkit to copy number changes identified by array comparative genomic hybridization. we packaged the components of cnvkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. cnvkit is freely available from",0
"background pancreatic cancer has an extremely poor prognosis and prolonged survival is achieved only by resection with macroscopic tumor clearance. there is a strong rationale for a neoadjuvant approach, since a relevant percentage of pancreatic cancer patients present with non-metastatic but locally advanced disease and microscopic incomplete resections are common. the objective of the present analysis was to systematically review studies concerning the effects of neoadjuvant therapy on tumor response, toxicity, resection, and survival percentages in pancreatic cancer. methods and findings trials were identified by searching medline, embase, and the cochrane central register of controlled trials from 1966 to december 2009 as well as through reference lists of articles and proceedings of major meetings. retrospective and prospective studies analyzing neoadjuvant radiochemotherapy, radiotherapy, or chemotherapy of pancreatic cancer patients, followed by re-staging, and surgical exploration/resection were included. two reviewers independently extracted data and assessed study quality. pooled relative risks and 95% confidence intervals were calculated using random-effects models. primary outcome measures were proportions of tumor response categories and percentages of exploration and resection. a total of 111 studies (n = 4,394) including 56 phase i-ii trials were analyzed. a median of 31 (interquartile range 19-46) patients per study were included. studies were subdivided into surveys considering initially resectable tumors (group 1) and initially non-resectable (borderline resectable/unresectable) tumors (group 2). neoadjuvant chemotherapy was given in 96.4% of the studies with the main agents gemcitabine, 5-fu (and oral analogues), mitomycin c, and platinum compounds. neoadjuvant radiotherapy was applied in 93.7% of the studies with doses ranging from 24 to 63 gy. averaged complete/partial response probabilities were 3.6% (95% ci 2%-5.5%)/30.6% (95% ci 20.7%-41.4%) and 4.8% (95% ci 3.5%-6.4%)/30.2% (95% ci 24.5%-36.3%) for groups 1 and 2, respectively; whereas progressive disease fraction was estimated to 20.9% (95% ci 16.9%-25.3%) and 20.8% (95% ci 14.5%-27.8%). in group 1, resectability was estimated to 73.6% (95% ci 65.9%-80.6%) compared to 33.2% (95% ci 25.8%-41.1%) in group 2. higher resection-associated morbidity and mortality rates were observed in group 2 versus group 1 (26.7%, 95% ci 20.7%-33.3% versus 39.1%, 95% ci 29.5%-49.1%; and 3.9%, 95% ci 2.2%-6% versus 7.1%, 95% ci 5.1%-9.5%). combination chemotherapies resulted in higher estimated response and resection probabilities for patients with initially non-resectable tumors (""non-resectable tumor patients"") compared to monotherapy. estimated median survival following resection was 23.3 (range 12-54) mo for group 1 and 20.5 (range 9-62) mo for group 2 patients. conclusions in patients with initially resectable tumors (""resectable tumor patients""), resection frequencies and survival after neoadjuvant therapy are similar to those of patients with primarily resected tumors and adjuvant therapy. approximately one-third of initially staged non-resectable tumor patients would be expected to have resectable tumors following neoadjuvant therapy, with comparable survival as initially resectable tumor patients. thus, patients with locally non-resectable tumors should be included in neoadjuvant protocols and subsequently re-evaluated for resection.",0
"rationale use of aceis (angiotensin-converting enzyme inhibitors) and arbs (angiotensin ii receptor blockers) is a major concern for clinicians treating coronavirus disease 2019 (covid-19) in patients with hypertension. objective to determine the association between in-hospital use of acei/arb and all-cause mortality in patients with hypertension and hospitalized due to covid-19. methods and results this retrospective, multi-center study included 1128 adult patients with hypertension diagnosed with covid-19, including 188 taking acei/arb (acei/arb group; median age 64 years; 53.2% men) and 940 without using acei/arb (non-acei/arb group; median age 64 ; 53.5% men), who were admitted to 9 hospitals in hubei province, china from december 31, 2019 to february 20, 2020. in mixed-effect cox model treating site as a random effect, after adjusting for age, gender, comorbidities, and in-hospital medications, the detected risk for all-cause mortality was lower in the acei/arb group versus the non-acei/arb group (adjusted hazard ratio, 0.42 ; p =0.03). in a propensity score-matched analysis followed by adjusting imbalanced variables in mixed-effect cox model, the results consistently demonstrated lower risk of covid-19 mortality in patients who received acei/arb versus those who did not receive acei/arb (adjusted hazard ratio, 0.37 ; p =0.03). further subgroup propensity score-matched analysis indicated that, compared with use of other antihypertensive drugs, acei/arb was also associated with decreased mortality (adjusted hazard ratio, 0.30 ; p =0.01) in patients with covid-19 and coexisting hypertension. conclusions among hospitalized patients with covid-19 and coexisting hypertension, inpatient use of acei/arb was associated with lower risk of all-cause mortality compared with acei/arb nonusers. while study interpretation needs to consider the potential for residual confounders, it is unlikely that in-hospital use of acei/arb was associated with an increased mortality risk.",0
"a new severe acute respiratory syndrome coronavirus 2 (sars-cov-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of wuhan in china. our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of sars-cov-2 using bioinformatics programs. information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. to understand the genomic structure and variations of the sars-cov-2. the study analyzed 95 sars-cov-2 complete genome sequences available in genbank, national microbiologydata center (nmdc) and ngdc genome warehouse from december-2019 until 05 of april-2020. the genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. we found 116 mutations, the three most common mutations were 8782c>t in orf1ab gene, 28144t>c in orf8 gene and 29095c>t in the n gene. the mutations might affect the severity and spread of the sars-cov-2. the finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with covid-19.",0
"for centuries, cell biology has been based on light microscopy and at the same time been limited by its optical resolution. however, several new technologies have been developed recently that bypass this limit. these new super-resolution technologies are either based on tailored illumination, nonlinear fluorophore responses, or the precise localization of single molecules. overall, these new approaches have created unprecedented new possibilities to investigate the structure and function of cells.",0
"sars-cov-2-specific memory t cells will likely prove critical for long-term immune protection against covid-19. here, we systematically mapped the functional and phenotypic landscape of sars-cov-2-specific t cell responses in unexposed individuals, exposed family members, and individuals with acute or convalescent covid-19. acute-phase sars-cov-2-specific t cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent-phase sars-cov-2-specific t cells were polyfunctional and displayed a stem-like memory phenotype. importantly, sars-cov-2-specific t cells were detectable in antibody-seronegative exposed family members and convalescent individuals with a history of asymptomatic and mild covid-19. our collective dataset shows that sars-cov-2 elicits broadly directed and functionally replete memory t cell responses, suggesting that natural exposure or infection may prevent recurrent episodes of severe covid-19.",0
"obesity is a chronic metabolic disease characterised by an increase of body fat stores. it is a gateway to ill health, and it has become one of the leading causes of disability and death, affecting not only adults but also children and adolescents worldwide. in clinical practice, the body fatness is estimated by bmi, and the accumulation of intra-abdominal fat (marker for higher metabolic and cardiovascular disease risk) can be assessed by waist circumference. complex interactions between biological, behavioural, social and environmental factors are involved in regulation of energy balance and fat stores. a comprehensive history, physical examination and laboratory assessment relevant to the patient's obesity should be obtained. appropriate goals of weight management emphasise realistic weight loss to achieve a reduction in health risks and should include promotion of weight loss, maintenance and prevention of weight regain. management of co-morbidities and improving quality of life of obese patients are also included in treatment aims. balanced hypocaloric diets result in clinically meaningful weight loss regardless of which macronutrients they emphasise. aerobic training is the optimal mode of exercise for reducing fat mass while a programme including resistance training is needed for increasing lean mass in middle-aged and overweight/obese individuals. cognitive behavioural therapy directly addresses behaviours that require change for successful weight loss and weight loss maintenance. pharmacotherapy can help patients to maintain compliance and ameliorate obesity-related health risks. surgery is the most effective treatment for morbid obesity in terms of long-term weight loss. a comprehensive obesity management can only be accomplished by a multidisciplinary obesity management team. we conclude that physicians have a responsibility to recognise obesity as a disease and help obese patients with appropriate prevention and treatment. treatment should be based on good clinical care, and evidence-based interventions; should focus on realistic goals and lifelong multidisciplinary management.",0
"background determinants of practice are factors that might prevent or enable improvements. several checklists, frameworks, taxonomies, and classifications of determinants of healthcare professional practice have been published. in this paper, we describe the development of a comprehensive, integrated checklist of determinants of practice (the ticd checklist). methods we performed a systematic review of frameworks of determinants of practice followed by a consensus process. we searched electronic databases and screened the reference lists of key background documents. two authors independently assessed titles and abstracts, and potentially relevant full text articles. we compiled a list of attributes that a checklist should have: comprehensiveness, relevance, applicability, simplicity, logic, clarity, usability, suitability, and usefulness. we assessed included articles using these criteria and collected information about the theory, model, or logic underlying how the factors (determinants) were selected, described, and grouped, the strengths and weaknesses of the checklist, and the determinants and the domains in each checklist. we drafted a preliminary checklist based on an aggregated list of determinants from the included checklists, and finalized the checklist by a consensus process among implementation researchers. results we screened 5,778 titles and abstracts and retrieved 87 potentially relevant papers in full text. several of these papers had references to papers that we also retrieved in full text. we also checked potentially relevant papers we had on file that were not retrieved by the searches. we included 12 checklists. none of these were completely comprehensive when compared to the aggregated list of determinants and domains. we developed a checklist with 57 potential determinants of practice grouped in seven domains: guideline factors, individual health professional factors, patient factors, professional interactions, incentives and resources, capacity for organisational change, and social, political, and legal factors. we also developed five worksheets to facilitate the use of the checklist. conclusions based on a systematic review and a consensus process we developed a checklist that aims to be comprehensive and to build on the strengths of each of the 12 included checklists. the checklist is accompanied with five worksheets to facilitate its use in implementation research and quality improvement projects.",0
"the integrins are a superfamily of cell adhesion receptors that bind to extracellular matrix ligands, cell-surface ligands, and soluble ligands. they are transmembrane alphabeta heterodimers and at least 18 alpha and eight beta subunits are known in humans, generating 24 heterodimers. members of this family have been found in mammals, chicken and zebrafish, as well as lower eukaryotes, including sponges, the nematode caenorhabditis elegans (two alpha and one beta subunits, generating two integrins) and the fruitfly drosophila melanogaster (five alpha and one beta, generating five integrins). the alpha and beta subunits have distinct domain structures, with extracellular domains from each subunit contributing to the ligand-binding site of the heterodimer. the sequence arginine-glycine-aspartic acid (rgd) was identified as a general integrin-binding motif, but individual integrins are also specific for particular protein ligands. immunologically important integrin ligands are the intercellular adhesion molecules (icams), immunoglobulin superfamily members present on inflamed endothelium and antigen-presenting cells. on ligand binding, integrins transduce signals into the cell interior; they can also receive intracellular signals that regulate their ligand-binding affinity. here we provide a brief overview that concentrates mostly on the organization, structure and function of mammalian integrins, which have been more extensively studied than integrins in other organisms.",0
"background prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. the community-wide critical assessment of structure prediction (casp) experiments have been designed to obtain an objective assessment of the state-of-the-art of the field, where i-tasser was ranked as the best method in the server section of the recent 7th casp experiment. our laboratory has since then received numerous requests about the public availability of the i-tasser algorithm and the usage of the i-tasser predictions. results an on-line version of i-tasser is developed at the ku center for bioinformatics which has generated protein structure predictions for thousands of modeling requests from more than 35 countries. a scoring function (c-score) based on the relative clustering structural density and the consensus significance score of multiple threading templates is introduced to estimate the accuracy of the i-tasser predictions. a large-scale benchmark test demonstrates a strong correlation between the c-score and the tm-score (a structural similarity measurement with values in ) of the first models with a correlation coefficient of 0.91. using a c-score cutoff > -1.5 for the models of correct topology, both false positive and false negative rates are below 0.1. combining c-score and protein length, the accuracy of the i-tasser models can be predicted with an average error of 0.08 for tm-score and 2 a for rmsd. conclusion the i-tasser server has been developed to generate automated full-length 3d protein structural predictions where the benchmarked scoring system helps users to obtain quantitative assessments of the i-tasser models. the output of the i-tasser server for each query includes up to five full-length models, the confidence score, the estimated tm-score and rmsd, and the standard deviation of the estimations. the i-tasser server is freely available to the academic community at",0
"cd4⁺t cells are crucial in achieving a regulated effective immune response to pathogens. naive cd4⁺t cells are activated after interaction with antigen-mhc complex and differentiate into specific subtypes depending mainly on the cytokine milieu of the microenvironment. besides the classical t-helper 1 and t-helper 2, other subsets have been identified, including t-helper 17, regulatory t cell, follicular helper t cell, and t-helper 9, each with a characteristic cytokine profile. for a particular phenotype to be differentiated, a set of cytokine signaling pathways coupled with activation of lineage-specific transcription factors and epigenetic modifications at appropriate genes are required. the effector functions of these cells are mediated by the cytokines secreted by the differentiated cells. this paper will focus on the cytokine-signaling and the network of transcription factors responsible for the differentiation of naive cd4⁺t cells.",0
"individuals make choices and prioritize goals using complex processes that assign value to rewards and associated stimuli. during pavlovian learning, previously neutral stimuli that predict rewards can acquire motivational properties, becoming attractive and desirable incentive stimuli. however, whether a cue acts solely as a predictor of reward, or also serves as an incentive stimulus, differs between individuals. thus, individuals vary in the degree to which cues bias choice and potentially promote maladaptive behaviour. here we use rats that differ in the incentive motivational properties they attribute to food cues to probe the role of the neurotransmitter dopamine in stimulus-reward learning. we show that intact dopamine transmission is not required for all forms of learning in which reward cues become effective predictors. rather, dopamine acts selectively in a form of stimulus-reward learning in which incentive salience is assigned to reward cues. in individuals with a propensity for this form of learning, reward cues come to powerfully motivate and control behaviour. this work provides insight into the neurobiology of a form of stimulus-reward learning that confers increased susceptibility to disorders of impulse control.",0
"background commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. we have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. however, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. we believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. such an initiative might then serve as a bridge between image analysis research and cardiovascular research. the aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (segment) and to announce its release in a source code format. results segment can be used for image analysis in magnetic resonance imaging (mri), computed tomography (ct), single photon emission computed tomography (spect) and positron emission tomography (pet). some of its main features include loading of dicom images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of mri flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. here we present an overview of the validation results and validation procedures for the functionality of the software. we describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. the software has been made freely available for research purposes in a source code format on the project home page conclusions segment is a well-validated comprehensive software package for cardiovascular image analysis. it is freely available for research purposes provided that relevant original research publications related to the software are cited.",0
"synapsin i (protein i) is a neuron-specific phosphoprotein, which is a substrate for camp-dependent and ca/calmodulin-dependent protein kinases. in two accompanying studies (de camilli, p., r. cameron, and p. greengard, and de camilli, p., s. m. harris, jr., w. b. huttner, and p. greengard, 1983, j. cell biol. 96:1337-1354 and 1355-1373) we have shown, by immunocytochemical techniques at the light microscopic and electron microscopic levels, that synapsin i is present in the majority of, and possibly in all, nerve terminals, where it is primarily associated with synaptic vesicles. in the present study we have prepared a highly purified synaptic vesicle fraction from rat brain by a procedure that involves permeation chromatography on controlled-pore glass as a final purification step. using immunological methods, synapsin i concentrations were determined in various subcellular fractions obtained in the course of vesicle purification. synapsin i was found to copurify with synaptic vesicles and to represent approximately 6% of the total protein in the highly purified synaptic vesicle fraction. the copurification of synapsin i with synaptic vesicles was dependent on the use of low ionic strength media throughout the purification. synapsin i was released into the soluble phase by increased ionic strength at neutral ph, but not by nonionic detergents. the highly purified synaptic vesicle fraction contained a calcium-dependent protein kinase that phosphorylated endogenous synapsin i in its collagenase-sensitive tail region. the phosphorylation of this region appeared to facilitate the dissociation of synapsin i from synaptic vesicles under the experimental conditions used.",0
"importance short-term and long-term persistent postacute sequelae of covid-19 (pasc) have not been systematically evaluated. the incidence and evolution of pasc are dependent on time from infection, organ systems and tissue affected, vaccination status, variant of the virus, and geographic region. objective to estimate organ system-specific frequency and evolution of pasc. evidence review pubmed (medline), scopus, the world health organization global literature on coronavirus disease, and coronacentral databases were searched from december 2019 through march 2021. a total of 2100 studies were identified from databases and through cited references. studies providing data on pasc in children and adults were included. the preferred reporting items for systematic reviews and meta-analyses (prisma) guidelines for abstracting data were followed and performed independently by 2 reviewers. quality was assessed using the newcastle-ottawa scale for cohort studies. the main outcome was frequency of pasc diagnosed by (1) laboratory investigation, (2) radiologic pathology, and (3) clinical signs and symptoms. pasc were classified by organ system, ie, neurologic; cardiovascular; respiratory; digestive; dermatologic; and ear, nose, and throat as well as mental health, constitutional symptoms, and functional mobility. findings from a total of 2100 studies identified, 57 studies with 250 351 survivors of covid-19 met inclusion criteria. the mean (sd) age of survivors was 54.4 (8.9) years, 140 196 (56%) were male, and 197 777 (79%) were hospitalized during acute covid-19. high-income countries contributed 45 studies (79%). the median (iqr) proportion of covid-19 survivors experiencing at least 1 pasc was 54.0% (45.0%-69.0%; 13 studies) at 1 month (short-term), 55.0% (34.8%-65.5%; 38 studies) at 2 to 5 months (intermediate-term), and 54.0% (31.0%-67.0%; 9 studies) at 6 or more months (long-term). most prevalent pulmonary sequelae, neurologic disorders, mental health disorders, functional mobility impairments, and general and constitutional symptoms were chest imaging abnormality (median , 62.2% ), difficulty concentrating (median , 23.8% ), generalized anxiety disorder (median , 29.6% ), general functional impairments (median , 44.0% ), and fatigue or muscle weakness (median , 37.5% ), respectively. other frequently reported symptoms included cardiac, dermatologic, digestive, and ear, nose, and throat disorders. conclusions and relevance in this systematic review, more than half of covid-19 survivors experienced pasc 6 months after recovery. the most common pasc involved functional mobility impairments, pulmonary abnormalities, and mental health disorders. these long-term pasc effects occur on a scale that could overwhelm existing health care capacity, particularly in low- and middle-income countries.",0
"alum (aluminum hydroxide) is the most widely used adjuvant in human vaccines, but the mechanism of its adjuvanticity remains unknown. in vitro studies showed no stimulatory effects on dendritic cells (dcs). in the absence of adjuvant, ag was taken up by lymph node (ln)-resident dcs that acquired soluble ag via afferent lymphatics, whereas after injection of alum, ag was taken up, processed, and presented by inflammatory monocytes that migrated from the peritoneum, thus becoming inflammatory dcs that induced a persistent th2 response. the enhancing effects of alum on both cellular and humoral immunity were completely abolished when cd11c(+) monocytes and dcs were conditionally depleted during immunization. mechanistically, dc-driven responses were abolished in myd88-deficient mice and after uricase treatment, implying the induction of uric acid. these findings suggest that alum adjuvant is immunogenic by exploiting ""nature's adjuvant,"" the inflammatory dc through induction of the endogenous danger signal uric acid.",0
"first released in 2009, metaboanalyst ( was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. with continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. metaboanalyst 2.0, which is the successor to metaboanalyst, represents just such an upgrade. metaboanalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. it also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. these new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. in developing metaboanalyst 2.0 we have also substantially improved its graphical presentation tools. all images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (png, tiff, pdf, postscript, or svg). to improve its performance, metaboanalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server's multi-core cpus for computationally intensive tasks. metaboanalyst 2.0 also maintains a collection of 50 or more faqs and more than a dozen tutorials compiled from user queries and requests. a downloadable version of metaboanalyst 2.0, along detailed instructions for local installation is now available as well.",0
"severe sepsis is a leading cause of death in the united states and the most common cause of death among critically ill patients in non-coronary intensive care units (icu). respiratory tract infections, particularly pneumonia, are the most common site of infection, and associated with the highest mortality. the type of organism causing severe sepsis is an important determinant of outcome, and gram-positive organisms as a cause of sepsis have increased in frequency over time and are now more common than gram-negative infections. recent studies suggest that acute infections worsen pre-existing chronic diseases or result in new chronic diseases, leading to poor long-term outcomes in acute illness survivors. people of older age, male gender, black race, and preexisting chronic health conditions are particularly prone to develop severe sepsis; hence prevention strategies should be targeted at these vulnerable populations in future studies.",0
"the connection matrix of the human brain (the human ""connectome"") represents an indispensable foundation for basic and applied neurobiological research. however, the network of anatomical connections linking the neuronal elements of the human brain is still largely unknown. while some databases or collations of large-scale anatomical connection patterns exist for other mammalian species, there is currently no connection matrix of the human brain, nor is there a coordinated research effort to collect, archive, and disseminate this important information. we propose a research strategy to achieve this goal, and discuss its potential impact.",0
"placental transfer of maternal igg antibodies to the fetus is an important mechanism that provides protection to the infant while his/her humoral response is inefficient. igg is the only antibody class that significantly crosses the human placenta. this crossing is mediated by fcrn expressed on syncytiotrophoblast cells. there is evidence that igg transfer depends on the following: (i) maternal levels of total igg and specific antibodies, (ii) gestational age, (iii) placental integrity, (iv) igg subclass, and (v) nature of antigen, being more intense for thymus-dependent ones. these features represent the basis for maternal immunization strategies aimed at protecting newborns against neonatal and infantile infectious diseases. in some situations, such as mothers with primary immunodeficiencies, exogenous igg acquired by intravenous immunoglobulin therapy crosses the placenta in similar patterns to endogenous immunoglobulins and may also protect the offspring from infections in early life. inversely, harmful autoantibodies may cross the placenta and cause transitory autoimmune disease in the neonate.",0
"the human gastrointestinal tract is colonised by a complex ecosystem of microorganisms. intestinal bacteria are not only commensal, but they also undergo a synbiotic co-evolution along with their host. beneficial intestinal bacteria have numerous and important functions, e.g., they produce various nutrients for their host, prevent infections caused by intestinal pathogens, and modulate a normal immunological response. therefore, modification of the intestinal microbiota in order to achieve, restore, and maintain favourable balance in the ecosystem, and the activity of microorganisms present in the gastrointestinal tract is necessary for the improved health condition of the host. the introduction of probiotics, prebiotics, or synbiotics into human diet is favourable for the intestinal microbiota. they may be consumed in the form of raw vegetables and fruit, fermented pickles, or dairy products. another source may be pharmaceutical formulas and functional food. this paper provides a review of available information and summarises the current knowledge on the effects of probiotics, prebiotics, and synbiotics on human health. the mechanism of beneficial action of those substances is discussed, and verified study results proving their efficacy in human nutrition are presented.",0
"the task of developing a new questionnaire or translating an existing questionnaire into a different language might be overwhelming. the greatest challenge perhaps is to come up with a questionnaire that is psychometrically sound, and is efficient and effective for use in research and clinical settings. this article provides guidelines for the development and translation of questionnaires for application in medical fields, with a special emphasis on perioperative and pain medicine. we provide a framework to guide researchers through the various stages of questionnaire development and translation. to ensure that the questionnaires are psychometrically sound, we present a number of statistical methods to assess the reliability and validity of the questionnaires.",0
"cloned cd4 t cell lines that recognize the ac1-16 peptide of myelin basic protein bound to i-au were isolated and used to analyze the immunopathogenesis of experimental autoimmune encephalomyelitis (eae). t helper type 1 (th1) clones induced disease, while th2 clones did not. using variants of a single cloned th1 line, the surface expression of alpha 4 integrins (very late antigen 4 ) was identified as a major pathogenic factor. encephalitogenic clones and nonencephalitogenic variants differ by 10-fold in their level of surface expression of alpha 4 integrin and in their ability to bind to endothelial cells and recombinant vascular cell adhesion molecule 1 (vcam-1). the alpha 4 integrin-high, disease-inducing cloned th1 t cells enter brain parenchyma in abundance, while alpha 4 integrin-low, nonencephalitogenic th1 cells do not. moreover, antibodies to alpha 4 integrin, its ligand vcam-1, and intercellular adhesion molecule 1 all influence the pathogenicity of this encephalitogenic clone in vivo. the importance of the expression of vla-4 for encephalitogenicity is not unique to cloned t cell lines, as similar results were obtained using myelin basic protein-primed lymph node t cells. alpha 4 integrin levels did not affect antigen responsiveness or production of the th1 cytokines interleukin 2, interferon gamma, and lymphotoxin/tumor necrosis factor beta; and antibodies against alpha 4 integrin did not block antigen recognition in vitro. thus, we conclude that surface expression of alpha 4 integrin is important in cd4 t cell entry into brain parenchyma. a general conclusion of these studies is that alpha 4 integrins may be crucial in allowing activated effector t cells to leave blood and enter the brain and other tissues to clear infections.",0
"the eskape pathogens (enterococcus faecium, staphylococcus aureus, klebsiella pneumoniae, acinetobacter baumannii, pseudomonas aeruginosa, and enterobacter species) are the leading cause of nosocomial infections throughout the world. most of them are multidrug resistant isolates, which is one of the greatest challenges in clinical practice. multidrug resistance is amongst the top three threats to global public health and is usually caused by excessive drug usage or prescription, inappropriate use of antimicrobials, and substandard pharmaceuticals. understanding the resistance mechanisms of these bacteria is crucial for the development of novel antimicrobial agents or other alternative tools to combat these public health challenges. greater mechanistic understanding would also aid in the prediction of underlying or even unknown mechanisms of resistance, which could be applied to other emerging multidrug resistant pathogens. in this review, we summarize the known antimicrobial resistance mechanisms of eskape pathogens.",0
"gold nanoparticles have attracted enormous scientific and technological interest due to their ease of synthesis, chemical stability, and unique optical properties. proof-of-concept studies demonstrate their biomedical applications in chemical sensing, biological imaging, drug delivery, and cancer treatment. knowledge about their potential toxicity and health impact is essential before these nanomaterials can be used in real clinical settings. furthermore, the underlying interactions of these nanomaterials with physiological fluids is a key feature of understanding their biological impact, and these interactions can perhaps be exploited to mitigate unwanted toxic effects. in this perspective we discuss recent results that address the toxicity of gold nanoparticles both in vitro and in vivo, and we provide some experimental recommendations for future research at the interface of nanotechnology and biological systems.",0
"sequence-specific nucleases represent valuable tools for precision genome engineering. traditionally, zinc-finger nucleases (zfns) and meganucleases have been used to specifically edit complex genomes. recently, the dna binding domains of transcription activator-like effectors (tales) from the bacterial pathogen xanthomonas have been harnessed to direct nuclease domains to desired genomic loci. in this study, we tested a panel of truncation variants based on the tale protein avrbs4 to identify tale nucleases (talens) with high dna cleavage activity. the most favorable parameters for efficient dna cleavage were determined in vitro and in cellular reporter assays. talens were designed to disrupt an egfp marker gene and the human loci ccr5 and il2rg. gene editing was achieved in up to 45% of transfected cells. a side-by-side comparison with zfns showed similar gene disruption activities by talens but significantly reduced nuclease-associated cytotoxicities. moreover, the ccr5-specific talen revealed only minimal off-target activity at the ccr2 locus as compared to the corresponding zfn, suggesting that the talen platform enables the design of nucleases with single-nucleotide specificity. the combination of high nuclease activity with reduced cytotoxicity and the simple design process marks talens as a key technology platform for targeted modifications of complex genomes.",0
"background curcumin is the major yellow pigment extracted from turmeric, a commonly-used spice in india and southeast asia that has broad anticarcinogenic and cancer chemopreventive potential. however, few systematic studies of curcumin's pharmacology and toxicology in humans have been performed. methods a dose escalation study was conducted to determine the maximum tolerated dose and safety of a single dose of standardized powder extract, uniformly milled curcumin (c3 complextrade mark, sabinsa corporation). healthy volunteers were administered escalating doses from 500 to 12,000 mg. results seven of twenty-four subjects (30%) experienced only minimal toxicity that did not appear to be dose-related. no curcumin was detected in the serum of subjects administered 500, 1,000, 2,000, 4,000, 6,000 or 8,000 mg. low levels of curcumin were detected in two subjects administered 10,000 or 12,000 mg. conclusion the tolerance of curcumin in high single oral doses appears to be excellent. given that achieving systemic bioavailability of curcumin or its metabolites may not be essential for colorectal cancer chemoprevention, these findings warrant further investigation for its utility as a long-term chemopreventive agent.",0
"background the lifetime risk of stroke has been calculated in a limited number of selected populations. we sought to estimate the lifetime risk of stroke at the regional, country, and global level using data from a comprehensive study of the prevalence of major diseases. methods we used the global burden of disease (gbd) study 2016 estimates of stroke incidence and the competing risks of death from any cause other than stroke to calculate the cumulative lifetime risks of first stroke, ischemic stroke, or hemorrhagic stroke among adults 25 years of age or older. estimates of the lifetime risks in the years 1990 and 2016 were compared. countries were categorized into quintiles of the sociodemographic index (sdi) used in the gbd study, and the risks were compared across quintiles. comparisons were made with the use of point estimates and uncertainty intervals representing the 2.5th and 97.5th percentiles around the estimate. results the estimated global lifetime risk of stroke from the age of 25 years onward was 24.9% (95% uncertainty interval, 23.5 to 26.2); the risk among men was 24.7% (95% uncertainty interval, 23.3 to 26.0), and the risk among women was 25.1% (95% uncertainty interval, 23.7 to 26.5). the risk of ischemic stroke was 18.3%, and the risk of hemorrhagic stroke was 8.2%. in high-sdi, high-middle-sdi, and low-sdi countries, the estimated lifetime risk of stroke was 23.5%, 31.1% (highest risk), and 13.2% (lowest risk), respectively; the 95% uncertainty intervals did not overlap between these categories. the highest estimated lifetime risks of stroke according to gbd region were in east asia (38.8%), central europe (31.7%), and eastern europe (31.6%), and the lowest risk was in eastern sub-saharan africa (11.8%). the mean global lifetime risk of stroke increased from 22.8% in 1990 to 24.9% in 2016, a relative increase of 8.9% (95% uncertainty interval, 6.2 to 11.5); the competing risk of death from any cause other than stroke was considered in this calculation. conclusions in 2016, the global lifetime risk of stroke from the age of 25 years onward was approximately 25% among both men and women. there was geographic variation in the lifetime risk of stroke, with the highest risks in east asia, central europe, and eastern europe. (funded by the bill and melinda gates foundation.).",0
"jaspar ( is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. the fifth major release greatly expands the heart of jaspar-the jaspar core subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in drosophila melanogaster, 10 in caenorhabditis elegans and 43 in arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in d. melanogaster and 4 in a. thaliana; a 9% update in total). the new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. in addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. finally, the new jaspar release is accompanied by a new biopython package, a new r tool package and a new r/bioconductor data package to facilitate access for both manual and automated methods.",0
"background raised blood pressure is an important risk factor for cardiovascular diseases and chronic kidney disease. we estimated worldwide trends in mean systolic and mean diastolic blood pressure, and the prevalence of, and number of people with, raised blood pressure, defined as systolic blood pressure of 140 mm hg or higher or diastolic blood pressure of 90 mm hg or higher. methods for this analysis, we pooled national, subnational, or community population-based studies that had measured blood pressure in adults aged 18 years and older. we used a bayesian hierarchical model to estimate trends from 1975 to 2015 in mean systolic and mean diastolic blood pressure, and the prevalence of raised blood pressure for 200 countries. we calculated the contributions of changes in prevalence versus population growth and ageing to the increase in the number of adults with raised blood pressure. findings we pooled 1479 studies that had measured the blood pressures of 19·1 million adults. global age-standardised mean systolic blood pressure in 2015 was 127·0 mm hg (95% credible interval 125·7-128·3) in men and 122·3 mm hg (121·0-123·6) in women; age-standardised mean diastolic blood pressure was 78·7 mm hg (77·9-79·5) for men and 76·7 mm hg (75·9-77·6) for women. global age-standardised prevalence of raised blood pressure was 24·1% (21·4-27·1) in men and 20·1% (17·8-22·5) in women in 2015. mean systolic and mean diastolic blood pressure decreased substantially from 1975 to 2015 in high-income western and asia pacific countries, moving these countries from having some of the highest worldwide blood pressure in 1975 to the lowest in 2015. mean blood pressure also decreased in women in central and eastern europe, latin america and the caribbean, and, more recently, central asia, middle east, and north africa, but the estimated trends in these super-regions had larger uncertainty than in high-income super-regions. by contrast, mean blood pressure might have increased in east and southeast asia, south asia, oceania, and sub-saharan africa. in 2015, central and eastern europe, sub-saharan africa, and south asia had the highest blood pressure levels. prevalence of raised blood pressure decreased in high-income and some middle-income countries; it remained unchanged elsewhere. the number of adults with raised blood pressure increased from 594 million in 1975 to 1·13 billion in 2015, with the increase largely in low-income and middle-income countries. the global increase in the number of adults with raised blood pressure is a net effect of increase due to population growth and ageing, and decrease due to declining age-specific prevalence. interpretation during the past four decades, the highest worldwide blood pressure levels have shifted from high-income countries to low-income countries in south asia and sub-saharan africa due to opposite trends, while blood pressure has been persistently high in central and eastern europe. funding wellcome trust.",0
"background extracellular matrix (ecm) is a dynamic and complex environment characterized by biophysical, mechanical and biochemical properties specific for each tissue and able to regulate cell behavior. stem cells have a key role in the maintenance and regeneration of tissues and they are located in a specific microenvironment, defined as niche. scope of review we overview the progresses that have been made in elucidating stem cell niches and discuss the mechanisms by which ecm affects stem cell behavior. we also summarize the current tools and experimental models for studying ecm-stem cell interactions. major conclusions ecm represents an essential player in stem cell niche, since it can directly or indirectly modulate the maintenance, proliferation, self-renewal and differentiation of stem cells. several ecm molecules play regulatory functions for different types of stem cells, and based on its molecular composition the ecm can be deposited and finely tuned for providing the most appropriate niche for stem cells in the various tissues. engineered biomaterials able to mimic the in vivo characteristics of stem cell niche provide suitable in vitro tools for dissecting the different roles exerted by the ecm and its molecular components on stem cell behavior. general significance ecm is a key component of stem cell niches and is involved in various aspects of stem cell behavior, thus having a major impact on tissue homeostasis and regeneration under physiological and pathological conditions. this article is part of a special issue entitled matrix-mediated cell behaviour and properties.",0
"macroautophagy, which is a lysosomal pathway for the turnover of organelles and long-lived proteins, is a key determinant of cell survival and longevity. in this study, we show that neuronal macroautophagy is induced early in alzheimer's disease (ad) and before beta-amyloid (abeta) deposits extracellularly in the presenilin (ps) 1/abeta precursor protein (app) mouse model of beta-amyloidosis. subsequently, autophagosomes and late autophagic vacuoles (avs) accumulate markedly in dystrophic dendrites, implying an impaired maturation of avs to lysosomes. immunolabeling identifies avs in the brain as a major reservoir of intracellular abeta. purified avs contain app and beta-cleaved app and are highly enriched in ps1, nicastrin, and ps-dependent gamma-secretase activity. inducing or inhibiting macroautophagy in neuronal and nonneuronal cells by modulating mammalian target of rapamycin kinase elicits parallel changes in av proliferation and abeta production. our results, therefore, link beta-amyloidogenic and cell survival pathways through macroautophagy, which is activated and is abnormal in ad.",0
"functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. it is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. to meet these requirements, we present here an updated version of our popular bioconductor package, clusterprofiler 4.0. this package has been enhanced considerably compared with its original version published 9 years ago. the new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. it also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization. other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. we anticipate that clusterprofiler 4.0 will be applied to a wide range of scenarios across diverse organisms.",0
"this guidance describes how the fda evaluates patient-reported outcome (pro) instruments used as effectiveness endpoints in clinical trials. it also describes our current thinking on how sponsors can develop and use study results measured by pro instruments to support claims in approved product labeling (see appendix point 1). it does not address the use of pro instruments for purposes beyond evaluation of claims made about a drug or medical product in its labeling. by explicitly addressing the review issues identified in this guidance, sponsors can increase the efficiency of their endpoint discussions with the fda during the product development process, streamline the fda's review of pro endpoint adequacy, and provide optimal information about the patient's perspective of treatment benefit at the time of product approval. a pro is a measurement of any aspect of a patient's health status that comes directly from the patient (i.e., without the interpretation of the patient's responses by a physician or anyone else). in clinical trials, a pro instrument can be used to measure the impact of an intervention on one or more aspects of patients' health status, hereafter referred to as pro concepts, ranging from the purely symptomatic (response of a headache) to more complex concepts (e.g., ability to carry out activities of daily living), to extremely complex concepts such as quality of life, which is widely understood to be a multidomain concept with physical, psychological, and social components. data generated by a pro instrument can provide evidence of a treatment benefit from the patient perspective. for this data to be meaningful, however, there should be evidence that the pro instrument effectively measures the particular concept that is studied. generally, findings measured by pro instruments may be used to support claims in approved product labeling if the claims are derived from adequate and well-controlled investigations that use pro instruments that reliably and validly measure the specific concepts at issue. the glossary defines many of the terms used in this guidance. in particular, the term instrument refers to the actual questions or items contained in a questionnaire or interview schedule along with all the additional information and documentation that supports the use of these items in producing a pro measure (e.g., interviewer training and instructions, scoring and interpretation manual). the term conceptual framework refers to how items are grouped according to subconcepts or domains (e.g., the item walking without help may be grouped with another item, walking with difficulty, within the domain of ambulation, and ambulation may be further grouped into the concept of physical ability). fda's guidance documents, including this guidance, do not establish legally enforceable responsibilities. instead, guidance documents describe the agency's current thinking on a topic and should be viewed only as recommendations, unless specific regulatory or statutory requirements are cited. the use of the word should in agency guidance documents means that something is suggested or recommended but not required. first publication of the draft guidance by the food and drug administration--february 2006.",0
"macropinocytosis is a highly conserved endocytic process by which extracellular fluid and its contents are internalized into cells through large, heterogeneous vesicles known as macropinosomes. oncogenic ras proteins have been shown to stimulate macropinocytosis but the functional contribution of this uptake mechanism to the transformed phenotype remains unknown. here we show that ras-transformed cells use macropinocytosis to transport extracellular protein into the cell. the internalized protein undergoes proteolytic degradation, yielding amino acids including glutamine that can enter central carbon metabolism. accordingly, the dependence of ras-transformed cells on free extracellular glutamine for growth can be suppressed by the macropinocytic uptake of protein. consistent with macropinocytosis representing an important route of nutrient uptake in tumours, its pharmacological inhibition compromises the growth of ras-transformed pancreatic tumour xenografts. these results identify macropinocytosis as a mechanism by which cancer cells support their unique metabolic needs and point to the possible exploitation of this process in the design of anticancer therapies.",0
"even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. here, we describe a major upgrade to eggnog-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. improvements in version 2 include a full update of both the genomes and functional databases to those from eggnog v5, as well as several efficiency enhancements and new features. most notably, eggnog-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated gff decoration. eggnog-mapper v2 is available as a standalone tool or as an online service at",0
"in order to understand the working brain as a network, it is essential to identify the mechanisms by which information is gated between regions. we here propose that information is gated by inhibiting task-irrelevant regions, thus routing information to task-relevant regions. the functional inhibition is reflected in oscillatory activity in the alpha band (8-13 hz). from a physiological perspective the alpha activity provides pulsed inhibition reducing the processing capabilities of a given area. active processing in the engaged areas is reflected by neuronal synchronization in the gamma band (30-100 hz) accompanied by an alpha band decrease. according to this framework the brain could be studied as a network by investigating cross-frequency interactions between gamma and alpha activity. specifically the framework predicts that optimal task performance will correlate with alpha activity in task-irrelevant areas. in this review we will discuss the empirical support for this framework. given that alpha activity is by far the strongest signal recorded by eeg and meg, we propose that a major part of the electrophysiological activity detected from the working brain reflects gating by inhibition.",0
"background cardiovascular disease (cvd) is a common comorbidity in type 2 diabetes (t2dm). cvd's prevalence has been growing over time. purpose to estimate the current prevalence of cvd among adults with t2dm by reviewing literature published within the last 10 years (2007-march 2017). methods we searched medline, embase, and proceedings of major scientific meetings for original research documenting the prevalence of cvd in t2dm. cvd included stroke, myocardial infarction, angina pectoris, heart failure, ischemic heart disease, cardiovascular disease, coronary heart disease, atherosclerosis, and cardiovascular death. no restrictions were placed on country of origin or publication language. two reviewers independently searched for articles and extracted data, adjudicating results through consensus. data were summarized descriptively. risk of bias was examined by applying the strobe checklist. results we analyzed data from 57 articles with 4,549,481 persons having t2dm. europe produced the most articles (46%), followed by the western pacific/china (21%), and north america (13%). overall in 4,549,481 persons with t2dm, 52.0% were male, 47.0% were obese, aged 63.6 ± 6.9 years old, with t2dm duration of 10.4 ± 3.7 years. cvd affected 32.2% overall (53 studies, n = 4,289,140); 29.1% had atherosclerosis (4 studies, n = 1153), 21.2% had coronary heart disease (42 articles, n = 3,833,200), 14.9% heart failure (14 studies, n = 601,154), 14.6% angina (4 studies, n = 354,743), 10.0% myocardial infarction (13 studies, n = 3,518,833) and 7.6% stroke (39 studies, n = 3,901,505). cvd was the cause of death in 9.9% of t2dm patients (representing 50.3% of all deaths). risk of bias was low; 80 ± 12% of strobe checklist items were adequately addressed. conclusions globally, overall cvd affects approximately 32.2% of all persons with t2dm. cvd is a major cause of mortality among people with t2dm, accounting for approximately half of all deaths over the study period. coronary artery disease and stroke were the major contributors.",0
"relion, for regularized likelihood optimization, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-em) data. whereas alternative approaches often rely on user expertise for the tuning of parameters, relion uses a bayesian approach to infer parameters of a statistical model from the data. this paper describes developments that reduce the computational costs of the underlying maximum a posteriori (map) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. a so-called gold-standard fourier shell correlation (fsc) procedure to prevent overfitting is also described. the resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.",0
"background mortality statistics are fundamental to public health decision making. mortality varies by time and location, and its measurement is affected by well known biases that have been exacerbated during the covid-19 pandemic. this paper aims to estimate excess mortality from the covid-19 pandemic in 191 countries and territories, and 252 subnational units for selected countries, from jan 1, 2020, to dec 31, 2021. methods all-cause mortality reports were collected for 74 countries and territories and 266 subnational locations (including 31 locations in low-income and middle-income countries) that had reported either weekly or monthly deaths from all causes during the pandemic in 2020 and 2021, and for up to 11 year previously. in addition, we obtained excess mortality data for 12 states in india. excess mortality over time was calculated as observed mortality, after excluding data from periods affected by late registration and anomalies such as heat waves, minus expected mortality. six models were used to estimate expected mortality; final estimates of expected mortality were based on an ensemble of these models. ensemble weights were based on root mean squared errors derived from an out-of-sample predictive validity test. as mortality records are incomplete worldwide, we built a statistical model that predicted the excess mortality rate for locations and periods where all-cause mortality data were not available. we used least absolute shrinkage and selection operator (lasso) regression as a variable selection mechanism and selected 15 covariates, including both covariates pertaining to the covid-19 pandemic, such as seroprevalence, and to background population health metrics, such as the healthcare access and quality index, with direction of effects on excess mortality concordant with a meta-analysis by the us centers for disease control and prevention. with the selected best model, we ran a prediction process using 100 draws for each covariate and 100 draws of estimated coefficients and residuals, estimated from the regressions run at the draw level using draw-level input data on both excess mortality and covariates. mean values and 95% uncertainty intervals were then generated at national, regional, and global levels. out-of-sample predictive validity testing was done on the basis of our final model specification. findings although reported covid-19 deaths between jan 1, 2020, and dec 31, 2021, totalled 5·94 million worldwide, we estimate that 18·2 million (95% uncertainty interval 17·1-19·6) people died worldwide because of the covid-19 pandemic (as measured by excess mortality) over that period. the global all-age rate of excess mortality due to the covid-19 pandemic was 120·3 deaths (113·1-129·3) per 100 000 of the population, and excess mortality rate exceeded 300 deaths per 100 000 of the population in 21 countries. the number of excess deaths due to covid-19 was largest in the regions of south asia, north africa and the middle east, and eastern europe. at the country level, the highest numbers of cumulative excess deaths due to covid-19 were estimated in india (4·07 million ), the usa (1·13 million ), russia (1·07 million ), mexico (798 000 ), brazil (792 000 ), indonesia (736 000 ), and pakistan (664 000 ). among these countries, the excess mortality rate was highest in russia (374·6 deaths per 100 000) and mexico (325·1 per 100 000), and was similar in brazil (186·9 per 100 000) and the usa (179·3 per 100 000). interpretation the full impact of the pandemic has been much greater than what is indicated by reported deaths due to covid-19 alone. strengthening death registration systems around the world, long understood to be crucial to global public health strategy, is necessary for improved monitoring of this pandemic and future pandemics. in addition, further research is warranted to help distinguish the proportion of excess mortality that was directly caused by sars-cov-2 infection and the changes in causes of death as an indirect consequence of the pandemic. funding bill & melinda gates foundation, j stanton, t gillespie, and j and e nordstrom.",0
"background isolation of extracellular vesicles from plasma is a challenge due to the presence of proteins and lipoproteins. isolation of vesicles using differential centrifugation or density-gradient ultracentrifugation results in co-isolation of contaminants such as protein aggregates and incomplete separation of vesicles from lipoproteins, respectively. aim to develop a single-step protocol to isolate vesicles from human body fluids. methods platelet-free supernatant, derived from platelet concentrates, was loaded on a sepharose cl-2b column to perform size-exclusion chromatography (sec; n=3). fractions were collected and analysed by nanoparticle tracking analysis, resistive pulse sensing, flow cytometry and transmission electron microscopy. the concentrations of high-density lipoprotein cholesterol (hdl) and protein were measured in each fraction. results fractions 9-12 contained the highest concentrations of particles larger than 70 nm and platelet-derived vesicles (46%±6 and 61%±2 of totals present in all collected fractions, respectively), but less than 5% of hdl and less than 1% of protein (4.8%±1 and 0.65%±0.3, respectively). hdl was present mainly in fractions 18-20 (32%±2 of total), and protein in fractions 19-21 (36%±2 of total). compared to the starting material, recovery of platelet-derived vesicles was 43%±23 in fractions 9-12, with an 8-fold and 70-fold enrichment compared to hdl and protein. conclusions sec efficiently isolates extracellular vesicles with a diameter larger than 70 nm from platelet-free supernatant of platelet concentrates. application sec will improve studies on the dimensional, structural and functional properties of extracellular vesicles.",0
"although mast cell functions have classically been related to allergic responses, recent studies indicate that these cells contribute to other common diseases such as multiple sclerosis, rheumatoid arthritis, atherosclerosis, aortic aneurysm and cancer. this study presents evidence that mast cells also contribute to diet-induced obesity and diabetes. for example, white adipose tissue (wat) from obese humans and mice contain more mast cells than wat from their lean counterparts. furthermore, in the context of mice on a western diet, genetically induced deficiency of mast cells, or their pharmacological stabilization, reduces body weight gain and levels of inflammatory cytokines, chemokines and proteases in serum and wat, in concert with improved glucose homeostasis and energy expenditure. mechanistic studies reveal that mast cells contribute to wat and muscle angiogenesis and associated cell apoptosis and cathepsin activity. adoptive transfer experiments of cytokine-deficient mast cells show that these cells, by producing interleukin-6 (il-6) and interferon-gamma (ifn-gamma), contribute to mouse adipose tissue cysteine protease cathepsin expression, apoptosis and angiogenesis, thereby promoting diet-induced obesity and glucose intolerance. our results showing reduced obesity and diabetes in mice treated with clinically available mast cell-stabilizing agents suggest the potential of developing new therapies for these common human metabolic disorders.",0
"some recent studies suggest that in progressive multiple sclerosis, neurodegeneration may occur independently from inflammation. the aim of our study was to analyse the interdependence of inflammation, neurodegeneration and disease progression in various multiple sclerosis stages in relation to lesional activity and clinical course, with a particular focus on progressive multiple sclerosis. the study is based on detailed quantification of different inflammatory cells in relation to axonal injury in 67 multiple sclerosis autopsies from different disease stages and 28 controls without neurological disease or brain lesions. we found that pronounced inflammation in the brain is not only present in acute and relapsing multiple sclerosis but also in the secondary and primary progressive disease. t- and b-cell infiltrates correlated with the activity of demyelinating lesions, while plasma cell infiltrates were most pronounced in patients with secondary progressive multiple sclerosis (spms) and primary progressive multiple sclerosis (ppms) and even persisted, when t- and b-cell infiltrates declined to levels seen in age matched controls. a highly significant association between inflammation and axonal injury was seen in the global multiple sclerosis population as well as in progressive multiple sclerosis alone. in older patients (median 76 years) with long-disease duration (median 372 months), inflammatory infiltrates declined to levels similar to those found in age-matched controls and the extent of axonal injury, too, was comparable with that in age-matched controls. ongoing neurodegeneration in these patients, which exceeded the extent found in normal controls, could be attributed to confounding pathologies such as alzheimer's or vascular disease. our study suggests a close association between inflammation and neurodegeneration in all lesions and disease stages of multiple sclerosis. it further indicates that the disease processes of multiple sclerosis may die out in aged patients with long-standing disease.",0
"context it is well established in the literature that healthier diets cost more than unhealthy diets. objective the aim of this review was to examine the contribution of food prices and diet cost to socioeconomic inequalities in diet quality. data sources a systematic literature search of the pubmed, google scholar, and web of science databases was performed. study selection publications linking food prices, dietary quality, and socioeconomic status were selected. data extraction where possible, review conclusions were illustrated using a french national database of commonly consumed foods and their mean retail prices. data synthesis foods of lower nutritional value and lower-quality diets generally cost less per calorie and tended to be selected by groups of lower socioeconomic status. a number of nutrient-dense foods were available at low cost but were not always palatable or culturally acceptable to the low-income consumer. acceptable healthier diets were uniformly associated with higher costs. food budgets in poverty were insufficient to ensure optimum diets. conclusions socioeconomic disparities in diet quality may be explained by the higher cost of healthy diets. identifying food patterns that are nutrient rich, affordable, and appealing should be a priority to fight social inequalities in nutrition and health.",0
"this paper reports and analyses the species diversity of vegetation in different environmental gradient in daming mountain. the results showed that the environmental heterogineity on the time and space is of great advantage to increasing species diversity, but its increase is nonlinear. the humans disturbance is advantageous to developing of species that life period are shorter and disadvantage to species that life period are longer. the same species in communities increase, similarity decrease and beta diversity increase with increasing of the environmental gradient.",0
"chronic obstructive pulmonary disease (copd) is characterised by progressive airflow obstruction that is only partly reversible, inflammation in the airways, and systemic effects or comorbities. the main cause is smoking tobacco, but other factors have been identified. several pathobiological processes interact on a complex background of genetic determinants, lung growth, and environmental stimuli. the disease is further aggravated by exacerbations, particularly in patients with severe disease, up to 78% of which are due to bacterial infections, viral infections, or both. comorbidities include ischaemic heart disease, diabetes, and lung cancer. bronchodilators constitute the mainstay of treatment: β(2) agonists and long-acting anticholinergic agents are frequently used (the former often with inhaled corticosteroids). besides improving symptoms, these treatments are also thought to lead to some degree of disease modification. future research should be directed towards the development of agents that notably affect the course of disease.",0
"background random forests are becoming increasingly popular in many scientific fields because they can cope with ""small n large p"" problems, complex interactions and even highly correlated predictor variables. their variable importance measures have recently been suggested as screening tools for, e.g., gene expression studies. however, these variable importance measures show a bias towards correlated predictor variables. results we identify two mechanisms responsible for this finding: (i) a preference for the selection of correlated predictors in the tree building process and (ii) an additional advantage for correlated predictor variables induced by the unconditional permutation scheme that is employed in the computation of the variable importance measure. based on these considerations we develop a new, conditional permutation scheme for the computation of the variable importance measure. conclusion the resulting conditional variable importance reflects the true impact of each predictor variable more reliably than the original marginal approach.",0
"t lymphocytes expressing the t cell receptor (tcr)-gammadelta recognize unknown antigens on tumor cells. here we identify metabolites of the mevalonate pathway as the tumor ligands that activate tcr-gammadelta cells. in tumor cells, blockade of hydroxy-methylglutaryl-coa reductase (hmgr), the rate limiting enzyme of the mevalonate pathway, prevents both accumulation of mevalonate metabolites and recognition by tcr-gammadelta cells. when metabolite accumulation is induced by overexpressing hmgr or by treatment with nitrogen-containing bisphosphonate drugs, tumor cells derived from many tissues acquire the capacity to stimulate the same tcr-gammadelta population. accumulation of mevalonate metabolites in tumor cells is a powerful danger signal that activates the immune response and may represent a novel target of tumor immunotherapy.",0
"cannabis sativa l. is an important herbaceous species originating from central asia, which has been used in folk medicine and as a source of textile fiber since the dawn of times. this fast-growing plant has recently seen a resurgence of interest because of its multi-purpose applications: it is indeed a treasure trove of phytochemicals and a rich source of both cellulosic and woody fibers. equally highly interested in this plant are the pharmaceutical and construction sectors, since its metabolites show potent bioactivities on human health and its outer and inner stem tissues can be used to make bioplastics and concrete-like material, respectively. in this review, the rich spectrum of hemp phytochemicals is discussed by putting a special emphasis on molecules of industrial interest, including cannabinoids, terpenes and phenolic compounds, and their biosynthetic routes. cannabinoids represent the most studied group of compounds, mainly due to their wide range of pharmaceutical effects in humans, including psychotropic activities. the therapeutic and commercial interests of some terpenes and phenolic compounds, and in particular stilbenoids and lignans, are also highlighted in view of the most recent literature data. biotechnological avenues to enhance the production and bioactivity of hemp secondary metabolites are proposed by discussing the power of plant genetic engineering and tissue culture. in particular two systems are reviewed, i.e., cell suspension and hairy root cultures. additionally, an entire section is devoted to hemp trichomes, in the light of their importance as phytochemical factories. ultimately, prospects on the benefits linked to the use of the -omics technologies, such as metabolomics and transcriptomics to speed up the identification and the large-scale production of lead agents from bioengineered cannabis cell culture, are presented.",0
"objective to examine the psychological effects on clinicians of working to manage novel viral outbreaks, and successful measures to manage stress and psychological distress. design rapid review and meta-analysis. data sources cochrane central register of controlled trials, pubmed/medline, psycinfo, scopus, web of science, embase, and google scholar, searched up to late march 2020. eligibility criteria for study selection any study that described the psychological reactions of healthcare staff working with patients in an outbreak of any emerging virus in any clinical setting, irrespective of any comparison with other clinicians or the general population. results 59 papers met the inclusion criteria: 37 were of severe acute respiratory syndrome (sars), eight of coronavirus disease 2019 (covid-19), seven of middle east respiratory syndrome (mers), three each of ebola virus disease and influenza a virus subtype h1n1, and one of influenza a virus subtype h7n9. of the 38 studies that compared psychological outcomes of healthcare workers in direct contact with affected patients, 25 contained data that could be combined in a pairwise meta-analysis comparing healthcare workers at high and low risk of exposure. compared with lower risk controls, staff in contact with affected patients had greater levels of both acute or post-traumatic stress (odds ratio 1.71, 95% confidence interval 1.28 to 2.29) and psychological distress (1.74, 1.50 to 2.03), with similar results for continuous outcomes. these findings were the same as in the other studies not included in the meta-analysis. risk factors for psychological distress included being younger, being more junior, being the parents of dependent children, or having an infected family member. longer quarantine, lack of practical support, and stigma also contributed. clear communication, access to adequate personal protection, adequate rest, and both practical and psychological support were associated with reduced morbidity. conclusions effective interventions are available to help mitigate the psychological distress experienced by staff caring for patients in an emerging disease outbreak. these interventions were similar despite the wide range of settings and types of outbreaks covered in this review, and thus could be applicable to the current covid-19 outbreak.",0
"somatically acquired epigenetic changes are present in many cancers. epigenetic regulation is maintained via post-translational modifications of core histones. here, we describe inactivating somatic mutations in the histone lysine demethylase gene utx, pointing to histone h3 lysine methylation deregulation in multiple tumor types. utx reintroduction into cancer cells with inactivating utx mutations resulted in slowing of proliferation and marked transcriptional changes. these data identify utx as a new human cancer gene.",0
"background although guidelines for critical appraisal of diagnostic research and meta-analyses have already been published, these may be difficult to understand for clinical researchers or do not provide enough detailed information. methods development of guidelines based on a systematic review of the evidence in reports of systematic searches of the literature for diagnostic research, of methodological criteria to evaluate diagnostic research, of methods for statistical pooling of data on diagnostic accuracy, and of methods for exploring heterogeneity. results guidelines for conducting diagnostic systematic reviews are presented in a stepwise fashion and are followed by comments providing further information. examples are given using the results of two systematic reviews on the accuracy of the urine dipstick in the diagnosis of urinary tract infections, and on the accuracy of the straight-leg-raising test in the diagnosis of intervertebral disc hernia.",0
"we propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-em) density maps that uses local sinusoidal features. our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. by evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-å range.",0
"background coronavirus disease 2019 (covid-19) is a novel infectious disease with lack of established laboratory markers available to evaluate illness severity. in this study, we investigate whether platelet count could differentiate between covid-19 patients with or without severe disease. additionally, we evaluate if thrombocytopenia is associated with severe covid-19. methods an electronic search in medline, scopus and web of science was performed to identify studies reporting data on platelet count in covid-19 patients. a meta-analysis was performed, with calculation of weighted mean difference (wmd) of platelet number in covid-19 patients with or without severe disease and odds ratio (or) of thrombocytopenia for severe form of covid-19. results nine studies with 1779 covid-19 patients, 399 (22.4%) with severe disease, were included in the meta-analysis. the pooled analysis revealed that platelet count was significantly lower in patients with more severe covid-19 (wmd -31 × 10 9 /l; 95% ci, from -35 to -29 × 10 9 /l). a subgroup analysis comparing patients by survival, found an even lower platelet count was observed with mortality (wmd, -48 × 10 9 /l; 95% ci, -57 to -39 × 10 9 /l. in the four studies (n = 1427) which reported data on rate of thrombocytopenia, a low platelet count was associated with over fivefold enhanced risk of severe covid-19 (or, 5.1; 95% ci, 1.8-14.6). conclusions low platelet count is associated with increased risk of severe disease and mortality in patients with covid-19, and thus should serve as clinical indicator of worsening illness during hospitalization.",0
"the local microenvironment, or niche, of a cancer cell plays important roles in cancer development. a major component of the niche is the extracellular matrix (ecm), a complex network of macromolecules with distinctive physical, biochemical, and biomechanical properties. although tightly controlled during embryonic development and organ homeostasis, the ecm is commonly deregulated and becomes disorganized in diseases such as cancer. abnormal ecm affects cancer progression by directly promoting cellular transformation and metastasis. importantly, however, ecm anomalies also deregulate behavior of stromal cells, facilitate tumor-associated angiogenesis and inflammation, and thus lead to generation of a tumorigenic microenvironment. understanding how ecm composition and topography are maintained and how their deregulation influences cancer progression may help develop new therapeutic interventions by targeting the tumor niche.",0
"multiplexed quantitation via isobaric chemical tags (e.g., tandem mass tags (tmt) and isobaric tags for relative and absolute quantitation (itraq)) has the potential to revolutionize quantitative proteomics. however, until recently the utility of these tags was questionable due to reporter ion ratio distortion resulting from fragmentation of coisolated interfering species. these interfering signals can be negated through additional gas-phase manipulations (e.g., ms/ms/ms (ms3) and proton-transfer reactions (ptr)). these methods, however, have a significant sensitivity penalty. using isolation waveforms with multiple frequency notches (i.e., synchronous precursor selection, sps), we coisolated and cofragmented multiple ms2 fragment ions, thereby increasing the number of reporter ions in the ms3 spectrum 10-fold over the standard ms3 method (i.e., multinotch ms3). by increasing the reporter ion signals, this method improves the dynamic range of reporter ion quantitation, reduces reporter ion signal variance, and ultimately produces more high-quality quantitative measurements. to demonstrate utility, we analyzed biological triplicates of eight colon cancer cell lines using the multinotch ms3 method. across all the replicates we quantified 8,378 proteins in union and 6,168 proteins in common. taking into account that each of these quantified proteins contains eight distinct cell-line measurements, this data set encompasses 174,704 quantitative ratios each measured in triplicate across the biological replicates. herein, we demonstrate that the multinotch ms3 method uniquely combines multiplexing capacity with quantitative sensitivity and accuracy, drastically increasing the informational value obtainable from proteomic experiments.",0
"mendelian randomization-egger (mr-egger) is an analysis method for mendelian randomization using summarized genetic data. mr-egger consists of three parts: (1) a test for directional pleiotropy, (2) a test for a causal effect, and (3) an estimate of the causal effect. while conventional analysis methods for mendelian randomization assume that all genetic variants satisfy the instrumental variable assumptions, the mr-egger method is able to assess whether genetic variants have pleiotropic effects on the outcome that differ on average from zero (directional pleiotropy), as well as to provide a consistent estimate of the causal effect, under a weaker assumption-the inside (instrument strength independent of direct effect) assumption. in this paper, we provide a critical assessment of the mr-egger method with regard to its implementation and interpretation. while the mr-egger method is a worthwhile sensitivity analysis for detecting violations of the instrumental variable assumptions, there are several reasons why causal estimates from the mr-egger method may be biased and have inflated type 1 error rates in practice, including violations of the inside assumption and the influence of outlying variants. the issues raised in this paper have potentially serious consequences for causal inferences from the mr-egger approach. we give examples of scenarios in which the estimates from conventional mendelian randomization methods and mr-egger differ, and discuss how to interpret findings in such cases.",0
"human and mouse lymphoid cells, stimulated by phytohemagglutinin (pha) or lipopolysaccharide w (lps), release supernatant factor(s) which are mitogenic for mouse thymocytes and which potentiate their responses to pha or concanavalin a (con a), the term laf (lymphocyte-activating factor) is proposed for this activity. laf not only enhances the mitotic responses of the less dense thymus subpopulations (a, b, and c) separable on discontinuous bovine serum albumin (bsa) gradients but also gives substantial responses in the otherwise inert cells of the denser fractions d and p. laf does not exert a potentiating stimulatory effect on the responses of unfractionated mouse spleen cells, but does act synergistically with pha on nonadherent spleen cells and on spleen cells of mice of several strains 5 days after irradiation and injection of thymocytes. similarly laf, which has no visible effect on unfractionated human peripheral blood cells, strongly potentiates the pha response of column-purified lymphocytes, when these are cultured at low concentration. we conclude that laf stimulates both central and peripheral t lymphocytes and enhances their responses to other stimulants.",0
"the molecular interaction database (mint, aims at storing, in a structured format, information about molecular interactions (mis) by extracting experimental details from work published in peer-reviewed journals. at present the mint team focuses the curation work on physical interactions between proteins. genetic or computationally inferred interactions are not included in the database. over the past four years mint has undergone extensive revision. the new version of mint is based on a completely remodeled database structure, which offers more efficient data exploration and analysis, and is characterized by entries with a richer annotation. over the past few years the number of curated physical interactions has soared to over 95 000. the whole dataset can be freely accessed online in both interactive and batch modes through web-based interfaces and an ftp server. mint now includes, as an integrated addition, homomint, a database of interactions between human proteins inferred from experiments with ortholog proteins in model organisms (",0
"accurate clinical course descriptions (phenotypes) of multiple sclerosis (ms) are important for communication, prognostication, design and recruitment of clinical trials, and treatment decision-making. standardized descriptions published in 1996 based on a survey of international ms experts provided purely clinical phenotypes based on data and consensus at that time, but imaging and biological correlates were lacking. increased understanding of ms and its pathology, coupled with general concern that the original descriptors may not adequately reflect more recently identified clinical aspects of the disease, prompted a re-examination of ms disease phenotypes by the international advisory committee on clinical trials of ms. while imaging and biological markers that might provide objective criteria for separating clinical phenotypes are lacking, we propose refined descriptors that include consideration of disease activity (based on clinical relapse rate and imaging findings) and disease progression. strategies for future research to better define phenotypes are also outlined.",0
"natural killer (nk) cell-mediated lysis is negatively regulated by killer cell inhibitory receptors specific for major histocompatibility complex (mhc) class i molecules. in this study, we characterize a novel inhibitory mhc class i receptor of the immunoglobulin-superfamily, expressed not only by subsets of nk and t cells, but also by b cells, monocytes, macrophages, and dendritic cells. this receptor, called ig-like transcript (ilt)2, binds mhc class i molecules and delivers a negative signal that inhibits killing by nk and t cells, as well as ca2+ mobilization in b cells and myelomonocytic cells triggered through the b cell antigen receptor and human histocompatibility leukocyte antigens (hla)-dr, respectively. in addition, myelomonocytic cells express receptors homologous to ilt2, which are characterized by extensive polymorphism and might recognize distinct hla class i molecules. these results suggest that diverse leukocyte lineages have adopted recognition of self-mhc class i molecules as a common strategy to control cellular activation during an immune response.",0
"human fas ligand (l) (cd95l) and tumor necrosis factor (tnf)-alpha undergo metalloproteinase-mediated proteolytic processing in their extracellular domains resulting in the release of soluble trimeric ligands (soluble fasl, stnf-alpha) which, in the case of sfasl, is thought to be implicated in diseases such as hepatitis and aids. here we show that the processing of sfasl occurs between ser126 and leu127. the apoptotic-inducing capacity of naturally processed sfasl was reduced by >1,000-fold compared with membrane-bound fasl, and injection of high doses of recombinant sfasl in mice did not induce liver failure. however, soluble fasl retained its capacity to interact with fas, and restoration of its cytotoxic activity was achieved both in vitro and in vivo with the addition of cross-linking antibodies. similarly, the marginal apoptotic activity of recombinant soluble tnf-related apoptosis-inducing ligand (strail), another member of the tnf ligand family, was greatly increased upon cross-linking. these results indicate that the mere trimerization of the fas and trail receptors may not be sufficient to trigger death signals. thus, the observation that sfasl is less cytotoxic than membrane-bound fasl may explain why in certain types of cancer, systemic tissue damage is not detected, even though the levels of circulating sfasl are high.",0
"1. osmotic shock disrupts particles of phage t2 into material containing nearly all the phage sulfur in a form precipitable by antiphage serum, and capable of specific adsorption to bacteria. it releases into solution nearly all the phage dna in a form not precipitable by antiserum and not adsorbable to bacteria. the sulfur-containing protein of the phage particle evidently makes up a membrane that protects the phage dna from dnase, comprises the sole or principal antigenic material, and is responsible for attachment of the virus to bacteria. 2. adsorption of t2 to heat-killed bacteria, and heating or alternate freezing and thawing of infected cells, sensitize the dna of the adsorbed phage to dnase. these treatments have little or no sensitizing effect on unadsorbed phage. neither heating nor freezing and thawing releases the phage dna from infected cells, although other cell constituents can be extracted by these methods. these facts suggest that the phage dna forms part of an organized intracellular structure throughout the period of phage growth. 3. adsorption of phage t2 to bacterial debris causes part of the phage dna to appear in solution, leaving the phage sulfur attached to the debris. another part of the phage dna, corresponding roughly to the remaining half of the dna of the inactivated phage, remains attached to the debris but can be separated from it by dnase. phage t4 behaves similarly, although the two phages can be shown to attach to different combining sites. the inactivation of phage by bacterial debris is evidently accompanied by the rupture of the viral membrane. 4. suspensions of infected cells agitated in a waring blendor release 75 per cent of the phage sulfur and only 15 per cent of the phage phosphorus to the solution as a result of the applied shearing force. the cells remain capable of yielding phage progeny. 5. the facts stated show that most of the phage sulfur remains at the cell surface and most of the phage dna enters the cell on infection. whether sulfur-free material other than dna enters the cell has not been determined. the properties of the sulfur-containing residue identify it as essentially unchanged membranes of the phage particles. all types of evidence show that the passage of phage dna into the cell occurs in non-nutrient medium under conditions in which other known steps in viral growth do not occur. 6. the phage progeny yielded by bacteria infected with phage labeled with radioactive sulfur contain less than 1 per cent of the parental radioactivity. the progeny of phage particles labeled with radioactive phosphorus contain 30 per cent or more of the parental phosphorus. 7. phage inactivated by dilute formaldehyde is capable of adsorbing to bacteria, but does not release its dna to the cell. this shows that the interaction between phage and bacterium resulting in release of the phage dna from its protective membrane depends on labile components of the phage particle. by contrast, the components of the bacterium essential to this interaction are remarkably stable. the nature of the interaction is otherwise unknown. 8. the sulfur-containing protein of resting phage particles is confined to a protective coat that is responsible for the adsorption to bacteria, and functions as an instrument for the injection of the phage dna into the cell. this protein probably has no function in the growth of intracellular phage. the dna has some function. further chemical inferences should not be drawn from the experiments presented.",0
"medium conditioned by chinese hamster ovary (cho) cells transfected with the simian pre-pro-tgf beta 1 cdna contains high levels of latent tgf beta 1. the amino-terminal region of the tgf beta 1 precursor is secreted and can be detected in the conditioned medium by immunoblotting using peptide antibodies specific for amino-terminal peptides. chemical cross-linking of cho-conditioned medium using bis-(sulfosuccinimidyl)-suberate (bs3) followed by immunoblot analyses indicates that latent recombinant tgf beta 1 contains both the cleaved amino-terminal glycopeptide and mature tgf beta 1 polypeptide in a noncovalent association and that this association confers latency. the data presented here do not support the involvement of a unique tgf beta binding protein(s) in latent recombinant tgf beta 1. plasmin treatment of cho-conditioned medium resulted in the appearance of tgf beta competing activity. in addition, immunoblot analysis of plasmin-treated cho-conditioned medium indicates that the amino-terminal glycopeptide is partially degraded and that mature tgf beta 1 is released. thus, activation of latent tgf beta 1 may occur by proteolytic nicking within the amino-terminal glycopeptide thereby causing a disruption of tertiary structure and noncovalent bonds, which results in the release of active, mature tgf beta 1. acid activation of latent tgf beta, in comparison, appears to be due to dissociation of the amino-terminal glycopeptide from the mature polypeptide.",0
"unlabelled the 2005 consensus proposal for the classification of hepatitis c virus (hcv) presented an agreed and uniform nomenclature for hcv variants and the criteria for their assignment into genotypes and subtypes. since its publication, the available dataset of hcv sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of hcv genetic variation in disease and treatment outcomes. the current study represents a major update to the previous consensus hcv classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of hcv available on public databases in may 2013. analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of hcv into seven confirmed genotypes and 67 subtypes. there are 21 additional complete coding region sequences of unassigned subtype. the study additionally describes the development of a web resource hosted by the international committee for taxonomy of viruses (ictv) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments ( the flaviviridae study group urges those who need to check or propose new genotypes or subtypes of hcv to contact the study group in advance of publication to avoid nomenclature conflicts appearing in the literature. while the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond ""w,"" and the nomenclature of intergenotypic recombinant. conclusion this study represents an important reference point for the consensus classification of hcv variants that will be of value to researchers working in clinical and basic science fields.",0
"a new, fluorescent, highly selective ca2+ indicator , ""quin2"", has been trapped inside intact mouse and pig lymphocytes, to measure and manipulate cytoplasmic free ca2+ concentrations, i. quin2 is a tetracarboxylic acid which binds ca2+ with 1:1 stoichiometry and an effective dissociation constant of 115 nm in a cationic background mimicking cytoplasm. its fluorescence signal (excitation 339 nm, emission 492 nm) increases about fivefold going from ca-free to ca-saturated forms. cells are loaded with quin2 by incubation with its acetoxymethyl ester, which readily permeates the membrane and is hydrolyzed in the cytoplasm, thus trapping the impermeant quin2 there. the intracellular quin2 appears to be free in cytoplasm, not bound to membranes and not sequestered inside organelles. the fluorescence signal from resting cells indicates a i of near 120 nm. the millimolar loadings of quin2 needed for accurately calibrated signals do not seem to perturb steady-state i, but do somewhat slow or blunt i transients. loadings of up to 2mm are without serious toxic effects, though above this level some lowering of cellular atp is observed. i was well stabilized in the face of large changes in external ca2+. alterations of na+ gradients, membrane potential, or intracellular ph had little effect. mitochondrial poisons produced a small increase in i, probably due mostly to the effects of severe atp depletion on the plasma membrane. thus intracellulary trapped chelators like quin2 offer a method to measure or buffer i in hitherto intractable cell types.",0
"effective navigation requires planning extended routes to remembered goal locations. hippocampal place cells have been proposed to have a role in navigational planning, but direct evidence has been lacking. here we show that before goal-directed navigation in an open arena, the rat hippocampus generates brief sequences encoding spatial trajectories strongly biased to progress from the subject's current location to a known goal location. these sequences predict immediate future behaviour, even in cases in which the specific combination of start and goal locations is novel. these results indicate that hippocampal sequence events characterized previously in linearly constrained environments as 'replay' are also capable of supporting a goal-directed, trajectory-finding mechanism, which identifies important places and relevant behavioural paths, at specific times when memory retrieval is required, and in a manner that could be used to control subsequent navigational behaviour.",0
"the mechanism of brain reorganization in pain chronification is unknown. in a longitudinal brain imaging study, subacute back pain (sbp) patients were followed over the course of 1 year. when pain persisted (sbpp, in contrast to recovering sbp and healthy controls), brain gray matter density decreased. initially greater functional connectivity of nucleus accumbens with prefrontal cortex predicted pain persistence, implying that corticostriatal circuitry is causally involved in the transition from acute to chronic pain.",0
"prostate cancer is the second most frequent cancer diagnosis made in men and the fifth leading cause of death worldwide. prostate cancer may be asymptomatic at the early stage and often has an indolent course that may require only active surveillance. based on globocan 2018 estimates, 1,276,106 new cases of prostate cancer were reported worldwide in 2018, with higher prevalence in the developed countries. differences in the incidence rates worldwide reflect differences in the use of diagnostic testing. prostate cancer incidence and mortality rates are strongly related to the age with the highest incidence being seen in elderly men (> 65 years of age). african-american men have the highest incidence rates and more aggressive type of prostate cancer compared to white men. there is no evidence yet on how to prevent prostate cancer; however, it is possible to lower the risk by limiting high-fat foods, increasing the intake of vegetables and fruits and performing more exercise. screening is highly recommended at age 45 for men with familial history and african-american men. up-to-date statistics on prostate cancer occurrence and outcomes along with a better understanding of the etiology and causative risk factors are essential for the primary prevention of this disease.",0
"prefrontal cortex is thought to have a fundamental role in flexible, context-dependent behaviour, but the exact nature of the computations underlying this role remains largely unknown. in particular, individual prefrontal neurons often generate remarkably complex responses that defy deep understanding of their contribution to behaviour. here we study prefrontal cortex activity in macaque monkeys trained to flexibly select and integrate noisy sensory inputs towards a choice. we find that the observed complexity and functional roles of single neurons are readily understood in the framework of a dynamical process unfolding at the level of the population. the population dynamics can be reproduced by a trained recurrent neural network, which suggests a previously unknown mechanism for selection and integration of task-relevant inputs. this mechanism indicates that selection and integration are two aspects of a single dynamical process unfolding within the same prefrontal circuits, and potentially provides a novel, general framework for understanding context-dependent computations.",0
"vps30p/apg6p is required for both autophagy and sorting of carboxypeptidase y (cpy). although vps30p is known to interact with apg14p, its precise role remains unclear. we found that two proteins copurify with vps30p. they were identified by mass spectrometry to be vps38p and vps34p, a phosphatidylinositol (ptdins) 3-kinase. vps34p, vps38p, apg14p, and vps15p, an activator of vps34p, were coimmunoprecipitated with vps30p. these results indicate that vps30p functions as a subunit of a vps34 ptdins 3-kinase complex(es). phenotypic analyses indicated that apg14p and vps38p are each required for autophagy and cpy sorting, respectively, whereas vps30p, vps34p, and vps15p are required for both processes. coimmunoprecipitation using anti-apg14p and anti-vps38p antibodies and pull-down experiments showed that two distinct vps34 ptdins 3-kinase complexes exist: one, containing vps15p, vps30p, and apg14p, functions in autophagy and the other containing vps15p, vps30p, and vps38p functions in cpy sorting. the vps34 and vps15 mutants displayed additional phenotypes such as defects in transport of proteinase a and proteinase b, implying the existence of another ptdins 3-kinase complex(es). we propose that multiple vps34p-vps15p complexes associated with specific regulatory proteins might fulfill their membrane trafficking events at different sites.",0
"objective to provide researchers with guidance on actions to take during intervention development. summary of key points based on a consensus exercise informed by reviews and qualitative interviews, we present key principles and actions for consideration when developing interventions to improve health. these include seeing intervention development as a dynamic iterative process, involving stakeholders, reviewing published research evidence, drawing on existing theories, articulating programme theory, undertaking primary data collection, understanding context, paying attention to future implementation in the real world and designing and refining an intervention using iterative cycles of development with stakeholder input throughout. conclusion researchers should consider each action by addressing its relevance to a specific intervention in a specific context, both at the start and throughout the development process.",0
"over the last 10-15 years, our understanding of the composition and functions of the human gut microbiota has increased exponentially. to a large extent, this has been due to new 'omic' technologies that have facilitated large-scale analysis of the genetic and metabolic profile of this microbial community, revealing it to be comparable in influence to a new organ in the body and offering the possibility of a new route for therapeutic intervention. moreover, it might be more accurate to think of it like an immune system: a collection of cells that work in unison with the host and that can promote health but sometimes initiate disease. this review gives an update on the current knowledge in the area of gut disorders, in particular metabolic syndrome and obesity-related disease, liver disease, ibd and colorectal cancer. the potential of manipulating the gut microbiota in these disorders is assessed, with an examination of the latest and most relevant evidence relating to antibiotics, probiotics, prebiotics, polyphenols and faecal microbiota transplantation.",0
"background an important feature of severe acute respiratory syndrome coronavirus 2 pathogenesis is covid-19-associated coagulopathy, characterised by increased thrombotic and microvascular complications. previous studies have suggested a role for endothelial cell injury in covid-19-associated coagulopathy. to determine whether endotheliopathy is involved in covid-19-associated coagulopathy pathogenesis, we assessed markers of endothelial cell and platelet activation in critically and non-critically ill patients admitted to the hospital with covid-19. methods in this single-centre cross-sectional study, hospitalised adult (≥18 years) patients with laboratory-confirmed covid-19 were identified in the medical intensive care unit (icu) or a specialised non-icu covid-19 floor in our hospital. asymptomatic, non-hospitalised controls were recruited as a comparator group for biomarkers that did not have a reference range. we assessed markers of endothelial cell and platelet activation, including von willebrand factor (vwf) antigen, soluble thrombomodulin, soluble p-selectin, and soluble cd40 ligand, as well as coagulation factors, endogenous anticoagulants, and fibrinolytic enzymes. we compared the level of each marker in icu patients, non-icu patients, and controls, where applicable. we assessed correlations between these laboratory results with clinical outcomes, including hospital discharge and mortality. kaplan-meier analysis was used to further explore the association between biochemical markers and survival. findings 68 patients with covid-19 were included in the study from april 13 to april 24, 2020, including 48 icu and 20 non-icu patients, as well as 13 non-hospitalised, asymptomatic controls. markers of endothelial cell and platelet activation were significantly elevated in icu patients compared with non-icu patients, including vwf antigen (mean 565% in icu patients vs 278% in non-icu patients; p interpretation our findings show that endotheliopathy is present in covid-19 and is likely to be associated with critical illness and death. early identification of endotheliopathy and strategies to mitigate its progression might improve outcomes in covid-19. funding this work was supported by a gift donation from jack levin to the benign hematology programme at yale, and the national institutes of health.",0
"since the year 2000, a concerted campaign against malaria has led to unprecedented levels of intervention coverage across sub-saharan africa. understanding the effect of this control effort is vital to inform future control planning. however, the effect of malaria interventions across the varied epidemiological settings of africa remains poorly understood owing to the absence of reliable surveillance data and the simplistic approaches underlying current disease estimates. here we link a large database of malaria field surveys with detailed reconstructions of changing intervention coverage to directly evaluate trends from 2000 to 2015, and quantify the attributable effect of malaria disease control efforts. we found that plasmodium falciparum infection prevalence in endemic africa halved and the incidence of clinical disease fell by 40% between 2000 and 2015. we estimate that interventions have averted 663 (542-753 credible interval) million clinical cases since 2000. insecticide-treated nets, the most widespread intervention, were by far the largest contributor (68% of cases averted). although still below target levels, current malaria interventions have substantially reduced malaria disease incidence across the continent. increasing access to these interventions, and maintaining their effectiveness in the face of insecticide and drug resistance, should form a cornerstone of post-2015 control strategies.",0
"the number of resting state functional connectivity mri studies continues to expand at a rapid rate along with the options for data processing. of the processing options, few have generated as much controversy as global signal regression and the subsequent observation of negative correlations (anti-correlations). this debate has motivated new processing strategies and advancement in the field, but has also generated significant confusion and contradictory guidelines. in this article, we work towards a consensus regarding global signal regression. we highlight several points of agreement including the fact that there is not a single ""right"" way to process resting state data that reveals the ""true"" nature of the brain. although further work is needed, different processing approaches likely reveal complementary insights about the brain's functional organisation.",0
"a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), was identified in wuhan, china, in december 2019. since then, the virus has made its way across the globe to affect over 180 countries. sars-cov-2 has infected humans in all age groups, of all ethnicities, both males and females while spreading through communities at an alarming rate. given the nature of this virus, there is much still to be learned; however, we know that the clinical manifestations range from a common cold to more severe diseases such as bronchitis, pneumonia, severe acute respiratory distress syndrome (ards), multi-organ failure, and even death. it is believed that covid-19, in those with underlying health conditions or comorbidities, has an increasingly rapid and severe progression, often leading to death. this paper examined the comorbid conditions, the progression of the disease, and mortality rates in patients of all ages, infected with the ongoing covid-19 disease. an electronic literature review search was performed, and applicable data was then collected from peer-reviewed articles published from january to april 20, 2020. from what is known at the moment, patients with covid-19 disease who have comorbidities, such as hypertension or diabetes mellitus, are more likely to develop a more severe course and progression of the disease. furthermore, older patients, especially those 65 years old and above who have comorbidities and are infected, have an increased admission rate into the intensive care unit (icu) and mortality from the covid-19 disease. patients with comorbidities should take all necessary precautions to avoid getting infected with sars cov-2, as they usually have the worst prognosis.",0
"objective to assess whether perceptions of the swine flu outbreak predicted changes in behaviour among members of the public in england, scotland, and wales. design cross sectional telephone survey using random digit dialling. setting interviews by telephone between 8 and 12 may. participants 997 adults aged 18 or more who had heard of swine flu and spoke english. main outcome measures recommended change in behaviour (increases in handwashing and surface cleaning or plans made with a ""flu friend"") and avoidance behaviours (engaged in one or more of six behaviours such as avoiding large crowds or public transport). results 37.8% of participants (n=377) reported performing any recommended behaviour change ""over the past four days . . . because of swine flu."" 4.9% (n=49) had carried out any avoidance behaviour. controlling for personal details and anxiety, recommended changes were associated with perceptions that swine flu is severe, that the risk of catching it is high risk, that the outbreak will continue for a long time, that the authorities can be trusted, that good information has been provided, that people can control their risk of catching swine flu, and that specific behaviours are effective in reducing the risk. being uncertain about the outbreak and believing that the outbreak had been exaggerated were associated with a lower likelihood of change. the strongest predictor of behaviour change was ethnicity, with participants from ethnic minority groups being more likely to make recommended changes (odds ratio 3.2, 95% confidence interval 2.0 to 5.3) and carry out avoidance behaviours (4.1, 2.0 to 8.4). conclusions the results support efforts to inform the public about specific actions that can reduce the risks from swine flu and to communicate about the government's plans and resources. tackling the perception that the outbreak has been ""over-hyped"" may be difficult but worthwhile. additional research is required into differing reactions to the outbreak among ethnic groups.",0
"the prevalence, age of onset, and symptomatology of many neuropsychiatric conditions differ between males and females. to understand the causes and consequences of sex differences it is important to establish where they occur in the human brain. we report the first meta-analysis of typical sex differences on global brain volume, a descriptive account of the breakdown of studies of each compartmental volume by six age categories, and whole-brain voxel-wise meta-analyses on brain volume and density. gaussian-process regression coordinate-based meta-analysis was used to examine sex differences in voxel-based regional volume and density. on average, males have larger total brain volumes than females. examination of the breakdown of studies providing total volumes by age categories indicated a bias towards the 18-59 year-old category. regional sex differences in volume and tissue density include the amygdala, hippocampus and insula, areas known to be implicated in sex-biased neuropsychiatric conditions. together, these results suggest candidate regions for investigating the asymmetric effect that sex has on the developing brain, and for understanding sex-biased neurological and psychiatric conditions.",0
"imgt, the international immunogenetics information system ( was created in 1989 by marie-paule lefranc, laboratoire d'immunogénétique moléculaire ligm (université montpellier 2 and cnrs) at montpellier, france, in order to standardize and manage the complexity of immunogenetics data. the building of a unique ontology, imgt-ontology, has made imgt the global reference in immunogenetics and immunoinformatics. imgt is a high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, t cell receptors, major histocompatibility complex, of human and other vertebrate species, proteins of the igsf and mhcsf, and related proteins of the immune systems of any species. imgt provides a common access to standardized data from genome, proteome, genetics and 3d structures. imgt consists of five databases (imgt/ligm-db, imgt/gene-db, imgt/3dstructure-db, etc.), fifteen interactive online tools for sequence, genome and 3d structure analysis, and more than 10,000 html pages of synthesis and knowledge. imgt is used in medical research (autoimmune diseases, infectious diseases, aids, leukemias, lymphomas and myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow-up of residual diseases) and therapeutical approaches (graft, immunotherapy, vaccinology). imgt is freely available at",0
"cultured bovine capillary endothelial (bce) cells were found to synthesize and secrete high molecular mass heparan sulfate proteoglycans and glycosaminoglycans, which bound basic fibroblast growth factor (bfgf). the secreted heparan sulfate molecules were purified by deae cellulose chromatography, followed by sepharose 4b chromatography and affinity chromatography on immobilized bfgf. most of the heparinase-sensitive sulfated molecules secreted into the medium by bce cells bound to immobilized bfgf at low salt concentrations. however, elution from bfgf with increasing salt concentrations demonstrated varying affinities for bfgf among the secreted heparan sulfate molecules, with part of the heparan sulfate requiring nacl concentrations between 1.0 and 1.5 m for elution. cell extracts prepared from bce cells also contained a bfgf-binding heparan sulfate proteoglycan, which could be released from the intact cells by a short proteinase treatment. the purified bfgf-binding heparan sulfate competed with 125i-bfgf for binding to low-affinity binding sites but not to high-affinity sites on the cells. heparan sulfate did not interfere with bfgf stimulation of plasminogen activator activity in bce cells in agreement with its lack of effect on binding of 125i-bfgf to high-affinity sites. soluble bfgf was readily degraded by plasmin, whereas bfgf bound to heparan sulfate was protected from proteolytic degradation. treatment of the heparan sulfate with heparinase before addition of plasmin abolished the protection and resulted in degradation of bfgf by the added proteinase. the results suggest that heparan sulfate released either directly by cells or through proteolytic degradation of their extracellular milieu may act as carrier for bfgf and facilitate the diffusion of locally produced growth factor by competing with its binding to surrounding matrix structures. simultaneously, the secreted heparan sulfate glycosaminoglycans protect the growth factor from proteolytic degradation by extracellular proteinases, which are abundant at sites of neovascularization or cell invasion.",0
"here, we report on the expression of programmed death (pd)-1 on human virus-specific cd8(+) t cells and the effect of manipulating signaling through pd-1 on the survival, proliferation, and cytokine function of these cells. pd-1 expression was found to be low on naive cd8(+) t cells and increased on memory cd8(+) t cells according to antigen specificity. memory cd8(+) t cells specific for poorly controlled chronic persistent virus (hiv) more frequently expressed pd-1 than memory cd8(+) t cells specific for well-controlled persistent virus (cytomegalovirus) or acute (vaccinia) viruses. pd-1 expression was independent of maturational markers on memory cd8(+) t cells and was not directly associated with an inability to produce cytokines. importantly, the level of pd-1 surface expression was the primary determinant of apoptosis sensitivity of virus-specific cd8(+) t cells. manipulation of pd-1 led to changes in the ability of the cells to survive and expand, which, over several days, affected the number of cells expressing cytokines. therefore, pd-1 is a major regulator of apoptosis that can impact the frequency of antiviral t cells in chronic infections such as hiv, and could be manipulated to improve hiv-specific cd8(+) t cell numbers, but possibly not all functions in vivo.",0
"the novel coronavirus disease (covid-19) has been rapidly transmitted in china, macau, hong kong, and other asian and european counterparts. this covid-19 epidemic has aroused increasing attention nationwide. patients, health professionals, and the general public are under insurmountable psychological pressure which may lead to various psychological problems, such as anxiety, fear, depression, and insomnia. psychological crisis intervention plays a pivotal role in the overall deployment of the disease control. the national health commission of china has summoned a call for emergency psychological crisis intervention and thus, various mental health associations and organizations have established expert teams to compile guidelines and public health educational articles/videos for mental health professionals and the general public alongside with online mental health services. in addition, mental health professionals and expert groups are stationed in designated isolation hospitals to provide on-site services. experts have reached a consensus on the admission of patients with severe mental illness during the covid-19 outbreak in mental health institutions. nevertheless, the rapid transmission of the covid-19 has emerged to mount a serious challenge to the mental health service in china.",0
"a novel severe acute respiratory syndrome (sars)-like coronavirus (sars-cov-2) recently emerged and is rapidly spreading in humans, causing covid-19 1,2 . a key to tackling this pandemic is to understand the receptor recognition mechanism of the virus, which regulates its infectivity, pathogenesis and host range. sars-cov-2 and sars-cov recognize the same receptor-angiotensin-converting enzyme 2 (ace2)-in humans 3,4 . here we determined the crystal structure of the receptor-binding domain (rbd) of the spike protein of sars-cov-2 (engineered to facilitate crystallization) in complex with ace2. in comparison with the sars-cov rbd, an ace2-binding ridge in sars-cov-2 rbd has a more compact conformation; moreover, several residue changes in the sars-cov-2 rbd stabilize two virus-binding hotspots at the rbd-ace2 interface. these structural features of sars-cov-2 rbd increase its ace2-binding affinity. additionally, we show that ratg13, a bat coronavirus that is closely related to sars-cov-2, also uses human ace2 as its receptor. the differences among sars-cov-2, sars-cov and ratg13 in ace2 recognition shed light on the potential animal-to-human transmission of sars-cov-2. this study provides guidance for intervention strategies that target receptor recognition by sars-cov-2.",0
"patients with coronavirus disease 2019 (covid-19) have elevated d-dimer levels. early reports describe high venous thromboembolism (vte) and disseminated intravascular coagulation (dic) rates, but data are limited. this multicenter retrospective study describes the rate and severity of hemostatic and thrombotic complications of 400 hospital-admitted covid-19 patients (144 critically ill) primarily receiving standard-dose prophylactic anticoagulation. coagulation and inflammatory parameters were compared between patients with and without coagulation-associated complications. multivariable logistic models examined the utility of these markers in predicting coagulation-associated complications, critical illness, and death. the radiographically confirmed vte rate was 4.8% (95% confidence interval , 2.9-7.3), and the overall thrombotic complication rate was 9.5% (95% ci, 6.8-12.8). the overall and major bleeding rates were 4.8% (95% ci, 2.9-7.3) and 2.3% (95% ci, 1.0-4.2), respectively. in the critically ill, radiographically confirmed vte and major bleeding rates were 7.6% (95% ci, 3.9-13.3) and 5.6% (95% ci, 2.4-10.7), respectively. elevated d-dimer at initial presentation was predictive of coagulation-associated complications during hospitalization (d-dimer >2500 ng/ml, adjusted odds ratio for thrombosis, 6.79 ; adjusted or for bleeding, 3.56 ), critical illness, and death. additional markers at initial presentation predictive of thrombosis during hospitalization included platelet count >450 × 109/l (adjusted or, 3.56 ), c-reactive protein (crp) >100 mg/l (adjusted or, 2.71 ), and erythrocyte sedimentation rate (esr) >40 mm/h (adjusted or, 2.64 ). esr, crp, fibrinogen, ferritin, and procalcitonin were higher in patients with thrombotic complications than in those without. dic, clinically relevant thrombocytopenia, and reduced fibrinogen were rare and were associated with significant bleeding manifestations. given the observed bleeding rates, randomized trials are needed to determine any potential benefit of intensified anticoagulant prophylaxis in covid-19 patients.",0
"bone tissue is continuously remodeled through the concerted actions of bone cells, which include bone resorption by osteoclasts and bone formation by osteoblasts, whereas osteocytes act as mechanosensors and orchestrators of the bone remodeling process. this process is under the control of local (e.g., growth factors and cytokines) and systemic (e.g., calcitonin and estrogens) factors that all together contribute for bone homeostasis. an imbalance between bone resorption and formation can result in bone diseases including osteoporosis. recently, it has been recognized that, during bone remodeling, there are an intricate communication among bone cells. for instance, the coupling from bone resorption to bone formation is achieved by interaction between osteoclasts and osteoblasts. moreover, osteocytes produce factors that influence osteoblast and osteoclast activities, whereas osteocyte apoptosis is followed by osteoclastic bone resorption. the increasing knowledge about the structure and functions of bone cells contributed to a better understanding of bone biology. it has been suggested that there is a complex communication between bone cells and other organs, indicating the dynamic nature of bone tissue. in this review, we discuss the current data about the structure and functions of bone cells and the factors that influence bone remodeling.",0
"background many causes of vision impairment can be prevented or treated. with an ageing global population, the demands for eye health services are increasing. we estimated the prevalence and relative contribution of avoidable causes of blindness and vision impairment globally from 1990 to 2020. we aimed to compare the results with the world health assembly global action plan (wha gap) target of a 25% global reduction from 2010 to 2019 in avoidable vision impairment, defined as cataract and undercorrected refractive error. methods we did a systematic review and meta-analysis of population-based surveys of eye disease from january, 1980, to october, 2018. we fitted hierarchical models to estimate prevalence (with 95% uncertainty intervals ) of moderate and severe vision impairment (msvi; presenting visual acuity from findings global crude prevalence of avoidable vision impairment and blindness in adults aged 50 years and older did not change between 2010 and 2019 (percentage change -0·2% ; 2019 prevalence 9·58 cases per 1000 people , 2010 prevalence 96·0 cases per 1000 people ). age-standardised prevalence of avoidable blindness decreased by -15·4% , while avoidable msvi showed no change (0·5% ). however, the number of cases increased for both avoidable blindness (10·8% ) and msvi (31·5% ). the leading global causes of blindness in those aged 50 years and older in 2020 were cataract (15·2 million cases ), followed by glaucoma (3·6 million cases ), undercorrected refractive error (2·3 million cases ), age-related macular degeneration (1·8 million cases ), and diabetic retinopathy (0·86 million cases ). leading causes of msvi were undercorrected refractive error (86·1 million cases ) and cataract (78·8 million cases ). interpretation results suggest eye care services contributed to the observed reduction of age-standardised rates of avoidable blindness but not of msvi, and that the target in an ageing global population was not reached. funding brien holden vision institute, fondation théa, the fred hollows foundation, bill & melinda gates foundation, lions clubs international foundation, sightsavers international, and university of heidelberg.",0
"shelxle is a graphical user interface for shelxl , currently the most widely used program for small-molecule structure refinement. it combines an editor with syntax highlighting for the shelxl-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (f(o)) and difference density (f(o)-f(c)) maps. special features of shelxle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. shelxle is completely compatible with all features of shelxl and is written entirely in c++ using the qt4 and fftw libraries. it is available at no cost for windows, linux and mac-os x and as source code.",0
"the amber lipid force field has been updated to create lipid14, allowing tensionless simulation of a number of lipid types with the amber md package. the modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. the lennard-jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. the force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, nmr order parameters, scattering data, and lipid lateral diffusion. as the derivation of this force field is consistent with the amber development philosophy, lipid14 is compatible with the amber protein, nucleic acid, carbohydrate, and small molecule force fields.",0
"the efficiency of producing timed pregnant or pseudopregnant mice can be increased by identifying those in proestrus or estrus. visual observation of the vagina is the quickest method, requires no special equipment, and is best used when only proestrus or estrus stages need to be identified. strain to strain differences, especially in coat color can make it difficult to determine the stage of the estrous cycle accurately by visual observation. presented here are a series of images of the vaginal opening at each stage of the estrous cycle for 3 mouse strains of different coat colors: black (c57bl/6j), agouti (cbyb6f1/j) and albino (balb/cbyj). when all 4 stages (proestrus, estrus, metestrus, and diestrus) need to be identified, vaginal cytology is regarded as the most accurate method. an identification tool is presented to aid the user in determining the stage of estrous when using vaginal cytology. these images and descriptions are an excellent resource for learning how to determine the stage of the estrous cycle by visual observation or vaginal cytology.",0
"some patients with positive chest ct findings may present with negative results of real-time reverse-transcription polymerase chain reaction (rt-pcr) tests for coronavirus disease 2019 (covid-19). in this study, the authors present chest ct findings from five patients with covid-19 infection who had initial negative rt-pcr results. all five patients had typical imaging findings, including ground-glass opacity (five patients) and/or mixed ground-glass opacity and mixed consolidation (two patients). after isolation for presumed covid-19 pneumonia, all patients were eventually confirmed to have covid-19 infection by means of repeated swab tests. a combination of repeated swab tests and ct scanning may be helpful for individuals with a high clinical suspicion of covid-19 infection but negative findings at rt-pcr screening.",0
"the concept of schizotypy or ""psychosis proneness"" captures individual differences in perceptual, cognitive, and affective experiences that may relate to a range of psychotic disorders. the concept is an important way to assess the contribution of pre-existing psychological and genetically based biological features to the development of illnesses such as schizophrenia (so called endophenotypes). the oxford-liverpool inventory of feelings and experiences (o-life) is a widely used multi-dimensional measure of the construct and consists of four scales which mirror several groups of psychotic symptoms: unusual experiences (unex; positive symptoms), cognitive disorganization (cogdis; cognitive symptoms), introvertive anhedonia (intan; negative symptoms), and impulsive nonconformity (impnon; impulsive and antisocial symptoms). for the purpose of evaluating the suitability of schizotypy as an endophenotype of schizophrenia the current version of the o-life was translated into german: its psychometric properties (including re-test reliability and construct validity) were examined in a large sample (n > 1200) and compared to those of the english original. the german version was both highly reliable and consistent with the original. the study aimed to show that schizotypy as measured by the o-life can indeed be regarded as an endophenotype of schizophrenia in terms of genetic associations regarding relevant dopamine-related candidate polymorphisms of schizotypy . we also wanted to compare the genetic associations of the o-life to those published using other operationalizations of schizotypy. our results show a large number of significant associations and borderline-significant trends between the o-life sub-scales and a range of genes, thereby supporting using the o-life in the search for endophenotypic markers.",0
"the aim of this study was to identify factors associated with the death of patients with covid-19 pneumonia caused by the novel coronavirus sars-cov-2.all clinical and laboratory parameters were collected prospectively from a cohort of patients with covid-19 pneumonia who were hospitalised to wuhan pulmonary hospital (wuhan city, hubei province, china) between 25 december 2019 and 7 february 2020. univariate and multivariate logistic regression analysis revealed that age ≥65 years (or 3.765, 95% ci 1.146–17.394; p=0.023), pre-existing concurrent cardiovascular or cerebrovascular diseases (or 2.464, 95% ci 0.755–8.044; p=0.007), cd3+cd8+ t-cells ≤75 cells·μl−1 (or 3.982, 95% ci 1.132–14.006; p + cd8 + t-cells ≤75 cells·μl -1 and cardiac troponin i ≥0.05 ng·ml -1 remained as predictors for high mortality from covid-19 pneumonia.we identified four risk factors: age ≥65 years, pre-existing concurrent cardiovascular or cerebrovascular diseases, cd3 + cd8 + t-cells ≤75 cells·μl -1 and cardiac troponin i ≥0.05 ng·ml -1 the latter two factors, especially, were predictors for mortality of covid-19 pneumonia patients.",0
"we have found that intradermal injection of native type ii collagen extracted from human, chick or rat cartilage induces an inflammatory arthritis in approximately 40% of rats of several strains whether complete freund's adjuvant or incomplete freund's adjuvant is used. type i or iii collagen extracted from skin, cartilage proteoglycans and alpha1(ii) chains were incapable of eliciting arthritis, as was type ii collagen injected without adjuvant. the disease is a chronic proliferative synovitis, resembling adjuvant arthritis in rats and rheumatoid arthritis in humans. native type ii co-lagen modified by limited pepsin digestion still produces arthritis, suggesting that type-specific determinants residing in the helical region of the molecule are responsible for the induction of disease. since homologous type ii collagen emulsified in oil without bacterial preparations regularly causes the disease, this new animal model of arthritis represents a unique example of experimentally-inducible autoimmunity to a tissue component.",0
"on march 13, 2020, the united states declared a national emergency to combat coronavirus disease 2019 (covid-19). as the number of persons hospitalized with covid-19 increased, early reports from austria (1), hong kong (2), italy (3), and california (4) suggested sharp drops in the numbers of persons seeking emergency medical care for other reasons. to quantify the effect of covid-19 on u.s. emergency department (ed) visits, cdc compared the volume of ed visits during four weeks early in the pandemic march 29-april 25, 2020 (weeks 14 to 17; the early pandemic period) to that during march 31-april 27, 2019 (the comparison period). during the early pandemic period, the total number of u.s. ed visits was 42% lower than during the same period a year earlier, with the largest declines in visits in persons aged ≤14 years, females, and the northeast region. health messages that reinforce the importance of immediately seeking care for symptoms of serious conditions, such as myocardial infarction, are needed. to minimize sars-cov-2, the virus that causes covid-19, transmission risk and address public concerns about visiting the ed during the pandemic, cdc recommends continued use of virtual visits and triage help lines and adherence to cdc infection control guidance.",0
"the outbreak of the 2019-ncov infection began in december 2019 in wuhan, hubei province, and rapidly spread to many provinces in china as well as other countries. here we report the epidemiological, clinical, laboratory, and radiological characteristics, as well as potential biomarkers for predicting disease severity in 2019-ncov-infected patients in shenzhen, china. all 12 cases of the 2019-ncov-infected patients developed pneumonia and half of them developed acute respiratory distress syndrome (ards). the most common laboratory abnormalities were hypoalbuminemia, lymphopenia, decreased percentage of lymphocytes (lym) and neutrophils (neu), elevated c-reactive protein (crp) and lactate dehydrogenase (ldh), and decreased cd8 count. the viral load of 2019-ncov detected from patient respiratory tracts was positively linked to lung disease severity. alb, lym, lym (%), ldh, neu (%), and crp were highly correlated to the acute lung injury. age, viral load, lung injury score, and blood biochemistry indexes, albumin (alb), crp, ldh, lym (%), lym, and neu (%), may be predictors of disease severity. moreover, the angiotensin ii level in the plasma sample from 2019-ncov infected patients was markedly elevated and linearly associated to viral load and lung injury. our results suggest a number of potential diagnosis biomarkers and angiotensin receptor blocker (arb) drugs for potential repurposing treatment of 2019-ncov infection.",0
"despite continuing debate about the amyloid β-protein (or aβ hypothesis, new lines of evidence from laboratories and clinics worldwide support the concept that an imbalance between production and clearance of aβ42 and related aβ peptides is a very early, often initiating factor in alzheimer's disease (ad). confirmation that presenilin is the catalytic site of γ-secretase has provided a linchpin: all dominant mutations causing early-onset ad occur either in the substrate (amyloid precursor protein, app) or the protease (presenilin) of the reaction that generates aβ. duplication of the wild-type app gene in down's syndrome leads to aβ deposits in the teens, followed by microgliosis, astrocytosis, and neurofibrillary tangles typical of ad apolipoprotein e4, which predisposes to ad in > 40% of cases, has been found to impair aβ clearance from the brain. soluble oligomers of aβ42 isolated from ad patients' brains can decrease synapse number, inhibit long-term potentiation, and enhance long-term synaptic depression in rodent hippocampus, and injecting them into healthy rats impairs memory. the human oligomers also induce hyperphosphorylation of tau at ad-relevant epitopes and cause neuritic dystrophy in cultured neurons. crossing human app with human tau transgenic mice enhances tau-positive neurotoxicity. in humans, new studies show that low cerebrospinal fluid (csf) aβ42 and amyloid-pet positivity precede other ad manifestations by many years. most importantly, recent trials of three different aβ antibodies (solanezumab, crenezumab, and aducanumab) have suggested a slowing of cognitive decline in post hoc analyses of mild ad subjects. although many factors contribute to ad pathogenesis, aβ dyshomeostasis has emerged as the most extensively validated and compelling therapeutic target.",0
"background : although post-traumatic stress disorder (ptsd) onset-persistence is thought to vary significantly by trauma type, most epidemiological surveys are incapable of assessing this because they evaluate lifetime ptsd only for traumas nominated by respondents as their 'worst.' objective : to review research on associations of trauma type with ptsd in the who world mental health (wmh) surveys, a series of epidemiological surveys that obtained representative data on trauma-specific ptsd. method : wmh surveys in 24 countries (n = 68,894) assessed 29 lifetime traumas and evaluated ptsd twice for each respondent: once for the 'worst' lifetime trauma and separately for a randomly-selected trauma with weighting to adjust for individual differences in trauma exposures. ptsd onset-persistence was evaluated with the who composite international diagnostic interview. results : in total, 70.4% of respondents experienced lifetime traumas, with exposure averaging 3.2 traumas per capita. substantial between-trauma differences were found in ptsd onset but less in persistence. traumas involving interpersonal violence had highest risk. burden of ptsd, determined by multiplying trauma prevalence by trauma-specific ptsd risk and persistence, was 77.7 person-years/100 respondents. the trauma types with highest proportions of this burden were rape (13.1%), other sexual assault (15.1%), being stalked (9.8%), and unexpected death of a loved one (11.6%). the first three of these four represent relatively uncommon traumas with high ptsd risk and the last a very common trauma with low ptsd risk. the broad category of intimate partner sexual violence accounted for nearly 42.7% of all person-years with ptsd. prior trauma history predicted both future trauma exposure and future ptsd risk. conclusions : trauma exposure is common throughout the world, unequally distributed, and differential across trauma types with respect to ptsd risk. although a substantial minority of ptsd cases remits within months after onset, mean symptom duration is considerably longer than previously recognized.",0
"objective neurofilament light chains (nfl) are unique to neuronal cells, are shed to the cerebrospinal fluid (csf), and are detectable at low concentrations in peripheral blood. various diseases causing neuronal damage have resulted in elevated csf concentrations. we explored the value of an ultrasensitive single-molecule array (simoa) serum nfl (snfl) assay in multiple sclerosis (ms). methods snfl levels were measured in healthy controls (hc, n = 254) and two independent ms cohorts: (1) cross-sectional with paired serum and csf samples (n = 142), and (2) longitudinal with repeated serum sampling (n = 246, median follow-up = 3.1 years, interquartile range = 2.0-4.0). we assessed their relation to concurrent clinical, imaging, and treatment parameters and to future clinical outcomes. results snfl levels were higher in both ms cohorts than in hc (p interpretation these results support the value of snfl as a sensitive and clinically meaningful blood biomarker to monitor tissue damage and the effects of therapies in ms. ann neurol 2017;81:857-870.",0
"the rising burden of type 2 diabetes is a major concern in healthcare worldwide. this research aimed to analyze the global epidemiology of type 2 diabetes. we analyzed the incidence, prevalence, and burden of suffering of diabetes mellitus based on epidemiological data from the global burden of disease (gbd) current dataset from the institute of health metrics, seattle. global and regional trends from 1990 to 2017 of type 2 diabetes for all ages were compiled. forecast estimates were obtained using the spss time series modeler. in 2017, approximately 462 million individuals were affected by type 2 diabetes corresponding to 6.28% of the world's population (4.4% of those aged 15-49 years, 15% of those aged 50-69, and 22% of those aged 70+), or a prevalence rate of 6059 cases per 100,000. over 1 million deaths per year can be attributed to diabetes alone, making it the ninth leading cause of mortality. the burden of diabetes mellitus is rising globally, and at a much faster rate in developed regions, such as western europe. the gender distribution is equal, and the incidence peaks at around 55 years of age. global prevalence of type 2 diabetes is projected to increase to 7079 individuals per 100,000 by 2030, reflecting a continued rise across all regions of the world. there are concerning trends of rising prevalence in lower-income countries. urgent public health and clinical preventive measures are warranted.",0
"in 2019, the international scientific association for probiotics and prebiotics (isapp) convened a panel of experts specializing in nutrition, microbial physiology, gastroenterology, paediatrics, food science and microbiology to review the definition and scope of postbiotics. the term 'postbiotics' is increasingly found in the scientific literature and on commercial products, yet is inconsistently used and lacks a clear definition. the purpose of this panel was to consider the scientific, commercial and regulatory parameters encompassing this emerging term, propose a useful definition and thereby establish a foundation for future developments. the panel defined a postbiotic as a ""preparation of inanimate microorganisms and/or their components that confers a health benefit on the host"". effective postbiotics must contain inactivated microbial cells or cell components, with or without metabolites, that contribute to observed health benefits. the panel also discussed existing evidence of health-promoting effects of postbiotics, potential mechanisms of action, levels of evidence required to meet the stated definition, safety and implications for stakeholders. the panel determined that a definition of postbiotics is useful so that scientists, clinical triallists, industry, regulators and consumers have common ground for future activity in this area. a generally accepted definition will hopefully lead to regulatory clarity and promote innovation and the development of new postbiotic products.",0
"aim the coronavirus disease 2019 (covid-19) pandemic has affected hundreds of thousands of people. data on symptoms and prognosis in children are rare. methods a systematic literature review was carried out to identify papers on covid-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), using the medline and embase databases between january 1 and march 18, 2020. results the search identified 45 relevant scientific papers and letters. the review showed that children have so far accounted for 1%-5% of diagnosed covid-19 cases, they often have milder disease than adults and deaths have been extremely rare. diagnostic findings have been similar to adults, with fever and respiratory symptoms being prevalent, but fewer children seem to have developed severe pneumonia. elevated inflammatory markers were less common in children, and lymphocytopenia seemed rare. newborn infants have developed symptomatic covid-19, but evidence of vertical intrauterine transmission was scarce. suggested treatment included providing oxygen, inhalations, nutritional support and maintaining fluids and electrolyte balances. conclusions the coronavirus disease 2019 has occurred in children, but they seemed to have a milder disease course and better prognosis than adults. deaths were extremely rare.",0
"biomarkers have become an essential component of alzheimer disease (ad) research and because of the pervasiveness of ad pathology in the elderly, the same biomarkers are used in cognitive aging research. a number of current issues suggest that an unbiased descriptive classification scheme for these biomarkers would be useful. we propose the ""a/t/n"" system in which 7 major ad biomarkers are divided into 3 binary categories based on the nature of the pathophysiology that each measures. ""a"" refers to the value of a β-amyloid biomarker (amyloid pet or csf aβ42); ""t,"" the value of a tau biomarker (csf phospho tau, or tau pet); and ""n,"" biomarkers of neurodegeneration or neuronal injury (-fluorodeoxyglucose-pet, structural mri, or csf total tau). each biomarker category is rated as positive or negative. an individual score might appear as a+/t+/n-, or a+/t-/n-, etc. the a/t/n system includes the new modality tau pet. it is agnostic to the temporal ordering of mechanisms underlying ad pathogenesis. it includes all individuals in any population regardless of the mix of biomarker findings and therefore is suited to population studies of cognitive aging. it does not specify disease labels and thus is not a diagnostic classification system. it is a descriptive system for categorizing multidomain biomarker findings at the individual person level in a format that is easy to understand and use. given the present lack of consensus among ad specialists on terminology across the clinically normal to dementia spectrum, a biomarker classification scheme will have broadest acceptance if it is independent from any one clinically defined diagnostic scheme.",0
"reproducible science requires transparent reporting. the arrive guidelines (animal research: reporting of in vivo experiments) were originally developed in 2010 to improve the reporting of animal research. they consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. here, we introduce arrive 2.0. the guidelines have been updated and information reorganised to facilitate their use in practice. we used a delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the ""arrive essential 10,"" which constitutes the minimum requirement, and the ""recommended set,"" which describes the research context. this division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. this helps journal editors and reviewers verify that the most important items are being reported in manuscripts. we have also developed the accompanying explanation and elaboration (e&e) document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. we aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.",0
"the international sharing of virus data is critical for protecting populations against lethal infectious disease outbreaks. scientists must rapidly share information to assess the nature of the threat and develop new medical countermeasures. governments need the data to trace the extent of the outbreak, initiate public health responses, and coordinate access to medicines and vaccines. recent outbreaks suggest, however, that the sharing of such data cannot be taken for granted - making the timely international exchange of virus data a vital global challenge. this article undertakes the first analysis of the global initiative on sharing all influenza data as an innovative policy effort to promote the international sharing of genetic and associated influenza virus data. based on more than 20 semi-structured interviews conducted with key informants in the international community, coupled with analysis of a wide range of primary and secondary sources, the article finds that the global initiative on sharing all influenza data contributes to global health in at least five ways: (1) collating the most complete repository of high-quality influenza data in the world; (2) facilitating the rapid sharing of potentially pandemic virus information during recent outbreaks; (3) supporting the world health organization's biannual seasonal flu vaccine strain selection process; (4) developing informal mechanisms for conflict resolution around the sharing of virus data; and (5) building greater trust with several countries key to global pandemic preparedness.",0
"iotbx.cif is a new software module for the development of applications that make use of the cif format. comprehensive tools are provided for input, output and validation of cifs, as well as for interconversion with high-level cctbx crystallographic objects. the interface to the library is written in python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (c++) with the benefits of using an interpreted language.",0
"since the completion of the genome sequence of saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast s. cerevisiae and its closest relative, saccharomyces paradoxus. we examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. we find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. s. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide s. cerevisiae isolates shows less differentiation and is comparable to a single s. paradoxus population. rather than one or two domestication events leading to the extant baker's yeasts, the population structure of s. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.",0
"structurally segregated and functionally specialized regions of the human cerebral cortex are interconnected by a dense network of cortico-cortical axonal pathways. by using diffusion spectrum imaging, we noninvasively mapped these pathways within and across cortical hemispheres in individual human participants. an analysis of the resulting large-scale structural brain networks reveals a structural core within posterior medial and parietal cerebral cortex, as well as several distinct temporal and frontal modules. brain regions within the structural core share high degree, strength, and betweenness centrality, and they constitute connector hubs that link all major structural modules. the structural core contains brain regions that form the posterior components of the human default network. looking both within and outside of core regions, we observed a substantial correspondence between structural connectivity and resting-state functional connectivity measured in the same participants. the spatial and topological centrality of the core within cortex suggests an important role in functional integration.",0
"results from genome-wide association studies (gwas) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample mendelian randomization (2smr) and bypassing the need for individual-level data. however, 2smr methods are evolving rapidly and gwas results are often insufficiently curated, undermining efficient implementation of the approach. we therefore developed mr-base ( ): a platform that integrates a curated database of complete gwas results (no restrictions according to statistical significance) with an application programming interface, web app and r packages that automate 2smr. the software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. the database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 gwas and is updated on a regular basis. integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies.",0
"the relative proportion of additive and non-additive variation for complex traits is important in evolutionary biology, medicine, and agriculture. we address a long-standing controversy and paradox about the contribution of non-additive genetic variation, namely that knowledge about biological pathways and gene networks imply that epistasis is important. yet empirical data across a range of traits and species imply that most genetic variance is additive. we evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close to 100%, of the total genetic variance. we present new theoretical results, based upon the distribution of allele frequencies under neutral and other population genetic models, that show why this is the case even if there are non-additive effects at the level of gene action. we conclude that interactions at the level of genes are not likely to generate much interaction at the level of variance.",0
"entry and progression through mitosis has traditionally been linked directly to the activity of cyclin-dependent kinase 1 (cdk1). in this study we utilized low doses of the cdk1-specific inhibitor, ro3306 from early g 2 phase onwards. addition of low doses of ro3306 in g 2 phase induced minor chromosome congression and segregation defects. in contrast, mild doses of ro3306 during g 2 phase resulted in cells entering an aberrant mitosis, with cells fragmenting centrosomes and failing to fully disassemble the nuclear envelope. cells often underwent cytokinesis and metaphase simultaneously, despite the presence of an active spindle assembly checkpoint, which prevented degradation of cyclin b1 and securin, resulting in the random partitioning of whole chromosomes. this highly aberrant mitosis produced a significant increase in the proportion of viable polyploid cells present up to 3 days post-treatment. furthermore, cells treated with medium doses of ro3306 were only able to reach the threshold of cdk1 substrate phosphorylation required to initiate nuclear envelope breakdown, but failed to reach the levels of phosphorylation required to correctly complete pro-metaphase. treatment with low doses of okadaic acid, which primarily inhibits pp2a, rescued the mitotic defects and increased the number of cells that completed a normal mitosis. this supports the current model that pp2a is the primary phosphatase that counterbalances the activity of cdk1 during mitosis. taken together these results show that continuous and subtle disruption of cdk1 activity from g 2 phase onwards has deleterious consequences on mitotic progression by disrupting the balance between cdk1 and pp2a.",0
"background monitoring the reasons why a considerable number of people do not receive recommended vaccinations allows identification of important trends over time, and designing and evaluating strategies to address vaccine hesitancy and increase vaccine uptake. existing validated measures assessing vaccine hesitancy focus primarily on confidence in vaccines and the system that delivers them. however, empirical and theoretical work has stated that complacency (not perceiving diseases as high risk), constraints (structural and psychological barriers), calculation (engagement in extensive information searching), and aspects pertaining to collective responsibility (willingness to protect others) also play a role in explaining vaccination behavior. the objective was therefore to develop a validated measure of these 5c psychological antecedents of vaccination. methods and findings three cross-sectional studies were conducted. study 1 uses factor analysis to develop an initial scale and assesses the sub-scales' convergent, discriminant, and concurrent validity (n = 1,445, two german convenience-samples). in study 2, a sample representative regarding age and gender for the german population (n = 1,003) completed the measure for vaccination in general and for specific vaccinations to assess the potential need for a vaccine-specific wording of items. study 3 compared the novel scale's performance with six existing measures of vaccine hesitancy (n = 350, us convenience-sample). as an outcome, a long (15-item) and short (5-item) 5c scale were developed as reliable and valid indicators of confidence, complacency, constraints, calculation, and collective responsibility. the 5c sub-scales correlated with relevant psychological concepts, such as attitude (confidence), perceived personal health status and invulnerability (complacency), self-control (constraints), preference for deliberation (calculation), and communal orientation (collective responsibility), among others. the new scale provided similar results when formulated in a general vs. vaccine-specific way (study 2). in a comparison of seven measures the 5c scale was constantly among the scales that explained the highest amounts of variance in analyses predicting single vaccinations (between 20% and 40%; study 3). the present studies are limited to the concurrent validity of the scales. conclusions the 5c scale provides a novel tool to monitor psychological antecedents of vaccination and facilitates diagnosis, intervention design and evaluation. its short version is suitable for field settings and regular global monitoring of relevant antecedents of vaccination.",0
"of the 70,237 drug overdose deaths in the united states in 2017, approximately two thirds (47,600) involved an opioid (1). in recent years, increases in opioid-involved overdose deaths have been driven primarily by deaths involving synthetic opioids other than methadone (hereafter referred to as synthetic opioids) (1). cdc analyzed changes in age-adjusted death rates from 2017 to 2018 involving all opioids and opioid subcategories* by demographic characteristics, county urbanization levels, u.s. census region, and state. during 2018, a total of 67,367 drug overdose deaths occurred in the united states, a 4.1% decline from 2017; 46,802 (69.5%) involved an opioid (2). from 2017 to 2018, deaths involving all opioids, prescription opioids, and heroin decreased 2%, 13.5%, and 4.1%, respectively. however, deaths involving synthetic opioids increased 10%, likely driven by illicitly manufactured fentanyl (imf), including fentanyl analogs (1,3). efforts related to all opioids, particularly deaths involving synthetic opioids, should be strengthened to sustain and accelerate declines in opioid-involved deaths. comprehensive surveillance and prevention measures are critical to reducing opioid-involved deaths, including continued surveillance of evolving drug use and overdose, polysubstance use, and the changing illicit drug market; naloxone distribution and outreach to groups at risk for imf exposure; linkage to evidence-based treatment for persons with substance use disorders; and continued partnerships with public safety.",0
"background coronavirus disease 2019 (covid-19) has widely spread all over the world since the beginning of 2020. it is desirable to develop automatic and accurate detection of covid-19 using chest ct. purpose to develop a fully automatic framework to detect covid-19 using chest ct and evaluate its performance. materials and methods in this retrospective and multicenter study, a deep learning model, the covid-19 detection neural network (covnet), was developed to extract visual features from volumetric chest ct scans for the detection of covid-19. ct scans of community-acquired pneumonia (cap) and other non-pneumonia abnormalities were included to test the robustness of the model. the datasets were collected from six hospitals between august 2016 and february 2020. diagnostic performance was assessed with the area under the receiver operating characteristic curve, sensitivity, and specificity. results the collected dataset consisted of 4352 chest ct scans from 3322 patients. the average patient age (±standard deviation) was 49 years ± 15, and there were slightly more men than women (1838 vs 1484, respectively; p = .29). the per-scan sensitivity and specificity for detecting covid-19 in the independent test set was 90% (95% confidence interval : 83%, 94%; 114 of 127 scans) and 96% (95% ci: 93%, 98%; 294 of 307 scans), respectively, with an area under the receiver operating characteristic curve of 0.96 ( p online supplemental material is available for this article.",0
"jpred4 ( is the latest version of the popular jpred protein secondary structure prediction server which provides predictions by the jnet algorithm, one of the most accurate methods for secondary structure prediction. in addition to protein secondary structure, jpred also makes predictions of solvent accessibility and coiled-coil regions. the jpred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. the jpred4 web server has been re-implemented in the bootstrap framework and javascript to improve its design, usability and accessibility from mobile devices. jpred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. predictions are now presented in svg format with options to view full multiple sequence alignments with and without gaps and insertions. finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.",0
"this article describes several features in the mafft online service for multiple sequence alignment (msa). as a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for msas with large numbers of sequences is increasing. to extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. we are working on development of mafft toward these two directions. here, we explain (i) the web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and msas.",0
"the effects of x-irradiation have been quantitatively studied on single cells of a human cervical carcinoma (hela) under conditions such that 100 per cent of the unirradiated cells reproduce in isolation to form macroscopic colonies. this technique eliminates complexities due to interactions of members of large cell populations. survival of single cells (defined as the ability to form a macroscopic colony within 15 days) yields a typical 2 hit curve when plotted against x-ray dose. the initial shoulder extends to about 75 r, after which a linear logarithmic survival rate is obtained, in which the dose needed to reduce survivors to 37 per cent is 96 r. this radiation sensitivity is tens to hundreds of times greater than that of any microorganism for which the equivalent function bas been studied. evidence, though not proof, is presented that the lethal effect is due to a radiation-induced genetic defect which, however, cannot be a simple single gene inactivation. the locus of the action could be chromosomal. beginning at doses of 100 r, or possibly earlier, growth-delaying effects of radiation are visible. cells in which the ability to reproduce has been destroyed by doses below 800 r, can still multiply several times. at higher doses even a single cell division is precluded. a large proportion of the cells killed by radiation at any dose gives rise to one or more giant cells. these metabolize actively, grow to huge proportions but never reproduce under the experimental conditions employed. methods of preparing large populations of giant cells are described. these giants are particularly susceptible to virus action. some of the irradiated cells disappear from the plate, presumably by disintegration. this action of radiation is by far the least efficient, since even after 10,000 r, 5 to 10 per cent of the original cell inoculum is recoverable as giants.",0
"ultracryotomy of fixed tissue has been investigated for a number of years but, so far, success has been limited for several reasons. the simple technique herein reported allows the ultracryotomy not only of a variety of tissues but also of single cells in suspension, with a preservation and visualization of ultrastructural detail at least equivalent to that obtained with conventional embedding procedures. in this technique, sucrose is infused into glutaraldehyde-fixed tissue pieces before freezing for the purpose of controlling the sectioning consistency. by choosing the proper combinations of sucrose concentration and sectioning temperature, a wide variety of tissues can be smoothly sectioned. isolated cells, suspended in a sucrose solution, are sectioned by sectioning the frozen droplet of the suspension. a small liquid droplet of a saturated or near-saturated sucrose solution, suspended on the tip of an eyelash probe, is used to transfer frozen sections from the knife edge onto a grid substrate or a water surface. upon melting of the sections on the surface of the sucrose droplet, they are spread flat and smooth due to surface tension. when the section of a suspension of single cells melts, individual sections of cells remain confined to the small area of the droplet surface. these devices make it possible to cut wide dry sections, and to avoid flotation on dimethyl sulfoxide solutions. with appropriate staining procedures, well-preserved ultrastructural detail can be observed. the technique is illustrated with a number of tissue preparations and with suspensions of erythrocytes and bacterial cells.",0
"the subcellular distribution of microtubules containing acetylated alpha-tubulin in mammalian cells in culture was analyzed with 6-11b-1, a monoclonal antibody specific for acetylated alpha-tubulin. cultures of 3t3, hela, and ptk2 cells were grown on coverslips and observed by immunofluorescence microscopy after double-staining by 6-11b-1 and b-5-1-2, a monoclonal antibody specific for all alpha-tubulins. the antibody 6-11b-1 binds to primary cilia, centrioles, mitotic spindles, midbodies, and to subsets of cytoplasmic microtubules in 3t3 and hela cells, but not in ptk2 cells. these observations confirm that the acetylation of alpha-tubulin is a modification occurring in different microtubule structures and in a variety of eukaryotic cells. some features of the acetylation of cytoplasmic microtubules of mammalian cells are also described here. first, acetylated alpha-tubulin is present in microtubules that, under depolymerizing conditions, are more stable than the majority of cytoplasmic microtubules. in addition to the specific microtubule frameworks already mentioned, cytoplasmic microtubules resistant to nocodazole or colchicine, but not cold-resistant microtubules, contain more acetylated alpha-tubulin than the rest of cellular microtubules. second, the alpha-tubulin in all cytoplasmic microtubules of 3t3 and hela cells becomes acetylated in the presence of taxol, a drug that stabilizes microtubules. third, acetylation and deacetylation of cytoplasmic microtubules are reversible in cells released from exposure to 0 degrees c or antimitotic drugs. fourth, the epitope recognized by the antibody 6-11b-1 is not absolutely necessary for cell growth and division. this epitope is absent in ptk2 cells. the acetylation of alpha-tubulin could regulate the presence of microtubules in specific intracellular spaces by selective stabilization.",0
"tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. however, inferring population structure in large modern data sets imposes severe computational challenges. here, we develop efficient algorithms for approximate inference of the model underlying the structure program using a variational bayesian framework. variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. in addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. we test the variational algorithms on simulated data and illustrate using genotype data from the ceph-human genome diversity panel. the variational algorithms are almost two orders of magnitude faster than structure and achieve accuracies comparable to those of admixture. furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. our algorithm, faststructure, is freely available online at",0
"naturally processed peptides were acid extracted from immunoaffinity-purified hla-dr2, dr3, dr4, dr7, and dr8. using the complementary techniques of mass spectrometry and edman microsequencing, > 200 unique peptide masses were identified from each allele, ranging from 1,200 to 4,000 daltons (10-34 residues in length), and a total of 201 peptide sequences were obtained. these peptides were derived from 66 different source proteins and represented sets nested at both the amino- and carboxy-terminal ends with an average length of 15-18 amino acids. strikingly, most of the peptides (> 85%) were derived from endogenous proteins that intersect the endocytic/class ii pathway, even though class ii molecules are thought to function mainly in the presentation of exogenous foreign peptide antigens. the predominant endogenous peptides were derived from major histocompatibility complex-related molecules. a few peptides derived from exogenous bovine serum proteins were also bound to every allele. four prominent promiscuous self-peptide sets (capable of binding to multiple hla-dr alleles) as well as 84 allele-specific peptide sets were identified. binding experiments confirmed that the promiscuous peptides have high affinity for the binding groove of all hla-dr alleles examined. a potential physiologic role for these endogenous self-peptides as immunomodulators of the cellular immune response is discussed.",0
"mcscan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. the mcscanx toolkit implements an adjusted mcscan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. applications of mcscanx to several sequenced plant genomes and gene families are shown as examples. mcscanx can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. an integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. the source code and documentation of mcscanx are freely available at",0
"human cd4+ t cells, activated by allogeneic monocytes in a primary mixed lymphocyte reaction in the presence of exogenous interleukin (il) 10, specifically failed to proliferate after restimulation with the same alloantigens. a comparable state of t cell unresponsiveness could be induced by activation of cd4+ t cells by cross-linked anti-cd3 monoclonal antibodies (mabs) in the presence of exogenous il-10. the anergic t cells failed to produce il-2, il-5, il-10, interferon gamma, tumor necrosis factor alpha, and granulocyte/macrophage colony-stimulating factor. the il-10-induced anergic state was long-lasting. t cell anergy could not be reversed after restimulation of the cells with anti-cd3 and anti-cd28 mabs, although cd3 and cd28 expression was normal. in addition, restimulation of anergized t cells with anti-cd3 mabs induced normal ca2+ fluxes and resulted in increased cd3, cd28, and class ii major histocompatibility complex expression, indicating that calcineurin-mediated signaling occurs in these anergic cells. however, the expression of the il-2 receptor alpha chain was not upregulated, which may account for the failure of exogenous il-2 to reverse the anergic state. interestingly, anergic t cells and their nonanergic counterparts showed comparable levels of proliferation and cytokine production after activation with phorbol myristate acetate and ca2+ ionophore, indicating that a direct activation of a protein kinase c-dependent pathway can overcome the tolerizing effect of il-10. taken together, these data demonstrate that il-10 induces t cell anergy and therefore may play an important role in the induction and maintenance of antigen-specific t cell tolerance.",0
"cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. current computational approaches find many false positives and require ad hoc postprocessing, especially for unusually shaped particles. to address these shortcomings, we develop topaz, an efficient and accurate particle-picking pipeline using neural networks trained with a general-purpose positive-unlabeled learning method. this framework enables particle detection models to be trained with few sparsely labeled particles and no labeled negatives. topaz retrieves many more real particles than conventional picking methods while maintaining low false-positive rates, is capable of picking challenging unusually shaped proteins (for example, small, non-globular and asymmetric particles), produces more representative particle sets and does not require post hoc curation. we demonstrate the performance of topaz on two difficult datasets and three conventional datasets. topaz is modular, standalone, free and open source ( ).",0
"background the mainstay of control of the coronavirus disease 2019 (covid-19) pandemic is vaccination against severe acute respiratory syndrome coronavirus 2 (sars-cov-2). within a year, several vaccines have been developed and millions of doses delivered. reporting of adverse events is a critical postmarketing activity. methods we report findings in 23 patients who presented with thrombosis and thrombocytopenia 6 to 24 days after receiving the first dose of the chadox1 ncov-19 vaccine (astrazeneca). on the basis of their clinical and laboratory features, we identify a novel underlying mechanism and address the therapeutic implications. results in the absence of previous prothrombotic medical conditions, 22 patients presented with acute thrombocytopenia and thrombosis, primarily cerebral venous thrombosis, and 1 patient presented with isolated thrombocytopenia and a hemorrhagic phenotype. all the patients had low or normal fibrinogen levels and elevated d-dimer levels at presentation. no evidence of thrombophilia or causative precipitants was identified. testing for antibodies to platelet factor 4 (pf4) was positive in 22 patients (with 1 equivocal result) and negative in 1 patient. on the basis of the pathophysiological features observed in these patients, we recommend that treatment with platelet transfusions be avoided because of the risk of progression in thrombotic symptoms and that the administration of a nonheparin anticoagulant agent and intravenous immune globulin be considered for the first occurrence of these symptoms. conclusions vaccination against sars-cov-2 remains critical for control of the covid-19 pandemic. a pathogenic pf4-dependent syndrome, unrelated to the use of heparin therapy, can occur after the administration of the chadox1 ncov-19 vaccine. rapid identification of this rare syndrome is important because of the therapeutic implications.",0
"the immune system is the most important protective physiological system of the organism. it has many connections with other systems and is, in fact, often considered as part of the larger neuro-endocrine-immune axis. most experimental data on immune changes with aging show a decline in many immune parameters when compared to young healthy subjects. the bulk of these changes is termed immunosenescence. immunosenescence has been considered for some time as detrimental because it often leads to subclinical accumulation of pro-inflammatory factors and inflamm-aging. together, immunosenescence and inflamm-aging are suggested to stand at the origin of most of the diseases of the elderly, such as infections, cancer, autoimmune disorders, and chronic inflammatory diseases. however, an increasing number of immune-gerontologists have challenged this negative interpretation of immunosenescence with respect to its significance in aging-related alterations of the immune system. if one considers these changes from an evolutionary perspective, they can be viewed preferably as adaptive or remodeling rather than solely detrimental. whereas it is conceivable that global immune changes may lead to various diseases, it is also obvious that these changes may be needed for extended survival/longevity. recent cumulative data suggest that, without the existence of the immunosenescence/inflamm-aging duo (representing two sides of the same phenomenon), human longevity would be greatly shortened. this review summarizes recent data on the dynamic reassessment of immune changes with aging. accordingly, attempts to intervene on the aging immune system by targeting its rejuvenation, it may be more suitable to aim to maintain general homeostasis and function by appropriately improving immune-inflammatory-functions.",0
"the emergence of the betacoronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), the causative agent of coronavirus disease 2019 (covid-19), represents a considerable threat to global human health. vaccine development is focused on the principal target of the humoral immune response, the spike (s) glycoprotein, which mediates cell entry and membrane fusion. the sars-cov-2 s gene encodes 22 n-linked glycan sequons per protomer, which likely play a role in protein folding and immune evasion. here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant sars-cov-2 s immunogen. this analysis enables mapping of the glycan-processing states across the trimeric viral spike. we show how sars-cov-2 s glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design.",0
"background immunohistochemical markers are often used to classify breast cancer into subtypes that are biologically distinct and behave differently. the aim of this study was to estimate mortality for patients with the major subtypes of breast cancer as classified using five immunohistochemical markers, to investigate patterns of mortality over time, and to test for heterogeneity by subtype. methods and findings we pooled data from more than 10,000 cases of invasive breast cancer from 12 studies that had collected information on hormone receptor status, human epidermal growth factor receptor-2 (her2) status, and at least one basal marker (cytokeratin 5/6 or epidermal growth factor receptor ) together with survival time data. tumours were classified as luminal and nonluminal tumours according to hormone receptor expression. these two groups were further subdivided according to expression of her2, and finally, the luminal and nonluminal her2-negative tumours were categorised according to expression of basal markers. changes in mortality rates over time differed by subtype. in women with luminal her2-negative subtypes, mortality rates were constant over time, whereas mortality rates associated with the luminal her2-positive and nonluminal subtypes tended to peak within 5 y of diagnosis and then decline over time. in the first 5 y after diagnosis the nonluminal tumours were associated with a poorer prognosis, but over longer follow-up times the prognosis was poorer in the luminal subtypes, with the worst prognosis at 15 y being in the luminal her2-positive tumours. basal marker expression distinguished the her2-negative luminal and nonluminal tumours into different subtypes. these patterns were independent of any systemic adjuvant therapy. conclusions the six subtypes of breast cancer defined by expression of five markers show distinct behaviours with important differences in short term and long term prognosis. application of these markers in the clinical setting could have the potential to improve the targeting of adjuvant chemotherapy to those most likely to benefit. the different patterns of mortality over time also suggest important biological differences between the subtypes that may result in differences in response to specific therapies, and that stratification of breast cancers by clinically relevant subtypes in clinical trials is urgently required.",0
"reactive oxygen species (ros) constitute a group of highly reactive molecules that have evolved as regulators of important signaling pathways. it is now well accepted that moderate levels of ros are required for several cellular functions, including gene expression. the production of ros is elevated in tumor cells as a consequence of increased metabolic rate, gene mutation and relative hypoxia, and excess ros are quenched by increased antioxidant enzymatic and nonenzymatic pathways in the same cells. moderate increases of ros contribute to several pathologic conditions, among which are tumor promotion and progression, as they are involved in different signaling pathways and induce dna mutation. however, ros are also able to trigger programmed cell death (pcd). our review will emphasize the molecular mechanisms useful for the development of therapeutic strategies that are based on modulating ros levels to treat cancer. specifically, we will report on the growing data that highlight the role of ros generated by different metabolic pathways as trojan horses to eliminate cancer cells.",0
"the kappa statistic is frequently used to test interrater reliability. the importance of rater reliability lies in the fact that it represents the extent to which the data collected in the study are correct representations of the variables measured. measurement of the extent to which data collectors (raters) assign the same score to the same variable is called interrater reliability. while there have been a variety of methods to measure interrater reliability, traditionally it was measured as percent agreement, calculated as the number of agreement scores divided by the total number of scores. in 1960, jacob cohen critiqued use of percent agreement due to its inability to account for chance agreement. he introduced the cohen's kappa, developed to account for the possibility that raters actually guess on at least some variables due to uncertainty. like most correlation statistics, the kappa can range from -1 to +1. while the kappa is one of the most commonly used statistics to test interrater reliability, it has limitations. judgments about what level of kappa should be acceptable for health research are questioned. cohen's suggested interpretation may be too lenient for health related studies because it implies that a score as low as 0.41 might be acceptable. kappa and percent agreement are compared, and levels for both kappa and percent agreement that should be demanded in healthcare studies are suggested.",0
"background the sars outbreak of 2002-2003 presented clinicians with a new, life-threatening disease for which they had no experience in treating and no research on the effectiveness of treatment options. the world health organization (who) expert panel on sars treatment requested a systematic review and comprehensive summary of treatments used for sars-infected patients in order to guide future treatment and identify priorities for research. methods and findings in response to the who request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (lpv/r), type i interferon (ifn), intravenous immunoglobulin (ivig), and sars convalescent plasma from both in vitro studies and in sars patients. we also searched for clinical trial evidence of treatment for acute respiratory distress syndrome. sources of data were the literature databases medline, embase, biosis, and the cochrane central register of controlled trials (central) up to february 2005. data from publications were extracted and evidence within studies was classified using predefined criteria. in total, 54 sars treatment studies, 15 in vitro studies, and three acute respiratory distress syndrome studies met our inclusion criteria. within in vitro studies, ribavirin, lopinavir, and type i ifn showed inhibition of sars-cov in tissue culture. in sars-infected patient reports on ribavirin, 26 studies were classified as inconclusive, and four showed possible harm. seven studies of convalescent plasma or ivig, three of ifn type i, and two of lpv/r were inconclusive. in 29 studies of steroid use, 25 were inconclusive and four were classified as causing possible harm. conclusions despite an extensive literature reporting on sars treatments, it was not possible to determine whether treatments benefited patients during the sars outbreak. some may have been harmful. clinical trials should be designed to validate a standard protocol for dosage and timing, and to accrue data in real time during future outbreaks to monitor specific adverse effects and help inform treatment.",0
"background knowledge of the number of deaths caused by risk factors is needed for health policy and priority setting. our aim was to estimate the mortality effects of the following 12 modifiable dietary, lifestyle, and metabolic risk factors in the united states (us) using consistent and comparable methods: high blood glucose, low-density lipoprotein (ldl) cholesterol, and blood pressure; overweight-obesity; high dietary trans fatty acids and salt; low dietary polyunsaturated fatty acids, omega-3 fatty acids (seafood), and fruits and vegetables; physical inactivity; alcohol use; and tobacco smoking. methods and findings we used data on risk factor exposures in the us population from nationally representative health surveys and disease-specific mortality statistics from the national center for health statistics. we obtained the etiological effects of risk factors on disease-specific mortality, by age, from systematic reviews and meta-analyses of epidemiological studies that had adjusted (i) for major potential confounders, and (ii) where possible for regression dilution bias. we estimated the number of disease-specific deaths attributable to all non-optimal levels of each risk factor exposure, by age and sex. in 2005, tobacco smoking and high blood pressure were responsible for an estimated 467,000 (95% confidence interval 436,000-500,000) and 395,000 (372,000-414,000) deaths, accounting for about one in five or six deaths in us adults. overweight-obesity (216,000; 188,000-237,000) and physical inactivity (191,000; 164,000-222,000) were each responsible for nearly 1 in 10 deaths. high dietary salt (102,000; 97,000-107,000), low dietary omega-3 fatty acids (84,000; 72,000-96,000), and high dietary trans fatty acids (82,000; 63,000-97,000) were the dietary risks with the largest mortality effects. although 26,000 (23,000-40,000) deaths from ischemic heart disease, ischemic stroke, and diabetes were averted by current alcohol use, they were outweighed by 90,000 (88,000-94,000) deaths from other cardiovascular diseases, cancers, liver cirrhosis, pancreatitis, alcohol use disorders, road traffic and other injuries, and violence. conclusions smoking and high blood pressure, which both have effective interventions, are responsible for the largest number of deaths in the us. other dietary, lifestyle, and metabolic risk factors for chronic diseases also cause a substantial number of deaths in the us.",0
"dna methylation is a defining feature of mammalian cellular identity and is essential for normal development. most cell types, except germ cells and pre-implantation embryos, display relatively stable dna methylation patterns, with 70-80% of all cpgs being methylated. despite recent advances, we still have a limited understanding of when, where and how many cpgs participate in genomic regulation. here we report the in-depth analysis of 42 whole-genome bisulphite sequencing data sets across 30 diverse human cell and tissue types. we observe dynamic regulation for only 21.8% of autosomal cpgs within a normal developmental context, most of which are distal to transcription start sites. these dynamic cpgs co-localize with gene regulatory elements, particularly enhancers and transcription-factor-binding sites, which allow identification of key lineage-specific regulators. in addition, differentially methylated regions (dmrs) often contain single nucleotide polymorphisms associated with cell-type-related diseases as determined by genome-wide association studies. the results also highlight the general inefficiency of whole-genome bisulphite sequencing, as 70-80% of the sequencing reads across these data sets provided little or no relevant information about cpg methylation. to demonstrate further the utility of our dmr set, we use it to classify unknown samples and identify representative signature regions that recapitulate major dna methylation dynamics. in summary, although in theory every cpg can change its methylation state, our results suggest that only a fraction does so as part of coordinated regulatory programs. therefore, our selected dmrs can serve as a starting point to guide new, more effective reduced representation approaches to capture the most informative fraction of cpgs, as well as further pinpoint putative regulatory elements.",0
"macroautophagy (referred to here as autophagy) is induced by starvation to capture and degrade intracellular proteins and organelles in lysosomes, which recycles intracellular components to sustain metabolism and survival. autophagy also plays a major homeostatic role in controlling protein and organelle quality and quantity. dysfunctional autophagy contributes to many diseases. in cancer, autophagy can be neutral, tumor-suppressive, or tumor-promoting in different contexts. large-scale genomic analysis of human cancers indicates that the loss or mutation of core autophagy genes is uncommon, whereas oncogenic events that activate autophagy and lysosomal biogenesis have been identified. autophagic flux, however, is difficult to measure in human tumor samples, making functional assessment of autophagy problematic in a clinical setting. autophagy impacts cellular metabolism, the proteome, and organelle numbers and quality, which alter cell functions in diverse ways. moreover, autophagy influences the interaction between the tumor and the host by promoting stress adaptation and suppressing activation of innate and adaptive immune responses. additionally, autophagy can promote a cross-talk between the tumor and the stroma, which can support tumor growth, particularly in a nutrient-limited microenvironment. thus, the role of autophagy in cancer is determined by nutrient availability, microenvironment stress, and the presence of an immune system. here we discuss recent developments in the role of autophagy in cancer, in particular how autophagy can promote cancer through suppressing p53 and preventing energy crisis, cell death, senescence, and an anti-tumor immune response.",0
"breast cancer is a heterogeneous disease in terms of histology, therapeutic response, dissemination patterns to distant sites, and patient outcomes. global gene expression analyses using high-throughput technologies have helped to explain much of this heterogeneity and provided important new classifications of cancer patients. in the last decade, genomic studies have established five breast cancer intrinsic subtypes (luminal a, luminal b, her2-enriched, claudin-low, basal-like) and a normal breast-like group. in this review, we dissect the most recent data on this genomic classification of breast cancer with a special focus on the claudin-low subtype, which appears enriched for mesenchymal and stem cell features. in addition, we discuss how the combination of standard clinical-pathological markers with the information provided by these genomic entities might help further understand the biological complexity of this disease, increase the efficacy of current and novel therapies, and ultimately improve outcomes for breast cancer patients.",0
"background vaccine development in the post-genomic era often begins with the in silico screening of genome information, with the most probable protective antigens being predicted rather than requiring causative microorganisms to be grown. despite the obvious advantages of this approach--such as speed and cost efficiency--its success remains dependent on the accuracy of antigen prediction. most approaches use sequence alignment to identify antigens. this is problematic for several reasons. some proteins lack obvious sequence similarity, although they may share similar structures and biological properties. the antigenicity of a sequence may be encoded in a subtle and recondite manner not amendable to direct identification by sequence alignment. the discovery of truly novel antigens will be frustrated by their lack of similarity to antigens of known provenance. to overcome the limitations of alignment-dependent methods, we propose a new alignment-free approach for antigen prediction, which is based on auto cross covariance (acc) transformation of protein sequences into uniform vectors of principal amino acid properties. results bacterial, viral and tumour protein datasets were used to derive models for prediction of whole protein antigenicity. every set consisted of 100 known antigens and 100 non-antigens. the derived models were tested by internal leave-one-out cross-validation and external validation using test sets. an additional five training sets for each class of antigens were used to test the stability of the discrimination between antigens and non-antigens. the models performed well in both validations showing prediction accuracy of 70% to 89%. the models were implemented in a server, which we call vaxijen. conclusion vaxijen is the first server for alignment-independent prediction of protective antigens. it was developed to allow antigen classification solely based on the physicochemical properties of proteins without recourse to sequence alignment. the server can be used on its own or in combination with alignment-based prediction methods. it is freely-available online at the url:",0
"background being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly from bacteria, fungi, viruses, nematodes and insects. to adapt to such adverse situations, plants have evolved well-developed mechanisms that help to perceive the stress signal and enable optimal growth response. phytohormones play critical roles in helping the plants to adapt to adverse environmental conditions. the elaborate hormone signaling networks and their ability to crosstalk make them ideal candidates for mediating defense responses. results recent research findings have helped to clarify the elaborate signaling networks and the sophisticated crosstalk occurring among the different hormone signaling pathways. in this review, we summarize the roles of the major plant hormones in regulating abiotic and biotic stress responses with special focus on the significance of crosstalk between different hormones in generating a sophisticated and efficient stress response. we divided the discussion into the roles of aba, salicylic acid, jasmonates and ethylene separately at the start of the review. subsequently, we have discussed the crosstalk among them, followed by crosstalk with growth promoting hormones (gibberellins, auxins and cytokinins). these have been illustrated with examples drawn from selected abiotic and biotic stress responses. the discussion on seed dormancy and germination serves to illustrate the fine balance that can be enforced by the two key hormones aba and ga in regulating plant responses to environmental signals. conclusions the intricate web of crosstalk among the often redundant multitudes of signaling intermediates is just beginning to be understood. future research employing genome-scale systems biology approaches to solve problems of such magnitude will undoubtedly lead to a better understanding of plant development. therefore, discovering additional crosstalk mechanisms among various hormones in coordinating growth under stress will be an important theme in the field of abiotic stress research. such efforts will help to reveal important points of genetic control that can be useful to engineer stress tolerant crops.",0
"objective to review the methods and dimensions of data quality assessment in the context of electronic health record (ehr) data reuse for research. materials and methods a review of the clinical research literature discussing data quality assessment methodology for ehr data was performed. using an iterative process, the aspects of data quality being measured were abstracted and categorized, as well as the methods of assessment used. results five dimensions of data quality were identified, which are completeness, correctness, concordance, plausibility, and currency, and seven broad categories of data quality assessment methods: comparison with gold standards, data element agreement, data source agreement, distribution comparison, validity checks, log review, and element presence. discussion examination of the methods by which clinical researchers have investigated the quality and suitability of ehr data for research shows that there are fundamental features of data quality, which may be difficult to measure, as well as proxy dimensions. researchers interested in the reuse of ehr data for clinical research are recommended to consider the adoption of a consistent taxonomy of ehr data quality, to remain aware of the task-dependence of data quality, to integrate work on data quality assessment from other fields, and to adopt systematic, empirically driven, statistically based methods of data quality assessment. conclusion there is currently little consistency or potential generalizability in the methods used to assess ehr data quality. if the reuse of ehr data for clinical research is to become accepted, researchers should adopt validated, systematic methods of ehr data quality assessment.",0
"new evidence and consensus has led to further revision of the mcdonald criteria for diagnosis of multiple sclerosis. the use of imaging for demonstration of dissemination of central nervous system lesions in space and time has been simplified, and in some circumstances dissemination in space and time can be established by a single scan. these revisions simplify the criteria, preserve their diagnostic sensitivity and specificity, address their applicability across populations, and may allow earlier diagnosis and more uniform and widespread use.",0
"cell junctions have been investigated in the amphibian epidermis, a stratified squamous epithelium, and compared to those described previously in simple columnar epithelia of mammalian cavitary organs. in adult frogs and toads, and in larvae approaching metamorphosis, belts of membrane fusion or zonulae occludentes of considerable depth are regularly found between adjoining cells of the outermost layer of the stratum corneum, binding the cells together into a continuous, uninterrupted sheet. another set of occluding zonules appears in the second cornified layer (when such a layer is present), and a third set usually occurs in the outermost layer of the stratum granulosum. specialized elements described as ""modified"" and ""composite"" desmosomes are encountered along the lateral and basal aspects, respectively, of the cornified cells; ordinary desmosomes and maculae occludentes (i.e., spots of membrane fusion) are found in all other strata. the usual 200 a intercellular gap is generally maintained between the cells of the stratum germinativum at the basal ends of the intercellular spaces. hence, the intercellular spaces of the epidermis form a largely continuous network, closed to the external medium and open to the dermal interstitia. the situation is comparable to that found in columnar epithelia, except that the intercellular spaces are much more extensive, and an extracellular subcompartment (or two) apparently exists in the stratum corneum and between the latter and the stratum granulosum. the last subcompartment is usually filled with a dense substance, probably derived from discharged secretory granules. the tripartite junctional complex characteristic of lumen-lining epithelia (i.e., a zonula occludens followed by a zonula adhaerens, and desmosome) is seen only in early larvae; in adults and in larvae approaching metamorphosis, the occluding zonule is followed directly by a series of modified desmosomes. interpreted in the light of current physiological data, these findings suggest that the diffusion of water, ions, and small, water-soluble molecules is impeded along the intercellular spaces of the epidermis by zonulae occludentes while it is facilitated from cell to cell within the epidermis by zonulae and maculae occludentes.",0
"cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. these genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. the stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. we find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. this phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.",0
"amyotrophic lateral sclerosis (als) is a neurodegenerative disease characterised by progressive muscular paralysis reflecting degeneration of motor neurones in the primary motor cortex, corticospinal tracts, brainstem and spinal cord. incidence (average 1.89 per 100,000/year) and prevalence (average 5.2 per 100,000) are relatively uniform in western countries, although foci of higher frequency occur in the western pacific. the mean age of onset for sporadic als is about 60 years. overall, there is a slight male prevalence (m:f ratio approximately 1.5:1). approximately two thirds of patients with typical als have a spinal form of the disease (limb onset) and present with symptoms related to focal muscle weakness and wasting, where the symptoms may start either distally or proximally in the upper and lower limbs. gradually, spasticity may develop in the weakened atrophic limbs, affecting manual dexterity and gait. patients with bulbar onset als usually present with dysarthria and dysphagia for solid or liquids, and limbs symptoms can develop almost simultaneously with bulbar symptoms, and in the vast majority of cases will occur within 1-2 years. paralysis is progressive and leads to death due to respiratory failure within 2-3 years for bulbar onset cases and 3-5 years for limb onset als cases. most als cases are sporadic but 5-10% of cases are familial, and of these 20% have a mutation of the sod1 gene and about 2-5% have mutations of the tardbp (tdp-43) gene. two percent of apparently sporadic patients have sod1 mutations, and tardbp mutations also occur in sporadic cases. the diagnosis is based on clinical history, examination, electromyography, and exclusion of 'als-mimics' (e.g. cervical spondylotic myelopathies, multifocal motor neuropathy, kennedy's disease) by appropriate investigations. the pathological hallmarks comprise loss of motor neurones with intraneuronal ubiquitin-immunoreactive inclusions in upper motor neurones and tdp-43 immunoreactive inclusions in degenerating lower motor neurones. signs of upper motor neurone and lower motor neurone damage not explained by any other disease process are suggestive of als. the management of als is supportive, palliative, and multidisciplinary. non-invasive ventilation prolongs survival and improves quality of life. riluzole is the only drug that has been shown to extend survival.",0
"purpose pembrolizumab monotherapy has demonstrated durable antitumor activity in advanced programmed death ligand 1 (pd-l1)-expressing non ‒ small-cell lung cancer (nsclc). we report 5-year outcomes from the phase ib keynote-001 study. these data provide the longest efficacy and safety follow-up for patients with nsclc treated with pembrolizumab monotherapy. patients and methods eligible patients had confirmed locally advanced/metastatic nsclc and provided a contemporaneous tumor sample for pd-l1 evaluation by immunohistochemistry using the 22c3 antibody. patients received intravenous pembrolizumab 2 mg/kg every 3 weeks or 10 mg/kg every 2 or 3 weeks. investigators assessed response per immune-related response criteria. the primary efficacy end point was objective response rate. overall survival (os) and duration of response were secondary end points. results we enrolled 101 treatment-naive and 449 previously treated patients. median follow-up was 60.6 months (range, 51.8 to 77.9 months). at data cutoff-november 5, 2018-450 patients (82%) had died. median os was 22.3 months (95% ci, 17.1 to 32.3 months) in treatment-naive patients and 10.5 months (95% ci, 8.6 to 13.2 months) in previously treated patients. estimated 5-year os was 23.2% for treatment-naive patients and 15.5% for previously treated patients. in patients with a pd-l1 tumor proportion score of 50% or greater, 5-year os was 29.6% and 25.0% in treatment-naive and previously treated patients, respectively. compared with analysis at 3 years, only three new-onset treatment-related grade 3 adverse events occurred (hypertension, glucose intolerance, and hypersensitivity reaction, all resolved). no late-onset grade 4 or 5 treatment-related adverse events occurred. conclusion pembrolizumab monotherapy provided durable antitumor activity and high 5-year os rates in patients with treatment-naive or previously treated advanced nsclc. of note, the 5-year os rate exceeded 25% among patients with a pd-l1 tumor proportion score of 50% or greater. pembrolizumab had a tolerable long-term safety profile with little evidence of late-onset or new toxicity.",0
"although kraken's k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. kraken 2 improves upon kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.",0
"background scoping studies are increasingly common for broadly searching the literature on a specific topic, yet researchers lack an agreed-upon definition of and framework for the methodology. in 2005, arksey and o'malley offered a methodological framework for conducting scoping studies. in their subsequent work, levac et al. responded to arksey and o'malley's call for advances to their framework. our paper builds on this collective work to further enhance the methodology. discussion this paper begins with a background on what constitutes a scoping study, followed by a discussion about four primary subjects: (1) the types of questions for which arksey and o'malley's framework is most appropriate, (2) a contribution to the discussion aimed at enhancing the six steps of arskey and o'malley's framework, (3) the strengths and challenges of our experience working with arksey and o'malley's framework as a large, inter-professional team, and (4) lessons learned. our goal in this paper is to add to the discussion encouraged by arksey and o'malley to further enhance this methodology. summary performing a scoping study using arksey and o'malley's framework was a valuable process for our research team even if how it was useful was unexpected. based on our experience, we recommend researchers be aware of their expectations for how arksey and o'malley's framework might be useful in relation to their research question, and remain flexible to clarify concepts and to revise the research question as the team becomes familiar with the literature. questions portraying comparisons such as between interventions, programs, or approaches seem to be the most suitable to scoping studies. we also suggest assessing the quality of studies and conducting a trial of the method before fully embarking on the charting process in order to ensure consistency. the benefits of engaging a large, inter-professional team such as ours throughout every stage of arksey and o'malley's framework far exceed the challenges and we recommend researchers consider the value of such a team. the strengths include breadth and depth of knowledge each team member brings to the study and time efficiencies. in our experience, the most significant challenges presented to our team were those related to consensus and resource limitations. effective communication is key to the success of a large group. we propose that by clarifying the framework, the purposes of scoping studies are attainable and the definition is enriched.",0
"antibodies specific for the insulin-regulatable glucose transporter (glut 4) were used to immunolocalize this protein in brown adipose tissue from basal- and insulin-treated rats. cryosections of fixed tissue were incubated with antibodies, which were subsequently labeled with protein a/gold and examined by em. antibodies against albumin and cathepsin d were also used with gold particles of different sizes to identify early and late endosomes, respectively. under basal conditions 99% of the glut 4 labeling was located within the cell. labeling was predominantly in the trans-golgi reticulum and tubulo-vesicular structures elsewhere in the cytoplasm. in insulin-stimulated cells approximately 40% of the glut 4 labeling was at the cell surface, where it was randomly distributed, except for occasional clustering in coated pits. moreover, after insulin treatment, glut 4 was also enriched in early endosomes. we conclude that translocation of glut 4 to the cell surface is the major mechanism by which insulin increases glucose transport. in addition, these results suggest that in the presence of insulin glut 4 recycles from the cell surface, probably via the coated pit-endosome pathway that has been characterized for cell surface receptors, and also that insulin causes the redistribution of glut 4 by stimulating exocytosis from glut 4-containing tubulo-vesicular structures, rather than by slowing endocytosis of glut 4.",0
"the iedb, contains information on immune epitopes--the molecular targets of adaptive immune responses--curated from the published literature and submitted by national institutes of health funded epitope discovery efforts. from 2004 to 2012 the iedb curation of journal articles published since 1960 has caught up to the present day, with >95% of relevant published literature manually curated amounting to more than 15,000 journal articles and more than 704,000 experiments to date. the revised curation target since 2012 has been to make recent research findings quickly available in the iedb and thereby ensure that it continues to be an up-to-date resource. having gathered a comprehensive dataset in the iedb, a complete redesign of the query and reporting interface has been performed in the iedb 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. we here present this most recent release of the iedb and describe the user testing procedures as well as the use of external ontologies that have enabled it.",0
"resting-state functional magnetic resonance imaging (fmri) has attracted more and more attention because of its effectiveness, simplicity and non-invasiveness in exploration of the intrinsic functional architecture of the human brain. however, user-friendly toolbox for ""pipeline"" data analysis of resting-state fmri is still lacking. based on some functions in statistical parametric mapping (spm) and resting-state fmri data analysis toolkit (rest), we have developed a matlab toolbox called data processing assistant for resting-state fmri (dparsf) for ""pipeline"" data analysis of resting-state fmri. after the user arranges the digital imaging and communications in medicine (dicom) files and click a few buttons to set parameters, dparsf will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (alff), and fractional alff. dparsf can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. in addition, users can also use dparsf to extract time courses from regions of interest.",0
"utility of vaccine campaigns to control coronavirus 2019 disease (covid-19) is not merely dependent on vaccine efficacy and safety. vaccine acceptance among the general public and healthcare workers appears to have a decisive role in the successful control of the pandemic. the aim of this review was to provide an up-to-date assessment of covid-19 vaccination acceptance rates worldwide. a systematic search of the peer-reviewed english survey literature indexed in pubmed was done on 25 december 2020. results from 31 peer-reviewed published studies met the inclusion criteria and formed the basis for the final covid-19 vaccine acceptance estimates. survey studies on covid-19 vaccine acceptance rates were found from 33 different countries. among adults representing the general public, the highest covid-19 vaccine acceptance rates were found in ecuador (97.0%), malaysia (94.3%), indonesia (93.3%) and china (91.3%). however, the lowest covid-19 vaccine acceptance rates were found in kuwait (23.6%), jordan (28.4%), italy (53.7), russia (54.9%), poland (56.3%), us (56.9%), and france (58.9%). only eight surveys among healthcare workers (doctors and nurses) were found, with vaccine acceptance rates ranging from 27.7% in the democratic republic of the congo to 78.1% in israel. in the majority of survey studies among the general public stratified per country (29/47, 62%), the acceptance of covid-19 vaccination showed a level of ≥70%. low rates of covid-19 vaccine acceptance were reported in the middle east, russia, africa and several european countries. this could represent a major problem in the global efforts to control the current covid-19 pandemic. more studies are recommended to address the scope of covid-19 vaccine hesitancy. such studies are particularly needed in the middle east and north africa, sub-saharan africa, eastern europe, central asia, middle and south america. addressing the scope of covid-19 vaccine hesitancy in various countries is recommended as an initial step for building trust in covid-19 vaccination efforts.",0
"in the last two years the pfam database ( has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. arguably the most significant of these changes is that pfam is now primarily based on the uniprotkb reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. it also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. matches to the full uniprotkb database are, however, still available and pfam annotations for individual uniprotkb sequences can still be retrieved. some pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with uniprot to see if sequences from them can be incorporated into reference proteomes. pfam-b, the automatically-generated supplement to pfam, has been removed. the current release (pfam 29.0) includes 16 295 entries and 559 clans. the facility to view the relationship between families within a clan has been improved by the introduction of a new tool.",0
"the number of deaths from colorectal cancer in japan continues to increase. colorectal cancer deaths exceeded 50,000 in 2016. in the 2019 edition, revision of all aspects of treatments was performed, with corrections and additions made based on knowledge acquired since the 2016 version (drug therapy) and the 2014 version (other treatments). the japanese society for cancer of the colon and rectum guidelines 2019 for the treatment of colorectal cancer (jsccr guidelines 2019) have been prepared to show standard treatment strategies for colorectal cancer, to eliminate disparities among institutions in terms of treatment, to eliminate unnecessary treatment and insufficient treatment and to deepen mutual understanding between healthcare professionals and patients by making these guidelines available to the general public. these guidelines have been prepared by consensuses reached by the jsccr guideline committee, based on a careful review of the evidence retrieved by literature searches and in view of the medical health insurance system and actual clinical practice settings in japan. therefore, these guidelines can be used as a tool for treating colorectal cancer in actual clinical practice settings. more specifically, they can be used as a guide to obtaining informed consent from patients and choosing the method of treatment for each patient. controversial issues were selected as clinical questions, and recommendations were made. each recommendation is accompanied by a classification of the evidence and a classification of recommendation categories based on the consensus reached by the guideline committee members. here, we present the english version of the jsccr guidelines 2019.",0
"on 11 march 2020, the world health organization (who) declared coronavirus disease 2019 (covid-19) a pandemic 1 . the strategies based on non-pharmaceutical interventions that were used to contain the outbreak in china appear to be effective 2 , but quantitative research is still needed to assess the efficacy of non-pharmaceutical interventions and their timings 3 . here, using epidemiological data on covid-19 and anonymized data on human movement 4,5 , we develop a modelling framework that uses daily travel networks to simulate different outbreak and intervention scenarios across china. we estimate that there were a total of 114,325 cases of covid-19 (interquartile range 76,776-164,576) in mainland china as of 29 february 2020. without non-pharmaceutical interventions, we predict that the number of cases would have been 67-fold higher (interquartile range 44-94-fold) by 29 february 2020, and we find that the effectiveness of different interventions varied. we estimate that early detection and isolation of cases prevented more infections than did travel restrictions and contact reductions, but that a combination of non-pharmaceutical interventions achieved the strongest and most rapid effect. according to our model, the lifting of travel restrictions from 17 february 2020 does not lead to an increase in cases across china if social distancing interventions can be maintained, even at a limited level of an on average 25% reduction in contact between individuals that continues until late april. these findings improve our understanding of the effects of non-pharmaceutical interventions on covid-19, and will inform response efforts across the world.",0
"we describe a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic dna alterations. the method, named absolute, can detect subclonal heterogeneity and somatic homozygosity, and it can calculate statistical sensitivity for detection of specific aberrations. we used absolute to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs. this analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes tp53 and nf1 and in a candidate tumor suppressor gene cdk12. we also used absolute to infer absolute allelic copy-number profiles from 3,155 diverse cancer specimens, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression (for example, with recessive inactivation of nf1 being less common after genome doubling). absolute will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.",0
"background surgical resection alone is regarded as the standard of care for patients with liver metastases from colorectal cancer, but relapse is common. we assessed the combination of perioperative chemotherapy and surgery compared with surgery alone for patients with initially resectable liver metastases from colorectal cancer. methods this parallel-group study reports the trial's final data for progression-free survival for a protocol unspecified interim time-point, while overall survival is still being monitored. 364 patients with histologically proven colorectal cancer and up to four liver metastases were randomly assigned to either six cycles of folfox4 before and six cycles after surgery or to surgery alone (182 in perioperative chemotherapy group vs 182 in surgery group). patients were centrally randomised by minimisation, adjusting for centre and risk score. the primary objective was to detect a hazard ratio (hr) of 0.71 or less for progression-free survival. primary analysis was by intention to treat. analyses were repeated for all eligible (171 vs 171) and resected patients (151 vs 152). this trial is registered with clinicaltrials.gov, number nct00006479. findings in the perioperative chemotherapy group, 151 (83%) patients were resected after a median of six (range 1-6) preoperative cycles and 115 (63%) patients received a median six (1-8) postoperative cycles. 152 (84%) patients were resected in the surgery group. the absolute increase in rate of progression-free survival at 3 years was 7.3% (from 28.1% to 35.4% ; hr 0.79 ; p=0.058) in randomised patients; 8.1% (from 28.1% to 36.2% ; hr 0.77 ; p=0.041) in eligible patients; and 9.2% (from 33.2% to 42.4% ; hr 0.73 ; p=0.025) in patients undergoing resection. 139 patients died (64 in perioperative chemotherapy group vs 75 in surgery group). reversible postoperative complications occurred more often after chemotherapy than after surgery (40/159 vs 27/170 ; p=0.04). after surgery we recorded two deaths in the surgery alone group and one in the perioperative chemotherapy group. interpretation perioperative chemotherapy with folfox4 is compatible with major liver surgery and reduces the risk of events of progression-free survival in eligible and resected patients.",0
"in a contemporary clinical laboratory it is very common to have to assess the agreement between two quantitative methods of measurement. the correct statistical approach to assess this degree of agreement is not obvious. correlation and regression studies are frequently proposed. however, correlation studies the relationship between one variable and another, not the differences, and it is not recommended as a method for assessing the comparability between methods. in 1983 altman and bland (b&a) proposed an alternative analysis, based on the quantification of the agreement between two quantitative measurements by studying the mean difference and constructing limits of agreement. the b&a plot analysis is a simple way to evaluate a bias between the mean differences, and to estimate an agreement interval, within which 95% of the differences of the second method, compared to the first one, fall. data can be analyzed both as unit differences plot and as percentage differences plot. the b&a plot method only defines the intervals of agreements, it does not say whether those limits are acceptable or not. acceptable limits must be defined a priori, based on clinical necessity, biological considerations or other goals. the aim of this article is to provide guidance on the use and interpretation of bland altman analysis in method comparison studies.",0
"background inanimate surfaces have often been described as the source for outbreaks of nosocomial infections. the aim of this review is to summarize data on the persistence of different nosocomial pathogens on inanimate surfaces. methods the literature was systematically reviewed in medline without language restrictions. in addition, cited articles in a report were assessed and standard textbooks on the topic were reviewed. all reports with experimental evidence on the duration of persistence of a nosocomial pathogen on any type of surface were included. results most gram-positive bacteria, such as enterococcus spp. (including vre), staphylococcus aureus (including mrsa), or streptococcus pyogenes, survive for months on dry surfaces. many gram-negative species, such as acinetobacter spp., escherichia coli, klebsiella spp., pseudomonas aeruginosa, serratia marcescens, or shigella spp., can also survive for months. a few others, such as bordetella pertussis, haemophilus influenzae, proteus vulgaris, or vibrio cholerae, however, persist only for days. mycobacteria, including mycobacterium tuberculosis, and spore-forming bacteria, including clostridium difficile, can also survive for months on surfaces. candida albicans as the most important nosocomial fungal pathogen can survive up to 4 months on surfaces. persistence of other yeasts, such as torulopsis glabrata, was described to be similar (5 months) or shorter (candida parapsilosis, 14 days). most viruses from the respiratory tract, such as corona, coxsackie, influenza, sars or rhino virus, can persist on surfaces for a few days. viruses from the gastrointestinal tract, such as astrovirus, hav, polio- or rota virus, persist for approximately 2 months. blood-borne viruses, such as hbv or hiv, can persist for more than one week. herpes viruses, such as cmv or hsv type 1 and 2, have been shown to persist from only a few hours up to 7 days. conclusion the most common nosocomial pathogens may well survive or persist on surfaces for months and can thereby be a continuous source of transmission if no regular preventive surface disinfection is performed.",0
"caveolae or noncoated plasmalemmal vesicles found in a variety of cells have been implicated in a number of important cellular functions including endocytosis, transcytosis, and potocytosis. their function in transport across endothelium has been especially controversial, at least in part because there has not been any way to selectively inhibit this putative pathway. we now show that the ability of sterol binding agents such as filipin to disassemble endothelial noncoated but not coated plasmalemmal vesicles selectively inhibits caveolae-mediated intracellular and transcellular transport of select macromolecules in endothelium. filipin significantly reduces the transcellular transport of insulin and albumin across cultured endothelial cell monolayers. rat lung microvascular permeability to albumin in situ is significantly decreased after filipin perfusion. conversely, paracellular transport of the small solute inulin is not inhibited in vitro or in situ. in addition, we show that caveolae mediate the scavenger endocytosis of conformationally modified albumins for delivery to endosomes and lysosomes for degradation. this intracellular transport is inhibited by filipin both in vitro and in situ. other sterol binding agents including nystatin and digitonin also inhibit this degradative process. conversely, the endocytosis and degradation of activated alpha 2-macroglobulin, a known ligand of the clathrin-dependent pathway, is not affected. interestingly, filipin appears to inhibit insulin uptake by endothelium for transcytosis, a caveolae-mediated process, but not endocytosis for degradation, apparently mediated by the clathrin-coated pathway. such selective inhibition of caveolae not only provides critical evidence for the role of caveolae in the intracellular and transcellular transport of select macromolecules in endothelium but also may be useful for distinguishing transport mediated by coated versus noncoated vesicles.",0
"background evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. astral is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. astral uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. results we introduce astral-iii, which substantially improves the running time of astral-ii and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). astral-iii limits the bipartition constraint set (x) to grow at most linearly with n and k. moreover, it handles polytomies more efficiently than astral-ii, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. the asymptotic running time of astral-iii in the presence of polytomies is where d=o(nk) is the sum of degrees of all unique nodes in input trees. the running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. in extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. we observe on a biological avian phylogenomic dataset of 14k genes that contracting low support branches greatly improve results. conclusions astral-iii is a faster version of the astral method for phylogenetic reconstruction and can scale up to 10,000 species. with astral-iii, low support branches can be removed, resulting in improved accuracy.",0
"the presence of inflammatory immune cells in human tumors raises a fundamental question in oncology: how do cancer cells avoid the destruction by immune attack? in principle, tumor development can be controlled by cytotoxic innate and adaptive immune cells; however, as the tumor develops from neoplastic tissue to clinically detectable tumors, cancer cells evolve different mechanisms that mimic peripheral immune tolerance in order to avoid tumoricidal attack. here, we provide an update of recent accomplishments, unifying concepts, and future challenges to study tumor-associated immune cells, with an emphasis on metastatic carcinomas.",0
"cancer of the pancreas remains one of the deadliest cancer types. based on the globocan 2012 estimates, pancreatic cancer causes more than 331000 deaths per year, ranking as the seventh leading cause of cancer death in both sexes together. globally, about 338000 people had pancreatic cancer in 2012, making it the 11 th most common cancer. the highest incidence and mortality rates of pancreatic cancer are found in developed countries. trends for pancreatic cancer incidence and mortality varied considerably in the world. a known cause of pancreatic cancer is tobacco smoking. this risk factor is likely to explain some of the international variations and gender differences. the overall five-year survival rate is about 6% (ranges from 2% to 9%), but this vary very small between developed and developing countries. to date, the causes of pancreatic cancer are still insufficiently known, although certain risk factors have been identified, such as smoking, obesity, genetics, diabetes, diet, inactivity. there are no current screening recommendations for pancreatic cancer, so primary prevention is of utmost importance. a better understanding of the etiology and identifying the risk factors is essential for the primary prevention of this disease.",0
"rapid innovations in cardiovascular magnetic resonance (cmr) now permit the routine acquisition of quantitative measures of myocardial and blood t1 which are key tissue characteristics. these capabilities introduce a new frontier in cardiology, enabling the practitioner/investigator to quantify biologically important myocardial properties that otherwise can be difficult to ascertain clinically. cmr may be able to track biologically important changes in the myocardium by: a) native t1 that reflects myocardial disease involving the myocyte and interstitium without use of gadolinium based contrast agents (gbca), or b) the extracellular volume fraction (ecv)-a direct gbca-based measurement of the size of the extracellular space, reflecting interstitial disease. the latter technique attempts to dichotomize the myocardium into its cellular and interstitial components with estimates expressed as volume fractions. this document provides recommendations for clinical and research t1 and ecv measurement, based on published evidence when available and expert consensus when not. we address site preparation, scan type, scan planning and acquisition, quality control, visualisation and analysis, technical development. we also address controversies in the field. while ecv and native t1 mapping appear destined to affect clinical decision making, they lack multi-centre application and face significant challenges, which demand a community-wide approach among stakeholders. at present, ecv and native t1 mapping appear sufficiently robust for many diseases; yet more research is required before a large-scale application for clinical decision-making can be recommended.",0
"using ca(2+) imaging in freely behaving mice that repeatedly explored a familiar environment, we tracked thousands of ca1 pyramidal cells' place fields over weeks. place coding was dynamic, as each day the ensemble representation of this environment involved a unique subset of cells. however, cells in the ∼15-25% overlap between any two of these subsets retained the same place fields, which sufficed to preserve an accurate spatial representation across weeks.",0
"mash extends the minhash dimensionality-reduction technique to include a pairwise mutation distance and p value significance test, enabling the efficient clustering and search of massive sequence collections. mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. we demonstrate several use cases, including the clustering of all 54,118 ncbi refseq genomes in 33 cpu h; real-time database search using assembled or unassembled illumina, pacific biosciences, and oxford nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition. mash is freely released under a bsd license ( ).",0
"phosphoinositide 3-kinase (pi 3-kinase) has been implicated in growth factor signal transduction and vesicular membrane traffic. it is thought to mediate the earliest steps leading from ligation of cell surface receptors to increased cell surface ruffling. we show here that inhibitors of pi 3-kinase inhibit endocytosis in macrophages, not by interfering with the initiation of the process but rather by preventing its completion. consistent with earlier studies, the inhibitors wortmannin and ly294002 inhibited fluid-phase pinocytosis and fc receptor-mediated phagocytosis, but they had little effect on the receptor-mediated endocytosis of dii-labeled, acetylated, low density lipoprotein. large solute probes of endocytosis reported greater inhibition by wortmannin than smaller probes did, indicating that macropinocytosis was affected more than micropinocytosis. since macropinocytosis and phagocytosis are actin-mediated processes, we expected that their inhibition by wortmannin resulted from deficient signaling from macrophage colony-stimulating factor (m-csf) receptors or fc receptors to the actin cytoskeleton. however, video microscopy showed cell surface ruffling in wortmannin-treated cells, and increased ruffling after addition of m-csf or phorbol myristate acetate. quantitative measurements of video data reported slightly diminished ruffling in wortmannin-treated cells. remarkably, the ruffles that formed in wortmannin-treated macrophages all receded into the cytoplasm without closing into macropinosomes. similarly, wortmannin and ly294002 did not inhibit the extension of actin-rich pseudopodia along igg-opsonized sheep erythrocytes, but instead prevented them from closing into phagosomes. these findings indicate that pi 3-kinase is not necessary for receptor-mediated stimulation of pseudopod extension, but rather functions in the closure of macropinosomes and phagosomes into intracellular organelles.",0
"to identify somatic mutations in pediatric diffuse intrinsic pontine glioma (dipg), we performed whole-genome sequencing of dna from seven dipgs and matched germline tissue and targeted sequencing of an additional 43 dipgs and 36 non-brainstem pediatric glioblastomas (non-bs-pgs). we found that 78% of dipgs and 22% of non-bs-pgs contained a mutation in h3f3a, encoding histone h3.3, or in the related hist1h3b, encoding histone h3.1, that caused a p.lys27met amino acid substitution in each protein. an additional 14% of non-bs-pgs had somatic mutations in h3f3a causing a p.gly34arg alteration.",0
"statistical models support medical research by facilitating individualized outcome prognostication conditional on independent variables or by estimating effects of risk factors adjusted for covariates. theory of statistical models is well-established if the set of independent variables to consider is fixed and small. hence, we can assume that effect estimates are unbiased and the usual methods for confidence interval estimation are valid. in routine work, however, it is not known a priori which covariates should be included in a model, and often we are confronted with the number of candidate variables in the range 10-30. this number is often too large to be considered in a statistical model. we provide an overview of various available variable selection methods that are based on significance or information criteria, penalized likelihood, the change-in-estimate criterion, background knowledge, or combinations thereof. these methods were usually developed in the context of a linear regression model and then transferred to more generalized linear models or models for censored survival data. variable selection, in particular if used in explanatory modeling where effect estimates are of central interest, can compromise stability of a final model, unbiasedness of regression coefficients, and validity of p-values or confidence intervals. therefore, we give pragmatic recommendations for the practicing statistician on application of variable selection methods in general (low-dimensional) modeling problems and on performing stability investigations and inference. we also propose some quantities based on resampling the entire variable selection process to be routinely reported by software packages offering automated variable selection algorithms.",0
"a variety of genetically encoded reporters use changes in fluorescence (or förster) resonance energy transfer (fret) to report on biochemical processes in living cells. the standard genetically encoded fret pair consists of cfps and yfps, but many cfp-yfp reporters suffer from low fret dynamic range, phototoxicity from the cfp excitation light and complex photokinetic events such as reversible photobleaching and photoconversion. we engineered two fluorescent proteins, clover and mruby2, which are the brightest green and red fluorescent proteins to date and have the highest förster radius of any ratiometric fret pair yet described. replacement of cfp and yfp with these two proteins in reporters of kinase activity, small gtpase activity and transmembrane voltage significantly improves photostability, fret dynamic range and emission ratio changes. these improvements enhance detection of transient biochemical events such as neuronal action-potential firing and rhoa activation in growth cones.",0
"background hydroxychloroquine or chloroquine, often in combination with a second-generation macrolide, are being widely used for treatment of covid-19, despite no conclusive evidence of their benefit. although generally safe when used for approved indications such as autoimmune disease or malaria, the safety and benefit of these treatment regimens are poorly evaluated in covid-19. methods we did a multinational registry analysis of the use of hydroxychloroquine or chloroquine with or without a macrolide for treatment of covid-19. the registry comprised data from 671 hospitals in six continents. we included patients hospitalised between dec 20, 2019, and april 14, 2020, with a positive laboratory finding for sars-cov-2. patients who received one of the treatments of interest within 48 h of diagnosis were included in one of four treatment groups (chloroquine alone, chloroquine with a macrolide, hydroxychloroquine alone, or hydroxychloroquine with a macrolide), and patients who received none of these treatments formed the control group. patients for whom one of the treatments of interest was initiated more than 48 h after diagnosis or while they were on mechanical ventilation, as well as patients who received remdesivir, were excluded. the main outcomes of interest were in-hospital mortality and the occurrence of de-novo ventricular arrhythmias (non-sustained or sustained ventricular tachycardia or ventricular fibrillation). findings 96 032 patients (mean age 53·8 years, 46·3% women) with covid-19 were hospitalised during the study period and met the inclusion criteria. of these, 14 888 patients were in the treatment groups (1868 received chloroquine, 3783 received chloroquine with a macrolide, 3016 received hydroxychloroquine, and 6221 received hydroxychloroquine with a macrolide) and 81 144 patients were in the control group. 10 698 (11·1%) patients died in hospital. after controlling for multiple confounding factors (age, sex, race or ethnicity, body-mass index, underlying cardiovascular disease and its risk factors, diabetes, underlying lung disease, smoking, immunosuppressed condition, and baseline disease severity), when compared with mortality in the control group (9·3%), hydroxychloroquine (18·0%; hazard ratio 1·335, 95% ci 1·223-1·457), hydroxychloroquine with a macrolide (23·8%; 1·447, 1·368-1·531), chloroquine (16·4%; 1·365, 1·218-1·531), and chloroquine with a macrolide (22·2%; 1·368, 1·273-1·469) were each independently associated with an increased risk of in-hospital mortality. compared with the control group (0·3%), hydroxychloroquine (6·1%; 2·369, 1·935-2·900), hydroxychloroquine with a macrolide (8·1%; 5·106, 4·106-5·983), chloroquine (4·3%; 3·561, 2·760-4·596), and chloroquine with a macrolide (6·5%; 4·011, 3·344-4·812) were independently associated with an increased risk of de-novo ventricular arrhythmia during hospitalisation. interpretation we were unable to confirm a benefit of hydroxychloroquine or chloroquine, when used alone or with a macrolide, on in-hospital outcomes for covid-19. each of these drug regimens was associated with decreased in-hospital survival and an increased frequency of ventricular arrhythmias when used for treatment of covid-19. funding william harvey distinguished chair in advanced cardiovascular medicine at brigham and women's hospital.",0
"we report a monomeric yellow-green fluorescent protein, mneongreen, derived from a tetrameric fluorescent protein from the cephalochordate branchiostoma lanceolatum. mneongreen is the brightest monomeric green or yellow fluorescent protein yet described to our knowledge, performs exceptionally well as a fusion tag for traditional imaging as well as stochastic single-molecule superresolution imaging and is an excellent fluorescence resonance energy transfer (fret) acceptor for the newest cyan fluorescent proteins.",0
"background there is overwhelming evidence that in vitro three-dimensional tumor cell cultures more accurately reflect the complex in vivo microenvironment than simple two-dimensional cell monolayers, not least with respect to gene expression profiles, signaling pathway activity and drug sensitivity. however, most currently available three-dimensional techniques are time consuming and/or lack reproducibility; thus standardized and rapid protocols are urgently needed. results to address this requirement, we have developed a versatile toolkit of reproducible three-dimensional tumor spheroid models for dynamic, automated, quantitative imaging and analysis that are compatible with routine high-throughput preclinical studies. not only do these microplate methods measure three-dimensional tumor growth, but they have also been significantly enhanced to facilitate a range of functional assays exemplifying additional key hallmarks of cancer, namely cell motility and matrix invasion. moreover, mutual tissue invasion and angiogenesis is accommodated by coculturing tumor spheroids with murine embryoid bodies within which angiogenic differentiation occurs. highly malignant human tumor cells were selected to exemplify therapeutic effects of three specific molecularly-targeted agents: pi-103 (phosphatidylinositol-3-kinase (pi3k)-mammalian target of rapamycin (mtor) inhibitor), 17-n-allylamino-17-demethoxygeldanamycin (17-aag) (heat shock protein 90 (hsp90) inhibitor) and cct130234 (in-house phospholipase c (plc)γ inhibitor). fully automated analysis using a celigo cytometer was validated for tumor spheroid growth and invasion against standard image analysis techniques, with excellent reproducibility and significantly increased throughput. in addition, we discovered key differential sensitivities to targeted agents between two-dimensional and three-dimensional cultures, and also demonstrated enhanced potency of some agents against cell migration/invasion compared with proliferation, suggesting their preferential utility in metastatic disease. conclusions we have established and validated a suite of highly reproducible tumor microplate three-dimensional functional assays to enhance the biological relevance of early preclinical cancer studies. we believe these assays will increase the translational predictive value of in vitro drug evaluation studies and reduce the need for in vivo studies by more effective triaging of compounds.",0
"background high-quality epidemiologic data worldwide are needed to improve our understanding of disease risk, support health policy to meet the diverse needs of people with multiple sclerosis (ms) and support advocacy efforts. objectives the atlas of ms is an open-source global compendium of data regarding the epidemiology of ms and the availability of resources for people with ms reported at country, regional and global levels. methods country representatives reported epidemiologic data and their sources via survey between september 2019 and march 2020, covering prevalence and incidence in males, females and children, and age and ms type at diagnosis. regional analyses and comparisons with 2013 data were conducted. results a total of 2.8 million people are estimated to live with ms worldwide (35.9 per 100,000 population). ms prevalence has increased in every world region since 2013 but gaps in prevalence estimates persist. the pooled incidence rate across 75 reporting countries is 2.1 per 100,000 persons/year, and the mean age of diagnosis is 32 years. females are twice as likely to live with ms as males. conclusions the global prevalence of ms has risen since 2013, but good surveillance data is not universal. action is needed by multiple stakeholders to close knowledge gaps.",0
"severe acute respiratory syndrome (sars) has been the first severe contagious disease to emerge in the 21st century. the available epidemic curves for sars show marked differences between the affected regions with respect to the total number of cases and epidemic duration, even for those regions in which outbreaks started almost simultaneously and similar control measures were implemented at the same time. the authors developed a likelihood-based estimation procedure that infers the temporal pattern of effective reproduction numbers from an observed epidemic curve. precise estimates for the effective reproduction numbers were obtained by applying this estimation procedure to available data for sars outbreaks that occurred in hong kong, vietnam, singapore, and canada in 2003. the effective reproduction numbers revealed that epidemics in the various affected regions were characterized by markedly similar disease transmission potentials and similar levels of effectiveness of control measures. in controlling sars outbreaks, timely alerts have been essential: delaying the institution of control measures by 1 week would have nearly tripled the epidemic size and would have increased the expected epidemic duration by 4 weeks.",0
"part i of this report appeared in the previous issue (br. j. cancer (1976) 34,585), and discussed the design of randomized clinical trials. part ii now describes efficient methods of analysis of randomized clinical trials in which we wish to compare the duration of survival (or the time until some other untoward event first occurs) among different groups of patients. it is intended to enable physicians without statistical training either to analyse such data themselves using life tables, the logrank test and retrospective stratification, or, when such analyses are presented, to appreciate them more critically, but the discussion may also be of interest to statisticians who have not yet specialized in clinical trial analyses.",0
"background children with autism have often been reported to have gastrointestinal problems that are more frequent and more severe than in children from the general population. methods gastrointestinal flora and gastrointestinal status were assessed from stool samples of 58 children with autism spectrum disorders (asd) and 39 healthy typical children of similar ages. stool testing included bacterial and yeast culture tests, lysozyme, lactoferrin, secretory iga, elastase, digestion markers, short chain fatty acids (scfa's), ph, and blood presence. gastrointestinal symptoms were assessed with a modified six-item gi severity index (6-gsi) questionnaire, and autistic symptoms were assessed with the autism treatment evaluation checklist (atec). results gastrointestinal symptoms (assessed by the 6-gsi) were strongly correlated with the severity of autism (assessed by the atec), (r = 0.59, p conclusions the strong correlation of gastrointestinal symptoms with autism severity indicates that children with more severe autism are likely to have more severe gastrointestinal symptoms and vice versa. it is possible that autism symptoms are exacerbated or even partially due to the underlying gastrointestinal problems. the low level of scfa's was partly associated with increased probiotic use, and probably partly due to either lower production (less sacchrolytic fermentation by beneficial bacteria and/or lower intake of soluble fiber) and/or greater absorption into the body (due to longer transit time and/or increased gut permeability).",0
"the endoplasmic reticulum (er) provides an environment that is highly optimized for oxidative protein folding. rather than relying on small molecule oxidants like glutathione, it is now clear that disulfide formation is driven by a protein relay involving ero1, a novel conserved fad-dependent enzyme, and protein disulfide isomerase (pdi); ero1 is oxidized by molecular oxygen and in turn acts as a specific oxidant of pdi, which then directly oxidizes disulfide bonds in folding proteins. while providing a robust driving force for disulfide formation, the use of molecular oxygen as the terminal electron acceptor can lead to oxidative stress through the production of reactive oxygen species and oxidized glutathione. how ero1p distinguishes between the many different pdi-related proteins and how the cell minimizes the effects of oxidative damage from ero1 remain important open questions.",0
"background in the early stages of the outbreak of coronavirus disease 2019 (covid-19) in hubei, china, the local health-care system was overwhelmed. physicians and nurses who had no infectious disease expertise were recruited to provide care to patients with covid-19. to our knowledge, no studies on their experiences of combating covid-19 have been published. we aimed to describe the experiences of these health-care providers in the early stages of the outbreak. methods we did a qualitative study using an empirical phenomenological approach. nurses and physicians were recruited from five covid-19-designated hospitals in hubei province using purposive and snowball sampling. they participated in semi-structured, in-depth interviews by telephone from feb 10 to feb 15, 2020. interviews were transcribed verbatim and analysed using haase's adaptation of colaizzi's phenomenological method. findings we recruited nine nurses and four physicians. three theme categories emerged from data analysis. the first was ""being fully responsible for patients' wellbeing-'this is my duty'"". health-care providers volunteered and tried their best to provide care for patients. nurses had a crucial role in providing intensive care and assisting with activities of daily living. the second category was ""challenges of working on covid-19 wards"". health-care providers were challenged by working in a totally new context, exhaustion due to heavy workloads and protective gear, the fear of becoming infected and infecting others, feeling powerless to handle patients' conditions, and managing relationships in this stressful situation. the third category was ""resilience amid challenges"". health-care providers identified many sources of social support and used self-management strategies to cope with the situation. they also achieved transcendence from this unique experience. interpretation the intensive work drained health-care providers physically and emotionally. health-care providers showed their resilience and the spirit of professional dedication to overcome difficulties. comprehensive support should be provided to safeguard the wellbeing of health-care providers. regular and intensive training for all health-care providers is necessary to promote preparedness and efficacy in crisis management. funding national key r&d program of china, project of humanities and social sciences of the ministry of education in china.",0
"quality healthcare outcomes depend upon patients' adherence to recommended treatment regimens. patient nonadherence can be a pervasive threat to health and wellbeing and carry an appreciable economic burden as well. in some disease conditions, more than 40% of patients sustain significant risks by misunderstanding, forgetting, or ignoring healthcare advice. while no single intervention strategy can improve the adherence of all patients, decades of research studies agree that successful attempts to improve patient adherence depend upon a set of key factors. these include realistic assessment of patients' knowledge and understanding of the regimen, clear and effective communication between health professionals and their patients, and the nurturance of trust in the therapeutic relationship. patients must be given the opportunity to tell the story of their unique illness experiences. knowing the patient as a person allows the health professional to understand elements that are crucial to the patient's adherence: beliefs, attitudes, subjective norms, cultural context, social supports, and emotional health challenges, particularly depression. physician-patient partnerships are essential when choosing amongst various therapeutic options to maximize adherence. mutual collaboration fosters greater patient satisfaction, reduces the risks of nonadherence, and improves patients' healthcare outcomes.",0
"background the mental disorders included in the global burden of diseases, injuries, and risk factors study (gbd) 2019 were depressive disorders, anxiety disorders, bipolar disorder, schizophrenia, autism spectrum disorders, conduct disorder, attention-deficit hyperactivity disorder, eating disorders, idiopathic developmental intellectual disability, and a residual category of other mental disorders. we aimed to measure the global, regional, and national prevalence, disability-adjusted life-years (dalys), years lived with disability (ylds), and years of life lost (ylls) for mental disorders from 1990 to 2019. methods in this study, we assessed prevalence and burden estimates from gbd 2019 for 12 mental disorders, males and females, 23 age groups, 204 countries and territories, between 1990 and 2019. dalys were estimated as the sum of ylds and ylls to premature mortality. we systematically reviewed psycinfo, embase, pubmed, and the global health data exchange to obtain data on prevalence, incidence, remission, duration, severity, and excess mortality for each mental disorder. these data informed a bayesian meta-regression analysis to estimate prevalence by disorder, age, sex, year, and location. prevalence was multiplied by corresponding disability weights to estimate ylds. cause-specific deaths were compiled from mortality surveillance databases. the cause of death ensemble modelling strategy was used to estimate death rate by age, sex, year, and location. the death rates were multiplied by the years of life expected to be remaining at death based on a normative life expectancy to estimate ylls. deaths and ylls could be calculated only for anorexia nervosa and bulimia nervosa, since these were the only mental disorders identified as underlying causes of death in gbd 2019. findings between 1990 and 2019, the global number of dalys due to mental disorders increased from 80·8 million (95% uncertainty interval 59·5-105·9) to 125·3 million (93·0-163·2), and the proportion of global dalys attributed to mental disorders increased from 3·1% (95% ui 2·4-3·9) to 4·9% (3·9-6·1). age-standardised daly rates remained largely consistent between 1990 (1581·2 dalys per 100 000 people) and 2019 (1566·2 dalys per 100 000 people). ylds contributed to most of the mental disorder burden, with 125·3 million ylds (95% ui 93·0-163·2; 14·6% of global ylds) in 2019 attributable to mental disorders. eating disorders accounted for 17 361·5 ylls (95% ui 15 518·5-21 459·8). globally, the age-standardised daly rate for mental disorders was 1426·5 (95% ui 1056·4-1869·5) per 100 000 population among males and 1703·3 (1261·5-2237·8) per 100 000 population among females. age-standardised daly rates were highest in australasia, tropical latin america, and high-income north america. interpretation gbd 2019 showed that mental disorders remained among the top ten leading causes of burden worldwide, with no evidence of global reduction in the burden since 1990. the estimated ylls for mental disorders were extremely low and do not reflect premature mortality in individuals with mental disorders. research to establish causal pathways between mental disorders and other fatal health outcomes is recommended so that this may be addressed within the gbd study. to reduce the burden of mental disorders, coordinated delivery of effective prevention and treatment programmes by governments and the global health community is imperative. funding bill & melinda gates foundation, australian national health and medical research council, queensland department of health, australia.",0
"human monocyte-derived interleukin 1 (il-1) was found to be a potent inducer of procoagulant activity in cultured human vascular endothelium. il-1-induced human umbilical vein endothelial cell procoagulant activity (hec-pca) was transiently expressed, manifest in intact cell monolayers, and required protein synthesis. data obtained with coagulation factor-deficient plasma and a goat anti-human apoprotein iii antiserum suggested that most, if not all, of il-1-induced endothelial cell procoagulant activity is tissue factor-like. il-1 induction of hec-pca may be important in the pathogenesis of intravascular coagulation in a variety of immunological and inflammatory conditions.",0
"within the context of screening tests, it is important to avoid misconceptions about sensitivity, specificity, and predictive values. in this article, therefore, foundations are first established concerning these metrics along with the first of several aspects of pliability that should be recognized in relation to those metrics. clarification is then provided about the definitions of sensitivity, specificity, and predictive values and why researchers and clinicians can misunderstand and misrepresent them. arguments are made that sensitivity and specificity should usually be applied only in the context of describing a screening test's attributes relative to a reference standard; that predictive values are more appropriate and informative in actual screening contexts, but that sensitivity and specificity can be used for screening decisions about individual people if they are extremely high; that predictive values need not always be high and might be used to advantage by adjusting the sensitivity and specificity of screening tests; that, in screening contexts, researchers should provide information about all four metrics and how they were derived; and that, where necessary, consumers of health research should have the skills to interpret those metrics effectively for maximum benefit to clients and the healthcare system.",0
"propensity score methods are increasingly being used to estimate causal treatment effects in observational studies. in medical and epidemiological studies, outcomes are frequently time-to-event in nature. propensity-score methods are often applied incorrectly when estimating the effect of treatment on time-to-event outcomes. this article describes how two different propensity score methods (matching and inverse probability of treatment weighting) can be used to estimate the measures of effect that are frequently reported in randomized controlled trials: (i) marginal survival curves, which describe survival in the population if all subjects were treated or if all subjects were untreated; and (ii) marginal hazard ratios. the use of these propensity score methods allows one to replicate the measures of effect that are commonly reported in randomized controlled trials with time-to-event outcomes: both absolute and relative reductions in the probability of an event occurring can be determined. we also provide guidance on variable selection for the propensity score model, highlight methods for assessing the balance of baseline covariates between treated and untreated subjects, and describe the implementation of a sensitivity analysis to assess the effect of unmeasured confounding variables on the estimated treatment effect when outcomes are time-to-event in nature. the methods in the paper are illustrated by estimating the effect of discharge statin prescribing on the risk of death in a sample of patients hospitalized with acute myocardial infarction. in this tutorial article, we describe and illustrate all the steps necessary to conduct a comprehensive analysis of the effect of treatment on time-to-event outcomes.",0
"systemic corticosteroids play an integral role in the management of many inflammatory and immunologic conditions, but these agents are also associated with serious risks. osteoporosis, adrenal suppression, hyperglycemia, dyslipidemia, cardiovascular disease, cushing's syndrome, psychiatric disturbances and immunosuppression are among the more serious side effects noted with systemic corticosteroid therapy, particularly when used at high doses for prolonged periods. this comprehensive article reviews these adverse events and provides practical recommendations for their prevention and management based on both current literature and the clinical experience of the authors.",0
"the development of immune checkpoint inhibitors has changed the treatment paradigm for advanced cancers across many tumor types. despite encouraging and sometimes durable responses in a subset of patients, most patients do not respond. tumors have adopted the pd-1/pd-l1 axis for immune escape to facilitate tumor growth, which can be leveraged as a potential target for immune checkpoint inhibitors. on this basis, pd-l1 protein expression on tumor or immune cells emerged as the first potential predictive biomarker for sensitivity to immune checkpoint blockade. the goal of our study was to evaluate pd-l1 as a predictive biomarker based on all us food and drug administration (fda) drug approvals of immune checkpoint inhibitors. we evaluated the primary studies associated with 45 fda drug approvals from 2011 until april 2019. in total, there were approvals across 15 tumor types. across all approvals, pd-l1 was predictive in only 28.9% of cases, and was either not predictive (53.3%) or not tested (17.8%) in the remaining cases. there were 9 fda approvals linked to a specific pd-l1 threshold and companion diagnostic: bladder cancer (n = 3), non-small cell lung cancer (n = 3), triple-negative breast cancer (n = 1), cervical cancer (n = 1), and gastric/gastroesophageal junction cancer (n = 1) with 8 of 9 (88.9%) with immune checkpoint inhibitor monotherapy. the pd-l1 thresholds were variable both within and across tumor types using several different assays, including approvals at the following pd-l1 thresholds: 1, 5, and 50%. pd-l1 expression was also measured in a variable fashion either on tumor cells, tumor-infiltrating immune cells, or both. in conclusion, our findings indicate that pd-l1 expression as a predictive biomarker has limitations and that the decision to pursue testing must be carefully implemented for clinical decision-making.",0
"phosphositeplus ( is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. it encompasses 1,30,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. the interface is designed for clarity and ease of navigation. from the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. a few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. pymol and chimera scripts that colorize reactive groups on residues that are modified can be downloaded. features designed to facilitate proteomic analyses include downloads of modification sites, kinase-substrate data sets, sequence logo generators, a cytoscape plugin and biopax download to enable pathway visualization of the kinase-substrate interactions in phosphositeplus®.",0
"although anaesthesiologists strive to avoid hypoxemia during surgery, reliably predicting future intraoperative hypoxemia is not currently possible. here, we report the development and testing of a machine-learning-based system that, in real time during general anaesthesia, predicts the risk of hypoxemia and provides explanations of the risk factors. the system, which was trained on minute-by-minute data from the electronic medical records of over fifty thousand surgeries, improved the performance of anaesthesiologists when providing interpretable hypoxemia risks and contributing factors. the explanations for the predictions are broadly consistent with the literature and with prior knowledge from anaesthesiologists. our results suggest that if anaesthesiologists currently anticipate 15% of hypoxemia events, with this system's assistance they would anticipate 30% of them, a large portion of which may benefit from early intervention because they are associated with modifiable factors. the system can help improve the clinical understanding of hypoxemia risk during anaesthesia care by providing general insights into the exact changes in risk induced by certain patient or procedure characteristics.",0
"background although the rising pandemic of obesity has received major attention in many countries, the effects of this attention on trends and the disease burden of obesity remain uncertain. methods we analyzed data from 68.5 million persons to assess the trends in the prevalence of overweight and obesity among children and adults between 1980 and 2015. using the global burden of disease study data and methods, we also quantified the burden of disease related to high body-mass index (bmi), according to age, sex, cause, and bmi in 195 countries between 1990 and 2015. results in 2015, a total of 107.7 million children and 603.7 million adults were obese. since 1980, the prevalence of obesity has doubled in more than 70 countries and has continuously increased in most other countries. although the prevalence of obesity among children has been lower than that among adults, the rate of increase in childhood obesity in many countries has been greater than the rate of increase in adult obesity. high bmi accounted for 4.0 million deaths globally, nearly 40% of which occurred in persons who were not obese. more than two thirds of deaths related to high bmi were due to cardiovascular disease. the disease burden related to high bmi has increased since 1990; however, the rate of this increase has been attenuated owing to decreases in underlying rates of death from cardiovascular disease. conclusions the rapid increase in the prevalence and disease burden of elevated bmi highlights the need for continued focus on surveillance of bmi and identification, implementation, and evaluation of evidence-based interventions to address this problem. (funded by the bill and melinda gates foundation.).",0
"we report that the dye nile red, 9-diethylamino-5h-benzophenoxazine-5-one, is an excellent vital stain for the detection of intracellular lipid droplets by fluorescence microscopy and flow cytofluorometry. the specificity of the dye for lipid droplets was assessed on cultured aortic smooth muscle cells and on cultured peritoneal macrophages that were incubated with acetylated low density lipoprotein to induce cytoplasmic lipid overloading. better selectivity for cytoplasmic lipid droplets was obtained when the cells were viewed for yellow-gold fluorescence (excitation, 450-500 nm; emission, greater than 528 nm) rather than red fluorescence (excitation, 515-560 nm; emission, greater than 590 nm). nile red-stained, lipid droplet-filled macrophages exhibited greater fluorescence intensity than did nile red-stained control macrophages, and the two cell populations could be differentiated and analyzed by flow cytofluorometry. such analyses could be performed with either yellow-gold or red fluorescence, but when few lipid droplets per cell were present, the yellow-gold fluorescence was more discriminating. nile red exhibits properties of a near-ideal lysochrome. it is strongly fluorescent, but only in the presence of a hydrophobic environment. the dye is very soluble in the lipids it is intended to show, and it does not interact with any tissue constituent except by solution. nile red can be applied to cells in an aqueous medium, and it does not dissolve the lipids it is supposed to reveal.",0
"pubchem ( is a key chemical information resource for the biomedical research community. substantial improvements were made in the past few years. new data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. pubchem released new web interfaces, such as pubchem target view page, sources page, bioactivity dyad pages and patent view page. pubchem also released a major update to pubchem widgets and introduced a new programmatic access interface, called pug-view. this paper describes these new developments in pubchem.",0
"background there is increasing international interest in the concept of mental well-being and its contribution to all aspects of human life. demand for instruments to monitor mental well-being at a population level and evaluate mental health promotion initiatives is growing. this article describes the development and validation of a new scale, comprised only of positively worded items relating to different aspects of positive mental health: the warwick-edinburgh mental well-being scale (wemwbs). methods wemwbs was developed by an expert panel drawing on current academic literature, qualitative research with focus groups, and psychometric testing of an existing scale. it was validated on a student and representative population sample. content validity was assessed by reviewing the frequency of complete responses and the distribution of responses to each item. confirmatory factor analysis was used to test the hypothesis that the scale measured a single construct. internal consistency was assessed using cronbach's alpha. criterion validity was explored in terms of correlations between wemwbs and other scales and by testing whether the scale discriminated between population groups in line with pre-specified hypotheses. test-retest reliability was assessed at one week using intra-class correlation coefficients. susceptibility to bias was measured using the balanced inventory of desired responding. results wemwbs showed good content validity. confirmatory factor analysis supported the single factor hypothesis. a cronbach's alpha score of 0.89 (student sample) and 0.91 (population sample) suggests some item redundancy in the scale. wemwbs showed high correlations with other mental health and well-being scales and lower correlations with scales measuring overall health. its distribution was near normal and the scale did not show ceiling effects in a population sample. it discriminated between population groups in a way that is largely consistent with the results of other population surveys. test-retest reliability at one week was high (0.83). social desirability bias was lower or similar to that of other comparable scales. conclusion wemwbs is a measure of mental well-being focusing entirely on positive aspects of mental health. as a short and psychometrically robust scale, with no ceiling effects in a population sample, it offers promise as a tool for monitoring mental well-being at a population level. whilst wemwbs should appeal to those evaluating mental health promotion initiatives, it is important that the scale's sensitivity to change is established before it is recommended in this context.",0
"governments are attempting to control the covid-19 pandemic with nonpharmaceutical interventions (npis). however, the effectiveness of different npis at reducing transmission is poorly understood. we gathered chronological data on the implementation of npis for several european and non-european countries between january and the end of may 2020. we estimated the effectiveness of these npis, which range from limiting gathering sizes and closing businesses or educational institutions to stay-at-home orders. to do so, we used a bayesian hierarchical model that links npi implementation dates to national case and death counts and supported the results with extensive empirical validation. closing all educational institutions, limiting gatherings to 10 people or less, and closing face-to-face businesses each reduced transmission considerably. the additional effect of stay-at-home orders was comparatively small.",0
"visual attention can improve behavioral performance by allowing observers to focus on the important information in a complex scene. attention also typically increases the firing rates of cortical sensory neurons. rate increases improve the signal-to-noise ratio of individual neurons, and this improvement has been assumed to underlie attention-related improvements in behavior. we recorded dozens of neurons simultaneously in visual area v4 and found that changes in single neurons accounted for only a small fraction of the improvement in the sensitivity of the population. instead, over 80% of the attentional improvement in the population signal was caused by decreases in the correlations between the trial-to-trial fluctuations in the responses of pairs of neurons. these results suggest that the representation of sensory information in populations of neurons and the way attention affects the sensitivity of the population may only be understood by considering the interactions between neurons.",0
"objective: the recent outbreak of novel coronavirus disease (covid-19) is reminiscent of the sars outbreak in 2003. we aim to compare the severity and mortality between male and female patients with covid-19 or sars. study design and setting: we extracted the data from: (1) a case series of 43 hospitalized patients we treated, (2) a public data set of the first 37 cases of patients who died of covid-19 and 1,019 patients who survived in china, and (3) data of 524 patients with sars, including 139 deaths, from beijing in early 2003. results: older age and a high number of comorbidities were associated with higher severity and mortality in patients with both covid-19 and sars. age was comparable between men and women in all data sets. in the case series, however, men's cases tended to be more serious than women's ( p = 0.035). in the public data set, the number of men who died from covid-19 is 2.4 times that of women (70.3 vs. 29.7%, p = 0.016). in sars patients, the gender role in mortality was also observed. the percentage of males were higher in the deceased group than in the survived group ( p = 0.015). conclusion: while men and women have the same prevalence, men with covid-19 are more at risk for worse outcomes and death, independent of age.",0
"although multiple sequence alignments (msas) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate msas for distantly related proteins remains a largely unsolved problem. the rapidly increasing database of spatial structures is a valuable source to improve alignment quality. we explore the use of 3d structural information to guide sequence alignments constructed by our msa program promals. the resulting tool, promals3d, automatically identifies homologs with known 3d structures for the input sequences, derives structural constraints through structure-based alignments and combines them with sequence constraints to construct consistency-based multiple sequence alignments. the output is a consensus alignment that brings together sequence and structural information about input proteins and their homologs. promals3d can also align sequences of multiple input structures, with the output representing a multiple structure-based alignment refined in combination with sequence constraints. the advantage of promals3d is that it gives researchers an easy way to produce high-quality alignments consistent with both sequences and structures of proteins. promals3d outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods.",0
"david moher and colleagues from the equator network offer guidance and recommended steps for developing health research reporting guidelines.",0
"interleukin 10 (il-10) decreases production of il-1, il-6, and tumor necrosis factor alpha (tnf-alpha) in vitro, and neutralization of il-10 in mice leads to elevation of the same monokines. we test here whether this monokine-suppressing property of il-10 confers on it the capacity to protect mice from lipopolysaccharide-induced shock, a monokine-mediated inflammatory reaction. a single injection of 0.5-1 microgram of recombinant murine il-10 reproducibly protected balb/c mice from a lethal intraperitoneal injection of endotoxin. this result was obtained whether the il-10 was administered concurrently with, or 30 min after the injection of endotoxin. the protective effect of il-10 was reversed by prior injection of neutralizing anti-il-10 antibodies, and correlated with a substantial decrease in endotoxin-induced tnf-alpha release. these data implicate il-10 as a candidate for treatment of bacterial sepsis, and more generally as an effective antiinflammatory reagent.",0
"purpose to present the findings of 21 coronavirus disease 2019 (covid-19) cases from two chinese centers with ct and chest radiographic findings, as well as follow-up imaging in five cases. materials and methods this was a retrospective study in shenzhen and hong kong. patients with covid-19 infection were included. a systematic review of the published literature on radiologic features of covid-19 infection was conducted. results the predominant imaging pattern was of ground-glass opacification with occasional consolidation in the peripheries. pleural effusions and lymphadenopathy were absent in all cases. patients demonstrated evolution of the ground-glass opacities into consolidation and subsequent resolution of the airspace changes. ground-glass and consolidative opacities visible on ct are sometimes undetectable on chest radiography, suggesting that ct is a more sensitive imaging modality for investigation. the systematic review identified four other studies confirming the findings of bilateral and peripheral ground glass with or without consolidation as the predominant finding at ct chest examinations. conclusion pulmonary manifestation of covid-19 infection is predominantly characterized by ground-glass opacification with occasional consolidation on ct. radiographic findings in patients presenting in shenzhen and hong kong are in keeping with four previous publications from other sites.© rsna, 2020see editorial by kay and abbara in this issue.",0
"cathie sudlow and colleagues describe the uk biobank, a large population-based prospective study, established to allow investigation of the genetic and non-genetic determinants of the diseases of middle and old age.",0
"background high tumor mutational burden (tmb) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to pd-1 and pd-l1 blockade immunotherapy than pd-1 or pd-l1 expression, as measured by immunohistochemistry (ihc). the distribution of tmb and the subset of patients with high tmb has not been well characterized in the majority of cancer types. methods in this study, we compare tmb measured by a targeted comprehensive genomic profiling (cgp) assay to tmb measured by exome sequencing and simulate the expected variance in tmb when sequencing less than the whole exome. we then describe the distribution of tmb across a diverse cohort of 100,000 cancer cases and test for association between somatic alterations and tmb in over 100 tumor types. results we demonstrate that measurements of tmb from comprehensive genomic profiling are strongly reflective of measurements from whole exome sequencing and model that below 0.5 mb the variance in measurement increases significantly. we find that a subset of patients exhibits high tmb across almost all types of cancer, including many rare tumor types, and characterize the relationship between high tmb and microsatellite instability status. we find that tmb increases significantly with age, showing a 2.4-fold difference between age 10 and age 90 years. finally, we investigate the molecular basis of tmb and identify genes and mutations associated with tmb level. we identify a cluster of somatic mutations in the promoter of the gene pms2, which occur in 10% of skin cancers and are highly associated with increased tmb. conclusions these results show that a cgp assay targeting ~1.1 mb of coding genome can accurately assess tmb compared with sequencing the whole exome. using this method, we find that many disease types have a substantial portion of patients with high tmb who might benefit from immunotherapy. finally, we identify novel, recurrent promoter mutations in pms2, which may be another example of regulatory mutations contributing to tumorigenesis.",0
"the virulence factor database (vfdb, is devoted to providing the scientific community with a comprehensive warehouse and online platform for deciphering bacterial pathogenesis. the various combinations, organizations and expressions of virulence factors (vfs) are responsible for the diverse clinical symptoms of pathogen infections. currently, whole-genome sequencing is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. however, the efficient characterization of pathogenomic compositions remains a challenge for microbiologists or physicians with limited bioinformatics skills. therefore, we introduced to vfdb an integrated and automatic pipeline, vfanalyzer, to systematically identify known/potential vfs in complete/draft bacterial genomes. vfanalyzer first constructs orthologous groups within the query genome and preanalyzed reference genomes from vfdb to avoid potential false positives due to paralogs. then, it conducts iterative and exhaustive sequence similarity searches among the hierarchical prebuilt datasets of vfdb to accurately identify potential untypical/strain-specific vfs. finally, via a context-based data refinement process for vfs encoded by gene clusters, vfanalyzer can achieve relatively high specificity and sensitivity without manual curation. in addition, a thoroughly optimized interactive web interface is introduced to present vfanalyzer reports in comparative pathogenomic style for easy online analysis.",0
"objectives to determine the quantitative efficacy of different classes of blood pressure lowering drugs in preventing coronary heart disease (chd) and stroke, and who should receive treatment. design meta-analysis. data source medline (1966-2007). study selection randomised trials of blood pressure lowering drugs recording chd events and strokes. 108 trials studied differences in blood pressure between study drug and placebo (or control group not receiving the study drug) (""blood pressure difference trials""), and 46 trials compared drugs (""drug comparison trials""). seven trials with three randomised groups fell into both categories. the results were interpreted in the context of those expected from the largest published meta-analysis of cohort studies, totalling 958 000 people. participants 464 000 people defined into three mutually exclusive categories: participants with no history of vascular disease, a history of chd, or a history of stroke. results in the blood pressure difference trials beta blockers had a special effect over and above that due to blood pressure reduction in preventing recurrent chd events in people with a history of chd: risk reduction 29% (95% confidence interval 22% to 34%) compared with 15% (11% to 19%) in trials of other drugs. the extra effect was limited to a few years after myocardial infarction, with a risk reduction of 31% compared with 13% in people with chd with no recent infarct (p=0.04). in the other blood pressure difference trials (excluding chd events in trials of beta blockers in people with chd), there was a 22% reduction in chd events (17% to 27%) and a 41% (33% to 48%) reduction in stroke for a blood pressure reduction of 10 mm hg systolic or 5 mm hg diastolic, similar to the reductions of 25% (chd) and 36% (stroke) expected for the same difference in blood pressure from the cohort study meta-analysis, indicating that the benefit is explained by blood pressure reduction itself. the five main classes of blood pressure lowering drugs (thiazides, beta blockers, angiotensin converting enzyme inhibitors, angiotensin receptor blockers, and calcium channel blockers) were similarly effective (within a few percentage points) in preventing chd events and strokes, with the exception that calcium channel blockers had a greater preventive effect on stroke (relative risk 0.92, 95% confidence interval 0.85 to 0.98). the percentage reductions in chd events and stroke were similar in people with and without cardiovascular disease and regardless of blood pressure before treatment (down to 110 mm hg systolic and 70 mm hg diastolic). combining our results with those from two other studies (the meta-analyses of blood pressure cohort studies and of trials determining the blood pressure lowering effects of drugs according to dose) showed that in people aged 60-69 with a diastolic blood pressure before treatment of 90 mm hg, three drugs at half standard dose in combination reduced the risk of chd by an estimated 46% and of stroke by 62%; one drug at standard dose had about half this effect. the present meta-analysis also showed that drugs other than calcium channel blockers (with the exception of non-cardioselective beta blockers) reduced the incidence of heart failure by 24% (19% to 28%) and calcium channel blockers by 19% (6% to 31%). conclusions with the exception of the extra protective effect of beta blockers given shortly after a myocardial infarction and the minor additional effect of calcium channel blockers in preventing stroke, all the classes of blood pressure lowering drugs have a similar effect in reducing chd events and stroke for a given reduction in blood pressure so excluding material pleiotropic effects. the proportional reduction in cardiovascular disease events was the same or similar regardless of pretreatment blood pressure and the presence or absence of existing cardiovascular disease. guidelines on the use of blood pressure lowering drugs can be simplified so that drugs are offered to people with all levels of blood pressure. our results indicate the importance of lowering blood pressure in everyone over a certain age, rather than measuring it in everyone and treating it in some.",0
"objective the a1c assay, expressed as the percent of hemoglobin that is glycated, measures chronic glycemia and is widely used to judge the adequacy of diabetes treatment and adjust therapy. day-to-day management is guided by self-monitoring of capillary glucose concentrations (milligrams per deciliter or millimoles per liter). we sought to define the mathematical relationship between a1c and average glucose (ag) levels and determine whether a1c could be expressed and reported as ag in the same units as used in self-monitoring. research design and methods a total of 507 subjects, including 268 patients with type 1 diabetes, 159 with type 2 diabetes, and 80 nondiabetic subjects from 10 international centers, was included in the analyses. a1c levels obtained at the end of 3 months and measured in a central laboratory were compared with the ag levels during the previous 3 months. ag was calculated by combining weighted results from at least 2 days of continuous glucose monitoring performed four times, with seven-point daily self-monitoring of capillary (fingerstick) glucose performed at least 3 days per week. results approximately 2,700 glucose values were obtained by each subject during 3 months. linear regression analysis between the a1c and ag values provided the tightest correlations (ag(mg/dl) = 28.7 x a1c - 46.7, r(2) = 0.84, p conclusions a1c levels can be expressed as eag for most patients with type 1 and type 2 diabetes.",0
"the clathrin-coated pit lattice is held onto the plasma membrane by an integral membrane protein that binds the clathrin ap-2 subunit with high affinity. in vitro studies have suggested that this protein controls the assembly of the pit because membrane bound ap-2 is required for lattice assembly. if so, the ap-2 binding site must be a resident protein of the coated pit and recycle with other receptors that enter cells through this pathway. proper recycling, however, would require the switching off of ap-2 binding to allow the binding site to travel through the endocytic pathway unencumbered. evidence for this hypothesis has been revealed by the cationic amphiphilic class of drugs (cad), which have previously been found to inhibit receptor recycling. incubation of human fibroblasts in the presence of these drugs caused clathrin lattices to assemble on endosomal membranes and at the same time prevented coated pit assembly at the cell surface. these effects suggest that cads reverse an on/off switch that controls ap-2 binding to membranes. we conclude that cells have a mechanism for switching on and off ap-2 binding during the endocytic cycle.",0
"background although ct scans are very useful clinically, potential cancer risks exist from associated ionising radiation, in particular for children who are more radiosensitive than adults. we aimed to assess the excess risk of leukaemia and brain tumours after ct scans in a cohort of children and young adults. methods in our retrospective cohort study, we included patients without previous cancer diagnoses who were first examined with ct in national health service (nhs) centres in england, wales, or scotland (great britain) between 1985 and 2002, when they were younger than 22 years of age. we obtained data for cancer incidence, mortality, and loss to follow-up from the nhs central registry from jan 1, 1985, to dec 31, 2008. we estimated absorbed brain and red bone marrow doses per ct scan in mgy and assessed excess incidence of leukaemia and brain tumours cancer with poisson relative risk models. to avoid inclusion of ct scans related to cancer diagnosis, follow-up for leukaemia began 2 years after the first ct and for brain tumours 5 years after the first ct. findings during follow-up, 74 of 178,604 patients were diagnosed with leukaemia and 135 of 176,587 patients were diagnosed with brain tumours. we noted a positive association between radiation dose from ct scans and leukaemia (excess relative risk per mgy 0·036, 95% ci 0·005-0·120; p=0·0097) and brain tumours (0·023, 0·010-0·049; p interpretation use of ct scans in children to deliver cumulative doses of about 50 mgy might almost triple the risk of leukaemia and doses of about 60 mgy might triple the risk of brain cancer. because these cancers are relatively rare, the cumulative absolute risks are small: in the 10 years after the first scan for patients younger than 10 years, one excess case of leukaemia and one excess case of brain tumour per 10,000 head ct scans is estimated to occur. nevertheless, although clinical benefits should outweigh the small absolute risks, radiation doses from ct scans ought to be kept as low as possible and alternative procedures, which do not involve ionising radiation, should be considered if appropriate. funding us national cancer institute and uk department of health.",0
"opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. these prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the g-protein-coupled µ-opioid receptor (µ-or) in the central nervous system. here we describe the 2.8 å crystal structure of the mouse µ-or in complex with an irreversible morphinan antagonist. compared to the buried binding pocket observed in most g-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. of particular interest, the µ-or crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. these high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.",0
"background clustered regularly interspaced palindromic repeats (crisprs) are a novel type of direct repeat found in a wide range of bacteria and archaea. crisprs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. existing repeat detection tools do a poor job of identifying crisprs due to the presence of unique spacer sequences separating the repeats. in this study, a new tool, crt, is introduced that rapidly and accurately identifies crisprs in large dna strings, such as genomes and metagenomes. results crt was compared to crispr detection tools, patscan and pilercr. in terms of correctness, crt was shown to be very reliable, demonstrating significant improvements over patscan for measures precision, recall and quality. when compared to pilercr, crt showed improved performance for recall and quality. in terms of speed, crt proved to be a huge improvement over patscan. both crt and pilercr were comparable in speed, however crt was faster for genomes containing large numbers of repeats. conclusion in this paper a new tool was introduced for the automatic detection of crispr elements. this tool, crt, showed some important improvements over current techniques for crispr identification. crt's approach to detecting repetitive sequences is straightforward. it uses a simple sequential scan of a dna sequence and detects repeats directly without any major conversion or preprocessing of the input. this leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being o(n) in space and o(nm/l) in time.",0
"in the hierarchy of data, information and knowledge, computational methods play a major role in the initial processing of data to extract information, but they alone become less effective to compile knowledge from information. the kyoto encyclopedia of genes and genomes (kegg) resource ( or has been developed as a reference knowledge base to assist this latter process. in particular, the kegg pathway maps are widely used for biological interpretation of genome sequences and other high-throughput data. the link from genomes to pathways is made through the kegg orthology system, a collection of manually defined ortholog groups identified by k numbers. to better automate this interpretation process the kegg modules defined by boolean expressions of k numbers have been expanded and improved. once genes in a genome are annotated with k numbers, the kegg modules can be computationally evaluated revealing metabolic capacities and other phenotypic features. the reaction modules, which represent chemical units of reactions, have been used to analyze design principles of metabolic networks and also to improve the definition of k numbers and associated annotations. for translational bioinformatics, the kegg medicus resource has been developed by integrating drug labels (package inserts) used in society.",0
"pubchem ( is a public repository for biological properties of small molecules hosted by the us national institutes of health (nih). pubchem bioassay database currently contains biological test results for more than 700 000 compounds. the goal of pubchem is to make this information easily accessible to biomedical researchers. in this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within pubchem. these web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure-activity analysis, and target selectivity examination. this article reviews these bioactivity analysis tools and discusses their uses. most of the tools described in this work can be directly accessed at urls for accessing other tools described in this work are specified individually.",0
"we set out a generalized linear model framework for the synthesis of data from randomized controlled trials. a common model is described, taking the form of a linear regression for both fixed and random effects synthesis, which can be implemented with normal, binomial, poisson, and multinomial data. the familiar logistic model for meta-analysis with binomial data is a generalized linear model with a logit link function, which is appropriate for probability outcomes. the same linear regression framework can be applied to continuous outcomes, rate models, competing risks, or ordered category outcomes by using other link functions, such as identity, log, complementary log-log, and probit link functions. the common core model for the linear predictor can be applied to pairwise meta-analysis, indirect comparisons, synthesis of multiarm trials, and mixed treatment comparisons, also known as network meta-analysis, without distinction. we take a bayesian approach to estimation and provide winbugs program code for a bayesian analysis using markov chain monte carlo simulation. an advantage of this approach is that it is straightforward to extend to shared parameter models where different randomized controlled trials report outcomes in different formats but from a common underlying model. use of the generalized linear model framework allows us to present a unified account of how models can be compared using the deviance information criterion and how goodness of fit can be assessed using the residual deviance. the approach is illustrated through a range of worked examples for commonly encountered evidence formats.",0
"background no therapy is approved for covid-19 pneumonia. the aim of this study was to assess the role of tocilizumab in reducing the risk of invasive mechanical ventilation and death in patients with severe covid-19 pneumonia who received standard of care treatment. methods this retrospective, observational cohort study included adults (≥18 years) with severe covid-19 pneumonia who were admitted to tertiary care centres in bologna and reggio emilia, italy, between feb 21 and march 24, 2020, and a tertiary care centre in modena, italy, between feb 21 and april 30, 2020. all patients were treated with the standard of care (ie, supplemental oxygen, hydroxychloroquine, azithromycin, antiretrovirals, and low molecular weight heparin), and a non-randomly selected subset of patients also received tocilizumab. tocilizumab was given either intravenously at 8 mg/kg bodyweight (up to a maximum of 800 mg) in two infusions, 12 h apart, or subcutaneously at 162 mg administered in two simultaneous doses, one in each thigh (ie, 324 mg in total), when the intravenous formulation was unavailable. the primary endpoint was a composite of invasive mechanical ventilation or death. treatment groups were compared using kaplan-meier curves and cox regression analysis after adjusting for sex, age, recruiting centre, duration of symptoms, and baseline sequential organ failure assessment (sofa) score. findings of 1351 patients admitted, 544 (40%) had severe covid-19 pneumonia and were included in the study. 57 (16%) of 365 patients in the standard care group needed mechanical ventilation, compared with 33 (18%) of 179 patients treated with tocilizumab (p=0·41; 16 of 88 patients treated intravenously and 17 of 91 patients treated subcutaneously). 73 (20%) patients in the standard care group died, compared with 13 (7%; p interpretation treatment with tocilizumab, whether administered intravenously or subcutaneously, might reduce the risk of invasive mechanical ventilation or death in patients with severe covid-19 pneumonia. funding none.",0
"background there are several methods of assessing nutritional status in cancer of which serum albumin is one of the most commonly used. in recent years, the role of malnutrition as a predictor of survival in cancer has received considerable attention. as a result, it is reasonable to investigate whether serum albumin has utility as a prognostic indicator of cancer survival in cancer. this review summarizes all available epidemiological literature on the association between pretreatment serum albumin levels and survival in different types of cancer. methods a systematic search of the literature using the medline database (january 1995 through june 2010) to identify epidemiologic studies on the relationship between serum albumin and cancer survival. to be included in the review, a study must have: been published in english, reported on data collected in humans with any type of cancer, had serum albumin as one of the or only predicting factor, had survival as one of the outcome measures (primary or secondary) and had any of the following study designs (case-control, cohort, cross-sectional, case-series prospective, retrospective, nested case-control, ecologic, clinical trial, meta-analysis). results of the 29 studies reviewed on cancers of the gastrointestinal tract, all except three found higher serum albumin levels to be associated with better survival in multivariate analysis. of the 10 studies reviewed on lung cancer, all excepting one found higher serum albumin levels to be associated with better survival. in 6 studies reviewed on female cancers and multiple cancers each, lower levels of serum albumin were associated with poor survival. finally, in all 8 studies reviewed on patients with other cancer sites, lower levels of serum albumin were associated with poor survival. conclusions pretreatment serum albumin levels provide useful prognostic significance in cancer. accordingly, serum albumin level could be used in clinical trials to better define the baseline risk in cancer patients. a critical gap for demonstrating causality, however, is the absence of clinical trials demonstrating that raising albumin levels by means of intravenous infusion or by hyperalimentation decreases the excess risk of mortality in cancer.",0
"the biology of cytokines is one of the most rapidly growing areas of biomedical research. it is understandable why the assumption was made several years ago that ep was equivalent to il-1 (both alpha and beta) and subsequently to il-1 alpha, il-1 beta, and tnf. however, as more data have been obtained, it has become clearer that many cytokines and hormones are capable of participating in the febrile response. it is also becoming apparent that eps and ecs might influence body temperature during nonpathological states, perhaps contributing to the elevation in temperature during or after exercise, the circadian variation in temperature, and others. medical textbooks have begun to list il-1 as the ep. as i attempted to make clear in this review, evidence that il-1 alpha is a circulating ep is poor. the evidence is considerably stronger that il-1 beta is an ep, at least during lps-induced fever in rodents. the point i have tried to emphasize is that before any cytokine or hormone can be characterized as an ep or ec (or, for that matter, as being involved in any of the acute phase responses), clearly established rules must be followed, which are patterned after the traditional criteria used by koch to distinguish a pathogenic microorganism from a benign one. as summarized in tables 4 and 5, there are many candidates for eps and ecs, but much more experimental evidence is essential before we gain a clear understanding of the relationship between contact with an exogenous pyrogen, the release of eps and ecs, and the development of fever.",0
"knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions. we have previously reported the development of an integrative interaction database called consensuspathdb ( that aims to fulfill this task. in this update article, we report its significant progress in terms of interaction content and web interface tools. consensuspathdb has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases. binary protein interactions are scored with our confidence assessment tool, intscore. the consensuspathdb web interface allows users to take advantage of these integrated interaction and pathway data in different contexts. recent developments include pathway analysis of metabolite lists, visualization of functional gene/metabolite sets as overlap graphs, gene set analysis based on protein complexes and induced network modules analysis that connects a list of genes through various interaction types. to facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of consensuspathdb using the cytoscape.js library.",0
"hsp90 is unique among molecular chaperones. the majority of its known substrates are signal transduction proteins, and recent work indicates that it uses a novel protein-folding strategy.",0
"background adolescents and young adults frequently experience mental disorders, yet tend not to seek help. this systematic review aims to summarise reported barriers and facilitators of help-seeking in young people using both qualitative research from surveys, focus groups, and interviews and quantitative data from published surveys. it extends previous reviews through its systematic research methodology and by the inclusion of published studies describing what young people themselves perceive are the barriers and facilitators to help-seeking for common mental health problems. methods twenty two published studies of perceived barriers or facilitators in adolescents or young adults were identified through searches of pubmed, psycinfo, and the cochrane database. a thematic analysis was undertaken on the results reported in the qualitative literature and quantitative literature. results fifteen qualitative and seven quantitative studies were identified. young people perceived stigma and embarrassment, problems recognising symptoms (poor mental health literacy), and a preference for self-reliance as the most important barriers to help-seeking. facilitators were comparatively under-researched. however, there was evidence that young people perceived positive past experiences, and social support and encouragement from others as aids to the help-seeking process. conclusions strategies for improving help-seeking by adolescents and young adults should focus on improving mental health literacy, reducing stigma, and taking into account the desire of young people for self-reliance.",0
"one of the most pressing challenges in genomic medicine is to understand the role played by genetic variation in health and disease. thanks to the exploration of genomic variants at large scale, hundreds of thousands of disease-associated loci have been uncovered. however, the identification of variants of clinical relevance is a significant challenge that requires comprehensive interrogation of previous knowledge and linkage to new experimental results. to assist in this complex task, we created disgenet ( a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, including the scientific literature. disgenet covers the full spectrum of human diseases as well as normal and abnormal traits. the current release covers more than 24 000 diseases and traits, 17 000 genes and 117 000 genomic variants. the latest developments of disgenet include new sources of data, novel data attributes and prioritization metrics, a redesigned web interface and recently launched apis. thanks to the data standardization, the combination of expert curated information with data automatically mined from the scientific literature, and a suite of tools for accessing its publicly available data, disgenet is an interoperable resource supporting a variety of applications in genomic medicine and drug r&d.",0
"dimerizers allowing inducible control of protein-protein interactions are powerful tools for manipulating biological processes. here we describe genetically encoded light-inducible protein-interaction modules based on arabidopsis thaliana cryptochrome 2 and cib1 that require no exogenous ligands and dimerize on blue-light exposure with subsecond time resolution and subcellular spatial resolution. we demonstrate the utility of this system by inducing protein translocation, transcription and cre recombinase-mediated dna recombination using light.",0
"background chronic obstructive pulmonary disease (copd) and asthma are common diseases with a heterogeneous distribution worldwide. here, we present methods and disease and risk estimates for copd and asthma from the global burden of diseases, injuries, and risk factors (gbd) 2015 study. the gbd study provides annual updates on estimates of deaths, prevalence, and disability-adjusted life years (dalys), a summary measure of fatal and non-fatal disease outcomes, for over 300 diseases and injuries, for 188 countries from 1990 to the most recent year. methods we estimated numbers of deaths due to copd and asthma using the gbd cause of death ensemble modelling (codem) tool. first, we analysed data from vital registration and verbal autopsy for the aggregate category of all chronic respiratory diseases. subsequently, models were run for asthma and copd relying on covariates to predict rates in countries that have incomplete or no vital registration data. disease estimates for copd and asthma were based on systematic reviews of published papers, unpublished reports, surveys, and health service encounter data from the usa. we used the global initiative of chronic obstructive lung disease spirometry-based definition as the reference for copd and a reported diagnosis of asthma with current wheeze as the definition of asthma. we used a bayesian meta-regression tool, dismod-mr 2.1, to derive estimates of prevalence and incidence. we estimated population-attributable fractions for risk factors for copd and asthma from exposure data, relative risks, and a theoretical minimum exposure level. results were stratified by socio-demographic index (sdi), a composite measure of income per capita, mean years of education over the age of 15 years, and total fertility rate. findings in 2015, 3·2 million people (95% uncertainty interval 3·1 million to 3·3 million) died from copd worldwide, an increase of 11·6% (95% ui 5·3 to 19·8) compared with 1990. there was a decrease in age-standardised death rate of 41·9% (37·7 to 45·1) but this was counteracted by population growth and ageing of the global population. from 1990 to 2015, the prevalence of copd increased by 44·2% (41·7 to 46·6), whereas age-standardised prevalence decreased by 14·7% (13·5 to 15·9). in 2015, 0·40 million people (0·36 million to 0·44 million) died from asthma, a decrease of 26·7% (-7·2 to 43·7) from 1990, and the age-standardised death rate decreased by 58·8% (39·0 to 69·0). the prevalence of asthma increased by 12·6% (9·0 to 16·4), whereas the age-standardised prevalence decreased by 17·7% (15·1 to 19·9). age-standardised daly rates due to copd increased until the middle range of the sdi before reducing sharply. age-standardised daly rates due to asthma in both sexes decreased monotonically with rising sdi. the relation between with sdi and daly rates due to asthma was attributed to variation in years of life lost (ylls), whereas daly rates due to copd varied similarly for ylls and years lived with disability across the sdi continuum. smoking and ambient particulate matter were the main risk factors for copd followed by household air pollution, occupational particulates, ozone, and secondhand smoke. together, these risks explained 73·3% (95% ui 65·8 to 80·1) of dalys due to copd. smoking and occupational asthmagens were the only risks quantified for asthma in gbd, accounting for 16·5% (14·6 to 18·7) of dalys due to asthma. interpretation asthma was the most prevalent chronic respiratory disease worldwide in 2015, with twice the number of cases of copd. deaths from copd were eight times more common than deaths from asthma. in 2015, copd caused 2·6% of global dalys and asthma 1·1% of global dalys. although there are laudable international collaborative efforts to make surveys of asthma and copd more comparable, no consensus exists on case definitions and how to measure disease severity for population health measurements like gbd. comparisons between countries and over time are important, as much of the chronic respiratory burden is either preventable or treatable with affordable interventions. funding bill & melinda gates foundation.",0
"in this paper, inspired by the plenary panel at the 2013 meeting of the international society for traumatic stress studies, dr. steven southwick (chair) and multidisciplinary panelists drs. george bonanno, ann masten, catherine panter-brick, and rachel yehuda tackle some of the most pressing current questions in the field of resilience research including: (1) how do we define resilience, (2) what are the most important determinants of resilience, (3) how are new technologies informing the science of resilience, and (4) what are the most effective ways to enhance resilience? these multidisciplinary experts provide insight into these difficult questions, and although each of the panelists had a slightly different definition of resilience, most of the proposed definitions included a concept of healthy, adaptive, or integrated positive functioning over the passage of time in the aftermath of adversity. the panelists agreed that resilience is a complex construct and it may be defined differently in the context of individuals, families, organizations, societies, and cultures. with regard to the determinants of resilience, there was a consensus that the empirical study of this construct needs to be approached from a multiple level of analysis perspective that includes genetic, epigenetic, developmental, demographic, cultural, economic, and social variables. the empirical study of determinates of resilience will inform efforts made at fostering resilience, with the recognition that resilience may be enhanced on numerous levels (e.g., individual, family, community, culture).",0
"protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. after decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally determined structure 1 . here we markedly expand the structural coverage of the proteome by applying the state-of-the-art machine learning method, alphafold 2 , at a scale that covers almost the entire human proteome (98.5% of human proteins). the resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. we introduce several metrics developed by building on the alphafold model and use them to interpret the dataset, identifying strong multi-domain predictions as well as regions that are likely to be disordered. finally, we provide some case studies to illustrate how high-quality predictions could be used to generate biological hypotheses. we are making our predictions freely available to the community and anticipate that routine large-scale and high-accuracy structure prediction will become an important tool that will allow new questions to be addressed from a structural perspective.",0
"the severe 2019 outbreak of novel coronavirus disease (covid-19), which was first reported in wuhan, would be expected to impact the mental health of local medical and nursing staff and thus lead them to seek help. however, those outcomes have yet to be established using epidemiological data. to explore the mental health status of medical and nursing staff and the efficacy, or lack thereof, of critically connecting psychological needs to receiving psychological care, we conducted a quantitative study. this is the first paper on the mental health of medical and nursing staff in wuhan. notably, among 994 medical and nursing staff working in wuhan, 36.9% had subthreshold mental health disturbances (mean phq-9: 2.4), 34.4% had mild disturbances (mean phq-9: 5.4), 22.4% had moderate disturbances (mean phq-9: 9.0), and 6.2% had severe disturbance (mean phq-9: 15.1) in the immediate wake of the viral epidemic. the noted burden fell particularly heavily on young women. of all participants, 36.3% had accessed psychological materials (such as books on mental health), 50.4% had accessed psychological resources available through media (such as online push messages on mental health self-help coping methods), and 17.5% had participated in counseling or psychotherapy. trends in levels of psychological distress and factors such as exposure to infected people and psychological assistance were identified. although staff accessed limited mental healthcare services, distressed staff nonetheless saw these services as important resources to alleviate acute mental health disturbances and improve their physical health perceptions. these findings emphasize the importance of being prepared to support frontline workers through mental health interventions at times of widespread crisis.",0
"basic local alignment search tool (blast) is a sequence similarity search program. the public interface of blast, at the ncbi website has recently been reengineered to improve usability and performance. key new features include simplified search forms, improved navigation, a list of recent blast results, saved search strategies and a documentation directory. here, we describe the blast web application's new features, explain design decisions and outline plans for future improvement.",0
"urine has long been a ""favored"" biofluid among metabolomics researchers. it is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. however, this chemical complexity has also made urine a particularly difficult substrate to fully understand. as a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. many of these compounds are poorly characterized and poorly understood. in an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. this involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. the experimental portion employed nmr spectroscopy, gas chromatography mass spectrometry (gc-ms), direct flow injection mass spectrometry (dfi/lc-ms/ms), inductively coupled plasma mass spectrometry (icp-ms) and high performance liquid chromatography (hplc) experiments performed on multiple human urine samples. this multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. the different analytical platforms were able to identify (quantify) a total of: 209 (209) by nmr, 179 (85) by gc-ms, 127 (127) by dfi/lc-ms/ms, 40 (40) by icp-ms and 10 (10) by hplc. our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. it also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. the literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. an online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at",0
"here, we describe the third major release of relion. cpu-based vector acceleration has been added in addition to gpu support, which provides flexibility in use of resources and avoids memory limitations. reference-free autopicking with laplacian-of-gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2d-classification, de novo model generation and 3d-classification. per-particle refinement of ctf parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. ewald sphere curvature correction improves resolution for large particles. we illustrate these developments with publicly available data sets: together with a bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 å compared to previous relion versions.",0
"the mesostriatal dopamine system is prominently implicated in model-free reinforcement learning, with fmri bold signals in ventral striatum notably covarying with model-free prediction errors. however, latent learning and devaluation studies show that behavior also shows hallmarks of model-based planning, and the interaction between model-based and model-free values, prediction errors, and preferences is underexplored. we designed a multistep decision task in which model-based and model-free influences on human choice behavior could be distinguished. by showing that choices reflected both influences we could then test the purity of the ventral striatal bold signal as a model-free report. contrary to expectations, the signal reflected both model-free and model-based predictions in proportions matching those that best explained choice behavior. these results challenge the notion of a separate model-free learner and suggest a more integrated computational architecture for high-level human decision-making.",0
"specific binding of aggregated gamma-globulin to a subpopulation of lymphocytes was demonstrated. this subpopulation was identified as the ig-staining or b lymphocytes. the binding was irreversible and independent of complement, ph, temperature, protein content of the medium, and divalent cations. aggregates of large size were needed for optimal visualization. evidence was obtained that the site on the lymphocyte membrane responsible for binding aggregates was distinct from surface ig.",0
"mendelian randomization (mr) permits causal inference between exposures and a disease. it can be compared with randomized controlled trials. whereas in a randomized controlled trial the randomization occurs at entry into the trial, in mr the randomization occurs during gamete formation and conception. several factors, including time since conception and sampling variation, are relevant to the interpretation of an mr test. particularly important is consideration of the ""missingness"" of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. testing for hardy-weinberg equilibrium (hwe) is a genetic approach that permits evaluation of missingness. in this paper, the authors demonstrate evidence of nonconformity with hwe in real data. they also perform simulations to characterize the sensitivity of hwe tests to missingness. unresolved missingness could lead to a false rejection of causality in an mr investigation of trait-disease association. these results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. the authors also present a web program ( for estimating possible missingness and an approach to evaluating missingness under different genetic models.",0
"regulatory t cells have been clearly implicated in the control of disease in murine models of autoimmunity. the paucity of data regarding the role of these lymphocytes in human autoimmune disease has prompted us to examine their function in patients with rheumatoid arthritis (ra). regulatory (cd4(+)cd25(+)) t cells isolated from patients with active ra displayed an anergic phenotype upon stimulation with anti-cd3 and anti-cd28 antibodies, and suppressed the proliferation of effector t cells in vitro. however, they were unable to suppress proinflammatory cytokine secretion from activated t cells and monocytes, or to convey a suppressive phenotype to effector cd4(+)cd25(-) t cells. treatment with antitumor necrosis factor alpha (tnfalpha; infliximab) restored the capacity of regulatory t cells to inhibit cytokine production and to convey a suppressive phenotype to ""conventional"" t cells. furthermore, anti-tnfalpha treatment led to a significant rise in the number of peripheral blood regulatory t cells in ra patients responding to this treatment, which correlated with a reduction in c reactive protein. these data are the first to demonstrate that regulatory t cells are functionally compromised in ra, and indicate that modulation of regulatory t cells by anti-tnfalpha therapy may be a further mechanism by which this disease is ameliorated.",0
"background the promoting action on research implementation in health services, or parihs framework, was first published in 1998. since this time, work has been ongoing to further develop, refine and test it. widely used as an organising or conceptual framework to help both explain and predict why the implementation of evidence into practice is or is not successful, parihs was one of the first frameworks to make explicit the multi-dimensional and complex nature of implementation as well as highlighting the central importance of context. several critiques of the framework have also pointed out its limitations and suggested areas for improvement. discussion building on the published critiques and a number of empirical studies, this paper introduces a revised version of the framework, called the integrated or i-parihs framework. the theoretical antecedents of the framework are described as well as outlining the revised and new elements, notably, the revision of how evidence is described; how the individual and teams are incorporated; and how context is further delineated. we describe how the framework can be operationalised and draw on case study data to demonstrate the preliminary testing of the face and content validity of the revised framework. this paper is presented for deliberation and discussion within the implementation science community. responding to a series of critiques and helpful feedback on the utility of the original parihs framework, we seek feedback on the proposed improvements to the framework. we believe that the i-parihs framework creates a more integrated approach to understand the theoretical complexity from which implementation science draws its propositions and working hypotheses; that the new framework is more coherent and comprehensive and at the same time maintains it intuitive appeal; and that the models of facilitation described enable its more effective operationalisation.",0
"introduction acute kidney injury (aki) is a complex disorder for which currently there is no accepted definition. having a uniform standard for diagnosing and classifying aki would enhance our ability to manage these patients. future clinical and translational research in aki will require collaborative networks of investigators drawn from various disciplines, dissemination of information via multidisciplinary joint conferences and publications, and improved translation of knowledge from pre-clinical research. we describe an initiative to develop uniform standards for defining and classifying aki and to establish a forum for multidisciplinary interaction to improve care for patients with or at risk for aki. methods members representing key societies in critical care and nephrology along with additional experts in adult and pediatric aki participated in a two day conference in amsterdam, the netherlands, in september 2005 and were assigned to one of three workgroups. each group's discussions formed the basis for draft recommendations that were later refined and improved during discussion with the larger group. dissenting opinions were also noted. the final draft recommendations were circulated to all participants and subsequently agreed upon as the consensus recommendations for this report. participating societies endorsed the recommendations and agreed to help disseminate the results. results the term aki is proposed to represent the entire spectrum of acute renal failure. diagnostic criteria for aki are proposed based on acute alterations in serum creatinine or urine output. a staging system for aki which reflects quantitative changes in serum creatinine and urine output has been developed. conclusion we describe the formation of a multidisciplinary collaborative network focused on aki. we have proposed uniform standards for diagnosing and classifying aki which will need to be validated in future studies. the acute kidney injury network offers a mechanism for proceeding with efforts to improve patient outcomes.",0
"macrophages are endowed with a variety of receptors for lineage-determining growth factors, t helper (th) cell cytokines, and b cell, host, and microbial products. in tissues, macrophages mature and are activated in a dynamic response to combinations of these stimuli to acquire specialized functional phenotypes. as for the lymphocyte system, a dichotomy has been proposed for macrophage activation: classic vs. alternative, also m1 and m2, respectively. in view of recent research about macrophage functions and the increasing number of immune-relevant ligands, a revision of the model is needed. here, we assess how cytokines and pathogen signals influence their functional phenotypes and the evidence for m1 and m2 functions and revisit a paradigm initially based on the role of a restricted set of selected ligands in the immune response.",0
"psychological health problems, especially emotional disorders, are common among adolescents. the epidemiology of emotional disorders is greatly influenced by stressful events. this study sought to assess the prevalence rate and socio-demographic correlates of depressive and anxiety symptoms among chinese adolescents affected by the outbreak of covid-19. we conducted a cross-sectional study among chinese students aged 12-18 years during the covid-19 epidemic period. an online survey was used to conduct rapid assessment. a total of 8079 participants were involved in the study. an online survey was used to collect demographic data, assess students' awareness of covid-19, and assess depressive and anxiety symptoms with the patient health questionnaire (phq-9) and the generalized anxiety disorder (gad-7) questionnaire, respectively. the prevalence of depressive symptoms, anxiety symptoms, and a combination of depressive and anxiety symptoms was 43.7%, 37.4%, and 31.3%, respectively, among chinese high school students during the covid-19 outbreak. multivariable logistic regression analysis revealed that female gender was the higher risk factor for depressive and anxiety symptoms. in terms of grades, senior high school was a risk factor for depressive and anxiety symptoms; the higher the grade, the greater the prevalence of depressive and anxiety symptoms. our findings show there is a high prevalence of psychological health problems among adolescents, which are negatively associated with the level of awareness of covid-19. these findings suggest that the government needs to pay more attention to psychological health among adolescents while combating covid-19.",0
"a number of cytoskeletal-associated proteins that are concentrated in focal contacts, namely alpha-actinin, vinculin, talin, and integrin, have been shown to interact in vitro such that they suggest a potential link between actin filaments and the membrane. because some of these interactions are of low affinity, we suspect the additional linkages also exist. therefore, we have used a synthetic peptide corresponding to the cytoplasmic domain of beta 1 integrin and affinity chromatography to identify additional integrin-binding proteins. here we report our finding of an interaction between the cytoplasmic domain of beta 1 integrin and the actin-binding protein alpha-actinin. beta 1-integrin cytoplasmic domain peptide columns bound several proteins from triton extracts of chicken embryo fibroblasts. one protein at approximately 100 kd was identified by immunoblot analysis as alpha-actinin. solid phase binding assays indicated that alpha-actinin bound specifically and directly to the beta 1 peptide with relatively high affinity. using purified heterodimeric chicken smooth muscle integrin (a beta 1 integrin) or the platelet integrin glycoprotein iib/iiia complex (a beta 3 integrin), binding of alpha-actinin was also observed in similar solid phase assays, albeit with a lower affinity than was seen using the beta 1 peptide. alpha-actinin also bound specifically to phospholipid vesicles into which glycoprotein iib/iiia had been incorporated. these results lead us to suggest that this integrin-alpha-actinin linkage may contribute to the attachment of actin filaments to the membrane in certain locations.",0
"cellular life emerged ∼3.7 billion years ago. with scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the earth's rotation. the advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. the molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: bacteria, archaea and eukaryota. here we show that oxidation-reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. furthermore, we explore the interconnectivity between these metabolic cycles and transcription-translation feedback loops of the clockwork in each system. our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the great oxidation event ∼2.5 billion years ago.",0
"background at the individual level, higher hiv viral load predicts sexual transmission risk. we evaluated san francisco's community viral load (cvl) as a population level marker of hiv transmission risk. we hypothesized that the decrease in cvl in san francisco from 2004-2008, corresponding with increased rates of hiv testing, antiretroviral therapy (art) coverage and effectiveness, and population-level virologic suppression, would be associated with a reduction in new hiv infections. methodology/principal findings we used san francisco's hiv/aids surveillance system to examine the trends in cvl. mean cvl was calculated as the mean of the most recent viral load of all reported hiv-positive individuals in a particular community. total cvl was defined as the sum of the most recent viral loads of all hiv-positive individuals in a particular community. we used poisson models with robust standard errors to assess the relationships between the mean and total cvl and the primary outcome: annual numbers of newly diagnosed hiv cases. both mean and total cvl decreased from 2004-2008 and were accompanied by decreases in new hiv diagnoses from 798 (2004) to 434 (2008). the mean (p = 0.003) and total cvl (p = 0.002) were significantly associated with new hiv cases from 2004-2008. conclusions/significance reductions in cvl are associated with decreased hiv infections. results suggest that wide-scale art could reduce hiv transmission at the population level. because cvl is temporally upstream of new hiv infections, jurisdictions should consider adding cvl to routine hiv surveillance to track the epidemic, allocate resources, and to evaluate the effectiveness of hiv prevention and treatment efforts.",0
"background observational studies suggest that male circumcision may provide protection against hiv-1 infection. a randomized, controlled intervention trial was conducted in a general population of south africa to test this hypothesis. methods and findings a total of 3,274 uncircumcised men, aged 18-24 y, were randomized to a control or an intervention group with follow-up visits at months 3, 12, and 21. male circumcision was offered to the intervention group immediately after randomization and to the control group at the end of the follow-up. the grouped censored data were analyzed in intention-to-treat, univariate and multivariate, analyses, using piecewise exponential, proportional hazards models. rate ratios (rr) of hiv incidence were determined with 95% ci. protection against hiv infection was calculated as 1 - rr. the trial was stopped at the interim analysis, and the mean (interquartile range) follow-up was 18.1 mo (13.0-21.0) when the data were analyzed. there were 20 hiv infections (incidence rate = 0.85 per 100 person-years) in the intervention group and 49 (2.1 per 100 person-years) in the control group, corresponding to an rr of 0.40 (95% ci: 0.24%-0.68%; p conclusion male circumcision provides a degree of protection against acquiring hiv infection, equivalent to what a vaccine of high efficacy would have achieved. male circumcision may provide an important way of reducing the spread of hiv infection in sub-saharan africa. (preliminary and partial results were presented at the international aids society 2005 conference, on 26 july 2005, in rio de janeiro, brazil.).",0
"background the outbreak of coronavirus disease-19 (covid-19) is a public health emergency of international concern. telehealth is an effective option to fight the outbreak of covid-19. the aim of this systematic review was to identify the role of telehealth services in preventing, diagnosing, treating, and controlling diseases during covid-19 outbreak. methods this systematic review was conducted through searching five databases including pubmed, scopus, embase, web of science, and science direct. inclusion criteria included studies clearly defining any use of telehealth services in all aspects of health care during covid-19 outbreak, published from december 31, 2019, written in english language and published in peer reviewed journals. two reviewers independently assessed search results, extracted data, and assessed the quality of the included studies. quality assessment was based on the critical appraisal skills program (casp) checklist. narrative synthesis was undertaken to summarize and report the findings. results eight studies met the inclusion out of the 142 search results. currently, healthcare providers and patients who are self-isolating, telehealth is certainly appropriate in minimizing the risk of covid-19 transmission. this solution has the potential to prevent any sort of direct physical contact, provide continuous care to the community, and finally reduce morbidity and mortality in covid-19 outbreak. conclusions the use of telehealth improves the provision of health services. therefore, telehealth should be an important tool in caring services while keeping patients and health providers safe during covid-19 outbreak.",0
"the body mass index (bmi) is the metric currently in use for defining anthropometric height/weight characteristics in adults and for classifying (categorizing) them into groups. the common interpretation is that it represents an index of an individual's fatness. it also is widely used as a risk factor for the development of or the prevalence of several health issues. in addition, it is widely used in determining public health policies.the bmi has been useful in population-based studies by virtue of its wide acceptance in defining specific categories of body mass as a health issue. however, it is increasingly clear that bmi is a rather poor indicator of percent of body fat. importantly, the bmi also does not capture information on the mass of fat in different body sites. the latter is related not only to untoward health issues but to social issues as well. lastly, current evidence indicates there is a wide range of bmis over which mortality risk is modest, and this is age related. all of these issues are discussed in this brief review.",0
"an in-depth annotation of the newly discovered coronavirus (2019-ncov) genome has revealed differences between 2019-ncov and severe acute respiratory syndrome (sars) or sars-like coronaviruses. a systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may have caused functional and pathogenic divergence of 2019-ncov.",0
"natural killer (nk) cells are the predominant innate lymphocyte subsets that mediate anti-tumor and anti-viral responses, and therefore possess promising clinical utilization. nk cells do not express polymorphic clonotypic receptors and utilize inhibitory receptors (killer immunoglobulin-like receptor and ly49) to develop, mature, and recognize "" self "" from "" non-self ."" the essential roles of common gamma cytokines such as interleukin (il)-2, il-7, and il-15 in the commitment and development of nk cells are well established. however, the critical functions of pro-inflammatory cytokines il-12, il-18, il-27, and il-35 in the transcriptional-priming of nk cells are only starting to emerge. recent studies have highlighted multiple shared characteristics between nk cells the adaptive immune lymphocytes. nk cells utilize unique signaling pathways that offer exclusive ways to genetically manipulate to improve their effector functions. here, we summarize the recent advances made in the understanding of how nk cells develop, mature, and their potential translational use in the clinic.",0
"background major depressive disorder is one of the most common, burdensome, and costly psychiatric disorders worldwide in adults. pharmacological and non-pharmacological treatments are available; however, because of inadequate resources, antidepressants are used more frequently than psychological interventions. prescription of these agents should be informed by the best available evidence. therefore, we aimed to update and expand our previous work to compare and rank antidepressants for the acute treatment of adults with unipolar major depressive disorder. methods we did a systematic review and network meta-analysis. we searched cochrane central register of controlled trials, cinahl, embase, lilacs database, medline, medline in-process, psycinfo, the websites of regulatory agencies, and international registers for published and unpublished, double-blind, randomised controlled trials from their inception to jan 8, 2016. we included placebo-controlled and head-to-head trials of 21 antidepressants used for the acute treatment of adults (≥18 years old and of both sexes) with major depressive disorder diagnosed according to standard operationalised criteria. we excluded quasi-randomised trials and trials that were incomplete or included 20% or more of participants with bipolar disorder, psychotic depression, or treatment-resistant depression; or patients with a serious concomitant medical illness. we extracted data following a predefined hierarchy. in network meta-analysis, we used group-level data. we assessed the studies' risk of bias in accordance to the cochrane handbook for systematic reviews of interventions, and certainty of evidence using the grading of recommendations assessment, development and evaluation framework. primary outcomes were efficacy (response rate) and acceptability (treatment discontinuations due to any cause). we estimated summary odds ratios (ors) using pairwise and network meta-analysis with random effects. this study is registered with prospero, number crd42012002291. findings we identified 28 552 citations and of these included 522 trials comprising 116 477 participants. in terms of efficacy, all antidepressants were more effective than placebo, with ors ranging between 2·13 (95% credible interval 1·89-2·41) for amitriptyline and 1·37 (1·16-1·63) for reboxetine. for acceptability, only agomelatine (or 0·84, 95% cri 0·72-0·97) and fluoxetine (0·88, 0·80-0·96) were associated with fewer dropouts than placebo, whereas clomipramine was worse than placebo (1·30, 1·01-1·68). when all trials were considered, differences in ors between antidepressants ranged from 1·15 to 1·55 for efficacy and from 0·64 to 0·83 for acceptability, with wide cris on most of the comparative analyses. in head-to-head studies, agomelatine, amitriptyline, escitalopram, mirtazapine, paroxetine, venlafaxine, and vortioxetine were more effective than other antidepressants (range of ors 1·19-1·96), whereas fluoxetine, fluvoxamine, reboxetine, and trazodone were the least efficacious drugs (0·51-0·84). for acceptability, agomelatine, citalopram, escitalopram, fluoxetine, sertraline, and vortioxetine were more tolerable than other antidepressants (range of ors 0·43-0·77), whereas amitriptyline, clomipramine, duloxetine, fluvoxamine, reboxetine, trazodone, and venlafaxine had the highest dropout rates (1·30-2·32). 46 (9%) of 522 trials were rated as high risk of bias, 380 (73%) trials as moderate, and 96 (18%) as low; and the certainty of evidence was moderate to very low. interpretation all antidepressants were more efficacious than placebo in adults with major depressive disorder. smaller differences between active drugs were found when placebo-controlled trials were included in the analysis, whereas there was more variability in efficacy and acceptability in head-to-head trials. these results should serve evidence-based practice and inform patients, physicians, guideline developers, and policy makers on the relative merits of the different antidepressants. funding national institute for health research oxford health biomedical research centre and the japan society for the promotion of science.",0
"single-particle tracking (spt) is often the rate-limiting step in live-cell imaging studies of subcellular dynamics. here we present a tracking algorithm that addresses the principal challenges of spt, namely high particle density, particle motion heterogeneity, temporary particle disappearance, and particle merging and splitting. the algorithm first links particles between consecutive frames and then links the resulting track segments into complete trajectories. both steps are formulated as global combinatorial optimization problems whose solution identifies the overall most likely set of particle trajectories throughout a movie. using this approach, we show that the gtpase dynamin differentially affects the kinetics of long- and short-lived endocytic structures and that the motion of cd36 receptors along cytoskeleton-mediated linear tracks increases their aggregation probability. both applications indicate the requirement for robust and complete tracking of dense particle fields to dissect the mechanisms of receptor organization at the level of the plasma membrane.",0
"although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. here, we present popgenome, a population genomics package for the r software environment (a de facto standard for statistical analyses). popgenome can efficiently process genome-scale data as well as large sets of individual loci. it reads dna alignments and single-nucleotide polymorphism (snp) data sets in most common formats, including those used by the hapmap, 1000 human genomes, and 1001 arabidopsis genomes projects. popgenome also reads associated annotation files in gff format, enabling users to easily define regions or classify snps based on their annotation; all analyses can also be applied to sliding windows. popgenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. popgenome is linked to hudson's ms and ewing's msms programs to assess statistical significance based on coalescent simulations. popgenome's integration in r facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. developers can easily incorporate new analyses methods into the popgenome framework. popgenome and r are freely available from cran ( for all major operating systems under the gnu general public license.",0
"background exposure to ambient air pollution increases morbidity and mortality, and is a leading contributor to global disease burden. we explored spatial and temporal trends in mortality and burden of disease attributable to ambient air pollution from 1990 to 2015 at global, regional, and country levels. methods we estimated global population-weighted mean concentrations of particle mass with aerodynamic diameter less than 2·5 μm (pm 2·5 ) and ozone at an approximate 11 km × 11 km resolution with satellite-based estimates, chemical transport models, and ground-level measurements. using integrated exposure-response functions for each cause of death, we estimated the relative risk of mortality from ischaemic heart disease, cerebrovascular disease, chronic obstructive pulmonary disease, lung cancer, and lower respiratory infections from epidemiological studies using non-linear exposure-response functions spanning the global range of exposure. findings ambient pm 2·5 was the fifth-ranking mortality risk factor in 2015. exposure to pm 2·5 caused 4·2 million (95% uncertainty interval 3·7 million to 4·8 million) deaths and 103·1 million (90·8 million 115·1 million) disability-adjusted life-years (dalys) in 2015, representing 7·6% of total global deaths and 4·2% of global dalys, 59% of these in east and south asia. deaths attributable to ambient pm 2·5 increased from 3·5 million (95% ui 3·0 million to 4·0 million) in 1990 to 4·2 million (3·7 million to 4·8 million) in 2015. exposure to ozone caused an additional 254 000 (95% ui 97 000-422 000) deaths and a loss of 4·1 million (1·6 million to 6·8 million) dalys from chronic obstructive pulmonary disease in 2015. interpretation ambient air pollution contributed substantially to the global burden of disease in 2015, which increased over the past 25 years, due to population ageing, changes in non-communicable disease rates, and increasing air pollution in low-income and middle-income countries. modest reductions in burden will occur in the most polluted countries unless pm 2·5 values are decreased substantially, but there is potential for substantial health benefits from exposure reduction. funding bill & melinda gates foundation and health effects institute.",0
"aspirin therapy inhibits prostaglandin biosynthesis without directly acting on lipoxygenases, yet via acetylation of cyclooxygenase 2 (cox-2) it leads to bioactive lipoxins (lxs) epimeric at carbon 15 (15-epi-lx, also termed aspirin-triggered lx ). here, we report that inflammatory exudates from mice treated with omega-3 polyunsaturated fatty acid and aspirin (asa) generate a novel array of bioactive lipid signals. human endothelial cells with upregulated cox-2 treated with asa converted c20:5 omega-3 to 18r-hydroxyeicosapentaenoic acid (hepe) and 15r-hepe. each was used by polymorphonuclear leukocytes to generate separate classes of novel trihydroxy-containing mediators, including 5-series 15r-lx(5) and 5,12,18r-trihepe. these new compounds proved to be potent inhibitors of human polymorphonuclear leukocyte transendothelial migration and infiltration in vivo (atl analogue > 5,12,18r-trihepe > 18r-hepe). acetaminophen and indomethacin also permitted 18r-hepe and 15r-hepe generation with recombinant cox-2 as well as omega-5 and omega-9 oxygenations of other fatty acids that act on hematologic cells. these findings establish new transcellular routes for producing arrays of bioactive lipid mediators via cox-2-nonsteroidal antiinflammatory drug-dependent oxygenations and cell-cell interactions that impact microinflammation. the generation of these and related compounds provides a novel mechanism(s) for the therapeutic benefits of omega-3 dietary supplementation, which may be important in inflammation, neoplasia, and vascular diseases.",0
"in recent years, photoredox catalysis has come to the forefront in organic chemistry as a powerful strategy for the activation of small molecules. in a general sense, these approaches rely on the ability of metal complexes and organic dyes to convert visible light into chemical energy by engaging in single-electron transfer with organic substrates, thereby generating reactive intermediates. in this perspective, we highlight the unique ability of photoredox catalysis to expedite the development of completely new reaction mechanisms, with particular emphasis placed on multicatalytic strategies that enable the construction of challenging carbon-carbon and carbon-heteroatom bonds.",0
"using a laser-induced endothelial injury model, we examined thrombus formation in the microcirculation of wild-type and genetically altered mice by real-time in vivo microscopy to analyze this complex physiologic process in a system that includes the vessel wall, the presence of flowing blood, and the absence of anticoagulants. we observe p-selectin expression, tissue factor accumulation, and fibrin generation after platelet localization in the developing thrombus in arterioles of wild-type mice. however, mice lacking p-selectin glycoprotein ligand 1 (psgl-1) or p-selectin, or wild-type mice infused with blocking p-selectin antibodies, developed platelet thrombi containing minimal tissue factor and fibrin. to explore the delivery of tissue factor into a developing thrombus, we identified monocyte-derived microparticles in human platelet-poor plasma that express tissue factor, psgl-1, and cd14. fluorescently labeled mouse microparticles infused into a recipient mouse localized within the developing thrombus, indicating that one pathway for the initiation of blood coagulation in vivo involves the accumulation of tissue factor- and psgl-1-containing microparticles in the platelet thrombus expressing p-selectin. these monocyte-derived microparticles bind to activated platelets in an interaction mediated by platelet p-selectin and microparticle psgl-1. we propose that psgl-1 plays a role in blood coagulation in addition to its known role in leukocyte trafficking.",0
"understanding the amazingly complex human cerebral cortex requires a map (or parcellation) of its major subdivisions, known as cortical areas. making an accurate areal map has been a century-old objective in neuroscience. using multi-modal magnetic resonance images from the human connectome project (hcp) and an objective semi-automated neuroanatomical approach, we delineated 180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults. we characterized 97 new areas and 83 areas previously reported using post-mortem microscopy or other specialized study-specific approaches. to enable automated delineation and identification of these areas in new hcp subjects and in future studies, we trained a machine-learning classifier to recognize the multi-modal 'fingerprint' of each cortical area. this classifier detected the presence of 96.6% of the cortical areas in new subjects, replicated the group parcellation, and could correctly locate areas in individuals with atypical parcellations. the freely available parcellation and classifier will enable substantially improved neuroanatomical precision for studies of the structural and functional organization of human cerebral cortex and its variation across individuals and in development, aging, and disease.",0
"many microorganisms produce natural products that form the basis of antimicrobials, antivirals, and other drugs. genome mining is routinely used to complement screening-based workflows to discover novel natural products. since 2011, the ""antibiotics and secondary metabolite analysis shell-antismash"" ( has supported researchers in their microbial genome mining tasks, both as a free-to-use web server and as a standalone tool under an osi-approved open-source license. it is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (bgcs) in bacteria and fungi. here, we present the updated version 6 of antismash. antismash 6 increases the number of supported cluster types from 58 to 71, displays the modular structure of multi-modular bgcs, adds a new bgc comparison algorithm, allows for the integration of results from other prediction tools, and more effectively detects tailoring enzymes in ripp clusters.",0
"background many ehealth technologies are not successful in realizing sustainable innovations in health care practices. one of the reasons for this is that the current development of ehealth technology often disregards the interdependencies between technology, human characteristics, and the socioeconomic environment, resulting in technology that has a low impact in health care practices. to overcome the hurdles with ehealth design and implementation, a new, holistic approach to the development of ehealth technologies is needed, one that takes into account the complexity of health care and the rituals and habits of patients and other stakeholders. objective the aim of this viewpoint paper is to improve the uptake and impact of ehealth technologies by advocating a holistic approach toward their development and eventual integration in the health sector. methods to identify the potential and limitations of current ehealth frameworks (1999-2009), we carried out a literature search in the following electronic databases: pubmed, sciencedirect, web of knowledge, picarta, and google scholar. of the 60 papers that were identified, 44 were selected for full review. we excluded those papers that did not describe hands-on guidelines or quality criteria for the design, implementation, and evaluation of ehealth technologies (28 papers). from the results retrieved, we identified 16 ehealth frameworks that matched the inclusion criteria. the outcomes were used to posit strategies and principles for a holistic approach toward the development of ehealth technologies; these principles underpin our holistic ehealth framework. results a total of 16 frameworks qualified for a final analysis, based on their theoretical backgrounds and visions on ehealth, and the strategies and conditions for the research and development of ehealth technologies. despite their potential, the relationship between the visions on ehealth, proposed strategies, and research methods is obscure, perhaps due to a rather conceptual approach that focuses on the rationale behind the frameworks rather than on practical guidelines. in addition, the web 2.0 technologies that call for a more stakeholder-driven approach are beyond the scope of current frameworks. to overcome these limitations, we composed a holistic framework based on a participatory development approach, persuasive design techniques, and business modeling. conclusions to demonstrate the impact of ehealth technologies more effectively, a fresh way of thinking is required about how technology can be used to innovate health care. it also requires new concepts and instruments to develop and implement technologies in practice. the proposed framework serves as an evidence-based roadmap.",0
"background there is little systematic operational guidance about how best to develop complex interventions to reduce the gap between practice and evidence. this article is one in a series of articles documenting the development and use of the theoretical domains framework (tdf) to advance the science of implementation research. methods the intervention was developed considering three main components: theory, evidence, and practical issues. we used a four-step approach, consisting of guiding questions, to direct the choice of the most appropriate components of an implementation intervention: who needs to do what, differently? using a theoretical framework, which barriers and enablers need to be addressed? which intervention components (behaviour change techniques and mode(s) of delivery) could overcome the modifiable barriers and enhance the enablers? and how can behaviour change be measured and understood? results a complex implementation intervention was designed that aimed to improve acute low back pain management in primary care. we used the tdf to identify the barriers and enablers to the uptake of evidence into practice and to guide the choice of intervention components. these components were then combined into a cohesive intervention. the intervention was delivered via two facilitated interactive small group workshops. we also produced a dvd to distribute to all participants in the intervention group. we chose outcome measures in order to assess the mediating mechanisms of behaviour change. conclusions we have illustrated a four-step systematic method for developing an intervention designed to change clinical practice based on a theoretical framework. the method of development provides a systematic framework that could be used by others developing complex implementation interventions. while this framework should be iteratively adjusted and refined to suit other contexts and settings, we believe that the four-step process should be maintained as the primary framework to guide researchers through a comprehensive intervention development process.",0
"background a high circulating concentration of interleukin 6 is associated with increased risk of coronary heart disease. blockade of the interleukin-6 receptor (il6r) with a monoclonal antibody (tocilizumab) licensed for treatment of rheumatoid arthritis reduces systemic and articular inflammation. however, whether il6r blockade also reduces risk of coronary heart disease is unknown. methods applying the mendelian randomisation principle, we used single nucleotide polymorphisms (snps) in the gene il6r to evaluate the likely efficacy and safety of il6r inhibition for primary prevention of coronary heart disease. we compared genetic findings with the effects of tocilizumab reported in randomised trials in patients with rheumatoid arthritis. findings in 40 studies including up to 133,449 individuals, an il6r snp (rs7529229) marking a non-synonymous il6r variant (rs8192284; p.asp358ala) was associated with increased circulating log interleukin-6 concentration (increase per allele 9·45%, 95% ci 8·34-10·57) as well as reduced c-reactive protein (decrease per allele 8·35%, 95% ci 7·31-9·38) and fibrinogen concentrations (decrease per allele 0·85%, 95% ci 0·60-1·10). this pattern of effects was consistent with il6r blockade from infusions of tocilizumab (4-8 mg/kg every 4 weeks) in patients with rheumatoid arthritis studied in randomised trials. in 25,458 coronary heart disease cases and 100,740 controls, the il6r rs7529229 snp was associated with a decreased odds of coronary heart disease events (per allele odds ratio 0·95, 95% ci 0·93-0·97, p=1·53×10(-5)). interpretation on the basis of genetic evidence in human beings, il6r signalling seems to have a causal role in development of coronary heart disease. il6r blockade could provide a novel therapeutic approach to prevention of coronary heart disease that warrants testing in suitably powered randomised trials. genetic studies in populations could be used more widely to help to validate and prioritise novel drug targets or to repurpose existing agents and targets for new therapeutic uses. funding uk medical research council; british heart foundation; rosetrees trust; us national heart, lung, and blood institute; du pont pharma; chest, heart and stroke scotland; wellcome trust; coronary thrombosis trust; northwick park institute for medical research; uclh/ucl comprehensive medical research centre; us national institute on aging; academy of finland; netherlands organisation for health research and development; sanco; dutch ministry of public health, welfare and sports; world cancer research fund; agentschap nl; european commission; swedish heart-lung foundation; swedish research council; strategic cardiovascular programme of the karolinska institutet; stockholm county council; us national institute of neurological disorders and stroke; medstar health research institute; glaxosmithkline; dutch kidney foundation; us national institutes of health; netherlands interuniversity cardiology institute of the netherlands; diabetes uk; european union seventh framework programme; national institute for healthy ageing; cancer research uk; macarthur foundation.",0
"remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets and deep convolutional neural networks (cnns). cnns enable learning data-driven, highly representative, hierarchical image features from sufficient training data. however, obtaining datasets as comprehensively annotated as imagenet in the medical imaging domain remains a challenge. there are currently three major techniques that successfully employ cnns to medical image classification: training the cnn from scratch, using off-the-shelf pre-trained cnn features, and conducting unsupervised cnn pre-training with supervised fine-tuning. another effective method is transfer learning, i.e., fine-tuning cnn models pre-trained from natural image dataset to medical image tasks. in this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. we first explore and evaluate different cnn architectures. the studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. we then evaluate the influence of dataset scale and spatial image context on performance. finally, we examine when and why transfer learning from pre-trained imagenet (via fine-tuning) can be useful. we study two specific computer-aided detection (cade) problems, namely thoraco-abdominal lymph node (ln) detection and interstitial lung disease (ild) classification. we achieve the state-of-the-art performance on the mediastinal ln detection, and report the first five-fold cross-validation classification results on predicting axial ct slices with ild categories. our extensive empirical evaluation, cnn model analysis and valuable insights can be extended to the design of high performance cad systems for other medical imaging tasks.",0
"background and aims there are increasing case reports of rhino-orbital mucormycosis in people with coronavirus disease 2019 (covid-19), especially from india. diabetes mellitus (dm) is an independent risk factor for both severe covid-19 and mucormycosis. we aim to conduct a systematic review of literature to find out the patient's characteristics having mucormycosis and covid-19. methods we searched the electronic database of pubmed and google scholar from inception until may 13, 2021 using keywords. we retrieved all the granular details of case reports/series of patients with mucormycosis, and covid-19 reported world-wide. subsequently we analyzed the patient characteristics, associated comorbidities, location of mucormycosis, use of steroids and its outcome in people with covid-19. results overall, 101 cases of mucormycosis in people with covid-19 have been reported, of which 82 cases were from india and 19 from the rest of the world. mucormycosis was predominantly seen in males (78.9%), both in people who were active (59.4%) or recovered (40.6%) from covid-19. pre-existing diabetes mellitus (dm) was present in 80% of cases, while concomitant diabetic ketoacidosis (dka) was present in 14.9%. corticosteroid intake for the treatment of covid-19 was recorded in 76.3% of cases. mucormycosis involving nose and sinuses (88.9%) was most common followed by rhino-orbital (56.7%). mortality was noted in 30.7% of the cases. conclusion an unholy trinity of diabetes, rampant use of corticosteroid in a background of covid-19 appears to increase mucormycosis. all efforts should be made to maintain optimal glucose and only judicious use of corticosteroids in patients with covid-19.",0
"background influenza vaccine hesitancy is a significant threat to global efforts to reduce the burden of seasonal and pandemic influenza. potential barriers of influenza vaccination need to be identified to inform interventions to raise awareness, influenza vaccine acceptance and uptake. objective this review aims to (1) identify relevant studies and extract individual barriers of seasonal and pandemic influenza vaccination for risk groups and the general public; and (2) map knowledge gaps in understanding influenza vaccine hesitancy to derive directions for further research and inform interventions in this area. methods thirteen databases covering the areas of medicine, bioscience, psychology, sociology and public health were searched for peer-reviewed articles published between the years 2005 and 2016. following the prisma approach, 470 articles were selected and analyzed for significant barriers to influenza vaccine uptake or intention. the barriers for different risk groups and flu types were clustered according to a conceptual framework based on the theory of planned behavior and discussed using the 4c model of reasons for non-vaccination. results most studies were conducted in the american and european region. health care personnel (hcp) and the general public were the most studied populations, while parental decisions for children at high risk were under-represented. this study also identifies understudied concepts. a lack of confidence, inconvenience, calculation and complacency were identified to different extents as barriers to influenza vaccine uptake in risk groups. conclusion many different psychological, contextual, sociodemographic and physical barriers that are specific to certain risk groups were identified. while most sociodemographic and physical variables may be significantly related to influenza vaccine hesitancy, they cannot be used to explain its emergence or intensity. psychological determinants were meaningfully related to uptake and should therefore be measured in a valid and comparable way. a compendium of measurements for future use is suggested as supporting information.",0
"we present translatorx, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. as protein-coding dna sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the dna than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. translatorx novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with gblocks based on protein information; and (v) a rich output, including jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. the translatorx server is freely available at",0
"evidence has amassed from both animal intracranial recordings and human electrophysiology that neural oscillatory mechanisms play a critical role in a number of cognitive functions such as learning, memory, feature binding and sensory gating. the wide availability of high-density electrical and magnetic recordings (64-256 channels) over the past two decades has allowed for renewed efforts in the characterization and localization of these rhythms. a variety of cognitive effects that are associated with specific brain oscillations have been reported, which range in spectral, temporal, and spatial characteristics depending on the context. our laboratory has focused on investigating the role of alpha-band oscillatory activity (8-14 hz) as a potential attentional suppression mechanism, and this particular oscillatory attention mechanism will be the focus of the current review. we discuss findings in the context of intersensory selective attention as well as intrasensory spatial and feature-based attention in the visual, auditory, and tactile domains. the weight of evidence suggests that alpha-band oscillations can be actively invoked within cortical regions across multiple sensory systems, particularly when these regions are involved in processing irrelevant or distracting information. that is, a central role for alpha seems to be as an attentional suppression mechanism when objects or features need to be specifically ignored or selected against.",0
"clinvar ( provides a freely available archive of reports of relationships among medically important variants and phenotypes. clinvar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. the database is tightly coupled with dbsnp and dbvar, which maintain information about the location of variation on human assemblies. clinvar is also based on the phenotypic descriptions maintained in medgen ( each clinvar record represents the submitter, the variation and the phenotype, i.e. the unit that is assigned an accession of the format scv000000000.0. the submitter can update the submission at any time, in which case a new version is assigned. to facilitate evaluation of the medical importance of each variant, clinvar aggregates submissions with the same variation/phenotype combination, adds value from other ncbi databases, assigns a distinct accession of the format rcv000000000.0 and reports if there are conflicting clinical interpretations. data in clinvar are available in multiple formats, including html, download as xml, vcf or tab-delimited subsets. data from clinvar are provided as annotation tracks on genomic refseqs and are used in tools such as variation reporter ( which reports what is known about variation based on user-supplied locations.",0
"objective in march 2020, several countries banned unnecessary outdoor activities during covid-19, commonly called 'lockdowns. these lockdowns have the potential to impact associated levels of physical activity and sedentary behaviour. given the numerous health outcomes associated with physical activity and sedentary behaviour, the aim of this review was to summarise literature that investigated differences in physical activity and sedentary behaviour before vs during the covid-19 lockdown. design data sources and eligibility criteria electronic databases were searched from november 2019 to october 2020 using terms and synonyms relating to physical activity, sedentary behaviour and covid-19. the coprimary outcomes were changes in physical activity and/or sedentary behaviour captured via device-based measures or self-report tools. risk of bias was measured using the newcastle-ottawa scale. results sixty six articles met the inclusion criteria and were included in the review (total n=86 981). changes in physical activity were reported in 64 studies, with the majority of studies reporting decreases in physical activity and increases in sedentary behaviours during their respective lockdowns across several populations, including children and patients with a variety of medical conditions. conclusion given the numerous physical and mental benefits of increased physical activity and decreased sedentary behaviour, public health strategies should include the creation and implementation of interventions that promote safe physical activity and reduce sedentary behaviour should other lockdowns occur.",0
"background hysterectomy and bilateral salpingo-oophorectomy (bso) is the standard surgery for stage i endometrial cancer. systematic pelvic lymphadenectomy has been used to establish whether there is extra-uterine disease and as a therapeutic procedure; however, randomised trials need to be done to assess therapeutic efficacy. the astec surgical trial investigated whether pelvic lymphadenectomy could improve survival of women with endometrial cancer. methods from 85 centres in four countries, 1408 women with histologically proven endometrial carcinoma thought preoperatively to be confined to the corpus were randomly allocated by a minimisation method to standard surgery (hysterectomy and bso, peritoneal washings, and palpation of para-aortic nodes; n=704) or standard surgery plus lymphadenectomy (n=704). the primary outcome measure was overall survival. to control for postsurgical treatment, women with early-stage disease at intermediate or high risk of recurrence were randomised (independent of lymph-node status) into the astec radiotherapy trial. analysis was by intention to treat. this study is registered, number isrctn 16571884. findings after a median follow-up of 37 months (iqr 24-58), 191 women (88 standard surgery group, 103 lymphadenectomy group) had died, with a hazard ratio (hr) of 1.16 (95% ci 0.87-1.54; p=0.31) in favour of standard surgery and an absolute difference in 5-year overall survival of 1% (95% ci -4 to 6). 251 women died or had recurrent disease (107 standard surgery group, 144 lymphadenectomy group), with an hr of 1.35 (1.06-1.73; p=0.017) in favour of standard surgery and an absolute difference in 5-year recurrence-free survival of 6% (1-12). with adjustment for baseline characteristics and pathology details, the hr for overall survival was 1.04 (0.74-1.45; p=0.83) and for recurrence-free survival was 1.25 (0.93-1.66; p=0.14). interpretation our results show no evidence of benefit in terms of overall or recurrence-free survival for pelvic lymphadenectomy in women with early endometrial cancer. pelvic lymphadenectomy cannot be recommended as routine procedure for therapeutic purposes outside of clinical trials.",0
"background the internet is increasingly used as a medium for the delivery of interventions designed to promote health behavior change. however, reviews of these interventions to date have not systematically identified intervention characteristics and linked these to effectiveness. objectives the present review sought to capitalize on recently published coding frames for assessing use of theory and behavior change techniques to investigate which characteristics of internet-based interventions best promote health behavior change. in addition, we wanted to develop a novel coding scheme for assessing mode of delivery in internet-based interventions and also to link different modes to effect sizes. methods we conducted a computerized search of the databases indexed by isi web of knowledge (including biosis previews and medline) between 2000 and 2008. studies were included if (1) the primary components of the intervention were delivered via the internet, (2) participants were randomly assigned to conditions, and (3) a measure of behavior related to health was taken after the intervention. results we found 85 studies that satisfied the inclusion criteria, providing a total sample size of 43,236 participants. on average, interventions had a statistically small but significant effect on health-related behavior (d(+) = 0.16, 95% ci 0.09 to 0.23). more extensive use of theory was associated with increases in effect size (p = .049), and, in particular, interventions based on the theory of planned behavior tended to have substantial effects on behavior (d(+) = 0.36, 95% ci 0.15 to 0.56). interventions that incorporated more behavior change techniques also tended to have larger effects compared to interventions that incorporated fewer techniques (p conclusions the review provides a framework for the development of a science of internet-based interventions, and our findings provide a rationale for investing in more intensive theory-based interventions that incorporate multiple behavior change techniques and modes of delivery.",0
"angiotensin converting enzyme-2 (ace2) receptors mediate the entry into the cell of three strains of coronavirus: sars-cov, nl63 and sars-cov-2. ace2 receptors are ubiquitous and widely expressed in the heart, vessels, gut, lung (particularly in type 2 pneumocytes and macrophages), kidney, testis and brain. ace2 is mostly bound to cell membranes and only scarcely present in the circulation in a soluble form. an important salutary function of membrane-bound and soluble ace2 is the degradation of angiotensin ii to angiotensin 1-7 . consequently, ace2 receptors limit several detrimental effects resulting from binding of angiotensin ii to at1 receptors, which include vasoconstriction, enhanced inflammation and thrombosis. the increased generation of angiotensin 1-7 also triggers counter-regulatory protective effects through binding to g-protein coupled mas receptors. unfortunately, the entry of sars-cov2 into the cells through membrane fusion markedly down-regulates ace2 receptors, with loss of the catalytic effect of these receptors at the external site of the membrane. increased pulmonary inflammation and coagulation have been reported as unwanted effects of enhanced and unopposed angiotensin ii effects via the ace→angiotensin ii→at1 receptor axis. clinical reports of patients infected with sars-cov-2 show that several features associated with infection and severity of the disease (i.e., older age, hypertension, diabetes, cardiovascular disease) share a variable degree of ace2 deficiency. we suggest that ace2 down-regulation induced by viral invasion may be especially detrimental in people with baseline ace2 deficiency associated with the above conditions. the additional ace2 deficiency after viral invasion might amplify the dysregulation between the 'adverse' ace→angiotensin ii→at1 receptor axis and the 'protective' ace2→angiotensin 1-7 →mas receptor axis. in the lungs, such dysregulation would favor the progression of inflammatory and thrombotic processes triggered by local angiotensin ii hyperactivity unopposed by angiotensin 1-7 . in this setting, recombinant ace2, angiotensin 1-7 and angiotensin ii type 1 receptor blockers could be promising therapeutic approaches in patients with sars-cov-2 infection.",0
"antibodies have become an indispensable tool for many biotechnological and clinical applications. they bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. the ability to predict epitopes from antigen sequences alone is a complex task. despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. here, we present bepipred-2.0 ( a web server for predicting b-cell epitopes from antigen sequences. bepipred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. this new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3d structures, and on a large collection of linear epitopes downloaded from the iedb database. the method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. we believe that bepipred-2.0 will be a valuable tool for the bioinformatics and immunology community.",0
"genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. we found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. we also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. we found consistency in time-to-speciation among plants and animals, ∼2 my, as measured by intervals of crown and stem species times. together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.",0
"importance immunotherapy checkpoint inhibitors have generated considerable interest because of durable responses in a number of hitherto intractable tumor types. objective to estimate the percentage of patients with cancer in the united states who are eligible for and respond to checkpoint inhibitor drugs approved for oncology indications by the us food and drug administration (fda). design, setting, and participants retrospective cross-sectional study performed from june 2018 through october 2018 using publicly available data to determine (1) demographic characteristics of patients with advanced or metastatic cancer, (2) fda data on checkpoint inhibitors approved from january 2011 through august 2018, (3) measures of response from drug labels, and (4) published reports estimating the frequency of various inclusion criteria. main outcomes and measures the estimated percentages of us patients with cancer who are eligible for and who respond to immunotherapy checkpoint inhibitor drugs, by year. results six checkpoint inhibitor drugs were approved for 14 indications between march 25, 2011, and august 17, 2018. the estimated percentage of patients with cancer who were eligible for checkpoint inhibitor drugs increased from 1.54% (95% ci, 1.51%-1.57%) in 2011 to 43.63% (95% ci, 43.51%-43.75%) in 2018. the percentage of patients with cancer estimated to respond to checkpoint inhibitor drugs was 0.14% (95% ci, 0.13%-0.15%) in 2011 when ipilimumab was approved for unresectable or metastatic melanoma and increased to 5.86% (95% ci, 5.80%-5.92%) by 2015. by 2018, the estimated percentage of responders increased to 12.46% (95% ci, 12.37%-12.54%). conclusions and relevance the estimated percentages of patients who are eligible for and who respond to checkpoint inhibitor drugs are higher than reported estimates for drugs approved for genome-driven oncology but remain modest. future research should explore biomarkers to maximize the benefit of immunotherapy among patients receiving it.",0
"purpose to estimate the burden of lifetime epilepsy (lte) and active epilepsy (ae) and examine the influence of study characteristics on prevalence estimates. methods we searched online databases and identified articles using prespecified criteria. random-effects meta-analyses were used to estimate the median prevalence in developed countries and in urban and rural settings in developing countries. the impact of study characteristics on prevalence estimates was determined using meta-regression models. results the median lte prevalence for developed countries was 5.8 per 1,000 (5th-95th percentile range 2.7-12.4) compared to 15.4 per 1,000 (4.8-49.6) for rural and 10.3 (2.8-37.7) for urban studies in developing countries. the median prevalence of ae was 4.9 per 1,000 (2.3-10.3) for developed countries and 12.7 per 1,000 (3.5-45.5) and 5.9 (3.4-10.2) in rural and urban studies in developing countries. the estimates of burden for lte and ae in developed countries were 6.8 million (5th-95th percentile range 3.2-14.7) and 5.7 million (2.7-12.2), respectively. in developing countries these were 45 (14-145) million lte and 17 (10-133) million ae in rural areas and 17 (5-61) million lte and 10 (5-17) million ae in urban areas. studies involving all ages or only adults showed higher estimates than pediatric studies. higher prevalence estimates were also associated with rural location and small study size. conclusions this study estimates the global burden of epilepsy and the proportions with ae, which may benefit from treatment. there are systematic differences in reported prevalence estimates, which are only partially explained by study characteristics.",0
"we introduce multi-trait analysis of gwas (mtag), a method for joint analysis of summary statistics from genome-wide association studies (gwas) of different traits, possibly from overlapping samples. we apply mtag to summary statistics for depressive symptoms (n eff = 354,862), neuroticism (n = 168,105), and subjective well-being (n = 388,538). as compared to the 32, 9, and 13 genome-wide significant loci identified in the single-trait gwas (most of which are themselves novel), mtag increases the number of associated loci to 64, 37, and 49, respectively. moreover, association statistics from mtag yield more informative bioinformatics analyses and increase the variance explained by polygenic scores by approximately 25%, matching theoretical expectations.",0
"fatal human respiratory disease associated with the 1918 pandemic influenza virus and potentially pandemic h5n1 viruses is characterized by severe lung pathology, including pulmonary edema and extensive inflammatory infiltrate. here, we quantified the cellular immune response to infection in the mouse lung by flow cytometry and demonstrate that mice infected with highly pathogenic (hp) h1n1 and h5n1 influenza viruses exhibit significantly high numbers of macrophages and neutrophils in the lungs compared to mice infected with low pathogenic (lp) viruses. mice infected with the 1918 pandemic virus and a recent h5n1 human isolate show considerable similarities in overall lung cellularity, lung immune cell sub-population composition, and cellular immune temporal dynamics. interestingly, while these similarities were observed, the hp h5n1 virus consistently elicited significantly higher levels of pro-inflammatory cytokines in whole lungs and primary human macrophages, revealing a potentially critical difference in the pathogenesis of h5n1 infections. primary mouse and human macrophages and dendritic cells were also susceptible to 1918 and h5n1 influenza virus infection in vitro. these results together indicate that infection with hp influenza viruses such as h5n1 and the 1918 pandemic virus leads to a rapid cell recruitment of macrophages and neutrophils into the lungs, suggesting that these cells play a role in acute lung inflammation associated with hp influenza virus infection.",0
"mesenchymal stem cell-mediated tissue regeneration is a promising approach for regenerative medicine for a wide range of applications. here we report a new population of stem cells isolated from the root apical papilla of human teeth (scap, stem cells from apical papilla). using a minipig model, we transplanted both human scap and periodontal ligament stem cells (pdlscs) to generate a root/periodontal complex capable of supporting a porcelain crown, resulting in normal tooth function. this work integrates a stem cell-mediated tissue regeneration strategy, engineered materials for structure, and current dental crown technologies. this hybridized tissue engineering approach led to recovery of tooth strength and appearance.",0
"the barcode of life data system (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of dna barcode records. by assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in dna barcoding. by providing specialized services, it aids the assembly of records that meet the standards needed to gain barcode designation in the global sequence databases. because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. this paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.",0
"background overweight and obesity are increasing worldwide. to help assess their relevance to mortality in different populations we conducted individual-participant data meta-analyses of prospective studies of body-mass index (bmi), limiting confounding and reverse causality by restricting analyses to never-smokers and excluding pre-existing disease and the first 5 years of follow-up. methods of 10 625 411 participants in asia, australia and new zealand, europe, and north america from 239 prospective studies (median follow-up 13·7 years, iqr 11·4-14·7), 3 951 455 people in 189 studies were never-smokers without chronic diseases at recruitment who survived 5 years, of whom 385 879 died. the primary analyses are of these deaths, and study, age, and sex adjusted hazard ratios (hrs), relative to bmi 22·5- findings all-cause mortality was minimal at 20·0-25·0 kg/m(2) (hr 1·00, 95% ci 0·98-1·02 for bmi 20·0- interpretation the associations of both overweight and obesity with higher all-cause mortality were broadly consistent in four continents. this finding supports strategies to combat the entire spectrum of excess adiposity in many populations. funding uk medical research council, british heart foundation, national institute for health research, us national institutes of health.",0
"large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and dna replication and repair. genomic techniques based on chromosome conformation capture (3c) assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. here we introduce single-cell hi-c, combined with genome-wide statistical analysis and structural modelling of single-copy x chromosomes, to show that individual chromosomes maintain domain organization at the megabase scale, but show variable cell-to-cell chromosome structures at larger scales. despite this structural stochasticity, localization of active gene domains to boundaries of chromosome territories is a hallmark of chromosomal conformation. single-cell hi-c data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organization underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns.",0
"two methods were used to demonstrate the presence of tumor-specific antigens in adenocarcinomata of the human colon: (a) rabbits were immunized with extracts of pooled colonic carcinomata, and the antitumor antisera thus produced were absorbed with a pooled extract of normal human colon and with human blood components; (b) newborn rabbits were made immunologically tolerant to normal colonic tissue at birth, and were then immunized with pooled tumor material in adult life. normal and tumor tissues were obtained from the same human donors in order to avoid misinterpretation of results due to individual-specific antigenic differences. the antisera prepared by both methods were tested against normal and tumor antigens by the techniques of agar gel diffusion, immunoelectrophoresis, hemagglutination, pca, and immunofluorescence. distinct antibody activity directed against at least two qualitatively tumor-specific antigens, or antigenic determinants, was detected in the antisera prepared by both methods and at least two additional tumor antigens were detected exclusively in antisera prepared by the tolerance technique. whether these additional antigens were qualitatively different from normal tissue antigens, or merely present in tumor tissue in higher concentrations than in normal tissue has not as yet been determined. furthermore, it was shown that the tumor-specific antibodies were not directed against bacterial contaminants or against the unusually high concentrations of fibrin found in many neoplastic tissues. it was concluded from these results that the pooled tumor extracts contained tumor-specific antigens not present in normal colonic tissue. identical tumor-specific antigens were also demonstrated in a number of individual colonic carcinomata obtained from different human donors.",0
"alcohol and tobacco consumption are closely correlated and published results on their association with breast cancer have not always allowed adequately for confounding between these exposures. over 80% of the relevant information worldwide on alcohol and tobacco consumption and breast cancer were collated, checked and analysed centrally. analyses included 58,515 women with invasive breast cancer and 95,067 controls from 53 studies. relative risks of breast cancer were estimated, after stratifying by study, age, parity and, where appropriate, women's age when their first child was born and consumption of alcohol and tobacco. the average consumption of alcohol reported by controls from developed countries was 6.0 g per day, i.e. about half a unit/drink of alcohol per day, and was greater in ever-smokers than never-smokers, (8.4 g per day and 5.0 g per day, respectively). compared with women who reported drinking no alcohol, the relative risk of breast cancer was 1.32 (1.19-1.45, p /=45 g per day alcohol. the relative risk of breast cancer increased by 7.1% (95% ci 5.5-8.7%; p<0.00001) for each additional 10 g per day intake of alcohol, i.e. for each extra unit or drink of alcohol consumed on a daily basis. this increase was the same in ever-smokers and never-smokers (7.1% per 10 g per day, p<0.00001, in each group). by contrast, the relationship between smoking and breast cancer was substantially confounded by the effect of alcohol. when analyses were restricted to 22 255 women with breast cancer and 40 832 controls who reported drinking no alcohol, smoking was not associated with breast cancer (compared to never-smokers, relative risk for ever-smokers=1.03, 95% ci 0.98-1.07, and for current smokers=0.99, 0.92-1.05). the results for alcohol and for tobacco did not vary substantially across studies, study designs, or according to 15 personal characteristics of the women; nor were the findings materially confounded by any of these factors. if the observed relationship for alcohol is causal, these results suggest that about 4% of the breast cancers in developed countries are attributable to alcohol. in developing countries, where alcohol consumption among controls averaged only 0.4 g per day, alcohol would have a negligible effect on the incidence of breast cancer. in conclusion, smoking has little or no independent effect on the risk of developing breast cancer; the effect of alcohol on breast cancer needs to be interpreted in the context of its beneficial effects, in moderation, on cardiovascular disease and its harmful effects on cirrhosis and cancers of the mouth, larynx, oesophagus and liver.",0
"metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. among the next-generation beneficial microbes that have been identified, akkermansia muciniphila is a promising candidate. indeed, a. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation. besides the numerous correlations observed, a large body of evidence has demonstrated the causal beneficial impact of this bacterium in a variety of preclinical models. translating these exciting observations to human would be the next logic step and it now appears that several obstacles that would prevent the use of a. muciniphila administration in humans have been overcome. moreover, several lines of evidence indicate that pasteurization of a. muciniphila not only increases its stability but more importantly increases its efficacy. this strongly positions a. muciniphila in the forefront of next-generation candidates for developing novel food or pharma supplements with beneficial effects. finally, a specific protein present on the outer membrane of a. muciniphila , termed amuc_1100, could be strong candidate for future drug development. in conclusion, as plants and its related knowledge, known as pharmacognosy, have been the source for designing drugs over the last century, we propose that microbes and microbiomegnosy, or knowledge of our gut microbiome, can become a novel source of future therapies.",0
"background although web-based interventions for promoting health and health-related behavior can be effective, poor adherence is a common issue that needs to be addressed. technology as a means to communicate the content in web-based interventions has been neglected in research. indeed, technology is often seen as a black-box, a mere tool that has no effect or value and serves only as a vehicle to deliver intervention content. in this paper we examine technology from a holistic perspective. we see it as a vital and inseparable aspect of web-based interventions to help explain and understand adherence. objective this study aims to review the literature on web-based health interventions to investigate whether intervention characteristics and persuasive design affect adherence to a web-based intervention. methods we conducted a systematic review of studies into web-based health interventions. per intervention, intervention characteristics, persuasive technology elements and adherence were coded. we performed a multiple regression analysis to investigate whether these variables could predict adherence. results we included 101 articles on 83 interventions. the typical web-based intervention is meant to be used once a week, is modular in set-up, is updated once a week, lasts for 10 weeks, includes interaction with the system and a counselor and peers on the web, includes some persuasive technology elements, and about 50% of the participants adhere to the intervention. regarding persuasive technology, we see that primary task support elements are most commonly employed (mean 2.9 out of a possible 7.0). dialogue support and social support are less commonly employed (mean 1.5 and 1.2 out of a possible 7.0, respectively). when comparing the interventions of the different health care areas, we find significant differences in intended usage (p=.004), setup (p conclusions using intervention characteristics and persuasive technology elements, a substantial amount of variance in adherence can be explained. although there are differences between health care areas on intervention characteristics, health care area per se does not predict adherence. rather, the differences in technology and interaction predict adherence. the results of this study can be used to make an informed decision about how to design a web-based intervention to which patients are more likely to adhere.",0
"autism spectrum disorders (asds) are highly prevalent neurodevelopmental disorders, but the underlying pathogenesis remains poorly understood. recent studies have implicated the cerebellum in these disorders, with post-mortem studies in asd patients showing cerebellar purkinje cell (pc) loss, and isolated cerebellar injury has been associated with a higher incidence of asds. however, the extent of cerebellar contribution to the pathogenesis of asds remains unclear. tuberous sclerosis complex (tsc) is a genetic disorder with high rates of comorbid asds that result from mutation of either tsc1 or tsc2, whose protein products dimerize and negatively regulate mammalian target of rapamycin (mtor) signalling. tsc is an intriguing model to investigate the cerebellar contribution to the underlying pathogenesis of asds, as recent studies in tsc patients demonstrate cerebellar pathology and correlate cerebellar pathology with increased asd symptomatology. functional imaging also shows that tsc patients with asds display hypermetabolism in deep cerebellar structures, compared to tsc patients without asds. however, the roles of tsc1 and the sequelae of tsc1 dysfunction in the cerebellum have not been investigated so far. here we show that both heterozygous and homozygous loss of tsc1 in mouse cerebellar pcs results in autistic-like behaviours, including abnormal social interaction, repetitive behaviour and vocalizations, in addition to decreased pc excitability. treatment of mutant mice with the mtor inhibitor, rapamycin, prevented the pathological and behavioural deficits. these findings demonstrate new roles for tsc1 in pc function and define a molecular basis for a cerebellar contribution to cognitive disorders such as autism.",0
"purpose to describe acute respiratory distress syndrome (ards) severity, ventilation management, and the outcomes of icu patients with laboratory-confirmed covid-19 and to determine risk factors of 90-day mortality post-icu admission. methods covid-icu is a multi-center, prospective cohort study conducted in 138 hospitals in france, belgium, and switzerland. demographic, clinical, respiratory support, adjunctive interventions, icu length-of-stay, and survival data were collected. results from february 25 to may 4, 2020, 4643 patients (median age 63 years and saps ii 37 ) were admitted in icu, with day-90 post-icu admission status available for 4244. on icu admission, standard oxygen therapy, high-flow oxygen, and non-invasive ventilation were applied to 29%, 19%, and 6% patients, respectively. 2635 (63%) patients were intubated during the first 24 h whereas overall 3376 (80%) received invasive mechanical ventilation (mv) at one point during their icu stay. median (iqr) positive end-expiratory and plateau pressures were 12 (10-14) cmh 2 o, and 24 (21-27) cmh 2 o, respectively. the mechanical power transmitted by the mv to the lung was 26.5 (18.6-34.9) j/min. paralyzing agents and prone position were applied to 88% and 70% of patients intubated at day-1, respectively. pulmonary embolism and ventilator-associated pneumonia were diagnosed in 207 (9%) and 1209 (58%) of these patients. on day 90, 1298/4244 (31%) patients had died. among patients who received invasive or non-invasive ventilation on the day of icu admission, day-90 mortality increased with the severity of ards at icu admission (30%, 34%, and 50% for mild, moderate, and severe ards, respectively) and decreased from 42 to 25% over the study period. early independent predictors of 90-day mortality were older age, immunosuppression, severe obesity, diabetes, higher renal and cardiovascular sofa score components, lower pao 2 /fio 2 ratio and a shorter time between first symptoms and icu admission. conclusion among more than 4000 critically ill patients with covid-19 admitted to our icus, 90-day mortality was 31% and decreased from 42 to 25% over the study period. mortality was higher in older, diabetic, obese and severe ards patients.",0
"the u.s. surgeon general has concluded that the burden of death and disease from tobacco use in the united states is overwhelmingly caused by cigarettes and other combusted tobacco products (1). cigarettes are the most commonly used tobacco product among u.s. adults, and about 480,000 u.s. deaths per year are caused by cigarette smoking and secondhand smoke exposure (1). to assess progress toward the healthy people 2020 target of reducing the proportion of u.s. adults aged ≥18 years who smoke cigarettes to ≤12.0% (objective tu-1.1),* cdc analyzed data from the 2016 national health interview survey (nhis). in 2016, the prevalence of current cigarette smoking among adults was 15.5%, which was a significant decline from 2005 (20.9%); however, no significant change has occurred since 2015 (15.1%). in 2016, the prevalence of cigarette smoking was higher among adults who were male, aged 25-64 years, american indian/alaska native or multiracial, had a general education development (ged) certificate, lived below the federal poverty level, lived in the midwest or south, were uninsured or insured through medicaid, had a disability/limitation, were lesbian, gay, or bisexual (lgb), or had serious psychological distress. during 2005-2016, the percentage of ever smokers who quit smoking increased from 50.8% to 59.0%. proven population-based interventions are critical to reducing the health and economic burden of smoking-related diseases among u.s. adults, particularly among subpopulations with the highest smoking prevalences (1,2).",0
"the propensity score is the probability of treatment assignment conditional on observed baseline characteristics. the propensity score allows one to design and analyze an observational (nonrandomized) study so that it mimics some of the particular characteristics of a randomized controlled trial. in particular, the propensity score is a balancing score: conditional on the propensity score, the distribution of observed baseline covariates will be similar between treated and untreated subjects. i describe 4 different propensity score methods: matching on the propensity score, stratification on the propensity score, inverse probability of treatment weighting using the propensity score, and covariate adjustment using the propensity score. i describe balance diagnostics for examining whether the propensity score model has been adequately specified. furthermore, i discuss differences between regression-based methods and propensity score-based methods for the analysis of observational data. i describe different causal average treatment effects and their relationship with propensity score analyses.",0
"pfam, available via servers in the uk ( and the usa ( is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the uniprot knowledgebase (uniprotkb) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. since our 2012 article describing pfam, we have also undertaken a comprehensive review of the features that are provided by pfam over and above the basic family data. for each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. as a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. here, we describe the changes to pfam content. notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive dna search interface. we also discuss the mapping between pfam and known 3d structures.",0
"these guidelines provide a strategy to manage unanticipated difficulty with tracheal intubation. they are founded on published evidence. where evidence is lacking, they have been directed by feedback from members of the difficult airway society and based on expert opinion. these guidelines have been informed by advances in the understanding of crisis management; they emphasize the recognition and declaration of difficulty during airway management. a simplified, single algorithm now covers unanticipated difficulties in both routine intubation and rapid sequence induction. planning for failed intubation should form part of the pre-induction briefing, particularly for urgent surgery. emphasis is placed on assessment, preparation, positioning, preoxygenation, maintenance of oxygenation, and minimizing trauma from airway interventions. it is recommended that the number of airway interventions are limited, and blind techniques using a bougie or through supraglottic airway devices have been superseded by video- or fibre-optically guided intubation. if tracheal intubation fails, supraglottic airway devices are recommended to provide a route for oxygenation while reviewing how to proceed. second-generation devices have advantages and are recommended. when both tracheal intubation and supraglottic airway device insertion have failed, waking the patient is the default option. if at this stage, face-mask oxygenation is impossible in the presence of muscle relaxation, cricothyroidotomy should follow immediately. scalpel cricothyroidotomy is recommended as the preferred rescue technique and should be practised by all anaesthetists. the plans outlined are designed to be simple and easy to follow. they should be regularly rehearsed and made familiar to the whole theatre team.",0
"interactive tree of life ( is a web-based tool for the display, manipulation and annotation of phylogenetic trees. it is freely available and open to everyone. the current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. numerous new features were introduced and several new data types are now supported. trees with up to 100,000 leaves can now be efficiently displayed. full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. itol 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. finally, itol's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.",0
"epigenetic control of gene transcription is critical for normal human development and cellular differentiation. while alterations of epigenetic marks such as dna methylation have been linked to cancers and many other human diseases, interindividual epigenetic variations in normal tissues due to aging, environmental factors, or innate susceptibility are poorly characterized. the plasticity, tissue-specific nature, and variability of gene expression are related to epigenomic states that vary across individuals. thus, population-based investigations are needed to further our understanding of the fundamental dynamics of normal individual epigenomes. we analyzed 217 non-pathologic human tissues from 10 anatomic sites at 1,413 autosomal cpg loci associated with 773 genes to investigate tissue-specific differences in dna methylation and to discern how aging and exposures contribute to normal variation in methylation. methylation profile classes derived from unsupervised modeling were significantly associated with age (p<0.0001) and were significant predictors of tissue origin (p<0.0001). in solid tissues (n = 119) we found striking, highly significant cpg island-dependent correlations between age and methylation; loci in cpg islands gained methylation with age, loci not in cpg islands lost methylation with age (p<0.001), and this pattern was consistent across tissues and in an analysis of blood-derived dna. our data clearly demonstrate age- and exposure-related differences in tissue-specific methylation and significant age-associated methylation patterns which are cpg island context-dependent. this work provides novel insight into the role of aging and the environment in susceptibility to diseases such as cancer and critically informs the field of epigenomics by providing evidence of epigenetic dysregulation by age-related methylation alterations. collectively we reveal key issues to consider both in the construction of reference and disease-related epigenomes and in the interpretation of potentially pathologically important alterations.",0
"purpose to estimate the strength and shape of the dose-response relationship between sedentary behaviour and all-cause, cardiovascular disease (cvd) and cancer mortality, and incident type 2 diabetes (t2d), adjusted for physical activity (pa). data sources: pubmed, web of knowledge, medline, embase, cochrane library and google scholar (through september-2016); reference lists. study selection: prospective studies reporting associations between total daily sedentary time or tv viewing time, and ≥ one outcome of interest. data extraction: two independent reviewers extracted data, study quality was assessed; corresponding authors were approached where needed. data synthesis: thirty-four studies (1,331,468 unique participants; good study quality) covering 8 exposure-outcome combinations were included. for total sedentary behaviour, the pa-adjusted relationship was non-linear for all-cause mortality (rr per 1 h/day: were 1.01 (1.00-1.01) ≤ 8 h/day; 1.04 (1.03-1.05) > 8 h/day of exposure), and for cvd mortality (1.01 (0.99-1.02) ≤ 6 h/day; 1.04 (1.03-1.04) > 6 h/day). the association was linear (1.01 (1.00-1.01)) with t2d and non-significant with cancer mortality. stronger pa-adjusted associations were found for tv viewing (h/day); non-linear for all-cause mortality (1.03 (1.01-1.04) ≤ 3.5 h/day; 1.06 (1.05-1.08) > 3.5 h/day) and for cvd mortality (1.02 (0.99-1.04) ≤ 4 h/day; 1.08 (1.05-1.12) > 4 h/day). associations with cancer mortality (1.03 (1.02-1.04)) and t2d were linear (1.09 (1.07-1.12)). conclusions independent of pa, total sitting and tv viewing time are associated with greater risk for several major chronic disease outcomes. for all-cause and cvd mortality, a threshold of 6-8 h/day of total sitting and 3-4 h/day of tv viewing was identified, above which the risk is increased.",0
"genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. these panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 genomes project produce larger and more diverse reference sets, which led us to develop an alternative framework. our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. this approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. using data from hapmap 3, we show that our framework produces accurate results in a wide range of human populations. we also use data from the malaria genetic epidemiology network (malariagen) to provide recommendations for imputation-based studies in africa. we demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. new methodology from this study is implemented in the impute2 software package.",0
"the nature and content of lytic bodies and the localization of acid phosphatase (acpase) activity were investigated in mammotrophic hormone-producing cells (mt) from rat anterior pituitary glands. mt were examined from lactating rats in which secretion of mth(1) was high and from postlactating rats in which mth secretion was suppressed by removing the suckling young. mt from lactating animals contained abundant stacks of rough-surfaced er, a large golgi complex with many forming secretory granules, and a few lytic bodies, primarily multivesicular bodies and dense bodies. mt from postlactating animals, sacrificed at selected intervals up to 96 hr after separation from their suckling young, showed (a) progressive involution of the protein synthetic apparatus with sequestration of er and ribosomes in autophagic vacuoles, and (b) incorporation of secretory granules into multivesicular and dense bodies. the content of mature granules typically was incorporated into dense bodies whereas that of immature granules found its way preferentially into multivesicular bodies. the secretory granules and cytoplasmic constituents segregated within lytic bodies were progressively degraded over a period of 24 to 72 hr to yield a common residual body, the vacuolated dense body. in mt from lactating animals, acpase reaction product was found in lytic bodies, and in several other sites not usually considered to be lysosomal in nature, i.e., inner golgi cisterna and associated vesicles, and around most of the immature, and some of the mature secretory granules. in mt from postlactating animals, acpase was concentrated in lytic bodies; reaction product and incorporated secretory granules were frequently recognizable within the same multivesicular or dense body which could therefore be identified as ""autolysosomes"" connected with the digestion of endogenous materials. several possible explanations for the occurrence of acpase in nonlysosomal sites are discussed. from the findings it is concluded that, in secretory cells, lysosomes function in the regulation of the secretory process by providing a mechanism which takes care of overproduction of secretory products.",0
"the propensity score is a subject's probability of treatment, conditional on observed baseline covariates. conditional on the true propensity score, treated and untreated subjects have similar distributions of observed baseline covariates. propensity-score matching is a popular method of using the propensity score in the medical literature. using this approach, matched sets of treated and untreated subjects with similar values of the propensity score are formed. inferences about treatment effect made using propensity-score matching are valid only if, in the matched sample, treated and untreated subjects have similar distributions of measured baseline covariates. in this paper we discuss the following methods for assessing whether the propensity score model has been correctly specified: comparing means and prevalences of baseline characteristics using standardized differences; ratios comparing the variance of continuous covariates between treated and untreated subjects; comparison of higher order moments and interactions; five-number summaries; and graphical methods such as quantile-quantile plots, side-by-side boxplots, and non-parametric density plots for comparing the distribution of baseline covariates between treatment groups. we describe methods to determine the sampling distribution of the standardized difference when the true standardized difference is equal to zero, thereby allowing one to determine the range of standardized differences that are plausible with the propensity score model having been correctly specified. we highlight the limitations of some previously used methods for assessing the adequacy of the specification of the propensity-score model. in particular, methods based on comparing the distribution of the estimated propensity score between treated and untreated subjects are uninformative.",0
"background the main problem in many model-building situations is to choose from a large set of covariates those that should be included in the ""best"" model. a decision to keep a variable in the model might be based on the clinical or statistical significance. there are several variable selection algorithms in existence. those methods are mechanical and as such carry some limitations. hosmer and lemeshow describe a purposeful selection of covariates within which an analyst makes a variable selection decision at each step of the modeling process. methods in this paper we introduce an algorithm which automates that process. we conduct a simulation study to compare the performance of this algorithm with three well documented variable selection procedures in sas proc logistic: forward, backward, and stepwise. results we show that the advantage of this approach is when the analyst is interested in risk factor modeling and not just prediction. in addition to significant covariates, this variable selection procedure has the capability of retaining important confounding variables, resulting potentially in a slightly richer model. application of the macro is further illustrated with the hosmer and lemeshow worchester heart attack study (whas) data. conclusion if an analyst is in need of an algorithm that will help guide the retention of significant covariates as well as confounding ones they should consider this macro as an alternative tool.",0
"antioxidants are substances that may protect cells from the damage caused by unstable molecules such as free radicals. flavonoids are phenolic substances widely found in fruits and vegetables. the previous studies showed that the ingestion of flavonoids reduces the risk of cardiovascular diseases, metabolic disorders, and certain types of cancer. these effects are due to the physiological activity of flavonoids in the reduction of oxidative stress, inhibiting low-density lipoproteins oxidation and platelet aggregation, and acting as vasodilators in blood vessels. free radicals are constantly generated resulting in extensive damage to tissues leading to various disease conditions such as cancer, alzheimer's, renal diseases, cardiac abnormalities, etc., medicinal plants with antioxidant properties play a vital functions in exhibiting beneficial effects and employed as an alternative source of medicine to mitigate the disease associated with oxidative stress. flavonoids have existed over one billion years and possess wide spectrum of biological activities that might be able to influence processes which are dysregulated in a disease. quercetin, a plant pigment is a potent antioxidant flavonoid and more specifically a flavonol, found mostly in onions, grapes, berries, cherries, broccoli, and citrus fruits. it is a versatile antioxidant known to possess protective abilities against tissue injury induced by various drug toxicities.",0
"polymicrobial sepsis alters the adaptive immune response and induces t cell suppression and th2 immune polarization. we identify a gr-1(+)cd11b(+) population whose numbers dramatically increase and remain elevated in the spleen, lymph nodes, and bone marrow during polymicrobial sepsis. phenotypically, these cells are heterogeneous, immature, predominantly myeloid progenitors that express interleukin 10 and several other cytokines and chemokines. splenic gr-1(+) cells effectively suppress antigen-specific cd8(+) t cell interferon (ifn) gamma production but only modestly suppress antigen-specific and nonspecific cd4(+) t cell proliferation. gr-1(+) cell depletion in vivo prevents both the sepsis-induced augmentation of th2 cell-dependent and depression of th1 cell-dependent antibody production. signaling through myd88, but not toll-like receptor 4, tir domain-containing adaptor-inducing ifn-beta, or the ifn-alpha/beta receptor, is required for complete gr-1(+)cd11b(+) expansion. gr-1(+)cd11b(+) cells contribute to sepsis-induced t cell suppression and preferential th2 polarization.",0
"introduction adverse events in hospitals constitute a serious problem with grave consequences. many studies have been conducted to gain an insight into this problem, but a general overview of the data is lacking. we performed a systematic review of the literature on in-hospital adverse events. methods a formal search of embase, cochrane and medline was performed. studies were reviewed independently for methodology, inclusion and exclusion criteria and endpoints. primary endpoints were incidence of in-hospital adverse events and percentage of preventability. secondary endpoints were adverse event outcome and subdivision by provider of care, location and type of event. results eight studies including a total of 74 485 patient records were selected. the median overall incidence of in-hospital adverse events was 9.2%, with a median percentage of preventability of 43.5%. more than half (56.3%) of patients experienced no or minor disability, whereas 7.4% of events were lethal. operation- (39.6%) and medication-related (15.1%) events constituted the majority. we present a summary of evidence-based interventions aimed at these categories of events. conclusions adverse events during hospital admission affect nearly one out of 10 patients. a substantial part of these events are preventable. since a large proportion of the in-hospital events are operation- or drug-related, interventions aimed at preventing these events have the potential to make a substantial difference.",0
"background this review examines recent evidence on mortality from elevated ambient temperature for studies published from january 2001 to december 2008. methods pubmed was used to search for the following keywords: temperature, apparent temperature, heat, heat index, and mortality. the search was limited to the english language and epidemiologic studies. studies that reported mortality counts or excess deaths following heat waves were excluded so that the focus remained on general ambient temperature and mortality in a variety of locations. studies focusing on cold temperature effects were also excluded. results thirty-six total studies were presented in three tables: 1) elevated ambient temperature and mortality; 2) air pollutants as confounders and/or effect modifiers of the elevated ambient temperature and mortality association; and 3) vulnerable subgroups of the elevated ambient temperature-mortality association. the evidence suggests that particulate matter with less than 10 um in aerodynamic diameter and ozone may confound the association, while ozone was an effect modifier in the warmer months in some locations. nonetheless, the independent effect of temperature and mortality was withheld. elevated temperature was associated with increased risk for those dying from cardiovascular, respiratory, cerebrovascular, and some specific cardiovascular diseases, such as ischemic heart disease, congestive heart failure, and myocardial infarction. vulnerable subgroups also included: black racial/ethnic group, women, those with lower socioeconomic status, and several age groups, particularly the elderly over 65 years of age as well as infants and young children. conclusion many of these outcomes and vulnerable subgroups have only been identified in recent studies and varied by location and study population. thus, region-specific policies, especially in urban areas, are vital to the mitigation of heat-related deaths.",0
"motivation quality control and preprocessing of fastq files are essential to providing clean data for downstream analysis. traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. these tools are often insufficiently fast as most are developed using high-level programming languages (e.g. python and java) and provide limited multi-threading support. reading and loading data multiple times also renders preprocessing slow and i/o inefficient. results we developed fastp as an ultra-fast fastq preprocessor with useful quality control and data-filtering features. it can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the fastq data. this tool is developed in c++ and has multi-threading support. based on our evaluation, fastp is 2-5 times faster than other fastq preprocessing tools such as trimmomatic or cutadapt despite performing far more operations than similar tools. availability and implementation the open-source code and corresponding instructions are available at",0
"glycogen synthase kinase 3 (gsk3) is a constitutively active, proline-directed serine/threonine kinase that plays a part in a number of physiological processes ranging from glycogen metabolism to gene transcription. gsk3 also plays a pivotal and central role in the pathogenesis of both sporadic and familial forms of alzheimer's disease (ad), an observation that has led us to coin the 'gsk3 hypothesis of ad'. according to this hypothesis, over-activity of gsk3 accounts for memory impairment, tau hyper-phosphorylation, increased beta-amyloid production and local plaque-associated microglial-mediated inflammatory responses; all of which are hallmark characteristics of ad. if our 'gsk3 hypothesis of ad' is substantiated and gsk3 is indeed a causal mediator of ad then inhibitors of gsk3 would provide a novel avenue for therapeutic intervention in this devastating disorder.",0
"background mucositis is a highly significant, and sometimes dose-limiting, toxicity of cancer therapy. the goal of this systematic review was to update the multinational association of supportive care in cancer and international society of oral oncology (mascc/isoo) clinical practice guidelines for mucositis. methods a literature search was conducted to identify eligible published articles, based on predefined inclusion/exclusion criteria. each article was independently reviewed by 2 reviewers. studies were rated according to the presence of major and minor flaws as per previously published criteria. the body of evidence for each intervention, in each treatment setting, was assigned a level of evidence, based on previously published criteria. guidelines were developed based on the level of evidence, with 3 possible guideline determinations: recommendation, suggestion, or no guideline possible. results the literature search identified 8279 papers, 1032 of which were retrieved for detailed evaluation based on titles and abstracts. of these, 570 qualified for final inclusion in the systematic reviews. sixteen new guidelines were developed for or against the use of various interventions in specific treatment settings. in total, the mascc/isoo mucositis guidelines now include 32 guidelines: 22 for oral mucositis and 10 for gastrointestinal mucositis. this article describes these updated guidelines. conclusions the updated mascc/isoo clinical practice guidelines for mucositis will help clinicians provide evidence-based management of mucositis secondary to cancer therapy.",0
"the normal function of poly (adp-ribose) polymerase-1 (parp-1) is the routine repair of dna damage by adding poly (adp ribose) polymers in response to a variety of cellular stresses. recently, it has become widely appreciated that parp-1 also participates in diverse physiological and pathological functions from cell survival to several forms of cell death and has been implicated in gene transcription, immune responses, inflammation, learning, memory, synaptic functions, angiogenesis and aging. in the cns, parp inhibition attenuates injury in pathologies like cerebral ischemia, trauma and excitotoxicity demonstrating a central role of parp-1 in these pathologies. parp-1 is also a preferred substrate for several 'suicidal' proteases and the proteolytic action of suicidal proteases (caspases, calpains, cathepsins, granzymes and matrix metalloproteinases (mmps)) on parp-1 produces several specific proteolytic cleavage fragments with different molecular weights. these parp-1 signature fragments are recognized biomarkers for specific patterns of protease activity in unique cell death programs. this review focuses on specific suicidal proteases active towards parp-1 to generate signature parp-1 fragments that can identify key proteases and particular forms of cell death involved in pathophysiology. the roles played by some of the parp-1 fragments and their associated binding partners in the control of different forms of cell death are also discussed.",0
"background many technological, biological, social, and information networks fall into the broad class of 'small-world' networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). this semi-quantitative definition leads to a categorical distinction ('small/not-small') rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network's small-world status. moreover, systems described by small-world networks are often studied using an equivalent canonical network model--the watts-strogatz (ws) model. however, the process of establishing an equivalent ws model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified. methodology/principal findings we defined a precise measure of 'small-world-ness' s based on the trade off between high local clustering and short path length. a network is now deemed a 'small-world' if s>1--an assertion which may be tested statistically. we then examined the behavior of s on a large data-set of real-world systems. we found that all these systems were linked by a linear relationship between their s values and the network size n. moreover, we show a method for assigning a unique watts-strogatz (ws) model to any real-world network, and show analytically that the ws models associated with our sample of networks also show linearity between s and n. linearity between s and n is not, however, inevitable, and neither is s maximal for an arbitrary network of given size. linearity may, however, be explained by a common limiting growth process. conclusions/significance we have shown how the notion of a small-world network may be quantified. several key properties of the metric are described and the use of ws canonical models is placed on a more secure footing.",0
"background postmastectomy radiotherapy was shown in previous meta-analyses to reduce the risks of both recurrence and breast cancer mortality in all women with node-positive disease considered together. however, the benefit in women with only one to three positive lymph nodes is uncertain. we aimed to assess the effect of radiotherapy in these women after mastectomy and axillary dissection. methods we did a meta-analysis of individual data for 8135 women randomly assigned to treatment groups during 1964-86 in 22 trials of radiotherapy to the chest wall and regional lymph nodes after mastectomy and axillary surgery versus the same surgery but no radiotherapy. follow-up lasted 10 years for recurrence and to jan 1, 2009, for mortality. analyses were stratified by trial, individual follow-up year, age at entry, and pathological nodal status. findings 3786 women had axillary dissection to at least level ii and had zero, one to three, or four or more positive nodes. all were in trials in which radiotherapy included the chest wall, supraclavicular or axillary fossa (or both), and internal mammary chain. for 700 women with axillary dissection and no positive nodes, radiotherapy had no significant effect on locoregional recurrence (two-sided significance level >0·1), overall recurrence (rate ratio , irradiated vs not, 1·06, 95% ci 0·76-1·48, 2p>0·1), or breast cancer mortality (rr 1·18, 95% ci 0·89-1·55, 2p>0·1). for 1314 women with axillary dissection and one to three positive nodes, radiotherapy reduced locoregional recurrence (2p interpretation after mastectomy and axillary dissection, radiotherapy reduced both recurrence and breast cancer mortality in the women with one to three positive lymph nodes in these trials even when systemic therapy was given. for today's women, who in many countries are at lower risk of recurrence, absolute gains might be smaller but proportional gains might be larger because of more effective radiotherapy. funding cancer research uk, british heart foundation, uk medical research council.",0
"we describe an intensity-based glutamate-sensing fluorescent reporter (iglusnfr) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. we engineered iglusnfr in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. in hippocampal culture, iglusnfr detected single field stimulus-evoked glutamate release events. in pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iglusnfr responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. in mouse retina, iglusnfr-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. in worms, glutamate signals preceded and predicted postsynaptic calcium transients. in zebrafish, iglusnfr revealed spatial organization of direction-selective synaptic activity in the optic tectum. finally, in mouse forelimb motor cortex, iglusnfr expression in layer v pyramidal neurons revealed task-dependent single-spine activity during running.",0
"translations for the chinese, french, german, and spanish translations of the abstract see supplementary materials section.",0
"during the innate response to many inflammatory and infectious stimuli, dendritic cells (dcs) undergo a differentiation process termed maturation. mature dcs activate antigen-specific naive t cells. here we show that both immature and mature dcs activate resting human natural killer (nk) cells. within 1 wk the nk cells increase two-- to fourfold in numbers, start secreting interferon (ifn)-gamma, and acquire cytolytic activity against the classical nk target lcl721.221. the dc-activated nk cells then kill immature dcs efficiently, even though the latter express substantial levels of major histocompatibility complex (mhc) class i. similar results are seen with interleukin (il)-2--activated nk cell lines and clones, i.e., these nk cells kill and secrete ifn-gamma in response to immature dcs. mature dcs are protected from activated nk lysis, but lysis takes place if the nk inhibitory signal is blocked by a human histocompatibility leukocyte antigen (hla)-a,b,c--specific antibody. the nk activating signal mainly involves the nkp30 natural cytotoxicity receptor, and not the nkp46 or nkp44 receptor. however, both immature and mature dcs seem to use a nkp30 independent mechanism to act as potent stimulators for resting nk cells. we suggest that dcs are able to control directly the expansion of nk cells and that the lysis of immature dcs can regulate the afferent limb of innate and adaptive immunity.",0
"1. from type iii pneumococci a biologically active fraction has been isolated in highly purified form which in exceedingly minute amounts is capable under appropriate cultural conditions of inducing the transformation of unencapsulated r variants of pneumococcus type ii into fully encapsulated cells of the same specific type as that of the heat-killed microorganisms from which the inducing material was recovered. 2. methods for the isolation and purification of the active transforming material are described. 3. the data obtained by chemical, enzymatic, and serological analyses together with the results of preliminary studies by electrophoresis, ultracentrifugation, and ultraviolet spectroscopy indicate that, within the limits of the methods, the active fraction contains no demonstrable protein, unbound lipid, or serologically reactive polysaccharide and consists principally, if not solely, of a highly polymerized, viscous form of desoxyribonucleic acid. 4. evidence is presented that the chemically induced alterations in cellular structure and function are predictable, type-specific, and transmissible in series. the various hypotheses that have been advanced concerning the nature of these changes are reviewed.",0
"the covid-19 pandemic has caused unprecedented changes in the lives of 1.6 billion children and adolescents. first non-representative studies from china, india, brazil, the us, spain, italy, and germany pointed to a negative mental health impact. the current study is the first nationwide representative study to investigate the impact of the covid-19 pandemic on health-related quality of life (hrqol) and mental health of children and adolescents in germany from the perspective of children themselves. a representative online survey was conducted among n = 1586 families with 7- to 17-year-old children and adolescents between may 26 and june 10. the survey included internationally established and validated instruments for measuring hrqol (kidscreen-10), mental health problems (sdq), anxiety (scared), and depression (ces-dc). results were compared with data from the nationwide, longitudinal, representative bella cohort study (n = 1556) conducted in germany before the pandemic. two-thirds of the children and adolescents reported being highly burdened by the covid-19 pandemic. they experienced significantly lower hrqol (40.2% vs. 15.3%), more mental health problems (17.8% vs. 9.9%) and higher anxiety levels (24.1% vs. 14.9%) than before the pandemic. children with low socioeconomic status, migration background and limited living space were affected significantly more. health promotion and prevention strategies need to be implemented to maintain children's and adolescents' mental health, improve their hrqol, and mitigate the burden caused by covid-19, particularly for children who are most at risk.",0
"the cortex is a complex system, characterized by its dynamics and architecture, which underlie many functions such as action, perception, learning, language, and cognition. its structural architecture has been studied for more than a hundred years; however, its dynamics have been addressed much less thoroughly. in this paper, we review and integrate, in a unifying framework, a variety of computational approaches that have been used to characterize the dynamics of the cortex, as evidenced at different levels of measurement. computational models at different space-time scales help us understand the fundamental mechanisms that underpin neural processes and relate these processes to neuroscience data. modeling at the single neuron level is necessary because this is the level at which information is exchanged between the computing elements of the brain; the neurons. mesoscopic models tell us how neural elements interact to yield emergent behavior at the level of microcolumns and cortical columns. macroscopic models can inform us about whole brain dynamics and interactions between large-scale neural systems such as cortical regions, the thalamus, and brain stem. each level of description relates uniquely to neuroscience data, from single-unit recordings, through local field potentials to functional magnetic resonance imaging (fmri), electroencephalogram (eeg), and magnetoencephalogram (meg). models of the cortex can establish which types of large-scale neuronal networks can perform computations and characterize their emergent properties. mean-field and related formulations of dynamics also play an essential and complementary role as forward models that can be inverted given empirical data. this makes dynamic models critical in integrating theory and experiments. we argue that elaborating principled and informed models is a prerequisite for grounding empirical neuroscience in a cogent theoretical framework, commensurate with the achievements in the physical sciences.",0
"the selection of appropriate outcomes is crucial when designing clinical trials in order to compare the effects of different interventions directly. for the findings to influence policy and practice, the outcomes need to be relevant and important to key stakeholders including patients and the public, health care professionals and others making decisions about health care. it is now widely acknowledged that insufficient attention has been paid to the choice of outcomes measured in clinical trials. researchers are increasingly addressing this issue through the development and use of a core outcome set, an agreed standardised collection of outcomes which should be measured and reported, as a minimum, in all trials for a specific clinical area.accumulating work in this area has identified the need for guidance on the development, implementation, evaluation and updating of core outcome sets. this handbook, developed by the comet initiative, brings together current thinking and methodological research regarding those issues. we recommend a four-step process to develop a core outcome set. the aim is to update the contents of the handbook as further research is identified.",0
"background the tehran lipid and glucose study (tlgs) is a long term integrated community-based program for prevention of non-communicable disorders (ncd) by development of a healthy lifestyle and reduction of ncd risk factors. the study begun in 1999, is ongoing, to be continued for at least 20 years. a primary survey was done to collect baseline data in 15005 individuals, over 3 years of age, selected from cohorts of three medical heath centers. a questionnaire for past medical history and data was completed during interviews; blood pressure, pulse rate, and anthropometrical measurements and a limited physical examination were performed and lipid profiles, fasting blood sugar and 2-hours-postload-glucose challenge were measured. a dna bank was also collected. for those subjects aged over 30 years, rose questionnaire was completed and an electrocardiogram was taken. data collected were directly stored in computers as database software- computer assisted system. the aim of this study is to evaluate the feasibility and effectiveness of lifestyle modification in preventing or postponing the development of ncd risk factors and outcomes in the tlgs population. design and methods in phase ii of the tlgs, lifestyle interventions were implemented in 5630 people and 9375 individuals served as controls. primary, secondary and tertiary interventions were designed based on specific target groups including schoolchildren, housewives, and high-risk persons. officials of various sectors such as health, education, municipality, police, media, traders and community leaders were actively engaged as decision makers and collaborators. interventional strategies were based on lifestyle modifications in diet, smoking and physical activity through face-to-face education, leaflets & brochures, school program alterations, training volunteers as health team and treating patients with ncd risk factors. collection of demographic, clinical and laboratory data will be repeated every 3 years to assess the effects of different interventions in the intervention group as compared to control group. conclusion this controlled community intervention will test the possibility of preventing or delaying the onset of non-communicable risk factors and disorders in a population in nutrition transition. trial registration isrctn52588395.",0
"the ontogeny of large-scale functional organization of the human brain is not well understood. here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar ""small-world"" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. we found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism.",0
"the gastrointestinal microbiota has an important role in human health, and there is increasing interest in utilizing dietary approaches to modulate the composition and metabolic function of the microbial communities that colonize the gastrointestinal tract to improve health, and prevent or treat disease. one dietary strategy for modulating the microbiota is consumption of dietary fiber and prebiotics that can be metabolized by microbes in the gastrointestinal tract. human alimentary enzymes are not able to digest most complex carbohydrates and plant polysaccharides. instead, these polysaccharides are metabolized by microbes which generate short-chain fatty acids (scfas), including acetate, propionate, and butyrate. this article reviews the current knowledge of the impact of fiber and prebiotic consumption on the composition and metabolic function of the human gastrointestinal microbiota, including the effects of physiochemical properties of complex carbohydrates, adequate intake and treatment dosages, and the phenotypic responses related to the composition of the human microbiota.",0
"mesenchymal stem cells (mscs), a non-hematopoietic stem cell population first discovered in bone marrow, are multipotent cells capable of differentiating into mature cells of several mesenchymal tissues, such as fat and bone. as common progenitor cells of adipocytes and osteoblasts, mscs are delicately balanced for their differentiation commitment. numerous in vitro investigations have demonstrated that fat-induction factors inhibit osteogenesis, and, conversely, bone-induction factors hinder adipogenesis. in fact, a variety of external cues contribute to the delicate balance of adipo-osteogenic differentiation of mscs, including chemical, physical, and biological factors. these factors trigger different signaling pathways and activate various transcription factors that guide mscs to commit to either lineage. the dysregulation of the adipo-osteogenic balance has been linked to several pathophysiologic processes, such as aging, obesity, osteopenia, osteopetrosis, and osteoporosis. thus, the regulation of msc differentiation has increasingly attracted great attention in recent years. here, we review external factors and their signaling processes dictating the reciprocal regulation between adipocytes and osteoblasts during msc differentiation and the ultimate control of the adipo-osteogenic balance.",0
"background biologists need to perform complex queries, often across a variety of databases. typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. therefore, many groups rely on local bioinformatics support to process queries by accessing the resource's programmatic interfaces if they exist. this is not an efficient solution in terms of cost and time. instead, it would be better if the biologist only had to learn one generic interface. biomart provides such a solution. results biomart enables scientists to perform advanced querying of biological data sources through a single web interface. the power of the system comes from integrated querying of data sources regardless of their geographical locations. once these queries have been defined, they may be automated with its ""scripting at the click of a button"" functionality. biomart's capabilities are extended by integration with several widely used software packages such as bioconductor, das, galaxy, cytoscape, taverna. in this paper, we describe all aspects of biomart from a user's perspective and demonstrate how it can be used to solve real biological use cases such as snp selection for candidate gene screening or annotation of microarray results. conclusion biomart is an easy to use, generic and scalable system and therefore, has become an integral part of large data resources including ensembl, uniprot, hapmap, wormbase, gramene, dictybase, pride, msd and reactome. biomart is freely accessible to use at",0
"it is urgent to understand the future of severe acute respiratory syndrome-coronavirus 2 (sars-cov-2) transmission. we used estimates of seasonality, immunity, and cross-immunity for human coronavirus oc43 (hcov-oc43) and hcov-hku1 using time-series data from the united states to inform a model of sars-cov-2 transmission. we projected that recurrent wintertime outbreaks of sars-cov-2 will probably occur after the initial, most severe pandemic wave. absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. to avoid this, prolonged or intermittent social distancing may be necessary into 2022. additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. longitudinal serological studies are urgently needed to determine the extent and duration of immunity to sars-cov-2. even in the event of apparent elimination, sars-cov-2 surveillance should be maintained because a resurgence in contagion could be possible as late as 2024.",0
"background open access websites which deliver cognitive and behavioral interventions for anxiety and depression are characterised by poor adherence. we need to understand more about adherence in order to maximize the impact of internet-based interventions on the disease burden associated with common mental disorders. objective the aims of this paper are to review briefly the adherence literature with respect to internet interventions and to investigate the rates of dropout and compliance in randomized controlled trials of anxiety and depression web studies. methods a systematic review of randomized controlled trials using internet interventions for anxiety and depression was conducted, and data was collected on dropout and adherence, predictors of adherence, and reasons for dropout. results relative to reported rates of dropout from open access sites, the present study found that the rates of attrition in randomized controlled trials were lower, ranging from approximately 1 - 50%. predictors of adherence included disease severity, treatment length, and chronicity. very few studies formally examined reasons for dropout, and most studies failed to use appropriate statistical techniques to analyze missing data. conclusions dropout rates from randomized controlled trials of web interventions are low relative to dropout from open access websites. the development of theoretical models of adherence is as important in the area of internet intervention research as it is in the behavioral health literature. disease-based factors in anxiety and depression need further investigation.",0
"repeated measures correlation (rmcorr) is a statistical technique for determining the common within-individual association for paired measures assessed on two or more occasions for multiple individuals. simple regression/correlation is often applied to non-independent observations or aggregated data; this may produce biased, specious results due to violation of independence and/or differing patterns between-participants versus within-participants. unlike simple regression/correlation, rmcorr does not violate the assumption of independence of observations. also, rmcorr tends to have much greater statistical power because neither averaging nor aggregation is necessary for an intra-individual research question. rmcorr estimates the common regression slope, the association shared among individuals. to make rmcorr accessible, we provide background information for its assumptions and equations, visualization, power, and tradeoffs with rmcorr compared to multilevel modeling. we introduce the r package (rmcorr) and demonstrate its use for inferential statistics and visualization with two example datasets. the examples are used to illustrate research questions at different levels of analysis, intra-individual, and inter-individual. rmcorr is well-suited for research questions regarding the common linear association in paired repeated measures data. all results are fully reproducible.",0
"scanpy is a scalable toolkit for analyzing single-cell gene expression data. it includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. its python-based implementation efficiently deals with data sets of more than one million cells ( ). along with scanpy, we present anndata, a generic class for handling annotated data matrices ( ).",0
"the profile of brain structural abnormalities in schizophrenia is still not fully understood, despite decades of research using brain scans. to validate a prospective meta-analysis approach to analyzing multicenter neuroimaging data, we analyzed brain mri scans from 2028 schizophrenia patients and 2540 healthy controls, assessed with standardized methods at 15 centers worldwide. we identified subcortical brain volumes that differentiated patients from controls, and ranked them according to their effect sizes. compared with healthy controls, patients with schizophrenia had smaller hippocampus (cohen's d=-0.46), amygdala (d=-0.31), thalamus (d=-0.31), accumbens (d=-0.25) and intracranial volumes (d=-0.12), as well as larger pallidum (d=0.21) and lateral ventricle volumes (d=0.37). putamen and pallidum volume augmentations were positively associated with duration of illness and hippocampal deficits scaled with the proportion of unmedicated patients. worldwide cooperative analyses of brain imaging data support a profile of subcortical abnormalities in schizophrenia, which is consistent with that based on traditional meta-analytic approaches. this first enigma schizophrenia working group study validates that collaborative data analyses can readily be used across brain phenotypes and disorders and encourages analysis and data sharing efforts to further our understanding of severe mental illness.",0
"magnetic resonance is an exceptionally powerful and versatile measurement technique. the basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (mrf)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. mrf thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. mrf can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. when paired with an appropriate pattern-recognition algorithm, mrf inherently suppresses measurement errors and can thus improve measurement accuracy.",0
"current methods for inferring population structure from genetic data do not provide formal significance tests for population differentiation. we discuss an approach to studying population structure (principal components analysis) that was first applied to genetic data by cavalli-sforza and colleagues. we place the method on a solid statistical footing, using results from modern statistics to develop formal significance tests. we also uncover a general ""phase change"" phenomenon about the ability to detect structure in genetic data, which emerges from the statistical theory we use, and has an important implication for the ability to discover structure in genetic data: for a fixed but large dataset size, divergence between two populations (as measured, for example, by a statistic like fst) below a threshold is essentially undetectable, but a little above threshold, detection will be easy. this means that we can predict the dataset size needed to detect structure.",0
"a major group of natural killer (nk) t cells express an invariant valpha14(+) t cell receptor (tcr) specific for the lipoglycan alpha-galactosylceramide (alpha-galcer), which is presented by cd1d. these cells may have an important immune regulatory function, but an understanding of their biology has been hampered by the lack of suitable reagents for tracking them in vivo. here we show that tetramers of mouse cd1d loaded with alpha-galcer are a sensitive and highly specific reagent for identifying valpha14(+) nk t cells. using these tetramers, we find that alpha-galcer-specific t lymphocytes are more widely distributed than was previously appreciated, with populations of largely nk1.1(-) but tetramer-binding t cells present in the lymph nodes and the intestine. injection of alpha-galcer leads to the production of both interferon gamma and interleukin 4 by nearly all nk t cells in the liver and the majority of the spleen within 2 h. these cells mostly disappear by 5 h, and they do not reappear after 1 wk. curiously, tetramer-positive thymocytes do not rapidly synthesize cytokines, nor do they undergo decreases in cell number after lipid antigen stimulation, although they express equivalent tcr levels. in summary, the data presented here demonstrate that alpha-galcer-specific nk t cells undergo a unique and highly compartmentalized response to antigenic stimulation.",0
"cancer prevention and treatment using traditional chinese medicines have attracted increasing interest. this study characterizes antioxidant activity and phenolic compounds of traditional chinese medicinal plants associated with anticancer, comprising 112 species from 50 plant families. the improved abts(*+) method was used to systematically assess the total antioxidant capacity (trolox equivalent antioxidant capacity, teac) of the medicinal extracts. the teac values and total phenolic content for methanolic extracts of herbs ranged from 46.7 to 17,323 micromol trolox equivalent/100 g dry weight (dw), and from 0.22 to 50.3 g of gallic acid equivalent/100 g dw, respectively. a positive, significant linear relationship between antioxidant activity and total phenolic content (all r(2) values>/=0.95) showed that phenolic compounds were the dominant antioxidant components in the tested medicinal herbs. major types of phenolic compounds from most of the tested herbs were preliminarily identified and analyzed, and mainly included phenolic acids, flavonoids, tannins, coumarins, lignans, quinones, stilbenes, and curcuminoids. these medicinal herbs exhibited far stronger antioxidant activity and contained significantly higher levels of phenolics than common vegetables and fruits. traditional chinese medicinal plants associated with anticancer might be potential sources of potent natural antioxidants and beneficial chemopreventive agents.",0
"background few observations exist with respect to the pro-coagulant profile of patients with covid-19 acute respiratory distress syndrome (ards). reports of thromboembolic complications are scarce but suggestive for a clinical relevance of the problem. objectives prospective observational study aimed to characterize the coagulation profile of covid-19 ards patients with standard and viscoelastic coagulation tests and to evaluate their changes after establishment of an aggressive thromboprophylaxis. methods sixteen patients with covid-19 ards received a complete coagulation profile at the admission in the intensive care unit. ten patients were followed in the subsequent 7 days, after increasing the dose of low molecular weight heparin, antithrombin levels correction, and clopidogrel in selected cases. results at baseline, the patients showed a pro-coagulant profile characterized by an increased clot strength (cs, median 55 hpa, 95% interquartile range 35-63), platelet contribution to cs (pcs, 43 hpa; interquartile range 24-45), fibrinogen contribution to cs (fcs, 12 hpa; interquartile range 6-13.5) elevated d-dimer levels (5.5 μg/ml, interquartile range 2.5-6.5), and hyperfibrinogenemia (794 mg/dl, interquartile range 583-933). fibrinogen levels were associated (r 2 = .506, p = .003) with interleukin-6 values. after increasing the thromboprophylaxis, there was a significant (p = .001) time-related decrease of fibrinogen levels, d-dimers (p = .017), cs (p = .013), pcs (p = .035), and fcs (p = .038). conclusion the pro-coagulant pattern of these patients may justify the clinical reports of thromboembolic complications (pulmonary embolism) during the course of the disease. further studies are needed to assess the best prophylaxis and treatment of this condition.",0
"genetically encoded calcium indicators (gecis) can be used to image activity in defined neuronal populations. however, current gecis produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. we developed a single-wavelength gcamp2-based geci (gcamp3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). we detected gcamp3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of gcamp2, d3cpvenus and tn-xxl. in caenorhabditis elegans chemosensory neurons and the drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with gcamp3 (4-6-fold). in somatosensory and motor cortical neurons in the intact mouse, gcamp3 detected calcium transients with amplitudes linearly dependent on action potential number. long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.",0
"microorganisms attach to surfaces and develop biofilms. biofilm-associated cells can be differentiated from their suspended counterparts by generation of an extracellular polymeric substance (eps) matrix, reduced growth rates, and the up- and down- regulation of specific genes. attachment is a complex process regulated by diverse characteristics of the growth medium, substratum, and cell surface. an established biofilm structure comprises microbial cells and eps, has a defined architecture, and provides an optimal environment for the exchange of genetic material between cells. cells may also communicate via quorum sensing, which may in turn affect biofilm processes such as detachment. biofilms have great importance for public health because of their role in certain infectious diseases and importance in a variety of device-related infections. a greater understanding of biofilm processes should lead to novel, effective control strategies for biofilm control and a resulting improvement in patient management.",0
"dna methylation is the most widely studied epigenetic mark and is known to be essential to normal development and frequently disrupted in disease. the illumina humanmethylation450 beadchip assays the methylation status of cpgs at 485,577 sites across the genome. here we present subset-quantile within array normalization (swan), a new method that substantially improves the results from this platform by reducing technical variation within and between arrays. swan is available in the minfi bioconductor package.",0
"summary the variant call format (vcf) is a generic format for storing dna polymorphism data such as snps, insertions, deletions and structural variants, together with rich annotations. vcf is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. the format was developed for the 1000 genomes project, and has also been adopted by other projects such as uk10k, dbsnp and the nhlbi exome project. vcftools is a software suite that implements various utilities for processing vcf files, including validation, merging, comparing and also provides a general perl api. availability",0
"although physical activity (pa) is a key element in the prevention and management of type 2 diabetes, many with this chronic disease do not become or remain regularly active. high-quality studies establishing the importance of exercise and fitness in diabetes were lacking until recently, but it is now well established that participation in regular pa improves blood glucose control and can prevent or delay type 2 diabetes, along with positively affecting lipids, blood pressure, cardiovascular events, mortality, and quality of life. structured interventions combining pa and modest weight loss have been shown to lower type 2 diabetes risk by up to 58% in high-risk populations. most benefits of pa on diabetes management are realized through acute and chronic improvements in insulin action, accomplished with both aerobic and resistance training. the benefits of physical training are discussed, along with recommendations for varying activities, pa-associated blood glucose management, diabetes prevention, gestational diabetes mellitus, and safe and effective practices for pa with diabetes-related complications.",0
"animal models of memory have been considered as the subject of many scientific publications at least since the beginning of the twentieth century. in humans, memory is often accessed through spoken or written language, while in animals, cognitive functions must be accessed through different kind of behaviors in many specific, experimental models of memory and learning. among them, the novel object recognition test can be evaluated by the differences in the exploration time of novel and familiar objects. its application is not limited to a field of research and enables that various issues can be studied, such as the memory and learning, the preference for novelty, the influence of different brain regions in the process of recognition, and even the study of different drugs and their effects. this paper describes the novel object recognition paradigms in animals, as a valuable measure of cognition. the purpose of this work was to review the neurobiology and methodological modifications of the test commonly used in behavioral pharmacology.",0
"we have developed cluego, an easy to use cytoscape plug-in that strongly improves biological interpretation of large lists of genes. cluego integrates gene ontology (go) terms as well as kegg/biocarta pathways and creates a functionally organized go/pathway term network. it can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. a one-click update option allows cluego to automatically download the most recent go/kegg release at any time. cluego provides an intuitive representation of the analysis results and can be optionally used in conjunction with the golorize plug-in.",0
"long noncoding rnas (lncrnas), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. rna-seq data were downloaded from geo of ncbi and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (icca). we investigated differences in lncrna and mrna profiles between 7 pairs of icca and adjacent normal tissues. 230 lncrnas were differentially expressed more than four-fold change in icca tissues. among these, 97 were upregulated and 133 downregulated relatively to normal tissues. moreover, 169 lncrnas and 597 mrnas formed the lncrna-mrna co-expression network which consist 766 network nodes and 769 connection edges. bioinformatics analysis identified these dysregulated lncrnas were associated with cholesterol homeostasis, insoluble fraction and lipid binding activity and were enriched in complement and coagulation cascades and ppar signaling pathway. these results uncovered the landscape of icca-associated lncrnas and co-expression network, providing insightful information about dysregulated lncrnas in icca.",1
"simple summary proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. the abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to dna or rna binding. these functions include the regulation of transcription, rna splicing, translation, stability and sequestration. cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between dna and rna. many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. abstract the cold-shock domain has a deceptively simple architecture but supports a complex biology. it is conserved from bacteria to man and has representatives in all kingdoms of life. bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. this conserved binding mode explains the cold-shock domains’ ability to associate with both dna and rna strands and their limited sequence selectivity. the promiscuous dna and rna binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and dna-damage repair as well as in regulating splicing, translation, mrna stability and rna sequestration.",0
"micrornas (mirnas/mirs) have been investigated as diagnostic and prognostic biomarkers for cancer; however, the significance of mirnas in colorectal cancer (crc) remains to be elucidated. the aim of the present study was to determine the genetic profiles of crc tissue, and screen for mirnas implicated in crc cell proliferation and migration. rna sequencing of 10 paired specimens was performed to for screen genes that were upregulated or downregulated in crc. mirna expression in crc specimens and cell lines was confirmed using qpcr analysis. the significance of indicated mirnas in crc cell proliferation and migration was evaluated using mtt and scratch wound-healing assays. online computational prediction, isobaric tags for relative and absolute quantification analysis and a luciferase reporter assay were applied to determine candidate targeted genes for the mirnas. rna-seq data revealed mir-1914 as the most prominent mirna in crc specimens. qpcr analysis also suggested that the expression of mir-1914, as well as its counterpart mir-647 were elevated in crc specimens and cell lines. suppression of mir-647/1914 using small interfering rnas inhibited crc sw480 and sw620 cell proliferation, and migration. nuclear factor i/x (nfix) was demonstrated to be a candidate for mir-647/1914 and mediated the oncogenic activity of mir-647/1914. in all, mir-647 and mir-1914 were demonstrated to promote the proliferation and migration of crc cells by directly targeting nfix. therapeutic delivery of sirnas targeting mir-647/1914 and overexpression of nfix may be feasible approaches for crc treatment.",1
"background reverse transcription quantitative pcr has become a powerful technique to monitor mrna transcription in response to different environmental conditions in many bacterial species. however, correct evaluation of data requires accurate and reliable use of reference genes whose transcription does not change during the course of the experiment. in the present study exposure to different growth conditions was used to validate the transcription stability of eight reference gene candidates in three strains from two subspecies of francisella noatunensis , a pathogen causing disease in both warm and cold water fish species. results relative transcription levels for genes encoding dna gyrase ( gyra ), rna polymerase beta subunit ( rpob ), dna polymerase i ( pola ), cell division protein ( ftsz ), outer membrane protein ( fopa ), riboflavin biosynthesis protein ( ribc ), 16s ribosomal rna ( 16s rrna ) and dna helicases ( uvrd ) were quantified under exponential, stationary and iron-restricted growth conditions. the suitability of selected reference genes for reliable interpretation of gene expression data was tested using the virulence-associated intracellular growth locus subunit c ( iglc ) gene. conclusion although the transcription stability of the reference genes was slightly different in the three strains studied, fopa , ftsz and pola proved to be the most stable and suitable for normalization of gene transcription in francisella noatunensis ssp.",0
"maternal obesity is a major risk factor for pregnancy complications, causing inflammatory cytokine release in the placenta, including interleukin-1β (il-1β), il-6, and il-8. pregnant women with obesity develop accelerated systemic and placental inflammation with elevated circulating advanced glycation end products (ages). il-1β is a pivotal inflammatory cytokine associated with obesity and pregnancy complications, and its production is regulated by nlr family pyrin domain-containing 3 (nlrp3) inflammasomes. here, we investigated whether ages are involved in the activation of nlrp3 inflammasomes using human placental tissues and placental cell line. in human placental tissue cultures, ages significantly increased il-1β secretion, as well as il-1β and nlrp3 mrna expression. in human placental cell culture, although age treatment did not stimulate il-1β secretion, ages significantly increased il-1β mrna expression and intracellular il-1β production. after pre-incubation with ages, nano-silica treatment (well known as an inflammasome activator) increased il-1β secretion in placental cells. however, after pre-incubation with lipopolysaccharide to produce pro-il-1β, age treatment did not affect il-1β secretion in placental cells. these findings suggest that ages stimulate pro-il-1β production within placental cells, but do not activate inflammasomes to stimulate il-1β secretion. furthermore, using pharmacological inhibitors, we demonstrated that age-induced inflammatory cytokines are dependent on mapk/nf-κb/ap-1 signaling and reactive oxygen species production in placental cells. in conclusion, ages regulate pro-il-1β production and inflammatory responses, resulting in the activation of nlrp3 inflammasomes in human placenta. these results suggest that ages, as an endogenous and sterile danger signal, may contribute to chronic placental cytokine production.",0
"background during mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. the identification of the complete changes has not been possible until the development of the next generation sequencing technology. results here we report comprehensive transcriptome dynamics of single matured bovine oocytes and pre-implantation embryos developed in vivo. surprisingly, more than half of the estimated 22,000 bovine genes, 11,488 to 12,729 involved in more than 100 pathways, is expressed in oocytes and early embryos. despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. a total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome is activated at this transition. additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in embryogenesis. using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. we also conducted the first comparison of embryonic expression profiles across three mammalian species, human, mouse and bovine, for which rna-seq data are available. we found that the three species share more maternally deposited genes than embryonic genome activated genes. more importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development. conclusions this study provides a comprehensive examination of gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-756) contains supplementary material, which is available to authorized users.",0
"abstract recent studies on the regulatory networks implicated in alzheimer’s disease (ad) evince long non-coding rnas (lncrnas) as crucial regulatory players, albeit a poor understanding of the mechanism. analyzing differential gene expression in the rna-seq data from the post-mortem ad brain hippocampus, we categorized a list of ad-dysregulated lncrna transcripts into functionally similar communities based on their k- mer profiles. using machine-learning-based algorithms, their subcellular localizations were mapped. we further explored the functional relevance of each community through ad-dysregulated mirna, rna-binding protein (rbp) interactors, and pathway enrichment analyses. further investigation of the mirna–lncrna and rbp–lncrna networks from each community revealed the top rbps, mirnas, and lncrnas for each cluster. the experimental validation community yielded elavl4 and mir-16-5p as the predominant rbp and mirna, respectively. five lncrnas emerged as the top-ranking candidates from the rbp/mirna-lncrna networks. further analyses of these networks revealed the presence of multiple regulatory triads where the rbp–lncrna interactions could be augmented by the enhanced mirna–lncrna interactions. our results advance the understanding of the mechanism of lncrna-mediated ad regulation through their interacting partners and demonstrate how these functionally segregated but overlapping regulatory networks can modulate the disease holistically. graphical abstract supplementary information the online version contains supplementary material available at 10.1007/s12031-024-02244-0.",1
"background the annual fish nothobranchius furzeri is characterized by a natural dichromatism with yellow-tailed and red-tailed male individuals. these differences are due to different distributions of xanthophores and erythrophores in the two morphs. previous crossing studies have showed that dichromatism in n. furzeri is inherited as a simple mendelian trait with the yellow morph dominant over the red morph. the causative genetic variation was mapped by linkage analysis in a chromosome region containing the mc1r locus. however, subsequent mapping showed that mc1r is most likely not responsible for the color difference in n. furzeri. to gain further insight into the molecular basis of this phenotype, we performed rna-seq on f2 progeny of a cross between n. furzeri male and n. kadleci female. results we identified 210 differentially-expressed genes between yellow and red fin samples. functional annotation analysis revealed that genes with higher transcript levels in the yellow morph are enriched for the melanin synthesis pathway indicating that xanthophores are more similar to melanophores than are the erythrophores. genes with higher expression levels in red-tails included xanthine dehydrogenase ( xdh ), coding for a biosynthetic enzyme in the pteridine synthesis pathway, and genes related to muscle contraction. comparison of degs obtained in this study with genes associated with pigmentation in the midas cichlid ( a. citrinellus ) reveal similarities like involvement of the melanin biosynthesis pathway, the genes ptgir , rasef (ras and ef-hand domain containing), as well as genes primarily expressed in muscle such as ttn and ttnb (titin, titin b). conclusions regulation of genes in the melanin synthetic pathway is an expected finding and shows that n. furzeri is a genetically-tractable species for studying the genetic basis of natural phenotypic variations. the current list of differentially-expressed genes can be compared with the results of fine-mapping, to reveal the genetic architecture of this natural phenotype. however, an evolutionarily-conserved role of muscle-related genes in tail fin pigmentation is novel finding and interesting perspective for the future. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-754) contains supplementary material, which is available to authorized users.",0
"to avoid organ dysfunction as a consequence of tissue diminution or tumorous growth, a tight balance between cell proliferation and differentiation is maintained in metazoans. however, cell-intrinsic gene expression mechanisms controlling adult tissue homeostasis remain poorly understood. by focusing on the adult caenorhabditis elegans reproductive tissue, we show that translational activation of mrnas is a fundamental mechanism to maintain tissue homeostasis. our genetic experiments identified the trf4/5-type cytoplasmic poly(a) polymerase (cytopap) gld-4 and its enzymatic activator gls-1 to perform a dual role in regulating the size of the proliferative zone. consistent with a ubiquitous expression of gld-4 cytopap in proliferative germ cells, its genetic activity is required to maintain a robust proliferative adult germ cell pool, presumably by regulating many mrna targets encoding proliferation-promoting factors. based on translational reporters and endogenous protein expression analyses, we found that gld-4 activity promotes glp-1/notch receptor expression, an essential factor of continued germ cell proliferation. rna-protein interaction assays documented also a physical association of the gld-4/gls-1 cytopap complex with glp-1 mrna, and ribosomal fractionation studies established that gld-4 cytopap activity facilitates translational efficiency of glp-1 mrna. moreover, we found that in proliferative cells the differentiation-promoting factor, gld-2 cytopap, is translationally repressed by the stem cell factor and puf-type rna-binding protein, fbf. this suggests that cytopap-mediated translational activation of proliferation-promoting factors, paired with puf-mediated translational repression of differentiation factors, forms a translational control circuit that expands the proliferative germ cell pool. our additional genetic experiments uncovered that the gld-4/gls-1 cytopap complex promotes also differentiation, forming a redundant translational circuit with gld-2 cytopap and the translational repressor gld-1 to restrict proliferation. together with previous findings, our combined data reveals two interconnected translational activation/repression circuitries of broadly conserved rna regulators that maintain the balance between adult germ cell proliferation and differentiation.",0
"endothelial dysfunction is a primary feature of several cardiovascular diseases. endothelial colony-forming cells (ecfcs) represent a highly proliferative subtype of endothelial progenitor cells (epcs), which are involved in neovascularization and vascular repair. statins are known to improve the outcome of cardiovascular diseases via pleiotropic effects. we hypothesized that treatment with the 3-hydroxy-3-methyl-glutaryl–coenzyme a (hmg-coa) reductase inhibitor pravastatin increases ecfcs’ functional capacities and regulates the expression of proteins which modulate endothelial health in a favourable manner. umbilical cord blood derived ecfcs were incubated with different concentrations of pravastatin with or without mevalonate, a key intermediate in cholesterol synthesis. functional capacities such as migration, proliferation and tube formation were addressed in corresponding in vitro assays. mrna and protein levels or phosphorylation of protein kinase b (akt), endothelial nitric oxide synthase (enos), heme oxygenase-1 (ho-1), vascular endothelial growth factor a (vegf-a), placental growth factor (plgf), soluble fms-like tyrosine kinase-1 (sflt-1) and endoglin (eng) were analyzed by real time pcr or immunoblot, respectively. proliferation, migration and tube formation of ecfcs were enhanced after pravastatin treatment, and akt- and enos-phosphorylation were augmented. further, expression levels of ho-1, vegf-a and plgf were increased, whereas expression levels of sflt-1 and eng were decreased. pravastatin induced effects were reversible by the addition of mevalonate. pravastatin induces beneficial effects on ecfc function, angiogenic signaling and protein expression. these effects may contribute to understand the pleiotropic function of statins as well as to provide a promising option to improve ecfcs’ condition in cell therapy in order to ameliorate endothelial dysfunction.",0
"proteins of the sm and sm-like (lsm) families, referred to collectively as (l)sm proteins, are found in all three domains of life and are known to promote a variety of rna processes such as base-pair formation, unwinding, rna degradation, and rna stabilization. in eukaryotes, (l)sm proteins have been studied, inter alia, for their role in pre-mrna splicing. in many organisms, the lsm proteins form two distinct complexes, one consisting of lsm1–7 that is involved in mrna degradation in the cytoplasm, and the other consisting of lsm2–8 that binds spliceosomal u6 snrna in the nucleus. we recently characterized the splicing proteins from the red alga cyanidioschyzon merolae and found that it has only seven lsm proteins. the identities of cmlsm2–cmlsm7 were unambiguous, but the seventh protein was similar to lsm1 and lsm8. here, we use in vitro binding measurements, microscopy, and affinity purification-mass spectrometry to demonstrate a canonical splicing function for the c. merolae lsm complex and experimentally validate our bioinformatic predictions of a reduced spliceosome in this organism. copurification of pat1 and its associated mrna degradation proteins with the lsm proteins, along with evidence of a cytoplasmic fraction of cmlsm complexes, argues that this complex is involved in both splicing and cytoplasmic mrna degradation. intriguingly, the pat1 complex also copurifies with all four snrnas, suggesting the possibility of a spliceosome-associated pre-mrna degradation complex in the nucleus.",0
"introduction glioblastoma (gbm) invasion studies have focused on coding genes, while few studies evaluate long non-coding rnas (lncrnas), transcripts without protein-coding potential, for role in gbm invasion. we leveraged crispr-interference (crispri) to evaluate invasive function of gbm-associated lncrnas in an unbiased functional screen, characterizing and exploring the mechanism of identified candidates. methods we implemented a crispri lncrna loss-of-function screen evaluating association of lncrna knockdown (kd) with invasion capacity in matrigel. top screen candidates were validated using crispri and oligonucleotide(aso)-mediated knockdown in three tumor lines. clinical relevance of candidates was assessed via the cancer genome atlas(tcga) and genotype-tissue expression(gtex) survival analysis. mediators of lncrna effect were identified via differential expression analysis following lncrna kd and assessed for tumor invasion using knockdown and rescue experiments. results forty-eight lncrnas were significantly associated with 33–83% decrease in invasion (p<0.01) upon knockdown. the top candidate, linc03045 , identified from effect size and p-value, demonstrated 82.7% decrease in tumor cell invasion upon knockdown, while linc03045 expression was significantly associated with patient survival and tumor grade(p<0.0001). rnaseq analysis of linc03045 knockdown revealed that wasf3 , previously implicated in tumor invasion studies, was highly correlated with lncrna expression, while wasf3 kd was associated with significant decrease in invasion. finally, wasf3 overexpression demonstrated rescue of invasive function lost with linc03045 kd. conclusion crispri screening identified linc03045 , a previously unannotated lncrna, as critical to gbm invasion. gene expression is significantly associated with tumor grade and survival. rna-seq and mechanistic studies suggest that this novel lncrna may regulate invasion via wasf3.",1
"mica is a small non-coding rna that regulates ompa mrna translation in escherichia coli. mica has an inhibitory function, base pairing to the translation initiation region of target mrnas through short sequences of complementarity, blocking their ribosome-binding sites. the mica structure contains two stem loops, which impede its interaction with target mrnas, and it is thought that the rna chaperone protein hfq, known to be involved in mica regulation of ompa , may structurally remodel mica to reveal the ompa- binding site for cognate pairing. to further characterize these interactions, we undertook biochemical and biophysical studies using native mica and a ‘stabilized’ version, modified to mimic the conformational state of mica where the ompa -binding site is exposed. our data corroborate two proposed roles for hfq: first, to bring both mica and ompa into close proximity, and second, to restructure mica to allow exposure of the ompa -binding site for pairing, thereby demonstrating the rna chaperone function of hfq. additionally, at accumulated mica levels, we identified a mg 2+ -dependent self-association that occludes the ompa -recognition region. we discuss the potential contribution of an mg 2+ -mediated conformational switch of mica for the regulation of mica function.",1
"oryza meyeriana ( o. meyeriana ), with a gg genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. it is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. however, limited genomic or transcriptomic data of o. meyeriana are currently available. in this study, we present the first comprehensive characterization of the o. meyeriana transcriptome using rna-seq and obtained 185,323 contigs with an average length of 1,692 bp and an n50 of 2,391 bp. through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. by similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. comparison with the oryza sativa ( japonica -type nipponbare and indica -type 93–11) genomes revealed that 13% of the o. meyeriana contigs had not been detected in o. sativa. many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. there are two kinds of rice bacterial blight-resistant genes ( xa1 and xa26 ) differentially or specifically expressed in o. meyeriana. the 4 xa1 contigs were all only expressed in root, while three of xa26 contigs have the highest expression level in leaves, two of xa26 contigs have the highest expression profile in stems and one of xa26 contigs was expressed dominantly in roots. the transcriptomic database of o. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in o. meyeriana.",0
"background sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. these sequences may be common in populations, and their absence in the reference genome may indicate rare variants in the genomes of individuals who served as donors for the human genome project. as the reference genome is used in probe design for microarray technology and mapping short reads in next generation sequencing (ngs), this missing sequence could be a source of bias in functional genomic studies and variant analysis. one end anchor (oea) and/or orphan reads from paired-end sequencing have been used to identify novel sequences that are absent in reference genome. however, there is no study to investigate the distribution, evolution and functionality of those sequences in human populations. results to systematically identify and study the missing common sequences (micseqs), we extended the previous method by pooling oea reads from large number of individuals and applying strict filtering methods to remove false sequences. the pipeline was applied to data from phase 1 of the 1000 genomes project. we identified 309 micseqs that are present in at least 1% of the human population, but absent in the reference genome. we confirmed 76% of these 309 micseqs by comparison to other primate genomes, individual human genomes, and gene expression data. furthermore, we randomly selected fifteen micseqs and confirmed their presence using pcr validation in 38 additional individuals. functional analysis using published rna-seq and chip-seq data showed that eleven micseqs are highly expressed in human brain and three micseqs contain transcription factor (tf) binding regions, suggesting they are functional elements. in addition, the identified micseqs are absent in non-primates and show dynamic acquisition during primate evolution culminating with most micseqs being present in africans, suggesting some micseqs may be important sources of human diversity. conclusions 76% of micseqs were confirmed by a comparative genomics approach. fourteen micseqs are expressed in human brain or contain tf binding regions. some micseqs are primate-specific, conserved and may play a role in the evolution of primates. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-685) contains supplementary material, which is available to authorized users.",0
"about half of the known mirna genes are located within protein-coding host genes, and are thus subject to co-transcription. accumulating data indicate that this coupling may be an intrinsic mechanism to directly regulate the host gene’s expression, constituting a negative feedback loop. inevitably, the cell requires a yet largely unknown repertoire of methods to regulate this control mechanism. we propose apa as one possible mechanism by which negative feedback of intronic mirna on their host genes might be regulated. using in-silico analyses, we found that host genes that contain seed matching sites for their intronic mirnas yield longer 32utrs with more polyadenylation sites. additionally, the distribution of polyadenylation signals differed significantly between these host genes and host genes of mirnas that do not contain potential mirna binding sites. we then transferred these in-silico results to a biological example and investigated the relationship between zfr and its intronic mirna mir-579 in a u87 cell line model. we found that zfr is targeted by its intronic mirna mir-579 and that alternative polyadenylation allows differential targeting. we additionally used bioinformatics analyses and rna-seq to evaluate a potential cross-talk between intronic mirnas and alternative polyadenylation. cpsf2, a gene previously associated with alternative polyadenylation signal recognition, might be linked to intronic mirna negative feedback by altering polyadenylation signal utilization.",1
"abstract co-infection with porcine reproductive and respiratory syndrome virus (prrsv) and haemophilus parasuis (hps) has severely restricted the healthy development of pig breeding. exploring disease resistance of non-coding rnas in pigs co-infected with prrsv and hps is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in kele piglets and to innovate the use of local pig germplasm resources in china. rna-seq of lungs from kele piglets with single-infection of prrsv or hps and co-infection of both pathogens was performed. two hundred and twenty-five differentially expressed long non-coding rnas (delncrnas) and 30 demicrornas (demirnas) were identified and characterized in the prrsv and hps co-infection (prrsv–hps) group. compared with the single-infection groups, 146 unique delncrnas, 17 unique demirnas, and 206 target differentially expressed genes (degs) were identified in the prrsv–hps group. the expression patterns of 20 demirnas and delncrnas confirmed by real-time quantitative polymerase chain reaction (rt-qpcr) were consistent with those determined by high-throughput sequencing. in the prrsv–hps group, the target degs were enriched in eight immune gene ontology terms relating to two unique demirnas and 16 delncrnas, and the unique target degs participated the host immune response to pathogens infection by affecting 15 immune-related kyoto encyclopedia of genes and genomes enrichment pathways. notably, competitive endogenous rna (cerna) networks of different groups were constructed, and the ssc-mir-671-5p mirna was validated as a potential regulatory factor to regulate dtx4 and aebp1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. these results provided insight into further study on the molecular mechanisms of resistance to prrsv and hps co-infection in kele piglets.",1
"background microrna (mirna)-related single nucleotide polymorphisms (snps) may compromise mirna binding affinity and modify mrna expression levels of the target genes, thus leading to cancer susceptibility. however, few studies have investigated roles of mirna-related snps in the etiology of cervical carcinoma. methods in this case–control study of 1,584 cervical cancer cases and 1,394 cancer-free female controls, we investigated associations between two mir-218 -related snps involved in the lamb3-mir-218 pathway and the risk of cervical carcinoma in eastern chinese women. results we found that the pri-mir-218 rs11134527 variant gg genotype was significantly associated with a decreased risk of cervical carcinoma compared with aa/ag genotypes (adjusted or=0.77, 95% ci=0.63-0.95, p =0.015). however, this association was not observed for the mir-218 binding site snp (rs2566) on lamb3. using the multifactor dimensionality reduction analysis, we observed some evidence of interactions of these two snps with other risk factors, especially age at primiparity and menopausal status, in the risk of cervical carcinoma. conclusions the pri-mir-218 rs11134527 snp was significantly associated with the risk of cervical carcinoma in eastern chinese women. larger, independent studies are warranted to validate our findings.",1
"natural antisense transcripts (nats) as one of the most diverse classes of long noncoding rnas (lncrnas), have been demonstrated involved in fundamental biological processes in human. here, we reported that human prohibitin gene pseudogene 1 ( phbp1 ) was upregulated in escc, and increased phbp1 expression in escc was associated with clinical advanced stage. functional experiments showed that phbp1 knockdown inhibited escc cells proliferation, colony formation and xenograft tumor growth in vitro and in vivo by causing cell-cycle arrest at the g1-g0 phase. mechanisms analysis revealed that phbp1 transcript as an antisense transcript of phb is partially complementary to phb mrna and formed an rna-rna hybrid with phb , consequently inducing an increase of phb expression at both the mrna and protein levels. furthermore, phbp1 expression is strongly correlated with phb expression in escc tissues. collectively, this study elucidates an important role of phbp1 in promoting escc partly via increasing phb expression.",1
"piwi-interacting rnas (pirnas) fulfill a critical, conserved role in defending the genome against foreign genetic elements. in many organisms, pirnas appear to be derived from processing of a long, polycistronic rna precursor. here, we establish that each caenorhabditis elegans pirna represents a tiny, autonomous transcriptional unit. remarkably, the minimal c. elegans pirna cassette requires only a 21 nucleotide (nt) pirna sequence and an ∼50 nt upstream motif with limited genomic context for expression. combining computational analyses with a novel, in vivo transgenic system, we demonstrate that this upstream motif is necessary for independent expression of a germline-enriched, piwi-dependent pirna. we further show that a single nucleotide position within this motif directs differential germline enrichment. accordingly, over 70% of c. elegans pirnas are selectively expressed in male or female germline, and comparison of the genes they target suggests that these two populations have evolved independently. together, our results indicate that c. elegans pirna upstream motifs act as independent promoters to specify which sequences are expressed as pirnas, how abundantly they are expressed, and in what germline. as the genome encodes well over 15,000 unique pirna sequences, our study reveals that the number of transcriptional units encoding pirnas rivals the number of mrna coding genes in the c. elegans genome.",1
"regulation of gene expression is one of several roles proposed for the stress-induced nucleotide diadenosine tetraphosphate (ap 4 a). we have examined this directly by a comparative rna-seq analysis of kbm-7 chronic myelogenous leukemia cells and kbm-7 cells in which the nudt2 ap 4 a hydrolase gene had been disrupted (nuko cells), causing a 175-fold increase in intracellular ap 4 a. 6,288 differentially expressed genes were identified with p < 0.05. of these, 980 were up-regulated and 705 down-regulated in nuko cells with a fold-change ≥ 2. ingenuity ® pathway analysis (ipa ® ) was used to assign these genes to known canonical pathways and functional networks. pathways associated with interferon responses, pattern recognition receptors and inflammation scored highly in the down-regulated set of genes while functions associated with mhc class ii antigens were prominent among the up-regulated genes, which otherwise showed little organization into major functional gene sets. tryptophan catabolism was also strongly down-regulated as were numerous genes known to be involved in tumor promotion in other systems, with roles in the epithelial-mesenchymal transition, proliferation, invasion and metastasis. conversely, some pro-apoptotic genes were up-regulated. major upstream factors predicted by ipa ® for gene down-regulation included nfκb, stat1/2, irf3/4 and sp1 but no major factors controlling gene up-regulation were identified. potential mechanisms for gene regulation mediated by ap 4 a and/or nudt2 disruption include binding of ap 4 a to the hint1 co-repressor, autocrine activation of purinoceptors by ap 4 a, chromatin remodeling, effects of nudt2 loss on transcript stability, and inhibition of atp-dependent regulatory factors such as protein kinases by ap 4 a. existing evidence favors the last of these as the most probable mechanism. regardless, our results suggest that the nudt2 protein could be a novel cancer chemotherapeutic target, with its inhibition potentially exerting strong anti-tumor effects via multiple pathways involving metastasis, invasion, immunosuppression and apoptosis.",0
"background the influenza rna dependent rna polymerase synthesizes viral rna in the nucleus as functional viral ribonucleoprotein (vrnp) complexes with rna and nucleoprotein (np). the n-terminus of np contains an unconventional nuclear localization signal (nls) important for initial vrnp nuclear localization but which also interacts with various host factors. methods to study the role of the n-terminus of np aside from nls function, we generated an n-terminal np deletion mutant, del20nls-np, encoding the conventional sv40 t-antigen nls in place of the first 20 amino acids of np. we characterized expression, location, and activity of del20nls-np compared to wild type np using reconstituted vrnp assays, cellular fractionation, western blotting, and reverse transcription-pcr. we assessed np nucleotide binding with gel-shift assays and analyzed np complexes using 1d blue native gel electrophoresis. results del20nls-np is expressed, localized in the nucleus and cytoplasm, and maintains ability to bind nucleic acids. despite this, del20nls-np exhibits a defect in viral rna expression exacerbated by increasing vrna template length. we find diminished del20nls-np high molecular weight complexes in protein extracts; evidence the defect is with functional vrnp formation. interestingly, the shortest template, ns vrna, exhibits a limited defect. however, this is not due to short template size, but rather activity of the ns protein(s). expression of ns1 rescues the gene expression defect primarily at the protein level, a finding consistent with the known role of ns1 as a viral mrna translational enhancer. ns1 mutant analysis confirms ns1-rna binding is not required for the translational enhancement and reveals the ns1-cpsf30 interaction surface is essential. conclusions del20nls-np is a nuclear localized np mutant able to bind nucleic acids but inefficient for assembly of functional vrnps inside the host cell. our results add to growing evidence the n-terminus of np plays important roles aside from vrnp nuclear localization. we demonstrate the utility of this partially functional np mutant to characterize the influence of additional proteins on viral gene expression. our studies reveal the ns1-cpsf30 interaction surface is required for the ability of ns1 to enhance viral protein translation, supporting a function for this ns1 domain in the cytoplasm.",0
"background one of the main goals in cancer studies including high-throughput microrna (mirna) and mrna data is to find and assess prognostic signatures capable of predicting clinical outcome. both mrna and mirna expression changes in cancer diseases are described to reflect clinical characteristics like staging and prognosis. furthermore, mirna abundance can directly affect target transcripts and translation in tumor cells. prediction models are trained to identify either mrna or mirna signatures for patient stratification. with the increasing number of microarray studies collecting mrna and mirna from the same patient cohort there is a need for statistical methods to integrate or fuse both kinds of data into one prediction model in order to find a combined signature that improves the prediction. results here, we propose a new method to fuse mirna and mrna data into one prediction model. since mirnas are known regulators of mrnas we used the correlations between them as well as the target prediction information to build a bipartite graph representing the relations between mirnas and mrnas. this graph was used to guide the feature selection in order to improve the prediction. the method is illustrated on a prostate cancer data set comprising 98 patient samples with mirna and mrna expression data. the biochemical relapse was used as clinical endpoint. it could be shown that the bipartite graph in combination with both data sets could improve prediction performance as well as the stability of the feature selection. conclusions fusion of mrna and mirna expression data into one prediction model improves clinical outcome prediction in terms of prediction error and stable feature selection. the r source code of the proposed method is available in the supplement.",1
"abstract ribosomal frameshifting on viral rnas relies on the mechanical properties of structural elements, often pseudoknots and more rarely stem-loops, that are unfolded by the ribosome during translation. in human immunodeficiency virus (hiv)-1 type b a long hairpin containing a three-nucleotide bulge is responsible for efficient frameshifting. this three-nucleotide bulge separates the hairpin in two domains: an unstable lower stem followed by a gc-rich upper stem. toeprinting and chemical probing assays suggest that a hairpin-like structure is retained when ribosomes, initially bound at the slippery sequence, were allowed multiple ef-g catalyzed translocation cycles. however, while the upper stem remains intact the lower stem readily melts. after the first, and single step of translocation of deacylated trna to the 30 s p site, movement of the mrna stem-loop in the 5′ direction is halted, which is consistent with the notion that the downstream secondary structure resists unfolding. mechanical stretching of the hairpin using optical tweezers only allows clear identification of unfolding of the upper stem at a force of 12.8 ± 1.0 pn. this suggests that the lower stem is unstable and may indeed readily unfold in the presence of a translocating ribosome.",1
"the wobble uridine of certain bacterial and mitochondrial trnas is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved mnme and gida proteins. the resulting modification (a methyluridine derivative) plays a critical role in decoding nng/a codons and reading frame maintenance during mrna translation. the lack of this trna modification produces a pleiotropic phenotype in bacteria and has been associated with mitochondrial encephalomyopathies in humans. in this work, we use in vitro and in vivo approaches to characterize the enzymatic pathway controlled by the escherichia coli mnme•gida complex. surprisingly, this complex catalyzes two different gtp- and fad-dependent reactions, which produce 5-aminomethyluridine and 5-carboxymethylamino-methyluridine using ammonium and glycine, respectively, as substrates. in both reactions, methylene-tetrahydrofolate is the most probable source to form the c5-methylene moiety, whereas nadh is dispensable in vitro unless fad levels are limiting. our results allow us to reformulate the bacterial mnme•gida dependent pathway and propose a novel mechanism for the modification reactions performed by the mnme and gida family proteins.",0
"in cattle, the corpus luteum (cl) is pivotal in maintaining early pregnancy by secreting progesterone. to establish pregnancy, the conceptus produces interferon-τ, preventing luteolysis and initiating the transformation of the cl spurium into a cl verum. although this transformation is tightly regulated, limited data are available on the expression of micrornas (mirnas) during and after this process. to address this gap, we re-analyzed previously published rna-seq data of cl from pregnant cows and regressed cl from non-pregnant cows. this analysis identified 44 differentially expressed mirnas. from this pool, three mirnas—bta-mir-222-3p, bta-mir-29c, and bta-mir-2411-3p—were randomly selected for relative quantification. using bovine ovaries (n = 14) obtained from an abattoir, total rna (including mirnas) was extracted and converted to cdna for rt-qpcr. the results revealed that bta-mir-222-3p was downregulated ( p = 0.016) in pregnant females compared to non-pregnant cows with regressed cl. however, no differences in mirna expression were observed between cl of pregnant and non-pregnant cows for bta-mir-29c ( p > 0.32) or bta-mir-2411-3p ( p > 0.60). in silico prediction approaches indicated that these mirnas are involved in pathways regulating pregnancy maintenance, such as the vegf- and foxo-signaling pathways. additionally, their biogenesis is regulated by gabpa and e2f4 transcription factors. the validation of selected mirna expression in the cl during pregnancy by rt-qpcr provides novel insights that could potentially lead to the identification of biomarkers related to cl physiology and pregnancy outcome.",1
"globally, epithelial ovarian cancer (eoc) is the most common gynecological malignancy with poor prognosis. the expression and oncogenic roles of ubiquitin specific peptidase 5 (usp5) have been reported in several cancers except eoc. in the current study, usp5 amplification was highly prevalent in patients with eoc and associated with higher mrna expression of usp5. usp5 amplification and overexpression was positively correlated with poor prognosis of patients of ovarian serous carcinomas. disruption of usp5 profoundly repressed cell proliferation by inducing cell cycle g0/g1 phase arrest in ovarian cancer cells. additionally, usp5 knockdown inhibited xenograft growth in nude mice. knockdown of usp5 decreased histone deacetylase 2 (hdac2) expression and increased p27 (an important cell cycle inhibitor) expression in vitro and in vivo. the promoting effects of usp5 overexpression on cell proliferation and cell cycle transition, as well as the inhibitory effects of usp5 overexpression on p27 expression were mediated by hdac2. moreover, usp5 interacted with hdac2, and disruption of usp5 enhanced the ubiquitination of hdac2. hdac2 protein was positively correlated usp5 protein, and negatively correlated with p27 protein in ovarian serous carcinomas tissues. collectively, our data suggest the oncogenic function of usp5 and the potential regulatory mechanisms in ovarian carcinogenesis.",0
"n6-methyladenosine (m6a) methylation, a prevalent eukaryotic post-transcriptional modification, is involved in multiple biological functions, including mediating variable splicing, rna maturation, transcription, and nuclear export, and also is vital for regulating rna translation, stability, and cytoplasmic degradation. for example, m6a methylation can regulate pre-mirna expression by affecting both splicing and maturation. non-coding rna (ncrna), which includes micrornas (mirnas), long non-coding rnas (lncrnas), and circular rnas (circrnas), does not encode proteins but has powerful impacts on transcription and translation. conversely, ncrnas may impact m6a methylation by affecting the expression of m6a regulators, including mirnas targeting mrna of m6a regulators, or lncrnas, and circrnas, acting as scaffolds to regulate transcription of m6a regulatory factors. dysregulation of m6a methylation is common in urinary tumors, and the regulatory role of ncrnas is also important for these malignancies. this article provides a systematic review of the role and mechanisms of action of m6a methylation and ncrnas in urinary tumors.",1
"background rna-seq, based on deep-sequencing techniques, has been widely employed to precisely measure levels of transcripts and their isoforms expressed under different conditions. however, robust statistical tools used to analyze these complex datasets are lacking. by grouping genes with similar expression profiles across treatments, cluster analysis provides insight into gene functions and networks that have become increasingly important. results we proposed and verified a cluster algorithm based on a skellam model for grouping genes into distinct groups based on the pattern of gene expression in response to changing conditions or in different tissues. this algorithm capitalizes on the skellam distribution to capture the count property of rna-seq data and clusters genes in different environments. a two-stage hierarchical expectation-maximization (em) algorithm was implemented to estimate the optimal number of groups and mean expression levels of each group across two environments. a procedure was formulated to test whether and how a given group shows a plastic response to environmental changes. the model was used to analyze an rna-seq dataset measured from reciprocal crosses of early arabidopsis thaliana embryos that respond differently based on the extent of maternal and paternal genome contributions, from which genes associated with maternal and paternal contributions were identified. simulation studies were also performed to validate the statistical behavior of the model. conclusions this model is a useful tool for clustering gene expression data by rna-seq, thus facilitating our understanding of gene functions and networks.",0
"proximal spinal muscular atrophy (sma) is an early onset, autosomal recessive motor neuron disease caused by loss of or mutation in smn1 ( survival motor neuron 1 ). despite understanding the genetic basis underlying this disease, it is still not known why motor neurons (mns) are selectively affected by the loss of the ubiquitously expressed smn protein. using a mouse embryonic stem cell (mesc) model for severe sma, the rna transcript profiles (transcriptomes) between control and severe sma ( smn2 +/+ ;msmn −/− ) mesc-derived mns were compared in this study using massively parallel rna sequencing (rna-seq). the mn differentiation efficiencies between control and severe sma mescs were similar. rna-seq analysis identified 3,094 upregulated and 6,964 downregulated transcripts in sma mesc-derived mns when compared against control cells. pathway and network analysis of the differentially expressed rna transcripts showed that pluripotency and cell proliferation transcripts were significantly increased in sma mns while transcripts related to neuronal development and activity were reduced. the differential expression of selected transcripts such as crabp1 , crabp2 and nkx2.2 was validated in a second mesc model for sma as well as in the spinal cords of low copy smn2 severe sma mice. furthermore, the levels of these selected transcripts were restored in high copy smn2 rescue mouse spinal cords when compared against low copy smn2 severe sma mice. these findings suggest that smn deficiency affects processes critical for normal development and maintenance of mns.",0
"abstract genetic elements encoded in nuclear dna determine the sex of an individual in many animals. in certain bivalve lineages that possess doubly uniparental inheritance (dui), mitochondrial dna (mtdna) has been hypothesized to contribute to sex determination. in these cases, females transmit a female mtdna to all offspring, while male mtdna (m mtdna) is transmitted only from fathers to sons. because m mtdna is inherited in the same way as y chromosomes, it has been hypothesized that mtdna may be responsible for sex determination. however, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in dui bivalves. in this study, we used dna, rna, and mitochondrial short noncoding rna (sncrna) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel potamilus streckersoni (bivalvia: unionida). we found that the m mtdna sheds a sncrna partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. rna-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncrnas in gene silencing. these findings support the hypothesis that m mtdna inhibits female development. genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.",1
"non-coding rna expression has shown to have cell type-specificity. the regulatory characteristics of these molecules are impacted by changes in their expression levels. we performed next-generation sequencing and examined small rna-seq data obtained from 6 different types of blood cells separated by fluorescence-activated cell sorting of severe covid−19 patients and healthy control donors. in addition to examining the behavior of pirna in the blood cells of severe sars-cov−2 infected patients, our aim was to present a distinct pirna differential expression portrait for each separate cell type. we observed that depending on the type of cell, different sorted control cells (erythrocytes, monocytes, lymphocytes, eosinophils, basophils, and neutrophils) have altering pirna expression patterns. after analyzing the expression of pirnas in each set of sorted cells from patients with severe covid−19, we observed 3 significantly elevated pirnas - pir−33,123, pir−34,765, pir−43,768 and 9 downregulated pirnas in erythrocytes. in lymphocytes, all 19 pirnas were upregulated. monocytes were presented with a larger amount of statistically significant pirna, 5 upregulated (pir−49039 pir−31623, pir−37213, pir−44721, pir−44720) and 35 downregulated. it has been previously shown that pir−31,623 has been associated with respiratory syncytial virus infection, and taking in account the major role of pirna in transposon silencing, we presume that the differential expression patterns which we observed could be a signal of indirect antiviral activity or a specific antiviral cell state. additionally, in lymphocytes, all 19 pirnas were upregulated. supplementary information the online version contains supplementary material available at 10.1186/s12920-024-01982-9.",1
"background rice is a salt-sensitive crop. complex gene regulatory cascades are likely involved in salinity stress in rice roots. microrna168 (mir168) is a conserved mirna among different plant species. it in-directly regulates the expression of all mirnas by targeting gene argonaute1(ago1). short tandem target mimic (sttm) technology is an ideal approach to study mirna functions by in-activating mature mirna in plants. results in this study, rice mir168 was inactivated by sttm. the t3 generation seedlings of sttm168 exhibited significantly enhanced salt resistance. direct target genes of rice mir168 were obtained by in silico prediction and further confirmed by degradome-sequencing. pinhead (osago1) , which was previously suggested to be a plant abiotic stress response regulator. rna-seq was performed in root samples of 150mm salt-treated sttm168 and control seedlings. among these screened 481 differentially expressed genes within sttm168 and the control, 44 abiotic stress response related genes showed significant difference, including four known salt-responsive genes. conclusion based on sequencing and qrt-pcr, a “mir168- ago1 -downstream” gene regulation model was proposed to be responsible for rice salt stress response. the present study proved mir168-ago1 cascade to play important role in rice salinity stress responding, as well as to be applied in agronomic improvement in further. supplementary information the online version contains supplementary material available at 10.1186/s12870-022-03959-1.",1
"background gametocyte carriage is essential for malaria transmission and endemicity of disease; thereby it is a target for malaria control strategies. malaria-infected individuals may harbour gametocytes below the microscopic detection threshold that can be detected by reverse transcription polymerase chain reaction (rt-pcr) targeting gametocyte-specific mrna. to date, rt-pcr has mainly been applied to the diagnosis of plasmodium falciparum gametocytes but very limited for that of plasmodium vivax. methods a multiplex-nested rt-pcr targeting pfs25 and pvs25 mrna specific to mature gametocytes of p. falciparum and p. vivax , respectively, was developed. the assay was evaluated using blood samples collected in rainy and dry seasons from febrile patients,in a malaria-endemic area in thailand. malaria diagnosis was performed by giemsa-stained blood smears and 18s rrna pcr. results the multiplex-nested rt-pcr detected pfs25 mrna in 75 of 86 (87.2%) p. falciparum -infected individuals and pvs25 mrna in 82 of 90 (91.1%) p. vivax malaria patients diagnosed by 18s rrna pcr. gametocytes were detected in 38 (eight p. falciparum and 30 p. vivax ) of 157 microscopy positive samples, implying that a large number of patients harbour sub-microscopic gametocytaemia. no seasonal differences in gametocyte carriage were observed for both malaria species diagnosed by multiplex-nested rt-pcr. with single-nested rt-pcr targeting pfs25 or pvs25 mrna as standard, the multiplex-nested rt-pcr offered sensitivities of 97.4% and 98.9% and specificities of 100% and 98.8% for diagnosing mature gametocytes of p. falciparum and p. vivax, respectively. the minimum detection limit of the multiplex-nested pcr was 10 copies of templates. conclusions the multiplex-nested rt-pcr developed herein is useful for simultaneous assessment of both p. falciparum and p. vivax gametocyte carriage that is prevalent and generally sympatric in several malaria-endemic areas outside africa.",1
"in this study, we investigated the role of ubiquitin-specific protease 22 (usp22) in the growth and progression of gastric cancer (gc). usp22 mrna and protein levels were significantly higher in gc tissue samples and gc cell lines than in adjacent noncancerous tissue samples and a normal gastric mucosal epithelial cell line (ges1), respectively. usp22 knockdown significantly decreased in vitro survival, proliferation, migration, and invasiveness of gc cells compared with the controls. western blot analysis of control and usp22-silenced gc cells showed that usp22 modulates the c-myc/nampt/sirt1-dependent foxo1 and yap signaling pathways. subcutanenous injection of usp22-silenced gc cells into scid mice generated significantly smaller xenograft tumors than did control cells. moreover, usp22-silenced gc cells showed less lung metastasis than the controls following tail vein injection in scid mice. in addition, high usp22 expression correlated positively with tumor size, advanced stage and metastasis, and correlated negatively with tumor differentiation and prognosis in gc patients. these results show that usp22 regulates growth and progression of gc via the c-myc/nampt/sirt1-dependent foxo1 and yap signaling pathways.",0
"strand-specific rna sequencing of s. pombe reveals a highly structured programme of ncrna expression at over 600 loci. functional investigations show that this extensive ncrna landscape controls the complex programme of sexual differentiation in s. pombe. the model eukaryote s. pombe features substantial numbers of ncrnas many of which are antisense regulatory transcripts (arts), ncrnas expressed on the opposing strand to coding sequences. individual arts are generated during the mitotic cycle, or at discrete stages of sexual differentiation to downregulate the levels of proteins that drive and coordinate sexual differentiation. antisense transcription occurring from events such as bidirectional transcription is not simply artefactual ‘chatter', it performs a critical role in regulating gene expression. regulation of the rna profile is a principal control driving sexual differentiation in the fission yeast schizosaccharomyces pombe. before transcription, rnai-mediated formation of heterochromatin is used to suppress expression, while post-transcription, regulation is achieved via the active stabilisation or destruction of transcripts, and through at least two distinct types of splicing control ( mata et al, 2002 ; shimoseki and shimoda, 2001 ; averbeck et al, 2005 ; mata and bähler, 2006 ; xue-franzen et al, 2006 ; moldon et al, 2008 ; djupedal et al, 2009 ; amorim et al, 2010 ; grewal, 2010 ; cremona et al, 2011 ). around 94% of the s. pombe genome is transcribed ( wilhelm et al, 2008 ). while many of these transcripts encode proteins ( wood et al, 2002 ; bitton et al, 2011 ), the majority have no known function. we used a strand-specific protocol to sequence total rna extracts taken from vegetatively growing cells, and at different points during a time course of sexual differentiation. the resulting data redefined existing gene coordinates and identified additional transcribed loci. the frequency of reads at each of these was used to monitor transcript abundance. transcript levels at 6599 loci changed in at least one sample (g-statistic; false discovery rate <5%). 4231 (72.3%), of which 4011 map to protein-coding genes, while 809 loci were antisense to a known gene. comparisons between haploid and diploid strains identified changes in transcript levels at over 1000 loci. at 354 loci, greater antisense abundance was observed relative to sense, in at least one sample (putative antisense regulatory transcripts—arts). since antisense mechanisms are known to modulate sense transcript expression through a variety of inhibitory mechanisms ( faghihi and wahlestedt, 2009 ), we postulated that the waves of antisense expression activated at different stages during meiosis might be regulating protein expression. to ask whether transcription factors that drive sense-transcript levels influenced art production, we performed rna-seq of a pat1.114 diploid meiosis in the absence of the transcription factors atf21 and atf31 (responsible for late meiotic transcription; mata et al, 2002 ). transcript levels at 185 ncrna loci showed significant changes in the knockout backgrounds. although meiotic progression is largely unaffected by removal of atf21 and atf31, viability of the resulting spores was significantly diminished, indicating that atf21- and atf31-mediated events are critical to efficient sexual differentiation. if changes to relative antisense/sense transcript levels during a particular phase of sexual differentiation were to regulate protein expression, then the continued presence of the antisense at points in the differentiation programme where it would normally be absent should abolish protein function during this phase. we tested this hypothesis at four loci representing the three means of antisense production: convergent gene expression, improper termination and nascent transcription from an independent locus. induction of the natural antisense transcripts that opposed spo4 + , spo6 + and dis1 + ( figures 3 and 7 ) in trans from a heterologous locus phenocopied a loss of function of the target protein. art overexpression decreased dis1 protein levels. antisense transcription opposing spk1 + originated from improper termination of the sense ups1 + transcript on the opposite strand ( figure 3b , left locus). expression of either the natural full-length ups1 + transcript or a truncated version, restricted to the portion of ups1 + overlapping spk1 + ( figure 3 , orange transcripts) in trans from a heterologous locus phenocopied the spk1. δ differentiation deficiency. convergent transcription from a neighbouring gene on the opposing strand is, therefore, an effective mechanism to generate rnai-mediated (below) silencing in fission yeast. further analysis of the data revealed, for many loci, substantial changes in utr length over the course of meiosis, suggesting that utr dynamics may have an active role in regulating gene expression by controlling the transcriptional overlap between convergent adjacent gene pairs. the rnai machinery ( grewal, 2010 ) was required for antisense suppression at each of the dis1, spk1 , spo4 and spo6 loci, as antisense to each locus had no impact in ago1. δ, dcr1. δ and rdp1. δ backgrounds. we conclude that rnai control has a key role in maintaining the fidelity of sexual differentiation in fission yeast. the histone h3 methyl transferase clr4 was required for antisense control from a heterologous locus. thus, a significant portion of the impact of ncrna upon sexual differentiation arises from antisense gene silencing. importantly, in contrast to the extensively characterised ability of the rnai machinery to operate in cis at a target locus in s. pombe ( grewal, 2010 ), each case of gene silencing generated here could be achieved in trans by expression of the antisense transcript from a single heterologous locus elsewhere in the genome. integration of an antibiotic marker gene immediately downstream of the dis1 + locus instigated antisense control in an orientation-dependent manner. pcr-based gene tagging approaches are widely used to fuse the coding sequences of epitope or protein tags to a gene of interest. not only do these tagging approaches disrupt normal 3′utr controls, but the insertion of a heterologous marker gene immediately downstream of an orf can clearly have a significant impact upon transcriptional control of the resulting fusion protein. thus, pcr tagging approaches can no longer be viewed as benign manipulations of a locus that only result in the production of a tagged protein product. repression of dis1 function by gene deletion or antisense control revealed a key role this conserved microtubule regulator in driving the horsetail nuclear migrations that promote recombination during meiotic prophase. non-coding transcripts have often been viewed as simple ‘chatter', maintained solely because evolutionary pressures have not been strong enough to force their elimination from the system. our data show that phenomena such as improper termination and bidirectional transcription are not simply interesting artifacts arising from the complexities of transcription or genome history, but have a critical role in regulating gene expression in the current genome. given the widespread use of rnai, it is reasonable to anticipate that future analyses will establish arts to have equal importance in other organisms, including vertebrates. these data highlight the need to modify our concept of a gene from that of a spatially distinct locus. this view is becoming increasingly untenable. not only are the 5′ and 3′ ends of many genes indistinct, but that this lack of a hard and fast boundary is actively used by cells to control the transcription of adjacent and overlapping loci, and thus to regulate critical events in the life of a cell. strand-specific rna sequencing of s. pombe revealed a highly structured programme of ncrna expression at over 600 loci. waves of antisense transcription accompanied sexual differentiation. a substantial proportion of ncrna arose from mechanisms previously considered to be largely artefactual, including improper 3′ termination and bidirectional transcription. constitutive induction of the entire spk1 + , spo4 + , dis1 + and spo6 + antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. this ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. consistently, insertion of a marker gene adjacent to the dis1 + antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent ‘horsetail' stage of meiosis. antisense production had no impact at any of these loci when the rna interference (rnai) machinery was removed. thus, far from being simply ‘genome chatter', this extensive ncrna landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in s. pombe.",1
"micrornas (mirnas) are ubiquitously expressed small non-coding rnas that, in most cases, negatively regulate gene expression at the post-transcriptional level. mirnas are involved in fine-tuning fundamental cellular processes such as proliferation, cell death and cell cycle control and are believed to confer robustness to biological responses. here, we investigated simultaneously the transcriptional changes of mirna and mrna expression levels over time after activation of the janus kinase/signal transducer and activator of transcription (jak/stat) pathway by interferon-γ stimulation of melanoma cells. to examine global mirna and mrna expression patterns, time-series microarray data were analysed. we observed delayed responses of mirnas (after 24–48 h) with respect to mrnas (12–24 h) and identified biological functions involved at each step of the cellular response. inference of the upstream regulators allowed for identification of transcriptional regulators involved in cellular reactions to interferon-γ stimulation. linking expression profiles of transcriptional regulators and mirnas with their annotated functions, we demonstrate the dynamic interplay of mirnas and upstream regulators with biological functions. finally, our data revealed network motifs in the form of feed-forward loops involving transcriptional regulators, mrnas and mirnas. additional information obtained from integrating time-series mrna and mirna data may represent an important step towards understanding the regulatory principles of gene expression.",1
"the tumor microenvironment is emerging as a key regulator of cancer growth and progression, however the exact mechanisms of interaction with the tumor are poorly understood. whilst the majority of genomic profiling efforts thus far have focused on the tumor, here we investigate rna-seq as a hypothesis-free tool to generate independent tumor and stromal biomarkers, and explore tumor-stroma interactions by exploiting the human-murine compartment specificity of patient-derived xenografts (pdx). across a pan-cancer cohort of 79 pdx models, we determine that mouse stroma can be separated into distinct clusters, each corresponding to a specific stromal cell type. this implies heterogeneous recruitment of mouse stroma to the xenograft independent of tumor type. we then generate cross-species expression networks to recapitulate a known association between tumor epithelial cells and fibroblast activation, and propose a potentially novel relationship between two hypoxia-associated genes, human mif and mouse ddx6. assessment of disease subtype also reveals mmp12 as a putative stromal marker of triple-negative breast cancer. finally, we establish that our ability to dissect recruited stroma from trans-differentiated tumor cells is crucial to identifying stem-like poor-prognosis signatures in the tumor compartment. in conclusion, rna-seq is a powerful, cost-effective solution to global analysis of human tumor and mouse stroma simultaneously, providing new insights into mouse stromal heterogeneity and compartment-specific disease markers that are otherwise overlooked by alternative technologies. the study represents the first comprehensive analysis of its kind across multiple pdx models, and supports adoption of the approach in pre-clinical drug efficacy studies, and compartment-specific biomarker discovery.",0
"state-of-the-art rare variant association testing methods aggregate the contribution of rare variants in biologically relevant genomic regions to boost statistical power. however, testing single genes separately does not consider the complex interaction landscape of genes, nor the downstream effects of non-synonymous variants on protein structure and function. here we present the network propagation-based assessment of genetic events (netpage), an integrative approach aimed at investigating the biological pathways through which rare variation results in complex disease phenotypes. we applied netpage to sporadic, late-onset alzheimer’s disease (ad), using whole-genome sequencing from the ad neuroimaging initiative (adni) cohort, as well as whole-exome sequencing from the ad sequencing project (adsp). netpage is based on network propagation, a framework that models information flow on a graph and simulates the percolation of genetic variation through tissue-specific gene interaction networks. the result of network propagation is a set of smoothed gene scores that can be tested for association with disease status through sparse regression. the application of netpage to ad enabled the identification of a set of connected genes whose smoothed variation profile was robustly associated to case-control status, based on gene interactions in the hippocampus. additionally, smoothed scores significantly correlated with risk of conversion to ad in mild cognitive impairment (mci) subjects. lastly, we investigated tissue-specific transcriptional dysregulation of the core genes in two independent rna-seq datasets, as well as significant enrichments in terms of gene sets with known connections to ad. we present a framework that enables enhanced genetic association testing for a wide range of traits, diseases, and sample sizes.",0
"the chromosomal passenger complex (cpc) is a key regulator of eukaryotic cell division, consisting of the protein kinase aurora b/ ipl1 in association with its activator (incenp/ sli15 ) and two additional proteins (survivin/ bir1 and borealin/ nbl1 ). here, we report a genome-wide genetic interaction screen in saccharomyces cerevisiae using the bir1 -17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. gene knockouts affecting the ctf19 kinetochore complex were identified as the strongest enhancers of bir1 -17 , while mutations affecting the large ribosomal subunit or the mrna nonsense-mediated decay pathway caused strong phenotypic suppression. thus, cells lacking a functional ctf19 complex become highly dependent on bir1 function and vice versa. the negative genetic interaction profiles of bir1 -17 and the cohesin mutant mcd1 -1 showed considerable overlap, underlining the strong functional connection between sister chromatid cohesion and chromosome biorientation. loss of some ctf19 components, such as iml3 or chl4 , impacted differentially on bir1 -17 compared with mutations affecting other cpc components: despite the synthetic lethality shown by either iml3 ∆ or chl4 ∆ in combination with bir1 -17 , neither gene knockout showed any genetic interaction with either ipl1 -321 or sli15 -3. our data therefore imply a specific functional connection between the ctf19 complex and bir1 that is not shared with ipl1.",0
"transcriptomics technologies are the techniques used to study an organism’s transcriptome , the sum of all of its rna transcripts. the information content of an organism is recorded in the dna of its genome and expressed through transcription. here, mrna serves as a transient intermediary molecule in the information network, whilst noncoding rnas perform additional diverse functions. a transcriptome captures a snapshot in time of the total transcripts present in a cell. the first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. transcriptomics has been defined by repeated technological innovations that transform the field. there are two key contemporary techniques in the field: microarrays , which quantify a set of predetermined sequences, and rna sequencing ( rna-seq ), which uses high-throughput sequencing to capture all sequences. measuring the expression of an organism’s genes in different tissues , conditions , or time points gives information on how genes are regulated and reveals details of an organism’s biology. it can also help to infer the functions of previously unannotated genes. transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. an analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.",1
"proton therapy allows to avoid excess radiation dose on normal tissues. however, there are some limitations. indeed, passive delivery of proton beams results in an increase in the lateral dose upstream of the tumor and active scanning leads to strong differences in dose delivery. this study aims to assess possible differences in the transcriptomic response of skin in c57bl/6 mice after tbi irradiation by active or passive proton beams at the dose of 6 gy compared to unirradiated mice. in that purpose, total rna was extracted from skin samples 3 months after irradiation and rna-seq was performed. results showed that active and passive delivery lead to completely different transcription profiles. indeed, 140 and 167 genes were differentially expressed after active and passive scanning compared to unirradiated, respectively, with only one common gene corresponding to riken cdna 9930021j03. moreover, protein–protein interactions performed by string analysis showed that 31 and 25 genes are functionally related after active and passive delivery, respectively, with no common gene between both types of proton delivery. analysis showed that active scanning led to the regulation of genes involved in skin development which was not the case with passive delivery. moreover, 14 ncrna were differentially regulated after active scanning against none for passive delivery. active scanning led to 49 potential mrna-ncrna pairs with one ncrna mainly involved, gm44383 which is a mirna. the 43 genes potentially regulated by the mirna gm44393 confirmed an important role of active scanning on skin keratin pathway. our results demonstrated that there are differences in skin gene expression still 3 months after proton irradiation versus unirradiated mouse skin. and strong differences do exist in late skin gene expression between scattered or scanned proton beams. further investigations are strongly needed to understand this discrepancy and to improve treatments by proton therapy.",1
"sam-pointed domain-containing ets transcription factor (spdef) is expressed in normal prostate epithelium. while its expression changes during prostate carcinogenesis (pca), the role of spdef in prostate cancer remains controversial due to the lack of genetic mouse models. in present study, we generated transgenic mice with the loss- or gain-of-function of spdef in prostate epithelium to demonstrate that spdef functions as tumor suppressor in prostate cancer. loss of spdef increased cancer progression and tumor cell proliferation, whereas over-expression of spdef in prostate epithelium inhibited carcinogenesis and reduced tumor cell proliferation in vivo and in vitro. transgenic over-expression of spdef inhibited mrna and protein levels of foxm1, a transcription factor critical for tumor cell proliferation, and reduced expression of foxm1 target genes, including cdc25b , cyclin b1 , cyclin a2, plk-1, aurorab, cks1 and topo2alpha. deletion of spdef in transgenic mice and cultures prostate tumor cells increased expression of foxm1 and its target genes. furthermore, an inverse correlation between spdef and foxm1 levels was found in human prostate cancers. the two-gene signature of low spdef and high foxm1 predicted poor survival in prostate cancer patients. mechanistically, spdef bound to, and inhibited transcriptional activity of foxm1 promoter by interfering with the ability of foxm1 to activate its own promoter through auto-regulatory site located in the −745/−660 bp foxm1 promoter region. re-expression of foxm1 restored cellular proliferation in the spdef-positive cancer cells and rescued progression of spdef-positive tumors in mouse prostates. altogether, spdef inhibits prostate carcinogenesis by preventing foxm1-regulated proliferation of prostate tumor cells. the present study identified novel crosstalk between spdef tumor suppressor and foxm1 oncogene and demonstrated that this crosstalk is required for tumor cell proliferation during progression of prostate cancer in vivo.",0
"background deregulated mirna expression plays a crucial role in carcinogenesis. recent studies show different mechanisms leading to mirna deregulation in cancer; however, alterations affecting mirnas by dna copy number variations (cnv) remain poorly studied. results our integrative analysis including data from high resolution snps arrays, mrna expression arrays, and mirnas expression profiles in 16 myeloid cell lines highlights that cnv are alternative mechanisms to deregulate the expression of mirnas in acute myeloid leukemia (aml), and represent a novel approach to identify novel candidate genes involved in aml. we found association between the expression levels of 19 mirnas and cnvs affecting their loci. functional analysis showed that nf1 is a direct target of mir-370, and that overexpression of mir-370 has similar effects that nf1 inactivation, increasing proliferation and colony formation in aml cells. moreover, real time rt-pcr showed that nf1 downregulation is a recurrent event in aml (30.8%), and western blot analysis confirmed this result. mir-370 overexpression and deletions affecting the nf1 locus were identified as alternative mechanisms to downregulate nf1. conclusions nf1 downregulation is a common event in aml, and both deletions in the nf1 locus and overexpression of mir-370 are alternative mechanisms to downregulate nf1 in this disease. our results suggest a leukemogenic role of mir-370 through nf1 downregulation in aml cells. since nf1 deficiency leads to ras activation, patients with aml and overexpression of mir-370 may potentially benefit from additional treatment with either ras or mtor inhibitors.",1
"background: glioblastoma is the most common type of malignant brain tumor. bioinformatics technology and structure biology were effectively and systematically used to identify specific targets in malignant tumors and screen potential drugs. results: gbm patients have higher aurka and kdr mrna expression compared with normal samples. then, we identified a small molecular compound, enmd-2076, could effectively inhibit aurora kinase a and vegfr-2 (encoded by kdr) activities. enmd-2076 is predicted without toxic properties and also has absorption and gratifying brain/blood barrier penetration ability. further results demonstrated that enmd-2076 could significantly inhibit gbm cell lines proliferation and vitality, it also suppressed gbm cells migration and invasion. enmd-2076 induced glioblastoma cell cycle arrest in g2-m phase and apoptosis by inhibiting pi3k/akt/mtor signaling pathways. additionally, enmd-2076 prolonged the median survival time of tumor-bearing rats and restrained growth rate of tumor volume in vivo. conclusions: our findings reveal that enmd-2076 is a promising drug in dealing with glioblastoma and have a perspective application. methods: we show that aurka and kdr genes are hub driver genes in glioblastoma with bioinformatics technology including wgcna analysis, ppi network, go, kegg analysis and gsea analysis. after identifying a compound via virtual screening analysis, further experiments were carried out to examine the anti-glioblastoma activities of the compound in vivo and in vitro.",0
"long-tailed pygmy rice rats ( oligoryzomys longicaudatus ) are principal reservoir hosts of andes virus (andv) ( bunyaviridae ), which causes most hantavirus cardiopulmonary syndrome cases in the americas. to develop tools for the study of the andv-host interactions, we used rna-seq to generate a de novo transcriptome assembly. splenic rna from five rice rats captured in chile, three of which were andv-infected, was used to generate an assembly of 66,173 annotated transcripts, including noncoding rnas. phylogenetic analysis of selected predicted proteins showed similarities to those of the north american deer mouse ( peromyscus maniculatus ), the principal reservoir of sin nombre virus (snv). one of the infected rice rats had about 50-fold more viral burden than the others, suggesting acute infection, whereas the remaining two had levels consistent with persistence. differential expression analysis revealed distinct signatures among the infected rodents. the differences could be due to 1) variations in viral load, 2) dimorphic or reproductive differences in splenic homing of immune cells, or 3) factors of unknown etiology. in the two persistently infected rice rats, suppression of the jak-stat pathway at stat5b and ccnot1 , elevation of casp1 , rig-i pathway factors ppp1cc and mff , and increased fc receptor-like transcripts occurred. caspase-1 and stat5b activation pathways have been shown to stimulate t helper follicular cell (t fh ) development in other species. these data are also consistent with reports suggestive of t fh stimulation in deer mice experimentally infected with hantaviruses. in the remaining acutely infected rice rat, the apoptotic pathway marker cox6a1 was elevated, and putative anti-viral factors abcb1a , fam46c , spp1 , rxra , rxrb , trmp2 and trim58 were modulated. transcripts for preproenkephalin ( prenk ) were reduced, which may be predictive of an increased t cell activation threshold. taken together, this transcriptome dataset will permit rigorous examination of rice rat-andv interactions and may lead to better understanding of virus ecology.",1
"a major objective of systems biology is to quantitatively integrate multiple parameters from genome-wide measurements. to integrate gene expression with dynamics in poly(a) tail length and adenylation site, we developed a targeted next-generation sequencing approach, p oly( a )- t est rna- seq uencing. pat-seq returns (i) digital gene expression, (ii) polyadenylation site/s, and (iii) the polyadenylation-state within and between eukaryotic transcriptomes. pat-seq differs from previous 3′ focused rna-seq methods in that it depends strictly on 3′ adenylation within total rna samples and that the full-native poly(a) tail is included in the sequencing libraries. here, total rna samples from budding yeast cells were analyzed to identify the intersect between adenylation state and gene expression in response to loss of the major cytoplasmic deadenylase ccr4. furthermore, concordant changes to gene expression and adenylation-state were demonstrated in the classic crabtree–warburg metabolic shift. because all polyadenylated rna is interrogated by the approach, alternative adenylation sites, noncoding rna and rna-decay intermediates were also identified. most important, the pat-seq approach uses standard sequencing procedures, supports significant multiplexing, and thus replication and rigorous statistical analyses can for the first time be brought to the measure of 3′-utr dynamics genome wide.",0
"background fetal growth restriction (fgr) is an important but poorly understood condition of pregnancy, which results in significant fetal, neonatal and long-term morbidity and mortality. novel research has suggested that altered mirna expression in the plasma and placenta is associated with adverse pregnancy. we hypothesized that aberrant expression of microrna-141 (mir-141) in the placenta is associated with fgr. additionally, expression levels of predicted target genes of mir-141 were also analyzed in placental tissues of fgr and normal controls. methodology/principal findings using quantitative real time pcr, we analyzed the expression level of mir-141 and its target genes in placentas of fgr pregnancies (n = 21) and normal controls (n = 34). western blot was used to detect the protein expression level of the target genes of mir-141. mir-141 showed significant up regulation in fgr and significant down regulation of its targets, i.e. e2f transcription factor 3 (e2f3) protein, pleiomorphic adenoma gene 1 (plag1) mrna and protein. moreover, a positive correlation was found between plag1 and insulin-like growth factor 2 ( igf2 ) expression levels (spearman r = 0.56, p <0.0001). mir-141 yields an auc of 0.83 with 88.5% sensitivity and 71.7% specificity for separating fgr from normal controls. this study indicates that mir-141 may be diagnostically important in fgr. conclusions/significance our results indicate that aberrant high expression level of mir-141 might play important roles in the pathogenesis of fgr by suppressing e2f3 and plag1. we propose that mir-141 may participate in a mir-141-plag1-igf2 network relating to fgr development. these findings may provide new targets via mir-141 in diagnosis and therapy of fgr in the future.",1
"recent studies have uncovered that noncoding sequence variants may relate to axenfeld-rieger syndrome (ars), a rare developmental anomaly with genetic heterogeneity. however, how these genomic regions are functionally and structurally associated with ars is still unclear. in this study, we performed genome-wide linkage analysis and whole-genome sequencing in a chinese family with ars and identified a heterozygous deletion of about 570 kb (termed loh-1) in the intergenic sequence between paired-like homeodomain transcription factor 2 ( pitx2 ) and family with sequence similarity 241 member a. knockout of loh-1 homologous sequences caused ars phenotypes in mice. rna-seq and real-time quantitative pcr revealed a significant reduction in pitx2 gene expression in loh-1 –/– mice, while forkhead box c1 expression remained unchanged. chip-seq and bioinformatics analysis identified a potential enhancer region (loh-e1) within loh-1. deletion of loh-e1 led to a substantial downregulation of the pitx2 gene. mechanistically, we found a sequence (hg38 chr4:111,399,594–111,399,691) that is on loh-e1 could regulate pitx2 by binding to rad21, a critical component of the cohesin complex. knockdown of rad21 resulted in reduced pitx2 expression. collectively, our findings indicate that a potential enhancer sequence that is within loh-1 may regulate pitx2 expression remotely through cohesin-mediated loop domains, leading to ars when absent. a potential enhancer sequence within loh-1 regulates pitx2 expression remotely through cohesin-mediated loop domains, and loss of the enhancer may lead to axenfeld-rieger syndrome.",1
"ewing sarcoma (es) is a highly aggressive pediatric cancer that may arise from neuronal precursors. neurotrophins stimulate neuronal devlopment and plasticity. here, we found that neurotrophins nerve growth factor (ngf) and brain-derived neurotrophic factor (bdnf), as well as their receptors (trka and trkb, respectively) are expressed in es tumors. treatment with trka (gw-441756) or trkb (ana-12) selective inhibitors decreased es cell proliferation, and the effect was increased when the two inhibitors were combined. es cells treated with a pan-trk inhibitor, k252a, showed changes in morphology, reduced levels of β-iii tubulin, and decreased mrna expression of ngf, bdnf, trka and trkb. furthermore, combining k252a with subeffective doses of cytotoxic chemotherapeutic drugs resulted in a decrease in es cell proliferation and colony formation, even in chemoresistant cells. these results indicate that trk inhibition may be an emerging approach for the treatment of es.",0
"differential rna localization and local protein synthesis regulate synapse function and plasticity in neurons. micrornas are a conserved class of regulatory rnas that control mrna stability and translation in tissues. they are abundant in the brain but the extent into which they are involved in synaptic mrna regulation is poorly known. herein, a computational analysis of the coding and 3′utr regions of 242 presynaptic and 304 postsynaptic proteins revealed that 91% of them are predicted to be microrna targets. analysis of the longest 3′utr isoform of synaptic transcripts showed that presynaptic mrnas have significantly longer 3′utr than control and postsynaptic mrnas. in contrast, the shortest 3′utr isoform of postsynaptic mrnas is significantly shorter than control and presynaptic mrnas, indicating they avert microrna regulation under specific conditions. examination of microrna binding site density of synaptic 3′utrs revealed that they are twice as dense as the rest of protein-coding transcripts and that approximately 50% of synaptic transcripts are predicted to have more than five different microrna sites. an interaction map exploring the association of micrornas and their targets revealed that a small set of ten micrornas is predicted to regulate 77% and 80% of presynaptic and postsynaptic transcripts, respectively. intriguingly, many of these micrornas have yet to be identified outside primate mammals, implicating them in cognition differences observed between high-level primates and non-primate mammals. importantly, the identified mirnas have been previously associated with psychotic disorders that are characterized by neural circuitry dysfunction, such as schizophrenia. finally, molecular dissection of their kegg pathways showed enrichment for neuronal and synaptic processes. adding on current knowledge, this investigation revealed the extent of mirna regulation at the synapse and predicted critical micrornas that would aid future research on the control of neuronal plasticity and etiology of psychiatric diseases.",1
"background the transcription factor sox11 is one of members of the sry box-containing (sox) family emerging as important transcriptional regulators. in recent years, up-regulation of sox11 has been detected in various types of solid tumors. in this study, the effects of promoter methylation of the sox11 gene on sox11 expression and cell growth and invasion of nasopharyngeal carcinoma were investigated. methods in this study,methylation-specific pcr and real time quantitative pcr have been applied to investigate the effect of promoter methylation of the sox11 gene on sox11 expression in the nasopharyngeal carcinoma and chronic inflammation tissues. the nasopharyngeal carcinoma cell line (cne2) was treated with 5-aza-2'-deoxycytidine. the effect of promoter methylation of sox11 on growth and invasion of nasopharyngeal carcinoma cells was detected with mtt test and boyden chamber matrigel invasion assay. results no or weak expression of sox11 mrna was detected in the nasopharyngeal carcinoma tissues of sox11 gene promoter methylation. strong expression of sox11 mrna was detected in the nasopharyngeal carcinoma tissues of sox11 gene promoter unmethylation and chronic inflammation tissues of pharynx nasalis. sox11 mrna and protein were re-expressed, sox11 gene was demethylated, and growth and invasion of cells were inhibited in cne2 cell line after 5-aza-2'-deoxycytidine treatment. conclusions the results of the study indicate that expression of sox11 mrna and protein were related to sox11 gene methylation status. sox11 gene methylation may be plays a role in growth and invasion of nasopharyngeal carcinoma cells.",0
"in mice, zygotic activation occurs for a wide variety of genes, mainly at the 2-cell stage. long noncoding rnas (lncrnas) are increasingly being recognized as modulators of gene expression. in this study, directional rna-seq of mii oocytes and 2-cell embryos identified more than 1000 divergently transcribed lncrna/mrna gene pairs. expression of these bidirectional promoter-associated noncoding rnas (pancrnas) was strongly associated with the upregulation of their cognate genes. conversely, knockdown of three abundant pancrnas led to reduced mrna expression, accompanied by sustained dna methylation even in the presence of enzymes responsible for dna demethylation. in particular, microinjection of sirna against the abundant pancrna partner of interleukin 17d ( il17d ) mrna at the 1-cell stage caused embryonic lethality, which was rescued by supplying il17d protein in vitro at the 4-cell stage. thus, this novel class of lncrnas can modulate the transcription machinery in cis to activate zygotic genes and is important for preimplantation development.",1
"micrornas (mirnas) comprise a gene-regulatory network through sequence complementarity with target mrnas. previous studies have shown that mammalian mirnas decrease many target mrna levels and reduce protein production predominantly by target mrna destabilization. however, it has not yet been fully assessed whether this scheme is widely applicable to more realistic conditions with multiple mirna fluctuations. by combining two analytical frameworks for detecting the enrichment of gene sets, gene set enrichment analysis (gsea) and functional assignment of mirnas via enrichment (fame), we developed gsea–fame analysis (gfa), which enables the prediction of mirna activities from mrna expression data using rank-based enrichment analysis and weighted evaluation of mirna–mrna interactions. this cooperative approach delineated a better widespread correlation between mirna expression levels and predicted mirna activities in cancer transcriptomes, thereby providing proof-of-concept of the mrna-destabilization scenario. in an integrative analysis of the cancer genome atlas (tcga) multidimensional data including profiles of both mrna and mirna, we also showed that gfa-based inference of mirna activity could be used for the selection of prognostic mirnas in the development of cancer survival prediction models. this approach proposes a next-generation strategy for the interpretation of mirna function and identification of target mirnas as biomarkers and therapeutic targets.",1
"background hemorrhagic stroke is a devastating cerebrovascular event with a high rate of early mortality and long-term disability. the therapeutic potential of mesenchymal stem cell-derived extracellular vesicles (msc-evs) for neurological conditions, such as intracerebral hemorrhage (ich), has garnered considerable interest, has garnered considerable interest, though their mechanisms of action remain poorly understood. methods evs were isolated from human umbilical cord mscs, and spect/ct was used to track the 99m tc-labeled evs in a mouse model of ich. a series of comprehensive evaluations, including magnetic resonance imaging (mri), histological study, rna sequencing (rna-seq), or mirna microarray, were performed to investigate the therapeutic action and mechanisms of msc-evs in both cellular and animal models of ich. results our findings show that intravenous injection of msc-evs exhibits a marked affinity for the ich-affected brain regions and cortical neurons. ev infusion alleviates the pathological changes observed in mri due to ich and reduces damage to ipsilateral cortical neurons. rna-seq analysis reveals that ev treatment modulates key pathways involved in the neuronal system and metal ion transport in mice subjected to ich. these data were supported by the attenuation of neuronal ferroptosis in neurons treated with hemin and in ich mice following ev therapy. additionally, mirna microarray analysis depicted the ev-mirnas targeting genes associated with ferroptosis, and mir-214-3p was identified as a regulator of neuronal ferroptosis in the ich cellular model. conclusions msc-evs offer neuroprotective effects against ich-induced neuronal damage by modulating ferroptosis highlighting their therapeutic potential for combating neuronal ferroptosis in brain disorders. supplementary information the online version contains supplementary material available at 10.1186/s13287-024-03879-x.",1
"in recent decades, mirna has been reported as a crucial modulator in some biology progressions. this work aims to assess the expression and role of mir-let-7a and pyruvate kinase muscle isozyme m2 (pkm2) in cc tissues and cell lines. here, we identified that mir-let-7a expression was decreased in cc tissues, and siha and hela cells (all p < 0.001), however, pkm2 expression was increased in these samples. statistically, mir-let-7a was inversely associated with pkm2 mrna or protein ( p = 0.013, p = 0.015, respectively). in-vitro assays revealed that ectopic mir-let-7a expression repressed siha and hela cell proliferation, migration and invasion, and enhanced siha and hela cell apoptosis. furthermore, luciferase reporter assays revealed the 3′-utr of pkm2 was identified a target of mir-let-7a, by which mir-let-7a affected the expression of pkm2 in siha and hela cells. besides, pkm2 plasmids partially abrogated the inhibitory effects of mir-let-7a, while si-pkm2 enhanced the inhibitory effects of mir-let-7a. in vivo , mir-let-7a mimics indeed repressed tumor growth in mice xenograft model. in conclusion, our results demonstrated that mir-let-7a inhibits cell proliferation, migration and invasion by down-regulation of pkm2 in cervical cancer. mir-let-7a/pkm2 pathway may be a useful therapeutic target for cc patients.",1
"during conditions of nutrient limitation bacteria undergo a series of global gene expression changes to survive conditions of amino acid and fatty acid starvation. rapid reallocation of cellular resources is brought about by gene expression changes coordinated by the signalling nucleotides' guanosine tetraphosphate or pentaphosphate, collectively termed (p)ppgpp and is known as the stringent response. the stringent response has been implicated in bacterial virulence, with elevated (p)ppgpp levels being associated with increased virulence gene expression. this has been observed in the highly pathogenic francisella tularensis sub spp. tularensis schu s4, the causative agent of tularaemia. here, we aimed to artificially induce the stringent response by culturing f. tularensis in the presence of the amino acid analogue l -serine hydroxamate. serine hydroxamate competitively inhibits trna ser aminoacylation, causing an accumulation of uncharged trna. the uncharged trna enters the a site on the translating bacterial ribosome and causes ribosome stalling, in turn stimulating the production of (p)ppgpp and activation of the stringent response. using the essential virulence gene iglc , which is encoded on the francisella pathogenicity island (fpi) as a marker of active stringent response, we optimized the culture conditions required for the investigation of virulence gene expression under conditions of nutrient limitation. we subsequently used whole genome rna-seq to show how f. tularensis alters gene expression on a global scale during active stringent response. key findings included up-regulation of genes involved in virulence, stress responses and metabolism, and down-regulation of genes involved in metabolite transport and cell division. f. tularensis is a highly virulent intracellular pathogen capable of causing debilitating or fatal disease at extremely low infectious doses. however, virulence mechanisms are still poorly understood. the stringent response is widely recognized as a diverse and complex bacterial stress response implicated in virulence. this work describes the global gene expression profile of f. tularensis schu s4 under active stringent response for the first time. herein we provide evidence for an association of active stringent response with fpi virulence gene expression. our results further the understanding of the molecular basis of virulence and regulation thereof in f. tularensis. these results also support research into genes involved in (p)ppgpp production and polyphosphate biosynthesis and their applicability as targets for novel antimicrobials.",1
"for over 130 years, invasive pneumococcal disease has been associated with the presence of extracellular planktonic pneumococci, i.e. diplococci or short chains in affected tissues. herein, we show that streptococcus pneumoniae that invade the myocardium instead replicate within cellular vesicles and transition into non-purulent biofilms. pneumococci within mature cardiac microlesions exhibited salient biofilm features including intrinsic resistance to antibiotic killing and the presence of an extracellular matrix. dual rna-seq and subsequent principal component analyses of heart- and blood-isolated pneumococci confirmed the biofilm phenotype in vivo and revealed stark anatomical site-specific differences in virulence gene expression; the latter having major implications on future vaccine antigen selection. our rna-seq approach also identified three genomic islands as exclusively expressed in vivo. deletion of one such island, region of diversity 12, resulted in a biofilm-deficient and highly inflammogenic phenotype within the heart; indicating a possible link between the biofilm phenotype and a dampened host-response. we subsequently determined that biofilm pneumococci released greater amounts of the toxin pneumolysin than did planktonic or rd12 deficient pneumococci. this allowed heart-invaded wildtype pneumococci to kill resident cardiac macrophages and subsequently subvert cytokine/chemokine production and neutrophil infiltration into the myocardium. this is the first report for pneumococcal biofilm formation in an invasive disease setting. we show that biofilm pneumococci actively suppress the host response through pneumolysin-mediated immune cell killing. as such, our findings contradict the emerging notion that biofilm pneumococci are passively immunoquiescent.",0
"basal-like breast cancer (blbc) is an aggressive and deadly subtype of human breast cancer that is highly metastatic, displays stem-cell like features, and has limited treatment options. therefore, developing and characterizing preclinical mouse models with tumors that resemble blbc is important for human therapeutic development. atf3 is a potent oncogene that is aberrantly expressed in most human breast cancers. in the bk5.atf3 mouse model, overexpression of atf3 in the basal epithelial cells of the mammary gland produces tumors that are characterized by activation of the wnt/β-catenin signaling pathway. here, we used rna-seq and microrna (mirna) microarrays to better define the molecular features of bk5.atf3-derived mammary tumors. these analyses showed that these tumors share many characteristics of human blbc including reduced expression of rb1 , esr1 , and pgr and increased expression of erbb2 , egfr , and the genes encoding keratins 5, 6, and 17. an analysis of mirna expression revealed reduced levels of mir145 and mir143 , leading to the upregulation of their target genes including both the pluripotency factors klf4 and sox2 as well as the cancer stem-cell-related gene kras. finally, we show through knock-down experiments that atf3 may directly modulate mir145/143 expression. taken together, our results indicate that the atf3 mouse mammary tumor model could provide a powerful model to define the molecular mechanisms leading to blbc, identify the factors that contribute to its aggressiveness, and, ultimately, discover specific genes and gene networks for therapeutic targeting.",1
"background colorectal cancer remains one of the leading causes of death from cancer in industrialized countries. integrins are a family of heterodimeric glycoproteins involved in bidirectional cell signaling and participate in the regulation of cell shape, adhesion, migration, differentiation, gene transcription, survival and proliferation. the α1 subunit is known to be involved in ras/erk proliferative pathway activation and plays an important role in mammary carcinoma cell proliferation and migration. in the small intestine, α1 is present in the crypt proliferative compartment and absent in the villus, but nothing is known about its expression in the colon mucosa, or in colorectal cancer. results in the present study, we demonstrated that in the colon mucosa, α1 is present in the basolateral domain of the proliferative cells of the crypt, and in the surrounding myofibroblasts. we found higher levels of α1 mrna in 86% of tumours compared to their corresponding matched margin tissues. immunohistochemical analysis showed that α1 staining was moderate to high in 65% of tumour cells and 97% of the reactive cells surrounding the tumour cells vs 23% of normal epithelial cells. conclusion our findings suggest an active role for the α1β1 integrin in colorectal cancer progression.",0
"we previously showed that myc promoted burkitt lymphoma (bl) growth by inhibiting the tumor suppressor mir-150, resulting in release of mir-150 targets myb and zdhhc11. the zdhhc11 gene encodes three different transcripts including a mrna (pczdhhc11), a linear long non-coding rna (lnczdhhc11) and a circular rna (circzdhhc11). all transcripts contain the same region with 18 mir-150 binding sites. here we studied the relevance of circzdhhc11, including this mir-150 binding site region, for growth of bl cells. circzdhhc11 was mainly present in the cytoplasmic fraction in bl cells and its localization was not altered upon mir-150 overexpression. knockdown of circzdhhc11 caused a strong inhibition of bl growth without affecting the expression levels of myc, myb, mir-150 and other genes. overexpression of circzdhhc11 neither affected cell growth, nor rescued the phenotype induced by mir-150 overexpression. genomic deletion of the mir-150 binding site region did not affect growth, nor did it change the effect of circzdhhc11 knockdown. this indicated that the mir-150 binding site region is dispensable for the growth promoting role of circzdhhc11. to conclude, our results show that circzdhhc11 is a crucial factor supporting bl cell growth independent of its ability to sponge mir-150.",1
"abstract the black sea urchin ( arbacia lixula ) is a keystone species inhabiting the coastal shallow waters of the mediterranean sea, which is a key driver of littoral communities’ structure. here, we present the first genome assembly and annotation of this species, standing as the first arbacioida genome, including both nuclear and mitochondrial genomes. to obtain a chromosome-level assembly, we used a combination of pacbio high fidelity (hifi) reads and chromatin capture reads (omni-c). in addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published rna-seq data from several individuals of a. lixula and gene models from closely related species. the nuclear genome assembly has a total span of 607.91 mb, being consistent with its experimentally estimated genome size. the assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. a total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncrna, snorna, and trnas. the circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rrna, and 22 trna. this reference genome will enhance ongoing a. lixula studies and benefit the wider sea urchin scientific community.",1
"background parasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized (“hard wired”) program of infection. assuming that large-scale functional plasticity would be discernible in the parasite transcriptome we have performed a dual rna-seq study of the lifecycle of eimeria falciformis using infected mice with different immune status as models for coccidian infections. results we compared parasite and host transcriptomes (dual transcriptome) between naïve and challenge infected mice, as well as between immune competent and immune deficient ones. mice with different immune competence show transcriptional differences as well as differences in parasite reproduction (oocyst shedding). broad gene categories represented by differently abundant host genes indicate enrichments for immune reaction and tissue repair functions. more specifically, tgf-beta, egf, tnf and il-1 and il-6 are examples of functional annotations represented differently depending on host immune status. much in contrast, parasite transcriptomes were neither different between coccidia isolated from immune competent and immune deficient mice, nor between those harvested from naïve and challenge infected mice. instead, parasite transcriptomes have distinct profiles early and late in infection, characterized largely by biosynthesis or motility associated functional gene groups, respectively. extracellular sporozoite and oocyst stages showed distinct transcriptional profiles and sporozoite transcriptomes were found enriched for species specific genes and likely pathogenicity factors. conclusion we propose that the niche and host-specific parasite e. falciformis uses a genetically canalized program of infection. this program is likely fixed in an evolutionary process rather than employing phenotypic plasticity to interact with its host. this in turn might limit the potential of the parasite to adapt to new host species or niches, forcing it to coevolve with its host. electronic supplementary material the online version of this article (10.1186/s12864-017-4095-6) contains supplementary material, which is available to authorized users.",0
"background in plants, rna- based gene silencing mediated by small rnas functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral rnas and/or transposon elements. post-transcriptional gene silencing (ptgs) or the rna interference (rnai) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded rna (dsrna). however, to our knowledge, successful rnai-application to knock-down endogenous genes has not been reported in the important staple food crop banana. results using embryogenic cell suspension (ecs) transformed with ß-glucuronidase (gus) as a model system, we assessed silencing of gusa int using three intron-spliced hairpin rna (ihprna) constructs containing gusa int sequences of 299-nt, 26-nt and 19-nt, respectively. their silencing potential was analysed in 2 different experimental set-ups. in the first, agrobacterium -mediated co-transformation of banana ecs with a gusa int containing vector and an ihprna construct resulted in a significantly reduced gus enzyme activity 6–8 days after co-cultivation with either the 299-nt and 19-nt ihprna vectors. in the second approach, these ihprna constructs were transferred to stable gus-expressing ecs and their silencing potential was evaluated in the regenerated in vitro plants. in comparison to control plants, transgenic plants transformed with the 299-nt gusa int targeting sequence showed a 4.5 fold down-regulated gusa mrna expression level, while gus enzyme activity was reduced by 9 fold. histochemical staining of plant tissues confirmed these findings. northern blotting used to detect the expression of sirna in the 299-nt ihprna vector transgenic in vitro plants revealed a negative relationship between sirna expression and gus enzyme activity. in contrast, no reduction in gus activity or gus mrna expression occurred in the regenerated lines transformed with either of the two gusa int oligo target sequences (26-nt and 19-nt). conclusions rnai-induced silencing was achieved in banana, both at transient and stable level, resulting in significant reduction of gene expression and enzyme activity. the success of silencing was dependent on the targeted region of the target gene. the successful generation of transgenic ecs for second transformation with (an)other construct(s) can be of value for functional genomics research in banana. electronic supplementary material the online version of this article (doi:10.1186/1756-0500-7-655) contains supplementary material, which is available to authorized users.",1
"background alpha-1 antitrypsin is the main inhibitor of neutrophil elastase in the lung. although it is principally synthesized by hepatocytes, alpha-1 antitrypsin is also secreted by bronchial epithelial cells. gene mutations can lead to alpha-1 antitrypsin deficiency, with the z variant being the most clinically relevant due to its propensity to polymerize. the ability of bronchial epithelial cells to produce z-variant protein and its polymers is unknown. we investigated the expression, accumulation, and secretion of z-alpha-1 antitrypsin and its polymers in cultures of transfected cells and in cells originating from alpha-1 antitrypsin-deficient patients. methods experiments using a conformation-specific antibody were carried out on m- and z-variant–transfected 16hbe cells and on bronchial biopsies and ex vivo bronchial epithelial cells from z and m homozygous patients. in addition, the effect of an inflammatory stimulus on z-variant polymer formation, elicited by oncostatin m, was investigated. comparisons of groups were performed using t -test or anova. non-normally distributed data were assessed by mann–whitney u test or the kruskal-wallis test, where appropriate. a p value of < 0.05 was considered to be significant. results alpha-1 antitrypsin polymers were found at a higher concentration in the culture medium of ex vivo bronchial epithelial cells from z-variant homozygotes, compared with m-variant homozygotes ( p < 0.01), and detected in the bronchial epithelial cells and submucosa of patient biopsies. oncostatin m significantly increased the expression of alpha-1 antitrypsin mrna and protein ( p < 0.05), and the presence of z-variant polymers in ex vivo cells ( p < 0.01). conclusions polymers of z-alpha-1 antitrypsin form in bronchial epithelial cells, suggesting that these cells may be involved in the pathogenesis of lung emphysema and in bronchial epithelial cell dysfunction. electronic supplementary material the online version of this article (doi:10.1186/s12931-014-0112-3) contains supplementary material, which is available to authorized users.",0
"background nucleolin, as a multifunctional protein, has been demonstrated to play an oncogenic role in human hepatocellular carcinoma (hcc). the aim of this study was to investigate the expression pattern of nucleolin in hcc and determine its correlation with tumor progression and prognosis. methods nucleolin expression at both mrna and protein levels in hcc and adjacent nonneoplastic tissues were respectively detected by quantitative real time polymerase chain reaction (q-pcr), immunohistochemistry and western blotting. results nucleolin expression, at both mrna and protein levels, was significantly higher in hcc tissues than in the adjacent nonneoplastic tissues (both p < 0.001). in addition, the elevated nucleolin expression was markedly correlated with advanced tumor stage (p = 0.001), high tumor grade (p = 0.02) and serum afp level (p = 0.008). moreover, hcc patients with high nucleolin expression had shorter 5-year disease-free survival and shorter 5-year overall survival than those with low expression (both p < 0.001). furthermore, the cox proportional hazards model showed that nucleolin expression was an independent poor prognostic factor for both 5-year disease-free survival (hazards ratio = 3.696, 95% confidence interval = 1.662-8.138, p = 0.01) and 5-year overall survival (hr = 3.872, ci = 1.681-8.392, p = 0.01) in hcc. conclusion these results showed that the markedly and consistently increasing expression of nucleolin may be associated with aggressive characteristics of hcc, and implied that nucleolin expression may serve as a promising biochemical marker for predicting the clinical outcome of patients with this malignancy. virtual slides the virtual slide(s) for this article can be found here:",0
"microorganisms evolve via mechanisms spanning sexual/parasexual reproduction, mutators, aneuploidy, hsp90, and even prions. mechanisms that may seem detrimental can be repurposed to generate diversity. here we show the human fungal pathogen mucor circinelloides develops spontaneous resistance to the antifungal drug fk506 (tacrolimus) via two distinct mechanisms. one involves mendelian mutations that confer stable drug resistance; the other occurs via an epigenetic rna interference (rnai)-mediated pathway resulting in unstable drug resistance. the peptidyl-prolyl isomerase fkbp12 interacts with fk506 forming a complex that inhibits the protein phosphatase calcineurin 1. calcineurin inhibition by fk506 blocks m. circinelloides transition to hyphae and enforces yeast growth 2. mutations in the fkba gene encoding fkbp12 or the calcineurin cnbr or cnaa genes confer fk506 resistance (fk506 r ) and restore hyphal growth. in parallel, rnai is spontaneously triggered to silence the fkbp12 fkba gene, giving rise to drug-resistant epimutants. fk506 r epimutants readily reverted to the drug-sensitive wild-type (wt) phenotype when grown without drug. the establishment of these epimutants is accompanied by generation of abundant fkba small rna (srna) and requires the rnai pathway as well as other factors that constrain or reverse the epimutant state. silencing involves generation of a double-stranded rna (dsrna) trigger intermediate from the fkba mature mrna to produce antisense fkba rna. this study uncovers a novel epigenetic rnai-based epimutation mechanism controlling phenotypic plasticity, with possible implications for antimicrobial drug resistance and rnai-regulatory mechanisms in fungi and other eukaryotes.",1
"background the white-eared opossum ( didelphis albiventris ) is widely distributed throughout brazil and south america. it has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of chagas disease, leishmaniasis and resistance against snake venom. as a marsupial, d. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. as neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of d. albiventris as an animal model is limited. in this work, we sequenced the d. albiventris transcriptome by rna-seq to obtain the first catalogue of differentially expressed (de) genes and gene ontology (go) annotations during the neonatal stages of marsupial development. results the d. albiventris transcriptome was obtained from whole neonates harvested at birth (p0), at 5 days of age (p5) and at 10 days of age (p10). the de novo assembly of these transcripts generated 85,338 transcripts. approximately 30% of these transcripts could be mapped against the amino acid sequences of m. domestica , the evolutionarily closest relative of d. albiventris to be sequenced thus far. among the expressed transcripts, 2077 were found to be de between p0 and p5, 13,780 between p0 and p10, and 1453 between p5 and p10. the enriched go terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the cns and limb development. conclusions the elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. this study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.",0
"emerging scientific evidence has suggested that the long non-coding (lnc)rna differentiation antagonizing non-protein coding rna ( dancr ) serves a significant role in human tumorigenesis and cancer progression; however, the precise mechanism of its function in breast cancer remains to be fully understood. therefore, the objective of the present study was to manipulate dancr expression in mcf7 and mda-mb-231 cells using lentiviral vectors to knock down or overexpress dancr. this manipulation, alongside the analysis of bioinformatics data, was performed to investigate the potential mechanism underlying the role of dancr in cancer. the mrna and/or protein expression levels of dancr, mir-34c-5p and e2f transcription factor 1 ( e2f1 ) were assessed using reverse transcription-quantitative pcr and western blotting, respectively. the interactions between these molecules were validated using chromatin immunoprecipitation and dual-luciferase reporter assays. additionally, fluorescence in situ hybridization was used to confirm the subcellular localization of dancr. cell proliferation, migration and invasion were determined using 5-ethynyl-2′-deoxyuridine, wound healing and transwell assays, respectively. the results of the present study demonstrated that dancr had a regulatory role as a competing endogenous rna and upregulated the expression of e2f1 by sequestering mir-34c-5p in breast cancer cells. furthermore, e2f1 promoted dancr transcription by binding to its promoter in breast cancer cells. notably, the dancr / mir-34c-5p / e2f1 feedback loop enhanced cell proliferation, migration and invasion in breast cancer cells. thus, these findings suggested that targeting dancr may potentially provide a promising future therapeutic strategy for breast cancer treatment.",1
"the myozenin family of proteins binds calcineurin, which is involved in myocyte differentiation of skeletal muscle. moreover, gene expression of myozenin is closely related to meat quality. to further understand the functions and effects of myozenin2 ( myoz2 ) and myozenin3 ( myoz3 ) genes in goat, we cloned them from tianfu goat longissimus dorsi muscle. sequence analyses revealed that full-length coding sequence of myoz2 consisted of 795 bp and encoded 264 amino acids, and full-length coding sequence of myoz3 consisted of 735 bp and encoded 244 amino acids. rt-qpcr analyses revealed that mrna expressions of myoz2 and myoz3 were detected in heart, liver, spleen, lung, kidney, leg muscle, abdominal muscle, and longissimus dorsi muscle. particularly high expression levels of myoz2 were seen in abdominal muscle and heart ( p 0.05) and very little expression were detected in liver, spleen, lung and kidney ( p >0.05). in addition, high expression levels of myoz3 were seen in abdominal muscle, leg muscle, lungs and kidney ( p 0.05). temporal mrna expression results showed that myoz2 and myoz3 gene expression varied across four muscle tissues with different ages of the goats. western blotting further revealed that myoz2 and myoz3 proteins were only expressed in goat muscle, with notable temporal expression differences in specialized muscle tissues from five development age stages. this work provides the first evidence that myoz2 and myoz3 genes are expressed abundantly in tianfu goat muscle tissues from different development age stages, and lay a foundation for understanding the functions of myoz2 and myoz3 genes in muscle fiber differentiation.",0
"abstract background: management of tumors has become more complex owing to tumor heterogeneity. fewer studies have been performed on intra-tumor heterogeneity of endometrial cancer (ec) until now. therefore, it is of great clinical value to explore the intra-tumor heterogeneity of ec based on clinical features and gene expression profiles. methods: a total of 1688 patients with ec were screened and 114 patients were finally selected, including specimens from 84 patients with primary ec without relapse (pe) and the paired metastases (p-m) specimens, as well as specimens from 30 patients with primary ec with relapse (rpe) and the paired relapsed ec (p-re) specimens. microarray and rna-seq were used to detect gene expression of ec samples. clinicopathological characteristics and molecular data were compared between pe and p-m groups and between rpe and p-re groups to explore the intra-tumor heterogeneity of ec. results: the clinical intra-tumor spatial heterogeneity of pathological type, grade, er status, and pr status between pe and p-m were 17.9%, 13.1%, 28.6%, and 28.6%, respectively. the clinical intra-tumor spatiotemporal heterogeneity of pathological type, grade, er status, and pr status between rpe and p-re were 16.7%, 33.3%, 25.0%, and 37.5%, respectively. cluster analysis sorts ec samples based on progression type of lesion and their pathological type. there were differentially expressed genes between pe and p-m and between rpe and p-re, of which gene ontology and kyoto encyclopedia of genes and genomes analysis were mainly enriched in cell proliferation, the p53 signaling pathway, etc. conclusions: clinical and molecular data showed that there was spatiotemporal heterogeneity in intra-tumor of ec, which may add to the complexity of diagnosis and therapeutics for ec. considering the intra-tumor heterogeneity, sequential chemotherapy and precision medicine may be a more suitable treatment plan for ec.",0
"the zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. a stronger defense response results in increased resistance. here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. xanthomonas vasicola pv. holcicola ( xvh ) causes sorghum bacterial leaf streak. despite being widespread, this disease has not been described in detail at the molecular level. we divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. to simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual rna-seq on xvh -infected sorghum. consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. surprisingly, bacterial virulence genes related to the type iii secretion system (t3ss) and type iii effectors (t3es) were also most highly expressed in the resistance interaction. this expression pattern was observed at multiple time points within the sorghum- xvh pathosystem. further, a similar expression pattern was observed in arabidopsis infected with pseudomonas syringae for effector-triggered immunity via avrrps4 but not avrrpt2. specific metabolites were able to repress the xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses.",0
"cephalotaxus hainanensis , an endangered plant, is known to contain several metabolites with anti-cancer activity. despite its clinical impact, the alkaloid metabolism of this species has remained largely uncharacterized. the potential of cephalotaxus for metabolic engineering of medically interesting compounds has, so far, not been exploited, due to the almost complete lack of molecular information. we have therefore performed a high throughput rna-seq analysis and assembled the transcriptome de novo. raw reads comprising 4.3 gbp were assembled de novo into 39,416 unique sequences (unigenes) with a mean length of 1,089.8 bp and a total assembly size of 45.8 mbp, which equals to more than 50 times the number of cephalotaxaceae sequences currently deposited in the genbank (as of august 2013). as proof of principle for medically interesting pathways, gene fragments related to paclitaxel biosynthesis were searched and detected. to verify their functionality, the metabolic product paclitaxel, and its precursor baccatin iii, were identified in the leaves of c. hainanensis by hplc, and shown to be induced by meja. this finding demonstrates exemplarily the potential of the annotated transcriptome as information resource for the biotechnological exploitation of plant secondary metabolism.",0
"background exosomes are small membranous vesicles secreted into body fluids by multiple cell types, including tumor cells, and in various disease conditions. tumor exosomes contain intact and functional mrnas, small rnas (including mirnas), and proteins that can alter the cellular environment to favor tumor growth. molecular profiling may increase our understanding of the role of exosomes in melanoma progression and may lead to discovery of useful biomarkers. methodology/principal findings in the present study, we used mrna array profiling to identify thousands of exosomal mrnas associated with melanoma progression and metastasis. similarly, mirna array profiling identified specific mirnas, such as hsa-mir-31, -185, and -34b, involved in melanoma invasion. we also used proteomic analysis and discovered differentially expressed melanoma exosomal proteins, including hapln1, grp78, syntenin-1, annexin a1, and annexin a2. importantly, normal melanocytes acquired invasion ability through molecules transported in melanoma cell-derived exosomes. conclusions/significance our results indicate that melanoma-derived exosomes have unique gene expression signatures, mirna and proteomics profiles compared to exosomes from normal melanocytes. to the best of our knowledge, this is the first in-depth screening of the whole transcriptome/mirnome/proteome expression in melanoma exosomes. these results provide a starting point for future more in-depth studies of tumor-derived melanoma exosomes, which will aid our understanding of melanoma biogenesis and new drug-targets that may be translated into clinical applications, or as non-invasive biomarkers for melanoma.",1
"background the 3′ untranslated regions (3′utrs) of mrnas contain cis elements involved in post-transcriptional regulation of gene expression. over half of all mammalian genes contain multiple polyadenylation sites that lead to different 3′utrs for a gene. studies have shown that the alternative polyadenylation (apa) pattern varies across tissues, and is dynamically regulated in proliferating or differentiating cells. generation of induced pluripotent stem (ips) cells, in which differentiated cells are reprogrammed to an embryonic stem (es) cell-like state, has been intensively studied in recent years. however, it is not known how 3′utrs are regulated during cell reprogramming. methods/main findings using a computational method that robustly examines apa across dna microarray data sets, we analyzed 3′utr dynamics in generation of ips cells from different cell types. we found that 3′utrs shorten during reprogramming of somatic cells, the extent of which depends on the type of source cell. by contrast, reprogramming of spermatogonial cells involves 3′utr lengthening. the alternative polyadenylation sites that are highly responsive to change of cell state in generation of ips cells are also highly regulated during embryonic development in opposite directions. compared with other sites, they are more conserved, can lead to longer alternative 3′utrs, and are associated with more cis elements for polyadenylation. consistently, reprogramming of somatic cells and germ cells involves significant upregulation and downregulation, respectively, of mrnas encoding polyadenylation factors, and rna processing is one of the most significantly regulated biological processes during cell reprogramming. furthermore, genes containing target sites of es cell-specific micrornas (mirnas) in different portions of 3′utr are distinctively regulated during cell reprogramming, suggesting impact of apa on mirna targeting. conclusions/significance taken together, these findings indicate that reprogramming of 3′utrs by apa, which result from regulation of both general polyadenylation activity and cell type-specific factors and can reset post-transcriptional gene regulatory programs in the cell, is an integral part of ips cell generation, and the apa pattern can be a good biomarker for cell type and state, useful for sample classification. the results also suggest that perturbation of the mrna polyadenylation machinery or rna processing activity may facilitate generation of ips cells.",1
"in barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. to change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. in this work, we used the barley cultivar gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment. a deep rna-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ∼14k genes, ∼90% of which were shared. an expression analysis identified a total of 3,382 differentially expressed genes (degs); of these, 2,155 and 2,281 degs were respectively identified when contrasting expression at days 0 and 2 and at days 2 and 5. these define 8 expression profiles in which degs share a common up- or down-regulation at these time points. up-regulation of numerous glutathione s-transferase and heat shock protein genes as well as down-regulation of ribosomal subunit protein genes was observed between days 0 and 2. the transition from microspores to developing embryos (days 2 vs. 5) was marked by the induction of transcription factor genes known to play important roles in early embryogenesis, numerous genes involved in hormone biosynthesis and plant hormonal signal transduction in addition to genes involved in secondary metabolism. this work sheds light on transcriptional changes accompanying an important developmental shift and provides candidate biomarkers for embryogenesis in barley.",0
"micrornas (mirnas) are a class of endogenous, non-coding rnas that mediate post-transcriptional gene silencing by inhibiting mrna translation and promoting mrna decay. dicer1, an rnase iii endonuclease encoded by dicer1 , is required for processing short 21–22 nucleotide mirnas from longer double-stranded rna precursors. here, we investigate the loss of dicer1 in mouse postnatal male germ cells to determine how disruptions in the mirna biogenesis pathway may contribute to infertility. reduced levels of dicer1 transcripts and dicer1 were confirmed in germ cell knock-out (gcko ) testes by postnatal day 18 (p18). compared to wild-type (wt) at 8 weeks, gcko males had no change in body weight; yet showed significant reductions in testis mass and sperm number. histology and fertility tests confirmed spermatogenic failure in gcko males. array analyses at p18 showed that in comparison to wt testes, 75% of mirna genes and 37% of protein coding genes were differentially expressed in gcko testes. among these, 96% of mirna genes were significantly down-regulated, while 4% mirna genes were overexpressed. interestingly, we observed preferential overexpression of genes encoded on the sex chromosomes in gcko testes, including more than 80% of previously identified targets of meiotic sex chromosome inactivation (msci). compared to wt, gcko mice showed higher percentages of germ cells at early meiotic stages (leptotene and zygotene) but lower percentages at later stages (pachytene, diplotene and metaphase i) providing evidence that deletion of dicer1 leads to disruptions in meiotic progression. therefore, deleting dicer1 in early postnatal germ cells resulted in deregulation of transcripts encoded by genes on the sex chromosomes, impaired meiotic progression and led to spermatogenic failure and infertility.",1
"serous epithelial ovarian cancer (eoc) patients often succumb to aggressive metastatic disease, yet little is known about the behavior and genetics of ovarian cancer metastasis. here, we aim to understand how omental metastases differ from primary tumors and how these differences may influence chemotherapy. we analyzed the mirna expression profiles of primary eoc tumors and their respective omental metastases from 9 patients using mirna taqman qpcr arrays. we find 17 mirnas with differential expression in omental lesions compared to primary tumors. mir-21, mir-150, and mir-146a have low expression in most primary tumors with significantly increased expression in omental lesions, with concomitant decreased expression of predicted mrna targets based on mrna expression. we find that mir-150 and mir-146a mediate spheroid size. both mir-146a and mir-150 increase the number of residual surviving cells by 2–4 fold when challenged with lethal cisplatin concentrations. these observations suggest that at least two of the mirnas, mir-146a and mir-150, up-regulated in omental lesions, stimulate survival and increase drug tolerance. our observations suggest that cancer cells in omental tumors express key mirnas differently than primary tumors, and that at least some of these micrornas may be critical regulators of the emergence of drug resistant disease.",1
"our previous studies had reported that morin, a bioflavanoid exhibited potent anti-inflammatory effect against adjuvant-induced arthritic rats. in this current study, we investigated the anti-inflammatory mechanism of morin against monosodium urate crystal (msu)-induced inflammation in raw 264.7 macrophage cells, an in vitro model for acute gouty arthritis. for comparison purpose, colchicine was used as a reference drug. we have observed that morin (100–300 μm) treatment significantly suppressed the levels of inflammatory cytokines (tnf-α, il-1β, il-6, mcp-1 and vegf), inflammatory mediators (no and peg 2 ), and lysosomal enzymes (acid phosphatase, β-galactosidase, n-acetyl glucosamindase and cathepsin d) in msu-crystals stimulated macrophage cells. the mrna expression of pro-inflammatory cytokines (tnf-α, il-1β, il-6, and mcp-1), inflammatory enzymes (inos and cox-2), and nf-κbp65 was found downregulated in msu crystal stimulated macrophage cells by morin treatment, however, the mrna expression of hypoxanthine phospho ribosyl transferse (hprt) was found to be increased. the flow cytometry analysis revealed that morin treatment decreased intracellular reactive oxygen species levels in msu crystal stimulated macrophage cells. the western blot analysis clearly showed that morin mainly exerts its anti-inflammatory effects by inhibiting the msu crystal-induced cox-2 and tnf-α protein expression through the inactivation of nf-κb signaling pathway in raw 264.7 macrophage cells similar to that of bay 11–7082 (iκb kinase inhibitor). our results collectively suggest that morin can be a potential therapeutic agent for inflammatory disorders like acute gouty arthritis.",0
"background herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. due to these properties this bacterium has great potential as a commercial inoculant for agriculture. the h. seropedicae smr1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding rnas (srnas) has not yet been done. we have conducted computational prediction and rna-seq analysis to select and confirm the expression of srna genes in the h. seropedicae smr1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants. results this approach resulted in a set of 117 srnas distributed in riboswitch, cis -encoded and trans -encoded categories and among them 20 have rfam homologs. the housekeeping srnas tmrna, ssrs and 4.5s were found and we observed that a large number of srnas are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. some srnas expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium. conclusions h. seropedicae smr1 express srnas in the presence of two nitrogen sources and/or in the presence of naringenin. the functions of most of these srnas remains unknown but their existence in this bacterium confirms the evidence that srnas are involved in many different cellular activities to adapt to nutritional and environmental changes.",1
"type 2 diabetes mellitus (t2dm) is a metabolic disease and comorbidity associated with several conditions, including cardiac dysfunction leading to heart failure with preserved ejection fraction (hfpef), in turn resulting in t2dm-induced cardiomyopathy (t2dm-cm). however, the molecular mechanisms underlying the development of t2dm-cm are poorly understood. it is hypothesized that molecular alterations in myopathic genes induced by diabetes promote the development of hfpef, whereas cardiac myosin inhibitors can rescue the resultant t2dm-mediated cardiomyopathy. to test this hypothesis, a leptin receptor-deficient db/db homozygous (lepr db/db ) mouse model was used to define the pathogenesis of t2dm-cm. echocardiographic studies at 4 and 6 months revealed that lepr db/db hearts started developing cardiac dysfunction by four months, and left ventricular hypertrophy with diastolic dysfunction was evident at 6 months. rna-seq data analysis, followed by functional enrichment, revealed the differential regulation of genes related to cardiac dysfunction in lepr db/db heart tissues. strikingly, the level of cardiac myosin binding protein-c phosphorylation was significantly increased in lepr db/db mouse hearts. finally, using isolated skinned papillary muscles and freshly isolated cardiomyocytes, camzyos ® (mavacamten, myk-461), a prescription heart medicine used for symptomatic obstructive hypertrophic cardiomyopathy treatment, was tested for its ability to rescue t2dm-cm. compared with controls, myk-461 significantly reduced force generation in papillary muscle fibers and cardiomyocyte contractility in the db/db group. this line of evidence shows that 1) t2dm-cm is associated with hyperphosphorylation of cardiac myosin binding protein-c and 2) myk-461 significantly lessened disease progression in vitro , suggesting its promise as a treatment for hfpef.",0
"background metastatic prostate cancer is a leading cause of cancer-related death in men. cancer stem cells (cscs) are involved in tumor progression and metastasis, including in prostate cancer. there is an obvious and urgent need for effective cancer stem cells specific therapies in metastatic prostate cancer. micrornas (mirnas) are an important class of pervasive genes that are involved in a variety of biological functions, especially in cancer. the goal of this study was to identify mirnas involved in prostate cancer metastasis and cancer stem cells. methods a microarray and qrt-pcr were performed to investigate the mirna expression profiles in pc-3 sphere cells and adherent cells. a transwell assay was used to evaluate the migration of pc-3 sphere cells and adherent cells. mir-143 was silenced with antisense oligonucleotides in pc-3, pc-3-m and lncap cells. the role of mir-143 in prostate cancer metastasis was measured by wound-healing and transwell assays in vitro and bioluminescence imaging in vivo. bioinformatics and luciferase report assays were used to identify the target of mir-143. results the expression of mir-143 and the migration capability were reduced in pc-3 sphere cells and progressively increased during sphere re-adherent culture. moreover, the down-regulation of mir-143 suppressed prostate cancer cells migration and invasion in vitro and systemically inhibited metastasis in vivo. fibronectin type iii domain containing 3b (fndc3b), which regulates cell motility, was identified as a target of mir-143. the inhibition of mir-143 increased the expression of fndc3b protein but not fndc3b mrna in vitro and vivo. conclusions these data demonstrate for the first time that mir-143 was up-regulated during the differentiation of prostate cancer stem cells and promoted prostate cancer metastasis by repressing fndc3b expression. this sheds a new insight into the post-transcriptional regulation of cancer stem cells differentiation by mirnas, a potential approach for the treatment of prostate cancer.",1
"background clear cell renal cell carcinoma (ccrcc) represents the most invasive and common adult kidney neoplasm. mounting evidence suggests that micrornas (mirnas) are important regulators of gene expression. but their function in tumourigenesis in this tumour type remains elusive. with the development of high throughput technologies such as microarrays and ngs, aberrant mirna expression has been widely observed in ccrcc. systematic and integrative analysis of multiple microrna expression datasets may reveal potential mechanisms by which micrornas contribute to ccrcc pathogenesis. methods we collected 5 public microrna expression datasets in ccrcc versus non-matching normal renal tissues from geo database and published literatures. we analyzed these data sets with an integrated bioinformatics framework to identify expression signatures. the framework incorporates a novel statistic method for abnormal gene expression detection and an in-house developed predictor to assess the regulatory activity of micrornas. we then mapped target genes of de-mirnas to different databases, such as go, kegg, genego etc, for functional enrichment analysis. results using this framework we identified a consistent panel of eleven deregulated mirnas shared by five independent datasets that can distinguish normal kidney tissues from ccrcc. after comparison with 3 rna-seq based microrna profiling studies, we found that our data correlated well with the results of next generation sequencing. we also discovered 14 novel molecular pathways that are likely to play a role in the tumourigenesis of ccrcc. conclusions the integrative framework described in this paper greatly improves the inter-dataset consistency of microrna expression signatures. consensus expression profile should be identified at pathway or network level to address the heterogeneity of cancer. the de-mirna signature and novel pathways identified herein could provide potential biomarkers for ccrcc that await further validation.",1
"background current practice in mass spectrometry (ms)-based proteomics is to identify peptides by comparison of experimental mass spectra with theoretical mass spectra derived from a reference protein database; however, this strategy necessarily fails to detect peptide and protein sequences that are absent from the database. we and others have recently shown that customized proteomic databases derived from rna-seq data can be employed for ms-searching to both improve ms analysis and identify novel peptides. while this general strategy constitutes a significant advance for the discovery of novel protein variations, it has not been readily transferable to other laboratories due to the need for many specialized software tools. to address this problem, we have implemented readily accessible, modifiable, and extensible workflows within galaxy-p, short for galaxy for proteomics, a web-based bioinformatic extension of the galaxy framework for the analysis of multi-omics (e.g. genomics, transcriptomics, proteomics) data. results we present three bioinformatic workflows that allow the user to upload raw rna sequencing reads and convert the data into high-quality customized proteomic databases suitable for ms searching. we show the utility of these workflows on human and mouse samples, identifying 544 peptides containing single amino acid polymorphisms (saps) and 187 peptides corresponding to unannotated splice junction peptides, correlating protein and transcript expression levels, and providing the option to incorporate transcript abundance measures within the ms database search process (reduced databases, incorporation of transcript abundance for protein identification score calculations, etc.). conclusions using rna-seq data to enhance ms analysis is a promising strategy to discover novel peptides specific to a sample and, more generally, to improve proteomics results. the main bottleneck for widespread adoption of this strategy has been the lack of easily used and modifiable computational tools. we provide a solution to this problem by introducing a set of workflows within the galaxy-p framework that converts raw rna-seq data into customized proteomic databases. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-703) contains supplementary material, which is available to authorized users.",0
"abstract we previously developed a web server cpgavas for annotation, visualization and genbank submission of plastome sequences. here, we upgrade the server into cpgavas2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petb, petd and rps16 and trans-splicing gene rps12 ; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. in particular, cpgavas2 provides two reference datasets for plastome annotation. the first dataset contains 43 plastomes whose annotation have been validated or corrected by rna-seq data. the second one contains 2544 plastomes curated with sequence alignment. two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. dna-seq and rna-seq data can be uploaded for identification of single-nucleotide polymorphism sites and rna-editing sites. the results of two case studies show that cpgavas2 annotates better than several other servers. cpgavas2 will likely become an indispensible tool for plastome research and can be accessed from",0
"regulation of gene expression by dna-binding transcription factors is essential for proper control of growth and development in all organisms. in this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus neurospora crassa. we identified 312 transcription factor genes, corresponding to 3.2% of the protein coding genes in the genome. the largest class was the fungal-specific zn 2 cys 6 (c6) binuclear cluster, with 135 members, followed by the highly conserved c2h2 zinc finger group, with 61 genes. viable knockout mutants were produced for 273 genes, and complete growth and developmental phenotypic data are available for 242 strains, with 64% possessing at least one defect. the most prominent defect observed was in growth of basal hyphae (43% of mutants analyzed), followed by asexual sporulation (38%), and the various stages of sexual development (19%). two growth or developmental defects were observed for 21% of the mutants, while 8% were defective in all three major phenotypes tested. analysis of available mrna expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type. inspection of this data also implicated cryptic roles in sexual development for several cotranscribed transcription factor genes that do not produce a phenotype when mutated.",0
"simple summary the evolution of colorectal cancer (crc) is influenced by complex interactions between tumor cells and tumor-infiltrating lymphocytes (tils). optimized immunotherapies to boost the potential anti-tumor t-cell response are still needed in crc. a good candidate is the inflammasome pathway that bridges innate and adaptive immunity via the caspase-1/interleukin-18 (il-18) axis, able to elicit a t-helper/cytotoxic (th1/tc1) anti-tumor response. this study aimed to determine the status of the caspase-1/il-18 axis in tumor cells and its potential modulatory role on tils in crc. using cohorts of crc patients and an ex vivo explant culture model allowing functional and multiparametric approaches, we demonstrate that tumor cells in the majority of crcs can be considered as innate immune cells that display a functional caspase-1/il-18 axis able to modulate the adaptive th1/tc1 anti-tumor response of tils. furthermore, the identification of three distinct subgroups of crc will provide a rationale for future strategies targeting the inflammasome pathway in crc. abstract in colorectal cancer (crc), a high density of t lymphocytes represents a strong prognostic marker in subtypes of crc. optimized immunotherapy strategies to boost this t-cell response are still needed. a good candidate is the inflammasome pathway, an emerging player in cancer immunology that bridges innate and adaptive immunity. its effector protein caspase-1 matures il-18 that can promote a t-helper/cytotoxic (th1/tc1) response. it is still unknown whether tumor cells from crc possess a functional caspase-1/il-18 axis that could modulate the th1/tc1 response. we used two independent cohorts of crc patients to assess il-18 and caspase-1 expression by tumor cells in relation to the density of tils and the microsatellite status of crc. functional and multiparametric approaches at the protein and mrna levels were performed on an ex vivo crc explant culture model. we show that, in the majority of crcs, tumor cells display an activated and functional caspase-1/il-18 axis that contributes to drive a th1/tc1 response elicited by tils expressing il-18rα. furthermore, unsupervised clustering identified three clusters of crcs according to the caspase-1/il-18/til density/interferon gamma (ifnγ) axis and microsatellite status. together, our results strongly suggest that targeting the caspase-1/il-18 axis can improve the anti-tumor immune response in subgroups of crc.",0
"background phosphorus (p) is an essential macronutrient for plant growth and development. several genes involved in phosphorus deficiency stress have been identified in various plant species. however, a whole genome understanding of the molecular mechanisms involved in plant adaptations to low p remains elusive, and there is particularly little information on the genetic basis of these acclimations in coniferous trees. masson pine ( pinus massoniana ) is grown mainly in the tropical and subtropical regions in china, many of which are severely lacking in inorganic phosphate (pi). in previous work, we described an elite p. massoniana genotype demonstrating a high tolerance to pi-deficiency. methodology/principal findings to further investigate the mechanism of tolerance to low p, rna-seq was performed to give an idea of extent of expression from the two mixed libraries, and microarray whose probes were designed based on the unigenes obtained from rna-seq was used to elucidate the global gene expression profiles for the long-term phosphorus starvation. a total of 70,896 unigenes with lengths ranging from 201 to 20,490 bp were assembled from 112,108,862 high quality reads derived from rna-seq libraries. we identified 1,396 and 943 transcripts that were differentially regulated (p<0.05) under p1 (0.01 mm p) and p2 (0.06 mm p) pi-deficiency conditions, respectively. numerous transcripts were consistently differentially regulated under pi deficiency stress, many of which were also up- or down-regulated in other species under the corresponding conditions, and are therefore ideal candidates for monitoring the p status of plants. the results also demonstrated the impact of different pi starvation levels on global gene expression in masson pine. conclusions/significance to our knowledge, this work provides the first insight into the molecular mechanisms involved in acclimation to long-term pi starvation and different pi availability levels in coniferous trees.",0
"pathophysiological states cause misfolded protein accumulation in the endoplasmic reticulum (er). then, er stress and the unfolded protein response (upr) are activated. targeting er stress may enhance the adaptive upr and then protect the cell against pathogenic environments. in the present study, we utilized nanotechnology to synthesize thapsigargin nanoparticles (tg nps) which induced er stress and the upr pathway, to study the role of er stress and autophagy in chronic kidney disease (ckd). we found that the mrna levels of er stress- and autophagy-related molecules were elevated in the renal tissue of ckd patients compared to those of healthy individuals. furthermore, tg nps induced the upr pathway and autophagy in hk-2 human kidney tubular epithelial cells. tg nps protected hk-2 cells against oxidative stress-induced cell death through the activation of nrf2 and foxo1. the sirna-mediated inhibition of nrf2 or foxo1 resulted in enhanced oxidative stress-induced cytotoxicity in hk-2 cells. in a mouse model of adenine diet-induced ckd, tg nps and kim-1-tg nps ameliorated renal injury through the stimulation of er stress and its downstream pathways. our findings suggest that the induction of er stress using pharmacological agents may offer a promising therapeutic strategy for preventing or interfering with ckd progression.",1
"objective this study aimed to identify differentially expressed genes (degs) by transcriptome analysis to elucidate a potential mechanism by which governor vessel electroacupuncture (gv-ea) promotes neuronal survival, axonal regeneration, and functional recovery after complete transection spinal cord injury (sci). methods sham, control, or gv-ea group adult female sprague dawley rats underwent a complete transection sci protocol. sci area rna-seq investigated the degs of coding and noncoding rnas 7 days post-sci. gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) enrichment analyses were used to classify degs functions, to explain a possible molecular mechanism. immunofluorescence and bbb (basso, beattie, and bresnahan) score were used to verify a gv-ea treatment effect following sci. results gv-ea treatment could regulate the expression of 173 mrna, 260 lncrna, and 153 circrna genes among these degs resulted by sci. go enrichment analysis showed that the degs were most enriched in membrane, actin binding, and regulation of toll-like receptor signaling pathway. kegg pathway analysis showed enriched pathways (e.g. , toll-like receptors, mapk, hippo signaling). according to the cerna network, mir-144-3p played a regulatory role by interacting with lncrna and circrna. gv-ea also promoted the injured spinal cord neuron survival, axonal regeneration, and functional improvement of hind limb locomotion. conclusion results of our rna-seq suggest that post-sci gv-ea may regulate characteristic changes in transcriptome gene expression, potential critical genes, and signaling pathways, providing clear directions for further investigation into the mechanism of gv-ea in subacute sci treatment. moreover, we found that gv-ea promotes neuronal survival, nerve fiber extension, and motor function recovery in subacute sci.",1
"post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. here, we use freshwater planarians as a model system to investigate this and uncover a role for ccr4-not mediated deadenylation of mrnas in stem cell differentiation. planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. while many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. we show that knockdown of planarian not1, the ccr4-not deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. this abrogation is primarily due to severe impairment of their differentiation potential. we describe a stem cell specific increase in the mrna levels of key neoblast genes after smed-not1 knock down, consistent with a role of the ccr4-not complex in degradation of neoblast mrnas upon the onset of differentiation. we also observe a stem cell specific increase in the frequency of longer poly(a) tails in these same mrnas, showing that stem cells after smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(a) tails. as other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mrnas by post-transcriptional regulators such as rna-binding proteins or micrornas. together, our results show that the ccr4-not complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mrnas, thus providing clear mechanistic insight into this aspect of neoblast biology.",1
"background many previous studies have shown that soybean wrky transcription factors are involved in the plant response to biotic and abiotic stresses. phakopsora pachyrhizi is the causal agent of asian soybean rust, one of the most important soybean diseases. there are evidences that wrkys are involved in the resistance of some soybean genotypes against that fungus. the number of wrky genes already annotated in soybean genome was underrepresented. in the present study, a genome-wide annotation of the soybean wrky family was carried out and members involved in the response to p. pachyrhizi were identified. results as a result of a soybean genomic databases search, 182 wrky -encoding genes were annotated and 33 putative pseudogenes identified. genes involved in the response to p. pachyrhizi infection were identified using supersage, rna-seq of microdissected lesions and microarray experiments. seventy-five genes were differentially expressed during fungal infection. the expression of eight wrky genes was validated by rt-qpcr. the expression of these genes in a resistant genotype was earlier and / or stronger compared with a susceptible genotype in response to p. pachyrhizi infection. soybean somatic embryos were transformed in order to overexpress or silence wrky genes. embryos overexpressing a wrky gene were obtained, but they were unable to convert into plants. when infected with p. pachyrhizi , the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants. conclusions the present study reports a genome-wide annotation of soybean wrky family. the participation of some members in response to p. pachyrhizi infection was demonstrated. the results contribute to the elucidation of gene function and suggest the manipulation of wrkys as a strategy to increase fungal resistance in soybean plants. electronic supplementary material the online version of this article (doi:10.1186/s12870-014-0236-0) contains supplementary material, which is available to authorized users.",0
"simple summary mirnas are endogenous, small, non-coding rna species that can be crucial regulators in a variety of biological processes, such as development, immunity, and metamorphosis. because one mirna may regulate hundreds of targets, nearly all genes are expected to be regulated by mirnas to some degree. since this is the case, mirna knockouts may show obvious symptoms, such as developmental defects and embryonic mortality. in this study, we reported that sex-mir-2766-3p knockout in s. exigua was non-lethal, confirming the theory that mirnas function redundantly with other mirnas or other pathways. abstract micrornas (mirnas) drive the post-transcriptional repression of target mrnas and play important roles in a variety of biological processes. mir-2766-3p is conserved and abundant in lepidopteran species and may be involved in a variety of biological activities. in this study, sex-mir-2766-3p was predicted to potentially bind to the 3′ untranslated region (utr) of cap ‘n’ collar isoform c (cncc) in spodoptera exigua , and sex-mir-2766-3p was confirmed to regulate the expression of secncc through screening with a luciferase reporter system. although crispr/cas9 has been extensively utilized to examine insect gene function, studies of mirna function are still relatively uncommon. thus, we employed crispr/cas9 to knock out sex-mir-2766-3p from s. exigua. however, the expression of secncc was not significantly altered in the knockout strain (2766-ko) compared with that of the whs strain. this result suggested that a mirna knockout might lack phenotypes because of genetic robustness. additionally, we used transcriptome analysis to examine how the global gene expression patterns of the sex-mir-2766-3p knockout strain varied. rna-seq data revealed 1746 upregulated and 2183 downregulated differentially expressed genes (degs) in the 2766-ko strain, which might be the result of sex-mir-2766-3p loss or dna lesions as the trigger for transcriptional adaptation. go function classification and kegg pathway analyses showed that these degs were enriched for terms related to binding, catalytic activity, metabolic process, and signal transduction. our findings demonstrated that s. exigua could compensate for the missing sex-mir-2766-3p by maintaining the expression of secncc by other pathways.",1
"abstract the innate immune response is the first line of defence against microbial infections. in drosophila , two major pathways of the innate immune system (the toll- and imd-mediated pathways) induce the synthesis of antimicrobial peptides (amps) within the fat body. recently, it has been reported that certain cationic amps exhibit selective cytotoxicity against human cancer cells; however, little is known about their anti-tumour effects. drosophila mxc mbn1 mutants exhibit malignant hyperplasia in a larval haematopoietic organ called the lymph gland (lg). here, using rna-seq analysis, we found many immunoresponsive genes, including those encoding amps, to be upregulated in these mutants. downregulation of these pathways by either a toll or imd mutation enhanced the tumour phenotype of the mxc mutants. conversely, ectopic expression of each of five different amps in the fat body significantly suppressed the lg hyperplasia phenotype in the mutants. thus, we propose that the drosophila innate immune system can suppress the progression of haematopoietic tumours by inducing amp gene expression. overexpression of any one of the five amps studied resulted in enhanced apoptosis in mutant lgs, whereas no apoptotic signals were detected in controls. we observed that two amps, drosomycin and defensin, were taken up by circulating haemocyte-like cells, which were associated with the lg regions and showed reduced cell-to-cell adhesion in the mutants. by contrast, the amp diptericin was directly localised at the tumour site without intermediating haemocytes. these results suggest that amps have a specific cytotoxic effect that enhances apoptosis exclusively in the tumour cells.",0
"background epstein-barr virus (ebv) is a human herpesvirus implicated in cancer and autoimmune disorders. little is known concerning the roles of rna structure in this important human pathogen. this study provides the first comprehensive genome-wide survey of rna and rna structure in ebv. results novel ebv rnas and rna structures were identified by computational modeling and rna-seq analyses of ebv. scans of the genomic sequences of four ebv strains (ebv-1, ebv-2, gd1, and gd2) and of the closely related macacine herpesvirus 4 using the rnaz program discovered 265 regions with high probability of forming conserved rna structures. secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. the analysis of rna-seq data uncovered the first observation of a stable intronic sequence rna (sisrna) in ebv. the abundance of this sisrna rivals that of the well-known and highly expressed ebv-encoded non-coding rnas (ebers). conclusion this work identifies regions of the ebv genome likely to generate functional rnas and rna structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. enhanced understanding of the ebv transcriptome will guide future experimental analyses of the discovered rnas and rna structures.",1
"the meganuclease i-scei has been effectively used to facilitate transgenesis in fish eggs for nearly a decade. i-scei-mediated transgenesis is simply via embryo cytoplasmic microinjection and only involves plasmid vectors containing i-scei recognition sequences, therefore regarding the transgenesis process and application of resulted transgenic organisms, i-scei-mediated transgenesis is of minimal bio-safety concerns. however, currently no transgenic mammals derived from i-scei-mediated transgenesis have been reported. in this work, we found that the native i-scei molecule was not capable of facilitating transgenesis in mammalian embryos via cytoplasmic microinjection as it did in fish eggs. in contrast, the i-scei molecule containing mammalian nuclear localization signal (nls-i-scei) was shown to be capable of transferring dna fragments from cytoplasm into nuclear in porcine embryos, and cytoplasmic microinjection with nls-i-scei mrna and circular i-scei recognition sequence-containing transgene plasmids resulted in transgene expression in both mouse and porcine embryos. besides, transfer of the cytoplasmically microinjected mouse and porcine embryos into synchronized recipient females both efficiently resulted in transgenic founders with germline transmission competence. these results provided a novel method to facilitate mammalian transgenesis using i-scei, and using the nls-i-scei molecule, a simple, efficient and species-neutral transgenesis technology based on embryo cytoplasmic microinjection with minimal bio-safety concerns can be established for mammalian species. as far as we know, this is the first report for transgenic mammals derived from i-scei-mediated transgenesis via embryo cytoplasmic microinjection.",1
"non-alcoholic fatty liver disease (nafld) is a common liver disease, characterized by the excess accumulation of lipids in the liver. it has been demonstrated that the dysregulation of lipid droplet (ld)-associated proteins may be involved in the development of nafld. adipose differentiation-related protein (adrp), as one of the major ld-associated proteins, is expressed in normal and steatotic livers; however, the exact role of adrp in the liver remains unknown. previous studies have indicated that metformin, as an antidiabetic drug, effectively ameliorates nafld. however, its cellular and molecular mechanisms of action remain to be elucidated. therefore, the aim of this study was to determine the role of adrp in the metformin-mediated regulation of hepatic steatosis. we examined the effects of meformin in vivo and in vitro using ob/ob mice and primary hepatocytes, respectively. lipid accumulation in the hepatocytes was induced by treatment with oleate. our results revealed that metformin prevented hepatic steatosis in ob/ob mice and inhibited oleate-induced lipid accumulation in primary hepatocytes. furthermore, using real-time pcr and western blot analysis, we examined the mrna and protein expression of adrp, respectively. we found that metformin significantly decreased the expression levels of adrp. in addition, to further clarify the role of adrp in lipid accumulation, we generated recombinant adenoviruses to induce the overexpression of adrp and to knockdown adrp. in the hepatocytes in which adrp was overexpressed, the reducing effects of metformin on lipid accumulation were diminished. however, the knockdown of adrp using sirna targeting adrp reduced the accumulation of triglycerides. taken together, our data demonstrate that metformin prevents hepatic steatosis by regulating the expression of adrp, which may be a key target in the treatment of nafld.",0
"abstract micrornas are key players involved in stress responses in plants and reports are available on the role of mirnas in drought stress response in rice. this work reports the development of a database, ricemetasys: drought-mir, based on the meta-analysis of publicly available srna datasets. from 28 drought stress-specific srna datasets, we identified 216 drought-responsive mirnas (drms). the major features of the database include genotype-, tissue- and mirna id-specific search options and comparison of genotypes to identify common mirnas. co-localization of the drms with the known quantitative trait loci (qtls), i.e., meta-qtl regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising drms. to identify the high confidence target genes of drms under drought stress, degradome datasets and web resource on drought-responsive genes (ricemetasys: drg) were used. out of the 216 unique drms, only 193 had targets with high stringent parameters. out of the 1081 target genes identified by degradome datasets, 730 showed differential expression under drought stress in at least one accession. to retrieve complete information on the target genes, the database has been linked with ricemetasys: drg. further, we updated the ricemetasys: drgv1 developed earlier with the addition of drgs identified from rna-seq datasets from five rice genotypes. we also identified 759 putative novel mirnas and their target genes employing stringent criteria. novel mirna search has all the search options of known mirnas and additionally, it gives information on their in silico validation features. simple sequence repeat markers for both the mirnas and their target genes have also been designed and made available in the database. network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. co-localization of the hub genes with the meta-qtl regions governing drought tolerance narrowed down this to 16 most promising drgs. database url : updated database of ricemetasys url:",1
"background osteoarthritis (oa) is the most common joint disorder in the world and represents the leading cause of pain and disability in the elderly population. advancing age remains the single greatest risk factor for oa. several studies have characterised disease development in the guinea pig ageing model of oa in terms of its joint histopathology and inflammatory cytokine profile. however, the quadriceps muscle has yet to be studied in relation to age-related disease onset or early disease progression. therefore, we examined whether the initiation of oa in the dunkin hartley guinea pig is associated with changes in the quadriceps skeletal muscle. male dunkin hartley guinea pigs (n = 24) were group housed with free access to standard guinea pig chow and water. at 2, 3, 5 and 7 months of age, six animals were selected based on their proximity to the median weight of the cohort. oa severity was graded at each time point by the assessment of toluidine blue stained step coronal sections of the total knee joint. serum ctx ii was measured as a potential biomarker of oa severity. myosin heavy chain (mhc) isoforms were determined by a validated real-time pcr assay. oxidative and glycolytic potential was determined in quadriceps homogenates via the measurement of icdh and ldh activity. results initiation of oa in the dh strain guinea pig occurred between 2 and 3 months of age and progressed until 7 months when the final analyses were conducted. serum ctx ii significantly decreased during this early period of oa initiation and levels were unrelated to the histopathological severity of knee oa at any of the time points assessed. mhc mrna measurements revealed a significant elevation in mhc iix mrna (associated with fast-twitch skeletal muscle fibres) coincident with the initiation of oa at 3 months of age, with preliminary findings suggestive of a positive correlation to oa severity at this time point. conclusions these preliminary findings suggest that disease initiation in the ageing guinea pig model of oa is not associated with overt quadriceps muscle atrophy but instead is coincident with altered expression of mrnas associated with quadriceps skeletal muscle contractile properties (specifically fast-twitch mhc iix).",0
"trypanosomes mostly regulate gene expression through post-transcriptional mechanisms, particularly mrna stability. however, much mrna degradation is cytoplasmic such that mrna nuclear export must represent an important level of regulation. ribosomal rnas must also be exported from the nucleus and the trypanosome orthologue of nmd3 has been confirmed to be involved in rrna processing and export, matching its function in other organisms. surprisingly, we found that tb nmd3 depletion also generates mrna accumulation of procyclin-associated genes (pags), these being co-transcribed by rna polymerase i with the procyclin surface antigen genes expressed on trypanosome insect forms. by whole transcriptome rna-seq analysis of tb nmd3-depleted cells we confirm the regulation of the pag transcripts by tb nmd3 and using reporter constructs reveal that pag1 regulation is mediated by its 5′utr. dissection of the mechanism of regulation demonstrates that it is not dependent upon translational inhibition mediated by tb nmd3 depletion nor enhanced transcription. however, depletion of the nuclear export factors xpo1 or mex67 recapitulates the effects of tb nmd3 depletion on pag mrnas and mrnas accumulated in the nucleus of tb nmd3-depleted cells. these results invoke a novel rna regulatory mechanism involving the nmd3-dependent nuclear export of mrna cargos, suggesting a shared platform for mrna and rrna export.",1
"to understand the molecular mechanisms of parasitism in vivo, it is essential to elucidate how the transcriptomes of the human hosts and the infecting parasites affect one another. here we report the rna-seq analysis of 116 indonesian patients infected with the malaria parasite plasmodium falciparum (pf). we extracted rnas from their peripheral blood as a mixture of host and parasite transcripts and mapped the rna-seq tags to the human and pf reference genomes to separate the respective tags. we were thus able to simultaneously analyze expression patterns in both humans and parasites. we identified human and parasite genes and pathways that correlated with various clinical data, which may serve as primary targets for drug developments. of particular importance, we revealed characteristic expression changes in the human innate immune response pathway genes including tlr2 and ticam2 that correlated with the severity of the malaria infection. we also found a group of transcription regulatory factors, jund , for example, and signaling molecules, tnfaip3 , for example, that were strongly correlated in the expression patterns of humans and parasites. we also identified several genetic variations in important anti-malaria drug resistance-related genes. furthermore, we identified the genetic variations which are potentially associated with severe malaria symptoms both in humans and parasites. the newly generated data should collectively lay a unique foundation for understanding variable behaviors of the field malaria parasites, which are far more complex than those observed under laboratory conditions.",0
"background the omentum is one of the initial sites for peritoneal metastasis because it possesses milky spots that provide a microenvironment for cancer cells to readily migrate and grow into micrometastases. this study investigated the role of the ccl22-ccr4 axis in gastric cancer cells selectively infiltrating into milky spots. methods gastric cancer mfc cells labelled with dii were injected intraperitoneally into strain 615 mice. the mice were euthanised at specified intervals and the omentum was excised for immunohistochemistry. the effects of ccl22 on the proliferation and migration of mfcs were assessed by mtt and trans-well assays. rt-pcr and western blot analysis detected ccr4 mrna and protein expression levels in mfcs. immunohistochemistry was used to analyse ccl22 and ccr4 expression in the milky spot micrometastases. results two weeks after intraperitoneal injection, the milky spot areas were completely occupied by proliferating gastric cancer cells and cell cluster-type micrometastases were observed. in contrast, cancer cells formed single cell-type micrometastases in the non-milky spot areas. mfcs expressed ccr4, which was localised on the cell surface and or in the cytoplasm. different concentrations of ccl22 significantly increased the proliferation ability of mfcs. additionally, concentrations of ccl22 between 10–100 ng/ml significantly increased the migration of mfcs. within omental milky spots, ccl22 was localised mainly on the cell surface and or in the cytoplasm. within sections of omental milky spot micrometastases, ccr4 was recognised on or in gastric cancer cells, constituent cells milky spots, blood cells and blood endothelial cells. conclusions omental milky spots are a congenial microenvironment for peritoneal free gastric cancer cells to migrate, survive, and establish cell cluster-type metastases. the ccl22-ccr4 axis contributes to this selective infiltration process.",0
"abstract changes in small non-coding rnas such as micro rnas (mirnas) can serve as indicators of disease and can be measured using next-generation sequencing of rna (rna-seq). here, we highlight the need for approaches that complement rna-seq, discover that northern blotting of small rnas is biased against short sequences and develop a protocol that removes this bias. we found that multiple small rna-seq datasets from the worm caenorhabditis elegans had shorter forms of mirnas that appear to be degradation products that arose during the preparatory steps required for rna-seq. when using northern blotting during these studies, we discovered that mirna-length probes can have ∼1000-fold bias against detecting even synthetic sequences that are 8 nt shorter. by using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable nearly equivalent detection of 24 to 14 nt rnas. our protocol can discriminate rnas that differ by a single nucleotide and can detect specific mirnas present in total rna from c. elegans and prnas in total rna from bacteria. this improved northern blotting is particularly useful to analyze products of rna processing or turnover, and functional rnas that are shorter than typical mirnas.",1
"background synthetic antisense molecules have an enormous potential for therapeutic applications in humans. the major aim of such strategies is to specifically interfere with gene function, thus modulating cellular pathways according to the therapeutic demands. among the molecules which can block mrna function in a sequence specific manner are peptide nucleic acids (pna). they are highly stable and efficiently and selectively interact with rna. however, some properties of non-modified aminoethyl glycine pnas (aegpna) hamper their in vivo applications. results we generated new backbone modifications of pnas, which exhibit more hydrophilic properties. when we examined the activity and specificity of these novel phosphonic ester pnas (pepna) molecules in medaka ( oryzias latipes ) embryos, high solubility and selective binding to mrna was observed. in particular, mixing of the novel components with aegpna components resulted in mixed pnas with superior properties. injection of mixed pnas directed against the medaka six3 gene, which is important for eye and brain development, resulted in specific six3 phenotypes. conclusions pnas are well established as powerful antisense molecules. modification of the backbone with phosphonic ester side chains further improves their properties and allows the efficient knock down of a single gene in fish embryos.",0
"background higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. this study utilized next generation sequencing (ngs) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (aba) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. results rna-seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (peg)-induced osmotic stress or exogenous aba. differential gene expression analyses in response to osmotic stress and aba revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. we successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed. conclusions the present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. we are providing an rna-seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. these resources will allow scientists to query gene expression and functional annotation in response to drought.",0
"background this study aimed to evaluate the effects of electro-acupuncture (ea) on neuroplasticity associated with the expressions of neurotrophic factors (ntfs) and their receptors in rats subjected to spinal cord transection (sct). material/methods a total of 144 rats were randomly divided into 3 groups (n=48 per group): sham-operated group, sct group, and ea (electro-acupuncture) group. rats in sct and ea groups received spinal cord transection at t 10 –t 11 vertebral levels. then, ea group rats received ea treatment. reverse transcription polymerase chain reaction was used to detect ntfs and receptors at the mrna level. in situ hybridization (ish) and immunohistochemistry (ihc) were used to detect the expression of ntfs and their receptors. basso, beattie, bresnahan (bbb) scores and cortical somato-sensory evoked potentials (csep) were evaluated to assess the recovery of motor and sensory functions. we also measured bda (biotinylated dextran amine) axonal tracing, cgrp (calcitonin gene-related peptide), gap-43 (growth-associated protein), and synaptophysin immunohistochemistry (ihc). results ea treatment led to obvious improvement in hindlimb locomotor and sensory functions. cntf, fgf-2, and trkb mrna were significantly upregulated, while ngf, pdgf, tgf-β1, igf-1, trka, and trkc mrna were concomitantly downregulated in the caudal spinal segment (css) following ea. immunohistochemistry demonstrated an increased number of cgrp fibers, gap-43, and synaptophysin profiles in the css in the ea rats. conclusions ea may promote the recovery of neuroplasticity in rats subjected to sct. this could be attributed to the systematic regulation of ntfs and their receptors after ea.",0
"we investigated the expression of receptor tyrosine kinase-like orphan receptor (ror) 2 and wnt5a and their prognostic significance in non-small cell lung cancer (nsclc). tissue microarray-based immunohistochemical analysis was performed to determine the expression of ror2 and wnt5a in 219 patients. mrna expression of ror2 and wnt5a was examined in 20 pairs of nsclc and matched adjacent normal tissues by real-time pcr. compared with non-tumorous tissues, both mrna expression and protein product of ror2 and wnt5a genes were significantly increased in nsclc. c 2 analysis revealed that high ror2 or wnt5a expression in nsclc was significantly associated with advanced tnm stage. high expression of both ror2 and wnt5a was also related to advanced tnm stage. multivariate analyses suggested that ror2, wnt5a and tnm stage were independent prognostic factors in nsclc. our clinical findings suggest that high ror2 or wnt5a expression is associated with poor prognosis in nsclc, and combined detection of ror2 and wnt5a is helpful in predicting the prognosis of nsclc.",0
"background & aims farnesoid x receptor (fxr, nr1h4 ) is a ligand-activated transcription factor, belonging to the nuclear receptor superfamily. fxr is highly expressed in the liver and is essential in regulating bile acid homeostasis. fxr deficiency is implicated in numerous liver diseases and mice with modulation of fxr have been used as animal models to study liver physiology and pathology. we have reported genome-wide binding of fxr in mice by chromatin immunoprecipitation - deep sequencing (chip-seq), with results indicating that fxr may be involved in regulating diverse pathways in liver. however, limited information exists for the functions of human fxr and the suitability of using murine models to study human fxr functions. methods in the current study, we performed chip-seq in primary human hepatocytes (phhs) treated with a synthetic fxr agonist, gw4064 or dmso control. in parallel, rna deep sequencing (rna-seq) and rna microarray were performed for gw4064 or control treated phhs and wild type mouse livers, respectively. results chip-seq showed similar profiles of genome-wide fxr binding in humans and mice in terms of motif analysis and pathway prediction. however, rna-seq and microarray showed more different transcriptome profiles between phhs and mouse livers upon gw4064 treatment. conclusions in summary, we have established genome-wide human fxr binding and transcriptome profiles. these results will aid in determining the human fxr functions, as well as judging to what level the mouse models could be used to study human fxr functions.",0
"objective the primary objective of this study is to elucidate the molecular mechanism underlying the reversal of peritoneal fibrosis (pf) by danshenol c, a natural compound derived from the traditional chinese medicine salvia miltiorrhiza. by comprehensively investigating the intricate interactions and signaling pathways involved in danshenol c's therapeutic effects on pf, we aim to unveil novel insights into its pharmacological actions. this investigation holds the potential to revolutionize the clinical application of salvia miltiorrhiza in traditional chinese medicine, offering promising new avenues for the treatment of pf and paving the way for evidence-based therapeutic interventions. methods firstly, we utilized the yatcm database to retrieve the structural formula of danshenol c, while the swisstargetprediction platform facilitated the prediction of its potential drug targets. to gain insights into the genetic basis of pf, we acquired the gse92453 dataset and gpl6480-9577 expression profile from the geo database, followed by obtaining disease-related genes of pf from major disease databases. r software was then employed to screen for deg associated with pf. to explore the intricate interactions between danshenol c's active component targets, we utilized the string database and cytoscape3.7.2 software to construct a ppi network. further analysis in cytoscape3.7.2 enabled the identification of core modules within the ppi network, elucidating key targets and molecular pathways critical to danshenol c's therapeutic actions. subsequently, we employed r to perform go and kegg pathway enrichment analyses, providing valuable insights into the functional implications and potential biological mechanisms of danshenol c in the context of pf. to investigate the binding interactions between the core active components and key targets, we conducted docking studies using chem3d, autodock1.5.6, sybyl2.0, and pymol2.4 software. we applied in vivo and in vitro experiments to prove that danshenol c can improve pf. in order to verify the potential gene and molecular mechanism of danshenol c to reverse pf, we used quantitative pcr, western blot, and apoptosis, ensuring robust and reliable verification of the results. results ① wogonin, sitosterol, and signal transducer and activator of transcription 5 (stat5) emerged as the most significant constituents among the small-molecule active compounds and gene targets investigated. ②38 targets intersected with the disease, among which mapk14, casp3, mapk8 and stat3 may be the key targets; the results of go and kegg analysis showed that there was a correlation between inflammatory pathway and apoptosis. ④real-time pcr showed that the mrna expressions of mapk8 (jnk1), mapk14 (p38) and stat3 were significantly decreased after danshenol c treatment ( p < 0.05), while the mrna expression of casp3 was significantly increased ( p < 0.05)⑤western blot showed that protein expressions of casp3 and mapk14 were significantly increased ( p < 0.05), while the expression of stat3 and mapk8 was decreased after danshenol c treatment ( p < 0.05). ⑥there was no significant difference in flow analysis of apoptosis among groups. conclusion the findings suggest that danshenol c may modulate crucial molecular pathways, including the mapk, apoptosis, calcium signaling, jak-stat signaling, and tnf signaling pathways. this regulation is mediated through the modulation of core targets such as stat3, mapk14, mapk8, casp3, and others. by targeting these key molecular players, danshenol c exhibits the potential to regulate cellular responses to chemical stress and inflammatory stimuli. the identification of these molecular targets and pathways represents a significant step forward in understanding the molecular basis of danshenol c's therapeutic effects in pf. this preliminary exploration provides novel avenues for the development of anti-pf treatment strategies and the discovery of potential therapeutic agents. by targeting specific core targets and pathways, danshenol c opens up new possibilities for the development of more effective and targeted drugs to combat pf. these findings have the potential to transform the landscape of pf treatment and offer valuable insights for future research and drug development endeavors. supplementary information the online version contains supplementary material available at 10.1186/s12906-023-04170-x.",0
"results of overexpression or downregulation of a microrna (mirna) on its target mrna expression are often validated by reverse-transcription and quantitative pcr analysis using an appropriate housekeeping gene as an internal control. the possible direct or indirect effects of a mirna on the expression of housekeeping genes are often overlooked. among many housekeeping genes, expressions of glyceraldehyde-3-phosphate dehydrogenase (gapdh) and β-actin have been used extensively for normalization of gene expression data. here, we show that gapdh and β-actin are direct targets of mir-644a. our data demonstrate the unsuitability of gapdh and β-actin as internal controls in mir-644a functional studies and emphasize the need to carefully consider the choice of a reference gene in mirna experiments.",1
"we generated parietal cortex rna-seq data from individuals with and without alzheimer disease (ad; n control = 13; n ad = 83) from the knight-adrc. using this and an independent (msbb) ad rna-seq dataset, we quantified cortical circular rna (circrna) expression in the context of ad. we identified significant associations between circrna expression and ad diagnosis, clinical dementia severity, and neuropathological severity. we demonstrated that a majority of circrna ad-associations are independent from changes in cognate linear mrna expression or brain cell-type proportions. we provided evidence for circrna expression changes occurring early in pre-symptomatic ad, and in autosomal dominant ad. we also observed ad-associated circrnas co-expressing with known ad genes. finally, we identified potential microrna binding sites in ad-associated circrnas for micrornas predicted to target ad genes. together, these results highlight the importance of analyzing non-linear rnas and support future studies exploring the potential roles of circrnas in ad pathogenesis.",1
"background iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. a lack of bioavailable iron in soil leads to iron deficiency chlorosis (idc), causing a reduction in photosynthesis and interveinal yellowing of leaves. soybeans ( glycine max (l.) merr.) grown in high ph soils often suffer from idc, resulting in substantial yield losses. iron efficient soybean cultivars maintain photosynthesis and have higher yields under idc-promoting conditions than inefficient cultivars. results to capture signaling between roots and leaves and identify genes acting early in the iron efficient cultivar clark, we conducted a rna-seq study at one and six hours after replacing iron sufficient hydroponic media (100 μm iron(iii) nitrate nonahydrate) with iron deficient media (50 μm iron(iii) nitrate nonahydrate). at one hour of iron stress, few genes were differentially expressed in leaves but many were already changing expression in roots. by six hours, more genes were differentially expressed in the leaves, and a massive shift was observed in the direction of gene expression in both roots and leaves. further, there was little overlap in differentially expressed genes identified in each tissue and time point. conclusions genes involved in hormone signaling, regulation of dna replication and iron uptake utilization are key aspects of the early iron-efficiency response. we observed dynamic gene expression differences between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. in roots, genes involved iron uptake and development of casparian strips were induced one hour after iron stress. in leaves, genes involved in dna replication and sugar signaling responded to iron deficiency. the differentially expressed genes (degs) and signaling components identified here represent new targets for soybean improvement. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-702) contains supplementary material, which is available to authorized users.",0
"background coronary artery disease (cad) is a leading cause of death and often presents as a complex systemic disease. the aim of the presents study was to determine the expression profiles of long non-coding rnas (lncrnas) in peripheral blood mononuclear cells (pbmc) of cad patients and controls. methods the lncrna expression profiling of pbmc obtained from 40 cad patients and 10 non-obstructive coronary atherosclerosis (noca) subjects were analyzed using the illumina hiseq 4000 sequencer. quantitative real-time polymerase chain reaction (qrt-pcr) was used to validate the differentially expressed lncrnas. gene ontology (go) enrichment and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analyses of mrna were conducted to predict biologic functions. results our results indicated that lncrnas were differentially expressed; 83 were upregulated lncrnas and 114 were downregulated lncrnas (p<0.05). a horizontal comparison of lncrna expression indicated that the change in the expression profile of 48 lncrnas was consistent with the degree of cad. six lncrnas were validated using qrt-pcr, confirming the accuracy of the rna sequencing analysis. go analysis indicated that these dysregulated lncrna transcripts were related to chromatin organization, cell and cell part, and protein heterodimerization activity. pathway analysis indicated that these differentially expressed genes mainly included viral carcinogenesis, systemic lupus erythematosus and alcoholism. conclusions our preliminary findings indicate that lncrnas could be used as potential biomarkers of subclinical cardiac abnormalities in the pbmc of cad patients. however, further studies are needed to verify our findings and hypothesis.",1
"background huntington disease (hd) is a progressive neurological disorder, with pathological manifestations in brain areas and in periphery caused by the ubiquitous expression of mutant huntingtin protein. transcriptional dysregulation is considered a key molecular mechanism responsible of hd pathogenesis but, although numerous studies investigated mrna alterations in hd, so far none evaluated a whole gene expression profile in blood of r6/2 mouse model. findings to discover novel pathogenic mechanisms and potential peripheral biomarkers useful to monitor disease progression or drug efficacy, a microarray study was performed in blood of r6/2 at manifest stage and wild type littermate mice. this approach allowed to propose new peripheral molecular processes involved in hd and to suggest different panels of candidate biomarkers. among the discovered deregulated processes, we focused on specific ones: complement and coagulation cascades, ppar signaling, cardiac muscle contraction, and dilated cardiomyopathy pathways. selected genes derived from these pathways were additionally investigated in other accessible tissues to validate these matrices as source of biomarkers, and in brain, to link central and peripheral disease manifestations. conclusions our findings validated the skeletal muscle as suitable source to investigate peripheral transcriptional alterations in hd and supported the hypothesis that immunological alteration may contribute to neurological degeneration. moreover, the identification of altered signaling in mouse blood enforce r6/2 transgenic mouse as a powerful hd model while suggesting novel disease biomarkers for pre-clinical investigation.",0
"xenobiotic activation of the aryl hydrocarbon receptor (ahr) by 2,3,7,8-tetrachlorodibenzo- p -dioxin (tcdd) prevents the proper formation of craniofacial cartilage and the heart in developing zebrafish. downstream molecular targets responsible for ahr-dependent adverse effects remain largely unknown; however, in zebrafish sox9b has been identified as one of the most-reduced transcripts in several target organs and is hypothesized to have a causal role in tcdd-induced toxicity. the reduction of sox9b expression in tcdd-exposed zebrafish embryos has been shown to contribute to heart and jaw malformation phenotypes. the mechanisms by which ahr2 (functional ortholog of mammalian ahr) activation leads to reduced sox9b expression levels and subsequent target organ toxicity are unknown. we have identified a novel long noncoding rna ( slincr ) that is upregulated by strong ahr ligands and is located adjacent to the sox9b gene. we hypothesize that slincr is regulated by ahr2 and transcriptionally represses sox9b. the slincr transcript functions as an rna macromolecule, and slincr expression is ahr2 dependent. antisense knockdown of slincr results in an increase in sox9b expression during both normal development and ahr2 activation, which suggests relief in repression. during development, slincr was expressed in tissues with sox9 essential functions, including the jaw/snout region, otic vesicle, eye, and brain. reducing the levels of slincr resulted in altered neurologic and/or locomotor behavioral responses. our results place slincr as an intermediate between ahr2 activation and the reduction of sox9b mrna in the ahr2 signaling pathway.",1
"background the spatiotemporal expression patterns of micrornas (mirnas) are important to the verification of their predicted function. rt-qpcr is the accepted technique for the quantification of mirna expression; however, stem-loop rt-pcr and poly(t)-adapter assay, the two most frequently used methods, are not very convenient in practice and have poor specificity, respectively. results we have developed an optimal approach that integrates these two methods and allows specific and rapid detection of tiny amounts of sample rna and reduces costs relative to other techniques. mirnas of the same sample are polyuridylated and reverse transcribed into cdnas using a universal poly(a)-stem-loop rt primer and then used as templates for sybr® green real-time pcr. the technique has a dynamic range of eight orders of magnitude with a sensitivity of up to 0.2 fm mirna or as little as 10 pg of total rna. virtually no cross-reaction is observed among the closely-related mirna family members and with mirnas that have only a single nucleotide difference in this highly specific assay. the spatial constraint of the stem-loop structure of the modified rt primer allowed detection of mirnas directly from cell lysates without laborious total rna isolation, and the poly(u) tail made it possible to use multiplex rt reactions of mrna and mirnas in the same run. conclusions the cost-effective rt-qpcr of mirnas with poly(a)-stem-loop rt primer is simple to perform and highly specific, which is especially important for samples that are precious and/or difficult to obtain.",1
"antisense transcripts were initially identified as transcriptional noise, but have since been reported to play an important role in the quality control of mirna functions. in this report, we tested the hypothesis that heterogeneous nuclear ribonucleoprotein k (hnrnpk) regulates mirna function via competitive endogenous rnas, such as pseudogenes, long non-coding rnas, and antisense transcripts. based on analyses of rna sequencing data, the knockdown of hnrnpk decreased the antisense ptov1-as1 transcript which harbors five binding sites for mir-1207-5p. we identified heme oxygenase-1 ( ho-1 ) mrna as a novel target of mir-1207-5p by western blotting and ago2 immunoprecipitation. the knockdown of hnrnpk or ptov1-as1 suppressed ho-1 expression by increasing the enrichment of ho-1 mrna in mir-1207-5p-mediated mirisc. downregulation of ho-1 by a mir-1207-5p mimic or knockdown of hnrnpk and ptov1- as1 inhibited the proliferation and clonogenic ability of hela cells. taken together, our results demonstrate that hnrnpk-regulated ptov1-as1 modulates ho-1 expression via mir-1207-5p.",1
"a hallmark of the immune system is the interplay among specialized cell types transitioning between resting and stimulated states. the gene regulatory landscape of this dynamic system has not been fully characterized in human cells. here, we collected atac-seq and rna-seq data under resting and stimulated conditions for up to 32 immune cell populations. stimulation caused widespread chromatin remodeling, including response elements shared between stimulated b and t cells. furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the importance of these cell states in autoimmunity. use of allele-specific read-mapping identified variants that alter chromatin accessibility in particular conditions, allowing us to observe evidence of function for a candidate causal variant that is undetected by existing large-scale studies in resting cells. our results provide a resource of chromatin dynamics and highlight the need for characterization of effects of genetic variation in stimulated cells.",0
"background a comprehensive understanding of the molecular mechanisms of adipogenesis is a critically important strategy for identifying new targets for obesity intervention. methods transcriptomic and lipidomic approaches were used to explore the functional genes regulating adipogenic differentiation and their potential mechanism of action in op9 cells and adipose-derived stem cells. oil red o staining was used to detect oil droplets in adipocytes. results rna sequencing (rna-seq) showed that slc25a5 expression was significantly upregulated in adipogenic differentiation. depletion of slc25a5 led to the suppressed expression of adipogenesis-related genes, reduced the accumulation of triglycerides, and inhibited pparγ protein expression. moreover, the knockdown of slc25a5 resulted in significant reduction of oxidative phosphorylation (oxphos) protein expression (atp5a1, cqcrc2, and mtco1) and atp production. the rna-seq and real-time quantitative polymerase chain reaction (rt–qpcr) results suggested that adipogenic differentiation is possibly mediated by erk1/2 phosphorylation, and this hypothesis was confirmed by intervention with pd98059 (an erk 1/2 inhibitor). conclusions this study indicates that slc25a5 inhibits adipogenesis and might be a new therapeutic target for the treatment of obesity. supplementary information the online version contains supplementary material available at 10.1186/s11658-022-00314-y.",0
"tea ( camellia sinensis l.) is a popular world beverage, and propagation of tea plants chiefly depends on the formation of adventitious roots in cuttings. to better understand potential mechanisms involved in adventitious root formation, we performed transcriptome analysis of single nodal cuttings of c. sinensis treated with or without indole-3-butyric acid (iba) using the illumina sequencing method. totally 42.5 million rna-seq reads were obtained and these were assembled into 59,931 unigenes, with an average length of 732 bp and an n50 of 1292 bp. in addition, 1091 differentially expressed unigenes were identified in the tea cuttings treated with iba compared to controls, including 656 up- and 435 down-regulated genes. further real time rt-pcr analysis confirmed rna-seq data. functional annotation analysis showed that many genes were involved in plant hormone signal transduction, secondary metabolism, cell wall organization and glutathione metabolism, indicating potential contributions to adventitious rooting. our study presents a global view of transcriptome profiles of tea cuttings in response to iba treatment and provides new insights into the fundamental mechanisms associated with auxin-induced adventitious rooting. our data will be a valuable resource for genomic research about adventitious root formation in tea cuttings, which can be used to improve rooting for difficult-to-root varieties.",0
"abstract aims oxidized phospholipids and micrornas (mirnas) are increasingly recognized to play a role in endothelial dysfunction driving atherosclerosis. nrf2 transcription factor is one of the key mediators of the effects of oxidized phospholipids, but the gene regulatory mechanisms underlying the process remain obscure. here, we investigated the genome-wide effects of oxidized phospholipids on transcriptional gene regulation in human umbilical vein endothelial cells and aortic endothelial cells with a special focus on mirnas. methods and results we integrated data from hic, chip-seq, atac-seq, gro-seq, mirna-seq, and rna-seq to provide deeper understanding of the transcriptional mechanisms driven by nrf2 in response to oxidized phospholipids. we demonstrate that presence of nrf2 motif and its binding is more prominent in the vicinity of up-regulated transcripts and transcriptional initiation represents the most likely mechanism of action. we further identified nrf2 as a novel regulator of over 100 endothelial pri-mirnas. among these, we characterize two hub mirnas mir-21-5p and mir-100-5p and demonstrate their opposing roles on mtor , vegfa , hif1a , and myc expressions. finally, we provide evidence that the levels of mir-21-5p and mir-100-5p in exosomes are increased upon senescence and exhibit a trend to correlate with the severity of coronary artery disease. conclusion altogether, our analysis provides an integrative view into the regulation of transcription and mirna function that could mediate the proatherogenic effects of oxidized phospholipids in endothelial cells.",1
"the transcription factor sox9 plays an essential role in determining the fate of several cell types and is a master factor in regulation of chondrocyte development. our aim was to determine which genes in the genome of chondrocytes are either directly or indirectly controlled by sox9. we used rna-seq to identify genes whose expression levels were affected by sox9 and used sox9 chip-seq to identify those genes that harbor sox9-interaction sites. for rna-seq, the rna expression profile of primary sox9 flox/flox mouse chondrocytes infected with ad-cmv- cre was compared with that of the same cells infected with a control adenovirus. analysis of rna-seq data indicated that, when the levels of sox9 mrna were decreased more than 8-fold by infection with ad-cmv- cre , 196 genes showed a decrease in expression of at least 4-fold. these included many cartilage extracellular matrix (ecm) genes and a number of genes for ecm modification enzymes (transferases), membrane receptors, transporters, and others. in chip-seq, 75% of the sox9-interaction sites had a canonical inverted repeat motif within 100 bp of the top of the peak. sox9-interaction sites were found in 55% of the genes whose expression was decreased more than 8-fold in sox9-depleted cells and in somewhat fewer of the genes whose expression was reduced more than 4-fold, suggesting that these are direct targets of sox9. the combination of rna-seq and chip-seq has provided a fuller understanding of the sox9-controlled genetic program of chondrocytes.",0
"complete transcriptomic data at high resolution are available only for a few model organisms with medical importance. the gene structures of non-model organisms are mostly computationally predicted based on comparative genomics with other species. as a result, more than half of the horse gene models are known only by projection. experimental data supporting these gene models are scarce. moreover, most of the annotated equine genes are single-transcript genes. utilizing rna sequencing (rna-seq) the experimental validation of predicted transcriptomes has become accessible at reasonable costs. to improve the horse genome annotation we performed rna-seq on 561 samples of peripheral blood mononuclear cells (pbmcs) derived from 85 warmblood horses. the mapped sequencing reads were used to build a new transcriptome assembly. the new assembly revealed many alternative isoforms associated to known genes or to those predicted by the ensembl and/or gnomon pipelines. we also identified 7,531 transcripts not associated with any horse gene annotated in public databases. of these, 3,280 transcripts did not have a homologous match to any sequence deposited in the ncbi est database suggesting horse specificity. the unknown transcripts were categorized as coding and noncoding based on predicted coding potential scores. among them 230 transcripts had high coding potential score, at least 2 exons, and an open reading frame of at least 300 nt. we experimentally validated 9 new equine coding transcripts using rt-pcr and sanger sequencing. our results provide valuable detailed information on many transcripts yet to be annotated in the horse genome.",0
"background high-throughput sequencing (hts) analysis of microbial communities from the respiratory airways has heavily relied on the 16s rrna gene. given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same rna-seq experiment, while accounting for variation in clinical metadata. methods transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and ncbi-nr protein reference databases. human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. concomitantly, microbial genes were mapped to metabolic databases (cog, seed, and kegg) to infer microbial functions differentially expressed in asthmatics and controls. finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. results and discussion our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. microbial adhesion (virulence) and proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator il1a; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.",0
"recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding rnas in zebrafish, a popular model organism for human diseases. these studies characterized lncrnas in critical developmental stages as well as adult tissues. each of the studies has uncovered a distinct set of lncrnas, with minor overlaps. the availability of the raw rna-seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncrnas. in the present report, we created a catalog of lncrnas in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncrna transcripts in zebrafish. the lncrnas were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincrnas. we created a comprehensive resource which houses the annotation of lncrnas as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. the resource also hosts a genome browser where the datasets could be browsed in the genome context. to the best of our knowledge, this is the first comprehensive resource providing a unified catalog of lncrnas in zebrafish. the resource is freely available at url:",1
"abstract methanogenic archaea play a key role in the global carbon cycle because these microorganisms remineralize organic compounds in various anaerobic environments. the microorganism methanosarcina barkeri is a metabolically versatile methanogen, which can utilize acetate, methanol, and h 2 /co 2 to synthesize methane. however, the regulatory mechanisms underlying methanogenesis for different substrates remain unknown. in this study, rna-seq analysis was used to investigate m. barkeri growth and gene transcription under different substrate regimes. according to the results, m. barkeri showed the best growth under methanol, followed by h 2 /co 2 and acetate, and these findings corresponded well with the observed variations in genes transcription abundance for different substrates. in addition, we identified a novel regulator, msbrm_rs03855 (designated as hdrr), which specifically activates the transcription of the heterodisulfide reductase hdrbca operon in m. barkeri. hdrr was able to bind to the hdrbca operon promoter to regulate transcription. furthermore, the structural model analyses revealed a helix-turn-helix domain, which is likely involved in dna binding. taken together, hdrr serves as a model to reveal how certain regulatory factors control the expression of key enzymes in the methanogenic pathway. importance the microorganism methanosarcina barkeri has a pivotal role in the global carbon cycle and contributes to global temperature homeostasis. the consequences of biological methanogenesis are far-reaching, including impacts on atmospheric methane and co 2 concentrations, agriculture, energy production, waste treatment, and human health. as such, reducing methane emissions is crucial to meeting set climate goals. the methanogenic activity of certain microorganisms can be drastically reduced by inhibiting the transcription of the hdrbca operon, which encodes heterodisulfide reductases. here, we provide novel insight into the mechanisms regulating hdrbca operon transcription in the model methanogen m. barkeri. the results clarified that hdrr serves as a regulator of heterodisulfide reductase hdrbca operon transcription during methanogenesis, which expands our understanding of the unique regulatory mechanisms that govern methanogenesis. the findings presented in this study can further our understanding of how genetic regulation can effectively reduce the methane emissions caused by methanogens.",0
"background trypanosoma brucei species are motile protozoan parasites that are cyclically transmitted by tsetse fly (genus glossina ) causing human sleeping sickness and nagana in livestock in sub-saharan africa. african trypanosomes display digenetic life cycle stages in the tsetse fly vector and in their mammalian host. experimental work on insect-stage trypanosomes is challenging because of the difficulty in setting up successful in vitro cultures. therefore, there is limited knowledge on the trypanosome biology during its development in the tsetse fly. consequently, this limits the development of new strategies for blocking parasite transmission in the tsetse fly. methods in this study, rna-seq data of insect-stage trypanosomes were used to construct a t. brucei gene co-expression network using the weighted gene co-expression analysis (wgcna) method. the study identified significant enriched modules for genes that play key roles during the parasite’s development in tsetse fly. furthermore, potential 3′ untranslated region (utr) regulatory elements for genes that clustered in the same module were identified using the finding informative regulatory elements (fire) tool. results a fraction of gene modules (12 out of 27 modules) in the constructed network were found to be enriched in functional roles associated with the cell division, protein biosynthesis, mitochondrion, and cell surface. additionally, 12 hub genes encoding proteins such as rna-binding protein 6 (rbp6), arginine kinase 1 (ak1), brucei alanine-rich protein (barp), among others, were identified for the 12 significantly enriched gene modules. in addition, the potential regulatory elements located in the 3′ untranslated regions of genes within the same module were predicted. conclusions the constructed gene co-expression network provides a useful resource for network-based data mining to identify candidate genes for functional studies. this will enhance understanding of the molecular mechanisms that underlie important biological processes during parasite’s development in tsetse fly. ultimately, these findings will be key in the identification of potential molecular targets for disease control.",0
"rna polymerase ii-interacting the set2 methyltransferase co-transcriptionally methylates histone h3 at lysine 36 within the body of genes. this modification facilitates histone deacetylation by rpd3s hdac in 3′ transcribed regions to suppress cryptic initiation and slow elongation. although this pathway is important for global deacetylation, no strong effects have been seen on genome-wide transcription under optimized laboratory conditions. in contrast, this pathway slows the kinetics of mrna induction when target genes are induced upon environmental changes. interestingly, a majority of set2-repressed genes are overlapped by a lncrna transcription that targets h3k36 methylation and deacetylation by rpd3s hdac to mrna promoters. furthermore, this pathway delays the induction of many cryptic transcripts upon environmental changes. therefore, the set2-rpd3s hdac pathway functions to fine-tune expression dynamics of mrnas and ncrnas.",1
"it is difficult to treat malignant melanoma because of its high malignancy. new and effective therapies for treating malignant melanoma are urgently needed. ergosterols are known for specific biological activities and have received widespread attention in cancer therapy. here, lh-1 , a kind of ergosterol from the secondary metabolites of the marine fungus pestalotiopsis sp., was extracted, isolated, purified, and further investigated the biological activities against melanoma. in vitro experiments, the anti-proliferation effect on tumor cells was detected by mtt and colony formation assay, and the anti-metastatic effect on tumor cells was investigated by wound healing assay and transwell assay. subcutaneous xenograft models, histopathology, and immunohistochemistry have been used to verify the anti-tumor, toxic, and side effect in vivo. besides, the anti-tumor mechanism of lh-1 was studied by mrna sequencing. in vitro , lh-1 could inhibit the proliferation and migration of melanoma cells a375 and b16-f10 in a dose-dependent manner and promote tumor cell apoptosis through the mitochondrial apoptosis pathway. in vivo assays confirmed that lh-1 could suppress melanoma growth by inducing cell apoptosis and reducing cell proliferation, and it did not have any notable toxic effects on normal tissues. lh-1 may play an anti-melanoma role by upregulating obscn gene expression. these findings suggest that lh-1 may be a potential for the treatment of melanoma.",0
"using rna-seq (rna sequencing) of ribosome-depleted rna, we have identified 1,273 lncrnas (long non-coding rnas) in p493-6 human b-cells. of these, 534 are either up- or downregulated in response to myc overexpression. an increase in myc occupancy near their tss (transcription start sites) was observed for myc-responsive lncrnas suggesting these are direct myc targets. myc binds to the same tss across several cell lines, but the number of tss bound depends on cellular myc levels and increases with higher myc concentrations. despite this concordance in promoter binding, a majority of expressed lncrnas are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of myc-bound lncrna promoters. a significant fraction of the lncrna transcripts lack polyadenylation. the rna-seq data were confirmed on eight selected lncrnas by nro (nuclear run-on) and rt-qpcr (quantitative reverse transcription pcr).",1
"we present a new approach to automatic training of a eukaryotic ab initio gene finding algorithm. with the advent of next-generation sequencing, automatic training has become paramount, allowing genome annotation pipelines to keep pace with the speed of genome sequencing. earlier we developed genemark-es, currently the only gene finding algorithm for eukaryotic genomes that performs automatic training in unsupervised ab initio mode. the new algorithm, genemark-et augments genemark-es with a novel method that integrates rna-seq read alignments into the self-training procedure. use of ‘assembled’ rna-seq transcripts is far from trivial; significant error rate of assembly was revealed in recent assessments. we demonstrated in computational experiments that the proposed method of incorporation of ‘unassembled’ rna-seq reads improves the accuracy of gene prediction; particularly, for the 1.3 gb genome of aedes aegypti the mean value of prediction sensitivity and specificity at the gene level increased over genemark-es by 24.5%. in the current surge of genomic data when the need for accurate sequence annotation is higher than ever, genemark-et will be a valuable addition to the narrow arsenal of automatic gene prediction tools.",0
"genistein has been shown to inhibit cancers both in vitro and in vivo, by altering the expression of several micrornas (mirnas). in this study, we focused on tumor suppressor mirnas regulated by genistein and investigated their function in prostate cancer (pca) and target pathways. using mirna microarray analysis and real-time rt-pcr we observed that mir-574-3p was significantly up-regulated in pca cells treated with genistein compared with vehicle control. the expression of mir-574-3p was significantly lower in pca cell lines and clinical pca tissues compared with normal prostate cells (rwpe-1) and adjacent normal tissues. low expression level of mir-574-3p was correlated with advanced tumor stage and higher gleason score in pca specimens. re-expression of mir-574-3p in pca cells significantly inhibited cell proliferation, migration and invasion in vitro and in vivo. mir-574-3p restoration induced apoptosis through reducing bcl-xl and activating caspase-9 and caspase-3. using genecodis software analysis, several pathways affected by mir-574-3p were identified, such as ‘pathways in cancer’, ‘jak-stat signaling pathway’, and ‘wnt signaling pathway’. luciferase reporter assays demonstrated that mir-574-3p directly binds to the 3′ utr of several target genes (such as rac1, egfr and ep300) that are components of ‘pathways in cancer’. quantitative real-time pcr and western analysis showed that the mrna and protein expression levels of the three target genes in pca cells were markedly down-regulated with mir-574-3p. loss-of-function studies demonstrated that the three target genes significantly affect cell proliferation, migration and invasion in pca cell lines. our results show that genistein up-regulates tumor suppressor mir-574-3p expression targeting several cell signaling pathways. these findings enhance understanding of how genistein regulates with mirna in pca.",1
"xist , a long non-coding rna, plays an important role in triggering x chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. however, a porcine xist has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. here, we present a full-length porcine xist sequence assembled using known sequences (genbank), rna-seq data (ncbi sra), and pcr/sequencing. the proposed porcine xist gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. transcription covering the entire xist region was observed specifically in female cells, but not in male cells. we also identified eight transcription starting sites (tsss) and evaluated cpg methylation patterns in the upstream (+2.0 kb) and downstream (−2.0 kb) regions. sixty-seven cg di-nucleotides identified in the target region were considered to be candidate cpg sites, and were enriched in the following two regions: −284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected tss. male 5` region of xist (64.5 sites, 96.26%) had a higher level of cpg methylation than female dna (33.4 sites, 49.85%). taken together, our results revealed that the porcine xist gene is expressed exclusively in female cells, which is influenced by the lower level of cpg methylation in the putative promoter region compared with male cells. the porcine xist presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.",1
"abstract salmonella pathogenicity island (spi) 2 type three secretion system (t3ss)-mediated effector molecules facilitate bacterial survival in phagocytes but their role in the intestinal epithelium in vivo remains ill-defined. using our neonatal murine infection model in combination with spi2 reporter technology and rna-seq of sorted primary enterocytes, we demonstrate expression of spi2 effector molecules by intraepithelial salmonella typhimurium (s. typhimurium). contrary to expectation, immunostaining revealed that infection with spi2 t3ss-mutants resulted in significantly enlarged intraepithelial salmonella -containing vacuoles (scv) with altered cellular positioning, suggesting impaired apical to basolateral transmigration. also, infection with isogenic tagged s. typhimurium strains revealed a reduced spread of intraepithelial spi2 t3ss mutant s. typhimurium to systemic body sites. these results suggest that spi2 t3ss effector molecules contribute to enterocyte apical to basolateral transmigration of the scv during the early stage of the infection.",0
"background microrna (mirna) directed gene repression is an important mechanism of posttranscriptional regulation. comprehensive analyses of how microrna influence biological processes requires paired mirna-mrna expression datasets. however, a review of both geo and arrayexpress repositories revealed few such datasets, which was in stark contrast to the large number of messenger rna (mrna) only datasets. it is of interest that numerous primary mirnas (precursors of microrna) are known to be co-expressed with coding genes (host genes). results we developed a mirna-mrna interaction analyses pipeline. the proposed solution is based on two mirna expression prediction methods – a scaling function and a linear model. additionally, mirna-mrna anti-correlation analyses are used to determine the most probable mirna gene targets ( i.e. the differentially expressed genes under the influence of up- or down-regulated microrna). both the consistency and accuracy of the prediction method is ensured by the application of stringent statistical methods. finally, the predicted targets are subjected to functional enrichment analyses including go, kegg and do, to better understand the predicted interactions. conclusions the mmpred pipeline requires only mrna expression data as input and is independent of third party mirna target prediction methods. the method passed extensive numerical validation based on the binding energy between the mature mirna and 3’ utr region of the target gene. we report that mmpred is capable of generating results similar to that obtained using paired datasets. for the reported test cases we generated consistent output and predicted biological relationships that will help formulate further testable hypotheses.",1
"the rna polymerase ii (rnapii) c-terminal domain kinase, cdk12, regulates genome stability, expression of dna repair genes, and cancer cell resistance to chemotherapy and immunotherapy. in addition to its role in mrna biosynthesis of dna repair genes, we show here that cdk12 phosphorylates the mrna 5′ cap-binding repressor, 4e-bp1, to promote translation of mtorc1-dependent mrnas. in particular, we found that phosphorylation of 4e-bp1 by mtorc1 (t37 and t46) facilitates subsequent cdk12 phosphorylation at two ser–pro sites (s65 and t70) that control the exchange of 4e-bp1 with eif4g at the 5′ cap of chk1 and other target mrnas. rna immunoprecipitation coupled with deep sequencing (rip-seq) revealed that cdk12 regulates release of 4e-bp1, and binding of eif4g, to many mtorc1 target mrnas, including those needed for myc transformation. genome-wide ribosome profiling (ribo-seq) further identified specific cdk12 “translation-only” target mrnas, including many mtorc1 target mrnas as well as many subunits of mitotic and centromere/centrosome complexes. accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of cdk12 or ccnk. we conclude that the nuclear rnapii-ctd kinase cdk12 cooperates with mtorc1, and controls a specialized translation network that is essential for mitotic chromosome stability.",0
"echinococcosis represents a major public health problem worldwide and is considered a neglected disease by the world health organization. the etiological agents are echinococcus tapeworms, which display elaborate developmental traits that imply a complex control of gene expression. micrornas (mirnas), a class of small regulatory rnas, are involved in the regulation of many biological processes such as development and metabolism. they act through the repression of messenger rnas (mrnas) usually by binding to the 3’ untranslated region (3’utr). previously, we described the mirnome of several echinococcus species and found that mirnas are highly expressed in all life cycle stages, suggesting an important role in gene expression regulation. however, studying the role of mirnas in helminth biology remains a challenge. to develop methodology for functional analysis of mirnas in tapeworms, we performed mirna knockdown experiments in primary cell cultures of echinococcus multilocularis , which mimic the development of metacestode vesicles from parasite stem cells in vitro. first, we analysed the mirna repertoire of e. multilocularis primary cells by small rna-seq and found that mir-71, a bilaterian mirna absent in vertebrate hosts, is one of the top five most expressed mirnas. using genomic information and bioinformatic algorithms for mirna binding prediction, we found a high number of potential mir-71 targets in e. multilocularis. inhibition of mirnas can be achieved by transfection of antisense oligonucleotides (anti-mirs) that block mirna function. to this end, we evaluated a variety of chemically modified anti-mirs for mir-71 knockdown. electroporation of primary cells with 2’-o-methyl modified anti-mir-71 led to significantly reduced mir-71 levels. transcriptomic analyses showed that several predicted mir-71 targets were up-regulated in anti-mir-treated primary cells, including genes potentially involved in parasite development, host parasite interaction, and several genes of as yet unknown function. notably, mir-71-silenced primary cell cultures showed a strikingly different phenotype from control cells and did not develop into fully mature metacestodes. these findings indicate an important function of mir-71 in echinococcus development and provide, for the first time, methodology to functionally study mirnas in a tapeworm.",1
"background the majority of published gene-expression studies have used rna isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. in this study, mrna fractions from the cytoplasm and from whole cells (total rna) were prepared from three human cell lines and sequenced using massive parallel sequencing. results for all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total rna fractions. transcripts detected at higher levels in the total rna fraction had longer coding sequences and higher number of mirna target sites. transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. nuclear retention of transcripts and mrna degradation via mirna pathway might contribute to this differential detection of genes. the consequence of the differential detection was further investigated by comparison to proteomics data. interestingly, the expression profiles of cytoplasmic and total rna correlated equally well with protein abundance levels indicating regulation at a higher level. conclusions we conclude that expression levels derived from the total rna fraction be regarded as an appropriate estimate of the amount of mrnas present in a given cell population, independent of the coding sequence length or utrs.",0
"micrornas (mirnas) are short non-coding rna regulators that control gene expression mainly through post-transcriptional silencing. we previously identified mir-205 in a signature for human cervical cancer using a deep sequencing approach. in this study, we confirmed that mir-205 expression was frequently higher in human cervical cancer than their matched normal tissue samples. functionally, we demonstrate that mir-205 promotes cell proliferation and migration in human cervical cancer cells. to further understand the biological roles of mir-205 , we performed in vivo crosslinking and argonaute 2 immunoprecipitation of mirna ribonucleoprotein complexes followed by microarray analysis (clip-chip) to identify its potential mrna targets. applying clip-chip on gain- and loss-of-function experiments, we identified a set of transcripts as potential targets of mir-205. several targets are functionally involved in cellular proliferation and migration. two of them, cyr61 and ctgf, were further validated by western blot analysis and quantification of mrna enrichment in the ago2 immunoprecipitates using qrt-pcr. furthermore, both cyr61 and ctgf were downregulated in cervical cancer tissues. in summary, our findings reveal novel functional roles and targets of mir-205 in human cervical cancer, which may provide new insights about its role in cervical carcinogenesis and its potential value for clinical diagnosis.",1
"background: circular rnas have been widely explored as potential biomarkers and therapeutic targets in bladder cancer; however, few have been functionally characterized. results: cirs-6 is expressed at low levels in cancer tissues and advanced tumor grades and stages, and its expression correlates with better outcomes for bladder cancer patients. in vitro and in vivo, cirs-6 was shown to suppress bladder cancer growth by sponging mir-653 to elevate march1 levels. march1 is an e3 ubiquitin ligase that has been proven to suppress bladder cancer growth; knocking down march1 in cirs-6 overexpressed bladder cancer cells reversed the tumor suppressive effect of cirs-6. conclusions: our study identifies an oncogenic role of cirs-6 and suggests its usefulness as a novel biomarker for bladder cancer diagnosis and prognosis and as a therapeutic target for bladder cancer. methods: cirs-6 was identified by rna-seq and qpcr; cck8 assays, clone forming assays and cell cycle analyses were performed to evaluate the in vitro effect of cirs-6 in bladder cancer; further, a mouse subcutaneous tumor model was designed for in vivo analysis. rna pulldown assays, mirna capture experiments and dual luciferase assessments were applied for mechanistic studies.",1
new methods employ rna-seq to study single cells within complex tissues by in situ sequencing or mrna capture from single photoactivated cells.,0
"integrin ανβ6 has emerged as a potential novel target for anticancer and plays a major role in promoting malignant tumor progression. recent studies indicate that integrin ανβ6 occurs in many cancers. however, whether and how ανβ6 is regulated by genetic and epigenetic mechanisms in breast cancer remain unknown. in the present study, two different short hairpin rnas (shrnas) targeting the β6 gene were designed and constructed into psuper, respectively, which were transfected into the mcf-7 human breast adenocarcinoma cell line. the β6-shrna stably transfected cells were successfully established, and significant lower levels of ανβ6 mrna and protein expression were confirmed. furthermore, inhibition of integrin ανβ6 markedly downregulated the expression of matrix metalloproteinase-9 (mmp-9), matrix metalloproteinase-3 (mmp-3) and urokinase plasminogen activator (upa) in tumor conditioned medium. furthermore, β6-shrna-mediated silencing of the ανβ6 gene obviously decreased the expression of erk1/2. in particular, supression of integrin ανβ6 caused significant downregulation of the degradation of basement membrane type iv collagen secretion via modulation of the plasminogen activation cascade. our results thus indicate that ανβ6 plays a fundamental role in promoting invasion and growth of breast adenocarcinoma cells. taken together, this study revealed that targeting of the β6 gene by rna interference (rnai) could efficiently downregulate ανβ6 expression and suppress the erk1/2-dependent extracellular matrix degradation in vitro , which is dependent upon inactivation of the mitogen-activated protein kinase (mapk) pathway. these findings may offer a useful therapeutic approach to block invasion and migration of breast cancer cells.",0
"abstract staphylococcus aureus is a leading cause of difficult-to-treat infections. the capacity of s. aureus to survive and persist within phagocytic cells is an important factor contributing to therapy failures and infection recurrence. therefore, interfering with s. aureus intracellular persistence is key to treatment success. in this study, we used a s. aureus strain carrying the reporter mkikumegr that enables the monitoring of the metabolic status of intracellular bacteria to achieve a better understanding of the molecular mechanisms facilitating s. aureus survival and persistence within macrophages. we found that shortly after bacteria internalization, a large fraction of macrophages harbored mainly s. aureus with high metabolic activity. this population decreased gradually over time with the concomitant increase of a macrophage subpopulation harboring s. aureus with low metabolic activity, which prevailed at later times. a dual rna-seq analysis performed in each macrophage subpopulation showed that the host transcriptional response was similar between both subpopulations. however, intracellular s. aureus exhibited disparate gene expression profiles depending on its metabolic state. whereas s. aureus with high metabolic activity exhibited a greater expression of genes involved in protein synthesis and proliferation, bacteria with low metabolic activity displayed a higher expression of oxidative stress response-related genes, silenced genes involved in energy-consuming processes, and exhibited a dormant-like state. consequently, we propose that reducing metabolic activity and entering into a dormant-like state constitute a survival strategy used by s. aureus to overcome the adverse environment encountered within macrophages and to persist in the intracellular niche.",0
"background recent studies indicated that a synthetic oligonucleotide containing un-methylated cpg oligodeoxynucleotides (cpg-odn) has a potential function for cancer therapy. in this study, we evaluated the chemosensitizing effects of cpg-odn in 5-fluorouracil (5-fu)-treated hepg2 human hepatoma cells. methods cell viability assay were utilized to evaluate the direct cytotoxicity of cpg-odn in the presence or absence of 5-fu in hepg2 cells, and apoptosis as well as cell-cycle was examined by flow cytometry analysis. the mrna expression of bcl-2, livin and survivin within hepg2 cells treated with cpg-odn and/or 5-fu were analyzed by real time pcr assay in vitro. results cpg-odn in combination with 5-fu could decrease cell viability, increase apoptosis and further induce hepg2 cells cycle arrest at s phase when compared with cpg-odn or 5-fu. cpg-odn or 5-fu could down-regulate the mrna expression of bcl-2 within hepg2 cells. the mrna expression of livin and survivin decreased in cells treated with cpg-odn alone but increased in cells treated with 5-fu alone. however, cpg-odn in combination with 5-fu could down-regulate the mrna expression of livin and survivin within hepg2 cells. conclusions our finding demonstrated that cpg-odn enhanced the chemosentivity of 5-fu in hepg2 human hepatoma cells at least in part by down-regulating the expression of livin and survivin, leading to apoptosis and further inducing cell cycle arrest at s phase. therefore, cpg-odn may be a potential candidate as chemosensitizer for human hepatocellular carcinoma.",0
"background the enhancer of zeste homolog 2 (ezh2) was found to be overexpressed and associated with tumor metastasis in esophageal squamous cell carcinoma (escc). on the other hand, it was reported that mir-26a, mir-98, mir-101, mir-124, mir-138 and mir-214 could inhibit the expression of ezh2 in some tumors. however, the role of mirnas in the regulation of ezh2 expression in human escc has not been documented. the aim of this study was to determine the role of these mirnas in the regulation of tumor metastasis via ezh2 overexpression in human escc. methods and results the expression of these mirnas and ezh2 mrna were examined by qpcr and the expression of ezh2 protein was detected by western blot. the role of these mirnas in migration and invasion was studied in escc cell line (eca109) transfected with mirna mimics or cotransfected with mirna mimics and pcdna-ezh2 plasmid (without the 3’-utr of ezh2). through clinical investigation, we found that mir-98 and mir-214 expression was significantly lower in escc tissues than in matched normal tissues, and the expression level of mir-98 and mir-214 was inversely correlated to ezh2 protein expression and the clinical features such as pathological grade, tumor stage and lymph node metastasis in escc. in eca109 cells, overexpression of mir-98 and mir-214 significantly inhibited the migration and invasion of escc cells, which was reversed by transfection of ezh2. conclusions these findings suggest that decreased expression of mir-98 and mir-214 might promote metastasis of human escc by inducing accumulation of ezh2 protein.",1
"kansenone is a triterpene from the root of the traditional chinese medicine, euphorbia kansui. however, kansenone exerts serious toxicity, but the exact mechanism was not clear. in this work, the effects of kansenone on cell proliferation, cell cycle, cell damage, and cell apoptosis were investigated. the suppression of cell proliferation was assessed via the colorimetric mtt assay, and cell morphology was visualized via inverted microscopy after iec-6 cells were incubated with different concentrations of kansenone. reactive oxygen species (ros), superoxide dismutase (sod) and malondialdehyde (mda) content were detected for evaluating cell damage. rnase/propidium iodide (pi) labeling for evaluation of cell cycle distribution was performed by flow cytometry analysis. annexin v-fluorescein isothiocyanate (fitc)/pi and hoechst 33342/annexin v-fitc/pi staining assay for cell apoptosis detection were performed using confocal laser scanning microscopy and high content screening. moreover, apoptosis induction was further confirmed by transmission electron microscope (tem) and jc-1 mitochondrial membrane potential, western blot and rt-pcr analysis. the results demonstrated that kansenone exerted high cytotoxicity, induced cell arrest at g0/g1 phase, and caused mitochondria damage. in addition, kansenone could up-regulate the apoptotic proteins bax, aif, apaf-1, cytochrome c , caspase-3, caspase-9, caspase-8, fasr, fasl, nf-κb, and tnfr1 mrna expression levels, and down-regulate the anti-apoptotic bcl-2 family proteins, revealing that kansenone induces apoptosis through both the death receptor and mitochondrial pathways.",0
"many studies have recently suggested that micrornas (mirnas) contribute to the development of various types of human cancers as well as to their invasive and metastatic capacities. previously, our mirna expression signature of renal cell carcinoma (rcc) revealed that microrna-138 ( mir-138 ) was significantly reduced in cancer cells. the aim of the present study was to investigate the functional significance of mir-138 and to identify its target genes in rcc cells. restoration of mature mir-138 in two rcc cell lines (a498 and 786-o) caused changes in the bleb-like cell morphology, characteristics of the epithelial-mesenchymal transition (emt). restoration also significantly inhibited migration and invasion in the two rcc cell lines, suggesting that mir-138 functions as a tumor suppressor. genome-wide gene expression analysis ( mir-138 transfectants and rcc clinical specimens) and targetscan database studies showed that vimentin ( vim ) is a promising candidate target gene of mir-138. it is well known that vim is one of the most widely expressed mammalian intermediate filament proteins. recent studies showed that vim functions in cell adhesion, migration, survival and cell signaling processes via dynamic assembly/disassembly in cancer cells. we focused on vim and investigated whether vim was regulated by tumor suppressive mir-138 and contributed to cancer cell migration and invasion in rcc cells. restoration of mir-138 in rcc cell lines suppressed vim expression at both the mrna and protein levels. silencing studies of vim in rcc cell lines demonstrated significant inhibition of cell migration and invasion activities in si-vim transfectants. in clinical specimens of rcc, the expression levels of vim were significantly upregulated in cancer tissues compared to adjacent non-cancerous tissues. furthermore, immunohistochemistry showed that vim expression levels in rcc specimens were significantly higher than those in normal renal tissues. these data suggest that vim may function as an oncogene and is regulated by tumor suppressive mir-138. the existence of a tumor suppressive mir-138 -mediated oncogenic pathway provides new insights into the potential mechanisms of rcc oncogenesis and metastasis.",1
"liver cirrhosis may lead to portal-systemic collateral formation and bleeding. the hemostatic effect is influenced by the response of collateral vessels to vasoconstrictors. diabetes and glucose also influence vasoresponsiveness, but their net effect on collaterals remains unexplored. this study investigated the impact of diabetes or glucose application on portal-systemic collateral vasoresponsiveness to arginine vasopressin (avp) in cirrhosis. spraque-dawley rats with bile duct ligation (bdl)-induced cirrhosis received vehicle (citrate buffer) or streptozotocin (diabetic, bdl/stz). the in situ collateral perfusion was done after hemodynamic measurements: both were perfused with krebs solution, d-glucose, or d-glucose and naf, with additional opc-31260 for the bdl/stz group. splenorenal shunt vasopressin receptors and g α proteins mrna expressions were evaluated. the survival rate of cirrhotic rats was decreased by stz injection. the collateral perfusion pressure changes to avp were lower in stz-injected groups, which were reversed by opc-31260 (a v 2 r antagonist) and overcome by naf (a g protein activator). the splenorenal shunt v 2 r mrna expression was increased while g α proteins mrna expressions were decreased in bdl/stz rats compared to bdl rats. the g αq and g α11 mrna expressions also correlated with the maximal perfusion pressure changes to avp. diabetes diminished the portal-systemic collateral vascular response to avp in rats with bdl-induced cirrhosis, probably via v 2 receptor up-regulation and g α proteins down-regulation.",0
"background hepatocellular carcinoma (hcc) still represents an unmet medical need. epigenetic inactivation of tumor suppressor genes like rassf1a or apc by overexpression of dna methyltransferases (dnmts) has been shown to be common in hcc and to be linked to the overall prognosis of patients. inhibitors of protein and histone deacetylases (daci) have been demonstrated to possess strong anti-tumor effects in hcc models. methods we therefore investigated whether daci also has any influence on the expression and activity of dnmts and methylated target genes in hepg2 and hep3b cell culture systems and in a xenograft model by immunohistochemistry, westernblotting, rt-qpcr and methylation-specific pcr. results our findings demonstrate a rapid inhibition of dnmt activity 6 h after treatment with 0.1 μm of the pan-daci panobinostat. a downregulation of dnmt mrnas and protein were also observed at later points in time. this loss of dnmt activity and expression was paralleled by a diminished methylation of the target genes rassf1a and apc and a concomitant re-expression of apc mrna and protein. analysis of hepg2 xenograft specimens confirmed these results in vivo. conclusion we suggest a dual mode of action of daci on dna methylation status: a rapid inhibition of enzyme activity due to interference with posttranslational acetylation and a delayed effect on transcriptional control of dnmt genes by hdac or mirna mechanisms.",0
"noninflammatory clearance of dying cells by professional phagocytes, termed efferocytosis, is fundamental in both homeostasis and inflammatory fibrosis disease but has not been confirmed to occur in chronic pancreatitis (cp). here, we investigated whether efferocytosis constitutes a novel regulatory target in cp and its mechanisms. prss1 transgenic ( prss1 tg ) mice were treated with caerulein to mimic cp development. phospholipid metabolite profiling and epigenetic assays were performed with prss1 tg cp models. the potential functions of atp8b1 in cp model were clarified using atp8b1-overexpressing adeno-associated virus, immunofluorescence, enzyme-linked immunosorbent assay(elisa), and lipid metabolomic approaches. atac-seq combined with rna-seq was then used to identify transcription factors binding to the atp8b1 promoter, and chip-qpcr and luciferase assays were used to confirm that the identified transcription factor bound to the atp8b1 promoter, and to identify the specific binding site. flow cytometry was performed to analyze the proportion of pancreatic macrophages. decreased efferocytosis with aggravated inflammation was identified in cp. the lysophosphatidylcholine (lpc) pathway was the most obviously dysregulated phospholipid pathway, and lpc and atp8b1 expression gradually decreased during cp development. h3k27me3 chip-seq showed that increased atp8b1 promoter methylation led to transcriptional inhibition. atp8b1 complementation substantially increased the lpc concentration and improved cp outcomes. bhlha15 was identified as a transcription factor that binds to the atp8b1 promoter and regulates phospholipid metabolism. our study indicates that the acinar atp8b1/lpc pathway acts as an important “find-me” signal for macrophages and plays a protective role in cp, with atp8b1 transcription promoted by the acinar cell-specific transcription factor bhlha15. bhlha15, atp8b1, and lpc could be clinically translated into valuable therapeutic targets to overcome the limitations of current cp therapies.",0
"in this study, we proposed a systems biology approach to investigate the pathogenic mechanism for identifying significant biomarkers as drug targets and a systematic drug discovery strategy to design a potential multiple-molecule targeting drug for type 2 diabetes (t2d) treatment. we first integrated databases to construct the genome-wide genetic and epigenetic networks (gwgens), which consist of protein–protein interaction networks (ppins) and gene regulatory networks (grns) for t2d and non-t2d (health), respectively. second, the relevant “real gwgens” are identified by system identification and system order detection methods performed on the t2d and non-t2d rna-seq data. to simplify network analysis, principal network projection (pnp) was thereby exploited to extract core gwgens from real gwgens. then, with the help of kegg pathway annotation, core signaling pathways were constructed to identify significant biomarkers. furthermore, in order to discover potential drugs for the selected pathogenic biomarkers (i.e., drug targets) from the core signaling pathways, not only did we train a deep neural network (dnn)-based drug–target interaction (dti) model to predict candidate drug’s binding with the identified biomarkers but also considered a set of design specifications, including drug regulation ability, toxicity, sensitivity, and side effects to sieve out promising drugs suitable for t2d.",0
"simple summary crossbreeding using exotic breeds is usually employed to improve the growth characteristics of indigenous chickens. this mating not only provides growth but adversely affects excess fat deposition as well. this deposition was regulated by a complicated cellular mechanism including peroxisome proliferator-activated receptors (ppars) function. thus, we hypothesized that native chickens breed percentage might be related to ppars gene expression. this study aimed to study the role of ppars on fat deposition in chickens which was the different native genetic background. our results indicated that increasing commercial breed percentage in the chicken leads to increased fat deposition via the increasing of pparg gene expression. therefore, the pparg gene notable as a major gene of cellular fat deposition and might be applied in further study. abstract this study aimed to study the role of ppars on fat deposition in native crossbred chicken. we studied the growth, abdominal, subcutaneous, and intramuscular fat, and mrna expression of ppara and pparg in adipose and muscle tissues of four chicken breeds (ch breed (100% thai native chicken), km1 (50% ch background), km2 (25% ch background), and broiler (br)). the result shows that the br chickens had higher abdominal fat than other breeds ( p < 0.05) and the km2 had an abdominal fat percentage higher than km1 and ch respectively ( p < 0.05). the intramuscular fat of br was greater than km1 and ch ( p < 0.05). in adipose tissue, ppara expression was different among the chicken breeds. however, there were breed differences in pparg expression. study of abdominal fat pparg expression showed the br breed, km1, and km2 breed significantly greater ( p < 0.05) than ch. in 8 to 12 weeks of age, the pparg expression of the ch breed is less than ( p < 0.05) km2. crossbreeding improved the growth of the thai native breed, there was also a corresponding increase in carcass fatness. however, there appears to be a relationship between pparg expression and fat deposition traits. therefore, pparg activity hypothesized to plays a key role in lipid accumulation by up-regulation.",0
"background: circular rnas (circrnas) are widely expressed non-coding rnas in eukaryotic cells, involved in regulating tumorigenesis of several types of cancers. however, the expression profiles and the precise functional role in glioblastoma remain unclear. results: circ-epb41l5 was downregulated in glioblastoma tissues and cell lines compared to the normal brain tissues and cell lines. low circ-epb41l5 expression was correlated to the poor prognosis of glioblastoma patients, while the overexpression inhibited proliferation, clone formation, migration, and invasion abilities of glioma cells, and the suppression had counter effects. furthermore, rna-seq results determined that the host gene was the target gene of circ-epb41l5, which served as a sponge against mir-19a and inhibited mir-19a activity from upregulating the expression of epb41l5. finally, we found that circ-epb41l5 regulated the rhoc expression and phosphorylation of akt through epb41l5. conclusion: the current study highlights a novel suppressive function of circ-epb41l5 and reveals that circ-epb41l5/mir-19a/epb41l5/p-akt regulatory axis plays a striking role in the progression of glioblastoma, which provides a novel insight into the mechanisms underlying glioblastoma. methods: the expression profiles of circrnas in glioblastoma were determined by illumina hiseq from six glioblastoma tissues and six normal brain tissues. then, the correlation between circ-epb41l5 expression and clinical features and the survival time of 45 glioblastoma patients was detected. the interaction between circ-epb41l5, mir-19a, and epb41l5 was assessed by luciferase reporter and rna pull-down assays. the effects of expression of the ectopic intervention of circ-epb41l5 or epb41l5 on proliferation, clone formation, migration, and invasion in vitro and tumorigenesis in vivo were observed to evaluate the function of circ-epb41l5 or epb41l5.",1
"parkinson’s disease (pd) is an age-dependent neurodegenerative condition. leucine-rich repeat kinase 2 (lrrk2) mutations are the most frequent cause of sporadic and autosomal dominant pd. the exact role of lrrk2 protective variants (r1398h, n551k) together with a pathogenic mutant (g2019s) in aging and neurodegeneration is unknown. we generated the following myc-tagged uas-lrrk2 transgenic drosophila: lrrk2 (wt), n551k, r1398h, g2019s single allele, and double-mutants (n551k/g2019s or r1398h/g2019s). the protective variants alone were able to suppress the phenotypic effects caused by the pathogenic lrrk2 mutation. next, we conducted rna-sequencing using mrna isolated from dopaminergic neurons of these different groups of transgenic drosophila. using pathway enrichment analysis, we identified the top 10 modules ( p < 0.05), with “lrrk2 in neurons in parkinson’s disease” among the candidates. further dissection of this pathway identified the most significantly modulated gene nodes such as eef1a2, actb, eef1a, and actin cytoskeleton reorganization. the induction of the pathway was successfully restored by the r1398h protective variant and r1398h-g2019s or n551k-g2019s rescue experiments. the oxidoreductase family of genes was also active in the pathogenic mutant and restored in protective and rescue variants. in summary, we provide in vivo evidence supporting the neuroprotective effects of lrrk2 variants. rna sequencing of dopaminergic neurons identified upregulation of specific gene pathways in the drosophila carrying the pathogenic variant, and this was restored in the rescue phenotypes. using protective gene variants, our study identifies potential new targets and provides proof of principle of a new therapeutic approach that will further our understanding of aging and neurodegeneration in pd.",0
"to assess the properties of lymphokine‐activated killer (lak) cells, we established mouse lak cell clones from lak cell lines induced from c57bl/6 mouse spleen cells. although these clones expressed similar phenotypes to the parent lak cells, lyt‐2 was expressed in a restricted portion of the clones. all clones were found to express t3 cd 3 and t cell receptor (tcr) αβ on their cell surface. rearrangement patterns of tcr were the same among the clones derived from the same parent cell line but differed in those from different cell lines as determined by using cβ 1 and jβ probes. the molecules responsible for lak‐target cell binding were examined by using a monoclonal antibody (mab) against lymphocyte function associated antigen 1 (lfa‐1). this mab (termed kba) showed inhibitory effects on both lak‐target cell binding and cytolytic activity of lak cell clones, indicating a principal role of lfa‐1 in lak cell clones. the magnitude of perform mrna expression in lak cell clones was unrelated to their cytolytic activities.",0
"the analysis of the tench growth hormone gene structure revealed a comparable organization of coding and non-coding regions than other from cyprinid species. based on the performed mrna and amino acid sequence alignments, gh tench is related to asian than to european representatives of cyprinidae family. second aim of the work was to characterize and predict protein structure of the tench growth hormone. tinca tinca gh share many common features with human gh molecule. the tench gh protein binds to the growth hormone receptor (ghr) using two regions i and ii that are situated at opposite sites of molecule. binding site i is placed in the central part of t. tinca gh and h 189 amino acid in the middle region of the iv helix is crucial for gh–ghr interactions.",0
"as a result of the development of high-throughput sequencing and efficient microarray analysis, global gene expression analysis has become an easy and readily available form of data collection. in many research and disease models however, steady state levels of target gene mrna does not always directly correlate with steady state protein levels. post-transcriptional gene regulation is a likely explanation of the divergence between the two. driven by the binding of rna binding proteins (rbp), post-transcriptional regulation affects mrna localization, stability and translation by forming a ribonucleoprotein (rnp) complex with target mrnas. identifying these unknown de novo mrna targets from cellular extracts in the rnp complex is pivotal to understanding mechanisms and functions of the rbp and their resulting effect on protein output. this protocol outlines a method termed rnp immunoprecipitation-microarray (rip-chip), which allows for the identification of specific mrnas associated in the ribonucleoprotein complex, under changing experimental conditions, along with options to further optimize an experiment for the individual researcher. with this important experimental tool, researchers can explore the intricate mechanisms associated with post-transcriptional gene regulation as well as other ribonucleoprotein interactions.",0
"while mrna stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene gc content; suggesting that structural dynamics of dna might also influence codon choice. because minor groove width is highly governed by 3-base periodicity in gc, the existence of triplet-based codons might imply a functional role for the optimization of local dna molecular dynamics via gc content at synonymous sites (≈gc3). we confirm a strong association between gc3-related intrinsic dna flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. we develop a novel test of natural selection targeting synonymous sites and demonstrate that gc3-related dna backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme dna backbone dynamics for their given protein space. this dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. we propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.",0
"objective increasing evidence suggests that mirnas have a profound impact on host defense to hepatitis c virus (hcv) infection and clinical outcome of standard hcv therapy. in this study, we investigated modulation of mirna expression in huh7.5 hepatoma cells by hcv infection and in vitro interferon-αtreatment. methods mirna expression profiling was determined using human mirna taqman® arrays followed by rigorous pairwise statistical analysis. mirna inhibitors assessed the functional effects of mirnas on hcv replication. computational analysis predicted anti-correlated mrna targets and their involvement in host cellular pathways. quantitative rtpcr confirmed the expression of predicted mirna-mrna correlated pairs in hcv-infected huh7.5 cells with and without interferon-α. results seven mirnas (mir-30b, mir-30c, mir-130a, mir-192, mir-301, mir-324-5p, and mir-565) were down-regulated in hcv-infected huh7.5 cells (p<0.05) and subsequently up-regulated following interferon-α treatment (p<0.01). the mir-30(a-d) cluster and mir-130a/301 and their putative mrna targets were predicted to be associated with cellular pathways that involve hepatitis c virus entry, propagation and host response to viral infection. conclusions hcv differentially modulates mirnas to facilitate entry and early establishment of infection in vitro. interferon-α appears to neutralize the effect of hcv replication on mirna regulation thus providing a potential mechanism of action in eradicating hcv from hepatocytes.",1
"background ltr retroelements (ltr res) constitute a major group of transposable elements widely distributed in eukaryotic genomes. through their own mechanism of retrotranscription ltr res enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. nonetheless, transcriptomic activity of ltr res still remains an obscure domain within cell, developmental, and organism biology. results here we present a first comparative analysis of ltr res for anuran amphibians based on a full depth coverage transcriptome of the european pool frog, pelophylax lessonae , the genome of the african clawed frog, silurana tropicalis (release v7.1), and additional transcriptomes of s. tropicalis and cyclorana alboguttata. we identified over 1000 copies of ltr res from all four families (bel/pao, ty1/copia, ty3/gypsy, retroviridae) in the genome of s. tropicalis and discovered transcripts of several of these elements in all rna-seq datasets analyzed. elements of the ty3/gypsy family were most active, especially amn-san elements, which accounted for approximately 0.27% of the genome in silurana. some elements exhibited tissue specific expression patterns, for example hydra1.1 and muerv-like elements in pelophylax. in s. tropicalis considerable transcription of ltr res was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. in the course of embryonic development the spectrum of transcribed ltr res changed; during gastrulation and neurulation muerv-like and snrv like retroviruses were abundantly transcribed while during organogenesis transcripts of the xen1 retroviruses became much more active. conclusions the differential expression of ltr res during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. our results support the meanwhile widely accepted concept that retroelements are not simple “junk dna” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-626) contains supplementary material, which is available to authorized users.",0
"transposable elements (tes) are an integral part of the host transcriptome. te-containing noncoding rnas (ncrnas) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. recent advances in single-cell rna-seq (scrna-seq) revolutionized cell type–specific gene expression analysis. however, effective scrna-seq quantification tools tailored for tes are lacking, limiting our ability to dissect te expression dynamics at single-cell resolution. to address this issue, we established a te expression quantification pipeline that is compatible with scrna-seq data generated across multiple technology platforms. we constructed te-containing ncrna references using bulk rna-seq data and showed that quantifying te expression at the transcript level effectively reduces noise. as proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. we further expanded our analysis to scrna-seq data from early stages of mouse embryogenesis. our results illustrated the dynamic te expression at preimplantation stages and revealed 146 te-containing ncrna transcripts with substantial tissue specificity during gastrulation and early organogenesis.",0
"dna methylome pattern is significantly different among tissues, ages, breeds, and genders. we assessed 20 methylome and transcriptome data in longissimus dorsi (ld) or testicles from bamaxiang (bmx) and large white pigs (lw) by deep sequencing technology. we identified ~55.7m cpgs and 5.30m, 0.20m, 1.20m, and 0.16m differential cpgs ( p <0.01) between tissues, ages, breeds, and genders, respectively. interestingly, 7.54% of differentially methylated regions (dmrs) are co-localized with promoters, which potentially regulate gene expression. rna-seq analysis revealed that 23.42% cpgs are significantly correlated with gene expression (mean |r|=0.58, p <0.01), most of which are enriched in tissue-specific functions. specially, we also found that the methylation levels in promoters of 655 genes were strongly associated with their expression levels (mean |r|=0.66, p <0.01). in addition, differentially methylated cpgs (dmcpgs) between breeds in hoxc gene cluster imply important regulatory roles in myocytes hypertrophy and intermuscular fat (imf) deposition. dramatically, higher similarity of methylation pattern was observed within pedigree than across pedigrees, which indicates the existence of heritable methylation regions. in summary, a part of cpgs in promoter can change its methylation pattern and play a marked regulatory function in different physiological or natural environments.",0
"wolbachia pipientis is an endosymbiotic bacterium that induces a wide range of effects in its insect hosts, including manipulation of reproduction and protection against pathogens. little is known of the molecular mechanisms underlying the insect- wolbachia interaction, though it is likely to be mediated via the secretion of proteins or other factors. there is an increasing amount of evidence that bacteria regulate many cellular processes, including secretion of virulence factors, using small non-coding rnas (srnas), but srnas have not previously been described from wolbachia. we have used two independent approaches, one based on comparative genomics and the other using rna-seq data generated for gene expression studies, to identify candidate srnas in wolbachia. we experimentally characterized the expression of one of these candidates in four wolbachia strains, and showed that it is differentially regulated in different host tissues and sexes. given the roles played by srnas in other host-associated bacteria, the conservation of the candidate srnas between different wolbachia strains, and the sex- and tissue-specific differential regulation we have identified, we hypothesise that srnas may play a significant role in the biology of wolbachia , and in particular in its interactions with its host.",1
"multi-omics datasets represent distinct aspects of the central dogma of molecular biology. such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. activepathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. as part of the icgc/tcga pan-cancer analysis of whole genomes (pcawg) consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. we also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. integration of chip-seq and rna-seq data for master regulators of the hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. activepathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.",0
"the mechanism by which the transcription factors inhibit the mirna expression in ovarian cancer chemoresistance is unclear. the present study investigated the mechanism underlying the transcriptional repression of mir-134 in chemoresistant serous epithelial ovarian cancer. the results demonstrate that nf-κb1, c-rel, and elk1 are involved as transcription factors in repressing mir-134 expression in paclitaxel-resistant ovarian cancer cells. knockdown of these transcription factors led to increased mir-134 expression, resulting in increased apoptosis and inhibition of proliferation in skov3-tr30 cells. nf-κb1, c-rel, and elk1 mrna expression was upregulated in chemoresistant specimens and negatively correlated with mir-134 expression. kaplan–meier analysis revealed that high nuclear expressions of nf-κb1, c-rel, elk1 were significantly associated with short survival in serous epithelial ovarian cancer patients. finally, tab1 was identified as a functional target of mir-134, and the expression of tab1 was increased by the transcription factors of nf-κb1, c-rel, and elk1 via mir-134. taken together, these results provide an insight into the mechanism of repressed mir-134 expression in chemoresistance of serous epithelial ovarian cancer.",1
"micrornas (mirnas), a class of endogenous small noncoding rnas, mediate posttranscriptional regulation of protein-coding genes by binding chiefly to the 3’ untranslated region of target mrnas, leading to translational inhibition, mrna destabilization or degradation. a single mirna concurrently downregulates hundreds of target mrnas designated “targetome”, and thereby fine-tunes gene expression involved in diverse cellular functions, such as development, differentiation, proliferation, apoptosis and metabolism. recently, we characterized the molecular network of the whole human mirna targetome by using bioinformatics tools for analyzing molecular interactions on the comprehensive knowledgebase. we found that the mirna targetome regulated by an individual mirna generally constitutes the biological network of functionally-associated molecules in human cells, closely linked to pathological events involved in cancers and neurodegenerative diseases. we also identified a collaborative regulation of gene expression by transcription factors and mirnas in cancer-associated mirna targetome networks. this review focuses on the workflow of molecular network analysis of mirna targetome in silico. we applied the workflow to two representative datasets, composed of mirna expression profiling of adult t cell leukemia (atl) and alzheimer’s disease (ad), retrieved from gene expression omnibus (geo) repository. the results supported the view that mirnas act as a central regulator of both oncogenesis and neurodegeneration.",1
"abstract diatom bloom is characterized by a rapid increase of population density. perception of population density and physiological responses can significantly influence their survival strategies, subsequently impacting bloom fate. the population density itself can serve as a signal, which is perceived through chemical signals or chlorophyll fluorescence signals triggered by high cell density, and their intracellular signaling mechanisms remain to be elucidated. in this study, we focused on the model diatom, phaeodactylum tricornutum , and designed an orthogonal experiment involving varying cell densities and light conditions, to stimulate the release of chemical signals and light-induced chlorophyll fluorescence signals. utilizing rna-seq and weighted gene co-expression network analysis, we identified four gene clusters displaying density-dependent expression patterns. within these, a potential hub gene, ptslc24a , encoding a na + /ca 2+ exchanger, was identified. based on molecular genetics, cellular physiology, computational structural biology, and in situ oceanic data, we propose a potential intracellular signaling mechanism related to cell density in marine diatoms using ca 2+ : upon sensing population density signals mediated by chemical cues, the membrane-bound ptslc24a facilitates the efflux of ca 2+ to maintain specific intracellular calcium levels, allowing the transduction of intracellular density signals, subsequently regulating physiological responses, including cell apoptosis, ultimately affecting algal blooms fate. these findings shed light on the calcium-mediated intracellular signaling mechanism of marine diatoms to changing population densities, and enhances our understanding of diatom bloom dynamics and their ecological implications.",0
"background rna-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. however, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains. results in order to fill this gap, an innovative software called ora (overlapped reads assembler) was developed. this software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. it can also determine the size and the position of the untranslated regions (utr) and of polycistronic transcripts. as a case study, we analyzed the transcriptional landscape of six s. cerevisiae strains in two different key steps of the fermentation process. this comparative analysis revealed differences in the utr regions of transcripts. by extending the transcriptome analysis to yeast species belonging to the saccharomyces genus, it was possible to examine the conservation level of unknown non-coding rnas and their putative functional role. conclusions by comparing the results obtained using ora with previous studies and with the transcriptome structure determined with other software, it was proven that ora has a remarkable reliability. the results obtained from the training set made it possible to detect the presence of transcripts with variable utrs between s. cerevisiae strains. finally, we propose a regulatory role for some non-coding transcripts conserved within the saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.",0
"objective: this study aimed to find the key genes and mirnas as potential biomarkers related to the progression of colorectal cancer (crc) from crohn’s disease (cd). background: cd is widely accepted as one of the main risk factors leading to crc. so, identifying the novel molecular pathways involved in the development of crc from cd can provide potential solutions for therapeutic interventions. methods: by implementing a systematic approach, we have analyzed mrna and mirna datasets containing crc and cd samples to determine differentially expressed genes (degs) and mirnas (demirna). then by selecting common genes involved in the progression from cd to crc, different downstream analyses including mrna-mirna network, functional enrichment analysis, gene set enrichment analysis, and survival analysis were performed. finally, quantitative real-time pcr (rt-pcr) analysis of tissue samples obtained from normal/crc samples was used to confirm the differential expression of selected genes and mirna. results: there were 10 de mirna and 181 genes degs common between progression from cd to crc. the genes obtained for each of the 10 mirnas were considered as the final target for downstream analyzes. in addition, analysis of rt-pcr indicated that mir-195-5p, phlpp2, and litaf were downregulated in the cancer group compared to the control group. conclusion: this study showed that phlpp2, litaf, and mir-195-5p may have key roles in the tumorigenesis of crc and they can be used as therapeutic targets and diagnostic biomarkers after further in-vitro and in-vivo evaluation.",1
"background the risk for recurrence and metastasis after treatment for urothelial carcinoma of the bladder (ucb) is high. therefore, identifying efficient prognostic markers and novel therapeutic targets is urgently needed. several long noncoding rnas (lncrnas) have been reported to be correlated with ucb progression. in this study, we found that the subtype-specific lncrna mir4435-2 host gene (mir4435-2hg) plays a novel oncogenic role in ucb. methods rna-seq data of tcga/blca were analyzed. the expression of mir4435-2hg was measured by qrt-pcr in 16 pairs of bladder cancer tissues and adjacent normal tissues. the clinical relecance of mir4435-2hg was validated via in situ hybridization performed on an in-house cohort of 116 ucb patient samples. rna pull-down followed by mass spectrometry was performed to identify mir4435-2hg-binding proteins. to identify signaling pathways involved in mir4435-2hg activity, comprehensive in vitro and in vivo studies and rna-seq assays were performed using ucb cells in which mir4435-2hg expression was knocked down or exogenously overexpressed. in addition, we performed rna immunoprecipitation and western blot analyses to validate the identified mir4435-2hg-binding proteins and to determine the molecular mechanisms by which mir4435-2hg promotes ucb progression. results we found that mir4435-2hg was significantly upregulated in the stromal-enriched subtype of ucb. increased mir4435-2hg expression was positively correlated with a high histological grade, advanced t stages, larger tumors, lymph node metastasis and a poor prognosis. in vitro experiments revealed that mir4435-2hg expression silencing suppressed cell proliferation and induced apoptosis. inhibition of mir4434-2hg delayed xenograft tumor growth, while mir4435-2hg overexpression reversed the mir4435-2hg silencing-induced inhibition of ucb tumor phenotype acquisition. mechanistically, we found that mir4435-2hg positively regulated the expression of a variety of cell cycle regulators, including brca2 and ccnd1. knocking down mir4435-2hg increased the sensitivity of tumor cells to the vegfr inhibitor cediranib. furthermore, we found that mir4435-2hg regulated mtor signaling and epithelial-mesenchymal transition (emt) signaling pathways by modulating the phosphorylation of mtor, 70s6k and 4ebp1. finally, we confirmed that mir4435-2hg enhances tumor metastasis through regulation of the emt pathway. conclusions our data indicate that upregulated mir4435-2hg expression levels are significantly correlated with a poor prognosis of ucb patients. mir4435-2hg promotes bladder cancer progression, mediates cell cycle (de)regulation and modulates mtor signaling. mir4435-2hg is an oncogenic lncrna in ucb that may serve as a diagnostic and therapeutic target. supplementary information the online version contains supplementary material available at 10.1007/s13402-023-00826-5.",1
"high-throughput sequencing technologies, including rna-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. while many statistical methods have been proposed for identifying novel transcriptional events with rna-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. few tools exist for the unsupervised discovery of such events without class labels. in this paper, we present sigfuge for identifying genomic loci exhibiting differential transcription patterns across many rna-seq samples. sigfuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. we apply sigfuge to rna-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the cancer genome atlas, and identify several cases of differential isoform usage including cdkn2a , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. by not restricting attention to known sample stratifications, sigfuge offers a novel approach to unsupervised screening of genetic loci across rna-seq cohorts. sigfuge is available as an r package through bioconductor.",0
"quantification of bcr-abl1 mrna levels in peripheral blood of chronic myeloid leukemia patients is a strong indicator of response to tyrosine-kinase inhibitors (tki) treatment. however, additional prognostic markers are needed in order to better classify patients. the hypothesis of leukemic stem cells (lscs) heterogeneity and persistence, suggests that their functional evaluation could be of clinical interest. in this work, we assessed the primitive and progenitor fractions in patients at diagnosis and during tki treatment using functional in vitro assays, defining a “functional leukemic burden” (flb). we observed that the flb was reduced in vivo in both fractions upon treatment. however, different flb levels were observed among patients according to their response to treatment, suggesting that quantification of the flb could complement early molecular monitoring. given that flb assessment is limited by bcr-abl1 mrna expression levels, we developed a novel detection method of primitive cells at the dna level, using patient-specific primers and direct nested pcr in colonies obtained from functional in vitro assays. we believe that this method could be useful in the context of discontinuation trials, given that it is unknown whether the persistent leukemic clone represents lscs, able to resume the leukemia upon tki removal.",0
"hypothalamic gonadotropin-releasing hormone (gnrh) is a major regulator of follicle-stimulating hormone (fsh) secretion in gonadotrope cell in the anterior pituitary gland. micrornas (mirnas) are small rna molecules that control gene expression by imperfect binding to the 3′-untranslated region (3′-utr) of mrna at the post-transcriptional level. it has been proven that mirnas play an important role in hormone response and/or regulation. however, little is known about mirnas in the regulation of fsh secretion. in this study, primary anterior pituitary cells were treated with 100 nm gnrh. the supernatant of pituitary cell was collected for fsh determination by enzyme-linked immunosorbent assay (elisa) at 3 hours and 6 hours post gnrh treatment respectively. results revealed that gnrh significantly promoted fsh secretion at 3 h and 6 h post-treatment by 1.40-fold and 1.80-fold, respectively. fshβ mrna at 6 h post gnrh treatment significantly increased by 1.60-fold. at 6 hours, cells were collected for mirna expression profile analysis using mircury lna array and quantitative pcr (qpcr). consequently, 21 up-regulated and 10 down-regulated mirnas were identified, and qpcr verification of 10 randomly selected mirnas showed a strong correlation with microarray results. chromosome location analysis indicated that 8 mirnas were mapped to chromosome 12 and 4 mirnas to chromosome x. target and pathway analysis showed that some mirnas may be associated with gnrh regulation pathways. in addition, in-depth analysis indicated that 10 up-regulated and 3 down-regulated mirnas probably target fshβ mrna 3′-utr directly, including mir-361-3p, a highly conserved x-linked mirna. most importantly, functional experimental results showed that mir-361-3p was involved in fsh secretion regulation, and up-regulated mir-361-3p expression inhibited fsh secretion, while down-regulated mir-361-3p expression promoted fsh secretion in pig pituitary cell model. these differentially expressed mirnas resolved in this study provide the first guide for post-transcriptional regulation of pituitary gonadotrope fsh secretion in pig, as well as in other mammals.",1
"abstract kaposi's sarcoma-associated herpesvirus is the etiologic agent of kaposi's sarcoma and two b-cell malignancies. recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. however, for kshv progress remained limited due to the overall low percentage of kshv transcripts, even during lytic replication. to address this challenge, we have developed a target enrichment method to increase the kshv-specific reads for both short- and long-read sequencing platforms. furthermore, we combined this approach with the transcriptome resolution through integration of multi-platform data (trimd) pipeline developed previously to annotate transcript structures. trimd first builds a scaffold based on long-read sequencing and validates each transcript feature with supporting evidence from illumina rna-seq and deepcage sequencing data. our stringent innovative approach identified 994 unique kshv transcripts, thus providing the first high-density kshv lytic transcriptome. we describe a plethora of novel coding and non-coding kshv transcript isoforms with alternative untranslated regions, splice junctions and open-reading frames, thus providing deeper insights on gene expression regulation of kshv. interestingly, as described for epstein-barr virus, we identified transcription start sites that augment long-range transcription and may increase the number of latency-associated genes potentially expressed in ks tumors.",1
"background few, if any, protozoan parasites are reported to exhibit extreme organ tropism like the flagellate tritrichomonas foetus. in cattle, t. foetus infects the reproductive system causing abortion, whereas the infection in cats results in chronic large bowel diarrhoea. in the absence of a t. foetus genome, we utilized a de novo approach to assemble the transcriptome of the bovine and feline genotype to identify host-specific adaptations and virulence factors specific to each genotype. furthermore, a subset of orthologs was used to characterize putative druggable targets and expose complications of in silico drug target mining in species with indefinite host-ranges. results illumina rna-seq reads were assembled into two representative bovine and feline transcriptomes containing 42,363 and 36,559 contigs, respectively. coding and non-coding regions of the genome libraries revealed striking similarities, with 24,620 shared homolog pairs reduced down to 7,547 coding orthologs between the two genotypes. the transcriptomes were near identical in functional category distribution; with no indication of selective pressure acting on orthologs despite differences in parasite origins/host. orthologs formed a large proportion of highly expressed transcripts in both genotypes (bovine genotype: 76%, feline genotype: 56%). mining the libraries for protease virulence factors revealed the cysteine proteases (cp) to be the most common. in total, 483 and 445 bovine and feline t. foetus transcripts were identified as putative proteases based on merops database, with 9 hits to putative protease inhibitors. in bovine t. foetus, cp8 is the preferentially transcribed cp while in the feline genotype, transcription of cp7 showed higher abundance. in silico druggability analysis of the two genotypes revealed that when host sequences are taken into account, drug targets are genotype-specific. conclusion gene discovery analysis based on rna-seq data analysis revealed prominent similarities between the bovine and feline t. foetus, suggesting recent adaptation to their respective host/niche. t. foetus represents a unique case of a mammalian protozoan expanding its parasitic grasp across distantly related host lineages. consequences of the host-range for in silico drug targeting are exposed here, demonstrating that targets of the parasite in one host are not necessarily ideal for the same parasite in another host. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-955) contains supplementary material, which is available to authorized users.",0
"single nucleotide polymorphisms (snps) in micrornas (mirnas) or their target sites (mir-snps) within the 3′-utr of mrnas are increasingly thought to play a major role in pathological dysregulation of gene expression. here, we studied the functional role of mir-snps on mirna-mediated post-transcriptional regulation of gene expression. first, analyses were performed on a snp located in the mir-155 target site within the 3′-utr of the angiotensin ii type 1 receptor ( agtr1 ; rs5186, a > c) mrna. second, a snp in the 3′-utr of the muscle ras oncogene homolog ( mras ; rs9818870, c > t) mrna was studied which is located outside of binding sites of mir-195 and mir-135. using these snps we investigated their effects on local rna structure, on local structural accessibility and on functional mirna binding, respectively. systematic computational rna folding analyses of the allelic mrnas in either case predicted significant changes of local rna structure in the vicinity of the cognate mirna binding sites. consistently, experimental in vitro probing of rna showing differential cleavage patterns and reporter gene-based assays indicated functional differences of mirna-mediated regulation of the two agtr1 and mras alleles. in conclusion, we describe a novel model explaining the functional influence of 3′-utr-located snps on mirna-mediated control of gene expression via snp-related changes of local rna structure in non-coding regions of mrna. this concept substantially extends the meaning of disease-related snps identified in non protein-coding transcribed sequences within or close to mirna binding sites.",1
"background lysine-specific demethylase 1 (lsd1, also known as kdm1a and aof2) is a chromatin-modifying activity that catalyzes the removal of methyl groups from lysine residues in histone and non-histone proteins, regulating gene transcription. lsd1 is overexpressed in several cancer types, and chemical inhibition of the lsd1 activity has been proposed as a candidate cancer therapy. here, we examine the levels of lsd1 mrna in human ovarian tumors and the cytotoxicity of several chemical lsd1 inhibitors in a panel of ovarian cancer cell lines. methods we measured lsd1 mrna levels in a cohort of n = 177 normal and heterogeneous tumor specimens by quantitative real time-pcr (qrt-pcr). tumors were classified by figo stage, figo grade, and histological subtypes. we tested the robustness of our analyses in an independent cohort of n = 573 serous tumor specimens (source: tcga, based on microarray). statistical analyses were based on kruskal-wallis/dunn’s and mann whitney tests. changes in lsd1 mrna levels were also correlated with transcriptomic alterations at genome-wide scale. effects on cell viability (mts/pms assay) of six lsd1 inhibitors (pargyline, tcp, rn-1, s2101, cas 927019-63-4, and cbb1007) were also evaluated in a panel of ovarian cancer cell lines (skov3, ovcar3, a2780 and cisplatin-resistant a2780cis). results we found moderate but consistent lsd1 mrna overexpression in stage iiic and high-grade ovarian tumors. lsd1 mrna overexpression correlated with a transcriptomic signature of up-regulated genes involved in cell cycle and down-regulated genes involved in the immune/inflammatory response, a signature previously observed in aggressive tumors. in fact, some ovarian tumors showing high levels of lsd1 mrna are associated with poor patient survival. chemical lsd1 inhibition induced cytotoxicity in ovarian cancer lines, which roughly correlated with their reported lsd1 inhibitory potential (rn-1,s2101 >> pargyline,tcp). conclusions our findings may suggest a role of lsd1 in the biology of some ovarian tumors. it is of special interest to find a correlation of lsd1 mrna overexpression with a transcriptomic signature relevant to cancer. our findings, therefore, prompt further investigation of the role of lsd1 in ovarian cancer, as well as the study of its enzymatic inhibition in animal models for potential therapeutic purposes in the context of this disease.",0
"background isomirs are mirna variants that vary in length and/or sequence when compared to their canonical forms. these variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5′ and/or 3′ end, internal editings or untemplated 3′ end additions. most available tools for small rna-seq data analysis do not allow the identification of isomirs and often require advanced knowledge of bioinformatics. to overcome this, we have developed isomir window, a platform that supports the systematic identification, quantification and functional exploration of isomir expression in small rna-seq datasets, accessible to users with no computational skills. methods isomir window enables the discovery of isomirs and identification of all annotated non-coding rnas in rna-seq datasets from animals and plants. it comprises two main components: the isomir window pipeline for data processing; and the isomir window browser interface. it integrates over ten third-party softwares for the analysis of small-rna-seq data and holds a new algorithm that allows the detection of all possible types of isomirs. these include 3′ and 5′end isomirs, 3′ end tailings, isomirs with single nucleotide polymorphisms (snps) or potential rna editings, as well as all possible fuzzy combinations. isomir window includes all required databases for analysis and annotation, and is freely distributed as a linux virtual machine, including all required software. results isomir window processes several datasets in an automated manner, without restrictions of input file size. it generates high quality interactive figures and tables which can be exported into different formats. the performance of isomir detection and quantification was assessed using simulated small-rna-seq data. for correctly mapped reads, it identified different types of isomirs with high confidence and 100% accuracy. the analysis of a small rna-seq data from basal cell carcinomas (bccs) using isomir window confirmed that mir-183-5p is up-regulated in nodular bccs, but revealed that this effect was predominantly due to a novel 5′end variant. this variant displays a different seed region motif and 1756 isoform-exclusive mrna targets that are significantly associated with disease pathways, underscoring the biological relevance of isomir-focused analysis. isomir window is available at",0
"simple summary gallbladder cancer (gbc) is a rare but lethal cancer. molecular characterization of gbc is insufficient so far, and a comprehensive molecular portrait is warranted to uncover new targets and classify gbc. clustering analysis of rna expression revealed two subclasses of 36 gbcs, which reflects the status of the tumor microenvironment (tme) and poor prognosis of gbc, including epithelial–mesenchymal transition (emt), immune suppression, and the tgf-β signaling pathway. the knockout of mir125b1 in gbc cell lines decreased its invasion ability and altered the emt pathway. mutations of the genes related to the tgf-β signaling pathway were enriched in the poor-prognosis/tme-rich cluster of gbcs. this comprehensive molecular analysis provides a new classification of gbcs based on the tme activity, which is involved with emt and immune suppression for poor prognosis of gbc. this information may be useful for gbc prognosis and therapeutic decision-making. abstract gallbladder cancer (gbc), a rare but lethal disease, is often diagnosed at advanced stages. so far, molecular characterization of gbc is insufficient, and a comprehensive molecular portrait is warranted to uncover new targets and classify gbc. we performed a transcriptome analysis of both coding and non-coding rnas from 36 gbc fresh-frozen samples. the results were integrated with those of comprehensive mutation profiling based on whole-genome or exome sequencing. the clustering analysis of rna-seq data facilitated the classification of gbcs into two subclasses, characterized by high or low expression levels of tme (tumor microenvironment) genes. a correlation was observed between gene expression and pathological immunostaining. tme-rich tumors showed significantly poor prognosis and higher recurrence rate than tme-poor tumors. tme-rich tumors showed overexpression of genes involved in epithelial-to-mesenchymal transition (emt) and inflammation or immune suppression, which was validated by immunostaining. one non-coding rna, mir125b1 , exhibited elevated expression in stroma-rich tumors, and mir125b1 knockout in gbc cell lines decreased its invasion ability and altered the emt pathway. mutation profiles revealed tp53 (47%) as the most commonly mutated gene, followed by elf3 (13%) and arid1a (11%). mutations of arid1a , erbb3 , and the genes related to the tgf-β signaling pathway were enriched in tme-rich tumors. this comprehensive analysis demonstrated that tme, emt, and tgf-β pathway alterations are the main drivers of gbc and provides a new classification of gbcs that may be useful for therapeutic decision-making.",1
"the 3′ untranslated regions (utrs), located at the end of mrna molecules, are believed to play a role in rna replication and/or protein translation. mutations in the tyrosinase ( tyr ) gene are known to cause recessive albinism in humans and other species. in this study, to test whether the crispr/cas9 system works on the mutation of the utrs regulatory region in rabbit, the 3′ utr of the rabbit tyr gene was deleted by a dual sgrna directed crispr/cas9 system. as expected, gray coat color and reduced melanin in hair follicles and irises was found in the mutated rabbit, thus increasing confidence in the association of the mutation of the tyr 3′ utr with graying in rabbit. the graying phenotype was also found in the f1 generation, suggesting that the mutated allele can be stably inherited by the offspring. thus, we provide the first evidence that reduced melanin and graying can be caused by deletion of the tyr 3′ utr in rabbits. additionally, crispr/cas9-mediated large fragment deletions can facilitate genotype to phenotype studies of utrs or non-coding rnas in future.",0
"in arabidopsis , variant in methylation (vim) proteins are required for the maintenance of dna methylation in the cpg dinucleotide context. vim1 acts as a cofactor of dna methyltransferase 1 (met1), although the mechanism for this co-regulation remains unclear. in this study, we used rna-seq analysis to profile the transcriptomes of vim1 , vim1 vim2 vim3 , and met1 null mutants. consistent with previous studies indicating functional redundancy between these vim proteins, we found no transcripts that were significantly misregulated in vim1 mutants. however, we identified a large set of vim protein regulatory targets through analysis of vim1 vim2 vim3 mutants, and we observed that this set is essentially identical to that regulated by met1. log 2 fold changes in gene expression relative to wild type are strongly correlated between vim1 vim2 vim3 and met1 mutants. while the largest subset of these transcripts is upregulated and enriched with transposable elements, we also found small subsets of downregulated genes in each mutant, which are enriched with protein-coding genes. together, these results expand on previous studies that profiled cytosine methylation in the vim1 vim2 vim3 mutant, and show that vim proteins function in transcriptional regulation via their roles in the met1 dna methylation pathway.",0
"recent studies reveal that circular rnas (circrnas) are a novel class of abundant, stable and ubiquitous noncoding rna molecules in animals. comprehensive detection of circrnas from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. here, we present a novel chiastic clipping signal-based algorithm, ciri, to unbiasedly and accurately detect circrnas from transcriptome data by employing multiple filtration strategies. by applying ciri to encode rna-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circrnas as well as fragments specific to them in the human transcriptome. electronic supplementary material the online version of this article (doi:10.1186/s13059-014-0571-3) contains supplementary material, which is available to authorized users.",1
"micrornas (mirnas) are noncoding small nucleic acids that contain ~22 nucleotides and are considered to promote the degradation or inhibit the translation of mrna by targeting its 3′-untranslated region. however, growing evidence has revealed that nuclear mirnas, combined with gene promoters or enhancers, are able to directly mediate gene transcription. these mirnas exert a critical influence on cancer progression by affecting cell growth, migration and invasion. in this review, the direct regulation of gene expression by nuclear mirnas at the transcriptional level was discussed and summarized, and their mechanisms of action in cancers were highlighted with reference to the various body systems.",1
"background pin2/trf1-interacting telomerase inhibitor1 (pinx1) was recently suggested as a putative tumor suppressor in several types of human cancer, based on its binding to and inhibition of telomerase. moreover, loss of pinx1 has been detected in many human malignancies. however, the possible involvement of pinx1 and its clinical/prognostic significance in urothelial carcinoma of the bladder (ucb) are unclear. methods the pinx1 expression profile was examined by quantitative real-time polymerase chain reaction (qrt-pcr), western blotting, and immunohistochemistry (ihc) in ucb tissues and adjacent normal urothelial bladder epithelial tissues. pinx1 was overexpressed and silenced in ucb cell lines to determine its role in tumorigenesis, development of ucb, and the possible mechanism. results pinx1 expression in ucb was significantly down-regulated at both mrna and protein level as compared with that in normal urothelial bladder epithelial tissues. pinx1 levels were inversely correlated with tumor multiplicity, advanced n classification, high proliferation index (ki-67), and poor survival ( p < 0.05). moreover, overexpression of pinx1 in ucb cells significantly inhibited cell proliferation in vitro and in vivo, whereas silencing pinx1 dramatically enhanced cell proliferation. overexpression of pinx1 resulted in g1/s phase arrest and cell growth/proliferation inhibition, while silencing pinx1 led to acceleration of g1/s transition, and cell growth/proliferation promotion by inhibiting/enhancing telomerase activity and via the p16/cyclin d1 pathway. conclusions these findings suggest that down-regulation of pinx1 play an important role in the tumorigenesis and development of ucb and that the expression of pinx1 as detected by ihc is an independent molecular marker in patients with ucb.",0
"abstract breast cancer is one of the most prevalent and recurring cancer types that leads to deaths in women. triple-negative breast cancer (tnbc) is difficult to treat due to the lack of therapeutic targets. many studies have focused on identifying drugs for use as alternative treatments for breast cancer. thioguanine (6-tg) exerts antitumor effects in cancer. increasing evidence has demonstrated that competitive endogenous ribonucleic acids (cernas) are involved in cancer processes. however, the mechanism by which 6-tg regulates lncrna–mirna–mrnas has not been elucidated. we evaluated the antitumor effect of 6-tg in mda-mb-231 cells and comprehensively analyzed the rna-seq data of mda-mb-231 cells treated with 6-tg. our results showed that most tumor pathways were blocked by 6-tg. the hub genes were fn1, flna, flnb, vcl, gsn, myh10, actn4, kdr and ereg , and they were all down-regulated after 6-tg treatment. the coexpression network consisted of 18 micrornas (mirnas), 9 long noncoding rnas (lncrnas) and 20 mrnas. hsa-mir-16-5p and hsa-mir-335-5p targeted the greatest number of mrnas in the network. these molecules could bind to pax8-as1 and eliminate the inhibition of target mrna expression. we showed that pax8-as1 is the main lncrna affected by 6-tg and that pax8-as1 regulates the hub genes in tumor pathways by competitively binding with mir-16-5p and mir-335-5p.",1
"micrornas are small, noncoding rna molecules that regulate gene expression at the post-transcriptional level and play an important role in various biological processes. although most micrornas expression profiles studies have been performed in humans or rodents, relatively limited knowledge also exists in other mammalian species. the identification of the full repertoire of micrornas expressed in the lactating mammary gland of capra hircus would significantly increase our understanding of the physiology of lactating mammary glands. in this study, two libraries were constructed using the lactating mammary gland tissues of laoshan dairy goats ( capra hircus ) during peak and late lactation. solexa high-throughput sequencing technique and bioinformatics were used to determine the abundance and differential expression of the micrornas between peak and late lactation. as a result, 19,044,002 and 7,385,833 clean reads were obtained, respectively, and 1,113 conserved known micrornas and 31 potential novel microrna candidates were identified. a total of 697 conserved micrornas were significantly differentially expressed with a p-value<0.01, 272 micrornas were up-regulated and 425 micrornas were down-regulated during peak lactation. the results were validated using real-time quantitative rt-pcr. 762,557 annotated mrna transcripts were predicted as putative target gene candidates. the go annotation and kegg pathway analysis suggested that differentially expressed micrornas were involved in mammary gland physiology, including signal transduction, and cell-cell and cell-extracellular communications. this study provided the first global of the microrna in capra hircus and expanded the repertoire of micrornas. our results have great significance and value for the elucidation of complex regulatory networks between micrornas and mrnas and for the study of mammary gland physiology and lactation.",1
"background syntrichia caninervis is a desiccation-tolerant moss and the dominant bryophyte of the biological soil crusts (bscs) found in the mojave and gurbantunggut deserts. next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available. results in this study, we employed next generation, high-throughput, illumina rna-seq to analyze the poly-(a) + mrna from hydrated, dehydrating and desiccated s. caninervis gametophores. approximately 58.0 million paired-end short reads were obtained and 92,240 unigenes were assembled with an average size of 493 bp, n50 value of 662 bp and a total size of 45.48 mbp. sequence similarity searches against five public databases (nr, swiss-prot, cosmoss, kegg and cog) found 54,125 unigenes (58.7%) with significant similarity to an existing sequence (e-value ≤ 1e-5) and could be annotated. gene ontology (go) annotation assigned 24,183 unigenes to the three go terms: biological process, cellular component or molecular function. go comparison between p. patens and s. caninervis demonstrated similar sequence enrichment across all three go categories. 29,370 deduced polypeptide sequences were assigned pfam domain information and categorized into 4,212 pfam domains/families. using the planttfdb, 778 unigenes were predicted to be involved in the regulation of transcription and were classified into 49 transcription factor families. annotated unigenes were mapped to the kegg pathways and further annotated using mapman. comparative genomics revealed that 44% of protein families are shared in common by s. caninervis , p. patens and arabidopsis thaliana and that 80% are shared by both moss species. conclusions this study is one of the first comprehensive transcriptome analyses of the moss s. caninervis. our data extends our knowledge of bryophyte transcriptomes, provides an insight to plants adapted to the arid regions of central asia, and continues the development of s. caninervis as a model for understanding the molecular aspects of desiccation-tolerance.",0
"hormone receptor status is of significant value when deciding on anti-estrogenic adjuvant therapy for breast cancer tumors. however, while estrogen receptor (er) regulation was intensively studied, the regulation of progesterone receptor (pr) levels has not been extensively investigated. micrornas (mirnas, mirs) are post-transcriptional negative regulators of gene expression involved in diverse cellular processes. the aim of this study was to identify mirnas that regulate pr in breast cancer. we mapped potential mirna binding sites for mir-181a, mir-23a and mir-26b on pr mrna and demonstrated a direct regulation of pr by these three mirnas by in-vitro luciferase binding assays. over-expression of each mirna in mcf-7 cells resulted in a reduction in the expression levels of pr mrna. then, expression levels of these mirnas were measured in formalin-fixed, paraffin-embedded (ffpe) samples of 29 er-positive breast cancer tumors and adjacent normal breast tissues. a significant reciprocal correlation between pr mrna and the mirna levels were identified suggesting a role for mir-181a, mir-23a and mir-26b in pr regulation in breast cancer. moreover, the average expression fold-changes of the three mirnas between cancerous and normal tissues displayed an opposite trend when analyzing according to immuno-histochemistry(ihc) status. furthermore, mir-181a and mir-26b were found to be over-expressed in most tumor tissues supporting their role in er-positive breast cancer development. we conclude that mir-181a, mir-23a and mir-26b act as negative regulators of pr expression in er-positive breast cancer. the diagnostic and prognostic potential of these mirnas in breast cancer should be further evaluated.",1
"lipopolysaccharide (lps) is one of the important pathogenic substances of e. coli and salmonella , which causes injury to the reproductive system. ovarian dysfunction due to gram-negative bacterial infections is a major cause of reduced reproductive performance in geese. however, the specific molecular mechanisms of lps-induced impairment of sex steroid hormone synthesis have not been determined. the regulatory mechanism of mirna has been proposed in many physiological and pathogenic mechanisms. therefore, the role of mirna in breeding geese exposed to lps during the peak laying period was investigated. in this study, twenty yangzhou geese at peak laying period were injected with lps for 0 h, 24 h, and 36 h. the follicular granulosa layer was taken for rna-seq and analyzed for differentially expressed mirnas. it was observed that lps changed the appearance of hierarchical follicles. mirna sequencing analysis was applied, and mir-21 and smad2 (smad family member 2) were selected from 51 differentially expressed mirnas through bioinformatics prediction. the results showed that mir-21 down-regulated smad2 expression and progesterone (p4) production in lps-treated goose granulosa cells (gcs). it also determined that overexpression of mir-21 or silence of smad2 suppressed the sex steroid biosynthesis pathway by decreasing star and cyp11a1 expression. down-regulation of mir-21 exacerbates the lps-induced decline in p4 synthesis and vice versa. the findings indicated that mir-21 was involved in lps regulation of p4 synthesis in goose granulosa cells by down-regulating smad2. this study provides theoretical support for the prevention of lps-induced ovarian dysfunction in geese.",1
"cirs-7 is an intensely studied, highly expressed and conserved circrna. essentially nothing is known about its biogenesis, including the location of its promoter. a prevailing assumption has been that cirs-7 is an exceptional circrna because it is transcribed from a locus lacking any mature linear rna transcripts of the same sense. to study the biogenesis of cirs-7, we developed an algorithm to define its promoter and predicted that the human cirs-7 promoter coincides with that of the long non-coding rna, linc00632. we validated this prediction using multiple orthogonal experimental assays. we also used computational approaches and experimental validation to establish that cirs-7 exonic sequence is embedded in linear transcripts that are flanked by cryptic exons in both human and mouse. together, this experimental and computational evidence generates a new model for regulation of this locus: (a) cirs-7 is like other circrnas, as it is spliced into linear transcripts; (b) expression of cirs-7 is primarily determined by the chromatin state of linc00632 promoters; (c) transcription and splicing factors sufficient for cirs-7 biogenesis are expressed in cells that lack detectable cirs-7 expression. these findings have significant implications for the study of the regulation and function of cirs-7, and the analytic framework we developed to jointly analyze rna-seq and chip-seq data reveal the potential for genome-wide discovery of important biological regulation missed in current reference annotations.",1
"bladder cancer is a very heterogeneous disease and the molecular mechanisms of carcinogenesis and progression are insufficiently investigated. from the dna sequencing analysis of matched non-muscle-invasive bladder cancer (nmibc) and muscle-invasive bladder cancer (mibc) samples from eight patients, we identified the tumour-associated gene slc35f2 to be mutated in the 5′ and 3′ untranslated region (utr). one mutation in 3′utr increased the luciferase activity reporter, suggesting its influence on the protein expression of slc35f2. the mrna level of slc35f2 was increased in mibc compared with nmibc. furthermore, in immunohistochemical staining, we observed a strong intensity of slc35f2 in single tumour cells and in the border cells of solid tumour areas with an atypical accumulation around the nucleus, especially in the mibc. this suggests that slc35f2 might be highly expressed in aggressive and invasive tumour cells. moreover, knockdown of slc35f2 repressed the growth of bladder cancer cells in the monolayer and spheroid model and suppressed migration and invasion of bladder cancer cells. in conclusion, we suggest that slc35f2 is involved in bladder cancer progression and might provide a new therapeutic approach, for example, by the anti-cancer drug ym155, a cargo of the slc35f2 transporter.",0
"background post-ischemic microglial activation may contribute to neuronal damage through the release of large amounts of pro-inflammatory cytokines and neurotoxic factors. the involvement of micrornas (mirnas) in the pathogenesis of disorders related to the brain and central nervous system has been previously studied, but it remains unknown whether the production of pro-inflammatory cytokines is regulated by mirnas. methods bv-2 and primary rat microglial cells were activated by exposure to oxygen-glucose deprivation (ogd). global cerebral ischemia was induced using the four-vessel occlusion (4-vo) model in rats. induction of pro-inflammatory and neurotoxic factors, such as tumor necrosis factor (tnf)-α, interleukin (il)-1β, and nitric oxide (no), were assessed by elisa, immunofluorescence, and the griess assay, respectively. the mirna expression profiles of ogd-activated bv-2 cells were subsequently compared with the profiles of resting cells in a mirna microarray. bv-2 and primary rat microglial cells were transfected with mir-181c to evaluate its effects on tnf-α production after ogd. in addition, a luciferase reporter assay was conducted to confirm whether tnf-α is a direct target of mir-181c. results ogd induced bv-2 microglial activation in vitro , as indicated by the overproduction of tnf-α, il-1β, and no. global cerebral ischemia/reperfusion injury induced microglial activation and the release of pro-inflammatory cytokines in the hippocampus. ogd also downregulated mir-181c expression and upregulated tnf-α expression. overproduction of tnf-α after ogd-induced microglial activation provoked neuronal apoptosis, whereas the ectopic expression of mir-181c partially protected neurons from cell death caused by ogd-activated microglia. rnainterference-mediated knockdown of tnf-α phenocopied the effect of mir-181c-mediated neuronal protection, whereas overexpression of tnf-α blocked the mir-181c-dependent suppression of apoptosis. further studies showed that mir-181c could directly target the 3′-untranslated region of tnf-α mrna, suppressing its mrna and protein expression. conclusions our data suggest a potential role for mir-181c in the regulation of tnf-α expression after ischemia/hypoxia and microglia-mediated neuronal injury.",1
"the single-cell analysis is becoming a powerful method for early detection of the abnormal variant in tissues, especially for profiling a small number of heterogeneous cells. with the advancement of sequencing technologies, many types of non-coding elements including mirnas and lncrnas which shed light on their heterogeneous patterns and functions among cells, have been profiled at the single-cell level. however, the complete picture of circrna profile at single-cell level is still lacking. in this study, rna-seq data obtained from single hek293t cells have been used to analyze expressions and functions of heterogeneous circrna profiles. the enrichment patterns of circrnas, interactions with mirnas and pathways such as erbb signaling pathway and protein processing in endoplasmic reticulum, have also been investigated. the results showed that circrnas had a specific distribution pattern which was implicated with expression, mirna and functional profiles at single-cell level. this assessment study of the expressions and functions of circrnas at single-cell level shed light on heterogeneities among single cells.",1
"to understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using illumina high-throughput transcriptome sequencing (rna-seq). rna was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. these have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the department of energy joint genome institute. over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. these were annotated as being related to many basic components and processes such as histones and proline-rich proteins. genes encoding storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (lea) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. more significantly, the power of rna-seq to detect genes expressed at low levels revealed hundreds of transcription factors with notable expression in at least one stage of seed development. results from a second biological replicate demonstrate high reproducibility of these data revealing a comprehensive view of the transciptome of seed development in the cultivar williams, the reference cultivar for the first soybean genome sequence.",0
"muscleblind-like (mbnl) proteins are key regulators of precursor and mature mrna metabolism in mammals. based on published and novel data, we explore models of tissue-specific mbnl interaction with rna. we portray mbnl domains critical for rna binding and splicing regulation, and the structure of mbnl's normal and pathogenic rna targets, particularly in the context of myotonic dystrophy (dm), in which expanded cug or ccug repeat transcripts sequester several nuclear proteins including mbnls. we also review the properties of mbnl/rna complex, including recent data obtained from uv cross-linking and immunoprecipitation (clip-seq), and discuss how this interaction shapes normal mbnl-dependent alternative splicing regulation. finally, we review how this acquired knowledge about the pathogenic rna structure and nature of mbnl sequestration can be translated into the design of therapeutic strategies against dm.",0
"the process of store-operated calcium entry (soce), whereby the release of intracellular ca 2+ from endoplasmic reticulum (er) activates ca 2+ influx channels in the plasma membrane, has been demonstrated to impact a diverse range of cell functions. in the present study, we investigated the potential protective effect of soce inhibition against 1-methyl-4-phenylpyridinium (mpp + ) injury by using pharmacological antagonists or specific small interfering rna (sirna) in pc12 cells. the results showed that both antagonists (15 μm mrs-1845 and 50 μm ml-9) and stromal interacting molecule-1 (stim1) targeted sirna (si-stim1) significantly increased cell viability, decreased apoptotic cell death and reduced intracellular reactive oxygen species (ros) production and lipid peroxidation in mpp + injured pc12 cells. soce inhibition also prevented mpp + induced mitochondrial dysfunction and activation of mitochondrial related apoptotic factors, while had no effect on mitochondrial biogenesis. moreover, inhibition of soce by antagonists and sirna increased the expression levels of homer1a mrna and protein, and knockdown of homer1a expression by specific sirna partly reversed the protective effects induced by soce inhibition in pc12 cells. all these results indicated that soce inhibition protected pc12 cells against mpp + insult through upregulation of homer1a expression, and soce might be an ideal target for investigating therapeutic strategy against neuronal injury in pd patients.",0
"despite advances in stem cell biology, there are few effective techniques to promote the osteogenic differentiation of human primary dedifferentiated fat (dfat) cells. we attempted to investigate whether epigallocatechin-3-gallate (egcg), the main component of green tea catechin, facilitates early osteogenic differentiation and mineralization on dfat cells in vitro. dfat cells were treated with egcg (1.25–10 μm) in osteogenic medium (om) with or without 100 nm dexamethasone (dex) for 12 days (hereafter two osteogenic media were designated as om(dex) and om). supplementation of 1.25 μm egcg to both the media effectively increased the mrna expression of collagen 1 ( col1a1 ) and runt-related transcription factor 2 ( runx2 ) and also increased proliferation and mineralization. compared to om(dex) with egcg, om with egcg induced earlier expression for col1a1 and runx2 at day 1 and higher mineralization level at day 12. om(dex) with 10 μm egcg remarkably hampered the proliferation of the dfat cells. these results suggest that om(without dex) with egcg might be a preferable medium to promote proliferation and to induce osteoblast differentiation of dfat cells. our findings provide an insight for the combinatory use of egcg and dfat cells for bone regeneration and stem cell-based therapy.",0
"background subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. methodology/principal findings we conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad beggiatoa spp. mat at mississippi canyon 118 (mc118) in the gulf of mexico. high process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. likewise, 16s ribosomal rrna, dsrab (dissimilatory sulfite reductase) and mcra (methyl coenzyme m reductase) mrna transcripts of sulfate-reducing bacteria (desulfobacteraceae and desulfobulbaceae) and methane-cycling archaea (anme-1 and anme-2) were prevalent at the sediment surface under the mat and at its edge. outside the mat at the surface, 16s rrna sequences indicated mostly aerobes commonly found in seawater. the seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16s rrna transcripts and v6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. conclusions/significance the visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. in contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes.",0
"abstract introduction objective biomarkers for the fatal neurodegenerative disease amyotrophic lateral sclerosis or motor neuron disease (als/mnd) are critical for diagnosis, drug development, clinical trials, and insight into disease pathology. key candidates for biomarkers present in biofluids include non-coding rna (ncrna) transcripts including microrna, piwi-interacting rna and transfer rna. to determine if the central nervous system was the source of the dysregulated ncrna biomarkers we previously observed in serum, we sought to identify dysregulated ncrna candidates in cerebrospinal fluid (csf) which may provide new insight into the disease pathology. methods and materials small rna sequencing (rna-seq) was undertaken on csf samples from healthy controls ( n = 18), disease mimics ( n = 8), and als patients ( n = 40) in our oxford study for biomarkers of als cohort, with rt-qpcr used to confirm their dysregulation. results we found a range of ncrna that were dysregulated in the rna-seq screen, but these failed to be validated or detected in some cases using reverse transcription-quantitative polymerase chain reaction (rt-qpcr). additionally, our previously identified serum ncrna biomarker showed no change in csf or correlation to serum. conclusions this study suggests the csf may not be the source of dysregulated ncrna in the serum and highlights the difficulty in identifying ncrna in csf as biomarkers for als. key messages in this current study, we investigated the expression of non-coding rna transcripts in the cerebrospinal fluid of als patients compared to healthy controls. rna-seq identified dysregulated non-coding rna transcripts, but these were not validated with rt-qpcr. we conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers.",1
"specific nuclear sub-compartments that are regions of fundamental processes such as gene expression or dna repair, contain phosphoinositides (pips). pips thus potentially represent signals for the localization of specific proteins into different nuclear functional domains. we performed limited proteolysis followed by label-free quantitative mass spectrometry and identified nuclear protein effectors of the most abundant pip—phosphatidylinositol 4,5-bisphosphate (pip2). we identified 515 proteins with pip2-binding capacity of which 191 ‘exposed’ proteins represent a direct pip2 interactors and 324 ‘hidden’ proteins, where pip2 binding was increased upon trypsin treatment. gene ontology analysis revealed that ‘exposed’ proteins are involved in the gene expression as regulators of pol ii, mrna splicing, and cell cycle. they localize mainly to non-membrane bound organelles—nuclear speckles and nucleolus and are connected to the actin nucleoskeleton. ‘hidden’ proteins are linked to the gene expression, rna splicing and transport, cell cycle regulation, and response to heat or viral infection. these proteins localize to the nuclear envelope, nuclear pore complex, or chromatin. bioinformatic analysis of peptides bound in both groups revealed that pip2-binding motifs are in general hydrophilic. our data provide an insight into the molecular mechanism of nuclear pip2 protein interaction and advance the methodology applicable for further studies of pips or other protein ligands.",0
"zika virus (zikv) infection can cause fetal developmental abnormalities and guillain–barré syndrome in adults. although progress has been made in understanding the link between zikv infection and microcephaly, the pathology of zikv, particularly the viral reservoirs in human, remains poorly understood. several studies have shown that compared to serum samples, patients’ urine samples often have a longer duration of zikv persistency and higher viral load. this finding suggests that an independent viral reservoir may exist in the human urinary system. despite the clinical observations, the host cells of zikv in the human urinary system are poorly characterized. in this study, we demonstrate that zikv can infect renal proximal tubular epithelial cells (rptepics) in immunodeficient mice in vivo and in both immortalized and primary human renal proximal tubular epithelial cells (hrptepics) in vitro. importantly, zikv infection in mouse kidneys caused caspase-3-mediated apoptosis of renal cells. similarly, in vitro infection of immortalized and primary hrptepics resulted in notable cytopathic effects. consistent with the clinical observations, we found that zikv infection can persist with prolonged duration in hrptepics. rna-seq analyses of infected hrptepics revealed a large number of transcriptional changes in response to zikv infection, including type i interferon signaling genes and anti-viral response genes. our results suggest that hrptepics are a potential reservoir of zikv in the human urinary system, providing a possible explanation for the prolonged persistency of zikv in patients’ urine.",0
"abstract the mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. here, we show deposition of one rna modification- n 2 -methylguanosine (m 2 g) on the g72 of u6 snrna (the catalytic center of the spliceosome) promotes efficient pre-mrna splicing activity in human cells. this modification was identified to be conserved among vertebrates. further, thumpd2 was demonstrated as the methyltransferase responsible for u6 m 2 g72 by explicitly recognizing the u6-specific sequences and structural elements. the knock-out of thumpd2 eliminated u6 m 2 g72 and impaired the pre-mrna splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mrnas in human cells. notably, the aberrantly spliced pre-mrna population elicited the nonsense-mediated mrna decay pathway. we further show that thumpd2 was associated with age-related macular degeneration and retinal function. our study thus demonstrates how an rna epigenetic modification of the major spliceosome regulates global pre-mrna splicing and impacts physiology and disease.",0
"plau codes for the urokinase-type plasminogen activator (upa), critical in cancer metastasis. while the mechanisms driving its overexpression in tumorigenic processes are unknown, it is regulated by the ap-1 transcriptional complex in diverse situations. the ap-1 component fra-1 being overexpressed in aggressive breast cancers, we have addressed its role in the overexpression of plau in the highly metastatic breast cancer model cell line mda-mb231 using chip, pharmacological and rnai approaches. plau transcription appears controlled by 2 ap-1 enhancers located -1.9 (abr-1.9) and -4.1 kb (abr-4.1) upstream of the transcription start site (tss) of the upa-coding mrna, plau-001, that bind fra-1. surprisingly, rna pol ii is not recruited only at the plau-001 tss but also upstream in the abr-1.9 and abr-4.1 region. most pol ii molecules transcribe short and unstable rnas while tracking down toward the tss, where there are converted into plau-001 mrna-productive species. moreover, a minority of pol ii molecules transcribes a low abundance mrna of unknown function called plau-004 from the abr-1.9 domain, whose expression is tempered by fra-1. thus, we unveil a heretofore-unsuspected transcriptional complexity at plau in a reference metastatic breast cancer cell line with pleiotropic effects for fra-1, providing novel information on ap-1 transcriptional action.",0
"background intrahepatic cholangiocarcinoma (icc) is a highly aggressive tumor of the bile duct, and a significant public health problem in east asia, where it is associated with infection by the parasite opisthorchis viverrini. icc is often detected at an advanced stage and with a poor prognosis, making a biomarker for early detection a priority. methods we have comprehensively profiled mirna expression levels in icc tumor tissue using small rna-seq and validated these profiles using quantitative pcr on matched plasma samples. results distinct mirna profiles were associated with increasing histological differentiation of icc tumor tissue. we also observed that histologically normal tissue adjacent to icc tumor displayed mirna expression profiles more similar to tumor than liver tissue from healthy donors. in plasma samples, an eight-mirna signature associated with icc, regardless of the degree of histological differentiation of its matched tissue, forming the basis of a circulating mirna-based biomarker for icc. conclusions the association of unique mirna profiles with different icc subtypes suggests the involvement of specific mirnas during icc tumor progression. in plasma, an eight-mirna signature associated with icc could form the foundation of an accessible (plasma-based) mirna-based biomarker for the early detection of icc. electronic supplementary material the online version of this article (doi:10.1186/s12885-015-1270-5) contains supplementary material, which is available to authorized users.",1
"increasing numbers of sars-cov-2-positive (sars-cov-2 pos ) subjects are detected at silent sars-cov-2 infection stage (ssis). yet, ssis represents a poorly examined time-window wherein unknown immunity patterns may contribute to the fate determination towards persistently asymptomatic or overt disease. here, we retrieved blood samples from 19 asymptomatic and 12 presymptomatic sars-cov-2 pos subjects, 47 age/gender-matched patients with mild or moderate covid-19 and 27 normal subjects, and interrogated them with combined assays of 44-plex cytof, rna-seq and olink. notably, both asymptomatic and presymptomatic subjects exhibited numerous readily detectable immunological alterations, while certain parameters including more severely decreased frequencies of cd107a low classical monocytes, intermediate monocytes, non-classical monocytes and cd62l hi cd8 + t naïve cells, reduced plasma stc1 level but an increased frequency of cd4 + nkt cells combined to distinguish the latter. intercorrelation analyses revealed a particular presymptomatic immunotype mainly manifesting as monocytic overactivation and differentiation blockage, a likely lymphocyte exhaustion and immunosuppression, yielding mechanistic insights into ssis fate determination, which could potentially improve sars-cov-2 management.",0
"abstract advances in high-throughput sequencing have resulted in a massive increase of rna-seq transcriptome data. however, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. to alleviate some of these challenges, we developed trapid 2.0, a web application for the fast and efficient processing of assembled transcriptome data. the initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. the exploratory phase enables downstream analyses from the web application. available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. a comparison with similar tools highlights trapid’s unique features. finally, analyses performed within trapid 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.",0
"the 3′ end of the small ribosomal rnas (ssu rrna) in bacteria is directly involved in the selection and binding of mrna transcripts during translation initiation via well-documented interactions between a shine-dalgarno (sd) sequence located upstream of the initiation codon and an anti-sd (asd) sequence at the 3′ end of the ssu rrna. consequently, the 3′ end of ssu rrna (3′tail) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes. escherichia coli and bacillus subtilis differ in their 3′ ends of ssu rrna, being gauc accuccuua 3′ in e. coli and gauc accuccuu ucu3′ or gauc accuccuu ucua3′ in b. subtilis. such differences in 3′tail lead to species-specific sds (designated sd ec for e. coli and sd bs for b. subtilis ) that can form strong and well-positioned sd/asd pairing in one species but not in the other. selection mediated by the species-specific 3′tail is expected to favor sd bs against sd ec in b. subtilis , but favor sd ec against sd bs in e. coli. among well-positioned sds, sd ec is used more in e. coli than in b. subtilis , and sd bs more in b. subtilis than in e. coli. highly expressed genes and genes of high translation efficiency tend to have longer sds than lowly expressed genes and genes with low translation efficiency in both species, but more so in b. subtilis than in e. coli. both species overuse sds matching the bolded part of the 3′tail shown above. the 3′tail difference contributes to the host specificity of phages.",1
"we downloaded the mrna expression profiles of patients with luad and corresponding clinical data from the cancer genome atlas (tcga) database and used the least absolute shrinkage and selection operator cox regression model to construct a multigene signature in the tcga cohort, which was validated with patient data from the geo cohort. results showed differences in the expression levels of 120 necroptosis-related genes between normal and tumor tissues. an eight-gene signature (cyld, fadd, h2ax, rbck1, ppia, ppid, vdac1, and vdac2) was constructed through univariate cox regression, and patients were divided into two risk groups. the overall survival of patients in the high-risk group was significantly lower than of the patients in the low-risk group in the tcga and geo cohorts, indicating that the signature has a good predictive effect. the time-roc curves revealed that the signature had a reliable predictive role in both the tcga and geo cohorts. enrichment analysis showed that differential genes in the risk subgroups were associated with tumor immunity and antitumor drug sensitivity. we then constructed an mrna–mirna–lncrna regulatory network, which identified lncrna al590666. 2/let-7c-5p/ppia as a regulatory axis for luad. real-time quantitative pcr (rt-qpcr) was used to validate the expression of the 8-gene signature. in conclusion, necroptosis-related genes are important factors for predicting the prognosis of luad and potential therapeutic targets.",1
"early human brain development can be affected by multiple prenatal factors that involve chemical exposures in utero, maternal health characteristics such as psychiatric disorders, and cancer. breast cancer is one of the most common cancers worldwide arising pregnancy. however, it is not clear whether the breast cancer might influence the brain development of fetus. exosomes secreted by breast cancer cells play a critical role in mediating intercellular communication and interplay between different organs. in this work, we engineered human induced pluripotent stem cells (hipscs)-derived brain organoids in an array of micropillar chip and probed the influences of breast cancer cell (mcf-7) derived-exosomes on the early neurodevelopment of brain. the formed brain organoids can recapitulate essential features of embryonic human brain at early stages, in terms of neurogenesis, forebrain regionalization, and cortical organization. treatment with breast cancer cell derived-exosomes, brain organoids exhibited enhanced expression of stemness-related marker oct4 and forebrain marker pax6. rna-seq analysis reflected several activated signaling pathways associated with breast cancer, medulloblastoma and neurogenesis in brain organoids induced by tumor-derived exosomes. these results suggested that breast cancer cell-derived exosomes might lead to the impaired neurodevelopment in the brain organoids and the carcinogenesis of brain organoids. it potentially implies the fetus of pregnant women with breast cancer has the risk of impaired neurodevelopmental disorder after birth. supplementary information the online version contains supplementary material available at 10.1186/s13619-021-00102-7.",1
"abstract ulcerative colitis (uc) is a prevalent relapsing-remitting inflammatory bowel disease whose pathogenetic mechanisms remain elusive. in the present study, colonic biopsies samples from three uc patients treated in the traditional chinese medicine hospital and three healthy controls were obtained. the genome-wide mrna and lncrna expression of the samples were profiled through agilent gene expression microarray. moreover, the genome-wide dna methylation dataset of normal and uc colon tissues was also downloaded from geo for a collaborative analysis. differential expression of lncrna (dels) and mrnas (dems) in uc samples compared with healthy samples were identified by using limma bioconductor package. differentially methylated promoters (dmps) in uc samples compared with controls were obtained through comparing the average methylation level of cpgs located at promoters by using t -test. functional enrichment analysis was performed by the david. string database was applied to the construction of gene functional interaction network. as a result, 2090 dems and 1242 dels were screened out in uc samples that were closely associated with processes related to complement and coagulation cascades, osteoclast differentiation vaccinia, and hemorrhagic diseases. a total of 90 dems and 72 dels were retained for the construction of functional network for the promoters of their corresponding genes were identified as dmps. s100a9, hecw2, sod3 and hix0114733 showed high interaction degrees in the functional network, and expression of s100a9 was confirmed to be significantly elevated in colon tissues of uc patients compared with that of controls by qrt-pcr that was consistent with gene microarray analysis. these indicate that s100a9 could potentially be used as predictive biomarkers in uc.",0
"the present study integrated microrna (mirna) and mrna expression data obtained from atrial fibrillation (af) tissues and healthy tissues, in order to identify mirnas and target genes that may be important in the development of af. the gse28954 mirna expression profile and gse2240 mrna gene expression profile were downloaded from the gene expression omnibus. differentially expressed mirnas and genes (degs) in af tissues, compared with in control samples, were identified and hierarchically clustered. subsequently, differentially expressed mirnas and degs were searched for in the mirecords database and tarbase, and were used to construct a regulatory network using cytoscape. finally, functional analysis of the mirna-targeted genes was conducted. after data processing, 71 differentially expressed mirnas and 390 degs were identified between af and normal tissues. a total of 3,506 mirna-mrna pairs were selected, of which 372 were simultaneously predicted by both mirecords and tarbase, and were therefore used to construct the mirna-mrna regulatory network. furthermore, 10 mirnas and 12 targeted mrnas were detected, which formed 14 interactive pairs. the mirna-targeted genes were significantly enriched into 14 gene ontology (go) categories, of which the most significant was gene expression regulation (go 10468), which was associated with 7 mirnas and 8 target genes. these results suggest that the screened mirnas and target genes may be target molecules in af development, and may be beneficial for the early diagnosis and future treatment of af.",1
"rna-binding proteins are frequently dysregulated in human cancer and able to modulate tumor cell proliferation as well as tumor metastasis through post-transcriptional regulation on target genes. abnormal dna damage response and repair mechanism are closely related to genome instability and cell transformation. here, we explore the function of the rna-binding protein muscleblind-like splicing regulator 2 (mbnl2) on tumor cell proliferation and dna damage response. transcriptome and gene expression analysis show that the pi3k/akt pathway is enriched in mbnl2-depleted cells, and the expression of cyclin-dependent kinase inhibitor 1a (p21 cdkn1a ) is significantly affected after mbnl2 depletion. mbnl2 modulates the mrna and protein levels of p21, which is independent of its canonical transcription factor p53. moreover, depletion of mbnl2 increases the phosphorylation levels of checkpoint kinase 1 (chk1) serine 345 (s345) and dna damage response, and the effect of mbnl2 on dna damage response is p21-dependent. mbnl2 would further alter tumor cell fate after dna damage, mbnl2 knockdown inhibiting dna damage repair and dna damage-induced senescence, but promoting dna damage-induced apoptosis.",0
"esophageal squamous cell carcinoma (escc) has a dismal prognosis because of atypical early symptoms and heterogeneous therapeutic responses. 5-methylcytosine (m 5 c) modification plays an important role in the onset and development of many tumors and is widespread in long non-coding rna (lncrna) transcripts. however, the functions of m 5 c and lncrnas in escc have not been completely elucidated. herein, this study aimed to explore the role of m 5 c-related lncrnas in escc. the rna-seq transcriptome profiles and clinical information were downloaded from the tcga-escc database. pearson analysis was used to identify m 5 c-related lncrnas. then we established the m 5 c-related lncrnas prognostic signature (m 5 c-lps) using univariate cox and least absolute shrinkage and selection operator (lasso) regression analysis. then, the prognostic value of m 5 c-lps was evaluated internally and externally using the tcga-escc and gse53622 databases through multiple methods. we also detected the expression of these lncrnas in escc cell lines and patient tissues. fluorescence in situ hybridization (fish) was used to detect the prognostic value of specific lncrna. in addition, clinical parameters, immune status, genomic variants, oncogenic pathways, enrichment pathways, and therapeutic response features associated with m 5 c-lps were explored using bioinformatics methods. we constructed and validated a prognostic signature based on 9 m 5 c-related lncrnas ( ac002091.2 , ac009275.1 , cahm , linc02057.1 , ac0006329.1 , ac037459.3 , ac064807.1 , atp2b1-as1 , and ubac2-as1 ). the quantitative real-time polymerase chain reaction (qrt-pcr) revealed that most lncrnas were upregulated in escc cell lines and patient tissues. and ac002091.2 was validated to have significant prognostic value in escc patients. a composite nomogram was generated to facilitate clinical practice by integrating this signature with the n stage. besides, patients in the low-risk group were characterized by good clinical outcomes, favorable immune status, and low oncogenic alteration. function enrichment analysis indicated that the risk score was associated with mrna splicing, ncrna processing, and dna damage repair response. at the same time, we found significant differences in the responses to chemoradiotherapy between the two groups, proving the value of m 5 c-lps in treatment decision-making in escc. this study established a novel prognostic signature based on 9 m 5 c-related lncrnas, which is a promising biomarker for predicting clinical outcomes and therapeutic response in escc.",1
"nontypeable haemophilus influenza e (nthi) are gram-negative commensal bacteria that reside in the nasopharynx. nthi can also cause multiple upper and lower respiratory tract diseases that include sinusitis, conjunctivitis, bronchitis, and otitis media. in numerous bacterial species the ferric uptake regulator (fur) acts as a global regulator of iron homeostasis by negatively regulating the expression of iron uptake systems. however in nthi strain 86-028np and numerous other bacterial species there are multiple instances where fur positively affects gene expression. it is known that many instances of positive regulation by fur occur indirectly through a small rna intermediate. however, no examples of small rnas have been described in nthi. therefore we used rna-seq analysis to analyze the transcriptome of nthi strain 86-028np rpsl and an isogenic 86-028np rpsl δ fur strain to identify fur-regulated intergenic transcripts. from this analysis we identified hrrf, the first small rna described in any haemophilus species. orthologues of this small rna exist only among other pasteurellaceae. our analysis showed that hrrf is maximally expressed when iron levels are low. additionally, fur was shown to bind upstream of the hrrf promoter. rna-seq analysis was used to identify targets of hrrf which include genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid biosynthesis. the stability of hrrf is not dependent on the rna chaperone hfq. this study is the first step in an effort to investigate the role small rnas play in altering gene expression in response to iron limitation in nthi.",1
"micrornas (mirnas) are small non-coding rnas that regulate gene expression through the binding of the 3′ untranslated region (3′utr) of specific mrnas. mirnas are post-transcriptional regulators and determine the repression of translation processes or the degradation of mrna targets. recently, another kind of mirna-mediated regulation of translation (repression or activation) involving the binding of mirna to the 5′utr of target gene has been reported. the possible interactions and the mechanism of action have been reported in many works that we reviewed here. moreover, we discussed also the available bioinformatics tools for predicting the mirna binding sites in the 5′utr and public databases collecting this information.",1
"simple summary piwi-interacting rnas (pirnas) exert crucial functions in maintaining the genomic stability and modulating gene expression and biological processes. however, study on pirnas in apis cerana is still lacking until now. here, systematic characterization of pirnas in the larval guts of apis cerana cerana was for the first time conducted, followed by in-depth investigation of the regulatory parts of differentially expressed pirnas (depirnas) in the gut developmente. a total of 621 pirnas were identified in the larval guts, with similar length distribution and first base bias to pirnas discovered in other insects and mammals. in addition, ten and 22 depirnas were respectively detected in the ac4 vs. ac5 and ac5 vs. ac6 comparison groups, with pir-ace-748815, pir-ace-512574, pir-ace-716466, and pir-ace-828146 targeting the highest number of mrnas. further, these targets were engaged in several vital pathways relevant to growth and development, such as the jak/stat, tgf-β, and wnt signaling pathways. our findings provide a new insight into the development of the a. cerana larval gut and a basis for illuminating the pirna-regulated mechanism underlying the gut development. abstract piwi-interacting rnas (pirnas), a class of small non-coding rnas (ncrnas), play pivotal roles in maintaining the genomic stability and modulating biological processes such as growth and development via the regulation of gene expression. however, the pirnas in the asian honeybee ( apis cerana ) are still largely unknown at present. in this current work, on the basis of previously gained high-quality small rna-seq datasets, pirnas in the larval gut of apis cerana cerana , the nominated species of a. cerana , were identified for the first time, followed by an in-depth investigation of the regulatory roles of differentially expressed pirnas (depirnas) in the developmental process of the a. c. cerana. here, a total of 621 pirnas were identified in a. c. cerana larval guts, among which 499 pirnas were shared by 4-(ac4 group), 5-(ac5 group), and 6-day-old (ac6 group) larval guts, while the numbers of unique ones equaled 79, 37, and 11, respectively. the pirnas in each group ranged from 24 nucleotides (nt) to 33 nt in length, and the first base of the pirnas had a cytosine (c) bias. additionally, five up-regulated and five down-regulated pirnas were identified in the ac4 vs. ac5 comparison group, nine of which could target 9011 mrnas; these targets were involved in 41 go terms and 137 pathways. comparatively, 22 up-regulated pirnas were detected in the ac5 vs. ac6 comparison group, 21 of which could target 28,969 mrnas; these targets were engaged in 46 functional terms and 164 pathways. the results suggested an overall alteration of the expression pattern of pirnas during the developmental process of a. c. cerana larvae. the regulatory network analysis showed that pir-ace-748815 and pir-ace-512574 in the ac4 vs. ac5 comparison group as well as pir-ace-716466 and pir-ace-828146 in the ac5 vs. ac6 comparison group were linked to the highest number of targets. further investigation indicated that targets of depirnas in the abovementioned two comparison groups could be annotated to several growth and development-associated pathways, such as the jak/stat, tgf-β, and wnt signaling pathways, indicating the involvement of depirnas in modulating larval gut development via these crucial pathways. moreover, the expression trends of six randomly selected depirnas were verified using a combination of stem-loop rt-pcr and rt-qpcr. these results not only provide a novel insight into the development of the a. c. cerana larval gut, but also lay a foundation for uncovering the epigenetic mechanism underlying larval gut development.",1
"background: lung cancer is the most frequent cancer globally with a high number of cancer-related deaths. the 4-and-a-half lim domain protein 2 (fhl2) is an oncogenic gene, which promotes the proliferation, invasion, and metastasis of cancer cells. in this study, we aimed to demonstrate that lung cancer patients with high fhl2 expression have worse overall survival (os) and relapse-free survival (rfs). methods: tcga was used to study fhl2 mrna expression. nomograms were used to predict the relationship between fhl2 expression levels and survival. the qrt-pcr was used to detect the fhl2 expression in lung cancer cells. in vitro experiments including cck-8 assay, wound healing, and transwell assay were performed. results: this study comprised rna-seq gene expression data and clinical features for 1018 lung cancer patients. fhl2 was found to be overexpressed in lung cancer tissues. fhl2 demonstrated moderate diagnostic ability for lung cancer (auc = 0.857). kaplan–meier curves and cox regression analysis revealed the higher fhl2 expression with the poorer os and rfs ( p < 0.001). the nomogram results indicated that fhl2 could be used to predict the survival of lung cancer patients. gsea analysis results show that high expression of fhl2 is related to glycolysis and unfolded protein reflection. fhl2 was highly expressed in lung cancer cells and related to their proliferation, migration, and invasion ability. conclusions: the high expression level of fhl2 in lung cancer can be used as an independent predictor of prognosis in clinical practice.",0
"the early onset and rapid progression of cutaneous squamous cell carcinoma (cscc) leads to high mortality rates in individuals with recessive dystrophic epidermolysis bullosa (rdeb). currently, the molecular mechanisms underlying cscc development in rdeb are not well understood and there are limited therapeutic options. rdeb-cscc arises through the accumulation of genetic mutations; however, previous work analyzing gene expression profiles have not been able to explain its aggressive nature. therefore, we generated a model to study rdeb-cscc development using cellular reprograming and re-differentiation technology. we compared rdeb-cscc to cscc that were first reprogrammed into induced pluripotent stem cells (rdeb-cscc-ipsc) and then differentiated back to keratinocytes (rdeb-cscc-ikc). the rdeb-cscc-ikc cell population had reduced proliferative capacities in vitro and in vivo, suggesting that reprogramming and re-differentiation leads to functional changes. finally, we performed rna-seq analysis for rdeb-cscc, rdeb-cscc-ipsc, and rdeb-cscc-ikc and identified different gene expression signatures between these cell populations. taken together, this cell culture model offers a valuable tool to study cscc and provides a novel way to identify potential therapeutic targets for rdeb-cscc.",0
"rna editing by adars can change the coding potential of protein-coding mrnas. so far, this type of rna editing has mainly been shown to affect rnas expressed in the nervous system with much lower editing levels being observed in other tissues. the actin crosslinking proteins filamin α and filamin β are widely expressed in most tissues. the mrnas encoding either protein are edited at the same position leading to a conserved q to r exchange in both proteins. using bar-coded next generation sequencing, we show that editing of filamin α is most abundant in the gastrointestinal tract and only to a lesser extent in the nervous system. using knockout mice, we show that adarb1 (adar2) is responsible for the majority of flna editing, while adar1 can edit filamin α mrna in some tissues quite efficiently. interestingly, editing levels of filamin α and β do not follow the same trend across tissues, suggesting a substrate-specific regulation of editing.",0
"follistatin (fst) performs several vital functions in the cells, including protection from apoptosis during stress. the expression of fst is up-regulated in response to glucose deprivation by an unknown mechanism. we herein showed that the induction of fst by glucose deprivation was due to an increase in the half-life of its mrna. we further identified an au-rich element (are) in the 3′utr of fst mrna that mediated its decay. the expression of fst was elevated after knocking down auf1 and reduced when auf1 was further expressed. in vitro binding assays and rna pull-down assays revealed that auf1 interacted with fst mrna directly via its are. during glucose deprivation, a majority of auf1 shuttled from cytoplasm to nucleus, resulting in dissociation of auf1 from fst mrna and thus stabilization of fst mrna. finally, knockdown of auf1 decreased whereas overexpression of auf1 increased glucose deprivation-induced apoptosis. the apoptosis promoting effect of auf1 was eliminated in fst expressing cells. collectively, this study provided evidence that auf1 is a negative regulator of fst expression and participates in the regulation of cell survival under glucose deprivation.",0
"background: breast cancer (bc) has become the leading cause of death for women’s malignancies and increasingly threatens the health of women worldwide. however, there is a lack of effective targeted drugs for basal-like bc. therefore, biomarkers related to the prognosis of early bc need to be identified. methods: the rna-seq data of 87 cases of early basal-like bc and 111 cases of normal breast tissue from the cancer genome atlas were explored by the weighted gene co-expression network analysis method and limma package. then, intersected genes were identified, and hub genes were selected by the maximal clique centrality method. the prognostic effect of the hub genes was also evaluated in early basal-like bc. results: in total, 601 igs were identified in this study. an appi network was constructed, and the top 10 hub genes were selected, namely, cyclin b1, cyclin a2, cyclin-dependent kinase 1, cell division cycle 20, dna topoisomerase ii alpha, bub1 mitotic checkpoint serine/threonine kinase, aurora kinase b (aurkb), cyclin b2, kinesin family member 11, and assembly factor for spindle microtubules. only aurkb was found to be significantly associated with the overall prognosis of early basal-like bc. the immune cell infiltration analysis showed that the infiltration numbers of cd4 + t cells and naïve cd8 + t cells were positively correlated with the aurkb expression level, while those of naïve b cells and macrophage m2 cells were negatively correlated with the aurkb expression level in basal-like bc. conclusion: aurkb might be a potential prognostic indicator in early basal-like bc.",0
"mutation-driven activation of kras is crucial to cancer development. the human gene yields four mrna splicing isoforms, 4a and 4b being translated to protein. their different properties and oncogenic potential have been studied, but the mechanisms deciding the ratio 4a/4b are not known. to address this issue, the expression of the four kras isoforms was determined in 9 human colorectal cancer cell lines. hct116 and sw48 were further selected because they present the highest difference in the ratio 4a/4b (twice as much in hct116 than in sw48). chromatin structure was analysed at the exon 4a, characteristic of isoform 4a, at its intronic borders and at the two flanking exons. the low nucleosome occupancy at exon 4a in both cell lines may result in a fast transcriptional rate, which would explain the general lower abundance of isoform 4a, also found in cells and tissues by other authors, but due to its similarity between both cell lines, chromatin structure does not influence alternative splicing. dna methylation downstream exon 4a significantly differs in hct116 and sw48 cells, but the ccctc-binding factor, which affects the processivity of rna polymerase and the alternative splicing, does not bind the differentially methylated sequences. quantitative epigenetic analysis at mononucleosomal level revealed significant differences between both cell lines in h3k4me3, h3k27me3, h3k36me3, h3k9ac, h3k27ac and h4k20me1, and the inhibition of some histone-modifying enzymes alters the ratio 4a/4b. it can be concluded that the epigenetic modification of histones has an influence on the selection of isoforms 4a and 4b.",0
"tea is one of the most popular non-alcoholic beverages worldwide. cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. however, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. using rna-seq, dge and srna-seq technologies, we performed an integrative analysis of mirna and mrna expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. differentially expressed (de) mirna and mrna profiles were obtained based on fold change analysis, mirnas and target mrnas were found to show both coherent and incoherent relationships in the regulatory network. furthermore, we compared several key pathways (e.g., ‘photosynthesis’), go terms (e.g., ‘response to karrikin’) and transcriptional factors (tfs, e.g., dreb1b/cbf1) which were identified as involved in the early chilling and/or freezing response of tea plants. intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (bpr), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. quantitative reverse transcriptase-polymerase chain reaction (qrt-pcr) analysis further confirmed the results from rna-seq and srna-seq analysis. this is the first study to simultaneously profile the expression patterns of both mirnas and mrnas on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. in addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mrna/mirna expression and profiling of non-model plant species using next-generation sequencing technology.",1
"background it was recently shown that niacin supplementation counteracts the obesity-induced muscle fiber transition from oxidative type i to glycolytic type ii and increases the number of type i fibers in skeletal muscle of obese zucker rats. these effects were likely mediated by the induction of key regulators of fiber transition, pparδ (encoded by ppard), pgc-1α (encoded by ppargc1a) and pgc-1β (encoded by ppargc1b), leading to type ii to type i fiber transition and upregulation of genes involved in oxidative metabolism. the aim of the present study was to investigate whether niacin administration also influences fiber distribution and the metabolic phenotype of different muscles in sheep as a model for ruminants. for this purpose, 16 male, 11 wk old rhoen sheep were randomly allocated to two groups of 8 sheep each administered either no (control group) or 1 g niacin per day (niacin group) for 4 wk. results after 4 wk, the percentage number of type i fibers in ld, sm and st muscles was greater in the niacin group, whereas the percentage number of type ii fibers was less in niacin group than in the control group ( p < 0.05). the mrna levels of ppargc1a, ppargc1b, and ppard and the relative mrna levels of genes involved in mitochondrial fatty acid uptake (cpt1b, slc25a20), tricarboxylic acid cycle (sdha), mitochondrial respiratory chain (cox5a, cox6a1), and angiogenesis (vegfa) in ld, sm and st muscles were greater ( p < 0.05) or tended to be greater ( p < 0.15) in the niacin group than in the control group. conclusions the study shows that niacin supplementation induces muscle fiber transition from type ii to type i, and thereby an oxidative metabolic phenotype of skeletal muscle in sheep as a model for ruminants. the enhanced capacity of skeletal muscle to utilize fatty acids in ruminants might be particularly useful during metabolic states in which fatty acids are excessively mobilized from adipose tissue, such as during the early lactating period in high producing cows.",0
"abstract genetically engineered silkworms have been widely used to obtain silk with modified characteristics especially by introducing spider silk genes. however, these attempts are still challenging due to limitations in transformation strategies and difficulties in integration of the large dna fragments. here, we describe three different transformation strategies in genetically engineered silkworms, including transcription-activator-like effector nuclease (talen)-mediated fibroin light chain (fibl) fusion (bmfibl-f), talen-mediated fibh replacement (bmfibh-r), and transposon-mediated genetic transformation with the silk gland-specific fibroin heavy chain (fibh) promoter (bmfibh-t). as the result, the yields of exogenous silk proteins, a 160 kda major ampullate spidroin 2 (masp2) from the orb-weaving spider nephila clavipes and a 226 kda fibroin heavy chain protein (evfibh) from the bagworm eumeta variegate , reach 51.02 and 64.13% in bmfibh-r transformed cocoon shells, respectively. moreover, the presence of masp2 or evfibh significantly enhances the toughness of genetically engineered silk fibers by ∼86% in bmfibh-t and ∼80% in bmfibh-r silkworms, respectively. structural analysis reveals a substantial ∼40% increase in fiber crystallinity, primarily attributed to the presence of unique polyalanines in the repetitive sequences of masp2 or evfibh. in addition, rna-seq analysis reveals that bmfibh-r system only causes minor impact on the expression of endogenous genes. our study thus provides insights into developing custom-designed silk production using the genetically engineered silkworm as the bioreactor.",0
"non-coding rnas (ncrnas), including the more recently identified stable unannotated transcripts (suts) and cryptic unstable transcripts (cuts), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. here, we carried out a large-scale screening of ncrnas in saccharomyces cerevisiae , and provide evidence for sut and cut function. phenotypic data on 372 ncrna deletion strains in 23 different growth conditions were collected, identifying ncrnas responsible for significant cellular fitness changes. transcriptome profiles were assembled for 18 haploid ncrna deletion mutants and 2 essential ncrna heterozygous deletants. guided by the resulting rna-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. novel functional ncrnas, sut125, sut126, sut035 and sut532 that act in trans by modulating transcription factors were identified. furthermore, we described the impact of suts and cuts in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (sut125, sut126, sut035, sut432), steroid biosynthesis (cut494, sut053, sut468) or rrna processing (sut075 and snr30). overall, these data capture and integrate the regulatory and phenotypic network of ncrnas and protein-coding genes, providing genome-wide evidence of the impact of ncrnas on cellular homeostasis.",1
"background three neuropeptides, gastrin releasing peptide (grp), natriuritic precursor peptide b (nppb), and neuromedin b (nmb) have been proposed to play roles in itch sensation. however, the tissues in which these peptides are expressed and their positions in the itch circuit has recently become the subject of debate. here we used next-gen rna-seq to examine the expression of transcripts coding for grp, nppb, nmb, and other peptides in drg, trigeminal ganglion, and the spinal cord as well as expression levels for their cognate receptors in these tissues. results rna-seq demonstrates that grp is not transcribed in mouse, rat, or human sensory ganglia. nppb, which activates natriuretic peptide receptor 1 (npr1), is well expressed in mouse drg and less so in rat and human, whereas nppa, which also acts on the npr1 receptor, is expressed in all three species. analysis of transcripts expressed in the spinal cord of mouse, rat, and human reveals no expression of nppb , but unambiguously detects expression of grp and the grp-receptor ( grpr ). the transcripts coding for nmb and tachykinin peptides are among the most highly expressed in drg. bioinformatics comparisons using the sequence of the peptides used to produce grp-antibodies with proteome databases revealed that the c-terminal primary sequence of nmb and substance p can potentially account for results from previous studies which showed grp-immunostaining in the drg. conclusions rna-seq corroborates a primary itch afferent role for nppb in mouse and potentially nppb and nppa in rats and humans, but does not support grp as a primary itch neurotransmitter in mouse, rat, or humans. as such, our results are at odds with the initial proposal of sun and chen (2007) that grp is expressed in drg. by contrast, our data strongly support an itch pathway where the itch-inducing actions of grp are exerted through its release from spinal cord neurons.",0
"abstract organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. next generation sequencing (ngs) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. however, most of the available eukaryotic rna-sequencing (rna-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. here, we use publicly available rna-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. our rna mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. in all cases, 85% or more of the organelle genome was recovered from the rna data, including noncoding (intergenic and intronic) regions. these results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. we explore the possibility that transcribed intergenic regions are producing functional noncoding rnas, and that organelle genome noncoding content might provide raw material for generating regulatory rnas.",1
"trans -translation, orchestrated by smpb and tmrna, is the principal eubacterial pathway for resolving stalled translation complexes. rnase r, the leading nonstop mrna surveillance factor, is recruited to stalled ribosomes in a trans- translation dependent process. to elucidate the contributions of smpb and tmrna to rnase r recruitment, we evaluated escherichia coli – francisella tularensis chimeric variants of tmrna and smpb. this evaluation showed that while the hybrid tmrna supported nascent polypeptide tagging and ribosome rescue, it suffered defects in facilitating rnase r recruitment to stalled ribosomes. to gain further insights, we used established tmrna and smpb variants that impact distinct stages of the trans- translation process. analysis of select tmrna variants revealed that the sequence composition and positioning of the ultimate and penultimate codons of the tmrna orf play a crucial role in recruiting rnase r to rescued ribosomes. evaluation of defined smpb c-terminal tail variants highlighted the importance of establishing the tmrna reading frame, and provided valuable clues into the timing of rnase r recruitment to rescued ribosomes. taken together, these studies demonstrate that productive rnase r-ribosomes engagement requires active trans -translation, and suggest that rnase r captures the emerging nonstop mrna at an early stage after establishment of the tmrna orf as the surrogate mrna template.",1
"here we report that the specificity of peptide release in the ribosome on a nonstop mrna by arfa and rf2 is achieved by an induced-fit mechanism. using rf2 that is methylated on the glutamine of its ggq motif (rf2 m ), we show that methylation substantially increases the rate of arfa/rf2-catalyzed peptide release on a nonstop mrna that does not occupy the ribosomal a site, but has only a modest effect on k cat by the same proteins on longer nonstop mrnas occupying the a site of the mrna channel in the ribosome. our data suggest that enhancement in the k cat of peptide release by arfa and rf2 under the cognate decoding condition is the result of favorable conformational changes in the nonstop complex. we demonstrate a shared mechanism between canonical and nonstop termination, supported by similarities in the kinetic mechanisms in antibiotic inhibition and methylation-correlated enhancement in the rate of peptide release. despite these similarities, our data suggest that nonstop termination differs from canonical pathway in the downstream event of recycling.",0
"xrn1 is a highly conserved exoribonuclease which degrades uncapped rnas in a 5′–3′ direction. degradation of rnas by xrn1 is important in many cellular and developmental processes and is relevant to human disease. studies in d. melanogaster demonstrate that xrn1 can target specific rnas, which have important consequences for developmental pathways. osteosarcoma is a malignancy of the bone and accounts for 2% of all pediatric cancers worldwide. five-year survival of patients has remained static since the 1970s and therefore furthering our molecular understanding of this disease is crucial. previous work has shown a down-regulation of xrn1 in osteosarcoma cells; however, the transcripts regulated by xrn1 which might promote osteosarcoma remain elusive. here, we confirm reduced levels of xrn1 in osteosarcoma cell lines and patient samples and identify xrn1-sensitive transcripts in human osteosarcoma cells. using rna-seq in xrn1-knockdown saos-2 cells, we show that 1178 genes are differentially regulated. using a novel bioinformatic approach, we demonstrate that 134 transcripts show characteristics of direct post-transcriptional regulation by xrn1. long noncoding rnas (lncrnas) are enriched in this group, suggesting that xrn1 normally plays an important role in controlling lncrna expression in these cells. among potential lncrnas targeted by xrn1 is hotair , which is known to be up-regulated in osteosarcoma and contributes to disease progression. we have also identified g-rich and gu motifs in post-transcriptionally regulated transcripts which appear to sensitize them to xrn1 degradation. our results therefore provide significant insights into the specificity of xrn1 in human cells which are relevant to disease.",1
"circadian clocks allow organisms to orchestrate the daily rhythms in physiology and behaviors, and disruption of circadian rhythmicity can profoundly affect fitness. the mammalian circadian oscillator consists of a negative primary feedback loop and is associated with some ‘auxiliary’ loops. this raises the questions of how these interlocking loops coordinate to regulate the period and maintain its robustness. here, we focused on the rev-erbα/ cry1 auxiliary loop, consisting of rev-erbα/ror-binding elements (rore) mediated cry1 transcription, coordinates with the negative primary feedback loop to modulate the mammalian circadian period. the silicon simulation revealed an unexpected rule: the intensity ratio of the primary loop to the auxiliary loop is inversely related to the period length, even when post-translational feedback is fixed. then we measured the mrna levels from two loops in 10-mutant mice and observed the similar monotonic relationship. additionally, our simulation and the experimental results in human osteosarcoma cells suggest that a coupling effect between the numerator and denominator of this intensity ratio ensures the robustness of circadian period and, therefore, provides an efficient means of correcting circadian disorders. this ratio rule highlights the contribution of the transcriptional architecture to the period dynamics and might be helpful in the construction of synthetic oscillators.",0
"diabetic nephropathy (dn) is characterized by metabolic disorder and inflammation. however, the regulatory effects that long noncoding rnas (lncrnas) have on the pathogenesis of dn and on the efficacy of rosiglitazone treatment have yet to be clearly defined. herein, we performed unbiased rna sequencing to characterize the transcriptomic profiles in db/db diabetic mouse model with or without rosiglitazone treatment that served to improve the phenotypes of dn. moreover, rna-seq profiling revealed that the development of dn caused an upregulation in the expression of 1176 mrnas and a downregulation in the expression of 1010 mrnas compared to controls, with the expression of 251 mrnas being returned to normal following treatment with rosiglitazone. further, 88 upregulated and 68 downregulated lncrnas were identified in db/db mice compared to controls, 10 of which had their normal expression restored following treatment with rosiglitazone. bioinformatic analysis revealed that the primary pathways involved in the pathogenesis of dn, and subsequently in the therapeutic effects of ppar γ , are related to inflammatory and metabolic processes. from bioinformatics analysis, lncrna-ai838599 emerged as a novel molecular mechanism for rosiglitazone treatment in dn through tnf α -nf κ b pathway. these findings may indicate a new molecular regulatory approach for the development of dn therapeutic agents.",1
"efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. a chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. to understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (acsh). to determine regulatory responses to the inhibitors normally present in acsh, we measured transcript and protein levels in an escherichia coli ethanologen using rna-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. our study identified four major regulators mediating these responses, the mara/soxs/rob network, aaer, frmr, and yqhc. induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of atp and nad(p)h, and an inhibition of xylose conversion. the aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.",0
"background the apoptosis-stimulating protein of p53 (aspp) family comprises three members, namely, aspp1, aspp2, and iaspp. they regulate the promotive effect of p53 on apoptosis. breast cancer (bc) remains as one of the leading causes of cancer or cancer-related mortality among women. however, the relationship between the aspp family members and p53, as well as the dissemination and expression pattern of aspp family members in p53 + bc, has not been elucidated. our objectives are to detect the expression of aspp family members in p53 + bc cell lines and determine its significance in tumor cell apoptosis. methods the mrna expression of aspp family members in five p53 + bc cell lines was detected through rt-pcr and assayed using quality-one software. the p53 protein expression was detected by immunohistochemistry. afterward, the apoptosis indices of the five bc cell lines were detected by flow cytometry. results the iaspp mrna was expressed in bcap-37, mcf-7, and hbl-100. compared with the human peripheral blood mononuclear cells, significant differences were found in the aspp1 mrna in bcap-37, mda-mb-231, mcf-7, and hbl-100 ( p 0.05). the aspp2 mrna was expressed in mda-mb-231, bcap-37, and mcf-7, but not in hbl-100 and zr-75-30. the p53 protein was expressed in five breast cancer cell lines. zr-75-30 and mda-mb-231 apoptosis indices were higher than those of other breast cancer cell line and peripheral blood mononuclear cells ( p < 0.01). conclusions the mrna expression of aspp family members varied in the five p53 + bc cell lines. the results also verified that the family members have an important function in apoptosis, which was promoted by p53 protein. zr-75-30 bc showed high apoptosis index, without expression of any aspp family members, indicating that the pathway of apoptosis in this cell line may be related to other cell transduction pathway. mda-mb-231, bcap37, and mcf-7 cell lines all expressed aspp1/2. however, the apoptosis pathway in mda-mb-231 is different from those of the other two cell lines. the status of the different cell lines should also be considered when the functions of the aspp family members are examined.",0
"the wnt-signaling pathway functions in regulating cell growth and thus is involved in the carcinogenic process of several cancers, including colorectal cancer. we tested the hypothesis that multiple genes in this signaling pathway are dysregulated and that mirnas are associated with these dysregulated genes. we used data from 217 colorectal cancer (crc) cases to evaluate differences in wnt-signaling pathway gene expression between paired crc and normal mucosa and identify mirnas that are associated with these genes. gene expression data from rna-seq and mirna expression data from agilent human mirna microarray v19.0 were analyzed. we focused on genes most strongly associated with crc (fold change (fc) of >1.5 or 1.50) after adjusting for multiple comparisons. thirteen of the 66 wnt-signaling genes that were differentially expressed in crc tumors were associated with differential expression of mirnas. a total of 93 mirna:mrna associations were detected for these 13 genes. of these 93 associations, 36 mirna seed-region matches were observed, suggesting that mirnas have both direct and indirect effects on wnt-signaling pathway genes. in summary, our data supports the hypothesis that the wnt-signaling pathway is dysregulated in crc and suggest that mirnas may importantly influence that dysregulation.",1
"background allergic asthma is characterized by airway inflammation in response to antigen exposure, leading to airway remodeling and lung dysfunction. epithelial-mesenchymal transition (emt) may play a role in airway remodeling through the acquisition of a mesenchymal phenotype in airway epithelial cells. tgf-β1 is known to promote emt; however, other cytokines expressed in severe asthma with extensive remodeling, such as il-22, may also contribute to this process. in this study, we evaluated the contribution of il-22 to emt in primary bronchial epithelial cells from healthy and asthmatic subjects. methods primary bronchial epithelial cells were isolated from healthy subjects, mild asthmatics and severe asthmatics (n=5 patients per group). the mrna and protein expression of epithelial and mesenchymal cell markers and emt-associated transcription factors was evaluated following stimulation with tgf-β1, il-22 and tgf-β1+il-22. results primary bronchial epithelial cells stimulated with tgf-β1 underwent emt, demonstrated by decreased expression of epithelial markers (e-cadherin and muc5ac) and increased expression of mesenchymal markers (n-cadherin and vimentin) and emt-associated transcription factors. il-22 alone had no effect on epithelial or mesenchymal gene expression. however, il-22+tgf-β1 promoted the expression of some emt transcription factors (snail1 and zeb1) and led to a more profound cadherin shift, but only in cells obtained from severe asthmatics. conclusion the impact of il-22 on airway epithelial cells depends on the cytokine milieu and the clinical phenotype of the patient. further studies are required to determine the molecular mechanism of il-22 and tgf-β1 cooperativity in driving emt in primary human bronchial epithelial cells.",0
"background: malignant glioma is the most common form of primary malignant brain cancer. heterogeneity is the hallmark of glioma. daz-interacting zinc finger 3 (dzip3), acts as an rna-binding ring-type ubiquitin ligase; however, its function in glioma is yet unclear. results: the dzip3 expression was related to the world health organization (who) grade and isocitrate dehydrogenase 1( idh1 ) status, as well as the clinical outcome. malignant cases exhibit lower dzip3 expression. dzip3 was an independent predictive factor of good prognosis in all grade and lower grade gliomas ( p < 0.0001). gene enrichment analysis and immunohistochemistry indicated that dzip3 affected the biological behavior of glioma through the angiogenesis pathway. moreover, based on dzip3 expression, idh1 wild-type lower-grade gliomas could be divided into two groups with different survival time. conclusion: in conclusion, the loss of dzip3 may be involved in the mechanism of angiogenesis in the invasive biological process of glioma. these findings laid an understanding of dzip3-specific clinical features in glioma. methods: a total of 325 glioma patients from the chinese glioma genome atlas (cgga) rna-seq cohort comprised the training cohort, while 265 patients from the gse 16011 array cohort formed the validation cohort. the mrna expression of dzip3 and clinical characteristics was assessed. dzip3 protein expression and microvessel density (mvd) were evaluated by immunohistochemistry (ihc).",0
"hemoglobinuria is associated with kidney injury in various hemolytic pathologies. currently, there is no treatment available and its pathophysiology is not completely understood. here we studied the potential detrimental effects of hemoglobin (hb) exposure to the distal nephron (dn). involvement of the dn in hb kidney injury was suggested by the induction of renal hepcidin synthesis ( p < 0.001) in mice repeatedly injected with intravenous hb. moreover, the hepcidin induction was associated with a decline in urinary kidney injury markers 24p3/ngal and kim1, suggesting a role for hepcidin in protection against hb kidney injury. we demonstrated that uptake of hb in the mouse cortical collecting duct cells (mccd cl1 ) is mediated by multi-protein ligand receptor 24p3r, as indicated by a significant 90% reduction in hb uptake ( p < 0.001) after 24p3r silencing. moreover, incubation of mccd cl1 cells with hb or hemin for 4 or 24 h resulted in hepcidin synthesis and increased mrna expression of markers for oxidative, inflammatory and er stress, but no cell death as indicated by apoptosis staining. a protective role for cellular hepcidin against hb-induced injury was demonstrated by aggravation of oxidative, inflammatory and er stress after 4 h hb or hemin incubation in hepcidin silenced mccd cl1 cells. hepcidin silencing potentiated hemin-mediated cell death that could be diminished by co-incubation of nec-1, suggesting that endogenous hepcidin prevents necroptosis. combined, these results demonstrate that renal hepcidin synthesis protects the dn against hemin and hemoglobin-mediated injury.",0
"objective activated mast cells in atherosclerotic lesions degranulate and release bioactive compounds capable of regulating atherogenesis. here we examined the ability of activated human primary mast cells to regulate the expression of the major scavenger receptors in cultured human primary monocyte-derived macrophages (hmdms). results components released by immunologically activated human primary mast cells induced a transient expression of lectin-like oxidized ldl receptor (lox-1) mrna in hmdms, while the expression of two other scavenger receptors, msr1 and cd36, remained unaffected. the lox-1-inducing secretory components were identified as histamine, tumor necrosis factor alpha (tnf-α), and transforming growth factor beta (tgf-β1), which exhibited a synergistic effect on lox-1 mrna expression. histamine induced a transient expression of lox-1 protein. mast cell –induced increase in lox-1 expression was not associated with increased uptake of oxidized ldl by the macrophages. conclusions mast cell-derived histamine, tnf-α, and tgf-β1 act in concert to induce a transient increase in lox-1 expression in human primary monocyte-derived macrophages. the lox-1-inducing activity potentially endows mast cells a hitherto unrecognized role in the regulation of innate immune reactions in atherogenesis.",0
"tuberous sclerosis complex (tsc) is an autosomal dominant tumor suppressor syndrome, characterized by tumor development in multiple organs, including renal angiomyolipoma. biallelic loss of tsc1 or tsc2 is a known genetic driver of angiomyolipoma development, however whether an altered transcriptional repertoire contributes to tsc-associated tumorigenesis is unknown. rna-seq analyses showed that mitf a isoform ( mitf-a) was consistently highly expressed in angiomyolipoma, immunohistochemistry showed mitf nuclear localization, and chip-seq analysis showed that the mitf-a transcriptional start site was highly enriched with h3k27ac marks. using the angiomyolipoma cell line 621-101, mitf knock out ( mitf.ko ) and mitf-a overexpressing ( mitf.oe ) cell lines were generated. mitf.ko cells showed markedly reduced growth and invasion in vitro , and were unable to form xenografted tumors. in contrast mitf.oe cells grew faster in vitro and as xenografted tumors compared to control cells. rna-seq analysis showed that both id2 and cyr61 expression were increased in the mitf.oe cells and reduced in the mitf.ko cells, and luciferase assays showed this was due to transcriptional effects. importantly, cyr61 overexpression rescued mitf.ko cell growth in vitro and tumor growth in vivo. these findings suggest that mitf-a is a transcriptional oncogenic driver of angiomyolipoma tumor development, acting through regulation of cyr61.",0
"abstract ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mrna translation. using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. for that reason, many recent studies omitted translation inhibitors in the culture medium. here, we investigate the influence of ranging cycloheximide concentrations on ribosome profiles in saccharomyces cerevisiae and demonstrate that increasing the drug concentration can overcome some of the artifacts. we subjected cells to various manipulations and show that neither oxidative stress nor heat shock nor amino acid starvation affect translation elongation. instead, the observations in the initial studies are the result of cycloheximide-inflicted artifacts. likewise, we find little support for short upstream reading frames to be involved in widespread protein synthesis regulation under stress conditions. our study highlights the need for better standardization of ribosome profiling methods.",0
"skeletal muscle is capable of phenotypic adaptation to environmental factors, such as nutrient availability, by altering the balance between muscle catabolism and anabolism that in turn coordinates muscle growth. small noncoding rnas, known as micrornas (mirnas), repress the expression of target mrnas, and many studies have demonstrated that mirnas regulate the mrnas of catabolic and anabolic genes. we evaluated muscle morphology, gene expression of components involved in catabolism, anabolism and energetic metabolism and mirnas expression in both the fast and slow muscle of juvenile pacu ( piaractus mesopotamicus ) during food restriction and refeeding. our analysis revealed that short periods of food restriction followed by refeeding predominantly affected fast muscle, with changes in muscle fiber diameter and mirnas expression. there was an increase in the mrna levels of catabolic pathways components ( fbxo25 , atg12 , bcl2 ) and energetic metabolism-related genes ( pgc1α and sdha ), together with a decrease in pparβ/δ mrna levels. interestingly, an increase in mrna levels of anabolic genes ( pi3k and mtorc1 complex: mtor , mlst8 and raptor ) was also observed during food restriction. after refeeding, muscle morphology showed similar patterns of the control group; the majority of genes were slightly up- or down-regulated in fast and slow muscle, respectively; the levels of all mirnas increased in fast muscle and some of them decreased in slow muscle. our findings demonstrated that a short period of food restriction in juvenile pacu had a considerable impact on fast muscle, increasing the expression of anabolic ( pi3k and mtorc1 complex: mtor , mlst8 and raptor ) and energetic metabolism genes. the mirnas (mir-1, mir-206, mir-199 and mir-23a) were more expressed during refeeding and while their target genes ( igf-1 , mtor , pgc1α and mafbx ), presented a decreased expression. the alterations in mtorc1 complex observed during fasting may have influenced the rates of protein synthesis by using amino acids from protein degradation as an alternative mechanism to preserve muscle phenotype and metabolic demand maintenance.",1
"β-lactam antibiotics are widely used in clinic. filamentous fungus acremonium chrysogenum is an important industrial fungus for the production of cpc, one of the major precursors of β-lactam antibiotics. although its fermentation yield has been bred significantly over the past decades, little is known regarding molecular changes between the industrial strain and the wild type strain. this limits the possibility to improve cpc production further by molecular breeding. comparative transcriptome is a powerful tool to understand the molecular mechanisms of cpc industrial high yield producer compared to wild type. a total of 57 million clean sequencing reads with an average length of 100 bp were generated from illumina sequencing platform. 22,878 sequences were assembled. among the assembled unigenes, 9502 were annotated and 1989 annotated sequences were assigned to 121 pathways by searching against the kyoto encyclopedia of genes and genomes pathway (kegg) database. furthermore, we compared the transcriptome differences between a high-yield and a wild-type strain during fermentation. a total of 4329 unigenes with significantly different transcription level were identified, among which 1737 were up-regulated and 2592 were down-regulated. 24 pathways were subsequently determined which involve glycerolipid metabolism, galactose metabolism, and pyrimidine metabolism. we also examined the transcription levels of 18 identified genes, including 11 up-regulated genes and 7 down-regulated genes using reverse transcription quantitative -pcr (rt-qpcr). the results of rt-qpcr were consistent with the illumina sequencing. in this study, the illumina sequencing provides the most comprehensive sequences for gene expression profile of acremonium chrysogenum and allows de novo transcriptome assembly while lacking genome information. comparative analysis of rna-seq data reveals the complexity of the transcriptome in the fermentation of different yield strains. this is an important public information platform which could be used to accelerate the research to improve cpc production in acremonium chrysogenum.",0
"background cytokine-induced killer (cik) cells are an emerging approach of cancer treatment. our previous study have shown that cik cells stimulated with combination of il-2 and il-15 displayed improved proliferation capacity and tumor cytotoxicity. however, the mechanisms of cik cell proliferation and acquisition of cytolytic function against tumor induced by il-2 and il-15 have not been well elucidated yet. methods cik il-2 and cik il-15 were generated from peripheral blood mononuclear cells primed with ifn-γ, and stimulated with il-2 and il-15 in combination with okt3 respectively. rna-seq was performed to identify differentially expressed genes, and gene ontology and pathways based analysis were used to identify the distinct roles of il-2 and il-15 in cik preparation. results the results indicated that cik il-15 showed improved cell proliferation capacity compared to cik il-2. however, cik il-2 has exhibited greater tumor cytotoxic effect than cik il-15. employing deep sequencing, we sequenced mrna transcripts in cik il-2 and cik il-15. a total of 374 differentially expressed genes (degs) were identified including 175 up-regulated genes in cik il-15 and 199 up-regulated genes in cik il-2. among degs in cik il-15 , wnt signaling and cell adhesion were significant go terms and pathways which related with their functions. in cik il-2 , type i interferon signaling and cytokine-cytokine receptor interaction were significant go terms and pathways. we found that the up-regulation of wnt 4 and pdgfd may contribute to enhanced cell proliferation capacity of cik il-15 , while inhibitory signal from interaction between ctla4 and cd80 may be responsible for the weak proliferation capacity of cik il-2. moreover, up-regulated expressions of cd40lg and irf7 may make for improved tumor cytolytic function of cik il-2 through type i interferon signaling. conclusions through our findings, we have preliminarily elucidated the cells proliferation and acquisition of tumor cytotoxicity mechanism of cik il-15 and cik il-2. better understanding of these mechanisms will help to generate novel cik cells with greater proliferation potential and improved tumor cytolytic function.",0
"hypopharyngeal carcinoma is the most malignant type of head and neck squamous cell carcinoma, and lncrnas play an important role in its formation and progression. however, the related specific mechanisms are rarely studied. lncrnas closely associated with hypopharyngeal cancer were examined by lncrna sequencing for in-depth exploration of the relationship between hoxc-as2 and hypopharyngeal cancer pathogenesis. the mrna expression of hoxc-as2 and related genes was measured by qrt-pcr, and the biological function of hoxc-as2 in hypopharyngeal carcinoma was demonstrated by gain- and loss-of-function experiments. rna pulldown, rna immunoprecipitation (rip) and gene body truncation experiments and transcriptome sequencing were used to investigate the potential mechanism of hoxc-as2 and its downstream genes, including p62, nf-kb and hmox1. finally, the biological function of hoxc-as2 was confirmed in animal experiments. hoxc-as2 and p62 expression was significantly upregulated in hypopharyngeal cancer tissues compared with normal hypopharyngeal tissues, while hmox1 expression was decreased. functionally, hoxc-as2 overexpression can promote the viability, proliferation, migration and invasion of hypopharyngeal cancer cells and facilitate hypopharyngeal cancer progression. it was confirmed that hoxc-as2 can bind to the p62 protein and activate the nf-kb signaling pathway, thereby affecting hmox1 expression and regulating autophagy in hypopharyngeal cancer cells, ultimately regulating the formation and progression of hypopharyngeal cancer. in conclusion, our findings suggest that hoxc-as2 regulates the progression of hypopharyngeal cancer by regulating autophagy and is abnormally highly expressed in hypopharyngeal cancer tissues. hoxc-as2 may become a new target for the diagnosis and treatment of hypopharyngeal cancer.",1
"prenatal cocaine exposure has been shown to alter cognitive processes of exposed individuals, presumed to be a result of long-lasting molecular alterations in the brain. in adult prenatal cocaine exposed (pcoc) mice we have identified a deficit in recall of fear extinction, a behavior that is dependent on the medial prefrontal cortex (mpfc) and the hippocampus. while we observed no change in the constitutive expression of brain derived neurotrophic factor (bdnf) protein and mrna in the mpfc and hippocampus of adult pcoc mice, we observed blunted bdnf signaling in the mpfc of adult pcoc mice after fear extinction compared to the control animals. specifically, during the consolidation phase of the extinction memory, we observed a decrease in bdnf protein and it’s phospho-trkb receptor expression. interestingly, at this same time point there was a significant increase in total bdnf mrna levels in the mpfc of pcoc mice as compared with controls. in the bdnf gene, we identified decreased constitutive binding of the transcription factors, mecp2 and p-creb at the promoters of bdnf exons i and iv in the mpfc of pcoc mice, that unlike control mice remained unchanged when measured during the behavior. finally, bilateral infusion of recombinant bdnf protein into the infralimbic subdivision of the mpfc during the consolidation phase of the extinction memory rescued the behavioral deficit in pcoc mice. in conclusion, these findings extend our knowledge of the neurobiologic impact of prenatal cocaine exposure on the mpfc of mice, which may lead to improved clinical recognition and treatment of exposed individuals.",0
"chromatin structure is an important factor in the functional coupling between transcription and mrna processing, not only by regulating alternative splicing events, but also by contributing to exon recognition during constitutive splicing. we observed that depolarization of neuroblastoma cell membrane potential, which triggers general histone acetylation and regulates alternative splicing, causes a concentration of sr proteins in nuclear speckles. this prompted us to analyze the effect of chromatin structure on splicing factor distribution and dynamics. here, we show that induction of histone hyper-acetylation results in the accumulation in speckles of multiple splicing factors in different cell types. in addition, a similar effect is observed after depletion of the heterochromatic protein hp1α, associated with repressive chromatin. we used advanced imaging approaches to analyze in detail both the structural organization of the speckle compartment and nuclear distribution of splicing factors, as well as studying direct interactions between splicing factors and their association with chromatin in vivo. the results support a model where perturbation of normal chromatin structure decreases the recruitment efficiency of splicing factors to nascent rnas, thus causing their accumulation in speckles, which buffer the amount of free molecules in the nucleoplasm. to test this, we analyzed the recruitment of the general splicing factor u2af65 to nascent rnas by iclip technique, as a way to monitor early spliceosome assembly. we demonstrate that indeed histone hyper-acetylation decreases recruitment of u2af65 to bulk 3′ splice sites, coincident with the change in its localization. in addition, prior to the maximum accumulation in speckles, ∼20% of genes already show a tendency to decreased binding, while u2af65 seems to increase its binding to the speckle-located ncrna malat1. all together, the combined imaging and biochemical approaches support a model where chromatin structure is essential for efficient co-transcriptional recruitment of general and regulatory splicing factors to pre-mrna.",1
"ribosomal profiling is a promising approach with increasing popularity for studying translation. this approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides. in this study, we focused on ribosomal density profiles of mouse embryonic stem cells. our analysis suggests, for the first time, that even in mammals such as m. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the trna pool; 2) the local mrna folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. in addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream. finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance.",0
"abstract the loss of skeletal muscle mass during aging is a significant health concern linked to adverse outcomes in older individuals. understanding the molecular basis of age‐related muscle loss is crucial for developing strategies to combat this debilitating condition. long noncoding rnas (lncrnas) are a largely uncharacterized class of biomolecules that have been implicated in cellular homeostasis and dysfunction across a many tissues and cell types. to identify lncrnas that might contribute to skeletal muscle aging, we screened for lncrnas whose expression was altered in vastus lateralis muscle from older compared to young adults. we identified frail1 as an aging‐induced lncrna with high abundance in human skeletal muscle. in healthy young and older adults, skeletal muscle frail1 was increased with age in conjunction with lower muscle function. forced expression of frail1 in mouse tibialis anterior muscle elicits a dose‐dependent reduction in skeletal muscle fiber size that is independent of changes in muscle fiber type. furthermore, this reduction in muscle size is dependent on an intact region of frail1 that is highly conserved across non‐human primates. unbiased transcriptional and proteomic profiling of the effects of frail1 expression in mouse skeletal muscle revealed widespread changes in mrna and protein abundance that recapitulate age‐related changes in pathways and processes that are known to be altered in aging skeletal muscle. taken together, these findings shed light on the intricate molecular mechanisms underlying skeletal muscle aging and implicate frail1 in age‐related skeletal muscle phenotypes.",1
"the basic region-leucine zipper (bzip) transcription factors (tfs) form homodimers and heterodimers via the coil–coil region. the bzip dimerization network influences gene expression across plant development and in response to a range of environmental stresses. the recent release of the most comprehensive potato reference genome was used to identify 80 stbzip genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. the stbzip genes have undergone 22 segmental and one tandem duplication events. ka/ks analysis suggested that most duplications experienced purifying selection. amino acid sequence alignments and phylogenetic comparisons made with the arabidopsis bzip family were used to assign the stbzip genes to functional groups based on the arabidopsis orthologs. the patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. inspection of the leucine repeat heptads within the bzip domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. these patterns of attractive and repulsive heptads were similar within each functional group for arabidopsis and s. tuberosum orthologs. high-throughput rna-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including potato virus x. these data provide useful information for further functional analysis of the stbzip gene family and their potential applications in crop improvement.",0
"epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (ibd) and colon tumor development. in the present work, dna methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the helicobacter hepaticus ( h. hepaticus ) -infected murine model of ibd. reduced representation bisulfite sequencing (rrbs) and oxidative rrbs (oxrrbs) analyses identified 1606 differentially methylated regions (dmr) and 3011 differentially hydroxymethylated regions (dhmr). these dmr/dhmr overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. rna-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. several genes including duox2 , tgm2 , cdhr5 , and hk2 exhibited changes in both dna methylation/hydroxymethylation and gene expression levels. overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.",0
"phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. single-cell transcriptomics using next-generation transcript sequencing (rna-seq) is now emerging as a powerful tool to profile cell-to-cell variability on a genomic scale. its application has already greatly impacted our conceptual understanding of diverse biological processes with broad implications for both basic and clinical research. different single-cell rna-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations. we further provide an overview of the biological questions single-cell rna-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field.",0
"simple summary the potential of primordial germ cells (pgcs) for multidirectional differentiation, together with their unique regeneration ability, makes them one of the most promising seed cells in clinical medicine and tissue engineering research. however, not enough pgcs can be obtained to meet the demand, which limits their application. we defined a novel long noncoding rna (lncrna) mediated by epigenetics, which could activate the mir-6577-5p/ btrc pathway to promote the formation of pgcs. the technical system we have established is a useful tool to obtain sufficient pgcs for scientific research. our study offers great theoretical and practical value in the production of transgenic animals or genomic imprinting in poultry. we believe that our study will help researchers in the fields of agricultural production, developmental biology, and cell biology. abstract although lncrnas have been identified as playing critical roles in the development of germ cells, their potential involvement in the development of pgcs in chickens remains poorly understood. differentially expressed lncrnas (dels) from previous rna-seq of embryonic stem cells (escs), pgcs, and spermatogonial stem cells (sscs) were analyzed by k-means clustering, from which a key candidate, lncrna (lncrna pgc regulator, lncpgcr ) was obtained. we confirmed that lncpgcr plays a positive role in the development of pgcs by increasing the expression of the pgc marker gene ( cvh and c-kit ), while downregulating the pluripotency-associated gene ( nanog ) in vitro and in vivo. the activation and expression of lncpgcr are regulated by histone acetylation, and transcription factor tcf7l2. mechanistically, a rescue assay was performed to further confirm that lncpgcr contributed to the development of pgcs by regulating the gga-mir-6577-5p/ btrc signaling pathway. adsorption of gga-mir-6577-5p activated the wnt signaling cascade by relieving the gga-mir-6577-5p-dependent inhibition of btrc expression. taken together, our study discovered the growth-expedited role of lncpgcr in pgcs development, showing the potential lncpgcr /mir-6577-5p/ btrc pathway. the results and findings provide a novel insight into the development of pgcs.",1
"to decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv. ‘abate fetel’, a rna-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages. these genes were grouped into 11 sota clusters based on their transcriptional pattern, of which three included genes upregulated while the other four were represented by downregulated genes. fruit ripening was furthermore investigated after 1 month of postharvest cold storage. the most important variation in fruit firmness, production of ethylene and volatile organic compounds were observed after 5 days of shelf-life at room temperature following cold storage. the role of ethylene in controlling the ripening of ‘abate fetel’ pears was furthermore investigated through the application of 1-methylcyclopropene, which efficiently delayed the progression of ripening by reducing fruit softening and repressing both ethylene and volatile production. the physiological response of the interference at the ethylene receptor level was moreover unraveled investigating the expression pattern of 12 candidate genes, initially selected to validate the rna-seq profile. this analysis confirmed the effective role of the ethylene competitor in downregulating the expression of cell wall (pg) and ethylene-related genes (acs, aco, ers1, and ers2), as well as inducing one element involved in the auxin signaling pathway (aux/iaa), highlighting a possible cross-talk between these two hormones. the expression patterns of these six elements suggest their use as molecular toolkit to monitor at molecular level the progression of the fruit on-tree maturation and postharvest ripening. pears: genes linked to fruit maturation and ripening numerous genes, including many involved in the production and signaling of key growth hormones, regulate the on-tree maturation and postharvest ripening of pear fruit. fabrizio costa from the edmund mach foundation in san michele all’adige, italy, and colleagues identified nearly 9,000 genes that were differentially expressed across four maturation stages of the abate fetel cultivar of european pear ( pyrus communis ). from this long list of genes, the researchers selected 12 involved in hormone signaling, cell wall metabolism or aromatic volatile compound production, and evaluated their expression pattern with and without application of a chemical added to delay ripening during postharvest storage. six of the genes, five of which controlled the activity of the hormones auxin and ethylene, showed differential expression, and could be informative as molecular biomarkers for improving fruit quality in pears.",0
"background formalin-fixed paraffin-embedded (ffpe) tissue samples are routinely archived in the course of patient care and can be linked to clinical outcomes with long-term follow-up. however, ffpe tissues have degraded rna which poses challenges for analyzing gene expression. next-generation sequencing (ngs) is rapidly becoming accepted as an effective tool for measuring gene expressions for research and clinical use. however, the feasibility of ngs has not been firmly established when using ffpe tissue. results we optimized strategies for whole transcriptome sequencing (rna-seq) using ffpe tissue. ribosomal rna (rrna) was successfully depleted by competitive hybridization using the ribo-zero™ kit (epicentre biotechnologies), and rrna sequence content was less than one percent for each library. gene expression measured by ffpe rna-seq was compared to two different standards: rna-seq from fresh frozen (ff) tissue and quantitative pcr (qpcr). both ff and ffpe tumors were sequenced on an illumina genome analyzer iix with an average of 10 million reads. the distribution of fpkms (fragments per kilobase of exon per million fragments mapped) and number of detected genes were similar between ffpe and ff. rna-seq expressions from ff and ffpe samples from the same renal cell carcinoma (rcc) correlated highly (r = 0.919 for tumor 1 and r = 0.954 for tumor 2). on hierarchical cluster analysis, samples clustered by patient identity rather than method of preservation. taqman qpcr of 424 rcc-related genes correlated highly with ffpe rna-seq expressions (r = 0.775 for ffpe tumor 1, r = 0.803 for ffpe tumor 2). expression fold changes were considered, to assess biologic relevance of gene expressions. expression fold changes between ffpe tumors (tumor 1/tumor 2) correlated well when comparing qpcr and rna-seq (r = 0.890). expression fold changes between tumors from different risk groups (our high risk rcc/the cancer genome atlas, tcga, low risk rcc) also correlated well when comparing rna-seq from ff and ffpe tumors (r = 0.887). conclusions ffpe rna-seq provides reliable genes expression data, comparable to that obtained from fresh frozen tissue. it represents a useful tool for discovery and validation of biomarkers. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-1087) contains supplementary material, which is available to authorized users.",0
"obesity is characterized by dysregulated adipogenesis that leads to increased number and/or size of adipocytes. understanding the molecular mechanisms governing adipogenesis is therefore key to designing therapeutic interventions against obesity. in our study, we analyzed 3’-end sequencing data that we generated from human preadipocytes and adipocytes, as well as previously published rna-seq datasets, to elucidate mechanisms of regulation via long non-coding rna (lncrna), alternative splicing (as) and alternative polyadenylation (apa). we discovered lncrnas that have not been previously characterized but may be key regulators of white adipogenesis. we also detected 100 as events and, using motif enrichment analysis, identified rna binding proteins (rbps) that could mediate exon skipping—the most prevalent as event. in addition, we show that usage of alternative poly(a) sites in introns or 3’-utrs of key adipogenesis genes leads to isoform diversity, which can have significant biological consequences on differentiation efficiency. we also identified rbps that may modulate apa and defined how 3’-utr apa can regulate gene expression through gain or loss of specific microrna binding sites. taken together, our bioinformatics-based analysis reveals potential therapeutic avenues for obesity through manipulation of lncrna levels and the profile of mrna isoforms via alternative splicing and polyadenylation.",1
"glioblastoma (gbm) is the most common malignant adult brain tumor generally associated with high level of cellular heterogeneity and a dismal prognosis. long noncoding rnas (lncrnas) are emerging as novel mediators of tumorigenesis. recently developed single-cell rna-seq provides an unprecedented way for analysis of the cell-to-cell variability in lncrna expression profiles. here we comprehensively examined the expression patterns of 2,003 lncrnas in 380 cells from five primary gbms and two glioblastoma stem-like cell (gsc) lines. employing the self-organizing maps, we displayed the landscape of the lncrna expression dynamics for individual cells. further analyses revealed heterogeneous nature of lncrna in abundance and splicing patterns. moreover, lncrna expression variation is also ubiquitously present in the established gsc lines composed of seemingly identical cells. through comparative analysis of gsc and corresponding differentiated cell cultures, we defined a stemness signature by the set of 31 differentially expressed lncrnas, which can disclose stemness gradients in five tumors. additionally, based on known classifier lncrnas for molecular subtypes, each tumor was found to comprise individual cells representing four subtypes. our systematic characterization of lncrna expression heterogeneity lays the foundation for future efforts to further understand the function of lncrna, develop valuable biomarkers, and enhance knowledge of gbm biology.",1
"the cholesterol-lowering drug atorvastatin is among the most prescribed drug in the world. alternative splicing in a number of genes has been reported to be associated with variable statin response. rna-seq has proven to be a powerful technique for genome-wide splice variant analysis. in the present study, we sought to investigate atorvastatin responsive splice variants in hepg2 cells using rna-seq analysis to identify novel candidate genes implicated in cholesterol homeostasis and in the statin response. hepg2 cells were treated with 10 µm atorvastatin for 24 hours. rna-seq and exon array analyses were performed. the validation of selected genes was performed using taqman gene expression assays. rna-seq analysis identified 121 genes and 98 specific splice variants, of which four were minor splice variants to be differentially expressed, 11 were genes with potential changes in their splicing patterns ( sycp3, znf195, znf674, myd88, whsc1, kif16b, znf92, ager, fcho1, slc6a12 and akap9 ), and one was a gene ( rap1gap ) with differential promoter usage. the il21r transcript was detected to be differentially expressed via rna-seq and rt-qpcr, but not in the exon array. in conclusion, several novel candidate genes that are affected by atorvastatin treatment were identified in this study. further studies are needed to determine the biological significance of the atorvastatin responsive splice variants that have been uniquely identified using rna-seq.",0
"digitalis purpurea ( d. purpurea ) is one of the most important medicinal plants and is well known in the treatment of heart failure because of the cardiac glycosides that are its main active compounds. however, in the absence of strand specific sequencing information, the post-transcriptional mechanism of gene regulation in d. purpurea thus far remains unknown. in this study, a strand-specific rna-seq library was constructed and sequenced using illumina hiseq platforms to characterize the transcriptome of d. purpurea with a focus on alternative splicing (as) events and the effect of as on protein domains. de novo rna-seq assembly resulted in 48,475 genes. based on the assembled transcripts, we reported a list of 3,265 as genes, including 5,408 as events in d. purpurea. interestingly, both glycosyltransferases and monooxygenase, which were involved in the biosynthesis of cardiac glycosides, are regulated by as. a total of 2,422 as events occurred in coding regions, and 959 as events were located in the regions of 882 unique protein domains, which could affect protein function. this d. purpurea transcriptome study substantially increased the expressed sequence resource and presented a better understanding of post-transcriptional regulation to further facilitate the medicinal applications of d. purpurea for human health.",0
"abundant neurochemical, neuropathological, and genetic evidence suggests that a critical number of proinflammatory and innate immune system-associated factors are involved in the underlying pathological pathways that drive the sporadic alzheimer's disease (ad) process. most recently, a series of epigenetic factors - including a select family of inducible, proinflammatory, nf-κb-regulated small noncoding rnas called mirnas - have been shown to be significantly elevated in abundance in ad brain. these upregulated mirnas appear to be instrumental in reshaping the human brain transcriptome. this reorganization of mrna speciation and complexity in turn drives proinflammatory and pathogenic gene expression programs. the ensuing, progressively altered immune and inflammatory signaling patterns in ad brain support immunopathogenetic events and proinflammatory features of the ad phenotype. this report will briefly review what is known concerning nf-κb-inducible mirnas that are significantly upregulated in ad-targeted anatomical regions of degenerating human brain cells and tissues. quenching of nf-κb-sensitive inflammatory mirna signaling using nf-κb-inhibitors such as the polyphenolic resveratrol analog trans -3,5,4'-trihydroxystilbene (cay10512) may have some therapeutic value in reducing inflammatory neurodegeneration. antagonism of nf-κb-inducing, and hence proinflammatory, epigenetic and environmental factors, such as the neurotrophic herpes simplex virus-1 and exposure to the potent neurotoxin aluminum, are briefly discussed. early reports further indicate that mirna neutralization employing anti-mirna (antagomir) strategies may hold future promise in the clinical management of this insidious neurological disorder and expanding healthcare concern.",1
"sus1 is a conserved protein involved in chromatin remodeling and mrna biogenesis. unlike most yeast genes, the sus1 pre-mrna of saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. sus1 splicing may allow the cell to control sus1 expression, but the mechanisms that regulate this process remain unknown. using in silico analyses together with nmr spectroscopy, gel electrophoresis, and uv thermal denaturation experiments, we show that the downstream intron (i2) of sus1 forms a weakly stable, 37-nucleotide stem–loop structure containing the branch site near its apical loop and the 3′ splice site after the stem terminus. a cellular assay revealed that two of four mutants containing altered i2 structures had significantly impaired sus1 expression. semiquantitative rt-pcr experiments indicated that all mutants accumulated unspliced sus1 pre-mrna and/or induced distorted levels of fully spliced mrna relative to wild type. concomitantly, sus1 cellular functions in histone h2b deubiquitination and mrna export were affected in i2 hairpin mutants that inhibited splicing. this work demonstrates that i2 structure is relevant for sus1 expression, and that this effect is likely exerted through modulation of splicing.",0
"organelle genomes are among the most sequenced kinds of chromosome. this is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. however, studies of organelle rna have not kept pace with those of dna, despite huge amounts of freely available eukaryotic rna-sequencing (rna-seq) data. little is known about organelle transcription in nonmodel species, and most of the available eukaryotic rna-seq data have not been mined for organelle transcripts. here, we use publicly available rna-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. mapping rna-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. for every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle dna—coding and noncoding—is transcriptionally active. these results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. our findings suggest that noncoding organelle dna can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available rna-seq data for recovering complete genome sequences. if pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle rnas are regulating fundamental processes within eukaryotic cells.",1
"the global shortening of mrnas through alternative polyadenylation (apa) that occurs during enhanced cellular proliferation represents an important, yet poorly understood mechanism of regulated gene expression 1 , 2. the 3′utr truncation of growth promoting mrna transcripts that relieves intrinsic microrna- and au-rich element-mediated repression has been observed to correlate with cellular transformation 3 ; however, the importance to tumorigenicity of rna 3′ end processing factors that potentially govern apa is unknown. here, we have identified cfim25 as a broad repressor of proximal poly(a) site usage that, when depleted, increases cell proliferation. applying a regression model on standard rna-seq data for novel apa events, we identified at least 1,450 genes with shortened 3′utrs after cfim25 knockdown, representing 11% of significantly expressed mrna in hela cells. dramatic increases in expression of several known oncogenes including cyclin d1 are observed as a consequence of cfim25 depletion. importantly, we identified a subset of cfim25-regulated apa genes with shortened 3′utrs in glioblastoma (gbm) tumors that have reduced cfim25 expression. downregulation of cfim25 expression in glioblastoma cells enhances their tumorigenic properties and increases tumor size while cfim25 overexpression reduces these properties and inhibits tumor growth. these findings identify a pivotal role of the cfim25 in governing apa and reveal a previously unknown connection between cfim25 and glioblastoma tumorigenicity.",0
"kashin-beck disease (kbd) is a chronic osteochondropathy with unclear pathogeny. in this study, we compared the microrna expression profiles of 16 kbd patients, 16 osteoarthritis (oa) patients and 16 rheumatoid arthritis (ra) patients and 16 healthy controls in their blood specimens. mirnas expression profiling was performed using exiqon mircury lnatm mirnas array. mirnas target genes were predicted using mirror suite. another independent mrna expression profile dataset of 20 kbd patients and 15 healthy controls were integrated with the mirna expression profiles of kbd. we identified 140 differently expressed mirnas in kbd vs. controls. go enrichment analysis found that hypoxia, wnt receptor signaling pathway and vitamin b6 biosynthesis related go terms were significantly overrepresented in the target genes of differently expressed mirnas in kbd vs. control. 18 differently expressed common mirnas were identified in kbd vs. control, kbd vs. oa and kbd vs. ra. integrating the lists of differently expressed mirna target genes and mrna differently expressed genes detected 6 common genes for kbd. our results demonstrated the altered mirnas expression profiles of kbd comparing to healthy controls, oa and ra, which provide novel clues for clarifying the mechanism of kbd.",1
"recently, large numbers of normal human tissues have been profiled for non-coding rnas and more than fourteen thousand long intergenic non-coding rnas (lincrnas) are found expressed in normal human tissues. the functional roles of these normal lincrnas (nlincrnas) in the regulation of protein coding genes in normal and disease biology are yet to be established. here, we have profiled two rna-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincrnas. we find 130 nlincrnas significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. interestingly, according to illumina body map, significant numbers of these nlincrnas display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. a number of the regulated nlincrnas share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. for example, in all cancer samples i) the nlincrna, tcons_00029157, and a neighboring tumor suppressor factor, sik1, are both down regulated; ii) several thyroid-specific nlincrnas in the neighborhood of the thyroid-specific gene tpo, are both up-regulated; and iii) the tcons_00010581, an isoform of heih, is down-regulated while the neighboring ezh2 gene is up-regulated in cancer. several nlincrnas from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including pcat-1, pvt1, and pcat-92. we observe that there is significant bias towards up-regulation of nlincrnas with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. considering that all reported cancer associated lincrnas (clincrnas) are biased towards up-regulation, we conclude that this bias may be functionally relevant.",1
"transportation of samples is essential for large-scale biobank projects. however, rna degradation during pre-analytical operations prior to transportation can cause systematic bias in transcriptome data, which may prevent subsequent biomarker identification. therefore, to collect high-quality biobank samples for expression analysis, specimens must be transported under stable conditions. in this study, we examined the effectiveness of rna-stabilizing reagents to prevent rna degradation during pre-analytical operations with an emphasis on rna from peripheral blood mononuclear cells (pbmcs) to establish a protocol for reducing systematic bias. to this end, we obtained pbmcs from 11 healthy volunteers and analyzed the purity, yield, and integrity of extracted rna after performing pre-analytical operations for freezing pbmcs at −80°c. we randomly chose 7 samples from 11 samples individually, and systematic bias in expression levels was examined by real-time quantitative reverse transcription polymerase chain reaction (qrt-pcr), rna sequencing (rna-seq) experiments and data analysis. our data demonstrated that omission of stabilizing reagents significantly lowered rna integrity, suggesting substantial degradation of rna molecules due to pre-analytical freezing. qrt-pcr experiments for 19 selected transcripts revealed systematic bias in the expression levels of five transcripts. rna-seq for 25,223 transcripts also suggested that about 40% of transcripts were systematically biased. these results indicated that appropriate reduction in systematic bias is essential in protocols for collection of rna from pbmcs for large-scale biobank projects. among the seven commercially available stabilizing reagents examined in this study, qrt-pcr and rna-seq experiments consistently suggested that rnalock, rna/dna stabilization reagent for blood and bone marrow, and 1-thioglycerol/homogenization solution could reduce systematic bias. on the basis of the results of this study, we established a protocol to reduce systematic bias in the expression levels of rna transcripts isolated from pbmcs. we believe that these data provide a novel methodology for collection of high-quality rna from pbmcs for biobank researchers.",0
"enhancer of zeste homolog 2 (ezh2), a dynamic chromatin regulator in cancer, represents a potential therapeutic target showing early signs of promise in clinical trials. ezh2 chip sequencing data in 19 cell lines and rna sequencing data in ten cancer types were downloaded from geo and tcga, respectively. integrated chip sequencing analysis and co-expressing analysis were conducted and both mrna and long noncoding rna (lncrna) targets were detected. we detected a median of 4,672 mrna targets and 4,024 lncrna targets regulated by ezh2 in 19 cell lines. 20 mrna targets and 27 lncrna targets were found in all 19 cell lines. these mrna targets were enriched in pathways in cancer, hippo, wnt, mapk and pi3k-akt pathways. co-expression analysis confirmed numerous targets, mrna genes (rras, tgfbr2, nuf2 and prc1) and lncrna genes (lncrna linc00261, dio3os, rp11-307c12.11 and rp11-98d18.9) were potential targets and were significantly correlated with ezh2. we predicted genome-wide potential targets and the role of ezh2 in regulating as a transcriptional suppressor or activator which could pave the way for mechanism studies and the targeted therapy of ezh2 in cancer.",1
"the classic g-quadruplex motif consists of a continuous array of 3–4 guanine residues with an intermittent loop size of 1–7 nucleotides (g 3–4 n 1–7 g 3–4 n 1–7 g 3–4 n 1–7 g 3–4 ). an rna g-quadruplex is able to attain only one parallel g-quadruplex topology owing to steric constraints. investigating the possibilities of the formation of rna g-quadruplexes with a stretch of sequences deviating from this classic motif will add to the overall conformations of rna g-quadruplexes, bestowing diversity to this structure. here, we report unusual combinations of guanine residues involved in rna g-quadruplex formation in the 5′ untranslated region (utr) of the von willebrand factor (vwf) mrna using the mutagenesis approach. different permutations and combinations of guanine residues form g-quadruplexes. upon investigation, g-quadruplexes in 5′ utr of vwf mrna are shown to exhibit an inhibitory function.",0
"background rna-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. however, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. results we present a method, in vitro transcription sequencing (ivt-seq), for identifying and assessing the technical biases in rna-seq library generation and sequencing at scale. we created a pool of over 1,000 in vitro transcribed rnas from a full-length human cdna library and sequenced them with polya and total rna-seq, the most common protocols. because each cdna is full length, and we show in vitro transcription is incredibly processive, each base in each transcript should be equivalently represented. however, with common rna-seq applications and platforms, we find 50% of transcripts have more than two-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. we also find greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. we use a combination of experimental and computational approaches to show rrna depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation. conclusions these results show the utility of ivt-seq for promoting better understanding of bias introduced by rna-seq. we find rrna depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. these biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting rna-seq results.",0
"selenocysteine, the 21st amino acid, has been found in 25 human selenoproteins and selenoenzymes important for fundamental cellular processes ranging from selenium homeostasis maintenance to the regulation of the overall metabolic rate. in all organisms that contain selenocysteine, both the synthesis of selenocysteine and its incorporation into a selenoprotein requires an elaborate synthetic and translational apparatus, which does not resemble the canonical enzymatic system employed for the 20 standard amino acids. in humans, three synthetic enzymes, a specialized elongation factor, an accessory protein factor, two catabolic enzymes, a trna, and a stem-loop structure in the selenoprotein mrna are critical for ensuring that only selenocysteine is attached to selenocysteine trna and that only selenocysteine is inserted into the nascent polypeptide in response to a context-dependent uga codon. the abnormal selenium homeostasis and mutations in selenoprotein genes have been causatively linked to a variety of human diseases, which, in turn, sparked a renewed interest in utilizing selenium as the dietary supplement to either prevent or remedy pathologic conditions. in contrast, the importance of the components of the selenocysteine-synthetic machinery for human health is less clear. emerging evidence suggests that enzymes responsible for selenocysteine formation and decoding the selenocysteine uga codon, which by extension are critical for synthesis of the entire selenoproteome, are essential for the development and health of the human organism.",0
"summary background micrornas (mirnas) are small non-coding nucleotides that regulate mrna stability and protein expression by imperfect base pairing with the 3′-untranslated region (3′utr) of target mrnas. many mirnas have been documented to be aberrantly expressed in human cancers, but the role of mirnas in endometrioid endometrial cancer (eec) remains poorly understood. the objective of this study was to investigate the effect of mir-125b on eec development and to explore its molecular mechanism in eec carcinogenesis. material/methods real-time quantitative pcr was applied to evaluate the expression level of mirna-125b in eec and normal endometrium (ne) samples. the invasion ability of mir-125b in eec hec1b cells was analyzed by transwell assay after pre-mir-125b or anti-mir-125b transfection. for the invasion mechanism analysis of mir-125b on hec1b cells, mirbase, targetscan, miranda and pictar were used to predict the possible target gene of mir-125b. luciferase activities assay, cotransfection and western blot were used to reveal that the predicted target genes of mir-125b were direct and specific. rna interference technology was used to confirm that the invasion inhibition of mir-125b was directly induced by erbb2. results our study showed that mir-125b was down-regulated in human eec specimens compared to that in nc specimens. over-expression of mir-125b in hec1b cells inhibited eec invasion and this inhibitory effect on hec1b cells could be restored by mir-125b knock down. mechanism analysis revealed that erbb2 was a direct and specific target of mir-125b. the inhibitory effect on eec cell invasion was mediated by mir-125b inhibition of the translation of a proto-oncogene, erbb2. conclusions aberrantly expressed mir-125b contributes to hec1b cells invasion partly through directly down-regulating erbb2 protein expression in eec. this mirna signature offers a novel potential therapeutic strategy for eec.",1
"the gram-positive bacterium listeria monocytogenes is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. l. monocytogenes causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. listeriosis has one of the highest mortality rates (up to 30%) of all food-borne infections. this human pathogenic bacterium is an important model organism for biomedical research to investigate cell-mediated immunity. l. monocytogenes is also one of the best characterised bacterial systems for the molecular analysis of intracellular parasitism. recently several transcriptomic studies have also made the ubiquitous distributed bacterium as a model to understand mechanisms of gene regulation from the environment to the infected host on the level of mrna and non-coding rnas (ncrnas). we have used semiconductor sequencing technology for rna-seq to investigate the repertoire of listerial ncrnas under extra- and intracellular growth conditions. furthermore, we applied a new bioinformatic analysis pipeline for detection, comparative genomics and structural conservation to identify ncrnas. with this work, in total, 741 ncrna locations of potential ncrna candidates are now known for l. monocytogenes , of which 611 ncrna candidates were identified by rna-seq. 441 transcribed ncrnas have never been described before. among these, we identified novel long non-coding antisense rnas with a length of up to 5,400 nt e.g. opposite to genes coding for internalins, methylases or a high-affinity potassium uptake system, namely the kdpabc operon, which were confirmed by qrt-pcr analysis. rna-seq, comparative genomics and structural conservation of l. monocytogenes ncrnas illustrate that this human pathogen uses a large number and repertoire of ncrna including novel long antisense rnas, which could be important for intracellular survival within the infected eukaryotic host.",1
"drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. in the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. we estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5′ ends of housekeeping genes. as a rule, interbands display preferential “head-to-head” orientation of genes. they are enriched for “broad” class promoters characteristic of housekeeping genes and associate with open chromatin proteins and origin recognition complex (orc) components. in two regions, 10a and 100b, coding sequences of genes whose 5′-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called “grey” bands. comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. analysis of rna-seq data (modencode-flybase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. we developed a special algorithm to computationally process protein localization data generated by the modencode project and show that drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.",0
"abstract cellular characteristics and their adjustment to a state of disease have become more evident due to recent advances in imaging, fluorescent reporter mice, and whole genome rna sequencing. the uncovered cellular heterogeneity and/or plasticity potentially complicates experimental studies and clinical applications, as markers derived from whole tissue ‘bulk’ sequencing is unable to yield a subtype transcriptome and specific markers. here, we propose definitions on heterogeneity and plasticity, discuss current knowledge thereof in the vasculature and how this may be improved by single-cell sequencing (scs). scs is emerging as an emerging technique, enabling researchers to investigate different cell populations in more depth than ever before. cell selection methods, e.g. flow assisted cell sorting, and the quantity of cells can influence the choice of scs method. smart-seq2 offers sequencing of the complete mrna molecule on a low quantity of cells, while drop-seq is possible on large numbers of cells on a more superficial level. scs has given more insight in heterogeneity in healthy vasculature, where it revealed that zonation is crucial in gene expression profiles among the anatomical axis. in diseased vasculature, this heterogeneity seems even more prominent with discovery of new immune subsets in atherosclerosis as proof. vascular smooth muscle cells and mesenchymal cells also share these plastic characteristics with the ability to up-regulate markers linked to stem cells, such as sca-1 or cd34. current scs studies show some limitations to the number of replicates, quantity of cells used, or the loss of spatial information. bioinformatical tools could give some more insight in current datasets, making use of pseudo-time analysis or rna velocity to investigate cell differentiation or polarization. in this review, we discuss the use of scs in unravelling heterogeneity in the vasculature, its current limitations and promising future applications.",0
"nf-y is a trimeric transcription factor -tf- which binds with high selectivity to the conserved ccaat element. individual chip-seq analysis as well as encode have progressively identified locations shared by other tfs. here, we have analyzed data introduced by encode over the last five years in k562, hela-s3 and gm12878, including several chromatin features, as well rna-seq profiling of hela cells after nf-y inactivation. we double the number of sequence-specific tfs and co-factors reported. we catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as rna-binding proteins. on the one hand, these data better define nf-y association with single members of major classes of tfs, on the other, they suggest that it might have a wider role in the control of mrna production.",0
"background histone deacetylase (hdac) inhibitors can attenuate acute kidney injury (aki)-mediated damage and reduce fibrosis in kidney disease models. the aim of the present study was to investigate the effects of the hdac inhibitor ms-275 on lipopolysaccharide (lps)-induced aki and the associated mechanisms. material/methods a lps-induced model in 6–8 weeks-old mice was established by intraperitoneal injection of lps (10 mg/kg), with pre-treatment of ms-275 (2 mg/kg/day) administered intraperitoneally for five days. in addition, hk-2 cells were exposed to lps (1 μg/ml) at 0.1 nm, 1 nm, 10 nm, and 100 nm. for our in vitro ms-275 study, detection programs included histology, biochemical, immunohistochemistry, mrna and protein expression as well as apoptosis. results ms-275 ameliorated renal damage, enhanced the survival rate of the lps-induced sepsis model, decreased the expressions of tnf-α, il-1β, il-6, cox-2, and nf-κbp65 nucleus translocation, suppressed the hdac activity which was enhanced in septic aki mice, and enhanced the acetylation of histone h3 and h4. reactive oxygen species (ros) production was enhanced in the kidney of lps mice compared to control mice, while ms-275 suppressed the production of ros in kidney tissue. in the in vitro studies, ms-275 reduced the lps-induced apoptosis of hk-2 cells, inhibited ros and mda production, increased the production gsh and sod activity, decreased the expressions of chop, grp78, caspase3, and capase12, which was related to endoplasmic reticulum stress in lps stimulated hk-2 cells. conclusions ms-275 pre-treatment improved renal function and ameliorated histological alterations, inflammation, and ros production in lps-induced aki mice and may act through inhibiting ros-oxidative stress and endoplasmic reticulum stress.",0
"micrornas (mirnas) contribute to cancer initiation and progression by silencing the expression of their target genes, causing either mrna molecule degradation or translational inhibition. intraductal epithelial proliferations of the breast are histologically and clinically classified into normal, atypical ductal hyperplasia (adh), ductal carcinoma in situ (dcis) and invasive ductal carcinoma (idc). to better understand the progression of ductal breast cancer development, we attempt to identify deregulated mirnas in this process using formalin-fixed, paraffin-embedded (ffpe) tissues from breast cancer patients. following tissue microdissection, we obtained 8 normal, 4 adh, 6 dcis and 7 idc samples, which were subject to rna isolation and mirna expression profiling analysis. we found that mir-21, mir-200b/c, mir-141, and mir-183 were consistently up-regulated in adh, dcis and idc compared to normal, while mir-557 was uniquely down-regulated in dcis. interestingly, the most significant mirna deregulations occurred during the transition from normal to adh. however, the data did not reveal a step-wise mirna alteration among discrete steps along tumor progression, which is in accordance with previous reports of mrna profiling of different stages of breast cancer. furthermore, the expression of msh2 and smad7, two important molecules involving tgf-β pathway, was restored following mir-21 knockdown in both mcf-7 and hs578t breast cancer cells. in this study, we have not only identified a number of potential candidate mirnas for breast cancer, but also found that deregulation of mirna expression during breast tumorigenesis might be an early event since it occurred significantly during normal to adh transition. consequently, we have demonstrated the feasibility of mirna expression profiling analysis using archived ffpe tissues, typically with rich clinical information, as a means of mirna biomarker discovery.",1
"abstract malignant melanoma (mm) is a highly malignant melanocytic tumor, it occurs mostly in the skin, the mucous membrane close to the skin, but also in the tunicae rhagoides and the pia mater. the uyghur is the largest ethnic group living in the xinjiang uyghur autonomous region of china, accounting for 46% of the total population of 20 million. large-scale studies on mms in asian countries are limited. this study aimed to investigate braf mrna expression and mutations in chinese uyghur patients with mms and to identify the clinical features associated with these parameters. formalin-fixed, paraffin wax-embedded tumor sections from 60 mms were analyzed for braf expression using reverse transcription polymerase chain reaction (rt-pcr). exons 11 and 15 of braf were analyzed for the presence of mutations using pcr and dna sequencing. sixty mms were followed by mobile phone for survival analysis. braf mrna expression was higher in mms than in pigmented moles and normal skin tissues. fourteen of 60 mms had braf mutations. the frequency of braf mutations was significantly higher in patients younger than 60 years (10/28, 4/32, p = .02). a significant difference was observed in the frequency of braf mutations among specimens of mucosal, acral, chronic sun-induced damage (csd), and non-csd mms (2/10, 3/19, 8/25, 1/6, p = .002). no significant association was found among braf mutations, sex, ulceration, or lymph node metastasis. mms lymph node metastasis (hazard ratio 2.54 , p = .01) affected survival. this study indicated that braf mutations and expression might serve as independent adverse prognostic factors in melanoma.",0
"micrornas (mirnas) play an important role in pancreatic development and adult β-cell physiology. our hypothesis is based on the assumption that each islet cell type has a specific pattern of mirna expression. we sought to determine the profile of mirna expression in α-and β-cells, the main components of pancreatic islets, because this analysis may lead to a better understanding of islet gene regulatory pathways. highly enriched (>98%) subsets of human α-and β-cells were obtained by flow cytometric sorting after intracellular staining with c-peptide and glucagon antibody. the method of sorting based on intracellular staining is possible because mirnas are stable after fixation. mirna expression levels were determined by quantitative high throughput pcr-based mirna array platform screening. most of the mirnas were preferentially expressed in β-cells. from the total of 667 mirnas screened, the significant analysis of microarray identified 141 mirnas, of which only 7 were expressed more in α-cells (α-mirnas) and 134 were expressed more in β-cells (β-mirnas). bioinformatic analysis identified potential targets of β-mirnas analyzing the beta cell gene atlas, described in the t1dbase, the web platform, supporting the type 1 diabetes (t1d) community. cmaf, a transcription factor regulating glucagon expression expressed selectively in α-cells (tfα) is targeted by β-mirnas; mir-200c, mir-125b and mir-182. min6 cells treated with inhibitors of these mirnas show an increased expression of cmaf rna. conversely, over expression of mir-200c, mir-125b or mir-182 in the mouse alpha cell line αtc6 decreases the level of cmaf mrna and protein. mir-200c also inhibits the expression of zfpm2, a tfα that inhibits the pi3k signaling pathway, at both rna and protein levels. in conclusion, we identified mirnas differentially expressed in pancreatic α- and β-cells and their potential transcription factor targets that could add new insights into different aspects of islet biology and pathophysiology.",1
"by introducing synonymous mutations into the coding sequences of gp64sp and fibhsp signal peptides, the influences of mrna secondary structure and codon usage of signal sequences on protein expression and secretion were investigated using baculovirus/insect cell expression system. the results showed that mrna structural stability of the signal sequences was not correlated with the protein production and secretion levels, and fibhsp was more tolerable to codon changes than gp64sp. codon bias analyses revealed that codons for gp64sp were well de-optimized and contained more non-optimal codons than fibhsp. synonymous mutations in gp64sp sufficiently increased its average codon usage frequency and resulted in dramatic reduction of the activity and secretion of luciferase. protein degradation inhibition assay with mg-132 showed that higher codon usage frequency in the signal sequence increased the production as well as the degradation of luciferase protein, indicating that the synonymous codon substitutions in the signal sequence caused misfolding of luciferase instead of slowing down the protein production. meanwhile, we found that introduction of more non-optimal codons into fibhsp could increase the production and secretion levels of luciferase, which suggested a new strategy to improve the production of secretory proteins in insect cells.",0
"micrornas (mirs) are small, endogenous, non-coding rnas that regulate the stability and/or translation of complementary mrna targets. mirs have emerged not only as critical modulators of normal physiologic processes, but their deregulation may significantly impact prostate and other cancers. the expression of mir-23b and mir-27b, which are encoded by the same mir cluster (mir-23b/-27b), are downregulated in metastatic, castration-resistant tumors compared to primary prostate cancer and benign tissue; however, their possible role in prostate cancer progression is unknown. we found that ectopic expression of mir-23b/-27b in two independent castration-resistant prostate cancer cell lines resulted in suppression of invasion and migration, as well as reduced survival in soft agar (a measure of anoikis). however, there was no effect of mir-23b/-27b on cell proliferation suggesting that these mirs function as metastasis (but not growth) suppressors in prostate cancer. conversely, inhibition of mir-23b/-27b in the less aggressive androgen-dependent lncap prostate cancer cell line resulted in enhanced invasion and migration also without affecting proliferation. mechanistically, we found that introduction of mir-23b/-27b in metastatic, castration-resistant prostate cancer cell lines resulted in a significant attenuation of rac1 activity without affecting total rac1 levels and caused increased levels of the tumor suppressor e-cadherin. inhibition of these mirs had the opposite effect in androgen-dependent lncap cells. these results suggest that mir-23b/-27b are metastasis suppressors that might serve as novel biomarkers and therapeutic agents for castration-resistant disease.",1
"background the biological function of lncrna elf3-as1 remains largely unknown in cancers. the cause of snai2 overexpression in tumor metastasis remains largely unclear. the molecular mechanisms underlying the high co-expression of antisense lncrnas and adjacent protein-coding genes remains unclear. methods rna-seq, chip and dual-luciferase reporter assay were performed to identify lncrnas regulated by snai2. microrna-seq and rna-seq studies were conducted to reveal the biological function of elf3-as1 in gc. rna pulldown and chirp assays were conducted to identify the protein that interacts with elf3-as1. results a total of 123 lncrnas were identified to be regulated by snai2 in gc by rna sequencing. the elf3 gene and antisense lncrna elf3-as1 were both transcriptionally repressed by snai2 or snai1. down-regulation of elf3-as1 and elf3 predicted poor prognosis in gc. nuclear localized lncrna elf3-as1 negatively regulated gc cell cycle progression via suppressing g1/s transition and histone synthesis. elf3-as1 mainly inhibited gc metastasis by repressing snai2 signaling. additionally, elf3-as1 modulated elf3 mrna stability by rna-rna interaction. the rna duplexes formed by elf3 mrna and lncrna elf3-as1 directly interacted with the double-stranded rna (dsrna) binding protein complex ilf2/ilf3 (nf45/nf90). in turn, the ilf2/ilf3 complex dynamically regulated the expression of elf3-as1 and elf3 by affecting the dsrna stability. conclusions the snai2-elf3-as1 feedback loop regulates elf3 expression at transcriptional and post-transcriptional levels and drives gastric cancer metastasis by maintaining snai2 overexpression. the ilf2/ilf3 complex plays a critical role in regulating dsrna stability. in addition, our work provides a direct evidence that head-to-head antisense lncrnas can share promoters with neighboring coding genes, which make their expression subject to similar transcriptional regulation, leading to high co-expression. supplementary information the online version contains supplementary material available at 10.1186/s13046-022-02541-9.",1
"background: chitinase-3-like protein 1 (chi3l1) is overexpressed in various types of tumors, especially in glioma, and contributes to tumor progression. however, the definite role of chi3l1 and involved pathway in glioma progression are not completely understood. methods: chi3l1 expression in human gliomas and its association with patient survival was determined using enzyme-linked immunosorbent assay, western blot, immunohistochemistry, and public databases. single-cell rna-seq was used to characterize the landscape of tumor and myeloid cells. human proteome microarray assay was applied to identify the binding partners of chi3l1. protein-protein interactions were analyzed by co-immunoprecipitation and cellular co-localization. the roles of chi3l1 in glioma proliferation and invasion were investigated in tumor cell lines by gain- and loss- of function, as well as in vivo animal experiments. results: chi3l1 was up-regulated in all disease stages of glioma, which was closely related with tumor survival, growth, and invasion. chi3l1 was primarily expressed in glioma cells, followed by neutrophils. moreover, glioma cells with high expression of chi3l1 were significantly enriched in nf-κb pathway. pseudo-time trajectory analysis revealed a gradual transition from chi3l1 low to chi3l1 high glioma cells, along with the nf-κb pathway gradually reversed from inhibition to activation. intriguingly, chi3l1 binds to actinin alpha 4 (actn4) and nfkb1, and enhances the nf-κb signaling pathway by promoting the nf-κb subunit nuclear translocation in glioma cells. further, chi3l1 were released into the tumor microenvironment (tme) and interacted with cd44 expressed on tumor-associated macrophages to activate akt pathway, thereby contributing to m2 macrophage polarization. in addition, chi3l1 positively correlated to the expression of immune checkpoints, such as cd274 (pd-l1) and havcr2 (lag3), which then remodeled the tme to an immunosuppressive phenotype. conclusion: our research revealed that chi3l1 facilitated nf-κb pathway activation within glioma cells and reprogramed the tme, thereby serving as a promising therapeutic target for glioma.",0
"ribo-seq maps the location of translating ribosomes on mature mrna transcripts. while during normal translation, ribosome density is constant along the length of the mrna coding region, this can be altered in response to translational regulatory events. in the present study, we developed a method to detect translational regulation of individual mrnas from their ribosome profiles, utilizing changes in ribosome density. we used mathematical modeling to show that changes in ribosome density should occur along the mrna at the point of regulation. we analyzed a ribo-seq data set obtained for mouse embryonic stem cells and showed that normalization by corresponding rna-seq can be used to improve the ribo-seq quality by removing bias introduced by deep-sequencing and alignment artifacts. after normalization, we applied a change point algorithm to detect changes in ribosome density present in individual mrna ribosome profiles. additional sequence and gene isoform information obtained from the ucsc genome browser allowed us to further categorize the detected changes into different mechanisms of regulation. in particular, we detected several mrnas with known post-transcriptional regulation, e.g., premature termination for selenoprotein mrnas and translational control of atf4 , but also several more mrnas with hitherto unknown translational regulation. additionally, our approach proved useful for identification of new transcript isoforms.",0
"brain aging frequently underlies cognitive decline and is a major risk factor for neurodegenerative conditions. the exact molecular mechanisms underlying brain aging, however, remain unknown. whole transcriptome sequencing provides unparalleled depth and sensitivity in gene expression profiling. it also allows non-coding rna and splice variant detection/comparison across phenotypes. using rna-seq to sequence the cerebral cortex transcriptome in 6-, 12- and 28-month-old rats, age-related changes were studied. protein-coding genes related to mhc ii presentation and serotonin biosynthesis were differentially expressed (de) in aging. relative to protein-coding genes, more non-coding genes were de over the three age-groups. rna-seq quantifies not only levels of whole genes but also of their individual transcripts. over the three age-groups, 136 transcripts were de, 37 of which were so-called dark matter transcripts that do not map to known exons. fourteen of these transcripts were identified as novel putative long non-coding rnas. evidence of isoform switching and changes in usage were found. promoter and coding sequence usage were also altered, hinting of possible changes to mitochondrial transport within neurons. therefore, in addition to changes in the expression of protein-coding genes, changes in transcript expression, isoform usage, and non-coding rnas occur with age. this study demonstrates dynamic changes in rna with age at various genomic levels, which may reflect changes in regulation of transcriptional networks and provides non-coding rna gene candidates for further studies. electronic supplementary material the online version of this article (doi:10.1007/s11357-012-9410-1) contains supplementary material, which is available to authorized users.",1
"nonsense-mediated mrna decay (nmd) eliminates different classes of mrna substrates including transcripts with long 3′ utrs. current models of nmd suggest that the long physical distance between the poly(a) tail and the termination codon reduces the interaction between cytoplasmic poly(a)-binding protein (pabpc1) and the eukaryotic release factor 3a (erf3a) during translation termination. in the absence of pabpc1 binding, erf3a recruits the nmd factor upf1 to the terminating ribosome, triggering mrna degradation. here, we have used the ms2 tethering system to investigate the suppression of nmd by pabpc1. we show that tethering of pabpc1 between the termination codon and a long 3′ utr specifically inhibits nmd-mediated mrna degradation. contrary to the current model, tethered pabpc1 mutants unable to interact with erf3a still efficiently suppress nmd. we find that the interaction of pabpc1 with eukaryotic initiation factor 4g (eif4g), which mediates the circularization of mrnas, is essential for nmd inhibition by tethered pabpc1. furthermore, recruiting either erf3a or eif4g in proximity to an upstream termination codon antagonizes nmd. while tethering of an erf3a mutant unable to interact with pabpc1 fails to suppress nmd, tethered eif4g inhibits nmd in a pabpc1-independent manner, indicating a sequential arrangement of nmd antagonizing factors. in conclusion, our results establish a previously unrecognized link between translation termination, mrna circularization, and nmd suppression, thereby suggesting a revised model for the activation of nmd at termination codons upstream of long 3′ utr.",0
"rapid and reliable methods for performing biological dosimetry are of paramount importance in the event of a large-scale nuclear event. traditional dosimetry approaches lack the requisite rapid assessment capability, ease of use, portability and low cost, which are factors needed for triaging a large number of victims. here we describe the results of experiments in which mice were acutely exposed to 60 co gamma rays at doses of 0 (control) to 10 gy. blood was obtained from irradiated mice 0.5, 1, 2, 3, 5, and 7 days after exposure. mrna expression levels of 106 selected genes were obtained by reverse-transcription real time pcr. stepwise regression of dose received against individual gene transcript expression levels provided optimal dosimetry at each time point. the results indicate that only 4–7 different gene transcripts are needed to explain ≥ 0.69 of the variance (r 2 ), and that receiver-operator characteristics, a measure of sensitivity and specificity, of ≥ 0.93 for these statistical models were achieved at each time point. these models provide an excellent description of the relationship between the actual and predicted doses up to 6 gy. at doses of 8 and 10 gy there appears to be saturation of the radiation-response signals with a corresponding diminution of accuracy. these results suggest that similar analyses in humans may be advantageous for use in a field-portable device designed to assess exposures in mass casualty situations.",0
"cardiovascular diseases (cvds) are seriously threatening to human life and health. polyunsaturated fatty acids (pufas) are known for their role in preventing cvds. it is beneficial to population health to promote the content of pufas in bovine milk. in recent years, limited research based on molecular mechanisms has focused on this field. the biological roles of numerous micrornas (mirnas) remain unknown. in this study, a promising and negatively correlated pair of the mirna (mirna-193a-5p) and a fatty acid desaturase 1 ( fads1 ) gene are identified and screened to explore whether they are potential factors of pufas’ synthesis in bovine milk. the targeted relationship between mirna-193a-5p and fads1 in bovine mammary epithelial cells (bmecs) is demonstrated by dual luciferase reporter assays. qrt-pcr and western blot assays indicate that both the expression of mrna and the protein fads1 show a negative correlation with mirna-193a-5p expression in bmecs. also, mir-193a-5p expression is positively correlated with the expression of genes associated with milk fatty acid metabolism, including elovl fatty acid elongase 6 ( elovl6 ) and diacylglycerol o-acyltransferase 2 ( dgat2 ). the expression of fatty acid desaturase 2 ( fads2 ) is negatively correlated with mir-193a-5p expression in bmecs. the contents of triglycerides (tag), eicosapentaenoic acid (epa), docosapentaenoic acid (dpa) and docosahexaenoic acid (dha) have a significant positive correlation with the expression of fads1 and a significant negative correlation with the expression of mir-193a-5p in bmecs. for the first time, this study confirms that mirna-193a-5p regulates pufas metabolism in bmecs by targeting fads1 , indicating that mirna-193a-5p and fads1 are underlying factors that improve pufas content in bovine milk.",1
"abstract pseudomonas stutzeri a1501 is a versatile nitrogen-fixing bacterium capable of living in diverse environments and coping with various oxidative stresses. nfis, a regulatory noncoding rna (ncrna) involved in the control of nitrogen fixation in a1501, was previously shown to be required for optimal resistance to h 2 o 2 ; however, the precise role of nfis and the target genes involved in the oxidative stress response is entirely unknown. in this work, we systematically investigated the nfis-based mechanisms underlying the response of this bacterium to h 2 o 2 at the cellular and molecular levels. a mutant strain carrying a deletion of nfis showed significant downregulation of oxidative stress response genes, especially katb , a catalase gene, and oxyr , an essential regulator for transcription of catalase genes. secondary structure prediction revealed two binding sites in nfis for katb mrna. complementation experiments using truncated nfis genes showed that each of two sites is functional, but not sufficient, for nfis-mediated regulation of oxidative stress resistance and nitrogenase activities. microscale thermophoresis assays further indicated direct base pairing between katb mrna and nfis at both sites 1 and 2, thus enhancing the half-life of the transcript. we also demonstrated that katb expression is dependent on oxyr and that both oxyr and katb are essential for optimal oxidative stress resistance and nitrogenase activities. h 2 o 2 at low concentrations was detoxified by katb, leaving o 2 as a by-product to support nitrogen fixation under o 2 -insufficient conditions. moreover, our data suggest that the direct interaction between nfis and katb mrna is a conserved and widespread mechanism among p. stutzeri strains. importance protection against oxygen damage is crucial for survival of nitrogen-fixing bacteria due to the extreme oxygen sensitivity of nitrogenase. this work exemplifies how the small ncrna nfis coordinates oxidative stress response and nitrogen fixation via base pairing with katb mrna and nifk mrna. hence, nfis acts as a molecular link to coordinate the expression of genes involved in oxidative stress response and nitrogen fixation. our study provides the first insight into the biological functions of nfis in oxidative stress regulation and adds a new regulation level to the mechanisms that contribute to the oxygen protection of the mofe nitrogenase.",1
"background and objectives: cytokine thymic stromal lymphopoietin (tslp) plays a pivotal role in the pathogenesis of atopic diseases such as atopic dermatitis, allergic rhinitis, and asthma. resveratrol (rsv) exerts various pharmacological effects such as antioxidant, anti-inflammatory, neuroprotective, and anticancer. although, it has been verified the beneficial effects of rsv on various subjects, the effect of rsv on thymic stromal lymphopoietin (tslp) regulation has not been elucidated. materials and methods: here, we examined how rsv regulates tslp in hmc-1 cells. enzyme-linked immunosorbent assay, real-time polymerase chain reaction, western blotting, and calcium assay were performed to evaluate the effect of rsv. results: tslp production and mrna expression were reduced by rsv. rsv down-regulated nuclear factor-κb activation, iκbα phosphorylation as well as activation of receptor-interacting protein2 and caspase-1 in hmc-1 cells. in addition, rsv treatment decreased the up-regulation of intracellular calcium in hmc-1 cells. conclusions: these results suggest that rsv might be useful for the treatment of atopic diseases through blocking of tslp.",0
"sepsis is one of the most common causes of death among critically ill patients in intensive care units worldwide; however, the micrornas (mirnas/mirs) involved in the sepsis process (and their target genes) are largely unknown. the present study integrated mirna and mrna datasets to elucidate key sepsis-related mirna-mrna pairs. the datasets, gse74952 and gse55238 were downloaded from the gene expression omnibus. by performing bioinformatics analysis such as geo2r, mirna target gene prediction, gene ontology analysis, kyoto encyclopedia of genes and genomes pathway analysis and mirna-mrna network analysis, a total of four sepsis-related mirna-mrna pairs were successfully obtained. mmu-mir-370-3p, cluster of differentiation (cd)8a, cd247, zap70 and inhibitor of nuclear factor κ b kinase subunit β (ikbkb) were identified as the components involved in these pairs, and these genes were enriched in the t-cell receptor signaling pathway. finally, reverse transcription-quantitative pcr results validated that the expression levels of the four genes (cd8a, cd247, zap70 and ikbkb) in the sepsis model mice were consistent with the microarray analysis. in conclusion, the present study identified four sepsis-related mirna-mrna pairs using bioinformatics analysis. these results indicated that the candidate mirna-mrna pairs may be involved in the regulation of immunity in sepsis, which may in turn act as indicators or therapeutic targets for sepsis.",1
"background: aberrant expression and alternative splicing of oncogenes are the driving events in tumor initiation and development. but how these events are regulated in cancer cells is largely unknown. functions of atp5a1, an important mitochondrial atp synthase gene, in transcriptional and posttranscriptional regulation were explored in this study. methods: atp5a1 was overexpressed using plasmid-transformed hela cells, and its influence on cell apoptosis and proliferation is evaluated. transcriptome sequencing was then performed using rna-seq to study the changes in gene expression and regulation of alternative splicing events. validation of the implicated genes was achieved using rt-qpcr analysis. results: it was found that atp5a1 could significantly promote cellular apoptosis, but it had no influence on cell proliferation. atp5a1 overexpression significantly increased the expression levels of genes associated with the innate immune response, angiogenesis, and collagen catabolic processes. this included enrichment of mmp2 and mmp19. it was also found that atp5a1 could interfere with the alternative splicing of hundreds of genes associated with glucose homeostasis, hif-1 signaling activation, and several pathways associated with cancers. eight atp5a1-regulated differentially expressed genes and 3 genes altered by splicing were selected and validated using rt-qpcr analysis. conclusions: in summary, we illustrate the regulatory functions of atp5a1 on the transcriptome of hela cells by exploring its influence on gene expression and alternative splicing. the results suggest that atp5a1 may play an important regulatory role in cervical cancer cells by regulating expression and alternative splicing of cancer-associated genes. this study provides novel insights into the current understanding of the mechanisms of atp5a1 on carcinogenesis and cancer progression.",0
"poly(a)-binding proteins are highly conserved among eukaryotes and regulate stability of mrna and translation. among c. elegans homologues, pab-1 mutants showed defects in germline mitotic proliferation. unlike pab-1 mutants, pab-1 rnai at every larval stage caused arrest of germline development at the following stage, indicating that pab-1 is required for the entire postembryonic germline development. this idea is supported by the observations that the mrna level of pab-1 increased throughout postembryonic development and its protein expression was germline-enriched. pab-1 localized to p granules and the cytoplasm in the germline. pab-1 colocalized with cgh-1 and car-1 and affected their localization, suggesting that pab-1 is a component of processing (p)-bodies that interacts with them. the mrna and protein levels of representative germline genes, rec-8 , glp-1 , rme-2 , and msp-152 , were decreased after pab-1 rnai. although the mrna level of msp-152 was increased in cgh-1 mutant, it was also significantly reduced by pab-1 rnai. our results suggest that pab-1 positively regulates the mrna levels of germline genes, which is likely facilitated by the interaction of pab-1 with other p-body components, cgh-1 and car-1.",0
"koi herpesvirus (khv, cyhv-3) causes severe economic losses in carp farms. its eradication is challenging due to the establishment of latency in blood leukocytes and other tissues. to understand the molecular mechanisms leading to khv infection in leukocytes, common carp were bath-exposed to khv at 17 °c. after confirming the presence of viral transcripts in blood leukocytes at ten days post infection, rna-seq was performed on peripheral blood leukocytes on the illumina novaseq. khv infection triggered a robust immune response mediated by pattern recognition receptors, mainly toll-like receptors ( tlr2 , tlr5 , tlr7, and tlr13 ), urokinase plasminogen activator surface receptor -like, galectin proteins, and lipid mediators such as leukotriene b4 receptor 1. enriched pathways showed increased mitochondria oxidative phosphorylation and the activation of signalling pathways such as mitogen-activated protein kinases (mapks) and vascular endothelial growth factor (vegf). khv-infected leukocytes showed low production of reactive oxygen species (ros) and glutathione metabolism, high iron export and phagocytosis activity, and low autophagy. macrophage polarization was deduced from the up-regulation of genes such as arginase non-hepatic 1 -like, macrophage mannose receptor-1 , crem , il-10 , and il-13 receptors, while markers for cytotoxic t cells were observed to be down-regulated. further work is required to characterise these leukocyte subsets and the molecular events leading to khv latency in blood leukocytes.",0
"background although regenerative capacity is evident throughout the animal kingdom, it is not equally distributed throughout evolution. for instance, complex limb/appendage regeneration is muted in mammals but enhanced in amphibians and teleosts. the defining characteristic of limb/appendage regenerative systems is the formation of a dedifferentiated tissue, termed blastema, which serves as the progenitor reservoir for regenerating tissues. in order to identify a genetic signature that accompanies blastema formation, we employ next-generation sequencing to identify shared, differentially regulated mrnas and noncoding rnas in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs. results these studies identified a core group of 5 micrornas (mirnas) that were commonly upregulated and 5 mirnas that were commonly downregulated, as well as 4 novel trnas fragments with sequences conserved with humans. to understand the potential function of these mirnas, we built a network of 1,550 commonly differentially expressed mrnas that had functional relationships to 11 orthologous blastema-associated genes. as mir-21 was the most highly upregulated and most highly expressed mirna in all three models, we validated the expression of known target genes, including the tumor suppressor, pdcd4 , and tgfβ receptor subunit, tgfbr2 and novel putative target genes such as the anti-apoptotic factor, bcl2l13 , choline kinase alpha, chka and the regulator of g-protein signaling, rgs5. conclusions our extensive analysis of rna-seq transcriptome profiling studies in three regenerative animal models, that diverged in evolution ~420 million years ago, reveals a common mirna-regulated genetic network of blastema genes. these comparative studies extend our current understanding of limb/appendage regeneration by identifying previously unassociated blastema genes and the extensive regulation by mirnas, which could serve as a foundation for future functional studies to examine the process of natural cellular reprogramming in an injury context.",1
"abstract araucaria angustifolia is endemic to southern brazil. known as brazilian pine, a. angustifolia is the only native conifer species with economic and social relevance in this country. due to massive exploitation, it has suffered a significant population decline and currently is classified as critically endangered. this encouraged the scientific community to investigate genetic features in brazilian pine to increase resources for management and preservation. in this work, rna-seq data was used to determine the complete nucleotide sequence of the a. angustifolia chloroplast genome (cpdna). the cpdna is 146,203 bp in length and contains 122 genes, including 80 protein-coding genes, 5 ribosomal rna genes, and 37 trna genes. coding regions comprise 45.02%, 4.96% correspond to rrnas and trnas, and 50.02% of the genome encompasses non-coding regions. genes found in the inverted repeat (ir) are present as single copy, with exception of the rrn5 and trn i-cau loci. the typical lsc, ssc, ira and irb organization reported in several land-plant groups is not present in a. angustifolia cpdna. phylogenetic analyses using bayesian and maximum likelihood methods clustered a. angustifolia in the araucariaceae family, with a. heterophylla and a. columnaris as congeneric species. the screening of a. angustifolia cpdna reveled 100 ssrs, 14 of them corresponding to tetrapolymer loci.",0
"huntington’s disease is an incurable neurodegenerative disorder caused by expansion of a cag trinucleotide repeat within one allele of the huntingtin ( htt ) gene. agents that block expression of mutant htt and preserve expression of wild-type htt target the cause of the disease and are an alternative for therapy. we have previously demonstrated that mismatch-containing duplex rnas complementary to the expanded trinucleotide repeat are potent and allele-selective inhibitors of mutant htt expression, but the mechanism of allele selectivity was not explored. we now report that anti-cag duplex rna preferentially recruits argonaute 2 (ago2) to mutant rather than wild-type htt mrna. efficient inhibition of mutant htt protein expression requires less ago2 than needed for inhibiting wild-type expression. in contrast, inhibiting the expression of mutant htt protein is highly sensitive to reduced expression of gw182 (tnrc6a) and its two paralogs, a protein family associated with mirna action. allele-selective inhibition may involve cooperative binding of multiple protein–rna complexes to the expanded repeat. these data suggest that allele-selective inhibition proceeds through an rna interference pathway similar to that used by mirnas and that discrimination between mutant and wild-type alleles of htt mrna is highly sensitive to the pool of ago2 and gw182 family proteins inside cells.",1
"proteins regulate gene expression by controlling mrna biogenesis, localization, translation and decay. identifying the composition, diversity and function of mrnps (mrna protein complexes) is essential to understanding these processes. in a global survey of s. cerevisiae mrna binding proteins we identified 120 proteins that cross-link to mrna, including 66 new mrna binding proteins. these include kinases, rna modification enzymes, metabolic enzymes, and trna and rrna metabolism factors. these proteins show dynamic subcellular localization during stress, including assembly into stress granules and p-bodies (processing-bodies). clip (cross-linking and immunoprecipitation) analyses of the p-body components pat1, lsm1, dhh1 and sbp1 identified sites of interaction on specific mrnas revealing positional binding preferences and co-assembly preferences. taken together, this work defines the major yeast mrnp proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for p-body mrnps.",0
"dis3l2 is a highly conserved 3’-5’ exoribonuclease which is mutated in the human overgrowth disorders perlman syndrome and wilms’ tumour of the kidney. using drosophila melanogaster as a model system, we have generated a new dis3l 2 null mutant together with wild-type and nuclease-dead genetic lines in drosophila to demonstrate that the catalytic activity of dis3l2 is required to control cell proliferation. to understand the cellular pathways regulated by dis3l2 to control proliferation, we used rna-seq on dis3l2 mutant wing discs to show that the imaginal disc growth factor idgf2 is responsible for driving the wing overgrowth. idgfs are conserved proteins homologous to human chitinase-like proteins such as chi3l1/ykl-40 which are implicated in tissue regeneration as well as cancers including colon cancer and non-small cell lung cancer. we also demonstrate that loss of dis3l2 in human kidney hek-293t cells results in cell proliferation, illustrating the conservation of this important cell proliferation pathway. using these human cells, we show that loss of dis3l2 results in an increase in the pi3-kinase/akt signalling pathway, which we subsequently show to contribute towards the proliferation phenotype in drosophila. our work therefore provides the first mechanistic explanation for dis3l2-induced overgrowth in humans and flies and identifies an ancient proliferation pathway controlled by dis3l2 to regulate cell proliferation and tissue growth.",0
"cephalotaxus oliveri is a tertiary relict conifer endemic to china, regarded as a national second-level protected plant in china. this species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. in view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. in this study, single-molecule real-time (smrt) sequencing and illumina rna sequencing were combined to generate the complete transcriptome of c. oliveri. using the rna-seq data to correct the smrt sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a n50 length of 2523, 3480, 3181, and 3267 bp, respectively. additionally, 35,887, 11,306, 36,422, and 25,439 ssrs were detected for the male cone, leaf, root, and stem, respectively. the number of long non-coding rnas predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. we also characterized the gene families and pathways related to abiotic factors. this work provides a comprehensive transcriptome resource for c. oliveri , and this resource will facilitate further studies on the functional genomics and adaptive evolution of c. oliveri.",1
"recent advances in the understanding of the genetics of type 2 diabetes (t2d) susceptibility have focused attention on the regulation of transcriptional activity within the pancreatic beta-cell. micrornas (mirnas) represent an important component of regulatory control, and have proven roles in the development of human disease and control of glucose homeostasis. we set out to establish the mirna profile of human pancreatic islets and of enriched beta-cell populations, and to explore their potential involvement in t2d susceptibility. we used illumina small rna sequencing to profile the mirna fraction in three preparations each of primary human islets and of enriched beta-cells generated by fluorescence-activated cell sorting. in total, 366 mirnas were found to be expressed (i.e. >100 cumulative reads) in islets and 346 in beta-cells; of the total of 384 unique mirnas, 328 were shared. a comparison of the islet-cell mirna profile with those of 15 other human tissues identified 40 mirnas predominantly expressed (i.e. >50% of all reads seen across the tissues) in islets. several highly-expressed islet mirnas, such as mir-375, have established roles in the regulation of islet function, but others (e.g. mir-27b-3p, mir-192-5p) have not previously been described in the context of islet biology. as a first step towards exploring the role of islet-expressed mirnas and their predicted mrna targets in t2d pathogenesis, we looked at published t2d association signals across these sites. we found evidence that predicted mrna targets of islet-expressed mirnas were globally enriched for signals of t2d association (p-values <0.01, q-values <0.1). at six loci with genome-wide evidence for t2d association ( ap3s2 , kcnk16 , notch2 , scl30a8 , vps26a , and wfs1 ) predicted mrna target sites for islet-expressed mirnas overlapped potentially causal variants. in conclusion, we have described the mirna profile of human islets and beta-cells and provide evidence linking islet mirnas to t2d pathogenesis.",1
"the effects of antibiotics on environment-originated nonpathogenic acinetobacter species have been poorly explored. to understand the antibiotic-resistance mechanisms that function in nonpathogenic acinetobacter species, we used an rna-sequencing (rna-seq) technique to perform global gene-expression profiling of soil-borne acinetobacter oleivorans dr1 after exposing the bacteria to 4 classes of antibiotics (ampicillin, amp; kanamycin, km; tetracycline, tc; norfloxacin, nor). interestingly, the well-known two global regulators, the soxr and the rpoe genes are present among 41 commonly upregulated genes under all 4 antibiotic-treatment conditions. we speculate that these common genes are essential for antibiotic resistance in dr1. treatment with the 4 antibiotics produced diverse physiological and phenotypic changes. km treatment induced the most dramatic phenotypic changes. examination of mutation frequency and dna-repair capability demonstrated the induction of the sos response in acinetobacter especially under nor treatment. based on the rna-seq analysis, the glyoxylate-bypass genes of the citrate cycle were specifically upregulated under amp treatment. we also identified newly recognized non-coding small rnas of the dr1 strain, which were also confirmed by northern blot analysis. these results reveal that treatment with antibiotics of distinct classes differentially affected the gene expression and physiology of dr1 cells. this study expands our understanding of the molecular mechanisms of antibiotic-stress response of environment-originated bacteria and provides a basis for future investigations.",1
"neuroblastoma is an aggressive pediatric cancer with a high rate of metastasis to the bm. despite intensive treatments including high-dose chemotherapy, the overall survival rate for children with metastatic neuroblastoma remains dismal. understanding the cellular and molecular mechanisms of the metastatic tumor microenvironment is crucial for developing new therapies and improving clinical outcomes. here, we used single-cell rna-seq to characterize immune and tumor cell alterations in neuroblastoma bm metastases by comparative analysis with patients without metastases. our results reveal remodeling of the immune cell populations and reprogramming of gene expression profiles in the metastatic niche. in particular, within the bm metastatic niche, we observed the enrichment of immune cells, including tumor-associated neutrophils, macrophages, and exhausted t cells, as well as an increased number of tregs and a decreased number of b cells. furthermore, we highlighted cell communication between tumor cells and immune cell populations, and we identified prognostic markers in malignant cells that are associated with worse clinical outcomes in 3 independent neuroblastoma cohorts. our results provide insight into the cellular, compositional, and transcriptional shifts underlying neuroblastoma bm metastases that contribute to the development of new therapeutic strategies. single-cell rna-sequencing identifies changes in immune cell populations and gene expression profiles in the neuroblastoma bone marrow metastatic niche, providing insight for potential therapeutic interventions.",0
"simple summary high levels of inorganic zn were supplemented to meet the nutritional requirements of zn in piglets, which results in the development of intestinal microbial resistance and environmental pollution. previous research indicated that organic zn sources had higher bioavailability than inorganic zn. there is limited information on the comparison of dietary zn source dissolved in water with other zn supplementation forms in piglets. therefore, the present study was designed to compare the effects of three zn supplementation forms (zn-met in the feed, znso 4 in the feed, and znso 4 dissolved in drinking water) on growth performance, zn accumulation, activities of zn-containing enzymes, expression of mt, and zn transporters in piglets. in conclusion, zn-met and znso 4 dissolved in drinking water had higher bioavailability in piglets. abstract the study aimed at determining the effect of different zinc (zn) supplementation forms on zn accumulation, activities of zn-containing enzymes, gene expression of metallothionein (mt), and zn transporters in piglets. eighteen piglets were randomly divided into three groups: (a) a basal diet supplemented with 150 mg/kg zn from zn methionine (zn-met) in the feed (zn-met group), (b) a basal diet supplemented with 150 mg/kg zn from zn sulfate (znso 4 ) in the feed (znso 4 , feed group), and (c) a basal diet supplemented with the same dose of zn as in znso4, feed group but in water (znso 4 , water group). the results showed that zn-met added in feed and znso 4 dissolved in drinking water significantly improved ( p < 0.05) the zn concentration in liver and jejunum and the apparent digestibility of zn in comparison with the znso 4 added in feed. in addition, dietary zn supplementation as zn-met significantly increased ( p < 0.05) the activity of alkaline phosphatase (akp) in the jejunum of piglets in comparison with the znso 4 , feed group. furthermore, the zn-met and znso 4 , water groups showed an improved total superoxide dismutase activity (t-sod) in the ileum as compared to the znso 4 , feed group. meanwhile, the qpcr and western blot results showed that zn-met and znso 4 dissolved in drinking water increased the expression of mt in the jejunum in comparison with the znso 4 added in the piglets’ feed. however, different zn supplementation forms had no effect on the mrna expressions of zip4 and znt1 transporters. in conclusion, zn-met added in feed and znso 4 dissolved in drinking water had higher bioavailability in piglets.",0
"accumulating evidence has indicated that noncoding rnas are involved in intervertebral disc degeneration (idd); however, the competing endogenous rna (cerna)-mediated regulatory mechanisms in idd remain rarely reported. the present study aimed to comprehensively investigate the alterations in expression levels of circular rna (circrna), long noncoding rna (lncrna), microrna (mirna/mir) and mrna in the nucleus pulposus (np) of patients with idd. in addition, crucial lncrna/circrna-mirna-mrna cerna interaction axes were screened using the gse67567 microarray dataset obtained from the gene expression omnibus database. after data preprocessing, differentially expressed circrnas (decs), lncrnas (dels), mirnas (dems) or genes (degs) between idd and normal controls were identified using the linear models for microarray data method. a protein-protein interaction (ppi) network was constructed for degs based on protein databases, followed by module analysis. the cerna network was constructed based on the interaction between mirnas and mrnas, and lncrnas/circrnas and mirnas. the underlying functions of mrnas were predicted using the database for annotation, visualization and integrated discovery database. the present study identified 636 decs, 115 dels, 84 dems and 1,040 degs between patients with idd and control individuals. ppi network analysis demonstrated that fos proto-oncogene, ap-1 transcription factor subunit (fos), mitogen-activated protein kinase 1 (mapk1), hypoxia inducible factor 1 subunit α (hif1a) and transforming growth factor β1 (tgfb1) were hub genes and enriched in modules. metastasis-associated lung adenocarcinoma transcript 1 (malat1)/hsa_circrna_102348-hsa- mir-185-5p-tgfb1/fos, malat1-hsa-mir-155-5p-hif1a, hsa_circrna_102399-hsa-mir-302a-3p-hif1a, malat1-hsa- mir-519d-3p-mapk1 and hsa_circrna_100086-hsa-mir-509-3p-mapk1 cerna axes were obtained by constructing the cerna networks. in conclusion, these identified cerna interaction axes may be crucial targets for the treatment of idd.",1
"haematopoietic stem cells (hscs) possess unique physiological adaptations to sustain blood cell production and cope with stress responses throughout life. to maintain these adaptations, hscs rely on maintaining a tightly controlled protein translation rate. however, the mechanism of how hscs regulate protein translation remains to be fully elucidated. in this study, we investigate the role of transfer rna (trna) m 1 a58 ‘writer’ proteins trmt6 and trmt61a in regulating hscs function. trmt6 deletion promoted hsc proliferation through aberrant activation of mtorc1 signaling. trmt6-deficient hscs exhibited an impaired self-renewal ability in competitive transplantation assay. mechanistically, single cell rna-seq analysis reveals that the mtorc1 signaling pathway is highly upregulated in hsc-enriched cell populations after trmt6 deletion. m 1 a-trna-seq and western blot analysis suggest that trmt6 promotes methylation modification of specific trna and expression of tsc1, fine-tuning mtorc1 signaling levels. furthermore, pharmacological inhibition of the mtorc1 pathway rescued functional defect in trmt6-deficient hscs. to our knowledge, this study is the first to elucidate a mechanism by which trmt6-trmt61a complex-mediated trna-m 1 a58 modification regulates hsc homeostasis.",1
"the outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding rnas (lncrnas). here we systematically inferred the regulatory functions of host lncrnas in response to influenza a virus and severe acute respiratory syndrome coronavirus (sars-cov) based on their similarity in expression with genes of known function. we performed total rna-seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. overall 5,329 lncrnas were differentially expressed after infection. most of the lncrnas were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. each lncrna was further individually annotated using a rank-based method, enabling us to associate 5,295 lncrnas to at least one gene set and to predict their potential cis effects. we validated the lncrnas predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. altogether, these results provide a broad categorization of potential lncrna functions and identify subsets of lncrnas with likely key roles in respiratory virus pathogenesis. these data are fully accessible through the mo use no n- c ode l ung interactive database ( monocldb ).",1
"lung adenocarcinoma (luad) is the most frequent histological subtype of lung cancer, which is the most common malignant tumor and the main cause of cancer-related mortality globally. recent reports revealed that long non-coding rna (lncrna) of metastasis-associated lung adenocarcinoma transcript 1 (malat1) plays a crucial role in tumorigenesis and metastasis development in lung cancer. however, the contribution of malat1 genetic variants to the development of luad is unclear, especially in epidermal growth factor receptor (egfr) mutation status. in this study, 272 ladc patients with different egfr status were recruited to dissect the allelic discrimination of the malat1 polymorphisms at rs3200401, rs619586, and rs1194338. the findings of the study showed that malat1 polymorphisms rs3200401, rs619586, and rs1194338 were not associated to luad susceptibility; however, rs3200401 polymorphisms was significantly correlated to egfr wild-type status and tumor stages in luad patients in dominant model (p=0.016). further analyses using the datasets from the cancer genome atlas (tcga) revealed that lower malat1 mrna levels were associated with the advanced stage, and lymph node metastasis in ladc patients. in conclusion, our results showed that malat1 rs3200401 polymorphisms dramatically raised the probability of luad development.",1
"background synthetic double-stranded rna poly(i:c) is a useful immune adjuvant and exhibits direct antitumor effects against several types of cancers. in this study, we elucidated the mechanisms underlying the effects induced in poly(i:c)-transfected human renal cell carcinoma (rcc) cells. results in contrast to the lack of an effect of adding poly(i:c), poly(i:c) transfection drastically decreased rcc cell viability. poly(i:c) transfection induced reactive oxygen species (ros)-dependent apoptosis in rcc cells and decreased the mitochondrial membrane potential (δψm). treatment with n -acetyl- l -cysteine (nac), a ros scavenger, suppressed apoptosis and restored the δψm. although the levels of phosphorylated γh2a.x, an indicator of dna damage, increased in poly(i:c)-transfected rcc cells, nac treatment decreased their levels, suggesting ros-mediated dna damage. furthermore, poly(i:c) transfection increased the levels of phosphorylated p53, noxa, and tbid. immunoblots and assays with a panel of caspase inhibitors revealed that poly(i:c) transfection-induced apoptosis was dependent on caspase-8 and -9, as well as caspase-2. alternatively, poly(i:c) transfection increased mrna expression of interferon (ifn)-β, and treatment with ifn-β suppressed growth of rcc cells without apoptosis. in addition, cyclind1 and c-myc expression decreased in poly(i:c)-transfected rcc cells. moreover, rna interference experiments revealed that poly(i:c) transfection exerted apoptotic effects on rcc cells through innate adjuvant receptors and the 2-5a system, the latter of which induces apoptosis in virus-infected cells. conclusions these results suggest that poly(i:c) transfection induced two types of effects against rcc cells such as apoptosis, as a result of ros-mediated dna damage, and ifn-β-mediated growth arrest, both of which were exerted via innate adjuvant receptors and the 2-5a system. electronic supplementary material the online version of this article (doi:10.1186/1476-4598-13-217) contains supplementary material, which is available to authorized users.",0
"biologists are required to integrate large amounts of data to construct a working model of the system under investigation. this model is often informal and stored mentally or textually, making it prone to contain undetected inconsistencies, inaccuracies, or even contradictions, not much less than a representation in free natural language. using object-process methodology (opm), a formal yet visual and humanly accessible conceptual modeling language, we have created an executable working model of the mrna decay process in saccharomyces cerevisiae , as well as the import of its components to the nucleus following mrna decay. we show how our model, which incorporates knowledge from 43 articles, can reproduce outcomes that match the experimental findings, evaluate hypotheses, and predict new possible outcomes. moreover, we were able to analyze the effects of the mrna decay model perturbations related to gene and interaction deletions, and predict the nuclear import of certain decay factors, which we then verified experimentally. in particular, we verified experimentally the hypothesis that rpb4p, lsm1p, and pan2p remain bound to the rna 3′-untralslated region during the entire process of the 5′ to 3′ degradation of the rna open reading frame. the model has also highlighted erroneous hypotheses that indeed were not in line with the experimental outcomes. beyond the scientific value of these specific findings, this work demonstrates the value of the conceptual model as an in silico vehicle for hypotheses generation and testing, which can reinforce, and often even replace, risky, costlier wet lab experiments.",0
"growth hormone (gh) is a key regulatory factor in animal growth, development and metabolism. based on the expression level of the gh receptor, the chicken liver is a major target organ of gh, but the biological effects of gh on the chicken liver are not fully understood. in this work we identified mrnas and mirnas that are regulated by gh in primary hepatocytes from female chickens through rna-seq, and analyzed the functional relevance of these mrnas and mirnas through go enrichment analysis and mirna target prediction. a total of 164 mrnas were found to be differentially expressed between gh-treated and control chicken hepatocytes, of which 112 were up-regulated and 52 were down-regulated by gh. a total of 225 chicken mirnas were identified by the rna-seq analysis. among these mirnas 16 were up-regulated and 1 mirna was down-regulated by gh. the gh-regulated mrnas were mainly involved in growth and metabolism. most of the gh-upregulated or gh-downregulated mirnas were predicted to target the gh-downregulated or gh-upregulated mrnas, respectively, involved in lipid metabolism. this study reveals that gh regulates the expression of many mrnas involved in metabolism in female chicken hepatocytes, which suggests that gh plays an important role in regulating liver metabolism in female chickens. the results of this study also support the hypothesis that gh regulates lipid metabolism in chicken liver in part by regulating the expression of mirnas that target the mrnas involved in lipid metabolism.",1
"riboregulation stands for rna-based control of gene expression. in bacteria, small non-coding rnas (srnas) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mrna genes. the rna chaperone hfq facilitates antisense interactions between target mrnas and regulatory srnas, thus influencing mrna stability and/or translation rate. in the α-proteobacterium sinorhizobium meliloti strain 2011, the identification and detection of multiple srnas genes and the broadly pleitropic phenotype associated to the absence of a functional hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. in order to identify target mrnas subject to hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type s. meliloti by quantitative proteomics following protein labelling with 15 n. among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of hfq. this profound proteomic impact implies a major role for hfq on regulation of diverse physiological processes in s. meliloti , from transport of small molecules to homeostasis of iron and nitrogen. changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. these results represent the first quantitative proteomic analysis in s. meliloti. the comparative analysis of the hfq mutant proteome allowed identification of novel strongly hfq-regulated genes in s. meliloti.",1
"the epigenetic writer lysine-specific demethylase 1 (lsd1) is aberrantly upregulated in many cancer types and its overexpression correlates with poor survival and tumor progression. in this study, we analysed lsd1 function in non-small cell lung cancer adenocarcinomas. expression profiling of 182 cases of lung adenocarcinoma proved a significant correlation of lsd1 overexpression with lung adenocarcinoma progression and metastasis. kras-mutated lung cancer cell clones were stably silenced for lsd1 expression. rna-seq and comprehensive pathway analysis revealed, that genes related to a recently described non-canonical integrin β3 pathway, were significantly downregulated by lsd1 silencing. hence, invasion and self-renewal capabilities were strongly decreased. notably, this novel defined lsd1/integrin β3 axis, was also detected in human lung adenocarcinoma specimens. furthermore, the linkage of lsd1 to an altered expression pattern of lung-lineage specific transcription factors and genes, which are involved in alveolar epithelial differentiation, was demonstrated. thus, our findings point to a lsd1-integrin β3 axis, conferring attributes of invasiveness and tumor progression to lung adenocarcinoma.",0
"gene regulation shapes the evolution of phenotypic diversity. we investigated the evolution of liver promoters and enhancers in six primate species using chip-seq (h3k27ac and h3k4me1) to profile cis -regulatory elements (cres) and using rna-seq to characterize gene expression in the same individuals. to quantify regulatory divergence, we compared cre activity across species by testing differential chip-seq read depths directly measured for orthologous sequences. we show that the primate regulatory landscape is largely conserved across the lineage, with 63% of the tested human liver cres showing similar activity across species. conserved cre function is associated with sequence conservation, proximity to coding genes, cell-type specificity, and transcription factor binding. newly evolved cres are enriched in immune response and neurodevelopmental functions. we further demonstrate that conserved cres bind master regulators, suggesting that while cres contribute to species adaptation to the environment, core functions remain intact. newly evolved cres are enriched in young transposable elements (tes), including long-terminal-repeats (ltrs) and sine-vntr- alu s (svas), that significantly affect gene expression. conversely, only 16% of conserved cres overlap tes. we tested the cis -regulatory activity of 69 te subfamilies by luciferase reporter assays, spanning all major te classes, and showed that 95.6% of tested tes can function as either transcriptional activators or repressors. in conclusion, we demonstrated the critical role of tes in primate gene regulation and illustrated potential mechanisms underlying evolutionary divergence among the primate species through the noncoding genome.",0
"glioblastoma multiforme (gbm) is the most malignant brain tumor with limited therapeutic options. temozolomide (tmz) is a novel cytotoxic agent used as first-line chemotherapy for gbm, however, some individual cells can't be isolated for surgical resection and show treatment-resistance, thus inducing poor prognosis. by using the hiseq sequencing and bioinformatics methods, we identified lncrnas showing different expression levels in tmz-resistant and non-resistant patients. rt-qpcr was then performed in tissues and serum samples, and lncrna malat1 was finally identified to show considerable discriminating potential to identify responding patients from non-responding patients. moreover, high serum malat1 expression was associated with poor chemoresponse and survival in gbm patients receiving tmz treatment. subsequently, the tmz resistant cell lines were established, and the cck8 assay showed that lncrna malat1 knockdown significantly reversed tmz resistance in gbm cells. the gain and loss-function experiments revealed that mir-203 was down-regulated by malat1 and this interaction has reciprocal effects. besides, thymidylate synthase (ts) mrna was identified as a direct target of mir-203. lncrna malat1 inhibition re-sensitized tmz resistant cells through up-regulating mir-203 and down-regulating ts expression. on the other hand, malat1 overexpression promoted resistance by suppressing mir-203 and promoting ts expression. in conclusion, our integrated approach demonstrates that enhanced expression of lncrna malat1 confers a potent poor therapeutic efficacy and inhibition of malat1 levels could be a future direction to develop a novel therapeutic strategy to overcome tmz resistance in gbm patients.",1
"curcumin, a natural product derived from the plant curcuma longa , has been found to have anti-inflammatory, antineoplastic and antifibrosis effects. it has been reported that curcumin attenuates allergic airway inflammation in mice through inhibiting nf-κb and its downstream transcription factor gata3. it also has been proved the antineoplastic effect of curcumin through down-regulating notch1 receptor and its downstream nuclear transcription factor nf-κb levels. in this study, we aimed to investigate the anti-inflammatory effect of curcumin on acute allergic asthma and its underlying mechanisms. 36 male balb/c mice were randomly divided into four groups (normal, asthma, asthma+budesonide and asthma+curcumin groups). balf (bronchoalveolar lavage fluid) and lung tissues were analyzed for airway inflammation and the expression of notch1, notch2, notch3, notch4 and the downstream transcription factor gata3. our findings showed that the levels of notch1 and notch2 receptors were up-regulated in asthma group, accompanied by the increased expression of gata3. but the expression of notch2 receptor was lower than notch1 receptor. curcumin pretreatment improved the airway inflammatory cells infiltration and reversed the increasing levels of notch1/2 receptors and gata3. notch3 receptor was not expressed in all of the four groups. notch4 receptor protein and mrna expression level in the four groups had no significant differences. the results of the present study suggested that notch1 and notch2 receptor, major notch1 receptor, played an important role in the development of allergic airway inflammation and the inhibition of notch1–gata3 signaling pathway by curcumin can prevent the development and deterioration of the allergic airway inflammation. this may be a possible therapeutic option of allergic asthma.",0
"plasma exosomal micrornas (mirnas) are considered as valid circulating biomarkers for cancer diagnosis and prognosis. quantitative real-time polymerase chain reaction (qrt-pcr), the most commonly used technique to assess circulating mirna levels, requires a normalization step involving uniformly expressed endogenous mirnas. however, there is still no consensus on reference mirnas for plasma exosomal mirna abundance normalization. in this study, we identified a panel of mirnas with stable abundance by analyzing public plasma exosome rna-seq data and selected mir-486-5p, mir-26a-5p, mir-423-5p and mir191-5p as candidate normalizers. next, we tested the abundance variation of these mirnas by qrt-pcr in plasma exosomes of healthy donors and pediatric patients with anaplastic large cell lymphoma, burkitt lymphoma, hodgkin lymphoma and mature b-cell acute lymphoblastic leukemia. mir-486-5p and mir-26a-5p showed the most stable levels, both between healthy controls and patients and among the malignancies analyzed. in light of previous reports on mirna stability in different exosome isolation methods, our data indicated that mir-26a-5p is a bona fide reference mirna for qrt-pcr normalization to evaluate mirna abundance from circulating plasma exosomes in studies of hematological malignancies.",1
"bacterial hfq-associated small regulatory rnas (srnas) parallel animal micrornas in their ability to control multiple target mrnas. the small non-coding mica rna represses the expression of several genes, including major outer membrane proteins such as omp a, tsx and ecn b. in this study, we have characterised the rna determinants involved in the stability of mica and analysed how they influence the expression of its targets. site-directed mutagenesis was used to construct mica mutated forms. the 5′linear domain, the structured region with two stem-loops, the a/u-rich sequence or the 3′ poly(u) tail were altered without affecting the overall secondary structure of mica. the stability and the target regulation abilities of the wild-type and the different mutated forms of mica were then compared. the 5′ domain impacted mica stability through an rnase iii-mediated pathway. the two stem-loops showed different roles and disruption of stem-loop 2 was the one that mostly affected mica stability and abundance. moreover, stem2 was found to be more important for the in vivo repression of both omp a and ecn b mrnas while stem1 was critical for regulation of tsx mrna levels. the a/u-rich linear sequence is not the only hfq-binding site present in mica and the 3′ poly(u) sequence was critical for srna stability. pnpase was shown to be an important exoribonuclease involved in srna degradation. in addition to the 5′ domain of mica, the stem-loops and the 3′ poly(u) tail are also shown to affect target-binding. disruption of the 3′u-rich sequence greatly affects all targets analysed. in conclusion, our results have shown that it is important to understand the “srna anatomy” in order to modulate its stability. furthermore, we have demonstrated that mica rna can use different modules to regulate its targets. this knowledge can allow for the engineering of non-coding rnas that interact differently with multiple targets.",1
"iron (fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. recently, long non-coding rnas (lncrnas) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. however, systematic screening of lncrnas responding to fe deficiency and their regulatory mechanism in plants has not been reported. in this work, 171 differently expressed lncrnas (de-lncrnas) were identified based on analysis of strand-specific rna-seq data from rice shoots and roots under fe-deficient conditions. we also found several lncrnas, which could generate mirnas or act as endogenous target mimics to regulate expression of fe-related genes. analysis of interaction networks and gene ontology enrichment revealed that a number of de-lncrnas were associated with iron transport and photosynthesis, indicating a possible role of lncrnas in regulation of fe homeostasis. moreover, we identified 76 potential lncrna targets of osbhlh156, a key regulator for transcriptional response to fe deficiency. this study provides insight into the potential functions and regulatory mechanism of fe-responsive lncrnas and would be an initial and reference for any further studies regarding lncrnas involved in fe deficiency in plants.",1
"background a major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mrnas, mirnas) into interpretable functional networks. however, employing a systems biology approach to better understand the complexities underlying drug resistance phenotypes in cancer continues to represent a significant challenge to the field. previously, we derived two drug-resistant breast cancer sublines (tamoxifen- and fulvestrant-resistant cell lines) from the mcf7 breast cancer cell line and performed genome-wide mrna and microrna profiling to identify differential molecular pathways underlying acquired resistance to these important antiestrogens. in the current study, to further define molecular characteristics of acquired antiestrogen resistance we constructed an “integrative network”. we combined joint mirna-mrna expression profiles, cancer contexts, mirna-target mrna relationships, and mirna upstream regulators. in particular, to reduce the probability of false positive connections in the network, experimentally validated, rather than prediction-oriented, databases were utilized to obtain connectivity. also, to improve biological interpretation, cancer contexts were incorporated into the network connectivity. results based on the integrative network, we extracted “substructures” (network clusters) representing the drug resistant states (tamoxifen- or fulvestrant-resistance cells) compared to drug sensitive state (parental mcf7 cells). we identified un-described network clusters that contribute to antiestrogen resistance consisting of mir-146a, -27a, -145, -21, -155, -15a, -125b, and let-7s, in addition to the previously described mir-221/222. conclusions by integrating mirna-related network, gene/mirna expression and text-mining, the current study provides a computational-based systems biology approach for further investigating the molecular mechanism underlying antiestrogen resistance in breast cancer cells. in addition, new mirna clusters that contribute to antiestrogen resistance were identified, and they warrant further investigation.",1
"grain production of rice ( oryza sativa l.) is a top priority in ensuring food security for human beings. one of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. micrornas (mirnas) are key regulators of aging and cellular senescence in eukaryotes. here, to help understand their biological role in rice leaf senescence, we report identification of mirnas and their putative target genes by deep sequencing of six small rna libraries, six rna-seq libraries and two degradome libraries from the leaves of two super hybrid rice, nei-2-you 6 (n2y6, age-resistant rice) and liang-you-pei 9 (lyp9, age-sensitive rice). in total 372 known mirnas, 162 mirna candidates and 1145 targets were identified. compared with the expression of mirnas in the leaves of lyp9, the numbers of mirnas up-regulated and down-regulated in the leaves of n2y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. six mirna families, osa-mir159, osa-mir160 osa-mir164, osa-mir167, osa-mir172 and osa-mir1848, targeting the genes encoding apetala2 (ap2), zinc finger proteins, salicylic acid-induced protein 19 (sip19), auxin response factors (arf) and nac transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. these results provided valuable information for understanding the mirna-mediated leaf senescence of rice, and offered an important foundation for rice breeding.",1
"background therapeutic interventions that optimize angiogenic activities may reduce rates of end-stage kidney disease, critical limb ischemia, and lower extremity amputations in individuals with diabetic kidney disease (dkd). infusion of autologous mesenchymal stromal cells (msc) is a promising novel therapy to rejuvenate vascular integrity. however, dkd-related factors, including hyperglycemia and uremia, might alter msc angiogenic repair capacity in an autologous treatment approach. methods to explore the angiogenic activity of msc in dkd, the transcriptome of adipose tissue-derived msc obtained from dkd subjects was compared to age-matched controls without diabetes or kidney impairment. next-generation rna sequencing (rna-seq) was performed on msc (dkd n = 29; controls n = 9) to identify differentially expressed (de; adjusted p 1) messenger rna (mrna) and microrna (mirna) involved in angiogenesis (genecards). paracrine-mediated angiogenic repair capacity of msc conditioned medium (msccm) was assessed in vitro using human umbilical vein endothelial cells incubated in high glucose and indoxyl sulfate for a hyperglycemic, uremic state. results rna-seq analyses revealed 133 de mrnas (77 upregulated and 56 down-regulated) and 208 de mirnas (119 up- and 89 down-regulated) in dkd-msc versus control-msc. interestingly, mirna let-7a-5p, which regulates angiogenesis and participates in dkd pathogenesis, interacted with 5 angiogenesis-associated mrnas (transgelin/ tagln , thrombospondin 1/ thbs1 , lysyl oxidase-like 4/ loxl4, collagen 4a1/ col4a1 and collagen 8a1/ col8a1 ). dkd-msccm incubation with injured endothelial cells improved tube formation capacity, enhanced migration, reduced adhesion molecules e-selectin, vascular cell adhesion molecule 1 and intercellular adhesion molecule 1 mrna expression in endothelial cells. moreover, angiogenic repair effects did not differ between treatment groups (dkd-msccm vs. control-msccm). conclusions msc from individuals with dkd show angiogenic transcriptome alterations compared to age-matched controls. however, angiogenic repair potential may be preserved, supporting autologous msc interventions to treat conditions requiring enhanced angiogenic activities such as dkd, diabetic foot ulcers, and critical limb ischemia. supplementary information the online version contains supplementary material available at 10.1186/s13287-023-03269-9.",1
"obesity is associated with metabolic perturbations including liver and adipose tissue inflammation, insulin resistance, and type 2 diabetes. omega-6 fatty acids (ω6) promote and omega-3 fatty acids (ω3) reduce inflammation as they can be metabolized to pro- and anti-inflammatory eicosanoids, respectively. 12/15-lipoxygenase (12/15-lo) enzymatically produces some of these metabolites and is induced by high fat (hf) diet. we investigated the effects of altering dietary ω6/ω3 ratio and 12/15-lo deficiency on hf diet-induced tissue inflammation and insulin resistance. we examined how these conditions affect circulating concentrations of oxidized metabolites of ω6 arachidonic and linoleic acids and innate and adaptive immune system activity in the liver. for 15 weeks, wild-type (wt) mice were fed either a soybean oil-enriched hf diet with high dietary ω6/ω3 ratio (11∶1, hfh), similar to western-style diet, or a fat kcal-matched, fish oil-enriched hf diet with a low dietary ω6/ω3 ratio of 2.7∶1 (hfl). importantly, the total saturated, monounsaturated and polyunsaturated fat content was matched in the two hf diets, which is unlike most published fish oil studies in mice. despite modestly increased food intake, wt mice fed hfl were protected from hfh-diet induced steatohepatitis, evidenced by decreased hepatic mrna expression of pro-inflammatory genes and genes involved in lymphocyte homing, and reduced deposition of hepatic triglyceride. furthermore, oxidized metabolites of ω6 arachidonic acid were decreased in the plasma of wt hfl compared to wt hfh-fed mice. 12/15-lo knockout (ko) mice were also protected from hfh-induced fatty liver and elevated mrna markers of inflammation and lymphocyte homing. 12/15-loko mice were protected from hfh-induced insulin resistance but reducing dietary ω6/ω3 ratio in wt mice did not ameliorate insulin resistance or adipose tissue inflammation. in conclusion, lowering dietary ω6/ω3 ratio in hf diet significantly reduces steatohepatitis.",0
"abstract respiratory syncytial virus (rsv) is the most common viral cause of severe lower respiratory tract illness in infants and children. the virus replicates in polarized epithelial cells in the airway and, to a lesser extent, infects airway antigen-presenting cells, such as dendritic cells (dcs). rsv possesses a number of expressed genes that antagonize the effect of type i interferons and other related host factor pathways that inhibit replication efficiency. virus infection alters host gene transcription and the translation of host transcripts through specific antagonism of the function of host proteins, through induction of rna stress granules, and through induction of altered patterns of host gene expression. in healthy cells, micrornas (mirnas) regulate gene expression by targeting the noncoding region of mrna molecules to cause silencing or degradation of transcripts. it is not known whether or not rsv infection alters the level of micrornas in cells. we profiled the pattern of expression of host cell micrornas in rsv-infected epithelial cells or dcs and found that rsv did alter microrna expression but in a cell-type-specific manner. the studies showed that let-7b was upregulated in dcs, while let-7i and mir-30b were upregulated in epithelial cells in a process that required viral replication. interestingly, we found that the rsv nonstructural genes ns1 and ns2 antagonized the upregulation of let-7i and mir-30b. rsv appears to manipulate host cell gene expression through regulation of expression of mirnas related to the interferon response. the data suggest a new mechanism of virus-host cell interactions for paramyxoviruses. importance respiratory syncytial virus (rsv) is the most common cause of serious lower respiratory tract illness in infants and children. the human innate immune response inhibits rsv replication early after inoculation, principally through the effect of substances called interferons. the virus, however, has developed several mechanisms for counteracting the host innate immune response. it is not known whether or not rsv infection alters the expression of host micrornas, which are short rna sequences that are posttranscriptional regulators. this paper shows that rsv does induce unique patterns of microrna expression related to the nf-κb pathway or interferon pathways. the microrna profiles differed depending on the cell type that was infected, airway cell or antigen-presenting cell. interestingly, the virus appears to counteract the microrna response by expressing nonstructural viral genes in the cell that reduce microrna induction. the data suggest a new way in which paramyxoviruses regulate the host cell response to infection.",1
"background rna sequencing technologies reveal that bacteria express rna molecules other than mrna, rrna or trna. during the last years genome-wide bacterial transcriptomes have been shown to comprise intergenic rna, antisense rna, and untranslated regions, all capable of performing diverse regulatory functions. results in this study we used rna-seq to identify 232 antisense rnas (asrnas) in the opportunistic pathogen pseudomonas aeruginosa grown under 13 different conditions. the conditions studied include exponential and stationary growth as well as osmotic, oxidative and antibiotic stress. we found a significant overrepresentation of asrnas that are transcribed opposite to genes involved in cell division and in cell wall, lipopolysaccharide (lps), and capsule biosynthesis, most likely reflecting the conditions used in this study. a substantial number of asrnas significantly changed their expression under osmotic, oxidative and antibiotic stress, suggesting that asrnas may play regulatory roles during these conditions. we also made a comparison between the asrnas detected in this study in p. aeruginosa pao1 with the asrnas detected in two previous studies in p. aeruginosa pa14, and found that the extent of overlap between the studies is very limited. conclusions rna-seq experiments are revealing hundreds of novel transcripts in all bacterial genomes investigated. the comparison between independent studies that used rna-seq to detect novel asrnas in p. aeruginosa shows that the overlap between the results reported is very narrow. it is necessary to address how reproducibility of these kind of studies should be reported in order to avoid misleading conclusions when comparing data generated by non-identical methods. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-783) contains supplementary material, which is available to authorized users.",1
"the molecular mechanism that regulates epicardial development has yet to be understood. in this study, we explored the function of cdx1, a caudal -related family member, in epicardial epithelial-to-mesenchymal transition (emt) and in the migration and the differentiation of epicardium-derived progenitors into vascular smooth muscle cells. we detected a transient expression of cdx1 in murine embryonic hearts at 11.5 days post coitum (dpc). using a doxycycline-inducible cdx1 mouse model, primary epicardium, and ex vivo heart culture, we further demonstrated that ectopic expression of cdx1 promoted epicardial emt. in addition, a low-dose cdx1 induction led to enhanced migration and differentiation of epicardium-derived cells into α-sma+ vascular smooth muscles. in contrast, either continued high-level induction of cdx1 or cdx1 deficiency attenuated the ability of epicardium-derived cells to migrate and to mature into smooth muscles induced by tgf-β1. further rna-seq analyses showed that cdx1 induction altered the transcript levels of genes involved in neuronal development, angiogenesis, and cell adhesions required for emt. our data have revealed a previously undefined role of cdx1 during epicardial development, and suggest that transient expression of cdx1 promotes epicardial emt, whereas subsequent down-regulation of cdx1 after 11.5 dpc in mice is necessary for further subepicardial invasion of epdcs and contribution to coronary vascular endothelium or smooth muscle cells.",0
"background: this study examined the metformin (mf) and/or chitosan stabilized selenium nanoparticles (ch-senps) efficacy to alleviate the male reproductive function impairment in a high-fat diet feed with low-dose streptozotocin (hfd/stz) induced type 2 diabetes mellitus (t2dm) diabetic rat model. methods: control non-diabetic, hfd/stz diabetic, hfd/stz+mf, hfd/stz+ch-senps, and hfd/stz+mf+ch-senps rat groups were used. after 60 days, semen evaluation, hormonal assay, enzymatic antioxidant, lipid peroxidation, testis histopathology, and the steroidogenesis-related genes mrna expressions were assessed. results: in the hfd/stz diabetic rats, sperm count and motility, male sexual hormones, and testicular antioxidant enzymes were significantly reduced. however, sperm abnormalities and testicular malondialdehyde were significantly incremented. the steroidogenesis-related genes, including steroidogenic acute regulatory protein (star), cytochrome11a1 (cyp11a1), cytochrome17a1 (cyp17a1), and hydroxysteroid 17-beta dehydrogenase 3 (hsd17b3), and the mitochondrial biogenesis related genes, including peroxisome proliferator-activated receptor gamma coactivator 1-alpha (pgcα) and sirtuin (sirt), were significantly downregulated in the hfd/stz diabetic rats. however, cyp19a1mrna expression was significantly upregulated. in contrast, mf and/or ch-senps oral dosing significantly rescued the t2dm-induced sperm abnormalities, reduced sperm motility, diminished sexual hormones level, testicular oxidative damage, and steroidogenesis-related genes dysregulation. in the mf and ch-senp co-treated group, many of the estimated parameters differ considerably from single mf or ch-senps treated groups. conclusions: the mf and ch-senps combined treatment could efficiently limit the diabetic complications largely than monotherapeutic approach and they could be considered a hopeful treatment option in the t2dm.",0
"ketamine has become a popular recreational drug due to its neuronal anesthesia effect and low price. the process of learning and memory is part of the distinctive high-level neural activities in animals. we investigated the effects of subanesthetic and anesthetic doses of ketamine on the learning and memory-related signal transduction mechanisms. we used the morris water maze test to execute rats’ learning and memory ability and detected changes of arc mrna and arc, camp-response element-binding protein (creb), phospho-creb (p-creb), extracellular signal-regulated kinase (erk), and phospho-erk (p-erk) protein expression in the hippocampus 10 min and 24 h after administration. ten min after ketamine injection, the arc gene and the protein expression levels increased in all groups; p-erk only increased in the chronic subanesthetic dose group. after 24 h, the arc gene and the protein expression levels of the subanesthetic dose group increased, but those of the chronic subanesthetic dose group and anesthetic dose group decreased. however, p-erk increased in all groups. a chronic subanesthetic dose of ketamine could increase learning and memory ability through erk, creb, and arc in a short time, and the high body temperature after the subanesthetic dose of ketamine injection was the main factor leading to changes in arc. the subanesthetic dose of ketamine regulated learning and memory through erk, creb, and arc 24 h after injection.",0
"the specialized protein synthesis functions of the cytosol and endoplasmic reticulum compartments are conferred by the signal recognition particle (srp) pathway, which directs the cotranslational trafficking of signal sequence-encoding mrnas from the cytosol to the endoplasmic reticulum (er). although subcellular mrna distributions largely mirror the binary pattern predicted by the srp pathway model, studies in mammalian cells, yeast, and drosophila have also demonstrated that cytosolic protein-encoding mrnas are broadly represented on er-bound ribosomes. a mechanism for such noncanonical mrna localization remains, however, to be identified. here, we examine the hypothesis that de novo translation initiation on er-bound ribosomes serves as a mechanism for localizing cytosolic protein-encoding mrnas to the er. as a test of this hypothesis, we performed single molecule rna fluorescence in situ hybridization studies of subcellular mrna distributions and report that a substantial fraction of mrnas encoding the cytosolic protein gapdh resides in close proximity to the er. consistent with these data, analyses of subcellular mrna and ribosome distributions in multiple cell lines demonstrated that cytosolic protein mrna-ribosome distributions were strongly correlated, whereas signal sequence-encoding mrna-ribosome distributions were divergent. ribosome footprinting studies of er-bound polysomes revealed a substantial initiation codon read density enrichment for cytosolic protein-encoding mrnas. we also demonstrate that eukaryotic initiation factor 2α is bound to the er via a salt-sensitive, ribosome-independent mechanism. combined, these data support er-localized translation initiation as a mechanism for mrna recruitment to the er.",0
"circular rnas (circrnas) comprise a novel class of widespread non-coding rnas that may regulate gene expression in eukaryotes. however, the characterization and function of circrnas remain elusive in human cancer, including oral squamous cell carcinoma (oscc). in this study, the expression level of circpvt1 in oscc was detected and define its functional role in initiation and progression of oscc. it was identified that circpvt1 was upregulated in oscc cells and specimens. knockdown of circpvt1 suppressed cell proliferation as evidenced by cell counting kit-8 assay and elevated ki-67 expression. mechanistically, it was demonstrated that circpvt1 possessed two targeting sites of microrna (mirna/mir)-125b and could effectively sponge mir-125b to release its downstream mrna targets. subsequently, the downstream target signal transducer and activator of transcription 3 (stat3) was verified as a direct target of mir-125b and stat3 expression was regulated by the circpvt1/mir-125b axis. circpvt1 functioned as competing endogenous rna (cerna) to increase the stat3 level and cell proliferation through sponging mir-125b. in conclusion, circpvt1 regulates cell proliferation and may serve as a promising therapeutic target for oscc patients. therefore, silencing of circpvt1 could be a future direction to develop a novel treatment strategy.",1
"background the vast majority of lncrnas have low expression abundance, which greatly limits their functional range and impact. as a high expression abundance lncrna, fgd5-as1’s non-cerna biological function in cancer is unclear. methods rna-seq studies and chromatin immunoprecipitation (chip) assays were performed to identify zeb1-regulated lncrnas. rna sequencing, rna pulldown, rna immunoprecipitation assays, and rescue assays were conducted to explore the molecular mechanisms of fgd5-as1 in gc. results as one of the most abundant lncrnas in cells, fgd5-as1 has been shown to be transcriptionally activated by zeb1, thus closely related to epithelial-mesenchymal transition (emt) signaling. clinical analysis showed that fgd5-as1 overexpression was clinically associated with lymph node metastasis, and predicted poor survival in gc. loss-of-function studies confirmed that fgd5-as1 knockdown inhibited gc proliferation and induced cisplatin chemosensibility, cell senescence, and dna damage in gc cells. mechanismically, fgd5-as1 is a ybx1-binding lncrna due to its mrna contains three adjacent structural motifs (uaauccca, accagccu, and cagugagc) that can be recognized and bound by ybx1. and this rna-protein interaction prolonged the half-life of the ybx1 protein in gc. additionally, a rescue assay showed that fgd5-as1 promotes gc by repressing cell senescence and ros production via ybx1. conclusion fgd5-as1 is a cellular high-abundant lncrna that is transcriptionally regulated by zeb1. fgd5-as1 overexpression promoted gc progression by inhibiting cell senescence and ros production through binding and stabilizing the ybx1 protein. supplementary information the online version contains supplementary material available at 10.1186/s13046-024-03103-x. highlights fgd5-as1 is an emt-related, cellularly abundant lncrna. the expression of fgd5-as1 is directly regulated by the transcription factor zeb1. fgd5-as1 overexpression was clinically associated with lymph node metastasis and a poor prognosis in gc. knockdown of fgd5-as1 causes senescence-associated secretory phenotypes, dna damage, cisplatin chemosensibility, and growth inhibition in gc cells. fgd5-as1 prolongs the half-life of the ybx1 protein by rna-protein interaction. the uaauccca, accagccu, and cagugagc linear 8-mer motifs in the fgd5-as1 transcript mediate the interaction between ybx1 and fgd5-as1. fgd5-as1 promotes gc proliferation by inhibiting cell senescence and ros production in a ybx1-dependent manner. supplementary information the online version contains supplementary material available at 10.1186/s13046-024-03103-x.",1
"one of the main causes of female infertility is a deregulated antral follicular atresia, a process of which the underlying molecular mechanisms are largely unknown. our objective was therefore to characterize the complex transcriptome changes in porcine granulosa cells of healthy antral (ha) and advanced antral atretic (aa) follicles, using elisa and rna-seq followed by qrt-pcr and immunohistochemistry. granulosa cell rna-seq data revealed 2160 differentially expressed genes, 1483 with higher and 677 with lower mrna concentrations in aa follicles. bioinformatic analysis showed that the upregulated genes in aa follicles were highly enriched in inflammation and apoptosis processes, while the downregulated transcripts were mainly highlighted in the steroid biosynthesis pathway and response to oxidative stress processes including antioxidant genes (e.g., gsta1 , gclc , gclm , idh1 , gpx8 ) involved in the glutathione metabolism pathway and other redox-related genes (e.g., rrm2b , ndufs4 ). these observations were confirmed by rt-qpcr and immunohistochemistry. additionally, the granulosa cells of aa follicles express significantly stronger 8-ohdg immunostaining, a marker of oxidative dna damage, implicating that oxidative stress may participate in follicular atresia. we hypothesize that the decrease in anti-apoptotic factors and steroid hormones coincides with increased oxidative stress markers and the expression of pro-apoptotic factors, all contributing to antral follicular atresia.",0
"facioscapulohumeral muscular dystrophy (fshd) is linked to abnormal derepression of the transcription activator dux4. this effect is localized to a low percentage of cells, requiring single-cell analysis. however, single-cell/nucleus rna-seq cannot fully capture the transcriptome of multinucleated large myotubes. to circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (merfish) spatial transcriptomics that allows profiling of rna transcripts at a subcellular resolution. we simultaneously examined spatial distributions of 140 genes, including 24 direct dux4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (mncs) of control, isogenic d4z4 contraction mutant and fshd patient samples, as well as the individual nuclei within them. we find myocyte nuclei segregate into two clusters defined by the expression of dux4 target genes, which is exclusively found in patient/mutant nuclei, whereas mncs cluster based on developmental states. patient/mutant myotubes are found in “fshd-hi” and “fshd-lo” states with the former signified by high dux4 target expression and decreased muscle gene expression. pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and fshd-hi myotube branches, with variable numbers of dux4 target-expressing nuclei found in multinucleated fshd-hi myotubes. gene coexpression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared with the control. we also identify distinct subpathways within the dux4 gene network that may differentially contribute to the disease transcriptomic phenotype. taken together, our merfish-based study provides effective gene network profiling of multinucleated cells and identifies fshd-induced transcriptomic alterations during myoblast differentiation.",0
"micrornas (mirnas) are key regulators of gene expression at the post-transcription level. the present study specifically explored and compared the mirna expression profiles of f. gigantica and f. hepatica using an integrated sequencing and bioinformatics platform and quantitative real-time pcr. nineteen and 16 mirna candidates were identified from f. gigantica and f. hepatica , respectively. the two parasites shared 11 mirnas, with 8 also showing similarity to mirnas of schistosoma japonicum. another 8 mirnas were identified as f. gigantica -specific and 5 as f. hepatica- specific, most of which were novel. predicted target analysis with 11465 mrna and est sequences of f. hepatica and f. gigantica revealed that all of the mirnas had more than one target, ranging from 2 to 398 with an average of 51 targets. some functions of the predicted targets were only found in f. gigantica , such as “transcription regulator”, while some others were only found in f. hepatica , such as “reproduction” and “response to stimulus”, indicating the different metabolism and gene regulation patterns of the two parasites. the present study represents the first global comparative characterization of mirna expression profiles of f. gigantica and f. hepatica , which has provided novel valuable resources for a better understanding of the two zoonotic trematodes.",1
"aims endothelial progenitor cells (epcs) are capable of proliferating and differentiating into mature endothelial cells, and they have been considered as potential candidates for coronary heart disease therapy. however, the transition of epcs to mesenchymal cells is not fully understood. this study aimed to explore the role of microrna 126 (mir-126) in the endothelial-to-mesenchymal transition (endmt) induced by transforming growth factor beta 1 (tgfβ1). methods and results endmt of rat bone marrow-derived epcs was induced by tgfβ1 (5 ng/ml) for 7 days. mir-126 expression was depressed in the process of epc endmt. the luciferase reporter assay showed that the pi3k regulatory subunit p85 beta (pik3r2) was a direct target of mir-126 in epcs. overexpression of mir-126 by a lentiviral vector (lenti-mir-126) was found to downregulate the mrna expression of mesenchymal cell markers (α-sma, sm22-a, and myocardin) and to maintain the mrna expression of progenitor cell markers (cd34, cd133). in the cellular process of endmt, there was an increase in the protein expression of pik3r2 and the nuclear transcription factors foxo3 and smad4; pi3k and phosphor-akt expression decreased, a change that was reversed markedly by overexpression of mir-126. furthermore, knockdown of pik3r2 gene expression level showed reversed morphological changes of the epcs treated with tgfβ1, thereby giving the evidence that pik3r2 is the target gene of mir-126 during endmt process. conclusions these results show that mir-126 targets pik3r2 to inhibit epc endmt and that this process involves regulation of the pi3k/akt signalling pathway. mir-126 has the potential to be used as a biomarker for the early diagnosis of intimal hyperplasia in cardiovascular disease and can even be a therapeutic tool for treating cardiovascular diseases mediated by the endmt process.",1
"noncoding rnas are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. while genomics is now a mature field, our capacity to identify noncoding rna elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. the emergence of new technologies for characterizing transcriptome outputs, notably rna-seq, are improving noncoding rna identification and expression quantification. however, a major challenge is to robustly distinguish functional outputs from transcriptional noise. to establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available rna-seq datasets spanning 37 different archaea and bacteria. using comparative tools, we identify close to a thousand highly-expressed candidate noncoding rnas. however, our analyses reveal that capacity to identify noncoding rna outputs is strongly dependent on phylogenetic sampling. surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding rnas from a null hypothesis of transcriptional noise. our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling.",1
"background most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. consequently, special types of non-canonical splicing events of short mrna regions (ire1α targeted) have not yet been thoroughly addressed at a genome-wide level using bioinformatics approaches in conjunction with next-generation technologies. during endoplasmic reticulum (er) stress, the gene encoding the rnase ire1 α is known to splice out a short 26 nt region from the mrna of the transcription factor xbp1 non-canonically within the cytosol. this causes an open reading frame-shift that induces expression of many downstream genes in reaction to er stress as part of the unfolded protein response (upr). we previously published an algorithm termed “read-split-walk” (rsw) to identify non-canonical splicing regions using rna-seq data and applied it to er stress-induced ire1 α heterozygote and knockout mouse embryonic fibroblast cell lines. in this study, we have developed an improved algorithm “read-split-run” (rsr) for detecting genome-wide ire1α -targeted genes with non-canonical spliced regions at a faster speed. we applied the rsr algorithm using different combinations of several parameters to the previously rsw tested mouse embryonic fibroblast cells (mef) and the human encyclopedia of dna elements (encode) rna-seq data. we also compared the performance of rsr with two other alternative splicing events identification tools (tophat (trapnell et al., bioinformatics 25:1105–1111, 2009) and alt event finder (zhou et al., bmc genomics 13:s10, 2012)) utilizing the context of the spliced xbp1 mrna as a positive control in the data sets we identified it to be the top cleavage target present in ire1α +/− but absent in ire1α −/− mef samples and this comparison was also extended to human encode rna-seq data. results proof of principle came in our results by the fact that the 26 nt non-conventional splice site in xbp1 was detected as the top hit by our new rsr algorithm in heterozygote (het) samples from both thapsigargin (tg) and dithiothreitol (dtt) treated experiments but absent in the negative control ire1 α knock-out (ko) samples. applying different combinations of parameters to the mouse mef rna-seq data, we suggest a general linear model (glm) for both tg and dtt treated experiments. we also ran rsr for a human encode rna-seq dataset and identified 32,597 spliced regions for regular chromosomes. tophat (trapnell et al., bioinformatics 25:1105–1111, 2009) and alt event finder (zhou et al., bmc genomics 13:s10, 2012) identified 237,155 spliced junctions and 9,129 exon skipping events (excluding chr14), respectively. our read-split-run algorithm also outperformed others in the context of ranking xbp1 gene as the top cleavage target present in ire1α +/− but absent in ire1α −/− mef samples. the rsr package including source codes is available at and its pipeline source codes are also freely available at for academic use. conclusions our new rsr algorithm has the capability of processing massive amounts of human encode rna-seq data for identifying novel splice junction sites at a genome-wide level in a much more efficient manner when compared to the previous rsw algorithm. our proposed model can also predict the number of spliced regions under any combinations of parameters. our pipeline can detect novel spliced sites for other species using rna-seq data generated under similar conditions. electronic supplementary material the online version of this article (doi:10.1186/s12864-016-2896-7) contains supplementary material, which is available to authorized users.",0
"background gastric intestinal metaplasia (im) is considered a precancerous lesion, and bile acids (ba) play a critical role in the induction of im. ectopic expression of hnf4α was observed in a ba-induced im cell model. however, the mechanisms underlying the upregulation of the protein in im cells remains to be elucidated. methods the effects of hnf4α on gastric mucosal cells in vivo were identified by a transgenic mouse model and rna-seq was used to screen downstream targets of deoxycholic acid (dca). the expression of pivotal molecules and mir-1 was detected by immunohistochemistry and in situ hybridization in normal, gastritis and im tissue slides or microarrays. the transcriptional regulation of hdac6 was investigated by chromatin immunoprecipitation (chip) and luciferase reporter assays. results the transgenic mouse model validated that hnf4α stimulated the hdac6 expression and mucin secretion in gastric mucosa. increased hdac6 and hnf4α expression was also detected in the gastric im cell model and patient specimens. hnf4α could bind to and activate hdac6 promoter. in turn, hdac6 enhanced the hnf4α protein level in ges-1 cells. furthermore, mir-1 suppressed the expression of downstream intestinal markers by targeting hdac6 and hnf4α. conclusions our findings show that the hdac6/hnf4α loop regulated by mir-1 plays a critical role in gastric im. blocking the activation of this loop could be a potential approach to preventing ba-induced gastric im or even gastric cancer (gc). electronic supplementary material the online version of this article (10.1007/s10120-020-01108-x) contains supplementary material, which is available to authorized users.",1
"recent studies have indicated that long non-coding rnas play crucial roles in numerous cancers, including thyroid cancer, while their function in the mechanism of thyroid cancer 131 i resistance has not been elucidated to date. the present study identified a functional long non-coding rna, slc6a9-5:2, which was involved in the radioactive therapy resistance of thyroid cancer. we demonstrated that slc6a9-5:2 was remarkably downregulated in 131 i-resistant thyroid cancer cell lines and 131 i-insensitive patients and was positively correlated with poly (adp-ribose) polymerase 1 (parp-1) expression and its activation. after downregulating slc6a9 or blocking parp-1 artificially, the sensitive thyroid cancer cells mostly displayed a tolerant phenotype under 131 i exposure. furthermore, slc6a9-5:2 overexpression was positively correlated with parp-1 mrna and protein levels, which restored the sensitivity of resistant thyroid cancer cells. the present study further revealed that cancer cell death was primarily caused by atp exhaustion in excessive dna repair with high parp-1 activity. in patients with thyroid cancer, a positive correlation between slc6a9-5:2 and parp-1 was identified, and low slc6a9-5:2 expression was associated with a worse prognosis of papillary thyroid carcinoma. hence, our data provide a new lncrna-mediated regulatory mechanism implying that slc6a9-5:2 can be used as a novel therapeutic target for 131 i-resistant thyroid cancer.",1
"microvesicles (mvs) play an important role in intercellular communication by carrying mrnas, micrornas (mirnas), non-coding rnas, proteins, and dna from cell to cell. to our knowledge, this is the first report of delivery of a therapeutic mrna/protein via mvs for treatment of cancer. we first generated genetically engineered mvs by expressing high levels of the suicide gene mrna and protein–cytosine deaminase (cd) fused to uracil phosphoribosyltransferase (uprt) in mv donor cells. mvs were isolated from these cells and used to treat pre-established nerve sheath tumors (schwannomas) in an orthotopic mouse model. we demonstrated that mv-mediated delivery of cd-uprt mrna/protein by direct injection into schwannomas led to regression of these tumors upon systemic treatment with the prodrug (5-fluorocytosine (5-fc)), which is converted within tumor cells to 5-fluorouracil (5-fu)–an anticancer agent. taken together, these studies suggest that mvs can serve as novel cell-derived “liposomes” to effectively deliver therapeutic mrna/proteins to treatment of diseases.",1
"pheochromocytomas (pc) and paragangliomas (pg) are rare neuroendocrine tumors associated with autonomic nerves. here we use single-nuclei rna-seq and bulk-tissue gene-expression data to characterize the cellular composition of pcpg and normal adrenal tissues, refine tumor gene-expression subtypes and make clinical and genotypic associations. we confirm seven pcpg gene-expression subtypes with significant genotype and clinical associations. tumors with mutations in vhl , sdh-encoding genes ( sdhx ) or maml3 -fusions are characterized by hypoxia-inducible factor signaling and neoangiogenesis. pcpg have few infiltrating lymphocytes but abundant macrophages. while neoplastic cells transcriptionally resemble mature chromaffin cells, early chromaffin and neuroblast markers are also features of some pcpg subtypes. the gene-expression profile of metastatic sdhx -related pcpg indicates these tumors have elevated cellular proliferation and a lower number of non-neoplastic schwann-cell-like cells, while gpr139 is a potential theranostic target. our findings therefore clarify the diverse transcriptional programs and cellular composition of pcpg and identify biomarkers of potential clinical significance.",0
"aim stomach adenocarcinoma (stad) is a common malignancy worldwide. this study aimed to identify the aberrantly expressed long non-coding rnas (lncrnas) in stad. results total of 74 delncrnas and 449 demrnas were identified in stad compared with paired non-tumor tissues. the delncrna/demrna co-expression network was constructed, which covered 519 nodes and 2993 edges. the qrt-pcr validation results of delncrnas were consistent with our bioinformatics analysis based on rna-sequencing. the demrnas co-expressed with delncrnas were significantly enriched in gastric acid secretion, complement and coagulation cascades, pancreatic secretion, cytokine-cytokine receptor interaction and jak-stat signaling pathway. the expression levels of the nine candidate delncrnas in tcga database were compatible with our rna-sequencing. fezf1-as1, hotair and linc01234 had the potential diagnosis value for stad. materials and methods the lncrna and mrna expression profile of 3 stad tissues and 3 matched adjacent non-tumor tissues was obtained through high-throughput rna-sequencing. differentially expressed lncrnas/mrnas (delncrnas/demrnas) were identified in stad. delncrna/demrna co-expression network construction, gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) enrichment analyses were conducted to predict the biological functions of delncrnas. quantitative real-time polymerase chain reaction (qrt-pcr) was subjected to validate the expression levels of demrnas and delncrnas. moreover, the expression of delncrnas was validated through the cancer genome atlas (tcga) database. the diagnosis value of candidate delncrnas was accessed by receiver operating characteristic (roc) analysis. conclusions our work might provide useful information for exploring the tumorigenesis mechanism of stad and pave the road for identification of diagnostic biomarkers in stad.",1
"background to study the role of microrna (mirna) in the regulation of chinese hamster ovary (cho) cell growth, qpcr, microarray and quantitative lc-ms/ms analysis were utilised for simultaneous expression profiling of mirna, mrna and protein. the sample set under investigation consisted of clones with variable cellular growth rates derived from the same population. in addition to providing a systems level perspective on cell growth, the integration of multiple profiling datasets can facilitate the identification of non-seed mirna targets, complement computational prediction tools and reduce false positive and false negative rates. results 51 mirnas were associated with increased growth rate (35 mirnas upregulated and 16 mirnas downregulated). gene ontology (go) analysis of genes (n=432) and proteins (n=285) found to be differentially expressed (de) identified biological processes driving proliferation including mrna processing and translation. to investigate the influence of mirna on these processes we combined the proteomic and transcriptomic data into two groups. the first set contained candidates where evidence of translational repression was observed (n=158). the second group was a mixture of proteins and mrnas where evidence of translational repression was less clear (n=515). the targetscan algorithm was utilised to predict potential targets within these two groups for anti-correlated de mirnas. conclusions the evidence presented in this study indicates that biological processes such as mrna processing and protein synthesis are correlated with growth rate in cho cells. through the integration of expression data from multiple levels of the biological system a number of proteins central to these processes including several hnrnps and components of the ribosome were found to be post-transcriptionally regulated. we utilised the expression data in conjunction with in - silico tools to identify potential mirna-mediated regulation of mrna/proteins involved in cho cell growth rate. these data have allowed us to prioritise candidates for cell engineering and/or biomarkers relevant to industrial cell culture. we also expect the knowledge gained from this study to be applicable to other fields investigating the role of mirnas in mammalian cell growth.",1
"a gene for the hfq protein is present in the majority of sequenced bacterial genomes. its characteristic hexameric ring-like core structure is formed by the highly conserved n-terminal regions. in contrast, the c-terminal forms an extension, which varies in length, lacks homology, and is predicted to be unstructured. in gram-negative bacteria, hfq facilitates the pairing of srnas with their mrna target and thus affects gene expression, either positively or negatively, and modulates srna degradation. in gram-positive bacteria, its role is still poorly characterized. numerous srnas have been detected in many gram-positive bacteria, but it is not yet known whether these srnas act in association with hfq. compared with all other hfqs, the c. difficile hfq exhibits an unusual c-terminal sequence with 75% asparagine and glutamine residues, while the n-terminal core part is more conserved. to gain insight into the functionality of the c. difficile hfq (cd-hfq) protein in processes regulated by srnas, we have tested the ability of cd-hfq to fulfill the functions of the e. coli hfq (ec-hfq) by examining various functions associated with hfq in both positive and negative controls of gene expression. we found that cd-hfq substitutes for most but not all of the tested functions of the ec-hfq protein. we also investigated the role of the c-terminal part of the hfq proteins. we found that the c-terminal part of both ec-hfq and cd-hfq is not essential but contributes to some functions of both the e. coli and c. difficile chaperons.",0
"salix matsudana koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in china. currently little transcriptomic and small rnaomic data are available to reveal the genes involve in the stress resistant in s. matsudana. here, we report the rna-seq analysis results of both transcriptome and small rnaome data using illumina deep sequencing of shoot tips from two willow variants( salix. matsudana and salix matsudana koidz. cultivar ‘tortuosa’). de novo gene assembly was used to generate the consensus transcriptome and small rnaome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 mb, and 166 known mirnas representing 35 mirna families. comparison of transcriptomes and small rnaomes combined with quantitative real-time pcr from the two salix libraries revealed a total of 292 different expressed genes(degs) and 36 different expressed mirnas (dems). among the degs and dems, 196 genes and 24 mirnas were up regulated, 96 genes and 12 mirna were down regulated in s. matsudana. functional analysis of degs and mirna targets showed that many genes were involved in stress resistance in s. matsudana. our global gene expression profiling presents a comprehensive view of the transcriptome and small rnaome which provide valuable information and sequence resources for uncovering the stress response genes in s. matsudana. moreover the transcriptome and small rnaome data provide a basis for future study of genetic resistance in salix.",1
"caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. we provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, rna-seq, global 5′-race, and liquid chromatography coupled with tandem mass spectrometry (lc-ms) data to the 4-megabase c. crescentus genome. we mapped transcript units at single base-pair resolution using rna-seq together with global 5′-race. additionally, using ribosome profiling and lc-ms, we mapped translation start sites and coding regions with near complete coverage. we found most start codons lacked corresponding shine-dalgarno sites although ribosomes were observed to pause at internal shine-dalgarno sites within the coding dna sequence (cds). these data suggest a more prevalent use of the shine-dalgarno sequence for ribosome pausing rather than translation initiation in c. crescentus. overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete c. crescentus genetic circuitry that controls asymmetric cell division.",0
"long noncoding rnas (lncrnas) are important regulators of transcription; however, their involvement in protein translation is not well known. here we explored whether the lncrna gas5 is associated with translation initiation machinery and regulates translation. gas5 was enriched with eukaryotic translation initiation factor-4e (eif4e) in an rna-immunoprecipitation assay using lymphoma cell lines. we identified two rna binding motifs within eif4e protein and the deletion of each motif inhibited the binding of gas5 with eif4e. to confirm the role of gas5 in translation regulation, gas5 sirna and in vitro transcribed gas5 rna were used to knock down or overexpress gas5, respectively. gas5 sirna had no effect on global protein translation but did specifically increase c-myc protein level without an effect on c-myc mrna. the mechanism of this increase in c-myc protein was enhanced association of c-myc mrna with the polysome without any effect on protein stability. in contrast, overexpression of in vitro transcribed gas5 rna suppressed c-myc protein without affecting c-myc mrna. interestingly, gas5 was found to be bound with c-myc mrna, suggesting that gas5 regulates c-myc translation through lncrna-mrna interaction. our findings have uncovered a role of gas5 lncrna in translation regulation through its interactions with eif4e and c-myc mrna.",1
"background long non-coding rnas (lncrnas) regulate embryonic development and cell fate decision in various ways, such as modulation of chromatin modification and post-transcription regulation of gene expression. however, the profiles and roles of lncrnas in early mammalian development have not yet been demonstrated. here, we reported a comprehensive analysis of mouse cleavage stage embryonic lncrna profiles based on public single-cell rna-seq data. results we reconstructed 50,006 high-confidence transcripts in 22,827 loci, and identified 5563 novel lncrnas from 3492 loci expressed in mouse cleavage stage embryos. these lncrnas share similar characteristics with previously reported vertebrate lncrnas, such as relatively short length, low exon number, low expression level and low sequence conservation. expression profile analysis revealed that the profiles of lncrna vary considerably at different stages of cleavage stage embryos, suggesting that many lncrnas in cleavage stage embryos are stage-specifically expressed. co-expression network analysis suggested many lncrnas in cleavage stage embryos are associated with cell cycle regulation, transcription, translation and oxidative phosphorylation to regulate the process of cleavage stage embryonic development. conclusions this study provides the first catalog of lncrnas expressed in mouse cleavage stage embryos and gives a revealing insight into the molecular mechanism responsible for early embryonic development. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-845) contains supplementary material, which is available to authorized users.",1
"identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. we developed a computational method, called iregulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis -regulatory sequence analysis. iregulon implements a genome-wide ranking-and-recovery approach to detect enriched transcription factor motifs and their optimal sets of direct targets. we increase the accuracy of network inference by using very large motif collections of up to ten thousand position weight matrices collected from various species, and linking these to candidate human tfs via a motif2tf procedure. we validate iregulon on gene sets derived from encode chip-seq data with increasing levels of noise, and we compare iregulon with existing motif discovery methods. next, we use iregulon on more challenging types of gene lists, including microrna target sets, protein-protein interaction networks, and genetic perturbation data. in particular, we over-activate p53 in breast cancer cells, followed by rna-seq and chip-seq, and could identify an extensive up-regulated network controlled directly by p53. similarly we map a repressive network with no indication of direct p53 regulation but rather an indirect effect via e2f and nfy. finally, we generalize our computational framework to include regulatory tracks such as chip-seq data and show how motif and track discovery can be combined to map functional regulatory interactions among co-expressed genes. iregulon is available as a cytoscape plugin from",0
"puberty is a complex physiological event by which animals mature into an adult capable of sexual reproduction. in order to enhance our understanding of the genes and regulatory pathways and networks involved in puberty, we characterized the transcriptome of five reproductive tissues (i.e. hypothalamus, pituitary gland, ovary, uterus, and endometrium) as well as tissues known to be relevant to growth and metabolism needed to achieve puberty (i.e., longissimus dorsi muscle, adipose, and liver). these tissues were collected from pre- and post-pubertal brangus heifers (3/8 brahman; bos indicus x 5/8 angus; bos taurus ) derived from a population of cattle used to identify quantitative trait loci associated with fertility traits (i.e., age of first observed corpus luteum (acl), first service conception (fsc), and heifer pregnancy (hpg)). in order to exploit the power of complementary omics analyses, pre- and post-puberty co-expression gene networks were constructed by combining the results from genome-wide association studies (gwas), rna-seq, and bovine transcription factors. eight tissues among pre-pubertal and post-pubertal brangus heifers revealed 1,515 differentially expressed and 943 tissue-specific genes within the 17,832 genes confirmed by rna-seq analysis. the hypothalamus experienced the most notable up-regulation of genes via puberty (i.e., 204 out of 275 genes). combining the results of gwas and rna-seq, we identified 25 loci containing a single nucleotide polymorphism (snp) associated with acl, fsc, and (or) hpg. seventeen of these snp were within a gene and 13 of the genes were expressed in uterus or endometrium. multi-tissue omics analyses revealed 2,450 co-expressed genes relative to puberty. the pre-pubertal network had 372,861 connections whereas the post-pubertal network had 328,357 connections. a sub-network from this process revealed key transcriptional regulators (i.e., pitx2 , foxa1 , dach2 , prop1, six6, etc. ). results from these multi-tissue omics analyses improve understanding of the number of genes and their complex interactions for puberty in cattle.",0
"background allograft inflammatory factor 1 (aif-1) is a putative obesity gene. our aim was to examine the expression of aif-1 in human white adipose tissue (wat) in relation to obesity and metabolic phenotypes in women. methods wat secretion of aif-1 was determined in subcutaneous adipose tissue pieces in vitro by elisa from 5 subjects. mrna expression of aif-1 was determined by rt-qpcr in the isolated cell fractions of adipose tissue (n = 5-6 per group), in subcutaneous and visceral wat pieces from non-obese (n = 12) and obese women (n = 23), and in some subcutaneous wat also before and after weight reduction (n = 10). finally, adipose aif-1 mrna was related to metabolic phenotypes in 96 subjects with a wide range of bmi. results aif-1 was secreted in a time dependent fashion from wat. the major source of aif-1 was wat resident macrophages. expression of aif-1 was similar in visceral and subcutaneous wat and was two-fold increased in obese women (p < 0.01). aif-1 mrna expression levels were normalized after weight reduction (p < 0.01). expression of aif-1 was inversely correlated with insulin sensitivity as assessed by insulin tolerance test (kitt), and circulating levels of adiponectin (p = 0.02), and positively correlated with insulin resistance as estimated by homa (=0.0042). conclusions aif-1 is a novel adipokine produced mainly by macrophages within human wat. its expression is increased in obese women and associates with unfavourable metabolic phenotypes. aif-1 may play a paracrine role in the regulation of wat function through cross-talk between macrophages and other cell types within the adipose tissue.",0
"epithelial organs are the first barrier against microorganisms and genotoxic stress, in which the p53 family members p63 and p73 have both overlapping and distinct functions. intriguingly, p73 displays a very specific localization to basal epithelial cells in human tissues, while p63 is expressed in both basal and differentiated cells. here, we analyse systematically the literature describing p63 and p73 protein–protein interactions to reveal distinct functions underlying the aforementioned distribution. we have found that p73 and p63 cooperate in the genome stability surveillance in proliferating cells; p73 specific interactors contribute to the transcriptional repression, anaphase promoting complex and spindle assembly checkpoint, whereas p63 specific interactors play roles in the regulation of mrna processing and splicing in both proliferating and differentiated cells. our analysis reveals the diversification of the rna and dna specific functions within the p53 family.",0
"abstract the upsurge of multidrug-resistant infections has rendered tuberculosis the principal cause of death among infectious diseases. a clonal outbreak multidrug-resistant triggering strain of mycobacterium tuberculosis was identified in kanchanaburi province, labelled “mkr superspreader,” which was found to subsequently spread to other regions, as revealed by prior epidemiological reports in thailand. herein, we showed that the mkr displayed a higher growth rate upon infection into host macrophages in comparison with the h37rv reference strain. to further elucidate mkr’s biology, we utilized rna-seq and differential gene expression analyses to identify host factors involved in the intracellular viability of the mkr. a set of host genes function in the cellular response to lipid pathway was found to be uniquely up-regulated in host macrophages infected with the mkr, but not those infected with h37rv. within this set of genes, the il-36 cytokines which regulate host cell cholesterol metabolism and resistance against mycobacteria attracted our interest, as our previous study revealed that the mkr elevated genes associated with cholesterol breakdown during its growth inside host macrophages. indeed, when comparing macrophages infected with the mkr to h37rv-infected cells, our rna-seq data showed that the expression ratio of il-36rn , the negative regulator of the il-36 pathway, to that of il-36g was greater in macrophages infected with the mkr. furthermore, the mkr’s intracellular survival and increased intracellular cholesterol level in the mkr-infected macrophages were diminished with decreased il-36rn expression. overall, our results indicated that il-36rn could serve as a new target against this emerging multidrug-resistant m. tuberculosis strain.",0
"background mica/b are major ligands for nk cell activating receptor nkg2d and previous studies showed that the serum level of soluble mica (smica) is an independent prognostic factor for advanced human hepatocellular carcinoma. however, the correlation between cellular mica/b expression pattern and human hepatocellular carcinoma progression has not been well explored. the unfolded protein response is one of the main causes of resistance to chemotherapy and radiotherapy in tumor cells. however, whether the upr in hcc could regulate the expression levels of mica/b and affect the sensitivity of hcc cells to nk cell cytolysis has not been established yet. methods mica/b expression pattern was evaluated by immunohistochemistry and kaplan-meier survival analysis was done to explore the relationship between mica/b expression level and patient survival. the protein and mrna expression levels of mica/b in smmc7721 and hepg2 cells treated by tunicamycin were evaluated by flow cytometry, western blot and rt-pcr. the cytotoxicity analysis was performed with the cytotox 96 non-radioactive ldh cytotoxicity assay. results mica/b was highly expressed in human hepatocellular carcinoma and the expression level was significantly and negatively associated with tumor-node metastasis (tnm) stages. patients with low level of mica/b expression showed a trend of shorter survival time. the unfolded protein response (upr) downregulated the expression of mica/b. this decreased protein expression occurred via post-transcriptional regulation and was associated with proteasomal degradation. moreover, decreased expression level of mica/b led to the attenuated sensitivity of human hcc to nk cell cytotoxicity. conclusion these new findings of the connection of mica/b, upr and nk cells may represent a new concrete theory of nk cell regulation in hcc, and suggest that targeting this novel nk cell-associated immune evasion pathway may be meaningful in treating patients with hcc. electronic supplementary material the online version of this article (doi:10.1186/s13046-014-0076-7) contains supplementary material, which is available to authorized users.",0
"long non-coding rna (lncrna) is a large class of gene transcripts with regulatory functions discovered in recent years. many more are expected to be revealed with accumulation of rna-seq data from diverse types of normal and diseased tissues. however, discovering novel lncrnas and accurately quantifying known lncrnas is not trivial from massive rna-seq data. herein we describe uclncr, an ultrafast and comprehensive lncrna detection pipeline to tackle the challenge. uclncr takes standard rna-seq alignment file, performs transcript assembly, predicts lncrna candidates, quantifies and annotates both known and novel lncrna candidates, and generates a convenient report for downstream analysis. the pipeline accommodates both un-stranded and stranded rna-seq so that lncrnas overlapping with other genes can be predicted and quantified. uclncr is fully parallelized in a cluster environment yet allows users to run samples sequentially without a cluster. the pipeline can process a typical rna-seq sample in a matter of minutes and complete hundreds of samples in a matter of hours. analysis of predicted lncrnas from two test datasets demonstrated uclncr’s accuracy and their relevance to sample clinical phenotypes. uclncr would facilitate researchers’ novel lncrna discovery significantly and is publically available at",1
"background recent studies have focused on the diagnostic and prognostic significance of cd24 and cd44 expression in human cancers. this study aimed to explore changes in cd44 and cd24 expression levels in patients with gastric cancer and to assess their prognostic values. methods cd44 and cd24 expression levels were investigated immunohistochemically in tumor samples from 290 patients with non-cardia gastric adenocarcinoma, of whom 77 had paired adjacent normal gastric mucosa. cd24 and cd44 mrna levels were determined by quantitative polymerase chain reaction in 34 patients. serum anti- helicobacter pylori igg was detected by enzyme-linked immunosorbent assay. relationships between cd44 and cd24 protein expression levels and tumor parameters were analyzed and their prognostic values were evaluated by cox proportional hazards models. results cd24 and cd44 expression levels were significantly higher in patients with gastric cancer compared with those in paired controls (45.5% vs. 0.0%, and 61.0% vs. 0.0%, p < 0.001). among 290 patients, the overall survival rate was significantly higher in cd44(−) compared with cd44(+) patients (log-rank test, p = 0.035). however, there was no significant correlation between cd24 expression and overall survival time (log-rank test, p = 0.115). multivariate regression analysis indicated that positive cd44 expression ( p = 0.029), tnm staging ( p < 0.001), and lymphovascular invasion ( p = 0.016), but not cd24 expression ( p = 0.065), were independent prognostic factors in gastric cancer. conclusions individual expression of cd44 was associated with poor survival in patients with gastric carcinoma. electronic supplementary material the online version of this article (doi:10.1186/1471-230x-14-157) contains supplementary material, which is available to authorized users.",0
"obesity, a characteristic of metabolic syndrome, is also associated with chronic inflammation and the development of autoimmune diseases. however, the relationship between obesity and autoimmune diseases remains to be investigated in depth. here, we compared hepatic gene expression profiles among high-fat diet (hfd) mice using the primary biliary cholangitis (pbc) mouse model based on the chronic expression of interferon gamma (ifnγ) (are-del -/- mice). the top differentially expressed genes affected by upstream transcriptional regulators ifnγ, lps, and tnfα displayed an overlap in hfd and are-del -/- mice, indicating that obesity-induced liver inflammation may be dependent on signaling via ifnγ. the top pathways altered in hfd mice were mostly involved in the innate immune responses, which overlapped with are-del -/- mice. in contrast, t cell-mediated signaling pathways were exclusively altered in are-del -/- mice. we further evaluated the therapeutic effect of luteolin, known as anti-inflammatory flavonoid, in hfd and are-del -/- mice. luteolin strongly suppressed the mhc i and ii antigen presentation pathways, which were highly activated in both hfd and are-del -/- mice. conversely, luteolin increased metabolic processes of fatty acid oxidation and oxidative phosphorylation in the liver, which were suppressed in are-del -/- mice. luteolin also strongly induced ppar signaling, which was downregulated in hfd and are-del -/- mice. using human gwas data, we characterized the genetic interaction between significant obesity-related genes and ifnγ signaling and demonstrated that ifnγ is crucial for obesity-mediated inflammatory responses. collectively, this study improves our mechanistic understanding of the relationship between obesity and autoimmune diseases. furthermore, it provides new methodological insights into how immune network-based analyses effectively integrate rna-seq and microarray data.",0
"escherichia coli endoribonuclease e has a major influence on gene expression. it is essential for the maturation of ribosomal and transfer rna as well as the rapid degradation of messenger rna. the latter ensures that translation closely follows programming at the level of transcription. recently, one of the hallmarks of rnase e, i.e. its ability to bind via a 5′-monophosphorylated end, was shown to be unnecessary for the initial cleavage of some polycistronic trna precursors. here we show using rna-seq analyses of ribonuclease-deficient strains in vivo and a 5′-sensor mutant of rnase e in vitro that, contrary to current models, 5′-monophosphate-independent, ‘direct entry’ cleavage is a major pathway for degrading and processing rna. moreover, we present further evidence that direct entry is facilitated by rnase e binding simultaneously to multiple unpaired regions. these simple requirements may maximize the rate of degradation and processing by permitting multiple sites to be surveyed directly without being constrained by 5′-end tethering. cleavage was detected at a multitude of sites previously undescribed for rnase e, including ones that regulate the activity and specificity of ribosomes. a potentially broad role for rnase g, an rnase e paralogue, in the trimming of 5′-monophosphorylated ends was also revealed.",0
"background rna sequencing (rna-seq) has revolutionized the detection of transcriptomic signatures due to its high-throughput sequencing ability. therefore, genomic annotations on different animal species have been rapidly updated using information from tissue-enriched novel transcripts and novel exons. results 34 putative novel transcripts and 236 putative tissue-enriched exons were identified using rna-seq datasets representing six tissues available in mouse databases. rt-pcr results indicated that expression of 21 and 2 novel transcripts were enriched in testes and liver, respectively, while 31 of the 39 selected novel exons were detected in the testes or heart. the novel isoforms containing the identified novel exons exhibited more dominant expression than the known isoforms in heart and testes. we also identified an example of pathology-associated exclusion of heart-enriched novel exons such as sorbs1 and cluh during pressure-overload cardiac hypertrophy. conclusion the present study depicted tissue-enriched novel transcripts, a tissue-specific isoform switch, and pathology-associated alternative splicing in a mouse model, suggesting tissue-specific genomic diversity and plasticity. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-592) contains supplementary material, which is available to authorized users.",0
"telomerase rnas (ters) are highly divergent between species, varying in size and sequence composition. here, we identify a candidate for the telomerase rna component of leishmania genus, which includes species that cause leishmaniasis, a neglected tropical disease. merging a thorough computational screening combined with rna-seq evidence, we mapped a non-coding rna gene localized in a syntenic locus on chromosome 25 of five leishmania species that shares partial synteny with both trypanosoma brucei ter locus and a putative ter candidate-containing locus of crithidia fasciculata. using target-driven molecular biology approaches, we detected a ∼2,100 nt transcript ( leish ter) that contains a 5′ spliced leader (sl) cap, a putative 3′ polya tail and a predicted c/d box snorna domain. leish ter is expressed at similar levels in the logarithmic and stationary growth phases of promastigote forms. a 5′sl capped leish ter co-immunoprecipitated and co-localized with the telomerase protein component (tert) in a cell cycle-dependent manner. prediction of its secondary structure strongly suggests the existence of a bona fide single-stranded template sequence and a conserved cguca motif-containing helix ii, representing the template boundary element. this study paves the way for further investigations on the biogenesis of parasite tert ribonucleoproteins (rnps) and its role in parasite telomere biology.",1
"localized mrna translation is thought to play a key role in synaptic plasticity, but the identity of the transcripts and the molecular mechanism underlying their function are still poorly understood. here, we show that syncrip, a regulator of localized translation in the drosophila oocyte and a component of mammalian neuronal mrna granules, is also expressed in the drosophila larval neuromuscular junction, where it regulates synaptic growth. we use rna-immunoprecipitation followed by high-throughput sequencing and qrt-pcr to show that syncrip associates with a number of mrnas encoding proteins with key synaptic functions, including msp-300, syd-1, neurexin-1, futsch, highwire, discs large, and α -spectrin. the protein levels of msp-300, discs large, and a number of others are significantly affected in syncrip null mutants. furthermore, syncrip mutants show a reduction in msp-300 protein levels and defects in muscle nuclear distribution characteristic of msp-300 mutants. our results highlight a number of potential new players in localized translation during synaptic plasticity in the neuromuscular junction. we propose that syncrip acts as a modulator of synaptic plasticity by regulating the translation of these key mrnas encoding synaptic scaffolding proteins and other important components involved in synaptic growth and function.",0
"vascular calcification is associated with significant cardiovascular morbidity and mortality, and has been demonstrated as an actively regulated process resembling bone formation. oxidized low density lipoprotein (ox-ldl) has been identified as a regulatory factor involved in calcification of vascular smooth muscle cells (vsmcs). additionally, over-expression of recombinant human neutral sphingomyelinase (n-smase) has been shown to stimulate vsmc apoptosis, which plays an important role in the progression of vascular calcification. the aim of this study is to investigate whether ceramide regulates ox-ldl-induced calcification of vsmcs via activation of p38 mitogen-activated protein kinase (mapk) pathway. ox-ldl increased the activity of n-smase and the level of ceramide in cultured vsmcs. calcification and the osteogenic transcription factor, msx2 mrna expression were reduced by n-smase inhibitor, gw4869 in the presence of ox-ldl. usage of gw4869 inhibited ox-ldl-induced apoptosis in vsmcs, an effect which was reversed by c2-ceramide. additionally, c2-ceramide treatment accelerated vsmc calcification, with a concomitant increase in alp activity. furthermore, c2-ceramide treatment enhanced ox-ldl-induced vsmc calcification. addition of caspase inhibitor, zvad-fmk attenuated ox-ldl-induced calcification. both ox-ldl and c2-ceramide treatment increased the phosphorylation of p38 mapk. inhibition of p38 mapk by sb203580 attenuated ox-ldl-induced calcification of vsmcs. these data suggest that ox-ldl activates n-smase-ceramide signaling pathway, and stimulates phosphorylation of p38 mapk, leading to apoptosis in vsmcs, which initiates vsmc calcification.",0
"abstract epithelial–mesenchymal transition (emt) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. although emt-regulatory roles for numerous mirnas and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct mirna targets from complex datasets and in deciding how to incorporate ‘indirect’ mirna effects that may, or may not, represent biologically relevant information. to better understand how mirnas exert effects throughout the transcriptome during emt, we employed exon–intron split analysis (eisa), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of rna-seq reads mapping to exons and introns. we find that in response to the manipulation of mirnas, a major effect on gene expression is transcriptional. we also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both emt and mesenchymal to epithelial transition (met) in response to tgf-β or mir-200c respectively. the prominent transcriptional influence of mirnas was also observed in other datasets where mirna levels were perturbed. this work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of eisa to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.",1
"humanity is in the midst of the coronavirus disease 2019 (covid-19) pandemic, and vaccines—including mrna vaccines—have been developed at an unprecedented speed. it is necessary to develop guidelines for vaccination for people undergoing treatment with assisted reproductive technology (art) and for pregnancy-related situations based on the extant laboratory and clinical data. covid-19 vaccines do not appear to adversely affect gametes, embryos, or implantation; therefore, active vaccination is recommended for women or men who are preparing for art. the use of intravenous immunoglobulin g (ivig) for the treatment of immune-related infertility is unlikely to impact the effectiveness of the vaccines, so covid-19 vaccines can be administered around art cycles in which ivig is scheduled. pregnant women have been proven to be at risk of severe maternal and neonatal complications from covid-19. it does not appear that covid-19 vaccines harm pregnant women or fetuses; instead, they have been observed to deliver antibodies against severe acute respiratory syndrome coronavirus 2 (sars-cov-2) to the fetus. accordingly, it is recommended that pregnant women receive covid-19 vaccination. there is no rationale for adverse effects, or clinical cases of adverse reactions, in mothers or neonates after covid-19 vaccination in lactating women. instead, antibodies to sars-cov-2 can be delivered through breast milk. therefore, breastfeeding mothers should consider vaccination. in summary, active administration of covid-19 vaccines will help ensure the safe implementation of art, pregnancy, and breastfeeding.",0
"abstract bacterial small noncoding rnas (srnas) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. generally, the rna-binding protein hfq helps srnas associate with target mrnas to modulate their translation and to modify global rna pools depending on physiological state. here, a combination of in vivo uv cross-linking immunoprecipitation followed by high-throughput sequencing (clip-seq) and total rna-seq showed that hfq interacts with different regions of the pseudomonas aeruginosa transcriptome under planktonic versus biofilm conditions. in the present approach, p. aeruginosa hfq preferentially interacted with repeats of the aan triplet motif at mrna 5′ untranslated regions (utrs) and srnas and u-rich sequences at rho-independent terminators. further transcriptome analysis suggested that the association of srnas with hfq is primarily a function of their expression levels, strongly supporting the notion that the pool of hfq-associated rnas is equilibrated by rna concentration-driven cycling on and off hfq. overall, our combinatorial clip-seq and total rna-seq approach highlights conditional srna associations with hfq as a novel aspect of posttranscriptional regulation in p. aeruginosa. importance the gram-negative bacterium p. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. although the presence of a large number of putative srnas and widely conserved rna chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of rna chaperones such as hfq in the p. aeruginosa transcriptome, especially under different environmental conditions. here, we characterize hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. a combinatorial comparative clip-seq and total rna-seq approach uncovered condition-dependent association of rnas with hfq in vivo and expands the potential direct regulatory targets of hfq in the p. aeruginosa transcriptome.",1
"background stevia ( stevia rebaudiana ) is an important medicinal plant that yields diterpenoid steviol glycosides (sgs). sgs are currently used in the preparation of medicines, food products and neutraceuticals because of its sweetening property (zero calories and about 300 times sweeter than sugar). recently, some progress has been made in understanding the biosynthesis of sgs in stevia , but little is known about the molecular mechanisms underlying this process. additionally, the genomics of stevia , a non-model species, remains uncharacterized. the recent advent of rna-seq, a next generation sequencing technology, provides an opportunity to expand the identification of stevia genes through in-depth transcript profiling. results we present a comprehensive landscape of the transcriptome profiles of three genotypes of stevia with divergent sg compositions characterized using rna-seq. 191,590,282 high-quality reads were generated and then assembled into 171,837 transcripts with an average sequence length of 969 base pairs. a total of 80,160 unigenes were annotated, and 14,211 of the unique sequences were assigned to specific metabolic pathways by the kyoto encyclopedia of genes and genomes. gene sequences of all enzymes known to be involved in sg synthesis were examined. a total of 143 udp-glucosyltransferase (ugt) unigenes were identified, some of which might be involved in sg biosynthesis. the expression patterns of eight of these genes were further confirmed by rt-qpcr. conclusion rna-seq analysis identified candidate genes encoding enzymes responsible for the biosynthesis of sgs in stevia, a non-model plant without a reference genome. the transcriptome data from this study yielded new insights into the process of sg accumulation in stevia. our results demonstrate that rna-seq can be successfully used for gene identification and transcript profiling in a non-model species. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-571) contains supplementary material, which is available to authorized users.",0
"piezo1 is a mechanosensitive cation channel with widespread physiological importance; however, its role in the heart is poorly understood. cardiac fibroblasts help preserve myocardial integrity and play a key role in regulating its repair and remodeling following stress or injury. here we investigated piezo1 expression and function in cultured human and mouse cardiac fibroblasts. rt-pcr experiments confirmed that piezo1 mrna in cardiac fibroblasts is expressed at levels similar to those in endothelial cells. the results of a fura-2 intracellular ca 2+ assay validated piezo1 as a functional ion channel that is activated by its agonist, yoda1. yoda1-induced ca 2+ entry was inhibited by piezo1 blockers (gadolinium and ruthenium red) and was reduced proportionally by sirna-mediated piezo1 knockdown or in murine piezo1 +/− cells. results from cell-attached patch clamp recordings on human cardiac fibroblasts established that they contain mechanically activated ion channels and that their pressure responses are reduced by piezo1 knockdown. investigation of yoda1 effects on selected remodeling genes indicated that piezo1 activation increases both mrna levels and protein secretion of il-6, a pro-hypertrophic and profibrotic cytokine, in a piezo1-dependent manner. moreover, piezo1 knockdown reduced basal il-6 expression from cells cultured on softer collagen-coated substrates. multiplex kinase activity profiling combined with kinase inhibitor experiments and phosphospecific immunoblotting established that piezo1 activation stimulates il-6 secretion via the p38 mitogen-activated protein kinase downstream of ca 2+ entry. in summary, cardiac fibroblasts express mechanically activated piezo1 channels coupled to secretion of the paracrine signaling molecule il-6. piezo1 may therefore be important in regulating cardiac remodeling.",0
"we present a network framework for analyzing multi-level regulation in higher eukaryotes based on systematic integration of various high-throughput datasets. the network, namely the integrated regulatory network, consists of three major types of regulation: tf→gene, tf→mirna and mirna→gene. we identified the target genes and target mirnas for a set of tfs based on the chip-seq binding profiles, the predicted targets of mirnas using annotated 3′utr sequences and conservation information. making use of the system-wide rna-seq profiles, we classified transcription factors into positive and negative regulators and assigned a sign for each regulatory interaction. other types of edges such as protein-protein interactions and potential intra-regulations between mirnas based on the embedding of mirnas in their host genes were further incorporated. we examined the topological structures of the network, including its hierarchical organization and motif enrichment. we found that transcription factors downstream of the hierarchy distinguish themselves by expressing more uniformly at various tissues, have more interacting partners, and are more likely to be essential. we found an over-representation of notable network motifs, including a ffl in which a mirna cost-effectively shuts down a transcription factor and its target. we used data of c. elegans from the modencode project as a primary model to illustrate our framework, but further verified the results using other two data sets. as more and more genome-wide chip-seq and rna-seq data becomes available in the near future, our methods of data integration have various potential applications.",1
"head and neck cancer is the sixth most common malignancy worldwide, with the relatively low 5-year survival rate, mainly because it is diagnosed at a late stage. infection with hpv is a well known aetiology, which affects the nature of these cancers and patients’ survival. besides, it is considered that the main driving force for this type of cancer could be epigenetics. in this study we aimed to find potential epigenetic biomarkers, by integrating mirnome, methylome, and transcriptome analyses. from the fresh head and neck cancer tissue samples, we chose a group for mirnome, methylome and transcriptome profiling, in comparison to adequate control samples. bioinformatics analyses are performed in r v4.2.2. count normalisation and group differential expression for mrna and the previously obtained mirna count data was performed with deseq2 v1.36. gene set enrichment analysis was performed and visualised using gprofiler2 v0.2.1 identification of mirna targets was performed by querying in mirtarbase using multimir v1.18.0. annotation of cpg sites merging into islands was obtained from rnbeads.hg19 v1.28.0. package. for the integrative analysis we performed kmeans clustering using stats v4.2.2 package, using 8–12 clusters and nstart 100. we found that transcriptome analysis divides samples into cancers and controls clusters, with no relation to hpv status or cancer anatomical location. differentially expressed genes (n = 2781) were predominantly associated with signalling pathways of tumour progression. we identified a cluster of genes under the control of the transcription factor e2f that are significantly underexpressed in cancer tissue, as well as t cell immunity genes and genes related to regulation of transcription. among overexpressed genes in tumours we found those that belong to cell cycle regulation and vasculature. a small number of genes were found significantly differentially expressed in hpv-positive versus hpv-negative tumours (for example nefh , zfr2 , taf7l , znf541 , and tyms ). in this comprehensive study on an overlapping set of samples where the integration of mirnome, methylome and transcriptome analysis were performed for head and neck cancer, we demonstrated that the majority of genes were associated exclusively with mirnome or methylome and, to a lesser extent, under the control of both epigenetic mechanisms.",1
"shellfish allergy affects 2% of the world’s population and persists for life in most patients. the diagnosis of shellfish allergy, in particular shrimp, is challenging due to the similarity of allergenic proteins from other invertebrates. despite the clinical importance of immunological cross-reactivity among shellfish species and between allergenic invertebrates such as dust mites, the underlying molecular basis is not well understood. here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. the transcriptomes were assembled de novo, using trinity, from raw rna-seq data of the whiteleg shrimp ( litopenaeus vannamei ), black tiger shrimp ( penaeus monodon ), banana shrimp ( fenneropenaeus merguiensis ), king shrimp ( melicertus latisulcatus ), and endeavour shrimp ( metapenaeus endeavouri ). blast searching using the two major allergen databases, who/iuis allergen nomenclature and allergenonline, successfully identified all seven known crustacean allergens. the analyses revealed up to 39 unreported allergens in the different shrimp species, including heat shock protein (hsp), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase a, and glyceraldehyde-3-phosphate dehydrogenase (g3pd). multiple sequence alignment (clustal omega) demonstrated high homology with allergens from other invertebrates including mites and cockroaches. this first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.",0
"radiation induced genomic instability is a well-studied phenomenon, the underlying mechanisms of which are poorly understood. persistent oxidative stress, mitochondrial dysfunction, elevated cytokine levels and epigenetic changes are among the mechanisms invoked in the perpetuation of the phenotype. to determine whether epigenetic aberrations affect genomic instability we measured dna methylation, mrna and microrna (mir) levels in well characterized chromosomally stable and unstable clonally expanded single cell survivors of irradiation. while no changes in dna methylation were observed for the gene promoters evaluated, increased line-1 methylation was observed for two unstable clones (ls12 and cs9) and decreased alu element methylation was observed for the other two unstable clones (115 and fe5.0–8). these relationships also manifested for mrna and mir expression. mrna identified for the ls12 and cs9 clones were most similar to each other (261 mrna), while the 115 and fe5.0–8 clones were more similar to each other, and surprisingly also similar to the two stable clones, 114 and 118 (286 mrna among these four clones). pathway analysis showed enrichment for pathways involved in mitochondrial function and cellular redox, themes routinely invoked in genomic instability. the commonalities between the two subgroups of clones were also observed for mir. the number of mir for which anti-correlated mrna were identified suggests that these mir exert functional effects in each clone. the results demonstrate significant genetic and epigenetic changes in unstable cells, but similar changes are almost as equally common in chromosomally stable cells. possible conclusions might be that the chromosomally stable clones have some other form of instability, or that some of the observed changes represent a sort of radiation signature and that other changes are related to genomic instability. irrespective, these findings again suggest that a spectrum of changes both drive genomic instability and permit unstable cells to persist and proliferate.",1
"rna sequencing (rna-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. current rna-seq protocols depend on high-throughput short-read sequencing of cdna. however, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in read length influence various transcriptome analyses. in this study, we generated two paired-end rna-seq datasets of differing read lengths (2×75 bp and 2×262 bp) for lymphoblastoid cell line gm12878 and compared the effect of read length on transcriptome analyses, including read-mapping performance, gene and transcript quantification, and detection of allele-specific expression (ase) and allele-specific alternative splicing (asas) patterns. our results indicate that, while the current long-read protocol is considerably more expensive than short-read sequencing, there are important benefits that can only be achieved with longer read length, including lower mapping bias and reduced ambiguity in assigning reads to genomic elements, such as mrna transcript. we show that these benefits ultimately lead to improved detection of cis -acting regulatory and splicing variation effects within individuals.",0
"gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. in the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. a total of 3131 putative duplicated gene pairs were identified, including 712 cattle-specific duplicate gene pairs unevenly distributed across the genome, which are significantly enriched for specific biological functions including immunity, growth, digestion, reproduction, embryonic development, inflammatory response, and defense response to bacterium. around 97.1% (87.8%) of (cattle-specific) duplicate gene pairs were found to have distinct exon-intron structures. analysis of gene expression by rna-seq and sequence divergence (synonymous or non-synonymous) revealed that expression divergence is correlated with sequence divergence, as has been previously observed in other species. this analysis also led to the identification of a subset of cattle-specific duplicate gene pairs exhibiting very high expression divergence. interestingly, further investigation revealed a significant relationship between structural and expression divergence while controlling for the effect of synonymous sequence divergence. together these results provide further insight into duplicate gene sequence and expression divergence in cattle, and their potential contributions to phenotypic divergence.",0
"synthetic analogs of the 5′ end of mrna (cap structure) are widely used in molecular studies on mechanisms of cellular processes such as translation, intracellular transport, splicing, and turnover. the best-characterized cap binding protein is translation initiation factor 4e (eif4e). recognition of the mrna cap by eif4e is a critical, rate-limiting step for efficient translation initiation and is considered a major target for anticancer therapy. here, we report a facile methodology for the preparation of n2-triazole-containing monophosphate cap analogs and present their biological evaluation as inhibitors of protein synthesis. five analogs possessing this unique hetero-cyclic ring spaced from the m7-guanine of the cap structure at a distance of one or three carbon atoms and/or additionally substituted by various groups containing the benzene ring were synthesized. all obtained compounds turned out to be effective translation inhibitors with ic 50 similar to dinucleotide triphosphate m 7 gpppg. as these compounds possess a reduced number of phosphate groups and, thereby, a negative charge, which may support their cell penetration, this type of cap analog might be promising in terms of designing new potential therapeutic molecules. in addition, an exemplary dinucleotide from a corresponding mononucleotide containing benzyl substituted 1,2,3-triazole was prepared and examined. the superior inhibitory properties of this analog (10-fold vs. m 7 gpppg) suggest the usefulness of such compounds for the preparation of mrna transcripts with high translational activity.",0
"studies of various mrnas have revealed that changes in the abundance of transcripts, through mrna degradation, act as a critical step in the control of various biological pathways. similarly, the regulation of non-coding rna (ncrna) levels is also considered to be important for their biological functions; however, far less is known about the mechanisms and biological importance of ncrna turnover for the regulation of ncrna functions. the growth arrest-specific 5 (gas5) ncrna accumulates during growth arrest induced by serum starvation and its transcript is degraded by the well characterized nonsense-mediated rna decay (nmd) pathway. historically, nmd was discovered as a rna quality control system to eliminate aberrant transcripts; however, accumulating evidence shows that nmd also regulates the abundance of physiological transcripts. interestingly, the gas5 transcript has the ability to bind the glucocorticoid receptor (gr), resulting in the inhibition of its ligand-dependent association with dna. the gr binds the promoters of various glucocorticoid-responsive genes, including apoptosis-related genes. in this study, we examined whether the rna degradation pathway can regulate this function of gas5. we measured the steady-state abundance and the decay rate of gas5 in upf1-depleted human cells using the 5′-bromo-uridine immunoprecipitation chase (bric) method, an inhibitor-free method for directly measuring rna stability. we found that levels of the gas5 transcript were elevated owing to prolonged decay rates in response to upf1 depletion, and consequently the apoptosis-related genes, ciap2 and sgk1, were down-regulated. in addition, serum starvation also increased the transcript levels of gas5 because of prolonged decay rates, and conversely decreased levels of ciap2 and sgk1 mrna. taken together, we found that the rna degradation pathway can regulate the function of the gas5 ncrna in mammalian cells.",1
"insulin resistance (ir) precedes the development of type 2 diabetes (t2d) and increases cardiovascular disease risk. although genome wide association studies (gwas) have uncovered new loci associated with t2d, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. thus, new approaches are necessary to explore the genetic architecture of insulin resistance. to that end, we generated an ipsc library across the spectrum of insulin sensitivity in humans. rna-seq based analysis of 310 induced pluripotent stem cell (ipsc) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive ipsc lines. analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. functional validation in human adipocytes and skeletal muscle cells (skmcs) confirmed the relevance of the key driver candidate genes for insulin responsiveness.",0
"background the application of next-generation sequencing technology to gene expression quantification analysis, namely, rna-sequencing, has transformed the way in which gene expression studies are conducted and analyzed. these advances are of particular interest to researchers studying organisms with missing or incomplete genomes, as the need for knowledge of sequence information is overcome. de novo assembly methods have gained widespread acceptance in the rna-seq community for organisms with no true reference genome or transcriptome. while such methods have tremendous utility, computational cost is still a significant challenge for organisms with large and complex genomes. results in this manuscript, we present a comparison of four reference-based mapping methods for non-human primate data. we utilize tophat2 and gsnap for mapping to the human genome, and bowtie2 and stampy for mapping to the human genome and transcriptome for a total of six mapping approaches. for each of these methods, we explore mapping rates and locations, number of detected genes, correlations between computed expression values, and the utility of the resulting data for differential expression analysis. conclusions we show that reference-based mapping methods indeed have utility in rna-seq analysis of mammalian data with no true reference, and the details of mapping methods should be carefully considered when doing so. critical algorithm features include short seed sequences, the allowance of mismatches, and the allowance of gapped alignments in addition to splice junction gaps. such features facilitate sensitive alignment of non-human primate rna-seq data to a human reference. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-570) contains supplementary material, which is available to authorized users.",0
"post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. it is mainly performed by rna binding proteins and micrornas, which target rnas and typically affect their stability. recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (clip), which facilitates identification of binding sites of these regulatory factors. however, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. in this work, we have performed a comprehensive analysis of 107 clip datasets from 49 different rbps in hek293 cells to shed light on the complex interactions that govern post-transcriptional regulation. by developing a more stringent clip analysis pipeline we have discovered the existence of conserved regulatory au-rich regions in the 3’utrs where mirnas and rbps that regulate several processes such as polyadenylation or mrna stability bind. analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mrna may depend on their relative concentrations. this hypothesis is supported by rbp knockdown experiments that alter the relative concentration of rbps in the cell. upon ago2 knockdown (kd), transcripts containing “free” target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for mirnas to bind. interestingly, these hotspots appear enriched in genes with regulatory functions such as dna binding and rna binding. taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer of regulation of post-transcriptional regulatory networks.",1
"polyamines are involved in the regulation of some trichomonas vaginalis virulence factors such as the transcript, proteolytic activity, and cytotoxicity of tvcp65, a cysteine proteinase (cp) involved in the trichomonal cytotoxicity. in this work, we reported the putrescine effect on tvcp39, other cp that also participate in the trichomonal cytotoxicity. parasites treated with 1,4-diamino-2-butanone (dab) (an inhibitor of putrescine biosynthesis), diminished the amount and proteolytic activity of tvcp39 as compared with untreated parasites. inhibition of putrescine biosynthesis also reduced ∼80% the tvcp39 mrna levels according to rt-pcr and qrt-pcr assays. additionally, actinomycin d-treatment showed that the tvcp39 mrna half-life decreased in the absence of putrescine. however, this reduction was restored by exogenous putrescine addition, suggesting that putrescine is necessary for tvcp39 mrna stability. tvcp39 was localized in the cytoplasm but, in dab treated parasites transferred into exogenous putrescine culture media, tvcp39 was re-localized to the nucleus and nuclear periphery of trichomonads. interestingly, the amount and proteolytic activity of tvcp39 was recovered as well as the tvcp39 mrna levels were restored when putrescine exogenous was added to the dab-treated parasites. in conclusion, our data show that putrescine regulate the tvcp39 expression, protein amount, proteolytic activity, and cellular localization.",0
"simple summary optimal reproductive performance on goat farms is an important trait in terms of production and economics. from a genetic perspective, understanding molecular mechanisms through the use of rna-seq technology can help us better understand goat herds. in this study, a whole-transcriptome sequencing approach was used to identify lncrna, circrna, mirna, and mrna expression in the ovaries of chongming white goats in terms of high and low fecundity during the estrus phase. these results were helpful in terms of further studying the molecular mechanisms of goat reproduction. abstract reproductive performance is one of the most important economic traits in the goat industry. increasing the number of goats is an effective measure to improve production efficiency and reduce production costs. ovaries are important reproductive organs in female mammals that directly affect the estrous cycle and reproductive abilities. understanding the complex transcription network of non-coding rnas (lncrnas, circrnas, and mirnas) and messenger rna (mrna) could lead to significant insights into the ovarian regulation of the reproductive processes of animals. however, the whole-transcriptome analysis of the non-coding rnas and mrna of the ovaries in chongming white goats between high-fecundity (hp) and low-fecundity (lp) groups is limited. in this study, a whole-transcriptome sequencing approach was used to identify lncrna, circrna, mirna, and mrna expression in the ovaries of chongming white goats during the estrus phase using rna-seq technology. more than 20,000 messenger rnas (mrnas), 10,000 long non-coding rnas (lncrnas), 3500 circular rnas (circrnas), and 1000 micro rnas (mirnas) were identified. a total of 1024 differential transcripts (724 mrnas, 112 lncrnas, 178 circrnas, and 10 mirnas) existing between the hp and the lp groups were revealed through a bioinformatics analysis. they were enriched in the prolactin signaling pathway, the jak–stat signaling pathway, and the gnrh signaling pathway, as well as various metabolic pathways. differentially expressed mrnas (such as lypd6 , vegfa , nos3 , tnxb , and epha2 ) and mirnas (such as mir-10a-5p ) play key roles in the regulation of goat ovaries during the estrus phase. the enrichment of pathways related to reproduction, such as the hippo, hedgehog, pi3k–akt, and mapk signaling pathways, suggests that they might be involved in the prolificacy of goat ovaries. overall, we identified several gene modules associated with goat fecundity and provided a basis for a molecular mechanism in the ovaries of chongming white goats.",1
"background micrornas (mirnas) are a class of small rna molecules that regulate expression of specific mrna targets. they can be released from cells, often encapsulated within extracellular vesicles (evs), and therefore have the potential to mediate intercellular communication. it has been suggested that certain mirnas may be selectively exported, although the mechanism has yet to be identified. manipulation of the mirna content of evs will be important for future therapeutic applications. we therefore wished to assess which endogenous mirnas are enriched in evs and how effectively an overexpressed mirna would be exported. results small rna libraries from hek293t cells and vesicles before or after transfection with a vector for mir-146a overexpression were analysed by deep sequencing. a subset of mirnas was found to be enriched in evs; pathway analysis of their predicted target genes suggests a potential role in regulation of endocytosis. rt-qpcr in additional cell types and analysis of publicly available data revealed that many of these mirnas tend to be widely preferentially exported. whilst overexpressed mir-146a was highly enriched both in transfected cells and their evs, the cellular:ev ratios of endogenous mirnas were not grossly altered. mir-451 was consistently the most highly exported mirna in many different cell types. intriguingly, argonaute2 (ago2) is required for mir-451 maturation and knock out of ago2 has been shown to decrease expression of other preferentially exported mirnas (eg mir-150 and mir-142-3p). conclusion the global expression data provided by deep sequencing confirms that specific mirnas are enriched in evs released by hek293t cells. observation of similar patterns in a range of cell types suggests that a common mechanism for selective mirna export may exist.",1
"development of the vasculature is a complex, dynamic process orchestrated by a balance of pro and anti-angiogenic signaling pathways. the same signaling pathways are mis-regulated and exploited during pathological angiogenesis in cancer, inflammation and cardiovascular diseases and contribute to disease progression. in the last decade, small non-coding rna molecules termed micrornas (mirs) have emerged as key regulators of several cellular processes including angiogenesis. it is becoming clear that mirs function in complex networks and regulate gene expression both at the mrna and protein levels thereby altering cellular signaling responses to specific stimuli. in the vasculature, mirs can function either in a pro-angiogenic manner and potentiate angiogenesis or act as anti-angiogenic mirs by enhancing cell death and decreasing endothelial proliferation. this review aims to provide an update on how micrornas regulate gene expression and illustrate mir function in the vasculature with a discussion of potential applications of mirs as anti-angiogenic therapeutics.",1
"objective here, we assess the usage of high throughput sequencing (hts) in rheumatic research and the availability of public hts data of rheumatic samples. methods we performed a semiautomated literature review on pubmed, consisting of an r-script and manual curation as well as a manual search on the sequence read archive for public available hts data. results of the 699 identified articles, rheumatoid arthritis (n=182 publications, 26%), systemic lupus erythematous (n=161, 23%) and osteoarthritis (n=152, 22%) are among the rheumatic diseases with the most reported use of hts assays. the most represented assay is rna-seq (n=457, 65%) for the identification of biomarkers in blood or synovial tissue. we also find, that the quality of accompanying clinical characterisation of the sequenced patients differs dramatically and we propose a minimal set of clinical data necessary to accompany rheumatological-relevant hts data. conclusion hts allows the analysis of a broad spectrum of molecular features in many samples at the same time. it offers enormous potential in novel personalised diagnosis and treatment strategies for patients with rheumatic diseases. being established in cancer research and in the field of mendelian diseases, rheumatic diseases are about to become the third disease domain for hts, especially the rna-seq assay. however, we need to start a discussion about reporting of clinical characterisation accompany rheumatological-relevant hts data to make clinical meaningful use of this data.",0
"objective sjögren’s disease (sjd) is an autoimmune disease characterised by inflammatory destruction of exocrine glands. patients with autoantibodies to ro/ssa (sjd ro+ ) exhibit more severe disease. long non-coding rnas (lncrnas) are a functionally diverse class of non-protein-coding rnas whose role in autoimmune disease pathology has not been well characterised. methods whole blood rna-sequencing (rna-seq) was performed on sjd cases (n=23 ro/ssa negative (sjd ro− ); n=27 ro/ssa positive (sjd ro+ ) and healthy controls (hcs; n=27). bioinformatics and pathway analyses of differentially expressed (de) transcripts (log 2 fold change ≥2 or ≤0.5; p adj <0.05) were used to predict lncrna function. linc01871 was characterised by rna-seq analyses of hsb-2 cells with crispr-targeted linc01871 deletion ( linc01871 −/ − ) and in vitro stimulation assays. results whole blood rna-seq revealed autoantibody-specific transcription profiles and disproportionate downregulation of de transcripts in sjd cases relative to hcs. sixteen de lncrnas exhibited correlated expression with the interferon (ifn)-regulated gene, rsad2 , in sjd ro+ (r≥0.65 or ≤−0.6); four antisense lncrnas exhibited ifn-regulated expression in immune cell lines. linc01871 was upregulated in all sjd cases. rna-seq and pathway analyses of linc01871 −/ − cells implicated roles in cytotoxic function, differentiation and ifnγ induction. linc01871 was induced by ifnγ in a myeloid cell line and regulated by calcineurin/nfat pathway and t cell receptor (tcr) signalling in primary human t cells. conclusion linc01871 influences expression of many immune cell genes and growth factors, is ifnγ inducible, and regulated by calcineurin signalling and tcr ligand engagement. altered linc01871 expression may influence the dysregulated t cell inflammatory pathways implicated in sjd.",1
"understanding the immune responses to sars-cov-2 vaccination is critical to optimizing vaccination strategies for individuals with autoimmune diseases, such as systemic lupus erythematosus (sle). here, we comprehensively analyzed innate and adaptive immune responses in 19 patients with sle receiving a complete 2-dose pfizer-biontech mrna vaccine (bnt162b2) regimen compared with a control cohort of 56 healthy control (hc) volunteers. patients with sle exhibited impaired neutralizing antibody production and antigen-specific cd4 + and cd8 + t cell responses relative to hc. interestingly, antibody responses were only altered in patients with sle treated with immunosuppressive therapies, whereas impairment of antigen-specific cd4 + and cd8 + t cell numbers was independent of medication. patients with sle also displayed reduced levels of circulating cxc motif chemokine ligands, cxcl9, cxcl10, cxcl11, and ifn-γ after secondary vaccination as well as downregulation of gene expression pathways indicative of compromised innate immune responses. single-cell rna-seq analysis reveals that patients with sle showed reduced levels of a vaccine-inducible monocyte population characterized by overexpression of ifn-response transcription factors. thus, although 2 doses of bnt162b2 induced relatively robust immune responses in patients with sle, our data demonstrate impairment of both innate and adaptive immune responses relative to hc, highlighting a need for population-specific vaccination studies. sars-cov-2 mrna vaccination reduces innate, t cell, and b cell immune responses in patients with systemic lupus erythematosus, highlighting a need for population-specific vaccination studies.",0
"uremic encephalopathy (ue) poses a significant challenge in neurology, leading to the need to investigate the involvement of non-coding rna (ncrna) in its development. this study employed ncrna-seq and rna-seq approaches to identify fundamental ncrnas, specifically circrna and mirna, in the pathogenesis of ue using a mouse model. in vitro and in vivo experiments were conducted to explore the circrna-ptpn4/mir-301a-3p/foxo3 axis and its effects on blood–brain barrier (bbb) function and cognitive abilities. the research revealed that circrna-ptpn4 binds to and inhibits mir-301a-3p, leading to an increase in foxo3 expression. this upregulation results in alterations in the transcriptional regulation of zo-1, affecting the permeability of human brain microvascular endothelial cells (hbmecs). the axis also influences the growth, proliferation, and migration of hbmecs. mice with ue exhibited cognitive deficits, which were reversed by overexpression of circrna-ptpn4, whereas silencing foxo3 exacerbated these deficits. furthermore, the uremic mice showed neuronal loss, inflammation, and dysfunction in the bbb, with the expression of circrna-ptpn4 demonstrating therapeutic effects. in conclusion, circrna-ptpn4 plays a role in promoting foxo3 expression by sequestering mir-301a-3p, ultimately leading to the upregulation of zo-1 expression and restoration of bbb function in mice with ue. this process contributes to the restoration of cognitive abilities. graphical abstract 1. the circrna-ptpn4/mir-301a-3p/foxo3 axis is identified as a key regulator of blood–brain barrier integrity and cognitive function in uremic encephalopathy. 2. circrna-ptpn4 sequestration of mir-301a-3p enhances foxo3 expression, leading to upregulation of zo-1 and improved endothelial permeability. 3. overexpression of circrna-ptpn4 in uremic mice restores cognitive abilities and reduces neuronal loss and inflammatory infiltration. supplementary information the online version contains supplementary material available at 10.1007/s10565-024-09865-6.",1
"the torrent of rna-seq data becoming available not only furnishes an overview of the entire transcriptome but also provides tools to focus on specific areas of interest. our focus on the synthesis of ribosomes asked whether the abundance of mrnas encoding ribosomal proteins (rps) matched the equimolar need for the rps in the assembly of ribosomes. we were at first surprised to find, in the mapping data of encode and other sources, that there were nearly 100-fold differences in the level of the mrnas encoding the different rps. however, after correcting for the mapping ambiguities introduced by the presence of more than 2000 pseudogenes derived from rp mrnas, we show that for 80%–90% of the rp genes, the molar ratio of mrnas varies less than threefold, with little tissue specificity. nevertheless, since the rps are needed in equimolar amounts, there must be sluggish or regulated translation of the more abundant rp mrnas and/or substantial turnover of unused rps. in addition, seven of the rps have subsidiary genes, three of which are pseudogenes that have been “rescued” by the introduction of promoters and/or upstream introns. several of these are transcribed in a tissue-specific manner, e.g., rpl10l in testis and rpl3l in muscle, leading to potential variation in ribosome structure from one tissue to another. of the 376 introns in the rp genes, a single one is alternatively spliced in a tissue-specific manner.",0
"flagellar synthesis is a highly regulated process in all motile bacteria. in escherichia coli and related species, the transcription factor flhdc is the master regulator of a multi-tiered transcription network. flhdc activates transcription of a number of genes, including some flagellar genes and the gene encoding the alternative sigma factor flia. genes whose expression is required late in flagellar assembly are primarily transcribed by flia, imparting temporal regulation of transcription and coupling expression to flagellar assembly. in this study, we use chip-seq and rna-seq to comprehensively map the e. coli flhdc and flia regulons. we define a surprisingly restricted flhdc regulon, including two novel regulated targets and two binding sites not associated with detectable regulation of surrounding genes. in contrast, we greatly expand the known flia regulon. surprisingly, 30 of the 52 flia binding sites are located inside genes. two of these intragenic promoters are associated with detectable noncoding rnas, while the others either produce highly unstable rnas or are inactive under these conditions. together, our data redefine the e. coli flagellar regulatory network, and provide new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process.",1
"abstract most common genetic variants associated with disease are located in non-coding regions of the genome. one mechanism by which they function is through altering transcription factor (tf) binding. in this study, we explore how genetic variation is connected to differences in the regulatory landscape of livers from c57bl/6j and 129s1/svimj mice fed either chow or a high-fat diet. to identify sites where regulatory variation affects tf binding and nearby gene expression, we employed an integrative analysis of h3k27ac chip-seq (active enhancers), atac-seq (chromatin accessibility) and rna-seq (gene expression). we show that, across all these assays, the genetically driven (i.e. strain-specific) differences in the regulatory landscape are more pronounced than those modified by diet. most notably, our analysis revealed that differentially accessible regions (dars, n = 29635, fdr 50%) are almost always strain-specific and enriched with genetic variation. moreover, proximal dars are highly correlated with differentially expressed genes. we also show that tf binding is affected by genetic variation, which we validate experimentally using chip-seq for tcf7l2 and ctcf. this study provides detailed insights into how non-coding genetic variation alters the gene regulatory landscape, and demonstrates how this can be used to study the regulatory variation influencing tf binding.",0
"background validation of physiologic mirna targets has been met with significant challenges. we employed hits-clip to identify which mirnas participate in liver regeneration, and to identify their target mrnas. results mirna recruitment to the risc is highly dynamic, changing more than five-fold for several mirnas. mirna recruitment to the risc did not correlate with changes in overall mirna expression for these dynamically recruited mirnas, emphasizing the necessity to determine mirna recruitment to the risc in order to fully assess the impact of mirna regulation. we incorporated rna-seq quantification of total mrna to identify expression-weighted ago footprints, and developed a microrna regulatory element (mre) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. these high confidence mres were used to generate candidate ‘competing endogenous rna’ (cerna) networks. conclusion hits-clip analysis provide novel insights into global mirna:mrna relationships in the regenerating liver.",1
"oomycetes in the class saprolegniomycetidae of the eukaryotic kingdom stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. we have sequenced the 63 mb genome of the fresh water fish pathogen, saprolegnia parasitica. approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. comparison of s. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. s. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from rna-seq data. in contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. the large gene families that are hallmarks of plant pathogenic oomycetes such as phytophthora appear to be lacking in s. parasitica , including those encoding rxlr effectors, crinkler's, and necrosis inducing-like proteins (nlp). s. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. moreover, s. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in s. parasitica.",0
"background sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. however, its large (10 gb), polyploid, complex genome has hindered genome based breeding efforts. here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. results three hundred and seventeen chiefly euchromatic bacs were sequenced. a reference set of one thousand four hundred manually-annotated protein-coding genes was generated. a small rna collection and a rna-seq library were used to explore expression patterns and the srna landscape. in the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. one of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. a diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. examination of hom(e)ologous loci indicate both sequence structural and srna landscape variation. a synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. conclusion this release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. electronic supplementary material the online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.",0
"background micrornas (mirnas) are a class of small non-coding rnas that regulate gene expression by targeting mrnas for translation repression or mrna degradation. although many mirnas have been discovered and studied in human and mouse, few studies focused on porcine mirnas, especially in genome wide. results here, we adopted computational approaches including support vector machine (svm) and homology searching to make a global scanning on the pre-mirnas of pigs. in our study, we built the svm-based porcine pre-mirnas classifier with a sensitivity of 100%, a specificity of 91.2% and a total prediction accuracy of 95.6%, respectively. moreover, 2204 novel porcine pre-mirna candidates were found by using svm-based pre-mirnas classifier. besides, 116 porcine pre-mirna candidates were detected by homology searching. conclusions we identified the porcine pre-mirna in genome-wide through computational approaches by utilizing the data sets of pigs and set up the porcine pre-mirnas library which may provide us a global scanning on the pre-mirnas of pigs in genome level and would benefit subsequent experimental research on porcine mirna functional and expression analysis.",1
"the spike protein in sars-cov-2 (sars-2-s) interacts with the human ace2 receptor to gain entry into a cell to initiate infection. both pfizer/biontech’s bnt162b2 and moderna’s mrna-1273 vaccine candidates are based on stabilized mrna encoding prefusion sars-2-s that can be produced after the mrna is delivered into the human cell and translated. sars-2-s is cleaved into s1 and s2 subunits, with s1 serving the function of receptor-binding and s2 serving the function of membrane fusion. here, i dissect in detail the various domains of sars-2-s and their functions discovered through a variety of different experimental and theoretical approaches to build a foundation for a comprehensive mechanistic understanding of how sars-2-s works to achieve its function of mediating cell entry and subsequent cell-to-cell transmission. the integration of structure and function of sars-2-s in this review should enhance our understanding of the dynamic processes involving receptor binding, multiple cleavage events, membrane fusion, viral entry, as well as the emergence of new viral variants. i highlighted the relevance of structural domains and dynamics to vaccine development, and discussed reasons for the spike protein to be frequently featured in the conspiracy theory claiming that sars-cov-2 is artificially created.",0
"eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. high-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding rnas with key roles in biological processes. long noncoding rnas (lncrnas) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. although a large set of lncrnas has been identified, the functional roles of lncrnas are only beginning to be recognized and the molecular mechanism of lncrna-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. using public and proprietary poly-(a) + rna-seq data as well as a collection of full length ests from several organs, developmental stages and stress conditions in three brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncrnas. here we provide a genome-wide characterization of lncrnas, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. this work represents a fundamental resource to deepen our knowledge on long noncoding rnas in c 3 cereals, allowing the brachypodium community to exploit these results in future research programs.",1
"ewing sarcoma is driven by fusion proteins containing a low-complexity (lc) domain that is intrinsically disordered and a powerful transcriptional regulator. the most common fusion protein found in ewing sarcoma, ews-fli1, takes its lc domain from the rna-binding protein ewsr1 (ewing sarcoma rna-binding protein 1) and a dna-binding domain from the transcription factor fli1 (friend leukemia virus integration 1). ews-fli1 can bind rna polymerase ii (rna pol ii) and self-assemble through its lc domain. the ability of rna-binding proteins like ewsr1 to self-assemble or phase separate in cells has raised questions about the contribution of this process to ews-fli1 activity. we examined ewsr1 and ews-fli1 activity in ewing sarcoma cells by sirna-mediated knockdown and rna-seq analysis. more transcripts were affected by the ewsr1 knockdown than expected and these included many ews-fli1 regulated genes. we reevaluated physical interactions between ews-fli1, ewsr1, and rna pol ii, and used a cross-linking-based strategy to investigate protein assemblies associated with the proteins. the lc domain of ews-fli1 was required for the assemblies observed to form in cells. these results offer new insights into a protein assembly that may enable ews-fli1 to bind its wide network of protein partners and contribute to regulation of gene expression in ewing sarcoma.",0
"background micrornas (mirnas) are noncoding rnas that direct post-transcriptional regulation of protein coding genes. recent studies have shown mirnas are important for controlling many biological processes, including nervous system development, and are highly conserved across species. given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (htp) mirna data in an increasing number of model species. the bioinformatics resource manager (brm) v2.3 is a software environment for data management, mining, integration and functional annotation of htp biological data. in this study, we report recent updates to brm for mirna data analysis and cross-species comparisons across datasets. results brm v2.3 has the capability to query predicted mirna targets from multiple databases, retrieve potential regulatory mirnas for known genes, integrate experimentally derived mirna and mrna datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. here we use brm to show that developmental exposure of zebrafish to 30 um nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative mirna gene targets in whole embryos at developmental stages that encompass early neurogenesis. we show typical workflows for using brm to integrate experimental zebrafish mirna and mrna microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. functional analysis of differentially regulated (p<0.05) gene targets in brm indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive mirnas. conclusions brm provides the ability to mine complex data for identification of candidate mirnas or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. the mirna workflow in brm allows for efficient processing of multiple mirna and mrna datasets in a single software environment with the added capability to interact with public data sources and visual analytic tools for htp data analysis at a systems level. brm is developed using java™ and other open-source technologies for free distribution ( ).",1
"significance aberrant lncrna expression is responsible for cancer progression and metastasis, positioning lncrnas not only as biomarkers but also as promising therapeutic targets for curing cancer. a number of lncrnas have been reported in escc but their mechanistic roles largely remain unknown. wnt signaling pathways are often dysregulated in escc; however, the role of lncrnas in such dysregulation was also undetermined. we found 6 lncrnas that are significantly dysregulated and correlated with outcomes in escc patients. the most upregulated lncrna, heres, promotes cancer progression and epigenetically regulates canonical and noncanonical wnt signaling pathways simultaneously through interaction with ezh2. these results show that heres represents an early diagnostic and therapeutic target for squamous-cell-type cancers caused by defects in wnt signaling pathways. wnt signaling through both canonical and noncanonical pathways plays a core role in development. dysregulation of these pathways often causes cancer development and progression. although the pathways independently contribute to the core processes, a regulatory molecule that commonly activates both of them has not yet been reported. here, we describe a long noncoding rna (lncrna), heres, that epigenetically regulates both canonical and noncanonical wnt signaling pathways in esophageal squamous cell carcinoma (escc). for this study, we performed rna-seq analysis on korean escc patients and validated these results on a larger escc cohort to identify lncrnas commonly dysregulated in esccs. six of the dysregulated lncrnas were significantly associated with the clinical outcomes of escc patients and defined 4 escc subclasses with different prognoses. heres reduction repressed cell proliferation, migration, invasion, and colony formation in escc cell lines and tumor growth in xenograft models. heres appears to be a transacting factor that regulates cacna2d3 , sfrp2 , and cxxc4 simultaneously to activate wnt signaling pathways through an interaction with ezh2 via its g-quadruple structure-like motif. our results suggest that heres holds substantial potential as a therapeutic target for escc and probably other cancers caused by defects in wnt signaling pathways.",1
"nocardithiocin is a thiopeptide compound isolated from the opportunistic pathogen nocardia pseudobrasiliensis. it shows a strong activity against acid-fast bacteria and is also active against rifampicin-resistant mycobacterium tuberculosis. here, we report the identification of the nocardithiocin gene cluster in n. pseudobrasiliensis ifm 0761 based on conserved thiopeptide biosynthesis gene sequence and the whole genome sequence. the predicted gene cluster was confirmed by gene disruption and complementation. as expected, strains containing the disrupted gene did not produce nocardithiocin while gene complementation restored nocardithiocin production in these strains. the predicted cluster was further analyzed using rna-seq which showed that the nocardithiocin gene cluster contains 12 genes within a 15.2-kb region. this finding will promote the improvement of nocardithiocin productivity and its derivatives production.",0